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Oil spills are a frequent perturbation to the marine environment that has rapid and significant impacts on the local microbiome. Previous studies have shown that exposure to synthetic dispersant alone did not enhance heterotrophic microbial activity or oxidation rates of specific hydrocarbon components but increased the abundance of some taxa (e.g., Colwellia). In contrast, exposure to oil, but not dispersants, increased the abundance of other taxa (e.g., Marinobacter) and stimulated hydrocarbon oxidation rates. Here, we advance these findings by interpreting metatranscriptomic data from this experiment to explore how and why specific components of the microbial community responded to distinct organic carbon exposure regimes. Dispersant alone was selected for a unique community and for dominant organisms that reflected treatment- and time-dependent responses. Dispersant amendment also led to diverging functional profiles among the different treatments. Similarly, oil alone was selected for a community that was distinct from treatments amended with dispersants. The presence of oil and dispersants with added nutrients led to substantial differences in microbial responses, likely suggesting increased fitness driven by the presence of additional inorganic nutrients. The oil-only additions led to a marked increase in the expression of phages, prophages, transposable elements, and plasmids (PPTEPs), suggesting that aspects of microbial community response to oil are driven by the mobilome, potentially through viral-associated regulation of metabolic pathways in ciliates and flagellates that would otherwise throttle the microbial community through grazing.IMPORTANCEMicrocosm experiments simulated the April 2010 Deepwater Horizon oil spill by applying oil and synthetic dispersants (Corexit EC9500A and EC9527A) to deep ocean water samples. The exposure regime revealed severe negative alterations in the treatments heterotrophic microbial activity and hydrocarbon oxidation rates. We expanded these findings by exploring metatranscriptomic signatures of the microbial communities during the chemical amendments in the microcosm experiments. Here we report how dominant organisms were uniquely associated with treatment- and time-dependent trajectories during the exposure regimes; nutrient availability was a significant factor in driving changes in metatranscriptomic responses. Remarkable signals associated with PPTEPs showed the potential role of mobilome and viral-associated survival responses. These insights underscore the time-dependent environmental perturbations of fragile marine environments under oil and anthropogenic stress.

The genus Marinobacter is very broadly distributed in global environments and is considered as aerobic heterotroph. In this study, six Marinobacter strains were identified with autotrophic thiosulfate oxidation capacity. These strains, namely Marinobacter guineae M3BT, Marinobacter aromaticivorans D15-8PT, Marinobacter vulgaris F01T, Marinobacter profundi PWS21T, Marinobacter denitrificans JB02H27T, and Marinobacter sp. ST-1M (with a 99.93% similarity to the 16S rDNA sequences of Marinobacter salsuginis SD-14BT), were screened out of 32 Marinobacter strains by autotrophic thiosulfate oxidization medium. The population of cells grew in a chemolithotrophic medium, increasing from 105 cells/mL to 107 cells/mL within 5 d. This growth was accompanied by the consumption of thiosulfate 3.59 mmol/L to 9.64 mmol/L and the accumulation of sulfate up to 0.96 mmol/L, and occasionally produced sulfur containing complex particles. Among these Marinobacter strains, it was also found their capability of oxidizing thiosulfate to sulfate in a heterotrophic medium. Notably, M. vulgaris F01T and M. antarcticus ZS2-30T showed highly significant production of sulfate at 9.45 mmol/L and 3.10 mmol/L. Genome annotation indicated that these Marinobacter strains possess a complete Sox cluster for thiosulfate oxidation. Further phylogenetic analysis of the soxB gene revealed that six Marinobacter strains formed a separate lineage within Gammaproteobacteria and close to obligate chemolithoautotroph Thiomicrorhabdus arctica. The results indicated that thiosulfate oxidizing and chemolithoautotrophic potential in Marinobacter genus, which may contribute to the widespread of Marinobacter in the global ocean. [ABSTRACT FROM AUTHOR]

Gram-negative, rod-shaped, and aerobic bacteria designated chi1T and chi5T were isolated from the root of Suaeda japonica Makino. Phylogenetics utilizing 16S rRNA and whole-genome sequences of the two novel strains chi1T and chi5T confirmed that they were related to the genera Marinobacter and Wenyingzhuangia, respectively. For the novel strains chi1T and chi5T, the digital DNA–DNA hybridization values (19–20% and 22.1–36.6%, respectively) and average nucleotide identity values (74.4–76.5% and 79.1–88.9%, respectively) fell within the range for the genera Marinobacter and Wenyingzhuangia, respectively. Pangenome analyses of the novel strains chi1T and chi5T revealed 357 and 368 singletons genes, respectively. The genomic DNA G + C contents of the strains chi1T and chi5T were 57.2% and 31.5%, respectively. The major fatty acids of strain chi1T were C12:0, C16:0, and summed feature 3 (C16:1 ω6c and/or C16:1ω7c), while those of the strain chi5T were iso-C15:0 3OH, iso-C17:0 3OH, and iso-C15:0. Data from the phylogenetic, phylogenomic, pangenome, genomic, physiological, and biochemical analyses indicated that the novel strains were distinct. Therefore, we propose the names Marinobacter suadae (type strain chi1T = KACC 23259T = TBRC 17652T) and Wenyingzhangia gilva (type strain chi5T = KACC 23262T = TBRC 17900T) for the studied bacterial strains. [ABSTRACT FROM AUTHOR]

Glucosylglycerol (GG) is a natural compatible solute that can be synthesized by many cyanobacteria and a few heterotrophic bacteria under high salinity conditions. In cyanobacteria, GG is synthesized by GG-phosphate synthase and GG-phosphate phosphatase, and a hydrolase GGHA catalyzes its degradation. In heterotrophic bacteria (such as some Marinobacter species), a fused form of GG-phosphate phosphatase and GG-phosphate synthase is present, but the cyanobacteria-like degradation pathway is not available. Instead, a phosphorylase GGP, of which the coding gene is located adjacent to the gene that encodes the GG-synthesizing enzyme, is supposed to perform the GG degradation function. In the present study, a GGP homolog from the salt-tolerant M. salinexigens ZYF650T was characterized. The recombinant GGP catalyzed GG decomposition via a two-step process of phosphorolysis and hydrolysis in vitro and exhibited high substrate specificity toward GG. The activity of GGP was enhanced by inorganic salts at low concentrations but significantly inhibited by increasing salt concentrations. While the investigation on the physiological role of GGP in M. salinexigens ZYF650T was limited due to the failed induction of GG production, the heterologous expression of ggp in the living cells of the GG-producing cyanobacterium Synechocystis sp. PCC 6803 significantly reduced the salt-induced GG accumulation. Together, these data suggested that GGP may represent a novel pathway of microbial GG catabolism. Key points: • GGP catalyzes GG degradation by a process of phosphorolysis and hydrolysis • GGP-catalyzed GG degradation is different from GGHA-based GG degradation • GGP represents a potential novel pathway of microbial GG catabolism [ABSTRACT FROM AUTHOR]

Extracellular vesicles are small (approximately 50 to 250 nm in diameter), membrane-bound structures that are released by cells into their surrounding environment. Heterogeneous populations of vesicles are abundant in the global oceans, and they likely play a number of ecological roles in these microbially dominated ecosystems. Here, we examine how vesicle production and size vary among different strains of cultivated marine microbes as well as explore the degree to which this is influenced by key environmental variables. We show that both vesicle production rates and vesicle sizes significantly differ among cultures of marine Proteobacteria, Cyanobacteria, and Bacteroidetes. Further, these properties vary within individual strains as a function of differences in environmental conditions, such as nutrients, temperature, and light irradiance. Thus, both community composition and the local abiotic environment are expected to modulate the production and standing stock of vesicles in the oceans. Examining samples from the oligotrophic North Pacific Gyre, we show depth-dependent changes in the abundance of vesicle-like particles in the upper water column in a manner that is broadly consistent with culture observations: the highest vesicle abundances are found near the surface, where the light irradiances and the temperatures are the greatest, and they then decrease with depth. This work represents the beginnings of a quantitative framework for describing extracellular vesicle dynamics in the oceans, which is essential as we begin to incorporate vesicles into our ecological and biogeochemical understanding of marine ecosystems. IMPORTANCE Bacteria release extracellular vesicles that contain a wide variety of cellular compounds, including lipids, proteins, nucleic acids, and small molecules, into their surrounding environment. These structures are found in diverse microbial habitats, including the oceans, where their distributions vary throughout the water column and likely affect their functional impacts within microbial ecosystems. Using a quantitative analysis of marine microbial cultures, we show that bacterial vesicle production in the oceans is shaped by a combination of biotic and abiotic factors. Different marine taxa release vesicles at rates that vary across an order of magnitude, and vesicle production changes dynamically as a function of environmental conditions. These findings represent a step forward in our understanding of bacterial extracellular vesicle production dynamics and provide a basis for the quantitative exploration of the factors that shape vesicle dynamics in natural ecosystems. [ABSTRACT FROM AUTHOR]

