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Angius F, Cremers G, Frank J, Witkowski C, Pol A, van Alen TA, Jetten MSM, Op den Camp HJM, Berben T. Gene-centered metagenome analysis of Vulcano Island soil (Aeolian archipelago, Italy) reveals diverse microbial key players in methane, hydrogen and sulfur cycles. Antonie Van Leeuwenhoek 2024; 117:94. [PMID: 38954064 PMCID: PMC11219375 DOI: 10.1007/s10482-024-01995-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/28/2024] [Indexed: 07/04/2024]
Abstract
The Aeolian archipelago is known worldwide for its volcanic activity and hydrothermal emissions, of mainly carbon dioxide and hydrogen sulfide. Hydrogen, methane, and carbon monoxide are minor components of these emissions which together can feed large quantities of bacteria and archaea that do contribute to the removal of these notorious greenhouse gases. Here we analyzed the metagenome of samples taken from the Levante bay on Vulcano Island, Italy. Using a gene-centric approach, the hydrothermal vent community appeared to be dominated by Proteobacteria, and Sulfurimonas was the most abundant genus. Metabolic reconstructions highlight a prominent role of formaldehyde oxidation and the reverse TCA cycle in carbon fixation. [NiFe]-hydrogenases seemed to constitute the preferred strategy to oxidize H2, indicating that besides H2S, H2 could be an essential electron donor in this system. Moreover, the sulfur cycle analysis showed a high abundance and diversity of sulfate reduction genes underpinning the H2S production. This study covers the diversity and metabolic potential of the microbial soil community in Levante bay and adds to our understanding of the biogeochemistry of volcanic ecosystems.
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Affiliation(s)
- Federica Angius
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Geert Cremers
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Jeroen Frank
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Caitlyn Witkowski
- Department of Marine Microbiology and Biogeochemistry, NIOZ, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands
- School of Earth Sciences, Wills Memorial Building, University of Bristol, Queens Road, Clifton, BS8 1RJ, UK
| | - Arjan Pol
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Theo A van Alen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
| | - Tom Berben
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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Rocha RA, Alexandrov K, Scott C. Rare earth elements in biology: From biochemical curiosity to solutions for extractive industries. Microb Biotechnol 2024; 17:e14503. [PMID: 38829373 PMCID: PMC11146143 DOI: 10.1111/1751-7915.14503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 04/28/2024] [Accepted: 05/11/2024] [Indexed: 06/05/2024] Open
Abstract
Rare earth elements (REEs) are critical for our modern lifestyles and the transition to a low-carbon economy. Recent advances in our understanding of the role of REEs in biology, particularly methylotrophy, have provided opportunities to explore biotechnological innovations to improve REE mining and recycling. In addition to bacterial accumulation and concentration of REEs, biological REE binders, including proteins (lanmodulin, lanpepsy) and small molecules (metallophores and cofactors) have been identified that enable REE concentration and separation. REE-binding proteins have also been used in several mechanistically distinct REE biosensors, which have potential application in mining and medicine. Notably, the role of REEs in biology has only been known for a decade, suggesting their considerable scope for developing new understanding and novel applications.
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Affiliation(s)
- Raquel A. Rocha
- ARC Centre of Excellence in Synthetic BiologyCanberraAustralian Capital TerritoryAustralia
- CSIRO Advanced Engineering Biology Future Science Platform, Black Mountain Science and Innovation ParkCanberraAustralian Capital TerritoryAustralia
| | - Kirill Alexandrov
- ARC Centre of Excellence in Synthetic BiologyCanberraAustralian Capital TerritoryAustralia
- Centre for Agriculture and the BioeconomyQueensland University of TechnologyBrisbaneQueenslandAustralia
- School of Biology and Environmental ScienceQueensland University of TechnologyBrisbaneQueenslandAustralia
| | - Colin Scott
- ARC Centre of Excellence in Synthetic BiologyCanberraAustralian Capital TerritoryAustralia
- CSIRO Advanced Engineering Biology Future Science Platform, Black Mountain Science and Innovation ParkCanberraAustralian Capital TerritoryAustralia
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3
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Chemodurova AA, Reshetnikov AS, Agafonova NV, Doronina NV. Genes of NAD+-Dependent Formate Dehydrogenases in Taxonomy of Aerobic Methylotrophic Bacteria of the Genus Ancylobacter. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722601932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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Daszczyńska A, Krucoń T, Stasiuk R, Koblowska M, Matlakowska R. Lanthanide-Dependent Methanol Metabolism of a Proteobacteria-Dominated Community in a Light Lanthanide-Rich Deep Environment. Int J Mol Sci 2022; 23:ijms23073947. [PMID: 35409305 PMCID: PMC8999231 DOI: 10.3390/ijms23073947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 02/01/2023] Open
Abstract
This study investigated the occurrence and diversity of proteobacterial XoxF-type methanol dehydrogenases (MDHs) in the microbial community that inhabits a fossil organic matter- and sedimentary lanthanide (Ln3+)-rich underground mine environment using a metagenomic and metaproteomic approach. A total of 8 XoxF-encoding genes (XoxF-EGs) and 14 protein sequences matching XoxF were identified. XoxF-type MDHs were produced by Alpha-, Beta-, and Gammaproteobacteria represented by the four orders Methylococcales, Nitrosomonadales, Rhizobiales, and Xanthomonadales. The highest number of XoxF-EG- and XoxF-matching protein sequences were affiliated with Nitrosomonadales and Rhizobiales, respectively. Among the identified XoxF-EGs, two belonged to the XoxF1 clade, five to the XoxF4 clade, and one to the XoxF5 clade, while seven of the identified XoxF proteins belonged to the XoxF1 clade, four to the XoxF4 clade, and three to the XoxF5 clade. Moreover, the accumulation of light lanthanides and the presence of methanol in the microbial mat were confirmed. This study is the first to show the occurrence of XoxF in the metagenome and metaproteome of a deep microbial community colonizing a fossil organic matter- and light lanthanide-rich sedimentary environment. The presented results broaden our knowledge of the ecology of XoxF-producing bacteria as well as of the distribution and diversity of these enzymes in the natural environment.
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Affiliation(s)
- Agnieszka Daszczyńska
- Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland; (A.D.); (R.S.)
| | - Tomasz Krucoń
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland;
| | - Robert Stasiuk
- Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland; (A.D.); (R.S.)
| | - Marta Koblowska
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland;
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Renata Matlakowska
- Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland; (A.D.); (R.S.)
