Reclassification of the Taxonomic Framework of Orders Cellvibrionales, Oceanospirillales, Pseudomonadales, and Alteromonadales in Class Gammaproteobacteria through Phylogenomic Tree Analysis

Genomic insights into novel predatory myxobacteria isolated from human feces

Myxobacteria are Gram-negative, spore-forming predatory bacteria isolated from diverse environmental samples that feed on other microbes for their survival and growth. However, no reports of cultured representatives from the human gut have been published to date, although previous investigations have revealed the presence of myxobacterial operational taxonomic units (OTUs) in skin and fecal samples. In this study, three myxobacterial strains designated as O35, O15, and Y35 were isolated and purified from fecal samples of two inflammatory bowel disease (IBD) patients. The 16S rRNA gene sequence analysis and phylogeny identified the strains as Myxococcus spp. belonging to two different clades. Genome-based phylogeny and overall genome-related indices, i.e., average amino acid identity and percentage of conserved proteins, confirmed the heterogeneity within the genus and placed the three strains within two different clades separated at the level of different genera. Digital DNA-DNA hybridization and average nucleotide identity values indicated that they belonged to two novel Myxococcus spp. The analysis of meta-barcoding data from IBD and control cohorts detected OTU lineages closely affiliated to the three novel strains. Based on evidence from detailed structural and functional genomics, we propose the novel species Myxococcus faecalis sp. nov. O35T and a new genus Pseudomyxococcus gen. nov. to accommodate the novel species Pseudomyxococcus flavus sp. nov. Y35T. Overall, these findings provide new information about the occurrence of myxobacteria in the human gut and lay the foundations for a new classification scheme for myxobacterial taxa.IMPORTANCEMyxobacteria have been described from a variety of niches ranging from terrestrial to marine habitats and are known to harbor a diverse portfolio of bioactive molecules. However, to date, there has been no report of isolating culturable representatives from the human gut. This study describes novel myxobacteria from the human gut based on phylogenomics and phenotypic description. The findings are complemented by sequence-based data, wherein operational taxonomic unit (OTU) lineages closely affiliated with the isolated strains have been identified, thus opening a Pandora's box of opportunities for research into the microbial ecology and functional potential of these taxa in the gut ecosystem. Additionally, the study also seeks to establish a new systematic framework, expanding our understanding of myxobacterial taxonomy.

Harmony in diversity: Reorganizing the families within the order Pseudomonadales

An accurate and coherent bacterial taxonomy is essential for studying the ecological aspects of microorganisms and for understanding microbial communities and their dynamics. The order Pseudomonadales is of particular importance in biological research due to its ability to interact with eukaryotic hosts, including taxa of clinical relevance (e.g.: Pseudomonas, Moraxella, Acinetobacter), or due to its functions in soil and water ecosystems. Despite their relevance, we have identified several inconsistencies in the organisation of genera within families in this order. Here, we perform comprehensive phylogenetic and phylogenomic analyses to reorganise these taxa. Average amino acid identity (AAI) values shared within and between families support our reclassifications. We propose seven new families, including new ecologically relevant families (e.g.: Oceanobacteraceae fam. nov.), as well as several taxonomic emendations. Our results also support the inclusion of Cellvibrionales and Oceanospirillales within Pseudomonadales. This revised organisation provides a robust delineation of these taxa into families, characterised by AAI values ranging from 60% to 77%. AAI distances between families are predominantly below 60%. This reclassification contributes to establishment of a more reliable taxonomic framework within Gammaproteobacteria, providing the basis for a more comprehensive understanding of their evolution.

Genomic-based taxonomic classification of the order Sphingomonadales

The order Sphingomonadales strains are globally distributed in various biomes and are renowned for their biodegradable and biosynthesis capabilities. At present, it consists of 4 families and 49 genera making it the third largest order within the class Alphaproteobacteria. However, their taxonomy remains complex, especially due to polyphyly in the family Sphingomonadaceae. In this study, we collected 429 Sphingomonadales type strain genomes, reconstructed robust phylogenomic relationships, and proposed delineation thresholds at the genus and family levels based on average amino acid identities (AAI) and evolutionary distances (ED). Based on the maximum-likelihood and Bayesian phylogenomic trees reconstructed by two molecular sets determined by orthologous sequence identity and the Genome Taxonomy Database, the consensus degree values were all higher than 90%, revealing that those phylogenomic trees had similar topological structures. By confirming monophyletic taxa and determining stable nodes, we reclassified the order Sphingomonadales into thirteen families including nine novel ones. AAI calculations indicated that the average intra-family AAI values ranged from 0.62 to 0.84, while inter-family ones were 0.51 to 0.60. ED summaries demonstrated that the average and median intra-family ED values were 0.16 to 0.57, and inter-family ones ranged from 0.50 to 1.22. Comparisons of AAI and ED values calculated by using genomic and phylogenetic analyses supported that those 13 families were significantly separated with p values < 2.2×10-16. Thus, it was speculated that the AAI and ED thresholds for distinguishing different families were <0.6 and >0.5, respectively. Additionally, we reclassified 163 species into new genera with their phylogenetic topologies, according to the previous genus AAI and ED boundaries of 0.7 and 0.4. Our study is the first genomic-based study of the order Sphingomonadales and will promote further insights into the evolution of this order.

