Microbial community composition across a coastal hydrological system affected by submarine groundwater discharge (SGD)

Microbial Community of a Sandy Beach Subterranean Estuary is Spatially Heterogeneous and Impacted by Winter Waves

Subterranean estuaries (STEs) are critical ecosystems at the interface of meteoric groundwater and subsurface seawater that are threatened by sea level rise. To characterize the influence of tides and waves on the STE microbial community, we collected porewater samples from a high-energy beach STE at Stinson Beach, California, USA, over the two-week neap-spring tidal transition during both a wet and dry season. The microbial community, analyzed by 16S rRNA gene (V4) amplicon sequencing, clustered according to consistent physicochemical features found within STEs. The porewater community harbored relatively abundant Proteobacteria, Verrucomicrobiota, and Bacteroidota, as well as members of the archaeal DPANN superphylum and bacterial Candidate Phyla Radiation (CPR). Tidal conditions were not associated with microbial community composition; however, a wave overtopping event significantly impacted the beach microbiome. As a baseline for environmental change, our results elucidate the unique dynamics of a STE microbiome with unprecedented temporal resolution, highlighting the transport of cellular material through beach porewater due to waves.

Dissemination of antimicrobial resistance in agricultural ecosystems following irrigation with treated municipal wastewater

The spread of antimicrobial resistance (AMR) in agricultural systems via irrigation water is a serious public health issue as it can be transmitted to humans through the food chain. Therefore, understanding the dissemination routes of antibiotic resistance genes (ARGs) in agricultural systems is crucial for the assessment of health risks associated with eating fresh vegetables such as spinach and radish irrigated with treated municipal wastewater (TMW). In this study, we investigated the bacterial community structure and resistome in the soil-plant-earthworm continuum after irrigation of spinach and radish with TMW containing the antibiotics trimethoprim (TMP), sulfamethoxazole (SMZ), and sulfapyridine (SPD) using 16S rRNA gene sequencing and high throughput quantitative PCR (HT-qPCR). The study was conducted in two phases: Phase I involved eight weeks of spinach and radish production using TMW for irrigation, whereas Phase II entailed three weeks of earthworm exposure to contaminated plant material obtained in Phase I. The 16S data indicated that the rhizosphere bacterial community composition and structure were more resilient to antibiotic residuals in the irrigated water, with radish showing less susceptibility than spinach than those of bulk soils. The HT-qPCR analysis revealed that a total of 271 ARGs (out of 285) and 9 mobile genetic elements (MGEs) (out of 10) were detected in all samples. Higher diversity and abundance of ARGs were observed for samples irrigated with higher concentrations of antibiotics in both spinach and radish treatments. However, compared to spinach, radish ARG dynamics in the soil biome were more stable due to the change of antibiotic introduction to the soil. At the class level, multi-drug resistance (MDR) class was altered significantly by the presence of antibiotics in irrigation water. Compared to earthworm fecal samples, their corresponding soil environments showed a higher number of detected ARGs, suggesting that earthworms could play a role in reducing ARG dissemination in the soil environments. These findings will not only provide insight into the dissemination of ARGs in agricultural environments due to antibiotic residuals in irrigated water but could help understand the potential human health risks associated with ARGs.

A culture-independent approach, supervised machine learning, and the characterization of the microbial community composition of coastal areas across the Bay of Bengal and the Arabian Sea

BACKGROUND

Coastal areas are subject to various anthropogenic and natural influences. In this study, we investigated and compared the characteristics of two coastal regions, Andhra Pradesh (AP) and Goa (GA), focusing on pollution, anthropogenic activities, and recreational impacts. We explored three main factors influencing the differences between these coastlines: The Bay of Bengal's shallower depth and lower salinity; upwelling phenomena due to the thermocline in the Arabian Sea; and high tides that can cause strong currents that transport pollutants and debris.

RESULTS

The microbial diversity in GA was significantly higher than that in AP, which might be attributed to differences in temperature, soil type, and vegetation cover. 16S rRNA amplicon sequencing and bioinformatics analysis indicated the presence of diverse microbial phyla, including candidate phyla radiation (CPR). Statistical analysis, random forest regression, and supervised machine learning models classification confirm the diversity of the microbiome accurately. Furthermore, we have identified 450 cultures of heterotrophic, biotechnologically important bacteria. Some strains were identified as novel taxa based on 16S rRNA gene sequencing, showing promising potential for further study.

