Microbial indicators for soil quality
Open accessAbstract
The living soil is instrumental to key life support functions (LSF) that safeguard life on Earth. The soil microbiome has a main role as a driver of these LSF. Current global developments, like anthropogenic threats to soil (e.g., via intensive agriculture) and climate change, pose a burden on soil functioning. Therefore, it is important to dispose of robust indicators that report on the nature of deleterious changes and thus soil quality. There has been a long debate on the best selection of biological indicators (bioindicators) that report on soil quality. Such indicators should ideally describe organisms with key functions in the system, or with key regulatory/connecting roles (so-called keystone species ). However, in the light of the huge functional redundancy in most soil microbiomes, finding specific keystone markers is not a trivial task. The current rapid development of molecular (DNA-based) methods that facilitate deciphering microbiomes with respect to key functions will enable the development of improved criteria by which molecular information can be tuned to yield molecular markers of soil LSF. This review critically examines the current state-of-the-art in molecular marker development and recommends avenues to come to improved future marker systems.
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A large proportion of soil organisms remains to be characterized in taxonomic and functional terms.
“since a large proportion of soil organisms yet remains to be characterized in taxonomic and functional terms (Schloter et al., 2018; Bouchez et al., 2016).”
From Soil quality – A critical review (2018) · cites this paper as Schloter et al., 2018
In “The soil microbiome—an ignored majority” (page unavailable), the paper says that efforts to characterize the soil microbiome in depth have been hindered by its complexity. In “Soil microbiome functions that drive nitrogen transformations” (page unavailable), it also says that knowledge of some organisms and their genes is lacking. These passages support the point for soil microorganisms, but not its extension to soil organisms generally. (LLM, conf=0.80)
Experimental — accuracy not yet measuredThe analysis of the 'big data' generated with sequencing poses a serious challenge in terms of time, computing capacities and interpretation.
“The analysis of the ' big data ' generated with sequencing also poses a serious challenge in terms of time, computing capacities and interpretation”
From Soil quality – A critical review (2018) · cites this paper as Schloter et al., 2018
In “The soil microbiome—an ignored majority” (page not provided), the paper says sequencing generates “big data” that challenge bioinformatics analysis. “Brave new world” also notes interpretational pitfalls for high-throughput sequencing. The cited passages do not specify analysis time or computing-capacity demands; their reference to time concerns sampling, not data analysis. (LLM, conf=0.88)
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Flagged first, then by citations
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Cited by
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Soil quality – A critical review
Bünemann, E. K., Bongiorno, G., Bai, Z., Creamer, R. E., De Deyn, G., de Goede, R., Fleskens, L., Geissen, V., Kuyper, T. W., Mäder, P., et al. (2018) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2018.01.030 · Cited by 2,960 · see citing works
- Authors
- Schloter, M., Nannipieri, P., Sørensen, S. J., & van Elsas, J. D.
- Affiliations
- Helmholtz Munich (DE)
- University of Florence (IT)
- University of Copenhagen (DK)
- Venue
- Biology and Fertility of Soils
- Published
- 2017-10-16
- Volume
- 54
- Issue
- 1
- Pages
- 1-10
- ISSN
- 0178-2762 (ISSN-L)
- 1432-0789
- OpenAlex
- W2765364657
- Cited by
- 540
- References
- 61
- Citations by year
- 2026: 49 · 2025: 65 · 2024: 72 · 2023: 61 · 2022: 79 · 2021: 83 · 2020: 61 · 2019: 44 · 2018: 16 · 2015: 1 · 2014: 1 · 2013: 1 · 2012: 1
- FWCI
- 36.29
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Biology and Fertility of Soils (publishedVersion, cc-by)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by)
- mediaTUM – the media and publications repository of the Technical University Munich (Technical University Munich) (submittedVersion, other-oa)
- Site cant be reached (submittedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, cc-by)
- PuSH - Publication Server of Helmholtz Zentrum München (submittedVersion)
- Funders
- University of Groningen
- Topics
- Life Sciences › Agricultural and Biological Sciences › Soil Science › Soil Carbon and Nitrogen Dynamics
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Mycorrhizal Fungi and Plant Interactions
- Keywords
- soil quality, bioindicators, soil microbiome, keystone species, functional redundancy, molecular markers, soil functions, DNA-based methods, anthropogenic soil disturbance, climate change impacts on soil
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