Two sulphur-oxidizing, chemolithoautotrophic aerobes were isolated from the chemocline of an anchialine sinkhole located within the Weeki Wachee River of Florida. Gram-stain-negative cells of both strains were motile, chemotactic rods. Phylogenetic analysis of the 16S rRNA gene and predicted amino acid sequences of ribosomal proteins, average nucleotide identities, and alignment fractions suggest the strains HH1 T and HH3 T represent novel species belonging to the genus Thiomicrorhabdus . The genome G+C fraction of HH1 T is 47.8 mol% with a genome length of 2.61 Mb, whereas HH3 T has a G+C fraction of 52.4 mol% and 2.49 Mb genome length. Major fatty acids of the two strains included C 16 : 1 , C 18 : 1 and C 16 : 0 , with the addition of C 10:0 3-OH in HH1 T and C 12 : 0 in HH3 T . Chemolithoautotrophic growth of both strains was supported by elemental sulphur, sulphide, tetrathionate, and thiosulphate, and HH1 T was also able to use molecular hydrogen. Neither strain was capable of heterotrophic growth or use of nitrate as a terminal electron acceptor. Strain HH1 T grew from pH 6.5 to 8.5, with an optimum of pH 7.4, whereas strain HH3 T grew from pH 6 to 8 with an optimum of pH 7.5. Growth was observed between 15–35 °C with optima of 32.8 °C for HH1 T and 32 °C for HH3 T . HH1 T grew in media with [NaCl] 80–689 mM, with an optimum of 400 mM, while HH3 T grew at 80–517 mM, with an optimum of 80 mM. The name Thiomicrorhabdus heinhorstiae sp. nov. is proposed, and the type strain is HH1 T (=DSM 111584 T =ATCC TSD-240 T ). The name Thiomicrorhabdus cannonii sp. nov is proposed, and the type strain is HH3 T (=DSM 111593 T =ATCC TSD-241 T ).
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Halobacterium bonnevillei sp. nov., Halobaculum saliterrae sp. nov. and Halovenus carboxidivorans sp. nov., three novel carbon monoxide-oxidizing Halobacteria from saline crusts and soils
Three novel carbon monoxide-oxidizing Halobacteria were isolated from Bonneville Salt Flats (Utah, USA) salt crusts and nearby saline soils. Phylogenetic analysis of 16S rRNA gene sequences revealed that strains PCN9 T , WSA2 T and WSH3 T belong to the genera Halobacterium , Halobaculum and Halovenus , respectively. Strains PCN9 T , WSA2 T and WSH3 T grew optimally at 40 °C (PCN9 T ) or 50 °C (WSA2 T , WSH3 T ). NaCl optima were 3 M (PCN9 T , WSA2 T ) or 4 M NaCl (WSH3 T ). Carbon monoxide was oxidized by all isolates, each of which contained a molybdenum-dependent CO dehydrogenase. G+C contents for the three respective isolates were 66.75, 67.62, and 63.97 mol% as derived from genome analyses. The closest phylogenetic relatives for PCN9 T , WSA2 T and WSH3 T were Halobacterium noricense A1 T , Halobaculum roseum D90 T and Halovenus aranensis EB27 T with 98.71, 98.19 and 95.95 % 16S rRNA gene sequence similarities, respectively. Genome comparisons of PCN9 T with Halobacterium noricense A1 T yielded an average nucleotide identity (ANI) of 82.0% and a digital DNA–DNA hybridization (dDDH) value of 25.7 %; comparisons of WSA2 T with Halobaculum roseum D90 T yielded ANI and dDDH values of 86.34 and 31.1 %, respectively. The ANI value for a comparison of WSH3 T with Halovenus aranensis EB27 T was 75.2 %. Physiological, biochemical, genetic and genomic characteristics of PCN9 T , WSA2 T and WSH3 T differentiated them from their closest phylogenetic neighbours and indicated that they represent novel species for which the names Halobaculum bonnevillei , Halobaculum saliterrae and Halovenus carboxidivorans are proposed, respectively. The type strains are PCN9 T (=JCM 32472=LMG 31022=ATCC TSD-126), WSA2 T (=JCM 32473=ATCC TSD-127) and WSH3 T (=JCM 32474=ATCC TSD-128).
