Jeff Bowman

Hydrostatic pressure defines the deep ocean, yet its role in structuring microbial activity across the subseafloor biosphere remains poorly understood. Here, we assessed pressure effects on anabolic activity in sediment communities across margin-proximal, bathyal, abyssal, and hadal settings of the Puerto Rico Trench (493-8,385 m water depth). Community-level responses to pressure reversed with burial, revealing an unrecognized shift toward piezophily in communities down to 20 meters below seafloor (mbsf). Atmospheric pressure yielded higher proportions of active cells in surficial sediments, whereas in situ pressure yielded higher proportions in the subseafloor. Pressure also structured active-community composition; in trench-axis sediments down to 8.35 mbsf, JS1/Atribacterota populations within widespread hadal lineages exhibited a physiological response to in situ pressure, indicative of subseafloor piezophily. These findings suggest that hydrostatic pressure acts as an ecological filter after burial, favoring piezophilic traits that may support microbial persistence in the deep subseafloor biosphere.

Extreme events reshape ocean ecosystems with significant implications for nutrient and carbon cycling. Here, we demonstrate that flooding on land can be a significant driver of biogeochemical variability in the open ocean, even in relatively dry climates. Using satellite observations, in situ measurements, and Lagrangian particle tracking, we present evidence that freshwater discharge from extreme precipitation during the 2023 water year was transported into the oligotrophic region of the California Current System. This transport was facilitated by submesoscale eddies and filaments and resulted in significant anomalies in surface salinity, stratification, nutrient concentrations, as well as phytoplankton and bacterioplankton community composition. These observations highlight the importance of episodic river discharge events in shaping offshore biogeochemical fluxes and ecosystem structure in eastern boundary current systems. With more frequent atmospheric river events projected, the likelihood of observing these specific hydrographic and biogeochemical conditions may be increasing.

Human norovirus GII (HuNoV GII) causes millions of gastrointestinal infections annually and persists for days to weeks in marine waters after wastewater discharge, raising transmission concerns in polluted coastal regions such as the San Diego–Tijuana border between the US and Mexico. We conducted a six-month ddPCR-based monitoring campaign in the Tijuana River Estuary and adjacent coastal ocean to quantify HuNoV GII’s spatial and temporal distribution. This is one of the first such spatially and temporally resolved studies in a coastal marine environment. Mean concentrations were ∼102 copies L–1, reaching > 105 copies L–1 near the mouth of the Tijuana River. HuNoV GII declined with increasing distance from shore and the pollution source, varying across gradients in shoreline proximity, river-mouth distance, alongshore wave-driven surfzone velocity, and river discharge. Concentrations correlated strongly with the widely used fecal indicator Enterococcus (ρ = 0.768), pointing to a shared wastewater source for both. Mean concentration-based swimmer illness risk ranged from 200–350 per 1000 swimmers, far exceeding the EPA benchmark of 32. These findings establish HuNoV GII as a persistent, spatially structured contaminant in this transboundary system and provide a baseline for tracking wastewater infrastructure improvements and informing pathogen risk forecasting models under development.

The San Diego/Tijuana (US/Mexico) coastal region has immense water quality issues due to untreated wastewater sources. Regular ddPCR Enterococcus sampling provides same-day water quality information for beachgoers but does not provide forecasts for decision making. We describe the Pathogen Forecast Model (PFM) V1.0, providing daily 5 day forecasts of swimmer illness risk along 30 km of shoreline on a web dashboard. PFM is based upon a hydrodynamic model using forecasted waves, winds, offshore currents, and Tijuana River flow as inputs. PFM accurately forecasts tides and waves and forecasts depth-averaged shelf currents moderately well. Modeled untreated wastewater concentration tracer C evolves with a constant decay rate representing Norovirus. Over 13 km of shoreline, forecasted C and observed EnterococcusE are moderately log-correlated (≈0.5) for day-1 and -5 forecasts. The C and E power-law relationship has an exponent of ≈0.5, possibly suggesting the tracer decays 2× slower than Enterococcus DNA, among other potential explanations. Using the cutoff C = 10–5, PFM classified advisory exceedances with nearly 80% raw accuracy, high sensitivity, and lower specificity. This is the first forecast model that resolves estuarine, surfzone, and shelf regions. PFM is a useful public health tool and is constantly being improved.

