Helen Parry

Immunological function in marine invertebrates: Responses to environmental perturbation

The inception of ecological immunology has led to an increase in the number of studies investigating the impact of environmental stressors on host immune defence mechanisms. This in turn has led to an increased understanding of the importance of invertebrate groups for immunological research. This review discusses the advances made within marine invertebrate ecological immunology over the past decade. By demonstrating the environmental stressors tested, the immune parameters typically investigated, and the species that have received the greatest level of investigation, this review provides a critical assessment of the field of marine invertebrate ecological immunology. In highlighting the methodologies employed within this field, our current inability to understand the true ecological significance of any immune dysfunction caused by environmental stressors is outlined. Additionally, a number of examples are provided in which studies successfully demonstrate a measure of immunocompetence through alterations in disease resistance and organism survival to a realized pathogenic threat. Consequently, this review highlights the potential to advance our current understanding of the ecological and evolutionary significance of environmental stressor related immune dysfunction. Furthermore, the potential for the advancement of our understanding of the immune system of marine invertebrates, through the incorporation of newly emerging and novel molecular techniques, is emphasized.

Next Generation Sequencing Reveals the Hidden Diversity of Zooplankton Assemblages

Background Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae. However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detection of long term changes in their community structure. The advent of massively parallel next generation sequencing technology allows DNA sequence data to be recovered directly from whole community samples. Here we assess the ability of such sequencing to quantify richness and diversity of a mixed zooplankton assemblage from a productive time series site in the Western English Channel. Methodology/Principle Findings Plankton net hauls (200 µm) were taken at the Western Channel Observatory station L4 in September 2010 and January 2011. These samples were analysed by microscopy and metagenetic analysis of the 18S nuclear small subunit ribosomal RNA gene using the 454 pyrosequencing platform. Following quality control a total of 419,041 sequences were obtained for all samples. The sequences clustered into 205 operational taxonomic units using a 97% similarity cut-off. Allocation of taxonomy by comparison with the National Centre for Biotechnology Information database identified 135 OTUs to species level, 11 to genus level and 1 to order, <2.5% of sequences were classified as unknowns. By comparison a skilled microscopic analyst was able to routinely enumerate only 58 taxonomic groups. Conclusions Metagenetics reveals a previously hidden taxonomic richness, especially for Copepoda and hard-to-identify meroplankton such as Bivalvia, Gastropoda and Polychaeta. It also reveals rare species and parasites. We conclude that Next Generation Sequencing of 18S amplicons is a powerful tool for elucidating the true diversity and species richness of zooplankton communities. While this approach allows for broad diversity assessments of plankton it may become increasingly attractive in future if sequence reference libraries of accurately identified individuals are better populated.

Permanent draft genome sequence of Vibrio tubiashii strain NCIMB 1337 (ATCC19106)

Vibrio tubiashii NCIMB 1337 is a major and increasingly prevalent pathogen of bivalve mollusks, and shares a close phylogenetic relationship with both V. orientalis and V. coralliilyticus. It is a Gram-negative, curved rod-shaped bacterium, originally isolated from a moribund juvenile oyster, and is both oxidase and catalase positive. It is capable of growth under both aerobic and anaerobic conditions. Here we describe the features of this organism, together with the draft genome and annotation. The genome is 5,353,266 bp long, consisting of two chromosomes, and contains 4,864 protein-coding and 86 RNA genes.

Shellsim: A Generic Model of Growth and Environmental Effects Validated Across Contrasting Habitats in Bivalve Shellfish

ABSTRACT Previous shellfish models have, in general, been calibrated for 1 location, unable to simulate growth across habitats that contrast in seston abundance and composition, as may vary between turbid, eutrophic and oligotrophic waters. Here, we describe the generic shellfish model ShellSIM, demonstrating how a common parameter set simulates growth effectively on calibration in the mussel Mytilus edulis and oyster Crassostrea gigas during normal culture across 9 different locations in Europe and China. Options enable the user to assess the relative values of chlorophyll a (CHL, measured in micrograms per liter), total particulate organic matter (POM; measured in milligrams per liter), and total particulate organic carbon (POC; measured in milligrams per liter) as codescriptors of the food available at separate locations. Using CHL as the sole proxy for available organics, together with an average carbon-to-CHL ratio of 50, growth in both M. edulis and C. gigas was predicted accurately at only 5 locations, primarily those with relatively low average food availability. In contrast, more than 74% of the observed variance in growth was predicted across all 9 locations in each species on inclusion of dynamic relations defining ingestion and absorption of both CHL-rich and all remaining organic matter such as may include bacteria, protozoans, colloids, and/or detritus, thereby helping to account for temporal and spatial changes in dietary composition. The energy content of the remaining organic matter (measured in Joules per milligram) ranged seasonally across all sites from about 2–25 J/mg, and could be predicted with growth from the relative abundance of CHL and POM alone, proving a viable alternative to more technically demanding measures of POC. Fractional contributions of the remaining organic matter to the energy absorbed in both species at each location ranged from less than about 0.4 during the spring to more than 0.8 from late autumn, in negative relation with CHL, thus helping to offset tissue wasting during winter months. We acknowledge model uncertainties, emphasizing the need to balance practicality and affordability against required accuracies. Last, we describe how the generic and multi-site capabilities afforded by ShellSIM, together with real-time outputs ready for integrated modeling of how shellfish influence ecosystem properties and processes, are saving time and resources across a variety of applications.

