Proposal of Cobetia marina gen. nov., comb. nov., within the family Halomonadaceae, to include the species Halomonas marina

In-Depth Genome Characterization and Pan-Genome Analysis of Strain KMM 296, a Producer of Highly Active Alkaline Phosphatase; Proposal for the Reclassification of Cobetia litoralis and Cobetia pacifica as the Later Heterotypic Synonyms of Cobetia amphilecti and Cobetia marina, and Emended Description of the Species Cobetia amphilecti and Cobetia marina

A strictly aerobic, Gram-stain-negative, rod-shaped, and motile bacterium, designated strain KMM 296, isolated from the coelomic fluid of the mussel Crenomytilus grayanus, was investigated in detail due to its ability to produce a highly active alkaline phosphatase CmAP of the structural family PhoA. A previous taxonomic study allocated the strain to the species Cobetia marina, a member of the family Halomonadaceae of the class Gammaproteobacteria. However, 16S rRNA gene sequencing showed KMM 296's relatedness to Cobetia amphilecti NRIC 0815T. The isolate grew with 0.5-19% NaCl at 4-42 °C and hydrolyzed Tweens 20 and 40 and L-tyrosine. The DNA G+C content was 62.5 mol%. The prevalent fatty acids were C18:1 ω7c, C12:0 3-OH, C18:1 ω7c, C12:0, and C17:0 cyclo. The polar lipid profile was characterized by the presence of phosphatidylethanolamine, phosphatidylglycerol, phosphatidic acid, and also an unidentified aminolipid, phospholipid, and a few unidentified lipids. The major respiratory quinone was Q-8. According to phylogenomic and chemotaxonomic evidence, and the nearest neighbors, the strain KMM 296 represents a member of the species C. amphilecti. The genome-based analysis of C. amphilecti NRIC 0815T and C. litoralis NRIC 0814T showed their belonging to a single species. In addition, the high similarity between the C. pacifica NRIC 0813T and C. marina LMG 2217T genomes suggests their affiliation to one species. Based on the rules of priority, C. litoralis should be reclassified as a later heterotypic synonym of C. amphilecti, and C. pacifica is a later heterotypic synonym of C. marina. The emended descriptions of the species C. amphilecti and C. marina are also proposed.

Marine versus Non-Marine Bacterial Exopolysaccharides and Their Skincare Applications

Bacteria are well-known to synthesize high molecular weight polysaccharides excreted in extracellular domain, which constitute their protective microenvironment. Several bacterial exopolysaccharides (EPS) are commercially available for skincare applications in cosmetic products due to their unique structural features, conferring valuable biological and/or textural properties. This review aims to give an overview of bacterial EPS, an important group of macromolecules used in cosmetics as actives and functional ingredients. For this purpose, the main chemical characteristics of EPS are firstly described, followed by the basics of the development of cosmetic ingredients. Then, a focus on EPS production, including upstream and downstream processes, is provided. The diversity of EPS used in the cosmetic industry, and more specifically of marine-derived EPS is highlighted. Marine bacteria isolated from extreme environments are known to produce EPS. However, their production processes are highly challenging due to high or low temperatures; yield must be improved to reach economically viable ingredients. The biological properties of marine-derived EPS are then reviewed, resulting in the highlight of the challenges in this field.

Biofilm Formation of Two Different Marine Bacteria on Modified PDMS Surfaces is Affected by Surface Roughness and Topography

Different strategies were tested to reduce biofilm formation of the model marine bacteria Cobetia marina and Marinobacter hydrocarbonoclasticus on cross-linked polydimethylsiloxane (PDMS) coated aluminum and cellulose acetate surfaces modified by addition of multi-walled carbon nanotubes (MWCNT) or exposure of the surfaces to bromine vapors in the presence and absence of UV irradiation. The three surface modifications explored led to important reductions in biofilm formation for the two marine bacteria, up to 30% in the case of exposure to Br₂(g). Biofouling reduction could be correlated to surface properties in all cases through the introduction of a quantitative theoretical model based on an effective roughness parameter, Ra_eff, that accounted for the different morphological changes observed. The model considers the possibility of bacterial inclusion into large surface wells, as observed by AFM in the case of Br₂(g) + UV light treatment. In addition, a linear relationship was observed between biofouling reduction and the Ra_eff effective roughness parameter.

Exploring the Potential Molecular Mechanisms of Interactions between a Probiotic Consortium and Its Coral Host

Beneficial microorganisms for corals (BMCs) have been demonstrated to be effective probiotics to alleviate bleaching and mitigate coral mortality in vivo. The selection of putative BMCs is traditionally performed manually, using an array of biochemical and molecular tests for putative BMC traits. We present a comprehensive genetic survey of BMC traits using a genome-based framework for the identification of alternative mechanisms that can be used for future in silico selection of BMC strains. We identify exclusive BMC traits associated with specific strains and propose new BMC mechanisms, such as the synthesis of glycine betaine and ectoines. Our roadmap facilitates the selection of BMC strains while increasing the array of genetic targets that can be included in the selection of putative BMC strains to be tested as coral probiotics. IMPORTANCE Probiotics are currently the main hope as a potential medicine for corals, organisms that are considered the marine "canaries of the coal mine" and that are threatened with extinction. Our experiments have proved the concept that probiotics mitigate coral bleaching and can also prevent coral mortality. Here, we present a comprehensive genetic survey of probiotic traits using a genome-based framework. The main outcomes are a roadmap that facilitates the selection of coral probiotic strains while increasing the array of mechanisms that can be included in the selection of coral probiotics.

Graphene-Based Coating to Mitigate Biofilm Development in Marine Environments

Due to its several economic and ecological consequences, biofouling is a widely recognized concern in the marine sector. The search for non-biocide-release antifouling coatings has been on the rise, with carbon-nanocoated surfaces showing promising activity. This work aimed to study the impact of pristine graphene nanoplatelets (GNP) on biofilm development through the representative marine bacteria Cobetia marina and to investigate the antibacterial mechanisms of action of this material. For this purpose, a flow cytometric analysis was performed and a GNP/polydimethylsiloxane (PDMS) surface containing 5 wt% GNP (G5/PDMS) was produced, characterized, and assessed regarding its biofilm mitigation potential over 42 days in controlled hydrodynamic conditions that mimic marine environments. Flow cytometry revealed membrane damage, greater metabolic activity, and endogenous reactive oxygen species (ROS) production by C. marina when exposed to GNP 5% (w/v) for 24 h. In addition, C. marina biofilms formed on G5/PDMS showed consistently lower cell count and thickness (up to 43% reductions) than PDMS. Biofilm architecture analysis indicated that mature biofilms developed on the graphene-based surface had fewer empty spaces (34% reduction) and reduced biovolume (25% reduction) compared to PDMS. Overall, the GNP-based surface inhibited C. marina biofilm development, showing promising potential as a marine antifouling coating.