- Correspondence:
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5
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Chaffron S, Delage E, Budinich M, Vintache D, Henry N, Nef C, Ardyna M, Zayed AA, Junger PC, Galand PE, Lovejoy C, Murray AE, Sarmento H, Acinas SG, Babin M, Iudicone D, Jaillon O, Karsenti E, Wincker P, Karp-Boss L, Sullivan MB, Bowler C, de Vargas C, Eveillard D. Environmental vulnerability of the global ocean epipelagic plankton community interactome. SCIENCE ADVANCES 2021; 7:eabg1921. [PMID: 34452910 PMCID: PMC8397264 DOI: 10.1126/sciadv.abg1921] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 07/09/2021] [Indexed: 05/05/2023]
Abstract
Marine plankton form complex communities of interacting organisms at the base of the food web, which sustain oceanic biogeochemical cycles and help regulate climate. Although global surveys are starting to reveal ecological drivers underlying planktonic community structure and predicted climate change responses, it is unclear how community-scale species interactions will be affected by climate change. Here, we leveraged Tara Oceans sampling to infer a global ocean cross-domain plankton co-occurrence network-the community interactome-and used niche modeling to assess its vulnerabilities to environmental change. Globally, this revealed a plankton interactome self-organized latitudinally into marine biomes (Trades, Westerlies, Polar) and more connected poleward. Integrated niche modeling revealed biome-specific community interactome responses to environmental change and forecasted the most affected lineages for each community. These results provide baseline approaches to assess community structure and organismal interactions under climate scenarios while identifying plausible plankton bioindicators for ocean monitoring of climate change.
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Affiliation(s)
- Samuel Chaffron
- Université de Nantes, CNRS UMR 6004, LS2N, F-44000 Nantes, France.
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
| | - Erwan Delage
- Université de Nantes, CNRS UMR 6004, LS2N, F-44000 Nantes, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
| | - Marko Budinich
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Sorbonne Université, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Damien Vintache
- Université de Nantes, CNRS UMR 6004, LS2N, F-44000 Nantes, France
| | - Nicolas Henry
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Sorbonne Université, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Charlotte Nef
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Mathieu Ardyna
- Department of Earth System Science, Stanford University, Stanford, CA 94305, USA
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, F-06230, Villefranche-sur-Mer, Paris, France
| | - Ahmed A Zayed
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Pedro C Junger
- Department of Hydrobiology, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, 13565-905 São Carlos, SP, Brazil
| | - Pierre E Galand
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques, LECOB, Banyuls-sur-Mer, 66500 Paris, France
| | - Connie Lovejoy
- Département de biologie, Faculté des sciences et Institut de biologie intégrative et des systèmes (IBIS) 1030, ave de la Médecine, Université Laval, Québec, QC, Canada
| | - Alison E Murray
- Division of Earth and Ecosystem Science, Desert Research Institute, Reno, NV 89512, USA
| | - Hugo Sarmento
- Department of Hydrobiology, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, 13565-905 São Carlos, SP, Brazil
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona 08003, Spain
| | - Marcel Babin
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, F-06230, Villefranche-sur-Mer, Paris, France
- Takuvik International Research Laboratory, Université Laval and CNRS, Québec, QC, Canada
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples 80121, Italy
| | - Olivier Jaillon
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, 91057 Paris, France
| | - Eric Karsenti
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Patrick Wincker
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, 91057 Paris, France
| | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA
| | - Chris Bowler
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Colomban de Vargas
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Sorbonne Université, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Damien Eveillard
- Université de Nantes, CNRS UMR 6004, LS2N, F-44000 Nantes, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
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6
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Izabel-Shen D, Höger AL, Jürgens K. Abundance-Occupancy Relationships Along Taxonomic Ranks Reveal a Consistency of Niche Differentiation in Marine Bacterioplankton With Distinct Lifestyles. Front Microbiol 2021; 12:690712. [PMID: 34262550 PMCID: PMC8273345 DOI: 10.3389/fmicb.2021.690712] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 05/25/2021] [Indexed: 01/23/2023] Open
Abstract
Abundance-occupancy relationships (AORs) are an important determinant of biotic community dynamics and habitat suitability. However, little is known about their role in complex bacterial communities, either within a phylogenetic framework or as a function of niche breadth. Based on data obtained in a field study in the St. Lawrence Estuary, we used 16S rRNA gene sequencing to examine the vertical patterns, strength, and character of AORs for particle-attached and free-living bacterial assemblages. Free-living communities were phylogenetically more diverse than particle-attached communities. The dominant taxa were consistent in terms of their presence/absence but population abundances differed in surface water vs. the cold intermediate layer. Significant, positive AORs characterized all of the surveyed communities across all taxonomic ranks of bacteria, thus demonstrating an ecologically conserved trend for both free-living and particle-attached bacteria. The strength of the AORs was low at the species level but higher at and above the genus level. These results demonstrate that an assessment of the distributions and population densities of finely resolved taxa does not necessarily improve determinations of apparent niche differences in marine bacterioplankton communities at regional scales compared with the information inferred from a broad taxonomic classification.
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Affiliation(s)
- Dandan Izabel-Shen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Department of Biological Oceanography Leibniz Institute for Baltic Sea Research, Rostock, Germany
| | - Anna-Lena Höger
- Department of Biological Oceanography Leibniz Institute for Baltic Sea Research, Rostock, Germany
- Department of Applied Biosciences and Process Engineering, Anhalt University of Applied Sciences, Köthen, Germany
| | - Klaus Jürgens
- Department of Biological Oceanography Leibniz Institute for Baltic Sea Research, Rostock, Germany
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A Novel Freshwater to Marine Evolutionary Transition Revealed within Methylophilaceae Bacteria from the Arctic Ocean. mBio 2021; 12:e0130621. [PMID: 34154421 PMCID: PMC8262872 DOI: 10.1128/mbio.01306-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteria inhabiting polar oceans, particularly the Arctic Ocean, are less studied than those at lower latitudes. Discovering bacterial adaptations to Arctic Ocean conditions is essential for understanding responses to the accelerated environmental changes occurring in the North. The Methylophilaceae are emerging as a model for investigating the genomic basis of habitat adaptation, because related lineages are widely distributed across both freshwater and marine ecosystems. Here, we investigated Methylophilaceae diversity in the salinity-stratified surface waters of the Canada Basin, Arctic Ocean. In addition to a diversity of marine OM43 lineages, we report on the genomic characteristics and evolution of a previously undescribed Methylophilaceae clade (BS01) common to polar surface waters yet related to freshwater sediment Methylotenera species. BS01 is restricted to the lower-salinity surface waters, while OM43 is found throughout the halocline. An acidic proteome supports a marine lifestyle for BS01, but gene content shows increased metabolic versatility compared to OM43 and evidence for ongoing genome-streamlining. Phylogenetic reconstruction shows that BS01 colonized the pelagic ocean independently of OM43 via convergent evolution. Salinity adaptation and differences in one-carbon and nitrogen metabolism may play a role in niche differentiation between BS01 and OM43. In particular, urea utilization by BS01 is predicted to provide an ecological advantage over OM43 given the limited amount of inorganic nitrogen in the Canada Basin. These observations provide further evidence that the Arctic Ocean is inhabited by distinct bacterial groups and that at least one group (BS01) evolved via a freshwater to marine environmental transition.
