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Map of the Houxi River watershed in Xiamen city, Southeast China, showing the ten sampling sites selected along the river continuum.
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Whether bacterioplankton are assembled in the same way as microeukaryotes is a key question that has been answered only partially in microbial ecology. In particular, relating distribution patterns to the underlying ecological processes for plankton communities in highly dynamic ecosystems, such as river–reservoirs subjected to anthropogenic impact...
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... samples were collected from the surface layer (<0.5 m) at the mid-point of the Houxi River, located northwest of Xiamen city, Fujian, China (24 • 34 -24 • 46 N and 117 • 56 -118 • 8 E; Figure 1. Houxi River watershed covers 205 km 2 of the surface area, with a river length of approximately 25 km. ...
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... total of 100 samples were collected in January and July of the years 2012-2016, during ten sampling visits at ten sampling sites. In the upstream, pristine area, one sampling site in the headwater (Site 1), and four sites (Sites 2-5) in the lacustrine and riverine zones of two reservoirs (Shidou and Bantou reservoirs; Figure 1) were selected. These reservoirs were constructed to supply drinking water for downstream urban population. ...
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... reservoirs were constructed to supply drinking water for downstream urban population. The remaining sites, located in the downstream urban area, included two sites in the peri-urban area (Sites 7 and 8) and two sites in the fully urban area (Sites 9 and 10; Figure 1). ...
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... resulting OTU tables were subjected to subsequent processing of singleton, archaea, and chloroplast deletion for bacterioplankton, and singleton deletion and taxa curation for microeukaryotes. The OTU tables were rarefied to the lowest number of sequences per sample, that is, 16,854 and 28,993 sequences for bacterioplankton and microeukaryotes, respectively ( Figure S1). ...
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... Houxi River system exhibited environmental heterogeneity as a result of landscape and hydrological changes in its watershed (Figure 1; Figure 2a). By averaging the values of the physical and chemical parameters over the ten sampling visits, our data confirmed this heterogeneity, as there were clear differences between the pristine upstream and the downstream sites in the urban areas (Figure 2a). ...
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... rarefying bacterioplankton and microeukaryotes OTU tables at the lowest sequences per sample, we retained 10,330 and 12,613 OTUs for bacterioplankton and microeukaryotes, respectively. The rarefaction curves tended to plateau, indicating that the efforts for sequencing depth were generally maximized ( Figure S1). Bacterioplankton were generally assigned to 36 phyla, 91 classes, 150 orders, 242 families, and 466 genera, while microeukaryotes were assigned to 29 phyla, 139 classes, 271 orders, 583 families, and 1854 genera. ...
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... Materials: The following are available online at http://www.mdpi.com/2073-4441/11/6/1127/s1, Figure S1: Rarefaction curves of the studied plankton communities in the Houxi River, Figure S2: Density plots exemplifying the spatial abundance distributions of typical core and random OTUs of bacteria and microeukaryotes, Figure S3: Heatmaps of taxonomic affiliation and site clustering of core and random bacterioplankton and microeukaryotes at phylum level, Figure S4: Upstream-downstream variation in the number of sequences assigned to different bacterial taxa, Figure S5: Upstream-downstream variation in the number of sequences assigned to different microeukaryotic taxa, Figure S6: Correlations between spatial proximity and core or random plankton community similarities within different distance classes, Figure S7: Relationships between Bray-Curtis dissimilarities of microeukaryotes and bacterioplankton in different taxa categories, Figure S8: Spearman correlations between the environmental variables and the number of OTUs for each plankton community facet. ...
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Introduction
Rapid environmental change driven by urbanisation offers a unique insight into the adaptive potential of urban‐dwelling organisms. Urban‐driven phenotypic differentiation is increasingly often demonstrated, but the impact of urbanisation (here modelled as the percentage of impervious surface (ISA) around each nestbox) on offspring deve...
Citations
... Therefore, planktonic microeukaryote communities are commonly employed as biomonitors for assessing aquatic ecosystem health and water quality (Foissner and Berger, 1996). Over the past decades, much effort has been made to unveil how the freshwater microeukaryotic communities are distributed and assembled Isabwe et al., 2019;Abdullah Al et al., 2022). The biogeography of microeukaryotic planktons can be shaped by abiotic factors (e.g., nutrients, temperature, light, pH, depth, spatial factors) and biotic factors (including top-down predation, competition, mutualism, and trade-offs) (Gong et al., 2015;Wang et al., 2015;Chen et al., 2019;Wang et al., 2020). ...