CONCLUSION

Thus, our study provides valuable insights into the microbial diversity and pollution levels of coastal areas in AP and GA. These findings contribute to a better understanding of the impact of anthropogenic activities and climate variations on biology of coastal ecosystems and biodiversity.

Microbial-induced MnO2 precipitation in a carbonate coastal aquifer

A study was carried out to identify biogeochemical reactions along a transect of a coastal dolomitic aquifer. In this transect, the physicochemical parameters of the groundwater as well as the microbial composition of samples taken at different depths and salinities were measured. Many of the dissolved ions measured in the groundwater follow a pattern that reflects the distribution of the water masses (fresh, interface and salt) in the aquifer, while others such as Ca and Mg ions deviate from this trend by identifying the zones of maximum dissolution of the carbonate matrix. The concentrations of minor ions, such as Fe and Mn, also follow a singular pattern, with maximum concentrations in the reducing zones of the aquifer and lower values in the oxidizing zones. Precipitates of Mn oxides along with other metals, such as Fe, Ba, Zn and Ni, were observed in the saline zone displaying oxidizing conditions close to the coastline, where a continuous core was recovered. This zone, which is located below the freshwater-seawater mixing zone and features percentages of seawater higher than 80 %, is characterized by the presence of Marinobacter as the predominant genus. These bacteria are also related to the formation of Mn-rich polymetallic oxides in other contexts such as the ocean floor (Wang et al., 2012; Cao et al., 2021). All in all, a biogeochemical reaction model is proposed that describes the formation of these oxides in areas close to the discharge zone of coastal aquifers. To do this, it has been necessary to integrate the results obtained from geochemical, hydrogeological and microbiological information.

The distinct phases of fresh-seawater mixing intricately regulate the nitrogen transformation processes in a high run-off estuary: Insight from multi-isotopes and microbial function analysis

Excessive anthropogenic nitrogen inputs lead to the accumulation of nitrogen, and significantly impact the nitrogen transformation processes in estuaries. However, the governing of nitrogen during its transport from terrestrial to estuary under the influence of diverse human activities and hydrodynamic environments, particularly in the fresh-seawater mixing zone, remains insufficient researched and lack of basis. To address this gap, we employed multi-isotopes, including δ15N-NO3-, δ18O-NO3-, δ15N-NH4+, and δ15N-PN, as well as microbial function analysis, to investigate the nitrogen transformation processes in the Pearl River Estuary (PRE), a highly anthropogenic and terrestrial estuary. Principle component analysis (PCA) confirmed that the PRE could clearly partitioned into three zone, e.g., terrestrial area (T zone), mixing area (M zone) and seawater area (S zone), in terms of nitrogen transportation and transformation processes. The δ15N-NO3- (3.38±0.60‰) and δ18O-NO3- (6.35±2.45‰) results in the inner estuary (T area) indicate that NO3-attributed to the domestic sewage and groundwater discharge in the river outlets lead to a higher nitrification rate in the outlets of the Pearl River than in the reaching and seawater intrusion areas, although nitrate is rapidly diluted by seawater after entering the estuary. The transformation of nitrogen in the T zone was under significant nitrogen fixation (0.61 ± 0.22 %) and nitrification processes (0.0043 ± 0.0032 %) (presumably driven by Exiguobacterium sp. (14.1 %) and Cyanobium_PCC-6307 (8.1 %)). In contrast, relatively low δ15N-NO3- (6.83 ± 1.24‰) and high δ18O-NO3- (22.13±6.01‰) imply that atmospheric deposition has increased its contribution to seawater nitrate and denitrification (0.53±0.13 %) was enhanced by phytoplankton/bacterial (such as Psychrobacter sp. and Rhodococcus) in the S zone. The assimilation of NH4 results from the ammonification of NO3- reduces δ15N-NH4+ (5.36 ± 1.49‰) and is then absorbed by particulate nitrogen (PN). The retention of nitrogen when fresh-seawater mixing enhances the elevation of δ15N-NH4+ (8.19 ± 2.19‰) and assimilation of NH4+, leading to an increase in PN and δ15N-PN (6.91 ± 1.52‰) from biological biomass (mainly Psychrobacter sp. and Rhodococcus). The results of this research demonstrate a clear and comprehensive characterization of the nitrogen transformation process in an anthropogenic dominated estuary, highlighting its importance for regulating the nitrogen dissipation in the fresh-seawater mixing process in estuarine ecosystems.

