Stanley Kim Juniper

The roles of DNA methylation in invertebrates are poorly characterized, and critical data are missing for the phylum Annelida. We fill this knowledge gap by conducting the first genome-wide survey of DNA methylation in the deep-sea polychaetes dominant in deep-sea vents and seeps: Paraescarpia echinospica, Ridgeia piscesae, and Paralvinella palmiformis. DNA methylation calls were inferred from Oxford Nanopore sequencing after assembling high-quality genomes of these animals. The genomes of these worms encode all the key enzymes of the DNA methylation metabolism and possess a mosaic methylome similar to that of other invertebrates. Transcriptomic data of these polychaetes support the hypotheses that gene body methylation strengthens the expression of housekeeping genes and that promoter methylation acts as a silencing mechanism but not the hypothesis that DNA methylation suppresses the activity of transposable elements. The conserved epigenetic profiles of genes responsible for maintaining homeostasis under extreme hydrostatic pressure suggest DNA methylation plays an important adaptive role in these worms.

The mechanisms by which large-scale microbial community function emerges from complex ecological interactions between individual taxa and functional groups remain obscure. We leveraged network analyses of 16S rRNA amplicon sequences obtained over a seven-month timeseries in seasonally anoxic Saanich Inlet (Vancouver Island, Canada) to investigate relationships between microbial community structure and water column N₂O cycling. Taxa separately broadly into three discrete subnetworks with contrasting environmental distributions. Oxycline subnetworks were structured around keystone aerobic heterotrophs that correlated with nitrification rates and N₂O supersaturations, linking N₂O production and accumulation to taxa involved in organic matter remineralization. Keystone taxa implicated in anaerobic carbon, nitrogen, and sulfur cycling in anoxic environments clustered together in a low-oxygen subnetwork that correlated positively with nitrification N₂O yields and N₂O production from denitrification. Close coupling between N₂O producers and consumers in the anoxic basin is indicated by strong correlations between the low-oxygen subnetwork, PICRUSt2-predicted nitrous oxide reductase (nosZ) gene abundances, and N₂O undersaturation. This study implicates keystone taxa affiliated with common ODZ groups as a potential control on water column N₂O cycling and provides a theoretical basis for further investigations into marine microbial interaction networks.

Indigenous knowledge is often disregarded and opportunities for positive change are lost. To protect the Ocean, a “two-eyed seeing” approach combining Indigenous and western knowledge systems can create advancements while empowering coastal Indigenous Peoples.

Many foundation species in chemosynthesis-based ecosystems rely on environmentally acquired symbiotic bacteria for their survival. Hence, understanding the biogeographic distributions of these symbionts at regional scales is key to understanding patterns of connectivity and predicting resilience of their host populations (and thus whole communities). However, such assessments are challenging because they necessitate measuring bacterial genetic diversity at fine resolutions. For this purpose, the recently discovered clustered regularly interspaced short palindromic repeats (CRISPR) constitutes a promising new genetic marker. These DNA sequences harboured by about half of bacteria hold their viral immune memory, and as such, might allow discrimination of different lineages or strains of otherwise indistinguishable bacteria. In this study, we assessed the potential of CRISPR as a hypervariable phylogenetic marker in the context of a population genetic study of an uncultured bacterial species. We used high-throughput CRISPR-based typing along with multi-locus sequence analysis (MLSA) to characterize the regional population structure of the obligate but environmentally acquired symbiont species Candidatus Endoriftia persephone on the Juan de Fuca Ridge. Mixed symbiont populations of Ca. Endoriftia persephone were sampled across individual Ridgeia piscesae hosts from contrasting habitats in order to determine if environmental conditions rather than barriers to connectivity are more important drivers of symbiont diversity. We showed that CRISPR revealed a much higher symbiont genetic diversity than the other housekeeping genes. Several lines of evidence imply this diversity is indicative of environmental strains. Finally, we found with both CRISPR and gene markers that local symbiont populations are strongly differentiated across sites known to be isolated by deep-sea circulation patterns. This research showed the high power of CRISPR to resolve the genetic structure of uncultured bacterial populations and represents a step towards making keystone microbial species an integral part of conservation policies for upcoming mining operations on the seafloor.

