Roseinatronobacter alkalisoli sp. nov., an alkaliphilic bacterium isolated from soda soil, and genome-based reclassification of the genera Rhodobaca and Roseinatronobacter

The genera Rhodobaca and Roseinatronobacter are phylogenetically related genera within the family Paracoccaceae. Species of these genera were described using 16S rRNA gene-based phylogeny and phenotypic characteristics. However, the 16S rRNA gene identity and phylogeny reveal the controversy of the taxonomic status of these two genera. In this work, we examined the taxonomic positions of members of both genera using 16S rRNA gene phylogeny, phylogenomic analysis and further validated using overall genome-related indexes, including digital DNA-DNA hybridization, average nucleotide identity, average amino acid identity and percentage of conserved proteins. Based on phylogenetic and phylogenomic results, the current four species of the two genera clustered tightly into one clade with high bootstrap values, suggesting that the genus Rhodobaca should be merged with Roseinatronobacter. In addition, a novel species isolated from a soda soil sample collected from Anda City, PR China, and designated as HJB301T was also described. Phenotypic, chemotaxonomic, genomic and phylogenetic properties suggested that strain HJB301T (=CCTCC AB 2021113T=KCTC 82977T) represents a novel species of the genus Roseinatronobacter, for which the name Roseinatronobacter alkalisoli sp. nov. is proposed.

Genomic Analysis of the Evolution of Phototrophy among Haloalkaliphilic Rhodobacterales

A characteristic feature of the order Rhodobacterales is the presence of a large number of photoautotrophic and photoheterotrophic species containing bacteriochlorophyll. Interestingly, these phototrophic species are phylogenetically mixed with chemotrophs. To better understand the origin of such variability, we sequenced the genomes of three closely related haloalkaliphilic species, differing in their phototrophic capacity and oxygen preference: the photoheterotrophic and facultatively anaerobic bacterium Rhodobaca barguzinensis, aerobic photoheterotroph Roseinatronobacter thiooxidans, and aerobic heterotrophic bacterium Natronohydrobacter thiooxidans. These three haloalcaliphilic species are phylogenetically related and share many common characteristics with the Rhodobacter species, forming together the Rhodobacter-Rhodobaca (RR) group. A comparative genomic analysis showed close homology of photosynthetic proteins and similarity in photosynthesis gene organization among the investigated phototrophic RR species. On the other hand, Rhodobaca barguzinensis and Roseinatronobacter thiooxidans lack an inorganic carbon fixation pathway and outer light-harvesting genes. This documents the reduction of their photosynthetic machinery towards a mostly photoheterotrophic lifestyle. Moreover, both phototrophic species contain 5-aminolevulinate synthase (encoded by the hemA gene) incorporated into their photosynthesis gene clusters, which seems to be a common feature of all aerobic anoxygenic phototrophic Alphaproteobacteria. Interestingly, the chrR-rpoE (sigma24) operon, which is part of singlet oxygen defense in phototrophic species, was found in the heterotrophic strain Natronohydrobacter thiooxidans. This suggests that this organism evolved from a photoheterotrophic ancestor through the loss of its photosynthesis genes. The overall evolution of phototrophy among the haloalkaliphilic members of the RR group is discussed.

Thioclava arenosa sp. nov., isolated from sea sand

A Gram-staining-negative, non-spore-forming, non-motile, rod-shaped, facultatively anaerobe bacterial strain, designated CAU 1312T, was isolated from sea sand of Eurwangri beach, South Korea. The strain's taxonomic position was investigated using a polyphasic approach. CAU 1312T grew at temperatures from 20 to 40 °C, in the range of pH 6.0-9.0 and at salinities from 1-4 % (w/v). The results of phylogenetic analysis based on the 16S rRNA gene sequence revealed that CAU 1312T represented a member of the genus Thioclava and was most closely related to Thioclava atlantica 13D2W-2T (similarity 96.53 %). The strain contained Q-10 as the predominant menaquinone and summed feature 8 (C18 : 1ω7c/ω6c) as the major fatty acid. The polar lipids of CAU 1312T consisted of phosphatidylethanolamine, phosphatidylglycerol, two aminophospholipids, a phosphoglycolipid, and two unidentified phospholipids. The DNA G+C content was 64.7 mol%. On the basis of phenotypic and chemotaxonomic properties and phylogenetic inference, CAU 1312T is considered to represent a novel species of the genus Thioclava, for which the name Thioclava arenosa sp. nov. is proposed. The type strain is CAU 1312T(=KCTC 52190T=NBRC 111989T).