Causality Verification for the Correlation between the Presence of Nonstarter Bacteria and Flavor Characteristics in Soft-Type Ripened Cheeses

Flavor characteristics of ripened cheese are established by various bacteria, such as lactic acid bacteria, Actinobacteria, and Proteobacteria, which spontaneously develop during the cheese-manufacturing process. We previously revealed the relationship between bacterial microbiota and flavor components in soft-type ripened cheeses by using a multiomics approach that combined metagenomics and metabolomics; however, we could not establish a causal relationship. This study aimed to substantiate the causal nature of the correlations revealed by the multiomics approach by using cheese-ripening tests with single isolate inoculation. The bacterial diversity and composition in surface mold-ripened cheeses from Japan and France varied, depending on the differences between the milks (pasteurized or raw), cheese positions (core or rind), and manufacturers. Although the volatile compounds did not clearly reflect the distinctive characteristics of the cheese samples, nonstarter lactic acid bacteria, Actinobacteria, and Proteobacteria positively correlated with ketones and sulfur compounds, as evidenced by a Spearman's correlation analysis. Cheese-ripening tests conducted after inoculation with single bacterial strains belonging to the above-mentioned taxa confirmed that these bacteria formed volatile compounds, in agreement with the correlations observed. In particular, various flavor compounds, such as acids, esters, ketones, and sulfur compounds, were detected in cheese inoculated with Pseudoalteromonas sp. TS-4-4 strain. These findings provide important insights into the role of nonstarter bacteria in the development of cheese flavor and into the effectiveness of the multiomics approach in screening for bacteria that can improve the quality of cheese products. IMPORTANCE Our previous study revealed that the existence of various bacteria, such as lactic acid bacteria, Actinobacteria, and Proteobacteria, clearly correlated with the abundance of flavor components, such as volatile compounds, in soft-type ripened cheeses via a multiomics approach that used 16S rRNA gene amplicon sequencing and headspace gas chromatography-mass spectrometry. However, this approach only showed correlations derived from statistical analyses rather than causal relationships. Therefore, in the present study, we performed cheese-ripening tests using nonstarter bacteria to substantiate the correlations revealed by the multiomics approach in soft-type ripened cheese. Our results suggest the capability of nonstarter bacteria, such as Proteobacteria, to impart flavor to cheese and the effectiveness of the multiomics approach in screening for microbial isolates that can improve the quality of cheese. Overall, our research provides new insights into the importance of bacteria in cheese production.

Complete genome sequencing and comparison of two nitrogen-metabolizing bacteria isolated from Antarctic deep-sea sediment

BACKGROUND

Bacteria are an essential component of the earth`s biota and affect circulation of matters through their metabolic activity. They also play an important role in the carbon and nitrogen cycle in the deep-sea environment. In this paper, two strains from deep-sea sediments were investigated in order to understand nitrogen cycling involved in the deep-sea environment.

RESULTS

In this paper, the basic genomic information of two strains was obtained by whole genome sequencing. The Cobetia amphilecti N-80 and Halomonas profundus 13 genome sizes are 4,160,095 bp with a GC content of 62.5% and 5,251,450 bp with a GC content of 54.84%. Through a comparison of functional analyses, we predicted the possible C and N metabolic pathways of the two strains and determined that Halomonas profundus 13 could use more carbon sources than Cobetia amphilecti N-80. The main genes associated with N metabolism in Halomonas profundus 13 are narG, narY, narI, nirS, norB, norC, nosZ, and nirD. On the contrast, nirD, using NH₄⁺ for energy, plays a main role in Cobetia amphilecti N-80. Both of them have the same genes for fixing inorganic carbon: icd, ppc, fdhA, accC, accB, accD, and accA.

CONCLUSION

In this study, the whole genomes of two strains were sequenced to clarify the basic characteristics of their genomes, laying the foundation for further studying nitrogen-metabolizing bacteria. Halomonas profundus 13 can utilize more carbon sources than Cobetia amphilecti N-80, as indicated by API as well as COG and KEGG prediction results. Finally, through the analysis of the nitrification and denitrification abilities as well as the inorganic carbon fixation ability of the two strains, the related genes were identified, and the possible metabolic pathways were predicted. Together, these results provide molecular markers and theoretical support for the mechanisms of inorganic carbon fixation by deep-sea microorganisms.

Halomonas alkalisoli sp. nov., a novel haloalkalophilic species from saline-alkaline soil, and reclassification of Halomonas daqingensis Wu et al. 2008 as a later heterotypic synonym of Halomonas desiderata Berendes et al. 1996

Two Gram-stain-negative, strictly aerobic, moderately halophilic, non-spore-forming and rod-shaped bacteria, designated M5N1S17T and M5N1S15, were isolated from saline soil in Baotou, China. A phylogenetic analysis based on 16S rRNA gene sequences showed that the two strains clustered closely with Halomonas montanilacus PYC7WT and shared 99.1 and 99.3% sequence similarities, respectively. The average nucleotide identity based on BLAST (ANIb) and MUMmer (ANIm) values of the two strains with each other were 95.5% and 96.7%, respectively, while the ANIb and ANIm values between the two strains and 15 closer Halomonas species were 74.8-91.3% and 84.1-92.6%, respectively. The major polar lipids of M5N1S17T are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, and an unidentified phospholipid. The major polar lipids of M5N1S15 are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, two unidentified phospholipids, and an unidentified lipid. The predominant ubiquinone in the two strains is Q-9. The major fatty acids of the two strains are C18:1ω6c and/or C18:1ω7c, C16:0, and C16:1ω7c and/or C16:1ω6c. Based on phylogenetic, phenotypic, and physiological results, strains M5N1S17T and M5N1S15 should be identified as a novel species of the genus Halomonas, for which Halomonas alkalisoli sp. nov. is proposed. The type strain is M5N1S17T (= CGMCC 1.19023T = KCTC 92130T). The phylogenetic trees showed that Halomonas daqingensis CGMCC 1.6443T clustered tightly with Halomonas desiderata FB2T, and the two strains shared >98.0% of ANI values with each other. Therefore, we propose the reclassification of H. daqingensis Wu et al. 2008 as a later heterotypic synonym of H. desiderata Berendes et al. 1996.

Turning mannitol-rich agricultural waste to poly(3-hydroxybutyrate) with Cobetia amphilecti fermentation and recovery with methyl levulinate as a green solvent

The present study explored the use of mannitol and mannitol-rich agro-industrial wastes as substrates for PHB production by Cobetia amphilecti isolated from the green Ulva sp. seaweed. Cultivation of C. amphilecti on mannitol, celery, and olive leaves (OLs) waste led to 4.20, 6.00, and 5.16 g L^-1 of cell dry mass (CDM), 76.3, 25.5, and 12.0% of PHB content in CDM and 3.2, 1.53, and 0.62 g L^-1 of PHB concentration, respectively; which suggested that they can be exploited as carbon substrates for the production of PHB. Extraction of PHB from C. amphilecti cultures by solubilization in the green solvent methyl levulinate (ML) (2% w/w, 140 °C, 1 h) indicated that the recovery yield and purity of PHB are above 97 and 90% w/w, respectively. The use of ML could be an attractive method for the recovery of PHB when safe and non-toxic solvents are required.

Everything Is Everywhere: Physiological Responses of the Mediterranean Sea and Eastern Pacific Ocean Epiphyte Cobetia Sp. to Varying Nutrient Concentration

Bacteria are essential in the maintenance and sustainment of marine environments (e.g., benthic systems), playing a key role in marine food webs and nutrient cycling. These microorganisms can live associated as epiphytic or endophytic populations with superior organisms with valuable ecological functions, e.g., seagrasses. Here, we isolated, identified, sequenced, and exposed two strains of the same species (i.e., identified as Cobetia sp.) from two different marine environments to different nutrient regimes using batch cultures: (1) Cobetia sp. UIB 001 from the endemic Mediterranean seagrass Posidonia oceanica and (2) Cobetia sp. 4B UA from the endemic Humboldt Current System (HCS) seagrass Heterozostera chilensis. From our physiological studies, both strains behaved as bacteria capable to cope with different nutrient and pH regimes, i.e., N, P, and Fe combined with different pH levels, both in long-term (12 days (d)) and short-term studies (4 d/96 h (h)). We showed that the isolated strains were sensitive to the N source (inorganic and organic) at low and high concentrations and low pH levels. Low availability of phosphorus (P) and Fe had a negative independent effect on growth, especially in the long-term studies. The strain UIB 001 showed a better adaptation to low nutrient concentrations, being a potential N₂-fixer, reaching higher growth rates (μ) than the HCS strain. P-acquisition mechanisms were deeply investigated at the enzymatic (i.e., alkaline phosphatase activity, APA) and structural level (e.g., alkaline phosphatase D, PhoD). Finally, these results were complemented with the study of biochemical markers, i.e., reactive oxygen species (ROS). In short, we present how ecological niches (i.e., MS and HCS) might determine, select, and modify the genomic and phenotypic features of the same bacterial species (i.e., Cobetia spp.) found in different marine environments, pointing to a direct correlation between adaptability and oligotrophy of seawater.