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- Award ID(s):
- 1634239
- NSF-PAR ID:
- 10182672
- Date Published:
- Journal Name:
- International Journal of Systematic and Evolutionary Microbiology
- Volume:
- 70
- Issue:
- 7
- ISSN:
- 1466-5026
- Page Range / eLocation ID:
- 4261 to 4268
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract A polyphasic taxonomic approach, incorporating analysis of phenotypic features, cellular fatty acid profiles, 16S rRNA gene sequences, and determination of average nucleotide identity (ANI) plus digital DNA–DNA hybridization (dDDH), was applied to characterize an anaerobic bacterial strain designated KD22Tisolated from human feces. 16S rRNA gene-based phylogenetic analysis showed that strain KD22Twas found to be most closely related to species of the genus
Gabonibacter. At the 16S rRNA gene level, the closest species from the strain KD22Tcorresponded withGabonibacter massiliensis GM7T, with a similarity of 97.58%. Cells of strain KD22T were Gram-negative coccobacillus, positive for indole and negative for catalase, nitrate reduction, oxidase, and urease activities. The fatty acid analysis demonstrated the presence of a high concentration of iso-C15: 0(51.65%). Next, the complete whole-genome sequence of strain KD22T was 3,368,578 bp long with 42 mol% of DNA G + C contents. The DDH and ANI values between KD22T and type strains of phylogenetically related species were 67.40% and 95.43%, respectively. These phylogenetic, phenotypic, and genomic results supported the affiliation of strain KD22Tas a novel bacterial species within the genusGabonibacter. The proposed name isGabonibacter chumensis and the type strain is KD22T(= CSUR Q8104T = DSM 115208 T). -
Background Cellulolytic, hemicellulolytic, and amylolytic (CHA) enzyme-producing halophiles are understudied. The recently defined taxon Iocasia fonsfrigidae consists of one well-described anaerobic bacterial strain: NS-1 T . Prior to characterization of strain NS-1 T , an isolate designated Halocella sp. SP3-1 was isolated and its genome was published. Based on physiological and genetic comparisons, it was suggested that Halocella sp. SP3-1 may be another isolate of I. fronsfrigidae . Despite being geographic variants of the same species, data indicate that strain SP3-1 exhibits genetic, genomic, and physiological characteristics that distinguish it from strain NS-1 T . In this study, we examine the halophilic and alkaliphilic nature of strain SP3-1 and the genetic substrates underlying phenotypic differences between strains SP3-1 and NS-1 T with focus on sugar metabolism and CHA enzyme expression. Methods Standard methods in anaerobic cell culture were used to grow strains SP3-1 as well as other comparator species. Morphological characterization was done via electron microscopy and Schaeffer-Fulton staining. Data for sequence comparisons ( e.g. , 16S rRNA) were retrieved via BLAST and EzBioCloud. Alignments and phylogenetic trees were generated via CLUTAL_X and neighbor joining functions in MEGA (version 11). Genomes were assembled/annotated via the Prokka annotation pipeline. Clusters of Orthologous Groups (COGs) were defined by eegNOG 4.5. DNA-DNA hybridization calculations were performed by the ANI Calculator web service. Results Cells of strain SP3-1 are rods. SP3-1 cells grow at NaCl concentrations of 5-30% (w/v). Optimal growth occurs at 37 °C, pH 8.0, and 20% NaCl (w/v). Although phylogenetic analysis based on 16S rRNA gene indicates that strain SP3-1 belongs to the genus Iocasia with 99.58% average nucleotide sequence identity to Iocasia fonsfrigida NS-1 T , strain SP3-1 is uniquely an extreme haloalkaliphile. Moreover, strain SP3-1 ferments D-glucose to acetate, butyrate, carbon dioxide, hydrogen, ethanol, and butanol and will grow on L-arabinose, D-fructose, D-galactose, D-glucose, D-mannose, D-raffinose, D-xylose, cellobiose, lactose, maltose, sucrose, starch, xylan and phosphoric acid swollen cellulose (PASC). D-rhamnose, alginate, and lignin do not serve as suitable culture substrates for strain SP3-1. Thus, the carbon utilization profile