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 Vertical stratification of microbial communities in woody plants

2021 ◽  
Author(s):  
Mohammad Bahram ◽  
Kati Kings ◽  
Mari Pent ◽  
Sergei Polme ◽  
Daniyal Gohar ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Community Assembly ◽  
Boreal Forests ◽  
Fungal Endophytes ◽  
Environmental Filtering ◽  
Dispersal Limitation ◽  
Distribution Patterns ◽  
Fungal Communities ◽  
Spatial Distance ◽  
Related Factors

Bacterial and fungal endophytes form diverse communities and contribute to the performance and health of their host plants. Recent evidence suggests that both host related factors and environmental conditions determine the community structure of plant endophytes. Yet, we know little about their distribution patterns, and underlying community assembly mechanisms across plant compartments. Here we analysed the structure of bacterial and fungal communities associated with tree compartments as well as their underlying soils across 12 tree individuals in boreal forests. We found that the structure of bacterial and fungal communities depends more strongly on the vertical location of tree compartments rather than the locality, species, and individuals of host trees. Microbial communities showed much stronger host specificity in aboveground than belowground compartments. While having lower compartment community variability compared to fungi, bacterial communities were markedly more distinct between below- and aboveground components but not between hosts, reflecting the greater importance of environmental filtering rather than dispersal limitation and host identity in their community assembly. Our data suggest that spatial distance from soil as a major microbiome source contributes to the formation of microbiomes in plants, and that bacterial and fungal communities may follow contrasting assembly processes.

scholarly journals Dynamic and Assembly of Benthic Bacterial Community in an Industrial-Scale In-Pond Raceway Recirculating Culture System

2021 ◽  
Vol 12 ◽  
Author(s):  
Yiran Hou ◽  
Bing Li ◽  
Gangchun Xu ◽  
Da Li ◽  
Chengfeng Zhang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Stochastic Processes ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Culture System ◽  
Null Model ◽  
Dispersal Limitation ◽  
Industrial Scale ◽  
Ecological Processes ◽  
Benthic Microbial Communities

To reduce water utilization, limit environmental pollution, and guarantee aquatic production and quality, the in-pond raceway recirculating culture system (IPRS) has been developed and is widely used. The effectiveness and sustainability of IPRSs rely on a good understanding of the ecological processes related to bacterial communities in the purification area. In this study, we investigated the dynamics and assembly mechanisms of benthic bacterial communities in the purification area of an industrial-scale IRPS. We found significant temporal and spatial variations in the sediment characteristics and benthic bacterial communities of the IPRS, although correlation analyses revealed a very limited relationship between them. Among the different culture stages, we identified numerous benthic bacteria with different abundances. Abundances of the phyla Bacteroidota and Desulfobacterota decreased whereas those of Myxococcota and Gemmatimonadota increased as the culture cycle progressed. Co-occurrence networks revealed that the bacterial community was less complex but more stable in the IPRS at the final stage compared with the initial stage. The neutral community model (NCM) showed that stochastic processes were the dominant ecological processes shaping the assembly of the benthic bacterial community. The null model suggested that homogenizing dispersal was more powerful than dispersal limitation and drift in regulating the assembly of the community. These findings indicate that the benthic microbial communities in purification areas of the IPRS may not be affected by the deposited wastes, and a more stable benthic microbial communities were formed and mainly driven by stochastic processes. However, the benthic microbial communities in the purification area at the end of the culturing stage was characterized by potentially inhibited organic matter degradation and carbon and sulfur cycling abilities, which was not corresponding to the purification area’s function. From this point on, the IPRS, especially the purification area was needed to be further optimized and improved.

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 Climate change will lead to pronounced shifts in the diversity of soil microbial communities

2017 ◽  
Author(s):  
Joshua Ladau ◽  
Yu Shi ◽  
Xin Jing ◽  
Jin-Sheng He ◽  
Litong Chen ◽  
...  
Keyword(s):  
Climate Change ◽  
North America ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Soil Bacteria ◽  
Soil Microbial Communities ◽  
Climatic Conditions ◽  
Climate Impacts ◽  
The Tibetan Plateau ◽  
Soil Microbial

