Current phylogeny of Rhodospirillaceae: A multi-approach study

Changes in the gut microbiota of pseudoxanthoma elasticum patients

OBJECTIVE

Pseudoxanthoma elasticum (PXE) is a rare autosomal disorder with a variable phenotype that may be modulated by environmental factors. Plasma vitamin K (VK) levels may be involved in the ectopic calcification process observed in PXE. Since VK2 is predominantly produced by the gut microbiota, we hypothesized that changes in the gut microbiota of PXE patients might exacerbate the calcification process and disease symptoms.

METHODS

Twenty PXE patients were included in the study and 60 gut microbiota profiles from the Biofortis laboratory database were used as controls.

RESULTS

The Rhodospirillaceae family was more abundant in the PXE group while the Sphingomonadaceae family was more abundant in the control group. In a PXE severity subgroup analysis, microbiota dispersion was lower in "severe" than in "non-severe" patients, which was confirmed by permutation multivariate analysis of variance at the phylum, family and genus ranks. However, no significant association was found in a model incorporating relative abundance of bacterial families, severity score, and different blood and fecal VK species.

CONCLUSION

These results suggest slight compositional changes in the gut microbiota of PXE patients. Further studies are needed to substantiate their impact on VK metabolism and the calcification process.

The phylogeny of Acetobacteraceae: photosynthetic traits and deranged respiratory enzymes

IMPORTANCE

Acetobacteraceae are one of the best known and most extensively studied groups of bacteria, which nowadays encompasses a variety of taxa that are very different from the vinegar-producing species defining the family. Our paper presents the most detailed phylogeny of all current taxa classified as Acetobacteraceae, for which we propose a taxonomic revision. Several of such taxa inhabit some of the most extreme environments on the planet, from the deserts of Antarctica to the Sinai desert, as well as acidic niches in volcanic sites like the one we have been studying in Patagonia. Our work documents the progressive variation of the respiratory chain in early branching Acetobacteraceae into the different respiratory chains of acidophilic taxa such as Acidocella and acetous taxa such as Acetobacter. Remarkably, several genomes retain remnants of ancestral photosynthetic traits and functional bc 1 complexes. Thus, we propose that the common ancestor of Acetobacteraceae was photosynthetic.

Multiple approaches of cellular metabolism define the bacterial ancestry of mitochondria

We breathe at the molecular level when mitochondria in our cells consume oxygen to extract energy from nutrients. Mitochondria are characteristic cellular organelles that derive from aerobic bacteria and carry out oxidative phosphorylation and other key metabolic pathways in eukaryotic cells. The precise bacterial origin of mitochondria and, consequently, the ancestry of the aerobic metabolism of our cells remain controversial despite the vast genomic information that is now available. Here, we use multiple approaches to define the most likely living relatives of the ancestral bacteria from which mitochondria originated. These bacteria live in marine environments and exhibit the highest frequency of aerobic traits and genes for the metabolism of fundamental lipids that are present in the membranes of eukaryotes, sphingolipids, and cardiolipin.

Bacterial Microbiota of Ostreobium, the Coral-Isolated Chlorophyte Ectosymbiont, at Contrasted Salinities

Microscopic filaments of the siphonous green algae Ostreobium (Ulvophyceae, Bryopsidales) colonize and dissolve the calcium carbonate skeletons of coral colonies in reefs of contrasted salinities. Here, we analyzed their bacterial community's composition and plasticity in response to salinity. Multiple cultures of Pocillopora coral-isolated Ostreobium strains from two distinct rbcL lineages representative of IndoPacific environmental phylotypes were pre-acclimatized (>9 months) to three ecologically relevant reef salinities: 32.9, 35.1, and 40.2 psu. Bacterial phylotypes were visualized for the first time at filament scale by CARD-FISH in algal tissue sections, within siphons, at their surface or in their mucilage. Ostreobium-associated microbiota, characterized by bacterial 16S rDNA metabarcoding of cultured thalli and their corresponding supernatants, were structured by host genotype (Ostreobium strain lineage), with dominant Kiloniellaceae or Rhodospirillaceae (Alphaproteobacteria, Rhodospirillales) depending on Ostreobium lineage, and shifted Rhizobiales' abundances in response to the salinity increase. A small core microbiota composed of seven ASVs (~1.5% of thalli ASVs, 19-36% cumulated proportions) was persistent across three salinities in both genotypes, with putative intracellular Amoebophilaceae and Rickettsiales_AB1, as well as Hyphomonadaceae and Rhodospirillaceae also detected within environmental (Ostreobium-colonized) Pocillopora coral skeletons. This novel knowledge on the taxonomic diversity of Ostreobium bacteria paves the way to functional interaction studies within the coral holobiont.

