Primer and Database Choice Affect Fungal Functional but Not Biological Diversity Findings in a National Soil Survey

George, Paul B. L.; Creer, Simon; Griffiths, Robert I.; Emmett, Bridget; Robinson, David A.; Jones, Davey L.

doi:10.3389/fenvs.2019.00173

Cited by 33 publications

(38 citation statements)

References 52 publications

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“…3D) compared to undisturbed control (ANOVA, p < 0.05 after FDR correction). However, we acknowledge that AMF are better characterized by the 18S rRNA region rather than the ITS region (George et al 2019). Detected AMF belonged to class Glomeromycetes (genera Diversispora, Racocetra, Claroideoglomus, Dominikia, Funneliformis, Glomus, Kamienskia, Rhizophagus) and class Archaeosporomycetes (genus Archaeospora).…”

Section: Resultsmentioning

confidence: 90%

Disturbance is more important than seeding or grazing in determining soil microbial communities in a semiarid grassland

Farrell

Barberán

Danielson

et al. 2020

Restoration Ecology

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A primary goal of ecological restoration is often to return processes and functions to degraded ecosystems. Soil, while often ignored in restoration, supports diverse communities of organisms and is a fundamental actor in providing ecosystem processes and services. We investigated the impact of seeding and livestock grazing on plant communities, soil microorganisms, and soil fertility 3 years after the restoration of a disturbed pipeline corridor in southeastern Arizona. The initial soil disturbance and topsoil treatment, regardless of seeding or grazing, was the most influential factor in determining differences in both plant and microbial communities. Compared with the control, the disturbed and restored sites had greater plant species richness, greater total herbaceous plant cover, greater soil organic matter, higher pH, and differed in soil nutrients. Bacteria and fungi appeared to generally correlate with micro‐environment and soil physiochemical properties rather than specific plant species. The undisturbed control had a smaller proportion of bacterial functional groups associated with the breakdown of plant biomass (polysaccharide decomposition) and a smaller proportion of arbuscular mycorrhizal fungi (AMF) compared with disturbed and restored sites. The ability of the unseeded disturbed site to recover robust vegetation may be due in part to the high presence of AMF. These differences show selection for soil microorganisms that thrive in disturbed and restored sites and may contribute to increased plant productivity. Restoration of specific plant species or ecological processes and services would both benefit from better understanding of the impacts of disturbance on soil microorganisms and soil fertility.

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Section: Resultsmentioning

confidence: 90%

Disturbance is more important than seeding or grazing in determining soil microbial communities in a semiarid grassland

Farrell

Barberán

Danielson

et al. 2020

Restoration Ecology

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“…This is consistent with studies that have found that ectomycorrhizal fungi were predominant in forested sites (Nguyen et al ; Detheridge et al ) and arbuscular mycorrhizal fungi in grassland sites (Nguyen et al ). Interpretation of these results needs to be approached with caution, however, as Acacia species can obfuscate data through their dual association with both arbuscular and ectomycorrhizal fungal species, and resolution of Glomeralean sequences using ITS alone has not proven comprehensive (Lekberg et al ; George et al ). The high abundance of ectomycorrhizal fungi sequences in our study was correlated to the high stem density (>3,000 stems/ha) of Acacia and eucalypt species (the main woody vegetation) (Ngugi et al ), and has been reported to be associated with accumulation of leaf litter (Glen et al ).…”

Section: Discussionmentioning

confidence: 99%

Successional dynamics of soil fungal diversity along a restoration chronosequence post‐coal mining

Ngugi

Fechner

Neldner

et al. 2020

Restoration Ecology

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Soil disruption from open-cut mining practices can adversely impact microbial communities and the ecosystem services that they mediate. Despite this, assessment of impacts of soil disruption, and the subsequent recovery of microbial communities is rarely studied. Monitoring of ecological restoration success on mine sites has traditionally focused on vegetation; however, most plants rely, at least in part, on associations with soil fungi for enhanced nutrient and water acquisition. Here, we used highthroughput phylogenetic marker gene sequencing to characterize the diversity of soil fungal communities along a restoration chronosequence ranging from 3 to 23 years at a rehabilitated mine site. We used nonmined analogue sites as a baseline for comparative purposes and examined the associations of soil fungal communities with soil physicochemical and aboveground vegetation variables. Fungal richness on rehabilitated sites was significantly larger than on nonmined sites, suggesting that mixing of topsoil during stockpiling resulted in a composite microbial community. Fungal community composition was significantly influenced by edaphic variables and the length of rehabilitation, with mined sites becoming more similar to nonmined sites over time. Fungal populations associated with ectomycorrhizae were relatively more abundant than those associated with arbuscular mycorrhizae and declined in response to disturbance, but recovered over time on the woody dominated sites indicating a strong coupling of these fungi with aboveground vegetation. Our data indicate that soil fungal diversity is a useful bioindicator of soil restoration in mined sites and may complement more traditional vegetation-based surveys.

