Production and utilization of pseudocobalamin in marine Synechococcus cultures and communities.

Cobalamin influences marine microbial communities because an exogenous source is required by most eukaryotic phytoplankton, and demand can exceed supply. Pseudocobalamin is a cobalamin analogue produced and used by most cyanobacteria but is not directly available to eukaryotic phytoplankton. Some microbes can remodel pseudocobalamin into cobalamin, but a scarcity of pseudocobalamin measurements impedes our ability to evaluate its importance for marine cobalamin production. Here, we perform simultaneous measurements of pseudocobalamin and methionine synthase (MetH), the key protein that uses it as a co-factor, in Synechococcus cultures and communities. In Synechococcus sp. WH8102, pseudocobalamin quota decreases in low temperature (17°C) and low nitrogen to phosphorus ratio, while MetH did not. Pseudocobalamin and MetH quotas were influenced by culture methods and growth phase. Despite the variability present in cultures, we found a comparably consistent quota of 300 ± 100 pseudocobalamin molecules per cyanobacterial cell in the Northwest Atlantic Ocean, suggesting that cyanobacterial cell counts may be sufficient to estimate pseudocobalamin inventories in this region. This work offers insights into cellular pseudocobalamin metabolism, environmental and physiological conditions that may influence it, and provides environmental measurements to further our understanding of when and how pseudocobalamin can influence marine microbial communities.

Hydrogenimonas leucolamina sp. nov., a hydrogen- and sulphur-oxidizing mesophilic chemolithoautotroph isolated from a deep-sea hydrothermal vent chimney at the Suiyo Seamount in the Western Pacific Ocean.

A novel mesophilic bacterium, strain SS33T, was isolated from a deep-sea hydrothermal vent chimney at Suiyo Seamount, Izu-Bonin Arc, Western Pacific Ocean. The cells of strain SS33T were motile short rods with a single polar flagellum. The growth of strain SS33T was observed at the temperature range between 33 and 55 °C (optimum growth at 45 °C), at the pH range between 5.0 and 7.1 (optimum growth at pH 6.0) and in the presence of between 2.0 and 4.5% (w/v) NaCl [optimum growth at 3.5% (w/v)]. Strain SS33T was a facultative anaerobic chemolithoautotroph using molecular hydrogen and elemental sulphur as the sole electron donor. Nitrate, nitrous oxide, sulphate, elemental sulphur and molecular oxygen were capable of serving as the sole electron acceptor. Phylogenetic analysis based on 16S rRNA gene sequences placed strain SS33T in the genus Hydrogenimonas belonging to the class Epsilonproteobacteria. The closely related species of strain SS33T were Hydrogenimonas urashimensis SSM-Sur55T (95.96%), Hydrogenimonas thermophila EP1-55-1%T (95.75%) and Hydrogenimonas cancrithermarum ISO32T (95.24%). According to the taxonomic and physiological characteristics, it is proposed that strain SS33T was classified into a novel species of genus Hydrogenimonas, Hydrogenimonas leucolamina sp. nov., with SS33T (=JCM 39184T =KCTC 25253T) as the type strain. Furthermore, the genome comparison of Epsilonproteobacteria revealed that their [NiFe] hydrogenase genes belonging to Group 1b could be divided into two phylogenetic lineages and suggested that the reverse gyrase gene has been lost after division to the genus Hydrogenimonas.

Agarose Degrading Potential and Whole Genome Sequence Analysis of Marine Bacterium Aliagarivorans sp. Strain DM1 Isolated from the Arabian Sea.

