scholarly journals Recurrent micropollutant exposure leads to divergent degradation abilities and community succession in a freshwater microbiome

2021 ◽  
Author(s):  
Dandan Izabel-Shen ◽  
Shuang Li ◽  
Tingwei Luo ◽  
Jianjun Wang ◽  
Yan Li ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Surface Waters ◽  
Community Assembly ◽  
High Volume ◽  
Aquatic Environments ◽  
Community Succession ◽  
Microbial Dynamics ◽  
Ecological Processes ◽  
Micropollutant Removal ◽  
Deterministic Processes

The high-volume release of micropollutants into natural surface waters has raised concern due to their environmental accumulation. Persisting micropollutants can impact multiple generations of organisms via press disturbances, but their microbially-mediated degradation and the influence on community assembly remain understudied. Here, freshwater microbial communities in microcosms were treated with four common micropollutants, alone or in combination, and then transferred in stages to fresh medium containing the same level of micropollutants to mimic the recurrent exposure of microbes under environmentally relevant conditions. Our results showed that the degradation of micropollutants was closely linked to the community succession, and that recurrent exposure to micropollutants enhanced the degradation capacity. The partitioning analysis of ecological processes revealed that community assembly was dominated by stochastic processes during early exposure, via random community changes, and by deterministic processes later in the exposure. Analyzing individual taxa abundances over time revealed two distinct bacterial responses, in which a larger proportion of sensitive than tolerant taxa was present in the disturbed communities, and the abundances of the most sensitive taxa were significantly associated with micropollutant degradation. This study clearly showed that microbial communities are generally vulnerable to persisting micropollutants in aquatic environments, which has important implications for pollution management, especially regarding microbial dynamics and ecosystem functioning in micropollutant removal.

scholarly journals Deterministic Selection Dominates Microbial Community Assembly in Termite Mounds Across a Large Spatial Area

2020 ◽  
Author(s):  
Qing-Lin Chen ◽  
Hang-Wei Hu ◽  
Zhen-Zhen Yan ◽  
Chao-Yu Li ◽  
Bao-Anh Thi Nguyen ◽  
...  
Keyword(s):  
Microbial Community ◽  
Stochastic Processes ◽  
Microbial Communities ◽  
Fungal Community ◽  
Community Assembly ◽  
Distance Decay ◽  
Termite Mounds ◽  
Deterministic Processes ◽  
Microbial Community Assembly

Abstract Background: Termites are ubiquitous insects in tropical and subtropical habitats, where they construct massive mounds from soil, their saliva and excreta. Termite mounds harbor an enormous amount of microbial inhabitants, which regulate multiple ecosystem functions such as mitigating methane emissions and increasing ecosystem resistance to climate change. However, we lack a mechanistic understanding about the role of termite mounds in modulating the microbial community assembly processes, which are essential to unravel the biological interactions of soil fauna and microorganisms, the major components of soil food webs. We conducted a large-scale survey across a >1500 km transect in northern Australia to investigate biogeographical patterns of bacterial and fungal community in 134 termite mounds and the relative importance of deterministic versus stochastic processes in microbial community assembly. Results: Microbial alpha (number of phylotypes) and beta (changes in bacterial and fungal community composition) significantly differed between termite mounds and surrounding soils. Microbial communities in termite mounds exhibited a significant distance-decay pattern, and fungal communities had a stronger distance-decay relationship (slope = -1.91) than bacteria (slope = -0.21). Based on the neutral community model (fitness < 0.7) and normalized stochasticity ratio index (NST) with a value below the 50% boundary point, deterministic selection, rather than stochastic forces, predominated the microbial community assembly in termite mounds. Deterministic processes exhibited significantly weaker impacts on bacteria (NST = 45.23%) than on fungi (NST = 33.72%), probably due to the wider habitat niche breadth and higher potential migration rate of bacteria. The abundance of antibiotic resistance genes (ARGs) was negatively correlated with bacterial/fungal biomass ratios, indicating that ARG content might be an important biotic factor that drove the biogeographic pattern of microbial communities in termite mounds. Conclusions: Deterministic processes play a more important role than stochastic processes in shaping the microbial community assembly in termite mounds, an unique habitat ubiquitously distributed in tropical and subtropical ecosystems. An improved understanding of the biogeographic patterns of microorganisms in termite mounds is crucial to decipher the role of soil faunal activities in shaping microbial community assembly, with implications for their mediated ecosystems functions and services.

scholarly journals Stochastic Community Assembly: Does It Matter in Microbial Ecology?

