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The 25 biodiversity hotspots (after Myers et al. 2000)
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Protists have scarcely been considered in traditional perspectives and strategies in environmental management and biodiversity
conservation. This is a remarkable omission given that these tiny organisms are highly diverse, and have performed as key
ecological players in evolutionary theatres for over a billion years of Earth history. Protists hold...
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The ability of harmful algal species to form dense, nearly monospecific blooms remains an ecological and evolutionary puzzle. We hypothesized that predation interacts with estuarine salinity gradients to promote blooms of Heterosigma akashiwo (Y. Hada) Y. Hada ex Y. Hara et M. Chihara, a cosmopolitan toxic raphidophyte. Specifically, H. akashiwo's...
Citations
... However, larger 261 incongruencies can be observed in the comparison of ED scores for certain species, which 262indicates that lacking phylogenetic information may have a greater impact on both ED and Among all the eukaryotic clades, the TSAR was identified as the clade containing the largest 265 mean evolutionary distinctiveness across all its individual species. However, even though there 266 are some advocates for conserving the biodiversity represented by microorganisms35,36 , the TSAR group still falls outside of the mainstream of conservation and there is almost no information about the extinction risk of TSAR species on the IUCN Red List. According to our estimation, the TSAR clade has the highest proportion of species whose ED score is higher than 95% of all described species (39.2%, 19194 species among 48964 TSAR species, see ...
In the face of rapid biodiversity loss, many approaches have been developed to measure biodiversity in ways that go beyond species richness. One prominent example is Phylogenetic Diversity (PD), which measures evolutionary history by summing the branches required to connect a set of species on a dated phylogenetic tree. PD may also capture other biodiversity measures by proxy such as the richness of biological features and their potential future benefits for humanity, sometimes known as ‘future options’. The total global PD is known for some well-studied groups, such as most vertebrates, but PD estimates are lacking for the majority of the tree of life. Here, we characterize the distribution of PD across the complete tree of life with over 2.2 million species. To do this we use data from the Open Tree of Life and a smoothing method to interpolate between nodes without date information. We estimate that the PD represented by all described species together is between 29 and 33 trillion years. We characterize the distribution of evolutionary distinctiveness, a measure of the fair share of PD captured by individual species, across all life and within selected clades. Many clades have bimodal distributions of evolutionary distinctiveness across species which may be due to changes in diversification rate within subclades. PD has previously been used as the basis for conservation prioritization schemes such as EDGE (Evolutionary Distinct and Globally Endangered) which synthesizes phylogenetic tree data with extinction risk data from the IUCN Red List of threatened species. Here we estimate EDGE scores for over 130,000 species, many more than have been done previously. The top EDGE species is Latimeria chalumnae, the critically endangered West Indian Ocean coelacanth. We hope this work will pave the way for more complete and automated analyses of PD and EDGE scores across the complete tree of life.
... Thus, we need an improved understanding of microbial processes and their response to climate change to ensure an environmentally secure future. Finally, in addition to being essential for soil functioning and natural soil fertility and hence to plant health and agricultural production, soil microorganisms also have intrinsic value as elements of biodiversity worthy of preservation (Averill et al., 2022;Cotterill et al., 2008). We therefore have moral as well as practical and economic reasons to better document soil microbial diversity as a basis for its conservation and understanding its functions. ...
... Due to their large population sizes, it used to be considered unlikely that any microbial species may be endangered (Finlay et al., 2004), but this view has been challenged (Cotterill et al., 2008). Extinction threat increases with decreasing population size and geographic range (MacArthur & Wilson, 1967) and it is now demonstrated that at least some soil microorganisms also have limited geographical ranges Mitchell and Meisterfeld (2005). ...
Aim
The diversity and distribution of soil microorganisms and their potential for long‐distance dispersal (LDD) are poorly documented, making the threats posed by climate change difficult to assess. If microorganisms do not disperse globally, regional endemism may develop and extinction may occur due to environmental changes. Here, we addressed this question using the testate amoeba Apodera vas, a morphologically conspicuous model soil microorganism in microbial biogeography, commonly found in peatlands and forests mainly of former Gondwana. We first documented its distribution. We next assessed whether its distribution could be explained by dispersal (i.e. matching its climatic niche) or vicariance (i.e. palaeogeography), based on the magnitude of potential range expansions or contractions in response to past and on‐going climatic changes. Last, we wanted to assess the likelihood of cryptic diversity and its potential threat from climate and land‐use changes (e.g. due to limited LDD).