Diversity of cultivable bacteria from deep-sea sediments of the Colombian Caribbean and their potential in bioremediation

The diversity of deep-sea cultivable bacteria was studied in seven sediment samples of the Colombian Caribbean. Three hundred and fifty two marine bacteria were isolated according to its distinct morphological character on the solid media, then DNA sequences of the 16S rRNA were amplified to identify the isolated strains. The identified bacterial were arranged in three phylogenetic groups, Firmicutes, Proteobacteria, and Actinobacteria, with 34 different OTUs defined at ≥ 97% of similarity and 70 OTUs at ≥ 98.65%, being the 51% Firmicutes, 34% Proteobacteria and 15% Actinobacteria. Bacillus and Fictibacillus were the dominant genera in Firmicutes, Halomonas and Pseudomonas in Proteobacteria and Streptomyces and Micromonospora in Actinobacteria. In addition, the strains were tested for biosurfactants and lipolytic enzymes production, with 120 biosurfactant producing strains (mainly Firmicutes) and, 56 lipolytic enzymes producing strains (Proteobacteria). This report contributes to the understanding of the diversity of the marine deep-sea cultivable bacteria from the Colombian Caribbean, and their potential application as bioremediation agents.

Fluid dynamics and cell‐bound Psl polysaccharide allows microplastic capture, aggregation and subsequent sedimentation by Pseudomonas aeruginosa in water

Decades after incorporating plastics into consumer markets, research shows that these polymers have spread worldwide. Fragmentation of large debris leads to smaller particles, collectively called microplastics (MPs), which have become ubiquitous in aquatic environments. A fundamental aspect of understanding the implications of MP contamination on ecosystems is resolving the complex interactions of these artificial substrates with microbial cells. Using polystyrene microparticles as model polymers, we conducted an exploratory study where these interactions are quantitatively analyzed using an in vitro system consisting of single‐bacterial species capturing and aggregating MPs in water. Here we show that the production of Psl exopolysaccharide by Pseudomonas aeruginosa (PA) does not alter MPs colloidal stability but plays a key role in microspheres adhesion to the cell surface. Further aggregation of MPs by PA cells depends on bacterial mobility and the presence of sufficient flow to prevent rapid sedimentation of early MP‐PA assembles. Surprisingly, cells in MP‐PA aggregates are not in a sessile state despite the production of Psl, enhancing the motility of the aggregates by an order of magnitude relative to passive diffusion. The generated data could inform the creation of predictive models that accurately describe the dynamics and influence of bacterial growth on plastics debris.

High natural PHA production from acetate in Cobetia sp. MC34 and Cobetia marina DSM 4741T and in silico analyses of the genus specific PhaC2 polymerase variant

BACKGROUND

Several members of the bacterial Halomonadacea family are natural producers of polyhydroxyalkanoates (PHA), which are promising materials for use as biodegradable bioplastics. Type-strain species of Cobetia are designated PHA positive, and recent studies have demonstrated relatively high PHA production for a few strains within this genus. Industrially relevant PHA producers may therefore be present among uncharacterized or less explored members. In this study, we characterized PHA production in two marine Cobetia strains. We further analyzed their genomes to elucidate pha genes and metabolic pathways which may facilitate future optimization of PHA production in these strains.

RESULTS

Cobetia sp. MC34 and Cobetia marina DSM 4741T were mesophilic, halotolerant, and produced PHA from four pure substrates. Sodium acetate with- and without co-supplementation of sodium valerate resulted in high PHA production titers, with production of up to 2.5 g poly(3-hydroxybutyrate) (PHB)/L and 2.1 g poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV)/L in Cobetia sp. MC34, while C. marina DSM 4741T produced 2.4 g PHB/L and 3.7 g PHBV/L. Cobetia marina DSM 4741T also showed production of 2.5 g PHB/L from glycerol. The genome of Cobetia sp. MC34 was sequenced and phylogenetic analyses revealed closest relationship to Cobetia amphilecti. PHA biosynthesis genes were located at separate loci similar to the arrangement in other Halomonadacea. Further genome analyses revealed some differences in acetate- and propanoate metabolism genes between the two strains. Interestingly, only a single PHA polymerase gene (phaC2) was found in Cobetia sp. MC34, in contrast to two copies (phaC1 and phaC2) in C. marina DSM 4741T. In silico analyses based on phaC genes show that the PhaC2 variant is conserved in Cobetia and contains an extended C-terminus with a high isoelectric point and putative DNA-binding domains.

CONCLUSIONS

Cobetia sp. MC34 and C. marina DSM 4741T are natural producers of PHB and PHBV from industrially relevant pure substrates including acetate. However, further scale up, optimization of growth conditions, or use of metabolic engineering is required to obtain industrially relevant PHA production titers. The putative role of the Cobetia PhaC2 variant in DNA-binding and the potential implications remains to be addressed by in vitro- or in vivo methods.

Quality and Safety Assessment of Edible Seaweeds Alaria esculenta and Saccharina latissima Cultivated in Scotland

Within Europe over the last 10 years, there has been an increase in seaweeds cultivated for human consumption. For food safety reasons, it is important to assess the microbiological and nutritional quality of the biomass. The fresh and dried edible seaweeds Alaria esculenta and Saccharina latissima were assessed over two consecutive years for the presence of microorganisms. Seaweed samples supplied from Scotland were stored under isothermal conditions for specific time intervals depending on the sample’s condition (fresh, dried or rehydrated). During storage, microbiological analyses were performed for the enumeration of Total Viable Counts (TVC), Pseudomonas spp., Enterobacteriaceae and Bacillus spp., as well as yeasts and molds. Additionally, bacterial colonies from the Marine Agar growth medium were isolated and subjected to PCR-RAPD analysis for characterization of the bacterial diversity of seaweeds. Bacterial isolates with different fingerprint patterns were further subjected to sequencing (16S rDNA, V1–V4 region). The presence of human pathogenic bacteria was also investigated. Results showed that the initial population of TVC was differentiated depending on the year of seaweed harvest, being closer to the enumeration limit (1.0 log CFU/g) in fresh samples from 2020 and higher in samples from 2019 (6.7 and 3.9 log CFU/g in A. esculenta and S. latissima, respectively). DNA-based analysis revealed the presence of Psychrobacter, Cobetia and Pseudomonas species in A. esculenta, while Psychrobacter and Micrococcus species were present in S. latissima.

Marine bacteria associated with the green seaweed Ulva sp. for the production of polyhydroxyalkanoates

This work aimed to isolate a series of bacterial strains associated with the green seaweed Ulva sp. and evaluate their capability to manufacture PHA. The effect of the type of supplemented sugars found to be in macroalgae, on the growth and PHA productivity of the strains was studied. Analysis of the 16S rRNA gene sequence of the isolated strains revealed that the PHA-producing bacteria were phylogenetically related to the genus Cobetia, Bacillus, Pseudoaltermonas and Sulfitobacter, which showed high PHA contents among the isolates. The highest PHA content was observed in the case of Cobetia strain, with up to 61% w/w in the presence of mannitol and 12% w/w on Ulva sp. acid hydrolysate as a substrate.

Are the Closely Related Cobetia Strains of Different Species?

