Methylotetracoccus oryzae Strain C50C1 Is a Novel Type Ib Gammaproteobacterial Methanotroph Adapted to Freshwater Environments
Methane-oxidizing microorganisms perform an important role in reducing emissions of the greenhouse gas methane to the atmosphere. To date, known bacterial methanotrophs belong to the , , and NC10 phyla. Within the phylum, they can be divided into type Ia, type Ib, and type II methanotrophs. Type Ia...
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creator | Ghashghavi, Mohammad Belova, Svetlana E Bodelier, Paul L E Dedysh, Svetlana N Kox, Martine A R Speth, Daan R Frenzel, Peter Jetten, Mike S M Lücker, Sebastian Lüke, Claudia |
description | Methane-oxidizing microorganisms perform an important role in reducing emissions of the greenhouse gas methane to the atmosphere. To date, known bacterial methanotrophs belong to the
,
, and NC10 phyla. Within the
phylum, they can be divided into type Ia, type Ib, and type II methanotrophs. Type Ia and type II are well represented by isolates. Contrastingly, the vast majority of type Ib methanotrophs have not been able to be cultivated so far. Here, we compared the distributions of type Ib lineages in different environments. Whereas the cultivated type Ib methanotrophs (
and
) are found in landfill and upland soils, lineages that are not represented by isolates are mostly dominant in freshwater environments, such as paddy fields and lake sediments. Thus, we observed a clear niche differentiation within type Ib methanotrophs. Our subsequent isolation attempts resulted in obtaining a pure culture of a novel type Ib methanotroph, tentatively named "
" C50C1. Strain C50C1 was further characterized to be an obligate methanotroph, containing C
ω9c as the major membrane phospholipid fatty acid, which has not been found in other methanotrophs. Genome analysis of strain C50C1 showed the presence of two
operon copies and XoxF5-type methanol dehydrogenase in addition to MxaFI. The genome also contained genes involved in nitrogen and sulfur cycling, but it remains to be demonstrated if and how these help this type Ib methanotroph to adapt to fluctuating environmental conditions in freshwater ecosystems.
Most of the methane produced on our planet gets naturally oxidized by a group of methanotrophic microorganisms before it reaches the atmosphere. These microorganisms are able to oxidize methane, both aerobically and anaerobically, and use it as their sole energy source. Although methanotrophs have been studied for more than a century, there are still many unknown and uncultivated groups prevalent in various ecosystems. This study focused on the diversity and adaptation of aerobic methane-oxidizing bacteria in different environments by comparing their phenotypic and genotypic properties. We used lab-scale microcosms to create a countergradient of oxygen and methane for preenrichment, followed by classical isolation techniques to obtain methane-oxidizing bacteria from a freshwater environment. This resulted in the discovery and isolation of a novel methanotroph with interesting physiological and genomic properties that could possibly make this bacterium able to cope with |
doi_str_mv | 10.1128/mSphere.00631-18 |
format | Article |
fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_6553558</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2305034459</sourcerecordid><originalsourceid>FETCH-LOGICAL-c424t-20751c8eb0a571a4b4a524156fa116f4ff219fa147d81339ac16ccbe3bfdf95a3</originalsourceid><addsrcrecordid>eNpdkc1v1DAQxSMEolXpnROyxIVLir-TXJCqVT9WKvTQcrYmzoSkSuJgO4uWQ__2etulKj3NaPyb53l6WfaR0RPGePl1vJk79HhCqRYsZ-Wb7JCLosoVlfzti_4gOw7hjlLKNNe60O-zA8GYLipFD7P77xi77eAiRg_WWbsE4vz2LyC5SZN-IitFV4ysAwHyw21wILfbGcm6JhcwjjD7tOpqsBF9DwPZycHkondzR04bmCM2JDpy7jF0fyBR5Gza9N5NI04xfMjetTAEPN7Xo-zn-dnt6jK_ur5Yr06vciu5jDmnhWK2xJqCKhjIWoLikindQnLSyrblrEq9LJqSCVGBZdraGkXdNm2lQBxl355056UesbHpbw-DmX0_gt8aB735_2XqO_PLbYxWSihVJoEvewHvfi8Yohn7YHEYYEK3BMMFVVRIqaqEfn6F3rnFT8me4VxWleRc6UTRJ8p6F4LH9vkYRs0uX7PP1zzma9juhk8vTTwv_EtTPABJzaTG</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2249942256</pqid></control><display><type>article</type><title>Methylotetracoccus oryzae Strain C50C1 Is a Novel Type Ib Gammaproteobacterial Methanotroph Adapted to Freshwater Environments</title><source>American Society for Microbiology</source><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>PubMed Central Open Access</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><creator>Ghashghavi, Mohammad ; Belova, Svetlana E ; Bodelier, Paul L E ; Dedysh, Svetlana N ; Kox, Martine A R ; Speth, Daan R ; Frenzel, Peter ; Jetten, Mike S M ; Lücker, Sebastian ; Lüke, Claudia</creator><contributor>Tamaki, Hideyuki</contributor><creatorcontrib>Ghashghavi, Mohammad ; Belova, Svetlana E ; Bodelier, Paul L E ; Dedysh, Svetlana N ; Kox, Martine A R ; Speth, Daan R ; Frenzel, Peter ; Jetten, Mike S M ; Lücker, Sebastian ; Lüke, Claudia ; Tamaki, Hideyuki</creatorcontrib><description>Methane-oxidizing microorganisms perform an important role in reducing emissions of the greenhouse gas methane to the atmosphere. To date, known bacterial methanotrophs belong to the
,
, and NC10 phyla. Within the
phylum, they can be divided into type Ia, type Ib, and type II methanotrophs. Type Ia and type II are well represented by isolates. Contrastingly, the vast majority of type Ib methanotrophs have not been able to be cultivated so far. Here, we compared the distributions of type Ib lineages in different environments. Whereas the cultivated type Ib methanotrophs (
and
) are found in landfill and upland soils, lineages that are not represented by isolates are mostly dominant in freshwater environments, such as paddy fields and lake sediments. Thus, we observed a clear niche differentiation within type Ib methanotrophs. Our subsequent isolation attempts resulted in obtaining a pure culture of a novel type Ib methanotroph, tentatively named "
" C50C1. Strain C50C1 was further characterized to be an obligate methanotroph, containing C
ω9c as the major membrane phospholipid fatty acid, which has not been found in other methanotrophs. Genome analysis of strain C50C1 showed the presence of two
operon copies and XoxF5-type methanol dehydrogenase in addition to MxaFI. The genome also contained genes involved in nitrogen and sulfur cycling, but it remains to be demonstrated if and how these help this type Ib methanotroph to adapt to fluctuating environmental conditions in freshwater ecosystems.
