MOLECULAR RESOLUTION OF MARINE NEMATODES FOR IMPROVED ASSESSMENT OF BIODIVERSITY

Free-living nematodes are abundant in all marine habitats, highly diverse and can be important ecological indicators for monitoring anthropogenic impacts on the environment. Despite such attributes, nematode diagnostics has traditionally relied on detailed comparison of morphological characters which is often difficult and laborious, and as a result there is an increasing 'black hole' in faunal inventories where the biodiversity of groups such as nematodes is typically underestimated. Molecular methods offer a potentially efficient alternative approach to studying the biodiversity of marine nematode communities, and the main focus of this thesis was to apply molecular ecological tools for improved understanding of nematode diversity in marine and estuarine environments. Denaturing gradient gel electrophoresis (DGGE) has been evaluated as a novel tool for the identification of marine nematodes and for rapid assessment of their diversity based on amplification of the nuclear 18S rRNA gene. This approach successfully identified nematode taxa based on banding pattern and was also able to detect the most abundant taxa in samples from marine and estuarine environments. A DNA barcoding approach based on the 18S rRNA gene was applied for the first time in marine nematology, in an attempt to speed up the identification process. The success rate of this approach, across a range of nematode groups, was found to be close to 97%. A combined morphometrics and molecular approach was also undertaken to investigate cosmopolitanism and cryptic speciation by analysing populations of a cosmopolitan marine nematode, Terschellingia longicaudata, from different geographical regions. Results suggest that Terschellingia longicaudata is indeed truly cosmopolitan, with a wide geographic distribution. Two haplotypes that were divergent from most T. longicaudata were also identified in this study, indicating possible novel cryptic lineages or previously undescribed species of the genus. The final focus of this thesis was to develop methods for the molecular investigation of nematodes stored in formalin and other organic compounds. The effectiveness of formalin as a short term preservative was first evaluated, since this would allow morphological and molecular work to be conducted on the same specimen. Amplifiable DNA could be routinely obtained from specimens stored in formalin for periods of up to nine days. In addition the effectiveness of other organic solvents for the preservation of both molecular and morphological integrity of marine nematodes was investigated. The final part of this study developed and optimized a novel DNA extraction technique that could be employed to recover DNA from archived formalin fixed marine nematode specimens so as to carry out subsequent molecular analysis such as PCR amplification and sequencing.Plymouth Marine Laborator

Minireview: algal natural compounds and extracts as antifoulants

Marine biofouling is a paramount phenomenon in the marine environment and causes serious problems to maritime industries worldwide. Marine algae are known to produce a wide variety of chemical compounds with antibacterial, antifungal, antialgal, and anti-macrofouling properties, inhibiting the settlement and growth of other marine fouling organisms. Significant investigations and progress have been made in this field in the last two decades and several antifouling extracts and compounds have been isolated from micro- and macroalgae. In this minireview, we have summarized and evaluated antifouling compounds isolated and identified from macroalgae and microalgae between January 2010 and June 2016. Future directions for their commercialization through metabolic engineering and industrial scale up have been discussed. Upon comparing biogeographical regions, investigations from Southeast Asian waters were found to be rather scarce. Thus, we have also discussed the need to conduct more chemical ecology based research in relatively less explored areas with high algal biodiversity like Southeast Asia

Molecular Diversity of Fungal Phylotypes Co-Amplified Alongside Nematodes from Coastal and Deep-Sea Marine Environments

Nematodes and fungi are both ubiquitous in marine environments, yet few studies have investigated relationships between these two groups. Microbial species share many well-documented interactions with both free-living and parasitic nematode species, and limited data from previous studies have suggested ecological associations between fungi and nematodes in benthic marine habitats. This study aimed to further document the taxonomy and distribution of fungal taxa often co-amplified from nematode specimens. A total of 15 fungal 18S rRNA phylotypes were isolated from nematode specimens representing both deep-sea and shallow water habitats; all fungal isolates displayed high pairwise sequence identities with published data in Genbank (99–100%) and unpublished high-throughput 454 environmental datasets (>95%). BLAST matches indicate marine fungal sequences amplified in this study broadly represent taxa within the phyla Ascomycota and Basidiomycota, and several phylotypes showed robust groupings with known taxa in phylogenetic topologies. In addition, some fungal phylotypes appeared to be present in disparate geographic habitats, suggesting cosmopolitan distributions or closely related species complexes in at least some marine fungi. The present study was only able to isolate fungal DNA from a restricted set of nematode taxa; further work is needed to fully investigate the taxonomic scope and function of nematode-fungal interactions

Molecular biodiversity of benthic communities in deep-sea sediments examples from the phylum Foraminifera and Nematoda

709-713Biodiversity in deep-sea environments is very high but often under-estimated to a large extent due to paucity in sampling and taxonomic intractability of certain faunal groups. In deep-sea benthic environments, two faunal groups namely Foraminifera and Nematoda often dominate in their abundance and contribute to major ecosystem processes. However, information at the species level and biogeographic patterns of these two major benthic faunal groups are largely unknown with some scattered studies undertaken so far based on the application of molecular techniques. This review highlights how application of molecular techniques, including next generation sequencing (NGS) methodologies have improved our understanding of biodiversity patterns of two major groups, namely Foraminifera and Nematoda from deep-sea benthic habitats