Geochemical factors impacting nitrifying communities in sandy sediments

Sandy sediment beaches covering 70% of non-ice-covered coastlines are important ecosystems for nutrient cycling along the land-ocean continuum. Subterranean estuaries (STEs), where groundwater and seawater meet, are hotspots for biogeochemical cycling within sandy beaches. The STE microbial community facilitates biogeochemical reactions, determining the fate of nutrients, including nitrogen (N), supplied by groundwater. Nitrification influences the fate of N, oxidising reduced dissolved inorganic nitrogen (DIN), making it available for N removal. We used metabarcoding of 16S rRNA genes and quantitative PCR (qPCR) of ammonia monooxygenase (amoA) genes to characterise spatial and temporal variation in STE microbial community structure and nitrifying organisms. We examined nitrifier diversity, distribution and abundance to determine how geochemical measurements influenced their distribution in STEs. Sediment microbial communities varied with depth (p-value = 0.001) and followed geochemical gradients in dissolved oxygen (DO), salinity, pH, dissolved inorganic carbon and DIN. Genetic potential for nitrification in the STE was evidenced by qPCR quantification of amoA genes. Ammonia oxidiser abundance was best explained by DIN, DO and pH. Our results suggest that geochemical gradients are tightly linked to STE community composition and nitrifier abundance, which are important to determine the fate and transport of groundwater-derived nutrients to coastal waters.

Hydrodynamic and anthropogenic disturbances co-shape microbiota rhythmicity and community assembly within intertidal groundwater-surface water continuum

Tidal hydrodynamics drive the groundwater-seawater exchange and shifts in microbiota structure in the coastal zone. However, how the coastal water microbiota structure and assembly patterns respond to periodic tidal fluctuations and anthropogenic disturbance remains unexplored in the intertidal groundwater-surface water (GW-SW) continuum, although it affects biogeochemical cycles and coastal water quality therein. Here, through hourly time-series sampling in the saltmarsh tidal creek, rhythmic patterns of microbiota structure in response to daily and monthly tidal fluctuations in intertidal surface water are disentangled for the first time. The similarity in archaeal community structures between groundwater and ebb-tide surface water (R2=0.06, p = 0.2) demonstrated archaeal transport through groundwater discharge, whereas multi-source transport mechanisms led to unique bacterial biota in ebb-tide water. Homogeneous selection (58.6%-69.3%) dominated microbiota assembly in the natural intertidal GW-SW continuum and the presence of 157 rhythmic ASVs identified at ebb tide and 141 at flood tide could be attributed to the difference in environmental selection between groundwater and seawater. For intertidal groundwater in the tidal creek affected by anthropogenically contaminated riverine inputs, higher microbial diversity and shift in community structure were primarily controlled by increased co-contribution of dispersal limitation and drift (jointly 57.8%) and enhanced microbial interactions. Overall, this study fills the knowledge gaps in the tide-driven water microbial dynamics in coastal transition zone and the response of intertidal groundwater microbiota to anthropogenic pollution of overlying waters. It also highlights the potential of microbiome analysis in enhancing coastal water quality monitoring and identifying anthropogenic pollution sources (e.g., pathogenic Vibrio in aquaculture) through the detection of rhythmic microbial variances associated with intertidal groundwater discharge and seawater intrusion.

Linking Groundwater to Surface Discharge Ecosystems: Archaeal, Bacterial, and Eukaryotic Community Diversity and Structure in Quebec (Canada)

Aquifer systems are composed of water flowing from surface recharge areas, to the subsurface and back to the surface in discharge regions. Groundwater habitats harbor a large microbial biomass and diversity, potentially contributing to surface aquatic ecosystems. Although this contribution has been widely studied in marine environments, very little is known about the connection between underground and surface microbial communities in freshwater settings. Therefore, in this study, we used amplicon sequencing to analyze the archaeal, bacterial, and eukaryotic community diversity and structure in groundwater and surface water samples, spanning the vast regions of the Laurentides and Lanaudières in the Quebec province (Canada). Our results show significant differences between subsurface and surface taxa; with more fungi, Amoebozoa, and chemolithoautotrophic prokaryotes involved in nitrogen-, sulfur-, and iron-cycling dominating the underground samples; while algae, ciliates, methanogens, and Actinobacteria dominate the surface discharge waters. Microbial source tracking suggested that only a small portion of the microbial communities in the groundwater contributed to the surface discharge communities. However, many taxa were shared between both habitats, with a large range of functional diversity, likely explaining their survival in both subsurface and surface water ecosystems.