Most of the methane produced on our planet gets naturally oxidized by a group of methanotrophic microorganisms before it reaches the atmosphere. These microorganisms are able to oxidize methane, both aerobically and anaerobically, and use it as their sole energy source. Although methanotrophs have been studied for more than a century, there are still many unknown and uncultivated groups prevalent in various ecosystems. This study focused on the diversity and adaptation of aerobic methane-oxidizing bacteria in different environments by comparing their phenotypic and genotypic properties. We used lab-scale microcosms to create a countergradient of oxygen and methane for preenrichment, followed by classical isolation techniques to obtain methane-oxidizing bacteria from a freshwater environment. This resulted in the discovery and isolation of a novel methanotroph with interesting physiological and genomic properties that could possibly make this bacterium able to cope with fluctuating environmental conditions.</description><identifier>ISSN: 2379-5042</identifier><identifier>EISSN: 2379-5042</identifier><identifier>DOI: 10.1128/mSphere.00631-18</identifier><identifier>PMID: 31167950</identifier><language>eng</language><publisher>United States: American Society for Microbiology</publisher><subject>Adaptation, Physiological ; Applied and Environmental Science ; Atmosphere ; Bacteria ; Bacterial Typing Techniques ; Carbon ; Deoxyribonucleic acid ; DNA ; DNA, Bacterial - genetics ; Ecosystems ; Environmental conditions ; Fatty acids ; Fatty Acids - chemistry ; Fresh Water - microbiology ; Freshwater ecosystems ; Freshwater environments ; Freshwater microorganisms ; Genome, Bacterial ; Genomes ; Genomics ; Greenhouse gases ; Membranes ; Metabolism ; Methane ; Methane - metabolism ; Methanol dehydrogenase ; Methanotrophic bacteria ; Methylococcaceae - classification ; Methylococcaceae - isolation & purification ; Methylococcaceae - physiology ; Microcosms ; Niches ; Phospholipids ; Phylogeny ; Physiology ; Proteobacteria ; Pure culture ; RNA, Ribosomal, 16S - genetics ; Sediments ; Sulfur</subject><ispartof>mSphere, 2019-06, Vol.4 (3)</ispartof><rights>Copyright © 2019 Ghashghavi et al.</rights><rights>Copyright © 2019 Ghashghavi et al. This work is published under https://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Copyright © 2019 Ghashghavi et al. 2019 Ghashghavi et al.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c424t-20751c8eb0a571a4b4a524156fa116f4ff219fa147d81339ac16ccbe3bfdf95a3</citedby><cites>FETCH-LOGICAL-c424t-20751c8eb0a571a4b4a524156fa116f4ff219fa147d81339ac16ccbe3bfdf95a3</cites><orcidid>0000-0001-5795-1411 ; 0000-0002-4691-7039 ; 0000-0002-2361-5935 ; 0000-0003-2935-4454</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6553558/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6553558/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,3188,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31167950$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Tamaki, Hideyuki</contributor><creatorcontrib>Ghashghavi, Mohammad</creatorcontrib><creatorcontrib>Belova, Svetlana E</creatorcontrib><creatorcontrib>Bodelier, Paul L E</creatorcontrib><creatorcontrib>Dedysh, Svetlana N</creatorcontrib><creatorcontrib>Kox, Martine A R</creatorcontrib><creatorcontrib>Speth, Daan R</creatorcontrib><creatorcontrib>Frenzel, Peter</creatorcontrib><creatorcontrib>Jetten, Mike S M</creatorcontrib><creatorcontrib>Lücker, Sebastian</creatorcontrib><creatorcontrib>Lüke, Claudia</creatorcontrib><title>Methylotetracoccus oryzae Strain C50C1 Is a Novel Type Ib Gammaproteobacterial Methanotroph Adapted to Freshwater Environments</title><title>mSphere</title><addtitle>mSphere</addtitle><description>Methane-oxidizing microorganisms perform an important role in reducing emissions of the greenhouse gas methane to the atmosphere. To date, known bacterial methanotrophs belong to the
,
, and NC10 phyla. Within the
phylum, they can be divided into type Ia, type Ib, and type II methanotrophs. Type Ia and type II are well represented by isolates. Contrastingly, the vast majority of type Ib methanotrophs have not been able to be cultivated so far. Here, we compared the distributions of type Ib lineages in different environments. Whereas the cultivated type Ib methanotrophs (
and
) are found in landfill and upland soils, lineages that are not represented by isolates are mostly dominant in freshwater environments, such as paddy fields and lake sediments. Thus, we observed a clear niche differentiation within type Ib methanotrophs. Our subsequent isolation attempts resulted in obtaining a pure culture of a novel type Ib methanotroph, tentatively named "
" C50C1. Strain C50C1 was further characterized to be an obligate methanotroph, containing C
ω9c as the major membrane phospholipid fatty acid, which has not been found in other methanotrophs. Genome analysis of strain C50C1 showed the presence of two
operon copies and XoxF5-type methanol dehydrogenase in addition to MxaFI. The genome also contained genes involved in nitrogen and sulfur cycling, but it remains to be demonstrated if and how these help this type Ib methanotroph to adapt to fluctuating environmental conditions in freshwater ecosystems.
