ArticleLiterature Review

Microbial diversity-productivity relationships in aquatic ecosystems

December 2007
FEMS Microbiology Ecology 62(2):181-6

December 2007
62(2):181-6

DOI:10.1111/j.1574-6941.2007.00381.x

Source
PubMed

Authors:

Val H. Smith

University of Kansas

Thanks to recent advances in molecular biology, one's knowledge of microbial co-occurrence patterns, microbial biogeography and microbial biodiversity is expanding rapidly. This MiniReview explores microbial diversity-productivity relationships in the light of what is known from the general ecology literature. Analyses of microbial diversity-productivity relationships from 70 natural, experimental, and engineered aquatic ecosystems reveal patterns that are strikingly similar to those that have long been documented for communities of macroorganisms. Microbial ecology and the general science of ecology are thus continuing to converge.

Diversity of benthic diatoms in the Baltic Sea: alpha and beta diversity, environmental drivers, and diversity–biomass relationships

Article

Jun 2023

Leena Virta

Benthic diatoms are crucial for the functioning of ecosystems, but their diversity patterns along large gradients are poorly studied. By using 3 self-collected data sets along large environmental gradients in the Baltic Sea, represented over spatial scales of 60, 1300, and 2300 km, I investigated whether different aspects of diversity follow general patterns or are context- and region-specific. General diversity patterns along different gradients would likely indicate high resilience of benthic diatoms against differences and changes in the environment, whereas context-dependent patterns would possibly suggest that environmental change is likely to modify diatom communities and that region-specific differences should be considered when designing ecosystem management. I investigated the effect of environmental conditions on taxonomic and functional diatom diversity with distance-based redundancy analyses, variability of taxonomic diversity with species accumulation curves, taxonomic and functional aspects of spatial beta diversity with pairwise Bray-Curtis dissimilarity indices and Mantel tests, and diversity-biomass relationships with generalized linear models. The effect of environment on diatom communities was context-dependent, and different factors controlled communities along different gradients. Diversity varied along gradients and correlated with salinity in a U-shaped way. Beta diversity followed a general pattern of high taxonomic but low functional beta diversity along all gradients. Relationships between diatom diversity and ecosystem biomass were weak along all gradients. These results suggest that although the regional diversity of diatoms seems resilient, environmental change is likely to modify the local diversity of diatom communities. Finding out how these changes will affect ecosystem functioning requires further investigation.

Relationships between fluid mixing, biodiversity, and chemosynthetic primary productivity in Yellowstone hot springs

Article

Full-text available

Jan 2023

The factors that influence biodiversity and productivity of hydrothermal ecosystems are not well understood. Here we investigate the relationship between fluid mixing, biodiversity, and chemosynthetic primary productivity in three co‐localized hot springs (RSW, RSN, and RSE) in Yellowstone National Park that have different geochemistry. All three springs are sourced by reduced hydrothermal fluid, but RSE and RSN receive input of vapor phase gas and oxidized groundwaters, with input of both being substantially higher in RSN. Metagenomic sequencing revealed that communities in RSN were more biodiverse than those of RSE and RSW in all dimensions evaluated. Microcosm activity assays indicate that rates of dissolved inorganic carbon uptake were also higher in RSN than in RSE and RSW. Together, these results suggest that increased mixing of reduced volcanic fluid with oxidized fluids generates additional niche space capable of supporting increasingly biodiverse communities that are more productive. These results provide insight into the factors that generate and maintain chemosynthetic biodiversity in hydrothermal systems and that influence the distribution, abundance, and diversity of microbial life in communities supported by chemosynthesis. These factors may also extend to other ecosystems not supported by photosynthesis, including the vast subterranean biosphere and biospheres beneath ice sheets and glaciers. This article is protected by copyright. All rights reserved.

Broadscale Variation of Phytoplankton Richness in Brazilian Inland Waters

Chapter

Full-text available

Oct 2022

Species richness is a primary biodiversity measure in ecosystem functioning studies. The main factors shaping broadscale patterns of phytoplankton species richness (PhyRich) are temperature, system area, productivity, and less assessed light, flushing, and grazing. Our understanding of how the environment affects PhyRich is limited on broad spatial scales because of the lack of data using the same sampling and analysis methods. We selected three essential factors and hypothesized that PhyRich increases with water temperature, light availability (as turbidity), and intermediate productivity (as total phosphorus) levels. We assessed PhyRich from samples taken by a specially equipped hydroplane at 1045 sites across subcontinental (entire dataset) and regional (hydrographic regions) scales in Brazil (4°N–33°S and 34°–73°W) by quantifying the species number per site (settling technique). We selected models using the Akaike Information Criterion to understand which combination of variables better described PhyRich patterns. On our subcontinental scale, PhyRich was positively related to water temperature and negatively to light availability and productivity, although PhyRich was similar in oligo- and mesotrophic conditions, approaching the expected unimodal relationship. The trend for a slight reduction at the end of all gradients (univariate models) may have implications for the ecological functioning of freshwater systems.

Responses of Functional and Taxonomic Phytoplankton Diversity to Environmental Gradients in Subtropical and Tropical Reservoirs

Article

Full-text available

Jul 2022

Understanding the influence of environmental conditions on biodiversity is a major task in ecology. We investigated how phytoplankton taxonomic (TD) and functional (FD) diversities vary with environmental factors in eight subtropical and tropical reservoirs. We hypothesized that i) environmental variables affect phytoplankton TD and FD; ii) FD provides better relationships to environmental changes than TD, and; iii) indices based on biomass are better related to the environment than those based on identities. The relationships between phytoplankton diversities and environmental drivers were assessed through generalized linear models. Our hypotheses were partly confirmed. TD and FD were, in fact, dependent on the environment, with higher values occurring in warmer, clearer, and more enriched systems, under lower zooplankton grazing pressure; but FD based on identities was not predicted better from environmental conditions than TD based on identities. As expected, indices based on biomass are better related to the environment than their counterpart based on identities.

Habitats and seasons differentiate the assembly of bacterial communities along a trophic gradient of freshwater lakes

Article

Full-text available

May 2021

• Freshwater lakes are subject to variable degrees of eutrophication. Within lakes, the planktonic bacterial community (PBC) and sediment bacterial community (SBC) are both significant participants in biogeochemical processes of lake ecosystems. However, how the assembly patterns of bacterial communities vary seasonally along a trophic gradient in freshwater lakes is poorly understood. • Here, we collected and analysed water and sediment samples from 13 shallow lakes located in an urban region of China during summer and winter, the trophic states of which ranged from mesotrophic to middle eutrophic in summer and oligo-mesotrophic to light eutrophic in winter. High-throughput sequencing of 16S ribosomal RNA genes was used to determine the diversity and composition of bacterial communities. • Our results indicated that bacterial communities derived from different habitats and seasons did not exhibit a uniform response to lake trophic states. Linear and nonlinear mixed effect models suggested that the α-diversity of PBC and SBC, respectively, showed a unimodal and monotonically decreasing trend with increasing eutrophication in summer, whereas that of PBC and SBC, respectively, exhibited no obvious trend or an increased pattern along the trophic gradient in winter. In addition, the taxonomic compositional dissimilarity of the PBC was most significantly related to lake trophic differences in summer. Phylogenetic structure analysis revealed that mostly environmental selection regulated the SBC and PBC in both seasons. Moreover, dispersal limitation and homogenising dispersal contributed more to the assembly of SBC and PBC in both seasons, respectively. Water temperature, associated with seasonal variability, was the most important variable driving the PBC assembly, while sediment pH overwhelmed nutrients in regulating the seasonal patterns of SBC assemblages. • Overall, we highlighted that the water and sediments, as well as the seasons, differentiated the diversity patterns and assembly processes of bacterial communities along a trophic gradient of freshwater lakes. Our findings provide novel information for understanding the ecological responses of lacustrine bacterial communities to trophic gradients and seasonal variations. This study also contributes an important reference for predicting the changes of microbial community biodiversity under future scenarios of eutrophication.

Nutrient levels and trade-offs control diversity in a serial dilution ecosystem

Article

Full-text available

Sep 2020

Microbial communities feature an immense diversity of species and this diversity is linked to outcomes ranging from ecosystem stability to medical prognoses. Yet the mechanisms underlying microbial diversity are under debate. While simple resource-competition models don't allow for coexistence of a large number of species, it was recently shown that metabolic trade-offs can allow unlimited diversity. Does this diversity persist with more realistic, intermittent nutrient supply? Here, we demonstrate theoretically that in serial dilution culture, metabolic trade-offs allow for high diversity. When a small amount of nutrient is supplied to each batch, the serial dilution dynamics mimic a chemostat-like steady state. If more nutrient is supplied, community diversity shifts due to an 'early-bird' effect. The interplay of this effect with different environmental factors and diversity-supporting mechanisms leads to a variety of relationships between nutrient supply and diversity, suggesting that real ecosystems may not obey a universal nutrient-diversity relationship.

Nutrient levels and trade-offs control diversity in a serial dilution ecosystem

Article

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Sep 2020

Nutrient levels and trade-offs control diversity in a serial dilution ecosystem

Article

Full-text available

Sep 2020
eLife

Bacterial communities at a groundwater‐surface water ecotone: gradual change or abrupt transition points along a contamination gradient?

Article

Full-text available

Aug 2021

Microbial communities contribute greatly to groundwater quality, but the impacts of land‐use practices on bacteria in groundwaters and groundwater‐dependent ecosystems remain poorly known. With 16S rRNA gene amplicon sequencing, we assessed bacterial community composition at the groundwater‐surface water ecotone of boreal springs impacted by urbanization and agriculture, using spring water nitrate‐N as a surrogate of contamination. We also measured the rate of a key ecosystem process, organic matter decomposition. We documented a recurrent pattern across all major bacterial phyla where diversity started to decrease at unexpectedly low nitrate‐N concentrations (100–300 μg L−1). At 400 NO3−‐N μg L−1, 25 bacterial exact sequence variants showed a negative response, resulting in a distinct threshold in bacterial community composition. Chthonomonas, Acetobacterales and Hyphomicrobium were the most sensitive taxa, while only three taxa (Duganella, Undibacterium and Thermoanaerobaculaceae) were enriched due to increased contamination. Decomposition rate responded unimodally to increasing nitrate‐N concentration, with a peak rate at ~400 NO3−‐N μg L−1, parallelly with a major shift in bacterial community composition. Our results emphasize the utility of bacterial communities in the assessment of groundwater‐dependent ecosystems. They also call for a careful reconsideration of threshold nitrate values for defining groundwater ecosystem health and protecting their microbial biodiversity.

Trade-off shapes diversity in eco-evolutionary dynamics

Preprint

Full-text available

Sep 2017

We introduce an Interaction and Trade-off based Eco-Evolutionary Model (ITEEM), in which species are competing for resources in a well-mixed system, and their evolution in interaction trait space is subject to a life-history trade-off between replication rate and competitive ability. We demonstrate that the strength of the trade-off has a fundamental impact on eco-evolutionary dynamics, as it imposes four phases of diversity, including a sharp phase transition. Despite its minimalism, ITEEM produces without further ad hoc features a remarkable range of observed patterns of eco-evolutionary dynamics. Most notably we find self-organization towards structured communities with high and sustainable diversity, in which competing species form interaction cycles similar to rock-paper-scissors games.

Linkage Between Dissolved Organic Matter Transformation, Bacterial Carbon Production, and Diversity in a Shallow Oligotrophic Aquifer: Results From Flow-Through Sediment Microcosm Experiments

Article

Full-text available

Nov 2020

Aquifers are important reservoirs for organic carbon. A fundamental understanding of the role of groundwater ecosystems in carbon cycling, however, is still missing. Using sediment flow-through microcosms, long-term (171d) experiments were conducted to test two scenarios. First, aquifer sediment microbial communities received dissolved organic matter (DOM) at low concentration and typical to groundwater in terms of composition (DOM-1x). Second, sediments received an elevated concentration of DOM originating from soil (DOM-5x). Changes in DOM composition were analyzed via NMR and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Carbon production, physiological adaptations and biodiversity of groundwater, and sediment prokaryotic communities were monitored by total cell counts, substrate use arrays, and deep amplicon sequencing. The experiments showed that groundwater microbial communities do not react very fast to the sudden availability of labile organic carbon from soil in terms of carbon degradation and biomass production. It took days to weeks for incoming DOM being efficiently degraded and pronounced cell production occurred. Once conditioned, the DOM-1x supplied sediments mineralized 294(±230) μgC L-1sed d-1, 10-times less than the DOM-5x fed sediment communities [2.9(±1.1) mgC L-1sed d-1]. However, the overall biomass carbon production was hardly different in the two treatments with 13.7(±4.8) μgC L-1sed d-1 and 14.3(±3.5) μgC L-1sed d-1, respectively, hinting at a significantly lower carbon use efficiency with higher DOM availability. However, the molecularly more diverse DOM from soil fostered a higher bacterial diversity. Taking the irregular inputs of labile DOM into account, shallow aquifers are assumed to have a low resilience. Lacking a highly active and responsive microbial community, oligotrophic aquifers are at high risk of contamination with organic chemicals.

Ecological assessment of groundwater ecosystems disturbed by recharge systems using organic matter quality, biofilm characteristics and bacterial diversity

Article

Full-text available

Jan 2020
ENVIRON SCI POLLUT R

Recharge of aquifers by urban stormwater may trigger significant ecological changes that can be detrimental to the biodiversity and functioning of groundwater ecosystems. Here, the effects of aquifer recharge (AR) on three levels of parameters were investigated: dissolved organic carbon (DOC) quantity and quality, global biofilm characteristics, and diversity changes of bacterial communities. As DOC enrichment by AR can be mitigated by vadose zone (VZ) thickness, three AR sites with thin VZ (< 3 m) and three sites with thick VZ (> 10 m) were selected. For each AR site, clay beads were incubated over a 10-day-long rainy period through wells in recharged and non-recharged groundwaters. Total proteins, dehydrogenase, and hydrolytic activities were monitored from clay beads to assess biofilm development. Bacterial richness on beads was estimated by 16S rRNA-based metabarcoding. AR was found to significantly increase DOC and biodegradable DOC (BDOC) concentrations, biofilm development, and bacterial richness especially in sites with thin VZ. VZ thickness was inversely related to microbial growth indicators and bacterial richness in groundwater, through a control of DOC availability. The proportion of Bacteroidetes 16S rRNA gene reads was higher in recharged groundwater than in non-recharged groundwater, suggesting that this phylum could be used as an indicator of DOC enrichment associated with AR. Quantitative PCR assays for Bacteroides DNA confirmed these trends and showed an enrichment of this bacterial group in DOC-rich aquifer waters. The positive linear relationships between BDOC concentrations and biofilm variables highlighted a strong C-limitation of groundwater impacting bacterial species sorting and activity.