Precipitation, submarine groundwater discharge of nitrogen, and red tides along the southwest Florida Gulf coast

Blooms of the dinoflagellate Karenia brevis occur almost every year along the southwest Florida Gulf coast. Long-duration blooms with especially high concentrations of K. brevis, known as red tides, destroy marine life through production of neurotoxins. Current hypotheses are that red tides originate in oligotrophic waters far offshore using nitrogen (N) from upwelling bottom water or, alternatively, from blooms of Trichodesmium, followed by advection to nearshore waters. But the amount of N available from terrestrial sources does not appear to be adequate to maintain a nearshore red tide. To explain this discrepancy, we hypothesize that contemporary red tides are associated with release of N from offshore submarine groundwater discharge (SGD) that has accumulated in benthic sediment biomass by dissimilatory nitrate reduction to ammonium (DNRA). The release occurs when sediment labile organic carbon (LOC), used as the electron donor in DNRA, is exhausted. Detritus from the resulting destruction of marine life restores the sediment LOC to continue the cycle of red tides. The severity of individual red tides increases with increased bloom-year precipitation in the geographic region where the SGD originates, while the severity of ordinary blooms is relatively unaffected.

Elevated CO2 aggravated polystyrene microplastics effects on the rice-soil system under field conditions

Polystyrene microplastics (PS) are decomposed very slowly due to their recalcitrance and inevitably interact with the changing climate. How the interaction between PS and increasing CO₂ concentration affects the plant-soil system is rarely investigated. Here, a free-air CO₂ enrichment system in farm fields was used to study the impacts of PS added to soil at 10 mg kg^-1 on rice and soil bacterial communities at different CO₂ levels (ambient∼390 ppm and elevated∼590 ppm). Results showed that single PS interfered with Fe, Mn and Zn uptake of rice, and it increased the abundances of bacteria taxa assigned to N turnover and urease activities, leading to altered soil N transformation and availability. Elevated CO₂ alone enhanced rice photosynthesis, decreased the abundances of nitrogen-fixation bacteria, and induced co-occurrence patterns between bacteria simplified and decentralized. Combined PS and elevated CO₂ significantly decreased rice stomatal conductance and transpiration rate by 56.70% and 29.46%, respectively, and further inhibited elements uptake. Besides, combined exposure significantly disturbed bacterial amino acid metabolism, and stimulated the adaptative responses of resistant bacteria. Overall, this study revealed that increasing CO₂ concentrations may exacerbate the impacts of PS on rice performance and soil bacterial communities, providing new insights into the interaction between microplastics and climate change.

Contaminant release, mixing and microbial fluctuations initiated by infiltrating water within a replica field-scale legacy radioactive waste trench

Numerous legacy near-surface radioactive waste sites dating from the mid 20th century have yet to be remediated and present a global contamination concern. Typically, there is insufficient understanding of contaminant release and redistribution, with invasive investigations often impractical due to the risk of disturbing the often significantly radiotoxic contaminants. Consequently, a replica waste trench (~5.4 m³), constructed adjacent to a legacy radioactive waste site (Little Forest Legacy Site, LFLS), was used to assist our understanding of the release and mixing processes of neodymium (Nd) - a chemical analogue for plutonium(III) and americium(III), two significant radionuclides in many contaminated environments. In order to clarify the behaviour of contaminants released from buried objects such as waste containers, a steel drum, representative of the hundreds of buried drums within the LFLS, was placed within the trench. Dissolved neodymium nitrate was introduced as a point-source contaminant to the base of the trench, outside the steel drum. Hydrologic conditions were manipulated to simulate natural rainfall intensities with dissolved lithium bromide added as a tracer. Neodymium was primarily retained both at its point of release at the bottom of the trench (>97 %) as well as at a steel container corrosion point, simulated through the emplacement of steel wool. However, over the 8-month field experiment, advective mixing initiated by surface water intrusions rapidly redistributed a small proportion of Nd to shallower waters (~1.5-1.7 %), as well as throughout the buried steel drum. Suspended particulate forms of Nd (>0.2 μm) were measured at all depths in the suboxic trench and were persistent across the entire study. Analyses of the microbial communities showed that their relative abundances and metabolic functions were strongly influenced by the prevailing geochemical conditions as a result of fluctuating water depths associated with rainfall events. The site representing steel corrosion exhibited divergent biogeochemical results with anomalous changes (sharp decrease) observed in both dissolved contaminant concentration as well as microbial diversity and functionality. This research demonstrates that experimental trenches provide a safe and unique method for simulating the behaviour of subsurface radioactive contaminants with results demonstrating the initial retention, partial shallow water redistribution, and stability of particulate form(s) of this radioactive analogue. These results have relevance for appropriate management and remediation strategies for the adjacent legacy site as well as for similar sites across the globe.

