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Copper is one of the essential trace dietary minerals for all living organisms, but is potentially toxic at higher concentrations, mainly due to the redox reactions in its transition state. Tolerance of microbes towards copper is primarily attributed to chelation and biosorption. In this study, marine-derived filamentous fungi were evaluated for their ability to remove Cu(ii) from a culture medium. Further, the cellular response of a select isolate to salinity stress (0, 35 and 100 PSU) and Cu(ii) stress (0, 100, and 500 ppm) was studied using the peptide mass fingerprinting technique, which revealed expression of 919 proteins, of which 55 proteins were commonly expressed across all conditions. Housekeeping proteins such as citrate synthase, pyruvate carboxylase, ribosomal proteins, ATP synthases, and more were expressed across all conditions. Reactive oxygen species scavenging proteins such as glutaredoxin, mitochondrial peroxiredoxins and thioredoxins were expressed under Cu(ii) and salinity stresses individually as well as in combination. Up-regulation of glutaredoxin under Cu(ii) stress with fold change values of 18.3 and 13.9 under 100 ppm and 500 ppm of Cu(ii) indicated active scavenging of free radicals to combat oxidative damage. The common mechanisms reported were enzymatic scavenging of free radicals, activation of DNA damage and repair proteins and probable intracellular metal chelation. This indicated multiple stress mechanisms employed by the isolate to combat the singular and synergistic effects of Cu(ii) and salinity stress.

The beaches of Goa state in India are frequently polluted with tarballs, specifically during pre-monsoon and monsoon seasons. Tarballs contain hydrocarbons, including polycyclic aromatic hydrocarbons, which pose significant environmental risks. Microbes associated with tarballs reportedly possess capabilities to degrade toxic hydrocarbons present in tarballs. In this study, bacterial diversity associated with tarballs from Vagator and Morjim beaches of north Goa was analysed based on V3-V4 regions of 16S rRNA gene sequenced using Illumina Miseq Platform. The Proteobacterial members were dominant in both Vagator (≥85.5%) and Morjim (≥94.0%) samples. Many of the identified taxa have been previously reported as hydrocarbon degraders (e.g. Halomonas, Marinobacter) or possible human pathogens (e.g. Acinetobacter, Klebsiella, Rhodococcus, Staphylococcus, Vibrio). This is the first study reported on a metagenomic analysis of bacteria associated with tarballs from Goa.

The eastern Arabian Sea has a unique and permanent oxygen minimum zone (OMZ) extending along the western continental margin of India. The Arabian Sea OMZ is a site of intense denitrification, contributing to 20% of the global oceanic denitrification, playing a significant role in the nitrogen cycle. This study reveals the members of the culturable marine bacterial communities thriving and functioning in the sediment underlying the Arabian Sea OMZ, through 16S rDNA phylogenetic analysis and elucidating their nitrate reduction potential. Phylogenetic analyses revealed that these cultured bacteria distributed into five phyla, viz. Firmicutes (45.7%) Gammaproteobacteria (36.84%), Actinobacteria (8.7%), Bacteroidetes (5.26%), and Alphaproteobacteria (3.5%). The presence of denitrification genes such as narG, nirS, and nosZ in the cultured bacteria (39%) explains their importance in this process. Present study on the diversity and distribution of bacterial communities in the OMZ surface sediment and their probable role in the nitrogen cycle will provide insight into the microbial biogeochemical processes occurring in this region.

Microbial community mediated denitrification leads to nitrate reduction and, its eventual removal from marine ecosystems. Therefore, it is necessary to understand the functional diversity in terms of the abundance and types of nitrate reductases in the microbial communities extant in the hypoxic/suboxic waters where organic matter oxidation is predominantly nitrate- reduction mediated. For this study, water samples from the surface, mid-depth and close to bottom were collected from three coastal locations along the west coast of India during Summer monsoon (SuM), Fall intermonsoon (FIM) and, Spring intermonsoon (SIM). The abundance of nitrate (narG), nitrite (nirS) and nitrous oxide (nosZ) reductase genes from these water samples were quantified by qPCR method. Besides the distinct spatio-temporal differences, the overall ranges of these three functional genes across the sampling sites ranged from 1.9 x 107 to 7.9 x 107 copies L-1 (narG), from 0.001 x 106 to 0.30 x 106 copies L-1 (nirS) and from 0.30 x 106 to 2.9 x 106 copies L-1 (nosZ). Functional gene sequencing of bacterial communities possessing these reductases were diverse and, dominated by members of Alpha-, Beta- and Gamma-proteobacteria, including taxonomic groups containing well known denitrifiers such as Pseudogulbenkiania, Kocuria, Pseudomonas, Herbaspirillum, Achromobacter, Rhodoferax, Mesorhizobium, Sinorhizobium, Shinella, Bradyrhizobiaceae, Rhodopseudomonas, Dinoroseobacter, Paracoccus, Rhodobacter, Ruegeria and Azospirillum sp. Assemblages of bacteria possessing narG, nirS, and nosZ indicated that complete denitrification could occur, particularly in the samples collected close to the bottom.

The subsurface waters of the northern Arabian Sea display a pronounced oxygen minimum layer associated with high nitrite maxima which provide an ideal niche for organisms that can respire nitrate. Culture-based studies elaborate the physiological characteristics of the organisms and their metabolic activities in biogeochemical cycles. In this study, the bacterial diversity and nitrate utilizing activity of the culturable heterotrophic bacteria inhabiting the water column oxygen minimum zone of Arabian Sea were investigated. Nitrate-reducing bacteria were isolated from the water column in the central Arabian Sea. Genotypic characterization of the isolates using 16 S rDNA gene sequencing grouped them into three phylogenetic groups i.e. Proteobacteria, Firmicutes, and Actinobacteria. Out of the 56 isolated bacteria, 45 strains belonged to Proteobacteria, 6 to Firmicutes and 5 to Actinobacteria. The nitrate reducing ability of the isolates was tested using Griess test. Thirty-six species belonging to genera Alcanivorax, Alteromonas, Halomonas, Pseudoalteromonas, Marinobacter, Bacillus, and Vibrio were positive for NO2-/NO3- reduction. Our results imply that cultivable bacteria capable of utilizing NO3 - available in the system are present in the Arabian Sea oxygen minimum zone and the conditions existing therein must be favorable for their growth and functionality.