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8
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Buchholz HH, Michelsen ML, Bolaños LM, Browne E, Allen MJ, Temperton B. Efficient dilution-to-extinction isolation of novel virus-host model systems for fastidious heterotrophic bacteria. THE ISME JOURNAL 2021; 15:1585-1598. [PMID: 33495565 PMCID: PMC8163748 DOI: 10.1038/s41396-020-00872-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 12/01/2020] [Accepted: 12/07/2020] [Indexed: 02/08/2023]
Abstract
Microbes and their associated viruses are key drivers of biogeochemical processes in marine and soil biomes. While viruses of phototrophic cyanobacteria are well-represented in model systems, challenges of isolating marine microbial heterotrophs and their viruses have hampered experimental approaches to quantify the importance of viruses in nutrient recycling. A resurgence in cultivation efforts has improved the availability of fastidious bacteria for hypothesis testing, but this has not been matched by similar efforts to cultivate their associated bacteriophages. Here, we describe a high-throughput method for isolating important virus-host systems for fastidious heterotrophic bacteria that couples advances in culturing of hosts with sequential enrichment and isolation of associated phages. Applied to six monthly samples from the Western English Channel, we first isolated one new member of the globally dominant bacterial SAR11 clade and three new members of the methylotrophic bacterial clade OM43. We used these as bait to isolate 117 new phages, including the first known siphophage-infecting SAR11, and the first isolated phage for OM43. Genomic analyses of 13 novel viruses revealed representatives of three new viral genera, and infection assays showed that the viruses infecting SAR11 have ecotype-specific host ranges. Similar to the abundant human-associated phage ɸCrAss001, infection dynamics within the majority of isolates suggested either prevalent lysogeny or chronic infection, despite a lack of associated genes, or host phenotypic bistability with lysis putatively maintained within a susceptible subpopulation. Broader representation of important virus-host systems in culture collections and genomic databases will improve both our understanding of virus-host interactions, and accuracy of computational approaches to evaluate ecological patterns from metagenomic data.
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Affiliation(s)
| | | | | | - Emily Browne
- School of Biosciences, University of Exeter, Exeter, UK
| | - Michael J Allen
- School of Biosciences, University of Exeter, Exeter, UK
- Plymouth Marine Laboratory, Plymouth, UK
| | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, UK.
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9
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Roszczenko-Jasińska P, Krucoń T, Stasiuk R, Matlakowska R. Occurrence of XoxF-type methanol dehydrogenases in bacteria inhabiting light lanthanide-rich shale rock. FEMS Microbiol Ecol 2021; 97:6047175. [PMID: 33547466 DOI: 10.1093/femsec/fiaa259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/22/2020] [Indexed: 11/12/2022] Open
Abstract
This study analyzed the occurrence of lanthanide-dependent (XoxF type) methanol dehydrogenases in the bacterial community dominated by Proteobacteria inhabiting shale rock. In total, 22 sequence matches of XoxF were identified in the metaproteome of the community. This enzyme was produced by bacteria represented by orders such as Rhizobiales, Rhodobacterales, Rhodospiralles, Burkholderiales and Nitrosomonadales. Among the identified XoxF proteins, seven belonged to XoxF1 clade and 15 to XoxF5 clade. This study is the first to show the occurrence of XoxF proteins in the metaproteome of environmental lithobiontic bacterial community colonizing an underground rock rich in light lanthanides. The presented results broaden our understanding of the ecology of XoxF producing bacteria as well as the distribution and diversity of these enzymes in the natural environment.
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Affiliation(s)
- Paula Roszczenko-Jasińska
- Faculty of Biology, Department of Bacterial Genetics, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Tomasz Krucoń
- Faculty of Biology, Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Robert Stasiuk
- Faculty of Biology, Department of Geomicrobiology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Renata Matlakowska
- Faculty of Biology, Department of Geomicrobiology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
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Fischer PQ, Sánchez‐Andrea I, Stams AJM, Villanueva L, Sousa DZ. Anaerobic microbial methanol conversion in marine sediments. Environ Microbiol 2021; 23:1348-1362. [PMID: 33587796 PMCID: PMC8048578 DOI: 10.1111/1462-2920.15434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 01/15/2023]
Abstract
Methanol is an ubiquitous compound that plays a role in microbial processes as a carbon and energy source, intermediate in metabolic processes or as end product in fermentation. In anoxic environments, methanol can act as the sole carbon and energy source for several guilds of microorganisms: sulfate-reducing microorganisms, nitrate-reducing microorganisms, acetogens and methanogens. In marine sediments, these guilds compete for methanol as their common substrate, employing different biochemical pathways. In this review, we will give an overview of current knowledge of the various ways in which methanol reaches marine sediments, the ecology of microorganisms capable of utilizing methanol and their metabolism. Furthermore, through a metagenomic analysis, we shed light on the unknown diversity of methanol utilizers in marine sediments which is yet to be explored.
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Affiliation(s)
- Peter Q. Fischer
- Laboratory of MicrobiologyWageningen University & Research, Stippeneng 4Wageningen6708 WEThe Netherlands
- Department of Marine Microbiology and BiogeochemistryRoyal Netherlands Institute for Sea Research, P.O. Box 59Den BurgTexel7197 ABThe Netherlands
| | - Irene Sánchez‐Andrea
- Laboratory of MicrobiologyWageningen University & Research, Stippeneng 4Wageningen6708 WEThe Netherlands
| | - Alfons J. M. Stams
- Laboratory of MicrobiologyWageningen University & Research, Stippeneng 4Wageningen6708 WEThe Netherlands
- Centre of Biological EngineeringUniversity of Minho, Campus de GualtarBraga4710‐057Portugal
| | - Laura Villanueva
- Department of Marine Microbiology and BiogeochemistryRoyal Netherlands Institute for Sea Research, P.O. Box 59Den BurgTexel7197 ABThe Netherlands
- Faculty of GeosciencesUtrecht University, Princetonlaan 8aUtrecht3584 CBThe Netherlands
| | - Diana Z. Sousa
- Laboratory of MicrobiologyWageningen University & Research, Stippeneng 4Wageningen6708 WEThe Netherlands
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11
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Discovery of lanthanide-dependent methylotrophy and screening methods for lanthanide-dependent methylotrophs. Methods Enzymol 2021; 650:1-18. [PMID: 33867018 DOI: 10.1016/bs.mie.2021.01.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The lanthanide elements (Lns) affect the physiology and growth of certain microorganisms known as "Ln-responsive microorganisms." Among them, in 2011, it was first reported that strains of Methylobacterium exhibited high methanol dehydrogenase (MDH) activity when grown in the presence of Lns; the purified Ln-inducible MDH was identified as XoxF-type MDH, whose catalytic function had previously been unknown. XoxF was the first enzyme to be identified as Ln-dependent, and its function in methylotrophy is more fundamental and important than that of the corresponding Ca2+-dependent MDH MxaFI. XoxF is encoded in the genomes of methylotrophic as well as non-methylotrophic bacteria. Thus, Lns are among the most fascinating and important growth factors for bacteria that potentially utilize methanol. Bacteria that require Lns for methanol growth are called "Ln-dependent methylotrophs." Recent findings indicate that these microorganisms comprise an "Ln-dependent ecosystem" that we have not been able to reconstruct under laboratory conditions without Lns. In this chapter, we summarize methods for (1) screening of Ln-responsive microorganisms, (2) purification of native XoxFs from Ln-dependent methylotrophs, and (3) screening of Ln-dependent methylotrophs from natural environments, while providing a history of the discovery of the Ln-dependent methylotrophs.
