Biodegradation of phenanthrene by piezotolerant Bacillus subtilis EB1 and genomic insights for bioremediation.

A marine strain B. subtilis EB1, isolated from Equator water, showed excellent degradation towards a wide range of hydrocarbons. Degradation studies revealed dense growth with 93 % and 83 % removal of phenanthrene within 72 h at 0.1 and 20 MPa, respectively. The identification of phenanthrene degradation metabolites by GC-MS combined with its whole genome analysis provided the pathway involved in the degradation process. Whole genome sequencing indicated a genome size of 3,983,989 bp with 4331 annotated genes. The genome provided the genetic compartments, which includes monooxygenase, dioxygenase, dehydrogenase, biosurfactant synthesis catabolic genes for the biodegradation of aromatic compounds. Detailed COG and KEGG pathway analysis confirmed the genes involved in the oxygenation reaction of hydrocarbons, piezotolerance, siderophores, chemotaxis and transporter systems which were specific to adaptation for survival in extreme marine habitat. The results of this study will be a key to design an optimal bioremediation strategy for oil contaminated extreme marine environment.

Genome sequence analysis of deep sea Aspergillus sydowii BOBA1 and effect of high pressure on biodegradation of spent engine oil.

A deep-sea fungus Aspergillus sydowii BOBA1 isolated from marine sediment at a depth of 3000 m was capable of degrading spent engine (SE) oil. The response of immobilized fungi towards degradation at elevated pressure was studied in customized high pressure reactors without any deviation in simulating in situ deep-sea conditions. The growth rate of A. sydowii BOBA1 in 0.1 MPa was significantly different from the growth at 10 MPa pressure. The degradation percentage reached 71.2 and 82.5% at atmospheric and high pressure conditions, respectively, within a retention period of 21 days. The complete genome sequence of BOBA1 consists of 38,795,664 bp in size, comprises 2582 scaffolds with predicted total coding genes of 18,932. A total of 16,247 genes were assigned with known functions and many families found to have a potential role in PAHs and xenobiotic compound metabolism. Functional genes controlling the pathways of hydrocarbon and xenobiotics compound degrading enzymes such as dioxygenase, decarboxylase, hydrolase, reductase and peroxidase were identified. The spectroscopic and genomic analysis revealed the presence of combined catechol, gentisate and phthalic acid degradation pathway. These results of degradation and genomic studies evidenced that this deep-sea fungus could be employed to develop an eco-friendly mycoremediation technology to combat the oil polluted marine environment. This study expands our knowledge on piezophilic fungi and offer insight into possibilities about the fate of SE oil in deep-sea.

Publisher Correction: Genome analysis of deep sea piezotolerant Nesiotobacter exalbescens COD22 and toluene degradation studies under high pressure condition.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Fatty acids-carotenoid complex: An effective anti-TB agent from the chlorella growth factor-extracted spent biomass of Chlorella vulgaris.