Marine bacteria of the genus Cobetia, which are promising sources of unique enzymes and secondary metabolites, were found to be complicatedly identified both by phenotypic indicators due to their ecophysiology diversity and 16S rRNA sequences because of their high homology. Therefore, searching for the additional methods for the species identification of Cobetia isolates is significant. The species-specific coding sequences for the enzymes of each functional category and different structural families were applied as additional molecular markers. The 13 closely related Cobetia isolates, collected in the Pacific Ocean from various habitats, were differentiated by the species-specific PCR patterns. An alkaline phosphatase PhoA seems to be a highly specific marker for C. amphilecti. However, the issue of C. amphilecti and C. litoralis, as well as C. marina and C. pacifica, belonging to the same or different species remains open.

Bacterial diversity in six species of fresh edible seaweeds submitted to high pressure processing and long-term refrigerated storage

Seaweeds are highly perishable foods due to their richness in nutrients. High pressure processing (HPP) has been applied for extending the shelf life of fresh seaweeds but there is no information on the effect of HPP on the bacterial diversity of seaweeds. The culturable bacteria of six species of fresh edible seaweeds (green seaweeds Codium fragile and Ulva lactuca, brown seaweeds Himanthalia elongata, Laminaria ochroleuca and Undaria pinnatifida, and red seaweed Chondrus crispus) were investigated and compared to those of HPP-treated (400 and 600 MPa for 5 min) seaweeds, at the start and end of their refrigerated storage period. A total of 523 and 506 bacterial isolates were respectively retrieved from untreated and HPP-treated seaweeds. Isolates from untreated seaweeds belonged to 18 orders, 35 families, 71 genera and 135 species whereas isolates from HPP-treated seaweeds belonged to 13 orders, 23 families, 43 genera and 103 species. HPP treatment significantly reduced the number of isolates belonging to 6 families and greatly increased the number of Bacillaceae isolates. At the end of storage, decreases in bacterial diversity at the genus and species level were observed for untreated as well as for HPP-treated seaweeds.

Cobetia sp. Bacteria, Which Are Capable of Utilizing Alginate or Waste Laminaria sp. for Poly(3-Hydroxybutyrate) Synthesis, Isolated From a Marine Environment

We isolated the Cobetia sp. strains IU 180733JP01 (5-11-6-3) and 190790JP01 (5-25-4-2) from seaweeds and showed that both strains accumulate poly(3-hydroxybutyrate) [P(3HB)] homopolymer in a nitrogen-limiting mineral salt medium containing alginate as a sole carbon source. Genome sequence analysis of the isolated strains showed that they have putative genes which encode enzymes relevant to alginate assimilation and P(3HB) synthesis, and the putative alginate-assimilating genes formed a cluster. Investigation of the optimum culture conditions for high accumulation of P(3HB) showed that when the 5-11-6-3 strain was cultured in a nitrogen-limiting mineral salt medium (pH 5.0) containing 6% NaCl and 3% (w/v) alginate as a sole carbon source for 2 days, the P(3HB) content and P(3HB) production reached 62.1 ± 3.4 wt% and 3.11 ± 0.16 g/L, respectively. When the 5-25-4-2 strain was cultured in a nitrogen-limiting mineral salt medium (pH 4.0) containing 5% NaCl and 3% (w/v) alginate for 2 days, the P(3HB) content and P(3HB) production reached 56.9 ± 2.1 wt% and 2.67 ± 0.11 g/L, respectively. Moreover, the 5-11-6-3 strain also produced P(3HB) in a nitrogen-limiting mineral salt medium (pH 5.0) containing 6% NaCl and freeze-dried and crushed waste Laminaria sp., which is classified into brown algae and contains alginate abundantly. The resulting P(3HB) content and P(3HB) productivity were 13.5 ± 0.13 wt% and 3.99 ± 0.15 mg/L/h, respectively. Thus, we demonstrated the potential application of the isolated strains to a simple P(3HB) production process from seaweeds without chemical hydrolysis and enzymatic saccharification.

Viral degradation of marine bacterial exopolysaccharides

The identification of the mechanisms by which marine dissolved organic matter (DOM) is produced and regenerated is critical to develop robust prediction of ocean carbon cycling. Polysaccharides represent one of the main constituents of marine DOM and their degradation is mainly attributed to polysaccharidases derived from bacteria. Here, we report that marine viruses can depolymerize the exopolysaccharides (EPS) excreted by their hosts using five bacteriophages that infect the notable EPS producer, Cobetia marina DSMZ 4741. Degradation monitorings as assessed by gel electrophoresis and size exclusion chromatography showed that four out of five phages carry structural enzymes that depolymerize purified solution of Cobetia marina EPS. The depolymerization patterns suggest that these putative polysaccharidases are constitutive, endo-acting and functionally diverse. Viral adsorption kinetics indicate that the presence of these enzymes provides a significant advantage for phages to adsorb onto their hosts upon intense EPS production conditions. The experimental demonstration that marine phages can display polysaccharidases active on bacterial EPS lead us to question whether viruses could also contribute to the degradation of marine DOM and modify its bioavailability. Considering the prominence of phages in the ocean, such studies may unveil an important microbial process that affects the marine carbon cycle.

Microbial Residents of the Atlantis Massif's Shallow Serpentinite Subsurface

The International Ocean Discovery Program Expedition 357—“Serpentinization and Life”—utilized seabed drills to collect rocks from the oceanic crust. The recovered rock cores represent the shallow serpentinite subsurface of the Atlantis Massif, where reactions between uplifted mantle rocks and water, collectively known as serpentinization, produce environmental conditions that can stimulate biological activity and are thought to be analogous to environments that were prevalent on the early Earth and perhaps other planets. The methodology and results of this project have implications for life detection experiments, including sample return missions, and provide a window into the diversity of microbial communities inhabiting subseafloor serpentinites.

The Atlantis Massif rises 4,000 m above the seafloor near the Mid-Atlantic Ridge and consists of rocks uplifted from Earth’s lower crust and upper mantle. Exposure of the mantle rocks to seawater leads to their alteration into serpentinites. These aqueous geochemical reactions, collectively known as the process of serpentinization, are exothermic and are associated with the release of hydrogen gas (H₂), methane (CH₄), and small organic molecules. The biological consequences of this flux of energy and organic compounds from the Atlantis Massif were explored by International Ocean Discovery Program (IODP) Expedition 357, which used seabed drills to collect continuous sequences of shallow (<16 m below seafloor) marine serpentinites and mafic assemblages. Here, we report the census of microbial diversity in samples of the drill cores, as measured by environmental 16S rRNA gene amplicon sequencing. The problem of contamination of subsurface samples was a primary concern during all stages of this project, starting from the initial study design, continuing to the collection of samples from the seafloor, handling the samples shipboard and in the lab, preparing the samples for DNA extraction, and analyzing the DNA sequence data. To distinguish endemic microbial taxa of serpentinite subsurface rocks from seawater residents and other potential contaminants, the distributions of individual 16S rRNA gene sequences among all samples were evaluated, taking into consideration both presence/absence and relative abundances. Our results highlight a few candidate residents of the shallow serpentinite subsurface, including uncultured representatives of the Thermoplasmata, Acidobacteria, Acidimicrobia, and Chloroflexi.

IMPORTANCE The International Ocean Discovery Program Expedition 357—“Serpentinization and Life”—utilized seabed drills to collect rocks from the oceanic crust. The recovered rock cores represent the shallow serpentinite subsurface of the Atlantis Massif, where reactions between uplifted mantle rocks and water, collectively known as serpentinization, produce environmental conditions that can stimulate biological activity and are thought to be analogous to environments that were prevalent on the early Earth and perhaps other planets. The methodology and results of this project have implications for life detection experiments, including sample return missions, and provide a window into the diversity of microbial communities inhabiting subseafloor serpentinites.

