Article

Warming and nutrient enrichment in combination increase stochasticity and beta diversity of bacterioplankton assemblages across freshwater mesocosms

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  • Guangdong Academy of Sciences
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Abstract

The current climate warming and eutrophication are known to interactively threaten freshwater biodiversity; however, the interactive effects on lacustrine bacterioplankton diversity remain to be determined. Here, we analyzed the spring bacterioplankton community composition (BCC) in 24 outdoor, flow-through mesocosms (mimicking shallow lake environments) under 3 temperature scenarios and 2 nutrient regimes. Our results revealed that neither long-term warming (8.5 years) nor nutrient enrichment had significant effects on bacterioplankton alpha diversity, whereas long-term enhanced warming (elevated 50% above the IPCC A2 climate scenario) and nutrient enrichment in combination increased bacterioplankton beta diversity. We also found that BCC shifted significantly under enhanced warming and nutrient-enriched conditions towards decreased relative abundances of Actinobacteria, Bacteroidetes and Betaproteobacteria, whereas the percentages of Cyanobacteria, total rare phyla and unclassified phyla significantly increased. Null-model tests indicated that deterministic processes played a more important role than stochastic processes in determining BCC. However, the relative importance of stochasticity, primarily ecological drift, was enhanced and contributed to the increased beta diversity of BCC under enhanced warming and nutrient-enriched conditions. Overall, our study suggests that the synergetic effects of warming and nutrient enrichment may result in high variability in the composition of bacterioplankton communities in lacustrine water bodies.

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... Exploring the mechanisms of bacterioplankton assembly is one of the major goals of marine microbial ecology (17)(18)(19). Generally, aquatic bacterioplankton community structure is shaped by environmental or dispersal-related processes (see, e.g., references 20 to 22). ...
... In summer seawater, we found lower percentages of Actinobacteria at sites with more thermal effluents, which was probably related to the obviously increased relative abundance of Cyanobacteria. This finding is consistent with previous reports showing negative relationships between the relative abundances of Cyanobacteria and Actinobacteria in aquatic ecosystems (19,41). Furthermore, Bacteroidetes have been found to be likely to attach to marine eukaryotic algae or animals (42,43). ...
... Among all the environmental factors examined, the spatially structured temperature created by thermal effluents played the strongest role in determining bacterioplankton metacommunity structure across thermal gradients in both seasons studied. Differences in traits cause different bacterial populations to have different sensitivities to temperature during their growth processes (44)(45)(46)(47); thus, temperature is one of the most important factors in shaping bacterioplankton community structure (19,35,48). This finding was further confirmed by the positive linear correlations between BCC dissimilarities and temperature differences in any pairwise comparison of sampling sites. ...
Article
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Understanding the mechanisms of bacterial community assembly across environmental gradients is one of the major goals of marine microbial ecology. Thermal effluents from two nuclear power plants have been present in the subtropical Daya Bay for more than 20 years and have generated a comparatively stable and long thermal gradient (a temperature increase from 0 to 10°C). The environmental patches across thermal gradients are heterogeneous and very strongly interconnected on a microbial scale; thus, this is a useful model for the study of the metacommunity processes (i.e., patch dynamics, species sorting, mass effects, and neutral processes) that underlie marine bacterioplankton assembly. The significance of our research is to reveal how environmental conditions and dispersal-related processes interact to influence bacterioplankton metacommunity processes and their seasonal differences across thermal gradients. Our results may advance the understanding of marine microbial ecology under future conditions of global warming.
... Previous evidence suggests that there is a combined effect of warming and nutrient enrichment on aquatic bacterial taxonomic (based on 16S rRNA gene sequencing) community composition (Ren et al. 2017), causing a dramatic change in the composition of bacterial communities toward increased percentages of cyanobacteria (Ren et al. 2017). However, changes in microbial composition do not always entail a functional shift due to microbial functional redundancy (Allison and Martiny 2008;He et al. 2012;Zhang et al. 2019). ...
... Previous evidence suggests that there is a combined effect of warming and nutrient enrichment on aquatic bacterial taxonomic (based on 16S rRNA gene sequencing) community composition (Ren et al. 2017), causing a dramatic change in the composition of bacterial communities toward increased percentages of cyanobacteria (Ren et al. 2017). However, changes in microbial composition do not always entail a functional shift due to microbial functional redundancy (Allison and Martiny 2008;He et al. 2012;Zhang et al. 2019). ...
... Sampling was conducted as described in detail by Ren et al. (2017). In brief, we collected 8 L pooled water samples from three uniformly distributed sites in each of the 16 mesocosms using a 1-m long tube water sampler that integrated the whole water column (twice on 02 April 2012). ...
Article
Shallow lakes, the most numerous waterbodies on Earth, are susceptible to climate warming and nutrient enrichment whose effects on the microbial functional potentials are not yet fully understood, however. Here, we applied a microarray-based technology termed GeoChip 5.0 to investigate microbial functional genes at the beginning of April in shallow lake ecosystems simulated in mesocosms that have been undergoing nutrient enrichment and warming for 9 yr. Our results showed that warming exacerbated the impact of nutrient enrichment on microbial metabolic potentials and significantly elevated the microbial autotrophy potentials, carbon degradation potentials (e.g., starch, hemicellulose, cellulose, and chitin), and polyphosphate mobilization potentials. We also observed that warming enhanced the impacts of nutrient enrichment on microbial functional gene structure. The combination of warming and nutrient enrichment increased the deterministic effect from phytoplankton, causing higher interlinking of microbial functional genes involved in the carbon, nitrogen , phosphorus, and sulfur cycling in correlation-based networks. Overall, we propose that the joint effect of warming and nutrient enrichment promoted the autotrophic carbon supply and the heterotrophic carbon demand and changed the carbon fluxes in the experimental mesocosms.
... Anthropogenic nutrient enrichment that resulted in eutrophication (Houseman et al., 2008) has been one of the more serious environmental problems in lake ecosystems (Smith et al., 2006;McCrackin et al., 2017). Previous investigations have highlighted the influences of nutrient enrichment and enhanced primary productivity on bacterial communities in aquatic ecosystems (Graves et al., 2016;Kearns et al., 2016;Wang et al., 2016;Dai et al., 2017;Ren et al., 2017) communities separately, and few studies considered the bacterial communities in water and sediments simultaneously along the same trophic gradient. ...
... A recent study reported that nutrient enrichment reduces active bacterial diversity but increases the proportion of dormant (low metabolic or inactive) taxa in sediments; consequently, the total bacterial diversity remains unaffected (Kearns et al., 2016). Here, our observed pattern that diversity is inversely correlated with higher nutrient supply may be due to the increased bacterial stochasticity (such as random extinction and death) (Ren et al., 2017). ...
... Thus, the PBC is more sensitive to lake eutrophication than the SBC, possibly due to the turbulent diffusion of water that favors the faster response of PBC to lake eutrophication than SBC. Typically, dissimilarities among bacterial communities are closely related to the trophic level (Dai et al., 2017;Ren et al., 2017), but some contradictory results are observed. Ren et al. (2017) showed that nutrient enrichment significantly increased PBC beta diversity in freshwater mesocosms. ...
Article
The water column (fluidic) and sediments (non-fluidic) represent two distinct habitats in lakes. Planktonic and sedimentary bacterial communities are fundamental components of the biogeochemical processes within freshwater lakes. Anthropogenic activities induced eutrophication has been recognized as one of the most severe environmental problems for the lake ecosystem. However, little is known regarding the responses of bacterial communities in fluidic and non-fluidic lake habitats to eutrophication nor the underlying ecological mechanisms. Here, we investigated the planktonic and sedimentary bacterial communities from a series of freshwater lakes across a range of trophic states. We observed a high heterogeneity in bacterial community composition between habitats and along the trophic gradient. Alpha diversity of the sedimentary bacterial community decreased monotonically with increased eutrophication, whereas that of planktonic bacterial community exhibited a downward arched (parabolic) pattern along the trophic gradient. Co-occurrence network analysis revealed that the network of planktonic bacterial community is more susceptible to eutrophication than the network of se-dimentary bacterial community. Null-model analysis suggested that eutrophication enhanced the contributions of stochastic processes in controlling the assembly of planktonic and sedimentary bacterial communities. However, the importance of stochastic processes in the assembly of planktonic bacterial community reduced within lakes experiencing extreme eutrophication. The differences in environmental characteristics and community assembly processes between water and sediment may account for the discrepancy in bacterial diversity patterns of the two lacustrine habitat types along the same trophic gradient. These results offer insights into the successional patterns of bacterial communities in freshwater lakes subjected to anthropogenic eutrophication. Moreover, the different distribution patterns and assembly processes of bacterial communities act as indicators of specific habitat responding to environmental gradients.
... Previous studies have manipulated nutrient enrichment in aquatic microcosms or mesocosms to identify bacterial community patterns across trophic gradients (Haukka et al., 2006;Horner-Devine et al., 2003;Ren et al., 2017;Wang et al., 2016). However, they may provide limited insight due to differences in microbial assemblages between manipulated experimental systems and actual freshwater ecosystems (Shade et al., 2012). ...
... Similarly, in the present study, we observed at the local (within-lake) scale that the β-diversity of summer PBC decreased along the lake trophic gradient, despite no significant relationship in other sample groups. In contrast with our findings on summer PBC, other studies showed an increase in compositional dissimilarity of bacterioplankton communities with increased productivity (as characterised by lake trophic state in this study) in natural and in experimental settings Ren et al., 2017). The conflicting results may be ascribed to the divergence in eutrophication conditions (Langenheder & Lindström, 2019). ...
... At colder temperatures (winter), we observed no clear pattern of α-diversity of PBC along the trophic gradient. This finding may be attributed to the following: first, the limited TSIc range in winter may have prevented us from determining whether winter PBC diversity could have a significant PDR pattern along a larger trophic gradient (Mittelbach et al., 2001); second, the marked variation in community compositions in the winter PBC may obscure differences in the distribution of α-diversity between the different trophic levels (Ren et al., 2017); last but not least, the high homogenising dispersal and other stochastic processes regulating the winter bacterioplankton communities possibly conceal the variation trend of α-diversity along the winter trophic gradient. However, along the same winter trophic gradient, a linear increasing PDR pattern was found for SBC, congruent with the positive effect F I G U R E 3 Relative importance of various ecological processes driving the assembly of bacterial community across different sample groups. ...
Article
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• 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.
... Except for the specific effects of the plant itself, temperature is likely the most important factor contributing to differences in the bacterial communities given that it changed markedly between the two seasons (8°C in winter and 32°C in summer) (Table S1). Temperature is one of the major determinants of bacterial assemblage composition, as the temperature optima of bacterial taxa differ greatly (64,65). In this study, the wide temperature difference between the two sampling times (24°C) could have resulted in the differences of bacterial community between the seasons. ...
