Long-lasting modification of soil fungal diversity associated with the introduction of rabbits to a remote sub-Antarctic archipelago

Pansu, Johan; Winkworth, Richard C.; Hennion, Françoise; Gielly, Ludovic; Taberlet, Pierre; Choler, Philippe

doi:10.1098/rsbl.2015.0408

Cited by 22 publications

(19 citation statements)

References 12 publications

(19 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The ability to resample allows for measurement of change through time. Across studies, we found a range of 2–100 subsamples taken per plot (Drummond et al., ; Pansu et al., ). Although the number of subsamples was generally easily determined, it was hard to find out how that number of subsamples was selected.…”

Section: Resultsmentioning

confidence: 99%

Towards robust and repeatable sampling methods in eDNA‐based studies

Dickie

Boyer

Buckley

et al. 2018

Molecular Ecology Resources

157

151

View full text Add to dashboard Cite

DNA-based techniques are increasingly used for measuring the biodiversity (species presence, identity, abundance and community composition) of terrestrial and aquatic ecosystems. While there are numerous reviews of molecular methods and bioinformatic steps, there has been little consideration of the methods used to collect samples upon which these later steps are based. This represents a critical knowledge gap, as methodologically sound field sampling is the foundation for subsequent analyses. We reviewed field sampling methods used for metabarcoding studies of both terrestrial and freshwater ecosystem biodiversity over a nearly three-year period (n = 75). We found that 95% (n = 71) of these studies used subjective sampling methods and inappropriate field methods and/or failed to provide critical methodological information. It would be possible for researchers to replicate only 5% of the metabarcoding studies in our sample, a poorer level of reproducibility than for ecological studies in general. Our findings suggest greater attention to field sampling methods, and reporting is necessary in eDNA-based studies of biodiversity to ensure robust outcomes and future reproducibility. Methods must be fully and accurately reported, and protocols developed that minimize subjectivity. Standardization of sampling protocols would be one way to help to improve reproducibility and have additional benefits in allowing compilation and comparison of data from across studies.

show abstract

Section: Resultsmentioning

confidence: 99%

Towards robust and repeatable sampling methods in eDNA‐based studies

Dickie

Boyer

Buckley

et al. 2018

Molecular Ecology Resources

157

151

View full text Add to dashboard Cite

show abstract

“…Details about the extraction procedure are available in Supplementary material Appendix 1. Four primer pairs were used to amplify specifically the v8-9 region of the 16S rRNA gene in archaea (Taberlet et al 2018), the v5-6 region of the 16S rRNA gene in bacteria (Fliegerova et al 2014), the ITS1 in fungi (Fung02 in Pansu et al 2015, Taberlet et al 2018) and the P6 loop of the chloroplast trnL intron in vascular plants (Taberlet et al 2007). Four primer pairs were used to amplify specifically the v8-9 region of the 16S rRNA gene in archaea (Taberlet et al 2018), the v5-6 region of the 16S rRNA gene in bacteria (Fliegerova et al 2014), the ITS1 in fungi (Fung02 in Pansu et al 2015, Taberlet et al 2018) and the P6 loop of the chloroplast trnL intron in vascular plants (Taberlet et al 2007).…”

Section: Dna Extraction Amplification and Sequencingmentioning

confidence: 99%

“…Each sample was subdivided into two subsamples of 10 g each, which were used as DNA extraction replicates to allow for controlling amplification biases (Ficetola et al 2015). Four primer pairs were used to amplify specifically the v8-9 region of the 16S rRNA gene in archaea (Taberlet et al 2018), the v5-6 region of the 16S rRNA gene in bacteria (Fliegerova et al 2014), the ITS1 in fungi (Fung02 in Pansu et al 2015, Taberlet et al 2018) and the P6 loop of the chloroplast trnL intron in vascular plants (Taberlet et al 2007). For each marker, we conducted two PCRs per extraction replicate (i.e.…”