ABSTRACTSoil bacteria are key to ecosystem function and maintenance of soil fertility. Leveraging associations of current geographic distributions of bacteria with historic climate, we predict that soil bacterial diversity will increase across the majority (~75%) of the Tibetan Plateau and northern North America if bacterial communities equilibrate with existing climatic conditions. This prediction is possible because the current distributions of soil bacteria have stronger correlations with climate from ~50 years ago than with current climate. This lag is likely associated with the time it takes for soil properties to adjust to changes in climate. The predicted changes are location specific and differ across bacterial taxa, including some bacteria that are predicted to have reductions in their distributions. These findings demonstrate the widespread influence that climate change will have on belowground diversity and highlight the importance of considering bacterial communities when assessing climate impacts on terrestrial ecosystems.IMPORTANCEThere have been many studies highlighting how plant and animal communities lag behind climate change, causing extinction and diversity debts that will slowly be paid as communities equilibrate. By virtue of their short generation times and dispersal abilities, soil bacteria might be expected to respond to climate change quickly and to be effectively in equilibrium with current climatic conditions. We found strong evidence to the contrary in Tibet and North America. These findings could significantly improve understanding of climate impacts on soil microbial communities.

scholarly journals Variation in denitrifying bacterial communities along a primary succession in the Hailuogou Glacier retreat area, China

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7356
Author(s):  
Yan Bai ◽  
Xiying Huang ◽  
Xiangrui Zhou ◽  
Quanju Xiang ◽  
Ke Zhao ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Community Composition ◽  
Bacterial Communities ◽  
Primary Succession ◽  
Abiotic Factors ◽  
Bacterial Community Composition ◽  
Living Environment ◽  
Available Phosphorus ◽  
The Tibetan Plateau ◽  
Successional Stages

Background The Hailuogou Glacier is located at the Gongga Mountain on the southeastern edge of the Tibetan Plateau, and has retreated continuously as a result of global warming. The retreat of the Hailuogou Glacier has left behind a primary succession along soil chronosequences. Hailuogou Glacier’s retreated area provides an excellent living environment for the colonization of microbes and plants, making it an ideal model to explore plant successions, microbial communities, and the interaction of plants and microbes during the colonization process. However, to date, the density of the nitrogen cycling microbial communities remain unknown, especially for denitrifiers in the primary succession of the Hailuogou Glacier. Therefore, we investigated the structural succession and its driving factors for denitrifying bacterial communities during the four successional stages (0, 20, 40, and 60 years). Methods The diversity, community composition, and abundance of nosZ-denitrifiers were determined using molecular tools, including terminal restriction fragment length polymorphism and quantitative polymerase chain reactions (qPCR). Results nosZ-denitrifiers were more abundant and diverse in soils from successional years 20–60 compared to 0–5 years, and was highest in Site3 (40 years). The denitrifying bacterial community composition was more complex in older soils (40–60 years) than in younger soils (≤20 years). The terminal restriction fragments (T-RFs) of Azospirillum (90 bp) and Rubrivivax (95 bp) were dominant in soisl during early successional stages (0–20 years) and in the mature phase (40–60 years), respectively. Specific T-RFs of Bradyrhizobium (100 bp) and Pseudomonas (275 bp) were detected only in Site3 and Site4, respectively. Moreover, the unidentified 175 bp T-RFs was detected only in Site3. Of the abiotic factors that were measured in this study, soil available phosphorus, available potassium and denitrifying enzyme activity (DEA) correlated significantly with the community composition of nosZ-denitrifiers (P < 0.05 by Monte Carlo permutation test within RDA analysis).

scholarly journals Diversity and Dynamics of Seaweed Associated Microbial Communities Inhabiting the Lagoon of Venice

2020 ◽  
Vol 8 (11) ◽  
pp. 1657
Author(s):  
Abdul-Salam Juhmani ◽  
Alessandro Vezzi ◽  
Mohammad Wahsha ◽  
Alessandro Buosi ◽  
Fabio De Pascale ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Host Response ◽  
Environmental Parameters ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Nutrient Concentrations ◽  
Lagoon Of Venice ◽  
Anthropogenic Stressors ◽  
Rich Diversity