Location
Documented records: Southern Hemisphere and intertropical zone; modelling: Global.
Methods
We first built an updated global distribution map of A. vas using 401 validated georeferenced records. We next used these data to develop a climatic niche model to predict its past (LGM, i.e. 21 ± 3 ka BP; PMIP3 IPSL‐CM5A‐LR), present and future (IPSL‐CMP6A‐LR predictions for 2071–2100, SSP3 and 5) potential distributions in responses to climate, by relating the species occurrences to climatic and topographic predictors. We then used these predictions to test our hypotheses (dispersal/vicariance, cryptic diversity, future threat from LDD limitation).
Results
Our models show that favourable climatic conditions for A. vas currently exist in the British Isles, an especially well‐studied region for testate amoebae where this species has never been found. This demonstrates a lack of interhemispheric LDD, congruent with the palaeogeography (vicariance) hypothesis. Longitudinal LDD is, however, confirmed by the presence of A. vas in isolated and geologically young peri‐Antarctic islands. Potential distribution maps for past, current and future climates show favourable climatic conditions existing on parts of all southern continents, with shifts to higher land from LGM to current in the tropics and a strong range contraction from current to future (global warming IPSL‐CM6A‐LR scenario for 2071–2100, SSP3.70 and SSP5.85) with favourable conditions developing on the Antarctic Peninsula.
Main Conclusions
This study illustrates the value of climate niche models for research on microbial diversity and biogeography, along with exploring the role played by historical factors and dispersal limitation in shaping microbial biogeography. We assess the discrepancy between latitudinal and longitudinal LDD for A. vas, which is possibly due to contrast in wind patterns and/or likelihood of transport by birds. Our models also suggest that climate change may lead to regional extinction of terrestrial microscopic organisms, thus illustrating the pertinence of including microorganisms in biodiversity conservation research and actions.
... 6). Therefore, biogeographical patterns of microorganisms provide a useful framework for understanding the overall ecology of microorganisms, as well as the ecological services they provide in the natural environment (Cotterill et al. 2007;Hanson 2017). Even though most biodiversity and conservation research has focused on the value and importance of macroorganisms, the huge abundance of microorganisms confers them a prime role in providing ecosystem services. ...
Biogeographical patterns provide insight into the evolutionary and ecological processes that shape biodiversity. Patterns of microbial biogeography have remained poorly described because adequate tools for measuring microbial diversity (such as molecular techniques and technologies) have emerged only recently. One aspect that has received a great attention in ecological biogeography is the latitudinal variation of biodiversity. Particularly, this chapter is focused on the biogeographical diversity patterns of planktonic prokaryotes and eukaryotes along a gradient of Patagonian water bodies, which also includes some Antarctic lakes. We provide evidence on the existence of biogeographic patterns of bacterial assemblages and the role of spatial and environmental factors controlling the bacterial community structure. Heterotrophic bacteria (HB), Archaea and photosynthetic picoplankton (PPP) abundances decreased towards higher latitudes. Nevertheless, HB and PPP cytometric diversity indexes did not. Light conditions and trophic status of the lakes were important in shaping the PPP structure, particularly in relation to the proportion of phycoerythrin- and phycocyanin-rich picocyanobacteria and picoeukaryotes. Using a polyphasic approach (morphologically based, functional and dominant molecular diversity), it was found that both geographical and environmental factors influenced phytoplankton diversity at large spatial scale, although the local effect was stronger. Generally, a decreasing biodiversity pattern with latitude was observed either for particular taxonomical microalgal groups or for the whole phytoplankton community. The studies showed the co-existence of a ‘core biosphere’ containing reduced number of dominant microeukaryote operational taxonomic units (OTUs) on which classical ecological rules apply, together with a much larger seedbank of rare OTUs driven by stochastic and reduced dispersal processes.
