Desulfolutivibrio sulfoxidireducens gen. nov., sp. nov., isolated from a pyrite-forming enrichment culture and reclassification of Desulfovibrio sulfodismutans as Desulfolutivibrio sulfodismutans comb. nov

Thiel, Joana; Spring, Stefan; Tindall, Brian J.; Spröer, Cathrin; Bunk, Boyke; Koeksoy, Elif; Ngugi, David Kamanda; Schink, Bernhard; Pester, Michael

doi:10.1016/j.syapm.2020.126105

Cited by 28 publications

(9 citation statements)

References 43 publications

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“…Genes were identified using Prodigal (Hyatt et al ., 2010) as part of the JGI genome annotation pipeline (Huntemann et al ., 2015). The complete genome of the reference strain Geovibrio thiophilus DSM 11263 T was determined at the Leibniz Institute DSMZ using a hybrid sequencing strategy involving long‐read PacBio and short‐read Illumina sequencing technologies as reported earlier (Thiel et al ., 2020). Genome sequences of strains L21‐Ace‐BES T , Seleniivibrio woodruffii DSM 24984 T and Geovibrio thiophilus DSM 11263 T are available in the NCBI GenBank database under the accession numbers ATWF00000000, SMGG00000000 and CP035108, respectively.…”

Section: Methodsmentioning

confidence: 99%

New insights into the energy metabolism and taxonomy ofDeferribacteresrevealed by the characterization of a new isolate from a hypersaline microbial mat

Spring

Rohde

Bunk

et al. 2022

Environmental Microbiology

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Summary Strain L21‐Ace‐BEST, isolated from a lithifying cyanobacterial mat, could be assigned to a novel species and genus within the class Deferribacteres. It is an important model organism for the study of anaerobic acetate degradation under hypersaline conditions. The metabolism of strain L21‐Ace‐BEST was characterized by biochemical studies, comparative genome analyses, and the evaluation of gene expression patterns. The central metabolic pathway is the citric acid cycle, which is mainly controlled by the enzyme succinyl‐CoA:acetate‐CoA transferase. The potential use of a reversed oxidative citric acid cycle to fix CO2 has been revealed through genome analysis. However, no autotrophic growth was detected in this strain, whereas sulfide and H2 can be used mixotrophically. Preferred electron acceptors for the anaerobic oxidation of acetate are nitrate, fumarate and dimethyl sulfoxide, while oxygen can be utilized only under microoxic conditions. Aerotolerant growth by fermentation was observed at higher oxygen concentrations. The redox cycling of sulfur/sulfide enables the generation of reducing power for the assimilation of acetate during growth and could prevent the over‐reduction of cells in stationary phase. Extracellular electron transfer appears to be an essential component of the respiratory metabolism in this clade of Deferribacteres and may be involved in the reduction of nitrite to ammonium.

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Section: Methodsmentioning

confidence: 99%

New insights into the energy metabolism and taxonomy ofDeferribacteresrevealed by the characterization of a new isolate from a hypersaline microbial mat

Spring

Rohde

Bunk

et al. 2022

Environmental Microbiology

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“…Thereafter, Desulfocurvus ( Klouche et al, 2009 ) and Desulfobaculum ( Zhao et al, 2012 ) were added. The addition of several new genera, namely Pseudodesulfovibrio ( Cao et al, 2016 ), Halodesulfovibrio ( Shivani et al, 2017 ), “Mailhella” ( Ndongo et al, 2017 ), Desulfohalovibrio , Desulfocurvibacter ( Spring et al, 2019 ), “ Paradesulfovibrio” ( Kim et al, 2020 ), and Desulfolutivibrio ( Thiel et al, 2020 ), finally led to a major reorganization based on the genome sequence data ( Waite et al, 2020 ), resulting in Desulfovibrionaceae currently comprising nine validly published genera ( Fundidesulfovibrio, Humidesulfovibrio, Maridesulfovibrio, Megalodesulfovibrio, Nitratidesulfovibrio, Oleidesulfovibrio, Paradesulfovibrio, Paucidesulfovibrio , and Solidesulfovibrio ) and three published but not validated genera ( “Alteridesulfovibrio,” “Aminidesulfovibrio,” and “Frigididesulfovibrio” ) besides the existing genera. Reorganizing the confusing taxonomy of the Desulfovibrionaceae family was completed by adding two valid [ Macrodesulfovibrio ( Galushko and Kuever, 2020b ), Oceanidesulfovibrio ( Galushko and Kuever, 2020c )] and one invalid genera [“ Psychrodesulfovibrio ” ( Galushko and Kuever, 2020d )] at the end of 2020 through Bergey’s manual ( Galushko and Kuever, 2020a ).…”

Section: Introductionmentioning

confidence: 99%

Establishment of Genome Based Criteria for Classification of the Family Desulfovibrionaceae and Proposal of Two Novel Genera, Alkalidesulfovibrio gen. nov. and Salidesulfovibrio gen. nov.

