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Genome Analysis and Description of Three Novel Diazotrophs Geomonas Species Isolated From Paddy Soils
Five strictly anaerobic strains, designated RG2 , RG3, RG10 , RF4 , and RG29, were isolated from paddy soils in China. Strains RG2 , RF4 , RG10 , RG3, and RG29 grew at temperatures ranging 5-42°C and pH ranging 5.5-8.5. Strains RG2 , RF4 , RG3, and RG29 could tolerate NaCl up to 0-0.7% (w/v) while s...
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| Published in: | Frontiers in microbiology 2022-02, Vol.12, p.801462-801462 |
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| container_title | Frontiers in microbiology |
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| creator | Liu, Guo-Hong Yang, Shang Tang, Rong Xie, Cheng-Jie Zhou, Shun-Gui |
| description | Five strictly anaerobic strains, designated RG2
, RG3, RG10
, RF4
, and RG29, were isolated from paddy soils in China. Strains RG2
, RF4
, RG10
, RG3, and RG29 grew at temperatures ranging 5-42°C and pH ranging 5.5-8.5. Strains RG2
, RF4
, RG3, and RG29 could tolerate NaCl up to 0-0.7% (w/v) while strain RG10
could tolerate NaCl up to 0-0.8% (w/v). The isolated strains showed the highest 16S rRNA gene sequence similarities to the type strains of
Red111
and
Red736
. In phylogenetic (based on 16S rRNA gene sequence) and phylogenomic trees, strains clustered with the members of the genus
Menaquinone-8 was the predominant quinone present in all strains. The major fatty acid profiles of all strains were C
ω6
, C
, iso-C
, and Summed Feature 3. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the isolated strains and the closely related
species were lower than the cutoff value (ANI 95-96% and dDDH 70%) for prokaryotic species delineation. Based on physiological, biochemical, and chemotaxonomic properties, strains RG2
, RG10
, and RF4
could easily be differentiated with the members of the genus
. Additionally, all the isolated strains possessed
clusters and catalytic compartments of nitrogenase. Based on the above results, the isolated five strains represent three novel species of the genus
, for which the names
sp. nov.,
sp. nov., and
sp. nov. are proposed. The type strains are RG10
(= GDMCC1.2537
= KCTC 26318
), RG2
(= GDMCC1.2536
= KCTC 25317
), and RF4
(= GDMCC 1.2547
= KCTC 25316
). |
| doi_str_mv | 10.3389/fmicb.2021.801462 |
| format | article |
| fullrecord | <record><control><sourceid>proquest_doaj_</sourceid><recordid>TN_cdi_doaj_primary_oai_doaj_org_article_f0aab9d399614f0c987041adc657f906</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><doaj_id>oai_doaj_org_article_f0aab9d399614f0c987041adc657f906</doaj_id><sourcerecordid>2632802719</sourcerecordid><originalsourceid>FETCH-LOGICAL-c531t-90f301c6c9c8bbe731b4db35a817161e02223f044c1a46e96189366e3a9ba1b23</originalsourceid><addsrcrecordid>eNpVkU1r3DAQQE1paUKaH9BL0bGX3WokWbYuhZCP7UJoC0mhNzGWx1kF2XIlb2D76-vNpiGZg2aQZt4IXlF8BL6UsjZfut67Zim4gGXNQWnxpjgGrdVCcvH77Yv6qDjN-Z7PobiYz_fFkSzBVEap44JWNMSe2NmAYZd9Zji07IKyS36cfBxY7NjtJhGx7_GBArvw-DdOKY6bzFYU-zhgZjcjOU-ZrXMMOFHLrlLs2U9s2x27iT7kD8W7DkOm06d8Uvy6urw9_7a4_rFan59dL1wpYVoY3kkOTjvj6qahSkKj2kaWWEMFGogLIWTHlXKASpPRUBupNUk0DUIj5EmxPnDbiPd2TL7HtLMRvX28iOnOYpq8C2Q7jtiYVpqZojruTF1xBdg6XVad4XpmfT2wxm3TU-tomBKGV9DXL4Pf2Lv4YOu6NKDNDPj8BEjxz5byZHufHYWAA8VttkJLUXNRwb4VDq0uxZwTdc9rgNu9bfto2-5t24PteebTy_89T_x3K_8By0CnAA</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2632802719</pqid></control><display><type>article</type><title>Genome