Most of the methane produced on our planet gets naturally oxidized by a group of methanotrophic microorganisms before it reaches the atmosphere. These microorganisms are able to oxidize methane, both aerobically and anaerobically, and use it as their sole energy source. Although methanotrophs have been studied for more than a century, there are still many unknown and uncultivated groups prevalent in various ecosystems. This study focused on the diversity and adaptation of aerobic methane-oxidizing bacteria in different environments by comparing their phenotypic and genotypic properties. We used lab-scale microcosms to create a countergradient of oxygen and methane for preenrichment, followed by classical isolation techniques to obtain methane-oxidizing bacteria from a freshwater environment. This resulted in the discovery and isolation of a novel methanotroph with interesting physiological and genomic properties that could possibly make this bacterium able to cope with fluctuating environmental conditions.</description><subject>Adaptation, Physiological</subject><subject>Applied and Environmental Science</subject><subject>Atmosphere</subject><subject>Bacteria</subject><subject>Bacterial Typing Techniques</subject><subject>Carbon</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA, Bacterial - genetics</subject><subject>Ecosystems</subject><subject>Environmental conditions</subject><subject>Fatty acids</subject><subject>Fatty Acids - chemistry</subject><subject>Fresh Water - microbiology</subject><subject>Freshwater ecosystems</subject><subject>Freshwater environments</subject><subject>Freshwater microorganisms</subject><subject>Genome, Bacterial</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Greenhouse gases</subject><subject>Membranes</subject><subject>Metabolism</subject><subject>Methane</subject><subject>Methane - metabolism</subject><subject>Methanol dehydrogenase</subject><subject>Methanotrophic bacteria</subject><subject>Methylococcaceae - classification</subject><subject>Methylococcaceae - isolation & purification</subject><subject>Methylococcaceae - physiology</subject><subject>Microcosms</subject><subject>Niches</subject><subject>Phospholipids</subject><subject>Phylogeny</subject><subject>Physiology</subject><subject>Proteobacteria</subject><subject>Pure culture</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>Sediments</subject><subject>Sulfur</subject><issn>2379-5042</issn><issn>2379-5042</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNpdkc1v1DAQxSMEolXpnROyxIVLir-TXJCqVT9WKvTQcrYmzoSkSuJgO4uWQ__2etulKj3NaPyb53l6WfaR0RPGePl1vJk79HhCqRYsZ-Wb7JCLosoVlfzti_4gOw7hjlLKNNe60O-zA8GYLipFD7P77xi77eAiRg_WWbsE4vz2LyC5SZN-IitFV4ysAwHyw21wILfbGcm6JhcwjjD7tOpqsBF9DwPZycHkondzR04bmCM2JDpy7jF0fyBR5Gza9N5NI04xfMjetTAEPN7Xo-zn-dnt6jK_ur5Yr06vciu5jDmnhWK2xJqCKhjIWoLikindQnLSyrblrEq9LJqSCVGBZdraGkXdNm2lQBxl355056UesbHpbw-DmX0_gt8aB735_2XqO_PLbYxWSihVJoEvewHvfi8Yohn7YHEYYEK3BMMFVVRIqaqEfn6F3rnFT8me4VxWleRc6UTRJ8p6F4LH9vkYRs0uX7PP1zzma9juhk8vTTwv_EtTPABJzaTG</recordid><startdate>20190605</startdate><enddate>20190605</enddate><creator>Ghashghavi, Mohammad</creator><creator>Belova, Svetlana E</creator><creator>Bodelier, Paul L E</creator><creator>Dedysh, Svetlana N</creator><creator>Kox, Martine A R</creator><creator>Speth, Daan R</creator><creator>Frenzel, Peter</creator><creator>Jetten, Mike S M</creator><creator>Lücker, Sebastian</creator><creator>Lüke, Claudia</creator><general>American Society for Microbiology</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0001-5795-1411</orcidid><orcidid>https://orcid.org/0000-0002-4691-7039</orcidid><orcidid>https://orcid.org/0000-0002-2361-5935</orcidid><orcidid>https://orcid.org/0000-0003-2935-4454</orcidid></search><sort><creationdate>20190605</creationdate><title>Methylotetracoccus