... In this study, the wide temperature difference between the two sampling times (24°C) could have resulted in the differences of bacterial community between the seasons. Moreover, almost all biological processes are affected by temperature increases, as the metabolic rates increase exponentially as temperatures rise (26,65,66). Increased temperature promotes the kinetic metabolic rate of microorganisms, thereby increasing the diversity and the stochasticity of the colonization and extinction of members of the bacterial community (65). ...
... Moreover, almost all biological processes are affected by temperature increases, as the metabolic rates increase exponentially as temperatures rise (26,65,66). Increased temperature promotes the kinetic metabolic rate of microorganisms, thereby increasing the diversity and the stochasticity of the colonization and extinction of members of the bacterial community (65). Therefore, we can explain why the bacterial communities within the same compartments were more affected by stochastic processes in summer marked by higher temperatures. ...
Article
The common reed (Phragmites australis), a cosmopolitan aquatic macrophyte, plays an important role in the structure and function of aquatic ecosystems. We compared bacterial community compositions (BCCs) and their assembly processes in the root-associated compartments (i.e., rhizosphere and endosphere) of reed and bulk sediment between summer and winter. The BCCs were analyzed using high-throughput sequencing of the bacterial 16S rRNA gene; meanwhile, nullmodel analysis was employed to characterize their assembly mechanisms. The sources of the endosphere BCCs were quantitatively examined using SourceTracker from bulk sediment, rhizosphere, and seed. We observed the highest-diversity and the lowest β-diversity of BCCs in the rhizosphere in both seasons. We also found a significant increase in α-and β-diversity in summer compared to that in winter among the three compartments. It was demonstrated that rhizosphere sediments were the main source (~70%) of root endosphere bacteria during both seasons. Null-model tests indicated that stochastic processes primarily affected endosphere BCCs, whereas both deterministic and stochastic processes dictated bacterial assemblages of the rhizosphere, with the relative importance of stochastic versus deterministic processes depending on the season. This study suggests that multiple mechanisms of bacterial selection and community assembly exist both inside and outside P. australis roots in different seasons.
... Though several laboratory manipulation studies have been conducted so far to address the effect of warming on bacterioplankton community, the results are inconsistent. For example, a few studies have shown significant community variations under rising temperature and warming conditions [13][14][15] , whereas others did not 16,17 . Similarly, number of long-term in situ studies have shown an influence of elevated temperature on bacterioplankton community composition 18,19 . ...
... Nevertheless, few studies have demonstrated that synergistic influence of two disturbing factors is greater than their individual influences. For example, Ren et al. 16 reported that www.nature.com/scientificreports/ elevated temperature alone had insignificant effects, whereas elevated temperature in combination with nutrient enrichment causes a significant shift in freshwater bacterioplankton community. ...
... However, a decreased proportion (> 10%) during most of the sampling months at thermal discharge-impacted areas was observed. A negative correlation between elevated temperature and Bacteroidetes abundance has also been previously reported in a freshwater mesocosms study 16 . Identification of taxonomic biomarkers for various anthropogenic factors is a critical task in ecology, especially in case of microbes owing to their extreme complexity and high diversity 45 . ...
Article
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Despite accumulating evidence on the impact of global climate warming on marine microbes, how increasing seawater temperature influences the marine bacterioplankton communities is elusive. As temperature gradient created by thermal discharges provides a suitable in situ model to study the influence of warming on marine microorganisms, surface seawater were sampled consecutively for one year (September-2016 to August-2017) from the control (unimpacted) and thermal discharge-impacted areas of a coastal power plant, located in India. The bacterioplankton community differences between control (n = 16) and thermal discharge-impacted (n = 26) areas, as investigated using 16S rRNA gene tag sequencing revealed reduced richness and varied community composition at thermal discharge-impacted areas. The relative proportion of Proteobacteria was found to be higher (average ~ 15%) while, Bacteroidetes was lower (average ~ 10%) at thermal discharge-impacted areas. Intriguingly, thermal discharge-impacted areas were overrepresented by several potential pathogenic bacterial genera (e.g. Pseudomonas, Acinetobacter, Sulfitobacter, Vibrio) and other native marine genera (e.g. Marinobacter, Pseudoalteromonas, Alteromonas, Pseudidiomarina, Halomonas). Further, co-occurrence networks demonstrated that complexity and connectivity of networks were altered in warming condition. Altogether, results indicated that increasing temperature has a profound impact on marine bacterioplankton richness, community composition, and inter-species interactions. Our findings are immensely important in forecasting the consequences of future climate changes especially, ocean warming on marine microbiota.
... Until now, more than a half of lakes in Asia and Europe have become eutrophicated as well as a sizable portion of lakes in North America, South America, and Africa. Some published papers paid more attention to the effect of nutrients or cyanobacteria biomass on the microbial community assemblages in lake ecosystems [32][33][34]; however, research about the influence of eutrophication on both planktonic and sedimentary bacterioplankton in one lake still need to be supplied. Therefore, five freshwater eutrophic lakes in Wuhan city, Hubei province were selected to compare the bacterial community composition and community assembly processes between the water and the sediments under eutrophication conditions. ...
... With the popularity of high-throughput studies on the microbial ecology, the mechanisms explaining eutrophic patterns of the planktonic and sedimental microbial composition have been published [33,43]. However, the driving factors that assemble the communities within and between different freshwater lakes in a larger pool are still not well-studied. ...
Article
Full-text available
The mechanism of bacterial community assembly has been the hot spot in the field of microbial ecology and it is difficult to quantitatively estimate the influences of different ecological processes. Here, a total of 23 pairs of planktonic and sedimentary samples were collected from five lakes in Wuhan, China. significant higher α-diversity (p < 0.001) and β-diversity (p < 0.001) of bacterial communities were observed in sediment than those in water. Some phylum had linear relationships with the comprehensive TSI (TSIc) by regression analysis. Non-metric multidimensional scaling (NMDS) and redundancy analysis (RDA) revealed that the depth of water, NO3−-N, NH4+-N, PO43−, and CODcr were the key environmental variables in planktonic bacterial communities, whereas in sediment they were the depth, NO3−-N, and NH4+-N. Furthermore, variation partitioning analysis (VPA) showed that spatial and environmental factors could only explain 40.2% and 27.9% of the variation in planktonic and sedimentary bacterial communities, respectively. More importantly, null model analysis suggested that different assembly mechanisms were found between in water and in sediment with the fact that planktonic bacterial community assembly was mainly driven by dispersal limitation process whereas variable selection process played a vital role in that of sediment.
... First, the terrestrial river water input carries abundant nutrients from aquaculture and human activities, which can create additional niches to stimulate the growth of various microorganisms, especially less abundant ones. Such growth could increase species diversity (Fig. 1B) and enhance stochastic processes like birth and death, the latter of which is consistent with the increased co-contribution of dispersal limitation (the influence of dispersal limitation acting in concert with drift [23]) and drift (the influence of drift acting alone) in the human-influenced groundwater, as noticed in prior studies on terrestrial freshwater [59] and groundwater [13]. Second, nutrient inputs could weaken niche selection by providing more resources and result in less-stressed groundwater conditions, partly resulting in decreased homogeneous selection, which was mainly driven by nutrient-associated factors in the humaninfluenced groundwater, as suggested by the relationships between homogeneous selection and DIC or DOC (Fig. 5). ...
Preprint
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Tidal hydrodynamics drive the groundwater-seawater exchange and shifts in microbiota structure in the coastal zone. However, how microbiota structure responds to periodic tidal fluctuations and anthropogenic disturbance is seldom evaluated in the intertidal groundwater-surface water (GW-SW) continuum, although it affects microbially driven biogeochemical cycles and ecosystem function therein. Here, we resolved the high-resolution spatiotemporal dynamics and assembly mechanisms along a GW-SW continuum in the natural tidal creek. Our results revealed an evident rhythmic pattern of microbiota structure in response to daily and monthly tidal fluctuations in intertidal surface water. The similarity in archaeal community structures among groundwater and ebb-tide surface water demonstrated archaeal transport through groundwater discharge, whereas multi-source transport mechanisms led to the occurrence of unique bacterial biota in ebb-tide water. Mechanistically, homogeneous selection (58.6%-69.3%) dominated microbiota assembly patterns in the intertidal GW-SW continuum, while biotic interactions were weaker in the groundwater microbiota than the surface water microbiota. Compared with the natural tidal creek, we found that microbiota biodiversity and community succession in intertidal groundwater under anthropogenic-induced terrestrial nutrient inputs and weakened tidal fluctuations were primarily controlled by increased dispersal limitation and consequent weakening of homogeneous selection, as well as enhanced biotic interactions. Overall, this study sheds light on the ecological rules guiding water microbiota assembly in the coastal transition zones and highlights periodic hydrodynamic and anthropogenic disturbances as prominent influencing factors of the microbiota structure, as well as the potential for enhancing coastal monitoring initiatives by incorporating only a few rhythmic but critical key microbial observations.
... We calculated and plotted the relative abundance of bacterial taxa for each sample using SigmaPlot 12.5. We applied the Jaccard distance (Ren et al., 2017) and weighted and unweighted UniFrac distance (Lozupone & Knight, 2005) to compare dissimilarities based on the taxonomic and phylogenetic distance between the FL and PA bacterial communities, respectively. Analysis of similarities (ANOSIM) tested differences in community composition between the two bacterial lifestyles during the bloom. ...
Article
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• Understanding the successional patterns of microbial communities during a phytoplankton bloom is crucial for predicting the compositional and functional stability of lake ecosystems in response to the disturbance of a bloom. Previous studies on bacterial communities associated with blooms have rarely studied the dynamics of these communities. The successional patterns of bacterial communities within different micro‐habitats (i.e. water column versus particles) and mechanisms that shape these communities that differ in composition and structure remain unclear. • We selected a eutrophic urban lake to investigate the succession of bacterial communities during a bloom. We divided the bacterial communities into free‐living (FL) and particle‐attached (PA) groups based on their different lifestyles. The amplicon‐based 16S rRNA gene high‐throughput sequencing technology was used to obtain bacterial community composition and phylogenetic structure. • Our study showed distinct successional patterns between FL and PA bacterial communities, and the two bacterial lifestyles showed different responses and resilience to the bloom, in terms of diversity and relative abundance of bacterial taxa. Alpha‐diversity of the PA bacterial community decreased during the bloom, whereas that of the FL bacterial community increased. More taxa in the FL bacterial community showed resilience after the disturbance than in the PA bacterial community. • The influence of phytoplankton blooms on the assembly of the bacterial community can be viewed as niche selection that led to the decrease in the relative importance of stochastic processes in shaping both FL and PA bacterial communities. This study shows the ecological significance of the bacterial community response to bloom events in lakes. It also shows that assembly processes differ for bacterial communities that have different lifestyles in lake ecosystems disturbed by phytoplankton blooms.