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12
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Lumpe H, Mayer P, Daumann LJ. Crystal structure of a calcium(II)-pyrroloquinoline quinone (PQQ) complex outside a protein environment. Acta Crystallogr C Struct Chem 2020; 76:1051-1056. [PMID: 33273141 PMCID: PMC7716187 DOI: 10.1107/s2053229620014278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 10/27/2020] [Indexed: 11/24/2022] Open
Abstract
Pyrroloquinoline quinone (PQQ) is an important cofactor of calcium- and lanthanide-dependent alcohol dehydrogenases, and has been known for over 30 years. Crystal structures of Ca-MDH enzymes (MDH is methanol dehydrogenase) have been known for some time; however, crystal structures of PQQ with biorelevant metal ions have been lacking in the literature for decades. We report here the first crystal structure analysis of a Ca-PQQ complex outside the protein environment, namely, poly[[undecaaquabis(μ-4,5-dioxo-4,5-dihydro-1H-pyrrolo[2,3-f]quinoline-2,7,9-tricarboxylato)tricalcium(II)] dihydrate], {[Ca3(C14H3N2O8)2(H2O)11]·2H2O}n. The complex crystallized as Ca3PQQ2·13H2O with Ca2+ in three different positions and PQQ3-, including an extensive hydrogen-bond network. Similarities and differences to the recently reported structure with biorelevant europium (Eu2PQQ2) are discussed.
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Affiliation(s)
- Henning Lumpe
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, Munich, Bavaria 81377, Germany
| | - Peter Mayer
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, Munich, Bavaria 81377, Germany
| | - Lena J. Daumann
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, Munich, Bavaria 81377, Germany
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13
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Glass JB, Cowan ET, Johannesson KH. Lanthanide rarity in natural waters: implications for microbial C1 metabolism. FEMS Microbiol Lett 2020; 367:5920214. [DOI: 10.1093/femsle/fnaa165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/07/2020] [Indexed: 01/01/2023] Open
Abstract
ABSTRACT
Research in the last decade has illuminated the important role that lanthanides play in microbial carbon metabolism, particularly methylotrophy. Environmental omics studies have revealed that lanthoenzymes are dominant in some environments, and laboratory studies have shown that lanthoenzymes are favored over their calcium-containing counterparts even when calcium is far more abundant. Lanthanide elements are common in rocks but occur at exceedingly low levels in most natural waters (picomolar to nanomolar range) with the exception of volcanic hot springs, which can reach micromolar concentrations. Calcium is orders of magnitude higher in abundance than lanthanide elements across natural settings. Bacteria that use lanthanides for growth on simple carbon compounds (e.g. methanol and ethanol) grow optimally at micromolar concentrations. It is highly likely that bacteria in the environment have evolved specialized lanthanide sequestration and high-affinity uptake systems to overcome lanthanide deprivation. Indeed, we identified genes in soil metagenomes encoding the lanthanide-binding protein lanmodulin, which may be important for cellular differentiation between calcium and lanthanides. More research is needed on microbial adaptations to lanthanide scarcity.
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Affiliation(s)
- Jennifer B Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA, 30332, USA
| | - Elizabeth T Cowan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, GA, 30332, USA
| | - Karen H Johannesson
- School for the Environment, University of Massachusetts, 100 Morrissey Blvd., Boston, MA, 02125, USA
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14
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Modelling Free-Living and Particle-Associated Bacterial Assemblages across the Deep and Hypoxic Lower St. Lawrence Estuary. mSphere 2020; 5:5/3/e00364-20. [PMID: 32434843 PMCID: PMC7380577 DOI: 10.1128/msphere.00364-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The Estuary and Gulf of St. Lawrence (EGSL) in eastern Canada is an appealing ecosystem for studying how microbial communities and metabolic processes are related to environmental change. Ocean and climate variability result in large spatiotemporal variations in environmental conditions and oceanographic processes. The EGSL is also exposed to a variety of additional human pressures that threaten its integrity and sustainable use, including shipping, aquiculture, coastal development, and oil exploration. To monitor and perhaps mitigate the impacts of these human activities on the EGSL, a comprehensive understanding of the biological communities is required. In this study, we provide the first comprehensive view of bacterial diversity in the EGSL and describe the distinct bacterial assemblages associated with different environmental habitats. This work therefore provides an important baseline ecological framework for bacterial communities in the EGSL useful for further studies on how these communities may respond to environmental change. The Estuary and Gulf of St. Lawrence (EGSL) in eastern Canada are among the largest and most productive coastal ecosystems in the world. Very little information on bacterial diversity exists, hampering our understanding of the relationships between bacterial community structure and biogeochemical function in the EGSL. During the productive spring period, we investigated free-living and particle-associated bacterial communities across the stratified waters of the Lower St. Lawrence Estuary, including the particle-rich surface and bottom boundary layers. Modelling of community structure based on 16S rRNA gene and transcript diversity identified bacterial assemblages specifically associated with four habitat types defined by water mass (upper water or lower water column) and size fraction (free living or particle associated). Assemblages from the upper waters represent sets of cooccurring bacterial populations that are widely distributed across Lower St. Lawrence Estuary surface waters and likely key contributors to organic matter degradation during the spring. In addition, we provide strong evidence that particles in deep hypoxic waters and the bottom boundary layer support a metabolically active bacterial community that is compositionally distinct from those of surface particles and the free-living communities. Among the distinctive features of the bacterial assemblage associated with lower-water particles was the presence of uncultivated lineages of Deltaproteobacteria, including marine myxobacteria. Overall, these results provide an important ecological framework for further investigations of the biogeochemical contributions of bacterial populations in this important coastal marine ecosystem. IMPORTANCE The Estuary and Gulf of St. Lawrence (EGSL) in eastern Canada is an appealing ecosystem for studying how microbial communities and metabolic processes are related to environmental change. Ocean and climate variability result in large spatiotemporal variations in environmental conditions and oceanographic processes. The EGSL is also exposed to a variety of additional human pressures that threaten its integrity and sustainable use, including shipping, aquiculture, coastal development, and oil exploration. To monitor and perhaps mitigate the impacts of these human activities on the EGSL, a comprehensive understanding of the biological communities is required. In this study, we provide the first comprehensive view of bacterial diversity in the EGSL and describe the distinct bacterial assemblages associated with different environmental habitats. This work therefore provides an important baseline ecological framework for bacterial communities in the EGSL useful for further studies on how these communities may respond to environmental change.
