Multi-targeted metagenetic analysis of the influence of climate and environmental parameters on soil microbial communities along an elevational gradient

Lanzén, Anders; Epelde, Lur; Blanco, F.; Martín, Iker; Artetxe, Unai; Garbisu, Carlos

doi:10.1038/srep28257

Cited by 69 publications

(58 citation statements)

References 57 publications

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“…In contrast, with a few exceptions (Bahram et al 2018), most studies find no increase in soil microbial diversity from polar to equatorial regions (Fenchel and Finlay 2004, Fuhrman 2009, Fierer et al 2011, Hendershot et al 2017. As a consequence, studies aiming to examine the relationship between plant diversity and soil microbial diversity across biogeographic scales find weak (Bryant et al 2008, Prober et al 2015, or even no correlations (Lanz en et al 2016, Cameron et al 2019. As a consequence, studies aiming to examine the relationship between plant diversity and soil microbial diversity across biogeographic scales find weak (Bryant et al 2008, Prober et al 2015, or even no correlations (Lanz en et al 2016, Cameron et al 2019.…”

Section: Introductionmentioning

confidence: 99%

“…Likewise, soil microbial diversity patterns vary widely along elevation gradients, where monotonic declines (Bryant et al 2008), unimodal patterns (Liu et al 2016a), and no relationships (Fierer et al 2011, Shen et al 2014 with increasing elevation have all been reported. As a consequence, studies aiming to examine the relationship between plant diversity and soil microbial diversity across biogeographic scales find weak (Bryant et al 2008, Prober et al 2015, or even no correlations (Lanz en et al 2016, Cameron et al 2019. These conflicting results suggest that the relationship between soil microbial diversity and plant diversity might differ across biomes and spatial scales.…”

Section: Introductionmentioning

confidence: 99%

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Relationships between plant diversity and soil microbial diversity vary across taxonomic groups and spatial scales

et al. 2020

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Citation: Liu, L., K. Zhu, N. Wurzburger, and J. Zhang. 2020. Relationships between plant diversity and soil microbial diversity vary across taxonomic groups and spatial scales. Ecosphere 11(1):Abstract. Plant diversity has long been assumed to predict soil microbial diversity. However, contradictory results have been found when examining their relationships, particularly at broad spatial scales. To address this issue, we conducted a meta-analysis to evaluate the patterns in the correlation between plant diversity and soil microbial diversity and the underlying factors driving the relationship. We collected correlation data from 84 studies covering more than 3900 natural terrestrial samples globally. Using the hierarchical mixed-effects model, we investigated factors including targeted taxonomic group, microbial examination method, sampling extent, biome type, soil type, and environmental factors to assess the patterns of the plant-microbial correlation and the determinants of their variations. We found that microbial richness displayed a modest but positive correlation with plant diversity (r = 0.333, CI = 0.220-0.437). In spite of variability among taxonomic groups and their relationship with plant diversity, positive correlations were more pronounced in the intermediate sampling extent of latitude and elevation coverage, and tropical forests. Among examined environmental factors, soil pH was negatively associated with the plant and soil microbial relationships at large spatial scales. The plant-microbial correlation appears more sensitive to edaphic factor variation in the poor nutrients and soil less compact systems. Collectively, our results point to key differences across taxonomic groups, spatial scales and biomes, and the modulating effects of climate and soil. The findings shed light on our deep understanding in plant-microbial diversity relationships at broad spatial scales and ecosystem sensitivity to biodiversity loss and environmental change.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Relationships between plant diversity and soil microbial diversity vary across taxonomic groups and spatial scales

et al. 2020

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“…Based on these observations, in our second iteration of this practical the THW cohort performed 16S rRNA gene amplification with primers targeting the V4 region. This approach resulted in similar soil-community profiles to other soil-microbiome studies (Lanzén et al, 2016;Thompson et al, 2017;Tian et al, 2017).…”