Marinicellulosiphila megalodicopiae gen. nov., sp. nov., a deep-sea alkaliphilic cellulolytic bacterium isolated from an endemic ascidian Megalodicopia hians

The strain TOYAMA8T is a deep-sea alkaliphilic cellulolytic bacterium isolated from a slurry-adhered epiphytic site of Megalodicopia hians. Cells of this strain are Gram-negative, aerobic, curved rods or spirilla, motile with monopolar flagella, and grow on cellulose as the sole carbon source. Compared to other closely related species, this bacterium is characterized by a large number of cellulase genes. Strain TOYAMA8T showed alkaliphilic growth within the pH range 7.5-9.0. The major cellular fatty acids were C18 : 1 ω7, C14 : 0, C16 : 0 and C16 : 1 ω7. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, unidentified phospholipids and aminolipids. A major respiratory lipoquinone was Q-9. Phylogenomic analysis using the 16S rRNA gene and whole-genome sequence data showed that the strain is related to the families Gynuellaceae, Saccharospirillaceae and Natronospirillaceae. The values of 16S rRNA gene sequence similarity, amino acid identity and percentage of conserved proteins between the strain TOYAMA8T and related species were low, with maximum values of 90.6, 48.1 and 34.6%, respectively. These results, together with differences in phenotypic and biochemical characteristics, indicate that the new isolate TOYAMA8T represents a novel genus and species, for which the name Marinicellulosiphila megalodicopiae gen. nov., sp. nov., is proposed. The type strain is TOYAMA8T (JCM 31119T=DSM 114864T).

Dynamic quinone repertoire accompanied the diversification of energy metabolism in Pseudomonadota

It is currently unclear how Pseudomonadota, a phylum that originated around the time of the Great Oxidation Event, became one of the most abundant and diverse bacterial phyla on Earth, with metabolically versatile members colonizing a wide range of environments with different O2 concentrations. Here, we address this question by studying isoprenoid quinones, which are central components of energy metabolism covering a wide range of redox potentials. We demonstrate that a dynamic repertoire of quinone biosynthetic pathways accompanied the diversification of Pseudomonadota. The low potential menaquinone (MK) was lost in an ancestor of Pseudomonadota while the high potential ubiquinone (UQ) emerged. We show that the O2-dependent and O2-independent UQ pathways were both present in the last common ancestor of Pseudomonadota, and transmitted vertically. The O2-independent pathway has a conserved genetic organization and displays signs of positive regulation by the master regulator "fumarate and nitrate reductase" (FNR), suggesting a conserved role for UQ in anaerobiosis across Pseudomonadota. The O2-independent pathway was lost in some lineages but maintained in others, where it favoured a secondary reacquisition of low potential quinones (MK or rhodoquinone), which promoted diversification towards aerobic facultative and anaerobic metabolisms. Our results support that the ecological success of Pseudomonadota is linked to the acquisition of the largest known repertoire of quinones, which allowed adaptation to oxic niches as O2 levels increased on Earth, and subsequent diversification into anoxic or O2-fluctuating environments.

Comparative genomics based exploration of xenobiotic degradation patterns in Glutamicibacter, Arthrobacter, and Pseudarthrobacter isolated from diverse ecological habitats

Xenobiotics pose a substantial threat to environmental integrity by disrupting normal ecosystems. The genus Arthrobacter, known for its metabolic versatility can degrade several xenobiotic compounds. Arthrobacter strains have also undergone frequent taxonomic revisions and reclassifications to strains including Pseudarthrobacter and Glutamicibacter. Here, we present the complete genome sequence of Glutamicibacter protophormiae strain NG4, isolated from a coastal area surrounded by chemical plants. Further, through comparative genomics involving 55 strains from Glutamicibacter, Arthrobacter, and Pseudarthrobacter, we elucidated taxonomic relationships and xenobiotic degradation potential. Our genomics-based findings revealed a generally even distribution of xenobiotic-degrading genes and pathways among the studied strains. Glutamicibacter species emerged as potential candidate for steroid degradation. A significant number of host-specific and environmental isolates predominantly possessed pathways for 4-hydroxybenzoate (4-HB) degradation and only the environmental isolates possessed benzoate degradation pathway. Certain Arthrobacter and Pseudarthrobacter species isolated from the environmental settings were identified as potential degraders of toluene, xylene, and phenanthrene. Notably, most strains contained pathways for azathioprine, capecitabine, and 5-fluorouridine pharmaceutical drug metabolism. Overall, our findings shed light on microbial metabolic diversity among 55 strains isolated from diverse sources and hint the importance of strict environmental monitoring. Further, for the application of the putative xenobiotic degrading strains, experimental validation is required in the future.