Microeukaryotes play crucial roles in the microbial loop of freshwater ecosystems, functioning both as primary producers and bacterivorous consumers. However, understanding the assembly of microeukaryotic communities and their functional composition in freshwater lake ecosystems across diverse environmental gradients remains limited. Here, we utilized amplicon sequencing of 18S rRNA gene and multivariate statistical analyses to examine the spatiotemporal and biogeographical patterns of microeukaryotes in water columns (at depths of 0.5, 5, and 10 m) within a subtropical lake in eastern China, covering a 40 km distance during spring and autumn of 2022. Our results revealed that complex and diverse microeukaryotic communities were dominated by Chlorophyta (mainly Chlorophyceae), Fungi, Alveolata, Stramenopiles, and Cryptophyta lineages. Species richness was higher in autumn than in spring, forming significant hump-shaped relationships with chlorophyll a concentration (Chl-a, an indicator of phytoplankton biomass). Microeukaryotic communities exhibited significant seasonality and distance-decay patterns. By contrast, the effect of vertical depth was negligible. Stochastic processes mainly influenced the assembly of microeukaryotic communities, explaining 63, 67, and 55% of community variation for spring, autumn, and both seasons combined, respectively. Trait-based functional analysis revealed the prevalence of heterotrophic and phototrophic microeukaryotic plankton with a trade-off along N:P ratio, Chl-a, and dissolved oxygen (DO) gradients. Similarly, the mixotrophic proportions were significantly and positively correlated with Chl-a and DO concentrations. Overall, our findings may provide useful insights into the assembly patterns of microeukaryotes in lake ecosystem and how their functions respond to environmental changes.
... We observed significant and strong negative correlations between geographical distance and Bray-Curtis similarity in these three communities (Fig. 7a-c), which align with findings from numerous previous studies Isabwe et al. 2019;Wu and Liu 2018;Zou et al. 2021). This significant and strong distance-decay relationship may arise from species sorting and dispersal capabilities (Hanson et al. 2012). ...
Although the Three Gorges Dam (TGD) is the world’s largest hydroelectric dam, little is known about the spatial–temporal patterns and community assembly mechanisms of meio- and micro-eukaryotes and its two subtaxa (zooplankton and zoobenthos). This knowledge gap is particularly evident across various habitats and during different water-level periods, primarily arising from the annual regular dam regulation. To address this inquiry, we employed mitochondrial cytochrome c oxidase I (COI) gene-based environmental DNA (eDNA) metabarcoding technology to systematically analyze the biogeographic pattern of the three communities within the Three Gorges Reservoir (TGR). Our findings reveal distinct spatiotemporal characteristics and complementary patterns in the distribution of meio- and micro-eukaryotes. The three communities showed similar biogeographic patterns and assembly processes. Notably, the diversity of these three taxa gradually decreased along the river. Their communities were less shaped by stochastic processes, which gradually decreased along the longitudinal riverine-transition-lacustrine gradient. Hence, deterministic factors, such as seasonality, environmental, and spatial variables, along with species interactions, likely play a pivotal role in shaping these communities. Environmental factors primarily drive seasonal variations in these communities, while hydrological conditions, represented as spatial distance, predominantly influence spatial variations. These three communities followed the distance-decay pattern. In winter, compared to summer, both the decay and species interrelationships are more pronounced. Taken together, this study offers fresh insights into the composition and diversity patterns of meio- and micro-eukaryotes at the spatial-temporal level. It also uncovers the mechanisms behind community assembly in various environmental niches within the dam-induced river-reservoir systems.
Key points
• Distribution and diversity of meio- and micro-eukaryotes exhibit distinct spatiotemporal patterns in the TGR.
• Contribution of stochastic processes in community assembly gradually decreases along the river.
• Deterministic factors and species interactions shape meio- and micro-eukaryotic community.
Graphical Abstract
... Interestingly, during the wet season, the compositions of eukaryotic communities were shown to be less dispersed than the prokaryotic communities. This reflected the stronger distance-decay relationships displayed by the eukaryotic communities than did the bacterial communities (shown in Supplementary Fig. 5), similar to those reported by Astorga et al. (2012) and Isabwe et al. (2019). The less discernible correlation between spatial distance and Mekong River's bacterial communities might reflect the high dispersal capabilities of bacteria and the flux of allochthonous bacterial populations from various sources (Meziti et al. 2019;Wang et al. 2019). ...
