scholarly journals Rapid and Stable Microbial Community Assembly in the Headwaters of a Third-Order Stream

2019 ◽  
Vol 85 (11) ◽  
Author(s):  
Morgan E. Teachey ◽  
Jacob M. McDonald ◽  
Elizabeth A. Ottesen
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Community Assembly ◽  
Fine Scale ◽  
Third Order ◽  
Order Stream ◽  
Bacterioplankton Community ◽  
Small Streams ◽  
Temporal And Spatial ◽  
Over Time

ABSTRACTSmall streams and their headwaters are key sources of microbial diversity in fluvial systems and serve as an entry point for bacteria from surrounding environments. Community assembly processes occurring in these streams shape downstream population structure and nutrient cycles. To elucidate the development and stability of microbial communities along the length of a first- through third-order stream, fine-scale temporal and spatial sampling regimes were employed along McNutt Creek in Athens, GA, USA. 16S rRNA amplicon libraries were constructed from samples collected on a single day from 19 sites spanning the first 16.76 km of the stream. To provide context for this spatial study and evaluate temporal variability, selected sites at the stream’s upper, mid, and lower reaches were sampled daily for 5 days preceding and following the spatial study. In a second study, three sites at and near the creek’s headwaters were sampled daily for 11 days to understand initial bacterioplankton community assembly. Both studies revealed decreasing alpha and beta diversity with increasing downstream distance. These trends were accompanied by the enrichment of a small fraction of taxa found at low abundance in headwater-proximal sites. Similar sets of taxa consistently increased in relative abundance in downstream samples over time scales ranging from 1 day to 1 year, many of which belong to clades known to be abundant in freshwater environments. These results underpin the importance of headwaters as the site of rapid in-stream selection that results in the reproducible establishment of a highly stable community of freshwater riverine bacteria.IMPORTANCEHeadwater streams are critical introduction points of microbial diversity for larger connecting rivers and play key roles in the establishment of taxa that partake in in-stream nutrient cycling. We examined the microbial community composition of a first- through third-order stream using fine-scale temporal and spatial regimes. Our results show that the bacterioplankton community develops rapidly and predictably from the headwater population with increasing total stream length. Along the length of the stream, the microbial community exhibits substantial diversity loss and enriches repeatedly for select taxa across days and years, although the relative abundances of individual taxa vary over time and space. This repeated enrichment of a stable stream community likely contributes to the stability and flexibility of downstream communities.

scholarly journals Rapid and stable microbial community assembly in the headwaters of third-order stream

2018 ◽  
Author(s):  
Morgan E. Teachey ◽  
Jacob M. McDonald ◽  
Elizabeth A. Ottesen
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Community Assembly ◽  
Fine Scale ◽  
Third Order ◽  
Order Stream ◽  
Bacterioplankton Community ◽  
Small Streams ◽  
Temporal And Spatial ◽  
Over Time

AbstractSmall streams and their headwaters are a key source of microbial diversity in fluvial systems and serve as an entry point for bacteria from the surrounding landscape. Community assembly processes occurring in these streams shape downstream population structure and nutrient cycles. To elucidate the development and stability of microbial communities along the length of a first through third order stream, fine-scale temporal and spatial sampling regimes were employed along McNutt Creek in Athens, Georgia, USA. 16S rRNA gene libraries were constructed from samples collected on a single day from 19 sites spanning the first 16.76 km of the stream. Selected sites at the upper, mid, and lower reaches of the stream were sampled daily for 11 days to evaluate community variability over time. In a second study, sites at and near the creek’s headwaters were sampled daily for 11 days to understand the initial stages of bacterioplankton community assembly. In all studies, we observed decreasing alpha and beta diversity with increasing downstream distance. These trends were accompanied by the enrichment of a small fraction of taxa found at low abundance in the furthest-upstream environments. Similar sets of taxa consistently increased significantly in relative abundance in downstream samples over time scales ranging from 1 day to 1 year, many of which belong to microbial clades known to be abundant in freshwater environments. These results underpin the importance of headwaters as the site of rapid in-stream selection that results in the reproducible establishment of a highly stable community of freshwater riverine bacteria.ImportanceHeadwater streams are critical introduction points of microbial diversity for larger connecting rivers and play key roles in the establishment of taxa that partake in in-stream nutrient cycling. We examined microbial community composition of a first- through third-order stream using fine-scale temporal and spatial regimes. Our results show that the bacterioplankton community develops rapidly and predictably from the headwater population with increasing total stream length. Along the length of the stream, the microbial community exhibits substantial diversity loss and enriches repeatedly for select taxa across days and years, although the relative abundances of individual taxa vary over time and space. This repeated enrichment of a stable stream community likely contributes to the stability and flexibility of downstream communities.