In recent years, agar-degrading bacteria have gained significant interest due to their biotechnological, environmental, microbiological, and industrial applications. Agar poses challenges such as marine waste accumulation, difficult industrial processing, limited natural degradability, and sustainability concerns due to high demand and overharvesting of red algae. The present study addresses the need for efficient agar-degrading microorganisms by isolating Aliagarivorans sp. strain DM1 from biofilm on fabric surfaces in the intertidal regions of the Arabian Sea, India. Phylogenetic analysis revealed that strain DM1 is closely related to Aliagarivorans taiwanensis AAT1T, and it exhibited significant agar-degrading activity on Zobell marine agar plates. Whole genome sequencing of Aliagarivorans sp. strain DM1, conducted using the Illumina NovaSeq platform, yielded a genome size of 4,898,415 bp with an average G + C content of 53.3%. The genome includes 4,518 predicted protein-coding genes (CDS), 86 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes, with thirteen predicted agarases identified. The highest enzyme activity recorded was 51.00 U mL-1 on the 6th day of incubation using 10% inoculum, with optimal conditions of pH 8-9, 0.8 M NaCl, and temperatures between 50 and 60 °C. These findings underscore the promise of Aliagarivorans sp. strain DM1 in developing efficient enzymatic processes that can be applied in various biotechnological and industrial fields, including waste management and agaro-oligosaccharide production. Furthermore, strain DM1 possesses several key characteristics that enhance its adaptability and utility in marine and industrial applications, surpassing closely related strains in enzyme stability, environmental tolerance, and industrial versatility.

Active-bromide and surfactant synergy for enhanced microfouling control.

Biofilms are structured microbial communities encased in a matrix of self-produced extracellular polymeric substance (EPS) and pose significant challenges in various industrial cooling systems. A nuclear power plant uses a biocide active-bromide for control of biological growth in its condenser cooling system. This study is aimed at evaluating the anti-bacterial and anti-biofilm efficacy of active-bromide against planktonic and biofilm-forming bacteria that are commonly encountered in seawater cooling systems. The results demonstrated that active-bromide at the concentration used at the power plant (1 ppm) exhibited minimal killing activity against Pseudomonas aeruginosa planktonic cells. The bacterial cell surface hydrophobicity assay using Staphylococcus aureus and P. aeruginosa indicated that Triton-X 100 significantly decreased the hydrophobicity of planktonic cells, enhancing the susceptibility of the cells to active-bromide. Biofilm inhibition assays revealed limited efficacy of active-bromide at 1 ppm concentration, but significant inhibition at 5 ppm and 10 ppm. However, the addition of a surfactant, Triton-X 100, in combination with 1 ppm active-bromide displayed a synergistic effect, leading to significant biofilm dispersal of pre-formed P. aeruginosa biofilms. This observation was substantiated by epifluorescence microscopy using a live/dead bacterial assay that showed the combination treatment resulted in extensive cell death within the biofilm, as indicated by a marked increase in red fluorescence, compared to treatments with either agent alone. These findings suggest that active bromide alone may be insufficient for microfouling control in the seawater-based condenser cooling system of the power plant. Including a biocompatible surfactant that disrupts established biofilms (microfouling) can significantly improve the efficacy of active bromide treatment.

Enterovibrio qingdaonensis sp. nov. and Enterovibrio gelatinilyticus sp. nov., two marine bacteria isolated from surface seawater of Qingdao offshore.

Two Gram-stain-negative, facultatively anaerobic, motile, and rod-shaped marine bacteria, designated strains ZSDZ35T and ZSDZ42T, were isolated from surface seawater of Qingdao offshore. Phylogenetic analysis of the 16S rRNA genes and whole genome data placed ZSDZ35T and ZSDZ42T within the genus Enterovibrio. Strain ZSDZ35T was most closely related to Enterovibrio nigricans DSM 22720T with 97.55% sequence similarity, whereas ZSDZ42T was most closely related to Enterovibrio calviensis DSM 14347T with 98.97% sequence similarity. Strain ZSDZ35T grew with 0-8% (w/v) NaCl (optimum 4%), at 16-37 °C (optimum 28 °C) and pH 6.0-9.0 (optimum pH 8.0); whereas strain ZSDZ42T grew with 1-7% (w/v) NaCl (5%), at 4-28 °C (8 °C) and pH 6.0-9.0 (pH 7.0). Both strains shared the same major fatty acid components of summed feature 3 (C16:1ω7c or/and C16:1ω6c), summed feature 8 (C18:1ω7c and C18:1ω6c) and C16:0, with different proportions. The DNA G + C contents of strains ZSDZ35T and ZSDZ42T were 47.2% and 46.7%, respectively. Based on the results of polyphasic analyses, ZSDZ35T and ZSDZ42T are considered to represent novel species, for which the names Enterovibrio qingdaonensis sp. nov. (type strain, ZSDZ35T = MCCC 1K06293T = KCTC 82887T) and Enterovibrio gelatinilyticus sp. nov. (type strain, ZSDZ42T = MCCC 1K06294T = KCTC 82886T) are proposed, respectively.

