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The communities of bacteria that assemble around marine microphytoplankton are predictably dominated by Rhodobacterales, Flavobacteriales, and families within the Gammaproteobacteria. Yet whether this consistent ecological pattern reflects the result of resource-based niche partitioning or resource competition requires better knowledge of the metabolites linking microbial autotrophs and heterotrophs in the surface ocean. We characterized molecules targeted for uptake by three heterotrophic bacteria individually co-cultured with a marine diatom using two strategies that vetted the exometabolite pool for biological relevance by means of bacterial activity assays: expression of diagnostic genes and net drawdown of exometabolites, the latter detected with mass spectrometry and nuclear magnetic resonance using novel sample preparation approaches. Of the more than 36 organic molecules with evidence of bacterial uptake, 53% contained nitrogen (including nucleosides and amino acids), 11% were organic sulfur compounds (including dihydroxypropanesulfonate and dimethysulfoniopropionate), and 28% were components of polysaccharides (including chrysolaminarin, chitin, and alginate). Overlap in phytoplankton-derived metabolite use by bacteria in the absence of competition was low, and only guanosine, proline, and N-acetyl-d-glucosamine were predicted to be used by all three. Exometabolite uptake pattern points to a key role for ecological resource partitioning in the assembly marine bacterial communities transforming recent photosynthate.

Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved in photosynthesis, central carbon metabolism, and nutrient cycling. While previous studies have focused on AMG diversity in the sunlit and dark ocean, less is known about the role of viruses in shaping metabolic networks along redox gradients associated with marine oxygen minimum zones (OMZs). Here, we analyzed relatively quantitative viral metagenomic datasets that profiled the oxygen gradient across Eastern Tropical South Pacific (ETSP) OMZ waters, assessing whether OMZ viruses might impact nitrogen (N) cycling via AMGs. Identified viral genomes encoded six N-cycle AMGs associated with denitrification, nitrification, assimilatory nitrate reduction, and nitrite transport. The majority of these AMGs (80%) were identified in T4-like Myoviridae phages, predicted to infect Cyanobacteria and Proteobacteria, or in unclassified archaeal viruses predicted to infect Thaumarchaeota. Four AMGs were exclusive to anoxic waters and had distributions that paralleled homologous microbial genes. Together, these findings suggest viruses modulate N-cycling processes within the ETSP OMZ and may contribute to nitrogen loss throughout the global oceans thus providing a baseline for their inclusion in the ecosystem and geochemical models.

Examination of dinitrogen (N₂) fixation in the Eastern Tropical South Pacific oxygen deficient zone has raised questions about the range of diazotrophs in the deep sea and their quantitative importance as a source of new nitrogen globally. However, technical considerations in the deployment of stable isotopes in quantifying N₂fixation rates have complicated interpretation of this research. Here, we report the findings of a comprehensive survey of N₂fixation within, above and below the Eastern Tropical South Pacific oxygen deficient zone. N₂fixation rates were measured using a robust¹⁵N tracer method (bubble removal) that accounts for the slow dissolution of N₂gas and calculated using a conservative approach. N₂fixation was only detected in a subset of samples (8 of 125 replicated measurements) collected within suboxic waters (< 20 μmol O₂kg⁻¹) or at the oxycline. Most of these detectable rates were measured at nearshore stations, or where surface productivity was high. These findings support the hypothesis that low oxygen/high organic carbon conditions favor non‐cyanobacterial diazotrophs. Nevertheless, this study indicates that N₂fixation is neither widespread nor quantitatively important throughout this region.

Recent work has suggested that the oxygen deficient zone (ODZ) and overlying surface waters of the eastern tropical South Pacific (ETSP) is a potential niche for dinitrogen (N₂) fixation. Rates of dinitrogen fixation were measured in the ETSP above and within the ODZ in July 2013 using a modified¹⁵N₂bubble addition method, wherein a bubble was added, mixed, and then removed, and the isotopic enrichment of the dissolved N₂was measured directly for each incubation. N₂fixation rates in the euphotic zone ranged from below detection to 3.9 nmol L⁻¹d⁻¹and were below detection at all depths surveyed within the ODZ. Depth‐integrated rates ranged from below detection to 289.7μmol m⁻²d⁻¹. DNA and RNA of diversenifHgenes were detected at both surface waters and in the ODZ. However, the results of this study suggest that N₂fixation rates were low and contribute little to N cycling in the ETSP.