Halomonas sambharensis sp. nov., a Moderately Halophilic Bacterium Isolated from the Saltern Crystallizer Ponds of the Sambhar Salt Lake in India

Two moderately halophilic strains SBS 10^T and SSO 06 were isolated from the saltern crystallizer ponds of the hypersaline Sambhar Salt Lake in India. Strains were aerobic, Gram-stain-negative, and rod shaped. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that two strains belong to the genus Halomonas in the Gammaproteobacteria, with highest 16S rRNA gene sequence similarities with Halomonas gudaonensis LMG 23610^T (98.2% similarity) and Halomonas campaniensis 5AG^T (99.0% similarity). Strains grew optimally at 37 °C, pH 7.5-8.0 in the presence of 5-8% (w/v) NaCl. The major fatty acids of the strain SBS 10^T were C_18:1ω7c (54.37%), C_16:0 (25.69%), C_16:1 × 7c/C_16:1 × 6c (13.28%), and C_12:0 (1.21%). The G+C content was 63.6 mol % (T_m). Phenotypic features, fatty acids profile, and DNA G+C content supported placement of the strain SBS 10^T in the genus Halomonas having distinct characteristics with related strains. Analysis of the housekeeping genes: gryB and rpoD and in silico DNA-DNA hybridization between the strain SBS 10^T and its type strain Halomonas gudaonensis (LMG 23610^T) further revealed the strain SBS 10^T to be a distinct species. On the basis of the phenotypic, chemotaxonomic and phylogenetic analysis, the strain SBS 10^T is considered to represent a novel species for which the name Halomonas sambharensis is proposed. The type strain is SBS 10^T (= MTCC 12313^T = LMG 30344^T).

Effects of cavitation on different microorganisms: The current understanding of the mechanisms taking place behind the phenomenon. A review and proposals for further research

A sudden decrease in pressure triggers the formation of vapour and gas bubbles inside a liquid medium (also called cavitation). This leads to many (key) engineering problems: material loss, noise, and vibration of hydraulic machinery. On the other hand, cavitation is a potentially useful phenomenon: the extreme conditions are increasingly used for a wide variety of applications such as surface cleaning, enhanced chemistry, and wastewater treatment (bacteria eradication and virus inactivation). Despite this significant progress, a large gap persists between the understanding of the mechanisms that contribute to the effects of cavitation and its application. Although engineers are already commercializing devices that employ cavitation, we are still not able to answer the fundamental question: What precisely are the mechanisms how bubbles can clean, disinfect, kill bacteria and enhance chemical activity? The present paper is a thorough review of the recent (from 2005 onward) work done in the fields of cavitation-assisted microorganism's destruction and aims to serve as a foundation to build on in the next years.

Betaine accumulation suppresses the de-novo synthesis of ectoine at a low osmotic concentration in Halomonas sp SBS 10, a bacterium with broad salinity tolerance

The study aims to find out osmoadaptive mechanism used to overcome the salinity stress by Halomonas sp SBS 10 isolated from the saltern crystallizer ponds of the Sambhar Salt Lake and its taxonomic position using neighbor-joining algorithm. The strain SBS 10 was tested for accumulation of two major compatable solutes betaine and ectoine and was observed that osmoprotection in the strain SBS 10 is achieved by the accumulation of betaine or by the de-novo synthesis of betaine or ectoine. Amount of endogenous content of the betaine and ectoine per milligram of cell biomass was estimated to be 581 µg, 587 µg, 588 µg, 617 µg, and 761 µg for betaine and 1.52 µg, 2.74 µg, 3.14 µg, 3.50 µg, and 52.67 µg for ectoine, when exposed to 5, 10, 15, 20 and 25% of NaCl concentration. Results obtained from HPLC analysis showed that the betaine accumulation suppresses the de-novo synthesis of ectoine partially at low NaCl concentration in the growth medium. However, at a high NaCl concentration, the ectoine concentration increases abruptly as compared to the betaine. This indicates that the ectoine accumulation is transcriptionally up-regulated by the salinity stress. Phylogenetic analysis based on the neighbor-joining algorithm included the strain SBS 10 in the genus Halomonas of the family Halomonadaceae belonging to the class Gammaproteobacteria. Most closely related type strain was found to be Halomonas gudaonensis SL014B-69^T (98.2% similarity). Ultrastructure characteristics showed the strain to be non-spore forming rod, 0.3-0.4 × 0.75-1.65 μm in size and motile with the help of peritrichous flagella.

Phytohalomonas tamaricis gen. nov., sp. nov., an endophytic bacterium isolated from Tamarix ramosissima roots growing in Kumtag desert

A gram-stain-negative, aerobic, non-spore-forming, rod-shaped, non-motile bacterium strain R4HLG17^T was isolated from Tamarix ramosissima roots growing in Kumtag desert. The strain grew at salinities of 0-16% (w/v) NaCl (optimum 5-6%), pH 5-9 (optimum 7) and at 16-45 °C. Based on 16S rRNA gene sequence similarity, strain R4HLG17^T belonged to the family Halomonadaceae and was most closely related to Halomonas lutea DSM 23508^T(95.1%), followed by Halotalea alkalilenta AW-7^T(94.8%), Salinicola acroporae S4-41^T(94.8%), Salinicola halophilus CG4.1^T(94.6%), and Larsenimonas salina M1-18^T(94.4%). Multilocus sequence analysis (MLSA) based on the partial sequences of 16S rRNA, atpA, gyrB, rpoD, and secA genes indicated that the strain R4HLG17^T formed an independent and monophyletic branch related to other genera of Halomonadaceae, supporting its placement as a new genus in this family. The draft genome of strain R4HLG17^T was 3.6 Mb with a total G + C content of 55.1%. The average nucleotide identity to Halomonas lutea DSM 23508^T was 83.5%. Q-9 was detected as the major respiratory quinone and summed feature 8 (C_18:1ω7c/C_18:1ω6c), summed feature 3 (C_16:1ω7c/C_16:1ω6c), and C_16:0 as predominant cellular fatty acids. On the basis of chemotaxonomic, phylogenetic, and phenotypic evidence, strain R4HLG17^T is concluded to represent a novel species of a new genus within Halomonadaceae, for which the name Phytohalomonas tamaricis gen. nov., sp. nov., is proposed. The type strain is R4HLG17^T (=ACCC 19929^T=KCTC 52415^T).

Characterization of a pH-Tolerant Strain Cobetia sp. SASS1 and Its Phenol Degradation Performance Under Salinity Condition

Biological treatment of complex saline phenolic wastewater remains a great challenge due to the low activity of bacterial populations under stressful conditions. Acid mine drainage (AMD) as a typically extreme environment, shaped unique AMD microbial communities. Microorganisms survived in the AMD environment have evolved various mechanisms of resistance to low pH, high salinity and toxic heavy metals. The primary goal of this work was to determine whether a strain isolated from an AMD could degrade phenol under stressful conditions such as low pH, high salinity and heavy metals. The results suggested that the strain Cobetia sp. SASS1 isolated from AMD presented different physiological characteristics in comparison with five most closely related species. SASS1 can efficiently degrade phenol at wide ranges of pH (3.0-9.0) and NaCl concentration (0-40 g/L), as well as the existence of Cu2+ and Mn2+. Specifically, the SASS1 could completely degrade 1500 mg/L phenol in 80 h at 10 g/L NaCl. Meanwhile, mineralization of phenol was achieved with complete degradation of 900 mg/L phenol and simultaneously COD decreasing from 2239 mg/L to 181.6 mg/L in 36 h. Based on biodegradation metabolites identification and enzyme activities analysis, both ortho-cleavage pathway and benzoic acid pathway for phenol degradation were proposed. These findings suggested that SASS1 was an efficient phenol degrader under salinity and acidic conditions, and could be considered as key population for bioremediation of industrial phenolic wastewaters under stressful conditions.

