Cladogram based on 16S rRNA gene sequences showing the position of <i>Deferrivibrio metallireducens</i> V6FE1T (ON783970) in the family <i>Deferrivibrionaceae</i>, related to the families <i>Deferribacteraceae</i> and <i>Geovibrionaceae</i> (Order <i

The evolutionary history was inferred using the Maximum Likelihood method and General Time Reversible model. The percentage of trees in which the associated taxa clustered is shown next to the branches. This analysis involved 23 nucleotide sequences. The outgroup was composed of the following type species: <i>Thermanaeromonas toyohensis</i> ToBE (AB062280), <i>Moorella humiferrea</i> 64 FGQ (GQ872425), <i>Desulfovibrio indonesiensis</i> Ind 1 (Y09504), <i>Desulfovibrio marinus</i> E-2 (DQ365924), <i>Desulfonatronum cooperativum</i> Z-7999 (AY725424), <i>Desulfonatronum thioautotrophicum</i> ASO4-1 (FJ469577), <i>Desulfonatronum thiodismutans</i> MLF1 (AF373920), <i>Desulfonatronum lacustre</i> DSM 10312 (AF418171), <i>Desulfonatronum buryatense</i> Ki5 (KC417374). There were a total of 2753 positions in the final dataset. Evolutionary analyses were conducted in MEGA 7 (35). Taxonomy is based on LPSN. <b>Figure S2. Polar lipids of strain V6Fe1T.</b> The polar lipid profile of strain V6Fe1T consisted of glycolipids, phospholipids, phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol. <b>Figure S3. Venn diagram of protein orthologs shared by the assembly of <i>D. autotrophicus</i> chromosome and plasmid of <i>D. desulfuricans</i> and <i>C. nitroreducens.</i></b> Orthology analysis was performed with OrthoVenn2 web server using 0.01 blast e-value and 1.5 orthoMCL grain value. Numbers indicate shared or unique protein clusters and singleton proteins. <b>Table S1. Primers used in this study, designed using Primer3 software version 4.1.0, targeting <i>cymA, hcp, napA, norV, nrfD</i> (present in two copies), <i>nrfA</i> genes encoding respectively a cytoplasmic membrane electron transport protein involved in nitrate reduction, a hydroxylamine reductase, a periplasmic nitrate reductase, a nitric oxide reductase, an integral transmembrane protein involved in the terminal transfer of electrons from the quinone pool into the terminal components of the Nrf pathway and a formate-dependent nitrite reductase.</b> <b>Table S2. General features and genome sequencing information for <i>Deferrivibrio metallireducens</i> V6Fe1T according to MIGS recommendations.</b>

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Figshare
Published
2025-03-11
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https://doi.org/10.1371/journal.pone.0315093.s001
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Genomics and Phylogenetic Studies
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article

Cladogram based on 16S rRNA gene sequences showing the position of Deferrivibrio metallireducens V6FE1T (ON783970) in the family Deferrivibrionaceae, related to the families Deferribacteraceae and Geovibrionaceae (Order <i

Figshare
Genomics and Phylogenetic Studies
article

Cladogram based on 16S rRNA gene sequences showing the position of Deferrivibrio metallireducens V6FE1T (ON783970) in the family Deferrivibrionaceae, related to the families Deferribacteraceae and Geovibrionaceae (Order <i

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Abstract

The evolutionary history was inferred using the Maximum Likelihood method and General Time Reversible model. The percentage of trees in which the associated taxa clustered is shown next to the branches. This analysis involved 23 nucleotide sequences. The outgroup was composed of the following type species: <i>Thermanaeromonas toyohensis</i> ToBE (AB062280), <i>Moorella humiferrea</i> 64 FGQ (GQ872425), <i>Desulfovibrio indonesiensis</i> Ind 1 (Y09504), <i>Desulfovibrio marinus</i> E-2 (DQ365924), <i>Desulfonatronum cooperativum</i> Z-7999 (AY725424), <i>Desulfonatronum thioautotrophicum</i> ASO4-1 (FJ469577), <i>Desulfonatronum thiodismutans</i> MLF1 (AF373920), <i>Desulfonatronum lacustre</i> DSM 10312 (AF418171), <i>Desulfonatronum buryatense</i> Ki5 (KC417374). There were a total of 2753 positions in the final dataset. Evolutionary analyses were conducted in MEGA 7 (35). Taxonomy is based on LPSN. <b>Figure S2. Polar lipids of strain V6Fe1T.</b> The polar lipid profile of strain V6Fe1T consisted of glycolipids, phospholipids, phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol. <b>Figure S3. Venn diagram of protein orthologs shared by the assembly of <i>D. autotrophicus</i> chromosome and plasmid of <i>D. desulfuricans</i> and <i>C. nitroreducens.</i></b> Orthology analysis was performed with OrthoVenn2 web server using 0.01 blast e-value and 1.5 orthoMCL grain value. Numbers indicate shared or unique protein clusters and singleton proteins. <b>Table S1. Primers used in this study, designed using Primer3 software version 4.1.0, targeting <i>cymA, hcp, napA, norV, nrfD</i> (present in two copies), <i>nrfA</i> genes encoding respectively a cytoplasmic membrane electron transport protein involved in nitrate reduction, a hydroxylamine reductase, a periplasmic nitrate reductase, a nitric oxide reductase, an integral transmembrane protein involved in the terminal transfer of electrons from the quinone pool into the terminal components of the Nrf pathway and a formate-dependent nitrite reductase.</b> <b>Table S2. General features and genome sequencing information for <i>Deferrivibrio metallireducens</i> V6Fe1T according to MIGS recommendations.</b>

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Cladogram based on 16S rRNA gene sequences showing the position of <i>Deferrivibrio metallireducens</i> V6FE1T (ON783970) in the family <i>Deferrivibrionaceae</i>, related to the families <i>Deferribacteraceae</i> and <i>Geovibrionaceae</i> (Order <i · Figshare (2025) | TGRS Research Map | TGRS