Analysis and Description of Three Novel Diazotrophs Geomonas Species Isolated From Paddy Soils</title><source>PubMed (Medline)</source><creator>Liu, Guo-Hong ; Yang, Shang ; Tang, Rong ; Xie, Cheng-Jie ; Zhou, Shun-Gui</creator><creatorcontrib>Liu, Guo-Hong ; Yang, Shang ; Tang, Rong ; Xie, Cheng-Jie ; Zhou, Shun-Gui</creatorcontrib><description>Five strictly anaerobic strains, designated RG2
, RG3, RG10
, RF4
, and RG29, were isolated from paddy soils in China. Strains RG2
, RF4
, RG10
, RG3, and RG29 grew at temperatures ranging 5-42°C and pH ranging 5.5-8.5. Strains RG2
, RF4
, RG3, and RG29 could tolerate NaCl up to 0-0.7% (w/v) while strain RG10
could tolerate NaCl up to 0-0.8% (w/v). The isolated strains showed the highest 16S rRNA gene sequence similarities to the type strains of
Red111
and
Red736
. In phylogenetic (based on 16S rRNA gene sequence) and phylogenomic trees, strains clustered with the members of the genus
Menaquinone-8 was the predominant quinone present in all strains. The major fatty acid profiles of all strains were C
ω6
, C
, iso-C
, and Summed Feature 3. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the isolated strains and the closely related
species were lower than the cutoff value (ANI 95-96% and dDDH 70%) for prokaryotic species delineation. Based on physiological, biochemical, and chemotaxonomic properties, strains RG2
, RG10
, and RF4
could easily be differentiated with the members of the genus
. Additionally, all the isolated strains possessed
clusters and catalytic compartments of nitrogenase. Based on the above results, the isolated five strains represent three novel species of the genus
, for which the names
sp. nov.,
sp. nov., and
sp. nov. are proposed. The type strains are RG10
(= GDMCC1.2537
= KCTC 26318
), RG2
(= GDMCC1.2536
= KCTC 25317
), and RF4
(= GDMCC 1.2547
= KCTC 25316
).</description><identifier>ISSN: 1664-302X</identifier><identifier>EISSN: 1664-302X</identifier><identifier>DOI: 10.3389/fmicb.2021.801462</identifier><identifier>PMID: 35197944</identifier><language>eng</language><publisher>Switzerland: Frontiers Media S.A</publisher><subject>Geomonas nitrogeniifigens ; Geomonas oryzisoli ; Geomonas subterranea ; iron reduction ; Microbiology ; nitrogen fixation activity ; paddy soil</subject><ispartof>Frontiers in microbiology, 2022-02, Vol.12, p.801462-801462</ispartof><rights>Copyright © 2022 Liu, Yang, Tang, Xie and Zhou.</rights><rights>Copyright © 2022 Liu, Yang, Tang, Xie and Zhou. 2022 Liu, Yang, Tang, Xie and Zhou</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c531t-90f301c6c9c8bbe731b4db35a817161e02223f044c1a46e96189366e3a9ba1b23</citedby><cites>FETCH-LOGICAL-c531t-90f301c6c9c8bbe731b4db35a817161e02223f044c1a46e96189366e3a9ba1b23</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8859169/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8859169/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35197944$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Liu, Guo-Hong</creatorcontrib><creatorcontrib>Yang, Shang</creatorcontrib><creatorcontrib>Tang, Rong</creatorcontrib><creatorcontrib>Xie, Cheng-Jie</creatorcontrib><creatorcontrib>Zhou, Shun-Gui</creatorcontrib><title>Genome Analysis and Description of Three Novel Diazotrophs Geomonas Species Isolated From Paddy Soils</title><title>Frontiers in microbiology</title><addtitle>Front Microbiol</addtitle><description>Five strictly anaerobic strains, designated RG2