et al. 2022

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Bacteria in the Desulfovibrionaceae family, which contribute to S element turnover as sulfate-reducing bacteria (SRB) and disproportionation of partially oxidized sulfoxy anions, have been extensively investigated since the importance of the sulfur cycle emerged. Novel species belonging to this taxon are frequently reported, because they exist in various environments and are easy to culture using established methods. Due to the rapid expansion of the taxon, correction and reclassification have been conducted. The development of high-throughput sequencing facilitated rapid expansion of genome sequence database. Genome-based criteria, based on these databases, proved to be potential classification standard by overcoming the limitations of 16S rRNA-based phylogeny. Although standards methods for taxogenomics are being established, the addition of a novel genus requires extensive calculations with taxa, including many species, such as Desulfovibrionaceae. Thus, the genome-based criteria for classification of Desulfovibrionaceae were established and validated in this study. The average amino-acid identity (AAI) cut-off value, 63.43 ± 0.01, was calculated to be an appropriate criterion for genus delineation of the family Desulfovibrionaceae. By applying the AAI cut-off value, 88 genomes of the Desulfovibrionaceae were divided into 27 genera, which follows the core gene phylogeny results. In this process, two novel genera (Alkalidesulfovibrio and Salidesulfovibrio) and one former invalid genus (“Psychrodesulfovibrio”) were officially proposed. Further, by applying the 95–96% average nucleotide identity (ANI) standard and the 70% digital DNA–DNA hybridization standard values for species delineation of strains that were classified as the same species, five strains have the potential to be newly classified. After verifying that the classification was appropriately performed through relative synonymous codon usage analysis, common characteristics were listed by group. In addition, by detecting metal resistance related genes via in silico analysis, it was confirmed that most strains display metal tolerance.

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“…Comparison of the characteristics of strain FSS-1 T with those of the reference strains Strains: 1, FSS-1 T ; 2, Fundidesulfovibrio putealis B7-43 T [64]; 3, Fundidesulfovibrio butyratiphilus BSY T[65]; 4, Desulfolutivibrio sulfoxidireducens DSM 107105 T[57]; 5, Desulfolutivibrio sulfodismutans ThAc01 T[66]; 6, Solidesulfovibrio magneticus RS-1 T[22]. +, Positive reaction; (+), weakly positive reaction; −, negative reaction; nd, not determined.…”

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confidence: 99%

Fundidesulfovibrio magnetotacticus sp. nov., a sulphate-reducing magnetotactic bacterium, isolated from sediments and freshwater of a pond

Shimoshige

Kobayashi

Shimamura

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

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A sulphate-reducing magnetotactic bacterium, designated strain FSS-1T, was isolated from sediments and freshwater of Suwa Pond located in Hidaka, Saitama, Japan. Strain FSS-1T was a motile, Gram-negative and curved rod-shaped bacterium that synthesizes bullet-shaped magnetite (Fe3O4) nanoparticles in each cell. Strain FSS-1T was able to grow in the range of pH 6.5–8.0 (optimum, pH 7.0), 22–34 °C (optimum, 28 °C) and with 0–8.0 g l−1 NaCl (optimum, 0–2.0 g l−1 NaCl). Strain FSS-1T grew well in the presence of 50 µM ferric quinate as an iron source. The major fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. The major menaquinone was MK-7 (H2). Strain FSS-1T contained desulfoviridin, cytochrome c 3 and catalase, but did not contain oxidase. Strain FSS-1T used fumarate, lactate, pyruvate, malate, formate/acetate, succinate, tartrate, ethanol, 1-propanol, peptone, soytone and yeast extract as electron donors, while the strain used sulphate, thiosulphate and fumarate as electron acceptors. Fumarate was fermented in the absence of electron acceptors. Analysis of the 16S rRNA gene sequence showed that strain FSS-1T is a member of the genus Fundidesulfovibrio . The gene sequence showed 96.7, 95.0, 92.0, 91.2 and 91.4% similarities to the most closely related members of the genera Fundidesulfovibrio putealis B7-43T, Fundidesulfovibrio butyratiphilus BSYT, Desulfolutivibrio sulfoxidireducens DSM 107105T, Desulfolutivibrio sulfodismutans ThAc01T and Solidesulfovibrio magneticus RS-1T, respectively. The DNA G+C content of strain FSS-1T was 67.5 mol%. The average nucleotide identity value between strain FSS-1T and F. putealis B7-43T was 80.7 %. Therefore, strain FSS-1T represents a novel species within the genus Fundidesulfovibrio , for which the name Fundidesulfovibrio magnetotacticus sp. nov. is proposed (=JCM 32405T=DSM 110007T).

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Desulfolutivibrio sulfoxidireducens gen. nov., sp. nov., isolated from a pyrite-forming enrichment culture and reclassification of Desulfovibrio sulfodismutans as Desulfolutivibrio sulfodismutans comb. nov

Cited by 28 publications

References 43 publications

New insights into the energy metabolism and taxonomy ofDeferribacteresrevealed by the characterization of a new isolate from a hypersaline microbial mat

New insights into the energy metabolism and taxonomy ofDeferribacteresrevealed by the characterization of a new isolate from a hypersaline microbial mat

Establishment of Genome Based Criteria for Classification of the Family Desulfovibrionaceae and Proposal of Two Novel Genera, Alkalidesulfovibrio gen. nov. and Salidesulfovibrio gen. nov.

Fundidesulfovibrio magnetotacticus sp. nov., a sulphate-reducing magnetotactic bacterium, isolated from sediments and freshwater of a pond

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