Georhizobium profundi gen. nov., sp. nov., a piezotolerant bacterium isolated from a deep-sea sediment sample of the New Britain Trench

Genomic insights into the alphaproteobacterium Georhizobium sp. MAB10 revealed a pathway of Mn(II) oxidation-coupled anoxygenic photoautotrophy: a novel understanding of the biotic process in deep-sea ferromanganese nodule formation

Under light conditions, Mn(II) facilitates the photoautotrophic growth of Georhizobium sp. MAB10, a strain derived from deep-sea ferromanganese nodules, along with the generation of dark Mn oxides (β-MnO2). This study investigated the genetic basis of Mn(II) oxidation-coupled anoxygenic photoautotrophy using genome sequencing and biochemical assays of strain MAB10. Preliminary results indicated the presence of genes encoding a functional pheophytin-quinone-type photosynthetic reaction center and a putative key enzyme for Mn(II) oxidation, namely FtsP/CotA-like multicopper oxidase GE001273. Under light conditions, Mn(II) significantly reduced the respiration rate and elevated the intracellular NADH/NADtotal ratio. This suggested that Mn(II)-derived electrons entered the cyclic photophosphorylation, partially replacing the oxidative phosphorylation for ATP production and enhancing the electron flow to complex I for NADH generation. In vitro enzymatic studies confirmed that GE001273 was a catalyst for Mn(II) oxidation in the outer membrane. Comprehensive genomic analyses of respiration and carbon and nitrogen metabolism revealed the high ecophysiological flexibility of strain MAB10 during Mn(II) oxidation-coupled anoxygenic photoautotrophy in deep-sea habitats. These analyses provided insights into bacterial Mn(II) oxidation-coupled anoxygenic photoautotrophy during microorganism-mediated deep-sea ferromanganese nodule formation.

IMPORTANCE

Microorganisms are believed to participate in the biotic process of deep-sea ferromanganese nodule formation [Mn(II) oxidation]. Despite the multitude of studies and reviews focusing on the details of Mn(II) oxidation catalyzed by diverse heterotrophs, the mechanistic roles of manganese chemolithotrophs from ferromanganese nodules remain unclear. We demonstrate that strain Georhizobium sp. MAB10 can utilize Mn(II)-derived electrons for photoautotrophic growth, with concomitant generation of dark β-MnO2 type Mn oxides under near-infrared light condition. This study uses genomic and biochemical assays to explore the genetic basis of Mn(II) oxidation-coupled anoxygenic photoautotrophy. The comprehensive analyses of respiration and carbon and nitrogen metabolism further elucidated the high ecophysiological flexibility of strain MAB10 in deep-sea habits. These findings expand our understanding of the role of chemolithotrophs in deep-sea ferromanganese nodule formation and justify further investigations into the molecular basis for Mn(II) oxidation-coupled anoxygenic photoautotrophy.

Characterization and Genomic Analysis of Fererhizobium litorale gen. nov., sp. nov., Isolated from the Sandy Sediments of the Sea of Japan Seashore

The taxonomic status of two gram-negative, whitish-pigmented motile bacteria KMM 9576T and KMM 9553 isolated from a sandy sediment sample from the Sea of Japan seashore was defined. Phylogenetic analysis revealed that strains KMM 9576T and KMM 9553 represent a distinct lineage within the family Rhizobiaceae, sharing 100% 16S rRNA sequence similarity and 99.5% average nucleotide identity (ANI) to each other. The strains showed the highest 16S rRNA sequence similarities of 97.4% to Sinorhizobium garamanticum LMG 24692T, 96.9% to Ensifer adhaerens NBRC 100388T, and 96.8% to Pararhizobium giardinii NBRC 107135T. The ANI values between strain KMM 9576T and Ensifer adhaerens NBRC 100388T, Sinorhizobium fredii USDA 205T, Pararhizobium giardinii NBRC 107135T, and Rhizobium leguminosarum NBRC 14778T were 79.9%, 79.6%, 79.4%, and 79.2%, respectively. The highest core-proteome average amino acid identity (cpAAI) values of 82.1% and 83.1% were estimated between strain KMM 9576T and Rhizobium leguminosarum NBRC 14778T and 'Rhizobium album' NS-104, respectively. The DNA GC contents were calculated from a genome sequence to be 61.5% (KMM 9576T) and 61.4% (KMM 9553). Both strains contained the major ubiquinone Q-10 and C18:1ω7c as the dominant fatty acid followed by 11-methyl C18:1ω7c and C19:0 cyclo, and polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, and two unidentified phospholipids. Based on phylogenetic and phylogenomic analyses, and phenotypic characterization, strains KMM 9576T and KMM 9553 are concluded to represent a novel genus and species, for which the name Fererhizobium litorale gen. nov., sp. nov. is proposed. The type strain of the type species is strain KMM 9576T (=NRIC 0957T).