Resource diversity disturbs marine Vibrio diversity and community stability, but loss of Vibrio diversity enhances community stability

Article

Full-text available

Apr 2024

Vibrio is a salt‐tolerant heterotrophic bacterium that occupies an important ecological niche in marine environments. However, little is known about the contribution of resource diversity to the marine Vibrio diversity and community stability. In this study, we investigated the association among resource diversity, taxonomic diversity, phylogenetic diversity, and community stability of marine Vibrio in the Beibu Gulf. V. campbellii and V. hangzhouensis were the dominant groups in seawater and sediments, respectively, in the Beibu Gulf. Higher alpha diversity was observed in the sediments than in the seawater. Marine Vibrio community assembly was dominated by deterministic processes. Pearson's correlation analysis showed that nitrite (‐N), dissolved inorganic nitrogen (DIN), ammonium (‐N), and pH were the main factors affecting marine Vibrio community stability in the surface, middle, and bottom layers of seawater and sediment, respectively. Partial least‐squares path models (PLS‐PM) demonstrated that resource diversity, water properties, nutrients, and geographical distance had important impacts on phylogenetic and taxonomic diversity. Regression analysis revealed that the impact of resource diversity on marine Vibrio diversity and community stability varied across different habitats, but loss of Vibrio diversity increases community stability. Overall, this study provided insights into the mechanisms underlying the maintenance of Vibrio diversity and community stability in marine environments.

Environmental forcing of phytoplankton carbon-to-diversity ratio and carbon-to-chlorophyll ratio: A case study in Jiaozhou Bay, the Yellow Sea

Article

Nov 2023
MAR POLLUT BULL

The relationships between phytoplankton carbon (C) biomass and diversity (i.e., C-to-H′ ratio) and chlorophyll a (i.e., C-to-Chl a ratio) are good indicators of marine ecosystem functioning and stability. Here we conducted four cruises spanning 2 years in Jiaozhou Bay to explore the dynamics of C-to-H′ and C-to-Chl a ratios. The results showed that the phytoplankton C biomass and diversity were dominated by diatoms, followed by dinoflagellates. The average C-to-H′ ratio ranged from 84.10 to 912.17, with high values occurring in the northern region of the bay. In contrast, the average C-to-Chl a ratio ranged between 15.55 and 89.47, and high values primarily appeared in the northern or northeastern part of the bay. In addition, the redundancy analysis showed that temperature and phosphate (DIP) were significantly correlated with both ratios in most cases, indicating that temperature and DIP may be key factors affecting the dynamics of C-to-H′ and C-to-Chl a ratios.

Towards a mechanistic understanding of variation in aquatic food chain length

Article

Full-text available

Sep 2023
ECOL LETT

Ecologists have long sought to understand variation in food chain length (FCL) among natural ecosystems. Various drivers of FCL, including ecosystem size, resource productivity and disturbance, have been hypothesised. However, when results are aggregated across existing empirical studies from aquatic ecosystems, we observe mixed FCL responses to these drivers. To understand this variability, we develop a unified competition‐colonisation framework for complex food webs incorporating all of these drivers. With competition‐colonisation tradeoffs among basal species, our model predicts that increasing ecosystem size generally results in a monotonic increase in FCL, while FCL displays non‐linear, oscillatory responses to resource productivity or disturbance in large ecosystems featuring little disturbance or high productivity. Interestingly, such complex responses mirror patterns in empirical data. Therefore, this study offers a novel mechanistic explanation for observed variations in aquatic FCL driven by multiple environmental factors.

Trajectories of freshwater microbial genomics and greenhouse gas saturation upon glacial retreat

Article

Full-text available

Jun 2023

Due to climate warming, ice sheets around the world are losing mass, contributing to changes across terrestrial landscapes on decadal time spans. However, landscape repercussions on climate are poorly constrained mostly due to limited knowledge on microbial responses to deglaciation. Here, we reveal the genomic succession from chemolithotrophy to photo- and heterotrophy and increases in methane supersaturation in freshwater lakes upon glacial retreat. Arctic lakes at Svalbard also revealed strong microbial signatures form nutrient fertilization by birds. Although methanotrophs were present and increased along lake chronosequences, methane consumption rates were low even in supersaturated systems. Nitrous oxide oversaturation and genomic information suggest active nitrogen cycling across the entire deglaciated landscape, and in the high Arctic, increasing bird populations serve as major modulators at many sites. Our findings show diverse microbial succession patterns, and trajectories in carbon and nitrogen cycle processes representing a positive feedback loop of deglaciation on climate warming.

From the Mountain to the Valley: Drivers of Groundwater Prokaryotic Communities along an Alpine River Corridor

Article

Full-text available

Mar 2023

Rivers are the “tip of the iceberg”, with the underlying groundwater being the unseen freshwater majority. Microbial community composition and the dynamics of shallow groundwater ecosystems are thus crucial, due to their potential impact on ecosystem processes and functioning. In early summer and late autumn, samples of river water from 14 stations and groundwater from 45 wells were analyzed along a 300 km transect of the Mur River valley, from the Austrian alps to the flats at the Slovenian border. The active and total prokaryotic communities were characterized using high-throughput gene amplicon sequencing. Key physico-chemical parameters and stress indicators were recorded. The dataset was used to challenge ecological concepts and assembly processes in shallow aquifers. The groundwater microbiome is analyzed regarding its composition, change with land use, and difference to the river. Community composition and species turnover differed significantly. At high altitudes, dispersal limitation was the main driver of groundwater community assembly, whereas in the lowland, homogeneous selection explained the larger share. Land use was a key determinant of the groundwater microbiome composition. The alpine region was more diverse and richer in prokaryotic taxa, with some early diverging archaeal lineages being highly abundant. This dataset shows a longitudinal change in prokaryotic communities that is dependent on regional differences affected by geomorphology and land use.

Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades

Article

Full-text available

Feb 2023

Background Microorganisms such as coliform-forming bacteria are commonly used to assess freshwater quality for drinking and recreational use. However, such organisms do not exist in isolation; they exist within the context of dynamic, interactive microbial communities which vary through space and time. Elucidating spatiotemporal microbial dynamics is imperative for discriminating robust community changes from ephemeral ecological trends, and for improving our overall understanding of the relationship between microbial communities and ecosystem health. We conducted a seven-year (2013–2019) microbial time-series investigation in the Chicago Area Waterways (CAWS): an urban river system which, in 2016, experienced substantial upgrades to disinfection processes at two wastewater reclamation plants (WRPs) that discharge into the CAWS and improved stormwater capture, to improve river water quality and reduce flooding. Using culture-independent and culture-dependent approaches, we compared CAWS microbial ecology before and after the intervention. Results Examinations of time-resolved beta distances between WRP-adjacent sites showed that community similarity measures were often consistent with the spatial orientation of site locations to one another and to the WRP outfalls. Fecal coliform results suggested that upgrades reduced coliform-associated bacteria in the effluent and the downstream river community. However, examinations of whole community changes through time suggest that the upgrades did little to affect overall riverine community dynamics, which instead were overwhelmingly driven by yearly patterns consistent with seasonality. Conclusions This study presents a systematic effort to combine 16S rRNA gene amplicon sequencing with traditional culture-based methods to evaluate the influence of treatment innovations and systems upgrades on the microbiome of the Chicago Area Waterway System, representing the longest and most comprehensive characterization of the microbiome of an urban waterway yet attempted. We found that the systems upgrades were successful in improving specific water quality measures immediately downstream of wastewater outflows. Additionally, we found that the implementation of the water quality improvement measures to the river system did not disrupt the overall dynamics of the downstream microbial community, which remained heavily influenced by seasonal trends. Such results emphasize the dynamic nature of microbiomes in open environmental systems such as the CAWS, but also suggest that the seasonal oscillations remain consistent even when perturbed.

Ciências Ambientais: desafios e perspectivas

Book

Full-text available

Aug 2021

Este livro traz um pouco do significado das relevantes pesquisas realizadas pela Rede de Pós-Graduação em Desenvolvimento e Meio Ambiente (PRODEMA). A Rede PRODEMA é formada por sete Universidades do nordeste do Brasil (UFPI, UFC, UFRN, UFPB, UFPE, UFS e UESC) e abrange as mais diversas linhas de investigação associadas à área de Ciências Ambientais. Esse livro nasce, então, do reflexo das discussões e das pesquisas dos nossos alunos de Mestrado e Doutorado. Vamos apresentar aqui produtos das dissertações e teses geradas no PRODEMA, destacando pesquisas em temáticas como a qualidade do meio ambiente, percepção ambiental, relações com os recursos naturais e valoração da natureza.

Trajectories of freshwater microbial genomics and greenhouse gas saturation upon glacial retreat

Preprint

Full-text available

Sep 2022

Due to climate warming, ice sheets around the world are losing mass, contributing to changes in runoff, loads of nutrients and organic carbon to recipient lakes and rivers, and on a longer time span to greening of terrestrial landscapes. These changes are expected to affect microbial communities and the release of greenhouse gases from these systems, and thus repercuss to climate. However, these repercussions are poorly constrained mostly due to limited knowledge on microbial responses to deglaciation. Using genomic and chemical data from freshwater chronosequences in Arctic Svalbard and Alpine Norway, we reveal the genomic succession from chemolithotrophic to photo- and heterotrophic microbial taxa upon glacial retreat and nutrient fertilization by birds. The highly resolved trait patterns were related to greenhouse gas concentrations including methane and carbon dioxide supersaturation. Although methanotrophs were present and increased along the chronosequence, methane consumption rates were low even in supersaturated systems. Nitrous oxide oversaturation and genomic information suggest active nitrogen cycling across the entire deglaciated landscape, and in the high Arctic, birds served as major modulators at many sites. Our findings show diverse microbial succession patterns, and trajectories in carbon and nitrogen cycle processes representing a positive feedback loop of deglaciation on climate warming.

Functional and taxonomic diversities are better early indicators of eutrophication than composition of freshwater phytoplankton

Article

Full-text available

Aug 2022
HYDROBIOLOGIA

Eutrophication is a key threat to aquatic biodiversity around the world, but especially in the Cerrado biome that has undergone intensive land use conversion and fertilizer use. In this study, we investigated how water conditions and different taxonomic and functional indicators of phytoplankton communities responded to eutrophication over time and also identified which of these variables can act as early indicators of eutrophication. We used a mesocosm experiment to simulate shallow lakes and added nutrients to produce eutrophic and oligo-mesotrophic environments. We found that conductivity and turbidity increased with the nutrient enrichment process. Eutrophication did not change species richness; however, it increased the total phytoplankton density and chlorophyll-a concentration and decreased the diversity indices (Shannon–Wiener diversity and Pielou’s equitability) over time, for both taxonomic and functional facets. Our results indicate that eutrophication may not have marked effects on the composition of the initially dominant organisms in the short term but does increase the density of certain organisms and exclude rare species and functional groups in eutrophic environments along the time. Furthermore, the diversity indices are more sensitive indicators of eutrophication compared to abiotic indicators and composition of species and functional groups. Therefore, they may be considered reliable early warnings of ecosystem changes.

Adsorption of Nutrient Ions into Biofilm Matrices of Natural Microbial Consortium

Article

Full-text available

Jun 2022

The presence of nutrient ions significantly affects the biotic components in the ecosystem, including the microbial consortium. Nutrient ions are an essential part of the aquatic ecosystem, which significantly affects microbial life. Most microbes live by forming biofilms that can uptake nutrient ions from the surrounding water. However, studies reporting the characteristics of uptake of nutrient ions by biofilms of the natural microbial consortium have been rarely reported. Understanding the uptake characteristics of cationic and anionic nutrients is an essential foundation for understanding biofilms as the predominant habitat of aquatic microbes. This study aims to analyze the adsorption characteristics of cationic nutrient (ammonium) and anionic nutrient (nitrate) by biofilm matrices. This study indicates that cationic nutrients can be adsorbed more into the biofilm matrix than anionic nutrients. The adsorption process of nutrient ions by biofilms is a fast process that allows the concentration of nutrient ions inside the biofilm matrix to be much higher than the surrounding water. According to the results of this study, the passive uptake of nutrient ions into the biofilm matrix is an important ecological factor providing nutrient ions for aquatic microbial life.

Bacterioplankton Assembly Along a Eutrophication Gradient Is Mainly Structured by Environmental Filtering, Including Indirect Effects of Phytoplankton Composition

Article

Full-text available

Mar 2022
MICROB ECOL

Biotic interactions are suggested to be key factors structuring bacterioplankton community assembly but are rarely included in metacommunity studies. Eutrophication of ponds and lakes provides a useful opportunity to evaluate how bacterioplankton assembly is affected by specific environmental conditions, especially also by biotic interactions with other trophic levels such as phytoplankton and zooplankton. Here, we evaluated the importance of deterministic and stochastic processes on bacterioplankton community assembly in 35 shallow ponds along a eutrophication gradient in Belgium and assessed the direct and indirect effects of phytoplankton and zooplankton community variation on bacterioplankton assembly through a path analysis and network analysis. Environmental filtering by abiotic factors (suspended matter concentration and pH) explained the largest part of the bacterioplankton community variation. Phytoplankton community structure affected bacterioplankton structure through its effect on variation in chlorophyll-a and suspended matter concentration. Bacterioplankton communities were also spatially structured through pH. Overall, our results indicate that environmental variation is a key component driving bacterioplankton assembly along a eutrophication gradient and that indirect biotic interactions can also be important in explaining bacterioplankton community composition. Furthermore, eutrophication led to divergence in community structure and more eutrophic ponds had a higher diversity of bacteria.

Knowledge Gaps, Obstacles, and Research Frontiers in Groundwater Microbial Ecology

Chapter

Jan 2022

Aim: The aim of this chapter is to critically highlight existing knowledge gaps, obstacles, and research frontiers in groundwater microbial ecology. Main concepts covered: We have identified and discuss below 10 topics where there is an urgent need for microbiological research in groundwater. Main methods covered: We consider the challenges in groundwater microbiology research, including the limited accessibility of aquifers, methods to robustly characterize communities, the importance of microbial interactions, and the current lack of underpinning ecological theory and the testing of basic concepts in groundwater. Conclusion/Outlook: There is enormous opportunity to progress fundamental ecological understanding through further research of microbiology in the terrestrial subsurface.