Gram-negative, rod-shaped, and aerobic bacteria designated chi1T and chi5T were isolated from the root of Suaeda japonica Makino. Phylogenetics utilizing 16S rRNA and whole-genome sequences of the two novel strains chi1T and chi5T confirmed that they were related to the genera Marinobacter and Wenyingzhuangia, respectively. For the novel strains chi1T and chi5T, the digital DNA–DNA hybridization values (19–20% and 22.1–36.6%, respectively) and average nucleotide identity values (74.4–76.5% and 79.1–88.9%, respectively) fell within the range for the genera Marinobacter and Wenyingzhuangia, respectively. Pangenome analyses of the novel strains chi1T and chi5T revealed 357 and 368 singletons genes, respectively. The genomic DNA G + C contents of the strains chi1T and chi5T were 57.2% and 31.5%, respectively. The major fatty acids of strain chi1T were C12:0, C16:0, and summed feature 3 (C16:1 ω6c and/or C16:1ω7c), while those of the strain chi5T were iso-C15:0 3OH, iso-C17:0 3OH, and iso-C15:0. Data from the phylogenetic, phylogenomic, pangenome, genomic, physiological, and biochemical analyses indicated that the novel strains were distinct. Therefore, we propose the names Marinobacter suadae (type strain chi1T = KACC 23259T = TBRC 17652T) and Wenyingzhangia gilva (type strain chi5T = KACC 23262T = TBRC 17900T) for the studied bacterial strains.

Azo dye-containing sewage is commonly detected at high salinity, temperature and pH. In this study, a halo-thermoalkalophilic azo dye decolorization consortium was enriched and named "consortium HL". Consortium HL which was dominated by Marinobacter (84.30%), Desulfocurvibacter (1.89%), and Pseudomonas (1.85%), was able to completely decolorize Direct Blue 5B (DB5) during incubation with the material at 5% salinity, 50 °C, and pH 9 for 30 h. The decolorization mechanism was proposed based on combined metagenomic analysis, GC‒MS, and enzymatic activity detection. The action of the consortium HL showed great tolerance to variations in salinity, temperature and pH. A phytotoxicity study indicated that the metabolic intermediates showed no significant toxicity to the generation of Cucumis sativus and Oryza sativa seeds. This study, in which azo dye decolorization and degradation under high-salt, high-temperature and high-alkalinity conditions were investigated and deeply analyzed by metagenomic information, is the first report regarding the ability of Marinobacter to decolorize azo dyes at high temperatures. [Display omitted] • Consortium HL was detected able to decolorize azo dye at high salinity, pH value and temperature. • Marinobacter was first discovered to play a key role under multi-extreme condition. • Decolorization mechanism was proposed by the combination of metagenomic analysis and GC-MS. • The functional enzyme contained in consortium HL was deeply analyzed. [ABSTRACT FROM AUTHOR]

The bacterium Marinobacter sp. RI1 was isolated from surface seawater through an enrichment culture using low-density polyethylene as the sole carbon source. Herein, we report its complete genomic sequence. Genomic annotation revealed that the strain harbors the genes encoding enzymes involved in alkane degradation, thus supporting polyethylene degradation., Competing Interests: The authors declare no conflict of interest.

During the exploitation of oil reservoirs with highly mineralized waters, water separated from oil is pumped back into the reservoirs, which in some cases leads to an increase in ambient salinity and limits the possibility of application of biotechnologies for the enhancement of oil recovery. The microbial community of such oil fields has been relatively scarcely studied. Two strains of halophilic hydrocarbon-oxidizing bacteria, Halomonas titanicae TAT1 and Marinobacter lutaoensis KAZ22 were isolated from oil fields with mineralized formation water. Their physiological and genomic characteristics determining their presence in these habitats and the possibility of biotechnological application were investigated. The strains H. titanicae TAT1 and M. lutaoensis KAZ22 grew aerobically on crude oil in the temperature range from 4 to 42 and from 22 to 55°C, respectively, and had growth optima at salinity levels of 2–12 and 5–10% NaCl (wt/vol). Phenomenological observations of the degradation of oil n-alkanes were confirmed by the detection of three genes (alkB1, alkB2, and almA) encoding alkane1-monooxygenases in the genome of strain KAZ22 and of one alkB gene in the genome of strain TAT1. In the genome of the H. titanicae TAT1, all the genes for formation of osmoprotectants betaine, ectoine, and hydroxyectoine were annotated, and in the genome of M. lutaoensis KAZ22, the genes for the formation of ectoine and hydroxyectoine were annotated. The growth of strain KAZ22 on oil was accompanied by a decrease in the surface tension of the medium by more than 20 mN/m. Due to the absence of the nirK nitrite reductase gene, anaerobic growth of strain H. titanicae TAT1 in a medium with acetate and nitrate resulted in accumulation of ~100 mg/L of nitrite, which can inhibit the growth of sulfidogens. Considering the biological features of the strains and the results of genome analysis, injection of nitrate and strain H. titanicae TAT1 can be recommended for bioaugmentation of oil reservoirs with mineralized formation waters to suppress corrosion and decrease sulfide content, and injection of M. lutaoensis KAZ22, for remediation of oil pollution and increasing oil recovery from reservoirs. [ABSTRACT FROM AUTHOR]

Marinobacter is a genus belonging to the class Gammaproteobacteria and the family Alteromonadaceae. This genus is a Gram-negative bacterium which can be found in a wide range of marine and saline water environments. Here, we present the genome sequence of Marinobacter sp. strain CA1 that was isolated from the indigenous diatom found in the whiteleg shrimp, Penaeus vannamei (Bonne 1931) pond in Malaysia. Genome sequencing was done using Pacbio and Illumina sequencing platforms. De novo hybrid assembly based on Pacbio long reads and high quality Illumina short reads yielded a complete circular chromosome with 4.7 M base pair (bp) in size. This genome was submitted to Genbank, NCBI database and can be accessed under accession number: NZ_CP071785 and the BioProject acession number PRJNA710741. This data could be useful for other studies on microalgae and bacteria interaction, and comparative genomics analysis of other Marinobacter species.

The aim of this study was to perform an in silico analysis of the available whole-genome sequencing data to detect syntenic genomic islands (GIs) having homology to Salmonella genomic island 1 (SGI1), analyze the genetic variations of their backbone, and determine their relatedness. Eighty-nine non-redundant SGI1-related elements (SGI1-REs) were identified among gamma-proteobacteria. With the inclusion of the thirty-seven backbones characterized to date, seven clusters were identified based on integrase homology: SGI1, PGI1, PGI2, AGI1 clusters, and clusters 5, 6, and 7 composed of GIs mainly harbored by waterborne or marine bacteria, such as Vibrio , Shewanella , Halomonas , Idiomarina , Marinobacter , and Pseudohongiella. The integrase genes and the backbones of SGI1-REs from clusters 6 and 7, and from PGI1, PGI2, and AGI1 clusters differed significantly from those of the SGI1 cluster, suggesting a different ancestor. All backbones consisted of two parts: the part from attL to the origin of transfer (oriT) harbored the DNA recombination, transfer, and mobilization genes, and the part from oriT to attR differed among the clusters. The diversity of SGI1-REs resulted from the recombination events between GIs of the same or other families. The oriT appeared to be a high recombination site. The multi-drug resistant (MDR) region was located upstream of the resolvase gene. However, most SGI1-REs in Vibrio , Shewanella , and marine bacteria did not harbor any MDR region. These strains could constitute a reservoir of SGI1-REs that could be potential ancestors of SGI1-REs encountered in pathogenic bacteria. Furthermore, four SGI1-REs did not harbor a resolvase gene and therefore could not acquire an integron. The presence of mobilization genes and AcaCD binding sites indicated that their conjugative transfer could occur with helper plasmids. The plasticity of SGI1-REs contributes to bacterial adaptation and evolution. We propose a more relevant classification to categorize SGI1-REs into different clusters based on their integrase gene similarity. [ABSTRACT FROM AUTHOR]