... The microbial community assembly, focusing on the contribution of stochastic (e.g., birth, death, and immigration) and deterministic (e.g., environmental factors and species interactions) processes to shaping the compositions and abundance of taxa in ecological communities, is a key issue in evaluating the influence of environmental changes on the microbial communities, which may in turn affect their functioning. Recent studies quantifying the importance of stochastic and deterministic processes for microbial community assembly mainly focused on soil [16,26] and water [27,28] environments, but limited studies reported the assembly of microbial community in the air or dust. Li et al. [29] have demonstrated a higher contribution of stochastic processes in shaping bacterial and fungal community assembly in urban dust. ...
Airborne microorganisms, including pathogens, would change with surrounding environments and become issues of global concern due to their threats to human health. Microbial communities typically contain a few abundant but many rare species. However, how the airborne abundant and rare microbial communities respond to environmental changes is still unclear, especially at hour scale. Here, we used a sequencing approach based on bacterial 16S rRNA genes and fungal ITS2 regions to investigate the high time‐resolved dynamics of airborne bacteria and fungi and to explore the responses of abundant and rare microbes to the atmospheric changes. Our results showed that air pollutants and microbial communities were significantly affected by human activities related to the Chinese New Year (CNY). Before CNY, significant hour‐scale changes in both abundant and rare subcommunities were observed, while only abundant bacterial subcommunity changed with hour time series during CNY. Air pollutants and meteorological parameters explained 61.5%−74.2% variations of abundant community but only 13.3%−21.6% variations of rare communities. These results suggested that abundant species were more sensitive to environmental changes than rare taxa. Stochastic processes predominated in the assembly of abundant communities, but deterministic processes determined the assembly of rare communities. Potential bacterial pathogens during CNY were the highest, suggesting an increased health risk of airborne microbes during CNY. Overall, our findings highlighted the “holiday effect” of CNY on airborne microbes and expanded the current understanding of the ecological mechanisms and health risks of microbes in a changing atmosphere.
... Eukaryotes were even less sensitive to geographical distances than Bacteria. These results have previously been observed in surface water (Isabwe et al., 2019;Liu et al., 2020;Logares et al., 2018;Vass et al., 2020). It is likely that water movement, and thus passive transport, was the primary mechanism of movement for the microorganisms in aquifers. ...
Aquifers are inhabited by microorganisms from the three major domains of life: archaea, eukaryotes and bacteria. Although interest in the processes that govern the assembly of these microbial communities is growing, their study is almost systematically limited to one of the three domains of life. Archaea, bacteria and eukaryotes are however interconnected and essential to understand the functioning of their living ecosystems. We, therefore, conducted a spatial study of the distribution of microorganisms by sampling 35 wells spread over an area of 10 000 km2 in the Quebec region (Canada). The obtained data allowed us to define the impact of geographic distance and geochemical water composition on the microbial communities. A null model approach was used to infer the relative influence of stochastic and determinist ecological processes on the assembly of the microbial community from all three domains. We found that the organisms from these three groups are mainly governed by stochastic mechanisms. However, this apparent similarity does not reflect the differences in the processes that govern the phyla assembly. The results obtained highlight the importance of considering all the microorganisms without neglecting their individual specificities. This article is protected by copyright. All rights reserved.
... This study was conducted in Xiamen, Fujian, China. Xiamen has a subtropical monsoon climate with an average annual temperature of 20.7°C and an average annual rainfall of 1335.8 mm [32]. Under rapid urban development, Xiamen has experienced a decrease in farmland and an increase in built-up land by, respectively, 14.0% and 15.7% from 1980 to 2015 [33]. ...
The size-plasticity hypothesis posits that larger size organisms are less plastic in their metabolic rates and therefore are more strongly environmental-filtered than smaller organisms. Many studies have supported this hypothesis by evaluating the relative roles of environmental filtration and dispersal for different taxonomic groups of soil organisms. Most observations are made at large spatial scales, which are assumed to have a wide array of varying habitats. However, since urbanization causes habitat fragmentation at smaller regional scales, testing the size-plasticity hypothesis at this scale would help better understand the spatial assortment of urban soil organisms which, in turn, would help to develop improved management and conservation strategies of urban soil health. Here, we used DNA metabarcoding on five groups of soil biota (bacteria, fungi, protists, nematodes, and soil invertebrates) to assess the relative importance of dispersal and environmental filters to examine the size-plasticity hypothesis at this spatial scale in an urban environment. We observed strong distance-decay of community similarities associated with higher levels of stochastic changes in bacteria, nematode and protist communities but not fungal or invertebrate communities. Bacterial communities occupied the widest niche followed by protists and nematodes, potentially because of their higher dispersal abilities compared to the larger soil organisms. Null deviation of communities varied with taxonomic groups where bacteria and nematodes were mainly driven by homogenizing dispersal, protists and fungi by drift and soil invertebrates by environmental selection. We further identified a small percentage of locally-adapted taxa (2.1%) that could be focal taxa for conservation and restoration efforts by, for example, restoring their habitats and enhancing their regional connectivity. These results support the size-plasticity hypothesis at the relatively unexplored regional scale in an urbanization context, and provide new information for improving urban soil health and sustainable city models and urban soil health.