Thaumarchaeota from deep-sea methane seeps provide novel insights into their evolutionary history and ecological implications.

BACKGROUND: Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota mediate the rate-limiting step of nitrification and remove the ammonia that inhibits the aerobic metabolism of methanotrophs. However, the AOA that inhabit deep-sea methane-seep surface sediments (DMS) are rarely studied. Here, we used global DMS metagenomics and metagenome-assembled genomes (MAGs) to investigate the metabolic activity, evolutionary history, and ecological contributions of AOA. Expression of AOA-specific ammonia-oxidizing gene (amoA) was examined in the sediments collected from the South China Sea (SCS) to identify their active ammonia metabolism in the DMS. RESULTS: Our analysis indicated that AOA contribute > 75% to the composition of ammonia-utilization genes within the surface layers (above 30 cm) of global DMS. The AOA-specific ammonia-oxidizing gene was actively expressed in the DMS collected from the SCS. Phylogenomic analysis of medium-/high-quality MAGs from 18 DMS-AOA indicated that they evolved from ancestors in the barren deep-sea sediment and then expanded from the DMS to shallow water forming an amoA-NP-gamma clade-affiliated lineage. Molecular dating suggests that the DMS-AOA origination coincided with the Neoproterozoic oxidation event (NOE), which occurred ~ 800 million years ago (mya), and their expansion to shallow water coincided with the Sturtian glaciation (~ 713 mya). Comparative genomic analysis suggests that DMS-AOA exhibit higher requirement of carbon source for protein synthesis with enhanced genomic capability for osmotic regulation, motility, chemotaxis, and utilization of exogenous organic compounds, suggesting it could be more heterotrophic compared with other lineages. CONCLUSION: Our findings provide new insights into the evolutionary history of AOA within the Thaumarchaeota, highlighting their critical roles in nitrogen cycling in the global DMS ecosystems. Video Abstract.

Thioclava arctica sp. nov. and Zhongshania arctica sp. nov., isolated from the surface sediment of the Arctic Ocean and reclassification of Marortus luteolus Yu et al. 2019 as a later heterotypic synonym of Zhongshania marina On et al. 2019.