Section: Dna Extraction Amplification and Sequencingmentioning

confidence: 99%

Environmental and biotic drivers of soil microbial β‐diversity across spatial and phylogenetic scales

et al. 2019

Self Cite

View full text Add to dashboard Cite

Soil microbial communities play a key role in ecosystem functioning but still little is known about the processes that determine their turnover (β-diversity) along ecological gradients. Here, we characterize soil microbial β-diversity at two spatial scales and at multiple phylogenetic grains to ask how archaeal, bacterial and fungal communities are shaped by abiotic processes and biotic interactions with plants. We characterized microbial and plant communities using DNA metabarcoding of soil samples distributed across and within eighteen plots along an elevation gradient in the French Alps. The recovered taxa were placed onto phylogenies to estimate microbial and plant β-diversity at different phylogenetic grains (i.e. resolution). We then modeled microbial β-diversities with respect to plant β-diversities and environmental dissimilarities across plots (landscape scale) and with respect to plant β-diversities and spatial distances within plots (plot scale). At the landscape scale, fungal and archaeal β-diversities were mostly related to plant β-diversity, while bacterial β-diversities were mostly related to environmental dissimilarities. At the plot scale, we detected a modest covariation of bacterial and fungal β-diversities with plant β-diversity; as well as a distance-decay relationship that suggested the influence of ecological drift on microbial communities. In addition, the covariation between fungal and plant β-diversity at the plot scale was highest at fine or intermediate phylogenetic grains hinting that biotic interactions between those clades depends on early-evolved traits.Altogether, we show how multiple ecological processes determine soil microbial community assembly at different spatial scales and how the strength of these processes change among microbial clades. In addition, we emphasized the imprint of microbial and plant evolutionary history on today's microbial community structure.

show abstract

“…The coevolutionary relationship between the soil microbiome and plants is well defined (Bonkowski et al 2009;Van Nuland et al 2016), and has been explored in the context of ecosystem restoration or recovery post-disturbance (Pansu et al 2015;Cavagnaro et al 2016;Hamonts et al 2017). Correlated succession of soil microbial and plant communities has also been shown from both natural succession and restoration interventions ( Fig.…”

Section: The Microbiome Rewilding Hypothesismentioning

confidence: 99%

Urban habitat restoration provides a human health benefit through microbiome rewilding: the Microbiome Rewilding Hypothesis

Mills

Weinstein

Gellie

et al. 2017

Restoration Ecology

146

107

View full text Add to dashboard Cite

Restoration aims to return ecosystem services, including the human health benefits of exposure to green space. The loss of such exposure with urbanization and industrialization has arguably contributed to an increase in human immune dysregulation. The Biodiversity and Old Friends hypotheses have described the possible mechanisms of this relationship, and suggest that reduced exposure to diverse, beneficial microorganisms can result in negative health consequences. However, it is unclear whether restoration of biodiverse habitat can reverse this effect, and what role the environmental microbiome might have in such recovery. Here, we propose the Microbiome Rewilding Hypothesis, which specifically outlines that restoring biodiverse habitats in urban green spaces can rewild the environmental microbiome to a state that enhances primary prevention of human disease. We support our hypothesis with examples from allied fields, including a case study of active restoration that reversed the degradation of the soil bacterial microbiome of a former pasture. This case study used high‐throughput amplicon sequencing of environmental DNA to assess the quality of a restoration intervention in restoring the soil bacterial microbiome. The method is rapid, scalable, and standardizable, and has great potential as a monitoring tool to assess functional outcomes of green‐space restoration. Evidence for the Microbiome Rewilding Hypothesis will help motivate health professionals, urban planners, and restoration practitioners to collaborate and achieve co‐benefits. Co‐benefits include improved human health outcomes and investment opportunities for biodiversity conservation and restoration.

show abstract

Long-lasting modification of soil fungal diversity associated with the introduction of rabbits to a remote sub-Antarctic archipelago

Cited by 22 publications

References 12 publications

Towards robust and repeatable sampling methods in eDNA‐based studies

Towards robust and repeatable sampling methods in eDNA‐based studies

Environmental and biotic drivers of soil microbial β‐diversity across spatial and phylogenetic scales

Urban habitat restoration provides a human health benefit through microbiome rewilding: the Microbiome Rewilding Hypothesis

Contact Info

Product

Resources

About