Oxygen‐deficient zones (ODZs) influence global nitrogen cycling as key sites for the removal of bioavailable nitrogen through denitrification and anammox. Despite their importance, many microbes and viruses in ODZs remain uncultivated, limiting our understanding of their ecological roles. This study employed Hi‐C proximity linkages, combined with long and short read metagenomic sequencing to characterise active viral interacti...

Oxygen deficient zones (ODZs) are subsurface marine systems that harbour distinct microbial communities, including populations of the picocyanobacteria Prochlorococcus that can form a secondary chlorophyll maximum (SCM), and low‐oxygen tolerant strains of the globally abundant heterotroph Pelagibacter (SAR11). Yet, the small labile molecules (metabolites) responsible for maintaining these ODZ communities are unknown. Here, we...

Introduction Assimilation of reduced nitrogen is less energetically costly than assimilation of oxidized forms. In the open ocean, ammonium is generally absent from the water column, including in oxygen-deficient zones (ODZs). Some microorganisms can use alternative organic reduced nitrogen forms like urea and cyanate, as indicated by the presence of cyanase ( cynS ) and urease ( ureC ) genes. Methods Here we examine the Hawai...

Marine snow and other particles are abundant in estuaries, where they drive biogeochemical transformations and elemental transport. Particles range in size, thereby providing a corresponding gradient of habitats for marine microorganisms. We used standard normalized amplicon sequencing, verified with microscopy, to characterize taxon‐specific microbial abundances, (cells per litre of water and per milligrams of particles), acr...

Picocyanobacteria contribute greatly to offshore primary production with cells extending through the deep euphotic zone. Literature indicates high viral infection of cyanobacteria in ocean transition zones. We postulate that the bottom of the euphotic zone is a transition zone, where communities transition from phototrophic to aphotic processes. We use single‐copy core genes to examine cyanophage to cyanobacteria ratios in cel...

Summary Ocean oxygen deficient zones (ODZs) host 30%–50% of marine N 2 production. Cyanobacteria photosynthesizing in the ODZ create a secondary chlorophyll maximum and provide organic matter to N 2 ‐producing bacteria. This chlorophyll maximum is thought to occur due to reduced grazing in anoxic waters. We first examine ODZ protists with long amplicon reads. We then use non‐primer‐based methods to examine the composition and...

Peptides are identified using a de novo‐discovery approach in suspended and sinking particles from the eastern tropical North Pacific oxygen‐deficient zone (ODZ) and in a culture of a dominant autotroph from the region, the cyanobacterium Prochlorococcus . The benchmarking experiment with Prochlorococcus shows de novo peptides to be taxonomically specific, and thus of value in augmenting database‐driven approaches. Analysis of...

Summary Cyanophages encode host‐derived genes that may increase their fitness. We examined the relative abundance of 18 host‐derived cyanophages genes in metagenomes and viromes along depth profiles from the Eastern Tropical North Pacific Oxygen Deficient Zone (ETNP ODZ) where Prochlorococcus dominates a secondary chlorophyll maximum within the ODZ. Cyanophages at the oxic primary chlorophyll maximum encoded genes related to l...

Summary During the productive Paleoproterozoic (2.4–1.8 Ga) and less productive Mesoproterozoic (1.8–1.0 Ga), the ocean was suboxic to anoxic and multicellular organisms had not yet evolved. Here, we link geologic information about the Proterozoic ocean to microbial processes in modern low‐oxygen systems. High iron concentrations and rates of Fe cycling in the Proterozoic are the largest differences from modern oxygen‐deficien...

Summary Chemical profiles of the Black Sea suboxic zone show a distribution of nitrogen species which is traditionally associated with denitrification, i.e. a secondary nitrite maximum associated with nitrate depletion and a N 2 gas peak. To better understand the distribution and diversity of the denitrifier community in the Black Sea suboxic zone, we combined a cultivation approach with cloning and sequencing of PCR‐amplified...