Using soil bacterial communities to predict physico-chemical variables and soil quality

Syrie M Hermans,Gavin Lear,Matthew Taylor,Hannah L Buckley,Fiona Curran-Cournane,Bradley S Case

doi:10.1186/s40168-020-00858-1

Syrie M Hermans, Gavin Lear + Show 4 more

Open Access

https://doi.org/10.1186/s40168-020-00858-1

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Abstract

BackgroundSoil ecosystems consist of complex interactions between biological communities and physico-chemical variables, all of which contribute to the overall quality of soils. Despite this, changes in bacterial communities are ignored by most soil monitoring programs, which are crucial to ensure the sustainability of land management practices. We applied 16S rRNA gene sequencing to determine the bacterial community composition of over 3000 soil samples from 606 sites in New Zealand. Sites were classified as indigenous forests, exotic forest plantations, horticulture, or pastoral grasslands; soil physico-chemical variables related to soil quality were also collected. The composition of soil bacterial communities was then used to predict the land use and soil physico-chemical variables of each site.ResultsSoil bacterial community composition was strongly linked to land use, to the extent where it could correctly determine the type of land use with 85% accuracy. Despite the inherent variation introduced by sampling across ~ 1300 km distance gradient, the bacterial communities could also be used to differentiate sites grouped by key physico-chemical properties with up to 83% accuracy. Further, individual soil variables such as soil pH, nutrient concentrations and bulk density could be predicted; the correlations between predicted and true values ranged from weak (R2 value = 0.35) to strong (R2 value = 0.79). These predictions were accurate enough to allow bacterial communities to assign the correct soil quality scores with 50–95% accuracy.ConclusionsThe inclusion of biological information when monitoring soil quality is crucial if we wish to gain a better, more accurate understanding of how land management impacts the soil ecosystem. We have shown that soil bacterial communities can provide biologically relevant insights on the impacts of land use on soil ecosystems. Furthermore, their ability to indicate changes in individual soil parameters shows that analysing bacterial DNA data can be used to screen soil quality.ByKu94ww1-1K9vBDz2Q4_dVideo

Highlights

Soil ecosystems consist of complex interactions between biological communities and physicochemical variables, all of which contribute to the overall quality of soils
Using an extensive dataset of soil samples collected from a variety of different natural and managed land uses across New Zealand, we aimed to (1) determine how bacterial communities in managed soils differ to those in natural, undisturbed environments, (2) determine the extent to which bacterial communities in managed soils can predict soil physico-chemical characteristics and (3) explore if these predictions are accurate and reliable enough to be applied for soil quality monitoring
The composition of soil bacterial communities was determined for 606 sites across New Zealand (Fig. S1, Additional file 1)

Summary

Introduction

Soil ecosystems consist of complex interactions between biological communities and physicochemical variables, all of which contribute to the overall quality of soils. Changes in bacterial communities are ignored by most soil monitoring programs, which are crucial to ensure the sustainability of land management practices. The composition of soil bacterial communities was used to predict the land use and soil physicochemical variables of each site. Despite the importance of living organisms for maintaining healthy soil ecosystems, most initiatives that directly monitor soil quality for applied purposes focus on changes in abiotic variables such as soil nutrients, metal pollutants and soil structure [8]. As well as relaying important information about the biological functioning of the ecosystem, soil organisms only respond to bioavailable nutrients and contaminants, unlike chemical measures which reflect the total proportion present [10]. Better incorporation of biological indicators in soil monitoring will provide a more sensitive, relevant and holistic insight into how anthropogenic activity impacts the soil environment

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