Seasonal variations, as well as depth-wise distribution patterns of bacterial and archaeal communities in the Arabian Sea oxygen minimum zone (AS-OMZ), were analyzed by examining 16S rRNA gene clones and their sequences. Sampling was carried out at the Arabian Sea Time Series (ASTS) location (17°0.126′ N, 67°59.772′ E) from five different depths during three different seasons. A total of 743 and 256 non-chimeric bacterial and archaeal 16S rRNA gene sequences were analyzed. Most of the bacterial 16S rRNA gene sequences were affiliated to Gammaproteobacteria (39.31%), Alphaproteobacteria (23.56%) and Cyanobacteria (20.2%). The archaeal 16S rRNA gene sequences mostly aligned with Marine Group II (MG-II, Euryarchaeota). An explicit vertical partitioning of bacterial communities between the surface (surface and DCM) and OMZ (250 m, 500 m, and 1000 m) was observed. Also evident was an apparent seasonal variation among surface bacterial communities but a minimal variation among OMZ bacterial and archaeal communities. LINKTREE and canonical correspondence analysis (CCA) indicates that differences in the concentrations of dissolved oxygen (DO) and total organic carbon (TOC) seem to cause the vertical separation among bacterial communities in the ASTS station. A higher number of shared OTUs affiliated mainly to Alteromonadales (bacteria) and Methanosarcinales (archaea) contributed towards seasonally stable community structure in the OMZ depths.

Bacterial community involved in nitrogen transformations in the oxygen minimum zones (OMZ) with dissolved oxygen (DO) levels below 0.5 ml L−1 is ascribed to be responsible for the reported 40% losses of fixed nitrogen. The Arabian Sea (AS) OMZ is among the largest suboxic regions accounting for a substantial loss of fixed nitrogen. Sampling was carried out at the Arabian Sea Time Series (ASTS) location (17°0.126′ N, 67°59.772′E) during three different seasons to document the diversity and abundance of both denitrifying and anammox bacteria, based on their molecular markers. Quantitative PCR (qPCR) was done to assess the abundance and distribution of genes encoding nitrite reductase (nirS) in denitrifying bacteria and hydrazine oxidoreductase (hzo) in anammox bacteria. Copy numbers of these genes had their maxima in the core OMZ depths of 250 and 500 m. The preponderance of nirS to the tune of 0.35 × 106 copy numbers L−1 and hzo, of 1.5 × 106 L−1 is indicative of simultaneous denitrification and anammox processes. The abundance of hzo was higher than nirS during all three seasons implying probable dominance of anammox process at this sampling location. Phylogenetic analysis revealed that nirS gene was present in bacteria belonging to Gammaproteobacteria, Alphaproteobacteria and Deltaproteobacteria. All the hzo sequences obtained in this study apparently imply that Candidatus Scalindua is the dominant anammox bacteria at the ASTS location.

Chromium (Cr) released from industrial units such as tanneries, textile and electroplating industries is detrimental to the surrounding ecosystems and human health. The focus of the present study was to check the Cr(VI) removal efficiency by marine-derived fungi from liquid broth. Amongst the three Cr(VI) tolerant isolates, #NIOSN-SK56-S19 (Aspergillus sydowii) showed Cr-removal efficiency of 0.01 mg Cr mg(−1) biomass resulting in 26% abatement of total Cr with just 2.8 mg of biomass produced during the growth in 300 ppm Cr(VI). Scanning Electron Microscopy revealed aggregation of mycelial biomass with exopolysaccharide, while Electron Dispersive Spectroscopy showed the presence of Cr(2)O(3) inside the biomass indicating presence of active Cr(VI) removal mechanisms. This was further supported when the Cr(VI) removal was monitored using DPC (1,5-diphenylcarbazide) method. The results of this study point to the potential of marine-derived fungal isolates for Cr(VI) removal. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12088-018-0719-z) contains supplementary material, which is available to authorized users.

Red clays of Central Indian Basin (CIB) under influence of trace of Rodriguez Triple Junction exhibited chemoautotrophy, low temperature hydrothermal alterations and photoautotrophic potential. Seamount flank TVBC-08, hosting such signatures revealed dominance of aerobic anoxygenic phototroph Erythrobacter, with 93% of total 454 pyrosequencing tags. Subsequently, enrichments for both aerobic (Erythrobacter) and anaerobic anoxygenic phototrophs (green and purple sulphur bacteria) under red and white LED light illumination, with average irradiance 30.66Wm-2, were attempted for three red-clay sediment cores. Successful enrichments were obtained after incubation for c.a. 120 days at 4°± 2°C and 25°± 2°C, representing ambient psychrophilic and low temperature hydrothermal alteration conditions respectively. During hydrothermal cooling, a microbial succession from anaerobic chemolithotrophy to oxygenic photoautotrophy through anaerobic/aerobic anoxygenic phototrophic microbes is indicated. Spectral absorbance patterns of the methanol extracted cell pellets showed peaks corresponding to metal sulphide precipitations, the Soret band of chlorosome absorbance by photosystem II and absence of peaks at Qy transition band. Dendritic nano-structures of metal sulphides are common in these sediments and are comparable with other sulphidic paleo-marine Martian analogues. Significant blue and redshifts have been observed for the experimental samples relative to the un-inoculated medium. These observations indicate the propensity of metal-sulphide deposits contributing to chemiluminiscence supporting the growth of phototrophs at least partially, in the otherwise dark abyss. The effects of other geothermal heat and light sources are also under further consideration. The potential of phototrophic microbial cells to exhibit Doppler shift in absorbance patterns is significant towards understanding planetary microbial habitability. Planetary desiccation could considerably influence Doppler effects and consequently spectral detection techniques exo-planetary microbial life.