Betaine accumulation suppresses the de-novo synthesis of ectoine at a low osmotic concentration in Halomonas sp SBS 10, a bacterium with broad salinity tolerance

The study aims to find out osmoadaptive mechanism used to overcome the salinity stress by Halomonas sp SBS 10 isolated from the saltern crystallizer ponds of the Sambhar Salt Lake and its taxonomic position using neighbor-joining algorithm. The strain SBS 10 was tested for accumulation of two major compatable solutes betaine and ectoine and was observed that osmoprotection in the strain SBS 10 is achieved by the accumulation of betaine or by the de-novo synthesis of betaine or ectoine. Amount of endogenous content of the betaine and ectoine per milligram of cell biomass was estimated to be 581 µg, 587 µg, 588 µg, 617 µg, and 761 µg for betaine and 1.52 µg, 2.74 µg, 3.14 µg, 3.50 µg, and 52.67 µg for ectoine, when exposed to 5, 10, 15, 20 and 25% of NaCl concentration. Results obtained from HPLC analysis showed that the betaine accumulation suppresses the de-novo synthesis of ectoine partially at low NaCl concentration in the growth medium. However, at a high NaCl concentration, the ectoine concentration increases abruptly as compared to the betaine. This indicates that the ectoine accumulation is transcriptionally up-regulated by the salinity stress. Phylogenetic analysis based on the neighbor-joining algorithm included the strain SBS 10 in the genus Halomonas of the family Halomonadaceae belonging to the class Gammaproteobacteria. Most closely related type strain was found to be Halomonas gudaonensis SL014B-69^T (98.2% similarity). Ultrastructure characteristics showed the strain to be non-spore forming rod, 0.3-0.4 × 0.75-1.65 μm in size and motile with the help of peritrichous flagella.

Draft Genome Sequence of the Crude Oil-Degrading and Biosurfactant-Producing Strain Cobetia sp. QF-1

We report here the draft genome of Cobetia sp. QF-1, a cold-adapted bacterium isolated from crude oil-contaminated seawater of the Yellow Sea, China. This genome is approximately 4.1 Mb (G+C content, 57.44%) with 3,513 protein-coding sequences. Cobetia sp. QF-1 shows crude oil degradation and biosurfactant production activity at low temperature.

Natural products and morphogenic activity of γ-Proteobacteria associated with the marine hydroid polyp Hydractinia echinata

Illumina 16S rRNA gene sequencing was used to profile the associated bacterial community of the marine hydroid Hydractinia echinata, a long-standing model system in developmental biology. 56 associated bacteria were isolated and evaluated for their antimicrobial activity. Three strains were selected for further in-depth chemical analysis leading to the identification of 17 natural products. Several γ-Proteobacteria were found to induce settlement of the motile larvae, but only six isolates induced the metamorphosis to the primary polyp stage within 24h. Our study paves the way to better understand how bacterial partners contribute to protection, homeostasis and propagation of the hydroid polyp.

Microbial Diversity in Extreme Marine Habitats and Their Biomolecules

Extreme marine environments have been the subject of many studies and scientific publications. For many years, these environmental niches, which are characterized by high or low temperatures, high-pressure, low pH, high salt concentrations and also two or more extreme parameters in combination, have been thought to be incompatible to any life forms. Thanks to new technologies such as metagenomics, it is now possible to detect life in most extreme environments. Starting from the discovery of deep sea hydrothermal vents up to the study of marine biodiversity, new microorganisms have been identified, and their potential uses in several applied fields have been outlined. Thermophile, halophile, alkalophile, psychrophile, piezophile and polyextremophile microorganisms have been isolated from these marine environments; they proliferate thanks to adaptation strategies involving diverse cellular metabolic mechanisms. Therefore, a vast number of new biomolecules such as enzymes, polymers and osmolytes from the inhabitant microbial community of the sea have been studied, and there is a growing interest in the potential returns of several industrial production processes concerning the pharmaceutical, medical, environmental and food fields.

Purification and characterization of a novel alginate lyase from the marine bacterium Cobetia sp. NAP1 isolated from brown algae

The application of marine resources, instead of fossil fuels, for biomass production is important for building a sustainable society. Seaweed is valuable as a source of marine biomass for producing biofuels such as ethanol, and can be used in various fields. Alginate is an anionic polysaccharide that forms the main component of brown algae. Various alginate lyases (e.g. exo- and endo-types and oligoalginate lyase) are generally used to degrade alginate. We herein describe a novel alginate lyase, AlgC-PL7, which belongs to the polysaccharide lyase 7 family. AlgC-PL7 was isolated from the halophilic Gram-negative bacterium Cobetia sp. NAP1 collected from the brown algae Padina arborescens Holmes. The optimal temperature and pH for AlgC-PL7 activity were 45 °C and 8, respectively. Additionally, AlgC-PL7 was thermostable and salt-tolerant, exhibited broad substrate specificity, and degraded alginate into monosaccharides. Therefore, AlgC-PL7 is a promising enzyme for the production of biofuels.

Pistricoccus aurantiacus gen. nov., sp. nov., a moderately halophilic bacterium isolated from a shark

A novel Gram-stain negative, non-motile, moderately halophilic, facultatively anaerobic and spherical bacterium designated strain SS9^T was isolated from the gill homogenate of a shark. Cells of SS9^T were observed to be 0.8-1.2 μm in diameter. The strain was found to grow optimally at 33 °C, pH 7.0-8.0 and in the presence of 6.0 % (w/v) NaCl. On the basis of 16S rRNA gene phylogeny, strain SS9^T can be affiliated with the family Halomonadaceae and is closely related to Chromohalobacter marismortui NBRC 103155^T (95.6 % sequence similarity), Halomonas ilicicola SP8^T (95.6 %) and Chromohalobacter salexigens DSM 3043^T (95.5 %). Multilocus sequence analysis of strain SS9^T using the housekeeping genes 16S rRNA, 23S rRNA, gyrB, rpoD and secA revealed the strain's distinct phylogenetic position, separate from other known genera of the family Halomonadaceae. Strain SS9^T was found to contain ubiquinone-9 (Q-9) as the predominant ubiquinone and C_18:1 ω7c, C_16:0 and summed feature 3 (C_16:1 ω7c and/or iso-C_15:0 2-OH) as the major fatty acids. The major polar lipids of strain SS9^T were identified as phosphatidylglycerol and phosphatidylethanolamine. The DNA G + C content of strain SS9^T was determined to be 60.4 mol%. It is evident from phylogenetic, genotypic, phenotypic and chemotaxonomic results that strain SS9^T represents a novel species in a new genus, for which the name Pistricoccus aurantiacus gen. nov., sp. nov. is proposed. The type strain is SS9^T (=KCTC 42586^T = MCCC 1H00111^T).

Draft Genome Sequence of Cobetia sp. UCD-24C, Isolated from Roots and Leaves of the Seagrass Zostera marina

Here, we present the 4,230,758-bp draft genome for Cobetia sp. UCD-24C. This strain was isolated from Zostera marina roots collected in Woods Hole, Massachusetts, USA.

Halomonas garicola sp. nov., isolated from saeu-jeot, a Korean salted and fermented shrimp sauce

A Gram-stain-negative, moderately halophilic and facultatively aerobic bacterium capable of respiration with nitrate, designated strain JJ-M1^T, was isolated from saeu-jeot, a traditional Korean fermented shrimp sauce. Cells of the strain were non-motile short rods showing oxidase-negative and catalase-positive reactions and the production of pale-yellow pigments. Growth of strain JJ-M1^T was observed at 20-37 °C (optimum, 30 °C), pH 5.5-9.5 (optimum, pH 7.0) and in the presence of 3-22.5 % (w/v) sea salts (optimum, 10 %). Strain JJ-M1^T contained ubiquinone 9 (Q-9) as the predominant isoprenoid quinone and summed feature 8 (comprising C_18 : 1ω7c and/or C_18 : 1ω6c), C_16 : 0, summed feature 3 (comprising C_16 : 1ω7c and/or C_16 : 1ω6c) and C_12 : 0 3-OH as the major cellular fatty acids. The polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphoglycolipid, diphosphatidylglycerol and four unidentified phospholipids. The genomic DNA G+C content of strain JJ-M1^T was 62.4 mol%. Phylogenetic and comparative analyses, based on 16S rRNA gene sequences, indicated that strain JJ-M1^T formed a tight phyletic lineage with Halomonas jeotgali Hwa^T within the genus Halomonas and was most closely related to Halomonas jeotgali Hwa^T with 96.2 % 16S rRNA gene sequence similarity. Based on phylogenetic, phenotypic and chemotaxonomic features, strain JJ-M1^T represents a novel species of the genus Halomonas, for which the name Halomonas garicola sp. nov. is proposed. The type strain is JJ-M1^T ( = KACC 18117^T = JCM 30151^T).