... The Dajiuhu peatland is located near to the middle reaches of Yangtze River, where the earliest archeological sites date back around 8,500 years BP and human habitation reached high levels in the Iron Age (Xie et al., 2013). Large areas of Dajiuhu were used for military bases, settlements, and agriculture starting from at least the Tang dynasty (618-907 CE) and human activities such as ditching, Sphagnum cutting, and pasture decreased the peatland size dramatically with negative effects on protist biodiversity (Cotterill et al., 2008;Qin et al., 2016;Duckert et al., 2021). ...
Anthropogenic peatland degradation is a global threat. As peatlands store large amounts of carbon (C) their potential for mitigation of climate change has been emphasized recently. Global C cycling is linked to silicon (Si) fluxes from the continents into the oceans. These fluxes in turn are driven by biosilicification, the incorporation of inorganic Si into living organisms, in terrestrial ecosystems. Biosilicification by testate amoeba (TA) communities and its potential for Si cycling has been highlighted since the beginning of the 21st century. However, the effects of peatland degradation on TA biodiversity and corresponding protozoic biosilicification on a continental scale remained unresolved so far. We show that TA biodiversity in Asian peatlands is strongly affected by the grade of human impact. This biodiversity decline was accompanied by an unexpected increase in protozoic biosilicification. Our findings provide new insights into the interactions between the biodiversity of soil microorganisms and biogeochemical Si cycling.
... Ciliates represent a monophyletic group of unicellular eukaryotes, the phylum Ciliophora Doflein, 1901. Their diversity comprises about 4500 free-living species, although it is estimated that there may be as many as 40,000 species on the planet (Cotterill et al. 2008). Many ciliate species appear to have ubiquitous geographic distributions, yet some appear to represent cryptic or pseudocryptic species complexes with more restricted geographic distributions (Cotterill et al. 2008;Dunthorn et al. 2012 Ciliates inhabit a wide range of terrestrial and aquatic habitats, such as soils, mosses, peatlands, phytotelmata, hypersaline pools, estuaries and lakes (Durán-Ramírez et al. 2015;Foissner et al. 2002;Lynn 2008). ...
... Their diversity comprises about 4500 free-living species, although it is estimated that there may be as many as 40,000 species on the planet (Cotterill et al. 2008). Many ciliate species appear to have ubiquitous geographic distributions, yet some appear to represent cryptic or pseudocryptic species complexes with more restricted geographic distributions (Cotterill et al. 2008;Dunthorn et al. 2012 Ciliates inhabit a wide range of terrestrial and aquatic habitats, such as soils, mosses, peatlands, phytotelmata, hypersaline pools, estuaries and lakes (Durán-Ramírez et al. 2015;Foissner et al. 2002;Lynn 2008). They also play a key role in microbial food webs by feeding on detritus and also by preying on bacteria and other protists (Finlay and Fenchel 1996;Schlegel and Meisterfeld 2003). ...
... As with other protist groups, there is currently a deficit of taxonomists trained in the identification of ciliates (Cotterill et al. 2008). Although this is a worldwide problem, this phenomenon is severe in most South American countries (Küppers et al. 2020). ...
There is a significant gap in research and knowledge on the diversity and distribution of Chilean ciliates. To tackle these issues, we used cultures and protargol preparations to describe the ciliates present in poorly explored areas. At these sites, we identified 45 ciliate morphospecies, 35 of which represent unprecedent records to Chile. Then, we brought together our records with literature data to construct a species checklist. This checklist summarises 132 years of data and describes the identity, habitat and distribution of 207 species, including 15 species potentially endemic to Chile. This checklist is far from complete: a diversity estimate suggests that at least two-thirds of the ciliate species occurring in Chile have yet to be described. The checklist is dominated by freshwater taxa because ciliates from marine, brackish and terrestrial environments have rarely been investigated in Chile. Finally, after controlling for sampling artefacts, we found that ciliates exhibit a bell-shaped latitudinal diversity gradient in Chile. This peculiar biogeographical pattern is common in Chile. Plants, animals and testate amoebae also exhibit a bell-shaped latitudinal diversity gradient in Chile. This finding suggests that the historical contingencies that drove the biogeography of the Chilean biota also shaped ciliate biogeography.
https://www.sciencedirect.com/science/article/abs/pii/S0932473922000293
... Describing the still mostly unknown diversity of protists requires a major effort in basic taxonomy (Heger et al., 2014). The magnitude of land-use changes and natural habitat destruction occurring throughout the world and the now well established existence of restricted geographical distribution patterns in free-living protists (Foissner, 2008) implies that a large proportion of protist diversity will likely disappear before it can be described, and thus the conservation of protists should indeed be a priority (Cotterill et al., 2008, Qin et al., 2016. Apodera angatakere is a highly conspicuous genus of testate amoeba and has to date only been found in New Zealand. ...