Phaeocystis globosa (P. globosa) is one of the dominant algae during harmful algal blooms (HABs) in coastal regions of Southern China. P. globosa exhibits complex heteromorphic life cycles that could switch between solitary cells and colonies. The ecological success of P. globosa has been attributed to its colony formation, although underlying mechanisms remain unknown. Here, we investigated different bacterial communities associated with P. globosa colonies and their influence on colony formation of two P. globosa strains isolated from coastal waters of Guangxi (GX) and Shantou (ST). Eight operational taxonomic units (OTUs) were observed in ST co-cultures and were identified as biomarkers based on Linear discriminant analysis Effect Size (LEfSe) analysis, while seven biomarkers were identified in P. globosa GX co-cultures. Bacterial communities associated with the P. globosa GX were more diverse than those of the ST strain. The most dominant phylum in the two co-cultures was Proteobacteria, within which Marinobacter was the most abundant genus in both GX and ST co-cultures. Bacteroidota were only observed in the GX co-cultures and Planctomycetota were only observed in the ST co-cultures. Co-culture experiments revealed that P. globosa colony formation was not influenced by low and medium cell densities of Marinobacter sp. GS7, but was inhibited by high cell densities of Marinobacter sp. GS7. Overall, these results indicated that the associated bacteria are selected by different P. globosa strains, which may affect the colony formation and development of P. globosa. [ABSTRACT FROM AUTHOR]

The present study was conducted to reveal specific bacterial consortium belong to same genus capable of mineralizing petroleum hydrocarbons and also act as a valid indicator to locate the oil reservoir in Red Sea, Saudi Arabia. The study focused on area consist of hydrocarbons in briny water and sediment. The sites included Port Sudan Deep, Suakin Deep, Hatiba Deep, and Brian salt in the Red Sea, Saudi Arabia. The concept of the study is to identify crude oil reservoir using the presence of hydrocarbon degrading bacterial strains. The Marinobacter strains isolated were grown in different media such as marine broth with crude oil, tryptic soy agar and mineral salt medium with phenanthrene as sole carbon source at 40 g/L of NaCl concentration. The strains present in hydrocarbon reservoirs of different deeps were isolated and identified as Marinobacter hydrocarbonoclasticus strain MAM1 (MF716467), Marinobacter sp. strain MAM2 (MF716468) and Marinobacter hydrocarbonoclasticus strain MAM3 (MF716469). Marinobacter consortium was pertained by the mixture of the above strains (MAM1, MAM2 and MAM3) from different deep samples. The consortium potentially utilized PAHs (polycyclic aromatic hydrocarbons) such as phenanthrene (PHN) and pyrene (PY). The consortium degraded 72 ± 1.5% of PHN at 1500 mg/L concentration in 16 days under saline condition (4%). The degradation of PY (300 mg/L) by the consortium was 86 ± 1.1% in 12 days under saline condition (4%). Also the presence of Marinobacter strains in the deep water samples and crude oil drilling rig (core) samples, confirmed the relationship between the bacterial strains and oil reservoir. Thus the study confirmed Marinobacter can be used as a potential indicator strain in different deeps at Red Sea to identify the crude oil reservoir. [ABSTRACT FROM AUTHOR]

Autotrophic bacteria utilizing Fe(II) as their energy and electron sources for growth affect multiple biogeochemical cycles. Some chemoheterotrophic bacteria have also been considered to exhibit an Fe(II) oxidation phenotype. For example, several Marinobacter strains have been reported to oxidize Fe(II) based on formation of oxidized iron bands in semi-solid gradient tubes that produce opposing concentration gradients of Fe(II) and oxygen. While gradient tubes are a simple and visually compelling method to test for Fe(II) oxidation, this method alone cannot confirm if, and to what extent, Fe(II) oxidation is linked to metabolism in chemoheterotrophic bacteria. Here we probe the possibility of protein-mediated and metabolic by-product-mediated Fe(II) oxidation in Marinobacter subterrani JG233, a chemoheterotroph previously proposed to oxidize Fe(II). Results from conditional and mutant studies, along with measurements of Fe(II) oxidation rates, suggest M. subterrani is unlikely to facilitate Fe(II) oxidation under microaerobic conditions. We conclude that the Fe(II) oxidation phenotype observed in gradient tubes inoculated with M. subterrani JG233 is a result of oligo-heterotrophic activity, shifting the location where oxygen dependent chemical Fe(II) oxidation occurs, rather than a biologically mediated process. [ABSTRACT FROM AUTHOR]

Phaeocystis globosa (P. globosa) is one of the dominant algae during harmful algal blooms (HABs) in coastal regions of Southern China. P. globosa exhibits complex heteromorphic life cycles that could switch between solitary cells and colonies. The ecological success of P. globosa has been attributed to its colony formation, although underlying mechanisms remain unknown. Here, we investigated different bacterial communities associated with P. globosa colonies and their influence on colony formation of two P. globosa strains isolated from coastal waters of Guangxi (GX) and Shantou (ST). Eight operational taxonomic units (OTUs) were observed in ST co-cultures and were identified as biomarkers based on Linear discriminant analysis Effect Size (LEfSe) analysis, while seven biomarkers were identified in P. globosa GX co-cultures. Bacterial communities associated with the P. globosa GX were more diverse than those of the ST strain. The most dominant phylum in the two co-cultures was Proteobacteria, within which Marinobacter was the most abundant genus in both GX and ST co-cultures. Bacteroidota were only observed in the GX co-cultures and Planctomycetota were only observed in the ST co-cultures. Co-culture experiments revealed that P. globosa colony formation was not influenced by low and medium cell densities of Marinobacter sp. GS7, but was inhibited by high cell densities of Marinobacter sp. GS7. Overall, these results indicated that the associated bacteria are selected by different P. globosa strains, which may affect the colony formation and development of P. globosa.

Marinobacter spp. are opportunitrophs with a broad metabolic range including interactions with metals and electrodes. Marinobacter atlanticus strain CP1 was previously isolated from a cathode biofilm microbial community enriched from a sediment microbial fuel cell. Like other Marinobacter spp., M. atlanticus generates small amounts of electrical current when grown as a biofilm on an electrode, which is enhanced by the addition of redox mediators. However, the molecular mechanism resulting in extracellular electron transfer is unknown. Here, RNA-sequencing was used to determine changes in gene expression in electrode-attached and planktonic cells of M. atlanticus when grown at electrode potentials that enable current production (310 and 510 mV vs. SHE) compared to a potential that enables electron uptake (160 mV). Cells grown at current-producing potentials had increased expression of genes for molybdate transport, regardless of planktonic or attached lifestyle. Electrode-attached cells at current-producing potentials showed increased expression of the major export protein for the type VI secretion system. Growth at 160 mV resulted in an increase in expression of genes related to stress response and DNA repair including both RecBCD and the LexA/RecA regulatory network, as well as genes for copper homeostasis. Changes in expression of proteins with PEP C-terminal extracellular export motifs suggests that M. atlanticus is remodeling the biofilm matrix in response to electrode potential. These results improve our understanding of the physiological adaptations required for M. atlanticus growth on electrodes, and suggest a role for metal acquisition, either as a requirement for metal cofactors of redox proteins or as a possible electron shuttling mechanism.

Marinobacter is the abundant and important algal-associated and hydrocarbon biodegradation bacteria in the ocean. However, little knowledge about their phages has been reported. Here, a novel siphovirus, vB_MalS-PS3, infecting Marinobacter algicola DG893(T), was isolated from the surface waters of the western Pacific Ocean. Transmission electron microscopy (TEM) indicated that vB_MalS-PS3 has the morphology of siphoviruses. VB_MalS-PS3 was stable from −20 to 55°C, and with the latent and rise periods of about 80 and 10 min, respectively. The genome sequence of VB_MalS-PS3 contains a linear, double-strand 42,168-bp DNA molecule with a G + C content of 56.23% and 54 putative open reading frames (ORFs). Nineteen conserved domains were predicted by BLASTp in NCBI. We found that vB_MalS-PS3 represent an understudied viral group with only one known isolate. The phylogenetic tree based on the amino acid sequences of whole genomes revealed that vB_MalS-PS3 has a distant evolutionary relationship with other siphoviruses, and can be grouped into a novel viral genus cluster with six uncultured assembled viral genomes from metagenomics, named here as Marinovirus. This study of the Marinobacter phage vB_MalS-PS3 genome enriched the genetic database of marine bacteriophages, in addition, will provide useful information for further research on the interaction between Marinobacter phages and their hosts, and their relationship with algal blooms and hydrocarbon biodegradation in the ocean.

