Life goes on: Spatial heterogeneity promotes biodiversity in an urbanized coastal marine ecosystem.

Both human populations and marine biodiversity are concentrated along coastlines, with growing conservation interest in how these ecosystems can survive intense anthropogenic impacts. Tropical urban centres provide valuable research opportunities because these megacities are often adjacent to mega-diverse coral reef systems. The Pearl River Delta is a prime exemplar, as it encompasses one of the most densely populated and impacted regions in the world and is located just northwest of the Coral Triangle. However, the spatial and taxonomic complexity of this biodiversity, most of which is small, cryptic in habitat and poorly known, make comparative analyses challenging. We deployed standardized settlement structures at seven sites differing in the intensity of human impacts and used COI metabarcoding to characterize benthic biodiversity, with a focus on metazoans. We found a total of 7184 OTUs, with an average of 665 OTUs per sampling unit; these numbers exceed those observed in many previous studies using comparable methods, despite the location of our study in an urbanized environment. Beta diversity was also high, with 52% of the OTUs found at just one site. As expected, we found that the sites close to point sources of pollution had substantially lower diversity (44% less) relative to sites bathed in less polluted oceanic waters. However, the polluted sites contributed substantially to the total animal diversity of the region, with 25% of all OTUs occurring only within polluted sites. Further analysis of Arthropoda, Annelida and Mollusca showed that phylogenetic clustering within a site was common, suggesting that environmental filtering reduced biodiversity to a subset of lineages present within the region, a pattern that was most pronounced in polluted sites and for the Arthropoda. The water quality gradients surrounding the PRD highlight the unique role of in situ studies for understanding the impacts of complex urbanization pressures on biodiversity.

Analysis of SARS-CoV-2 amino acid mutations in New York City Metropolitan wastewater (2020-2022) reveals multiple traits with human health implications across the genome and environment-specific distinctions

We characterize variant diversity, amino acid mutation frequency, functionality and associations with COVID-19 infections in one of the largest datasets of SARS-CoV-2 genome sequences collected from wastewater in the New York metropolitan area. Variant diversity differed within parts of the New York City sewershed and between wastewater sludge and influent samples. P314L, D614G and T3255I occurred in >95% of wastewater samples. Enhanced infectivity, transmissibility and escape from antibody neutralization were dominant traits in the wastewater. Strikingly, over 60% of the most frequently occurring mutations were found in regions other than the spike (S) protein, and nearly 50% remain uncharacterized for functional impacts warranting further investigation. We demonstrate strong correlations between P314L, D614G, T95I, G50E, G50R, G204R, R203K, G662S, P10S, P13L and mortality rates, percent positive test results, hospitalization rates and % of population fully vaccinated. The results from our study suggest that there are relatively understudied mutations in the spike protein (H655Y, T95I) and understudied mutations occurring in non-spike proteins (N, ORF1b, ORF9b and ORF9c), that are enhancing transmissibility and infectivity among human populations, warranting further investigation.

Modification of fatty acid profile and biosynthetic pathway in symbiotic corals under eutrophication.

Symbiotic corals receive energy not only by ingesting food (e.g. plankton, inorganic/organic matter, i.e. heterotrophy), but also by endosymbiosis, which supplies photosynthates (dissolved inorganic carbon, i.e. autotrophy). These two sources of energy have distinct fatty acid (FA) profiles, which can be used to differentiate corals by their primary feeding mode. FA profiles have been applied as biomarkers to evaluate the quality of nutrition in the midst of environmental change. However, species-specific responses of coral FA profiles and biosynthetic pathway under cultural eutrophication are still unknown. We collected two coral species (Acropora samoensis, Platygyra carnosa) from sites with different levels of eutrophication to test for variations in FA profiles. Gas Chromatography-Mass Spectrometry (GC-MS) was performed to identify FA profiles and quantify their concentration. Our main findings are threefold: 1) chronic eutrophication inhibits corals' ability to synthesize essential FA; 2) PUFA:SFA ratio and certain FA biomarkers or their pathway can be successfully utilized to determine the relative degree of autotrophy and heterotrophy in corals; 3) under eutrophication, different FA profiles of coral host tissue are attributed to different feeding strategies. Thus, our research provides significant new insights into the roles of FA as a risk assessment tool in coral reef ecosystems under the pressure of eutrophication.

Investigating the link between Pearl River-induced eutrophication and hypoxia in Hong Kong shallow coastal waters.

We present geochemical analysis of 75 surface water samples collected in 2016 in Hong Kong coastal waters. We found that nitrogen distribution around Hong Kong can be characterized by two regimes driven by the influence of the Pearl River: 1) a regime where nitrate is the dominant species of nitrogen, associated with lower salinity and more faecal coliform and 2) a regime where dissolved organic nitrogen is dominant, associated with higher salinity and fewer faecal coliform. While the impact of the Pearl River on Hong Kong coastal waters is well characterized, we used the sharp contrast between the nitrogen regimes to produce new evidence about the role of the Pearl River on the generation of local hypoxia in Hong Kong. The impact of nitrate originating from the Pearl River on the generation of hypoxia in Hong Kong might be less important than previously thought, as no sign of eutrophication was found within the zones dominated by dissolved organic nitrogen and an historical decoupling of surface processes and bottom water oxygenation was observed. Moreover, we measured elevated ammonium levels and rapid cycling of ammonium and dissolved organic nitrogen in Victoria Harbour suggesting local sources, such as wastewater, might be rapidly oxidized and thus play an important role in the consumption of oxygen locally. A first-order calculation highlighted the potential for wastewater to drive the observed seasonal decline in oxygen. Taken together, these evidences suggest that eutrophication might not be the primary driver in the generation of seasonal hypoxia and that oxidation of ammonium released locally might play a bigger role than initially thought.

