Aestuariicella hydrocarbonica gen. nov., sp. nov., an aliphatic hydrocarbon-degrading bacterium isolated from a sea tidal flat

Mechanisms of intestinal injury in polychaete Perinereis aibuhitensis caused by low-concentration fluorene pollution: Microbiome and metabonomic analyses

The polychaete Perinereis aibuhitensis is used for bioremediation; however, its ability to remove fluorene, a common environmental pollutant, from sediments remains unclear, especially at low concentrations of fluorene (10 mg/kg). In this study, we explored the mechanism of intestinal injury induced by low concentrations of fluorene and the reason intestinal injury is alleviated in high fluorene concentration groups (100 and 1000 mg/kg) using histology, ecological biomarkers, gut microbiome, and metabolic response analyses. The results show that P. aibuhitensis showed high tolerance to fluorene in sediments, with clearance rates ranging 25-50 %. However, the remediation effect at low fluorene concentrations (10 mg/kg) was poor. This is attributed to promoting the growth of harmful microorganisms such as Microvirga, which can cause metabolic disorders, intestinal flora imbalances, and the generation of harmful substances such as 2-hydroxyfluorene. These can result in severe intestinal injury in P. aibuhitensis, reducing its fluorene clearance rate. However, high fluorene concentrations (100 and 1000 mg/kg) may promote the growth of beneficial microorganisms such as Faecalibacterium, which can replace the dominant harmful microorganisms and improve metabolism to reverse the intestinal injury caused by low fluorene concentrations, ultimately restoring the fluorene-removal ability of P. aibuhitensis. This study demonstrates an effective method for evaluating the potential ecological risks of fluorene pollution in marine sediments and provides guidance for using P. aibuhitensis for remediation.

Surface-associated bacterial assemblages on marine anthropogenic litter in the intertidal zone of the Arabian Sea, India

Anthropogenic marine litter (mainly plastic pollution) is a serious concern globally. The interactions between terrestrial and marine ecosystems lead to the accumulation of marine litter in the intertidal zone. The biofilm-forming bacteria tend to colonize on surfaces of marine litter which are composed of diverse bacteria and are less studied. The present study investigated the bacterial community composition using both culturable and non-culturable (Next-generation sequencing (NGS)) approaches associated with the marine litter (polyethylene (PE), styrofoam (SF) and fabric (FB)) at three distinct locations (Alang, Diu and Sikka) of the Arabian Sea, Gujarat, India. Predominant bacteria observed using culturable and NGS techniques belonged to Proteobacteria phyla. Alphaproteobacteria class dominated on polyethylene and styrofoam surfaces in the culturable fraction among the sites while the Bacillus dominated fabric surfaces. In the metagenomics fraction, Gammaproteobacteria dominated the surfaces except for PE and SF surfaces from Sikka and Diu, respectively. The PE surface at Sikka was dominated by Fusobacteriia while SF surface from Diu was dominated by Alphaproteobacteria. Both culture-dependent and NGS approaches identified hydrocarbon-degrading bacteria as well as pathogenic bacteria on the surfaces. The outcome of the present study illustrates diverse bacterial assemblages which occur on marine litter and increases our understanding of the plastisphere community.

Aestuariicella albida sp. nov., isolated from surface water of the Yellow Sea, and proposal of the genus Aestuariicella as a member of the family Cellvibrionaceae

A Gram-stain-negative, non-motile and aerobic bacterium, designated HHU G3-2T, was isolated from surface water of the Yellow Sea, PR China. Strain HHU G3-2T was positive for oxidase activity and negative for catalase. Optimal growth occurred at 28 °C (range, 20–37 °C), pH 7.0 (range, pH 6.0–9.0) and in the presence of 2–5 % (w/v) NaCl (range, 1–7%). Phylogenetic analysis based on 16S rRNA gene sequences and 120 ubiquitous single-copy protein-coding genes indicated that strain HHU G3-2T formed a distinct phylogenetic lineage with Aestuariicella hydrocarbonica JCM 30134T, sharing a 16S rRNA gene sequence similarity of 98.05%. Average nucleotide identity and digital DNA–DNA hybridization values between strain HHU G3-2T and A. hydrocarbonica JCM 30134T were 75.74 and 17.80%, respectively, which were below the threshold values of 95–96 and 70 %, respectively. The DNA G+C content of the genomic DNA was 51.17 mol%. The major fatty acids (>10 %) were C17 : 1 ω8c (19.8 %), summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c; 15.9 %), summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c; 13.8 %) and C17 : 0 (10.3 %). The predominant isoprenoid quinone was ubiquinone-8. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Based on the polyphasic taxonomic data, strain HHU G3-2T represents a novel species of the genus Aestuariicella , for which the name Aestuariicella albida sp. nov. is proposed. The type strain is HHU G3-2T (=MCCC 1K04224T=JCM 34652T=GDMCC 1.2418T=CGMCC 1.17397T). In addition, we proposed the genus Aestuariicella as a member of the family Cellvibrionaceae .

