A methodological framework to embrace soil biodiversity

Geisen, Stefan; Briones, Maria J.I.; Gan, Huijie; Behan‐Pelletier, Valerie M.; Friman, Ville‐Petri; Groot, G.A. de; Hannula, S. Emilia; Lindo, Zoë; Philippot, Laurent; Tiunov, Alexei V.; Wall, Diana H.

doi:10.1016/j.soilbio.2019.107536

Cited by 120 publications

(85 citation statements)

References 183 publications

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“…The future success of metagenomics in soil surveys will mainly depend on the possibilities to standardise bioinformatics pipelines as well as on the availability of tools for big data analysis and artificial intelligence. However, it must be mentioned that even a well-standardised and automated workflow will generate only data on the relative abundance of nucleotide sequences and not absolute values (Geisen et al, 2019). Thus at the moment for the assessment of new methods linked to Functions 4 to 8, qPCR from soil DNA extracts (ISO 17601, 2016) plays a very important role in determining the abun-dance of single-marker gene sequences, which are indicative of specific transformation processes or soil functions.…”

Section: Microbial Biomass and Respiration (Some Relations To Functiomentioning

confidence: 99%

“…Consequently, this technique does not reflect the full spectrum of microbial species within a mixed soil community. Additionally, due to the artificial growth conditions required in the test, it is argued that the method does not reflect the microbial community diversity and its function of a given soil (Glimm et al, 1997). On the other hand, however, standardised conditions allow for direct comparisons between microbial communities in different sites, for example, independent of the abiotic conditions, thus making CLPP a popular method for toxicology testing (Preston-Mafham et al, 2002).…”

Section: Microbial Biomass and Respiration (Some Relations To Functiomentioning

confidence: 99%

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Identification of new microbial functional standards for soil quality assessment

Thiele‐Bruhn¹,

Schloter

Wilke

et al. 2020

SOIL

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Abstract. The activity of microorganisms in soil is important for a robust functioning of soil and related ecosystem services. Hence, there is a necessity to identify the composition, diversity, and function of the soil microbiome in order to determine its natural properties, functioning, and operating range as well as to assess ecotoxicological effects due to anthropogenic activities. Numerous microbiological methods currently exist in the literature and new, more advanced methods continue to be developed; however, only a limited number of these methods are standardised. Consequently, there is a need to identify the most promising non-standardised methods for assessing soil quality and to transform them into standards. In agreement with the “Ecosystem Service Approach”, new methods should focus more on soil microbial functions, including nutrient cycling and greenhouse gas emission, pest control and plant growth promotion, carbon cycling and sequestration, as well as soil structure development and filter function. The few existing standardised methods available that focus on the function of the soil microbiome mostly include measurements, like basal respiration, enzyme activities, and biodegradation of organic matter, under well-defined conditions in the lab. This paper sets out to summarise and expand on recent discussions within the International Organization for Standardization (ISO), Soil Quality – Biological Characterization sub-committee (ISO TC 190/SC 4), where a need was identified to develop scientifically sound methods which would best fulfil the practical needs of future users for assessing soil quality, going beyond the existing test systems. Of particular note is the current evolution of molecular methods in microbial ecology that use quantitative real-time PCR (qPCR) to produce a large number of new functional endpoints which are more sensitive as compared to “classical” methods. Quantitative PCR assesses the abundance of microbes that catalyse major transformation steps in nitrogen and phosphorus cycling, greenhouse gas emissions, chemical transformations including pesticide degradation, and plant growth promotion pathways based on the assessment of marker gene sequences that drive the related processes. In the assessment of soil quality methods, it was found that most methods focus on bacteria and related endpoints. Techniques to describe fungal communities as well as their functional traits are far less represented. As such, techniques to analyse fungal enzyme activities are proposed. Additionally, methods for the determination of microbial growth rates and efficiencies, including the use of glomalin as a biochemical marker for soil aggregation, are discussed. Furthermore, field methods indicative of carbon turnover, including the litter bag test and a modification to the tea bag test, are presented. However, it is obvious that with increasing developments in high throughput sequencing technologies and big data analyses, including metagenomics analysis, it will be possible to implement these technologies into the standardisation process for assessing the functions of the soil microbiome. Overall, it is suggested that endpoints should represent a potential function of soil microorganisms rather than actual activity levels, as the latter can largely be dependent on short-term variable soil properties such as pedoclimatic conditions, nutrient availability, and anthropogenic soil cultivation activities.