... Here, the increase in temperature (warming) gradually enhanced stochastic assembly of bacteria in autumn cruise, probably related to the increased activity of bacteria in colonization, extinction, reproduction, and dispersal resulted from faster metabolic kinetics in warmer conditions (Allen, Brown, & Gillooly, 2002;Brown, Gillooly, Allen, Savage, & West, 2004). A mesocosm-based study in freshwater lakes found that warming and nutrient enrichment in combination increased stochasticity in bacterioplankton assembly (Ren et al., 2017). Many studies across various ecosystems have suggested that bacterial communities tented to more strongly governed by stochastic processes in more eutrophic environments (Chase, 2010;Liu et al., 2015;Zhou et al., 2014). ...
Article
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Marine planktonic bacteria and archaea commonly exhibit pronounced seasonal succession in community composition. But the existence of seasonality in their assembly processes and between‐domain differences in underlying mechanism are largely unassessed. Using a high‐coverage sampling strategy (including single sample for each station during four cruises in different seasons), 16S rRNA gene sequencing, and null models, we investigated seasonal patterns in the processes governing spatial turnover of bacteria and archaea in surface coastal waters across a sampling grid over ~300 km in the East China Sea. We found that archaea only bloomed in prokaryotic communities during autumn and winter cruises. Seasonality mostly overwhelmed spatial variability in the compositions of both domains. Bacterial and archaeal communities were dominantly governed by deterministic and stochastic assembly processes, respectively, in autumn cruise, likely due to the differences in niche breadths (bacteria < archaea) and relative abundance (bacteria > archaea). Stochasticity dominated assembly mechanisms of both domains but was driven by distinct processes in winter cruise. Determinism‐dominated assembly mechanisms of bacteria rebounded in spring and summer cruises, reflecting seasonal variability in bacterial community assembly. This could be attributed to seasonal changes in bacterial niche breadths and habitat heterogeneity across study area. There were seasonal changes in environmental factors mediating the determinism‐stochasticity balance of bacterial community assembly, holding a probability of the existence of unmeasured mediators. Our results suggest contrasting assembly mechanisms of bacteria and archaea in terms of determinism‐versus‐stochasticity pattern and its seasonality, highlighting the importance of seasonal perspective on microbial community assembly in marine ecosystems.
... Meanwhile, some bacteria, such as flavobacteria and other γ-proteobacteria, produce algicidal compounds that shift the interaction from mutualistic to pathogenic. Previous studies (Zhou et al., 2014;Ren et al., 2017) also indicated that an increase in nutrients in water may disrupt the metabolic kinetics and growth rate of the bacterial community, leading to random colonization or extinction, unpredictable perturbations, and amplification of the initial differences in bacterial composition. Therefore, the influence of stochastic processes increased with these uncertain factors, disrupting the metabolic kinetics and growth rates of abundant and rare species at the end stage of the blooms. ...
Article
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Phaeocystis globosa blooms are recognized as playing an essential role in shaping the structure of the marine community and its functions in marine ecosystems. In this study, we observed variation in the alpha diversity and composition of marine free-living bacteria during P. globosa blooms and identified key microbial community assembly patterns during the blooms. The results showed that the Shannon index was higher before the blooming of P. globosa in the subtropical bay. Marinobacterium (γ-proteobacteria), Erythrobacter (α-proteobacteria), and Persicobacter (Cytophagales) were defined as the most important genera, and they were more correlated with environmental factors at the terminal stage of P. globosa blooms. Furthermore, different community assembly processes were observed. Both the mean nearest relatedness index (NRI) and nearest taxon index (NTI) revealed the dominance of deterministic factors in the non-blooming and blooming periods of P. globosa, while the bacterial communities in marine waters after the blooms tended to be controlled by stochastic factors. Our findings revealed that the assembly of the bacterial community in marine P. globosa blooms is a complex process with mixture effects of marine microbiomes and environmental parameters.
... Lake Taihu is identified as a eutrophic lake and composed of several connected lake zones that maintaining a gradient level of nutrition loading (Qin et al. 2007). The extremely eutrophic state in the MLB could weaken environmental selection by delivering plenty of living materials and therefore reducing the competition among species (Smith et al. 1999;Ren et al. 2017), which could attribute to the higher alpha diversity in the MLB for abundant bacterial (Haukka et al. 2006;Wang et al. 2016). The rare taxa were observed to be comparable, and encompass much more unique OTUs in the two lake zones. ...
Article
Aims: To reveal whether the patterns of abundant and rare subcommunity composition of both bacteria and microeukaryotes vary between connected regions with different levels of nutrient loading in freshwater lakes. Methods and results: We investigated the abundant and rare subcommunity composition of both bacteria and microeukaryotes in two connected zones [(Meiliang Bay (MLB) and Xukou Bay (XKB)] of a large shallow freshwater Lake Taihu via the high-throughput sequencing of bacterial 16S rRNA and microeukaryotic 18S rRNA genes. Even though these two lake zones are connected and share a species bank, they diverge in community composition. Significantly higher alpha-diversity was observed for the abundant bacterial subcommunity in the MLB. However, no significant difference in alpha-diversity between the rare bacterial subcommunities, as well as both rare and abundant microeukaryotic subcommunities were observed between MLB and XKB. It is demonstrated that both environmental factors and geographic distance play central roles in controlling the rare and abundant microbial subcommunities in the two connected lake zones. Conclusions: The abundant subcommunity composition of bacteria and microeukaryotes vary between connected regions with different levels of nutrient loading. Dispersal limitation plays a vital role in shaping microbial communities even in connected zones of freshwater lakes. Significance and impact of the study: Leading to a comprehensive understanding of the characteristics of microbial community in connected lake regions with different levels of nutrient loading.
... Bacterial communities normally comprise a few abundant and many rare species ( Logares et al., 2014), and abundant and rare subcommunities may show fundamentally distinct characteristics and have different ecological roles (Pedros-Alio, 2012). Biodiversity is an important issue in community ecology, underpinning ecosystem functioning ( Ren et al., 2017;Wilhelm et al., 2013;Zhang et al., 2019). Characterising species diversity and its variation along environmental gradients and understanding the forces that structure bacterial communities are fundamental components of ecological research Cottenie, 2005;Dumbrell et al., 2010). ...
Article
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Dissolved organic matter (DOM) released from permafrost thaw greatly influences the biogeochemical cycles of, among others, downstream carbon, nitrogen and phosphorus cycles; yet, knowledge of the linkages between bacterial communities with permafrost DOM heterogeneity is limited. Here, we aim at unravelling the responses of bacterial diversities and metabolic profiles to DOM quantity and composition across permafrost thawing gradients by coupling an extensive field investigation with bio-incubation experiments. Richness, evenness and dissimilarities of the whole and rare communities decreased from thermokarst pits to headstreams and to downstream rivers. The assemblages of the abundant subcommunities were mainly determined by ecological drift-driven stochastic processes. Both the optical and the molecular composition of DOM were significantly related to the changes of the whole (rare) bacterial communities (Mantel's correlation > 0.5, p < 0.01). Diversity indices of the whole and rare communities decreased with decreasing relative abundance of tannins, condensed aromatics and more aromatic and oxidized lignins as well as with decreased dissolved organic carbon and intensities of all fluorescence components. Laboratory DOM bio-incubation experiments further confirmed microbial consumption of more aromatic and oxidized compounds as well as decreasing metabolic diversities in terms of microbial degradation and production along permafrost thawing gradients. Our findings suggest that changes in the sources of permafrost-derived DOM induced by global warming can have different influences on the diversity and metabolism of bacterial communities and thus on permafrost carbon climate feedbacks along permafrost thawing gradients.
... Due to the phytoplankton generation time and the duration of the T shift event in our experiment, we noted no changes in phytoplankton community composition towards more temperature-tolerant species, as found in longer microcosm experiments 56,57 . Although we have no data on bacteria diversity, changes in bacterial (shorter generation time) composition, with increased biodiversity under warming and nutrient addition, might have been possible 58 , enabling the proliferation of rare bacterial phyla more tolerant to higher temperatures. Changes in bacterioplankton community composition frequently are mediated by phytoplankton response to environmental changes through EOC availability 59 . ...
Article
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Global-change stressors act under different timing, implying complexity and uncertainty in the study of interactive effects of multiple factors on planktonic communities. We manipulated three types of stressors acting in different time frames in an in situ experiment: ultraviolet radiation (UVR); phosphorus (P) concentration; temperature (T) in an oligotrophic Mediterranean high-mountain lake. The aim was to examine how the sensitivity of phytoplankton and bacterioplankton to UVR and their trophic relationship change under nutrient acclimation and abrupt temperature shifts. Phytoplankton and bacteria showed a common pattern of metabolic response to UVR × P addition interaction, with an increase in their production rates, although evidencing an inhibitory UVR effect on primary production (PP) but stimulatory on bacterial production (HBP). An abrupt T shift in plankton acclimated to UVR and P addition decreased the values of PP, evidencing an inhibitory UVR effect, whereas warming increased HBP and eliminated the UVR effect. The weakening of commensalistic and predatory relationship between phyto- and bacterioplankton under all experimental conditions denotes the negative effects of present and future global-change conditions on planktonic food webs towards impairing C flux within the microbial loop.
... In this case, trophic changes may exert a random effect on the Vibrio species. Lateral pieces of evidence uncovered in investigations of planktonic bacteria in lake ecosystems indicated that the importance of stochastic processes was increased with nutrient enrichment due to a disorder in metabolic kinetics and growth rate between abundant and rare species (Ren et al. 2017;Zeng et al. 2019a). In addition, stochastic-dominant results are commonly found in studies of aquatic systems (e.g. ...
Article
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Understanding the effects of eutrophication on heterotrophic bacteria, a primary responder to eutrophication, is critical for predicting the responses of ecosystems to marine environmental pollution. Vibrio are indigenous in coastal water and of significance to geochemical cycling and public health. In this study, we investigated the diversity and assembly features of Vibrio, as well as their relationship with the environmental factors in the subtropical Beibu Gulf. We found that the alpha-diversity of Vibrio increased in parallel with the trophic state they occupy. A Mantel test indicated that the trophic state was correlated to Vibrio beta-diversity, and the correlation gradually strengthened at higher trophic states. Variation partitioning analysis suggested that the geographic distance was an important factor impacting the variables of Vibrio communities in all the samples, but nutrients exerted more influence in the more highly eutrophic samples. Our results demonstrated that stochastic processes govern the turnover of marine Vibrio communities in the Beibu Gulf, and that ecological drift was the most important process for the assembly of the Vibrio communities.
... Mantel and Partial Mantel tests indicated that the BCC in both the MD and PD communities is strongly related to the levels of nitrogen and phosphorus as well as DOC. Significant difference in microbial community composition due to disparate environmental variables has been widely observed in lake water (Velghe et al. 2012;Comte et al. 2013;Ren et al. 2016). Phytoplankton blooms caused by high concentrations of phosphorus in eutrophic lakes are believed to lead to a significant increase in the DOC concentration, which can provide important labile carbon sources for bacterial growth (Kim et al. 2000;Yoshioka et al. 2002). ...