A taxonomic note on the order Caryophanales: description of 12 novel families and emended description of 21 families

The order Caryophanales, belonging to class Bacilli, is globally distributed in various ecosystems. Currently, this order comprised 12 families that show vast phenotypic, ecological and genotypic variation. The classification of Caryophanales at the family level is currently mainly based on 16S rRNA gene sequencing analysis and the presence of shared phenotypic characteristics, resulting in noticeable anomalies. Our present study revises the taxonomy of Caryophanales based on 1080 available high-quality genome sequences of type strains. The evaluated parameters included the core-genome phylogeny, pairwise average aa identity, lineage-specific core genes, physiological criteria and ecological parameters. Based on the results of this polyphasic approach, we propose that the order Caryophanales be reclassified into 41 families, which include the existing 12 families, 17 families in a recent Validation List in the IJSEM (Validation List no. 215) and 12 novel families for which we propose the names Aureibacillaceae, Cytobacillaceae, Domibacillaceae, Falsibacillaceae, Heyndrickxiaceae, Lottiidibacillaceae, Oxalophagaceae, Pradoshiaceae, Rossellomoreaceae, Schinkiaceae, Sulfoacidibacillaceae and Sutcliffiellaceae. This work represents a genomic sequence-based and systematic framework for classifying the order Caryophanales at the family level, providing new insights into its evolution.

Phylogenomic evaluation of Mangrovimicrobium sediminis gen. nov. sp. nov., the first nitrogen fixing member of the family Halieaceae adapted to mangrove habitat and reclassification of Halioglobus pacificus to Pseudohaliglobus pacificus comb. nov

The taxonomic position and genomic characteristics of a nitrogen fixing and polymer degrading marine bacterium, strain SAOS 164 isolated from a mangrove sediment sample was investigated. Sequence analysis based on 16S rRNA gene identified it as a member of family Halieaceae with closest similarity to Haliea salexigens DSM 19537T (96.3 %), H. alexandrii LZ-16-2T (96.2 %) and Parahaliea maris HSLHS9T (96.0 %) but was distantly related to the genera Haliea, Parahaliea and Halioglobus in phylogenetic trees. In order to ascertain the exact taxonomic position, phylogeny based on RpoBC proteins, whole genome, core and orthologous genes, and comparative analysis of metabolic potential retrieved the strain in an independent lineage clustering along with the genera Halioglobus, Pseudohalioglobus and Seongchinamella. Further, various genome based delimitation parameters represented by mol % GC content, percentage of conserved proteins (POCP), and amino acid identity (AAI) along with chemotaxonomic markers (i.e. fatty acids and polar lipids) supported the inferences of genome based phylogeny and indicated that the strain SAOS 164 belongs to a novel genus. The genome was mapped to 4.8 Mb in size with 65.1 % DNA mol% G + C content. In-silico genomic investigation and phenotyping revealed diverse metabolite genes/pathways related to polymer hydrolysis, nitrogen fixation, light induced growth, carbohydrate, sulfur, phosphorus and amino acid metabolism, virulence factors, defense mechanism, and stress-responsive elements facilitating survival in the mangrove habitat. Based on polyphasic taxonomic approach including genome analyses, a novel genus Mangrovimicrobium sediminis gen. nov. sp. nov. (=SAOS 164T = MTCC 12907T = KCTC 52755T = JCM 32136T) is proposed. Additionally, the reclassification of Halioglobus pacificus (=DSM 27932T = KCTC 23430T = S1-72T) to Pseudhalioglobus pacificus comb. nov. is also proposed.

The Description of Pseudoalteromonas apostichopi sp. nov., Vibrio apostichopi sp. nov., and Marinobacter apostichopi sp. nov. from the Fertilized Eggs and Larvae of Apostichopus japonicus

Three novel bacterial strains, FE4T, FE10T, and LA51T, which are phylogenetically affiliated to the genera Pseudoalteromonas, Vibrio, or Marinobacter, respectively, isolated from fertilized eggs and juveniles of sea cucumber Apostichopus japonicus were characterized by a genome-based taxonomical approach including multilocus sequence analysis (MLSA) combined with classical phenotypic and chemotaxonomic characterizations. A molecular network reconstructed on the basis of nucleotide sequences of four phylogenetic maker protein genes revealed that the strains FE4T, FE10T, and LA51T were closely related to Pseudoalteromonas shioyasakiensis, Vibrio lentus, and Marinobacter similis, respectively. Average nucleotide identity (ANI) comparisons against phylogenetically related species to FE4T, FE10T, and LA51T demonstrated that each newly described strain could not be identified as any previously described species within each genus showing < 95% ANI: 91.3% of FE4T against P. shioyasakiensis JCM 18891 T, 92.6% of FE10T against "V. bathopelagicus" Sal10, and 92.6% of LA51T against M. similis A3d10T, in maximum, respectively. Here, we show molecular phylogenetic, genomic, phenotypic, and chemotaxonomic features of the newly described species FE4T, FE10T, and LA51T. We also propose Pseudoalteromonas apostichopi sp. nov. with FE4T (JCM 36173 T = LMG 33143 T) as the type strain, Vibrio apostichopi sp. nov. with FE10T (JCM 36174 T = LMG 33144 T) as the type strain, and Marinobacter apostichopi sp. nov. with LA51T (JCM 36175 T = LMG 33145 T) as the type strain.

