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Mobile Bay, the fourth largest estuary in the USA located in the northern Gulf of Mexico, is known for extreme hypoxia in the water column during dry season caused by NH4+-rich and anoxic submarine groundwater discharge (SGD). Nutrient dynamics in the coastal ecosystem point to potentially elevated microbial activities; however, little is known about microbial community composition and their functional roles in this area. In this study, we investigated microbial community composition, distribution, and metabolic prediction along the coastal hydrological compartment of Mobile Bay using 16S rRNA gene sequencing. We collected microbial samples from surface (river and bay water) and subsurface water (groundwater and coastal pore water from two SGD sites with peat and sandy lithology, respectively). Salinity was identified as the primary factor affecting the distribution of microbial communities across surface water samples, while DON and PO43- were the major predictor of community shift within subsurface water samples. Higher microbial diversity was found in coastal pore water in comparison to surface water samples. Gammaproteobacteria, Bacteroidia, and Oxyphotobacteria dominated the bacterial community. Among the archaea, methanogens were prevalent in the peat-dominated SGD site, while the sandy SGD site was characterized by a higher proportion of ammonia-oxidizing archaea. Cyanobium PCC-6307 and unclassified Thermodesulfovibrionia were identified as dominant taxa strongly associated with trends in environmental parameters in surface and subsurface samples, respectively. Microbial communities found in the groundwater and peat layer consisted of taxa known for denitrification and dissimilatory nitrate reduction to ammonium (DNRA). This finding suggested that microbial communities might also play a significant role in mediating nitrogen transformation in the SGD flow path and in affecting the chemical composition of SGD discharging to the water column. Given the ecological importance of microorganisms, further studies at higher taxonomic and functional resolution are needed to accurately predict chemical biotransformation processes along the coastal hydrological continuum, which influence water quality and environmental condition in Mobile Bay., Competing Interests: DM and Geosyntec Consultants declare no competing interest regarding the publication of all information and data included in this manuscript. DM and Geosyntec Consultants declare that no employment, consultancy, patent, product development, or marketed products will be implemented in relation with this publication. DM’s affiliation with Geosyntec Consultants does not alter our adherence to PLOS ONE policies on sharing data and materials.

Submarine groundwater discharge (SGD) can be an important pathway for chemical or biological pollutants from land to the ocean around the world. However, studies on the microbial communities associated with SGD in Southeast Asia, which has been hypothesized as SGD hotspot, remain scarce. In this study, we examined the microbial community composition with 16S rRNA gene sequencing along the hydrological continuum of an SGD site in a tropical urban area of Indonesia. Of the observed parameters in this study, salinity and temperature were the most determinant variables explaining patterns in microbial community composition. The bacterial taxon Burkholderiaceae was predominantly found in low salinity samples, including those from terrestrial groundwater and brackish pore water, while cyanobacteria of the genus Synechococcus sp. CC9902 were indicative of saline SGD and seawater samples. The composition of microbial taxa in each sample pointed to the influence of shallow terrestrial groundwater in the beach pore water, while seawater recirculation dominated the SGD sampling points situated further offshore. We identified taxa containing fecal indicators and potential pathogens at the SGD compartments; however, while a likely explanation, we could not conclude with certainty that SGD was a conduit for these bacteria. Overall, the results from this study show that microbial community analysis can highlight hydrological processes and water quality at the SGD site; thus, they could be useful for environmental policymakers to formulate water management strategies in coastal areas., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Fresh submarine groundwater discharge (FSGD) is an important pathway for nutrients andother forms of pollutants from land to the ocean. Microbial communities in SGD may have aneffect on sediments and coastal waters. In this study, we examined microbial communitycomposition along the hydrological continuum of a SGD site in an urban tropical area inIndonesia. Microbial communities in coastal water were clustered according to salinity. The bacterialtaxa Novosphingobium, Flavobacterium and Burkholderiaceae were predominantly found inlow salinity samples, including those from terrestrial groundwater and brackish SGD, whilecyanobacteria of the genus Synechococcus CC9902 were indicative of saline SGD andseawater samples. The microbial community composition of each sample pointed towards amixture of shallow and deep groundwater contribution into the SGD sites, as well as a highinfluence of seawater recirculation. Ammonia oxidation and denitrification likely were thedominant biochemical processes occurring along the SGD pathway based on the taxonomiccomposition of the microbial community. The identification of fecal and potentiallypathogenic bacteria along the land-ocean interface also suggested biological contaminationfrom anthropogenic activities. Results from this study suggest that groundwater and coastal pore water were relatedbased on their microbial community composition and it supports previous findingsregarding the occurrence of fresh SGD in the area. Furthermore, microbial analyses inSGD studies can determine the quality of SGD; thus, it could be a useful tool forenvironmental policy makers in formulating water management strategies in coastal areas. [ABSTRACT FROM AUTHOR]