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Shallow lakes often exhibit a macrophyte‐dominated (MD) clear state or a phytoplankton‐dominated (PD) turbid state, each of which has profound impacts on biological communities, including bacterioplankton community composition (BCC). However, the response of microbial functional gene structure (FGS) to regime shift has not been thoroughly elucidated to date. In this study, we used a functional gene array (GeoChip 5.0) in combination with high‐throughput sequencing of the bacterial 16S rRNA gene to investigate the FGS and BCC between the two regimes in Lake Taihu, a large shallow freshwater lake in China. A simultaneous change in the BCC and FGS was observed between the two different regimes. We observed higher numbers of bacterial operational taxonomic units and functional genes detected by the GeoChip 5.0 in the MD samples than in the PD samples. By performing network analyses, we observed stronger microbe‐microbe interactions but weaker functional gene interactions involved in nutrient metabolism in the MD community than in the PD community. We speculate that at higher concentrations of phosphorus, the domination of Microcystis bloom may weaken the interactions among microbial species by releasing more labile dissolved organic carbon, but enhance the selection and interactions of functional genes involved in carbon cycling in the PD community. In contrast, the lower levels of phosphorus may enhance microbe‐microbe interactions but weaken the interactions between the primary nutrients and particular genes. Overall, this study demonstrated contrasting patterns in the BCC and FGS between the MD and PD communities in a large shallow freshwater lake.
... This was also confirmed by the high nucleic acid sequence similarity between the moraine lake and the stream from Yala Glacier melt (Liu et al. 2016). Thus, these glacier-originated autotrophs likely influence the ecological functions and community assembly in downstream aquatic ecosystems (Dubnick et al. 2017;Ren et al. 2017). ...
Article
Glaciers harbour diverse microbes and autotrophic microbes play a key role in sustaining the glacial ecosystems by providing organic carbon. The succession of glacier-originated autotrophic microbes and their effects on downstream aquatic ecosystems remain unknown. We herein investigated the shift of autotrophic microbial communities in waters (not biofilms) along a glacier meltwater transect consisting of a glacier terminus outflow (subglacial), a glacial stream, two glacier-fed lakes (upper and lower) and their outflow on the Tibetan Plateau. The autotrophic community was characterized by cbbL gene using qPCR, T-RFLP and clone library/sequencing methods. The results demonstrated that form IC and ID autotrophic microbes exhibited a much higher abundance than form IAB in all waters along the transect. Form IAB autotrophic abundance in waters gradually decreased, while the form IC exhibited a substantial increase in the upper lake waters, and ID exhibited a substantial increase in the lower lake waters. The water form IC autotrophic community structure exhibited a distinguished shift from the glacier terminus outflow to the stream, while the form ID showed a dramatic shift from the stream to the lower lake. Our results revealed the succession patterns of glacier-originated autotrophic microbial communities and possible effects on downstream aquatic ecosystems.
... In our study, 58.5% and 14.5% of microbial variations could not be explained by the selected environmental variables in horizontal and vertical soil samples, respectively, which might be caused by the unmeasured biotic and abiotic factors (such as light, temperature, nutrient content, salinity, oxygen level, land use, and soil texture and structure) (Fierer, 2017;Rooney-Varga et al., 2007;Wu et al., 2017a). Besides, high-throughput MiSeq sequencing has some technical stochastic effects and possible sequencing bias, such as PCR amplification, sequencing errors, and chimeric sequences ( Ren et al., 2016). Additionally, the high intraspecific diversity may result in high ecological differentiation within the population ( Hahn et al., 2005;Wu and Hahn, 2006), which may contribute to the microbial community and support the ecological redundancy in the genetically diverse populations (bib_Thompso-n_et_al_2005 Thompson et al., 2005). ...
... With the increased feed input and associated waste materials, elevated concentrations of nutrients were observed in the three other seasons (Table S5, e.g., TP: 0.126 ± 0.050 mg/L in summer, DOC: 10.42 ± 2.09 mg/L and 13.14 ± 3.50 mg/L in autumn and winter, respectively). Previous studies have reported that diversity is greater with increased productivity due to a greater supply of resources potentially supporting more specialized organisms, 'the larger pie can be divided into more pieces' (Brown, 1981;Fuhrman et al., 2008;Ren et al., 2017). In agreement with these studies, we noted a higher diversity of the bacterial communities in eastern Lake Taihu in the summer, autumn, and winter samples. ...
Article
Aquaculture accounts for an extremely valuable and rapidly expanding sector of global food production, yet its environmental impacts on aquatic ecosystems have attracted much concern. In this study, we collected water samples from eastern Lake Taihu, China. We targeted sites varying in their intensity of aquacultural activities and sampled them over multiple seasons. For each sample, we measured physicochemical variables, and we sequenced the 16S rRNA gene of the respective bacterial communities using an Illumina second-generation sequencing platform. Marked differences in diversity and bacterial community composition were observed between seasons, whereas we observed relatively weak differences between sites. Remarkable differences in the abundance of the bacterial community were observed at the phylum and genus levels across the different seasons. Stochastic processes dominated the assembly of bacterial communities in the aquaculture-influenced systems, and the assembly processes of bacterial community differed between seasons. Our observations highlight the effect of seasonality on bacterial communities and provide a more complete knowledge base for the proper assessment of the effects of aquacultural activities on freshwater ecosystems.
... Ávila et al. (2017) asserted that thermal stratification and oxygen depletion dictated the bacterioplankton diversity in two tropical shallow lakes in the Brazilian Atlantic Forest. Ren et al. (2017) found that spring bacterioplankton community composition shifted significantly under enhanced warming and nutrient-enriched conditions. ...
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River damming influences the hydro‐physicochemical variations in karst water; however, such disruption in bacterioplankton communities has seldom been studied. Here, three sampling sites (city‐river section, reservoir area, and outflow area) of the Ca2+–Mg2+–HCO3−–SO42− water type in the dammed Liu River were selected to investigate the bacterioplankton community composition as identified by high‐throughput 16S rRNA gene sequencing. In the dammed Liu River, thermal regimes have been altered, which has resulted in considerable spatial‐temporal differences in total dissolved solids (TDSs), oxidation‐reduction potential (Eh), dissolved oxygen (DO), and pH and in a different microenvironment for bacterioplankton. Among the dominant bacterioplankton phyla, Proteobacteria, Actinobacteria, Bacteroidetes, and Cyanobacteria account for 38.99%–87.24%, 3.75%–36.55%, 4.77%–38.90%, and 0%–14.44% of the total reads (mean relative frequency), respectively. Bacterioplankton communities are dominated by Brevundimonas, Novosphingobium, Zymomonas, the Actinobacteria hgcIclade, the CL500‐29 marine group, Sediminibacterium, Flavobacterium, Pseudarcicella, Cloacibacterium, and Prochlorococcus. Their abundances covary with spatial‐temporal variations in hydro‐physicochemical factors, as also demonstrated by beta diversity analyses. In addition, temperature plays a pivotal role in maintaining bacterioplankton biodiversity and hydro‐physicochemical variations. This result also highlights the concept that ecological niches for aquatic bacteria in dammed karst rivers do not accidentally occur but are the result of a suite of environmental forces. In addition, bacterioplankton can alter the aquatic carbon/nitrogen cycle and contribute to karst river metabolism. Temperature plays a pivotal role in maintaining bacterioplankton biodiversity and hydro‐physicochemical variations from dammed Liu river.
... Thus, microbial communities are endowed with more function traits by the accelerated evolutional heterogeneity. It is supported by our findings that the βMPD, which represents phylogenetic heterogeneity of community assemblage (Carvajal-Endara et al., 2017;Ren et al., 2016), is correlated with the first component (PC1) of biological properties (Table 2). This indicated that diversified function traits of soil microorganisms can lead to more efficient microbial function, which is correlated with carbon sequestration efficiency (Zheng et al., 2009). ...
Article
Recent works have shown that long-term fertilization has a critical influence on soil microbial communities; however, the underlying ecological assemblage of microbial community as well as its linkage with soil fertility and crop yield are still poorly understood. In this study, using analysis of high-throughput sequencing of 16S rRNA gene amplicons, we investigate mean pairwise phylogenetic distance (MPD), nearest relative index (NRI), taxonomic compositions and network topological properties to evaluate the assembly of the soil microbial community developed in 30-year fertilized soils. The phylogenetic signal indicates that environmental filtering was a more important assembly process that structure the microbial community than the stochastic process. Increase of soil fertility indexes, such as cation exchange capacity (CEC), soil organic matter (SOM) and available P (AP), driven by balanced fertilizations and straw returning amendment, result in the decrease of environmental filtering on the bacterial community assembly. Network parameters show that the amendment of straw returning provides with more niches, which lead to more complex phylotype co-occurrence. Increase of crop yield under balanced fertilizations might due to the increase of soil microbial function traits, which is associated with decreasing influence of environmental filtering. The significantly increased bacterial genera, Candidatus Koribacter, Candidatus Solibacter, and Fimbriimonas, in straw returning treatments, might be the key species in the competition caused by long-term environmental filtering. These results are helpful for a unified understanding of the ecological processes for microbial communities in different fertilized agroecosystem and the development of sustainable agriculture.
... To reduce noise, spare OTUs comprising single sequences (singletons) were filtered out from OTU table using filter_-otus_from_otu_table.py script in QIIME [53]. Differences in sequencing depth of individual sample was equalized by rarifying the whole dataset to equal number of sequences as we aimed to conduct comparative analysis. ...
Article
Meta-omics approaches such as high-throughput sequencing of 16S hypervariable region(s) [HVR(s)] is extensively applied for profiling microbial community. Several studies have deciphered the influence of HVR(s) on bacterial diversity; most of these were devoted to human body habitats. Extent to which targeted HVR(s) influences the diversity estimates of environmental samples is rather unclear. Here, we evaluated the performance of five widely used universal primer pairs spanning V1-V3, V3-V4, V4, V5-V6 and V7-V9 HVRs to characterize bacterial diversity and predictive functionality of complex marine sediments. Obtained results revealed that the HVR(s) V4 and V5-V6 represented the higher species richness than others while, V1-V3 and V7-V9 were unsuccessful to detect Bacteroidetes and Planctomycetes. Further, PICRUSt analysis showed that the selected HVR(s) also had significant impact on the predictive functional profile. Conclusively, this study proved that HVR selection has a profound effect on overall results and thus should be selected with utmost caution.