Marinobacter is the abundant and important algal-associated and hydrocarbon biodegradation bacteria in the ocean. However, little knowledge about their phages has been reported. Here, a novel siphovirus, vB_MalS-PS3, infecting Marinobacter algicola DG893(T), was isolated from the surface waters of the western Pacific Ocean. Transmission electron microscopy (TEM) indicated that vB_MalS-PS3 has the morphology of siphoviruses. VB_MalS-PS3 was stable from −20 to 55°C, and with the latent and rise periods of about 80 and 10 min, respectively. The genome sequence of VB_MalS-PS3 contains a linear, double-strand 42,168-bp DNA molecule with a G + C content of 56.23% and 54 putative open reading frames (ORFs). Nineteen conserved domains were predicted by BLASTp in NCBI. We found that vB_MalS-PS3 represent an understudied viral group with only one known isolate. The phylogenetic tree based on the amino acid sequences of whole genomes revealed that vB_MalS-PS3 has a distant evolutionary relationship with other siphoviruses, and can be grouped into a novel viral genus cluster with six uncultured assembled viral genomes from metagenomics, named here as Marinovirus. This study of the Marinobacter phage vB_MalS-PS3 genome enriched the genetic database of marine bacteriophages, in addition, will provide useful information for further research on the interaction between Marinobacter phages and their hosts, and their relationship with algal blooms and hydrocarbon biodegradation in the ocean. [ABSTRACT FROM AUTHOR]

Abstract Background In comparison to synthetically derived surfactants, biosurfactants produced from microbial culture are generally regarded by industry as being more sustainable and possess lower toxicity. One major class of biosurfactants are rhamnolipids primarily produced by Pseudomonas aeruginosa. Due to its pathogenicity rhamnolipid synthesis by this species is viewed as being commercially nonviable, as such there is a significant focus to identify alternative producers of rhamnolipids. Results To achieve this, we phenotypically screened marine bacteria for biosurfactant production resulting in the identification of rhamnolipid biosynthesis in a species belonging to the Marinobacter genus. Preliminary screening showed the strain to reduce surface tension of cell-free supernatant to 31.0 mN m−1. A full-factorial design was carried out to assess the effects of pH and sea salt concentration for optimising biosurfactant production. When cultured in optimised media Marinobacter sp. MCTG107b produced 740 ± 28.3 mg L−1 of biosurfactant after 96 h of growth. Characterisation of this biosurfactant using both HPLC–MS and tandem MS showed it to be a mixture of different rhamnolipids, with di-rhamnolipid, Rha-Rha-C10-C10 being the most predominant congener. The strain exhibited no pathogenicity when tested using the Galleria mellonella infection model. Conclusions This study expands the paradigm of rhamnolipid biosynthesis to a new genus of bacterium from the marine environment. Rhamnolipids produced from Marinobacter have prospects for industrial application due to their potential to be synthesised from cheap, renewable feed stocks and significantly reduced pathogenicity compared to P. aeruginosa strains.

Abstract Background The group of the so-called obligate hydrocarbonoclastic bacteria (OHCB) are marine microorganisms affiliated with the genera Alcanivorax, Cycloclasticus, Oleiphilus and Thalassolituus. This small group plays a major role in oil-bioremediation in marine ecosystems. Marinobacter and Planomicrobium are considered related to this group. The OHCB are claimed to be obligate to hydrocarbon nutrition. This study argues against this claim. Results Four Alcanivorax species, three Marinobacter species and Planomicrobium okeanokoites from the Arabian/Persian Gulf proved to be not obligate to hydrocarbon nutrition. Although the eight strains grew on crude oil, n-octadecane and phenanthrene as sole carbon substrates, their growth was weaker than on certain nonhydrocarbon, organic compounds viz. peptone, glutamic acid, pyruvic acid, sucrose, mannose and others. Glucose and lactose failed to support the growth of seven of the eight tested strains. Mannose was utilized by five and sucrose by six strains. The well-known intermediate metabolite; pyruvic acid was utilized by all the eight strains, and lactic acid by five strains. In batch cultures, all the tested species consumed higher proportions of peptone than of n-alkanes and phenanthrene. When peptone and crude oil were provided together into the medium, the OHCB started to consume peptone first, and the enriched bacterial populations consumed oil effectively. Added nonhydrocarbon substrates biostimulated oil-consumption by all OHCB species. Conclusion The tested OHCB species are not obligate hydrocarbon-utilizers. This provides them with the merit of survival, should their marine ecosystems become oil- or hydrocarbon-free. The fact that conventional, organic substrates biostimulated hydrocarbon-consumption by the tested bacterial species confirms the facultative nature of those organisms and is interesting from the practical point of view.

The biosynthesis of lipid-based biofuels is an important aspect of developing sustainable alternatives to conventional oils derived from fossil fuel reserves. Many biosynthetic approaches to biodiesel fuels and oils involve fatty acid derivatives as a precursor, and thioesterases have been employed in various strategies to increase fatty acid pools. Thioesterases liberate fatty acids from fatty acyl-coenzyme A or fatty acyl-acyl carrier protein substrates. The role played by thioesterases has not been extensively studied in model bacteria that accumulate elevated levels of biological oils based on fatty acid precursors. In this report, two primary thioesterases from the wax ester accumulating bacterium Marinobacter aquaeolei VT8 were heterologously expressed, isolated and characterized. These genes were further analyzed at the transcriptional level in the native bacterium during wax ester accumulation, and their genes were disrupted to determine the effect these changes had on wax ester levels. Combined, these results indicate that these two thioesterases do not play an integral role in wax ester accumulation in this natural lipid-accumulating model bacterium. [ABSTRACT FROM AUTHOR]

As diazotrophic cyanobacteria of tremendous biomass, Trichodesmium continuously provide a nitrogen source for carbon-fixing cyanobacteria and drive the generation of primary productivity in marine environments. However, ocean iron deficiencies limit growth and metabolism of Trichodesmium . Recent studies have shown the co-occurrence of Trichodesmium and siderophore-producing Synechococcus in iron-deficient oceans, but whether siderophores secreted by Synechococcus can be used by Trichodesmium to adapt to iron deficiency is not clear. We constructed a mutant Synechococcus strain unable to produce siderophores to explore this issue. Synechococcus filtrates with or without siderophores were added into a Trichodesmium microbial consortium consisting of Trichodesmium erythraeum IMS 101 as the dominant microbe with chronic iron deficiency. By analyzing the physiological phenotype, metagenome, and metatranscriptome, we investigated the interactions between the nitrogen-fixing cyanobacterium Tricodesmium and siderophore-producing cyanobacterium Synechococcus under conditions of iron deficiency. The results indicated that siderophores secreted by Synechococcus are likely to chelate with free iron in the culture medium of the Trichodesmium consortium, reducing the concentration of bioavailable iron and posing greater challenges to the absorption of iron by Trichodesmium . These findings revealed the characteristics of iron-competitive utilization between diazotrophic cyanobacteria and siderophore-producing cyanobacteria, as well as potential interactions, and provide a scientific basis for understanding the regulatory effects of nutrient limitation on marine primary productivity., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

A Gram-stain-negative, aerobic, rod-shaped and halotolerant bacterium, designated as strain ASW11-75 T , was isolated from intertidal sediments in Qingdao, PR China, and identified using a polyphasic taxonomic approach. Growth of strain ASW11-75 T occurred at 10-45 °C (optimum, 37 °C), pH 6.5-9.0 (optimum, pH 8.0) and 0.5-18.0 % NaCl concentrations (optimum, 2.5 %). Phylogenetic analyses based on 16S rRNA gene sequences and 1179 single-copy orthologous clusters indicated that strain ASW11-75 T is affiliated with the genus Marinobacter . Strain ASW11-75 T showed highest 16S rRNA gene sequence similarity to ' Marinobacter arenosus ' CAU 1620 T (98.5 %). The digital DNA-DNA hybridization and average nucleotide identity values between strain ASW11-75 T and its closely related strains ( Marinobacter salarius R9SW1 T , Marinobacter similis A3d10 T , ' Marinobacter arenosus ' CAU 1620 T , Marinobacter sediminum R65 T , Marinobacter salinus Hb8 T , Marinobacter alexandrii LZ-8 T and Marinobacter nauticus ATCC 49840 T ) were 19.8-24.5 % and 76.6-80.7 %, respectively. The predominant cellular fatty acids were C 16 : 0 , C 18 : 1  ω 9 c and C 16 : 0  N alcohol. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminophospholipid and two unidentified lipids. The major isoprenoid quinone was ubiquinone-9. The genomic DNA G+C content was 62.2 mol%. Based on genomic and gene function analysis, strain ASW11-75 T had lower protein isoelectric points with higher ratios of acidic residues to basic residues and possessed genes related to ion transport and organic osmoprotectant uptake, implying its potential tolerance to salt. The results of polyphasic characterization indicated strain ASW11-75 T represents a novel Marinobacter species, for which the name Marinobacter qingdaonensis sp. nov. with the type strain ASW11-75 T is proposed. The type strain is ASW11-75 T (=KCTC 82497 T =MCCC 1K05587 T ).