Would that it were so simple: Interactions between multiple traits undermine classical single‐trait‐based predictions of microbial community function and evolution

Article

Full-text available

Aug 2021
ECOL LETT

Understanding how microbial traits affect the evolution and functioning of microbial communities is fundamental for improving the management of harmful microorganisms, while promoting those that are beneficial. Decades of evolutionary ecology research has focused on examining microbial cooperation, diversity, productivity and virulence but with one crucial limitation. The traits under consideration, such as public good production and resistance to antibiotics or predation, are often assumed to act in isolation. Yet, in reality, multiple traits frequently interact, which can lead to unexpected and undesired outcomes for the health of macroorganisms and ecosystem functioning. This is because many predictions generated in a single‐trait context aimed at promoting diversity, reducing virulence or controlling antibiotic resistance can fail for systems where multiple traits interact. Here, we provide a much needed discussion and synthesis of the most recent research to reveal the widespread and diverse nature of multi‐trait interactions and their consequences for predicting and controlling microbial community dynamics. Importantly, we argue that synthetic microbial communities and multi‐trait mathematical models are powerful tools for managing the beneficial and detrimental impacts of microbial communities, such that past mistakes, like those made regarding the stewardship of antimicrobials, are not repeated. Decades of evolutionary ecology research has focused on examining microbial cooperation, diversity, productivity and virulence but with one crucial limitation. The traits under consideration, such as public good production and resistance to antibiotics or predation, are often assumed to act in isolation. Yet, in reality, multiple traits frequently interact, which can lead to unexpected and undesired outcomes for the health of macroorganisms and ecosystem functioning.

Occurrence, sources, bioaccumulation, and air–water exchange fluxes of polycyclic aromatic hydrocarbons in Lake Hongze, China

Article

Full-text available

Jun 2021
J SOIL SEDIMENT

PurposeCompared with deep oligotrophic waters, the distribution and geochemical processes of polycyclic aromatic hydrocarbons (PAHs) in shallow eutrophic waters are more complicated. The fourth largest freshwater lake in China (Lake Hongze) was taken as an example to study distribution, sources, bioaccumulation, and air–water exchange of PAHs in shallow eutrophic waters.Materials and methodsEighty samples of surface sediments, air, water, and plankton were collected simultaneously from 15 sampling sites in November 2018. PAHs were extracted, concentrated, and analyzed using GC–MS.Results and discussionAverage concentrations of ∑PAH16 in the surface sediments, atmosphere, water, phytoplankton, zooplankton, and suspended particle matter were 511 ± 212 ng g−1, 119 ng m−3, 232 ± 91.2 ng L−1, 12,500 ± 70,000 ng g−1, 102,000 ± 83,600 ng g−1, and 35,100 ± 24,700 ng g−1. Log BCF of PAHs in phytoplankton ranged from 6.7 ± 7.8 to 16.0 ± 4.4. Log BAF of PAHs in zooplankton ranged from 8.2 ± 8.1 to 16.8 ± 3.9. Log BMF of PAHs from phytoplankton to zooplankton varied from − 0.25 ± 0.39 to 0.25 ± 0.55.Conclusions Combustion of petroleum and coal was the main source for the PAHs in the surface sediments of Lake Hongze. Concentrations of PAHs in phytoplankton and zooplankton were negatively correlated to the trophic level index. Bioaccumulation of PAHs by plankton was observed. No biomagnification occurred from phytoplankton to zooplankton for most PAHs during this sampling period. The net air–water flux of low molecular weight PAHs was from water to air. The net air–water flux of high molecular weight PAHs was from air to water.

Computational Design of Synthetic Microbial Communities

Conference Paper

Apr 2021

Behzad Darius Karkaria

In naturally occurring microbial systems, species rarely exist in isolation. There is strong ecological evidence for a positive relationship between species diversity and the functional output of communities. The pervasiveness of these communities in nature highlights that there may be advantages for engineered strains to exist in cocultures as well. Building synthetic microbial communities allows us to create distributed systems that mitigate issues often found in engineering a monoculture, especially when functional complexity is increasing. The establishment of synthetic microbial communities is a major challenge we must overcome in order to implement coordinated multicellular systems. Here I present computational tools that help us design engineering strategies for establishing synthetic microbial communities. Using these tools I identify promising candidates for several design scenarios. This work highlights the importance of parameter inference and model selection to build robust communities. The findings highlight important interaction motifs that provide stability, and identify requirements for selecting genetic parts and tuning the community composition. Additionally, I show that fundamental interactions in small synthetic communities can produce chaotic behaviour that is unforecastable. Together these findings have important ramifications for how we build synthetic communities in the lab, and the considerations of interactions in microbiomes we manipulate.

Investigating the microbial ecology of coastal hotspots of marine nitrogen fixation in the western North Atlantic

Article

Full-text available

Mar 2021

Variation in the microbial cycling of nutrients and carbon in the ocean is an emergent property of complex planktonic communities. While recent findings have considerably expanded our understanding of the diversity and distribution of nitrogen (N2) fixing marine diazotrophs, knowledge gaps remain regarding ecological interactions between diazotrophs and other community members. Using quantitative 16S and 18S V4 rDNA amplicon sequencing, we surveyed eukaryotic and prokaryotic microbial communities from samples collected in August 2016 and 2017 across the Western North Atlantic. Leveraging and significantly expanding an earlier published 2015 molecular dataset, we examined microbial community structure and ecological co-occurrence relationships associated with intense hotspots of N2 fixation previously reported at sites off the Southern New England Shelf and Mid-Atlantic Bight. Overall, we observed a negative relationship between eukaryotic diversity and both N2 fixation and net community production (NCP). Maximum N2 fixation rates occurred at sites with high abundances of mixotrophic stramenopiles, notably Chrysophyceae. Network analysis revealed such stramenopiles to be keystone taxa alongside the haptophyte diazotroph host Braarudosphaera bigelowii and chlorophytes. Our findings highlight an intriguing relationship between marine stramenopiles and high N2 fixation coastal sites.

Spatial analysis of gut microbiome reveals a distinct ecological niche associated with the mucus layer

Article

Full-text available

Jan 2021

Mucus-associated bacterial communities are critical for determining disease pathology and promoting colonization resistance. Yet the key ecological properties of mucus resident communities remain poorly defined. Using an approach that combines in situ hybridization, laser microdissection and 16s rRNA sequencing of spatially distinct regions of the mouse gut lumen, we discovered that a dense microbial community resembling a biofilm is embedded in the mucus layer. The mucus-associated biofilm-like community excluded bacteria belonging to phylum Proteobacteria. Additionally, it was significantly more diverse and consisted of bacterial species that were unique to it. By employing germ-free mice deficient in T and B lymphocytes we found that formation of biofilm-like structure was independent of adaptive immunity. Instead the integrity of biofilm-like community depended on Gram-positive commensals such as Clostridia. Additionally, biofilm-like community in the mucus lost fewer Clostridia and showed smaller bloom of Proteobacteria compared to the lumen upon antibiotic treatment. When subjected to time-restricted feeding biofilm-like structure significantly enhanced in size and showed enrichment of Clostridia. Taken together our work discloses that mucus-associated biofilm-like community represents a specialized community that is structurally and compositionally distinct that excludes aerobic bacteria while enriching for anaerobic bacteria such as Clostridia, exhibits enhanced stability to antibiotic treatment and that can be modulated by dietary changes.

Multiple stressors shape invertebrate assemblages and reduce their trophic niche: A case study in a regulated stream

Article

Feb 2021
SCI TOTAL ENVIRON

Few studies have addressed how the diversity of basal resources change with stream regulation and the potential consequences on river biota. We sampled invertebrates above and below a series of dams, over two years, at both downwelling and upwelling zones. In each zone, we recorded the daily temperature and flow variations, estimated the algal development, measured the available resources, and analysed carbon and nitrogen stable isotope compositions of the invertebrate community. The number of hydrological pulses were typically higher below the dams than above the dams especially during high-flow periods whereas the groundwater outlets had minor effects on invertebrate assemblages. Invertebrate abundance, richness and diversity tended to decrease below the dams. Co-inertia analysis showed that flow and temperature variations, and eutrophication explained most of the variance in the invertebrate assemblages, which comprised a higher number of resilient taxa below than above the dams. The proportions of pesticide-sensitive invertebrates were lower below the dams and ovoviviparous and more generalist taxa were prominent. We did not observe the expected CPOM decrease and FPOM increase downstream. Accordingly, the proportions of each functional feeding group were remarkably similar above and below the dams despite the long distance between the sectors (>100 kms). The diversity of basal resources used within assemblages progressively increased downstream above dams. In contrast, the diversity of resources used by organisms below the dams decreased from upstream to downstream suggesting a significant influence of flow regulation on aquatic food webs. Finally, the shorter trophic chains for the invertebrate assemblages below the dams suggests that the effects of stream regulation and eutrophication induced a simplification of food webs. To our knowledge, this study is the first to connect taxonomic and functional trait changes in response to multiple stressors with the associated modifications in isotopic niches within aquatic invertebrate assemblages. Context Understanding how stream regulation and associated anthropogenic pressures act on aquatic assemblages and trophic niches is necessary to guide management actions. Goal We aimed to investigate the functional responses (traits and trophic niches) of aquatic invertebrate assemblages to stream regulation and eutrophication. Methods We used univariate and multivariate analyses to compare the invertebrate assemblages above and below the dams and to assess the contributions of hydrology (including groundwater supplies to the river), temperature and eutrophication to the variability in the composition of invertebrate assemblages. We also considered the relative utilization of a selected set of traits describing invertebrate resilience, resistance and specialization to address the potential functional effects of stream regulation on invertebrate assemblages. Finally, carbon and nitrogen isotope analyses allowed us to characterize the length and width of invertebrate assemblage food webs as related to the availability and diversity of basal resources. Results Invertebrate abundance and richness generally decreased below the dams, with the highest impacts on insect taxa. Co-inertia analysis showed that stream regulation and eutrophication were main drivers of the aquatic invertebrate assemblages. The analysis separated the sites above and below the dams according to flow and temperature variation, whereas eutrophication appeared as a secondary stressor that separated the sites within each sector. Furthermore, the series of dams resulted in (i) a higher proportion of resilient (e.g., multivoltine) and resistant (ovoviviparous) taxa and a majority of generalists in assemblages below dams, (ii) an impact on the classical dynamics of CPOM (decrease) and FPOM (increase) sources from upstream to downstream, and (iii) a reduction in the diversity of resource use and in the trophic chain length of invertebrate assemblages below dams. The cooler and less oxygenated upwelling zones had lower invertebrate abundance; however, contrary to our expectation, the variation in the groundwater supply did not affect the composition of epigean invertebrate assemblages. Conclusion This study provides insights about the impacts of flow regime alteration and eutrophication on food webs that may have been caused by regulation of permanent streams. To our knowledge, this is the first to connect taxonomic and functional trait changes in response to multiple stressors with the associated modifications in energy fluxes in aquatic invertebrate assemblages. This study suggests that bed stability, which is associated with a reduction in channel mobility below the dams and with moderate eutrophication, may provide the shelter and resources that can locally favour invertebrate assemblage dynamics and lessen the effects of flow regulation. In addition, the study suggests that the biological trait-based approach and isotope analysis are complementary approaches for addressing ecosystem functioning. The relative utilization of traits indicates the functional potential of aquatic invertebrate assemblages to face multiple stressors whereas isotope analysis is an expression of the actual effect of the stressors on the trophic structure of aquatic invertebrate assemblages.

Community biofilm-formation, stratification and productivity in serially-transferred microcosms

Article

Nov 2020

The establishment of O2 gradients in liquid columns by bacterial metabolic activity produces a spatially-structured environment. This produces a high-O2 region at the top that represents an un-occupied niche which could be colonised by biofilm-competent strains. We have used this to develop an experimental model system using soil-wash inocula and a serial-transfer approach to investigate changes in community-based biofilm-formation and productivity. This involved ten transfers of mixed-community or biofilm-only samples over a total of 10–60 days incubation. In all final-transfer communities the ability to form biofilms was retained, though in longer incubations the build-up of toxic metabolites limited productivity. Measurements of microcosm productivity, biofilm-strength and attachment levels were used to assess community-aggregated traits which showed changes at both the community and individual-strain levels. Final-transfer communities were stratified with strains demonstrating a plastic phenotype when migrating between the high and low-O2 regions. The majority of community productivity came from the O2-depleted region rather than the top of the liquid column. This model system illustrates the complexity we expect to see in natural biofilm-forming communities. The connection between biofilms and the liquid column seen here has important implications for how these structures form and respond to selective pressure.

Organic Matter Composition at Ocean Station Papa Affects Its Bioavailability, Bacterioplankton Growth Efficiency and the Responding Taxa

Article

Full-text available

Dec 2020

The bioavailability of organic matter (OM) to marine heterotrophic bacterioplankton is determined by both the chemical composition of OM and the microbial community composition. In the current study, changes in OM bioavailability were identified at Ocean Station Papa as part of the 2018 Export Processes in the Ocean from Remote Sensing (EXPORTS) field study. Removal rates of carbon (C) in controlled experiments were significantly correlated with the initial composition of total hydrolyzable amino acids, and C removal rates were high when the amino acid degradation index suggested a more labile composition. Carbon remineralization rates averaged 0.19 ± 0.08 μmol C L–1 d–1 over 6–10 days while bacterial growth efficiencies averaged 31 ± 7%. Amino acid composition and tandem mass spectrometry analysis of compound classes also revealed transformations to a more degraded OM composition during experiments. There was a log2-fold increase in the relative abundances of 16S rDNA-resolved bacterioplankton taxa in most experiments by members of the Methylophilaceae family (OM43 genus) and KI89A order. Additionally, when OM was more bioavailable, relative abundances increased by at least threefold for the classes Bacteroidetes (Flavobacteriaceae NS2b genus), Alphaproteobacteria (Rhodobacteraceae Sulfitobacter genus), and Gammaproteobacteria (Alteromonadales and Ectothiorhodospiraceae orders). Our data suggest that a diverse group of bacterioplankton was responsible for removing organic carbon and altering the OM composition to a more degraded state. Elevated community diversity, as inferred from the Shannon–Wiener H index, may have contributed to relatively high growth efficiencies by the bacterioplankton. The data presented here shed light on the interconnections between OM bioavailability and key bacterioplankton taxa for the degradation of marine OM.