Taxonomic Reframe of Some Species of the Genera Haloferax and Halobellus

Haloferax and Halobellus are the representatives of the family Haloferacaceae and they are dominant in hypersaline ecosystems. Some Haloferax and Halobellus species exhibit a close evolutionary relationship. Genomic, phylogenetic (based on 16S rRNA gene sequence), and phylogenomic analysis were performed to evaluate the taxonomic positions of the genera Haloferax and Halobellus. Based on the results we propose to reclassify Halobellus ramosii as a later heterotypic synonym of Halobellus inordinatus; Haloferax lucentense and Haloferax alexandrinum as later heterotypic synonyms of Haloferax volcanii.

Marortus luteolus Yu et al. 2019 is a later heterotypic synonym of Zhongshania marina On et al. 2019

Phylogeny of 16S rRNA gene sequences showed that Marortus luteolus ZX-21T and Zhongshania marina DSW25-10T are closely related, and form a monophyletic clade affiliated with the genus Zhongshania. Whole genome sequence comparisons showed that M. luteolus ZX-21T and Z. marina DSW25-10T shared 78.8 % digital DNA-DNA hybridization, 97.6 % average nucleotide identity and 98.1 % average amino acid identity. These values exceeded the recommended threshold values for species delineation. Thus, based on the principle of priority, we propose the reclassification of Marortus luteolus Yu et al. 2019 as a later heterotypic synonym of Zhongshania marina On et al. 2019.

Marinobacter azerbaijanicus sp. nov., a moderately halophilic bacterium from Urmia Lake, Iran

A novel moderately halophilic, Gram-stain-negative and facultatively anaerobic bacterium, designated as strain TBZ242T, was isolated from water of Urmia Lake in the Azerbaijan region of Iran. The cells were found to be rod-shaped and motile by a single polar flagellum, producing circular and yellowish colonies. The strain could grow in the presence of 0.5-10 % (w/v) NaCl (optimum, 2.5-5 %). The temperature and pH ranges for growth were 15-45 °C (optimum 30 °C) and pH 7.0-11.0 (optimum pH 8.0) on marine agar. The 16S rRNA gene sequence analysis revealed that strain TBZ242T belonged to the genus Marinobacter, showing the highest similarities to Marinobacter algicola DG893T (98.8 %), Marinobacter vulgaris F01T (98.8 %), Marinobacter salarius R9SW1T (98.5 %), Marinobacter panjinensis PJ-16T (98.4 %), Marinobacter orientalis W62T (98.0 %) and Marinobacter denitrificans JB2H27T (98.0 %). The 16S rRNA and core-genome phylogenetic trees showed that strain TBZ242T formed a distinct branch, closely related to a subclade accommodating M. vulgaris, M. orientalis, M. panjinensis, M. denitrificans, M. algicola, M. salarius and M. iranensis, within the genus Marinobacter. Average nucleotide identity and digital DNA-DNA hybridization values between strain TBZ242T and the type strains of the related species of Marinobacter were ≤85.0 and 28.6 %, respectively, confirming that strain TBZ242T represents a distinct species. The major cellular fatty acids of strain TBZ242T were C16 : 0 and C16 : 1  ω7c/C16 : 1 ω6c and the quinone was ubiquinone Q-9. The genomic DNA G+C content of strain TBZ242T is 57.2 mol%. Based on phenotypic, chemotaxonomic and genomic data, strain TBZ242T represents a novel species within the genus Marinobacter, for which the name Marinobacter azerbaijanicus sp. nov. is proposed. The type strain is TBZ242T (= CECT 30649T = IBRC-M 11466T). Genomic fragment recruitment analysis showed that this species prefers aquatic saline environments with intermediate salinities, being detected on metagenomic databases of Lake Meyghan (Iran) with 5 and 18 % salinity, respectively.