, RG3, RG10
, RF4
, and RG29, were isolated from paddy soils in China. Strains RG2
, RF4
, RG10
, RG3, and RG29 grew at temperatures ranging 5-42°C and pH ranging 5.5-8.5. Strains RG2
, RF4
, RG3, and RG29 could tolerate NaCl up to 0-0.7% (w/v) while strain RG10
could tolerate NaCl up to 0-0.8% (w/v). The isolated strains showed the highest 16S rRNA gene sequence similarities to the type strains of
Red111
and
Red736
. In phylogenetic (based on 16S rRNA gene sequence) and phylogenomic trees, strains clustered with the members of the genus
Menaquinone-8 was the predominant quinone present in all strains. The major fatty acid profiles of all strains were C
ω6
, C
, iso-C
, and Summed Feature 3. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the isolated strains and the closely related
species were lower than the cutoff value (ANI 95-96% and dDDH 70%) for prokaryotic species delineation. Based on physiological, biochemical, and chemotaxonomic properties, strains RG2
, RG10
, and RF4
could easily be differentiated with the members of the genus
. Additionally, all the isolated strains possessed
clusters and catalytic compartments of nitrogenase. Based on the above results, the isolated five strains represent three novel species of the genus
, for which the names
sp. nov.,
sp. nov., and
sp. nov. are proposed. The type strains are RG10
(= GDMCC1.2537
= KCTC 26318
), RG2
(= GDMCC1.2536
= KCTC 25317
), and RF4
(= GDMCC 1.2547
= KCTC 25316
).</description><subject>Geomonas nitrogeniifigens</subject><subject>Geomonas oryzisoli</subject><subject>Geomonas subterranea</subject><subject>iron reduction</subject><subject>Microbiology</subject><subject>nitrogen fixation activity</subject><subject>paddy soil</subject><issn>1664-302X</issn><issn>1664-302X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>DOA</sourceid><recordid>eNpVkU1r3DAQQE1paUKaH9BL0bGX3WokWbYuhZCP7UJoC0mhNzGWx1kF2XIlb2D76-vNpiGZg2aQZt4IXlF8BL6UsjZfut67Zim4gGXNQWnxpjgGrdVCcvH77Yv6qDjN-Z7PobiYz_fFkSzBVEap44JWNMSe2NmAYZd9Zji07IKyS36cfBxY7NjtJhGx7_GBArvw-DdOKY6bzFYU-zhgZjcjOU-ZrXMMOFHLrlLs2U9s2x27iT7kD8W7DkOm06d8Uvy6urw9_7a4_rFan59dL1wpYVoY3kkOTjvj6qahSkKj2kaWWEMFGogLIWTHlXKASpPRUBupNUk0DUIj5EmxPnDbiPd2TL7HtLMRvX28iOnOYpq8C2Q7jtiYVpqZojruTF1xBdg6XVad4XpmfT2wxm3TU-tomBKGV9DXL4Pf2Lv4YOu6NKDNDPj8BEjxz5byZHufHYWAA8VttkJLUXNRwb4VDq0uxZwTdc9rgNu9bfto2-5t24PteebTy_89T_x3K_8By0CnAA</recordid><startdate>20220207</startdate><enddate>20220207</enddate><creator>Liu, Guo-Hong</creator><creator>Yang, Shang</creator><creator>Tang, Rong</creator><creator>Xie, Cheng-Jie</creator><creator>Zhou, Shun-Gui</creator><general>Frontiers Media S.A</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20220207</creationdate><title>Genome Analysis and Description of Three Novel Diazotrophs Geomonas Species Isolated From Paddy Soils</title><author>Liu, Guo-Hong ; Yang, Shang ; Tang, Rong ; Xie, Cheng-Jie ; Zhou, Shun-Gui</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c531t-90f301c6c9c8bbe731b4db35a817161e02223f044c1a46e96189366e3a9ba1b23</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Geomonas