... These highly dynamic landscapes suffer from plant biomass destruction by stochastic disturbances in addition to large variation in resource availability over a short period of time; processes that may break established environment-plantecosystem relationships (Kleyer et al. 2014). Studies on rivers and wetlands found that neutral processes and dispersal limitation better explain species diversity in highly dynamic ecosystems than environmental filtering (Isabwe et al. 2019, Schöpke et al. 2019. ...
The influence of island dynamics and characteristics on taxonomic diversity, particularly species richness, are well studied. Yet, our knowledge on the influence of island dynamics and characteristics on other facets of diversity, namely functional and phylogenetic diversity, is limited, constraining our understanding of assembly processes on islands (e.g. biogeographic history, dispersal and environmental filtering and species interactions). Using barrier islands, a highly dynamic and so far, understudied island type, we investigate how multiple facets of vascular plant diversity (functional, phylogenetic and taxonomic diversity) are shaped by island geomorphology, modern and historic area, and habitat heterogeneity. In line with our expectation, historical dynamics in island geomorphology affected phylogenetic and taxonomic diversity via habitat heterogeneity. However, island area was the best predictor across all facets of diversity. Specifically, larger islands had higher functional and phylogenetic diversity than expected by chance while most of the smaller islands had lower diversity. The influence of area on functional diversity acted via habitat heterogeneity, with habitat heterogeneity influencing negatively functional diversity. Our results suggest that larger islands accumulate functionally and phylogenetically unique species. Further, results for functional diversity pointed towards potential area–heterogeneity trade‐offs, with these trade‐offs likely resulting from increased interspecific competition favoring a specific set of trait values (of stronger competitors), particularly on smaller islands. Together, these results demonstrate that going beyond taxonomic diversity contributes to identifying underlying processes shaping diversity–area relationships.
... Due to the rapid urbanization of Xiamen city, Houxi River has undergone a strong impact of human activities for twenty years. Due to the typical characteristic of an urbanizing river that originates from a rural area and flows through an urban area (Isabwe et al., 2019), Houxi River is an ideal system for deeply understanding the influence of human activities on CEC behaviors at the watershed scale. ...
The distribution and fate of contaminants of emerging concern (CECs) was studied in relation to hydrological conditions, land use characteristics, and spatial contiguity in Houxi River. Thirty-four CECs were detected in the surface water during a three-year sampling campaign. Caffeine was most prevalent (99% frequency), while bisphenol A had the highest median concentration (78.2 ng/L) among the detected CECs. Caffeine and the other prevalent CECs lincomycin and bisphenol A, with median concentrations of 3.89 ng/L, 0.26 ng/L, and 78.2 ng/L, respectively, were positively correlated with land use types related to anthropogenic activities (grass, barren, built up, and cropland areas and landscape indexes for human activities). The analysis of similarities revealed significant annual variations, with increasing trends in both the concentrations and detection frequencies of CECs. Spatial variations were demonstrated by higher concentrations and detection frequencies downstream compared to upstream. The singular value decomposition analysis revealed that the downstream sites were the major contributors (55.6%–100%) to the spatial variability of most CECs. Moran's I analysis based on downstream contiguity indicated strong spatial autocorrelation among the connected sites for most CECs. This was further supported by longer correlation lengths for 18 CECs than the average distance between the sampling sites. The spatial autocorrelation can be attributed to the physicochemical properties of CECs and local hydrological dynamics, including temperature, wind speed, and sunshine hours. For most CECs, local contribution predominated over neighbor influence with an average value of 75.5%. The results of this study provide new insight to evaluate CEC distributions and will be beneficial policymakers for the management and prioritization of CEC contaminants in the Houxi watershed.
... Studies of marine microbial biogeography have benefited greatly from the rapid progress that has been made in genomic sequencing and theoretical microbial ecology (11). Among the various spatial distribution patterns (e.g., latitudinal diversity patterns and taxa-area relationships), distance-decay patterns have frequently been reported based on studies of communities of bacteria and microeukaryotes in a variety of aquatic habitats, including rivers (12,13), lakes (9,14), intertidal zones (15), coastal ocean (8,16), and open ocean (16,17). However, there have been few studies of microbial biogeographic patterns in oligotrophic marine waters, especially at the trans-basin scale (17). ...