ETHNOPHARMACOLOGICAL RELEVANCE: The multidrug-resistant (MDR) pathogen, Mycobacterium tuberculosis, still remains as one of the major threat to mankind, despite the availability of a live attenuated vaccine and effective antibiotics. Marine microalgae, at all times, act as a key resource for valuable therapeutic compounds with limited side effects. AIM OF THE STUDY: The present explorative attempt is to isolate the biomolecules of pharmacological importance from the marine microalgae, Chlorella vulgaris, and to evaluate its effect on the ever dreadful disease, Tuberculosis. The study is also aimed to develop an economically feasible methodology for by-products extraction from microalgae. MATERIALS AND METHODS: Fatty acids-carotenoid complexes (FACC), namely, FACC-1 (red oil) and FACC-2 (brown oil) were isolated, in addition to lipid and lutein from the Chlorella Growth Factor (CGF, a protein fraction enriched with vitamins, minerals and carbohydrates)-extracted spent biomass through column chromatography. RESULTS: FACC-1 is a complex of fatty acids such as oleic and linoleic acids, and carotenoids such as canthaxanthin and neoxanthin. FACC-2 is a complex of oleic, linoleic and linolenic acids and carotenoids (cryptoxanthin and echinenone). Initial screening for evaluation of minimum bactericidal concentration (MBC) of FACC-1 and -2 was performed against Mycobacterium tuberculosis strains such as H37Rv, SHRE sensitive clinical isolate and SHRE resistant clinical isolate. MBC was noted at 10 µg/mL by FACC-1 and at 5 µg/mL by FACC-2, determined using colony forming and Lucipherase Reporter Mycobacteriophages (LRP) assay. Testing in the PAN sensitive isolates indicated that the MBC was noted at 5 µg/mL by FACC-1 and at 2.5 µg/mL by FACC-2. Complete inhibition (100%) was observed at 100 µg/mL by FACC-1 and at 50 µg/mL by FACC-2. Testing of FACC-1 and FACC-2 individually as well as in combination on two different types of MDR strains confirmed the efficacy of the algal oils, wherein in MDR-strain 1, FACC-1 revealed 50% inhibition at 10 µg/mL, while FACC-2 exhibited the same at 5 µg/mL. Conversely, in the case of MDR strain-2, MBC of FACC-1 was at 500 µg/mL and MBCof FACC-2 to be at 250 µg/mL. No significant synergistic effect was observed on combining both the oils. CONCLUSION: The study signifies the development of a potent therapeutic agent comprising of a complex of anti-TB agent (fatty acids) and antioxidants (carotenoids) from the CGF-extracted spent biomass of C. vulgaris.

Genome analysis of deep sea piezotolerant Nesiotobacter exalbescens COD22 and toluene degradation studies under high pressure condition.

A marine isolate, Nesiotobacter exalbescens COD22, isolated from deep sea sediment (2100 m depth) was capable of degrading aromatic hydrocarbons. The Nesiotobacter sp. grew well in the presence of toluene at 0.1 MPa and 10 MPa at a rate of 0.24 h-1 and 0.12 h-1, respectively, in custom designed high pressure reactors. Percentage of hydrocarbon degradation was found to be 87.5% at ambient pressure and it reached 92% under high pressure condition within a short retention period of 72 h. The biodegradation of hydrocarbon was confirmed by the accumulation of dicarboxylic acid, benzoic acid, benzyl alcohol and benzaldehyde which are key intermediates in toluene catabolism. The complete genome sequence consists of 4,285,402 bp with 53% GC content and contained 3969 total coding genes. The complete genome analysis revealed unique adaptation and degradation capabilities for complex aromatic compounds, biosurfactant synthesis to facilitate hydrocarbon emulsification, advanced mechanisms for chemotaxis and presence of well developed flagellar assembly. The genomic data corroborated with the results of hydrocarbon biodegradation at high pressure growth conditions and confirmed the biotechnological potential of Nesiotobacter sp. towards bioremediation of hydrocarbon polluted deep sea environments.

Evaluation of trace metals in seawater, sediments, and bivalves of Nellore, southeast coast of India, by using multivariate and ecological tool.

Urbanization in recent years has driven us to investigate metal contamination on Nellore coast by collecting seawater, sediment, and bivalve samples monthly at five stations from 2015 to 2017. Non-metric multidimensional scaling and cluster analysis indicated that open sea (OS) samples were markedly different from the samples collected at other stations. Strong factor loadings of Al (0.76), Mn (0.79), and Cd (0.78) showed variability in seawater, while those for Fe (0.76), Ni (0.77), Zn (0.85), and Pb (0.81) showed variability in sediment. The mean values of Fe (346 ppm) and Mn (21 ppm) were high in bivalves compared to the mean values of other metals. A higher contamination factor was observed for Cd at Buckingham Canal, while the lowest was observed for sediment in OS. The order of trace metals in sediments according to risk index was Cd > Pb > Cu > Cr > Zn. The results obtained are essential to establish a reference for better comparison of tropical environments.

Biodegradation of crude oil using self-immobilized hydrocarbonoclastic deep sea bacterial consortium.

