Copepods are the dominant members of the zooplankton community and the most abundant form of life. It is imperative to obtain insights into the copepod-associated bacteriobiomes (CAB) in order to ...identify specific bacterial taxa associated within a copepod, and to understand how they vary between different copepods. Analysing the potential genes within the CAB may reveal their intrinsic role in biogeochemical cycles. For this, machine-learning models and PICRUSt2 analysis were deployed to analyse 16S rDNA gene sequences (approximately 16 million reads) of CAB belonging to five different copepod genera viz., Acartia spp., Calanus spp., Centropages sp., Pleuromamma spp., and Temora spp.. Overall, we predict 50 sub-OTUs (s-OTUs) (gradient boosting classifiers) to be important in five copepod genera. Among these, 15 s-OTUs were predicted to be important in Calanus spp. and 20 s-OTUs as important in Pleuromamma spp.. Four bacterial s-OTUs Acinetobacter johnsonii, Phaeobacter, Vibrio shilonii and Piscirickettsiaceae were identified as important s-OTUs in Calanus spp., and the s-OTUs Marinobacter, Alteromonas, Desulfovibrio, Limnobacter, Sphingomonas, Methyloversatilis, Enhydrobacter and Coriobacteriaceae were predicted as important s-OTUs in Pleuromamma spp., for the first time. Our meta-analysis revealed that the CAB of Pleuromamma spp. had a high proportion of potential genes responsible for methanogenesis and nitrogen fixation, whereas the CAB of Temora spp. had a high proportion of potential genes involved in assimilatory sulphate reduction, and cyanocobalamin synthesis. The CAB of Pleuromamma spp. and Temora spp. have potential genes accountable for iron transport.
The red palm weevil, Rhynchophorus ferrugineus (Olivier 1790) caused a high economic loos in date palm in gulf region especially in Saudi Arabia. Previous estimations of palm weevil haplotype ...diversity in Saudi Arabia was not satisfactory because of choice of marker and small sampling area. Assessing haplotype diversity using COI gene was found ineffective. The present study was carried out to estimate the haplotypes of R. ferrugineus using internal transcribed spacer (ITS) sequences. Results showed 3 haplo-groups, among which, the haplotype UT9 was a singleton haplotype. The haplotypes UT16, UT2, UT6 UT10, UT14 and UT5 formed the second haplo-group whereas the remaining haplotypes were clustered as third group. K2P distance varied between 0 and 0.06 among the sequenced haplotypes and the maximum distance was recorded between two sets of haplotypes; viz; UT4 and UT3, UT4 and UT8. The overall distance of all the sequenced haplotypes were 0.02. Tajima’s neutrality value was < 0 indicating the potentiality for further haplotype diversification. Median joining haplotype network diagram reveals the presence of 10 haplotypes and most mutations were at 244th and 381st nucleotide positions. Overall, total number of mutations leading to the evolution of the documented 10 haplotypes was 34. Through genetic data, we have provided a strong evidence that there were multiple haplotypes of R. ferrugineus which were bound to expand its diversity. Higher nucleotide diversity and Tajima’s neutrality test values suggest that there were higher movement of infested palm trees, as desserts were natural barriers for movement of H. ferrugineus. The findings of this study will be useful for pest controlling agencies and to the workers involved in infested date palm quarantining.
Bacterial diversity studies in hypersaline soil often yield novel organisms and contribute to our understanding of this extreme environment. Soil from Mad Boon is previously uncharacterized, with ...dense mangrove forest in one side and hypersaline soil in another side of backwater located in Southeast coast of Tamil Nadu, India. We surveyed to characterize the structure and diversity of the bacterial community. Samples were collected in a partially vegetated upland, exposed backwater sedimentation and water-logged location. In this study, we investigate the bacterial community structure using pyrosequence analysis of the V5- V9 gene region. After quality checks a total of 3919, 7298 and 7399 reads were obtained. About 42 phyla were observed, among them Proteobacteria were dominant phylum followed by Acidobacteria, Firmicutes and Chloroflexi. Classes including Deltaproteobacteria and Gammaproteobacteriawere observed. All sequences generated in this study were submitted to NCBI SRA under the accession numbers SRR627695, SRR63011 and SRR631012.