... First, the latitudinal β-diversity gradient may be partially due to the direct effects of temperature, as temperature had more explanatory power than any of the geochemical properties for the changes in microbial β-diversity in this study. On the one hand, higher temperatures will enhance the stochasticity in community assemblies (Ren et al., 2017), which may increase the variation in microbial communities under similar or even identical conditions, causing higher β-diversity. On the other hand, regions that experience colder extremes may impose harsher environmental filtering on species (Silva et al., 2015), which leads to more homogeneous selection for cold-tolerant taxa at higher latitudes, reducing β-diversity. ...
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Aim The β‐diversity of plants and animals generally decreases with increasing latitudes. Here, we tested whether this relationship also holds for soil microbes at both functional and taxonomic levels. Location China. Time period Between June and October 2013. Major taxa studied Soil archaea, bacteria, and functional genes. Methods We used a spatially explicit ‘L‐shaped’ sampling strategy in 39 paddy fields in China to study the pattern of soil microbial β‐diversity (i.e., species turnover, βz) across a latitudinal gradient (19.75° N to 47.58° N), with 11 soil samples taken within a 100 m × 100 m plot from each field. Archaeal and bacterial communities were analysed by sequencing 16S ribosomal RNA gene amplicons using Illumina MiSeq; microbial functional genes involved in C/N/P/S cycling were detected by GeoChip. Results We showed that the microbial β‐diversity varied considerably across taxonomic and functional groups. For both soil microbial communities and functional genes, β‐diversity decreased significantly along elevated latitudes at the continental scale. Woesearchaeota of archaeal communities, Bacteroidetes of bacterial communities, and the functional genes involved in methane production displayed the greatest decreases. Both mean temperature during the growing season of rice plants and paddy soil heterogeneity contributed to the latitudinal patterns. Further analyses indicated that temperature was more important than soil heterogeneity in driving the β‐diversity of microbial communities and functional genes. Main conclusions These results highlight the importance of temperature‐driven soil microbial β‐diversity and suggest the potential to predict the changes of microbial diversity with climate change.
... This mirrors our long-term observation that warming led to the community's divergent succession and accelerated temporal scaling 7,8 , as well as reported in a montane community and a coastal ecosystem 42,43 . Based on the metabolic theory of ecology, temperature determines metabolic rates and thus affects nearly all biological processes, including species turnover 44,45 . Thus, the trend of an increase in community variation among months and across experimental plots can be directly predicted by elevated temperature. ...
Article
Abstract Soil microbial community's responses to climate warming alter the global carbon cycle. In temperate ecosystems, soil microbial communities function along seasonal cycles. However, little is known about how the responses of soil microbial communities to warming vary when the season changes. In this study, we investigated the seasonal dynamics of soil bacterial community under experimental warming in a temperate tall‐grass prairie ecosystem. Our results showed that warming significantly (p = 0.001) shifted community structure, such that the differences of microbial communities between warming and control plots increased nonlinearly (R2 = 0.578, p = 0.021) from spring to winter. Also, warming significantly (p
... It has been reported that the effect of temperature on species richness is greatest at extreme nutrient levels whereas the effects of nutrients on species richness are strongest at intermediate temperatures (Wang et al., 2016). Moreover, slight warming may not significantly change the bacterial community composition in the mesocosms by itself but the bacterial community composition shifts when warming acts in concert with nutrient enrichment (Ren et al., 2017). It should be noted that nutrients and temperature may influence lake microbial communities largely independently (Schulhof et al., 2020). ...
Article
Eutrophication substantially influences the community structure of aquatic organisms and has become a major threat to biodiversity. However, whether eutrophication is linked to homogenization of microbial communities and the possible underlying mechanisms are poorly understood. Here, we studied bacterial and fungal communities from water and sediments of 40 shallow lakes in the Yangtze-Huaihe River basin, a representative area characterized by intensifying eutrophication in China, and further examined the beta diversity patterns and underlying mechanisms under eutrophication conditions. Our results indicate that eutrophication generally caused biotic homogenization of bacterial and fungal communities in both habitats showing decreased community variations for the sites with a higher trophic state index (TSI). In the two habitats, community dissimilarities were positively correlated with TSI changes for both taxonomic groups, while the local contribution to beta diversity (LCBD) remarkably declined with increasing TSI for the fungal community. These phenomena were consistent with the pivotal importance of the TSI in statistically accounting for beta diversity of bacterial and fungal communities in both habitats. In addition, we found that physicochemical factors such as water temperature and pH were also important for bacterial and fungal communities in water, while heavy metal elements were important for the communities in sediments. Interestingly, generalist species, rather than specialist species, were revealed to more dominantly affect the variations in beta diversity along the trophic gradient, which were quantified by Bray-Curtis dissimilarity and LCBD. Collectively, our findings reveal the importance of generalist species in contributing to the change of beta diversity of microbial communities along trophic gradients, which have profound implications for a comprehensive understanding of the effects of eutrophication on microbial community.
... This was also confirmed by the high nucleic acid sequence similarity between the moraine lake and the stream from Yala Glacier melt (Liu et al. 2016). Thus, these glacier-originated autotrophs likely influence the ecological functions and community assembly in downstream aquatic ecosystems (Dubnick et al. 2017;Ren et al. 2017). ...
Article
One sentence summary: Form IC autotrophic microbial community distinguishedly shifted from the glacier terminus to the stream waters, while ID dramatically shifted at the site where meltwaters flowing into downstream big lake. Editor: Andrew McMinn † Weidong Kong, http://orcid.org/0000 ABSTRACT Glaciers harbour diverse microbes and autotrophic microbes play a key role in sustaining the glacial ecosystems by providing organic carbon. The succession of glacier-originated autotrophic microbes and their effects on downstream aquatic ecosystems remain unknown. We herein investigated the shift of autotrophic microbial communities in waters (not biofilms) along a glacier meltwater transect consisting of a glacier terminus outflow (subglacial), a glacial stream, two glacier-fed lakes (upper and lower) and their outflow on the Tibetan Plateau. The autotrophic community was characterized by cbbL gene using qPCR, T-RFLP and clone library/sequencing methods. The results demonstrated that form IC and ID autotrophic microbes exhibited a much higher abundance than form IAB in all waters along the transect. Form IAB autotrophic abundance in waters gradually decreased, while the form IC exhibited a substantial increase in the upper lake waters, and ID exhibited a substantial increase in the lower lake waters. The water form IC autotrophic community structure exhibited a distinguished shift from the glacier terminus outflow to the stream, while the form ID showed a dramatic shift from the stream to the lower lake. Our results revealed the succession patterns of glacier-originated autotrophic microbial communities and possible effects on downstream aquatic ecosystems.
... Cyanobacteria was obvious summer-associated taxa in this eutrophic bay. Previous research showed that warming caused an increase in the abundance and biomass of Cyanobacteria in eutrophic waters (9,27), which is consistent with our findings (Fig. S4, Table S1). The predominance of Cyanobacteria in summer was largely due to Synechococcus and Prochlorococcus (Fig. 1). ...
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A growing number of studies have examined roles of microbial community assembly in modulating community composition. However, the relationships between community assembly and microbial interactions are not fully understood and rarely tested, especially in eutrophic waters.
... predation, mutualism, parasitism, and competition;Zhou and Ning 2017). Previous experimental studies have revealed that the relative importance of stochastic assembly processes increased under nutrient-enriched conditions in freshwater ecosystems (Chase 2010, Ren et al. 2017. Conversely, opposite results were observed in other field studies by indicating that deterministic processes played a stronger role in the assembly of bacterioplankton communities in enriched nutrient environments (Langenheder et al. 2012, Liu et al. 2021. ...
Article
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Unveiling the rules of bacterioplankton community assembly in anthropogenically disturbed lakes is a crucial issue in aquatic ecology. However, it is unclear how the ecological processes underlying the seasonally driven bacterioplankton community structure respond to varying degrees of lake eutrophication. We therefore collected water samples from three subtropical freshwater lakes with various trophic states (i.e. oligo-mesotrophic, mesotrophic and eutrophic states) on a quarterly basis between 2017 and 2018. To innovatively increase our understanding of bacterioplankton community assembly along the trophic state gradient, the total bacterioplankton community dissimilarity was subdivided into balanced variation in abundances and abundance gradients. The results indicated that balanced-variation component rather than abundance-gradient component dominated the total temporal β-diversity of bacterioplankton communities across all trophic categories. Ecological stochasticity contributed more to the overall bacterioplankton community assembly in the oligo-mesotrophic and mesotrophic lakes than in the eutrophic lake. The reduced bacterioplankton network complexity at the eutrophic level was closely associated with the enhancement of environmental filtering, showing that bacterioplankton communities in eutrophic lakes are likely to be less stable and more vulnerable to water quality degradation. Together, this study offers essential clues for biodiversity conservation in subtropical lakes under future intensified eutrophication.
... The increase in temperature causes the metabolic rate to increase exponentially, so nearly all biological processes are more or less affected by temperature (Bowen et al., 2017;He et al., 2020;Schulte, 2015). Increased temperature can promote the dynamic metabolism of microorganisms, such that the stochasticity and diversity of colonization and extinction of members of the microbial community also increase (Ren et al., 2017). More frequent hydrologic exchange in the rainy season also increases the probability of free diffusion of microorganisms in the entire watershed. ...
Article
The differences in bacterial community assembly mechanism between surface water and groundwater, as well as the driving factors of environmental factors, are still unknown. Here we aimed to answer these questions by analyzing microbial community samples from surface water and groundwater. We observed a strong connection between microbial communities in surface water and groundwater and several human pathogens are shared between surface water and groundwater; however, the richness and diversity of groundwater microbial communities were greater than those of surface water, regardless of the season. Additionally, bacterial community compositions of surface water and groundwater differed significantly between seasons. Most importantly, the groundwater community exhibited a highly deterministic assembly process (56% contributed by deterministic process, with neutral community model R² = 0.277) compared with surface water (51% contributed by deterministic process, with R² = 0.526). This study provides a deep understanding of the effects of environmental factors on surface water and groundwater microbial communities, to better protect water resources.
... We mainly used Functional Annotation of Prokaryotic Taxa (FAPROTAX) to the predict response of ecologically relevant functional groups of bacterial communities in water and sediment [18]. In this work, we hypothesized that (1) climate warming may result in high variability in the composition of bacterioplankton communities in lacustrine water [51,52], while warming (constant and variable warming) may alter the metabolic functional structure of bacteria involved in nutrient cycling. (2) During the low-temperature period, temperature is the main limiting factor driving bacterial activity and, with the increase in temperature, nutrients may become the main limiting factor of microbial activity [27,53,54]. ...