nitrogeniifigens</topic><topic>Geomonas oryzisoli</topic><topic>Geomonas subterranea</topic><topic>iron reduction</topic><topic>Microbiology</topic><topic>nitrogen fixation activity</topic><topic>paddy soil</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Liu, Guo-Hong</creatorcontrib><creatorcontrib>Yang, Shang</creatorcontrib><creatorcontrib>Tang, Rong</creatorcontrib><creatorcontrib>Xie, Cheng-Jie</creatorcontrib><creatorcontrib>Zhou, Shun-Gui</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>Frontiers in microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Liu, Guo-Hong</au><au>Yang, Shang</au><au>Tang, Rong</au><au>Xie, Cheng-Jie</au><au>Zhou, Shun-Gui</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome Analysis and Description of Three Novel Diazotrophs Geomonas Species Isolated From Paddy Soils</atitle><jtitle>Frontiers in microbiology</jtitle><addtitle>Front Microbiol</addtitle><date>2022-02-07</date><risdate>2022</risdate><volume>12</volume><spage>801462</spage><epage>801462</epage><pages>801462-801462</pages><issn>1664-302X</issn><eissn>1664-302X</eissn><abstract>Five strictly anaerobic strains, designated RG2
, RG3, RG10
, RF4
, and RG29, were isolated from paddy soils in China. Strains RG2
, RF4
, RG10
, RG3, and RG29 grew at temperatures ranging 5-42°C and pH ranging 5.5-8.5. Strains RG2
, RF4
, RG3, and RG29 could tolerate NaCl up to 0-0.7% (w/v) while strain RG10
could tolerate NaCl up to 0-0.8% (w/v). The isolated strains showed the highest 16S rRNA gene sequence similarities to the type strains of
Red111
and
Red736
. In phylogenetic (based on 16S rRNA gene sequence) and phylogenomic trees, strains clustered with the members of the genus
Menaquinone-8 was the predominant quinone present in all strains. The major fatty acid profiles of all strains were C
ω6
, C
, iso-C
, and Summed Feature 3. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the isolated strains and the closely related
species were lower than the cutoff value (ANI 95-96% and dDDH 70%) for prokaryotic species delineation. Based on physiological, biochemical, and chemotaxonomic properties, strains RG2
, RG10
, and RF4
could easily be differentiated with the members of the genus
. Additionally, all the isolated strains possessed
clusters and catalytic compartments of nitrogenase. Based on the above results, the isolated five strains represent three novel species of the genus
, for which the names
sp. nov.,
sp. nov., and
sp. nov. are proposed. The type strains are RG10
(= GDMCC1.2537
= KCTC 26318
), RG2
(= GDMCC1.2536
= KCTC 25317
), and RF4
(= GDMCC 1.2547
= KCTC 25316
).</abstract><cop>Switzerland</cop><pub>Frontiers Media S.A</pub><pmid>35197944</pmid><doi>10.3389/fmicb.2021.801462</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1664-302X |
| ispartof | Frontiers in microbiology, 2022-02, Vol.12, p.801462-801462 |
| issn | 1664-302X 1664-302X |
| language | eng |
| recordid | cdi_doaj_primary_oai_doaj_org_article_f0aab9d399614f0c987041adc657f906 |
| source | PubMed (Medline) |
| subjects | Geomonas nitrogeniifigens Geomonas oryzisoli Geomonas subterranea iron reduction Microbiology nitrogen fixation activity paddy soil |
| title | Genome Analysis and Description of Three Novel Diazotrophs Geomonas Species Isolated From Paddy Soils |
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