Oxygen minimum zones are results of oxygen consumption exceeding the oxygen availability in stratified water columns of the marine environment. We compared the ammonia monooxygenase subunit A (amoA) ...gene abundance and the diversity of ammonia-oxidising archaea (AOA) in the Arabian Sea (AS) with those of the Bay of Bengal (BoB). Three primer pairs targeting amoA genes of water column A (WCA), water column B (WCB) and total AOA (amoAt) captured different densities of gene copy numbers in both marginal seas. Water column A (WCA) ecotypes were more abundant in the AS than in the BoB. Core-OMZ depths of the BoB contained 10 times lower amoA copy numbers than those of the AS. Along with sampling depth, concentration of ammonia shapes the WCA/WCB ecotypes in AS/BoB. Among the total AOA populations, WCB ecotypes were more abundant. The amoA gene sequences were either of Nitrosopumilales or Ca. Nitrosotaleales members and belonged to NP-γ, NP-δ, NS-β, NS-γ and NS-ε sub-clades. Pairwise distance and nucleotide diversity index analysis reveals that BoB nurtures two times more diverse amoA sequences than the AS. The core OMZ region of the BoB contains a two-fold higher diversity of amoA gene sequences compared to the AS, whereas the AS contains 13 times more abundant amoA copies than the BoB.
Due to their large size, bathynomids (Crustacea, Isopoda, Cirolanidae), belonging to the “supergiant group” of isopods, have long been prominent. The distribution of giant isopods from inshore to ...deep-sea environments has been reported. There was a shortage of molecular taxonomic data for these species. While DNA barcoding has proven to accelerate species identification, due to lack of reference sequences in the database, the results of environmental DNA barcoding remain mysterious. The present is therefore aimed at identifying giant isopods and generating barcode sequences for the four species that occur on India’s southeast coast. The trawl by-catches have been used for DNA extraction, amplification of COI genes and sequencing. Basic Local Alignment Search Tool (BLAST) and neighbor joining tree analysis showed that the sequences of Bathynomus kensleyi and B. decemspinosus were barcoded for the first time. DNA barcodes of B. giganteus and B. doederleinii has <3% variation compared to DNA barcodes of the same species sequenced elsewhere and made available through Genbank, whereas B. kensleyi and B. decemspinosus exhibited >7% variation to other species of the genus Bathynomus. Analysis of Kimura-2 parametric genetic distance includes 6 species of Bathynomus genera barcoded to date and an average distance of 2.1% has been found. We recommend a minimum of 3% variation based on genetic distances as a barcoding gap to differentiate and identify species in Bathynomus genera or until a new barcoding gap has been suggested after sequencing more species.
The structural and genetic variation of morphologically adapted polychaetes from the Bay of Bengal continental shelf (North Indian Ocean) including Oxygen Minimum Zone (OMZ) are described. The ...density and biomass of polychaetes such as Aricidea curviseta (Paronidae), Lumberineris aberrans (Lumberineridae), Prionospio malmgreni, Paraprionospio pinnata, and Prinospio sexoculata (Spionidae) were significantly differed (P<0.05) in depths (Non-Oxygen Minimum Zone - NOMZ and OMZ), transects and cruises. The response and morphometric measures of branchiae structures were inconsistent between OMZ and NOMZ depths. The species Aricidea curviseta (OR450003 - OR450005), Paraprionospio pinnata (OR436939, OR436941, OR436952 and OR436953), and Prionospio malmgreni (OR436956, OR436957, OR436945, OR436946, OR436947) were barcoded for the first time. The Maximum likelihood tree analysis indicated low ranges of similarity indices among the NOMZ (0.255–0.446 %) and OMZ (0.257–0.443) depths. The total number of mutations and polymorphic sites were 395 and 268, with low haplotypes (12) and nucleotide diversity (among depths: 0.228–0.246, and regions: 0.826–0.100). The groups of haplotypes were also independent of the geographical locations. The AMOVA revealed that the variation among populations was low (regions: −5 %, and depths: −1.86 %) and within populations were high (regions:105.45 % and depths: 101.86 %, respectively). The nMDS indicated that the oxygen factor significantly separated the distribution of density and biomass of polychaetes within transects (density: biomass: F=3.57) and cruises (biomass: F=2.41, P<0.05). Generally, 70–80 % of the total variation was described in four pCCAs by salinity (PSU), pressure, Co, Cu, Fe, Mn, Ni, Pb, Zn, Hg (ppm), and clay (%) with NOMZ and OMZ depths, different cruises, transects and or the interaction between this three. OMZs might not influence the genetic variations. Several additional studies, such as physiological, metabolic, enzymatic, and biochemical, are also be essential for understanding the ecology and evolution of organisms in this habitat.
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