Diversification of Ubiquinone Biosynthesis via Gene Duplications, Transfers, Losses, and Parallel Evolution

The availability of an ever-increasing diversity of prokaryotic genomes and metagenomes represents a major opportunity to understand and decipher the mechanisms behind the functional diversification of microbial biosynthetic pathways. However, it remains unclear to what extent a pathway producing a specific molecule from a specific precursor can diversify. In this study, we focus on the biosynthesis of ubiquinone (UQ), a crucial coenzyme that is central to the bioenergetics and to the functioning of a wide variety of enzymes in Eukarya and Pseudomonadota (a subgroup of the formerly named Proteobacteria). UQ biosynthesis involves three hydroxylation reactions on contiguous carbon atoms. We and others have previously shown that these reactions are catalyzed by different sets of UQ-hydroxylases that belong either to the iron-dependent Coq7 family or to the more widespread flavin monooxygenase (FMO) family. Here, we combine an experimental approach with comparative genomics and phylogenetics to reveal how UQ-hydroxylases evolved different selectivities within the constrained framework of the UQ pathway. It is shown that the UQ-FMOs diversified via at least three duplication events associated with two cases of neofunctionalization and one case of subfunctionalization, leading to six subfamilies with distinct hydroxylation selectivity. We also demonstrate multiple transfers of the UbiM enzyme and the convergent evolution of UQ-FMOs toward the same function, which resulted in two independent losses of the Coq7 ancestral enzyme. Diversification of this crucial biosynthetic pathway has therefore occurred via a combination of parallel evolution, gene duplications, transfers, and losses.

Marinobacter iranensis sp. nov., a slightly halophilic bacterium from a hypersaline lake

A novel halophilic bacterium, strain 71-iT, was isolated from Inche-Broun hypersaline lake in Golestan province, in the north of Iran. It was a Gram-stain-negative, non-endospore forming, rod-shaped bacterium. It grew at 4-40 °C (optimum 30 °C), pH 6.0-11.0 (optimum pH 7.5) and with 0.5-15 % (w/v) NaCl [optimum 3 % (w/v) NaCl]. The results of phylogenetic analyses based on the 16S rRNA gene sequence comparison indicated its affiliation to the genus Marinobacter and the low percentage of identity with the most closely related species (97.5 %), indicated its placement as a novel species within this genus. Digital DNA-DNA hybridization (dDDH) values and average nucleotide identity (ANI) analyses of this strain against closely related species confirmed its condition of novel taxon. On the other hand, the percentage of the average amino acid identity (AAI) affiliated strain 71-iT within the genus Marinobacter. The DNA G+C content of this isolate was 57.7 mol%. The major fatty acids were C16 : 0 and C16 : 1ω7c and/or C16 : 1 ω6c. Ubiquinone-9 was the major isoprenoid quinone and diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylethanolamine (PE) were the main polar lipids of this strain. On the basis of the phylogenomic and phenotypic (including chemotaxonomic) features, we propose strain 71-iT (= IBRC M 11023T = CECT 30160T = LMG 29252T) as the type strain of a novel species within the genus Marinobacter, with the name Marinobacter iranensis sp. nov. Genomic detections of this strain in various metagenomic databases indicate that it is a relatively abundant species in environments with low salinities (approximately 5 % salinity), but not in hypersaline habitats with high salt concentrations.

Marinagarivorans cellulosilyticus sp. nov., a cellulolytic bacterium isolated from the deep-sea off Noma-misaki, Japan

Cells from strain GE09^T, isolated from an artificially immersed nanofibrous cellulose plate in the deep sea, were Gram-stain-negative, motile, aerobic cells that could grow with cellulose as their only nutrient. Strain GE09^T was placed among members of Cellvibrionaceae, in the Gammaproteobacteria, with Marinagarivorans algicola Z1^T, a marine degrader of agar, as the closest relative (97.4 % similarity). The average nucleotide identity and digital DNA-DNA hybridization values between GE09^T and M. algicola Z1^T were 72.5 and 21.2 %, respectively. Strain GE09^T degraded cellulose, xylan and pectin, but not starch, chitin and agar. The different carbohydrate-active enzymes encoded in the genomes of strain GE09^T and M. algicola Z1^T highlights their differences in terms of target energy sources and reflects their isolation environments. The major cellular fatty acids of strain GE09^T were C_18 : 1  ω7c, C_16 : 0 and C_16 : 1  ω7c. The polar lipid profile showed phosphatidylglycerol and phosphatidylethanolamine. The major respiratory quinone was Q-8. Based on these distinct taxonomic characteristics, strain GE09^T represents a new species in the genus Marinagarivorans, for which we propose the name Marinagarivorans cellulosilyticus sp. nov. (type strain GE09^T=DSM 113420^T=JCM 35003^T).

Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea

Background

Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen that are mainly accumulated in oil reservoirs. As the introduction of all classes of hydrocarbons including crude oil and oil products into the environment has increased significantly, oil pollution has become a global ecological problem. However, our perception of pathways for biotic degradation of major HCs and key enzymes in these bioconversion processes has mainly been based on cultured microbes and is biased by uneven taxonomic representation. Here we used Annotree to provide a gene-centric view of the aerobic degradation ability of aliphatic and aromatic HCs in 23,446 genomes from 123 bacterial and 14 archaeal phyla. 