A novel moderately halophilic, Gram-stain-negative and facultatively anaerobic bacterium, designated as strain TBZ242 T , 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 TBZ242 T belonged to the genus Marinobacter , showing the highest similarities to Marinobacter algicola DG893 T (98.8 %), Marinobacter vulgaris F01 T (98.8 %), Marinobacter salarius R9SW1 T (98.5 %), Marinobacter panjinensis PJ-16 T (98.4 %), Marinobacter orientalis W62 T (98.0 %) and Marinobacter denitrificans JB2H27 T (98.0 %). The 16S rRNA and core-genome phylogenetic trees showed that strain TBZ242 T 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 TBZ242 T and the type strains of the related species of Marinobacter were ≤85.0 and 28.6 %, respectively, confirming that strain TBZ242 T represents a distinct species. The major cellular fatty acids of strain TBZ242 T were C 16 : 0 and C 16 : 1  ω 7 c /C 16 : 1  ω6 c and the quinone was ubiquinone Q-9. The genomic DNA G+C content of strain TBZ242 T is 57.2 mol%. Based on phenotypic, chemotaxonomic and genomic data, strain TBZ242 T represents a novel species within the genus Marinobacter , for which the name Marinobacter azerbaijanicus sp. nov. is proposed. The type strain is TBZ242 T (= CECT 30649 T = IBRC-M 11466 T ). 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.

Las lipasas de la familia I son reconocidas a nivel industrial por sus actividades catalíticas de esterificación, interesterificación y transesterificación. En esta investigación se caracterizó por análisis in silico a la lipasa de Marinobacter sp. LB aislado de las Salinas de Pilluana, San Martín. Con tal finalidad, se amplificó el gen lip mediante la reacción en cadena de la polimerasa (PCR) de punto final y la secuencia nucleotídica fue analizada in silico. Se elucidó la estructura terciaria empleando como molde a la lipasa 1EX9 de Pseudomonas aeruginosa PAO1 y se ejecutó el acoplamiento molecular con tres sustratos. El gen lip presentó 927 pb y la proteína madura, 284 aminoácidos. La lipasa posee un peso molecular de 29.99 kDa y un pI de 8.89. Asimismo, se identificaron residuos Ser78, Asp229 e His251, típicos de la triada catalítica de una lipasa de la familia I. Además, se evidenciaron once α-hélices periféricas y siete láminas-β internas. La región del bolsillo de unión y su afinidad por lípidos fue demostrada realizando acoplamientos moleculares con trioctanoina, tributirina y trioleina, con energías de -314.28, -248.11 y -215.44 kcal/mol, respectivamente; siendo los aminoácidos de interacción Asn167, Lys106, Trp172, Thr164, Ala179. En conclusión, la estructura tridimensional de la lipasa de Marinobacter sp. LB fue construida por modelamiento homólogo y validada en base a la calidad estereoquímica y el entorno de sus aminoácidos; mientras que, los análisis de acoplamiento con sustratos de lipasas permitieron evidenciar los aminoácidos que participan en el bolsillo de unión.

Abstract With the close relationship between saline environments and industry, polycyclic aromatic hydrocarbons (PAHs) accumulate in saline/hypersaline environments. Therefore, PAHs degradation by halotolerant/halophilic bacteria has received increasing attention. In this study, the metabolic pathway of phenanthrene degradation by halophilic consortium CY-1 was first studied which showed a single upstream pathway initiated by dioxygenation at the C1 and C2 positions, and at several downstream pathways, including the catechol pathway, gentisic acid pathway and protocatechuic acid pathway. The effects of salinity on the community structure and expression of catabolic genes were further studied by a combination of high-throughput sequencing, catabolic gene clone library and real-time PCR. Pure cultures were also isolated from consortium CY-1 to investigate the contribution made by different microbes in the PAH-degrading process. Marinobacter is the dominant genus that contributed to the upstream degradation of phenanthrene especially in high salt content. Genus Halomonas made a great contribution in transforming intermediates in the subsequent degradation of catechol by using catechol 1,2-dioxygenase (C12O). Other microbes were predicted to be mediating bacteria that were able to utilize intermediates via different downstream pathways. Salinity was investigated to have negative effects on both microbial diversity and activity of consortium CY-1 and consortium CY-1 was found with a high degree of functional redundancy in saline environments.

Although interactions between microalgae and bacteria are observed in both natural environment and the laboratory, the modalities of coexistence of bacteria inside microalgae phycospheres in laboratory cultures are mostly unknown. Here, we focused on well-controlled cultures of the model green picoalga Ostreococcus tauri and the most abundant member of its phycosphere, Marinobacter algicola. The prevalence of M. algicola in O. tauri cultures raises questions about how this bacterium maintains itself under laboratory conditions in the microalga culture. The results showed that M. algicola did not promote O. tauri growth in the absence of vitamin B12 while M. algicola depended on O. tauri to grow in synthetic medium, most likely to obtain organic carbon sources provided by the microalgae. M. algicola grew on a range of lipids, including triacylglycerols that are known to be produced by O. tauri in culture during abiotic stress. Genomic screening revealed the absence of genes of two particular modes of quorum-sensing in Marinobacter genomes which refutes the idea that these bacterial communication systems operate in this genus. To date, the ‘opportunistic’ behaviour of M. algicola in the laboratory is limited to several phytoplanktonic species including Chlorophyta such as O. tauri. This would indicate a preferential occurrence of M. algicola in association with these specific microalgae under optimum laboratory conditions.

Homoacetogens are efficient CO2 fixing bacteria using H2 as electron donor to produce acetate. These organisms can be enriched at the biocathode of microbial electrosynthesis (MES) for electricity-driven CO2 reduction to acetate. Studies exploring homoacetogens in MES are mainly conducted using pure or mix-culture anaerobic inocula from samples with standard environmental conditions. Extreme marine environments host unique microbial communities including homoacetogens that may have unique capabilities due to their adaptation to harsh environmental conditions. Anaerobic deep-sea brine pools are hypersaline and metalliferous environments and homoacetogens can be expected to live in these environments due to their remarkable metabolic flexibility and energy-efficient biosynthesis. However, brine pools have never been explored as inocula for the enrichment of homacetogens in MES. Here we used the saline water from a Red Sea brine pool as inoculum for the enrichment of halophilic homoacetogens at the biocathode (−1 V vs. Ag/AgCl) of MES. Volatile fatty acids, especially acetate, along with hydrogen gas were produced in MES systems operated at 25 and 10% salinity. Acetate concentration increased when MES was operated at a lower salinity ∼3.5%, representing typical seawater salinity. Amplicon sequencing and genome-centric metagenomics of matured cathodic biofilm showed dominance of the genus Marinobacter and phylum Firmicutes at all tested salinities. Seventeen high-quality draft metagenome-assembled genomes (MAGs) were extracted from the biocathode samples. The recovered MAGs accounted for 87 ± 4% of the quality filtered sequence reads. Genome analysis of the MAGs suggested CO2 fixation via Wood–Ljundahl pathway by members of the phylum Firmicutes and the fixed CO2 was possibly utilized by Marinobacter sp. for growth by consuming O2 escaping from the anode to the cathode for respiration. The enrichment of Marinobacter sp. with homoacetogens was only possible because of the specific cathodic environment in MES. These findings suggest that in organic carbon-limited saline environments, Marinobacter spp. can live in consortia with CO2 fixing bacteria such as homoacetogens, which can provide them with fixed carbon as a source of carbon and energy.

The marine heterotroph, Marinobacter atlanticus strain CP1, was recently isolated from the electroautotrophic Biocathode MCL community, named for the three most abundant members: Marinobacter, an uncharacterized member of the Chromatiaceae, and Labrenzia. Biocathode MCL catalyzes the production of cathodic current coupled to carbon fixation through the activity of the uncharacterized Chromatiaceae, renamed as “Candidatus Tenderia electrophaga,” but the contribution of M. atlanticus is currently unknown. Here, we report on the electrochemical characterization of pure culture M. atlanticus biofilms grown under aerobic conditions and supplemented with succinate as a carbon source at applied potentials ranging from 160 to 510 mV vs. SHE, and on three different electrode materials (graphite, carbon cloth, and indium tin oxide). M. atlanticus was found to produce either cathodic or anodic current that was an order of magnitude lower than that of the Biocathode MCL community depending on the oxygen concentration, applied potential, and electrode material. Cyclic voltammetry, differential pulse voltammetry (DPV), and square wave voltammetry (SWV) were performed to characterize putative redox mediators at the electrode surface; however no definitive redox peaks were observed. No effect on current was observed when genes encoding a putative rubredoxin (ACP86_RS07295), as well as a putative NADH:flavorubredoxin oxidoreductase (ACP86_RS07290), were deleted to evaluate their role in EET. The addition of either riboflavin or excess trace mineral solution increased anodic current by ca. an order of magnitude under the conditions in which Biocathode MCL is typically grown. These results indicate that M. atlanticus has a non-negligible ability to utilize electrodes as an electron acceptor, which can be enhanced by the presence of excess trace minerals already available in the growth medium. The ability of M. atlanticus to utilize trace minerals as electron shuttles with extracellular electron acceptors may have broader implications for its natural role in biogeochemical cycling.