2017 ◽  
Vol 81 (4) ◽  
Author(s):  
Jizhong Zhou ◽  
Daliang Ning
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Ecology ◽  
Community Assembly ◽  
Community Diversity ◽  
Ecological Processes ◽  
Experimental Approaches ◽  
Deterministic Processes ◽  
Deterministic Components ◽  
Microbial Community Assembly

SUMMARY Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly in microbial ecology. Although stochastic processes are believed to play nonnegligible roles in shaping community structure, their importance relative to deterministic processes is hotly debated. The importance of ecological stochasticity in shaping microbial community structure is far less appreciated. Some of the main reasons for such heavy debates are the difficulty in defining stochasticity and the diverse methods used for delineating stochasticity. Here, we provide a critical review and synthesis of data from the most recent studies on stochastic community assembly in microbial ecology. We then describe both stochastic and deterministic components embedded in various ecological processes, including selection, dispersal, diversification, and drift. We also describe different approaches for inferring stochasticity from observational diversity patterns and highlight experimental approaches for delineating ecological stochasticity in microbial communities. In addition, we highlight research challenges, gaps, and future directions for microbial community assembly research.

scholarly journals Neutral Processes Dominate Microbial Community Assembly in Atlantic Salmon, Salmo salar

2020 ◽  
Vol 86 (8) ◽  
Author(s):  
C. Heys ◽  
B. Cheaib ◽  
A. Busetti ◽  
R. Kazlauskaite ◽  
L. Maier ◽  
...  
Keyword(s):  
Life Cycle ◽  
Microbial Community ◽  
Atlantic Salmon ◽  
Salmo Salar ◽  
Community Assembly ◽  
Wild Fish ◽  
Ecological Processes ◽  
Deterministic Processes ◽  
Microbial Community Assembly

ABSTRACT In recent years, a wealth of studies has examined the relationships between a host and its microbiome across diverse taxa. Many studies characterize the host microbiome without considering the ecological processes that underpin microbiome assembly. In this study, the intestinal microbiota of Atlantic salmon, Salmo salar, sampled from farmed and wild environments was first characterized using 16S rRNA gene MiSeq sequencing analysis. We used neutral community models to determine the balance of stochastic and deterministic processes that underpin microbial community assembly and transfer across life cycle stage and between gut compartments. Across gut compartments in farmed fish, neutral models suggest that most microbes are transient with no evidence of adaptation to their environment. In wild fish, we found declining taxonomic and functional microbial community richness as fish mature through different life cycle stages. Alongside neutral community models applied to wild fish, we suggest that declining richness demonstrates an increasing role for the host in filtering microbial communities that is correlated with age. We found a limited subset of gut microflora adapted to the farmed and wild host environment among which Mycoplasma spp. are prominent. Our study reveals the ecological drivers underpinning community assembly in both farmed and wild Atlantic salmon and underlines the importance of understanding the role of stochastic processes, such as random drift and small migration rates in microbial community assembly, before considering any functional role of the gut microbes encountered. IMPORTANCE A growing number of studies have examined variation in the microbiome to determine the role in modulating host health, physiology, and ecology. However, the ecology of host microbial colonization is not fully understood and rarely tested. The continued increase in production of farmed Atlantic salmon, coupled with increased farmed-wild salmon interactions, has accentuated the need to unravel the potential adaptive function of the microbiome and to distinguish resident from transient gut microbes. Between gut compartments in a farmed system, we found a majority of operational taxonomic units (OTUs) that fit the neutral model, with Mycoplasma species among the key exceptions. In wild fish, deterministic processes account for more OTU differences across life stages than those observed across gut compartments. Unlike previous studies, our results make detailed comparisons between fish from wild and farmed environments, while also providing insight into the ecological processes underpinning microbial community assembly in this ecologically and economically important species.

scholarly journals Soil plastispheres as hotpots of antibiotic resistance genes and potential pathogens

2021 ◽  
Author(s):  
Dong Zhu ◽  
Jun Ma ◽  
Gang Li ◽  
Matthias C. Rillig ◽  
Yong-Guan Zhu
Keyword(s):  
Antibiotic Resistance ◽  
Microbial Communities ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Plastic Pollution ◽  
Ecological Processes ◽  
Operational Taxonomic Units ◽  
Soil Ecosystems ◽  
Potential Pathogen ◽  
Deterministic Processes