Halomonas salicampi sp. nov., a halotolerant and alkalitolerant bacterium isolated from a saltern soil

A Gram-stain-negative, halotolerant and alkalitolerant bacterium, designated strain BH103T, was isolated from saltern soil in Gomso, Korea. Cells of strain BH103T were strictly aerobic, motile, straight rods and grew at pH 7.0-10.8 (optimum, pH 8.5), at 10-55 °C (optimum, 28 °C) and at salinities of 0-23 % (w/v) NaCl (optimum, 14 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain BH103T belongs to the genus Halomonas, showing highest sequence similarity to Halomonas boliviensis LC1T (97.7 %), Halomonas neptunia Eplume1T (97.7 %), Halomonas variabilis IIIT (97.7 %), Halomonas alkaliantarctica CRSST (97.7 %), Halomonas olivaria TYRC17T (97.5 %), Halomonas titanicae BH1T (97.2 %) and Halomonas sulfidaeris Esulfide1T (96.2 %). The predominant ubiquinone was Q-9. The major fatty acids were C18 : 1ω7c, C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C12 : 0 3-OH. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and an unknown phospholipid. The DNA G+C content of this novel isolate was 54.7 mol%. DNA-DNA relatedness between strain BH103T and H. boliviensis KACC 16615T, H. neptunia KCTC 2888T, H. variabilis KCTC 2889T, H. alkaliantarctica KCTC 22844T, H. olivaria DSM 19074T, H. titanicae JCM 16411T and H. sulfidaeris DSM 15722T was 45, 41, 39, 32, 38, 45 and 35 %, respectively. On the basis of polyphasic analysis from this study, strain BH103T represents a novel species of the genus Halomonas, for which the name Halomonas salicampi sp. nov. is proposed. The type strain is BH103T ( = KACC 17609T = NBRC 109914T = NCAIM B 02528T).

High-quality permanent draft genome sequence of the extremely osmotolerant diphenol degrading bacterium Halotalea alkalilenta AW-7(T), and emended description of the genus Halotalea

Members of the genus Halotalea (family Halomonadaceae) are of high significance since they can tolerate the greatest glucose and maltose concentrations ever reported for known bacteria and are involved in the degradation of industrial effluents. Here, the characteristics and the permanent-draft genome sequence and annotation of Halotalea alkalilenta AW-7(T) are described. The microorganism was sequenced as a part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project at the DOE Joint Genome Institute, and it is the only strain within the genus Halotalea having its genome sequenced. The genome is 4,467,826 bp long and consists of 40 scaffolds with 64.62 % average GC content. A total of 4,104 genes were predicted, comprising of 4,028 protein-coding and 76 RNA genes. Most protein-coding genes (87.79 %) were assigned to a putative function. Halotalea alkalilenta AW-7(T) encodes the catechol and protocatechuate degradation to β-ketoadipate via the β-ketoadipate and protocatechuate ortho-cleavage degradation pathway, and it possesses the genetic ability to detoxify fluoroacetate, cyanate and acrylonitrile. An emended description of the genus Halotalea Ntougias et al. 2007 is also provided in order to describe the delayed fermentation ability of the type strain.

Biological treatment of fish processing wastewater: A case study from Sfax City (Southeastern Tunisia)

The present work presents a study of the biological treatment of fish processing wastewater at salt concentration of 55 g/L. Wastewater was treated by both continuous stirred-tank reactor (CSTR) and membrane bioreactor (MBR) during 50 and 100 days, respectively. These biological processes involved salt-tolerant bacteria from natural hypersaline environments at different organic loading rates (OLRs). The phylogenetic analysis of the corresponding excised DGGE bands has demonstrated that the taxonomic affiliation of the most dominant species includes Halomonadaceae and Flavobacteriaceae families of the Proteobacteria (Gamma-proteobacteria class) and the Bacteroidetes phyla, respectively. The results of MBR were better than those of CSTR in the removal of total organic carbon with efficiencies from 97.9% to 98.6%. Nevertheless, salinity with increasing OLR aggravates fouling that requires more cleaning for a membrane in MBR while leads to deterioration of sludge settleability and effluent quality in CSTR.

The marine bacteria Cobetia marina DSMZ 4741 synthesizes an unexpected K-antigen-like exopolysaccharide

We have studied the exopolysaccharide produced by Cobetia marina DSMZ 4741, a marine bacterium isolated from coastal seawater. This strain is able to produce a polysaccharide in presence of carbon sources as glucose, mannitol and alginate. The maximum production occurs in aerobic condition, during the end of the exponential phase. The polymer is a non-viscous, acidic heteropolysaccharide of 270kDa constituted of a repeating unit of: This kind of chemical structure is generally related to K-antigen polysaccharide of pathogenic Escherichia coli strains. This is the first time this type of EPS is described from a marine bacterium. Moreover the polysaccharide exhibits a pyruvate substitution on its 3-deoxy-d-manno-oct-2-ulosonic acid (KDO) residue never encountered before. The discovery of such an unexpected EPS with high biotechnological potential is a new incentive for a better exploration of bioactive marine resources.

Hydration and chain entanglement determines the optimum thickness of poly(HEMA-co-PEG₁₀MA) brushes for effective resistance to settlement and adhesion of marine fouling organisms

Understanding how surface physicochemical properties influence the settlement and adhesion of marine fouling organisms is important for the development of effective and environmentally benign marine antifouling coatings. We demonstrate that the thickness of random poly(HEMA-co-PEG10MA) copolymer brushes affect antifouling behavior. Films of thicknesses ranging from 50 to 1000 Å were prepared via surface-initiated atom-transfer radical polymerization and characterized using infrared spectroscopy, ellipsometry, atomic force microscopy and contact angle measurements. The fouling resistance of these films was investigated by protein adsorption, attachment of the marine bacterium Cobetia marina, settlement and strength of attachment tests of zoospores of the marine alga Ulva linza and static immersion field tests. These assays show that the polymer film thickness influenced the antifouling performance, in that there is an optimum thickness range, 200-400 Å (dry thickness), where fouling of all types, as well as algal spore adhesion, was lower. Field test results also showed lower fouling within the same thickness range after 2 weeks of immersion. Studies by quartz crystal microbalance with dissipation and underwater captive bubble contact angle measurements show a strong correlation between lower fouling and higher hydration, viscosity and surface energy of the poly(HEMA-co-PEG10MA) brushes at thicknesses around 200-400 Å. We hypothesize that the reduced antifouling performance is caused by a lower hydration capacity of the polymer for thinner films, and that entanglement and crowding in the film reduces the conformational freedom, hydration capacity and fouling resistance for thicker films.

Microbiology and epidemiology of Halomonas species

Halomonas has been organized as a genus since 1980, and comprises halophilic and/or halotolerant Gram-negative aerobic bacteria, typically found in saline environments. The genus is enlarging: at present, 76 species are taxonomically recognized, with more to be added. Increasing industrial uses have been found, largely in bioremediation and the production of desirable compounds. Originally seen as environmental contaminants, pathogenicity was initially not recognized; however, disease in algae, animals and humans has now been described. As the biotechnological use of these species increases, and the ability to isolate and recognize them improves, one might expect further pathogenic encounters with humans to be described.