Results

Apart from the widespread genetic potential for HC degradation in Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes, genomes from an additional 18 bacterial and 3 archaeal phyla also hosted key HC degrading enzymes. Among these, such degradation potential has not been previously reported for representatives in the phyla UBA8248, Tectomicrobia, SAR324, and Eremiobacterota. Genomes containing whole pathways for complete degradation of HCs were only detected in Proteobacteria and Actinobacteriota. Except for several members of Crenarchaeota, Halobacterota, and Nanoarchaeota that have tmoA, ladA, and alkB/M key genes, respectively, representatives of archaeal genomes made a small contribution to HC degradation. None of the screened archaeal genomes coded for complete HC degradation pathways studied here; however, they contribute significantly to peripheral routes of HC degradation with bacteria.

Conclusion

Phylogeny reconstruction showed that the reservoir of key aerobic hydrocarbon-degrading enzymes in Bacteria and Archaea undergoes extensive diversification via gene duplication and horizontal gene transfer. This diversification could potentially enable microbes to rapidly adapt to novel and manufactured HCs that reach the environment.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08906-w.

Aestuariicella albida sp. nov., isolated from surface water of the Yellow Sea, and proposal of the genus Aestuariicella as a member of the family Cellvibrionaceae

A Gram-stain-negative, non-motile and aerobic bacterium, designated HHU G3-2T, was isolated from surface water of the Yellow Sea, PR China. Strain HHU G3-2T was positive for oxidase activity and negative for catalase. Optimal growth occurred at 28 °C (range, 20–37 °C), pH 7.0 (range, pH 6.0–9.0) and in the presence of 2–5 % (w/v) NaCl (range, 1–7%). Phylogenetic analysis based on 16S rRNA gene sequences and 120 ubiquitous single-copy protein-coding genes indicated that strain HHU G3-2T formed a distinct phylogenetic lineage with Aestuariicella hydrocarbonica JCM 30134T, sharing a 16S rRNA gene sequence similarity of 98.05%. Average nucleotide identity and digital DNA–DNA hybridization values between strain HHU G3-2T and A. hydrocarbonica JCM 30134T were 75.74 and 17.80%, respectively, which were below the threshold values of 95–96 and 70 %, respectively. The DNA G+C content of the genomic DNA was 51.17 mol%. The major fatty acids (>10 %) were C17 : 1 ω8c (19.8 %), summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c; 15.9 %), summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c; 13.8 %) and C17 : 0 (10.3 %). The predominant isoprenoid quinone was ubiquinone-8. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Based on the polyphasic taxonomic data, strain HHU G3-2T represents a novel species of the genus Aestuariicella , for which the name Aestuariicella albida sp. nov. is proposed. The type strain is HHU G3-2T (=MCCC 1K04224T=JCM 34652T=GDMCC 1.2418T=CGMCC 1.17397T). In addition, we proposed the genus Aestuariicella as a member of the family Cellvibrionaceae .

Past, present and future of the boundaries of the Pseudomonas genus: Proposal of Stutzerimonas gen. Nov

Pseudomonas is one the best studied bacterial genera, and it is the genus with the highest number of species among the gram-negative bacteria. Pseudomonas spp. are widely distributed and play relevant ecological roles; several species are commensal or pathogenic to humans, animals and plants. The main aim of the present minireview is the discussion of how the Pseudomonas taxonomy has evolved with the development of bacterial taxonomy since the first description of the genus in 1894. We discuss how the successive implementation of novel methodologies has influenced the taxonomy of the genus and, vice versa, how the taxonomic studies developed in Pseudomonas have introduced novel tools and concepts to bacterial taxonomy. Current phylogenomic analyses of the family Pseudomonadaceae demonstrate that a considerable number of named Pseudomonas spp. are not monophyletic with P. aeruginosa, the type species of the genus, and that a reorganization of several genera can be foreseen. Phylogenomics of Pseudomonas, Azomonas and Azotobacter within the Pseudomonadaceae is presented as a case study. Five new genus names are delineated to accommodate five well-defined phylogenetic branches that are supported by the shared genes in each group, and two of them can be differentiated by physiological and ecological properties: the recently described genus Halopseudomonas and the genus Stutzerimonas proposed in the present study. Five former Pseudomonas species are transferred to Halopseudomonas and 10 species to Stutzerimonas.

Proposal of Zooshikellaceae fam. nov. to accommodate the genera Zooshikella and Spartinivicinus and reclassification of Zooshikella marina as a later heterotypic synonym of Zooshikella ganghwensis based on whole genome sequence analysis