Lead resistant Providencia vermicola strain SJ2A was isolated from the waste of a battery manufacturing industry which could tolerate upto 3.0mM lead nitrate in the minimal medium. Interestingly, this isolate showed presence of a plasmid borne metallothionein gene, bmtA that matched significantly (96%) with that of Pseudomonas aeruginosa. Scanning electron micrographs of bacterial cells exposed to lead revealed a unique alteration in the cell morphology from rods to long inter-connected filaments. On the other hand, electron dispersive X-ray spectroscopy (EDX) clearly indicated no significant lead adsorption therefore, we speculated intracellular sequestration in this bacterial strain. Transmission electron micrographs of the bacterial cells exposed to lead evidently demonstrated periplasmic sequestration of lead which was also supported by Fourier transformed infrared spectroscopic (FTIR) analysis. The bacterium internalised 155.12mg Pb2+/g biomass as determined by atomic absorption spectroscopy. Subsequently, the accumulated lead was identified as lead sulfite by X-ray diffraction studies. Therefore P. vermicola strain SJ2A has potential to bioremediate lead contaminated environmental sites.

Tarballs, the remnants of crude oil which change into semi-solid phase due to various weathering processes in the sea, are rich in hydrocarbons, including toxic and almost non-degradable hydrocarbons. Certain microorganisms such as fungi are known to utilize hydrocarbons present in tarballs as sole source of carbon for nutrition. Previous studies have reported 53 fungal taxa associated with tarballs. There is apparently no gene sequence-data available for the published taxa so as to verify the fungal identification using modern taxonomic tools. The objective of the present study is to isolate fungi from tarballs collected from Candolim beach in Goa, India and investigate their phylogenetic diversity based on 5.8S rRNA gene and the flanking internal transcribed spacer regions (ITS) sequence analysis. In the ITS-based NJ tree, eight tarball-associated fungal isolates clustered with 3 clades of Dothideomycetes and 2 clades of Saccharomycetes. To the best of our knowledge, this is the first study that has employed ITS-based phylogeny to characterize the fungal diversity associated with tarballs. Further studies are warranted to investigate the role of the tarball-associated fungi in degradation of recalcitrant hydrocarbons present in tarballs and the role of tarballs as carriers of human pathogenic fungi.

Culturable bacteria associated with marine sponges and coral mucus (collected from Gulf of Mannar and Palk Bay) were screened for their prospective antimicrobial compounds against 9 bacterial pathogens (Bacillus megaterium, B. cereus, Salmonella typhimurium, Staphylococcus aureus, Proteus vulgaris, Klebsillla pneumoniae, Escherichia coli, Pseudomonas aeruginosa and Acinetobacter baumannii) and a fungal pathogen (Candida albicans). Of the 263 bacterial isolates obtained during this study, 52 isolates displayed antimicrobial activity against one or more pathogens. 16S rRNA gene sequencing revealed that these 52 strains affiliated to 14 genera from three phyla Proteobacteria, Firmicutes and Actinobacteria. Sponge associated bacterial strains F-04, I-23, I-33 and G-03 inhibited the growth of all the bacterial pathogens tested in this study and significantly the former 2 strains inhibited the growth of fungal pathogen also. Majority of the potential strains (88.4% out of 52 strains) inhibited the growth of Bacillus cereus. Interestingly, an actinomycete strain F-04 (isolated from sponge Orina sagittaria) inhibited the growth of methicillin resistant Staphylococcus aureus. In total, 10 volatile organic compounds were determined from the ethyl acetate and hexane extract of the strain F-04 using GC-MS. Overall, marine bacteria isolated during this study demonstrate the potential for the development of broad spectrum antibiotics.

There are regions in the world oceans where oxygen saturation is at its lowest, evident at depths between shelf to upper bathyal zone. These regions are known as Oxygen Minimum Zones (OMZs), which reportedly support phylogenetically diverse microbes. In this study, we aimed to characterize prokaryotic diversity in the water samples collected from 43, 200 and 1000 m depth of the Bay of Bengal Time Series location (BoBTS—18.0027°N, 89.0174°E) in the OMZ region. Illumina sequencing generated 3,921,854 reads of 16S rRNA gene amplicons, which corresponded to 5778 operational taxonomic units. The distribution of bacteria at class level varied with depth and oxygen concentration. α-Proteobacteria was found in abundance in 43 m and 1000 m depth water samples. γ-Proteobacteria was prominently detected in oxygen-depleted depths of 200 m and 1000 m. AB16 (Marine Group A, originally SAR406) was restricted at dissolved oxygen concentration of 1.5 μM at 200 m. Archaeal members were observed in low abundance (2%), with a high occurrence of phylum Euryarchaeota at 43 m, while Crenarchaeota was detected only at 200 m depth. Select bacterial cultures were screened for their ability to reduce nitrate in vitro, to obtain insights into their possible role in the nitrogen cycle. A total of 156 bacterial isolates clustered majorly with Alcanivorax, Bacillus, Erythrobacter, Halomonas, Idiomarina and Marinobacter. Among them, 11 bacterial genera showed positive nitrate reduction in the Griess test. A large percentage (63.55%) of 16S rRNA gene amplicons corresponded to unidentified OTUs at genus or higher taxonomic levels, suggesting a greater undiscovered prokaryotic diversity in this oxygen depleted region. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12088-019-00786-1) contains supplementary material, which is available to authorized users.