An appraisal of early stage biofilm-forming bacterial community assemblage and diversity in the Arabian Sea, India

The community composition and distribution of early-stage (24 h) biofilm-forming bacteria on two different surfaces (glass slide and polystyrene plastic slide) at three different locations (Diu, Alang and Sikka) were studied using a culture-dependent and next-generation sequencing (NGS) approach in the Arabian Sea, Gujarat, India. The most dominant phyla observed using the NGS approach were the Proteobacteria among the sampling sites. Gammaproteobacteria class dominated both the surfaces among the sites and accounted for 46.7% to 89.2% of total abundance. The culture-dependent analysis showed Proteobacteria and Firmicutes as the dominant phyla on the surfaces within the sampling sites. During the initial colonization, hydrocarbon-degrading bacterial strains have also attached to the surfaces. The outcome of this study would be of great importance for targeting the early stage biofilm-forming and hydrocarbon-degrading bacterial isolates may help to degrade plastic in the marine environment.

Electrochemical Bacterial Enrichment from Natural Seawater and Its Implications in Biocorrosion of Stainless-Steel Electrodes

Microbial electrochemical technologies have revealed the opportunity of electrochemical enrichment for specific bacterial groups that are able to catalyze reactions of interest. However, there are unsolved challenges towards their application under aggressive environmental conditions, such as in the sea. This study demonstrates the impact of surface electrochemical potential on community composition and its corrosivity. Electrochemical bacterial enrichment was successfully carried out in natural seawater without nutrient amendments. Experiments were carried out for ten days of exposure in a closed-flow system over 316L stainless steel electrodes under three different poised potentials (−150 mV, +100 mV, and +310 mV vs. Ag/AgCl). Weight loss and atomic force microscopy showed a significant difference in corrosion when +310 mV (vs. Ag/AgCl) was applied in comparison to that produced under the other tested potentials (and an unpoised control). Bacterial community analysis conducted using 16S rRNA gene profiles showed that poised potentials are more positive as +310 mV (vs. Ag/AgCl) resulted in strong enrichment for Rhodobacteraceae and Sulfitobacter. Hence, even though significant enrichment of the known electrochemically active bacteria from the Rhodobacteraceae family was accomplished, the resultant bacterial community could accelerate pitting corrosion in 316 L stainless steel, thereby compromising the durability of the electrodes and the microbial electrochemical technologies.

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

A Gram-stain-negative, non-spore-forming, aerobic, curved rod-shaped bacterium, designed strain R142^T, was isolated from a coralline algae Tricleocarpa sp. in the Beibu Gulf, China. Optimal growth occurred with 0-0.5 % (w/v) NaCl, at 25 °C and at pH 8. Global alignment based on 16S rRNA gene sequences indicated that strain R142^T shared 93.8 % similarity with its closest type strain, Pseudomaricurvus alkylphenolicus KU14G^T. Phylogenetic analyses showed that strain R142^T forms a distinct branch alongside Maricurvus nonylphenolicus KU41E^T, Pseudoteredinibacter isoporae SW-11^T, Pseudomaricurvus alkylphenolicus KU14G^T, Pseudomaricurvus alcaniphilus MEBiC06469^T and Aestuariicella hydrocarbonica SM-6^T. The major polar lipids of strain R142^T were phosphatidylethanolamine and phosphatidylglycerol. The primary cellular fatty acids were C_16 : 0, C_16 : 1ω7c, C_18 : 1ω7c, C_18 : 0 and C_14 : 0. The genome DNA G+C ratio was 56.4 mol%. The only detected respiratory quinone was ubiquinone 8. The low 16S rRNA gene sequence similarity and differences in cellular fatty acids readily distinguished strain R142^T from all validly published type strains. Strain R142^T is therefore suggested to represent a novel species of a new genus, for which the name Exilibacterium tricleocarpae gen. nov., sp. nov. is proposed. The type strain of Exilibacterium tricleocarpae is R142^T (=MCCC 1K03816^T=KCTC 72138^T).

