Genome Study of α-, β-, and γ-Carbonic Anhydrases from the Thermophilic Microbiome of Marine Hydrothermal Vent Ecosystems

Carbonic anhydrases (CAs) are metalloenzymes that can help organisms survive in hydrothermal vents by hydrating carbon dioxide (CO₂). In this study, we focus on alpha (α), beta (β), and gamma (γ) CAs, which are present in the thermophilic microbiome of marine hydrothermal vents. The coding genes of these enzymes can be transferred between hydrothermal-vent organisms via horizontal gene transfer (HGT), which is an important tool in natural biodiversity. We performed big data mining and bioinformatics studies on α-, β-, and γ-CA coding genes from the thermophilic microbiome of marine hydrothermal vents. The results showed a reasonable association between thermostable α-, β-, and γ-CAs in the microbial population of the hydrothermal vents. This relationship could be due to HGT. We found evidence of HGT of α- and β-CAs between Cycloclasticus sp., a symbiont of Bathymodiolus heckerae, and an endosymbiont of Riftia pachyptila via Integrons. Conversely, HGT of β-CA genes from the endosymbiont Tevnia jerichonana to the endosymbiont Riftia pachyptila was detected. In addition, Hydrogenovibrio crunogenus SP-41 contains a β-CA gene on genomic islands (GIs). This gene can be transferred by HGT to Hydrogenovibrio sp. MA2-6, a methanotrophic endosymbiont of Bathymodiolus azoricus, and a methanotrophic endosymbiont of Bathymodiolus puteoserpentis. The endosymbiont of R. pachyptila has a γ-CA gene in the genome. If α- and β-CA coding genes have been derived from other microorganisms, such as endosymbionts of T. jerichonana and Cycloclasticus sp. as the endosymbiont of B. heckerae, through HGT, the theory of the necessity of thermostable CA enzymes for survival in the extreme ecosystem of hydrothermal vents is suggested and helps the conservation of microbiome natural diversity in hydrothermal vents. These harsh ecosystems, with their integral players, such as HGT and endosymbionts, significantly impact the enrichment of life on Earth and the carbon cycle in the ocean.

PpCas9 from Pasteurella pneumotropica - a compact Type II-C Cas9 ortholog active in human cells

CRISPR-Cas defense systems opened up the field of genome editing due to the ease with which effector Cas nucleases can be programmed with guide RNAs to access desirable genomic sites. Type II-A SpCas9 from Streptococcus pyogenes was the first Cas9 nuclease used for genome editing and it remains the most popular enzyme of its class. Nevertheless, SpCas9 has some drawbacks including a relatively large size and restriction to targets flanked by an 'NGG' PAM sequence. The more compact Type II-C Cas9 orthologs can help to overcome the size limitation of SpCas9. Yet, only a few Type II-C nucleases were fully characterized to date. Here, we characterized two Cas9 II-C orthologs, DfCas9 from Defluviimonas sp.20V17 and PpCas9 from Pasteurella pneumotropica. Both DfCas9 and PpCas9 cleave DNA in vitro and have novel PAM requirements. Unlike DfCas9, the PpCas9 nuclease is active in human cells. This small nuclease requires an 'NNNNRTT' PAM orthogonal to that of SpCas9 and thus potentially can broaden the range of Cas9 applications in biomedicine and biotechnology.

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.

Physiological and genomic features of Paraoceanicella profunda gen. nov., sp. nov., a novel piezophile isolated from deep seawater of the Mariana Trench

A novel piezophilic alphaproteobacterium, strain D4M1^T, was isolated from deep seawater of the Mariana Trench. 16S rRNA gene analysis showed that strain D4M1^T was most closely related to Oceanicella actignis PRQ‐67^T (94.2%), Oceanibium sediminis O448^T (94.2%), and Thioclava electrotropha ElOx9^T (94.1%). Phylogenetic analyses based on both 16S rRNA gene and genome sequences showed that strain D4M1^T formed an independent monophyletic branch paralleled with the genus Oceanicella in the family Rhodobacteraceae. Cells were Gram‐stain‐negative, aerobic short rods, and grew optimally at 37°C, pH 6.5, and 3.0% (w/v) NaCl. Strain D4M1^T was piezophilic with the optimum pressure of 10 MPa. The principal fatty acids were C_18:1ω7c/C_18:1ω6c and C_16:0, major respiratory quinone was ubiquinone‐10, and predominant polar lipids were phosphatidylglycerol, phosphatidylethanolamine, and an unidentified aminophospholipid. The complete genome contained 5,468,583‐bp with a G + C content of 70.2 mol% and contained 4,855 protein‐coding genes and 78 RNA genes. Genomic analysis revealed abundant clues on bacterial high‐pressure adaptation and piezophilic lifestyle. The combined evidence shows that strain D4M1^T represents a novel species of a novel genus in the family Rhodobacteraceae, for which the name Paraoceanicella profunda gen. nov., sp. nov. is proposed (type strain D4M1^T = MCCC 1K03820^T = KCTC 72285^T).

