Biogeography of soil bacteria and archaea across France

Karimi, Battle; Terrat, Sébastien; Dequiedt, Samuel; Saby, Nicolas P.A.; Horrigue, Walid; Lelièvre, Mélanie; Nowak, Virginie; Jolivet, Claudy; Arrouays, Dominique; Wincker, Patrick; Cruaud, Corinne; Bispo, Antonio; Maron, Pierre‐Alain; Bouré, Nicolas Chemidlin Prévost; Ranjard, Lionel

doi:10.1126/sciadv.aat1808

Cited by 191 publications

(174 citation statements)

References 62 publications

(117 reference statements)

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“…The genus Mycobacterium is ubiquitous and reasonably abundant in soil as determined by our cultivation-independent 16S rRNA gene analyses. We found that Mycobacterium was typically one of the more abundant named genera of bacteria found in soil, confirming results reported in comparable studies (13, 19, 21). However, the relative abundance of mycobacteria was highly variable across soils ranging from 0.03 to 2.9% of 16S rRNA gene reads, a range similar to that reported previously (19–21).…”

Section: Discussionsupporting

confidence: 92%

“…Members of the Mycobacterium genus are commonly detected across a broad range of soil types using both cultivation-dependent and cultivation-independent methods. We know from cultivation-independent surveys of soil bacterial communities that mycobacteria are nearly ubiquitous in soil and the genus Mycobacterium is consistently one of the more abundant genera of soil bacteria, ranging in relative abundance from ~0.5-3.0% of the total community (19–21). For instance, the Mycobacterium genus has been detected in soils from bogs (22), forests (13, 23, 24), croplands (25, 26) and livestock farms (27–29), and even in potting soil (30).…”

Section: Introductionmentioning

confidence: 99%

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A global survey of mycobacterial diversity in soil

Walsh

Gebert

Delgado‐Baquerizo

et al. 2019

Preprint

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Section: Discussionsupporting

confidence: 92%

Section: Introductionmentioning

confidence: 99%

A global survey of mycobacterial diversity in soil

Walsh

Gebert

Delgado‐Baquerizo

et al. 2019

Preprint

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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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“…Large-scale spatial variation in the composition of the soil biota has been associated with difference in edaphic and climatic conditions 9 . Particularly, local edaphic factors such as soil pH primarily predict geographic distribution of soil bacteria 10, 11, 12 , whereas climatic variables better predict fungal distribution in soil 13 . However, systematic field studies exploring and disentangling the extent to which variation in soil and climatic conditions impacts root microbiota composition and adaptive differentiation in plants are lacking.…”

Section: Introductionmentioning

confidence: 99%

Root microbiota assembly and adaptive differentiation among European Arabidopsis populations

Thiergart

Durán

Ellis

et al. 2019

Preprint

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20Factors that drive continental-scale variation in root microbiota and plant adaptation are poorly 21 understood. We monitored root-associated microbial communities in Arabidopsis thaliana and co-22 occurring grasses at 17 European sites across three years. Analysis of 5,625 microbial community 23 profiles demonstrated strong geographic structuring of the soil biome, but not of the root microbiota. 24Remarkable similarity in bacterial community composition in roots of A. thaliana and grasses was 25 explained by the presence of a few diverse and geographically widespread taxa that disproportionately 26 colonize roots across sites. In a reciprocal transplant between two A. thaliana populations in Sweden 27and Italy, we uncoupled soil from location effects and tested their respective contributions to root 28 2 microbiota variation and plant adaptation. The composition of the root microbiota was affected by 29 location and soil origin, and to a lesser degree by host genotype. The filamentous eukaryotes were 30 particularly strongly affected by location. Strong local adaptation between the two A. thaliana 31 populations was observed, with difference in soil properties and microbes of little importance for the 32 observed magnitude of adaptive differentiation. Our results suggest that, across large spatial scales, 33 climate is more important than are soil conditions for plant adaptation and variation in root-associated 34 filamentous eukaryotic communities. 35 36 differentiation among plant populations is still limited beyond classical examples of adaptation to 57 extreme soil conditions 25 . 58 59Here, we tested whether roots of A. thaliana and co-occurring grasses growing in various soils and 60 climatic environments establish stable associations with bacterial and filamentous eukaryotic 61 communities across a latitudinal gradient in Europe. In a reciprocal transplant between two A. thaliana 62 populations in Sweden and Italy, we uncoupled soil from location effects and experimentally tested the 63 hypothesis that soil properties and climate drive root microbiota assembly and adaptive differentiation 64 between the two A. thaliana populations. 65 66We found that a widespread set of bacteria, but not filamentous eukaryotes, establish stable associations 67 with roots of A. thaliana and grasses across 17 sites in Europe, despite strong geographical structuring 68 and variation in the surrounding soil communities. The reciprocal transplant of soil and plant genotypes 69 between two native A. thaliana populations in northern and southern Europe showed that the 70 composition of root microbiota was more affected by soil properties and location than by host genotype. 71The effect of soil was stronger than that of location for root-associated bacteria, whereas the effect of 72 location was stronger for root-associated fungi and oomycetes. Transplant location, rather than origin 73 of soil, also largely accounted for strong selection against the nonlocal A. thaliana genotype at each site. 74Our results suggest that climat...

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Biogeography of soil bacteria and archaea across France

Abstract: Each soil bacterial taxon exhibits a specific wide scale distribution explained by particular environmental filters.

Cited by 191 publications

References 62 publications

A global survey of mycobacterial diversity in soil

A global survey of mycobacterial diversity in soil

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

Root microbiota assembly and adaptive differentiation among European Arabidopsis populations

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