Phycoremediation is the use of algae for removal or reduction of inorganic nutrients and xenobiotics from wastewaters. It is a reliable process for biotransformation and detoxification of a variety of pollutants. This study focused on the potential of a strain of the green microalga, Chlorella vulgaris, to reduce various pollutants in tannery wastewater (TW). The microalga was grown in TW for a culture period of 21 days and the resultant removal/reduction/biotransformation of biochemical oxygen demand (BOD), chemical oxygen demand (COD), nitrates (NO3–N), phosphates (PO4–P), sulphates (SO4–S), dissolved solids and chromium (Cr) was monitored. The isolate was efficient in the removal of excess nutrients in wastewater. Most notably, complete removal (100 % reduction) of NO3–N and Cr was observed by the 6th and 12th day of culture period, respectively. Removal of phosphates was as high as 91.73 % by day 6 and over 99 % by day 21. This strain also reduced sulphate concentrations to 67.4 % by day 21. Levels of chemical oxygen demand (COD) and biochemical oxygen demand (BOD) in TW were reduced by 94.74 and 95.93 %, respectively, after 21 days. Our results are useful to suggest that this isolate of C. vulgaris is promising for bioremediating and detoxifying tannery wastewater to improve its quality to meet up recommended effluent discharge limits.

Nitrate reduction plays a key role in the biogeochemical dynamics and microbial ecology of coastal upwelling systems. Seasonal upwelling in the eastern Arabian Sea entrains nitrate rich waters to the surface, the intense productivity that follows leads to oxygen depletion and then denitrification. Heterotrophic bacteria comprise diverse functional groups. Both aerobic and facultative anaerobic heterotrophic bacteria capable of nitrate reduction are important functional groups in the nitrogen cycle due to their ability to respire anaerobically using nitrogen oxides as electron acceptors, which are reduced to nitrous oxide and dinitrogen. However little is known from the coastal Arabian Sea on the types/species of culturable bacteria catalyzing this crucial step. To recognize the species composition of the culturable fractions involved in nitrate reduction and nitrous oxide production, as many as 360 cultures of native heterotrophic bacteria were isolated and screened for nitrate reduction. Isolates were identified by sequencing their 16S rRNA gene and the rate of nitrate reduction and production of nitrous oxide by representatives of 30 different species of bacteria were measured. Close to 77% (or 277 of 360) of the cultures were found to be nitrate reducers, which grouped into 30 different species. Further, the nitrate reduction rates and nitrous oxide production by these 30 representative nitrate reducing species were measured. Cultures were capable of nitrate reduction up to 2.40 (×10−14) mol cell−1 and 5.54 (×10−15) mol cell−1 of nitrous oxide. This high fraction of culturable bacteria reducing nitrate and producing N2O in low oxygen conditions ought to reflect their important role in biogeochemical processes in the tropical coastal water experiencing hypoxia during SuM (Summer monsoon) and FIM (Fall intermonsoon) in the monsoon affected regions.

Sedimentary bacteria play a role in polymetallic nodule formation and growth. There are, however, limited reports on bacterial diversity in nodule-rich areas of the Central Indian Ocean Basin (CIOB). In this study, bacterial abundance in thirteen sediment cores collected from the CIOB was enumerated, followed by phylogenetic characterisation and, screening of select heterotrophic bacteria for extracellular enzyme activities. Total bacterial counts (TBC) were in the order of 107 cells g−1; there was a significant difference (p > 0.05) among the cores but not within the sub-sections of the cores. The retrievable heterotrophic counts ranged from non-detectable to 5.33 × 105 g−1; the heterotrophic bacteria clustered within the phyla Firmicutes, Proteobacteria and Actinobacteria. Bacillus was the most abundant genus. The extracellular enzyme activities were in the order: amylase > lipase > protease > phosphatase > Dnase > urease. Major findings are compared with previous studies from the CIOB and other areas.

Ten fungal isolates with an ability to degrade crude oil were isolated from select marine substrates, such as mangrove sediments, Arabian Sea sediments, and tarballs. Out of the ten isolates, six belonged to Aspergillus, two to Fusarium and one each to Penicillium and Acremonium as identified using ITS rDNA sequencing. The selected ten fungal isolates were found to degrade the long-chain n-alkanes as opposed to short-chain n-alkanes from the crude oil. Mangrove fungus #NIOSN-M126 (Penicillium citrinum) was found to be highly efficient in biodegradation of crude oil, reducing the total crude oil content by 77% and the individual n-alkane fraction by an average of 95.37%, indicating it to be a potential candidate for the development into a bioremediation agent.

In a shipboard microcosm experiment we manipulated cobalt (Co), copper (Cu), iron (Fe), and Fe+Co availability in surface water samples collected during austral summer of 2013 from a Polar front (PF) location in the Indian Sector of Southern Ocean, to examine the responses of phytoplankton as well as bacterial community (BC) to these micronutrient amendments. Total chlorophyll a (Chl a) concentration increased significantly (P

The effects of micronutrient amendments such as cobalt (Co), copper (Cu), iron (Fe) and their mixture (CoþCuþFe) on bacterial abundance, phytoplankton, bacterial community (BC) composition were examined at a subtropical front (STF) location in the Indian Sector of the Southern Ocean (ISSO) during the austral summer of 2012. From the 15-day on-board experiment it became evident that there was no significant increase in total chlorophyll a concentration or phytoplankton cell numbers in micronutrient enriched microcosms (MEM) compared to the control microcosms (CM) with no added micronutrients. Highest bacterial abundance was observed in the Fe-enriched microcosm within 5 days of incubation unlike in other microcosms. Interestingly, significant differences in the BC composition were observed between MEM and CM. In that an increase of � 10 unique phylotypes affiliated with Psychrobacter sp