Eukaryotic microbial diversity is known to be extensive but remains largely undescribed and uncharted. While much of this unknown diversity is composed of inconspicuous flagellates and parasites, larger and morphologically distinct protists are regularly discovered, most notably from poorly studied regions.
Here we report a new flagship species of hyalospheniid (Amoebozoa; Arcellinida; Hyalospheniformes) testate amoeba from New Zealand and an unusual story of overlooked description under a pre-occupied name and subsequent oversight for nearly one century. Through a process involving The Māori Language Commission, we named the species Apodera angatakere, meaning “a shell with a keel”. This species resembles Apodera vas but differs by the presence of a distinctive hollow keel. Cytochrome Oxidase Subunit 1 (COI) sequence data shows that this species forms a distinct clade nested within genus Apodera.
This conspicuous species is so far known only from New Zealand and is restricted to peatlands. It is one of the few examples of endemic microorganisms from this biodiversity hotspot and biogeographer’s paradise. As over 90% of New Zealand’s peatlands have been lost since European colonisation and much of the remaining surfaces are threatened, Apodera angatakere could be a flagship species not only for microbial biogeography but also for island biodiversity conservation.
... Conversely, the study of non-photosynthetic protists in inland waters was mostly focused on taxonomic and broad ecological aspects of selected groups and populations (see e.g., Foissner and Berger, 1996;Wujek, 2005). In general, the knowledge of the key ecological roles of freshwater planktic microeukaryote communities has been limited by incomplete inventories of diversity (Cotterill et al., 2008;Grossmann et al., 2016). ...
The structure of microbial communities, microalgae, heterotrophic protozoa and fungi contributes to characterize food webs and productivity and, from an anthropogenic point of view, the qualitative characteristics of water bodies. Traditionally, in freshwater environments many investigations have been directed to the study of pelagic microalgae (“phytoplankton”) and periphyton (i.e., photosynthetic and mixotrophic protists) through the use of light microscopy (LM). While the number of studies on bacterioplankton communities have shown a substantial increase after the advent of high-throughput sequencing (HTS) approaches, the study of the composition, structure, and spatio-temporal patterns of microbial eukaryotes in freshwater environments was much less widespread. Moreover, the understanding of the correspondence between the relative phytoplankton abundances estimated by HTS and LM is still incomplete. Taking into account these limitations, this study examined the biodiversity and seasonality of the community of eukaryotic microplankton in the epilimnetic layer of a large and deep perialpine lake (Lake Garda) using HTS. The analyses were carried out at monthly frequency during 2014 and 2015. The results highlighted the existence of a rich and well diversified community and the presence of numerous phytoplankton taxa that were never identified by LM in previous investigations. Furthermore, the relative abundances of phytoplankton estimated by HTS and LM showed a significant relationship at different taxonomic ranks. In the 2 years of investigation, the temporal development of the whole micro-eukaryotic community showed a clear non-random and comparable distribution pattern, with the main taxonomic groups coherently distributed in the individual seasons. In perspective, the results obtained in this study highlight the importance of HTS approaches in assessing biodiversity and the relative importance of the main protist groups along environmental gradients, including those caused by anthropogenic impacts (e.g., eutrophication and climate change).
... SegundoCotterill et al. (2008), cerca de 89% da diversidade de protozoários permanece desconhecida, número que ressalta a necessidade de se investir no conhecimento desses organi smos, visto que apresentam importantes funções nos variados ecossistemas que habitam e são negligenciados em programas de conservação. ...
Neste trabalho foi realizado um inventário de ciliados bentônicos em ecossistemas límnicos, localizados no município de Juiz de Fora (MG), com amostragens mensais, no período entre março e agosto de 2018. Os ciliados foram identificados com base em observações in vivo e, quando necessário, foi realizada impregnação pela prata e pela coloração por DAPI. Vinte e uma morfoespécies, distribuídas em cinco classes de Ciliophora, foram identificadas. Destas, Euplotes sp. 2, Euplotes eurystomus, Paramecium bursaria e Paramecium caudatum foram as espécies encontradas que poderiam ser facilmente mantidas sob condições in vitro.