Marinobacter nanhaiticus D15-8W is known for its ability to metabolize polycyclic aromatic hydrocarbons. Here, we report the complete circular genome sequence of this strain to be 5,336,660 bp (G + C content, 58.6%; 4,869 protein-coding sequences) with one plasmid (69,655 bp)., Competing Interests: Ayako Fukazawa is an employee of Shiseido Co., Ltd.

Here, we report on the development of a genetic system for Marinobacter sp. strain CP1, previously isolated from the Biocathode MCL community and shown to oxidize iron and grow as a cathodic biofilm. Sequence analysis of the small and large subunits of the 16S rRNA gene of CP1, as well as comparison of select conserved proteins, indicate that it is most closely related to Marinobacter adhaerens HP15 and Marinobacter sp. ES.042. In silico DNA–DNA hybridization using the genome-to-genome distance calculator (GGDC) predicts CP1 to be a new species of Marinobacter described here as Marinobacter atlanticus. CP1 is competent for transformation with plasmid DNA using conjugation with Escherichia coli donor strain WM3064 and constitutive expression of green fluorescent protein (GFP) is stable in the absence of antibiotic selection. Targeted double deletion mutagenesis of homologs for the M. aquaeoli fatty acyl-CoA reductase (acrB) and fatty aldehyde reductase (farA) genes resulted in a loss of production of wax esters; however, single deletion mutants for either gene resulted in an increase in total wax esters recovered. Genetic tools presented here for CP1 will enable further exploration of wax ester synthesis for biotechnological applications, as well as furthering our efforts to understand the role of CP1 within the Biocathode MCL community.

Homoacetogens are efficient CO2 fixing bacteria using H2 as electron donor to produce acetate. These organisms can be enriched at the biocathode of microbial electrosynthesis (MES) for electricity-driven CO2 reduction to acetate. Studies exploring homoacetogens in MES are mainly conducted using pure or mix-culture anaerobic inocula from samples with standard environmental conditions. Extreme marine environments host unique microbial communities including homoacetogens that may have unique capabilities due to their adaptation to harsh environmental conditions. Anaerobic deep-sea brine pools are hypersaline and metalliferous environments and homoacetogens can be expected to live in these environments due to their remarkable metabolic flexibility and energy-efficient biosynthesis. However, brine pools have never been explored as inocula for the enrichment of homacetogens in MES. Here we used the saline water from a Red Sea brine pool as inoculum for the enrichment of halophilic homoacetogens at the biocathode (−1 V vs. Ag/AgCl) of MES. Volatile fatty acids, especially acetate, along with hydrogen gas were produced in MES systems operated at 25 and 10% salinity. Acetate concentration increased when MES was operated at a lower salinity ∼3.5%, representing typical seawater salinity. Amplicon sequencing and genome-centric metagenomics of matured cathodic biofilm showed dominance of the genus Marinobacter and phylum Firmicutes at all tested salinities. Seventeen high-quality draft metagenome-assembled genomes (MAGs) were extracted from the biocathode samples. The recovered MAGs accounted for 87 ± 4% of the quality filtered sequence reads. Genome analysis of the MAGs suggested CO2 fixation via Wood–Ljundahl pathway by members of the phylum Firmicutes and the fixed CO2 was possibly utilized by Marinobacter sp. for growth by consuming O2 escaping from the anode to the cathode for respiration. The enrichment of Marinobacter sp. with homoacetogens was only possible because of the specific cathodic environment in MES. These findings suggest that in organic carbon-limited saline environments, Marinobacter spp. can live in consortia with CO2 fixing bacteria such as homoacetogens, which can provide them with fixed carbon as a source of carbon and energy. [ABSTRACT FROM AUTHOR]

Beneficial plant-growth-promoting bacteria (PGPB) have been reasonably applied to rescue crucial issue for agriculture by salinity soil. Observed most of PGPB was found in endophyte, rhizosphere and soil. Indole acetic acid (IAA)-producing bacteria could naturally stimulate and facilitate plant growth. The knowledge of IAA production and content of bacteria resident in the marine environment has been typically insufficient and limited to date. In recent years, unwarrantable intrusions of sea water have been enlarged in the Mekong River Delta of Vietnam, threatening productive rice fields, local fruits, and cash crops. Therefore, finding PGPB in the coastal regions in the Mekong River Delta as a creative resource for sustainable agriculture is necessary and is a prompt challenge. In this study, IAA-producing bacteria from coastal regions of Ben Tre and Tra Vinh Provinces were isolated and adequately identified. Out of 202 bacterial isolates, 10 isolates showed the possible ability to produce IAA from L-tryptophan. These 10 isolates were objectively evaluated the capacity to produce IAA under 5% (w/v) NaCl in King B and marine broths. The results revealed that IAA production decreased in 5% NaCl, even though bacterial growth increased. These 10 IAA-producing bacteria were classified at the species level, Marinobacter hydrocarbonoclasticus, M. pelagius, M. daepoensis, and Mameliella phaeodactyli by 16S rRNA gene analysis. The most IAA producer in King's B broth, the isolate C7, was investigated in more detail. The isolate C7 produced the maximum IAA amount (192.2 ± 1.14 µg/ml) under the presence of 20 g/l yeast extract, 2 g/l of L-tryptophan and 1% NaCl. The isolate C7 was able to grow at 1-17% (w/v) NaCl (optimum, 4%), but not in the absence of NaCl, indicating it is a moderate halophilic bacterium. This study highlighted the considerable ability to produce IAA of marine bacteria, which could be thoughtfully considered to use naturally as biofertilizers to promote plant growth in saline intrusion lands. [ABSTRACT FROM AUTHOR]

Hydrocarbon (HC) pollution is a threat to the marine environment and bioremediation strategies based on microbial degradation have been developed for pollution clean-up. Effectiveness of bioaugmentation, i.e. the addition of suitable HC-degrading microorganisms to the polluted matrix, strongly depends on the metabolic and physiological versatility of cultivable HC-degrading microorganisms and on their adaptation capacity. The aim of this work was to investigate the potential of laboratory enrichment approaches to obtain cultivable HC-degrading bacteria having versatility breadth. Despite we used as inoculum marine samples of different origin and contamination history, and applied different enrichment strategies, we brought into culture 183 hydrocarbonoclastic bacterial strains strongly dominated by only the two genera Alcanivorax and Marinobacter. These isolates, screened for traits related to HC degradation, biostimulation and abiotic stress tolerance, demonstrated nevertheless to have a diverse functional potential, correlated to the adopted enrichment strategy. Although the obtained strains resulted phylogenetically similar, we showed that multiple cultivation approaches enhanced their metabolic diversification with potential benefits for bioaugmentation effectiveness. • Physiological diversity of microbial isolates is needed for bioagumentation set up. • Alcanivorax and Marinobacter are common isolates from HC contaminated environments. • Diverse hydrocarbon enrichment strategies select bacteria with functional versatility. [ABSTRACT FROM AUTHOR]

Bacteria from the genus Marinobacter are ubiquitous throughout the worlds’ oceans as “opportunitrophs” capable of surviving a wide range of conditions, including colonization of surfaces of marine snow and algae. To prevent too many bacteria from occupying this ecological niche simultaneously, some sort of population dependent control must be operative. Here, we show that while Marinobacter do not produce or utilize an acylhomoserine lactone (AHL)-based quorum sensing system, “sibling” colonies of many species of Marinobacter exhibit a form of non-lethal chemical communication that prevents colonies from overrunning each other’s niche space. Evidence suggests that this inhibition is the result of a loss in motility for cells at the colony interfaces. Although not the signal itself, we have identified a protein, glycerophosphoryl diester phosphodiesterase, that is enriched in the inhibition zone between the spreading colonies that may be part of the overall response.

The surface of marine eukaryotic phytoplankton can harbour communities of hydrocarbon-degrading bacteria; however, this algal–bacterial association has, hitherto, been only examined with non-axenic laboratory cultures of micro-algae. In this study, we isolated an operationally-defined community of phytoplankton, of cell size 50–70 μm, from a natural community in sea surface waters of a subarctic region in the northeast Atlantic. Using MiSeq 16S rRNA sequencing, we identified several recognized (Alcanivorax, Marinobacter, Oleispira, Porticoccus, Thalassospira) and putative hydrocarbon degraders (Colwelliaceae, Vibrionaceae) tightly associated with the phytoplankton population. We combined fluorescence in situ hybridisation with flow-cytometry (FISH-Flow) to examine the association of Marinobacter with this natural eukaryotic phytoplankton population. About 1.5% of the phytoplankton population contained tightly associated Marinobacter. The remaining Marinobacter population were loosely associated with either eukaryotic phytoplankton cells or non-chlorophyll particulate material. This work is the first to show the presence of obligate, generalist and putative hydrocarbonoclastic bacteria associated with natural populations of eukaryotic phytoplankton directly from sea surface water samples. It also highlights the suitability of FISH-Flow for future studies to examine the spatial and temporal structure and dynamics of these and other algal–bacterial associations in natural seawater samples.