scholarly journals Stochastic Assembly Leads to Alternative Communities with Distinct Functions in a Bioreactor Microbial Community

mBio ◽  
2013 ◽  
Vol 4 (2) ◽  
Author(s):  
Jizhong Zhou ◽  
Wenzong Liu ◽  
Ye Deng ◽  
Yi-Huei Jiang ◽  
Kai Xue ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Diversity ◽  
Microbial Community Structure ◽  
Community Assembly ◽  
Ecosystem Functioning ◽  
Dominant Role ◽  
Microbial Biodiversity ◽  
Stochastic Assembly

ABSTRACTThe processes and mechanisms of community assembly and its relationships to community functioning are central issues in ecology. Both deterministic and stochastic factors play important roles in shaping community composition and structure, but the connection between community assembly and ecosystem functioning remains elusive, especially in microbial communities. Here, we used microbial electrolysis cell reactors as a model system to examine the roles of stochastic assembly in determining microbial community structure and functions. Under identical environmental conditions with the same source community, ecological drift (i.e., initial stochastic colonization) and subsequent biotic interactions created dramatically different communities with little overlap among 14 identical reactors, indicating that stochastic assembly played dominant roles in determining microbial community structure. Neutral community modeling analysis revealed that deterministic factors also played significant roles in shaping microbial community structure in these reactors. Most importantly, the newly formed communities differed substantially in community functions (e.g., H2production), which showed strong linkages to community structure. This study is the first to demonstrate that stochastic assembly plays a dominant role in determining not only community structure but also ecosystem functions. Elucidating the links among community assembly, biodiversity, and ecosystem functioning is critical to understanding ecosystem functioning, biodiversity preservation, and ecosystem management.IMPORTANCEMicroorganisms are the most diverse group of life known on earth. Although it is well documented that microbial natural biodiversity is extremely high, it is not clear why such high diversity is generated and maintained. Numerous studies have established the roles of niche-based deterministic factors (e.g., pH, temperature, and salt) in shaping microbial biodiversity, the importance of stochastic processes in generating microbial biodiversity is rarely appreciated. Moreover, while microorganisms mediate many ecosystem processes, the relationship between microbial diversity and ecosystem functioning remains largely elusive. Using a well-controlled laboratory system, this study provides empirical support for the dominant role of stochastic assembly in creating variations of microbial diversity and the first explicit evidence for the critical role of community assembly in influencing ecosystem functioning. The results presented in this study represent important contributions to the understanding of the mechanisms, especially stochastic processes, involved in shaping microbial biodiversity.

scholarly journals A quantitative framework reveals ecological drivers of grassland microbial community assembly in response to warming

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Daliang Ning ◽  
Mengting Yuan ◽  
Linwei Wu ◽  
Ya Zhang ◽  
Xue Guo ◽  
...  
Keyword(s):  
Animal Ecology ◽  
Microbial Community ◽  
Community Assembly ◽  
Null Model ◽  
High Accuracy ◽  
Relative Importance ◽  
Experimental Warming ◽  
Community Based ◽  
Microbial Community Assembly ◽  
Over Time

