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Azemtsop Matanfack G, Taubert M, Reilly-Schott V, Küsel K, Rösch P, Popp J. Phenotypic Differentiation of Autotrophic and Heterotrophic Bacterial Cells Using Raman-D 2O Labeling. Anal Chem 2022; 94:7759-7766. [PMID: 35608509 DOI: 10.1021/acs.analchem.1c04097] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Carbon cycling is one of the major biogeochemical processes driven by bacteria. Autotrophic bacteria convert carbon dioxide (CO2) into organic compounds that are used by heterotrophs. Mixotrophic bacteria can employ both autotrophy and heterotrophy for growth. The characterization of the lifestyle of individual cells is essential to understand the microbial activity and thus reveal the implication of bacteria in the carbon flux. In this study, we used groundwater bacteria to investigate the potential of Raman-D2O labeling in combination with chemometrics to identify the carbon assimilation strategies of bacteria. Classification models were built using principal component analysis (PCA) followed by linear discriminant analysis (LDA). Autotrophs assimilated a significantly higher amount (mean C-D ratio between 16.63 and 21.69%) of deuterium than heterotrophs. The C-D signal only provides information about the activity since it appears in the Raman-silent region, where no interference with the taxonomic information is expected. The classification between autotrophs and heterotrophs achieved an overall accuracy of 96.3%. In the validation step with an independent dataset containing species not included in the model, the PCA-LDA model achieved 100% accuracy. This demonstrated that the C-D signal contributed to the identification of autotrophic and heterotrophic bacterial cells. This work reports a robust, rapid, and nondestructive approach for the identification of single cells based on their carbon acquisition strategies. The present study foresees the potential of Raman-D2O labeling as a promising method for automated discrimination of in situ functional activities of bacteria in environmental systems.
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Affiliation(s)
- Georgette Azemtsop Matanfack
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Helmholtzweg 4, 07743 Jena, Germany.,Leibniz Institute of Photonic Technology (Leibniz-IPHT), Albert-Einstein-Straße 9, 07745 Jena, Germany.,Research Campus Infectognostics e.V., 07743 Jena, Germany
| | - Martin Taubert
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany
| | - Vincent Reilly-Schott
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Petra Rösch
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Helmholtzweg 4, 07743 Jena, Germany.,Research Campus Infectognostics e.V., 07743 Jena, Germany
| | - Jürgen Popp
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Helmholtzweg 4, 07743 Jena, Germany.,Leibniz Institute of Photonic Technology (Leibniz-IPHT), Albert-Einstein-Straße 9, 07745 Jena, Germany.,Research Campus Infectognostics e.V., 07743 Jena, Germany
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Louca S, Hawley AK, Katsev S, Torres-Beltran M, Bhatia MP, Kheirandish S, Michiels CC, Capelle D, Lavik G, Doebeli M, Crowe SA, Hallam SJ. Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone. Proc Natl Acad Sci U S A 2016; 113:E5925-E5933. [PMID: 27655888 PMCID: PMC5056048 DOI: 10.1073/pnas.1602897113] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Microorganisms are the most abundant lifeform on Earth, mediating global fluxes of matter and energy. Over the past decade, high-throughput molecular techniques generating multiomic sequence information (DNA, mRNA, and protein) have transformed our perception of this microcosmos, conceptually linking microorganisms at the individual, population, and community levels to a wide range of ecosystem functions and services. Here, we develop a biogeochemical model that describes metabolic coupling along the redox gradient in Saanich Inlet-a seasonally anoxic fjord with biogeochemistry analogous to oxygen minimum zones (OMZs). The model reproduces measured biogeochemical process rates as well as DNA, mRNA, and protein concentration profiles across the redox gradient. Simulations make predictions about the role of ubiquitous OMZ microorganisms in mediating carbon, nitrogen, and sulfur cycling. For example, nitrite "leakage" during incomplete sulfide-driven denitrification by SUP05 Gammaproteobacteria is predicted to support inorganic carbon fixation and intense nitrogen loss via anaerobic ammonium oxidation. This coupling creates a metabolic niche for nitrous oxide reduction that completes denitrification by currently unidentified community members. These results quantitatively improve previous conceptual models describing microbial metabolic networks in OMZs. Beyond OMZ-specific predictions, model results indicate that geochemical fluxes are robust indicators of microbial community structure and reciprocally, that gene abundances and geochemical conditions largely determine gene expression patterns. The integration of real observational data, including geochemical profiles and process rate measurements as well as metagenomic, metatranscriptomic and metaproteomic sequence data, into a biogeochemical model, as shown here, enables holistic insight into the microbial metabolic network driving nutrient and energy flow at ecosystem scales.