Groundwater Microbial Communities in Times of Climate Change

Article

Full-text available

Oct 2020
CURR ISSUES MOL BIOL

Climate change has a massive impact on the global water cycle. Subsurface ecosystems, the earth largest reservoir of liquid freshwater, currently experience a significant increase in temperature and serious consequences from extreme hydrological events. Extended droughts as well as heavy rains and floods have measurable impacts on groundwater quality and availability. In addition, the growing water demand puts increasing pressure on the already vulnerable groundwater ecosystems. Global change induces undesired dynamics in the typically nutrient and energy poor aquifers that are home to a diverse and specialized microbiome and fauna. Current and future changes in subsurface environmental conditions, without doubt, alter the composition of communities, as well as important ecosystem functions, for instance the cycling of elements such as carbon and nitrogen. A key role is played by the microbes. Understanding the interplay of biotic and abiotic drivers in subterranean ecosystems is required to anticipate future effects of climate change on groundwater resources and habitats. This review summarizes potential threats to groundwater ecosystems with emphasis on climate change and the microbial world down below our feet in the water saturated subsurface.

Taxonomic Diversity of Pico-/Nanoeukaryotes Is Related to Dissolved Oxygen and Productivity, but Functional Composition Is Shaped by Limiting Nutrients in Eutrophic Coastal Oceans

Article

Full-text available

Nov 2020

Pico-/nanoeukaryotes (P/NEs) comprise both primary producers and bacterial predators, playing important biogeochemical and ecological roles in the marine microbial loop. Besides the difference in size, these small sized fractions can be distinguished from microplankton by certain functional and ecological traits. Nevertheless, little information is available regarding patterns of their taxonomic and functional diversity and community composition along environmental gradients in coastal marine ecosystems. In this study, we applied high-throughput sequencing of 18S rRNA gene to assess the taxonomic species richness and community composition of P/NEs in surface waters of Bohai Sea and North Yellow Sea, northern China spanning a 600-km distance during summer and winter of 2011. The richness of operational taxonomic units (OTUs) formed a U-shaped relationship with concentration of chlorophyll a (Chl-a, a proxy of primary productivity), but a stronger, negative relationship with concentration of dissolved oxygen (DO). These two factors also significantly co-varied with the OTU-based community composition of P/NEs. The effect of geographic distance on community composition of P/NEs was negligible. Among the three functional groups defined by trophic traits, heterotrophs had the highest OTU richness, which exhibited a U-shaped relationship with both DO and Chl-a. The community of P/NEs was dominated by heterotrophs and mixotrophs in terms of read numbers, which showed a trade-off along the gradient of phosphate, but no significant changes along DO and Chl-a gradients, indicating functional redundancy. Similarly, the proportion of phototrophs was significantly and positively correlated with the concentration of silicate. Our results indicate that taxonomic and functional composition of P/NEs are decoupled on a regional scale, and limiting nutrients are important factors in modulating functional composition of these microorganisms in the studied area. These findings contribute towards gaining a better understanding of how diversity of small eukaryotes and their functions are structured in coastal oceans and the effect of environmental changes on the structuring process.

Biodiversity and Host–Parasite (Co)Extinction

Chapter

Full-text available

Dec 2021

Parasitism is one of the most common modes of life, and yet it is often disregarded or ignored in nature conservation. We are at the brink of the sixth mass extinction and in order to assess the extinction risk of both parasites and their hosts, we first need to fully understand the role and function of parasites in ecosystems. Parasites might play an active role in their host’s extinction, and coextinction has been postulated to be the most common mode of extinction. However, parasites may be able to survive their host’s extinction through host switching, perhaps to a more abundant host, for example. The dilution effect has been described as an important natural defense mechanism for the host: higher biodiversity is associated with lower infection risk. Discussed here is the importance of biodiversity and host–parasite associations and (co)extinction, and the role the fossil record has in filling the knowledge gap regarding deep-time host–parasite interactions.

Groundwater Microbial Communities in Times of Climate Change

Chapter

Full-text available

Oct 2020

Climate change has a massive impact on the global water cycle. Subsurface ecosystems, the earth largest reservoir of liquid freshwater, currently experience a significant increase in temperature and serious consequences from extreme hydrological events. Extended droughts as well as heavy rains and floods have measurable impacts on groundwater quality and availability. In addition, the growing water demand puts increasing pressure on the already vulnerable groundwater ecosystems. Global change induces undesired dynamics in the typically nutrient and energy poor aquifers that are home to a diverse and specialized microbiome and fauna. Current and future changes in subsurface environmental conditions, without doubt, alter the composition of communities, as well as important ecosystem functions, for instance the cycling of elements such as carbon and nitrogen. A key role is played by the microbes. Understanding the interplay of biotic and abiotic drivers in subterranean ecosystems is required to anticipate future effects of climate change on groundwater resources and habitats. This chapter summarizes potential threats to groundwater ecosystems with emphasis on climate change and the microbial world down below our feet in the water saturated subsurface.

Fundamental research questions in subterranean biology

Article

Nov 2020

Five decades ago, a landmark paper in Science titled The Cave Environment heralded caves as ideal natural experimental laboratories in which to develop and address general questions in geology, ecology, biogeography, and evolutionary biology. Although the 'caves as laboratory' paradigm has since been advocated by subterranean biologists, there are few examples of studies that successfully translated their results into general principles. The contemporary era of big data, modelling tools, and revolutionary advances in genetics and (meta)genomics provides an opportunity to revisit unresolved questions and challenges, as well as examine promising new avenues of research in subterranean biology. Accordingly, we have developed a roadmap to guide future research endeavours in subterranean biology by adapting a well-established methodology of 'horizon scanning' to identify the highest priority research questions across six subject areas. Based on the expert opinion of 30 scientists from around the globe with complementary expertise and of different academic ages, we assembled an initial list of 258 fundamental questions concentrating on macroecology and microbial ecology, adaptation , evolution, and conservation. Subsequently, through online surveys, 130 subterranean biologists with various backgrounds assisted us in reducing our list to 50 top-priority questions. These research questions are broad in scope and ready to be addressed in the next decade. We believe this exercise will stimulate research towards a deeper understanding of subterranean biology and foster hypothesis-driven studies likely to resonate broadly from the traditional boundaries of this field.

Microbialites of Great Salt Lake

Chapter

Jul 2020

Fossilized organo-sedimentary structures (microbialites) have been identified in sedimentary rocks dated to 3.5 Ga, with some reports of putative microbialite structures in rocks that are even older. These findings have spurred significant interest in understanding the role of biology in the formation of microbialites and the role of microbialites in sustaining biodiverse contemporary and non-contemporary ecosystems. Microbialites in Great Salt Lake (GSL) form reef-like structures that cover an estimated 20% of the lake bottom and thus represent the most extensive assemblage of extant microbialites on Earth. GSL microbialites are colonized by complex photosynthetic microbial mats consisting of both Cyanobacteria and algae (diatoms) that contribute fixed carbon supporting a diversity of heterotrophic microorganisms also within these mats. These diverse microbial communities are also thought to be involved in the formation of carbonate minerals that can then lithify and preserve microbialite structure. Biomass produced by these complex microbial communities supports a variety of higher forms of life, including brine flies and brine shrimp that themselves serve as food sources for a diverse array of shore and migratory birds. Consequently, the microbialites and associated mat communities represent integral components of the aquatic ecosystem at GSL and represent useful analogs for understanding microbialite ecology in past Earth environments. This chapter overviews the key microbial taxa that comprise microbialite mat communities and the metabolic processes that support them, highlighting the importance of these “living fossils” and their linkages with the health of the greater GSL ecosystem and their significance as analogs for understanding ecosystem function on early Earth.

Environmental and Spatial Influences on Biogeography and Community Structure of Saltmarsh Benthic Diatoms

Article

Jul 2020

Benthic microalgae play important roles in energy flow and biogeochemistry of coastal ecosystems; however, factors influencing community composition remain largely unknown. Our purpose was to identify and compare spatial and environmental influences on benthic diatom biogeography at regional scales. In summer 2018, we sampled sediment at various spatial scales (0.0001–180 km) from five saltmarshes in South Carolina, USA, and characterized diatom assemblages using DNA metabarcoding. Twenty-three environmental variables from marsh sediments, adjacent creeks, and atmosphere were recorded. Multivariate analyses revealed that the saltmarsh communities were clearly distinct. Community dissimilarity was compared to both geographic distance and environmental differences to determine influences on community structure. Mantel tests and redundancy analysis revealed that spatial influences, in addition to several environmental factors (phosphate, grain size, sediment sorting, sediment moisture, and creek salinity), were significant. Variation partitioning revealed that 26% of community variation was explained by geographic distance alone, whereas 60% could be explained by combined spatial/environmental factors. In contrast, the independent explanatory power of individual environmental factors was negligible. Our findings suggest that spatially structured environmental variation mainly conditioned the saltmarsh diatom biogeography in this region. Dispersal limitation, as evinced by the large pure spatial effect and distance-decay pattern, was also important. Spatial effects were stronger relative to that previously observed in other microbial groups (marine bacteria and phytoplankton) and detected at finer spatial scales. Results support prior studies that suggest body size and dispersal mode are important drivers of metacommunity structure and therefore must be considered when studying aquatic microbial biogeography.

Effets conjoints de facteurs physiques (lumière et vitesse du courant) et chimiques (pesticides) sur la structure et la composition du périphyton : Une approche multi-échelle

Thesis

Full-text available

Dec 2008

Villeneuve Aurelie

Cette thèse s’articule autour de l’hypothèse générale selon laquelle une modification des facteurs physiques des milieux aquatiques (intensité lumineuse et vitesse du courant) peut entraîner une modification de la dynamique et/ou de la structure, de la composition et du fonctionnement du périphyton et donc de sa réponse à la présence de polluants. Cette hypothèse a été testée 1) dans des systèmes de complexité croissante allant d’approches expérimentales (microcosmes et mésocosmes) à des approches in situ, et 2) pour des variations de faible intensité des facteurs physiques et chimiques telles qu’observées sur le terrain. * L’effet de la lumière (éclairé/ombragé) et l’effet de la présence de diuron (herbicide) à faible concentration (1 μg.L-1) ont été testés en microcosmes de laboratoire. Nous avons ainsi : - observé un décalage du développement des biofilms placés sous ombrage. - caractérisé des espèces plus aptes à se développer dans des conditions limitantes de lumière, notamment parmi les diatomées. - mis en évidence qu’à ces changements de diversité et de structure, sont associés une modification de la réponse et un changement de la tolérance des communautés périphytiques à un même stress toxique * La vitesse du courant est un autre facteur physique d’intérêt pour la structuration des biofilms. Les petits milieux lotiques sont composés d’une succession de différents faciès hydrauliques, radier, mouille, cascade…. Chacun de ces faciès est, en théorie, caractérisé par des communautés microbiennes adaptées aux conditions environnementales locales. Au sein de mésocosmes d’extérieur, nous avons créé des zones d’hydraulique très contrastée avec comme objectif l’établissement de communautés différentes. L’application d’un mélange de pesticides nous a ensuite permis d’évaluer la tolérance de ces différentes communautés. Nous avons observé : - un retard d’installation et une moindre densité du périphyton au sein de zones d’hydraulique rapide - un changement de diversité algale (développement plus important d’algues filamenteuses en zone de faible courant) qui entraîne une différence de réponse et de tolérance aux pesticides. - une répercussion de la présence de micro-habitats physiques diversifiés à l’échelle locale (décimètre) à une échelle plus globale (rivières artificielles hétérogènes ou homogènes sur le plan hydraulique). - un effet des variations saisonnières (printemps / automne) qui entraînent des différences de structure, de diversité et de fonctionnement des biofilms et finalement une différence de sensibilité à la présence de molécules polluantes. * Une étude in situ, a permis d’approfondir ces résultats, dans le contexte plus complexe d’une petite rivière, en caractérisant les communautés périphytiques et leurs réponses au stress chimique en fonction du régime hydraulique. Ces travaux ont été menés sur la Morcille, petite rivière d’ordre 1, qui traverse un bassin versant occupé à 60-70 % par de la vigne. Les communautés périphytiques de ce cours d’eau sont soumises à deux types de pollution: les phytosanitaires et la pollution organique. Des études antérieures ont montré un changement global et permanent de diversité et de tolérance des communautés périphytiques le long d’un gradient amont-aval de pollution, sans toutefois aborder les interactions entre niveaux de contaminations et facteurs hydrauliques. Cette étude de terrain permet également d’évaluer la pertinence des résultats obtenus lors de nos essais en microcosmes et mésocosmes. Ainsi, nous avons : - Confirmé une différence de structure des communautés périphytiques entre l’amont et l’aval. - Observé, en accord avec nos expérimentations en rivières artificielles, des différences de structuration et de diversité des communautés issues de zones d’hydraulique différente. - Caractérisé des réponses différentes au mélange in situ de polluants de la part des communautés issues de zones d’hydraulique différente. - Enregistré une modification de la réponse des communautés en lien avec des changements saisonniers. Une analyse « transversale » de ces résultats, s’appuyant sur les différents niveaux d’études abordés (du microcosme à l’in situ) nous a également permis, de préciser les méthodologies expérimentales nécessaire

Stable Seasonal and Annual Alpha Diversity of Benthic Diatom Communities Despite Changing Community Composition

Article

Full-text available

Feb 2020

The global biodiversity loss has raised interest in the different facets of diversity, and the importance of diversity for ecosystem functions has been recognized. However, our knowledge on seasonal and inter-annual variation in the composition and diversity of communities is still poor. Here, we investigated the seasonal and inter-annual changes in taxonomic and functional community composition and diversity of benthic diatoms in a coastal habitat of the northern Baltic Sea, where seasonal and inter-annual variation of climate is pronounced. We found that the taxonomic and functional alpha diversity remained stable at seasonal and inter-annual level despite strong changes in community composition. However, alpha diversity decreased during an exceptionally warm winter possibly due to disturbances induced by the lack of ice. This may suggest that climate warming and consequently limited ice cover will affect the diversity of benthic communities.