of strain SP3-1 differs from that of I. fronsfrigidae strain NS-1 T . Differences between these two strains are also noted in their lipid composition. Genomic data reveal key differences between the genetic profiles of strain SP3-1 and NS-1 T that likely account for differences in morphology, sugar metabolism, and CHA-enzyme potential. Important to this study, I. fonsfrigidae SP3-1 produces and extracellularly secretes CHA enzymes at different levels and composition than type strain NS-1 T . The high salt tolerance and pH range of SP3-1 makes it an ideal candidate for salt and pH tolerant enzyme discovery.more » « less
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The genus Rosenbergiella is one of the most frequent bacterial inhabitants of flowers and a usual member of the insect microbiota worldwide. To date, there is only one publicly available Rosenbergiella genome, corresponding to the type strain of Rosenbergiella nectarea (8N4 T ), which precludes a detailed analysis of intra-genus phylogenetic relationships. In this study, we obtained draft genomes of the type strains of the other Rosenbergiella species validly published to date ( R. australiborealis , R. collisarenosi and R. epipactidis ) and 23 additional isolates of flower and insect origin. Isolate S61 T , retrieved from the nectar of an Antirrhinum sp. flower collected in southern Spain, displayed low average nucleotide identity (ANI) and in silico DNA–DNA hybridization (isDDH) values when compared with other Rosenbergiella members (≤86.5 and ≤29.8 %, respectively). Similarly, isolate JB07 T , which was obtained from the floral nectar of Metrosideros polymorpha plants in Hawaii (USA) had ≤95.7 % ANI and ≤64.1 % isDDH with other Rosenbergiella isolates. Therefore, our results support the description of two new Rosenbergiella species for which we propose the names Rosenbergiella gaditana sp. nov. (type strain: S61 T =NCCB 100789 T =DSM 111181 T ) and Rosenbergiella metrosideri sp. nov. (JB07 T =NCCB 100888 T =LMG 32616 T ). Additionally, some R. epipactidis and R. nectarea isolates showed isDDH values<79 % with other conspecific isolates, which suggests that these species include subspecies for which we propose the names Rosenbergiella epipactidis subsp. epipactidis subsp. nov. (S256 T =CECT 8502 T =LMG 27956 T ), Rosenbergiella epipactidis subsp. californiensis subsp. nov. (FR72 T =NCCB 100898 T =LMG 32786 T ), Rosenbergiella epipactidis subsp. japonicus subsp. nov. (K24 T =NCCB 100924 T =LMG 32785 T ), Rosenbergiella nectarea subsp. nectarea subsp. nov. (8N4 T = DSM 24150 T = LMG 26121 T ) and Rosenbergiella nectarea subsp. apis subsp. nov. (B1A T =NCCB 100810 T = DSM 111763 T ), respectively. Finally, we present the first phylogenomic analysis of the genus Rosenbergiella and update the formal description of the species R. australiborealis , R. collisarenosi , R. epipactidis and R. nectarea based on new genomic and phenotypic information.more » « less
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null (Ed.)A detailed evaluation of eight bacterial isolates from floral nectar and animal visitors to flowers shows evidence that they represent three novel species in the genus Acinetobacter . Phylogenomic analysis shows the closest relatives of these new isolates are Acinetobacter apis , Acinetobacter boissieri and Acinetobacter nectaris , previously described species associated with floral nectar and bees, but high genome-wide sequence divergence defines these isolates as novel species. Pairwise comparisons of the average nucleotide identity of the new isolates compared to known species is extremely low (<83 %), thus confirming that these samples are representative of three novel Acinetobacter species, for which the names Acinetobacter pollinis sp. nov., Acinetobacter baretiae sp. nov. and Acinetobacter rathckeae sp. nov. are proposed. The respective type strains are SCC477 T (=TSD-214 T =LMG 31655 T ), B10A T (=TSD-213 T =LMG 31702 T ) and EC24 T (=TSD-215 T =LMG 31703 T =DSM 111781 T ).more » « less
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1099/ijsem.0.004282