oryzae Strain C50C1 Is a Novel Type Ib Gammaproteobacterial Methanotroph Adapted to Freshwater Environments</title><author>Ghashghavi, Mohammad ; Belova, Svetlana E ; Bodelier, Paul L E ; Dedysh, Svetlana N ; Kox, Martine A R ; Speth, Daan R ; Frenzel, Peter ; Jetten, Mike S M ; Lücker, Sebastian ; Lüke, Claudia</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c424t-20751c8eb0a571a4b4a524156fa116f4ff219fa147d81339ac16ccbe3bfdf95a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Adaptation, Physiological</topic><topic>Applied and Environmental Science</topic><topic>Atmosphere</topic><topic>Bacteria</topic><topic>Bacterial Typing Techniques</topic><topic>Carbon</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA, Bacterial - genetics</topic><topic>Ecosystems</topic><topic>Environmental conditions</topic><topic>Fatty acids</topic><topic>Fatty Acids - chemistry</topic><topic>Fresh Water - microbiology</topic><topic>Freshwater ecosystems</topic><topic>Freshwater environments</topic><topic>Freshwater microorganisms</topic><topic>Genome, Bacterial</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Greenhouse gases</topic><topic>Membranes</topic><topic>Metabolism</topic><topic>Methane</topic><topic>Methane - metabolism</topic><topic>Methanol dehydrogenase</topic><topic>Methanotrophic bacteria</topic><topic>Methylococcaceae - classification</topic><topic>Methylococcaceae - isolation & purification</topic><topic>Methylococcaceae - physiology</topic><topic>Microcosms</topic><topic>Niches</topic><topic>Phospholipids</topic><topic>Phylogeny</topic><topic>Physiology</topic><topic>Proteobacteria</topic><topic>Pure culture</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>Sediments</topic><topic>Sulfur</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ghashghavi, Mohammad</creatorcontrib><creatorcontrib>Belova, Svetlana E</creatorcontrib><creatorcontrib>Bodelier, Paul L E</creatorcontrib><creatorcontrib>Dedysh, Svetlana N</creatorcontrib><creatorcontrib>Kox, Martine A R</creatorcontrib><creatorcontrib>Speth, Daan R</creatorcontrib><creatorcontrib>Frenzel, Peter</creatorcontrib><creatorcontrib>Jetten, Mike S M</creatorcontrib><creatorcontrib>Lücker, Sebastian</creatorcontrib><creatorcontrib>Lüke, Claudia</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Biological Science Database</collection><collection>Access via ProQuest (Open Access)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>mSphere</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ghashghavi, Mohammad</au><au>Belova, Svetlana E</au><au>Bodelier, Paul L E</au><au>Dedysh, Svetlana N</au><au>Kox, Martine A R</au><au>Speth, Daan R</au><au>Frenzel, Peter</au><au>Jetten, Mike S M</au><au>Lücker, Sebastian</au><au>Lüke, Claudia</au><au>Tamaki, Hideyuki</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Methylotetracoccus oryzae Strain C50C1 Is a Novel Type Ib Gammaproteobacterial Methanotroph Adapted to Freshwater Environments</atitle><jtitle>mSphere</jtitle><addtitle>mSphere</addtitle><date>2019-06-05</date><risdate>2019</risdate><volume>4</volume><issue>3</issue><issn>2379-5042</issn><eissn>2379-5042</eissn><abstract>Methane-oxidizing microorganisms perform an important role in reducing emissions of the greenhouse gas methane to the atmosphere. To date, known bacterial methanotrophs belong to the
,
, and NC10 phyla. Within the
phylum, they can be divided into type Ia, type Ib, and type II methanotrophs. Type Ia and type II are well represented by isolates. Contrastingly, the vast majority of type Ib methanotrophs have not been able to be cultivated so far. Here, we compared the distributions of type Ib lineages in different environments. Whereas the cultivated type Ib methanotrophs (