Novel hydrolytic extremely halotolerant alkaliphiles from mature landfill leachate with key involvement in maturation process

Mature landfill leachate is a heavily-polluted wastewater due to its recalcitrant nature of organic matter, and high ammonia and salt content. Despite the moderate saline and alkaline nature of this habitat, no attention has been paid to the isolation and functional role of extremophiles in such environment. In this work, a total of 73 and 29 bacterial strains were isolated by using alkaline and saline media, respectively, while bacteria from mature landfill leachate growing in these media were enumerated as 1.5 ± 0.1 (×10⁸) and 5.8 ± 0.9 (×10⁸) cfu/L. Based on their pH and salt ranges and optima for growth, all bacterial isolates were halotolerant alkaliphiles (either facultative or obligate), with the majority of them being extremely halotolerant bacteria. These halotolerant alkaliphiles were classified into 14 operational taxonomic units (OTUs). Of these, 12 are placed within known halophilic and alkaliphilic species of the genera Dietzia, Glycocaulis, Halomonas, Marinobacter, Piscibacillus and Rhodobacter, while the remaining OTUs represented two novel phylogenetic linkages among the families Cyclobacteriaceae and Rhodobacteraceae. Examination of their hydrolytic ability through the performance of lipase, protease and β-glucosidase assays using landfill leachate as the growth substrate revealed that all halotolerant alkaliphiles isolated exhibited extremely high lipolytic activities (up to 78,800 U g^-1 protein), indicating a key involvement of extremophilic microbiota at the late landfill maturation stage. The wide extremely lipolytic halotolerant alkaliphilic community identified also makes mature landfill leachate an ideal microbial pool for the isolation of novel extremophiles of biotechnological interest.

Paenirhodobacter enshiensis gen. nov., sp. nov., a non-photosynthetic bacterium isolated from soil, and emended descriptions of the genera Rhodobacter and Haematobacter

A Gram-reaction-negative, facultatively anaerobic, non-motile, rod-shaped, non-photosynthetic bacterial strain, DW2-9(T), was isolated from soil. The highest 16S rRNA gene sequence similarities were found to Rhodobacter capsulatus ATCC 11166(T) (97.1%), Rhodobacter viridis JA737(T) (96.4%), Rhodobacter maris JA276(T) (96.2%), Rhodobacter veldkampii ATCC 35703(T) (96.0%), Haematobacter massiliensis CCUG 47968(T) (96.0%), Haematobacter missouriensis CCUG 52307(T) (95.9%) and Rhodobacter aestuarii JA296(T) (95.7%). The genomic DNA G+C content was 67.2 mol% and the major respiratory quinone was ubiquinone 10 (Q-10). The major cellular fatty acids (>5%) were C(18 : 1)ω7c, C(16 : 0), C(19 : 0) cyclo ω8c and summed feature 3 (one or more of iso-C(15 : 0) 2-OH, C(16 : 1)ω6c and C(16 : 1)ω7c). However, unlike species of the genus Rhodobacter, strain DW2-9(T) neither formed internal photosynthetic membranes nor produced photosynthetic pigments. DNA-DNA hybridization between strain DW2-9(T) and R. capsulatus JCM 21090(T) showed a relatedness of 33%. Strain DW2-9(T) contained phosphatidylethanolamine, phosphatidylglycerol and an unknown aminophospholipid as major polar lipids, which differed from those of species of the genera Rhodobacter and Haematobacter. In addition to the differences in phylogenetic position and polar lipid types, strain DW2-9(T) could be distinguished from species of the genus Haematobacter by the cultivation conditions. On the basis of our polyphasic taxonomic analysis, strain DW2-9(T) is considered to represent a novel genus and species, for which the name Paenirhodobacter enshiensis gen. nov., sp. nov. is proposed. The type strain of Paenirhodobacter enshiensis is DW2-9(T) ( = CCTCC AB 2011145(T) = KCTC 15169(T)). Emended descriptions of the genera Rhodobacter and Haematobacter are also proposed.