... Sample clustering by regions revealed significant distance-decay patterns ( Fig. 3A-C, Fig. 4). Significant distance-decay patterns of bacteria and/or microeukaryotes have been found in rivers (12,13), lakes (9,14), intertidal zones (15), coastal seas (8,16), and open oceans (16,17). The underling mechanisms responsible for distance-decay patterns have been shown to differ between domains and between ecosystems (8,13,15). ...
... Significant distance-decay patterns of bacteria and/or microeukaryotes have been found in rivers (12,13), lakes (9,14), intertidal zones (15), coastal seas (8,16), and open oceans (16,17). The underling mechanisms responsible for distance-decay patterns have been shown to differ between domains and between ecosystems (8,13,15). The fact that environmental factors varied spatially in the TNPO during our study (Fig. 1B, Fig. S2 and S4) may have led to distinct variations in bacterial and microeukaryotic community structures between the WTNP and CTNP. ...
Marine microbiota are critical components of global biogeochemical cycles. However, the biogeographic patterns and ecological processes that structure them remain poorly understood, especially in the oligotrophic ocean. In this study, we used high-throughput sequencing of 16S and 18S rRNA genes to investigate the distribution patterns of bacterial and microeukaryotic communities and their assembly mechanisms in the surface waters of the tropical North Pacific Ocean. The fact that both the bacterial and the microeukaryotic communities showed similar distribution patterns (i.e., similar distance-decay patterns) and were clustered according to their geographic origin (i.e., the western tropical North Pacific and central tropical North Pacific) suggested that there was a significant biogeographic pattern of microbiota in the North Pacific Ocean. Indices of alpha diversity such as species richness, phylogenetic diversity, and the Shannon diversity index also differed significantly between regions. The correlations were generally similar between spatial and environmental variables and the alpha and beta diversities of bacteria and microeukaryotes across the entire region. The relative importance of ecological processes differed between bacteria and microeu-karyotes: ecological drift was the principal mechanism that accounted for the structure of bacterial communities; heterogeneous selection, dispersal limitation, and ecological drift collectively explained much of the turnover of the microeu-karyote communities. IMPORTANCE Bacteria and microeukaryotes are extremely diverse groups in the ocean, where they regulate elemental cycling and energy flow. Studies of marine microbial ecology have benefited greatly from the rapid progress that has been made in genomic sequencing and theoretical microbial ecology. However, the spatial distribution of marine bacteria and microeukaryotes and the nature of the assembly mechanisms that determine their distribution patterns in oligotrophic marine waters are poorly understood. In this study, we used high-throughput sequencing methods to identify the distribution patterns and ecological processes of bacteria and microeukaryotes in an oligotrophic, tropical ocean. Our study showed that contrasting community assembly mechanisms underlaid similar bio-geographic patterns of surface bacterial and microeukaryotic communities in the tropical North Pacific Ocean.
... The |βNTI| < 2 and RC bray < −0.95 or the |βNTI| < 2 and RC bray ≥ 0.95 RCbray were identified as homogenizing dispersal and dispersal limitation, respectively. When the |βNTI| < 2 and |RC bray | < 0.95 were identified as "Undominated" (Dini-Andreote et al., 2015;Stegen et al., 2015;Isabwe et al., 2019). To demonstrate which process contributed more to the DDR slopes between the core and satellite sub-communities, samples controlled by dispersal limitation and heterogeneous selection were separately extracted from both sub-communities according to the results of Stegen's null model. ...
Microbial communities normally comprise a few core species and large numbers of satellite species. These two sub-communities have different ecological and functional roles in natural environments, but knowledge on the assembly processes and co-occurrence patterns of the core and satellite species in Tibetan lakes is still sparse. Here, we investigated the ecological processes and co-occurrence relationships of the core and satellite bacterial sub-communities in the Tibetan lakes via 454 sequencing of 16S rRNA gene. Our studies indicated that the core and satellite bacterial sub-communities have similar dominant phyla (Proteobacteria, Bacteroidetes, and Actinobacteria). But the core sub-communities were less diverse and exhibited a stronger distance-decay relationship than the satellite sub-communities. In addition, topological properties of nodes in the network demonstrated that the core sub-communities had more complex and stable co-occurrence associations and were primarily driven by stochastic processes (58.19%). By contrast, the satellite sub-communities were mainly governed by deterministic processes (62.17%). Overall, this study demonstrated the differences in the core and satellite sub-community assembly and network stability, suggesting the importance of considering species traits to understand the biogeographic distribution of bacterial communities in high-altitude lakes.