The application of chemical dispersants during marine oil spills can affect the community composition and activity of marine microorganisms. Several studies have indicated that certain marine hydrocarbon-degrading bacteria, such as Marinobacter spp., can be inhibited by chemical dispersants, resulting in lower abundances and/or reduced biodegradation rates. However, a major knowledge gap exists regarding the mechanisms underlying these physiological effects. Here, we performed comparative proteomics of the Deepwater Horizon isolate Marinobacter sp. TT1 grown under different conditions. Strain TT1 received different carbon sources (pyruvate vs. n-hexadecane) with and without added dispersant (Corexit EC9500A). Additional treatments contained crude oil in the form of a water-accommodated fraction (WAF) or chemically-enhanced WAF (CEWAF; with Corexit). For the first time, we identified the proteins associated with alkane metabolism and alginate biosynthesis in strain TT1, report on its potential for aromatic hydrocarbon biodegradation and present a protein-based proposed metabolism of Corexit components as carbon substrates. Our findings revealed that Corexit exposure affects hydrocarbon metabolism, chemotactic motility, biofilm formation, and induces solvent tolerance mechanisms, like efflux pumps, in strain TT1. This study provides novel insights into dispersant impacts on microbial hydrocarbon degraders that should be taken into consideration for future oil spill response actions.

During marine oil spills, chemical dispersants are used routinely to disperse surface slicks, transferring the hydrocarbon constituents of oil into the aqueous phase. Nonetheless, a comprehensive understanding of how dispersants affect natural populations of hydrocarbon-degrading bacteria, particularly under environmentally relevant conditions, is lacking. We investigated the impacts of the dispersant Corexit EC9500A on the marine hydrocarbon degrader Marinobacter sp. TT1 when pre-adapted to either low n-hexadecane concentrations (starved culture) or high n-hexadecane concentrations (well-fed culture). The growth of previously starved cells was inhibited when exposed to the dispersant, as evidenced by 55% lower cell numbers and 30% lower n-hexadecane biodegradation efficiency compared to cells grown on n-hexadecane alone. Cultures that were well-fed did not exhibit dispersant-induced inhibition of growth or n-hexadecane degradation. In addition, fluorescence microscopy revealed amorphous cell aggregate structures when the starved culture was exposed to dispersants, suggesting that Corexit affected the biofilm formation behavior of starved cells. Our findings indicate that (previous) substrate limitation, resembling oligotrophic open ocean conditions, can impact the response and hydrocarbon-degrading activities of oil-degrading organisms when exposed to Corexit, and highlight the need for further work to better understand the implications of environmental stressors on oil biodegradation and microbial community dynamics.

Background Denitrification is one of the main pathways of the N-cycle, during which nitrate is converted to dinitrogen gas, in four consecutive reactions that are each catalyzed by a different metalloenzyme. One of the intermediate metabolites is nitrous oxide, which has a global warming impact greater then carbon dioxide and which atmospheric concentration has been increasing in the last years. The four denitrification enzymes have been isolated and biochemically characterized from Marinobacter hydrocarbonoclasticus in our lab. Methods Bioinformatic analysis of the M. hydrocarbonoclasticus genome to identify the genes involved in the denitrification pathway. The relative gene expression of the gene encoding the catalytic subunits of those enzymes was analyzed during the growth under microoxic conditions. The consumption of nitrate and nitrite, and the reduction of nitric oxide and nitrous oxide by whole-cells was monitored during anoxic and microoxic growth in the presence of 10 mM sodium nitrate at pH 7.5. Results The bioinformatic analysis shows that genes encoding the enzymes and accessory factors required for each step of the denitrification pathway are clustered together. An unusual feature is the co-existence of genes encoding a q- and a c-type nitric oxide reductase, with only the latter being transcribed at similar levels as the ones encoding the catalytic subunits of the other denitrifying enzymes, when cells are grown in the presence of nitrate under microoxic conditions. Using either a batch- or a closed system, nitrate is completely consumed in the beginning of the growth, with transient formation of nitrite, and whole-cells can reduce nitric oxide and nitrous oxide from mid-exponential phase until being collected (time-point 50 h). Discussion M. hydrocarbonoclasticus cells can reduce nitric and nitrous oxide in vivo, indicating that the four denitrification steps are active. Gene expression profile together with promoter regions analysis indicates the involvement of a cascade regulatory mechanism triggered by FNR-type in response to low oxygen tension, with nitric oxide and nitrate as secondary effectors, through DNR and NarXL, respectively. This global characterization of the denitrification pathway of a strict marine bacterium, contributes to the understanding of the N-cycle and nitrous oxide release in marine environments.

Phytoplankton blooms can cause acute effects on marine ecosystems either due to their production of endogenous toxins or due to their enormous biomass leading to major impacts on local economies and public health. Despite years of effort, the causes of harmful algal blooms (HAB) are still not fully understood. Our hypothesis is that bacteria that produce photoactive siderophores may provide a bioavailable form of iron to commensally associated phytoplankton, which could in turn affect algal growth and bloom dynamics. Here we report a laboratory-based study of binary cultures of the dinoflagellate Lingulodinium polyedrum, a major HAB species, with Marinobacter algicola DG893, a phytoplankton-associated bacterium that produces the photoactive siderophore vibrioferrin. Comparing binary cultures of L. polyedrum with both the wild type and the vibrioferrin minus mutant of M. algicola shows that bacteria are necessary to promote dinoflagellate growth and that this growth promotion effect is at least partially related to the ability of the bacterium to supply bioavailable iron via the siderophore vibrioferrin. These results support the notion of a carbon for iron mutualism in some bacterial-algal interactions.

A complete genome sequence of Marinobacter shengliensis D49 in the class Gamma-proteobacteria was isolated from activated sludge treating landfill leachate. The genome encodes the functional genes for the biosynthesis of ectoine ( ectABC ), a compatible solute for cosmetics. Deciphering the genome helps pave the way for ectoine production by the isolate., Competing Interests: The authors declare no conflict of interest.

A novel halophilic bacterium, strain 71-i T , 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-i T within the genus Marinobacter . The DNA G+C content of this isolate was 57.7 mol%. The major fatty acids were C 16 : 0 and C 16 : 1 ω 7c and/or C 16 : 1  ω6 c . 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-i T (= IBRC M 11023 T = CECT 30160 T = LMG 29252 T ) 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.

The analysis of ribosomal genes has been applied to study microbiomes of two soils of the solonetzic soil complex in the northern Caspian region. These soils—solonetz and quasigleyic chestnut soil—drastically differ in their salinity characteristics. The specificity of the vertical distribution of prokaryotes by the genetic soil horizons from the surface to the depth of 120 cm in these soils is discussed. The differences in the structure of microbiomes in the upper soil horizons can be related to the differences in the vegetation cover of the two soils, whereas the differentiation of microbiomes along the soil profiles is affected by the soil salinization. The solonetz is characterized by a much sharper decrease in the abundance and diversity of microorganisms down the soil profile in comparison with the leached quasigleyic chestnut soil. The total number of prokaryotes is mainly limited by the organic carbon content. In the upper soil horizons, Archaea from the phylum Thaumarchaeota are relatively abundant; their percentage decreases down the soil profiles. In the lower horizons of the solonetz, the genes of Marinobacter bacteria, which are considered marine inhabitants, have been found. It is probable that they persist in the soil since the previous transgression of the Caspian Sea. [ABSTRACT FROM AUTHOR]

