Rhodobacter thermarum sp. nov., a novel phototrophic bacterium isolated from sediment of a hot spring

Overlooked pathways of endogenous simultaneous nitrification and denitrification in anaerobic/aerobic/anoxic sequencing batch reactors with organic supplementation

The anaerobic/aerobic/anoxic (A/O/A) process is a promising biotechnology to intensify denitrification in low carbon/nitrogen (C/N) wastewater treatment, but the neglected typical rate-limiting step-nitrification-would hinder its wider application. Heterotrophic nitrification driven by intracellular carbon (PHAs) could enhance nitrification and achieve endogenous simultaneous nitrification and denitrification (ESND) in the A/O/A process, but its feasibility remains unexamined. Here we established four A/O/A-SBRs at different C/N ratios (3, 7.5, 12, and 16.5) to address the above-mentioned knowledge gaps. The results showed that organic supplementation promoted both nitrification and denitrification (performance and relevant enzymatic activities) until organic overdose (C/N = 16.5) exacerbated niche competitions from other non-functional heterotrophs. qPCR and batch tests indicated that high C/N ratios inhibited autotrophic nitrifiers, and heterotrophic nitrifiers (HNB) dominated in the enhanced nitrification. Given the high HNB contribution (43.7%) and low COD variation (< 10 mg L^-1) in the SND (76.4%) of CN12, we proposed a potential SND pathway based on heterotrophic nitrification and denitrification driven by PHAs and verified it with batch tests. Microbial and functional analyses suggested that CN12 favored the intracellular carbon transformation and harbored the minimum autotrophic nitrifiers, supporting the dominance of ESND in the enhanced SND. Our findings expand the understanding of the relationships between intracellular carbon transformation and SND and provide a novel nitrogen removal pathway for the practical application of the A/O/A process.

Genome Sequence and Characterization of a Xanthorhodopsin-Containing, Aerobic Anoxygenic Phototrophic Rhodobacter Species, Isolated from Mesophilic Conditions at Yellowstone National Park

The genus Rhodobacter consists of purple nonsulfur photosynthetic alphaproteobacteria known for their diverse metabolic capabilities. Here, we report the genome sequence and initial characterization of a novel Rhodobacter species, strain M37P, isolated from Mushroom hot spring runoff in Yellowstone National Park at 37 °C. Genome-based analyses and initial growth characteristics helped to define the differentiating characteristics of this species and identified it as an aerobic anoxygenic phototroph (AAP). This is the first AAP identified in the genus Rhodobacter. Strain M37P has a pinkish-red pigmentation that is present under aerobic dark conditions but disappears under light incubation. Whole genome-based analysis and average nucleotide identity (ANI) comparison indicate that strain M37P belongs to a specific clade of recently identified species that are genetically and physiologically unique from other representative Rhodobacter species. The genome encodes a unique xanthorhodopsin, not found in any other Rhodobacter species, which may be responsible for the pinkish-red pigmentation. These analyses indicates that strain M37P is a unique species that is well-adapted to optimized growth in the Yellowstone hot spring runoff, for which we propose the name Rhodobacter calidifons sp. nov.

Reclassification of 11 Members of the Family Rhodobacteraceae at Genus and Species Levels and Proposal of Pseudogemmobacter hezensis sp. nov

A novel Gram-stain-negative, aerobic, motile bacterial strain, D13-10-4-6^T, was isolated from the bark sample of Populus × euramericana. The strain could grow at 15-35°C, at pH 6-10 and in 0-4% (w/v) NaCl, and the strain tested positive for oxidase and catalase activities. The main polar lipids were phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The main respiratory quinone was Q-10, and the predominant fatty acid was C_18:1 ω7c. The phylogenetic analyses showed that the strain belonged to the genus Pseudogemmobacter of the family Rhodobacteraceae. The family Rhodobacteraceae is an ecologically diverse group that includes bacteria from aquatic to terrestrial ecosystems. As a consequence, the classification of the family Rhodobacteraceae is difficult, not least when the early taxonomy work relied heavily on 16S rRNA gene analysis. Recently, the taxonomic status of many members of the family has been revised based on the genome analysis; however, there are still some classification conflicts due to the lack of genome sequences and parallel publication time. In this study, phylogenetic trees based on 16S rRNA gene, gyrB gene, and 120 concatenated proteins, the average amino acid identity (AAI) and percentage of conserved proteins (POCP) have been used for the analysis of strain D13-10-4-6^T and other members of 15 genera within the family to further clarify their taxonomic relationships. For the data of phylogeny, AAI, and POCP, the taxonomic proposals are (1) reclassification of Rhodobacter tardus as the type species of a novel genus, Stagnihabitans gen. nov., as Stagnihabitans tardus comb. nov.; (2) reclassification of Tabrizicola alkalilacus, Tabrizicola sediminis, Tabrizicola algicola into a novel genus, Pseudotabrizicola gen. nov., as Pseudotabrizicola alkalilacus comb. nov., Pseudotabrizicola sediminis comb. nov., Pseudotabrizicola algicola comb. nov.; (3) reclassification of Rhodobacter sediminicola into the genus Cereibacter as Cereibacter sediminicola comb. nov.; (4) reclassification of Rhodobacter flagellatus, Rhodobacter thermarum, and Xinfangfangia soli into the genus Tabrizicola as Tabrizicola flagellatus comb. nov., Tabrizicola thermarum comb. Nov., and Tabrizicola soli comb. nov.; (5) reclassification of Xinfangfangia humi into the genus Pseudogemmobacter as Pseudogemmobacter humicola comb. nov.; (6) classification of strain D13-10-4-6^T as a novel species of the genus Pseudogemmobacter, for which the name P. hezensis sp. nov. is proposed, the type strain is D13-10-4-6^T (= CFCC 12033^T = KCTC 82215^T).