Hydrocarbonoclastic bacterial consortium that utilizes crude oil as carbon and energy source was isolated from marine sediment collected at a depth of 2100 m. Molecular characterization by 16S rRNA gene sequences confirmed that these isolates as Oceanobacillus sp., Nesiotobacter sp., Ruegeria sp., Photobacterium sp., Enterobacter sp., Haererehalobacter sp., Exiguobacterium sp., Acinetobacter sp. and Pseudoalteromonas sp. Self-immobilized consortium degraded more than 85% of total hydrocarbons after 10 days of incubation with 1% (v/v) of crude oil and 0.05% (v/v) of Tween 80 (non-ionic surfactant) at 28 ±â€¯2 °C. The addition of nitrogen and phosphorus sources separately i.e. 0.1% (v/v) of CO (NH2)2 or K2HPO4 enhanced the hydrocarbon utilization percentage. The pathways of microbial degradation of hydrocarbons were confirmed by FTIR, GC-MS, 1H and 13C NMR spectroscopy analyses. These results demonstrated a novel approach using hydrocarbonoclastic self-immobilized deep sea bacterial consortium for eco-friendly bioremediation.

Studies on the antifungal and serotonin receptor agonist activities of the secondary metabolites from piezotolerant deep-sea fungus Ascotricha sp.

The potent antifungal agent sesquiterpenes and serotonin 5-HT2C agonist ascotricin were produced by a newly isolated deep-sea fungus Ascotricha sp. This fungus was isolated from deep-sea sediment collected at a depth of 1235 m and characterized. Piezotolerance was successfully tested under high pressure-low temperature (100 bar pressure and 20ºC) microbial cultivation system. Production of secondary metabolites was enhanced at optimized culture conditions. The in-vivo antifungal activity of sesquiterpenes was studied using the Caenorhabditis elegans - Candida albicans model system. The sesquiterpenes affected the virulence of C. albicans and prolonged the life of the host C. elegans. These findings suggest that sesquiterpenes are attractive antifungal drug candidates. The 5-HT2C receptor agonist is a potential target for the development of drugs for a range of central nervous system disorders. The interaction of 5-HT2C agonist ascotricin with the receptor was studied through bioinformatic analysis. The in silico molecular docking and molecular dynamic simulation studies demonstrated that they fit into the serotonin 5-HT2C active site and the crucial amino acid residues involved in the interactions were identified. To our knowledge, this is first report of in vivo antifungal analysis of sesquiterpenes and in silico studies of serotonin 5-HT2C receptor-ascotricin complex.

Genomic insights of Vibrio harveyi RT-6 strain, from infected "Whiteleg shrimp" (Litopenaeus vannamei) using Illumina platform.

The pathogenicity of "Vibriosis" in shrimps imposes prominent menace to the sustainable growth of mariculture economy. Often the disease outbreak is associated speciously with Vibrio harveyi and its closely related species. The present study investigated the complete genome of the strain V. harveyi RT-6 to explore the molecular mechanism of pathogenesis. The genome of V. harveyi possesses a single chromosome of 6,374,398 bp in size, G + C content (44.7%) and 5730 protein coding genes. The reads of 1.3 Gb were retained from Illumina Hiseq 2500 sequencing method, assembled into 5912 predicted genes, 114 tRNAs genes, and 11 rRNAs genes. Unigenes were annotated by matching against Clusters of Orthologous Groups of proteins (COG)-5730, Gene ontology (GO)-1088, and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases-3401. Furthermore, 13 insertion sequences-(IS), virulence factors and prophage regions were also identified. A total of 94 pathogenic genes and 36 virulence factor genes were mainly identified using Virulence Factors Database (VFDB). Out of the 36 virulence factors, 23 genes responsible for encoding flagella-based motility protein were exclusively predicted to take part in pathogenic mechanism. The Whole Genome Sequencing (WGS) of the strain RT-6 (accession number: SRR5410471) highlighted the underlying genes and specifically accountable functional genes that were responsible for pathogenic infections in shrimps.

PYRROLO isolated from marine sponge associated bacterium Halobacillus kuroshimensis SNSAB01 - Antifouling study based on molecular docking, diatom adhesion and mussel byssal thread inhibition.