Dimensions of marine phytoplankton diversity

Article

Full-text available

Feb 2020
BG

Biodiversity of phytoplankton is important for ecosystem stability and marine biogeochemistry. However, the large-scale patterns of diversity are not well understood and are often poorly characterized in terms of statistical relationships with factors such as latitude, temperature and productivity. Here we use ecological theory and a global trait-based ecosystem model to provide mechanistic understanding of patterns of phytoplankton diversity. Our study suggests that phytoplankton diversity across three dimensions of trait space (size, biogeochemical function and thermal tolerance) is controlled by disparate combinations of drivers: the supply rate of the limiting resource, the imbalance in different resource supplies relative to competing phytoplankton demands, size-selective grazing and transport by the moving ocean. Using sensitivity studies we show that each dimension of diversity is controlled by different drivers. Models including only one (or two) of the trait dimensions will have different patterns of diversity than one which incorporates another trait dimension. We use the results of our model exploration to infer the controls on the diversity patterns derived from field observations along meridional transects in the Atlantic and to explain why different taxa and size classes have differing patterns.

Key role of plankton species and nutrients on biomagnification of PAHs in the micro-food chain: A case study in plateau reservoirs of Guizhou, China

Article

Jun 2024
J HAZARD MATER

A circumpolar study of surface zooplankton biodiversity of the Southern Ocean based on eDNA metabarcoding

Article

May 2024
ENVIRON RES

Resource availability governs polyhydroxyalkanoate (PHA) accumulation and diversity of methanotrophic enrichments from wetlands

Article

Full-text available

Jul 2023

Aquatic environments account for half of global CH4 emissions, with freshwater wetlands being the most significant contributors. These CH4 fluxes can be partially offset by aerobic CH4 oxidation driven by methanotrophs. Additionally, some methanotrophs can convert CH4 into polyhydroxyalkanoate (PHA), an energy storage molecule as well as a promising bioplastic polymer. In this study, we investigate how PHA-accumulating methanotrophic communities enriched from wetlands were shaped by varying resource availability (i.e., C and N concentrations) at a fixed C/N ratio. Cell yields, PHA accumulation, and community composition were evaluated in high (20% CH4 and 10 mM NH4 ⁺) and low resource (0.2% CH4 and 0.1 mM NH4 ⁺) conditions simulating engineered and environmental settings, respectively. High resource availability decreased C-based cell yields, while N-based cell yields remained stable, suggesting nutrient exchange patterns differed between methanotrophic communities at different resource concentrations. PHA accumulation was only observed in high resource enrichments, producing approximately 12.6% ± 2.4% (m/m) PHA, while PHA in low resource enrichments remained below detection. High resource enrichments were dominated by Methylocystis methanotrophs, while low resource enrichments remained significantly more diverse and contained only a minor population of methanotrophs. This study demonstrates that resource concentration shapes PHA-accumulating methanotrophic communities. Together, this provides useful information to leverage such communities in engineering settings as well as to begin understanding their role in the environment.

Linking satellites to genes with machine learning to estimate major phytoplankton groups from space

Preprint

Full-text available

Dec 2022

Ocean color remote sensing offers two decades-long time series of information on phytoplankton abundance. However , determining the structure of the phytoplankton community from this signal is not straightforward, and many uncertainties remain to be evaluated, despite multiple intercomparison efforts of the different available algorithms. Here, we use remote sensing and machine learning to infer the abundance of seven phytoplankton groups at global scale based on a new molecular method from Tara Oceans. Our dataset is to our knowledge the most comprehensive and complete, available to describe phy-5 toplankton community structure at global scale using a molecular marker that defines relative abundances of all phytoplankton groups simultaneously. The methodology shows satisfying performances to provide robust estimates of phytoplankton groups using satellite data, with few limitations regarding the global generalization of the method. Furthermore, this new satellite-based methodology allows a valuable global intercomparison with the pigment-based approach used in in-situ and satellite data to identify phytoplankton groups. Nevertheless, these datasets show different, yet coherent information on the phyto-10 plankton, valuable for the understanding of community structure. This makes remote sensing observations excellent tools to collect Essential Biodiversity Variables and provide a foundation for developing marine biodiversity forecasts.

Comparison in phytoplankton diversity-productivity-community stability between river-type reservoir and lake-type reservoir

Article

Full-text available

Jul 2022

Relationship between biodiversity and ecosystem function is one of the core issues in ecological research. Phytoplankton, as the main producer of aquatic ecosystem, its diversity, productivity, and community stability are of great significance to reveal ecosystem function. There are significant differences in hydrodynamics, water retention time, and phytoplankton community structure between river-type reservoir and newly built lake-type reservoir. The comparative analysis of phytoplankton community stability between the two types of reservoir has not been reported. Jiuquwan Reservoir (river-type) and Taihu Reservoir (laketype), the two reservoirs in the Dongjiang River source area of Zhujiang (Pearl) River Basin, were selected for comparison in terms of multi-year operation vs. new impoundment, river-type vs. lake-type, and shallow water vs. sub-deep water reservoirs. Samples were collected in dry season (December 2019), normal season (March 2020), and wet season (August 2020), on which the phytoplankton diversity and productivity of the two reservoirs, and the relationship and difference of community stability were examined. Results show that (1) the number of phytoplankton species in Jiuquwan Reservoir decreased comparing that before algal bloom and the restoration treatment, while that in Taihu Reservoir increased compared with that before the impoundment of the reservoir. There was no significant difference in functional groups and species number between the two reservoirs ( P >0.05); (2) the biological stability, diversity, productivity, and resource utilization efficiency of newly built lake-type reservoir were higher than those of multi-year river-type reservoir. In addition, the utilization efficiency of phytoplankton resources was the highest in wet season in both reservoirs. The increases in biodiversity, richness, and evenness promoted the stability of the community, while increases in productivity and resource utilization efficiency weakened the stability of the community; (3) community stability was affected by both biotic and abiotic factors, and hydrodynamic index was the main factor. This study is helpful to understand the relationship and differences in phytoplankton diversity, productivity and community stability in different types of reservoirs, and provides a guidance for maintaining the stability of reservoir water ecosystem and protecting the biodiversity. The relationships between phytoplankton diversity, productivity, and community stability will be investigated in depth, for which a long-term observation will be conducted on the impact of environmental factors and diversity on the local biostability in different types of reservoirs.

Long-term trends in diatom diversity and palaeoproductivity: a 16 000-year multidecadal record from Lake Baikal, southern Siberia

Article

Full-text available

Feb 2022
CLIM PAST

Biological diversity is inextricably linked to community stability and ecosystem functioning, but our understanding of these relationships in freshwater ecosystems is largely based on short-term observational, experimental, and modelling approaches. Using a multidecadal diatom record for the past ca. 16 000 years from Lake Baikal, we investigate how diversity and palaeoproductivity have responded to climate change during periods of both rapid climate fluctuation and relative climate stability. We show dynamic changes in diatom communities during the past 16 000 years, with decadal shifts in species dominance punctuating millennial-scale seasonal trends. We describe for the first time in Lake Baikal a gradual shift from spring to autumnal diatom communities that started during the Younger Dryas and peaked during the Late Holocene, which likely represents orbitally driven ecosystem responses to long-term changes in seasonality. Using a multivariate classification tree, we show that trends in planktonic and tychoplanktonic diatoms broadly reflect both long-term climatic changes associated with the demise of Northern Hemisphere ice sheets and abrupt climatic changes associated with, for example, the Younger Dryas stadial. Indeed, diatom communities are most different before and after the boundary between the Early and Middle Holocene periods of ca. 8.2 cal kyr BP, associated with the presence and demise of Northern Hemisphere ice sheets respectively. Diatom richness and diversity, estimated using Hill's species numbers, are also shown to be very responsive to periods characterized by abrupt climate change, and using knowledge of diatom autecologies in Lake Baikal, diversity trends are interpreted in terms of resource availability. Using diatom biovolume accumulation rates (BVARs; µm3 cm−2 yr−1), we show that spring diatom crops dominate palaeoproductivity for nearly all of our record, apart from a short period during the Late Holocene, when autumnal productivity dominated between 1.8–1.4 cal kyr BP. Palaeoproductivity was especially unstable during the Younger Dryas, reaching peak rates of 18.3 × 103 µm3 cm−2 yr−1 at ca. 12.3 cal kyr BP. Generalized additive models (GAMs), which explore productivity–diversity relationships (PDRs) during pre-defined climate periods, reveal complex relationships. The strongest statistical evidence for GAMs were found during the Younger Dryas, the Early Holocene, and the Late Holocene, i.e. periods of rapid climate change. We account for these differences in terms of climate-mediated resource availability, and the ability of endemic diatom species in Lake Baikal to adapt to extreme forms of living in this unique ecosystem. Our analyses offer insight into how productivity–diversity relationships may develop in the future under a warming climate.

Linking soil bacterial diversity to satellite‐derived vegetation productivity: a case study in arid and semi‐arid desert areas

Article

Jul 2021

Increasing studies have begun to focus on biodiversity‐productivity relationships for soil microorganisms through molecular ecology methods. However, most of these studies involve controlled experiments, and whether the relationship remains at large spatial scales is still largely unknown. To unravel this issue, archived desert soils from long‐term experiments were analysed using high‐throughput sequencing, and satellite‐derived vegetation datasets were acquired to quantify productivity. Most of the abundant genera were significantly different between low‐ and high‐productivity conditions, and soil bacterial communities were strongly impacted by productivity. Soil bacterial biodiversity, including observed OTUs (operational taxonomic units) and the Chao1, Shannon, and Faith's PD indexes, increased rapidly with productivity at low levels and then reached a relatively stable state, and similar phenomena were observed at multiple taxonomic ranks and for most of the dominant groups. Furthermore, we discovered that the mechanisms resulting in the observed relationship might be ecosystem resource availability in large‐scale regions and species competition in local regions. Collectively, these results enhance our understanding of the linkage between belowground microorganisms and aboveground vegetation in arid and semi‐arid areas and confirm the potential value of satellite‐derived datasets in research on soil microbial diversity at large spatial scales. This article is protected by copyright. All rights reserved.

Analyzing the Diversity of Microbial Communities Residing in Marine Ecosystems

Article

Full-text available

Aug 2020

Marine biotechnology is a scientifically escalating enterprise, which is poised to harness the huge but unexplored marine life with its innovative and extensive array of bioanalytical and biosynthetic capabilities. Marine biotechnology involves establishment of products and processes from marine organisms. In the past few decades it has contributed immensely in the consistent supply of products for various sectors like food, feed, energy, nutrition, medicine, bioremediation, and nanomaterials, etc. The marine ecosystem encompasses huge genetic diversity with the potential of forming newer products and processes. This genetic diversity also ensures the stability and fidelity of the marine ecosystem by providing biological insurance against environmental change. Coupled with the discovery of a huge microbial diversity, there has been a growing recognition of the eco‐value (both ecological as well as economic) of microbes. However, only a small fraction of the earth's vast oceanic environment has been scientifically investigated. Additionally, rather sparse information is available to link up biodiversity with the environmental and other challenging issues. Presently, the marine ecosystem has been acknowledged as a perpetual source of marine biological resources that need to be unraveled. Keeping these issues in mind, the present review provides an insight into the investigations carried out after exploring the microbial diversity of the marine world using traditional as well as modern methods. It aims to enhance the understanding of microbial diversity, interactions and processes that occur in the marine ecosystem.

WHAT IS THE OBSERVED RELATIONSHIP BETWEEN SPECIES RICHNESS AND PRODUCTIVITY?

Article

Full-text available

Sep 2001

Energy supply and patterns of species richness on local and regional scales

Article

Full-text available

Jan 1993

Effects of energy on species richness are a common, albeit complex, phenomenon, deserving of deeper and more systematic investigation by ecologists. A mechanism for species-energy relationships should be sought in the way that usable energy is divided among species, and in how the resulting patterns of local abundance affect incidence and richness in the landscape. Of particular interest is the very general model result that regional species-energy patterns have a stronger tendency to be positive than do local patterns, given a heterogeneous landscape. It is possible for the regional species-energy relationship in a heterogeneous landscape to be positive even when local relationships are hump-shaped or negative, a finding that agrees well with the empirically observed scale-dependence of the relation between species richness and measures of energy. This potential for diverse and conflicting yet mechanistic patterns at different scales may explain why it has been so difficult for ecologists to reach a consensus about the importance of energy in controlling species richness. -from Authors

Regional and local impact on species diversity - from pattern to processes

Article

Full-text available

Aug 2002

The impact of regional factors (such as speciation or dispersal) on the species richness in local communities (SL) has received increasing attention. A prominent method to infer the impact of regional factors is the comparison of species richness in local assemblages (SL) with the total number of species in the region (SR). Linear relations between SR and SL have been interpreted as an indication of strong regional influence and weak influence of interactions within local communities. We propose that two aspects bias the outcome of such comparisons: (1) the spatial scale of local and regional sampling, and (2) the body size of the organisms. The impact of the local area reflects the scales of ecological interactions, whereas the ratio between local and regional area reflects the inherent moment of autocorrelation. A proposed impact of body size on the relation is based on the high dispersal and high abundance of small organisms. We predict strongest linearity between SR and SL for large organisms, for large local areas (less important ecological interactions) and for sampling designs where the local habitat area covers a high proportion of the regional area (more important autocorrelation). We conducted a meta-analysis on 63 relations obtained from the literature. As predicted, the linearity of the relationship between SL and SR increased with the proportion of local to regional sampling area. In contrast, neither the body size of the organisms nor the local area itself was significantly related to the relation between SL and SR. This indicated that ecological interactions played a minor role in the shape of local to regional richness plots, which instead was mainly influenced by the sampling design. We found that the studies published so far were highly biased towards larger organisms and towards high similarity between the local and regional area. The proposed prevalence of linear relationships may thus be an artefact and plots of SL to SR are not a suitable tool with which to infer the strength of local interactions.

Intermediate disturbance in the ecology of phytoplankton and the maintenance of species diversity

Article

Full-text available

Jan 1993

This paper concludes a collection of contributions presented at the 8th Workshop of the International Association of Phytoplankton Taxonomy and Ecology. It derives a consensus as to the virtues and strengths of J. H. Connell's Intermediate Disturbance Hypothesis (IDH), its applicability to phytoplankton ecology and its theoretical and practical weaknesses. The view is expressed that the IDH is too useful a concept to reject and that, as a word model, it provides a powerful link between diversity and disturbance. The more robust investigations that are necessary to consolidate the tenancy of IDH need to concentrate upon the separation and quantification of the stimulus- and response-components of disturbance.