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15
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Lv H, Sahin N, Tani A. Methylotenera oryzisoli sp. nov., a lanthanide-dependent methylotrophic bacteria isolated from rice field soil. Int J Syst Evol Microbiol 2020; 70:2713-2718. [DOI: 10.1099/ijsem.0.004098] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A new lanthanide (Ln3+)-dependent methanol-utilizing bacterial strain, La3113T, was isolated from rice field soil and its taxonomic position was investigated using polyphasic approaches. The strain was aerobic, Gram-stain-negative, strongly motile, catalase-positive and cytochrome oxidase-positive. It could neither catalyse the hydrolysis of urea nor reduce nitrate to nitrite. Growth was observed within a temperature range of 10–40 °C and a pH range of 6–8, with optimum growth at 28 °C and pH 7. Methylamine was utilized as the single source of energy, carbon and nitrogen, and it was oxidized by methylamine dehydrogenase. C16 : 1
ω7c, C16 : 1
ω6c and C16 : 0 were the dominant cellular fatty acids. Its draft genome (2.67 Mbp and 44.9 mol% G+C content) encodes genes including three Ln3+-dependent methanol dehydrogenase (XoxF-type MDH) genes, those for formaldehyde assimilation (ribulose monophosphate pathway), formate dehydrogenases and methylamine dehydrogenases, but not Ca2+-dependent MDH (MxaFI-MDH), which characterizes the species as a Ln3+-dependent methylotroph. The 16S rRNA gene sequence showed that strain La3113T belongs to the genus
Methylotenera
and is closely related to
Methylotenera mobilis
JLW8T (98.29 % identity). The digital DNA–DNA hybridization (dDDH) values (less than 30 %) and average nucleotide identity (ANI) values (less than 85 %) between genomes of strain La3113T and related type strains were lower than the thresholds for species delineation (70 % for dDDH and 95–96 % for ANI). On the basis of these polyphasic approaches, we propose a novel
Methylotenera
species, Methylotenera oryzisoli sp. nov. (type strain La3113T=NBRC 111954T=DSM 103219T).
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Affiliation(s)
- Haoxin Lv
- College of Food Science and Technology, Henan University of Technology, Zhengzhou, PR China
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Nurettin Sahin
- Egitim Fakultesi, Mugla Sitki Kocman University, Kotekli, Mugla, Turkey
| | - Akio Tani
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
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16
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Chen WM, Cai CY, Li ZH, Young CC, Sheu SY. Methylobacterium oryzihabitans sp. nov., isolated from water sampled from a rice paddy field. Int J Syst Evol Microbiol 2019; 69:3843-3850. [PMID: 31483751 DOI: 10.1099/ijsem.0.003693] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain TER-1T was isolated from water sampled from a rice paddy field in Taiwan. Cells were Gram-negative, aerobic, motile, rod-shaped and formed pink-coloured colonies. Optimal growth occurred at 25-30 °C, pH 6-7 and in the presence of 0.5 % NaCl. Strain TER-1T could grow on C1 compounds such as methanol, formic acid, methylamine and dimethylamine as sole carbon source, and carry methanol dehydrogenase gene, which supports its methylotrophic metabolism. The results of phylogenetic analyses based on the 16S rRNA gene sequence, methanol dehydrogenase gene sequence and coding sequences of 92 protein clusters indicated that strain TER-1T formed a phylogenetic lineage in the genus Methylobacterium. Strain TER-1T was most closely related to Methylobacterium isbiliense AR24T with 96.8 % 16S rRNA gene sequence similarity. Strain TER-1T showed 77.1-82.8 % average nucleotide identity and 16.4-20.2 % digital DNA-DNA hybridization identity with the strains of other Methylobacterium species. The major fatty acid of strain TER-1T was C18 : 1ω7c. The predominant hydroxy fatty acid was C18 : 0 3-OH. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and two uncharacterized lipids. The only isoprenoid quinone was Q-10. The genomic DNA G+C content of strain TER-1T was 71.9 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain TER-1T should be classified in a novel species of the genus Methylobacterium, for which the name Methylobacterium oryzihabitans sp. nov. is proposed. The type strain is TER-1T (=BCRC 81157T=LMG 30931T=KCTC 62864T).
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Affiliation(s)
- Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung City 811, Taiwan ROC
| | - Cheng-Ye Cai
- Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, Nan-Tzu, Kaohsiung City 811, Taiwan ROC
| | - Zhi-Hao Li
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung City 811, Taiwan ROC
| | - Chiu-Chung Young
- College of Agriculture and Natural Resources, Department of Soil and Environmental Sciences, National Chung Hsing University, Taichung 402, Taiwan ROC
| | - Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, Nan-Tzu, Kaohsiung City 811, Taiwan ROC
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17
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Salcher MM, Schaefle D, Kaspar M, Neuenschwander SM, Ghai R. Evolution in action: habitat transition from sediment to the pelagial leads to genome streamlining in Methylophilaceae. THE ISME JOURNAL 2019; 13:2764-2777. [PMID: 31292537 PMCID: PMC6794327 DOI: 10.1038/s41396-019-0471-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/14/2019] [Accepted: 06/21/2019] [Indexed: 12/15/2022]
Abstract
The most abundant aquatic microbes are small in cell and genome size. Genome-streamlining theory predicts gene loss caused by evolutionary selection driven by environmental factors, favouring superior competitors for limiting resources. However, evolutionary histories of such abundant, genome-streamlined microbes remain largely unknown. Here we reconstruct the series of steps in the evolution of some of the most abundant genome-streamlined microbes in freshwaters ("Ca. Methylopumilus") and oceans (marine lineage OM43). A broad genomic spectrum is visible in the family Methylophilaceae (Betaproteobacteria), from sediment microbes with medium-sized genomes (2-3 Mbp genome size), an occasionally blooming pelagic intermediate (1.7 Mbp), and the most reduced pelagic forms (1.3 Mbp). We show that a habitat transition from freshwater sediment to the relatively oligotrophic pelagial was accompanied by progressive gene loss and adaptive gains. Gene loss has mainly affected functions not necessarily required or advantageous in the pelagial or is encoded by redundant pathways. Likewise, we identified genes providing adaptations to oligotrophic conditions that have been transmitted horizontally from pelagic freshwater microbes. Remarkably, the secondary transition from the pelagial of lakes to the oceans required only slight modifications, i.e., adaptations to higher salinity, gained via horizontal gene transfer from indigenous microbes. Our study provides first genomic evidence of genome reduction taking place during habitat transitions. In this regard, the family Methylophilaceae is an exceptional model for tracing the evolutionary history of genome streamlining as such a collection of evolutionarily related microbes from different habitats is rare in the microbial world.
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Affiliation(s)
- Michaela M Salcher
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 37005, České Budějovice, Czech Republic.
