Soil parameters, land use, and geographical distance drive soil bacterial communities along a European transect

Plassart, Pierre; Prévost-Bouré, Nicolas Chemidlin; Uroz, Stéphane; Dequiedt, Samuel; Stone, D.; Creamer, Rachel; Griffiths, Robert I.; Bailey, Mark; Ranjard, Lionel; Lemanceau, Philippe

doi:10.1038/s41598-018-36867-2

Cited by 70 publications

(63 citation statements)

References 68 publications

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“…This larger role of microenvironment versus stochastic factors has repeatedly been seen in soil communities, where soils with similar environmental characteristics have similar microbial communities regardless of geographic distance (Fierer and Jackson, 2006;Lauber et al, 2009;Xu et al, 2014;Lladó et al, 2018;Plassart et al, 2019). Interestingly, we see this same trend in the bacterial communities of the soil-dwelling salamanders sampled in this study.…”

Section: Community Diversity and Compositionsupporting

confidence: 83%

“…An emerging approach to study how microbial communities respond to environmental differences at both local and regional spatial scales is analyzing the effects of land use change. Habitat destruction, intensification of agriculture, and urbanization all alter edaphic properties, with correlated effects on microbial community composition (Zhao and Guo, 2010;Suleiman et al, 2013;Hawkes and Keitt, 2015;Plassart et al, 2019). In particular, urbanization may markedly alter the physicochemical properties of soil, leading to changes in the abundance and taxa of soil microbes (Zhao and Guo, 2010;Xu et al, 2014;Reese et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

“…Studies of genes linked to key environmental processes have related disturbances to changes in both microbial taxonomic and functional diversity (Bissett et al, 2011;Paula et al, 2014;Plassart et al, 2019), yet microbiomes usually are classified solely using the 16S rRNA gene. As others note, this gene alone is not a reliable indicator of the functional ability of a microbiome (Mollet et al, 1997;Fukushima et al, 2002;Hilario et al, 2004;Janda and Abbott, 2007;Becker et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

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Predicting Microbiome Function Across Space Is Confounded by Strain-Level Differences and Functional Redundancy Across Taxa

Barnes

Carter

2020

Front. Microbiol.

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Variation in the microbiome among individual organisms may play a critical role in the relative susceptibility of those organisms to infection, disease, and death. However, predicting microbiome function is difficult because of spatial and temporal variation in microbial diversity, and taxonomic diversity is not predictive of microbiome functional diversity. Addressing this issue may be particularly important when addressing pandemic diseases, such as the global amphibian die-off associated with Bd. Some of the most important factors in probiotic development for disease treatment are whether bacteria with desired function can be found on native amphibians in the local environment. To address this issue, we isolated, sequenced, and assayed the cutaneous bacterial communities of Plethodon cinereus along a gradient of land use change. Our results suggest that cutaneous community composition, but not overall diversity, change with changes in land use, but this does not correspond to significant change in Bd-inhibitory function. We found that Bd-inhibition is a functionally redundant trait, but that level of inhibition varies over phylogenetic, spatial, and temporal scales. This research provides further evidence for the importance of continued examination of amphibian microbial communities across environmental gradients, including biotic and abiotic interactions, when considering disease dynamics.

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Section: Community Diversity and Compositionsupporting

confidence: 83%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Predicting Microbiome Function Across Space Is Confounded by Strain-Level Differences and Functional Redundancy Across Taxa

Barnes

Carter

2020

Front. Microbiol.

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“…Bacterivores and eukaryvores were differentially influenced by three edaphic factors, i.e. pH, texture and organic carbon content (Figure 4), the very same major drivers of bacterial community structure at national and continental scales (Bahram et al, 2018;Karimi et al, 2018;Plassart et al, 2019).…”

Section: Opposite Responses Of Trophic Guilds In Forestmentioning

confidence: 99%

Contrasting responses of protistan plant parasites and phagotrophs to ecosystems, land management and soil properties

Fiore-Donno

Richter-Heitmann

Bonkowski

2020

Preprint

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Highlights  Protistan plant parasites of worldwide importance (Phytomyxea) are absent from forest  Protistan plant parasites are enhanced by land use intensification in grassland  Opposite responses of protistan trophic guilds to environmental conditions in forest  Drastic differences in protistan community composition between grassland and forest Abstract Functional traits are increasingly used in ecology to link the structure of microbial communities to ecosystem processes. We investigated two important protistan lineages, Cercozoa and Endomyxa (Rhizaria) in soil using Illumina sequencing and analysed their diversity and functional traits along with their responses to environmental factors in grassland and forest across Germany. From 600 soil samples, we obtained 2,101 Operational Taxonomy Units representing ~18 million Illumina reads (region V4, 18S rRNA gene). All major taxonomic and functional groups were present, dominated by small bacterivorous flagellates (Glissomonadida). Endomyxan plant parasites were absent from forest. In grassland, they were promoted by more intensive land use management. Grassland and forest strikingly differed in community composition. Relative abundances of bacterivores and eukaryvores were contrastingly influenced by environmental factors, indicating bottom-up regulation by food resources. These patterns provide new insights into the functional organization of soil biota and indications for a more sustainable land-use management.

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“…The fungi cultivation can be taken as one kind of land use. Land use was considered as a main driving factor of bacteria for multiple land uses (arable, forest, grasslands) 25 . Previous studies also showed that microbial indexes could be influenced by land-use in many scale [26][27][28] .…”

Section: Discussionmentioning

confidence: 99%

Ganoderma lucidum cultivation affect microbial community structure of soil, wood segments and tree roots

Ren

Zhang

et al. 2020

Sci Rep

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The popular medicinal mushroom Ganoderma lucidum (Fr.) Karst. [Ling Zhi] has been widely used for the general promotion of health and longevity in Asian countries. Continuous cultivation may affect soil microbe and soil properties. However, the effect of G. lucidum cultivation on related wood segments, soil and tree roots microbial communities and soil properties is remain unknown. In our study, the microbial communities of soils, wood segments, and tree roots before and after G. lucidum cultivation were investigated by Illumina Miseq sequencing of both ITS and 16S rDNA, and taxonomic composition of eukaryotic and prokaryotic microorganisms were observed. Indices of microbial richness, diversity and evenness significantly differed between before and after G. lucidum cultivation. Each of the investigated sampling type harbored a distinctive microbial community and differed remarkably before and after G. lucidum cultivation. Ascomycota and Basidiomycota (fungi), Proteobacteria and Actinobacteria (bacteria) showed significant differences after Ling Zhi cultivation. The soil property values also changed after cultivation. The redundancy analysis (RDA) showed that both the fungal and bacterial community structure significantly correlated with soil humus, pH, nitrogen, carbon and trace elements (Fe, Zn, Mn, Cu) contents. The results indicated that G. lucidum cultivation may have significant differed the associated microbial community structures and soil properties. The study will provide useful information for G. lucidum cultivation and under-forest economic development.

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Soil parameters, land use, and geographical distance drive soil bacterial communities along a European transect

Cited by 70 publications

References 68 publications

Predicting Microbiome Function Across Space Is Confounded by Strain-Level Differences and Functional Redundancy Across Taxa

Predicting Microbiome Function Across Space Is Confounded by Strain-Level Differences and Functional Redundancy Across Taxa

Contrasting responses of protistan plant parasites and phagotrophs to ecosystems, land management and soil properties

Ganoderma lucidum cultivation affect microbial community structure of soil, wood segments and tree roots

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