The Relationship Between Productivity and Species Richness

Article

Full-text available

Nov 1999
Annu Rev Ecol Systemat

Recent overviews have suggested that the relationship between species richness and productivity (rate of conversion of resources to biomass per unit area per unit time) is unimodal (hump-shaped). Most agree that productivity affects species richness at large scales, but unanimity is less regarding underlying mechanisms. Recent studies have examined the possibility that variation in species richness within communities may influence productivity, leading roan exploration of the relative effect of alterations in species number per se as contrasted to the addition of productive species. Reviews of the literature concerning deserts, boreal forests, tropical forests, lakes, and wetlands lead to the conclusion that extant data are insufficient to conclusively resolve the relationship between diversity and productivity, or that patterns are variable with mechanisms equally varied and complex. A more comprehensive survey of the ecological literature uncovered approximately 200 relationships, of which 30% were unimodal, 26% were positive linear, 12% were negative linear, and 32% were not significant. Categorization of studies with respect to geographic extent, ecological extent, taxonomic hierarchy, or energetic basis of productivity similarly yielded a heterogeneous distribution of relationships. Theoretical and empirical approaches increasingly suggest scale-dependence in the relationship between species richness and productivity; consequently, synthetic understanding may be contingent on explicit considerations of scale in analytical studies of productivity and diversity.

Biogeography of aquatic microbes

Article

Full-text available

Nov 2005

John R Dolan

Aquatic microbes, like all organisms, have biogeographies, but this subject has attracted relatively little attention. In this review, recent results exploiting techniques of molecular biology are summarized to place in perspective the studies of this Theme Section. The studies considered concern large-scale patterns of spatial distribution among heterotrophic planktonic prokaryotic and eukaryotic microbes. For freshwater bacterioplankton communities, reported patterns are inconsistent. Taxonomic richness may increase with system size, and composition may be related among neighboring bodies of water. However, inconsistencies in patterns may be due to differences in the temporal and spatial scales considered. Among planktonic marine prokaryotes, biogeographic patterns are known only in terms of high level groups, e.g. Archea are perhaps dominant in deep oceanic waters. However, studies of large-scale patterns have just begun and they suggest that some ribotypes or species may be restricted to certain oceanic areas. Eukaryotic microbes appear to characterised by high capacities for both dispersal and gene flow. Recent studies appear to conclude that we can form morphological, genetic and physiological groupings but their inter-relationships are obscure at this point in time.

What Is the Observed Relationship between Species Richness and Productivity?

Article

Full-text available

Sep 2001

Understanding the relationship between species richness & productivity is fundamental to the management & preservation of biodiversity. Yet despite years of study & intense theoretical interest, this relationship remains controversial. Here, we present the results of a literature survey in which we examined the relationship between betweens species richness & productivity in 171 published studies. We extracted the raw data from published tables & graphs & subjected these to a standardised analysis, using ordinary least squares (OLS) regression and generalised linear-model (GLIM) regression to test for significant positive, negative, or curvilinear relationships between productivity & species diversity. If the relationship was curvilinear, we tested whether the maximum (or minimum) of the curve occurred within the range of productivity values observed(i.e. was there evidence of a hump). A meta-analysis conducted on the distribution of standardised quadratic regression coefficients showed that the average quadratic coefficient was negative (i.e. the average species richness-productivity relationship was curvilinear & decelerating), and that the distribution of standardised quadratic regression coefficients was significantly heterogeneous (i.e.the studies did not sample the same underlying species richness-productivity relationship). Looking more closely at the patterns of productivity-diversity relationships, we found that, for vascular plants at geographical scales smaller than continents, humped-shaped relationships occurred most frequently (41-45% of all studies). A positive relationship between productivity & species richness was the next most common pattern, & positive & hump-shaped patterns co-dominated at the continental scale. For animals, positive , negative & humped-shaped patterns were common at most geographical scales , & no one pattern predominated. For both plants & animals, hump-shaped curves were relatively more common in studies that crossed community boundaries compared to studies conducted within a community type, & plant studies that crossed community types tended to span a greater range of productivity compared to studies within community types. Sample size and plot size did not affect the probability of finding a particular probability--diversity relationship (e.g. positive, hump-shaped, etc.). However, hump-shaped curves were especially common(65%)in studies of plant diversity that used plant biomass as a measure of productivity, and in studies conducted in aquatic systems.

Kassen, R., Buckling, A., Bell, G. & Rainey, P. B. Diversity peaks at intermediate productivity in a laboratory microcosm. Nature 406, 508−512

Article

Full-text available

Sep 2000

The species diversity of natural communities is often strongly related to their productivity. The pattern of this relationship seems to vary: diversity is known to increase monotonically with productivity, to decrease monotonically with productivity, and to be unimodally related to productivity, with maximum diversity occurring at intermediate levels of productivity. The mechanism underlying these patterns remains obscure, although many possibilities have been suggested. Here we outline a simple mechanism--involving selection in a heterogeneous environment--to explain these patterns, and test it using laboratory cultures of the bacterium Pseudomonas fluorescens. We grew diverse cultures over a wide range of nutrient concentrations, and found a strongly unimodal relationship between diversity and productivity in heterogeneous, but not in homogeneous, environments. Our result provides experimental evidence that the unimodal relationship often observed in natural communities can be caused by selection for specialized types in a heterogeneous environment.

Chase JM, Leibold MA.. Spatial scale dictates the productivity-biodiversity relationship. Nature 416: 427-430

Article

Full-text available

Apr 2002

The diversity of life is heterogeneously distributed across the Earth. A primary cause for this pattern is the heterogeneity in the amount of energy, or primary productivity (the rate of carbon fixed through photosynthesis), available to the biota in a given location. But the shape of the relationship between productivity and species diversity is highly variable. In many cases, the relationship is 'hump-shaped', where diversity peaks at intermediate productivity. In other cases, diversity increases linearly with productivity. A possible reason for this discrepancy is that data are often collected at different spatial scales. If the mechanisms that determine species diversity vary with spatial scale, then so would the shape of the productivity-diversity relationship. Here, we present evidence for scale-dependent productivity-diversity patterns in ponds. When the data were viewed at a local scale (among ponds), the relationship was hump-shaped, whereas when the same data were viewed at a regional scale (among watersheds), the relationship was positively linear. This dependence on scale results because dissimilarity in local species composition within regions increased with productivity.

Curtis TP, Sloan WT, Scannell JW.. Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci 99: 10494-10499

Article

Full-text available

Sep 2002

The absolute diversity of prokaryotes is widely held to be unknown and unknowable at any scale in any environment. However, it is not necessary to count every species in a community to estimate the number of different taxa therein. It is sufficient to estimate the area under the species abundance curve for that environment. Log-normal species abundance curves are thought to characterize communities, such as bacteria, which exhibit highly dynamic and random growth. Thus, we are able to show that the diversity of prokaryotic communities may be related to the ratio of two measurable variables: the total number of individuals in the community and the abundance of the most abundant members of that community. We assume that either the least abundant species has an abundance of 1 or Preston's canonical hypothesis is valid. Consequently, we can estimate the bacterial diversity on a small scale (oceans 160 per ml; soil 6,400-38,000 per g; sewage works 70 per ml). We are also able to speculate about diversity at a larger scale, thus the entire bacterial diversity of the sea may be unlikely to exceed 2 x 10(6), while a ton of soil could contain 4 x 10(6) different taxa. These are preliminary estimates that may change as we gain a greater understanding of the nature of prokaryotic species abundance curves. Nevertheless, it is evident that local and global prokaryotic diversity can be understood through species abundance curves and purely experimental approaches to solving this conundrum will be fruitless.

Productivity-biodiversity relationships depend on the history of community assembly

Article

Full-text available

Aug 2003
NATURE

Identification of the causes of productivity-species diversity relationships remains a central topic of ecological research. Different relations have been attributed to the influence of disturbance, consumers, niche specialization and spatial scale. One unexplored cause is the history of community assembly, the partly stochastic sequential arrival of species from a regional pool of potential community members. The sequence of species arrival can greatly affect community structure. If assembly sequence interacts with productivity to influence diversity, different sequences can contribute to variation in productivity-diversity relationships. Here we report a test of this hypothesis by assembling aquatic microbial communities at five productivity levels using four assembly sequences. About 30 generations after assembly, productivity-diversity relationships took various forms, including a positive, a hump-shaped, a U-shaped and a non-significant pattern, depending on assembly sequence. This variation resulted from idiosyncratic joint effects of assembly sequence, productivity and species identity on species abundances. We suggest that the history of community assembly should be added to the growing list of factors that influence productivity-biodiversity patterns.

An ecological perspective on bacterial diversity

Article

Full-text available

Feb 2004

Bacteria may be one of the most abundant and species-rich groups of organisms, and they mediate many critical ecosystem processes. Despite the ecological importance of bacteria, past practical and theoretical constraints have limited our ability to document patterns of bacterial diversity and to understand the processes that determine these patterns. However, recent advances in molecular techniques that allow more thorough detection of bacteria in nature have made it possible to examine such patterns and processes. Here, we review recent studies of the distribution of free-living bacterial diversity and compare our current understanding with what is known about patterns in plant and animal diversity. From these recent studies a preliminary picture is emerging: bacterial diversity may exhibit regular patterns, and in some cases these patterns may be qualitatively similar to those observed for plants and animals.

Global biodiversity patterns of marine phytoplankton and zooplankton

Article

Full-text available

Jul 2004
NATURE

Although the oceans cover 70% of the Earth's surface, our knowledge of biodiversity patterns in marine phytoplankton and zooplankton is very limited compared to that of the biodiversity of plants and herbivores in the terrestrial world. Here, we present biodiversity data for marine plankton assemblages from different areas of the world ocean. Similar to terrestrial vegetation, marine phytoplankton diversity is a unimodal function of phytoplankton biomass, with maximum diversity at intermediate levels of phytoplankton biomass and minimum diversity during massive blooms. Contrary to expectation, we did not find a relation between phytoplankton diversity and zooplankton diversity. Zooplankton diversity is a unimodal function of zooplankton biomass. Most strikingly, these marine biodiversity patterns show a worldwide consistency, despite obvious differences in environmental conditions of the various oceanographic regions. These findings may serve as a new benchmark in the search for global biodiversity patterns of plants and herbivores.

Ecology: Larger islands house more bacterial taxa

Article

Full-text available

Jul 2005
SCIENCE

The power law that describes the relationship between species richness and area size is one of the few generalizations in ecology, but recent studies show that this relationship differs for microbes. We demonstrate that the natural bacterial communities inhabiting small aquatic islands (treeholes) do indeed follow the species-area law. The result requires a re-evaluation of the current understanding of how natural microbial communities operate and implies that analogous processes structure both microbial communities and communities of larger organisms.

Developing Unified Theories in Ecology as Exemplified with Diversity Gradients

Article

Full-text available

Nov 2005
AM NAT

A scientific field matures as its theoretical underpinnings consolidate around unified theories: conceptual structures consisting of a few general propositions that encompass a wide domain of phenomena and from which can be derived an array of models. We demonstrate this process with a synthetic theory of ecological gradients and species richness. Our unified theory rests on four propositions. First, variation in some environmental factor effects variation in the number of individuals creating a gradient. Second, in a uniform environment of fixed area, more individuals lead to more species. Third, the variance of an environmental factor increases with its mean for sites of equal area. Fourth, all nonmonotonic relationships (i.e., hump shaped or U shaped) require a trade-off in organismal performance or in population characteristics with respect to the environmental gradient. We identify 17 models that link environmental gradients with diversity, show their relationship to our framework, and describe issues surrounding their empirical testing. We illustrate how a general theory can be used to build new models such as that for the U-shaped productivity-diversity relationship. Finally, we discuss how our theory could be unified further with other theories of diversity and indicate other areas of ecology that are ripe for unification. By providing an example of the process of theory unification, we hope to encourage such efforts throughout ecology.

Predicting microbial species richness

Article

Full-text available

Feb 2006

Microorganisms are spectacularly diverse phylogenetically, but available estimates of their species richness are vague and problematic. For example, for comparable environments, the estimated numbers of species range from a few dozen or hundreds to tens of thousands and even half a million. Such estimates provide no baseline information on either local or global microbial species richness. We argue that this uncertainty is due in large part to the way statistical tools are used, if not indeed misused, in biodiversity research. Here we develop a powerful synthetic statistical approach to quantify biodiversity. It provides statistically sound estimates of microbial richness at any level of taxonomic hierarchy. We apply this approach to a large original 16S rRNA dataset on marine bacterial diversity and show that the number of bacterial species in a sample from marine sediments is (2.4 ± 0.5 SE) × 10³. We argue that our methodology provides estimates of microbial richness that are reliable and general, have biologically meaningful SEs, and meet other fundamental statistical standards. This approach can be an essential tool in biodiversity research, and the estimates of microbial richness presented here can serve as a baseline in microbial diversity studies. • global biodiversity • microorganisms • number of species

Microbial biogeography: putting microorganisms on the map

Article

Full-text available

Mar 2006

We review the biogeography of microorganisms in light of the biogeography of macroorganisms. A large body of research supports the idea that free-living microbial taxa exhibit biogeographic patterns. Current evidence confirms that, as proposed by the Baas-Becking hypothesis, 'the environment selects' and is, in part, responsible for spatial variation in microbial diversity. However, recent studies also dispute the idea that 'everything is everywhere'. We also consider how the processes that generate and maintain biogeographic patterns in macroorganisms could operate in the microbial world.

OpinionMicrobial landscapes: new paths to biofilm research

Article

Full-text available

Feb 2007
NAT REV MICROBIOL

It is the best of times for biofilm research. Systems biology approaches are providing new insights into the genetic regulation of microbial functions, and sophisticated modelling techniques are enabling the prediction of microbial community structures. Yet it is also clear that there is a need for ecological theory to contribute to our understanding of biofilms. Here, we suggest a concept for biofilm research that is spatially explicit and solidly rooted in ecological theory, which might serve as a universal approach to the study of the numerous facets of biofilms.

An ecological perspective on bacterial biodiversity

Article

Jan 2003

Phytoplankton Diversity in Inland Waters of Different Trophic Status

Article

Jan 1984

Phytoplankton diversity in 23 water bodies of different trophic status was evaluated by the SHANNON index. High diversity was obtained in meso- and slightly eutrophic waters, whereas a low diversity was observed in oligo- or highly eutrophic waters.