- Limnological Station, Institute of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Switzerland.
| | - Daniel Schaefle
- Limnological Station, Institute of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Switzerland
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, 8006, Zurich, Switzerland
| | - Melissa Kaspar
- Limnological Station, Institute of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Switzerland
| | - Stefan M Neuenschwander
- Limnological Station, Institute of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Switzerland
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001, Bern, Switzerland
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 37005, České Budějovice, Czech Republic
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18
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Pseudomethylobacillus aquaticus gen. nov., sp. nov., a new member of the family Methylophilaceae isolated from an artificial reservoir. Int J Syst Evol Microbiol 2019; 69:3551-3559. [DOI: 10.1099/ijsem.0.003661] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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19
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Taubert M, Grob C, Crombie A, Howat AM, Burns OJ, Weber M, Lott C, Kaster AK, Vollmers J, Jehmlich N, von Bergen M, Chen Y, Murrell JC. Communal metabolism by Methylococcaceae and Methylophilaceae is driving rapid aerobic methane oxidation in sediments of a shallow seep near Elba, Italy. Environ Microbiol 2019; 21:3780-3795. [PMID: 31267680 DOI: 10.1111/1462-2920.14728] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/14/2019] [Accepted: 06/29/2019] [Indexed: 11/29/2022]
Abstract
The release of abiotic methane from marine seeps into the atmosphere is a major source of this potent greenhouse gas. Methanotrophic microorganisms in methane seeps use methane as carbon and energy source, thus significantly mitigating global methane emissions. Here, we investigated microbial methane oxidation at the sediment-water interface of a shallow marine methane seep. Metagenomics and metaproteomics, combined with 13 C-methane stable isotope probing, demonstrated that various members of the gammaproteobacterial family Methylococcaceae were the key players for methane oxidation, catalysing the first reaction step to methanol. We observed a transfer of carbon to methanol-oxidizing methylotrophs of the betaproteobacterial family Methylophilaceae, suggesting an interaction between methanotrophic and methylotrophic microorganisms that allowed for rapid methane oxidation. From our microcosms, we estimated methane oxidation rates of up to 871 nmol of methane per gram sediment per day. This implies that more than 50% of methane at the seep is removed by microbial oxidation at the sediment-water interface, based on previously reported in situ methane fluxes. The organic carbon produced was further assimilated by different heterotrophic microbes, demonstrating that the methane-oxidizing community supported a complex trophic network. Our results provide valuable eco-physiological insights into this specialized microbial community performing an ecosystem function of global relevance.
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Affiliation(s)
- Martin Taubert
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159 07743, Jena, Germany.,School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Carolina Grob
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Andrew Crombie
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Alexandra M Howat
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Oliver J Burns
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Miriam Weber
- HYDRA Marine Sciences GmbH, Sinzheim, Germany.,HYDRA Field Station Elba, Italy.,Microsensor Group, Max Plank Institute for Marine Microbiology, 28359, Celsiusstr. 1, Bremen, Germany
| | - Christian Lott
- HYDRA Marine Sciences GmbH, Sinzheim, Germany.,HYDRA Field Station Elba, Italy.,Department of Symbiosis, Max Plank Institute for Marine Microbiology, 28359, Celsiusstr. 1, Bremen, Germany
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces (IBG5), Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Karlsruhe, Germany.,Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, 38124, Inhoffenstrasse 7B, Braunschweig, Germany
| | - John Vollmers
- Institute for Biological Interfaces (IBG5), Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Karlsruhe, Germany.,Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, 38124, Inhoffenstrasse 7B, Braunschweig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, 04103, Brüderstraße 32, Leipzig, Germany.,Department of Chemistry and Bioscience, University of Aalborg, 9220, Fredrik Bajers Vej 7H, Aalborg East, Denmark
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - John Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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20
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Linz AM, He S, Stevens SLR, Anantharaman K, Rohwer RR, Malmstrom RR, Bertilsson S, McMahon KD. Freshwater carbon and nutrient cycles revealed through reconstructed population genomes. PeerJ 2018; 6:e6075. [PMID: 30581671 PMCID: PMC6292386 DOI: 10.7717/peerj.6075] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 11/05/2018] [Indexed: 02/01/2023] Open
Abstract
Although microbes mediate much of the biogeochemical cycling in freshwater, the categories of carbon and nutrients currently used in models of freshwater biogeochemical cycling are too broad to be relevant on a microbial scale. One way to improve these models is to incorporate microbial data. Here, we analyze both genes and genomes from three metagenomic time series and propose specific roles for microbial taxa in freshwater biogeochemical cycles. Our metagenomic time series span multiple years and originate from a eutrophic lake (Lake Mendota) and a humic lake (Trout Bog Lake) with contrasting water chemistry. Our analysis highlights the role of polyamines in the nitrogen cycle, the diversity of diazotrophs between lake types, the balance of assimilatory vs. dissimilatory sulfate reduction in freshwater, the various associations between types of phototrophy and carbon fixation, and the density and diversity of glycoside hydrolases in freshwater microbes. We also investigated aspects of central metabolism such as hydrogen metabolism, oxidative phosphorylation, methylotrophy, and sugar degradation. Finally, by analyzing the dynamics over time in nitrogen fixation genes and Cyanobacteria genomes, we show that the potential for nitrogen fixation is linked to specific populations in Lake Mendota. This work represents an important step towards incorporating microbial data into ecosystem models and provides a better understanding of how microbes may participate in freshwater biogeochemical cycling.
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Affiliation(s)
- Alexandra M Linz
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Shaomei He
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.,Department of Geoscience, University of Wisconsin-Madison, Madison, WI, USA
| | - Sarah L R Stevens
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Robin R Rohwer
- Environmental Chemistry and Technology Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Rex R Malmstrom
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Stefan Bertilsson
- Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Katherine D McMahon
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.,Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
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21
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Genomic characterization of methylotrophy of Oharaeibacter diazotrophicus strain SM30T. J Biosci Bioeng 2018; 126:667-675. [DOI: 10.1016/j.jbiosc.2018.05.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 05/22/2018] [Accepted: 05/28/2018] [Indexed: 11/21/2022]
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22
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Smith GJ, Angle JC, Solden LM, Borton MA, Morin TH, Daly RA, Johnston MD, Stefanik KC, Wolfe R, Gil B, Wrighton KC. Members of the Genus Methylobacter Are Inferred To Account for the Majority of Aerobic Methane Oxidation in Oxic Soils from a Freshwater Wetland. mBio 2018; 9:e00815-18. [PMID: 30401770 PMCID: PMC6222125 DOI: 10.1128/mbio.00815-18] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 10/01/2018] [Indexed: 11/20/2022] Open
Abstract
Microbial carbon degradation and methanogenesis in wetland soils generate a large proportion of atmospheric methane, a highly potent greenhouse gas. Despite their potential to mitigate greenhouse gas emissions, knowledge about methane-consuming methanotrophs is often limited to lower-resolution single-gene surveys that fail to capture the taxonomic and metabolic diversity of these microorganisms in soils. Here our objective was to use genome-enabled approaches to investigate methanotroph membership, distribution, and in situ activity across spatial and seasonal gradients in a freshwater wetland near Lake Erie. 16S rRNA gene analyses demonstrated that members of the methanotrophic Methylococcales were dominant, with the dominance largely driven by the relative abundance of four taxa, and enriched in oxic surface soils. Three methanotroph genomes from assembled soil metagenomes were assigned to the genus Methylobacter and represented the most abundant methanotrophs across the wetland. Paired metatranscriptomes confirmed that these Old Woman Creek (OWC) Methylobacter members accounted for nearly all the aerobic methanotrophic activity across two seasons. In addition to having the capacity to couple methane oxidation to aerobic respiration, these new genomes encoded denitrification potential that may sustain energy generation in soils with lower dissolved oxygen concentrations. We further show that Methylobacter members that were closely related to the OWC members were present in many other high-methane-emitting freshwater and soil sites, suggesting that this lineage could participate in methane consumption in analogous ecosystems. This work contributes to the growing body of research suggesting that Methylobacter may represent critical mediators of methane fluxes in freshwater saturated sediments and soils worldwide.IMPORTANCE Here we used soil metagenomics and metatranscriptomics to uncover novel members within the genus Methylobacter We denote these closely related genomes as members of the lineage OWC Methylobacter Despite the incredibly high microbial diversity in soils, here we present findings that unexpectedly showed that methane cycling was primarily mediated by a single genus for both methane production ("Candidatus Methanothrix paradoxum") and methane consumption (OWC Methylobacter). Metatranscriptomic analyses revealed that decreased methanotrophic activity rather than increased methanogenic activity possibly contributed to the greater methane emissions that we had previously observed in summer months, findings important for biogeochemical methane models. Although members of this Methylococcales order have been cultivated for decades, multi-omic approaches continue to illuminate the methanotroph phylogenetic and metabolic diversity harbored in terrestrial and marine ecosystems.