Tarballs are semisolid blobs of crude oil, normally formed due to weathering of crude-oil in the sea after any kind of oil spills. Microorganisms are believed to thrive on hydrocarbon-rich tarballs and possibly assist in biodegradation. The taxonomy of ecologically and economically important tarball-associated microbes, however, needs improvement as DNA-based identification and phylogenetic characterization have been scarcely incorporated into it. In this study, bacteria and fungi associated with tarballs from touristic Betul beach in Goa, India were isolated, followed by phylogenetic analyses of 16S rRNA gene and the ITS sequence-data to decipher their clustering patterns with closely-related taxa. The gene-sequence analyses identified phylogenetically diverse 20 bacterial genera belonging to the phyla Proteobacteria (14), Actinobacteria (3), Firmicutes (2) and Bacteroidetes (1), and 8 fungal genera belonging to the classes Eurotiomycetes (6), Sordariomycetes (1) and Leotiomycetes (1) associated with the Betul tarball samples. Future studies employing a polyphasic approach, including multigene sequence-data, are needed for species-level identification of culturable tarball-associated microbes. This paper also discusses potentials of tarball-associated microbes to degrade hydrocarbons.

Deep-sea sediments can reveal much about the last 200 million years of Earth history, including the history of ocean life and climate. Microbial diversity in Afanasy Nikitin seamount located at Equatorial East Indian Ocean (EEIO) was investigated. Deep sea sediment collected at 150 cm depth (∼67 ky BP) exhibited a dominance of clones clustering in the phylum Firmicutes (63%), followed by γ-Proteobacteria (37%). The bacterial diversity within sediment at 200 cm depth (∼84 ky BP) was dominated by γ-Proteobacteria (66%) followed by β- Proteobacteria (34%), whereas no Firmicutes clones were retrieved. Notably, 29% clones from 150 cm and 18% of clones from 200 cm sediment showed high identity to sequences previously reported from mining sites, while 21% of clones from 150 cm depth and 10% from 200 cm sediments showed identity to sequences previously reported from volcanic areas. Further, many of the sequences were from uncultured clones. Overall, these data may help elucidate the nature of microorganisms inhab...

Longtail tuna Thunnus tonggol is a neritic species of the family Scombridae, having a confined coastal distribution to tropical and temperate waters of the Indo-Pacific region. In the present study, the population structure of longtail tuna was examined using sequence analysis of the mtDNA control region from two geographically distinct locations along the northwest coast of India. A 500 bp segment of the D-loop region was sequenced and analysed for 98 longtail tuna individuals. Analysis of population differentiation showed no significant genetic differentiation between the two sampling localities (ΦST = 0.005, P = 0.200). Results were further corroborated by a non-significant nearest-neighbour statistic (Snn = 0.489, P = 0.549). Phylogeographic analysis revealed two haplogroups, but there was no obvious phylogeographic pattern separating the samples of the two localities. The present study suggests a single panmictic population of longtail tuna in the northwest coastal waters of India.

A low-temperature shallow-water hydrothermal vent field was discovered during the summer of 2010 in the Faial-Pico channel off the Espalamaca headland, Faial Island, Azores, Portugal, NE Atlantic. The present study analyses bacterial communities present in shallowwater hydrothermal vent of Espalamaca using SSU rRNA-based clone library approach. Clones of shallow vent sediment sample revealed the dominance of Proteobacteria (including α, γ, e, δ, ζ subdivisions) and Bacteroidetes with 36% and 28% of the whole community respectively. The dominance of γ-Proteobacteria is the unique characteristic of this shallow vent and it coincides with the South Tonga Arc and Bahia Concepcion (Pacific Ocean), whereas e- Proteobacteria groups were reported to be high in the majority of the hydrothermal vents. Though the sampling sites of the venting and non-venting regions of Espalamaca were only 500 m apart, high variation (>80%) of phylotypes was found between the regions.

As many as 71 marine bacterial DNA extracts were PCR screened for L-asparaginase (ansA), a key gene in anti-cancer molecular-searches. Over 62% (44) of them were positive for ansA gene. The positive cultures were from genera Bacillus and Staphylococcus. The ansA gene cloned from isolate NIOS4 belonging to recently described Bacillus tequilensis is 1099 bp in length with a 990 bp ORF coding for 329 amino acids. BLASTx analysis revealed this sequence to be 98% similar to earlier reported ansA sequence from B. subtilis (Accession no. NP390239.1). By comparing its deduced amino acid sequence with other bacterial asparaginase sequences six substitutions at positions 305(Thr), 313(Lys), 314(Leu), 315(Asp), 318(Arg), and 320(Gln) are observed. Key residues like Thr(12), Thr(85), Asp(86), Lys(156), and Phe(165) taking part in active-site formation and imparting catalytic properties are conserved. The phylogenetic tree based of the ansA amino acid sequences revealed close relatedness of the NIOS4 ansA sequence with B. subtilis (Accession no. NP 390239.1). It's very close genetic resemblance to B. subtilis and conservation of certain key amino acid residues suggest it as a prospective candidate for evaluation and, production of L-asparaginases.

Yellowfin tuna (Thunnus albacares) is an epipelagic, oceanic species of family Scombridae found in tropical and subtropical region of Pacific, Indian and Atlantic Ocean. It is commercially important fish and accounts for 19 % of total tuna catches in Indian waters. In present study, population structure of yellowfin tuna was examined using sequence analysis of mitochondrial DNA from seven geographically distinct locations along the Indian coast. A 500 bp segment of D-loop region was sequenced and analysed for 321 yellowfin samples. Hierarchical analysis of molecular variance showed significant genetic differentiation among three groups (VE); (AG); (KO, TU, PO, VI, PB) analyzed (Φ ST = 0.03844, P ≤ 0.001). In addition, spatial analysis of molecular variance identified three genetically heterogeneous groups of yellowfin tuna in Indian waters. Results were further corroborated by significant value of nearest neighbour statistic (S nn = 0.261, P ≤ 0.001). Thus finding of this study rejects the null hypothesis of single panmictic population of yellowfin tuna in Indian waters.

