Analysis of soil eDNA functional genes: potential to increase profitability and sustainability of pastoral agriculture

Wakelin, Steven A.; Cave, Vanessa M.; Dignam, Bryony E.A.; D’Ath, C; Tourna, Maria; Condron, L. M.; Zhou, Jizhong; Nostrand, JD Van; O’Callaghan, Maureen

doi:10.1080/00288233.2016.1209529

Cited by 12 publications

(8 citation statements)

References 36 publications

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“…The gene categories defined above were used collectively (All Genes) and individually to assess the influence of soil properties on functional gene composition among soils (general analysis approach described in [ 39 ]). To compare the abundance of individual genes among soil samples, signal intensities were first standardized by the number of probes per gene (to account for disproportionate numbers of probes) and expressed as per gram of soil.…”

Section: Methodsmentioning

confidence: 99%

Effect of land use and soil organic matter quality on the structure and function of microbial communities in pastoral soils: Implications for disease suppression

et al. 2018

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Cropping soils vary in extent of natural suppression of soil-borne plant diseases. However, it is unknown whether similar variation occurs across pastoral agricultural systems. We examined soil microbial community properties known to be associated with disease suppression across 50 pastoral fields varying in management intensity. The composition and abundance of the disease-suppressive community were assessed from both taxonomic and functional perspectives. Pseudomonas bacteria were selected as a general taxonomic indicator of disease suppressive potential, while genes associated with the biosynthesis of a suite of secondary metabolites provided functional markers (GeoChip 5.0 microarray analysis). The composition of both the Pseudomonas communities and disease suppressive functional genes were responsive to land use. Underlying soil properties explained 37% of the variation in Pseudomonas community structure and up to 61% of the variation in the abundance of disease suppressive functional genes. Notably, measures of soil organic matter quality, C:P ratio, and aromaticity of the dissolved organic matter content (carbon recalcitrance), influenced both the taxonomic and functional disease suppressive potential of the pasture soils. Our results suggest that key components of the soil microbial community may be managed on-farm to enhance disease suppression and plant productivity.

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Section: Methodsmentioning

confidence: 99%

Effect of land use and soil organic matter quality on the structure and function of microbial communities in pastoral soils: Implications for disease suppression

et al. 2018

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“…These host × microbiome × environment relationships in agricultural production systems involve extremely broad and complex interactions along the soil-plant and animal continuum, and its investigation needs to be divided into more specific research questions to enable detailed dissection and analysis. In this context, an “ecological genomics” approach is appropriate, whereby the microbiomes associated with soil, plants and animals are recognized as an integral part of an interconnected system that influence the functions of their hosts and thereby contribute significantly to productive processes in the pastoral sector (71). The key features of, and interactions between the soil-plant-animal microbiomes need to be identified so that their contributions to these agricultural processes and their impacts on the environment can be quantified.…”

Section: Introductionmentioning

confidence: 99%

Applications of the Soil, Plant and Rumen Microbiomes in Pastoral Agriculture

et al. 2019

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The production of dairy, meat, and fiber by ruminant animals relies on the biological processes occurring in soils, forage plants, and the animals' rumens. Each of these components has an associated microbiome, and these have traditionally been viewed as distinct ecosystems. However, these microbiomes operate under similar ecological principles and are connected via water, energy flows, and the carbon and nitrogen nutrient cycles. Here, we summarize the microbiome research that has been done in each of these three environments (soils, forage plants, animals' rumen) and investigate what additional benefits may be possible through understanding the interactions between the various microbiomes. The challenge for future research is to enhance microbiome function by appropriate matching of plant and animal genotypes with the environment to improve the output and environmental sustainability of pastoral agriculture.

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“…The extent of association between organic S and the soil ecosystem function was unexpected, as this has rarely been reported, although the organic S status of soils is rarely measured as part of soil microbial ecology studies (Wakelin et al 2008). In studies where various sulphur forms are measured, such as a survey of 50 New Zealand pasture soils, associations between bacterial abundance (Dignam et al 2018) and function (Wakelin et al 2016) have been evident. These findings indicate that sulphur may have a regulatory influence on the biogeochemical processes underpinning a range soil functions (including C, N and P cycling) and should be routinely measured in soil microbial ecology.…”

Section: Discussionmentioning

confidence: 99%

“…For the sample collected from under native bush at Eyrewell, there was insufficient DNA to conduct GeoChip analysis. Although whole community genome amplification could be used to increase total DNA content (Wang et al 2011), the bias associated with this method can be large and obfuscate underlying biological trends (Wakelin et al 2016). As such, this sample was not included for processing or subsequent data analysis.…”

Section: Soil Functional Genomicsmentioning

confidence: 99%

Protecting the unseen majority: Land cover and environmental factors linked with soil bacterial communities and functions in New Zealand

Wakelin¹,

Scion²,

Forrester³

et al. 2021

NZJE

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The biodiversity in soil ecosystems is simultaneously incredibly rich and poorly described. In countries such as New Zealand, where high endemism in plant species emerged following extended geographical isolation, it is likely similar evolutionary pressures extended to soil microbial communities (our biodiversity 'dark matter'). However, we have little understanding of the extent of microbial life in New Zealand soils, let alone estimates of endemism, rates of species loss or gain, or implications for systems where plants and their microbiomes have co-evolved. In this study, we tested for the impacts of land-cover type (native forest, planted forest with exotic conifers, and pastoral agriculture) on soil bacterial communities and their functional potential, using environmental microarrays (PhyloChip and GeoChip, respectively). This evaluation was conducted across four environmentally different locations (Hokitika, Banks Peninsula, Craigieburn, and Eyrewell). The environment from which samples were collected was the largest and most significant factor associated with variation in bacterial community assemblage and function. As such, novel pockets of bacterial biodiversity, with discrete ecosystem function, may be present in New Zealand. There was some evidence to suggest that change in land cover affected soil bacterial species, but not their functions. Secondary testing found this effect was restricted to differences between native forest and agricultural land use. Bacterial communities and functions between native and planted forests were similar. Analysis of soil environmental properties among samples found that land cover effects were underpinned by changes in soil pH that typically accompanies application of lime in agricultural systems, but is uncommon in planted forests. When compared with other studies conducted in New Zealand, we conclude that: (1) different locations can harbour distinct communities of soil microbial diversity, and (2) land-use intensification, not land cover change per se, shifts microbial biodiversity through alteration of primary habitat conditions, particularly soil pH.

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Analysis of soil eDNA functional genes: potential to increase profitability and sustainability of pastoral agriculture

Cited by 12 publications

References 36 publications

Effect of land use and soil organic matter quality on the structure and function of microbial communities in pastoral soils: Implications for disease suppression

Effect of land use and soil organic matter quality on the structure and function of microbial communities in pastoral soils: Implications for disease suppression

Applications of the Soil, Plant and Rumen Microbiomes in Pastoral Agriculture

Protecting the unseen majority: Land cover and environmental factors linked with soil bacterial communities and functions in New Zealand

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