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Affiliation(s)
- Garrett J Smith
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Jordan C Angle
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Lindsey M Solden
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Mikayla A Borton
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
- Environmental Science Graduate Program, The Ohio State University, Columbus, Ohio, USA
| | - Timothy H Morin
- Department of Environmental Resources Engineering, State University of New York College of Environmental Science and Forestry, Syracuse, New York, USA
| | - Rebecca A Daly
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Michael D Johnston
- National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Kay C Stefanik
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Department of Civil and Environmental Engineering and Geodetic Sciences, The Ohio State University, Columbus, Ohio, USA
| | - Richard Wolfe
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Bohrer Gil
- Environmental Science Graduate Program, The Ohio State University, Columbus, Ohio, USA
- Department of Civil and Environmental Engineering and Geodetic Sciences, The Ohio State University, Columbus, Ohio, USA
| | - Kelly C Wrighton
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
- Environmental Science Graduate Program, The Ohio State University, Columbus, Ohio, USA
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23
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Lumpe H, Pol A, Op den Camp HJM, Daumann LJ. Impact of the lanthanide contraction on the activity of a lanthanide-dependent methanol dehydrogenase - a kinetic and DFT study. Dalton Trans 2018; 47:10463-10472. [PMID: 30020281 PMCID: PMC6085770 DOI: 10.1039/c8dt01238e] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/14/2018] [Indexed: 01/15/2023]
Abstract
Interest in the bioinorganic chemistry of lanthanides is growing rapidly as more and more lanthanide-dependent bacteria are being discovered. Especially the earlier lanthanides have been shown to be preferentially utilized by bacteria that need these Lewis acids as cofactors in their alcohol dehydrogenase enzymes. Here, we investigate the impact of the lanthanide ions lanthanum(iii) to lutetium(iii) (excluding Pm) on the catalytic parameters (vmax, KM, kcat/KM) of a methanol dehydrogenase (MDH) isolated from Methylacidiphilum fumariolicum SolV. Kinetic experiments and DFT calculations were used to discuss why only the earlier lanthanides (La-Gd) promote high MDH activity. Impact of Lewis acidity, coordination number preferences, stability constants and other properties that are a direct result of the lanthanide contraction are discussed in light of the two proposed mechanisms for MDH.
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Affiliation(s)
- Henning Lumpe
- Ludwig-Maximilians-Universität München
, Department Chemie
,
Butenandtstr. 5-13
, 81377 München
, Germany
.
| | - Arjan Pol
- Department of Microbiology
, Institute of Wetland and Water Research
, Radboud University Nijmegen
,
The Netherlands
| | - Huub J. M. Op den Camp
- Department of Microbiology
, Institute of Wetland and Water Research
, Radboud University Nijmegen
,
The Netherlands
| | - Lena J. Daumann
- Ludwig-Maximilians-Universität München
, Department Chemie
,
Butenandtstr. 5-13
, 81377 München
, Germany
.
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry
, Ludwig-Maximilians-Universität München
,
Germany
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24
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Facile Arsenazo III-Based Assay for Monitoring Rare Earth Element Depletion from Cultivation Media for Methanotrophic and Methylotrophic Bacteria. Appl Environ Microbiol 2018; 84:AEM.02887-17. [PMID: 29453257 PMCID: PMC5881054 DOI: 10.1128/aem.02887-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 02/07/2018] [Indexed: 01/31/2023] Open
Abstract
Recently, methanotrophic and methylotrophic bacteria were found to utilize rare earth elements (REEs). To monitor the REE content in culture media of these bacteria, we have developed a rapid screening method using the Arsenazo III (AS III) dye for spectrophotometric REE detection in the low μM (0.1 to 10 μM) range. We designed this assay to follow LaIII and EuIII depletion from the culture medium by the acidophilic verrucomicrobial methanotroph Methylacidiphilum fumariolicum strain SolV. The assay can also be modified to screen the uptake of other REEs, such as PrIII, or to monitor the depletion of LaIII from growth media in neutrophilic methylotrophs such as Methylobacterium extorquens strain AM1. The AS III assay presents a convenient and fast detection method for REE levels in culture media and is a sensitive alternative to inductively coupled plasma mass spectrometry (ICP-MS) or atomic absorption spectroscopy (AAS). IMPORTANCE REE-dependent bacterial metabolism is a quickly emerging field, and while the importance of REEs for both methanotrophic and methylotrophic bacteria is now firmly established, many important questions, such as how these insoluble elements are taken up into cells, are still unanswered. Here, an Arsenazo III dye-based assay has been developed for fast, specific, and sensitive determination of REE content in different culture media. This assay presents a useful tool for optimizing cultivation protocols, as well as for routine REE monitoring during bacterial growth without the need for specialized analytical instrumentation. Furthermore, this assay has the potential to promote the discovery of other REE-dependent microorganisms and can help to elucidate the mechanisms for acquisition of REEs by methanotrophic and methylotrophic bacteria.
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25
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Lv H, Sahin N, Tani A. Isolation and genomic characterization ofNovimethylophilus kurashikiensisgen. nov. sp. nov., a new lanthanide-dependent methylotrophic species ofMethylophilaceae. Environ Microbiol 2018; 20:1204-1223. [DOI: 10.1111/1462-2920.14062] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 01/17/2018] [Indexed: 01/22/2023]
Affiliation(s)
- Haoxin Lv
- Institute of Plant Science and Resources, Okayama University; Okayama Japan
| | - Nurettin Sahin
- Egitim Fakultesi, Mugla Sitki Kocman University; 48170 Kotekli, Mugla Turkey
| | - Akio Tani
- Institute of Plant Science and Resources, Okayama University; Okayama Japan
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26
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Abstract
Aerobic methanotrophs have long been known to play a critical role in the global carbon cycle, being capable of converting methane to biomass and carbon dioxide. Interestingly, these microbes exhibit great sensitivity to copper and rare-earth elements, with the expression of key genes involved in the central pathway of methane oxidation controlled by the availability of these metals. That is, these microbes have a "copper switch" that controls the expression of alternative methane monooxygenases and a "rare-earth element switch" that controls the expression of alternative methanol dehydrogenases. Further, it has been recently shown that some methanotrophs can detoxify inorganic mercury and demethylate methylmercury; this finding is remarkable, as the canonical organomercurial lyase does not exist in these methanotrophs, indicating that a novel mechanism is involved in methylmercury demethylation. Here, we review recent findings on methanotrophic interactions with metals, with a particular focus on these metal switches and the mechanisms used by methanotrophs to bind and sequester metals.