Two Gram-stain-negative bacterial strains, 15-R06ZXC-3T and R06B22T, were isolated from the surface sediment of the Arctic Ocean. Phylogenetic analyses based on the 16S rRNA gene and genome sequences indicated that strain 15-R06ZXC-3T belongs to the genus Thioclava, while strain R06B22T belongs to the genus Zhongshania. Strain 15-R06ZXC-3T showed the closest relationship to Thioclava indica DT23-4T. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain 15-R06ZXC-3T and all of the type strains of the genus Thioclava ranged from 20.8 to 30.4% and 79.1 to 85.7%, respectively. Strain R06B22T was most closely related to Zhongshania marina DSW25-10T. The dDDH and ANI values between strain R06B22T and all of the type strains of the genus Zhongshania ranged from 18.6 to 20.4% and 77.5 to 79.4%, respectively. These dDDH and ANI values were all below the standard cutoff criteria for the delineation of bacterial species, indicating that the two strains may represent novel species within their respective genera. Furthermore, their phenotypic and chemotaxonomic characteristics also differentiated them from closely related species. Based on the polyphasic analyses, strains 15-R06ZXC-3T and R06B22T separately represent novel species of the genera Thioclava and Zhongshania, for which the names Thioclava arctica sp. nov. (type strain 15-R06ZXC-3T = MCCC 1A07434T= KCTC 8342T) and Zhongshania arctica sp. nov. (type strain R06B22T = MCCC 1A08273T= KCTC 8343T) are proposed. Additionally, phylogenomic analyses showed that the strain Marortus luteolus ZX-21T was clustered with the strain Z. marina DSW25-10T and all other type strains of the genus Zhongshania. Furthermore, the ANI and dDDH values between strains ZX-21T and DSW25-10T were 97.6% and 78.8±2.5%, respectively, strongly indicating that they represented a single species. Therefore, it is proposed that M. luteolus Yu et al. 2019 be recognized as a later heterotypic synonym of Z. marina On et al. 2019.

Widespread production of plant growth-promoting hormones among marine bacteria and their impacts on the growth of a marine diatom.

BACKGROUND: Reciprocal exchanges of metabolites between phytoplankton and bacteria influence the fitness of these microorganisms which ultimately shapes the productivity of marine ecosystems. Recent evidence suggests that plant growth-promoting hormones may be key metabolites within mutualistic phytoplankton-bacteria partnerships, but very little is known about the diversity of plant growth-promoting hormones produced by marine bacteria and their specific effects on phytoplankton growth. Here, we aimed to investigate the capacity of marine bacteria to produce 7 plant growth-promoting hormones and the effects of these hormones on Actinocyclus sp. growth. RESULTS: We examined the plant growth-promoting hormone synthesis capabilities of 14 bacterial strains that enhance the growth of the common diatom Actinocyclus. Plant growth-promoting hormone biosynthesis was ubiquitous among the bacteria tested. Indeed all 14 strains displayed the genomic potential to synthesise multiple hormones, and mass-spectrometry confirmed that each strain produced at least 6 out of the 7 tested plant growth-promoting hormones. Some of the plant growth-promoting hormones identified here, such as brassinolide and trans-zeatin, have never been reported in marine microorganisms. Importantly, all strains produced the hormone indole-3 acetic acid (IAA) in high concentrations and released it into their surroundings. Furthermore, indole-3 acetic acid extracellular concentrations were positively correlated with the ability of each strain to promote Actinocyclus growth. When inoculated with axenic Actinocyclus cultures, only indole-3 acetic acid and gibberellic acid enhanced the growth of the diatom, with cultures exposed to indole-3 acetic acid exhibiting a two-fold increase in cell numbers. CONCLUSION: Our results reveal that marine bacteria produce a much broader range of plant growth-promoting hormones than previously suspected and that some of these compounds enhance the growth of a marine diatom. These findings suggest plant growth-promoting hormones play a large role in microbial communication and broaden our knowledge of their fuctions in the marine environment. Video Abstract.

Cable bacteria colonise new sediment environments through water column dispersal.

Cable bacteria exhibit a unique metabolism involving long-distance electron transport, significantly impacting elemental cycling in various sediments. These long filamentous bacteria are distributed circumglobally, suggesting an effective mode of dispersal. However, oxygen strongly inhibits their activity, posing a challenge to their dispersal through the water column. We investigated the effective dispersal of marine cable bacteria in a compartmentalised microcosm experiment. Cable bacteria were grown in natural 'source' sediment, and their metabolic activity was recorded in autoclaved 'destination' cores, which were only accessible through oxygenated seawater. Colonisation occurred over weeks, and destination cores contained only one cable bacterium strain. Filament 'snippets' (fragments with a median size of ~15 cells) accumulated in the microcosm water, with about 30% of snippets attached to sediment particles. Snippet release was also observed in situ in a salt marsh creek. This provides a model for the dispersal of cable bacteria through oxygenated water: snippets are formed by filament breakage in the sediment, released into the overlying water and transported with sediment particles that likely offer protection. These insights are informative for broader theories on microbial community assembly and prokaryotic biogeography in marine sediments.