Haematospirillum jordaniae Cellulitis and Bacteremia

We isolated Haematospirillum jordaniae from a positive blood culture from a 57-year-old man in Slovenia who had bacteremia and bullous cellulitis of lower extremities. The infection was successfully treated with ciprofloxacin. Our findings signal the need for increased awareness about the clinical course of H. jordaniae and its potential effects as a human pathogen.

New Alphaproteobacteria Thrive in the Depths of the Ocean with Oxygen Gradient

We survey here the Alphaproteobacteria, a large class encompassing physiologically diverse bacteria which are divided in several orders established since 2007. Currently, there is considerable uncertainty regarding the classification of an increasing number of marine metagenome-assembled genomes (MAGs) that remain poorly defined in their taxonomic position within Alphaproteobacteria. The traditional classification of NCBI taxonomy is increasingly complemented by the Genome Taxonomy Database (GTDB), but the two taxonomies differ considerably in the classification of several Alphaproteobacteria, especially from ocean metagenomes. We analyzed the classification of Alphaproteobacteria lineages that are most common in marine environments, using integrated approaches of phylogenomics and functional profiling of metabolic features that define their aerobic metabolism. Using protein markers such as NuoL, the largest membrane subunit of complex I, we have identified new clades of Alphaproteobacteria that are specific to marine niches with steep oxygen gradients (oxycline). These bacteria have relatives among MAGs found in anoxic strata of Lake Tanganyika and together define a lineage that is distinct from either Rhodospirillales or Sneathiellales. We characterized in particular the new 'oxycline' clade. Our analysis of Alphaproteobacteria also reveals new clues regarding the ancestry of mitochondria, which likely evolved in oxycline marine environments.

Pacificispira spongiicola gen. nov., sp. nov., a nitrate-reducing bacterium isolated from tropical western Pacific

The Gram-stain-negative, strictly aerobic, curved-to-spiral rod-shaped bacterial strain, designated KN72^T, was isolated from the Caroline Seamounts in the Pacific Ocean. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain KN72^T was a member of the family Rhodospirillaceae and formed a distinct lineage. Strain KN72^T contained ubiquinone-10 as the major respiratory quinone. The polar lipid profiles contained phosphatidylethanolamine, phosphatidylglycerol, one aminolipid and three phospholipids. The predominant cellular fatty acids were C_16:0 and summed feature 8 (comprising C_18:1ω7c/C_18:1ω6c). The strain KN72^T displayed highest 16S rRNA gene sequence similarities with Hwanghaeella grinnelliae Gri0909^T (92.3%), Marivibrio halodurans ZB80^T (91.0%) and Aestuariispira insulae AH-MY2^T (90.1%). The DNA G+C content of strain KN72^T was 61.1%. Collectively, based on phenotypic, chemotaxonomic, phylogenetic and genomic evidence presented, strain KN72^T represents a novel species of a novel genus of the family Rhodospirillaceae, for which the name Pacificispira spongiicola gen. nov., sp. nov. is proposed. The type strain is KN72^T (= CGMCC 1.17142^T = KCTC 72429^T).

Denitrobaculum tricleocarpae gen. nov., sp. nov., a marine bacterium from coralline algae Tricleocarpa sp

A Gram-stain-negative, non-spore-forming, aerobic, motile, curved rod-shaped bacterium, designed strain R148^T was isolated from a coralline algae Tricleocarpa sp. collected from Weizhou island, PR China. The optimal growth of R148^T occurred at 25 °C, pH 8-9 in the presence of 0.5 % (w/v) NaCl on the basis of amended marine broth 2216. The genomic DNA G+C content was 59.5 mol%. The only detected respiratory quinone was Q-10. The major polar lipids were phosphatidylmethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, and three unidentified ninhydrin-positive lipids. The major cellular fatty acids were C_18 : 1ω7c, C_16 : 1ω7c, C_19 : 0cyclo 9, 10 DMA and C_18 : 0. The results of 16S rRNA gene-based global alignment indicated that the closest neighbour of strain R148^T was Pelagibius litoralis DSM 21314^T (93.1 % similarity), the second is Limibacillus halophilus KCTC 42420^T (92.2 %). The results of phylogenetic analysis indicated that R148^T forms a distinct branch in the robust clade of R148^T and P. litoralis DSM 21314^T, while the taxonomic position of this clade in the family Rhodospirillaceae is ambiguous among phylogenetic approaches. The low 16S rRNA gene similarity and distinct polar lipid and cellular fatty acid profile could readily distinguish R148^T from closely related type strains. So R148^T is suggested to represent a novel species in a novel genus, for which the name Denitrobaculum tricleocarpae gen. nov., sp. nov. is proposed. The type strain is R148^T (=MCCC 1K03781^T=KCTC 72137^T).