... In addition, economic and sanitary management could benefit from microbes spatial modelling, for instance by predicting zones at risk of disease outbreaks and therefore make the use of a potential treatment more parsimonious. A third outcome of spatial modelling of soil microbes could also focus on their conservation by identifying microbe diversity hotspots or refine distribution zones of endemic microorganisms (Cotterill, Al-Rasheid, & Foissner, 2008). ...
Aim
Trends in spatial patterns of diversity in macroscopic organisms can be well predicted from correlative models, using topo‐climatic variables for plants and animals allowing inference over large scales. By contrast, diversity in soil microorganisms is generally considered as mostly driven by edaphic variables and, therefore, difficult to extrapolate on a large spatial scale based on predictive models. Here, we compared the power of topo‐climatic versus edaphic variables for predicting the diversity of various soil protist groups at the regional scale.
Location
Swiss western Alps.
Taxa
Full protist community and nine clades belonging respectively to three functional groups: parasites (Apicomplexa, Peronosporomycetes and Phytomyxea), phagotrophs (Sarcomonadea, Tubulinea and Spirotrichea) and phototrophs (Chlorophyta, Trebouxiophyceae and Diatomeae).
Methods
We extracted soil DNA from 178 sites along a wide range of elevations with a random‐stratified sampling design. We defined protist Operational Taxonomic Units assemblages by metabarcoding of the V4 region of the rRNA small subunit gene. We assessed and modelled the diversity (Shannon index) patterns of all above‐mentioned taxonomic groups based on topo‐climatic (topography, slope southness, slope steepness and average summer temperature) and edaphic (soil temperature, relative humidity, pH, electroconductivity, phosphorus percentage, carbon/nitrogen, loss on ignition and shale percentage) variables in Generalized Additive Models (GAM).
Results
The respective significance of topo‐climatic and edaphic variables varied among taxonomic and—to a certain extent—functional groups: while many variables explained significantly the diversity of the three phototrophs this was less the case for the three parasites. Topo‐climatic variables had a better predictive power than edaphic variables, yet predictive power varied among taxonomic groups.
Main conclusions
Topo‐climatic variables (particularly slope steepness and summer temperature if we consider their significance in the GAMs) were, on average, better predictors of protist diversity at the landscape scale than edaphic variables. However, the predictive power of these variables on diversity differed considerably among taxonomic groups; such relationships may be due to direct and/or indirect (e.g. biotic) influences (like with parasitic taxa, where low predictive power is most likely explained by the absence of information on the hosts’ distribution). Future prospects include using such spatial models to predict hotspots of diversity and disease outbreaks.
... The global diversity of free-living protists is not known, although estimates range from < 30 000 ( Mora et al. 2011) to over 1 million species ( Adl et al. 2007, Cotterill et al. 2008, Larsen et al. 2017, with many in between (Appeltans et al. 2012, Pawlowski et al. 2012, de Vargas et al. 2015). Improved understanding of protistan diversity of soils in ice-free regions around Antarctica (c. ...
Heterotrophic soil protists encompass lineages that are both evolutionarily ancient and highly diverse, providing an untapped wealth of scientific insight. Yet the diversity of free-living heterotrophic terrestrial protists is still largely unknown. To contribute to our understanding of this diversity, we present a checklist of heterotrophic protists currently reported from terrestrial Antarctica, for which no comprehensive evaluation currently exists. As a polar continent, Antarctica is especially susceptible to rising temperatures caused by anthropogenic climate change. Establishing a baseline for future conservation efforts of Antarctic protists is therefore important. We performed a literature search and found 236 taxa identified to species and an additional 303 taxa identified to higher taxonomic levels in 54 studies spanning over 100 years of research. Isolated by distance, climate and the circumpolar vortex, Antarctica is the most extreme continent on Earth: it is not unreasonable to think that it may host physiologically and evolutionarily unique species of protists, yet currently most species discovered in Antarctica are considered cosmopolitan. Additional sampling of the more extreme intra-continental zones will probably result in the discovery of more novel and unique taxa.