Identification of microbial key-indicators of oil contamination at sea through tracking of oil biotransformation: An Arctic field and laboratory study

In this paper, a molecular analytical approach for detecting hydrocarbonoclastic bacteria in water is suggested as a proxy measurement for tracking petroleum discharges in industrialized or pristine aquatic environments. This approach is tested for general application in cold marine regions (freezing to 5 °C). We used amplicon sequencing and qPCR to quantify 16S rRNA and GyrB genes from oleophilic bacteria in seawater samples from two different crude oil enrichments. The first experiment was conducted in a controlled environment using laboratory conditions and natural North Sea fjord seawater (NSC) at a constant temperature of 5 °C. The second was performed in the field with natural Arctic seawater (ARC) and outdoor temperature conditions from -7 °C to around 4 °C. Although the experimental conditions for NSC and ARC differed, the temporal changes in bacterial communities were comparable and reflected oil biotransformation processes. The common bacterial OTUs for NSC and ARC had the highest identity to Colwellia rossensis and Oleispira antarctica rRNA sequences and were enriched within a few days in both conditions. Other typical oil degrading bacteria such as Alcanivorax (n-alkane degrader) and Cycloclasticus (polycyclic aromatic hydrocarbons degrader) were rapidly enriched only in NSC conditions. Both the strong correlation between Oleispira SSU gene copies and oil concentration, and the specificity of the Oleispira assay suggest that this organism is a robust bioindicator for seawater contaminated by petroleum in cold water environments. Further optimization for automation of the Oleispira assay for in situ analysis with a genosensing device is underway. The assay for Colwellia quantification requires more specificity to fewer Colwellia OTUs and a well-established dose-response relationship before those taxa are used for oil tracking purposes.

Colonization of Non-biodegradable and Biodegradable Plastics by Marine Microorganisms

Plastics are ubiquitous in the oceans and constitute suitable matrices for bacterial attachment and growth. Understanding biofouling mechanisms is a key issue to assessing the ecological impacts and fate of plastics in marine environment. In this study, we investigated the different steps of plastic colonization of polyolefin-based plastics, on the first one hand, including conventional low-density polyethylene (PE), additivated PE with pro-oxidant (OXO), and artificially aged OXO (AA-OXO); and of a polyester, poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV), on the other hand. We combined measurements of physical surface properties of polymers (hydrophobicity and roughness) with microbiological characterization of the biofilm (cell counts, taxonomic composition, and heterotrophic activity) using a wide range of techniques, with some of them used for the first time on plastics. Our experimental setup using aquariums with natural circulating seawater during 6 weeks allowed us to characterize the successive phases of primo-colonization, growing, and maturation of the biofilms. We highlighted different trends between polymer types with distinct surface properties and composition, the biodegradable AA-OXO and PHBV presenting higher colonization by active and specific bacteria compared to non-biodegradable polymers (PE and OXO). Succession of bacterial population occurred during the three colonization phases, with hydrocarbonoclastic bacteria being highly abundant on all plastic types. This study brings original data that provide new insights on the colonization of non-biodegradable and biodegradable polymers by marine microorganisms.

