Geographic Scale Influences the Interactivities Between Determinism and Stochasticity in the Assembly of Sedimentary Microbial Communities on the South China Sea Shelf

Liu, Hualin; Lin, Genmei; Gao, Di; Chen, Hongyu; He, Miao; Lü, Jianguo

doi:10.1007/s00248-021-01946-x

Cited by 6 publications

(6 citation statements)

References 75 publications

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“…Dispersal limitation was the primary process in shaping the microbial community structure for the plastisphere, which was consistent with those found in the freshwater and seawater environments [71] , [72] . Our result was in agreement with a previous study showing that the dispersion limitation would be the main assembly process when the physiochemical properties among sites were heterogeneous [32] . Moreover, the dispersion limitation acting in concert with the undominated process ( i.e.…”

Section: Discussionsupporting

confidence: 94%

Enrichment of antibiotic resistant genes and pathogens in face masks from coastal environments

Cheng

Xing

Wang

et al. 2023

Journal of Hazardous Materials

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Section: Discussionsupporting

confidence: 94%

Enrichment of antibiotic resistant genes and pathogens in face masks from coastal environments

Cheng

Xing

Wang

et al. 2023

Journal of Hazardous Materials

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“…Therefore, we proposed that in canyon C4, the nutrient content in the surface sediments should be lower than that in the middle and bottom layers, which is also supported by the recent low deposition rate reflected by the unpublished dating data of the sediments. Diverse and abundant substrates could significantly enhance microbial diversity ( 47 , 48 ), which may explain why microbial diversity is lowest in surface sediments.…”

Section: Discussionmentioning

confidence: 99%

“…The heatmap based on Bray-Curtis distance was drawn with the R package pheatmap ( 78 ). The community assembly framework based on the null model test was conducted as previously described ( 48 ). Scripts used for these analyses can be found at https://github.com/liaochenlanruo/SY179_Canyon/tree/master/Amplicon .…”

Section: Methodsmentioning

confidence: 99%

Microbial Diversity, Community Turnover, and Putative Functions in Submarine Canyon Sediments under the Action of Sedimentary Geology

et al. 2023

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“…Numerous studies have explored assembly as based on taxonomic groups (e.g. OTU or ASV) derived from 16S rRNA gene sequencing (Liu et al, 2023;Thompson et al, 2017;Wu et al, 2019). It is well-recognized that multiple environmental factors influence the variations of microbial community diversity and composition, and further drive microbial community assembly (Righetti et al, 2019;Thompson et al, 2017).…”

Section: Highly Deterministic Lignin-degrading Communities At the Fun...mentioning

confidence: 99%

Metagenomic‐based discovery and comparison of the lignin degrading potential of microbiomes in aquatic and terrestrial ecosystems via the LCdb database

Chen,

Lin,

et al. 2024

Molecular Ecology Resources

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Lignin, as an abundant organic carbon, plays a vital role in the global carbon cycle. However, our understanding of the global lignin‐degrading microbiome remains elusive. The greatest barrier has been absence of a comprehensive and accurate functional gene database. Here, we first developed a curated functional gene database (LCdb) for metagenomic profiling of lignin degrading microbial consortia. Via the LCdb, we draw a clear picture describing the global biogeography of communities with lignin‐degrading potential. They exhibit clear niche differentiation at the levels of taxonomy and functional traits. The terrestrial microbiomes showed the highest diversity, yet the lowest correlations. In particular, there were few correlations between genes involved in aerobic and anaerobic degradation pathways, showing a clear functional redundancy property. In contrast, enhanced correlations, especially closer inter‐connections between anaerobic and aerobic groups, were observed in aquatic consortia in response to the lower diversity. Specifically, dypB and dypA, are widespread on Earth, indicating their essential roles in lignin depolymerization. Estuarine and marine consortia featured the laccase and mnsod genes, respectively. Notably, the roles of archaea in lignin degradation were revealed in marine ecosystems. Environmental factors strongly influenced functional traits, but weakly shaped taxonomic groups. Null mode analysis further verified that composition of functional traits was deterministic, while taxonomic composition was highly stochastic, demonstrating that the environment selects functional genes rather than taxonomic groups. Our study not only develops a useful tool to study lignin degrading microbial communities via metagenome sequencing but also advances our understanding of ecological traits of these global microbiomes.

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Geographic Scale Influences the Interactivities Between Determinism and Stochasticity in the Assembly of Sedimentary Microbial Communities on the South China Sea Shelf

Cited by 6 publications

References 75 publications

Enrichment of antibiotic resistant genes and pathogens in face masks from coastal environments

Enrichment of antibiotic resistant genes and pathogens in face masks from coastal environments

Microbial Diversity, Community Turnover, and Putative Functions in Submarine Canyon Sediments under the Action of Sedimentary Geology

Metagenomic‐based discovery and comparison of the lignin degrading potential of microbiomes in aquatic and terrestrial ecosystems via the LCdb database

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