Based on distinct colony morphology, color, size, shape and certain other traits, 92 bacterial isolates were investigated to understand their managerial ability on iron from the Arabian Sea and Equatorial Indian Ocean samples. The ARDRA (amplified rDNA restriction analysis) applied to eliminate the duplication of the bacterial strains, resulted 39 different banding patterns. The 16S rRNA gene sequencing data indicate the dominancy of three phylogenetic groups, alpha-Proteobacteria (10.25%), gamma-Proteobacteria (35.89%) and Bacilli (53.84%) in these waters. Marinobacter and Bacillus were the only common genera from both of the regions. Pseudoalteromonas, Halomonas, Rheinheimera, Staphylococcus and Idiomarina were some of the other genera obtained from the Arabian Sea. Erythrobacter, Roseovarius, Sagittula and Nitratireductor were found mostly in Equatorial Indian Ocean. In addition, 16S rRNA gene sequence data of some of our iron bacterial strains belong to novel species and one isolate ASS2A could form a new genus. Close to 23% of the isolates were able to produce high affinity sets of ligands like siderophores to mediate iron transport into the cell. The current study indicated that the Equatorial Indian Ocean species were well adapted to oxidize iron as an electron acceptor and the Arabian Sea species preferably go through siderophore production.

Frigate tuna Auxis thazard thazard is a cosmopolitan species and one of the smallest members of the tribe Thunnini (the true tunas), and currently managed as a single stock. In the present study, genetic variation was surveyed using sequence data of mitochondrial DNA D-loop region to test for the presence of genetic stock structure of frigate tuna along the Indian coast. A total of 364 individuals were sampled from 8 major fishing zones along the Indian coast. Significant genetic heterogeneity was observed for the sequence data (ΦST = 0.0439, P = < 0.001). Analysis of molecular variance (AMOVA) showed significant genetic variation among the three groups analysed (ΦCT = 0.1223, P = < 0.05), which was also supported by spatial AMOVA results. Therefore, the null hypothesis of single panmictic population of frigate tuna along the Indian coast can be rejected. Phylogenetic analysis of nucleotide sequences demonstrated that frigate tuna can be grouped into three different mitochondrial clades (Clades I...

Contributions of microbial communities to biogeochemical processes in oxygen minimum oceanic zones are being realized through the applications of molecular techniques. To understand seasonal and depth-wise variations in bacterial community structure (BCS) in the Arabian Sea oxygen minimum region, extensive sampling and molecular analyses were carried out. 16S rRNA gene sequencing was done to profile the BCS from five depths, surface (5 m), deep chorophyll maximum (43–50 m, DCM), 250 m, 500 m and 1000 m during Spring intermonsoon (SIM), Fall intermonsoon (FIM), and Northeast monsoon (NEM) seasons. Sequencing of 743 chimera-free clones revealed a clear vertical partitioning of BCS between the surface (surface + DCM) and OMZ (250 + 500 + 1000 m) layers. There was no distinct seasonal difference in the BCS. Most 16S rRNA gene sequences were affiliated to Gammaproteobacteria (39.31 %), Alphaproteobacteria (23.56 %) and Cyanobacteria (20.2 %). Higher diversity and OTUs in OMZ predominantly consisting of Alteromonodales, Sphinogomonadales, Rhodobacterales, Burkholderales, and Acidimicrobiales we observed might be due to their microaerophilic metabolism, ability to degrade recalcitrant substrates and assimilate sinking particulate matter. Further hitherto undescribed diversity both in surface and OMZ layers was evidenced. Implicit role of extant bacterial community in denitrification and anammox and in sulphur oxidation is highlighted.

Lichens are complex symbiotic association of mycobionts, photobionts, and bacteriobionts, including chemolithotropic bacteria. In the present study, 46 lichenized bacteria were isolated by conventional and enrichment culture methods on nitrogen-free bromothymol blue (NFb) medium. Only 11 of the 46 isolates fixed nitrogen on NFb and had reduced acetylene. All these 11 isolates had also produced siderophore and 10 of them the IAA. Further, ammonia production was recorded from nine of these nitrogen fixers (NF). On molecular characterization, 16 S rRNA sequencing recorded that, nine NF belonged to Proteobacteria, within Gammaproteobacteria, and were closely related to Enterobacter sp. with a maximum similarity to Enterobacter cloacae. Each one of our NF isolates was aligned closely to Enterobacter pulveris strain E443, Cronobacter sakazakii strain PNP8 and Providencia rettgeri strain ALK058. Notably, a few strains we examined found to possess plant growth promoting properties. This is the first report of Enterobacter sp. from lichens which may be inhabit lichen thalli extrinsically or intrinsically.

Diversity of fungi from deep biosphere is recently gaining an increasing attention. We investigated fungal diversity in two sediment cores ∼40 cmbsf (cm below seafloor) at a depth of ∼5 000 m in the Central Indian Basin (CIB), by culture-dependent as well as culture-independent approaches. This resulted in recovering a total of 19 culturable fungi and 46 operational taxonomic units (OTUs) respectively. Two of the cultured fungi showed similarity to Hortaea werneckii and Aspergillus versicolor , and 11 OTUs from environmental libraries showed high divergence (86–97 %) from the existing sequences in the GenBank (NCBI database). Some of the fungi, such as Cerrena , Hortaea and Aspergillus sp., were recovered by culture-dependent as well as culture-independent approaches. Together, culture-dependent and culture-independent approaches detected a total of 12 distinct fungal genera and 42 OTUs respectively from two sediment cores indicating presence of a high fungal diversity in deep-sea sediments.

