Search

Oysters play an important role in coastal ecology and are a globally popular seafood source. However, their filter feeding lifestyle enables coastal pathogens, toxins, and pollutants to accumulate in their tissues, potentially endangering human health. For example, bacterial pathogens from both marine and terrestrial sources concentrate in oysters and can cause human illness when oysters are consumed raw. While pathogen concentrations in coastal waters are often linked to environmental conditions and runoff events, these do not always correlate with pathogen concentrations in oysters. Additional factors related to oyster hosts and the microbial ecology of pathogenic bacteria likely play a role in accumulation but are poorly understood. In this study, we investigated whether microbial communities in water and oysters were linked to accumulation of fecal indicators,Vibrio parahaemolyticus, andVibrio vulnificus. Site-specific environmental conditions significantly influenced the composition and diversity of water microbial communities, which were linked to the highest concentrations of bothVibriospp. and fecal indicator bacteria. Oyster microbial communities, however, were less impacted by environmental variability and exhibited less variability in microbial community diversity and accumulation of target bacteria. Instead, changes in specific microbial taxa in oyster and water samples, particularly in oyster digestive glands, were linked to elevated potential pathogens in oysters, especiallyV. parahaemolyticus. This included an increase in cyanobacteria in both water and oyster digestive gland microbial communities, which could represent an environmental vector forVibriospp. transport and decreased relative abundance ofMycoplasmaand other key members of the oyster digestive gland microbiota. These findings suggest that host and microbial factors, in addition to environmental variables, may influence pathogen accumulation in oysters.

Fish are the most diverse and widely distributed vertebrates, yet little is known about the microbial ecology of fishes nor the biological and environmental factors that influence the fish microbiome. The microbiota from 101 species of Southern California marine fishes, spanning 22 orders, 55 families, and 83 genera representing ~ 25% of local marine fish diversity, was analyzed to identify patterns that explain microbial diversity patterns in a geographical subset of marine fish biodiversity. We compared fish microbiomes (gill, skin, midgut, and hindgut) using alpha, beta, and gamma diversity along with establishing a novel method to estimate microbial biomass (Qiime2 plugin katharoseq). For oceanic fishes from the neritic zone, host size and distance from shore were negatively associated with microbial biomass densities and diversity in the gills. Body site was the strongest driver for beta diversity with strong evidence of phylosymbiosis observed across the gill, skin, and hindgut, but not midgut. The majority of microbes from all fish body sites were of unknown origin but overall sea water generally contributes more microbes to fish mucus compared to marine sediment. In a meta-analysis of vertebrate hindguts (569 species), mammals had the highest gamma diversity when controlling for host species number while fishes had the highest percent of unique microbial taxa (92%). In fishes, the midgut, gill, and skin contains the majority of microbial diversity which collectively can be 5.5 times higher than the hindgut. The composite dataset will be useful to vertebrate microbiome researchers and fish biologists interested in microbial ecology with applications in aquaculture and fisheries management.

The Olympia oyster (Ostrea lurida) of the Puget Sound suffered a dramatic population crash, but restoration efforts hope to revive this native species. One overlooked variable in the process of assessing ecosystem health is association of bacteria with marine organisms and the environments they occupy. Oyster microbiomes are known to differ significantly between species, tissue type, and the habitat in which they are found. The goals of this study were to determine the impact of field site and habitat on the oyster microbiome and to identify core oyster-associated bacteria in the Puget Sound. Olympia oysters from one parental family were deployed at four sites in the Puget Sound both inside and outside of eelgrass (Zostera marina) beds. Using 16S rRNA gene amplicon sequencing of the oyster gut, shell, surrounding seawater and sediment, we demonstrate that gut-associated bacteria are distinct from the surrounding environment and vary by field site. Furthermore, regional differences in the gut microbiota are associated with the survival rates of oysters at each site after two months of field exposure. However, habitat type had no influence on microbiome diversity. Further work is needed to identify the specific bacterial dynamics that are associated with oyster physiology and survival rates.ImportanceThe outcomes of this study demonstrate the need to monitor microbial ecology at potential oyster restoration sites, specifically for the native Olympia oyster in the Puget Sound. Some areas of Puget Sound may be less amenable to Olympia oyster restoration than others due to microbiome colonization trends. Furthermore, this study puts the oyster microbiome in the context of its surroundings, providing a holistic perspective on the factors that may influence oyster performance and microbial ecology.

