Microbial genomics of the global ocean system

Kostka, Joel E.; Joye, Samantha B.

doi:10.1002/essoar.10502548.1

Cited by 17 publications

(15 citation statements)

References 48 publications

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“…Sulfate is typically present in higher concentration than the other electron acceptors, leading to the domination of sulfate reduction in anaerobic metabolism in these systems. However, biologically mediated reactions occur in tandem with abiotic reactions, making it difficult in some cases to assess the driving force behind the observed biogeochemical reactions (Joye and Kostka, 2020).…”

Section: Biogeochemical Reactions In Coastal Aquifersmentioning

confidence: 99%

“…There are a number of ways to assess the importance of abiotic versus microbially mediated processes in aquifers. Assessing microbial community composition using genomics data (Joye and Kostka, 2020) provides information on genomic capacity for a particular reaction by tracking gene abundance (e.g., probing for genes or assessing metagenomes) or by tracking the presence of transcripts associated with a particular process (e.g., metatranscriptomics). While some studies utilized such techniques in coastal aquifers (Santoro et al, 2006(Santoro et al, , 2008Rogers and Casciotti, 2010;Sáenz et al, 2012;Adyasari et al, 2019Adyasari et al, , 2020, this approach holds tremendous potential.…”

Section: Biogeochemical Reactions In Coastal Aquifersmentioning

confidence: 99%

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Saltwater Intrusion and Submarine Groundwater Discharge: Acceleration of Biogeochemical Reactions in Changing Coastal Aquifers

Moore

Joye

2021

Front. Earth Sci.

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Intrusion of saltwater into freshwater coastal aquifers poisons an essential resource. Such intrusions are occurring along coastlines worldwide due largely to the over-pumping of freshwater and sea level rise. Saltwater intrusion impacts drinking water, agriculture and industry, and causes profound changes in the biogeochemistry of the affected aquifers, the dynamic systems called subterranean estuaries. Subterranean estuaries receive freshwater from land and saltwater from the ocean and expose this fluid mixture to intense biogeochemical dynamics as it interacts with the aquifer and aquiclude solids. Increased saltwater intrusion alters the ionic strength and oxidative capacity of these systems, resulting in elevated concentrations of certain chemical species in the groundwater, which flows from subterranean estuaries into the ocean as submarine groundwater discharge (SGD). These highly altered fluids are enriched in nutrients, carbon, trace gases, sulfide, metals, and radionuclides. Seawater intrusion expands the subterranean estuary. Climate change amplifies sea level variations on short and seasonal time scales. These changes may result in higher SGD fluxes, further accelerating release of nutrients and thus promoting biological productivity in nutrient-depleted waters. But this process may also adversely affect the environment and alter the local ecology. Research on saltwater intrusion and SGD has largely been undertaken by different groups. We demonstrate that these two processes are linked in ways that neither group has articulated effectively to date.

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Section: Biogeochemical Reactions In Coastal Aquifersmentioning

confidence: 99%

Section: Biogeochemical Reactions In Coastal Aquifersmentioning

confidence: 99%

Saltwater Intrusion and Submarine Groundwater Discharge: Acceleration of Biogeochemical Reactions in Changing Coastal Aquifers

Moore

Joye

2021

Front. Earth Sci.

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“…Despite a recent burst in knowledge and understanding of the diversity, behavior, and function of marine microbial communities in response to hydrocarbon contamination in marine environments ( 4 , 7 – 9 ), regions like the Arctic, sub-Arctic, and deep ocean basins remain largely underexplored in this respect, due mainly to the challenge of sampling and unpredictability associated with these environments. Past major oil spills (e.g., Exxon Valdez and Deepwater Horizon) highlighted the need for a prerequisite understanding of the structure, diversity, and dynamics of prespill baseline bacterial communities ( 4 , 10 , 11 ).…”

Section: Introductionmentioning

confidence: 99%

Inter- and Intra-Annual Bacterioplankton Community Patterns in a Deepwater Sub-Arctic Region: Persistent High Background Abundance of Putative Oil Degraders

