Using soil bacterial communities to predict physico-chemical variables and soil quality
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RESEARCH
Open Access
Using soil bacterial communities to predict physico-chemical variables and soil quality Syrie M. Hermans1, Hannah L. Buckley2, Bradley S. Case2, Fiona Curran-Cournane3, Matthew Taylor4 and Gavin Lear1*
Abstract Background: Soil ecosystems consist of complex interactions between biological communities and physicochemical 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 physicochemical variables of each site. Results: Soil 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. Conclusions: The 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. Keywords: Bacterial communities, Bacterial indicators, Biomonitoring, Environmental monitoring, Random forest analysis, Soil health, Soil microbiology
* Correspondence: [email protected] 1 School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third part
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