Seaweeds are a group of essential photosynthetic organisms that harbor a rich diversity of associated microbial communities with substantial functions related to host health and defense. Environmental and anthropogenic stressors may disrupt the microbial communities and their metabolic activity, leading to host physiological alterations that negatively affect seaweeds’ performance and survival. Here, the bacterial communities associated with one of the most common seaweed, Ulva laetevirens Areshough, were sampled over a year at three sites of the lagoon of Venice affected by different environmental and anthropogenic stressors. Bacterial communities were characterized through Illumina sequencing of the V4 hypervariable region of 16S rRNA genes. The study demonstrated that the seaweed associated bacterial communities at sites impacted by environmental stressors were host-specific and differed significantly from the less affected site. Furthermore, these communities were significantly distinct from those of the surrounding seawater. The bacterial communities’ composition was significantly correlated with environmental parameters (nutrient concentrations, dissolved oxygen saturation, and pH) across sites. This study showed that several more abundant bacteria on U. laetevirens at stressed sites belonged to taxa related to the host response to the stressors. Overall, environmental parameters and anthropogenic stressors were shown to substantially affect seaweed associated bacterial communities, which reflect the host response to environmental variations.

scholarly journals Environment drives high phylogenetic turnover among oceanic bacterial communities

2012 ◽  
Vol 8 (4) ◽  
pp. 562-566 ◽  
Author(s):  
Thomas Pommier ◽  
Emmanuel J. P. Douzery ◽  
David Mouillot
Keyword(s):  
Bacterial Communities ◽  
Environmental Gradient ◽  
Regional Scale ◽  
Environmental Filtering ◽  
Species Level ◽  
Geographical Distance ◽  
Abiotic Conditions ◽  
High Connectivity ◽  
Phylogenetic Lineages ◽  
Marine Microbial Communities

Although environmental filtering has been observed to influence the biodiversity patterns of marine bacterial communities, it was restricted to the regional scale and to the species level, leaving the main drivers unknown at large biogeographic scales and higher taxonomic levels. Bacterial communities with different species compositions may nevertheless share phylogenetic lineages, and phylogenetic turnover (PT) among those communities may be surprisingly low along any biogeographic or environmental gradient. Here, we investigated the relative influence of environmental filtering and geographical distance on the PT between marine bacterial communities living more than 8000 km apart in contrasted abiotic conditions. PT was high between communities and was more structured by local environmental factors than by geographical distance, suggesting the predominance of a lineage filtering process. Strong phenotype-environment mismatches observed in the ocean may surpass high connectivity between marine microbial communities.

scholarly journals Assembly processes of gastropod community change with horizontal and vertical zonation in ancient Lake Ohrid: a metacommunity speciation perspective

2016 ◽  
Vol 13 (10) ◽  
pp. 2901-2911 ◽  
Author(s):  
Torsten Hauffe ◽  
Christian Albrecht ◽  
Thomas Wilke
Keyword(s):  
Community Composition ◽  
Community Assembly ◽  
Environmental Filtering ◽  
Dispersal Limitation ◽  
Species Interaction ◽  
Relative Importance ◽  
Lake Depth ◽  
Ancient Lake ◽  
Lake Ohrid ◽  
Speciation Model

Abstract. The Balkan Lake Ohrid is the oldest and most diverse freshwater lacustrine system in Europe. However, it remains unclear whether species community composition, as well as the diversification of its endemic taxa, is mainly driven by dispersal limitation, environmental filtering, or species interaction. This calls for a holistic perspective involving both evolutionary processes and ecological dynamics, as provided by the unifying framework of the “metacommunity speciation model”.The current study used the species-rich model taxon Gastropoda to assess how extant communities in Lake Ohrid are structured by performing process-based metacommunity analyses. Specifically, the study aimed (1) to identifying the relative importance of the three community assembly processes and (2) to test whether the importance of these individual processes changes gradually with lake depth or discontinuously with eco-zone shifts.Based on automated eco-zone detection and process-specific simulation steps, we demonstrated that dispersal limitation had the strongest influence on gastropod community composition. However, it was not the exclusive assembly process, but acted together with the other two processes – environmental filtering and species interaction. The relative importance of the community assembly processes varied both with lake depth and eco-zones, though the processes were better predicted by the latter.This suggests that environmental characteristics have a pronounced effect on shaping gastropod communities via assembly processes. Moreover, the study corroborated the high importance of dispersal limitation for both maintaining species richness in Lake Ohrid (through its impact on community composition) and generating endemic biodiversity (via its influence on diversification processes). However, according to the metacommunity speciation model, the inferred importance of environmental filtering and biotic interaction also suggests a small but significant influence of ecological speciation. These findings contribute to the main goal of the Scientific Collaboration on Past Speciation Conditions in Lake Ohrid (SCOPSCO) deep drilling initiative – inferring the drivers of biotic evolution – and might provide an integrative perspective on biological and limnological dynamics in ancient Lake Ohrid.

scholarly journals Do soil bacterial communities respond differently to abrupt or gradual additions of copper?

