Niche and Neutrality Work Differently in Microbial Communities in Fluidic and Non-fluidic Ecosystems

Wang, Lixiao; Han, Maozhen; Xi, Li; Ginawi, Amjed; Ning, Kang; Yan, Yunjun

doi:10.1007/s00248-019-01439-y

Cited by 15 publications

(10 citation statements)

References 38 publications

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“…A PowerWater DNA Isolation Kit (MoBio Laboratories) was used to extract the total genomic DNA from the filters in triplicate according to the manufacturer's instructions. The 156 DNA samples were quantified with a Qubit 2.0 Fluorimeter (Invitrogen) before amplifying the hypervariable regions V3–V5 of bacteria and archaea 16S rRNA gene (the V3–V4 regions were amplified using forward primers 5′‐CCTACGGRRBGCASCAGKVRVGAAT‐3′ and reverse primers 5′‐GGACTACNVGGGTWTCTAATCC‐3′; while forward primers 5′‐GTGYCAGCMGCCGCGGTAA‐3′ and reverse primers 5′‐CTTGTGCGGKCCCCCGYCAATTC‐3′ were used to amplify V4–V5 regions; Wang, Han, Li, Ginawi, et al, 2019, Wang, Han, Li, Yu, et al, 2019). NGS library preparations and Illumina MiSeq paired‐end sequencing were executed at GENEWIZ.…”

Section: Methodsmentioning

confidence: 99%

“…For each taxon, the relationship between its occurrence frequency and its average relative abundance across local communities was plotted and fitted to the NCM in R (Burns et al, 2016; Wang, Han, Li, Ginawi, et al, 2019; Wang, Han, Li, Yu, et al, 2019), with the hmisc package to calculate the 95% confidence intervals and minpack.lm package to estimate m , the migration rate, which indicated the degree of dispersal limitation (Sloan et al, 2006, 2007). Here, for each transect, 36 local communities (three triplicates in each site and each season) were involved, and they comprised the metacommunity of the specific transect.…”

Section: Methodsmentioning

confidence: 99%

“…Ofiteru et al (2010) applied this NCM analysis in both heterotrophic and ammonia‐oxidizing bacteria communities from a wastewater treatment plant with a calibration, and explained 28% and 37% of the variance of two kinds of communities respectively, verifying the significant role of neutral dynamics. Wang, Han, Li, Ginawi, et al (2019), Wang, Han, Li, Yu, et al (2019) also compared the niche‐neutrality dynamics of microbial communities from a waterbody and sediment of freshwater ecosystems using both SAD analysis and the NCM method, drawing the conclusion that neutrality was much more involved in water microbial communities than counterparts in sediment, where microbial dispersal was highly restricted. Sloan's NCM was also tested on microbial communities from intestines of fish at different life cycle stages, and the resulting niche‐neutrality balancing dynamics indicated that along with the growth and development of the hosts, the effect of neutral processes decreased while deterministic selection worked more on intestinal microbial communities (Burns et al, 2016; Hey et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

“…Therefore, by investigating the dispersal dynamics of microbial assemblages living in an ecological continuum in freshwater rivers, the main objectives of this study were: (i) to explore how the niche‐based selections and neutral processes cooperate with each other in microbial community assembling. Based on previous studies (Burns et al, 2016; Hey et al, 2020; Ofiteru et al, 2010; Wang, Han, Li, Ginawi, et al, 2019; Wang, Han, Li, Yu, et al, 2019), it was supposed that neutrality played greater roles in mild environments than in harsh conditions, whereas niche‐based selection could exert a stronger influence on communities under stress than in regular circumstances. (ii) To elucidate the differences and the internal successional mechanisms of microbial community networks in healthy circumstances and under environmental pressures.…”

Section: Introductionmentioning

confidence: 99%

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Mechanisms of niche‐neutrality balancing can drive the assembling of microbial community

Wang

Han

et al. 2021

Molecular Ecology

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One hotspot of present community ecology is to uncover the mechanisms of community succession. In this study, two popular concepts, niche‐neutrality dynamic balancing and co‐occurrence network analysis, were integrated to investigate the dispersal dynamics of microbial communities in a freshwater river continuum in subtropical China. Results showed that when habitat conditions were mild and appropriate, such as in the clean upstream river, free of heavy pollution or long‐lasting extreme disturbances, stochastic processes could increase species diversities, and organize communities into relatively loosely linked and stable networks with higher modularity and more modules. However, when conditions became degraded under heavy pollution, the influence of neutrality diminished, and niche‐based selection imposed more constraints on communities and guided the assembling processes in certain directions: depleting species richness, strengthening interspecies connections and breaking boundaries of modules. Consequently, communities became more sensitive to fluctuations so as to deal with the harsh conditions efficiently. Another interesting finding was that, both as keystone taxa of communities, module hubs were mostly neutrally distributed generalists with high abundances, and were beneficial to many related operational taxonomic units. In contrast, connectors were less abundant and their distributions were more subjected to the environments. Therefore, connectors were probably responsible for the information transmission between microbial communities and environments, as well as between different modules, and thus could restrict the dispersal of microbes and guide the direction of community assembly.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Mechanisms of niche‐neutrality balancing can drive the assembling of microbial community