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“…Animal richness was governed by intensive land use and unaffected by soil properties, while microbial richness was driven by environmental properties across land uses. The efficacy of 18S and ITS1 barcodes in capturing fungal biological and functional diversity has been compared, revealing barcode biases that influenced metrics of functional but not biological diversity (George et al, 2019b). Investigations of bacterial functional groups in the 16S marker gene dataset showed changes in sulphate-reducing bacterial community across land uses, with highest richness in grasslands (George et al, 2020).…”

Section: Additional Published Work To Datementioning

confidence: 99%

Integrated ecological monitoring in Wales: the Glastir Monitoring and Evaluation Programme field survey

Wood¹,

Alison²,

Botham³

et al. 2021

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Abstract. The Glastir Monitoring and Evaluation Programme (GMEP) ran from 2013 until 2016, and was probably the most comprehensive programme of ecological study ever undertaken at a national scale in Wales. The programme aimed to (1) set up an evaluation of the environmental effects of the Glastir agri-environment scheme and (2) quantify environmental status and trends across the wider countryside of Wales. The focus was on outcomes for climate change mitigation, biodiversity, soil and water quality, woodland expansion and cultural landscapes. As such, GMEP included a large field survey component, collecting data on a range of elements including vegetation, land cover and use, soils, freshwaters, birds and insect pollinators from up to 300 1 km squares throughout Wales. The field survey capitalised upon the UKCEH Countryside Survey of Great Britain, which has provided an extensive set of repeated, standardised ecological measurements since 1978. The design of both GMEP and the UKCEH Countryside Survey involved stratified-random sampling of squares from a 1 km grid, ensuring proportional representation from land classes with distinct climate, geology and physical geography. Data were collected from different land cover types and landscape features by trained professional surveyors, following standardised and published protocols. Thus, GMEP was designed so that surveys could be repeated at regular intervals to monitor the Welsh environment, including the impacts of agri-environment interventions. One such repeat survey is scheduled for 2021 under the Environment and Rural Affairs Monitoring and Modelling Programme (ERAMMP). Data from GMEP have been used to address many applied policy questions, but there is major potential for further analyses. The precise locations of data collection are not publicly available, largely for reasons of landowner confidentiality. However, the wide variety of available datasets can be (1) analysed at coarse spatial resolutions and (2) linked to each other based on square-level and plot-level identifiers, allowing exploration of relationships, trade-offs and synergies. This paper describes the key sets of raw data arising from the field survey at co-located sites, 2013 to 2016. Data from each of these survey elements are available with the following Digital Object Identifiers. Landscape features, https://doi.org/10.5285/82c63533-529e-47b9-8e78-51b27028cc7f, https://doi.org/10.5285/9f8d9cc6-b552-4c8b-af09-e92743cdd3de, https://doi.org/10.5285/f481c6bf-5774-4df8-8776-c4d7bf059d40; Vegetation plots, https://doi.org/10.5285/71d3619c-4439-4c9e-84dc-3ca873d7f5cc; Topsoil physico-chemical properties, https://doi.org/10.5285/0fa51dc6-1537-4ad6-9d06-e476c137ed09; Topsoil meso-fauna, https://doi.org/10.5285/1c5cf317-2f03-4fef-b060-9eccbb4d9c21; Topsoil particle size distribution https://doi.org/10.5285/d6c3cc3c-a7b7-48b2-9e61-d07454639656; Headwater stream quality metrics, https://doi.org/10.5285/e305fa80-3d38-4576-beef-f6546fad5d45 ; Pond quality metrics, https://doi.org/10.5285/687b38d3-2278-41a0-9317-2c7595d6b882; Insect pollinator and flower data, https://doi.org/10.5285/3c8f4e46-bf6c-4ea1-9340-571fede26ee8; Bird counts, https://doi.org/10.5285/31da0a94-62be-47b3-b76e-4bdef3037360.

show abstract

Primer and Database Choice Affect Fungal Functional but Not Biological Diversity Findings in a National Soil Survey

Cited by 33 publications

References 52 publications

Disturbance is more important than seeding or grazing in determining soil microbial communities in a semiarid grassland

Disturbance is more important than seeding or grazing in determining soil microbial communities in a semiarid grassland

Successional dynamics of soil fungal diversity along a restoration chronosequence post‐coal mining

Integrated ecological monitoring in Wales: the Glastir Monitoring and Evaluation Programme field survey

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