Urbanization along coastlines alters marine ecosystems including contributing molecules of anthropogenic origin to the coastal dissolved organic matter (DOM) pool. A broad assessment of the nature and extent of anthropogenic impacts on coastal ecosystems is urgently needed to inform regulatory guidelines and ecosystem management. Recently, non-targeted tandem mass spectrometry approaches are gaining momentum for the analysis of global organic matter composition (chemotypes) including a wide array of natural and anthropogenic compounds. In line with these efforts, we developed a non-targeted liquid chromatography tandem mass spectrometry (LC-MS/MS) workflow that utilizes advanced data analysis approaches such as feature-based molecular networking and repository-scale spectrum searches. This workflow allows the scalable comparison and mapping of seawater chemotypes from large-scale spatial surveys as well as molecular family level annotation of unknown compounds. As a case study, we visualized organic matter chemotype shifts in coastal environments in northern San Diego, USA, after notable rain fall in winter 2017/2018 and highlight potential anthropogenic impacts. The observed seawater chemotype, consisting of 4384 LC-MS/MS features, shifted significantly after a major rain event. Molecular drivers of this shift could be attributed to multiple anthropogenic compounds, including pesticides (Imazapyr and Isoxaben), cleaning products (Benzyl-tetradecyl-dimethylammonium) and chemical additives (Hexa (methoxymethyl)melamine) and potential degradation products. By expanding the search of identified xenobiotics to other public tandem mass spectrometry datasets, we further contextualized their possible origin and show their importance in other ecosystems. The mass spectrometry and data analysis pipelines applied here offer a scalable framework for future molecular mapping and monitoring of marine ecosystems, which will contribute to a deliberate assessment of how chemical pollution impacts our oceans.

Anthropogenic pollutants inundate marine ecosystems as human population growth and urbanization rapidly increase along the coast. The analytical methods applied to detect anthropogenic imprints in coastal seawater are historically aimed at measuring and monitoring a restricted number of compounds. More recently applied non-targeted approaches are typically still limited by spectral and structure library coverage. To prioritize anthropogenic impacts in marine systems beyond compounds present in libraries and suspect lists, we applied non-targeted liquid chromatography tandem mass spectrometry in combination with molecular networking. We integrated an advanced data analysis pipeline that allows scalable comparison of chemotypes between samples in addition to expanded compound annotation using molecular networking. Using this workflow, we explored the chemical impacts of a major rain event in January 2018 in coastal San Diego, USA in a total of 120 samples. We detected 4384 ion features and could annotate 92 MS/MS spectra by spectrum library matching of which 40 annotations were putative xenobiotics. The observed seawater chemotype shifted significantly after the rain event. Molecular drivers of this shift could be attributed to multiple anthropogenic compounds, such as pesticides (Imazapyr and Isoxaben), cleaning products (Benzyl-tetradecyl-dimethylammonium) and chemical additives (Hexa(methoxymethyl)melamine). Expanding the search of identified xenobiotics to other public tandem mass spectrometry datasets, we could further contextualize their possible origin and show their potential importance in other ecosystems. Ultimately, the mass spectrometry and data analysis pipelines applied here offer a scalable framework for future molecular mapping and monitoring of marine ecosystems, which we hope will contribute to a more deliberate assessment of how chemical pollution impacts marine environments.

Anthropogenic pollutants inundate marine ecosystems as human population growth and urbanization rapidly increase along the coast. Our analytical methods are typically aimed at measuring and monitoring a restricted number of compounds. To prioritize coastal anthropogenic impacts in a comprehensive fashion, we applied large-scale non-targeted liquid chromatography tandem mass spectrometry. We integrated an advanced data analysis pipeline that allows scalable comparison of chemotypes between samples in addition to expanded compound annotation using molecular networking. Using this workflow, we explored the chemical impacts of a major rain event in January 2018 in coastal San Diego, USA. We observed the seawater chemotype shift significantly after the rain event. Molecular drivers of this shift could be attributed to multiple anthropogenic compounds, such as pesticides, cleaning products, drugs and chemical additives that could be connected to potential point sources. Expanding the search of identified xenobiotics to other public tandem mass spectrometry datasets, we could further contextualize their origin and show their potential importance in other ecosystems. Ultimately, the mass spectrometry and data analysis pipeline applied here offer a scalable framework for future molecular mapping and monitoring of marine ecosystems, which we hope will contribute to a more deliberate assessment of how chemical pollution impacts marine environments.