The genus Spartinivicinus, affiliated to the class Gammaproteobacteria, is an important marine member that produces prodiginines. Currently, its taxonomic assignment to family level is not well presented. Phylogeny of 16S rRNA gene sequences indicated that Spartinivicinus forms a monophyletic clade with Zooshikella, which is neighboured by Aestuariirhabdus of the family Aestuariirhabdaceae and another monophyletic clade of the family Endozoicomonadaceae. The 16S rRNA gene of Spartinivicinus ruber S2-4-1H^T had sequence similarities to those of Aestuariirhabdus litorea GTF13^T, Zooshikella members and Endozoicomonas members of 93.4%, 93.2-93.4  and <92.5 %, respectively. Phylogenomic analysis based on 120 bacterial conserved single-copy genes highly supported placing Spartinivicinus as a sister member of Zooshikella, neighboured by Aestuariirhabdaceae and Endozoicomonadaceae members, indicating that Spartinivicinus and Zooshikella could be considered to belong to the same family. Thus, Zooshikellaceae fam. nov. is proposed to accommodate the two genera. Colonies of Spartinivicinus and Zooshikella are red-pigmented, which is different from Aestuariirhabdus (pale-yellow pigmented). The major respiratory quinone of S. ruber was ubiquinone (Q-9), similar to Zooshikella, but distinct from Aestuariirhabdus (Q-9 and Q-8). The predominant fatty acids and polar lipids of Spartinivicinus also showed a similar patterns to Zooshikella, but they were different from Aestuariirhabdus. Lastly, Spartinivicinus possessed a genome size of 6.68 Mbp and DNA G+C content of 40.1mol%, similar to Zooshikella, but much larger than Aestuariirhabdus. In addition, the 16S rRNA genes of Z. ganghwensis JC2044^T and Z. marina JC333^T possess sequence similarity of 99.79 %. Whole genome comparisons indicated that they shared 79.8 % digital DNA-DNA hybridization, 97.78 % average nucleotide identity and 97.31 % average amino acid identity values. Activities of catalase and oxidase for the two strains were positive. Hydrolysis of skimmed milk and Tweens (40, 60 and 80) was positive. Interestingly, the two strains produced different kinds of prodiginines. We propose that Z. marina is a later heterotypic synonym of Zooshikella ganghwensis.

Deep phylo-taxono genomics reveals Xylella as a variant lineage of plant associated Xanthomonas and supports their taxonomic reunification along with Stenotrophomonas and Pseudoxanthomonas

Genus Xanthomonas is a group of phytopathogens that is phylogenetically related to Xylella, Stenotrophomonas, and Pseudoxanthomonas, having diverse lifestyles. Xylella is a lethal plant pathogen with a highly reduced genome, atypical GC content and is taxonomically related to these three genera. Deep phylo-taxono genomics reveals that Xylella is a variant Xanthomonas lineage that is sandwiched between Xanthomonas clades. Comparative studies suggest the role of unique pigment and exopolysaccharide gene clusters in the emergence of Xanthomonas and Xylella clades. Pan-genome analysis identified a set of unique genes associated with sub-lineages representing plant-associated Xanthomonas clade and nosocomial origin Stenotrophomonas clade. Overall, our study reveals the importance of reconciling classical phenotypic data and genomic findings in reconstituting the taxonomic status of these four genera. SIGNIFICANCE STATEMENT: Xylella fastidiosa is a devastating pathogen of perennial dicots such as grapes, citrus, coffee, and olives. An insect vector transmits the pathogen to its specific host wherein the infection leads to complete wilting of the plants. The genome of X. fastidiosa is significantly reduced both in terms of size (2 Mb) and GC content (50%) when compared with its relatives such as Xanthomonas, Stenotrophomonas, and Pseudoxanthomonas that have higher GC content (65%) and larger genomes (5 Mb). In this study, using systematic and in-depth genome-based taxonomic and phylogenetic criteria and comparative studies, we assert the need to unify Xanthomonas with its relatives (Xylella, Stenotrophomonas and Pseudoxanthomonas). Interestingly, Xylella revealed itself as a minor variant lineage embedded within two major Xanthomonas lineages comprising member species of different hosts.

Yangia mangrovi sp. nov., a novel member of the Roseobacter clade isolated from mangrove soil and emended description of Yangia pacifica Dai et al. 2006

During a study of the bacterial diversity of mangrove habitats, a novel Gram-stain-negative, rod-shaped bacterium designated as SAOS 153D^T was isolated. Sequence alignment and molecular phylogenetic analyses based on 16S rRNA and core gene sequence of strain SAOS 153D^T with closely related taxa revealed a sequence identity of 99.4 % and clustering with Yangia pacifica DX5-10^T. The fatty acids summed feature 8 (C_18:1 ω7c/C_18:1 ω6c) and the lipids phosphatidylglycerol, phosphatidylethanolamine and an unknown phospholipid were the major components of the cell wall. The only ubiquinone type present was Q-10. The genomic DNA G+C content of the strain calculated from whole genome sequencing was 66.9 mol%. These chemotaxonomic and genomic characteristics supported the molecular phylogenetic analysis and placed the strain well within the radiation of the genus Yangia. The overall genome related indices using digital DNA-DNA hybridization (35.4 %) and ortho-average nucleotide identity (88.1 %) values were much lower than the recommended thresholds for species delineation, which further consolidated the novel species status of strain SAOS 153D^T within the genus Yangia as Yangia mangrovi sp. nov. The type strain is SAOS 153D^T (=JCM 31345^T=KCTC 52280^T=MTCC 12749^T).