Novel oil-associated bacteria in Arctic seawater exposed to different nutrient biostimulation regimes.

The Arctic Ocean is an oligotrophic ecosystem facing escalating threats of oil spills as ship traffic increases owing to climate change-induced sea ice retreat. Biostimulation is an oil spill mitigation strategy that involves introducing bioavailable nutrients to enhance crude oil biodegradation by endemic oil-degrading microbes. For bioremediation to offer a viable response for future oil spill mitigation in extreme Arctic conditions, a better understanding of the effects of nutrient addition on Arctic marine microorganisms is needed. Controlled experiments tracking microbial populations revealed a significant decline in community diversity along with changes in microbial community composition. Notably, differential abundance analysis highlighted the significant enrichment of the unexpected genera Lacinutrix, Halarcobacter and Candidatus Pseudothioglobus. These groups are not normally associated with hydrocarbon biodegradation, despite closer inspection of genomes from closely related isolates confirming the potential for hydrocarbon metabolism. Co-occurrence analysis further revealed significant associations between these genera and well-known hydrocarbon-degrading bacteria, suggesting potential synergistic interactions during oil biodegradation. While these findings broaden our understanding of how biostimulation promotes enrichment of endemic hydrocarbon-degrading genera, further research is needed to fully assess the suitability of nutrient addition as a stand-alone oil spill mitigation strategy in this sensitive and remote polar marine ecosystem.

Yoonia algicola sp. nov., Yoonia rhodophyticola sp. nov. and Yoonia phaeophyticola sp. nov., isolated from marine algae.

Three Gram-stain-negative, strictly aerobic, non-motile, oxidase- and catalase-positive, short-rod-shaped bacteria, designated as strains G8-12T, SS1-5T and BS5-3T, were isolated from marine algae in South Korea. Strain G8-12T exhibited optimal growth at 20-25 °C, pH 8.0 and 2.0-2.5% (w/v) NaCl, while strains SS1-5T and BS5-3T grew optimally at 25 °C, pH 7.0 and 1.5% NaCl. All strains contained ubiquinone-10 as the sole respiratory quinone, with phosphatidylglycerol and phosphatidylcholine as major polar lipids, and C18 : 1 ω7c and C16 : 0 as major fatty acids (>5 %); C18 : 1 ω7c 11-methyl and C18 : 1 2-OH were additionally identified as major fatty acids in strain SS1-5T. The genomic DNA G+C contents were 57.0, 58.3 and 56.4% for strains G8-12T, SS1-5T and BS5-3T, respectively. Strains G8-12T, SS1-5T and BS5-3T exhibited less than 74.8% average nucleotide identity (ANI) and 19.7% digital DNA-DNA hybridization (dDDH) values with each other, indicating that they represent different species. Phylogenetic analyses based on both 16S rRNA gene and genome sequences revealed that strains G8-12T, SS1-5T and BS5-3T form distinct phylogenetic lineages within the genus Yoonia. Relative to other closely related Yoonia species, these strains exhibited ANI and dDDH values below 83.5 and 26.9%, respectively, suggesting that they constitute novel species within the genus Yoonia. Based on their phenotypic, chemotaxonomic and phylogenetic characteristics, strains G8-12T, SS1-5T and BS5-3T represent three novel species of the genus Yoonia, for which the names Yoonia algicola sp. nov. (G8-12T=KACC 22753T=JCM 35790T), Yoonia rhodophyticola sp. nov. (SS1-5T=KACC 22649T=JCM 35753T) and Yoonia phaeophyticola sp. nov. (BS5-3T=KACC 22648T=JCM 35751T) are proposed, respectively.