Szabonella alba gen. nov., sp. nov., a motile alkaliphilic bacterium of the family Rhodobacteraceae isolated from a soda lake

A Gram-stain-negative, oxidase- and catalase-positive, rod-shaped, creamy white coloured bacterial strain, DMG-N-6T, was isolated from a water sample of Lake Fertő/Neusiedler See (Hungary). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain forms a distinct linage within the family Rhodobacteraceae . Its closest relatives are Tabrizicola alkalilacus DJCT (96.76% similarity) and Tabrizicola piscis K13M18T (96.76%), followed by Tabrizicola sediminis DRYC-M-16T (96.69 %), Rhodobacter sediminicola JA983T (96.62 %), Tabrizicola aquatica RCRI19T (96.47 %) and Cereibacter johrii JA192T (96.18 %). The novel bacterial strain favours an alkaline environment (pH 8.0-12.0) and grows optimally at 18–28°C in the presence of 2–4 % (w/v) NaCl. Cells of DMG-N-6T were motile by a single subpolar flagellum. Bacteriochlorophyll a was not detected. The predominant respiratory quinone was ubiquinone Q-10. The major cellular fatty acid was C18:1 ω7c. The polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, phosphatidylcholine, an unidentified phospholipid and five unidentified lipids. The assembled draft genome of strain DMG-N-6T had 52 contigs with a total length of 4 219 778 bp and a G+C content of 64.3 mol%. Overall genome-related indices (ANI <77.8 %, AAI <69.0 %, dDDH <19.6 %) with respect to close relatives were all significantly below the corresponding threshold to demarcate bacterial genus and species. Strain DMG-N-6T (=DSM 108208T=NCAIM B.02645T) is strongly different from its closest relatives and is suggested as the type strain of a novel species of a new genus in the family Rhodobacteraceae , for which the name Szabonella alba gen. nov., sp. nov. is proposed.

Rhodobacter amnigenus sp. nov. and Rhodobacter ruber sp. nov., isolated from freshwater habitats

Two bacterial strains, designated HSP-20^T and CCP-1^T, isolated from freshwater habitats in Taiwan, were characterized by polyphasic taxonomy. Both strains were Gram-stain-negative, aerobic, non-motile and rod-shaped. Cells of strains HSP-20^T and CCP-1^T formed pink and dark red coloured colonies, respectively. Both strains contained bacteriochlorophyll a, and showed optimum growth under anaerobic conditions by photoheterotrophy, but no growth by photoautotrophy. Phylogenetic analyses based on 16S rRNA gene and whole-genome sequences indicated that both strains belonged to the genus Rhodobacter. Analysis of 16S rRNA gene sequences showed that strains HSP-20^T and CCP-1^T shared 98.3 % sequence similarity and were closely related to Rhodobacter tardus CYK-10^T (96.0 %) and Rhodobacter flagellatus SYSU G03088^T (96.0 %), respectively. Both strains shared common chemotaxonomic characteristics including Q-10 as the major isoprenoid quinone, C_18 : 1  ω7c as the predominant fatty acid, and phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine as the main polar lipids. The DNA G+C content of both strains was 66.2 mol%. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between these two novel isolates and their closest relatives were below the cut-off values of 95-96, 90 and 70 %, respectively, used for species demarcation. On the basis of phenotypic and genotypic properties and phylogenetic inference, both strains should be classified as novel species within the genus Rhodobacter, for which the names Rhodobacter amnigenus sp. nov. (=BCRC 81193^T=LMG 31334^T) and Rhodobacter ruber sp. nov. (=BCRC 81189^T=LMG 31335^T) are proposed.