In the present study, an attempt has been made to explore the antifouling potential of bioactive compound isolated from sponge associated bacterium Halobacillus kuroshimensis SNSAB01. The crude extract of SNSAB01 strongly inhibited the growth of fouling bacterial strains with least minimal inhibitory concentration (MIC) and minimum bactericidal concentration (MBC). The bioactive compound was characterized through FT-IR, HPLC, GCMS and NMR predicted as 'pyrrolo". From the mass spectral library, structure was elucidated as pyrrolo [1, 2-a] pyrazine-1, 4-dione, hexahydro. The in silico studies provided encouraging docking scores with two interactions by GLN 200 and GLU 304. The extract inhibited 89% diatom adhesion at 350 µg/ml concentration against Amphora sp. An EC50 value of 150 µg/ml for 50% inhibition of byssal thread of Perna viridis and LC50 was found to be 500 µg/ml. The LC50/EC50 ratio of 3.0 indicated nontoxic to nature. The result suggested that pyrrolo[1,2-a]pyrazine-1,4-dione can be used for antifouling coating.

De novo assembly and annotation of the whole genomic analysis of Vibrio campbellii RT-1 strain, from infected shrimp: Litopenaeus vannamei.

OBJECTIVES: This study aimed to sequence the whole genome of Vibrio campbellii RT-1 strain. METHODS: V. campbellii strain was isolated from an infected shrimp, Litopenaeus vannamei collected from aquaculture ponds, India (12.1899° N, 79.9249° E). The whole genome sequencing (WGS) was performed using the Illumina Hiseq 2500 platform and assembled de novo using SPAdes and Velvet optimiser. Furthermore, the gene prediction and annotation were performed by a rapid prokaryotic genome tool-Prokka. RESULTS: The genome of V. campbellii RT-1 strain has one circular chromosome with 6327218 bp long. V. campbellii RT-1 strain contains 5787 predicted genes with an average of 45% GC content. A total of 86 known genes associated with pathogenicity were identified and 28 genes were found to be responsible for virulence factors. Furthermore, 1112 unigenes were subjected to Gene Ontology (GO) terms, and 4895 predicted proteins were annotated with Clusters of orthologous (COGs) functional groups. CONCLUSIONS: The phylogenetic position of V. campbellii RT-1 strain was established through whole genome sequencing and genomic tools which provides a strong platform to further study on genomic alterations and phenotype of V. campbellii.

Dataset on the importation of the exotic shrimp Penaeus vannamei broodstock (Boone, 1931) to India.

Penaeus vannamei is an exotic shrimp species that has gained high culture momentum, since its introduction to India [1]. Currently, the culture of the species in the Country is being done by the shrimp farmers by importation of Specific Pathogen Free (SPF) vannamei broodstock from approved suppliers, which are located overseas. The value of one brooder normally ranges from 50 to 61 US $, excluding the custom duty, processing fee and other charges for the transboundary shipment of the stock to India. The P. vannamei stock are permitted to be imported to the Country by the hatchery operators only through the single declared port of entry, i.e. Chennai in Tamil Nadu in the Country. The imported parent shrimps are then to be quarantined at the Aquatic Quarantine Facility before being transported to the vannamei hatcheries [2]. This article reports the data available on import of vannamei broodstock to India since its importation to India in 2009. The dataset presented here contains information on transit and quarantine mortality of the brooders following the shipment of the stock by the various broodstock suppliers from the overseas.

Ultrasonic-assisted green synthesis of flower like silver nanocolloids using marine sponge extract and its effect on oral biofilm bacteria and oral cancer cell lines.

The knowhow followed for synthesis, characterization and application of nanomaterials has become an important branch of nanoscience. The use of marine sponges for the synthesis of metal nanoparticles is still in the budding level of current nanobiotechnology. This paper reports a single step one pot biosynthesis utilizing marine sponge (Haliclona exigua) extract as a reducing agent by means of a conventional ultrasonic bath on the formation and growth of flower like silver nanocolloids. These silver nanocolloids were characterized through UV visible spectroscopy, High Resolution Transmission Electron Microscope, Fourier Transform Infrared spectroscopy and X-ray Diffractometer. Further, antibacterial activity and antiproliferative activity were done against oral biofilm bacteria and oral cancer cell lines for the biosynthesized flower like silver nanocolloids. Water soluble organic amines were responsible for the syntheses of nanomaterials which have a size range from 100 to 120 nm. An average size of 9.1 mm zone of inhibition was recorded with 10.0 µg of silver nanocolloids against oral biofilm bacteria. The estimated half maximal inhibitory concentration value for flower like silver nanocolloids was 0.6 µg/ml for oral cancer cell lines.