A Biofilm Channel Origin for Vermiform Microstructure in Carbonate Microbialites.

A three-dimensional tubular fabric known as "vermiform microstructure" in Phanerozoic and Neoproterozoic carbonate microbialites has been hypothesized to represent the body fossil of nonspicular keratose demosponges. If correct, this interpretation extends the sponge body fossil record and origin of animals to ~890 Ma. However, the veracity of the keratose sponge interpretation for vermiform microstructure remains in question, and the origin of the tubular fabric is enigmatic. Here we compare exceptionally well-preserved microbialite textures from the Upper Triassic to channel networks created by modern microbial biofilms. We demonstrate that anastomosing channel networks of similar size and geometries are produced by microbial biofilms in the absence of sponges, suggesting the origin for vermiform microstructure in ancient carbonates is not unique to sponges and perhaps best interpreted conservatively as likely microbial in origin. We present a taphonomic model of early biofilm lithification in seawater with anomalously high carbonate saturation necessary to preserve delicate microbial textures. This work has implications for the understanding of three-dimensional biofilm architecture that goes beyond the current micro-scale observations available from living biofilm experiments and suggests that biofilm channel networks have an extensive fossil record.

Low microbial abundance and community diversity in the egg capsule of the oviparous cloudy catshark (Scyliorhinus torazame) during oviposition.

Vertebrate embryos are protected from bacterial infection by various maternally derived factors, yet little is known about the defence mechanisms in elasmobranchs. This study aimed to characterize the intracapsular environment of freshly laid eggs of the oviparous catshark (Scyliorhinus torazame) by investigating the microbial abundance and microbiota to understand its potential contribution to embryonic defence. The egg capsule of oviparous elasmobranchs is tightly sealed until pre-hatching, after which seawater flows into the capsule, exposing the embryos to the surrounding seawater. We found that early embryos were highly vulnerable to environmental pathogens, suggesting that the embryos are somehow protected from infection before pre-hatching. Indeed, the intracapsular environment of freshly laid eggs exhibited significantly low bacterial density, maintained until pre-hatching. Furthermore, the microbiome inside eggs just after oviposition differed markedly from those of rearing seawater and adult oviducal gland epithelia; these eggs were predominantly populated by an unidentified genus of Sphingomonadaceae. Overall, this study provides compelling evidence that early embryos of oviparous cloudy catshark are incubated in a clean intracapsular environment that potentially plays a significant role in embryonic development in oviparous elasmobranchs.

Mapping the spread of antibiotic resistance genes in the coastal microbiome.

StandfirstCoastal environments are becoming increasingly exposed to antibiotics through anthropogenic inputs. But how could emerging metagenomic techniques be used to map the spread of antibiotic resistance genes in the coastal microbiome?[Formula: see text].

Biosurfactant production by Bacillus cereus GX7 utilizing organic waste and its application in the remediation of hydrocarbon-contaminated environments.

The use of biosurfactants represents a promising technology for remediating hydrocarbon pollution in the environment. This study evaluated a highly effective biosurfactant strain-Bacillus cereus GX7's ability to produce biosurfactants from industrial and agriculture organic wastes. Bacillus cereus GX7 showed poor utilization capacity for oil soluble organic waste but effectively utilized of water- soluble organic wastes such as starch hydrolysate and wheat bran juice as carbon sources to enhance biosurfactant production. This led to significant improvements in surface tension and emulsification index. Corn steep liquor was also effective as a nitrogen source for Bacillus cereus GX7 in biosurfactant production. The biosurfactants produced by strain Bacillus cereus GX7 demonstrated a remediation effect on oily beach sand, but are slightly inferior to chemical surfactants. Inoculation with Bacillus cereus GX7 (70.36%) or its fermentation solution (94.38%) effectively enhanced the degradation efficiency of diesel oil in polluted seawater, surpassing that of indigenous degrading bacteria treatments (57.62%). Moreover, inoculation with Bacillus cereus GX7's fermentation solution notably improved the community structure by increasing the abundance of functional bacteria such as Pseudomonas and Stenotrophomonas in seawater. These findings suggest that the Bacillus cereus GX7 as a promising candidate for bioremediation of petroleum hydrocarbons.