Description of Flavimaribacter sediminis gen. nov., sp. nov., a New Member of the Family Rhizobiaceae Isolated from Marine Sediment

A novel Gram-staining-negative, aerobic and rod-shaped bacterium, designated WL0058T, was isolated from coastal sediment sample collected in Nantong city, Jiangsu province of China (120° 51' 13″ E, 32° 6' 26″ N) in October 2020. Strain WL0058T was found to grow at 4-37 °C (optimum, 28 °C) with 1.5-4.0% NaCl (optimum, 4.0%) and displayed alkaliphilic growth with the pH range of pH 6.0-10.0 (optimum, pH 6.0). Phylogenetic trees constructed based on 16S rRNA gene sequence indicated that strain WL0058T is a member of the family Rhizobiaceae, shared the highest similarity with "Hoeflea prorocentri" CCTCC AB 2016294T (97.7%) and constituted a sub-cluster within the family with it, while the similarity with others in the family Rhizobiaceae was lower than 97.0%. The G + C content of genomic DNA was 59.5 mol%. Polar lipids profile of strain WL0058T included phosphatidylcholine (PC), phosphatidylethanolamine (PE), and glycolipid (GL), phosphatidylmonomethylethanolamine (PME) and two unidentified polar lipids (L). The major isoprenoid quinone was determined to be Q-10 and the major fatty acids were C16:0, C18:0, summed features 4 (iso-C17:1 and/or anteiso-C17:1), and summed features 8 (C18:1ω6c and/or C18:1ω7c). As inferred from the morphology, physiology, and biochemical analysis, genotypic characteristics, and the phylogenetic trees, strain WL0058T ought to be recognized as a novel genus in the family Rhizobiaceae, for which the name Flavimaribacter sediminis gen. nov., sp. nov. The type strain of Flavimaribacter sediminis gen. nov., sp. nov. is WL0058T (= MCCC 1K06063T = JCM 34659T = GDMCC 1.2448T).

Deep-sea plastisphere: Long-term colonization by plastic-associated bacterial and archaeal communities in the Southwest Atlantic Ocean

Marine plastic pollution is a global concern because of continuous release into the oceans over the last several decades. Although recent studies have made efforts to characterize the so-called plastisphere, or microbial community inhabiting plastic substrates, it is not clear whether the plastisphere is defined as a core community or as a random attachment of microbial cells. Likewise, little is known about the influence of the deep-sea environment on the plastisphere. In our experimental study, we evaluated the microbial colonization on polypropylene pellets and two types of plastic bags: regular high density polyethylene (HDPE) and HDPE with the oxo-biodegradable additive BDA. Gravel was used as control. Samples were deployed at three sites at 3300 m depth in the Southwest Atlantic Ocean and left for microbial colonization for 719 days. For microbial communities analysis, DNA was extracted from the biofilm on plastic and gravel substrates, and then the 16S rRNA was sequenced through the Illumina Miseq platform. Cultivation was performed to isolate strains from the plastic and gravel substrates. Substrate type strongly influenced the microbial composition and structure, while no difference between sites was detected. Although several taxa were shared among plastics, we observed some groups specific for each plastic substrate. These communities comprised taxa previously reported from both epipelagic zones and deep-sea benthic ecosystems. The core microbiome (microbial taxa shared by all plastic substrates) was exclusively composed by low abundance taxa, with some members well-described in the plastisphere and with known plastic-degradation capabilities. Additionally, we obtained bacterial strains that have been previously reported inhabiting plastic substrates and/or degrading hydrocarbon compounds, which corroborates our metabarcoding data and suggests the presence of microbial members potentially active and involved with degradation of these plastics in the deep sea.