Evaluation of zinc oxide nanoparticles toxicity on marine algae chlorella vulgaris through flow cytometric, cytotoxicity and oxidative stress analysis.

The increasing industrial use of nanomaterials during the last decades poses a potential threat to the environment and in particular to organisms living in the aquatic environment. In the present study, the toxicity of zinc oxide nanoparticles (ZnO NPs) was investigated in Marine algae Chlorella vulgaris (C. vulgaris). High zinc dissociation from ZnONPs, releasing ionic zinc in seawater, is a potential route for zinc assimilation and ZnONPs toxicity. To examine the mechanism of toxicity, C. vulgaris were treated with 50mg/L, 100mg/L, 200mg/L and 300 mg/L ZnO NPs for 24h and 72h. The detailed cytotoxicity assay showed a substantial reduction in the viability dependent on dose and exposure. Further, flow cytometry revealed the significant reduction in C. vulgaris viable cells to higher ZnO NPs. Significant reductions in LDH level were noted for ZnO NPs at 300 mg/L concentration. The activity of antioxidant enzyme superoxide dismutase (SOD) significantly increased in the C. vulgaris exposed to 200mg/L and 300 mg/L ZnO NPs. The content of non-enzymatic antioxidant glutathione (GSH) significantly decreased in the groups with a ZnO NPs concentration of higher than 100mg/L. The level of lipid peroxidation (LPO) was found to increase as the ZnO NPs dose increased. The FT-IR analyses suggested surface chemical interaction between nanoparticles and algal cells. The substantial morphological changes and cell wall damage were confirmed through microscopic analyses (FESEM and CM).

Biodegradation of complex hydrocarbons in spent engine oil by novel bacterial consortium isolated from deep sea sediment.

Complex hydrocarbon and aromatic compounds degrading marine bacterial strains were isolated from deep sea sediment after enrichment on spent engine (SE) oil. Phenotypic characterization and phylogenetic analysis of 16S rRNA gene sequences showed the isolates were related to members of the Pseudoalteromonas sp., Ruegeria sp., Exiguobacterium sp. and Acinetobacter sp. Biodegradation using 1% (v/v) SE oil with individual and mixed strains showed the efficacy of SE oil utilization within a short retention time. The addition of non-ionic surfactant 0.05% (v/v) Tween 80 as emulsifying agent enhanced the solubility of hydrocarbons and renders them more accessible for biodegradation. The degradation of several compounds and the metabolites formed during the microbial oxidation process were confirmed by Fourier transform infrared spectroscopy and Gas chromatography-mass spectrometry analyses. The potential of this consortium to biodegrade SE oil with and without emulsifying agent provides possible application in bioremediation of oil contaminated marine environment.

Multivariate statistical approach to identify significant sources influencing the physico-chemical variables in Aerial Bay, North Andaman, India.

Aerial Bay is one of the harbor towns of Andaman and Nicobar Islands, the union territory of India. Nevertheless, it is least studied marine environment, particularly for physico-chemical assessment. Therefore, to evaluate the annual spatiotemporal variations of physico-chemical parameters, seawater samples collected from 20 sampling stations covering three seasons were analyzed. Multivariate statistics is applied to the investigated data in an attempt to understand the causes of variation in physico-chemical parameters. Cluster analysis distinguished mangrove and open sea stations from other areas by considering distinctive physico-chemical characteristics. Factor analysis revealed 79.5% of total variance in physico-chemical parameters. Strong loading included transparency, TSS, DO, BOD, salinity, nitrate, nitrite, inorganic phosphate, total phosphorus and silicate. In addition, box-whisker plots and Geographical Information System based land use data further facilitated and supported multivariate results.

