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 -