AbstractIn the Anthropocene, increasing pervasive plastic pollution is creating a new environmental compartment, the plastisphere. How the plastisphere affects microbial communities and antibiotic resistance genes (ARGs) is an issue of global concern. Although this has been studied in aquatic ecosystems, our understanding of plastisphere microbiota in soil ecosystems remains poor. Here, we investigated plastisphere microbiota and ARGs of four types of microplastics (MPs) from diverse soil environments, and revealed effects of manure, temperature, and moisture on them. Our results showed that the MPs select for microbial communities in the plastisphere, and that these plastisphere communities are involved in diverse metabolic pathways, indicating that they could drive diverse ecological processes in the soil ecosystem. The relationship within plastisphere bacterial zero-radius operational taxonomic units (zOTUs) was predominantly positive, and neutral processes appeared to dominate community assembly. However, deterministic processes were more important in explaining the variance in ARGs in plastispheres. A range of potential pathogens and ARGs were detected in the plastisphere, which were enriched compared to the soil but varied across MPs and soil types. We further found that the addition of manure and elevation of soil temperature and moisture all enhance ARGs in plastispheres, and potential pathogens increase with soil moisture. These results suggested that plastispheres are habitats in which an increased potential pathogen abundance is spatially co-located with an increased abundance of ARGs under global change. Our findings provided new insights into the community ecology of the microbiome and antibiotic resistome of the soil plastisphere.

scholarly journals Trophic States Regulate Assembly Processes and Network Structures of Picophytoplankton Communities in Subtropical Coastal Ecosystems

2020 ◽  
Author(s):  
Xing Chen ◽  
Huaxian Zhao ◽  
Gonglingxia Jiang ◽  
Jinli Tang ◽  
Qiangsheng Xu ◽  
...  
Keyword(s):  
Community Assembly ◽  
Anthropogenic Activities ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Coastal Ecosystems ◽  
Network Structures ◽  
Coastal Eutrophication ◽  
Nitrogen And Phosphorus ◽  
Ecological Processes ◽  
Deterministic Processes

Abstract Background: Long-term coastal eutrophication especially in semi-enclosed marine areas is driven by increased amounts of nutrients derived from anthropogenic activities. Given that accelerating nutrients may constitute a strong environmental filter, understanding the diversity, assembly process and co-occurrence pattern of picophytoplankton communities in response to increasing coastal eutrophication is clearly of great importance. Results: We investigated picophytoplankton community changes using rbcL gene amplicon sequencing. The results exhibited that the alpha diversity (ANOVA, p < 0.001) and beta diversity (ANOSIM, p < 0.001) were significantly different among eutrophic states. Further, phylogenetic based β-nearest taxon distance analyses revealed that stochastic processes mainly provided 69.26% contribution to picophytoplankton community assembly, whereas deterministic processes dominated community assembly in a heavy eutrophic state. Integrated co-occurrence networks modularly responded to eutrophic states and revealed that keystone taxa mainly belonged to the oligo eutrophic group, which may play fundamental roles in network persistence. Importantly, increased environmental disturbances, such as nitrogen and phosphorus nutrients, could alter picophytoplankton community structure and disrupt ecological processes. Conclusion: Stochastic and deterministic processes simultaneously influenced the assembly of picophytoplankton communities in the subtropical coastal ecosystems. Eutrophic disturbances alert the assembly processes and network structures of picophytoplankton community. Our findings promote the understanding of fundamental ecological processes along eutrophic gradients in subtropical coastal ecosystems.

Microbial Communities’ Characterization in Urban Recreational Surface Waters Using Next Generation Sequencing

2021 ◽  
Author(s):  
Laura Vega ◽  
Jesús Jaimes ◽  
Duvan Morales ◽  
David Martínez ◽  
Lissa Cruz-Saavedra ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Microbial Communities ◽  
Surface Waters ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Phylogenetic and Functional Traits Verify the Combined Effect of Deterministic and Stochastic Processes in the Community Assembly of Temperate Forests along an Elevational Gradient