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Extreme climatic events, such as heat wave and large temperature fluctuations, are predicted to increase in frequency and intensity during the next hundred years, which may rapidly alter the composition and function of lake bacterial communities. Here, we conducted a year-long experiment to explore the effect of warming on bacterial metabolic function of lake water and sediment. Predictions of the metabolic capabilities of these communities were performed with FAPROTAX using 16S rRNA sequencing data. The results indicated that the increase in temperature changed the structure of bacterial metabolic functional groups in water and sediment. During periods of low temperature, the carbon degradation pathway decreased, and the synthesis pathway increased, under the stimulation of warming, especially under the conditions temperature fluctuation. We also observed that nitrogen fixation ability was especially important in the warming treatments during the summer season. However, an elevated temperature significantly led to reduced nitrogen fixation abilities in winter. Compared with the water column, the most predominant functional groups of nitrogen cycle in sediment were nitrite oxidation and nitrification. Variable warming significantly promoted nitrite oxidation and nitrification function in winter, and constant warming was significantly inhibited in spring, with control in sediments. Co-occurrence network results showed that warming, especially variable warming, made microbial co-occurrence networks larger, more connected and less modular, and eventually functional groups in the water column and sediment cooperated to resist warming. We concluded that warming changed bacterial functional potentials important to the biogeochemical cycling in the experimental mesocosms in winter and spring with low temperature. The effect of different bacteria metabolism functions in water column and sediment may change the carbon and nitrogen fluxes in aquatic ecosystems. In conclusion, the coupling response between different bacterial metabolic functions in water and sediment may improve the ability to mitigate climate change.
... Such disordered growth rates between abundant and rare taxa may enhance stochastic processes of birth, death, colonization, extinction and random changes (i.e. drift) in species abundance [40,44,45]. ...
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Revealing planktonic fungal ecology under coastal eutrophication is crucial to our understanding of microbial community shift in marine pollution background. We investigated the diversity, putative interspecies interactions, assembly processes and environmental responses of abundant and rare planktonic fungal communities along a eutrophication gradient present in the Beibu Gulf. The results showed that Dothideomycetes and Agaricomycetes were the predominant classes of abundant and rare fungi, respectively. We found that eutrophication significantly altered the planktonic fungal communities and affected the abundant taxa more than the rare taxa. The abundant and rare taxa were keystone members in the co-occurrence networks, and their interaction was enhanced with increasing nutrient concentrations. Stochastic processes dominated the community assembly of both abundant and rare planktonic fungi across the eutrophication gradient. Heterogeneous selection affected abundant taxa more than rare taxa, whereas homogenizing dispersal had a greater influence on rare taxa. Influences of environmental factors involving selection processes were detected, we found that abundant fungi were mainly influenced by carbon compounds, whereas rare taxa were simultaneously affected by carbon, nitrogen and phosphorus compounds in the Beibu Gulf. Overall, these findings highlight the distinct ecological adaptations of abundant and rare fungal communities to marine eutrophication.
... The results suggested that deterministic processes may play an important role in maintaining the diversity and function of epiphytic bacteria in aquatic ecosystems. Concurrently, the increase in temperature enhanced the metabolic dynamics and molecular irregular movement of the bacterial community, increasing the stochasticity of the colonization and extinction of bacterial community members [77]. Consistent with our results, the bacterial community may be more affected by stochasticity in summer. ...
Article
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In shallow macrophytic lakes, epiphytic biofilms are formed on the surface of submerged plant stems and leaves because of algae and bacterial accumulation. Epiphytic biofilms significantly impact the health of the host vegetation and the biogeochemical cycling of lake elements. However, community diversity, species interactions, and community assembly mechanisms in epiphytic bacterial communities (EBCs) of plants during different growth periods are not well understood. We investigated the successional dynamics, co-occurrence patterns, and community assembly processes of epiphytic biofilm bacterial communities of submerged plants, Najas marina and Potamogeton lucens, from July to November 2020. The results showed a significant seasonal variation in EBC diversity and richness. Community diversity and richness increased from July to November, and the temperature was the most important driving factor for predicting seasonal changes in EBC community structure. Co-occurrence network analysis revealed that the average degree and graph density of the network increased from July to November, indicating that the complexity of the EBC network increased. The bacterial community co-occurrence network was limited by temperature, pH, and transparency. The phylogeny-based null model analysis showed that deterministic processes dominated the microbial community assembly in different periods, increasing their contribution. In addition, we found that as the dominance of deterministic processes increased, the microbial co-occurrence links increased, and the potential interrelationships between species became stronger. Thus, the findings provide insights into the seasonal variability of EBC assemblage and co-occurrence patterns in lacustrine ecosystems.
... The intensive bacterial competition for EPS in the bulk soil might lead to the negative correlations between Cyanobacteria and other bacteria. Previous studies have observed that nutrient variations oppositely impact the relative abundances of Cyanobacteria and Actinobacteria (Ghai et al. 2014;Ren et al. 2017). This inverse relationship between the members of Cyanobacteria and Proteobacteria was also observed in the coastal water of northern China ). ...
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Understanding interspecies interactions is essential to predict the response of microbial communities to exogenous perturbation. Herein, rhizospheric and bulk soils were collected from five developmental stages of soybean, which grew in soils receiving 16-year nitrogen inputs. Bacterial communities and functional profiles were examined using high-throughput sequencing and quantitative PCR, respectively. The objective of this study was to identify the key bacterial interactions that influenced community dynamics and functions. We found that the stages of soybean development outcompeted nitrogen fertilization management in shaping bacterial community structure, while fertilization treatments significantly shaped the abundance distribution of nitrogen functional genes. Temporal variations in bacterial abundances increased in bulk soils, especially at the stage of soybean branching, which helps to infer underlying negative interspecies interactions. Members of Cyanobacteria and Actinobacteria actively engaged in inter-phylum negative interactions in bulk soils and soybean rhizosphere, respectively. Furthermore, the negative interactions between nitrogen-fixing functional groups and the reduction of nifH gene abundance were coupled during soybean development, which may help to explain the linkages between population dynamics and functions. Overall, these findings highlight the importance of inter-phylum negative interactions in shaping the correlation patterns of bacterial communities and in determining soil functional potential.
... Under this conceptual framework, a review by Cross et al. (2015) proposes that rising temperature accelerates the metabolic rates regardless of nutrient availability because the first driver masks or counteracts the effect of the second one. This proposal is supported by recent findings reflecting a strong stimulatory warming effect on key processes such as primary (Lee and Kang, 2020;Schubert et al., 2019) and bacterial (Scofield et al., 2015) production or on microbial communities' β-diversity (Ren et al., 2017) regardless of nutrient status. Contrary to the proposal of Cross et al. (2015), ocean-scale evidence supports the contention that nutrient availability controls the temperature dependence of metabolism and thus temperature may be far less decisive than expected under nutrient limitation (Marañón et al., 2014). ...
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Multiple drivers are threatening the functioning of the microbial food webs and trophic interactions. Our understanding about how temperature, CO2, nutrient inputs, and solar ultraviolet radiation (UVR) availability interact to alter ecosystem functioning is scarce because research has focused on single and double interactions. Moreover, the role that the degree of in situ nutrient limitation could play in the outcome of these interactions has been largely neglected, despite it is predominant in marine ecosystems. We address these uncertainties by combining remote-sensing analyses, and a collapsed experimental design with natural microbial communities from Mediterranean Sea and Atlantic Ocean exposed to temperature, nutrients, CO2, and UVR interactions. At the decade scale, we found that more intense and frequent (and longer lasting) Saharan dust inputs (and marine heatwaves) were only coupled with reduced phytoplankton biomass production. When microbial communities were concurrently exposed to future temperature, CO2, nutrient, and UVR conditions (i.e. the drivers studied over long-term scales), we found shifts from net autotrophy [primary production:respiration (PP:R) ratio > 1] towards a metabolic equilibrium (PP:R ratio ~ 1) or even a net heterotrophy (PP:R ratio < 1), as P-limitation degree was higher (i.e. Atlantic Ocean). These changes in the metabolic balance were coupled with a weakened phytoplankton-bacteria interaction (i.e. bacterial carbon demand exceeded phytoplankton carbon supply. Our work reveals that an accentuated in situ P limitation may promote reductions both in carbon uptake and fluxes between trophic levels in microbial plankton communities under global-change conditions. We show that considering long-term series can aid in identifying major local environmental drivers (i.e. temperature and nutrients in our case), easing the design of future global-change studies, but also that the abiotic environment to which microbial plankton communities are acclimated should be taken into account to avoid biased predictions concerning the effects of multiple interacting global-change drivers on marine ecosystems.
... The inconsistent effect of constant warming and heatwave on litter bacterial may be due to a consensus conclusions drawn in a varies of studies examining disturbance: the microbial communities are not resistant to many factors but highly resilient to disturbance [22,47], Finlay indicated that the composition of the microbial community usually changes when environmental factors change at high amplitude or high frequency. For example, in similar mesocosm experiments, the researchers found that heating induced a positive effect on the bacteria within a few days [48] and long-term warming had not significant effects on bacterial alpha diversity but significantly shifted bacterial community composition [49]. In addition, some studies reported the increase in bacterial diversity during the late stage of organic matter decomposition [50,51]. ...
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Global climate change scenarios predict that lake water temperatures will increase up to 4 °C and extreme weather events, such as heat waves and large temperature fluctuations, will occur more frequently. Such changes may result in the increase of aquatic litter decomposition and on shifts in diversity and structure of bacteria communities in this period. We designed a two-month mesocosm experiment to explore how constant (+4 °C than ambient temperature) and variable (randomly +0~8 °C than ambient temperature) warming treatment will affect the submerged macrophyte litter decomposition process. Our data suggests that warming treatments may accelerate the decomposition of submerged macrophyte litter in shallow lake ecosystems, and increase the diversity of decomposition-related bacteria with community composition changed the relative abundance of Proteobacteria, especially members of Alphaproteobacteria increased while that of Firmicutes (mainly Bacillus) decreased.
... Environmental heterogeneity includes spatial differences in environmental characteristics (e.g., eutrophic gradients among lakes) and temporal changes in these environmental characteristics along with temporal beta diversity (e.g., the amplitude of seasonal temperature differences among lakes) (O'Reilly et al., 2015). Previous studies have found that eutrophication reduces the seasonal variation in macroinvertebrate assemblages (Cook et al., 2018), while warming increases the spatial beta diversity of macroinvertebrates, benthic diatoms, macrophytes and bacterioplankton (Ren et al., 2017). However, the contributions of these two aspects to temporal beta diversity are unclear. ...
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... In addition, the standardized effect size (SES) was calculated as the differences in beta diversity between the real communities and the mean value of null communities divided by the standardized deviation of the beta diversity in the null communities. The relative importance of stochastic processes increases when SES is closer to zero (Ren et al., 2017). Null model analysis and PERMANOVA were performed using Vegan and Parallel packages in the R platform. ...
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... It has been shown that agricultural practices and environmental changes can alter the balance between stochastic and deterministic processes governing microbial community assembly. For example, fertilization and warming can increase while tillage and drought can decrease the relative importance of stochastic processes (Chase, 2007;Feng et al., 2018;Ren et al., 2017;Zhou et al., 2014). However, multiple perturbations factors can interact with each other, yielding synergistic or antagonistic effects on biological community assembly (Houseman et al., 2008). ...
