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

Abstract

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.

Taxogenomic status of phylogenetically distant Frankia clusters warrants their elevation to the rank of genus: A description of Protofrankia gen. nov., Parafrankia gen. nov., and Pseudofrankia gen. nov. as three novel genera within the family Frankiaceae

“…A cut-off AAI value at 72.2 ± 0.03%, which is within the 60–80% threshold recommended for the delineation of genera ( Konstantinidis and Tiedje, 2005 ; Rodriguez-R and Konstantinidis, 2014 ), permitted a congruent regrouping with phylogenetic clusters. The POCP threshold of 50% originally proposed for genus delineation by Qin et al (2014) has been shown to be inappropriate for multiple taxa ( Aliyu et al, 2016 ; Pannekoek et al, 2016 ; Li et al, 2017 ; Lopes-Santos et al, 2017 ; Orata et al, 2018 ; Wirth and Whitman, 2018 ; Park et al, 2022 ). Sangal et al (2022) considered this POCP cutoff as overly stringent and proposed its reappraisement to 58–66%.…”

“…When ANI values are compared between more divergent taxa than species, they are prone to saturation and loss of information and, hence, considered inappropriate standards for genus delineation ( Konstantinidis and Tiedje, 2007 ; Kim et al, 2014 ; Qin et al, 2014 ; Rodriguez-R and Konstantinidis, 2014 ; Gosselin et al, 2022 ; Park et al, 2022 ). The ANI values in the present study (78–81.5%) were consistently lower than the ANI species thresholds of 95–96.5%.…”

Pseudodesulfovibrio nedwellii sp. nov., a mesophilic sulphate-reducing bacterium isolated from a xenic culture of an anaerobic heterolobosean protist

“…The genus Desulfovibrio (family Desulfovibrionaceae , order Desulfovibrionales , class Desulfovibrionia ) was later reclassified to include 13 genera [6]. Thereafter, the family Desulfovibrionaceae has been divided into 27 genera according to the results of genome analyses, and some species of the genus Pseudodesulfovibrio have been proposed to be members of the novel genus ‘ Salidesulfovibrio ’ [7]. However, the genus ‘ Salidesulfovibrio ’ is not a validity published name to date.…”

“…However, the genus ‘ Salidesulfovibrio ’ is not a validity published name to date. Although ‘ Desulfovibrio dechloracetivorans ’ belongs to a linage of the the genus Pseudodesulfovibrio [6, 7], the change of its name cannot be validly published because of absence of its type culture from public culture collections.…”

Genome Sequence of the Sulfate-Reducing Bacterium Pseudodesulfovibrio portus JCM 14722 T

“…Dissimilatory sulfate-reducing bacteria are obligate anaerobic prokaryotes which play a significant role in the biogeochemical cycling of sulfur and carbon in anoxic environments ( 1 , 2 ). The sulfate-reducing bacterial genus Pseudodesulfovibrio includes 11 Gram stain-negative, mesophilic species that are characterized by dissimilatory sulfate reduction with incomplete oxidation of low-molecular-weight fatty acids ( 3 – 5 ). The genomes of all the type strains of the Pseudodesulfovibrio species have been sequenced, except for that of Pseudodesulfovibrio portus JCM 14722 T (=MSL79 T ), which was isolated from estuarine sediments in the Sea of Japan ( 6 ).…”