and
) are found in landfill and upland soils, lineages that are not represented by isolates are mostly dominant in freshwater environments, such as paddy fields and lake sediments. Thus, we observed a clear niche differentiation within type Ib methanotrophs. Our subsequent isolation attempts resulted in obtaining a pure culture of a novel type Ib methanotroph, tentatively named "
" C50C1. Strain C50C1 was further characterized to be an obligate methanotroph, containing C
ω9c as the major membrane phospholipid fatty acid, which has not been found in other methanotrophs. Genome analysis of strain C50C1 showed the presence of two
operon copies and XoxF5-type methanol dehydrogenase in addition to MxaFI. The genome also contained genes involved in nitrogen and sulfur cycling, but it remains to be demonstrated if and how these help this type Ib methanotroph to adapt to fluctuating environmental conditions in freshwater ecosystems.
Most of the methane produced on our planet gets naturally oxidized by a group of methanotrophic microorganisms before it reaches the atmosphere. These microorganisms are able to oxidize methane, both aerobically and anaerobically, and use it as their sole energy source. Although methanotrophs have been studied for more than a century, there are still many unknown and uncultivated groups prevalent in various ecosystems. This study focused on the diversity and adaptation of aerobic methane-oxidizing bacteria in different environments by comparing their phenotypic and genotypic properties. We used lab-scale microcosms to create a countergradient of oxygen and methane for preenrichment, followed by classical isolation techniques to obtain methane-oxidizing bacteria from a freshwater environment. This resulted in the discovery and isolation of a novel methanotroph with interesting physiological and genomic properties that could possibly make this bacterium able to cope with fluctuating environmental conditions.</abstract><cop>United States</cop><pub>American Society for Microbiology</pub><pmid>31167950</pmid><doi>10.1128/mSphere.00631-18</doi><orcidid>https://orcid.org/0000-0001-5795-1411</orcidid><orcidid>https://orcid.org/0000-0002-4691-7039</orcidid><orcidid>https://orcid.org/0000-0002-2361-5935</orcidid><orcidid>https://orcid.org/0000-0003-2935-4454</orcidid><oa>free_for_read</oa></addata></record> |
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source | American Society for Microbiology; MEDLINE; DOAJ Directory of Open Access Journals; PubMed Central Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central |
subjects | Adaptation, Physiological Applied and Environmental Science Atmosphere Bacteria Bacterial Typing Techniques Carbon Deoxyribonucleic acid DNA DNA, Bacterial - genetics Ecosystems Environmental conditions Fatty acids Fatty Acids - chemistry Fresh Water - microbiology Freshwater ecosystems Freshwater environments Freshwater microorganisms Genome, Bacterial Genomes Genomics Greenhouse gases Membranes Metabolism Methane Methane - metabolism Methanol dehydrogenase Methanotrophic bacteria Methylococcaceae - classification Methylococcaceae - isolation & purification Methylococcaceae - physiology Microcosms Niches Phospholipids Phylogeny Physiology Proteobacteria Pure culture RNA, Ribosomal, 16S - genetics Sediments Sulfur |
title | Methylotetracoccus oryzae Strain C50C1 Is a Novel Type Ib Gammaproteobacterial Methanotroph Adapted to Freshwater Environments |
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