Thousands of saline to hypersaline lakes exist across the Yilgarn Craton in Western Australia, representing potential Mars analogs with diverse and varying salinity, pH, and oxygen conditions that remain poorly constrained. Here, we report geochemical trends in lake waters that vary across wet‐dry cycles as well as with regional location and geomorphic setting within the craton's paleovalley system. We identify two different geochemical regimes: (a) lakes where groundwater is more acidic than lake water, and shifts in composition reflect changing precipitation, and (b) lakes that are more acidic than local groundwater due to subsurface and surface geochemical interactions. Elevated salinity in all lakes relative to groundwater occurs due to cyclic evaporation driven by strong seasonal forcing. Most lakes occupy shallow, surficial basins that lack exposed outcrops. Lakes that are deeply incised expose truncated lateritic profiles dominated by clay minerals, quartz veins, and Fe‐oxides. These contrasting settings represent geologic and geochemical endmembers across the region, for which interactions between evaporative concentration and acidic groundwater shape the geochemical evolution of lake systems differently. These factors, in turn, influence microbial habitability, the deposition of salts and other surficial indicators of environmental change. Our observations reveal visible signatures of prolonged acidic‐groundwater interactions, including features consistent with Fe redox cycling, and recurring wet‐dry cycles. These findings suggest that paleodrainage systems within and near craters in Mars' Terra Sirenum, which host similar layered and bleached Al‐rich clay outcrops with smaller exposures of acidic weathered minerals, may record evaporitic concentration and potentially long‐duration groundwater interactions.

Identifying sources of ice nucleating particles (INPs) in the central Arctic is important for understanding controls on the phase of Arctic mixed‐phase clouds (AMPCs). We show meltwater samples collected from the Arctic pack ice in July 2020 contain biological INPs active at relatively warm temperatures ( T ≥ −10°C). We attribute the meltwater INPs to organisms and processes unique to a meltwater habitat. Concentrations of biological INPs active at T ≥ −10°C on filters deployed downwind of meltwater sites showed an enhancement associated with surface proximity. We hypothesize that time over the melt‐pond‐covered pack ice may have influenced the higher concentrations of biological INPs on the aerosol filters. More work to resolve emission mechanisms from melt ponds is necessary for understanding the extent of this potential source, which may increase importance as melt seasons extend spatiotemporally.

Phosphorus is a vital nutrient required for the functioning of living organisms. In aquatic environments, dissolved inorganic phosphate is considered its most bioavailable form. However, phosphate can be scarce, which has the potential to limit microbial metabolism and ecosystem functioning. To overcome phosphate scarcity, microbes produce alkaline phosphatase (AP) to access dissolved organic phosphorus (DOP). Here, we conducted a year-long study of alkaline phosphatase activity (APA) at the Ellen Browning Scripps Memorial Pier, a nutrient-rich coastal site. APA was observed throughout the year despite phosphate-replete conditions, suggesting that the role of APs in microbial nutrition is not completely understood. We tested the hypothesis that APA may promote acquisition of organic carbon liberated from DOP hydrolysis by growing the heterotrophic marine bacterium Ruegeria pomeroyi on three DOP compounds as sole carbon sources and assessing APA. Controlling for carbon concentration, all DOP sources supported growth, but at lower levels than glucose, with the highest growth observed on glucose-6-phosphate (G6P), followed by adenosine monophosphate (AMP) and adenosine triphosphate (ATP). Moreover, cell-specific APA was significantly enhanced in carbon-deplete conditions and during growth on G6P, relative to cultures grown on replete glucose or nucleotides. These findings suggest alkaline phosphatases (APs) are part of a generic carbon stress response and likely play a role in acquiring certain forms of organic carbon by R. pomeroyi , with implications for other taxa. Overall, this study helps advance the current state of knowledge regarding microbial phosphorus cycling and carbon utilization in aquatic environments.