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The fungi associated with leaf litter play a key role in decomposition and can be affected both by the warming water and the invasion of non-native species in riparian vegetation. Warming water and invasion of non-native riparian species on stream fungal communities have been studied, mainly in temperate ecosystems. We tested the effects of warming water and non-native plant Psidium guajava on leaf litter decomposition, conidia density, species richness and beta diversity of tropical stream fungi. Thus, we carried out an experiment using the current mean temperature of streams from northwestern Paraná in South Brazil (22 °C) and two temperatures above the current mean temperature (26 °C and 29 °C). We also used the debris of a non-native plant (P. guajava), and two native plants (one of similar nutritional quality, and the other of higher nutritional quality than the non-native species) occurring in Neotropical streams riparian vegetation. Warming water accelerated leaf litter decomposition and reduced conidia density and fungal richness in native and non-native plants. However, species composition and beta diversity were not affected by water temperature. Our study showed that warming affects the fungi of streams, the main microorganisms responsible for decomposition and that the nutritional quality of the leaves may be more important than the origin of riparian plant species. Despite this, further investigations should be conducted on the interaction of P. guajava with the flow of nutrients in these environments and how it can affect other ecosystem processes and the food chain. Efforts to study the effects of water warming and biological invasion on the attributes and distribution of fungi in streams are vital, making them a tool for the conservation of riparian ecosystems.
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Chronic exposures to tobacco and biomass smoke are the most prevalent risk factors for COPD development. Although microbial diversity in tobacco smoke-associated COPD (TSCOPD) has been investigated, microbiota in biomass smoke-associated COPD (BMSCOPD) is still unexplored. We aimed to compare the nasal and oral microbiota between healthy, TSCOPD, and BMSCOPD subjects from a rural population in India. Nasal swabs and oral washings were collected from healthy (n = 10), TSCOPD (n = 11), and BMSCOPD (n = 10) subjects. The downstream analysis was performed using QIIME pipeline (v1.9). In nasal and oral microbiota no overall differences were noted, but there were key taxa that had differential abundance in either Healthy vs COPD and/or TSCOPD vs. BMSCOPD. Genera such as Actinomyces, Actinobacillus, Megasphaera, Selenomonas, and Corynebacterium were significantly higher in COPD subjects. This study suggests that microbial community undergoes dysbiosis which may further contribute to the progression of disease. Thus, it is important to identify etiological agents for such a polymicrobial alterations which contribute highly to the disease manifestation.
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From an extensive study, we determined that heterotrophic bacterial production (HBP) variance in Sierra Nevada (Spain) lakes was explained mainly by excretion of organic carbon by algae (EOC), underlining a bacterial dependence on algal carbon. Subsequently, we studied how the interaction among global change factors such as ultraviolet radiation (UVR), nutrient inputs, and increased temperature affected this phytoplankton-bacteria coupling through in situ factorial experiments in two model high-mountain lakes, La Caldera, and Las Yeguas. Bacterioplankton were more sensitive than phytoplankton because the joint action of increased temperature and nutrient-addition unmasked an inhibitory UVR effect on HBP while reducing the inhibitory UVR effect on primary production (PP) (in La Caldera) or augmenting the net PP values (in Las Yeguas). The interaction among the three factors had a different effect on phytoplankton-bacteria coupling depending on the lake. Thus, in the colder lake (La Caldera), EOC was not adequate to meet the bacterial carbon demand (BCD), leading to a mismatch in phytoplankton-bacteria coupling. Contrarily, in the warmer lake (Las Yeguas), the phytoplankton-bacteria coupling was accentuated by the interaction among the three factors, with EOC exceeding BCD. These contrasting responses of phytoplankton-bacteria coupling may affect the microbial loop development, becoming reinforced in warmer and less UVR-transparent high-mountain lakes, but weakened in colder and more UVR-transparent high-mountain lakes, with implications in the C-flux of these sentinel ecosystems in a scenario of global change. © 2015 Association for the Sciences of Limnology and Oceanography.
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The vegan package (available from: https://cran.r-project.org/package=vegan) provides tools for descriptive community ecology. It has most basic functions of diversity analysis, community ordination and dissimilarity analysis. Most of its multivariate tools can be used for other data types as well. The functions in the vegan package contain tools for diversity analysis, ordination methods and tools for the analysis of dissimilarities. Together with the labdsv package, the vegan package provides most standard tools of descriptive community analysis. Package ade4 provides an alternative comprehensive package, and several other packages complement vegan and provide tools for deeper analysis in specific fields. Package https://CRAN.R-project.org/package=BiodiversityR provides a Graphical User Interface (GUI) for a large subset of vegan functionality. The vegan package is developed at GitHub (https://github.com/vegandevs/vegan/). GitHub provides up-to-date information and forums for bug reports. Most important changes in vegan documents can be read with news(package="vegan") and vignettes can be browsed with browseVignettes("vegan"). The vignettes include a vegan FAQ, discussion on design decisions, short introduction to ordination and discussion on diversity methods. A tutorial of the package at http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf provides a more thorough introduction to the package. To see the preferable citation of the package, type citation("vegan").
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Understanding the structure, functions, activities and dynamics of microbial communities in natural environments is one of the grand challenges of 21st century science. To address this challenge, over the past decade, numerous technologies have been developed for interrogating microbial communities, of which some are amenable to exploratory work (e.g., high-throughput sequencing and phenotypic screening) and others depend on reference genes or genomes (e.g., phylogenetic and functional gene arrays). Here, we provide a critical review and synthesis of the most commonly applied "open-format" and "closed-format" detection technologies. We discuss their characteristics, advantages, and disadvantages within the context of environmental applications and focus on analysis of complex microbial systems, such as those in soils, in which diversity is high and reference genomes are few. In addition, we discuss crucial issues and considerations associated with applying complementary high-throughput molecular technologies to address important ecological questions. Copyright © 2015 Zhou et al.
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Freshwater ecosystems and their biodiversity are presently seriously threatened by global development and population growth, leading to increases in nutrient inputs and intensification of eutrophication-induced problems in receiving fresh waters, particularly in lakes. Climate change constitutes another threat exacerbating the symptoms of eutrophication and species migration and loss. Unequivocal evidence of climate change impacts is still highly fragmented despite the intensive research, in part due to the variety and uncertainty of climate models and underlying emission scenarios but also due to the different approaches applied to study its effects. We first describe the strengths and weaknesses of the multi-faceted approaches that are presently available for elucidating the effects of climate change in lakes, including space-for-time substitution, time series, experiments, palaeoecology and modelling. Reviewing combined results from studies based on the various approaches, we describe the likely effects of climate changes on biological communities, trophic dynamics and the ecological state of lakes. We further discuss potential mitigation and adaptation measures to counteract the effects of climate change on lakes and, finally, we highlight some of the future challenges that we face to improve our capacity for successful prediction.
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Freshwaters ecosystems are critical but fragile environments directly affecting society and its welfare. However, our understanding of genuinely freshwater microbial communities, constrained by our capacity to manipulate its prokaryotic participants in axenic cultures, remains very rudimentary. Even the most abundant components, freshwater Actinobacteria, remain largely unknown. Here, applying deep metagenomic sequencing to the microbial community of a freshwater reservoir, we were able to circumvent this traditional bottleneck and reconstruct de novo seven distinct streamlined actinobacterial genomes. These genomes represent three new groups of photoheterotrophic, planktonic Actinobacteria. We describe for the first time genomes of two novel clades, acMicro (Micrococcineae, related to Luna2,) and acAMD (Actinomycetales, related to acTH1). Besides, an aggregate of contigs belonged to a new branch of the Acidimicrobiales. All are estimated to have small genomes (~1.2 Mb) and their GC content varied from 40-61%. One of the Micrococcineae genomes encodes a proteorhodopsin, a rhodopsin type reported for the first time in Actinobacteria.The remarkable potential capacity of some of these genomes to transform recalcitrant plant detrital material, particularly lignin derived compounds, suggests close linkages between the terrestrial and aquatic realms. Moreover, abundances of Actinobacteria correlate inversely to those of Cyanobacteria that are responsible for prolonged and frequently irretrievable damage to freshwater ecosystems. This suggests that they might serve as sentinels of impending ecological catastrophes.This article is protected by copyright. All rights reserved.
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Current practice in the normalization of microbiome count data is inefficient in the statistical sense. For apparently historical reasons, the common approach is either to use simple proportions (which does not address heteroscedasticity) or to use rarefying of counts, even though both of these approaches are inappropriate for detection of differentially abundant species. Well-established statistical theory is available that simultaneously accounts for library size differences and biological variability using an appropriate mixture model. Moreover, specific implementations for DNA sequencing read count data (based on a Negative Binomial model for instance) are already available in RNA-Seq focused R packages such as edgeR and DESeq. Here we summarize the supporting statistical theory and use simulations and empirical data to demonstrate substantial improvements provided by a relevant mixture model framework over simple proportions or rarefying. We show how both proportions and rarefied counts result in a high rate of false positives in tests for species that are differentially abundant across sample classes. Regarding microbiome sample-wise clustering, we also show that the rarefying procedure often discards samples that can be accurately clustered by alternative methods. We further compare different Negative Binomial methods with a recently-described zero-inflated Gaussian mixture, implemented in a package called metagenomeSeq. We find that metagenomeSeq performs well when there is an adequate number of biological replicates, but it nevertheless tends toward a higher false positive rate. Based on these results and well-established statistical theory, we advocate that investigators avoid rarefying altogether. We have provided microbiome-specific extensions to these tools in the R package, phyloseq.
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Determining the composition and function of subgingival dental plaque is crucial to understanding human periodontal health and disease, but it is challenging because of the complexity of the interactions between human microbiomes and human body. Here, we examined the phylogenetic and functional gene differences between periodontal and healthy individuals using MiSeq sequencing of 16S rRNA gene amplicons and a specific functional gene array (a combination of GeoChip 4.0 for biogeochemical processes and HuMiChip 1.0 for human microbiomes). Our analyses indicated that the phylogenetic and functional gene structure of the oral microbiomes were distinctly different between periodontal and healthy groups. Also, 16S rRNA gene sequencing analysis indicated that 39 genera were significantly different between healthy and periodontitis groups, and Fusobacterium, Porphyromonas, Treponema, Filifactor, Eubacterium, Tannerella, Hallella, Parvimonas, Peptostreptococcus and Catonella showed higher relative abundances in the periodontitis group. In addition, functional gene array data showed that a lower gene number but higher signal intensity of major genes existed in periodontitis, and a variety of genes involved in virulence factors, amino acid metabolism and glycosaminoglycan and pyrimidine degradation were enriched in periodontitis, suggesting their potential importance in periodontal pathogenesis. However, the genes involved in amino acid synthesis and pyrimidine synthesis exhibited a significantly lower relative abundance compared with healthy group. Overall, this study provides new insights into our understanding of phylogenetic and functional gene structure of subgingival microbial communities of periodontal patients and their importance in pathogenesis of periodontitis.The ISME Journal advance online publication, 27 March 2014; doi:10.1038/ismej.2014.28.