On the hidden diversity and niche specialization of the microbial realm of subterranean estuaries

Subterranean estuaries (STEs) modulate the chemical composition of continental groundwater before it reaches the coast, but their microbial community is poorly known. Here, we explored the microbial ecology of two neighbouring, yet contrasting STEs (Panxón and Ladeira STEs; Ría de Vigo, NW Iberian Peninsula). We investigated microbial composition (16S rRNA gene sequencing), abundance, heterotrophic production and their geochemical drivers. A total of 10,150 OTUs and 59 phyla were retrieved from porewater sampled during four surveys covering each STE seepage face. In both STEs, we find a very diverse microbial community composed by abundant cosmopolitans and locally restricted rare taxa. Porewater oxygen and dissolved organic matter are the main environmental predictors of microbial community composition. More importantly, the high variety of benthic microbiota links to biogeochemical processes of different elements in STEs. The oxygen-rich Panxón beach showed strong associations of the ammonium oxidizing archaea Nitrosopumilales with the heterotrophic community, thus acting as a net source of nitrogen to the coast. On the other hand, the prevailing anoxic conditions of Ladeira beach promoted the dominance of anaerobic heterotrophs related to the degradation of complex and aromatic compounds, such as Dehalococcoidia and Desulfatiglans, and the co-occurrence of methane oxidizers and methanogens.

Structural shifts in sea ice prokaryotic communities across a salinity gradient in the subarctic

Current knowledge of the processes that shape prokaryotic community assembly in sea ice across polar ecosystems is scarce. Here, we coupled culture-dependent (bacterial isolation on R2A medium) and culture-independent (high-throughput 16S rRNA gene sequencing) approaches to provide the first comprehensive assessment of prokaryotic communities in the late winter ice and its underlying water along a natural salinity gradient in coastal Hudson Bay, an iconic cryo-environment that marks the ecological transition between Canadian Subarctic and Arctic biomes. We found that prokaryotic community assembly processes in the ice were less selective at low salinity since typical freshwater taxa such as Frankiales, Burkholderiales, and Chitinophagales dominated both the ice and its underlying water. In contrast, there were sharp shifts in community structure between the ice and underlying water samples at sites with higher salinity, with the orders Alteromonadales and Flavobacteriales dominating the ice, while the abovementioned freshwater taxa dominated the underlying water communities. Moreover, primary producers including Cyanobium (Cyanobacteria, Synechococcales) may play a role in shaping the ice communities and were accompanied by known Planctomycetes and Verrucomicrobiae taxa. Culture-dependent analyses showed that the ice contained pigment-producing psychrotolerant or psychrophilic bacteria from the phyla Proteobacteria, Actinobacteriota, and Bacteroidota, likely favored by the combination of low temperatures and the seasonal increase in sunlight. Our findings suggest that salinity, photosynthesis and dissolved organic matter are the main drivers of prokaryotic community structure in the late winter ice of coastal Hudson Bay, the ecosystem with the fastest sea ice loss rate in the Canadian North.

Many Questions Remain Unanswered About the Role of Microbial Transmission in Epizootic Shell Disease in American Lobsters (Homarus americanus)

Despite decades of research on lobster species’ biology, ecology, and microbiology, there are still unresolved questions about the microbial communities which associate in or on lobsters under healthy or diseased states, microbial acquisition, as well as microbial transmission between lobsters and between lobsters and their environment. There is an untapped opportunity for metagenomics, metatranscriptomics, and metabolomics to be added to the existing wealth of knowledge to more precisely track disease transmission, etiology, and host-microbe dynamics. Moreover, we need to gain this knowledge of wild lobster microbiomes before climate change alters environmental and host-microbial communities more than it likely already has, throwing a socioeconomically critical industry into disarray. As with so many animal species, the effects of climate change often manifest as changes in movement, and in this perspective piece, we consider the movement of the American lobster (Homarus americanus), Atlantic Ocean currents, and the microorganisms associated with either.