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Section: Microbial Biomass and Respiration (Some Relations To Functiomentioning

confidence: 99%

Section: Microbial Biomass and Respiration (Some Relations To Functiomentioning

confidence: 99%

Identification of new microbial functional standards for soil quality assessment

Thiele‐Bruhn¹,

Schloter

Wilke

et al. 2020

SOIL

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“…To be able to cope with this high diversity, species can be grouped into functional groups, under the assumption that if species occur at the same location in the soil and share the same resources and predators they should perform the same function (review: Briones, 2014 ). Research has so far focused on the importance of each one of these functional groups to the ecosystem, but this highly specialised information is not integrated into the more plant-based ecosystem models ( Geisen et al, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

KEYLINK: towards a more integrative soil representation for inclusion in ecosystem scale models. I. review and model concept

Deckmyn

Flores

Mayer

et al. 2020

PeerJ

Self Cite

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The relatively poor simulation of the below-ground processes is a severe drawback for many ecosystem models, especially when predicting responses to climate change and management. For a meaningful estimation of ecosystem production and the cycling of water, energy, nutrients and carbon, the integration of soil processes and the exchanges at the surface is crucial. It is increasingly recognized that soil biota play an important role in soil organic carbon and nutrient cycling, shaping soil structure and hydrological properties through their activity, and in water and nutrient uptake by plants through mycorrhizal processes. In this article, we review the main soil biological actors (microbiota, fauna and roots) and their effects on soil functioning. We review to what extent they have been included in soil models and propose which of them could be included in ecosystem models. We show that the model representation of the soil food web, the impact of soil ecosystem engineers on soil structure and the related effects on hydrology and soil organic matter (SOM) stabilization are key issues in improving ecosystem-scale soil representation in models. Finally, we describe a new core model concept (KEYLINK) that integrates insights from SOM models, structural models and food web models to simulate the living soil at an ecosystem scale.

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“…Soils host the vast majority of life on Earth including microorganisms and animals, such as viruses, bacteria, fungi, protists, nematodes, and earthworms (Geisen et al, 2019). Microorganisms (bacteria and fungi) may serve as possible bio-indicators for monitoring soil ecosystem functions in close association with changes in the physicochemical and biological conditions during the ecological restoration of degraded areas (Mendez, García, Maestre, & Escudero, 2008;Wang et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Revegetation by sowing reduces soil bacterial and fungal diversity

Wang

Zhang

Zhao

et al. 2019

Ecology and Evolution

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Aim:The aim of this study was to understand the effects of revegetation on the diversity of bacteria and fungi in soil by sowing a single species and exploring the underlying mechanism.Location: Beijing, China. Taxon: Plants and Microbes.Methods: In a short-term ecological restoration experiment, one natural recovery treatment and three seed sowing treatments were chosen to assess their effects on the alteration of fungal and bacterial diversity. Plant species richness, abundance, and height were investigated. The diversity of fungi and bacteria was analyzed by high-throughput sequencing technologies. Linear mixed-effects model analysis was used to examine the effects of different restoration methods on biodiversity and ecosystem functions. Pearson's correlation analysis, analysis of covariance, and structural equation modeling (SEM) were used to examine the relationship between biodiversity and environmental factors. Results: Species richness and the Shannon-Wiener Index (H′) of plants in the sown treatments were lower than in the natural recovery treatment, especially with sowing of Medicago sativa L. Similarly, the sum of the observed species and H′ of fungi and bacteria significantly decreased in the sown treatments. Moreover, plant density, community coverage, and soil moisture increased markedly, while soil bulk density decreased in the sown treatments. Importantly, SEM showed that sown treatments reduced the diversity of plants through increasing plant density, while it decreased the diversity of fungi and bacteria through decreasing the plant diversity and increasing soil moisture.Main conclusions: Our findings confirm that ecological restoration by sowing could improve soil conditions, but may be unfavorable to the amelioration of soil microbial diversity in the short-term. Restoration practitioners should consider long-term studies on the dynamics of biodiversity in the above-and belowground after revegetation by native species to achieve goals related to biodiversity conservation.

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A methodological framework to embrace soil biodiversity

Cited by 120 publications

References 183 publications

Identification of new microbial functional standards for soil quality assessment

Identification of new microbial functional standards for soil quality assessment

KEYLINK: towards a more integrative soil representation for inclusion in ecosystem scale models. I. review and model concept

Revegetation by sowing reduces soil bacterial and fungal diversity

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