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Affiliation(s)
- Stilianos Louca
- Institute of Applied Mathematics, University of British Columbia, Vancouver, BC, Canada V6T1Z2
| | - Alyse K Hawley
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T1Z3
| | - Sergei Katsev
- Large Lakes Observatory, University of Minnesota Duluth, Duluth, MN 55812; Department of Physics and Astronomy, University of Minnesota Duluth, Duluth, MN 55812
| | - Monica Torres-Beltran
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T1Z3
| | - Maya P Bhatia
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T1Z3; Canadian Institute for Advanced Research Program in Integrated Microbial Biodiversity, Canadian Institute for Advanced Research, Toronto, ON, Canada M5G1Z8
| | - Sam Kheirandish
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T1Z3
| | - Céline C Michiels
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T1Z3
| | - David Capelle
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada V6T1Z4
| | - Gaute Lavik
- Biogeochemistry Group, Max Planck Institute for Marine Microbiology, Bremen D-28359, Germany
| | - Michael Doebeli
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada V6T1Z4; Department of Mathematics, University of British Columbia, Vancouver, BC, Canada V6T1Z4
| | - Sean A Crowe
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T1Z3; Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada V6T1Z4; Ecosystem Services, Commercialization Platforms, and Entrepreneurship (ECOSCOPE) Training Program, University of British Columbia, Vancouver, BC, Canada V6T1Z3;
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T1Z3; Canadian Institute for Advanced Research Program in Integrated Microbial Biodiversity, Canadian Institute for Advanced Research, Toronto, ON, Canada M5G1Z8; Ecosystem Services, Commercialization Platforms, and Entrepreneurship (ECOSCOPE) Training Program, University of British Columbia, Vancouver, BC, Canada V6T1Z3; Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada V6T1Z3; Peter Wall Institute for Advanced Studies, University of British Columbia, Vancouver, BC, Canada V6T1Z2
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Liu JF, Sun XB, Yang GC, Mbadinga SM, Gu JD, Mu BZ. Analysis of microbial communities in the oil reservoir subjected to CO2-flooding by using functional genes as molecular biomarkers for microbial CO2 sequestration. Front Microbiol 2015; 6:236. [PMID: 25873911 PMCID: PMC4379918 DOI: 10.3389/fmicb.2015.00236] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 03/10/2015] [Indexed: 11/13/2022] Open
Abstract
Sequestration of CO2 in oil reservoirs is considered to be one of the feasible options for mitigating atmospheric CO2 building up and also for the in situ potential bioconversion of stored CO2 to methane. However, the information on these functional microbial communities and the impact of CO2 storage on them is hardly available. In this paper a comprehensive molecular survey was performed on microbial communities in production water samples from oil reservoirs experienced CO2-flooding by analysis of functional genes involved in the process, including cbbM, cbbL, fthfs, [FeFe]-hydrogenase, and mcrA. As a comparison, these functional genes in the production water samples from oil reservoir only experienced water-flooding in areas of the same oil bearing bed were also analyzed. It showed that these functional genes were all of rich diversity in these samples, and the functional microbial communities and their diversity were strongly affected by a long-term exposure to injected CO2. More interestingly, microorganisms affiliated with members of the genera Methanothemobacter, Acetobacterium, and Halothiobacillus as well as hydrogen producers in CO2 injected area either increased or remained unchanged in relative abundance compared to that in water-flooded area, which implied that these microorganisms could adapt to CO2 injection and, if so, demonstrated the potential for microbial fixation and conversion of CO2 into methane in subsurface oil reservoirs.
