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Falkenberg R, Sigl L, Fochler M. From 'making lists' to conducting 'well-rounded' studies: Epistemic re-orientations in soil microbial ecology. SOCIAL STUDIES OF SCIENCE 2024; 54:78-104. [PMID: 37387230 PMCID: PMC10832317 DOI: 10.1177/03063127231179700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Soil microbial ecology is a relatively young research field that became established around the middle of the 20th century and has grown considerably since then. We analyze two epistemic re-orientations in the field, asking how possibilities for creating do-able problems within current conditions of research governance and researchers' collective sense-making about new, more desirable modes of research were intertwined in these developments. We show that a first re-orientation towards molecular omics studies was comparably straightforward to bring about, because it allowed researchers to gain resources for their work and to build careers-in other words, to create do-able problems. Yet, over time this mode of research developed into a scientific bandwagon from which researchers found it difficult to depart, even as they considered this kind of work as producing mostly descriptive studies rather than exploring interesting and important ecological questions. Researchers currently wish to re-orient their field again, towards a new mode of conducting 'well-rounded' interdisciplinary and ecologically-relevant studies. This re-orientation is, however, not easy to put into practice. In contrast to omics studies, this new mode of research does not easily enable the creation of do-able problems for two reasons. First, it is not as readily 'packaged' and hence more difficult to align with institutional and funding frameworks as well as with demands for productivity and career building. Second, while the first re-orientation was part of a broader exciting bandwagon across the life sciences and promised apparent discoveries, the current re-orientation goes along with a different sense of novelty, exploring complex environmental relations and building an understanding at the intersection of disciplines, instead of pushing a clearly circumscribed frontier. Ultimately, our analysis raises questions about whether current conditions of research governance structurally privilege particular kinds of scientific re-orientation over others.
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Affiliation(s)
| | - Lisa Sigl
- University of Vienna, Vienna, Austria
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Merges D, Schmidt A, Schmitt I, Neuschulz EL, Dal Grande F, Bálint M. Metatranscriptomics reveals contrasting effects of elevation on the activity of bacteria and bacterial viruses in soil. Mol Ecol 2023; 32:6552-6563. [PMID: 36321191 DOI: 10.1111/mec.16756] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 08/24/2022] [Accepted: 10/13/2022] [Indexed: 11/21/2022]
Abstract
Soil microbial diversity affects ecosystem functioning and global biogeochemical cycles. Soil bacterial communities catalyse a diversity of biogeochemical reactions and have thus sparked considerable scientific interest. One driver of bacterial community dynamics in natural ecosystems has so far been largely neglected: the predator-prey interactions between bacterial viruses (bacteriophages) and bacteria. To generate ground level knowledge on environmental drivers of these particular predator-prey dynamics, we propose an activity-based ecological framework to simultaneous capture community dynamics of bacteria and bacteriophages in soils. An ecological framework and specifically the analyses of community dynamics across latitudinal and elevational gradients have been widely used in ecology to understand community-wide responses of innumerable taxa to environmental change, in particular to climate. Here, we tested the hypothesis that the activity of bacteria and bacteriophages codeclines across an elevational gradient. We used metatranscriptomics to investigate bacterial and bacteriophage activity patterns at five sites across 400 elevational metres in the Swiss Alps in 2015 and 2017. We found that metabolic activity (transcription levels) of bacteria declined significantly with increasing elevation, but activity of bacteriophages did not. We showed that bacteriophages are consistently active in soil along the entire gradient, making bacteriophage activity patterns divergent from that of their putative bacterial prey. Future efforts will be necessary to link the environment-activity relationship to predator-prey dynamics, and to understand the magnitude of viral contributions to carbon, nitrogen and phosphorus cycling when infection causes bacterial cell death, a process that may represent an overlooked component of soil biogeochemical cycles.
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Affiliation(s)
- Dominik Merges
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Alexandra Schmidt
- Department of Biology, Limnological Institute, University Konstanz, Konstanz, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Eike Lena Neuschulz
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Department of Biology, University of Padova, Padua, Italy
| | - Miklós Bálint
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Institute of Insect Biotechnology, Justus Liebig University Gießen, Gießen, Germany
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Timsy T, Behrendt U, Ulrich A, Foesel BU, Spanner T, Neumann-Schaal M, Wolf J, Schloter M, Horn MA, Kolb S. Genomic evidence for two pathways of formaldehyde oxidation and denitrification capabilities of the species Paracoccus methylovorus sp. nov. Int J Syst Evol Microbiol 2022; 72. [PMID: 36861375 DOI: 10.1099/ijsem.0.005581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Three strains (H4-D09T, S2-D11 and S9-F39) of a member of the genus Paracoccus attributed to a novel species were isolated from topsoil of temperate grasslands. The genome sequence of the type strain H4-D09T exhibited a complete set of genes required for denitrification as well as methylotrophy. The genome of H4-D09T included genes for two alternative pathways of formaldehyde oxidation. Besides the genes for the canonical glutathione (GSH)-dependent formaldehyde oxidation pathway, all genes for the tetrahydrofolate-formaldehyde oxidation pathway were identified. The strain has the potential to utilize methanol and/or methylamine as a single carbon source as evidenced by the presence of methanol dehydrogenase (mxaFI) and methylamine dehydrogenase (mau) genes. Apart from dissimilatory denitrification genes (narA, nirS, norBC and nosZ), genes for assimilatory nitrate (nasA) and nitrite reductases (nirBD) were also identified. The results of phylogenetic analysis based on 16S rRNA genes coupled with riboprinting revealed that all three strains represented the same species of genus Paracoccus. Core genome phylogeny of the type strain H4-D09T indicated that Paracoccus thiocyanatus and Paracoccus denitrificans are the closest phylogenetic neighbours. The average nucleotide index (ANI) and digital DNA-DNA hybridization (dDDH) with the closest phylogenetic neighbours revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. The major respiratory quinone is Q-10, and the predominant cellular fatty acids are C18 : 1ω7c, C19 : 0cyclo ω7c, and C16 : 0, which correspond to those detected in other members of the genus. The polar lipid profile consists of a diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), aminolipid (AL), glycolipid (GL) and an unidentified lipid (L).On the basis of our results, we concluded that the investigated isolates represent a novel species of the genus Paracoccus, for which the name Paracoccus methylovorus sp. nov. (type strain H4-D09T=LMG 31941T= DSM 111585T) is proposed.
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Affiliation(s)
- Timsy Timsy
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany.,Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Undine Behrendt
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Andreas Ulrich
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Bärbel U Foesel
- Research Unit Molecular Epidemiology, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Tobias Spanner
- Institute of Microbiology, Leibniz University of Hannover, Hannover, Germany
| | - Meina Neumann-Schaal
- Research Group Bacterial Metabolomics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Jacqueline Wolf
- Research Group Bacterial Metabolomics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Marcus A Horn
- Institute of Microbiology, Leibniz University of Hannover, Hannover, Germany
| | - Steffen Kolb
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany.,Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
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Dong Y, Tebo BM. Editorial: Insights in Microbiological Chemistry and Geomicrobiology: 2021. Front Microbiol 2022; 13:970474. [PMID: 35903475 PMCID: PMC9325411 DOI: 10.3389/fmicb.2022.970474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Yiran Dong
- School of Environmental Studies, China University of Geosciences, Wuhan, China
- *Correspondence: Yiran Dong
| | - Bradley M. Tebo
- Department of Chemistry, University of Washington, Seattle, WA, United States
- Bradley M. Tebo
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