Description of Rhodobacter flavimaris sp. nov. and proposal of the genera Paenirhodobacter, Sedimentimonas, and Sinirhodobacter as synonyms of Rhodobacter.

Two Gram-stain-negative, aerobic, ovoid to short rod-shaped bacterial strains, designated as WL0062T and WL0115, were isolated from coastal zone of the Yellow Sea, Jiangsu Province, PR China, respectively. Strain WL0062T grew optimally at 28 °C, pH 7.0-8.0 and with 1.0-3.0% (w/v) NaCl. Strain WL0115 grew optimally at 28 °C, pH 6.0-7.0 and with 1.0-3.0% (w/v) NaCl. In the bac120 tree, strains WL0062T and WL0115 clustered together with Sedimentimonas flavescens B57T. The respiratory quinone of both strains was ubiquinone-10. The major polar lipids of both strains were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, glycolipid, phosphatidylmonomethylethanolamine, and one unidentified polar lipid. The major fatty acids of strain WL0062T were summed features 8 (C18 : 1 ω6c and/or C18 : 1 ω7c). The major fatty acids of strain WL0115 were summed features 8 (C18 : 1 ω6c and/or C18 : 1 ω7c), C18 : 0, iso-C17 : 1 ω5c and C20 : 4 ω6/9/12/15c (arachidonic acid). The G+C content of genomic DNA of strains WL0062T and WL0115 was 64.0 mol% in both of them. Combined with the analysis of average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization, strain WL0062T represents a novel species of the genus Rhodobacter, for which the name Rhodobacter flavimaris sp. nov is proposed. The type strain is WL0062T (=MCCC 1K06014T=JCM 34676T=GDMCC 1.2427T). Strain WL0115 (=MCCC 1K07531=JCM 35568=GDMCC 1.3088) should belong to the same species as Sedimentimonas flavescens B57T. In addition, on the basis of phylogenomic relationship and phenotypical characteristics, the genera Paenirhodobacter, Sedimentimonas, and Sinirhodobacter are proposed as synonyms of Rhodobacter.

Seasonal dynamics in microbial trace metals transporters during phytoplankton blooms in the Southern Ocean.

Trace metals are required as cofactors in metalloproteins that are essential in microbial metabolism and growth. The microbial requirements of diverse metals and the capabilities of prokaryotic taxa to acquire these metals remain poorly understood. We present here results from metagenomic observations over an entire productive season in the region off Kerguelen Island (Indian Sector of the Southern Ocean). We observed seasonal patterns in the abundance of prokaryotic transporters of seven trace elements (zinc [Zn], manganese [Mn], nickel [Ni], molybdenum [Mo], tungsten [W], copper [Cu] and cobalt [Co]) and the consecutive spring and summer phytoplankton blooms were strong drivers of these temporal trends. Taxonomic affiliation of the functional genes revealed that Rhodobacteraceae had a broad repertoire of trace metal transporters (Mn, Zn, Ni, W and Mo) and a more restricted set was observed for other prokaryotic groups, such as Flavobacteriaceae (Zn), Nitrincolaceae (Ni and W) and Thioglobaceae (Mo). The prevalence of trace metal transporters within a prokaryotic group, as determined on the family level, was overall confirmed in representative metagenome-assembled genomes. We discuss the potential involvement of prokaryotic groups in processes related to organic matter utilisation that require these metals and the consequences on carbon and trace metal cycling in surface waters of the Southern Ocean.

Microbial responses on upwelling signature across reversal wind pattern in tropical coastal environment off Mumbai, India.