2018 ◽  
Vol 95 (1) ◽  
Author(s):  
Michael McTee ◽  
Lorinda Bullington ◽  
Matthias C Rillig ◽  
Philip W Ramsey
Keyword(s):  
Heavy Metals ◽  
Soil Respiration ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Diversity Indices ◽  
Microbial Populations ◽  
Metal Concentrations ◽  
Soil Bacterial Communities ◽  
Bacterial Richness

ABSTRACTMany experiments that measure the response of microbial communities to heavy metals increase metal concentrations abruptly in the soil. However, it is unclear whether abrupt additions mimic the gradual and often long-term accumulation of these metals in the environment where microbial populations may adapt. In a greenhouse experiment that lasted 26 months, we tested whether bacterial communities and soil respiration differed between soils that received an abrupt or a gradual addition of copper or no copper at all. Bacterial richness and other diversity indices were consistently lower in the abrupt treatment compared to the ambient treatment that received no copper. The abrupt addition of copper yielded different initial bacterial communities than the gradual addition; however, these communities appeared to converge once copper concentrations were approximately equal. Soil respiration in the abrupt treatment was initially suppressed but recovered after four months. Afterwards, respiration in both the gradual and abrupt treatments wavered between being below or equal to the ambient treatment. Overall, our study indicates that gradual and abrupt additions of copper can yield similar bacterial communities and respiration, but these responses may drastically vary until copper concentrations are equal.

scholarly journals Lack of evidence for microbiota in the placental and fetal tissues of rhesus macaques

2020 ◽  
Author(s):  
Kevin R. Theis ◽  
Roberto Romero ◽  
Andrew D. Winters ◽  
Alan H. Jobe ◽  
Nardhy Gomez-Lopez
Keyword(s):  
Dna Sequencing ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Rhesus Macaques ◽  
Uterine Wall ◽  
Bacterial Burden ◽  
Multiple Modes ◽  
Fetal Tissues ◽  
Microbial Invasion ◽  
Cutibacterium Acnes

ABSTRACTThe prevailing paradigm in obstetrics has been the sterile womb hypothesis. However, some are asserting that the placenta, intra-amniotic environment, and fetus harbor microbial communities. The objective of this study was to determine if the fetal and placental tissues of rhesus macaques harbor viable bacterial communities. Fetal, placental, and uterine wall samples were obtained from cesarean deliveries without labor (∼130/166 days gestation). The presence of viable bacteria in the fetal intestine and placenta was investigated through culture. The bacterial burden and profile of the placenta, umbilical cord, and fetal brain, heart, liver, and colon were determined through quantitative real-time PCR and DNA sequencing. These data were compared with those of the uterine wall, as well as to negative and positive technical controls. Bacterial cultures of fetal and placental tissues yielded only a single colony of Cutibacterium acnes. This bacterium was detected at a low relative abundance (0.02%) in the 16S rRNA gene profile of the villous tree sample from which it was cultured, yet it was also identified in 12/29 background technical controls. The bacterial burden and profile of fetal and placental tissues did not exceed or differ from those of background technical controls. In contrast, the bacterial burden and profiles of positive controls exceeded and differed from those of background controls. Among the macaque samples, distinct microbial signals were limited to the uterine wall. Therefore, using multiple modes of microbiologic inquiry, there was not consistent evidence of viable bacterial communities in the fetal and placental tissues of rhesus macaques.IMPORTANCEMicrobial invasion of the amniotic cavity (i.e. intra-amniotic infection) has been causally linked to pregnancy complications, especially preterm birth. Therefore, if the placenta and the fetus are typically populated by low biomass yet viable microbial communities, current understanding of the role of microbes in reproduction and pregnancy outcomes will need to be fundamentally reconsidered. Could these communities be of benefit by competitively excluding potential pathogens or priming the fetal immune system for the microbial bombardment it will experience upon delivery? If so, what properties (e.g. microbial load, community membership) of these microbial communities preclude versus promote intra-amniotic infection? Given the ramifications of the in utero colonization hypothesis, critical evaluation is required. In this study, using multiple modes of microbiologic inquiry (i.e. culture, qPCR, DNA sequencing) and controlling for potential background DNA contamination, we did not find consistent evidence for microbial communities in the placenta and fetal tissues of rhesus macaques.

Sign in / Sign up

Export Citation Format

Share Document