Diversity-productivity relationships in streams vary as a function of the natural disturbance regime

Article

Mar 2005

Understanding the key ecological factors that moderate the relationship be- tween biodiversity and the productivity of ecosystems is a major challenge for ecological research. Here we show that the relationship between the species richness of primary producers and net rates of biomass production in streams depends on the history of dis- charge-related disturbances. Using common methods to study 83 streams in the mid-Atlantic United States, we demonstrate that a positive relationship between producer richness and the net production of biomass only occurs in streams characterized by highly variable, unpredictable discharge regimes that represent frequently disturbed environments to benthic organisms. This pattern is partly explained by predictable changes in the composition of species assemblages among disturbed streams. The pattern also results because, in disturbed systems, species have faster rates of biomass accumulation when they are a part of species- rich assemblages. We discuss several possible explanations for this result. Our study sup- ports qualitative predictions from theoretical and small-scale experimental work that the strength of the diversity-productivity relationship will depend explicitly on the disturbance regime of an ecosystem. The results have important implications for the management and conservation of aquatic resources as they suggest that changes to the productivity and diversity of streams may have their greatest impacts on organisms and systems that are most sensitive to disturbance.

Comparative Ecology of Microorganisms and Macroorganisms

Book

Jan 1991

John H. Andrews

Influence of inlet bacteria on bacterioplankton assemblage composition in lakes of different hydraulic retention time

Article

Jan 2004

The influence of inlet bacteria on the assemblage composition of bacterioplankton was investigated in two Swed- ish forest lakes of different hydraulic retention time. Assemblage composition of the bacteria in lakes and running waters was determined by denaturing gradient gel electrophoresis (DGGE) and sequencing of polymerase chain reaction (PCR)-amplified 16S rDNA. The amount of bacterial cells imported via the inlets in relation to bacterio- plankton cells produced in the epilimnion of the lakes was also determined. In the lake with short retention time (theoretical hydraulic retention time of 0.3 yr) the lake bacterioplankton assemblage largely resembled the riverine assemblages, although the extent of similarity varied among inlets, depending on water flow. In the lake with long retention time (theoretical hydraulic retention time of 10 yr) the bacterioplankton assemblage in the lake had low similarity to the inlet assemblages. The degree of similarity between inlets and lakes was well correlated to the amount of imported cells. Thus, our data suggest that import of inlet bacteria could have a large effect on the composition of lake bacterioplankton assemblages and that hydrological factors determined the magnitude of this effect. Since short hydraulic retention times are very common in lakes in the boreal zone, input of allochthonous bacteria can be one major factor influencing bacterioplankton assemblage composition in boreal lakes.

The Ubiquity of Small Species: Patterns of Local and Global Diversity

Article

Jan 2009

TOM FENCHEL BLAND J. FINLAY

Small organisms (less than 1 millimeter in length) tend to have a cosmopolitan distribution. This is a consequence of huge absolute population sizes rather than any inherent properties of particular taxonomic groups. At the local scale, the diversity of small species exceeds that of larger organisms, but at the global scale this relation is reversed, because endemism is largely responsible for the species richness of large organisms. For small organisms, the relationship between species and area is flat, and a latitudinal diversity gradient is absent or weak. These patterns are explained by some of the assumptions underlying the unified neutral community model.

The Relationship in Lake Communities between Primary Productivity and Species Richness

Article

Oct 2000

An understanding of the relationship between species richness and productivity is crucial to understanding biodiversity in lakes. We investigated the relationship between the primary productivity of lake ecosystems and the number of species for lacustrine phytoplankton, rotifers, cladocerans, copepods, macrophytes, and fish. Our study includes two parts: (1) a survey of 33 well-studied lakes for which data on six major taxonomic groups were available; and (2) a comparison of the effects of short- and long-term whole-lake nutrient addition on primary productivity and planktonic species richness. In the survey, species richness of all six taxa showed a significant quadratic response to increased annual primary productivity (C-14 estimate, g C.m(-2).yr(-1)) when lake area is taken into account. However, the richness-productivity relationship for phytoplankton and fish was strongly dependent on lake area. The relationship for phytoplankton, rotifers, cladocerans, copepods, and macrophytes was significantly unimodal. Species richness generally peaked at levels of primary productivity in the range of 30-300 g C.m(-2).yr(-1). For the average lake size, the highest biodiversity tended to occur in lakes with relatively low primary productivity, such as those found in the Northern Temperate Lakes Long-Term Ecological Research (LTER) site in the upper Midwest (United States) and in the Experimental Lakes Area of Ontario (Canada). Based on short-term (3 yr) and long-term (21-24 yr) experiments, we tested whether individual lakes respond to whole-lake enrichment experiments in the manner suggested by analyses of survey data. Experimental addition of nutrients produced varied and unpredictable responses in species richness, probably due to transient dynamics and time lags. Responses to nutrient addition were taxon and lake specific. Phytoplankton showed a variety of relationships between species richness and pelagic primary productivity (PPR), depending on the history of enrichment and recovery. No significant effect of primary productivity on rotifer richness occurred in any of the experimental lakes, whereas richness of crustacean zooplankton was negatively correlated with primary productivity in both the short- and long-term experiments.

Does ecosystem size determine aquatic bacterial richness? Ecology

Article

Jul 2005

With the advent of DNA-based molecular technologies, microbial ecologists now have the tools to test whether general ecological patterns apply to microorganisms. In this study, we selected 11 high-mountain lakes from Sierra Nevada (Spain) to test the predictions of island-biogeography theory in relation to ecosystem size and isolation, and to assess the influence of other factors (i.e., ecosystem productivity, resource richness, and biotic interactions) on bacterial community structure. Bacterial operational taxonomic units (OTUs), generated by denaturing-gradient gel electrophoresis of polymerase chain-reaction-amplified 16S rRNA genes, were used as a surrogate of predominant ''biodiversity units.'' OTU composition among lakes was heterogeneous, and the number of site-specific OTUs was near 50%. Lake remoteness did not affect the number of bacterial OTUs although the spatial distribution of the lakes significantly influenced bacterial composition. Lakes that were closer together had more similar bacterial fingerprints. We found a consistent positive association between bacterial OTU richness and lake area. The slope of this relationship (0.161 0.026, including literature data) was similar to slopes obtained for organisms with high dispersion rates.

Does ecosystem size determine aquatic bacteria richness? Reply

Article

Jan 2007

If the two remaining data sets from Reche et al. (2005), i.e., the DGGE data sets, are merged there is a significant correlation between DGGE band numbers and lake surface area (linear correlation of log-transformed data, P ¼ 0.002, r 2 ¼ 0.379, n ¼ 23). Although DGGE band numbers do not reflect richness of a community, and it is unclear what it reflects as discussed above, a significant correlation between DGGE band numbers and lake surface area might still have some ecological meaning. However, we question the merging of these two datasets into one analysis. One-way ANOVA analyses show that DGGE band numbers differ significantly between the two sub-studies (P ¼ 0.004), and there was also very little overlap in lake sizes between sub-studies (0.0001–0.02 and 0.01–6.2 km 2 , respectively; P , 0.001). Hence, it is plausible that a significant correlation between lake area and DGGE band numbers was obtained only because both lake area and DGGE band numbers depended on sub-study, and instead alternative explanations to the relationship found should be evaluated. The laboratory protocols used in the two sub-studies differed (Lindstro and Leskinen 2002, Reche et al. 2005). For instance different primer pairs were used, and thereby most likely different bacterial populations were detected (see, e.g., Forney et al. 2004). Thus, due to the differences in methodology, the two different studies could have had different resolution and/or thresholds of detection in their estimates of numbers of DGGE bands. Further, we cannot exclude that the Spanish high mountain lakes studied by Reche et al. (2005) for some other reason than lake area harbored bacterial commu-nities giving rise to fewer bands than the communities in the Swedish and Norwegian lakes studied by Lindstro and Leskinen (2002). Thus, we cannot tangle out which factors cause the difference in number of DGGE bands between the two sub-studies. However, it is clear that lake surface area is not the only possible explanation, and there is no solid support for the idea of a causal relationship between lake surface area and DGGE band numbers. To summarize, we argue that it still remains to be shown if ecosystem size determines aquatic bacterial richness.

Regional occupancy in unicellular eukaryotes: A reflection of niche breadth, habitat availability or size-related dispersal capacity?

Article

Mar 2006
FRESHWATER BIOL

1. The distribution patterns of unicellular and multicellular organisms have recently been shown to differ profoundly, with the former probably being mostly cosmopolitan, whereas the latter are mostly restricted to certain regions. However, the within-region distribution patterns of these two organism groups may be rather similar. 2. We predicted that the degree of regional occupancy in unicellular eukaryotes would be related to niche characteristics, dispersal ability and size, as has been found previously for multicellular organisms. The niche characteristics we considered were niche position, that measures marginality in species habitat distribution, and niche breadth, that measures amplitude in species habitat distribution. Niche characteristics were determined using Outlying Mean Index (OMI) analysis. 3. We found that the regional occupancy in our model group of unicellular eukaryotes, stream diatoms, was primarily a reflection of the niche position of a species or, more generally, habitat availability. Thus, non-marginal species (i.e. species that occupied common habitat conditions across the region) tended to be more widely distributed than marginal species (i.e. species that were restricted to a limited range of rare habitat conditions). This finding was further supported by the general linear model, with niche position, niche breadth, maximum size and attachment mode as explanatory variables: niche position was by far the most important variable accounting for variability in regional occupancy, with significant amounts of additional variation related to niche breadth and maximum size of diatoms. 4. Thus, the degree of regional occupancy among unicellular eukaryotes may be primarily governed by habitat availability, supporting former findings for multicellular organisms.

Connectivity, Scale-Dependence, and the Productivity–Diversity Relationship

Article

Jul 2004
ECOL LETT

We surveyed freshwater ponds (localities) nested within watersheds (regions) to evaluate the relationship between productivity and animal species richness at different spatial scales. In watersheds where the ponds were relatively distant from one another (likely reducing the level of interpond dispersal of many organisms), we found a scale-dependent productivity–diversity relationship; at local scales (among ponds), diversity was a hump-shaped function of productivity, whereas at regional scales (among watersheds), diversity monotonically increased with productivity. Furthermore, this relationship emerged because there was a strong relationship between productivity and pond-to-pond species compositional differences. Alternatively, in watersheds where ponds were relatively close together (likely leading to higher rates of dispersal of many organisms), we found no scale-dependence; diversity was a hump-shaped function of productivity at both local and regional scales. Here, the relationship between species compositional dissimilarity and productivity was much weaker. We conclude that whether or not scale-dependence is observed in productivity–diversity relationships will depend, at least in part, on the degree of connectivity among localities within regions.

The Role Of Spatial Scale And The Perception Of Large-Scale Species-Richness Patterns

Article

Dec 2004
ECOL LETT

Carsten Rahbek

Despite two centuries of exploration, our understanding of factors determining the distribution of life on Earth is in many ways still in its infancy. Much of the disagreement about governing processes of variation in species richness may be the result of differences in our perception of species-richness patterns. Until recently, most studies of large-scale species-richness patterns assumed implicitly that patterns and mechanisms were scale invariant. Illustrated with examples and a quantitative analysis of published data on altitudinal gradients of species richness (n = 204), this review discusses how scale effects (extent and grain size) can influence our perception of patterns and processes. For example, a hump-shaped altitudinal species-richness pattern is the most typical (c. 50%), with a monotonic decreasing pattern (c. 25%) also frequently reported, but the relative distribution of patterns changes readily with spatial grain and extent. If we are to attribute relative impact to various factors influencing species richness and distribution and to decide at which point along a spatial and temporal continuum they act, we should not ask only how results vary as a function of scale but also search for consistent patterns in these scale effects. The review concludes with suggestions of potential routes for future analytical exploration of species-richness patterns.

Opposing effects of grazing and nutrients on diversity

Article

Apr 2003
OIKOS

Helmut Hillebrand

Conceptual models predict counteractive effects of herbivores and nutrient enrichment on plant diversity and reversed effects of grazers under different nutrient regimes. I tested these hypotheses in 11 field experiments with periphyton communities in three different aquatic habitats (a highly eutrophic lake, an meso-eutrophic lake, and an meso-eutrophic part of the Baltic Sea coast) and in different seasons. Grazer access and nutrient supply were manipulated in a factorial design. Species richness and evenness were chosen as response variables. Both manipulated factors had significant and contrasting effects on diversity, with variable effect strength between sites and seasons. From the two aspects of diversity, evenness well reflected the changes in community composition. Fertilization tended to increase the dominance of few species and thus to decrease evenness, whereas grazers counteracted these effects by removing dominant life forms. The response of species richness was not as expected, since grazers decreased richness throughout, whereas nutrients had weaker effects but tended to increase richness. Species richness rather reflected changes in periphyton architecture. Grazers reduced algal richness presumably by co-consumption of rare species in the tightly connected periphyton assemblages, whereas enrichment may increase richness by providing more structure via increased dominance of filamentous species. Although grazer and nutrient effects on richness and evenness were opposing, there was no change in the effect of one factor by manipulation of the other.

Patterns of diversity in microscopic animals: Are they comparable to those in protists or in larger animals?

Article

Feb 2006
GLOBAL ECOL BIOGEOGR

Aim General patterns of biodiversity, such as latitudinal gradients and species-area relationships, are found consistently in a wide range of organisms, but recent results for protist diversity suggest that organisms shorter than 2 mm do not display such patterns. We tested this prediction in bdelloid rotifers, pluricellular metazoans smaller than 2 mm, but with size and ecology comparable to protists. Location A single valley in northern Italy was surveyed in detail and compared to all available faunistic data on bdelloids worldwide. Methods We analysed 171 local assemblages of bdelloid rotifers living in 5 systems of dry mosses and submerged mosses in running water and in lakes. We compared patterns of alpha, beta, and gamma diversity, and nestedness of metacommunities, with those known from protists and larger organisms. Results Bdelloid rotifers showed low local species richness (alpha diversity), with strong habitat selection, as observed in larger organisms. The number of species differed among systems, with a higher number of species in dry than in aquatic mosses. There was no hierarchical structure or exclusion of species in the metacommunity pattern within each system. Local diversity for the entire valley was surprisingly high compared with worldwide bdelloid diversity, similar to observed patterns in protists. Main Conclusions Bdelloid rotifers have some of the peculiarities of protist biodiversity, although at slightly different spatial scales, thus confirming the idea of a major change in biodiversity patterns among organisms shorter than 2 mm. However, bdelloids show stronger habitat selection than protists. We suggest two possible explanations for the observed patterns: (1) dispersal is very rare, and not all bdelloid clones are arriving everywhere; and (2) dispersal is effective in displacing propagules, but environmental heterogeneity is very high and prevents many species from colonizing a given patch of moss.

