Details
| Original language | English |
|---|---|
| Article number | 625697 |
| Journal | Frontiers in microbiology |
| Volume | 12 |
| Publication status | Published - 28 Oct 2021 |
Abstract
In this review, we introduce microbially-mediated soil processes, players, their functional traits, and their links to processes at biogeochemical interfaces [e.g., rhizosphere, detritusphere, (bio)-pores, and aggregate surfaces]. A conceptual view emphasizes the central role of the rhizosphere in interactions with other biogeochemical interfaces, considering biotic and abiotic dynamic drivers. We discuss the applicability of three groups of traits based on microbial physiology, activity state, and genomic functional traits to reflect microbial growth in soil. The sensitivity and credibility of modern molecular approaches to estimate microbial-specific growth rates require further development. A link between functional traits determined by physiological (e.g., respiration, biomarkers) and genomic (e.g., genome size, number of ribosomal gene copies per genome, expression of catabolic versus biosynthetic genes) approaches is strongly affected by environmental conditions such as carbon, nutrient availability, and ecosystem type. Therefore, we address the role of soil physico-chemical conditions and trophic interactions as drivers of microbially-mediated soil processes at relevant scales for process localization. The strengths and weaknesses of current approaches (destructive, non-destructive, and predictive) for assessing process localization and the corresponding estimates of process rates are linked to the challenges for modeling microbially-mediated processes in heterogeneous soil microhabitats. Finally, we introduce a conceptual self-regulatory mechanism based on the flexible structure of active microbial communities. Microbial taxa best suited to each successional stage of substrate decomposition become dominant and alter the community structure. The rates of decomposition of organic compounds, therefore, are dependent on the functional traits of dominant taxa and microbial strategies, which are selected and driven by the local environment.
Keywords
- (bio)-pores, detritusphere, mycorrhizosphere, rhizosphere, soil aggregates, soil priming, statistical analysis of process locations, trophic interactions
ASJC Scopus subject areas
- Immunology and Microbiology(all)
- Microbiology
- Medicine(all)
- Microbiology (medical)
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In: Frontiers in microbiology, Vol. 12, 625697, 28.10.2021.
Research output: Contribution to journal › Review article › Research › peer review
}
TY - JOUR
T1 - Bridging Microbial Functional Traits With Localized Process Rates at Soil Interfaces
AU - Blagodatskaya, Evgenia
AU - Tarkka, Mika
AU - Knief, Claudia
AU - Koller, Robert
AU - Peth, Stephan
AU - Schmidt, Volker
AU - Spielvogel, Sandra
AU - Uteau, Daniel
AU - Weber, Matthias
AU - Razavi, Bahar S.
N1 - Funding Information: This research was carried out in inspiration of the framework of the priority programme 2089 “Rhizosphere spatiotemporal organization—a key to rhizosphere functions” funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) Projects: 403664478, 403670038, 403641192, and 403637614. This publication was supported by the RUDN University Strategic Academic Leadership Program. The work of VS and MW was supported by the DFG grant No. SCHM 997/33-1. RK acknowledges support from the Helmholtz Association for the Forschungszentrum Jülich. The contribution of CK was additionally supported by Germany’s Excellence Strategy—EXC 2070–390732324.
PY - 2021/10/28
Y1 - 2021/10/28
N2 - In this review, we introduce microbially-mediated soil processes, players, their functional traits, and their links to processes at biogeochemical interfaces [e.g., rhizosphere, detritusphere, (bio)-pores, and aggregate surfaces]. A conceptual view emphasizes the central role of the rhizosphere in interactions with other biogeochemical interfaces, considering biotic and abiotic dynamic drivers. We discuss the applicability of three groups of traits based on microbial physiology, activity state, and genomic functional traits to reflect microbial growth in soil. The sensitivity and credibility of modern molecular approaches to estimate microbial-specific growth rates require further development. A link between functional traits determined by physiological (e.g., respiration, biomarkers) and genomic (e.g., genome size, number of ribosomal gene copies per genome, expression of catabolic versus biosynthetic genes) approaches is strongly affected by environmental conditions such as carbon, nutrient availability, and ecosystem type. Therefore, we address the role of soil physico-chemical conditions and trophic interactions as drivers of microbially-mediated soil processes at relevant scales for process localization. The strengths and weaknesses of current approaches (destructive, non-destructive, and predictive) for assessing process localization and the corresponding estimates of process rates are linked to the challenges for modeling microbially-mediated processes in heterogeneous soil microhabitats. Finally, we introduce a conceptual self-regulatory mechanism based on the flexible structure of active microbial communities. Microbial taxa best suited to each successional stage of substrate decomposition become dominant and alter the community structure. The rates of decomposition of organic compounds, therefore, are dependent on the functional traits of dominant taxa and microbial strategies, which are selected and driven by the local environment.
AB - In this review, we introduce microbially-mediated soil processes, players, their functional traits, and their links to processes at biogeochemical interfaces [e.g., rhizosphere, detritusphere, (bio)-pores, and aggregate surfaces]. A conceptual view emphasizes the central role of the rhizosphere in interactions with other biogeochemical interfaces, considering biotic and abiotic dynamic drivers. We discuss the applicability of three groups of traits based on microbial physiology, activity state, and genomic functional traits to reflect microbial growth in soil. The sensitivity and credibility of modern molecular approaches to estimate microbial-specific growth rates require further development. A link between functional traits determined by physiological (e.g., respiration, biomarkers) and genomic (e.g., genome size, number of ribosomal gene copies per genome, expression of catabolic versus biosynthetic genes) approaches is strongly affected by environmental conditions such as carbon, nutrient availability, and ecosystem type. Therefore, we address the role of soil physico-chemical conditions and trophic interactions as drivers of microbially-mediated soil processes at relevant scales for process localization. The strengths and weaknesses of current approaches (destructive, non-destructive, and predictive) for assessing process localization and the corresponding estimates of process rates are linked to the challenges for modeling microbially-mediated processes in heterogeneous soil microhabitats. Finally, we introduce a conceptual self-regulatory mechanism based on the flexible structure of active microbial communities. Microbial taxa best suited to each successional stage of substrate decomposition become dominant and alter the community structure. The rates of decomposition of organic compounds, therefore, are dependent on the functional traits of dominant taxa and microbial strategies, which are selected and driven by the local environment.
KW - (bio)-pores
KW - detritusphere
KW - mycorrhizosphere
KW - rhizosphere
KW - soil aggregates
KW - soil priming
KW - statistical analysis of process locations
KW - trophic interactions
UR - http://www.scopus.com/inward/record.url?scp=85119081108&partnerID=8YFLogxK
U2 - 10.3389/fmicb.2021.625697
DO - 10.3389/fmicb.2021.625697
M3 - Review article
AN - SCOPUS:85119081108
VL - 12
JO - Frontiers in microbiology
JF - Frontiers in microbiology
SN - 1664-302X
M1 - 625697
ER -