Salinity tolerance a key factor helps in understanding the ionic homeostasis in general, which is a fundamental cellular phenomenon in all living cells. Here, a marine derived pathogenic fungus was examined for its adaptation under salt stress using antioxidant properties. The aqueous extracts of halophilic fungus exhibited different levels of antioxidant activity in all the in vitro tests such as α,α-diphenyl-β-picrylhydrazyl (DPPH(·)), Hydroxyl Radical Scavenging Assay (HRSA), Metal chelating assay and β-carotene-linoleic acid model system. The antioxidant capacity of marine fungus exposed to high salt condition showed an increase in activity. In addition, the production of intra and extracellular antioxidant enzymes of the fungus at various salt stresses were analyzed and discussed for their possible role in the stress mechanism. The marine derived fungus was identified as Phialosimplex genus, which is associated with infections in dogs. Thus the present study elucidates that the scavenging activity is one of the protective mechanisms developed in the fungus to avoid the deleterious effect of salt stress. In addition, the study also helps in understanding how the pathogenic fungus tackles the oxidative burst i.e. hypersensitivity reaction performed by host to kill the pathogens.

Kawakawa Euthynnus affinis is an epipelagic migratory tuna species, widely distributed in the tropical and subtropical waters of the Indo-Pacific region. Kawakawa constitutes the largest tuna fishery in the Indian waters. In the present study, genetic variation was assessed using sequence analyses of Mitochondrial DNA (mtDNA) D-loop region. A 500 bp segment of D-loop region was sequenced in 400 samples collected from eight localities (Veraval (VE), Ratnagiri (RA), Kochi (KO), Kavaratti (KA), Port-Blair (PB), Tuticorin (TU), Pondicherry (PO), and Vizag (VI)) along the Indian coast. Analysis of molecular variance of mtDNA data revealed no significant genetic differentiation among sites the (ΦST = 0.0028, P = 0.20723) indicating a single population along the Indian coast. Phylogenetic analysis revealed no obvious phylogeographic pattern separating the eight samples of kawakawa. However, the genealogical relationships demonstrated that mtDNA D-loop sequences belong to two different clades (clade I and clade II). Clade I is the major clade which consists of more than 98 % specimens from each regional population while clade II has individuals from only three populations (VE, PO, and VI). Results of genetic analyses of the present study support a single stock management of kawakawa along the Indian coast.

Coastal and estuarine waters are highly productive and dynamic ecosystems. The complex carbohydrate composition of the ecosystem would lead to colonisation of microbial communities with abilities to produce an array of complex carbohydrate degrading enzymes. We have examined the abundance and phylogenetic diversity of culturable bacteria with abilities to produce complex carbohydrate degrading enzymes in the Mondovi and Zuari eustauri. It was interesting to note that 65% of isolated bacteria could produce complex carbohydrate degrading enzymes. A majority of these bacteria belonged to Bacillus genera followed by Vibrio, Marinobacter, Exiquinobacterium, Alteromonas, Enterobacter and Aeromonas. Most abundant bacterial genus to degrade hemicellulose and cellulose were Bacillus and Vibrio respectively. Most abundant bacterial genus to degrade hemicellulose and cellulose were Bacillus and Vibrio respectively. It was seen that 46 % of Bacillus had ability to degrade both the substrate while only 14 % of Vibrio had bifunctionality.

We identified 38 genes and eight hypothetical proteins by sequencing of 1200 clones from a Vibrio harveyi challenged Fenneropenaeus indicus subtracted cDNA library. Based on physiological roles and functions these genes were categorized into 10 groups with ∼29% of the sequences having no matches in the databases. Immune related transcripts in the library were carboxypeptidase B, ferritin, translationally controlled tumor proteins (TCTP), hemocyanin, chitinase and serine carboxy peptidase. Remarkably, qPCR results imply 4.15, 3.45 and 1.86-fold rises in expression of ferritin, TCTP and hemocyanin transcripts respectively. Additionally, minor upregulation of other immune relevant genes lectin, penaeidin, crustin, MnSOD was observed in the challenged postlarvae.

Butyltins (TBT, DBT, MBT) were measured in water and sediment samples collected from various locations in the Mandovi (ten stations) and Zuari (nine stations) estuaries during November 2007. The total butyltin (TB) in water samples varied between approximately 12 and 73 and from 0.5 to 77 ng Sn l(-1), whereas for the sediments, it varied from approximately 15 to 118 and 6 to 119 ng Sn g(-1) dry weight for the Mandovi and the Zuari estuaries, respectively. The average TB concentration in the sediments from the Zuari estuary was higher as compared to the Mandovi estuary, whereas for the water samples, it was vice versa. For both the water and sediment samples, MBT was generally the most predominant butyltin in these two estuaries. This suggests that the butyltin contamination was not freshly derived. Fairly good relationships between the concentrations of TB and organic carbon in water and sediment samples of these estuaries implicate the importance of adsorption/desorption processes in controlling the levels of TB in these estuaries.

Surface seawaters from the Dona Paula Bay, were collected at weekly intervals during March 2007 to March 2008, and analyzed for butyltins (BT) such as tributyltin (TBT), dibutyltin (DBT), monobutyltin (MBT) using a GC-MS system. The mean concentrations of TBT, DBT, MBT and total BT varied from1-37, 4-19, 6-28 and 21-84 ng Sn L(-1), respectively. Highest levels of BTs were recorded during May followed by April 2007 and March 2007 probably because the shipping and tourism activities are very high during these months.

Reports on the active role of fungi as denitrifiers in terrestrial ecosystems have stimulated an interest in the study of the role of fungi in oxygen-deficient marine systems. In this study, the culturable diversity of fungi was investigated from 4 stations within the permanent, oceanic, oxygen minimum zone of the Arabian Sea. The isolated cultures grouped within the 2 major fungal phyla Ascomycota and Basidiomycota; diversity estimates in the stations sampled indicated that the diversity of the oxygen-depleted environments is less than that of mangrove regions and deep-sea habitats. Phylogenetic analyses of 18S rRNA sequences revealed a few divergent isolates that clustered with environmental sequences previously obtained by others. This is significant, as these isolates represent phylotypes that so far were known only from metagenomic studies and are of phylogenetic importance. Nitrate reduction activity, the first step in the denitrification process, was recorded for isolates under simulated anoxic, deep-sea conditions showing ecological significance of fungi in the oxygen-depleted habitats. This report increases our understanding of fungal diversity in unique, poorly studied habitats and underlines the importance of fungi in the oxygen-depleted environments.