Bacterial Indicators Are Ubiquitous Members of Pelagic Microbiome in Anthropogenically Impacted Coastal Ecosystem

Coastal zones are exposed to various anthropogenic impacts, such as different types of wastewater pollution, e.g., treated wastewater discharges, leakage from sewage systems, and agricultural and urban runoff. These various inputs can introduce allochthonous organic matter and microbes, including pathogens, into the coastal marine environment. The presence of fecal bacterial indicators in the coastal environment is usually monitored using traditional culture-based methods that, however, fail to detect their uncultured representatives. We have conducted a year-around in situ survey of the pelagic microbiome of the dynamic coastal ecosystem, subjected to different anthropogenic pressures to depict the seasonal and spatial dynamics of traditional and alternative fecal bacterial indicators. To provide an insight into the environmental conditions under which bacterial indicators thrive, a suite of environmental factors and bacterial community dynamics were analyzed concurrently. Analyses of 16S rRNA amplicon sequences revealed that the coastal microbiome was primarily structured by seasonal changes regardless of the distance from the wastewater pollution sources. On the other hand, fecal bacterial indicators were not affected by seasons and accounted for up to 34% of the sequence proportion for a given sample. Even more so, traditional fecal indicator bacteria (Enterobacteriaceae) and alternative wastewater-associated bacteria (Lachnospiraceae, Ruminococcaceae, Arcobacteraceae, Pseudomonadaceae and Vibrionaceae) were part of the core coastal microbiome, i.e., present at all sampling stations. Microbial source tracking and Lagrangian particle tracking, which we employed to assess the potential pollution source, revealed the importance of riverine water as a vector for transmission of allochthonous microbes into the marine system. Further phylogenetic analysis showed that the Arcobacteraceae in our data set was affiliated with the pathogenic Arcobacter cryaerophilus, suggesting that a potential exposure risk for bacterial pathogens in anthropogenically impacted coastal zones remains. We emphasize that molecular analyses combined with statistical and oceanographic models may provide new insights for environmental health assessment and reveal the potential source and presence of microbial indicators, which are otherwise overlooked by a cultivation approach.

Planktonic bacteria in white shrimp (Litopenaeus vannamei) and channel catfish (Letalurus punetaus) aquaculture ponds in a salt-alkaline region

Aquaculture in salt-alkaline regions is encouraged in China, and culture of many aquatic species has been introduced into these areas. In this study, we cultured two species, white shrimp (Litopenaeus vannamei) and channel catfish (Letalurus punetaus) separately in aquaculture ponds in a salt-alkaline region in northwest China and assessed the impacts of the aquaculture operations on the planktonic bacterial community in the culture ponds. Culture of both species decreased the planktonic bacterial diversity and altered the bacterial community structure in the aquaculture ponds compared with the source water. Among the 10 dominant bacterial phyla, 8 were significantly correlated with environmental parameters; the exception was Actinobacteriota, the most dominant phylum, and Firmicutes. Proteobacteria and Bacteroidota abundances showed significant positive correlations with alkalinity, whereas Patescibacteria, Cyanobacteria, Planctomycetota, and Verrucomicrobiota abundance were positively correlated with salinity. Linear regression analysis showed that alkalinity was positively correlated with bacterial beta diversity and salinity was negatively correlated with that. In addition, white shrimp aquaculture significantly lowered the alkalinity, which suggests that culture of this species in inland salt-alkaline regions is a potential dealkalization solution.

The microbial dimension of submarine groundwater discharge: current challenges and future directions

Despite the relevance of submarine groundwater discharge (SGD) for ocean biogeochemistry, the microbial dimension of SGD remains poorly understood. SGD can influence marine microbial communities through supplying chemical compounds and microorganisms, and in turn, microbes at the land–ocean transition zone determine the chemistry of the groundwater reaching the ocean. However, compared with inland groundwater, little is known about microbial communities in coastal aquifers. Here, we review the state of the art of the microbial dimension of SGD, with emphasis on prokaryotes, and identify current challenges and future directions. Main challenges include improving the diversity description of groundwater microbiota, characterized by ultrasmall, inactive and novel taxa, and by high ratios of sediment-attached versus free-living cells. Studies should explore microbial dynamics and their role in chemical cycles in coastal aquifers, the bidirectional dispersal of groundwater and seawater microorganisms, and marine bacterioplankton responses to SGD. This will require not only combining sequencing methods, visualization and linking taxonomy to activity but also considering the entire groundwater–marine continuum. Interactions between traditionally independent disciplines (e.g. hydrogeology, microbial ecology) are needed to frame the study of terrestrial and aquatic microorganisms beyond the limits of their presumed habitats, and to foster our understanding of SGD processes and their influence in coastal biogeochemical cycles.