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confidence: 63%

“…Based on these observations, in our second iteration of this practical the THW cohort performed 16S rRNA gene amplification with primers targeted to the V4 region and used the higher fidelity Q5 polymerase. This approach resulted in similar soil-community profiles to other soil-microbiome studies (Lanzén et al, 2016;Thompson et al, 2017;Tian et al, 2017). We maintained sterility in these negative controls by returning soil samples to the laboratory and assembling the iChips in laminar flow cabinets before returning the samples to the field for initial growth.…”

Section: Protocol Pitfalls and Improvementsmentioning

confidence: 96%

A practical introduction to microbial molecular ecology through the use of isolation chips

Alessi

Redeker

Chong

2018

Ecology and Evolution

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In the context of antimicrobial resistance as one of the most serious issues faced globally by health providers, we explored a practical introduction to molecular microbial ecology. We designed field work and practical experiments for third year members of a 4 year undergraduate Masters Program, in which the students employed traditional and novel isolation techniques to identify antimicrobial activities from soil dwelling microorganisms. Students gained experience in isolating DNA from complex microbial communities, amplifying 16S rRNA genes and applied richness/diversity indices as well as principal coordinate analyses to the interpretation of the data they obtained from high throughput sequencing. Our results confirmed that isolation chips facilitate the growth of a greater diversity and different species subset from the complex soil microorganism community than traditional plate spreading techniques. However, rarefaction of 16S rRNA amplicon sequencing data showed that the majority of observed species in soil remain unculturable by current methods. Based on the written reports produced by the students carrying out the work, we concluded that the described protocols are robust and informative, that these activities provide a good practical introduction to the theories and practice of molecular ecology and can be easily deployed to groups of six or more students in a cost‐effective manner.

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“…Several distinct patterns have been also described for archaeal (Singh et al, 2014;Wang et al, 2015a;Siles and Margesin, 2016;Bardelli et al, 2017) and fungal communities (Meng et al, 2013;Wang et al, 2015b;Siles and Margesin, 2016). The processes driving this variation in microbial communities have been mainly related to abiotic factors (Lanz en et al, 2016;Siles and Margesin, 2016), and the role of biotic interactions such as competition has long been neglected. However, there is no good reason to reject a role for biotic processes in driving elevational patterns exhibited by microbial communities (Goberna et al, 2014a).…”

Section: Introductionmentioning

confidence: 99%

Competition and habitat filtering jointly explain phylogenetic structure of soil bacterial communities across elevational gradients

Zhang

Goberna

et al. 2018

Environmental Microbiology

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The importance of assembly processes in shaping biological communities is poorly understood, especially for microbes. Here, we report on the forces that structure soil bacterial communities along a 2000 m elevational gradient. We characterized the relative importance of habitat filtering and competition on phylogenetic structure and turnover in bacterial communities. Bacterial communities exhibited a phylogenetically clustered pattern and were more clustered with increasing elevation. Biotic factors (i.e., relative abundance of dominant bacterial lineages) appeared to be most important to the degree of clustering, evidencing the role of the competitive ability of entire clades in shaping the communities. Phylogenetic turnover showed the greatest correlation to elevation. After controlling the elevation, biotic factors showed greater correlation to phylogenetic turnover than all the habitat variables (i.e., climate, soil and vegetation). Structural equation modelling also identified that elevation and soil organic matter exerted indirect effects on phylogenetic diversity and turnover by determining the dominance of microbial competitors. Our results suggest that competition among bacterial taxa induced by soil carbon contributes to the phylogenetic pattern across elevational gradient in the Tibetan Plateau. This highlights the importance of considering not only abiotic filtering but also biotic interactions in soil bacterial communities across stressful elevational gradients.

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Multi-targeted metagenetic analysis of the influence of climate and environmental parameters on soil microbial communities along an elevational gradient

Cited by 69 publications

References 57 publications

Relationships between plant diversity and soil microbial diversity vary across taxonomic groups and spatial scales

Relationships between plant diversity and soil microbial diversity vary across taxonomic groups and spatial scales

A practical introduction to microbial molecular ecology through the use of isolation chips

Competition and habitat filtering jointly explain phylogenetic structure of soil bacterial communities across elevational gradients

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