Roseitranquillus sediminis gen. nov., sp. nov. a novel genus and species of the family Rhodobacteraceae, isolated from sediment of an Arctic fjord

A Gram-negative, aerobic, non-motile, oxidase-positive, catalase-positive, rod-shaped bacterium, designated strain MCCB 386^T was isolated from sediment samples collected from Kongsfjorden, an Arctic fjord. The strain MCCB 386^T showed growth at 4-37 °C (optimum 27°C) in the presence of 1-8% NaCl (w/v, optimum 3.5%) and at pH 6.0-8.0 (optimum pH 7.0). The major fatty acids were C_18:1ω7c (54.0%) and 11-methyl C_18:1ω7c (22.6%). The dominant respiratory quinone was Q-10. The major polar lipids comprised of phosphatidylcholine (PC), diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphoglycolipid (PGL), one unidentified aminolipid, two glycolipids and two unidentified lipids. The genomic G+C content of the strain MCCB 386^T was 68.1 mol%. The 16 S rRNA gene sequences based phylogenetic analysis of MCCB 386^T showed that Psychromarinibacter halotolerans YBW34^T (95.88%) is the most closely related species. In addition, overall genome relatedness indices (OGRI) of MCCB 386^T with closely related strains were lower than threshold level for species and genus delineation. The analysis of Biosynthetic Gene clusters (BGCs) revealed the potential of this strain for production of novel bioactive secondary metabolites. As per polyphasic taxonomic characterisation, strain MCCB 386^T represents a novel species of a novel genus for which the name Roseitranquillus sediminis gen. nov., sp. nov. is suggested. The type strain of the species is MCCB 386^T (= JCM 33,538^T= KACC 21,531^T).

Peteryoungia gen. nov. with four new species combinations and description of Peteryoungia desertarenae sp. nov., and taxonomic revision of the genus Ciceribacter based on phylogenomics of Rhizobiaceae

A novel bacterial strain designated as ADMK78^T was isolated from the saline desert soil. The cells were rod-shaped, Gram-stain-negative, and non-motile. The strain ADMK78^T grows best at 28 °C. Phylogeny of 16S rRNA gene placed the strain ADMK78^T with the members of genera Ciceribacter and Rhizobium, while the highest sequence similarity was with Rhizobium wuzhouense W44^T (98.7%) and Rhizobium ipomoeae shin9-1 ^T (97.9%). Phylogenetic analysis based on 92 core-genes extracted from the genome sequences and average amino acid identity (AAI) revealed that the strain ADMK78^T forms a distinct cluster including five species of Rhizobium, which is separate from the cluster of the genera Rhizobium and Ciceribacter. We propose re-classification of Rhizobium ipomoeae, R. wuzhouense, R. rosettiformans and R. rhizophilum into the novel genus Peteryoungia. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of ADMK78^T were less than 82 and 81%, respectively, among all type strains included in the genus Peteryoungia. The strain ADMK78^T showed differences in physiological, phenotypic, and protein profiles estimated by MALDI-TOF MS to its closest relatives. Based on the phenotypic, chemotaxonomic properties, and phylogenetic analyses, the strain ADMK78^T represents a novel species, Peteryoungia desertarenae sp. nov. The type strain is ADMK78^T (= MCC 3400^T; KACC 21383^T; JCM 33657^T). We also proposed the reclassification of Rhizobium daejeonense, R. naphthalenivorans and R. selenitireducens, into the genus Ciceribacter, based on core gene phylogeny and AAI values.

Genome Analysis of Endobacterium cerealis, a Novel Genus and Species Isolated from Zea mays Roots in North Spain

In the present work, we analyse the genomic and phenotypic characteristics of a strain named RZME27^T isolated from roots of a Zea mays plant grown in Spain. The phylogenetic analyses of 16S rRNA gene and whole genome sequences showed that the strain RZME27^T clustered with the type strains of Neorhizobium galegae and Pseudorhizobium pelagicum from the family Rhizobiaceae. This family encompasses several genera establishing symbiosis with legumes, but the genes involved in nodulation and nitrogen fixation are absent in its genome. Nevertheless, genes related to plant colonization, such as those involved in motility, chemotaxis, quorum sensing, exopolysaccharide biosynthesis and hydrolytic enzymes production were found. The comparative pangenomic analyses showed that 78 protein clusters present in the strain RZME27^T were not found in the type strains of its closest relatives N. galegae and P. pelagicum. The calculated average nucleotide identity (ANI) values between the strain RZME27^T and the type strains of N. galegae and P. pelagicum were 75.61% and 75.1%, respectively, similar or lower than those found for other genera from family Rhizobiaceae. Several phenotypic differences were also found, highlighting the absence of the fatty acid C_19:0 cyclo ω8c and propionate assimilation. These results support the definition of a novel genus and species named Endobacterium cerealis gen. nov. sp. nov. whose type strain is RZME27^T.