Rhodobacter kunshanensis sp. nov., a Novel Bacterium Isolated from Activated Sludge

Strain HX-7-19^T was isolated from the activated sludge collected from an abandoned herbicide manufacturing plant in Kunshan, China. Cells were Gram-reaction-negative, rod-shaped, and non-motile. The phylogenetic analysis based on 16S rRNA gene indicated that strain HX-7-19^T formed a clade with Rhodobacter blasticus CGMCC 1.3365^T (96.3% sequence similarity). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain HX-7-19^T and R. blasticus CGMCC 1.3365^T were 76.2% and 20.3%, respectively. The genomic DNA G + C content of strain HX-7-19^T was 65.9%. The major fatty acids (> 10% of the total fatty acids) were C_18:1 ω7c and C_18:1 ω7c 11-methyl. The major respiratory quinone was quinone Q-10. The major polar lipid profile consists of phosphatidylglycerol (PG), diphosphatidyl-glycerol (DPG), phosphatidylethanolamine (PE), and phosphatidylcholine (PC). Photosynthesis pigments bacteriochlorophyll a and carotenoids were formed and photosynthesis genes pufL and pufM were detected. On the basis of phenotypic and phylogenetic evidences, strain HX-7-19^T is considered as a novel species in the genus Rhodobacter, for which the name Rhodobacter kunshanensis sp. nov. is proposed. The type strain is HX-7-19^T (= KCTC 72471^T = CCTCC AB 2020148^T).

Tabrizicola oligotrophica sp. nov. and Rhodobacter tardus sp. nov., two new species of bacteria belonging to the family Rhodobacteraceae

Two Gram-stain-negative, aerobic, non-motile bacteria, designated KMS-5^T and CYK-10^T, were isolated from freshwater environments. 16S rRNA gene sequence similarity results indicated that these two novel strains belong to the family Rhodobacteraceae. Strain KMS-5^T is closely related to species within the genus Tabrizicola (96.1-96.8 % sequence similarity) and Cypionkella (96.5-97.0 %). Strain CYK-10^T is closest to Rhodobacter thermarum YIM 73036^T with 96.6 % sequence similarity. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set showed that strain KMS-5^T is affiliated with species in the genus Tabrizicola and strain CYK-10^T is placed in a distinct clade with Rhodobacter blasticus ATCC 33485^T, Rhodobacter thermarum YIM 73036^T and Rhodobacter flagellatus SYSU G03088^T. These two strains shared common chemotaxonomic features comprising Q-10 as the major quinone, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine as the principal polar lipids, and C_18 : 1  ω7c as the main fatty acid. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between these two novel isolates and their closest relatives were below the cut-off values of 95-96, 90 and 70 %, respectively, used for species demarcation. The obtained polyphasic taxonomic data suggested that strain KMS-5^T represents a novel species within the genus Tabrizicola, for which the name Tabrizicola oligotrophica sp. nov. is proposed with KMS-5^T (=BCRC 81196^T=LMG 31337^T) as the type strain, and strain CYK-10^T should represent a novel species of the genus Rhodobacter, for which the name Rhodobacter tardus sp. nov. is proposed with CYK-10^T (=BCRC 81191^T=LMG 31336^T) as the type strain.

Rhodobacter flagellatus sp. nov., a thermophilic bacterium isolated from a hot spring

A thermophilic bacterium, designated SYSU G03088^T, was isolated from Moincer hot spring, Tibet, PR China. Polyphasic taxonomic analyses and whole-genome sequencing were used to determine the taxonomic position and genomic profiles of the strain. Phylogenetic analysis using 16S rRNA gene sequence indicated that SYSU G03088^T showed highest sequence similarity to Rhodobacter blasticus CGMCC 1.3365^T (96.0 % sequence identity). The strain could be differentiated from most recognized species of the genus Rhodobacter by its slightly purple colony colour, distinct phenotypic characters and low ANI values. Cells were Gram-staining negative, and oval-to-rod shaped. Poly-β-hydroxybutyrate and vesicular intracytoplasmic membrane structures were formed inside cells. Growth occurred optimally at 45 °C and pH 7.0. Ubiquinone 10 was the only respiratory quinone. The major fatty acids (>10 %) were C_18 : 0, C_18 : 1ω7c 11-methyl and summed feature 8 (C_18 : 1ω7c and/or C_18 : 1ω6c). The detected polar lipids of SYSU G03088^T included diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylmethylethanolamine. The DNA G+C content of SYSU G03088^T was 67.7 % (genome). On the basis of the differences in the phenotypic characteristics and phylogenetic analyses, SYSU G03088^T is considered to represent a novel species of the genus Rhodobacter, for which the name Rhodobacter flagellatus sp. nov. is proposed. The type strain is SYSU G03088^T (=CGMCC 1.16876^T=KCTC 72354^T).