Scaling of SARS-CoV-2 RNA in Settled Solids from Multiple Wastewater Treatment Plants to Compare Incidence Rates of Laboratory-Confirmed COVID-19 in Their Sewersheds.

Published and unpublished reports show that SARS-CoV-2 RNA in publicly owned treatment work (POTW) wastewater influent and solids is associated with new COVID-19 cases or incidence in associated sewersheds, but methods for comparing data collected from diverse POTWs to infer information about the relative incidence of laboratory-confirmed COVID-19 cases, and scaling to allow such comparisons, have not been previously established. Here, we show that SARS-CoV-2 N1 and N2 concentrations in solids normalized by concentrations of PMMoV RNA in solids can be used to compare incidence of laboratory confirmed new COVID-19 cases across POTWs. Using data collected at seven POTWs along the United States West Coast, Midwest, and East Coast serving ∼3% of the U.S. population (9 million people), we show that a 1 log change in N gene/PMMoV is associated with a 0.24 (range 0.19 to 0.29) log10 change in incidence of laboratory confirmed COVID-19. Scaling of N1 and N2 by PMMoV is consistent, conceptually, with a mass balance model relating SARS-CoV-2 RNA to the number of infected individuals shedding virus in their stool. This information should support the application of wastewater-based epidemiology to inform the response to the COVID-19 pandemic and potentially future viral pandemics.

A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments.

BACKGROUND: Coastal marine environments are one of the most productive ecosystems on Earth. However, anthropogenic impacts exert significant pressure on coastal marine biodiversity, contributing to functional shifts in microbial communities and human health risk factors. However, relatively little is known about the impact of eutrophication-human-derived nutrient pollution-on the marine microbial biosphere. RESULTS: Here, we tested the hypothesis that benthic microbial diversity and function varies along a pollution gradient, with a focus on human pathogens and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG annotation revealed that zinc, lead, total volatile solids, and ammonia nitrogen were correlated with microbial diversity and function. We propose several microbes, including Planctomycetes and sulfate-reducing microbes as candidates to reflect pollution concentration. Annotation of antibiotic resistance genes showed that the highest abundance of efflux pumps was found at the most polluted site, corroborating the relationship between pollution and human health risk factors. This result suggests that sediments at polluted sites harbor microbes with a higher capacity to reduce intracellular levels of antibiotics, heavy metals, or other environmental contaminants. CONCLUSIONS: Our findings suggest a correlation between pollution and the marine sediment microbiome and provide insight into the role of high-turnover microbial communities as well as potential pathogenic organisms as real-time indicators of water quality, with implications for human health and demonstrate the inner functional shifts contributed by the microcommunities.

Nitrogen sources and cycling revealed by dual isotopes of nitrate in a complex urbanized environment.

Elevated nutrient inputs have led to increased eutrophication in coastal marine ecosystems worldwide. An understanding of the relative contribution of different nutrient sources is imperative for effective water quality management. Stable isotope values of nitrate (δ15NNO3-, δ18ONO3-) can complement conventional water quality monitoring programs to help differentiate natural sources of NO3- from anthropogenic inputs and estimate the processes involved in N cycling within an ecosystem. We measured nutrient concentrations, δ15NNO3-, and δ18ONO3- in 76 locations along a salinity gradient from the lower end of the Pearl River Estuary, one of China's largest rivers discharging into the South China Sea, towards the open ocean. NO3- concentrations decreased with increasing salinity, indicative of conservative mixing of eutrophic freshwater and oligotrophic seawater. However, our data did not follow conservative mixing patterns. At salinities <20 psu, samples exhibited decreasing NO3-concentrations with almost unchanged NO3- isotope values, indicating simple dilution. At salinities >20 psu, NO3- concentrations decreased, while dual NO3- isotopes increased, suggesting mixing and/or other transformation processes. Our analysis yielded mean estimates for isotope enrichment factors (15ε = -2.02‰ and 18ε = -3.37‰), Δ(15,18) = -5.5‰ and δ15NNO3- - δ15NNO2- = 12.3‰. After consideration of potential alternative sources (sewage, atmospheric deposition and groundwater) we concluded that there are three plausible interpretations for deviations from conservative mixing behaviour (1) NO3- uptake by assimilation (2) in situ NO3- production (from fixation-derived nitrogen and nitrification of sewage-derived effluents) and (3) input of groundwater nitrate carrying a denitrification signal. Through this study, we propose a simple workflow that incorporates a synthesis of numerous isotope-based studies to constrain sources and behaviour of NO3- in urbanized marine environments.