Upwelling promotes marine productivity through water column mixing. The process disturbs the ecosystem, causing oxygen depletion and thermal variability. This study analyses effect of upwelling processes on microbial signature in coastal waters off Mumbai. The coastal environment with seasonal reversal winds was analysed using data during ten cruises. Coastal metocean processes are examined using water quality parameters and the Ekman approximation with wind stress. This analysis explains oxygen depletion and coastal upwelling, influenced by seasonal reversal wind pattern. The study connects hypoxia in the coastal water column to wind-induced upwelling. Concurrently, microbial structure is assessed through metrics such as Total Viable Count, Total Bacterial Count, Sulfate Reducing Bacteria (SRB), and denitrifiers. Notably, high levels of SRB are observed during hypoxia associated with coastal upwelling. This study investigates microbial level with combined result of physical processes and water quality parameters.

Whole cell affinity for 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) in the marine bacterium Candidatus Pelagibacter st. HTCC7211 explains marine dissolved HMP concentrations.

Vitamin B1 is a universally required coenzyme in carbon metabolism. However, most marine microorganisms lack the complete biosynthetic pathway for this compound and must acquire thiamin, or precursor molecules, from the dissolved pool. The most common version of Vitamin B1 auxotrophy is for thiamin's pyrimidine precursor moiety, 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP). Frequent HMP auxotrophy in plankton and vanishingly low dissolved concentrations (approximately 0.1-50 pM) suggest that high-affinity HMP uptake systems are responsible for maintaining low ambient HMP concentrations. We used tritium-labelled HMP to investigate HMP uptake mechanisms and kinetics in cell cultures of Candidatus Pelagibacter st. HTCC7211, a representative of the globally distributed and highly abundant SAR11 clade. A single protein, the sodium solute symporter ThiV, which is conserved across SAR11 genomes, is the likely candidate for HMP transport. Experimental evidence indicated transport specificity for HMP and mechanistically complex, high-affinity HMP uptake kinetics. Km values ranged from 9.5 pM to 1.2 nM and were dramatically lower when cells were supplied with a carbon source. These results suggest that HMP uptake in HTCC7211 is subject to complex regulation and point to a strategy for high-affinity uptake of this essential growth factor that can explain natural HMP levels in seawater.

Temporal enrichment of comammox Nitrospira and Ca. Nitrosocosmicus in a coastal plastisphere.

Plastic marine debris is known to harbor a unique microbiome (termed the "plastisphere") that can be important in marine biogeochemical cycles. However, the temporal dynamics in the plastisphere and their implications for marine biogeochemistry remain poorly understood. Here, we characterized the temporal dynamics of nitrifying communities in the plastisphere of plastic ropes exposed to a mangrove intertidal zone. The 39-month colonization experiment revealed that the relative abundances of Nitrospira and Candidatus Nitrosocosmicus representatives increased over time according to 16S rRNA gene amplicon sequencing analysis. The relative abundances of amoA genes in metagenomes implied that comammox Nitrospira were the dominant ammonia oxidizers in the plastisphere, and their dominance increased over time. The relative abundances of two metagenome-assembled genomes of comammox Nitrospira also increased with time and positively correlated with extracellular polymeric substances content of the plastisphere but negatively correlated with NH4+ concentration in seawater, indicating the long-term succession of these two parameters significantly influenced the ammonia-oxidizing community in the coastal plastisphere. At the end of the colonization experiment, the plastisphere exhibited high nitrification activity, leading to the release of N2O (2.52 ng N2O N g-1) in a 3-day nitrification experiment. The predicted relative contribution of comammox Nitrospira to N2O production (17.9%) was higher than that of ammonia-oxidizing bacteria (4.8%) but lower than that of ammonia-oxidizing archaea (21.4%). These results provide evidence that from a long-term perspective, some coastal plastispheres will become dominated by comammox Nitrospira and thereby act as hotspots of ammonia oxidation and N2O production.