Wang

Han

et al. 2021

Molecular Ecology

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“…The V3-V4 hypervariable regions of the 16S rRNA gene of microbes for each rhizosphere soil sample were ampli ed and sequenced to pro le the taxonomical structure of the blueberry rhizosphere microbial community. Speci cally, approximately 50 ng DNA was used as PCR template, and the forward primer 5¢-CCTACGGRRBGCASCAGKVRVGAAT-3¢ and reverse primer 5¢-GGACTACNVGGGTWTCTAATCC-3¢ were used to amplify the V3-V4 amplicon (29,30). Indexed adapters were added to the ends of 16S rDNA amplicons and the sequencing library was constructed.…”

Section: Dna Extraction and Amplicon Sequencingmentioning

confidence: 99%

Comparison and Interpretation of Characteristics of Rhizosphere Microbial Communities in Three Blueberry Varieties: The Benefits to Blueberry Production

Zhang¹,

Wang²,

Shen³

et al. 2020

Preprint

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Background: Rhizosphere microbiota play a critical role in biogeochemical cycles and carry out various vital functions in plant production. Studies on the rhizosphere microbiome of various plants proved that rhizosphere microbiota can regulate the growth and improve the yield of plants. However, the rhizosphere microbiome of commercial blueberry remains elusive. Hence, the characteristics of rhizosphere microbial communities of blueberry should be compared and interpreted for improving production. Methods: We collected 15 rhizosphere soil samples of three different blueberry varieties and five bulk soil samples to profile the composition of blueberry microbial communities by high-throughput sequencing. Results: Our results demonstrated significant differences in both alpha diversity and beta diversity of rhizosphere microbial communities of different blueberry varieties and bulk soil. We found that the distribution patterns of taxonomical, functional, and phenotypic composition of rhizosphere microbiome differ across the blueberry varieties. The rhizosphere microbial communities of three different blueberry varieties could be distinctly separated and 28 discriminative biomarkers were selected to distinguish these three blueberry varieties. Core rhizosphere microbiota for blueberry was identified, and it contained 201 OTUs, which were mainly affiliated with Proteobacteria, Actinobacteria, and Acidobacteria. Moreover, we explored the interactions between OTUs of blueberry rhizosphere microbial communities by constructing the co-occurrence network of OTUs from an ecological perspective. Conclusions: This pilot study explored the characteristics of blueberry’s rhizosphere microbial community, such as the beneficial microorganisms, and provided an integrative perspective on blueberry’s rhizosphere microbiome, which was beneficial to blueberry health and production.

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Biogeographic responses and niche occupancy of microbial communities following long-term land-use change

Goss‐Souza

Tsai

Rodrigues

et al. 2022

Antonie van Leeuwenhoek

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Understanding the effects of forest-to-agriculture conversion on microbial diversity has been a major goal in soil ecological studies. However, linking community assembly to the ruling ecological processes at local and regional scales remains challenging. Here, we evaluated bacterial community assembly patterns and the ecological processes governing niche specialization in a gradient of geography, seasonality, and land-use change, totalizing 324 soil samples, 43 habitat characteristics (abiotic factors), and 16 metabolic and co-occurrence patterns (biotic factors), in the Brazilian Atlantic Rainforest, a subtropical biome recognized as one the world's largest and most threatened hotspots of biodiversity. We observed no significant shifts in alpha diversity due to land-use change.Meanwhile, pairwise beta diversities and distance decays were lower in pastures than those observed for forest and no-till soils. Pasture communities showed a predominantly neutral model, regarding stochastic processes, with moderate dispersion, leading to biotic homogenization. Most no-till and forest microbial communities followed a niche-based model, with low rates of dispersal and weak homogenizing selection, indicating niche specialization or variable selection. Historical and evolutionary contingencies, as represented by soil type, season, and dispersal process were the main drivers of microbial assembly and processes at the local scale, markedly correlated with the occurrence of endemic microbes. Our results indicate that the patterns of assembly and their governing processes are dependent on the niche occupancy of the taxa evaluated (generalists or specialists). They are also more correlated with historical/evolutionary contingencies and the interactions among taxa (i.e. co-occurrence patterns) than the land-use change itself.

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Niche and Neutrality Work Differently in Microbial Communities in Fluidic and Non-fluidic Ecosystems

Cited by 15 publications

References 38 publications

Mechanisms of niche‐neutrality balancing can drive the assembling of microbial community

Mechanisms of niche‐neutrality balancing can drive the assembling of microbial community

Comparison and Interpretation of Characteristics of Rhizosphere Microbial Communities in Three Blueberry Varieties: The Benefits to Blueberry Production

Biogeographic responses and niche occupancy of microbial communities following long-term land-use change

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