Polyphasic Taxonomic Analysis of Pontitalea aquivivens gen. nov., sp. nov., Isolated from Seawater

A Gram-stain-negative, rod-shaped, strictly aerobic, non-motile, and chemo-organoheterotrophic alphaproteobacterium, designated KMU-169T, was isolated from coastal seawater in the Republic of Korea. The novel isolate was able to grow at 0-2.0% NaCl concentrations (w/v), pH 6.0-9.5, and 15-40 °C. The analysis based on 16S rRNA gene sequences indicated that strain KMU-169T belongs to the family Paracoccaceae and shared the highest similarity (97.0%) with "Defluviimonas salinarum" CAU 1641T. The major (> 10%) cellular fatty acids were C18:1 ω7c and summed feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c). The predominant respiratory quinone was ubiquinone-10. Strain KMU-169T comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid, an unidentified phospholipid, and an unidentified lipid. The assembled draft genome size of strain KMU-169T was 4.1 Mbp with a DNA G + C content of 65.0%. The average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) values between the genomes of strain KMU-169T and its closely related taxa were 71.9-76.8%, 60.9-76.1%, and 18.4-21.0%, respectively. The genome of the strain KMU-169T revealed the presence of numerous genes involved in bio-macromolecule degradation, indicating a high potential for producing industrially valuable enzymes. Based on the polyphasic taxonomic data reported in this study, a novel genus and a new species of the family Paracoccaceae, for which the name Pontitalea aquivivens gen. nov., sp. nov., is proposed with the type strain KMU-169T (= KCCM 90598T = NBRC 117093T).

Description of Albidovulum litorale sp. nov., Albidovulum marisflavi sp. nov., Albidovulum salinarum sp. nov., and Albidovulum sediminicola sp. nov., and proposal for reclassification of the genus Defluviimonas as a later heterotypic synonym of Albidovulum

Four Gram-stain-negative, aerobic, rod-shaped bacteria, designated WL0002T, WL0024T, WL0050T, and WL0075T, were isolated from sediment in the coastal areas of Nantong City, China. Metagenomic analysis revealed higher relative abundance of taxa closely related to the four strains in sediment (0.79-2.0 %) than in water (0.34-1.3 %) (Mann-Whitney U test: p < 0.001). Phylogenetic analysis based on 16S rRNA gene and the bac120 gene set both suggested that the four strains are closely related to the genus Defluviimonas. Additionally, Albidovulum inexpectatum DSM 12048T formed a distinct branch within Defluviimonas. The evolutionary distance (ED) and percentage of conserved proteins (POCP) analysis indicated that the four strains and the genus strains of Albidovulum and Defluviimonas should be recognized as a single genus. Genomic relatedness analysis among the four strains and type strains of the genera Albidovulum and Defluviimonas was below species delimitation thresholds, except for strains WL0024T and "D. salinarum" CAU 1641T, which should belong to the same species. Based on phenotypic and genotypic characterization, the four strains should be recognized as novel species in Albidovulum, and it is reasonable to reclassify the genus Defluviimonas as a later heterotypic synonym of Albidovulum, consistent with the classification of the Genome Taxonomy Database (GTDB). Four names are proposed as follows: Albidovulum marisflavi sp. nov. (type strain WL0002T = MCCC 1K06013T = JCM 34653T = GDMCC 1.2437T), Albidovulum salinarum sp. nov. (WL0024T = MCCC 1K06062T = JCM 34656T = GDMCC 1.2438T), Albidovulum litorale sp. nov. (WL0050T = MCCC 1K07524T = JCM 35566T = GDMCC 1.3084T), and Albidovulum sediminicola sp. nov. (WL0075T = MCCC 1K06064T = JCM 34660T = GDMCC 1.2419T).

Different responses of mesophilic and thermophilic anaerobic digestion of waste activated sludge to PVC microplastics

The effect of microplastics (MPs) retained in waste activated sludge (WAS) on anaerobic digestion (AD) performance has attracted more and more attention. However, their effect on thermophilic AD remains unclear. Here, the influence of polyvinyl chloride (PVC) MPs on methanogenesis and active microbial communities in mesophilic (37 °C) and thermophilic (55 °C) AD was investigated. The results showed that 1, 5, and 10 mg/L PVC MPs significantly promoted the cumulative methane yield in mesophilic AD by 5.62%, 7.36%, and 8.87%, respectively, while PVC MPs reduced that in thermophilic AD by 13.30%, 18.82%, and 19.99%, respectively. Moreover, propionate accumulation was only detected at the end of thermophilic AD with PVC MPs. Microbial community analysis indicated that PVC MPs in mesophilic AD enriched hydrolytic and acidifying bacteria (Candidatus Competibacter, Lentimicrobium, Romboutsia, etc.) together with acetoclastic methanogens (Methanosarcina, Methanosaeta). By contrast, most carbohydrate-hydrolyzing bacteria, propionate-oxidizing bacterium (Pelotomaculum), and Methanosarcina were inhibited by PVC MPs in thermophilic AD. Network analysis further suggested that PVC MPs significantly changed the relationship of key microorganisms in the AD process. A stronger correlation among the above genera occurred in mesophilic AD, which may promote the methanogenic performance. These results suggested that PVC MPs affected mesophilic and thermophilic AD of WAS via changing microbial activities and interaction.