Abstract Unraveling the drivers controlling community assembly is a central issue in ecology. Although it is generally accepted that selection, dispersal, diversification and drift are major community assembly processes, defining their relative importance is very challenging. Here, we present a framework to quantitatively infer community assembly mechanisms by phylogenetic bin-based null model analysis (iCAMP). iCAMP shows high accuracy (0.93–0.99), precision (0.80–0.94), sensitivity (0.82–0.94), and specificity (0.95–0.98) on simulated communities, which are 10–160% higher than those from the entire community-based approach. Application of iCAMP to grassland microbial communities in response to experimental warming reveals dominant roles of homogeneous selection (38%) and ‘drift’ (59%). Interestingly, warming decreases ‘drift’ over time, and enhances homogeneous selection which is primarily imposed on Bacillales. In addition, homogeneous selection has higher correlations with drought and plant productivity under warming than control. iCAMP provides an effective and robust tool to quantify microbial assembly processes, and should also be useful for plant and animal ecology.

scholarly journals Prokaryotic Diversity in Mangrove Sediments across Southeastern China Fundamentally Differs from That in Other Biomes

mSystems ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Cui-Jing Zhang ◽  
Jie Pan ◽  
Chang-Hai Duan ◽  
Yong-Ming Wang ◽  
Yang Liu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Community Assembly ◽  
Alpha Diversity ◽  
Mean Annual Precipitation ◽  
Mangrove Sediments ◽  
Southeastern China ◽  
Deterministic Process ◽  
Deterministic Processes ◽  
Microbial Community Assembly

ABSTRACT Mangroves, as a blue carbon reservoir, provide an environment for a variety of microorganisms. Mangroves lie in special locations connecting coastal and estuarine areas and experience fluctuating conditions, which are expected to intensify with climate change, creating a need to better understand the relative roles of stochastic and deterministic processes in shaping microbial community assembly. Here, a study of microbial communities inhabiting mangrove sediments across southeastern China, spanning mangroves in six nature reserves, was conducted. We performed high-throughput DNA sequencing of these samples and compared them with data of 1,370 sediment samples collected from the Earth Microbiome Project (EMP) to compare the microbial diversity of mangroves with that of other biomes. Our results showed that prokaryotic alpha diversity in mangroves was significantly higher than that in other biomes and that microbial beta diversity generally clustered according to biome types. The core operational taxonomic units (OTUs) in mangroves were mostly assigned to Gammaproteobacteria, Deltaproteobacteria, Chloroflexi, and Euryarchaeota. The majority of beta nearest-taxon index values were higher than 2, indicating that community assembly in mangroves was better explained through a deterministic process than through a stochastic process. Mean annual precipitation (MAP) and total organic carbon (TOC) were main deterministic factors explaining variation in the microbial community. This study fills a gap in addressing the unique microbial diversity of mangrove ecosystems and their microbial community assembly mechanisms. IMPORTANCE Understanding the underlying mechanisms of microbial community assembly patterns is a vital issue in microbial ecology. Mangroves, as an important and special ecosystem, provide a unique environment for examining the relative importance of stochastic and deterministic processes. We made the first global-scale comparison and found that microbial diversity was significantly different in mangrove sediments compared to that of other biomes. Furthermore, our results suggest that a deterministic process is more important in shaping microbial community assembly in mangroves.

scholarly journals Stochastic changes over time and not founder effects drive cage effects in microbial community assembly in a mouse model

2013 ◽  
Vol 7 (11) ◽  
pp. 2116-2125 ◽  
Author(s):  
Jonathan McCafferty ◽  
Marcus Mühlbauer ◽  
Raad Z Gharaibeh ◽  
Janelle C Arthur ◽  
Ernesto Perez-Chanona ◽  
...  
Keyword(s):  
Microbial Community ◽  
Mouse Model ◽  
Community Assembly ◽  
Founder Effects ◽  
Changes Over Time ◽  
Microbial Community Assembly ◽  
Cage Effects ◽  
Over Time

scholarly journals Deciphering Centimeter-Scale Microbial Biogeographic Patterns and Community Assembly Processes From A 3D Perspective

2020 ◽  
Author(s):  
Ran Xue ◽  
Kankan Zhao ◽  
Xiuling Yu ◽  
Erinne Stirling ◽  
Shan Liu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Variable Selection ◽  
Microbial Diversity ◽  
Community Assembly ◽  
Sampling Strategy ◽  
Sampling Scheme ◽  
Ecological Processes ◽  
Soil Matrix ◽  
Biogeographic Patterns ◽  
2D To 3D

