Salipiger mangrovisoli sp. nov., isolated from mangrove soil and the proposal for the reclassification of Paraphaeobacter pallidus as Salipiger pallidus comb. nov.
A novel Gram-stain-negative, aerobic and rod-shaped bacterial strain designated as 6D45AT was isolated from mangrove soil and characterized using a polyphasic taxonomic approach. Strain 6D45AT was found to grow at 10–37 °C (optimum, 28 °C), at pH 6.0–9.0 (optimum, 7.0) and in 0–5 % (w/v) NaCl (optimum, 2%). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 6D45AT fell into the genus Salipiger and shared 99.1 % identity with the closest type strain Salipiger pacificus CGMCC 1.3455T and less than 97.2 % identity with other type strains of this genus. The 34.8 % digital DNA–DNA hybridization (dDDH) and 88.3 % average nucleotide identity (ANI) values between strain 6D45AT and the closest relative above were well below recognized thresholds of 70 % DDH and 95–96 % ANI for species definition, implying that strain 6D45AT should represent a novel genospecies. The phylogenomic analysis indicated that strain 6D45AT formed an independent branch distinct from reference strains. The predominant cellular fatty acid of strain 6D45AT was summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c, 66.9 %); the polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, two unidentified glycolipids and an unknown lipid; the respiratory quinone was Q-10. The genomic DNA G+C content was 66.5 mol %. Based on the phenotypic and genotypic characteristics, strain 6D45AT is concluded to represent a novel species of the genus Salipiger, for which the name Salipiger mangrovisoli sp. nov., is proposed. The type strain of the species is 6D45AT (=GDMCC 1.1960T=KCTC 82334T). We also propose the reclassification of Paraphaeobacter pallidus as Salipiger pallidus comb. nov. and ‘Pelagibaca abyssi’ as a species of the genus Salipiger.
WirthJS, WhitmanWB. Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera. Int J Syst Evol Microbiol2018; 68:2393–2411 [View Article] [PubMed]
OrenA, GarrityGM. Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 68, part 7, of the IJSEM. Int J Syst Evol Microbiol2018; 68:3077–3079 [View Article] [PubMed]
OrenA, GarrityG. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol2020; 70:4043–4049 [View Article] [PubMed]
ParteAC, Sardà CarbasseJ, Meier-KolthoffJP, ReimerLC, GökerM. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol2020; 70:5607–5612 [View Article] [PubMed]
RajasabapathyR, MohandassC, DastagerSG, LiuQ, LiW-J et al.Citreicella manganoxidans sp. nov., a novel manganese oxidizing bacterium isolated from a shallow water hydrothermal vent in Espalamaca (Azores. Antonie van Leeuwenhoek2015; 108:1433–1439 [View Article]
LiS, TangK, LiuK, JiaoN. Thiobacimonas profunda gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from deep-sea water. Int J Syst Evol Microbiol2015; 65:359–364 [View Article] [PubMed]
LinY, TangK, LiS, LiuK, SunJ et al.Pelagibaca abyssi sp. nov., of the family Rhodobacteraceae, isolated from deep-sea water. Antonie van Leeuwenhoek2014; 106:507–513 [View Article] [PubMed]
DaiX, WangBJ, YangQX, JiaoNZ, LiuSJ. Yangia pacifica gen. nov., sp. nov., a novel member of the Roseobacter clade from coastal sediment of the East China Sea. Int J Syst Evol Microbiol2006; 56:529–533 [View Article] [PubMed]
SorokinDY, TourovaTP, MuyzerG. Citreicella thiooxidans gen. nov., sp. nov., a novel lithoheterotrophic sulfur-oxidizing bacterium from the Black Sea. Syst Appl Microbiol2005; 28:679–687 [View Article] [PubMed]
LlamasI, MataJA, TallonR, BressollierP, UrdaciMC et al. Characterization of the exopolysaccharide produced by Salipiger mucosus A3T, a halophilic species belonging to the Alphaproteobacteria, isolated on the Spanish Mediterranean seaboard. Mar Drugs2010; 8:2240–2251 [View Article] [PubMed]
YoonS-H, HaS-M, KwonS, LimJ, KimY et al. Introducing Ezbiocloud: A taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol2017; 67:1613–1617
MinhBQ, SchmidtHA, ChernomorO, SchrempfD, WoodhamsMD et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol2020; 37:1530–1534 [View Article] [PubMed]
KalyaanamoorthyS, MinhBQ, WongTKF, von HaeselerA, JermiinLS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods2017; 14:587–589 [View Article] [PubMed]
RzhetskyA, NeiM. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol1993; 10:1073–1095 [View Article] [PubMed]
BankevichA, NurkS, AntipovD, GurevichAA, DvorkinM et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol2012; 19:455–477 [View Article] [PubMed]
ParksDH, ImelfortM, SkennertonCT, HugenholtzP, TysonGW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res2015; 25:1043–1055 [View Article] [PubMed]
AuchAF, von JanM, KlenkHP, GökerM. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci2010; 2:117–134 [View Article] [PubMed]
ChenC, ChenH, ZhangY, ThomasHR, FrankMH et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant2020; 13:1194–1202 [View Article] [PubMed]
OverbeekR, OlsonR, PuschGD, OlsenGJ, DavisJJ et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST. Nucleic Acids Res2014; 42:D206–214 [View Article] [PubMed]
NaS-I, KimYO, YoonSH, HaS-M, BaekI et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol2018; 56:280–285
ChunJ, OrenA, VentosaA, ChristensenH, ArahalDR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol2018; 68:461–466 [View Article] [PubMed]
WayneLG, BrennerDJ, ColwellRR, GrimontPAD, KandlerO et al. Report of the Ad Hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol1987; 37:463–464
RichterM, Rosselló-MóraR. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A2009; 106:19126 [View Article] [PubMed]
BarcoRA, GarrityGM, ScottJJ, AmendJP, NealsonKH et al. A genus definition for bacteria and archaea based on a standard genome relatedness index. mBio2020; 11:e02475–02419 [View Article] [PubMed]
KonstantinidisKT, TiedjeJM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A2005; 102:2567–2572 [View Article] [PubMed]
MinnikinDE, O’DonnellAG, GoodfellowM, AldersonG, AthalyeM et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods1984; 2:233–241 [View Article]
CollinsMD, PirouzT, GoodfellowM, MinnikinDE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol1977; 100:221–230 [View Article] [PubMed]
ChoJC, GiovannoniSJ. Pelagibaca bermudensis gen. nov., sp. nov., a novel marine bacterium within the Roseobacter clade in the order Rhodobacterales. Int J Syst Evol Microbiol2006; 56:855–859 [View Article] [PubMed]
Salipiger mangrovisoli sp. nov., isolated from mangrove soil and the proposal for the reclassification of Paraphaeobacter pallidus as Salipiger pallidus comb. nov.