A resource-based conceptual model of plant diversity that reassesses causality in the productivity–diversity relationship

Article

Apr 2006
GLOBAL ECOL BIOGEOGR

Biogeographical studies frequently reveal positive correlations between species richness and estimates of environmental water and/or energy. A popular interpretation of this relationship relates the supply of water and energy to productivity, and then, in turn, to richness. Productivity–diversity theories are now legion, yet none has proved sufficiently intuitive to gain broad acceptance. Like productivity, heterogeneity is known to influence diversity at fine spatial scales, yet the possibility that richness might relate to water–energy dynamics at coarse spatial scales via a heterogeneity-generating mechanism has received little attention. In this paper we outline such a conceptual model for plants that is internally consistent and testable. We believe it may help to explain the capacity of environments receiving different inputs of water and energy to support variable numbers of species at a range of spatial scales, the pervasive correlation between productivity and richness, some exceptions to the productivity–diversity relationship, the form of productivity–diversity curves and the link between richness and environmental ‘harshness’. The model may also provide an answer to one of the most venerable puzzles in the field of diversity studies: why high inputs of water and energy correspond to more species rather than simply more individuals.

Hillebrand H, Watermann F, Karez R, Berninger UG.. Differences in species richness patterns between unicellular and multicellular organisms. Oecologia 126: 114-124

Article

Jul 2001

For unicellular organisms, a lack of effects of local species richness on ecosystem function has been proposed due to their locally high species richness and their ubiquitous distribution. High dispersal ability and high individual numbers may enable unicellular taxa to occur everywhere. Using our own and published data sets on uni- and multicellular organisms, we conducted thorough statistical analyses to test whether (1) unicellular taxa show higher relative local species richness compared to multicellular taxa, (2) unicellular taxa show lower slopes of the species:area relationships and species:individuals relationships, and (3) the species composition of unicellular taxa is less influenced by geographic distance compared to multicellular taxa. We found higher local species richness compared to the global species pool for unicellular organisms than for metazoan taxa. The difference was significant if global species richness was conservatively estimated but not if extrapolated, and therefore higher richness estimates were used. Both microalgae and protozoans showed lower slopes between species richness and sample size (area or individuals) compared to macrozoobenthos, also indicating higher local species richness for unicellular taxa. The similarity of species composition of both benthic diatoms and ciliates decreased with increasing geographic distance. This indicated restricted dispersal ability of protists and the absence of ubiquity. However, a steeper slope between similarity and distance was found for polychaetes and corals, suggesting a stronger effect of distance on the dispersal of metazoans compared to unicellular taxa. In conclusion, we found partly different species richness patterns among uni- and multicellular eukaryotes, but no strict ubiquity of unicellular taxa. Therefore, the effect of local unicellular species richness on ecosystem function has to be reanalyzed. Macroecological patterns suggested for multicellular organisms may differ in unicellular communities.

Biodiversity and nutrient enrichment in pond communities

Article

Jan 1999
EVOL ECOL RES

Mathew Leibold

There are at least four mathematically developed models that predict unimodal diversity -productivity relations in local communities. I attempt to distinguish among these theories using data from surveys of planktonic organisms in 31 fishless ponds in southern Michigan by relating plant and herbivore diversity and composition to pond nutrient levels. The density of plants (phytoplankton) was positively correlated with nutrient levels and the density of herbivores (zooplankton) was positively correlated with the density of plants. Species richness of plants and of herbivores were declining or unimodal functions of nutrient levels. The composition of each trophic level changed significantly with eutrophication as indicated by significant correlations between nutrient levels and site scores (obtained by reciprocal averaging ordination on occurrences). A concomitant lack of correlation between site scores and species richness for both trophic levels further shows that the patterns of species distributions form gradients of species replacements rather than nested subsets. Taxonomic ordination scores also showed that the algae found at low nutrient levels consisted disproportionately of small, unprotected forms (thought to be fast-growing but grazer-susceptible), whereas the algae found at high nutrient levels were larger and often sheathed or gelatinous (thought to be slow-growing but more resistant to grazers). The results of this analysis of changes in the patterns of distribution of planktonic organisms are consistent with a hypothesis of productivity-dependent 'keystqne-predation' causing the unimodal relation between diversity and productivity.

Monotonic or Unimodal Diversity-Productivity Gradients: What Does Competition Theory Predict?

Article

Oct 1995

Peter A Abrams

This article discusses two types of proposed relationships between resource productivity and the diversity of coexisting Consumer species. Monotonically increasing curves have recently been dismissed on both empirical and theoretical grounds, while unimodal (''hump-shaped'') curves have been supported. Unimodal curves have been attributed to increased competitive exclusion, usually as the result of decreased heterogeneity in limiting resources at high productivities. This article argues that: (1) there are many viable mechanisms that can produce monotonic curves in the presence of competition; (2) there is little empirical support for any of the major variants of the hypothesis that productivity decreases heterogeneity, which increases competitive exclusion; and (3) there are alternative reasons for unimodal curves, some or all of which are consistent with previously observed productivity-diversity relationships. Additional theoretical and empirical work is required to understand what relationships follow from different mechanisms of competition, and what relationships are most frequently observed under different observational protocols.

Species Diversity In Space And Time

Article

May 1995

Michael L. Rosenzweig

Why do larger areas have more species? What makes diversity so high near the equator? Has the number of species grown during the past 600 million years? Does habitat diversity support species diversity, or is it the other way around? What reduces diversity in ecologically productive places? At what scales of space and time do diversity patterns hold? Do the mechanisms that produce them vary with scale? This book examines these questions and many others, by employing both theory and data in the search for answers. Surprisingly, many of the questions have reasonably likely answers. By identifying these, attention can be turned toward life's many, still-unexplained diversity patterns. As evolutionary ecologists race to understand biodiversity before it is too late, this book will help set the agenda for diversity research into the next century.

Chesson P.. Mechanisms of maintenance of species diversity. Annu Rev Ecol Evol Syst 31: 343-366

Article

Nov 2000
Annu Rev Ecol Systemat

Peter Chesson

The focus of most ideas on diversity maintenance is species coexistence, which may be stable or unstable. Stable coexistence can be quantified by the long-term rates at which community members recover from low density. Quantification shows that coexistence mechanisms function in two major ways: they may be a) equalising because they tend to minimise average fitness differences between species b) stabilising because they tend to increase negative intraspecific interactions relative to negative interspecific interactions Stabilising mechanisms are essential for species coexistence and include traditional mechanisms such as resource partitioning and frequency-dependent predation, as well as mechanisms that depend on fluctuations of population densities and environemntal factors in space and time. Equalising mechanisms contribute to stable coexistence because they reduce average fitness inequalities which might negate the effects of stabilising mechanisms. Models of unstable coexistence, in which species diversity decays over time, have focused almost exclusively on equalising mechanisms. These models would be more robust if they included stabilising mechanisms, which arise in many and varied ways but need not be adequate for full stability of a system. Models of unstable coexistence invite a briader view of diversity maintenence incorporating species turnover.

Horner-Devine MC, Leibold MA, Smith VH, Bohann BJM.. Bacterial diversity patterns along a gradient of primary productivity. Ecol Lett 6: 613-622

Article

Jul 2003

Primary productivity is a key determinant of biodiversity patterns in plants and animals but has not previously been shown to affect bacterial diversity. We examined the relationship between productivity and bacterial richness in aquatic mesocosms designed to mimic small ponds. We observed that productivity could influence the composition and richness of bacterial communities. We showed that, even within the same system, different bacterial taxonomic groups could exhibit different responses to changes in productivity. The richness of members of the Cytophaga-Flavobacteria-Bacteroides group exhibited a significant hump-shaped relationship with productivity, as is often observed for plant and animal richness in aquatic systems. In contrast, we observed a significant U-shaped relationship between richness and productivity for a-proteobacteria and no discernable relationship for b-proteobacteria. We show, for the first time, that bacterial diversity varies along a gradient of primary productivity and thus make an important step towards understanding processes responsible for the maintenance of bacterial biodiversity.

Microbial Ecology: Fundamentals and Applications.

Article

Jul 1982

Chapter 1 contains a short historical introduction. Chapter 2, represents an updated review of microbial diversity and systematics. It also provides essential information required for the understanding of the form, function, and systematic relationship of microorganisms. Chapter 3 is devoted to the formation and structure of microbial communities, and deals with this subject both in the evolutionary and successional senses. Chapter 4 describes the interactions between microorganisms, and Chapters 5 and 6 explore the interactions of microorganisms with plants and with animals, respectively. Chapter 7 discusses the quantitative measurement of numbers, biomass, and activity of microorganisms; Chapter 8 examines the influence and the measurement of their environmental determinants. Chapter 9 presents air, water, and soil as microbial habitats and describes the typical composition of their communities. Chapters 10 and 11 contain an expanded discussion of the biogeochemical cycling activities performed by microbial communities. Chapters 12-15 deal with applied aspects of microbial ecology evident in biodeterioration control, sanitation, soil conservation, pollution control, resource recovery, and biological control.

Ward BB. How many species of prokaryotes are there? Proc Natl Acad Sci USA 99: 10234-10236

Article

Sep 2002

Bess B Ward

Bohannan BJM, Hughes JB.. New approaches to analyzing microbial biodiversity data. Curr Opin Microbiol 6: 282-287

Article

Jul 2003
CURR OPIN MICROBIOL

Modern molecular techniques have revealed an extraordinary diversity of microorganisms, most of which are as yet uncharacterized. This poses a major challenge to microbial ecologists: how can one compare the microbial diversity of different environments when the vast majority of microbial taxa are usually unknown? Three statistical approaches developed by ecologists and evolutionary biologists--parametric estimation, nonparametric estimation and community phylogenetics--are proving to be promising tools to meet this challenge. The combination of these tools with molecular biology techniques allow the rigorous estimation and comparison of microbial diversity in different environments.

Phytoplankton species richness scales consistently from laboratory microcosms to the world's oceans

Article

Mar 2005

Species-area relationships have been observed for virtually all major groups of macroorganisms that have been studied to date but have not been explored for microscopic phytoplankton algae, which are the dominant producers in many freshwater and marine ecosystems. Our analyses of data from 142 different natural ponds, lakes, and oceans and 239 experimental ecosystems reveal a strong species-area relationship with an exponent that is invariant across ecosystems that span >15 orders of magnitude in spatial extent. A striking result is that the species-area relationship derived from small-scale experimental studies correctly scales up to natural aquatic ecosystems. These results significantly broaden our knowledge of the effects of island size on biodiversity and also confirm the relevance of experimentally derived data to the analysis and understanding of larger-scale ecological patterns. In addition, they confirm that patterns in microbial diversity are strongly consistent with those that have been repeatedly reported in the literature for macroorganisms. • biodiversity • island biogeography • species-area • scale-invariance

Big questions, small worlds: microbial model systems in ecology

Article

May 2004
TRENDS ECOL EVOL

Although many biologists have embraced microbial model systems as tools to address genetic and physiological questions, the explicit use of microbial communities as model systems in ecology has traditionally been more restricted. Here, we highlight recent studies that use laboratory-based microbial model systems to address ecological questions. Such studies have significantly advanced our understanding of processes that have proven difficult to study in field systems, including the genetic and biochemical underpinnings of traits involved in ecological interactions, and the ecological differences driving evolutionary change. It is the simplicity of microbial model systems that makes them such powerful tools for the study of ecology. Such simplicity enables the high degrees of experimental control and replication that are necessary to address many questions that are inaccessible through field observation or experimentation.

Theory and the microbial world

Article

Feb 2007

Tom Curtis

Does ecosystem size determine aquatic bacterial richness? Comment

Article

Feb 2007

Toward an Ecological Classification of Soil Bacteria

Article

Jul 2007

Although researchers have begun cataloging the incredible diversity of bacteria found in soil, we are largely unable to interpret this information in an ecological context, including which groups of bacteria are most abundant in different soils and why. With this study, we examined how the abundances of major soil bacterial phyla correspond to the biotic and abiotic characteristics of the soil environment to determine if they can be divided into ecologically meaningful categories. To do this, we collected 71 unique soil samples from a wide range of ecosystems across North America and looked for relationships between soil properties and the relative abundances of six dominant bacterial phyla (Acidobacteria, Bacteroidetes, Firmicutes, Actinobacteria, alpha-Proteobacteria, and the beta-Proteobacteria). Of the soil properties measured, net carbon (C) mineralization rate (an index of C availability) was the best predictor of phylum-level abundances. There was a negative correlation between Acidobacteria abundance and C mineralization rates (r2 = 0.26, P < 0.001), while the abundances of beta-Proteobacteria and Bacteroidetes were positively correlated with C mineralization rates (r2 = 0.35, P < 0.001 and r2 = 0.34, P < 0.001, respectively). These patterns were explored further using both experimental and meta-analytical approaches. We amended soil cores from a specific site with varying levels of sucrose over a 12-month period to maintain a gradient of elevated C availabilities. This experiment confirmed our survey results: there was a negative relationship between C amendment level and the abundance of Acidobacteria (r2 = 0.42, P < 0.01) and a positive relationship for both Bacteroidetes and beta-Proteobacteria (r2 = 0.38 and 0.70, respectively; P < 0.01 for each). Further support for a relationship between the relative abundances of these bacterial phyla and C availability was garnered from an analysis of published bacterial clone libraries from bulk and rhizosphere soils. Together our survey, experimental, and meta-analytical results suggest that certain bacterial phyla can be differentiated into copiotrophic and oligotrophic categories that correspond to the r- and K-selected categories used to describe the ecological attributes of plants and animals. By applying the copiotroph-oligotroph concept to soil microorganisms we can make specific predictions about the ecological attributes of various bacterial taxa and better understand the structure and function of soil bacterial communities.

Big Questions for a Small Planet

Article

Aug 1995

Microbial landscapes

Battin TJ
Sloan WT
Kjelleberg S
Daims H
Head IM
Curtis TP
Eberl L
Battin TJ
Sloan WT
Kjelleberg S
Daims H
Head IM
Curtis TP
Eberl L

Patterns of diversity in microscopic animals

Fontaneto D
Francesco Ficetola G
Ambrosini R
Ricci C
Fontaneto D
Francesco Ficetola G
Ambrosini R
Ricci C

Microbial diversity-productivity relationships in aquatic ecosystems

Abstract

No full-text available

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