Forests ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 591
Author(s):  
Wensong Zhou ◽  
Yuxin Zhang ◽  
Shuang Zhang ◽  
Basil N. Yakimov ◽  
Keming Ma
Keyword(s):  
Stochastic Processes ◽  
Functional Traits ◽  
Community Assembly ◽  
Woody Plants ◽  
Elevational Gradient ◽  
Combined Effect ◽  
Abiotic Environment ◽  
Spatial Factors ◽  
Assembly Mechanism ◽  
Deterministic Processes

Explaining community assembly mechanisms along elevational gradients dominated by deterministic processes or stochastic processes is a pressing challenge. Many studies suggest that phylogenetic and functional diversity are significant indicators of the process. In this study, we analyzed the structure and beta diversity of phylogenetic and functional traits along an elevational gradient and discussed the effects of environmental and spatial factors. We found that the phylogenetic and functional traits showed inconsistent changes, and their variations were closely related to the abiotic environment. The results suggested that the community assembly of woody plants was obviously affected by the combined effect of deterministic processes and the stochastic hypothesis (primarily by the latter). Phylogenetic and functional traits had a certain relationship but changed according to different rules. These results enhance our understanding of the assembly mechanism of forest communities by considering both phylogenetic and functional traits.

scholarly journals Forfeiting the founder effect: turnover defines biofilm community succession

2018 ◽  
Author(s):  
Colin J. Brislawn ◽  
Emily B. Graham ◽  
Karl Dana ◽  
Peter Ihardt ◽  
Sarah J. Fansler ◽  
...  
Keyword(s):  
Bacterial Colonization ◽  
Amplicon Sequencing ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Community Succession ◽  
Ecological Processes ◽  
Functional Capabilities ◽  
Resolution Imaging ◽  
Successional Stages ◽  
Almost All

ABSTRACTMicrobial community succession is a fundamental process that effects underlying functions of almost all ecosystems; yet the roles and fates of the most abundant colonizers are poorly understood. Does early abundance spur long term persistence? How do deterministic and stochastic processes influence the roles of founder species? We performed a succession experiment within a hypersaline microbial mat ecosystem to investigate how ecological processes contributed to the turnover of founder species. Bacterial and micro-eukaryotic founder species were identified from primary succession and tracked through a defined maturation period using 16S and 18S rRNA gene amplicon sequencing in combination with high resolution imaging that utilized stable isotope tracers to evaluate basic functional capabilities. The majority of the founder species did not maintain high relative abundances in later stages of succession. Turnover (versus nestedness) was the dominant process shaping the final community structure. We also asked if different ecological processes acted on bacteria versus eukaryotes during successional stages and found that deterministic and stochastic forces corresponded more with eukaryote and bacterial colonization, respectively. Our results show that taxa from different kingdoms, that share habitat in the tight spatial confines of a biofilm, were influenced by different ecological forces and time scales of succession.

scholarly journals Local versus site-level effects of algae on coral microbial communities

2021 ◽  
Vol 8 (9) ◽  
pp. 210035
Author(s):  
Amy A. Briggs ◽  
Anya L. Brown ◽  
Craig W. Osenberg
Keyword(s):  
Microbial Communities ◽  
Spatial Scales ◽  
French Polynesia ◽  
Negative Effects ◽  
Ecological Processes ◽  
Antagonistic Effects ◽  
Alpha And Beta Diversity ◽  
Macroalgal Cover ◽  
Coral Microbiome ◽  
Turf Algae

Microbes influence ecological processes, including the dynamics and health of macro-organisms and their interactions with other species. In coral reefs, microbes mediate negative effects of algae on corals when corals are in contact with algae. However, it is unknown whether these effects extend to larger spatial scales, such as at sites with high algal densities. We investigated how local algal contact and site-level macroalgal cover influenced coral microbial communities in a field study at two islands in French Polynesia, Mo'orea and Mangareva. At 5 sites at each island, we sampled prokaryotic microbial communities (microbiomes) associated with corals, macroalgae, turf algae and water, with coral samples taken from individuals that were isolated from or in contact with turf or macroalgae. Algal contact and macroalgal cover had antagonistic effects on coral microbiome alpha and beta diversity. Additionally, coral microbiomes shifted and became more similar to macroalgal microbiomes at sites with high macroalgal cover and with algal contact, although the microbial taxa that changed varied by island. Our results indicate that coral microbiomes can be affected by algae outside of the coral's immediate vicinity, and local- and site-level effects of algae can obscure each other's effects when both scales are not considered.

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