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Affiliation(s)
- Jin-Feng Liu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology Shanghai, China
| | - Xiao-Bo Sun
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology Shanghai, China
| | - Guang-Chao Yang
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology Shanghai, China
| | - Serge M Mbadinga
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology Shanghai, China
| | - Ji-Dong Gu
- School of Biological Sciences, University of Hong Kong Hong Kong, China
| | - Bo-Zhong Mu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology Shanghai, China
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Huang CH, Ye M. The Rh protein family: gene evolution, membrane biology, and disease association. Cell Mol Life Sci 2010; 67:1203-18. [PMID: 19953292 PMCID: PMC11115862 DOI: 10.1007/s00018-009-0217-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Revised: 11/10/2009] [Accepted: 11/12/2009] [Indexed: 11/25/2022]
Abstract
The Rh (Rhesus) genes encode a family of conserved proteins that share a structural fold of 12 transmembrane helices with members of the major facilitator superfamily. Interest in this family has arisen from the discovery of Rh factor's involvement in hemolytic disease in the fetus and newborn, and of its homologs widely expressed in epithelial tissues. The Rh factor and Rh-associated glycoprotein (RhAG), with epithelial cousins RhBG and RhCG, form four subgroups conferring upon vertebrates a genealogical commonality. The past decade has heralded significant advances in understanding the phylogenetics, allelic diversity, crystal structure, and biological function of Rh proteins. This review describes recent progress on this family and the molecular insights gleaned from its gene evolution, membrane biology, and disease association. The focus is on its long evolutionary history and surprising structural conservation from prokaryotes to humans, pointing to the importance of its functional role, related to but distinct from ammonium transport proteins.
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Affiliation(s)
- Cheng-Han Huang
- Laboratory of Biochemistry and Molecular Genetics, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA.
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Dos Santos VAPM, Heim S, Moore ERB, Strätz M, Timmis KN. Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440. Environ Microbiol 2004; 6:1264-86. [PMID: 15560824 DOI: 10.1111/j.1462-2920.2004.00734.x] [Citation(s) in RCA: 217] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
A major challenge in microbiology is the elucidation of the genetic and ecophysiological basis of habitat specificity of microbes. Pseudomonas putida is a paradigm of a ubiquitous metabolically versatile soil bacterium. Strain KT2440, a safety strain that has become a laboratory workhorse worldwide, has been recently sequenced and its genome annotated. By drawing on both published information and on original in silico analysis of its genome, we address here the question of what genomic features of KT2440 could explain or are consistent with its ubiquity, metabolic versatility and adaptability. The genome of KT2440 exhibits combinations of features characteristic of terrestrial, rhizosphere and aquatic bacteria, which thrive in either copiotrophic or oligotrophic habitats, and suggests that P. putida has evolved and acquired functions that equip it to thrive in diverse, often inhospitable environments, either free-living, or in close association with plants. The high diversity of protein families encoded by its genome, the large number and variety of small aralogous families, insertion elements, repetitive extragenic palindromic sequences, as well as the mosaic structure of the genome (with many regions of 'atypical' composition) and the multiplicity of mobile elements, reflect a high functional diversity in P. putida and are indicative of its evolutionary trajectory and adaptation to the diverse habitats in which it thrives. The unusual wealth of determinants for high affinity nutrient acquisition systems, mono- and di-oxygenases, oxido-reductases, ferredoxins and cytochromes, dehydrogenases, sulfur metabolism proteins, for efflux pumps and glutathione-S-transfereases, and for the extensive array of extracytoplasmatic function sigma factors, regulators, and stress response systems, constitute the genomic basis for the exceptional nutritional versatility and opportunism of P. putida , its ubiquity in diverse soil, rhizosphere and aquatic systems, and its renowned tolerance of natural and anthropogenic stresses. This metabolic diversity is also the basis of the impressive evolutionary potential of KT2440, and its utility for the experimental design of novel pathways for the catabolism of organic, particularly aromatic, pollutants, and its potential for bioremediation of soils contaminated with such compounds as well as for its application in the production of high-added value compounds.
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Affiliation(s)
- V A P Martins Dos Santos
- Department of Environmental Microbiology, GBF - German Research Centre for Biotechnology, Braunschweig, Germany.
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