Proposal for transfer of Defluviimonas alba to the genus Frigidibacter as Frigidibacter mobilis nom. nov

A polyphasic taxonomic study was undertaken to clarify the exact position of the type strain cai42^T of the species Defluviimonas alba Pan et al. 2015. The results of the 16S rRNA gene sequence analysis indicated that the two sequences from cai42^T shared 99.6 and 99.7 % similarity to that of the type strain SP32^T of the species Frigidibacter albus and formed a coherent clade in the phylogenetic tree. Whole genomic comparison between cai42^T and SP32^T yielded a digital DNA-DNA hybridization estimate of 36.3 %, an average nucleotide identity of 88.8 % and an average amino acid identity of 89.8 %, clearly indicating that the two strains should belong to two genospecies of the same genus. The close relationship between the two strains was underpinned by the results of genome-based phylogenetic analysis. Although cai42^T and SP32^T shared similar physiological and biochemical properties, some striking differences, such as mobility, the temperature range for growth and the polar lipid components, could distinguish them as separate species. Therefore, the comparative phenotypic and genotypic analyses supported the incorporation of Defluviimonas alba into the genus Frigidibacter as Frigidibacter mobilis nom. nov. with the type strain cai42^T (=CGMCC 1.12518^T=LMG 27406^T).

Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria

The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.

Solirhodobacter olei gen. nov., sp. nov., a nonphotosynthetic bacterium isolated from oil-contaminated soil

A nonphotosynthetic, Gram-stain-negative, rod-shaped and motile strain, designated Pet-1^T, was isolated from oil-contaminated soil collected from Daqing oil field in China. Optimal growth occurred at 37 °C, pH 5.5 and in 1 % (w/v) NaCl. Q-10 was the sole respiratory quinone. The most abundant fatty acid was C_{18 : 1}ɷ7c/C_{18 : 1}ɷ6c (67.4 %). The major polar lipids were phosphatidylglycerol, aminolipid, phosphatidylethanolaine, phosphatidycholine, two unidentified lipids and two unidentified phospholipids. The genomic DNA G+C content was 69.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that Pet-1^T shared the highest similarity (95.1 %) to Rhodobacter vinaykumarii DSM 18714^T, followed by Sinorhodobacter populi sk2b1^T (95.0 %) and Haematobacter massiliensis CCUG 47968^T (95.0 %). In the phylogenetic tree, strain Pet-1^T formed a separate branch from the closely related genera Rhodobacter, Pararhodobacter, Defluviimonas and Rhodovulum within the family Rhodobacteraceae. Based on the data from the current polyphasic study, it is proposed that the isolate is a novel species of a novel genus within the family Rhodobacteraceae, with the name Solirhodobacter olei gen. nov., sp. nov. The type strain of the type species is Pet-1^T (=KCTC 72074^T =CCTCC AB 2018368^T).

Pseudopontivivens aestuariicola gen. nov., sp. nov., a Novel Bacterium of the Class Alphaproteobacteria Isolated from a Tidal Flat

A Gram-stain-negative, non-motile and coccoid, ovoid or rod-shaped bacterial strain, OITF-57^T, which was isolated from a tidal flat sediment in South Korea, was characterized taxonomically. Strain OITF-57^T grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of 2.0% (w/v) NaCl. Strain OITF-57^T exhibited the highest 16S rRNA gene sequence similarity value (94.2%) to the type strain of Pontivivens insulae forming a cluster in the neighbour-joining phylogenetic tree. In the maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences and the phylogenetic tress based on gyrB sequences, strain OITF-57^T formed evolutionary lineages independent of those of other taxa. Strain OITF-57^T contained Q-10 as the predominant ubiquinone and C_18:1 ω7c as the major fatty acid. The major polar lipids of strain OITF-57^T were phosphatidylcholine and phosphatidylglycerol. The DNA G + C content of strain OITF-57^T was 66.0 mol%. The chemotaxonomic data and other differential phenotypic properties made it possible to distinguish strain OITF-57^T from the genus Pontivivens and other phylogenetically related genera. On the basis of the data presented, strain OITF-57^T constitutes a new genus and species within the class Alphaproteobacteria, for which the name Pseudopontivivens aestuariicola gen. nov., sp. nov. is proposed. The type strain is OITF-57^T (= KACC 19570^T = CGMCC 1.13481^T).

Defluviimonas alba sp. nov., isolated from an oilfield

Two Gram-stain-negative, rod-shaped bacterial strains, cai42T and b45, were isolated from oil-production water taken from Xinjiang Oilfield, China. Optimum growth was observed at 30 °C, at pH 8 and with 1–3 % (w/v) NaCl. According to phylogenetic analyses, the two strains were members of the genus Defluviimonas , with 16S rRNA gene sequence similarities of 95.5−96.3 % with the type strains of species of the genus. The major cellular fatty acids of strains cai42T and b45 were C10 : 0 3-OH, C16 : 0 and summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), and the predominant ubiquinone was Q-10, all of these data being typical for the genus Defluviimonas . The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, glycolipid, phosphatidylcholine, two unidentified aminolipids, an unidentified phospholipid and two unidentified lipids. The mean genomic DNA G+C contents of strains cai42T and b45 were 60.8±1.1 and 60.4±1.0 mol%, respectively. On the basis of phylogenetic, physiological and chemotaxonomic analyses, strains cai42T and b45 represent a novel species of the genus Defluviimonas , for which the name Defluviimonas alba sp. nov. is proposed. The type strain is cai42T ( = CGMCC 1.12518T = LMG 27406T).