Effects of ocean acidification on marine invertebrates- a review

454-464<span style="font-size:9.0pt;line-height: 115%;font-family:" times="" new="" roman";mso-fareast-font-family:calibri;mso-bidi-font-family:="" "times="" roman";mso-ansi-language:en-us;mso-fareast-language:en-us;="" mso-bidi-language:ar-sa"="" lang="EN-US">Present review discusses about the effects of ocean acidification on key marine invertebrates groups which are major players of ecosystem processes across different coastal environments ranging from mangroves to coral reefs. Effects of ocean acidification on important calcifying marine invertebrate groups such as echinoderms, molluscs and crustaceans have been thoroughly discussed based on observations rendered from laboratory CO2 manipulation experiments as well as from the field. Majority of the experiments have shown sub-lethal effects on larval development and size which could ultimately affect adult population recruitment in coastal ecosystems. Particularly studies which have used ‘omics' based approaches to investigate effects of ocean acidification on marine invertebrates have been thoroughly discussed in this review. </span

Marine barcoding- how will it help Indian marine benthic studies?

645-647DNA barcoding has unraveled issues related to cryptic species complexes, assigning life history stages of unidentified organisms and also towards better understanding of evolutionary relationships between organismal groups. Given the advantages of DNA barcoding, one can strongly argue that barcodes may prove to be extremely useful for marine meiobenthic studies particularly for taxonomic groups such as free-living marine nematodes and polychaetes from the Indian subcontinent. An integrative taxonomic approach based on morphological traits based taxonomy and DNA barcoding would be ideal for studying the meiobenthic groups from Indian sedimentary environments

Molecular diversity of benthic foraminifera from tropical and subtropical coastal settings- a concise review

951-960Benthic foraminiferal diversity in coastal environments representing tropical and sub-tropical latitudes is important from the context of community development under an ecotonal setting. Even after two decades since the introduction of molecular techniques in marine biology, investigations delineating diversity and biogeography of benthic foraminifer communities are highly dependent on morpho-taxonomy. Nevertheless, application of molecular techniques in benthic foraminiferal research is starting to yield vital information on aspects ranging from diversity to ecophysiology. Coastal environments from tropical and subtropical regions are known to harbor rich marine biodiversity and the same stands for benthic foraminifer. In this review an effort has been made to provide an overview on the evolutionary origin, diversity and hidden biodiversity of benthic foraminifer communities from tropical and subtropical coastal settings based on published studies which have incorporated molecular based approaches

Insights into bacterioplankton community structure from Sundarbans mangrove ecoregion using Sanger and Illumina MiSeq sequencing approaches: A comparative analysis

AbstractNext generation sequencing using platforms such as Illumina MiSeq provides a deeper insight into the structure and function of bacterioplankton communities in coastal ecosystems compared to traditional molecular techniques such as clone library approach which incorporates Sanger sequencing. In this study, structure of bacterioplankton communities was investigated from two stations of Sundarbans mangrove ecoregion using both Sanger and Illumina MiSeq sequencing approaches. The Illumina MiSeq data is available under the BioProject ID PRJNA35180 and Sanger sequencing data under accession numbers KX014101-KX014140 (Stn1) and KX014372-KX014410 (Stn3). Proteobacteria-, Firmicutes- and Bacteroidetes-like sequences retrieved from both approaches appeared to be abundant in the studied ecosystem. The Illumina MiSeq data (2.1GB) provided a deeper insight into the structure of bacterioplankton communities and revealed the presence of bacterial phyla such as Actinobacteria, Cyanobacteria, Tenericutes, Verrucomicrobia which were not recovered based on Sanger sequencing. A comparative analysis of bacterioplankton communities from both stations highlighted the presence of genera that appear in both stations and genera that occur exclusively in either station. However, both the Sanger sequencing and Illumina MiSeq data were coherent at broader taxonomic levels. Pseudomonas, Devosia, Hyphomonas and Erythrobacter-like sequences were the abundant bacterial genera found in the studied ecosystem. Both the sequencing methods showed broad coherence although as expected the Illumina MiSeq data helped identify rarer bacterioplankton groups and also showed the presence of unassigned OTUs indicating possible presence of novel bacterioplankton from the studied mangrove ecosystem

Study of diatom assemblages in Sundarbans mangrove water based on light microscopy and rbcL gene sequencing

Sundarbans, the world's largest mangrove deltaic region, is one of the most productive ecosystems in tropical and subtropical latitudes and also serve as a nursery ground for rich coastal fisheries. In this study, we highlighted diatom assemblages from the Indian part of Sundarbans Biosphere Reserve (SBR) area for the first time based on light microscopy and rbcL gene sequencing and phylogeny. In total, 15 diatom species (11 centric forms and 4 pennate forms) were documented using light microscopy, and 3 major clades of diatoms were detected in rbcL phylogeny. Out of 15 diatom species, 7 were the first record from Sundarbans mangrove water. One of the species, Thalassiosira ferelineata Hasle and Fryxell, was reported for the first time in an Asian mangrove ecosystem based on light microscopy. Our study suggests the importance of establishing cultures and their polyphasic taxonomy are the future necessity to create an authenticated diatom database from mangrove water, which is still overlooked globally