The sfp gene responsible for surfactin production was screened from the DNA extracts of 37 Bacillus spp. whose identity was confirmed by 16S rRNA gene sequence analyses. PCR screening revealed amplification of sfp gene fragments in a total of 25 isolates. Several isolates belonging to Bacillus tequilensis were found to be positive for this gene. A gene fragment coding for the sfp gene was amplified and cloned from genomic DNA of the isolate B. tequilensis NIOS11. The cloned gene has an open reading frame of 675 bp coding for 224 amino acids with a theoretical molecular weight of 26,166.33 Da and a predicted isolectric point (pI) of 5.51. BLASTP analysis revealed 99% similarity to the earlier reported sfp gene of B. subtilis. Conserved domains of the sfp type PPTase family of proteins like P1a, P1b, P2, and P3 involved in biosynthesis of polyketides and nonribosomal peptides were observed. Phylogenetic analysis revealed a close relatedness of this gene with earlier reported sequences of B. subtilis. Results from the molecular characterization and substantial similarities with surfactins produced from B. subtilis make the B. tequilensis identified in this study a suitable candidate for exploring the potential of its application in the production of biosurfactants.

The relationship of the marine heterokont stramenopilan protists, the aplanochytrids, with the zooplankton was studied in coastal waters. The aplanochytrids were fed to the zooplankton specimens and observed for grazing by two different approaches: [1] using fluorescently-labeled prey approach and [2] using internal transcribed spacer-based molecular probe and in situ hybridization approach. The aplanochytrid cells were detected in the guts as well as fecal pellets of the zooplankton, thus serving as prey to them. Aplanochytrids were consistently isolated from zooplankton specimens. The isolates did not produce a wide array of enzymes, implicating that they may not play a major role in degradation of zooplankton exoskeleton. They were found to produce only protease considerably and sometimes lipase too. The amplified rDNA restriction analysis showed similar patterns, suggesting that most of the isolates might be same strains of Aplanochytrium spp. The existence of aplanochytrids with the zooplankton in marine waters points towards their probable association either as predator–prey or as commensalistic rather than saprophytic type of association.

As many as 71 marine bacterial DNA extracts were PCR screened for L-asparaginase (ansA), a key gene in anti-cancer molecular-searches. Over 62% (44) of them were positive for ansA gene. The positive cultures were from genera Bacillus and Staphylococcus. The ansA gene cloned from isolate NIOS4 belonging to recently described Bacillus tequilensis is 1099 bp in length with a 990 bp ORF coding for 329 amino acids. BLASTx analysis revealed this sequence to be 98% similar to earlier reported ansA sequence from B. subtilis (Accession no. NP390239.1). By comparing its deduced amino acid sequence with other bacterial asparaginase sequences six substitutions at positions 305(Thr), 313(Lys), 314(Leu), 315(Asp), 318(Arg), and 320(Gln) are observed. Key residues like Thr(12), Thr(85), Asp(86), Lys(156), and Phe(165) taking part in active-site formation and imparting catalytic properties are conserved. The phylogenetic tree based of the ansA amino acid sequences revealed close relatedness of the NIOS4 ansA sequence with B. subtilis (Accession no. NP 390239.1). It's very close genetic resemblance to B. subtilis and conservation of certain key amino acid residues suggest it as a prospective candidate for evaluation and, production of L-asparaginases.

Elucidation, through molecular analyses, of bacterial afflictions in commercially important aquaculture-reared shrimps is pivotal for the prevention and/or control of disease outbreaks. In this study, we examined the phylogenetic relatedness and compared the possible immune-related functional roles of both translationally controlled tumour protein (TCTP) and ferritin genes with previous studies. Both TCTP and ferritin genes were substantially upregulated in the Indian white prawn, Fenneropenaeus indicus (H. Milne Edwards), post-larvae following bath challenge with the virulent strain of bacteria, Vibrio harveyi D3. Full-length cloning of these genes by rapid amplification of complementary DNA ends -polymerase chain reaction (RACE-PCR) yielded 727-base pair (bp)-long TCTP and 1212-bp-long ferritin gene sequences. Their open reading frames (ORFs) were 507 and 510 bp, respectively. The TCTP-ORF coded for 168 amino acids with three substitutions at positions 37, 141, 155, and the ferritin ORF coded for 170 amino acids with no species-specific substitutions. Phylogenetic analysis suggested the closest relatedness of both TCTP and ferritin from F. indicus to Chinese white prawn, Fenneropenaeus chinensis (Osbeck). In addition to reporting the full-length sequences of these immune-relevant genes, this study highlighted their conserved natures, which perhaps make them important defence-related proteins in the innate immune system of F. indicus.

Water and surface sediment samples were analyzed for butyltins (TBT, DBT, MBT) from various ports along the east and west coast of India. The total butyltin (TB) in water samples varied between ~1.7 and 342 ng S nl⁻¹, whereas for sediments it varied between below detection limit to 14861 ng S ng⁻¹ dry weight of sediment. On an average Chennai port recorded the highest level of butyltins in the sediments while Paradip recorded the highest level of butylins in the waters. A fairly good relationship between the TB in the sediment and overlying water samples, as well as between organic carbon and TB, implicates the importance of adsorption/desorption process in controlling the levels of TBT in these port areas. In India the data on organotin pollution is very sparse; most of the port areas have been surveyed for butyltins for the first time during this study.