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Significance The study of ecological succession remains at the core of ecology. Understanding the trajectories and mechanisms controlling ecological succession is crucial to predicting the responses of ecosystems to environmental change and projecting their future states. By definition, deterministic succession is expected under homogeneous abiotic and biotic starting conditions. This study, however, shows that the succession of groundwater microbial communities in response to nutrient amendment is primarily stochastic, but that the drivers controlling biodiversity and succession are dynamic rather than static. By identifying the mechanisms controlling microbial community assembly and succession, this study makes fundamental contribution to the mechanistic understanding essential for a predictive microbial ecology of many systems ranging from microbiomes of humans and plants to natural and managed ecosystems.
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1930 Climate change may have profound eff ects on phosphorus (P) transport in streams and on lake eutrophication. Phosphorus loading from land to streams is expected to increase in northern temperate coastal regions due to higher winter rainfall and to a decline in warm temperate and arid climates. Model results suggest a 3.3 to 16.5% increase within the next 100 yr in the P loading of Danish streams depending on soil type and region. In lakes, higher eutrophication can be expected, reinforced by temperature-mediated higher P release from the sediment. Furthermore, a shift in fi sh community structure toward small and abundant plankti-benthivorous fi sh enhances predator control of zooplankton, resulting in higher phytoplankton biomass. Data from Danish lakes indicate increased chlorophyll a and phytoplankton biomass, higher dominance of dinophytes and cyanobacteria (most notably of nitrogen fi xing forms), but lower abundance of diatoms and chrysophytes, reduced size of copepods and cladocerans, and a tendency to reduced zooplankton biomass and zooplankton:phytoplankton biomass ratio when lakes warm. Higher P concentrations are also seen in warm arid lakes despite reduced external loading due to increased evapotranspiration and reduced infl ow. Th erefore, the critical loading for good ecological state in lakes has to be lowered in a future warmer climate. Th is calls for adaptation measures, which in the northern temperate zone should include improved P cycling in agriculture, reduced loading from point sources, and (re)-establishment of wetlands and riparian buff er zones. In the arid Southern Europe, restrictions on human use of water are also needed, not least on irrigation. O n average, global surface temperatures have increased by about 0.74°C over the past 100 yr (Trenberth et al., 2007), with the majority of the increase (0.55°C) occurring over the past 30 yr. We may expect marked changes to occur in the global climate during this century (IPCC, 2007). Increasingly reliable regional climate projections are available for many regions of the world, but fewer projections are available for many developing countries than for the developed world (Christensen et al., 2007). Th e warming generally increases the spatial variability of precipitation with reduced rainfall in the subtropics and increases at higher latitudes and in parts of the tropics. Th e changes in temperature and rainfall lead to changes in agricul-tural land use and management, including changes in soil cultivation and in the rates and timing of fertilization (Howden et al., 2007). Th ese changes have cascading eff ects on the P cycling, directly and indirectly, that aff ect the aquatic environment. Th e direct eff ects are related to the increased temperatures, increased rainfall intensity, and changes in winter rainfall that are expected to enhance the P loading to freshwaters in the temperate zone (IPCC, 2007) and the Arctic (Arctic Climate Impact Assessment, 2002) and to reduce the loading, but not the concentrations, in streams and freshwater lakes in the Mediterranean region. However, a few quantitative studies are avail-able (Chang, 2004; Andersen et al., 2006). Th e indirect eff ects are related to changes in the choice of crops, crop rotations, use of catch crops, and agricultural practices, including tillage and fertilization. In northern temperate areas, new heat-demanding, warm-season crops (e.g., maize and sunfl ower) will replace many of the present grain cereals and oilseed crops (Olesen and Bindi, 2002). At the same time, changes occur in planting and harvesting times (Olesen, 2005) and in fertilization rates and strategies (Olesen et al., 2007). Crop rotation must be adapted to changes in crop choices, in crop maturing, and in the need to control weeds, pests, and diseases. Th is will aff ect the amount of P released to freshwaters and its seasonal pattern. More-Abbreviation: TP, total phosphorus.
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1. We followed microbial and other planktonic communities during a 4-month period (February–May) in 12 outdoor flow-through mesocosms designed to elucidate the effect of global warming and nutrient enrichment. The mesocosms were established in 2003. 2. Warming had a smaller effect than nutrients on the biomass of the microbial and planktonic communities, and warming and nutrients together exhibited complex interactions. 3. We did not find direct effects of warming on the biomass of bacterioplankton or ciliates; however, warming significantly added to the positive effect of nutrients on these organisms and on heterotrophic nanoflagellates (HNF). No warming effects on any of the other planktonic groups analysed were detected. 4. The zooplankton: phytoplankton biomass ratio was lowest, and the HNF: bacteria and rotifer: bacteria biomass ratios highest in the heated, nutrient-rich mesocosms. We attribute this to higher fish predation on large-bodied zooplankton, releasing the predation on HNF and competition for rotifers. 5. The proportion of phytoplankton to the total plankton biomass increased with nutrients, but decreased with warming. The opposite pattern was observed for the proportion of phytoplankton to the total microbial biomass. 6. As climate warming may lead to eutrophication, major changes may occur in the pelagic food web and the microbial community due to changes in trophic state and in combination with warming.
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Planktonic heterotrophic prokaryotes play an essential role in all aquatic ecosystems due to their short generation times and access to dissolved organic carbon and nutrients. In order to understand how rising temperatures and nutrient loading affect the biogeochemistry of whole lake ecosystems, it is essential to understand the interactive effects that temperature and resources have on the metabolism of natural bacterioplankton communities. To address this question we sampled bacterial communities from 1 mesotrophic and 1 oligotrophic lake in Clearwater County, Minnesota, USA, in winter and summer. Each community was exposed to a combination of carbon, nitrogen and phosphorus additions at 4 different levels (ambient, 2 x, 5 x, and 10 x ambient) and 4 temperatures (4, 14, 24 and 34 degrees C). Community metabolic response to temperature depended on the resource treatment, and the season when the community was sampled. Bacterial respiration increased more with temperature than bacterial growth, resulting in decreased bacterial growth efficiencies at higher temperatures. This result was most pronounced in the high resource treatments, while at lower resource levels the results were more ambiguous. In addition, differences between seasons and lakes suggested that the bacterial communities had adapted or acclimated to in situ temperature such that communities sampled from cold temperature environments had higher respiration at high temperatures than those sampled from warmer environments. These results suggest that the effect of temperature on carbon cycling mediated by the bacterial community depends on both the in situ resource pool and the extent to which the bacterial community is acclimated to a specific temperature regime.
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A series of seawater culture experiments was carried out during the Phaeocystis antarctica bloom in the Ross Sea polynya (76.5°S, 180°W; November to December 1994 and December 1995 to January 1996) to examine bacterioplankton growth and derive empirical factors for estimating bacterial production rates. Bacterial growth was exponential over 3 to 10 d in all experiments, at rates of ca 0.1 to 0.7 d-1, even in persistently cold waters (-2 to + 1°C). Growth rates were lower in the early part of the bloom (early to mid-November) and highest during the period of peak primary productivity (2 to 4 g C m-2 d-1 in late November through December). Apparent lag phases in the growth curves lasting 1 to 7 d could be accounted for mathematically by subpopulations in the bacterial assemblages growing exponentially at different rates, with no need to invoke inactive, nondividing or nonviable populations. Lags were absent during the period of peak primary production, suggesting adaptation of the bacteria to ambient DOM. Growth was not stimulated by small temperature increases (Δ+2 to 4°C), and was not balanced by removal processes in untreated 'whole' water samples. Growth rates were broadly similar to other directly observed bacterial growth rates in the Antarctic and did not appear to differ from rates in warmer waters. Conversion factors for thymidine and leucine averaged 8 and 0.8 x 1017 cells mol-1, respectively, not dissimilar to estimates from temperate waters. These findings suggest that bacteria were growing actively in 0 to -2°C waters under rich bloom conditions, and lend strong support to the hypothesis that bacterioplankton metabolism controls DOC accumulation in Antarctic waters, at least at the low rates of DOM supply we infer from field and experimental observations. Bacterioplankton responded within 10 to 20 d to the evolving F antarctica bloom and did not appear to behave substantially differently from lower latitude bloom systems.
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Predicting the ecological causes and consequences of global climate change requires a variety of approaches, including the use of experiments, models, and surveys. Among experiments, mesocosms have become increasingly popular because they provide an important bridge between smaller, more tightly-controlled, microcosm experiments (which can suffer from limited realism) and the greater biological complexity of natural systems (in which mechanistic relationships often cannot be identified). A new evaluation of the contribution of the mesocosm approach, its potential for future research, as well as its limitations, is timely. As part of this review, we constructed a new database of over 250 post-1990 studies that have explored different components of climate change across a range of organisational levels, scales, and habitats. Issues related to realism, reproducibility and control are assessed in marine, freshwater and terrestrial systems. Some general patterns emerged, particularly at the ecosystem level, such consistent and predictable effects on whole-system respiration rates. There are, however, also many seemingly idiosyncratic, contingent responses, especially at the community level, both within and among habitat types. These similarities and differences in both the drivers and responses highlight the need for caution before making generalizations. Finally, we assess future directions and prospects for new methodological advances and the need for greater international co-ordination and interdisciplinarity.
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Rapid advances in sequencing technology have changed the experimental landscape of microbial ecology. In the last 10 years the field has moved from sequencing hundreds of 16S rRNA gene fragments per study using clone libraries to the sequencing of millions of fragments per study using next generation sequencing technologies from 454 and Illumina. As these technologies advance it is critical to assess the strengths, weaknesses and overall suitability of these platforms for the interrogation of microbial communities. Here we present an improved method for sequencing variable regions within the 16S rRNA gene using Illumina's MiSeq platform, which is currently capable of producing paired 250-nt reads. We evaluated three overlapping regions of the 16S rRNA gene that vary in their length (i.e. V34, V4, and V45) by re-sequencing a mock community and natural samples from human feces, mouse feces, and soil. By titrating the concentration of 16S rRNA gene amplicons applied to the flow cell and using a quality score-based approach to correct discrepancies between reads used to construct contigs, we were able to reduce error rates by as much as two orders of magnitude. Finally, we re-processed samples from a previous study to demonstrate that large numbers of samples could be multiplexed and sequenced in parallel with shotgun metagenomes. These analyses demonstrate that our approach can provide data that are at least as good as that generated by the 454 platform while providing considerably higher sequencing coverage for a fraction of the cost.
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