Abstract Background: Revealing the effects of multi-dimensional spatial distribution on microorganisms is crucial for the further understanding of microbial diversity, turnover and ecological processes. However, microbial community assembly and the factors that shape it are still unknown from a three dimensional (3D) perspective. Here, a 3D model was created by performing an exhaustive sampling strategy to a 4x4x4 soil matrix. We examined the dynamics of microbial diversity, biogeographic patterns and microbial assembly processes when transfroming sampling scheme from 2D to 3D.Results: Our results indicated that dispersion of microbial community and significance of distance decay relationship was higher in the 3D compared with 2D sampling scheme, suggesting increased microbial turnover when transforming the model from 2D to 3D. Only a small fraction of community variation can be explained by environmental, spatial factors and spatial canonical axes, possibly due to unmeasured environmental variables. The assembly of microbial community was dominated by deterministic processes that shifted from homogeneous selection to variable selection as we transformed the model from 2D to 3D. The importance of stochasticity increased when homogeneous and variable selection processes were well balanced. However, heterogeneity of existing environmental and spatial variables failed to explain the dynamics of community assembly.Conclusions: Our study revealed significant dynamics of microbial diversity and assembly processes when assessed from 2D and 3D perspectives. As microorganisms are spatially distributed in soil, this spatial dependent diversity and assembly suggests that microbial ecological questions need to be considered in more dimensions than they usually are. Further, new models that integrate all data sets are still needed to disengle the microbial processes in multiple dimensions.

scholarly journals Hierarchical control of microbial community assembly

2021 ◽  
Author(s):  
Sammy Pontrelli ◽  
Rachel Szabo ◽  
Shaul Pollak ◽  
Julia A Schwartzman ◽  
Daniela Ledezma-Tejeida ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Resource Availability ◽  
Community Assembly ◽  
Hierarchical Control ◽  
Complex Forms ◽  
Chain Lengths ◽  
Changes Over Time ◽  
Microbial Community Assembly ◽  
Over Time

Metabolic processes that fuel the growth of heterotrophic microbial communities are initiated by specialized biopolymer degraders that decompose complex forms of organic matter. It is unclear, however, to what extent degraders control the downstream assembly of the community that follows polymer breakdown. Investigating a model marine microbial community that degrades chitin, we show that chitinases secreted by different degraders produce oligomers of specific chain lengths that not only select for specialized consumers but also influence the metabolites secreted by these consumers into a shared resource pool. Each species participating in the breakdown cascade exhibits unique hierarchical preferences for substrates, which underlies the sequential colonization of metabolically distinct groups as resource availability changes over time. By identifying the metabolic underpinnings of microbial community assembly, we reveal a hierarchical crossfeeding structure that allows biopolymer degraders to shape the dynamics of community assembly.

scholarly journals Disturbance and recovery: a synthesis of microbial community reassembly following disturbance across realms

2021 ◽  
Author(s):  
Stephanie Jurburg ◽  
Shane Blowes ◽  
Ashley Shade ◽  
Nico Eisenhauer ◽  
Jonathan Chase
Keyword(s):  
Time Series ◽  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Community Assembly ◽  
Disturbance And Recovery ◽  
Microbial Community Assembly ◽  
Community Reassembly ◽  
Over Time

Disturbances alter the diversity and composition of microbial communities, but whether microbiomes from different environments exhibit similar degrees of resistance or rates of recovery has not been evaluated. Here, we synthesized 86 time series of disturbed mammalian, aquatic, and soil microbiomes to examine how the recovery of microbial richness and community composition differed after disturbance. We found no general patterns in compositional variance (i.e., dispersion) in any microbiomes over time. Only mammalian microbiomes consistently exhibited decreases in richness following disturbance. Importantly, they tended to recover this richness, but not their composition, over time. In contrast, aquatic microbiomes tended to diverge from their pre-disturbance composition following disturbance. By synthesizing microbiome responses across environments, our study aids in the reconciliation of disparate microbial community assembly frameworks, and highlights the role of the environment in microbial community reassembly following disturbance.