Background. Denitrification is one of the main pathways of the N-cycle, during which nitrate is converted to dinitrogen gas, in four consecutive reactions that are each catalyzed by a different metalloenzyme. One of the intermediate metabolites is nitrous oxide, which has a global warming impact greater then carbon dioxide and which atmospheric concentration has been increasing in the last years. The four denitrification enzymes have been isolated and biochemically characterized from Marinobacter hydrocarbonoclasticus in our lab. Methods. Bioinformatic analysis of the M. hydrocarbonoclasticus genome to identify the genes involved in the denitrification pathway. The relative gene expression of the gene encoding the catalytic subunits of those enzymes was analyzed during the growth under microoxic conditions. The consumption of nitrate and nitrite, and the reduction of nitric oxide and nitrous oxide by whole-cells was monitored during anoxic and microoxic growth in the presence of 10 mM sodium nitrate at pH 7.5. Results. The bioinformatic analysis shows that genes encoding the enzymes and accessory factors required for each step of the denitrification pathway are clustered together. An unusual feature is the co-existence of genes encoding a q- and a c-type nitric oxide reductase, with only the latter being transcribed at similar levels as the ones encoding the catalytic subunits of the other denitrifying enzymes, when cells are grown in the presence of nitrate under microoxic conditions. Using either a batch- or a closed system, nitrate is completely consumed in the beginning of the growth, with transient formation of nitrite, and whole-cells can reduce nitric oxide and nitrous oxide from mid-exponential phase until being collected (time-point 50 h). Discussion. M. hydrocarbonoclasticus cells can reduce nitric and nitrous oxide in vivo, indicating that the four denitrification steps are active. Gene expression profile together with promoter regions analysis indicates the involvement of a cascade regulatory mechanism triggered by FNR-type in response to low oxygen tension, with nitric oxide and nitrate as secondary effectors, through DNR and NarXL, respectively. This global characterization of the denitrification pathway of a strict marine bacterium, contributes to the understanding of the N-cycle and nitrous oxide release in marine environments. [ABSTRACT FROM AUTHOR]

Acquisition of ecologically relevant genes is common among ocean bacteria, but whether it has a major impact on genome evolution in marine environments remains unknown. Here, we analyzed the core genomes of 16 phylogenetically diverse and ecologically relevant bacterioplankton lineages, each consisting of up to five genomes varying at the strain level. Statistical approaches identified from each lineage up to ~50 loci showing anomalously high divergence at synonymous sites, which is best explained by recombination with distantly related organisms. The enriched gene categories in these outlier loci match well with the characteristics previously identified as the key phenotypes of these lineages. Examples are antibiotic synthesis and detoxification in Phaeobacter inhibens, exopolysaccharide production in Alteromonas macleodii, hydrocarbon degradation in Marinobacter hydrocarbonoclasticus, and cold adaptation in Pseudoalteromonas haloplanktis. Intriguingly, the outlier loci feature polysaccharide catabolism in Cellulophaga baltica but not in Cellulophaga lytica, consistent with their primary habitat preferences in macroalgae and beach sands, respectively. Likewise, analysis of Prochlorococcus showed that photosynthesis-related genes listed in the outlier loci are found only in the high-light-adapted ecotype and not in the low-light adapted ecotype. These observations strongly suggest that recombination with distant relatives is a key mechanism driving the ecological diversification among marine bacterial lineages. [ABSTRACT FROM AUTHOR]

Antarctic subice environments are diverse, underexplored microbial habitats. Here, we describe the ecophysiology and annotated genome of a Marinobacter strain isolated from a cold, saline, iron-rich subglacial outflow of the Taylor Glacier, Antarctica. This strain (BF04_ CF4) grows fastest at neutral pH (range 6-10), is psychrophilic (range: 0°C-20°C), moderately halophilic (range: 0.8%-15% NaCl) and hosts genes encoding potential low temperature and high salt adaptations. The predicted proteome suggests it utilizes fewer charged amino acids than a mesophilic Marinobacter strain. BF04_ CF4 has increased concentrations of membrane unsaturated fatty acids including palmitoleic (33%) and oleic (27.5%) acids that may help maintain cell membrane fluidity at low temperatures. The genome encodes proteins for compatible solute biosynthesis and transport, which are known to be important for growth in saline environments. Physiological verification of predicted metabolic functions demonstrate BF04 CF4 is capable of denitrification and may facilitate iron oxidation. Our data indicate that strain BF04_ CF4 represents a new Marinobacter species, Marinobacter gelidimuriae sp. nov., that appears well suited for the subglacial environment it was isolated from. Marinobacter species have been isolated from other cold, saline environments in the McMurdo Dry Valleys and permanently cold environments globally suggesting that this lineage is cosmopolitan and ecologically relevant in icy brines. [ABSTRACT FROM AUTHOR]

Marinobacter hydrocarbonoclasticus nitric oxide reductase, c NOR, is an integral membrane protein composed of two subunits with different roles, NorC (electron transfer) and NorB (catalytic) that receives electrons from the soluble cytochrome c 552 and reduces nitric oxide to nitrous oxide in the denitrification pathway. The solvent-exposed domain of NorC, harboring a c -type heme was heterologously produced, along with its physiological electron donor, cytochrome c 552 . These two proteins were spectroscopically characterized and shown to be similar to the native proteins, both being low-spin and Met-His coordinated, with the soluble domain of NorC presenting some additional features of a high-spin heme, which is consistent with the higher solvent accessibility of its heme and weaker coordination of the methionine axial ligand. The electron transfer complex between the two proteins has a 1:1 stoichiometry, and an upper limit for the dissociation constant was estimated by 1 H NMR titration to be 1.2 ± 0.4 μM. Electrochemical techniques were used to characterize the interaction between the proteins, and a model structure of the complex was obtained by molecular docking. The electrochemical observations point to the modulation of the NorC reduction potential by the presence of NorB, tuning its ability to receive electrons from cytochrome c 552 . [ABSTRACT FROM AUTHOR]

The microbial degradation of crude oil stranded on seashores is usually much slower than that of dispersed oil at sea. This is usually attributed to nutrient limitation and higher oil concentrations on beaches than in dispersed plumes, in addition to the low moisture content and transient hypersaline conditions of the upper intertidal and supratidal zones. Here, we investigated the effect of hypersaline conditions, oil concentration, and nutrient limitation on the hydrocarbonoclastic activity. Beach sand, with oil concentrations of 1 and 10 mL/kg, was infiltrated with seawater at salinities of 30, 90, and 160 g/L to 20% saturation, with and without the addition of nutrients. Oil chemistry, 16 S rRNA gene amplicon, and metagenomic sequencing analyses were conducted every 30 days for 180 days. The biodegradation of aromatic hydrocarbons was much slower at higher salinities, while that of alkanes was not noticeably affected, and the addition of nutrients only marginally enhanced the biodegradation of hydrocarbons. The relative abundance and diversity of genera varied substantially with the increase in pore water salinity, whereby halophilic hydrocarbon-degrading microorganisms, particularly in the Marinobacter genus, were significantly abundant only under hypersaline conditions. The enzymes were considerably less abundant at high salinities, mainly for those associated to aromatic hydrocarbon degradation pathways. Consequently, occasional inundation of the upper parts of oiled sandy beaches with seawater to decrease the pore water salinity and reseed the contaminated region with indigenous hydrocarbon degraders, along with the concomitant addition of fertilizers, could be a suitable, non-destructive, and inexpensive response tool for enhancing the biodegradation of beached crude oil, particularly that of the aromatic fraction. [Display omitted] • Hydrocarbonoclastic activity is much slower in beaches relative to dispersed plumes. • Biodegradation of aromatics in sandy beaches is noticeably slower at higher salinity. • Biodegradation of alkanes in sandy beaches is not affected by salinity. • Marinobacter genus were significantly abundant only under hypersaline conditions. • Enzymes associated to aromatic degradation pathways were much less abundant at high salinities. [ABSTRACT FROM AUTHOR]

Enzymes involved in lipid biosynthesis and metabolism play an important role in energy conversion and storage and in the function of structural components such as cell membranes. The fatty aldehyde dehydrogenase (FAldDH) plays a central function in the metabolism of lipid intermediates, oxidizing fatty aldehydes to the corresponding fatty acid and competing with pathways that would further reduce the fatty aldehydes to fatty alcohols or require the fatty aldehydes to produce alkanes. In this report, the genes for four putative FAldDH enzymes from Marinobacter aquaeolei VT8 and an additional enzyme from Acinetobacter baylyi were heterologously expressed in Escherichia coli and shown to display FAldDH activity. Five enzymes (Maqu_0438, Maqu_3316, Maqu_3410, Maqu_3572, and the enzyme reported under RefSeq accession no. WP_004927398) were found to act on aldehydes ranging from acetaldehyde to hexadecanal and also acted on the unsaturated long-chain palmitoleyl and oleyl aldehydes. A comparison of the specificities of these enzymes with various aldehydes is presented. Crystallization trials yielded diffraction-quality crystals of one particular FAldDH (Maqu_3316) from M. aquaeolei VT8. Crystals were independently treated with both the NAD+ cofactor and the aldehyde substrate decanal, revealing specific details of the likely substrate binding pocket for this class of enzymes. A likely model for how catalysis by the enzyme is accomplished is also provided. IMPORTANCE This study provides a comparison of multiple enzymes with the ability to oxidize fatty aldehydes to fatty acids and provides a likely picture of how the fatty aldehyde and NAD+ are bound to the enzyme to facilitate catalysis. Based on the information obtained from this structural analysis and comparisons of specificities for the five enzymes that were characterized, correlations to the potential roles played by specific residues within the structure may be drawn. [ABSTRACT FROM AUTHOR]