scholarly journals Biogeographic Patterns and Assembly Mechanisms of Bacterial Communities Differ Between Habitat Generalists and Specialists Across Elevational Gradients

2019 ◽  
Vol 10 ◽  
Author(s):  
Zhengming Luo ◽  
Jinxian Liu ◽  
Pengyu Zhao ◽  
Tong Jia ◽  
Cui Li ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Elevational Gradients ◽  
Biogeographic Patterns ◽  
Habitat Generalists

Integrated biogeography and assembly process of planktonic and sedimentary bacterial communities in the Yangtze River

2020 ◽  
Author(s):  
Tang Liu ◽  
Jiawen Wang ◽  
Shufeng Liu ◽  
Qian Chen ◽  
Chunmiao Zheng ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Yangtze River ◽  
Selection Process ◽  
Anthropogenic Impacts ◽  
Spatiotemporal Pattern ◽  
Assembly Process ◽  
The Yangtze River ◽  
Species Sorting ◽  
Biogeographic Patterns ◽  
Water And Sediment

<p>Bacterial communities are essential to the biogeochemical cycle in riverine ecosystems. However, the integrated biogeography and assembly process of planktonic and sedimentary bacterial communities in large rivers is still poorly understood. Here, the study provided the spatiotemporal pattern of bacterial communities in the Yangtze River of 4300 km continuum, which is the largest river in Asia. We found that the taxa in sediments are the main contributors to the bacterial diversity of the river ecosystem since sediments sub-group took 98.8% of the total 38, 904 Operational Taxonomic Units (OTUs) observed in 280 samples. Seasonal differences in bacterial communities were statistically significant in water, whereas bacterial communities in both water and sediment were geographically clustered according to five types of landforms: mountain, foothill, basin, foothill-mountain, and plain. Interestingly, the presence of two huge dams resulted in a drastic fall of bacterial taxa in sediment immediately downstream due to severe riverbed scouring. The integrity of the biogeography was satisfactorily interpreted by the combination of neutral and species sorting perspectives in meta-community theory for bacterial communities in flowing water and sediment. Although deterministic process had dominant influence on assembly processes in water and sediment communities, homogeneous selection was the main contributor in water, while combination of homogeneous selection and variable selection contributed selection process in sediment. In addition, homogenizing dispersal played more important role in community assembly process in sediment than water. Our study fills a gap in understanding of biogeography and assembly process of bacterial communities in one of the world’s largest river and highlights the importance of both planktonic and sedimentary communities to the integrity of bacterial biogeographic patterns in a river subject to varying natural and anthropogenic impacts.</p>

scholarly journals Different community assembly mechanisms underlie similar biogeography of bacteria and microeukaryotes in Tibetan lakes

2020 ◽  
Vol 96 (6) ◽  
Author(s):  
Keshao Liu ◽  
Yongqin Liu ◽  
Anyi Hu ◽  
Feng Wang ◽  
Yuying Chen ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Environmental Filtering ◽  
Dispersal Limitation ◽  
Dispersal Ability ◽  
Similar Distribution ◽  
The Tibetan Plateau ◽  
Biogeographic Patterns ◽  
Geographic Patterns ◽  
Related Process

ABSTRACT Geographic patterns of bacteria and microeukaryotes have attracted increasing attention. However, mechanisms underlying geographic patterns in the community composition of both microbial groups are still poorly resolved. In particular, knowledge of whether bacterial communities and microeukaryotic communities are subject to the same or different assembly mechanisms is still limited. In this study, we investigated the biogeographic patterns of bacterial and microeukaryotic communities of 23 lakes on the Tibetan Plateau and quantified the relative influence of assembly mechanisms in shaping both microbial communities. Results showed that water salinity was the major driving force in controlling the community structures of bacteria and microeukaryotes. Although bacterial and microeukaryotic communities exhibited similar distance-decay patterns, the bacterial communities were mainly governed by environmental filtering (a niche-related process), whereas microeukaryotic communities were strongly driven by dispersal limitation (a neutral-related process). Furthermore, we found that bacteria exhibited wider niche breadths and higher dispersal ability but lower community stabilities than microeukaryotes. The similar distribution patterns but contrasting assembly mechanisms effecting bacteria and microeukaryotes resulted from the differences in dispersal ability and community stability. Our results highlight the importance of considering organism types in studies of the assembly mechanisms that shape microbial communities in microbial ecology.

scholarly journals Soil Bacterial Communities Exhibit Strong Biogeographic Patterns at Fine Taxonomic Resolution

mSystems ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Sean K. Bay ◽  
Melodie A. McGeoch ◽  
Osnat Gillor ◽  
Nimrod Wieler ◽  
David J. Palmer ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Taxonomic Resolution ◽  
Rrna Gene ◽  
Data Sets ◽  
Soil Biodiversity ◽  
Biogeographic Patterns ◽  
Soil Bacterial Communities ◽  
Rare Biosphere ◽  
Local Soil ◽  
Soil Bacterial