Angelova

Berx

Bresnan

et al. 2021

mBio

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Hydrocarbon-degrading bacteria naturally degrade and remove petroleum pollutants, yet baselines do not currently exist for these critical microorganisms in many regions where the oil and gas industry is active. Furthermore, understanding how a baseline community changes across the seasons and its potential to respond to an oil spill event are prerequisites for predicting their response to elevated hydrocarbon exposures. In this study, 16S rRNA gene-based profiling was used to assess the spatiotemporal variability of baseline bacterioplankton community composition in the Faroe-Shetland Channel (FSC), a deepwater sub-Arctic region where the oil and gas industry has been active for the last 40 years. Over a period of 2 years, we captured the diversity of the bacterioplankton community within distinct water masses (defined by their temperature and salinity) that have a distinct geographic origin (Atlantic or Nordic), depth, and direction of flow. We demonstrate that bacterioplankton communities were significantly different across water samples of contrasting origin and depth. Taxa of known hydrocarbon-degrading bacteria were observed at higher-than-anticipated abundances in water masses originating in the Nordic Seas, suggesting these organisms are sustained by an unconfirmed source of oil input in that region. In the event of an oil spill, our results suggest that the response of these organisms is severely hindered by the low temperatures and nutrient levels that are typical for the FSC. IMPORTANCE Oil spills at sea are one of the most disastrous anthropogenic pollution events, with the Deepwater Horizon spill providing a testament to how profoundly the health of marine ecosystems and the livelihood of its coastal inhabitants can be severely impacted by spilled oil. The fate of oil in the environment is largely dictated by the presence and activities of natural communities of oil-degrading bacteria. While a significant effort was made to monitor and track the microbial response and degradation of the oil in the water column in the wake of the Deepwater Horizon spill, the lack of baseline data on the microbiology of the Gulf of Mexico confounded scientists’ abilities to provide an accurate assessment of how the system responded relative to prespill conditions. This data gap highlights the need for long-term microbial ocean observatories in regions at high risk of oil spills. Here, we provide the first microbiological baseline established for a subarctic region experiencing high oil and gas industry activity, the northeast Atlantic, but with no apparent oil seepage or spillage. We also explore the presence, relative abundances, and seasonal dynamics of indigenous hydrocarbon-degrading communities. These data will advance the development of models to predict the behavior of such organisms in the event of a major oil spill in this region and potentially impact bioremediation strategies by enhancing the activities of these organisms in breaking down the oil.

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“…comm.). Such persistent surface oil slicks suggest naturally occurring oil seepage, which may contribute to elevated (above background) levels of an oil-degrading bacterioplankton population, including Alcanivorax , in the FSC; a similar situation is well documented in the Gulf of Mexico [ 64 ]. However, we do not exclude the likelihood that such a community is in part also supported by the close coupling of these organisms with hydrocarbon-producing phytoplankton, such as Synechococcus .…”

Section: Resultsmentioning

confidence: 99%

Hydrocarbon-Degrading Bacteria Found Tightly Associated with the 50–70 μm Cell-Size Population of Eukaryotic Phytoplankton in Surface Waters of a Northeast Atlantic Region

2020

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The surface of marine eukaryotic phytoplankton can harbour communities of hydrocarbon-degrading bacteria; however, this algal–bacterial association has, hitherto, been only examined with non-axenic laboratory cultures of micro-algae. In this study, we isolated an operationally-defined community of phytoplankton, of cell size 50–70 μm, from a natural community in sea surface waters of a subarctic region in the northeast Atlantic. Using MiSeq 16S rRNA sequencing, we identified several recognized (Alcanivorax, Marinobacter, Oleispira, Porticoccus, Thalassospira) and putative hydrocarbon degraders (Colwelliaceae, Vibrionaceae) tightly associated with the phytoplankton population. We combined fluorescence in situ hybridisation with flow-cytometry (FISH-Flow) to examine the association of Marinobacter with this natural eukaryotic phytoplankton population. About 1.5% of the phytoplankton population contained tightly associated Marinobacter. The remaining Marinobacter population were loosely associated with either eukaryotic phytoplankton cells or non-chlorophyll particulate material. This work is the first to show the presence of obligate, generalist and putative hydrocarbonoclastic bacteria associated with natural populations of eukaryotic phytoplankton directly from sea surface water samples. It also highlights the suitability of FISH-Flow for future studies to examine the spatial and temporal structure and dynamics of these and other algal–bacterial associations in natural seawater samples.

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Microbial genomics of the global ocean system

Cited by 17 publications

References 48 publications

Saltwater Intrusion and Submarine Groundwater Discharge: Acceleration of Biogeochemical Reactions in Changing Coastal Aquifers

Saltwater Intrusion and Submarine Groundwater Discharge: Acceleration of Biogeochemical Reactions in Changing Coastal Aquifers

Inter- and Intra-Annual Bacterioplankton Community Patterns in a Deepwater Sub-Arctic Region: Persistent High Background Abundance of Putative Oil Degraders

Hydrocarbon-Degrading Bacteria Found Tightly Associated with the 50–70 μm Cell-Size Population of Eukaryotic Phytoplankton in Surface Waters of a Northeast Atlantic Region

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