Silver nanoparticles with anti microfouling effect: a study against marine biofilm forming bacteria.

Marine biofilms are the preliminary entities due to attachment of bacteria on surfaces immersed in seawater and aggregated in a hydrated polymeric matrix. Such biofilms or microfouling play a major role in the succession of marine biofouling which attracts the larvae of barnacles, mussels and other sessile invertebrates. Different approaches have been used to prevent micro and macrofouling on marine industrial settings. Silver nanoparticles are renowned for their influential antimicrobial activity. On this back drop the present work is focused on the effect of biosynthesized silver nanoparticles against marine biofilm forming bacterial species. Aspects such as circular zone of inhibition, quantification of biofilm formation and bacterial growth were assessed for bacterial species isolated from the marine biofilm in the presence and sabsence of silver nanoparticles. The size of the circular zone formation was directly proportional to the concentration of biosynthesized silver nanoparticles that reflected the antimicrobial effect. The crystal violet staining on biofilm formation and its optical density revealed the effect on biofilm inhibition. The growth of bacteria in the presence and absence of silver nanoparticles concluded the bactericidal ability of the silver nanoparticles. However, further research is required to examine these factors.

Evaluation of significant sources influencing the variation of physico-chemical parameters in Port Blair Bay, South Andaman, India by using multivariate statistics.

Port Blair is the capital city of Andaman & Nicobar Islands, the union territory of India. More than 50% of the population of these islands lives around Port Blair Bay. Therefore the anthropogenic effects in the bay water were studied for monitoring purpose from seven stations. Physico-chemical parameters of seawater were analyzed in samples collected once in every 3 months for 2 years from seven sampling stations located in Port Blair Bay, South Andaman Island to evaluate the spatial and tidal variation. Cluster analysis and factor analysis were applied to the experimental data in an attempt to understand the sources of variation of physico-chemical parameters. In cluster analysis, the stations Junglighat Bay and Phoenix Bay having high anthropogenic influence formed a separate group. The factors obtained from factor analysis indicated that the parameters responsible for physico-chemical variations are mainly related to land run-off, sewage outfall and tidal flow.

Four new records of Conidae (Mollusca: Caenogastropoda) from the Andaman Islands, India.

The Andaman and Nicobar archipelago comprises 572 islands spread over an area of 8,249 sq. km. These islands are within the 'Indo-Malayan region' and near the 'faunistic centre' from which other Indo-West Pacific regions recruit their tropical marine fauna (Ekman, 1953). The topographically complex nature of the nearshore environments of these islands creates a plethora of niches that support a rich and diverse molluscan fauna. Many of the Conus species (e.g., C. geographus Linnaeus, 1758; C. miles Linnaeus, 1758; and C. striatus Linnaeus, 1758) that occupy these islands are broadly distributed throughout the Indo-West Pacific. However, a few Indo-West Pacific species (e.g., Conus andamanensis Smith, 1878; and C. araneosus nicobaricus Hwass in Bruguière, 1792) are restricted to small geographic regions (Röckel et. al. 1995). Early oceanographic expeditions of the Andaman and Nicobar Islands that began in 1788 report only 10 Conus species from these islands (Smith, 1878; Melvill & Sykes, 1898; Preston, 1908). More recently, Subba Rao (1980) of the Zoological Survey of India (ZSI) reports a total of 51 Conus species from this region. In the past two decades, the Conus fauna has not been studied extensively due to lack of focused studies in the Andaman and Nicobar Islands. Several recent surveys conducted by the Andaman and Nicobar Centre for Ocean Science and Technology investigated the intertidal and subtidal macrobenthic fauna of the Andaman Islands. The present study reports four Conus species for the first time from this location. The observations of multiple living specimens of each species confirm this report. Three species (Conus leopardus Röding, 1798, C. litoglyphus Hwass in Bruguière, 1792 and C. striatellus Link, 1807) are new records from Andaman Islands and one (Conus coffeae Gmelin, 1791) represents a new record for India. One specimen of each species was deposited in the National Zoological Collections, ZSI/ANRC, Port Blair, India.