Pacificibacter aestuarii sp. nov., isolated from a tidal flat

A Gram-stain-negative, strictly aerobic bacterium, designated KJ21T, was isolated from a tidal flat in South Korea. Cells were non-motile rods showing oxidase- and catalase-positive activities. Growth of strain KJ21T was observed at 10-35 °C (optimum, 30 °C), at pH 6.0-8.5 (optimum, pH 7.0) and in the presence of 1-5 % (w/v) NaCl (optimum, 2 %). Strain KJ21T contained summed feature 8 (comprising C18 : 1ω7c/C18 : 1ω6c), C16 : 0, 10-methyl C19 : 0 and C10 : 0 3-OH as the major fatty acids and ubiquinone-10 as the major isoprenoid quinone. Phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unknown aminolipid and an unknown lipid were detected as the major polar lipids. The G+C content of the genomic DNA was 53.9 mol%. Phylogenic analysis based on 16S rRNA gene sequences showed that strain KJ21T formed a tight phylogenetic lineage with the members of the genus Pacificibacter with a 100 % bootstrap value. Strain KJ21T was most closely related to Pacificibacter maritimus KMM 9031T (98.7 %) and Pacificibacter marinus HDW-9T (98.4 %), and the DNA-DNA relatedness values between strain KJ21T and the type strains of P. maritimus and P. marinus were 46.9±4.2 % and 39.8±5.7, respectively. On the basis of phenotypic, chemotaxonomic and molecular properties, it is clear that strain KJ21T represents a novel species of the genus Pacificibacter, for which the name Pacificibacter aestuarii sp. nov. is proposed. The type strain is KJ21T (=KACC 19098T=JCM 31805T).

Microbial community composition of deep-sea corals from the Red Sea provides insight into functional adaption to a unique environment

Microbes associated with deep-sea corals remain poorly studied. The lack of symbiotic algae suggests that associated microbes may play a fundamental role in maintaining a viable coral host via acquisition and recycling of nutrients. Here we employed 16 S rRNA gene sequencing to study bacterial communities of three deep-sea scleractinian corals from the Red Sea, Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus typus. We found diverse, species-specific microbiomes, distinct from the surrounding seawater. Microbiomes were comprised of few abundant bacteria, which constituted the majority of sequences (up to 58% depending on the coral species). In addition, we found a high diversity of rare bacteria (taxa at <1% abundance comprised >90% of all bacteria). Interestingly, we identified anaerobic bacteria, potentially providing metabolic functions at low oxygen conditions, as well as bacteria harboring the potential to degrade crude oil components. Considering the presence of oil and gas fields in the Red Sea, these bacteria may unlock this carbon source for the coral host. In conclusion, the prevailing environmental conditions of the deep Red Sea (>20 °C, <2 mg oxygen L-1) may require distinct functional adaptations, and our data suggest that bacterial communities may contribute to coral functioning in this challenging environment.

A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments

Many microbial ecology experiments use sequencing data to measure a community’s response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samples and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method’s validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of “bottle effects”.

Pseudomaricurvus alcaniphilus sp. nov., a marine bacterium isolated from tidal flat sediment and emended descriptions of the genus Pseudomaricurvus, Pseudomaricurvus alkylphenolicus Iwaki et al. 2014 and Maricurvus nonylphenolicus Iwaki et al. 2012

A novel Gram-reaction-negative, rod-shaped, aerobic and motile strain, designated MEBiC06469T, was isolated from tidal flat sediment of the Taean province, South Korea. Strain MEBiC06469T produced ivory-coloured colonies on marine agar 2216 medium and could degrade carboxymethyl-cellulose. On the basis of 16S rRNA gene sequence similarity, the closest relative was Pseudomaricurvus alkylphenolicus KU41GT with 96.5 % similarity. The isolate was catalase-positive but oxidase-negative. Growth was observed at 16-38 °C (optimum, 32 °C), at pH 6.0-9.0 (optimum, pH 7.5) and in the presence of 0.0-8.0 % (w/v) NaCl (optimum, 1.5 %). The only isoprenoid quinone was Q-8.The dominant fatty acids were summed feature 3 (comprised of C15 : 0 2-OH and/or C16 : 1ω7c; 20.4 %) and C17 : 1ω8c (30.9 %), summed feature 8 (comprised of C18 : 1ω7c and/or C18 : 1ω6c; 9.5 %), C16 : 0 (9.0 %), C15 : 1ω8c (5.3 %), and C11 : 0 3-OH (5.2 %). Based on these phenotypic properties and phylogenetic data, strain MEBiC06469T should be classified as a novel species within the genus Pseudomaricurvus for which the name Pseudomaricurvus alcaniphilus sp. nov. is proposed. The type strain is MEBiC06469T ( = KCCM 42976T = JCM 18313T). Emended descriptions of the genus Pseudomaricurvus, Pseudomaricurvus alkylphenolicusIwaki et al. 2014, and Maricurvus nonylphenolicusIwaki et al. 2012 are also provided.