Viruses are the most abundant biological entities on Earth and exert powerful controls on ecosystem ecology, biogeochemical cycling, and microbial evolution. Hypersaline environments host the highest reported viral abundances of any aquatic system, yet little is known about how salinity and other environmental extremes influence viral ecology. In these systems, salinity alongside acidity strongly influence the isoelectric point (pI) of viral particles – the pH at which a virion carries no net surface charge – which affects viral particle electrostatic interactions and stability. When environmental pH approaches the pI of the viral structural proteome, virions lose surface charge, aggregate, and adsorb to particles, reducing viral infectivity. This, in turn, greatly influences microbial ecology and ecosystem-scale biogeochemical cycling. In this study, we use acidic and alkaline hypersaline lakes in Western Australia as a natural Earth-system laboratory to test how pH and salinity shape viral ecogenomics and microbial evolution. We analyzed metagenomes and viromes from 37 polyextreme lakes spanning pH 2.3-9.4 and 30-465 ppt salinity across wet and dry seasons, recovering 11,804 viral populations from 50 families along with 645 microbial metagenome-assembled genomes. We calculated the pI for viral structural proteomes and placed these data in a global context using viral genomes from environments spanning freshwater, soda lakes, acidic meromictic lakes, and deep-sea hydrothermal vents. Across all environments, viral structural pI distributions were strongly skewed toward more acidic values, with the most acidic capsids occurring in hypersaline and alkaline brines. Even modest shifts in viral structural pIs (~0.8 pH units) correspond to order-of-magnitude changes in proton concentration, suggesting physicochemical selection. Within cosmopolitan viral families, structural pI shifted systematically across pH-salinity regimes, demonstrating that structural traits are not fixed by phylogeny alone but respond to environmental geochemistry. Viruses infecting halophilic archaea exhibited the most acidic and most tightly constrained structural pI values, pointing to host envelope chemistry and host ecology as an additional filter on viral evolution. To understand how viruses may influence microbial adaptation to these environmental extremes, we also functionally characterized viral auxiliary metabolic genes (AMGs) and genes encoded on plasmids. Viral AMGs primarily supported host energy metabolism rather than stress tolerance, whereas plasmids encoded extensive osmotic and acid-stress pathways that were strongly structured across pH-salinity space, identifying plasmids as key agents of microbial adaptation in extreme brines. By linking viral and plasmid omics to geochemical gradients across a natural Earth-system laboratory, this work shows how molecular-scale traits scale up to shape ecosystem function and biogeochemical dynamics across the planet.

Anaerobic methane oxidation, typically mediated by consortia of archaea and bacteria, is a key process in the global methane cycle, but little is known about its upper salinity limits. We characterized the microbial methane cycle in the anoxic, hypersaline Orca Basin using metagenomics, metatranscriptomics, fluorescence in situ hybridization, and geochemical measurements at sub-meter resolution. In the brine, we detected transcriptional activity of the halophilic methylotrophic methanogen Methanohalophilus , consistent with a biological source for Orca Basin methane. In the particle-rich halocline (∼2 M Cl ^- ; ∼2235 meters depth), high mcrA transcription by a novel ANME-2a species was co-located with a positive shift in δ ¹³ C-CH ₄ consistent with anaerobic oxidation of methane. ANME-2a also transcribed genes for biosynthesis of the osmolyte N(ε)-acetyl-β-L-lysine, supporting adaptation to hypersaline conditions. At the same depth, consortia of sarcina-like archaea, likely ANME-2a, were observed in association with vibrioid and filamentous bacteria. Members of a halotolerant Desulfobulbales genus (family SURF-16, which includes the previously identified ANME partner Seep-DBB) were active at the same depth. At and above the oxic-anoxic interface, aerobic methane oxidation appears to be mediated by three genera of uncultivated Methylococcales bacteria. Our results extend the known upper salinity range of ANME-2a to ∼2 M Cl ^- and reveal the key microbial players in the methane bio-filter between the Orca Basin brine and overlying seawater.

Protists and bacteriophages exert top‐down control on bacterial populations. Previous work in the coastal Antarctic demonstrates the potential for intra‐seasonal variability of this top‐down control driven by the extreme seasonal contrast in bacterial growth rates. We evaluated whether predators ‘kill the winner’ wherein protists and phages preferentially impact the most abundant members of bacterial assemblages over an austral summer with weekly dilution experiments. Seawater from 10 m was divided into two serial dilutions with either 0.2 μm (to evaluate protist grazing) or 30 kDa (to evaluate protist grazing and lysis from bacteriophage) filtered water. We observed strong intra‐seasonal change of bacteriophage and protistan contributions to mortality. A comparison of activity per ASV from amplicon sequencing over our dilution experiments to a predicted minimal doubling time indicates that ‘kill the winner’ is occurring during the top‐down control of only a few bacteria. As not all bacterial taxa with a predicted low mean doubling time demonstrated high activity in our dilution experiments, our results indicate protists and phage selectively target some fast‐growing or abundant bacteria which we term ‘kill select winners’ (KsW). Overall, our evaluation of bacterial abundance and community structure provides unprecedented knowledge of top‐down control of marine bacteria.