ABSTRACT Bacteria have been inferred to exhibit relatively weak biogeographic patterns. To what extent such findings reflect true biological phenomena or methodological artifacts remains unclear. Here, we addressed this question by analyzing the turnover of soil bacterial communities from three data sets. We applied three methodological innovations: (i) design of a hierarchical sampling scheme to disentangle environmental from spatial factors driving turnover; (ii) resolution of 16S rRNA gene amplicon sequence variants to enable higher-resolution community profiling; and (iii) application of the new metric zeta diversity to analyze multisite turnover and drivers. At fine taxonomic resolution, rapid compositional turnover was observed across multiple spatial scales. Turnover was overwhelmingly driven by deterministic processes and influenced by the rare biosphere. The communities also exhibited strong distance decay patterns and taxon-area relationships, with z values within the interquartile range reported for macroorganisms. These biogeographical patterns were weakened upon applying two standard approaches to process community sequencing data: clustering sequences at 97% identity threshold and/or filtering the rare biosphere (sequences lower than 0.05% relative abundance). Comparable findings were made across local, regional, and global data sets and when using shotgun metagenomic markers. Altogether, these findings suggest that bacteria exhibit strong biogeographic patterns, but these signals can be obscured by methodological limitations. We advocate various innovations, including using zeta diversity, to advance the study of microbial biogeography. IMPORTANCE It is commonly thought that bacterial distributions show lower spatial variation than for multicellular organisms. In this article, we present evidence that these inferences are artifacts caused by methodological limitations. Through leveraging innovations in sampling design, sequence processing, and diversity analysis, we provide multifaceted evidence that bacterial communities in fact exhibit strong distribution patterns. This is driven by selection due to factors such as local soil characteristics. Altogether, these findings suggest that the processes underpinning diversity patterns are more unified across all domains of life than previously thought, which has broad implications for the understanding and management of soil biodiversity.

scholarly journals Geographic Patterns of Bacterioplankton among Lakes of the Middle and Lower Reaches of the Yangtze River Basin, China

2020 ◽  
Vol 86 (6) ◽  
Author(s):  
Chengrong Bai ◽  
Jian Cai ◽  
Lei Zhou ◽  
Xingyu Jiang ◽  
Yang Hu ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Yangtze River ◽  
Yangtze River Basin ◽  
Assembly Process ◽  
Wet Season ◽  
Rare Taxa ◽  
Biogeographic Patterns ◽  
Geographic Patterns ◽  
Lower Yangtze ◽  
Rare Bacteria

ABSTRACT The revolution of molecular techniques has revealed that the composition of natural bacterial communities normally includes a few abundant taxa and many rare taxa. Unraveling the mechanisms underlying the spatial assembly process of both abundant and rare bacterial taxa has become a central goal in microbial ecology. Here, we used high-throughput sequencing to explore geographic patterns and the relative importance of ecological processes in the assembly of abundant and rare bacterial subcommunities from 25 lakes across the middle and lower reaches of Yangtze River basin (MLYB), located in Southeast China, where most of the lakes are interconnected by river networks. We found similar biogeographic patterns of abundant and rare subcommunities which could significantly distinguish the community compositions of the two lake groups that were far from each other but which could not distinguish the community compositions of the nearby lakes. Both abundant and rare bacteria followed a strong distance-decay relationship. These findings suggest that the interconnectivity between lakes homogenizes the bacterial communities in local areas, and the abundant and rare taxa therein may be affected by the same ecological process. In addition, based on the measured environmental variables, the deterministic processes explain a small fraction of variation within both abundant and rare subcommunities, while both neutral and null models revealed a high stochasticity ratio for the spatial distribution patterns of both abundant and rare taxa. These findings indicate that the stochastic processes exhibited a greater influence on both abundant and rare bacterial subcommunity assemblies among interconnected lakes. IMPORTANCE The middle and lower Yangtze Plain is a typical floodplain in which many lakes connect with each other, especially in the wet season. More importantly, with the frequent change of regional water level in the wet season, there is a mutual hydrodynamic exchange among these lakes. The microbial biogeography among these interconnected lakes is still poorly understood. This study aims to unravel the mechanisms underlying the assembly process of abundant and rare bacteria among the interconnected lakes in the middle and lower Yangtze Plain. Our findings will provide a deeper understanding of the biogeographic patterns of rare and abundant bacterial taxa and their determined processes among interconnected aquatic habitats.

scholarly journals Geographical Distribution of Iron Redox Cycling Bacterial Community in Peatlands: Distinct Assemble Mechanism Across Environmental Gradient

2021 ◽  
Vol 12 ◽  
Author(s):  
Liang Yang ◽  
Ming Jiang ◽  
Yuanchun Zou ◽  
Lei Qin ◽  
Yingyi Chen
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Geographic Distance ◽  
Null Model ◽  
Redox Cycling ◽  
Biogeographic Patterns ◽  
Deterministic Processes ◽  
Iron Redox ◽  
Soil And Water

Microbial-mediated iron (Fe) oxidation and reduction greatly contribute to the biogeochemistry and mineralogy of ecosystems. However, knowledge regarding the composition and distribution patterns of iron redox cycling bacteria in peatlands remains limited. Here, using high-throughput sequencing, we compared biogeographic patterns and assemblies of the iron redox cycling bacterial community between soil and water samples obtained from different types of peatland across four regions in Northeast China. A total of 48 phylotypes were identified as potential iron redox bacteria, which had greater than 97% similarity with Fe(II)-oxidizing bacteria (FeOB) and Fe(III)-reducing bacteria (FeRB). Among them, Rhodoferax, Clostridium, Geothrix, Sideroxydans, Geobacter, Desulfovibrio, and Leptothrix could be used as bioindicators in peatlands for characterizing different hydrological conditions and nutrient demands. Across all samples, bacterial communities associated with iron redox cycling were mainly affected by pH, dissolved organic carbon (DOC), and Fe2+. Distance–decay relationship (DDR) analysis indicated that iron redox cycling bacterial communities in soil, but not in water, were highly correlated with geographic distance. Additionally, null model analysis revealed that stochastic processes substituted deterministic processes from minerotrophic fens to ombrotrophic bogs in soils, whereas deterministic processes were dominant in water. Overall, these observations suggest that bacteria involved in iron redox cycling are widespread in diverse habitats and exhibit distinct patterns of distribution and community assembly mechanisms between soil and water in peatlands.

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