Temporal changes in microbial ecology and geochemistry in produced water from hydraulically fractured Marcellus shale gas wells

Microorganisms play several important roles in unconventional gas recovery, from biodegradation of hydrocarbons to souring of wells and corrosion of equipment. During and after the hydraulic fracturing process, microorganisms are subjected to harsh physicochemical conditions within the kilometer-deep hydrocarbon-bearing shale, including high pressures, elevated temperatures, exposure to chemical additives and biocides, and brine-level salinities. A portion of the injected fluid returns to the surface and may be reused in other fracturing operations, a process that can enrich for certain taxa. This study tracked microbial community dynamics using pyrotag sequencing of 16S rRNA genes in water samples from three hydraulically fractured Marcellus shale wells in Pennsylvania, USA over a 328-day period. There was a reduction in microbial richness and diversity after fracturing, with the lowest diversity at 49 days. Thirty-one taxa dominated injected, flowback, and produced water communities, which took on distinct signatures as injected carbon and electron acceptors were attenuated within the shale. The majority (>90%) of the community in flowback and produced fluids was related to halotolerant bacteria associated with fermentation, hydrocarbon oxidation, and sulfur-cycling metabolisms, including heterotrophic genera Halolactibacillus, Vibrio, Marinobacter, Halanaerobium, and Halomonas, and autotrophs belonging to Arcobacter. Sequences related to halotolerant methanogenic genera Methanohalophilus and Methanolobus were detected at low abundance (<2%) in produced waters several months after hydraulic fracturing. Five taxa were strong indicators of later produced fluids. These results provide insight into the temporal trajectory of subsurface microbial communities after "fracking" and have important implications for the enrichment of microbes potentially detrimental to well infrastructure and natural gas fouling during this process.

Halomonas songnenensis sp. nov., a moderately halophilic bacterium isolated from saline and alkaline soils

A moderately halophilic bacterium (strain NEAU-ST10-39T) was isolated from saline and alkaline soils in the oilfield of Daqing City, Heilongjiang Province, China. The strain was strictly aerobic, Gram-stain-negative, rod-shaped and motile by peritrichous flagella. Its colonies were yellow. It grew at NaCl concentrations of 0.2–15 % (w/v) (optimum 4 %, w/v), at temperatures of 4–40 °C (optimum 35 °C) and at pH 5–10 (optimum pH 7). It did not produce acids from sugars or alcohols. Its DNA G+C content was 57.4 mol%. Phylogenetic analyses based on 16S rRNA gene sequences and concatenated 16S rRNA, gyrB and rpoD gene sequences indicated that it belonged to the genus Halomonas in the class Gammaproteobacteria . The most phylogenetically related species were Halomonas axialensis , Halomonas meridiana and Halomonas aquamarina , whose types shared 98.3 % (16S rRNA), 82.7 % (gyrB) and 83.9–84.5 % (rpoD) sequence similarity with strain NEAU-ST10-39T. The results of DNA–DNA hybridization assays showed 20±2 %–50±1 % relatedness between strain NEAU-ST10-39T and the most closely related species including Halomonas axialensis DSM 15723T, Halomonas meridiana DSM 5425T, Halomonas aquamarina DSM 30161T, Halomonas johnsoniae DSM 21197T, Halomonas stevensii DSM 21198T, Halomonas nanhaiensis CCTCC AB 2012911T, Halomonas hamiltonii DSM 21196T and Halomonas arcis CGMCC 1.6494T. The major fatty acids were C18 : 1ω7c (47.2 %), C16 : 1ω7c and/or C16 : 1ω6c (18.9 %) and C16 : 0 (16.3 %), the only respiratory quinone detected was ubiquinone 9 and polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unknown phospholipids and three unknown lipids. The new isolate is proposed to represent a novel species with the name Halomonas songnenensis sp. nov., NEAU-ST10-39T ( = CGMCC 1.12152T = DSM 25870T) being the type strain.

Halomonas huangheensis sp. nov., a moderately halophilic bacterium isolated from a saline–alkali soil

A novel, Gram-stain-negative, aerobic, rod-shaped, non-motile and moderately halophilic bacterium, designated strain BJGMM-B45T, was isolated from a saline–alkali soil collected from Shandong Province, China. Growth of strain BJGMM-B45T occurred at 10–45 °C (optimum, 30 °C) and pH 5.0–12.0 (optimum, pH 7.0) on Luria–Bertani agar medium with 1–20 % (w/v) NaCl (optimum, 7–10 %). The predominant respiratory quinone was Q-9. The major cellular fatty acids (>5 %) were C18 : 1ω7c, C16 : 0, C19 : 0 cyclo ω8c, summed feature 3, C12 : 0 3-OH and C12 : 0. The genomic DNA G+C content was 57.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BJGMM-B45T belonged to the genus Halomonas in the class Gammaproteobacteria . The closest relatives were Halomonas cupida DSM 4740T (98.2 % 16S rRNA gene sequence similarity) and Halomonas denitrificans M29T (97.8 %). Levels of DNA–DNA relatedness between strain BJGMM-B45T and Halomonas cupida CGMCC 1.2312T and Halomonas denitrificans DSM 18045T were 57.0 and 58.9 %, respectively. On the basis of phenotypic, chemotaxonomic and phylogenetic features, strain BJGMM-B45T is considered to represent a novel species of the genus Halomonas , for which the name Halomonas huangheensis sp. nov. is proposed. The type strain is BJGMM-B45T ( = ACCC 05850T = KCTC 32409T).

Halomonas zincidurans sp. nov., a heavy-metal-tolerant bacterium isolated from the deep-sea environment

A Gram-stain-negative, aerobic, rod-like, motile by peritrichous flagella and moderately halophilic bacterium, designated strain B6(T), was isolated a deep-sea sediment collected from the South Atlantic Ocean. The isolate grew with 0.5-15 % (w/v) NaCl, at 4-37 °C and pH 5.0-8.5 and showed a high tolerance to zinc, manganese, cobalt and copper ions. The major fatty acids were C16 : 0, C19 : 0 cyclo ω8c, C12 : 0 3-OH and C12 : 0. The predominant ubiquinone was Q-9. The genomic DNA G+C content was 61.1 mol%. Phylogenetic analysis based on 16S rRNA gene comparisons indicated that strain B6(T) belonged to the genus Halomonas, and the closest relative was Halomonas xinjiangensis TRM 0175(T) (96.1 %). Based upon the phenotypic, chemotaxonomic and genetic data, strain B6(T) represents a novel species from the genus Halomonas, for which the name Halomonas zincidurans sp. nov. is proposed. The type strain is B6(T) ( = CGMCC 1.12450(T) = JCM 18472(T)).

Seasonal variation in the antifouling defence of the temperate brown alga Fucus vesiculosus

The important role of marine epibiotic biofilms in the interactions of the host with its environment has been acknowledged recently. Previous studies with the temperate brown macroalga Fucus vesiculosus have identified polar and non-polar compounds recovered from the algal surface that have the potential to control such biofilms. Furthermore, both the fouling pressure and the composition of the epibiotic bacterial communities on this macroalga varied seasonally. The extent to which this reflects a seasonal fluctuation of the fouling control mechanisms of the host is, however, unexplored in an ecological context. The present study investigated seasonal variation in the anti-settlement activity of surface extracts of F. vesiculosus against eight biofilm-forming bacteria isolated from rockweed-dominated habitats, including replication of two populations from two geographically distant sites. The anti-settlement activity at both sites was found to vary temporally, reaching a peak in summer/autumn. Anti-settlement activity also showed a consistent and strong difference between sites throughout the year. This study is the first to report temporal variation of antifouling defence originating from ecologically relevant surface-associated compounds.