Host–symbiont relationships in hydrothermal vent ecosystems, supported by chemoautotrophic bacteria as primary producers, have been extensively studied. However, the process by which densely populated co‐occurring invertebrate hosts form symbiotic relationships with bacterial symbionts remains unclear. Here, we analyzed gill‐associated symbiotic bacteria (gill symbionts) of five co‐occurring hosts, three mollusks (“Bathymodiolus” manusensis, B. brevior, and Alviniconcha strummeri) and two crustaceans (Rimicaris variabilis and Austinograea alayseae), collected together at a single vent site in the Tonga Arc. We observed both different compositions of gill symbionts and the presence of unshared operational taxonomic units (OTUs). In addition, the total number of OTUs was greater for crustacean hosts than for mollusks. The phylogenetic relationship trees of gill symbionts suggest that γ‐proteobacterial gill symbionts have coevolved with their hosts toward reinforcement of host specificity, while campylobacterial Sulfurovum species found across various hosts and habitats are opportunistic associates. Our results confirm that gill symbiont communities differ among co‐occurring vent invertebrates and indicate that hosts are closely related with their gill symbiont communities. Considering the given resources available at a single site, differentiation of gill symbionts seems to be a useful strategy for obtaining nutrition and energy while avoiding competition among both hosts and gill symbionts.

Continental margin sediments are important sites of marine nitrogen cycling and potential contributors to atmospheric N₂O emissions. We employed trace‐level N₂O microsensors to measure vertical N₂O profiles at submillimeter resolutions in intact cores from outer continental margin sediments underlying the NE Pacific oxygen minimum zone. We used mathematical modeling to estimate depth‐dependent rates of N₂O production and fluxes to the overlying water along a transect of diminishing bottom water oxygen concentrations. Net sediment efflux was observed at all sites on the outer continental margin, with a mean value of 524 nmol m⁻² d⁻¹. N₂O efflux increased with decreased oxygen penetration depth in sediments. Enhanced N₂O production and efflux were obtained when outer continental shelf sediments were experimentally exposed to lower bottom‐water O₂ concentrations, to simulate upwelling conditions. Our results underline the need for further investigation of the drivers of N₂O production in continental margin sediments, and the relative importance of these environments to the global N₂O budget.

Deep‐sea marine protected areas (MPAs) present particular challenges for management. Their remote location means there is limited knowledge of species and habitat distribution, and rates and scales of change. Yet, evaluating the attainment of conservation objectives and managing the impact of human activities both require a quantitative understanding of natural variability in species composition/abundance and habitat conditions. Ocean Networks Canada (ONC) and Fisheries and Oceans Canada are collaborating in the development of remote monitoring tools for the Endeavour Hydrothermal Vents MPA in the north‐east Pacific. This 98.5 km² MPA, located 250 km offshore Vancouver Island, encompasses five major fields of hydrothermal vents, at depths of 2200–2400 m. A real‐time cabled observatory was installed at the Endeavour site in 2010. Scientific research for the conservation, protection and understanding of the area is permitted within the MPA and is the primary activity impacting the area. Research activities require the use of submersibles for sampling, surveying and observatory infrastructure maintenance. Data and imagery from remotely operated vehicle dives and fixed subsea observatory sensors are archived in real time using ONC's Oceans 2.0 software system, enabling evaluation of the spatial footprint of research activity in the MPA and the baseline level of natural ecosystem change. Recent examples of database queries that support MPA management include: (1) using ESRI ArcGIS spatial analysis tools to create kernel density ‘heat maps’ to quantify the intensity of sampling and survey activity within the MPA; and (2) quantifying high‐frequency variability in vent fauna and habitat using sensor and fixed camera data. Collaboration between researchers and MPA managers can help mitigate the logistical challenges of monitoring remote MPAs. Recognition at the policy level of the importance of such partnerships could facilitate the extension of scientific missions to support more formal monitoring programmes.