scholarly journals Soil multifunctionality is negatively related to microbial community stochasticity in restored grasslands

2021 ◽  
Author(s):  
Yongyong Zhang ◽  
Monika Resch ◽  
Martin Schuetz ◽  
Ziyan Liao ◽  
Beat Frey ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Fungal Community ◽  
Community Assembly ◽  
Soil Microbial Community ◽  
Ecosystem Functions ◽  
Grassland Restoration ◽  
Soil Microbial ◽  
Topsoil Removal ◽  
The Relationship

It is generally assumed that there is a relationship between microbial diversity and multiple ecosystem functions. Although it is indisputable that microbial diversity is controlled by stochastic and deterministic ecological assembly processes, the relationship between these processes and soil multifunctionality (SMF) remains less clear. In this study, we examined how different grassland restoration treatments, namely harvest only, topsoil removal and topsoil removal plus propagule addition, affected i) soil bacterial and fungal community stochasticity, ii) SMF, and iii) the relationship between community stochasticity and SMF. Results showed that soil microbial community stochasticity decreased in all the three restoration treatments, while SMF increased. Soil multifunctionality was found to be significantly and negatively correlated with soil microbial community stochasticity. Plant diversity and plant C/N indirectly influenced SMF by regulating the microbial community stochasticity. Our findings provide empirical evidence that when deterministic community assembly processes dominate in soils, then higher microbial functioning is expected.

scholarly journals Salinity Is a Key Determinant for Soil Microbial Communities in a Desert Ecosystem

mSystems ◽  
2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Kaoping Zhang ◽  
Yu Shi ◽  
Xiaoqing Cui ◽  
Ping Yue ◽  
Kaihui Li ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Community Assembly ◽  
Salinity Gradient ◽  
Soil Microbial Communities ◽  
Desert Ecosystem ◽  
Desert Ecosystems ◽  
Soil Microbial ◽  
Deterministic Processes ◽  
Community Dissimilarity

ABSTRACT Soil salinization is a growing environmental problem caused by both natural and human activities. Excessive salinity in soil suppresses growth, decreases species diversity, and alters the community composition of plants; however, the effect of salinity on soil microbial communities is poorly understood. Here, we characterize the soil microbial community along a natural salinity gradient in Gurbantunggut Desert, Northwestern China. Microbial diversity linearly decreased with increases in salinity, and community dissimilarity significantly increased with salinity differences. Soil salinity showed a strong effect on microbial community dissimilarity, even after controlling for the effects of spatial distance and other environmental variables. Microbial phylotypes (n = 270) belonging to Halobacteria, Nitriliruptoria, [Rhodothermi], Gammaproteobacteria, and Alphaproteobacteria showed a high-salinity niche preference. Out of nine potential phenotypes predicted by BugBase, oxygen-related phenotypes showed a significant relationship with salinity content. To explore the community assembly processes, we used null models of within-community (nearest-taxon index [NTI]) and between-community (βNTI) phylogenetic composition. NTI showed a significantly negative relationship with salinity, suggesting that the microbial community was less phylogenetically clustered in more-saline soils. βNTI, the between-community analogue of NTI, showed that deterministic processes have overtaken stochastic processes across all sites, suggesting the importance of environmental filtering in microbial community assembly. Taken together, these results suggest the importance of salinity in soil microbial community composition and assembly processes in a desert ecosystem. IMPORTANCE Belowground microorganisms are indispensable components for nutrient cycling in desert ecosystems, and understanding how they respond to increased salinity is essential for managing and ameliorating salinization. Our sequence-based data revealed that microbial diversity decreased with increasing salinity, and certain salt-tolerant phylotypes and phenotypes showed a positive relationship with salinity. Using a null modeling approach to estimate microbial community assembly processes along a salinity gradient, we found that salinity imposed a strong selection pressure on the microbial community, which resulted in a dominance of deterministic processes. Studying microbial diversity and community assembly processes along salinity gradients is essential in understanding the fundamental ecological processes in desert ecosystems affected by salinization.

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