Emergent properties of microbial activity in heterogeneous soil microenvironments: Different research approaches are slowly converging, yet major challenges remain
Author | Baveye P.C. |
Author | Otten W. |
Author | Kravchenko A. |
Author | Balseiro-Romero M. |
Author | Beckers E. |
Author | Chalhoub M. |
Author | Darnault C. |
Author | Eickhorst T. |
Author | Garnier P. |
Author | Hapca S. |
Author | Kiranyaz S. |
Author | Monga O. |
Author | Mueller C.W. |
Author | Nunan N. |
Author | Pot V. |
Author | Schluter S. |
Author | Schmidt H. |
Author | Vogel H.-J. |
Available date | 2020-03-18T08:10:07Z |
Publication Date | 2018 |
Publication Name | Frontiers in Microbiology |
Resource | Scopus |
ISSN | 1664302X |
Abstract | Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the bulk, macroscopic parameters (e.g., granulometry, pH, soil organic matter, and biomass contents) commonly used to characterize soils provide insufficient information to describe quantitatively the activity of soil microorganisms and some of its outcomes, like the emission of greenhouse gasses. Clearly, new, more appropriate macroscopic parameters are needed, which reflect better the spatial heterogeneity of soils at the microscale (i.e., the pore scale) that is commensurate with the habitat of many microorganisms. For a long time, spectroscopic and microscopic tools were lacking to quantify processes at that scale, but major technological advances over the last 15 years have made suitable equipment available to researchers. In this context, the objective of the present article is to review progress achieved to date in the significant research program that has ensued. This program can be rationalized as a sequence of steps, namely the quantification and modeling of the physical-, (bio)chemical-, and microbiological properties of soils, the integration of these different perspectives into a unified theory, its upscaling to the macroscopic scale, and, eventually, the development of new approaches to measure macroscopic soil characteristics. At this stage, significant progress has been achieved on the physical front, and to a lesser extent on the (bio)chemical one as well, both in terms of experiments and modeling. With regard to the microbial aspects, although a lot of work has been devoted to the modeling of bacterial and fungal activity in soils at the pore scale, the appropriateness of model assumptions cannot be readily assessed because of the scarcity of relevant experimental data. For significant progress to be made, it is crucial to make sure that research on the microbial components of soil systems does not keep lagging behind the work on the physical and (bio)chemical characteristics. Concerning the subsequent steps in the program, very little integration of the various disciplinary perspectives has occurred so far, and, as a result, researchers have not yet been able to tackle the scaling up to the macroscopic level. Many challenges, some of them daunting, remain on the path ahead. Fortunately, a number of these challenges may be resolved by brand new measuring equipment that will become commercially available in the very near future. |
Sponsor | TE acknowledges gratefully the financial support received from the German Research Foundation (DFG; ZK/14/M8-Plus) and German Academic Research Service (DAAD; K/15/464342). Finally, PCB, SS, TE, and CM acknowledge the financial support by the German Soil Science Society (DBG) for the workshop "Combined analysis of biochemistry and structural complexity of soil via imaging", held at the UFZ in July 2016 and during which many aspects of the topic reviewed in this article were discussed The research described in this article was made possible in part through NPRP grant #9-390-1-088 from the Qatar National Research Fund (Project Simupor), as well as through a grant from the Agence Nationale de la Recherche (ANR, France) to project Soil?3D. WO acknowledges funding from the National Environment and Research Council (NE/P014208/1). MB-R's contribution was made possible by a postdoctoral fellowship (Programa de axudas ? etapa posdoutoral; ED481B 2017/073) awarded by the Conseller?a de Cultura, Educaci?n e Ordenaci?n Universitaria (Xunta de Galicia, Spain) |
Language | en |
Publisher | Frontiers Media S.A. |
Subject | Biodiversity NanoSIMS imaging Single-cell genomics Soil microbiology Tomography Upscaling X-ray computed |
Type | Article Review |
Issue Number | AUG |
Volume Number | 9 |
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