The potential interplay between the glandular microbiome and scent marking behavior in owl monkeys (Aotus nancymaae)

In mammals, scent marking behavior is a pervasive form of chemical communication that regulates social interactions within and between groups. Glandular microbiota consist of bacterial communities capable of producing chemical cues used in olfactory communication. Despite countless studies on scent marking in primates, few have examined the microbiota associated with glandular secretions. Nancy Ma's owl monkeys (Aotus nancymaae) are nocturnal, socially monogamous primates that frequently scent mark using their subcaudal glands. Previous analyses revealed that unique chemical signatures of Aotus may convey information about sex and age. We used positive reinforcement to sample the subcaudal glands of 23 captive owl monkeys to describe their glandular microbiomes and examine how patterns in these bacterial communities vary with age, sex, rearing environment and/or social group (pair identity). We coupled these analyses with behavioral observations to examine patterns in their scent marking behavior. We isolated 31 bacterial species from Phyla Firmicutes, Proteobacteria, and Actinobacteria, consistent with the dermal and glandular microbiomes of other primates. Several bacterial taxa we identified produce volatile organic compounds, which may contribute to olfactory communication. These bacterial communities are best predicted by an interaction between sex, rearing environment and pair identity rather than any of these variables alone. Within mated pairs of A. nancymaae, males and females scent mark their nest boxes at similar frequencies. In some pairs, rates of scent marking by males and females fluctuated over time in a similar manner. Pairs that had been together longer tended to exhibit the greatest similarities in their rates of scent marking. Together, these findings suggest that scent marking behavior and close social interactions with pair mates in Aotus may influence bacterial transmission and their glandular microbiomes. Chemical communication, including coordinated scent marking, may play a role in strengthening pair bonds, signaling pair status and/or in mate guarding in this socially monogamous primate.

Nitrogeniibacter mangrovi gen. nov., sp. nov., a novel anaerobic and aerobic denitrifying betaproteobacterium and reclassification of Azoarcus pumilus as Aromatoleum pumilum comb. nov

Denitrification is a vital link in the global bio-nitrogen cycle. Here, we isolated a strain (M9-3-2^T) that is a novel benzo[a]pyrene (BaP)-tolerant, anaerobic and aerobic denitrifying bacterium from a continuous BaP-enrichment cultured mangrove sediment. In silico comparative genomics and taxonomic analysis clearly revealed that strain M9-3-2^T (=MCCC 1K03313^T=JCM 32045^T) represents a novel species of a novel genus named as Nitrogeniibacter mangrovi gen. nov., sp. nov., belonging to family Zoogloeaceae, order Rhodocyclales. In addition, the species Azoarcus pumilus is transferred into genus Aromatoleum and named Aromatoleum pumilum comb. nov. The predominant respiratory quinone of strain M9-3-2^T was ubiquinone-8 and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified phospholipids and three unidentified aminophospholipids. In this study, the capacity of strain M9-3-2^T to eliminate nitrate was detected under anaerobic and aerobic conditions, and the removal rates of nitrate were 6.1×10^-6 µg N/l/h/cell and 3×10^-7 µg N/l/h/cell, respectively. Our results suggested that strain M9-3-2^T could play an important role in the nitrogen removal regardless of the presence of oxygen in natural or/and man-made ecosystems.

Cosmopolitan Distribution of Endozoicomonas-Like Organisms and Other Intracellular Microcolonies of Bacteria Causing Infection in Marine Mollusks

Intracellular microcolonies of bacteria (IMC), in some cases developing large extracellular cysts (bacterial aggregates), infecting primarily gill and digestive gland, have been historically reported in a wide diversity of economically important mollusk species worldwide, sometimes associated with severe lesions and mass mortality events. As an effort to characterize those organisms, traditionally named as Rickettsia or Chlamydia-like organisms, 1950 specimens comprising 22 mollusk species were collected over 10 countries and after histology examination, a selection of 99 samples involving 20 species were subjected to 16S rRNA gene amplicon sequencing. Phylogenetic analysis showed Endozoicomonadaceae sequences in all the mollusk species analyzed. Geographical differences in the distribution of Operational Taxonomic Units (OTUs) and a particular OTU associated with pathology in king scallop (OTU_2) were observed. The presence of Endozoicomonadaceae sequences in the IMC was visually confirmed by in situ hybridization (ISH) in eight selected samples. Sequencing data also indicated other symbiotic bacteria. Subsequent phylogenetic analysis of those OTUs revealed a novel microbial diversity associated with molluskan IMC infection distributed among different taxa, including the phylum Spirochetes, the families Anaplasmataceae and Simkaniaceae, the genera Mycoplasma and Francisella, and sulfur-oxidizing endosymbionts. Sequences like Francisella halioticida/philomiragia and Candidatus Brownia rhizoecola were also obtained, however, in the absence of ISH studies, the association between those organisms and the IMCs were not confirmed. The sequences identified in this study will allow for further molecular characterization of the microbial community associated with IMC infection in marine mollusks and their correlation with severity of the lesions to clarify their role as endosymbionts, commensals or true pathogens.