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27
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Nolte TM, Pinto-Gil K, Hendriks AJ, Ragas AMJ, Pastor M. Quantitative structure-activity relationships for primary aerobic biodegradation of organic chemicals in pristine surface waters: starting points for predicting biodegradation under acclimatization. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2018; 20:157-170. [PMID: 29192704 DOI: 10.1039/c7em00375g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Microbial biomass and acclimation can affect the removal of organic chemicals in natural surface waters. In order to account for these effects and develop more robust models for biodegradation, we have compiled and curated removal data for un-acclimated (pristine) surface waters on which we developed quantitative structure-activity relationships (QSARs). Global analysis of the very heterogeneous dataset including neutral, anionic, cationic and zwitterionic chemicals (N = 233) using a random forest algorithm showed that useful predictions were possible (Qext2 = 0.4-0.5) though relatively large standard errors were associated (SDEP ∼0.7). Classification of the chemicals based on speciation state and metabolic pathway showed that biodegradation is influenced by the two, and that the dependence of biodegradation on chemical characteristics is non-linear. Class-specific QSAR analysis indicated that shape and charge distribution determine the biodegradation of neutral chemicals (R2 ∼ 0.6), e.g. through membrane permeation or binding to P450 enzymes, whereas the average biodegradation of charged chemicals is 1 to 2 orders of magnitude lower, for which degradation depends more directly on cellular uptake (R2 ∼ 0.6). Further analysis showed that specific chemical classes such as peptides and organic halogens are relatively less biodegradable in pristine surface waters, resulting in the need for the microbial consortia to acclimate. Additional literature data was used to verify an acclimation model (based on Monod-type kinetics) capable of extrapolating QSAR predictions to acclimating conditions such as in water treatment, downstream lakes and large rivers under μg L-1 to mg L-1 concentrations. The framework developed, despite being based on multiple assumptions, is promising and needs further validation using experimentation with more standardised and homogenised conditions as well as adequate characterization of the inoculum used.
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Affiliation(s)
- Tom M Nolte
- Department of Environmental Science, Institute for Water and Wetland Research, Radboud University Nijmegen, P. O. Box 9010, 6500 GL Nijmegen, The Netherlands.
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28
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Shiller AM, Chan EW, Joung DJ, Redmond MC, Kessler JD. Light rare earth element depletion during Deepwater Horizon blowout methanotrophy. Sci Rep 2017; 7:10389. [PMID: 28871146 PMCID: PMC5583346 DOI: 10.1038/s41598-017-11060-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 08/17/2017] [Indexed: 11/30/2022] Open
Abstract
Rare earth elements have generally not been thought to have a biological role. However, recent work has demonstrated that the light REEs (LREEs: La, Ce, Pr, and Nd) are essential for at least some methanotrophs, being co-factors in the XoxF type of methanol dehydrogenase (MDH). We show here that dissolved LREEs were significantly removed in a submerged plume of methane-rich water during the Deepwater Horizon (DWH) well blowout. Furthermore, incubation experiments conducted with naturally methane-enriched waters from hydrocarbon seeps in the vicinity of the DWH wellhead also showed LREE removal concurrent with methane consumption. Metagenomic sequencing of incubation samples revealed that LREE-containing MDHs were present. Our field and laboratory observations provide further insight into the biochemical pathways of methanotrophy during the DWH blowout. Additionally, our results are the first observations of direct biological alteration of REE distributions in oceanic systems. In view of the ubiquity of LREE-containing MDHs in oceanic systems, our results suggest that biological uptake of LREEs is an overlooked aspect of the oceanic geochemistry of this group of elements previously thought to be biologically inactive and an unresolved factor in the flux of methane, a potent greenhouse gas, from the ocean.
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Affiliation(s)
- A M Shiller
- Center for Trace Analysis, University of Southern Mississippi, Stennis Space Center, Mississippi, 39529, United States.
| | - E W Chan
- Earth and Environmental Sciences, University of Rochester, Rochester, NY, 14627, USA
| | - D J Joung
- Center for Trace Analysis, University of Southern Mississippi, Stennis Space Center, Mississippi, 39529, United States
| | - M C Redmond
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - J D Kessler
- Earth and Environmental Sciences, University of Rochester, Rochester, NY, 14627, USA
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29
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Chu F, Beck DAC, Lidstrom ME. MxaY regulates the lanthanide-mediated methanol dehydrogenase switch in Methylomicrobium buryatense. PeerJ 2016; 4:e2435. [PMID: 27651996 PMCID: PMC5018670 DOI: 10.7717/peerj.2435] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/12/2016] [Indexed: 01/12/2023] Open
Abstract
Many methylotrophs, microorganisms that consume carbon compounds lacking carbon-carbon bonds, use two different systems to oxidize methanol for energy production and biomass accumulation. The MxaFI methanol dehydrogenase (MDH) contains calcium in its active site, while the XoxF enzyme contains a lanthanide in its active site. The genes encoding the MDH enzymes are differentially regulated by the presence of lanthanides. In this study, we found that the histidine kinase MxaY controls the lanthanide-mediated switch in Methylomicrobium buryatense 5GB1C. MxaY controls the transcription of genes encoding MxaFI and XoxF at least partially by controlling the transcript levels of the orphan response regulator MxaB. We identify a constitutively active version of MxaY, and identify the mutated residue that may be involved in lanthanide sensing. Lastly, we find evidence to suggest that tight control of active MDH production is required for wild-type growth rates.
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Affiliation(s)
- Frances Chu
- Department of Chemical Engineering, University of Washington , Seattle , WA , United States
| | - David A C Beck
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States; eScience Institute, University of Washington, Seattle, WA, United States
| | - Mary E Lidstrom
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States; Department of Microbiology, University of Washington, Seattle, WA, United States
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30
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Martinez-Gomez NC, Vu HN, Skovran E. Lanthanide Chemistry: From Coordination in Chemical Complexes Shaping Our Technology to Coordination in Enzymes Shaping Bacterial Metabolism. Inorg Chem 2016; 55:10083-10089. [DOI: 10.1021/acs.inorgchem.6b00919] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Norma Cecilia Martinez-Gomez
- Department
of Microbiology and Molecular Genetics, Michigan State University, 567 Wilson Road, East Lansing, Michigan 48824, United States
| | - Huong N. Vu
- Department of Biological Sciences, San José State University, 1 Washington Square, San José, California 95192, United States
| | - Elizabeth Skovran
- Department of Biological Sciences, San José State University, 1 Washington Square, San José, California 95192, United States
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31
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Chistoserdova L. Lanthanides: New life metals? World J Microbiol Biotechnol 2016; 32:138. [DOI: 10.1007/s11274-016-2088-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 05/18/2016] [Indexed: 11/28/2022]
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