COMPARATIVE FEEDING ON CHLOROPHYLL-RICH VERSUS REMAINING ORGANIC MATTER IN BIVALVE SHELLFISH

ABSTRACT Filter feeding was compared in the blue mussel Mytilus edulis, Mediterranean mussel Mytilus galloprovincialis, Pacific oyster Crassostrea gigas, Chinese pleated oyster Crassostrea plicatula, Chinese scallop Chlamys farreri,Manila clam Tapes phillipinarum, razor clam Sinonvacula constricta, and blood cockle Tegillarca granosa over 95 dietary conditions across nine locations in Europe and China. Conditions included natural seawater enhanced, on occasion, with variable additions of microalgal monoculture and/or natural silt collected from the surface of nearby mudflats, thereby ensuring that diets ranged from oligotrophic to hypereutrophic (>325 µg chlorophyll a/L) and highly turbid (>1,250 mg total particulate matter/L). Building on past insights into differential particle processing, we resolved the availability, filtration, and ingestion of organic matter rich in chlorophyll a, and which matter is known to be ingested selectively, from all remaining organics, such as detritus, bacteria, protozoans, and/or colloids. The forms of fitted relations that best described feeding responses were different for chlorophyll-rich versus remaining organics, that difference being consistent in all eight bivalve species, including when measured in the same species across different locations. Throughout, positive linear relations between net ingestion of chlorophyll-rich organic matter and the availability of that chlorophyll-rich organic matter indicated that each species ingested constant proportions of the organics associated with chlorophyll a, with no limitation evident to such ingestion over our experimental range. Alternatively, ingestion of the remaining organics by each species increased as saturating functions of the availability of those remaining organics alone. Differences were evident between species both in the proportions of available chlorophyll-rich organic matter that were ingested and in saturated ingestion rates for the remaining organics. Comparison of those differences suggests an evolutionary trade-off among species between their relative abilities to process chlorophyll-rich versus remaining organics. Differences also suggest congeneric adaptation to natural habitat, impressing a need for careful appraisal of each and every bivalve species. Significant costs of particle sorting, digestion, and absorption, evidenced as metabolically derived material egested and assayed within feces, were greatest in species with higher saturated capacities for the ingestion of remaining organics. Last, we describe how, compared with predictions based on chlorophyll a or total particulate organic matter alone, our approach resolving coincident differential availabilities and processing of chlorophyll-rich versus remaining organic matter has improved the accuracy of growth simulations when applying single calibrations of the generic shellfish model ShellSIM across coastal habitats that contrast in seston composition.

Marine Microbial Gene Abundance and Community Composition in Response to Ocean Acidification and Elevated Temperature in Two Contrasting Coastal Marine Sediments

Marine ecosystems are exposed to a range of human-induced climate stressors, in particular changing carbonate chemistry and elevated sea surface temperatures as a consequence of climate change. More research effort is needed to reduce uncertainties about the effects of global-scale warming and acidification for benthic microbial communities, which drive sedimentary biogeochemical cycles. In this research, mesocosm experiments were set up using muddy and sandy coastal sediments to investigate the independent and interactive effects of elevated carbon dioxide concentrations (750 ppm CO2) and elevated temperature (ambient +4°C) on the abundance of taxonomic and functional microbial genes. Specific quantitative PCR primers were used to target archaeal, bacterial, and cyanobacterial/chloroplast 16S rRNA in both sediment types. Nitrogen cycling genes archaeal and bacterial ammonia monooxygenase (amoA) and bacterial nitrite reductase (nirS) were specifically targeted to identify changes in microbial gene abundance and potential impacts on nitrogen cycling. In muddy sediment, microbial gene abundance, including amoA and nirS genes, increased under elevated temperature and reduced under elevated CO2 after 28 days, accompanied by shifts in community composition. In contrast, the combined stressor treatment showed a non-additive effect with lower microbial gene abundance throughout the experiment. The response of microbial communities in the sandy sediment was less pronounced, with the most noticeable response seen in the archaeal gene abundances in response to environmental stressors over time. 16S rRNA genes (amoA and nirS) were lower in abundance in the combined stressor treatments in sandy sediments. Our results indicated that marine benthic microorganisms, especially in muddy sediments, are susceptible to changes in ocean carbonate chemistry and seawater temperature, which ultimately may have an impact upon key benthic biogeochemical cycles.

A Leucine Aminopeptidase Gene of the Pacific Oyster Crassostrea gigas Exhibits an Unusually High Level of Sequence Variation, Predicted to Affect Structure, and Hence Activity, of the Enzyme

Abstract Leucine aminopeptidase (LAP) belongs to a family of ubiquitous peptidases, with roles in growth and development, stress responses and adaptation to changing environmental conditions. The LAP gene was sequenced from a commercially important marine bivalve: the Pacific oyster Crassostrea gigas, and sequence polymorphisms were identified. This study identified 21 single nucleotide polymorphisms (SNPs), which would alter the encoded amino acid sequence, one 3 base deletion, one single base deletion, which would create a truncated protein (predicted to be nonfunctional), and a further 50 silent SNPs. The 23 polymorphisms altering protein sequence were found to occur in 34 different combinations, which we designated as 34 alleles: many more than the 6 alleles predicted previously by allozyme analysis. Predictions of protein structure and stability were used to identify which of the changes in the protein sequence are most likely to affect enzyme function. The sequence of the LAP gene noncoding regions was also analyzed and simple sequence repeats (microsatellites) were found in introns 1 and 9. The intron 1 microsatellite region was also found in another species of oyster: Crassostrea hongkongensis. We have demonstrated that the LAP gene region of the Pacific oyster, C. gigas is highly variable, and have identified new, potentially useful, genetic markers.