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).

Acidimangrovimonas sediminis gen. nov., sp. nov., isolated from mangrove sediment and reclassification of Defluviimonas indica as Acidimangrovimonas indica comb. nov. and Defluviimonas pyrenivorans as Acidimangrovimonas pyrenivorans comb. nov

A Gram-stain-negative, aerobic, non-motile, short-rod bacterium, strain MS2-2^T, was isolated from mangrove sediment sampled at Jiulong River Estuary, Fujian province, PR China. 16S rRNA gene sequence similarity analysis showed that strain MS2-2^T was most closely related to Defluviimonas indica 20V17^T (97.41 %) and Defluviimonas pyrenivorans PrR001^T (96.18 %). Phylogenetic trees based on 16S rRNA genes and genome sequences both revealed that strain MS2-2^T formed a distinct cluster with D. indica 20V17^T and D. pyrenivorans PrR001^T within family Rhodobacteracea, quite separate from other type species in the genus Defluviimonas. The average nucleotide identity value between strain MS2-2^T and D. indica 20V17^T was 78.35 %. Growth of strain MS2-2^T was observed at 16-41 ° C (optimum, 34 ° C), pH 3.6-7.5 (pH 6.0) and 0.5-10.0 % (w/v) NaCl (4.0 %). The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and C18 : 0. Ubiquinone 10 was the sole quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 67.9 mol%. The combined genotypic and phenotypic data show that strain MS2-2^T represents a novel species of a novel genus in the family Rhodobacteraceae, for which the name Acidimangrovimonassediminis gen. nov., sp. nov. is proposed, with the type strain MS2-2^T (=MCCC 1K02682^T=NBRC 112978^T). We also propose the reclassification of Defluviimonas indica as Acidimangrovimonas indica comb. nov. and Defluviimonas pyrenivorans as Acidimangrovimonas pyrenivorans comb. nov.

Extant microbial communities in the partially desiccated Rincon de Parangueo maar crater lake in Mexico

Rincon de Parangueo is a maar where a perennial lake was present until the 1980s. A conspicuous feature of the lake’s sediments is the presence of bioherms and organo-sedimentary deposits produced by microbial communities. The gradual lake desiccation during the last 40 years has produced dramatic environmental changes inside the maar basin, which resulted in the formation of a highly saline-alkaline system with extant microorganisms. In this paper we succinctly describe the geologic setting where the microbial communities have developed inside of the maar crater and the results obtained from high-throughput sequencing methods to characterize the microbial component (Bacteria, Eukarya and Archaea) in endolithic mats of calcareous sediments, and microbial mats and free-living microorganisms in the soda ponds. The studied sites displayed different microbial communities with a diverse number of phylotypes belonging to Bacteria and Eukarya, contrasting with a much less diverse component in Archaea. The sequences here detected were related to environmental sequences from sites with extreme life conditions such as high alkalinity (alkaliphiles), high salinity (halophiles) and high temperature (thermophiles). Moreover, our results indicate an important unexplored endemic microbial biodiversity in the vestiges of the former lake that need to be studied.

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).

Defluviimonas aquaemixtae sp. nov., isolated from the junction between a freshwater spring and the ocean

A Gram-stain-negative, coccoid- or short-rod-shaped and non-gliding bacterial strain, designated CDM-7T, was isolated from the zone where the ocean meets a freshwater spring at Jeju island, South Korea, and was subjected to a polyphasic taxonomic study. Strain CDM-7T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2–3 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain CDM-7T falls within the clade comprising species of the genus Defluviimonas, clustering with the type strain of Defluviimonas aestuarii , with which it exhibited the highest 16S rRNA gene sequence similarity value (98.4 %). The 16S rRNA gene sequence similarity values between strain CDM-7T and the type strains of Defluviimonas denitrificans and Defluviimonas indica were 97.1 and 96.2 %, respectively. The genomic DNA G+C content was 66.8 mol% and the mean DNA–DNA relatedness values between strain CDM-7T and the type strains of D. aestuarii and D. denitrificans were 15.6±2.5 and 6.7±3.2 %, respectively. Strain CDM-7T contained Q-10 as the predominant ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as the major fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid, an unidentified phospholipid and an unidentified lipid. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, demonstrated that strain CDM-7T is distinguishable from other species of the genus Defluviimonas . On the basis of the data presented, strain CDM-7T is considered to represent a novel species of the genus Defluviimonas , for which the name Defluviimonas aquaemixtae sp. nov. is proposed. The type strain is CDM-7T ( = KCTC 42108T = CECT 8626T).

Draft Genome Sequence of Defluviimonas indica Strain 20V17T, Isolated from a Deep-Sea Hydrothermal Vent Environment in the Southwest Indian Ocean

Here, we present the draft genome sequence of Defluviimonas indica 20V17^T, which was isolated from a deep-sea hydrothermal vent chimney sample in the southwest Indian Ocean. The draft genome sequence contains 4,268,338 bp, with a G+C content of 66.33%.