Falsirhodobacter halotolerans gen. nov., sp. nov., isolated from dry soils of a solar saltern

Two bacterial strains (JA744T and JA745) were isolated from dry soil samples collected from solar salterns at Humma, Odisha, India. Both strains were Gram-stain-negative, catalase- and oxidase-positive, motile rods. Major fatty acids in both strains included C18 : 1ω7c, C18 : 0 and C16 : 0, while minor amounts of C10 : 0 3-OH, C12 : 0, C12 : 0 3-OH, C14 : 0 and C16 : 0 were also present. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, an unidentified glycolipid, five unidentified lipids, an unidentified aminolipid and an unidentified phospholipid made up the polar lipids of both strains. Both strains had bacteriohopane derivatives (BHD1,2) and diploptene as major hopanoids. Mean genomic DNA G+C content was 75±1 mol% and the two strains were closely related (mean DNA–DNA hybridization >90 %). Phylogenetic analysis based on the 16S rRNA gene sequence showed that the two strains clustered with species of the genus Rhodobacter belonging to the family Rhodobacteraceae of the class Alphaproteobacteria . The highest sequence similarity was observed with Rhodobacter sphaeroides ATH2.4.1T (96 %) and other members of the genera Rhodobacter and Pseudorhodobacter (<96 %). However, the two strains were positioned distinctly outside the group formed by the other genera of the family Rhodobacteraceae . Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of these isolates as representatives of a novel species in a new genus, for which the name Falsirhodobacter halotolerans gen. nov., sp. nov. is proposed. The type strain of Falsirhodobacter halotolerans is JA744T ( = KCTC 32158T  = NBRC 108897T).

Humitalea rosea gen. nov., sp. nov., an aerobic bacteriochlorophyll-containing bacterium of the family Acetobacteraceae isolated from soil

A Gram-staining-negative, pale-pink-pigmented, non-motile, obligately aerobic and rod-shaped bacterium, designated strain W37T, was isolated from soil and subjected to a taxonomic investigation using a polyphasic approach. The strain grew at 1–30 °C, oxidized thiosulfate and accumulated polyhydroxyalkanoates. Photosynthetic pigments were represented by bacteriochlorophyll a and carotenoids. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain W37T was most closely related to members of the genera Roseococcus and Rubritepida (with sequence similarities of <92.8 %) but formed a distinct lineage in the family Acetobacteraceae . The polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, three unidentified aminolipids and one other unidentified lipid. The predominant cellular fatty acids were C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The DNA G+C content of strain W37T was 68.2 mol%. On the basis of phenotypic characteristics and phylogenetic analysis, strain W37T represents a novel species of a new genus in the family Acetobacteraceae , for which the name Humitalea rosea gen. nov., sp. nov. is proposed. The type strain of the type species is W37T ( = CIP 110261T = LMG 26243T).

Albirhodobacter marinus gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from sea shore water of Visakhapatnam, India

A novel marine, Gram-negative, rod-shaped bacterium, designated strain N9(T), was isolated from a water sample of the sea shore at Visakhapatnam, Andhra Pradesh (India). Strain N9(T) was found to be positive for oxidase and catalase activities. The fatty acids were found to be dominated by C(16:0), C(18:1) ω7c and summed in feature 3 (C(16:1) ω7c and/or C(16:1) ω6c). Strain N9(T) was determined to contain Q-10 as the major respiratory quinone and phosphatidylethanolamine, phosphatidylglycerol, two aminophospholipids, two phospholipids and four unidentified lipids as polar lipids. The DNA G+C content of the strain N9(T) was found to be 63 mol%. 16S rRNA gene sequence analysis indicated that Rhodobacter sphaeroides, Rhodobacter johrii, Pseudorhodobacter ferrugineus, Rhodobacter azotoformans, Rhodobacter ovatus and Pseudorhodobacter aquimaris were the nearest phylogenetic neighbours, with pair-wise sequence similarities of 95.43, 95.36, 94.24, 95.31, 95.60 and 94.74 %, respectively. Phylogenetic analysis showed that strain N9(T) formed a distinct branch within the family Rhodobacteraceae and clustered with the clade comprising species of the genus Pseudorhodobacter, together with species of the genera Roseicitreum, Roseinatronobacter, Roseibaca and Rhodobaca. Species of the genus Pseudorhodobacter are phylogenetically close with a 16S rRNA gene sequence dissimilarity of 5.9-7.3 % (92.7-94.1 % similarity). Based on the above-mentioned phenotypic characteristics and on phylogenetic inference, strain N9(T) is proposed as a representative of a new genus and a novel species of the family Rhodobacteraceae as Albirhodobacter marinus gen. nov., sp. nov. The type strain of Albirhodobacter marinus is N9 (= MTCC 11277(T) = JCM 17680(T)).