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Microorganisms in marine oxygen minimum zones (OMZs) drive globally impactful biogeochemical processes. One such process is multistep denitrification (NO₃^–→NO₂^–→NO→N₂O→N₂), which dominates OMZ bioavailable nitrogen (N) loss and nitrous oxide (N₂O) production. Denitrification-derived N loss is typically measured and modeled as a single step, but observations reveal that most denitrifiers in OMZs contain subsets (“modules”) of the complete pathway. Here, we identify the ecological mechanisms sustaining diverse denitrifiers, explain the prevalence of certain modules, and examine the implications for N loss. We describe microbial functional types carrying out diverse denitrification modules by their underlying redox chemistry, constraining their traits with thermodynamics and pathway length penalties, in an idealized OMZ ecosystem model. Biomass yields of single-step modules increase along the denitrification pathway when organic matter (OM) limits growth, which explains the viability of populations respiring NO₂^–and N₂O in a NO₃^–-filled ocean. Results predict denitrifier community succession along environmental gradients: Pathway length increases as the limiting substrate shifts from OM to N, suggesting a niche for the short NO₃^–→NO₂^–module in free-living, OM-limited communities, and for the complete pathway in organic particle-associated communities, consistent with observations. The model captures and mechanistically explains the observed dominance and higher oxygen tolerance of the NO₃^–→NO₂^–module. Results also capture observations that NO₃^–is the dominant source of N₂O. Our framework advances the mechanistic understanding of the relationship between microbial ecology and N loss in the ocean and can be extended to other processes and environments. 

ABSTRACT Archaea belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have been found in an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise a sizeable fraction of the archaeal community within marine oxygen-deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes (MAGs) belonging to the DPANN phyla Nanoarchaeota, Pacearchaeota, Woesearchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and the Arabian Sea. We find these archaea to be permanent, stable residents of all three major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25%–50% of archaea as estimated from read mapping to MAGs. ODZ DPANN appear to be capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs. IMPORTANCEArchaea from the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have diverse metabolic capabilities and participate in multiple biogeochemical cycles. While metagenomics and enrichments have revealed that many DPANN are characterized by ultrasmall genomes, few biosynthetic genes, and episymbiotic lifestyles, much remains unknown about their biology. We report 33 new DPANN metagenome-assembled genomes originating from the three global marine oxygen-deficient zones (ODZs), the first from these regions. We survey DPANN abundance and distribution within the ODZ water column, investigate their biosynthetic capabilities, and report potential roles in the cycling of organic carbon, methane, and nitrogen. We test the hypothesis that nitrous oxide reductases found within several ODZ DPANN genomes may enable ultrasmall episymbionts to serve as nitrous oxide consumers when attached to a host nitrous oxide producer. Our results indicate DPANN archaea as ubiquitous residents within the anoxic core of ODZs with the potential to produce or consume key compounds. 

The end of Dennard scaling and the slowing of Moore's Law has put the energy use of datacenters on an unsustainable path. Datacenters are already a significant fraction of worldwide electricity use, with application demand scaling at a rapid rate. We argue that substantial reductions in the carbon intensity of datacenter computing are possible with a software-centric approach: by making energy and carbon visible to application developers on a fine-grained basis, by modifying system APIs to make it possible to make informed trade offs between performance and carbon emissions, and by raising the level of application programming to allow for flexible use of more energy efficient means of compute and storage. We also lay out a research agenda for systems software to reduce the carbon footprint of datacenter computing. 

Abstract Sinking marine particles drive the biological pump that naturally sequesters carbon from the atmosphere. Despite their small size, the compartmentalized nature of particles promotes intense localized metabolic activity by their bacterial colonizers. Yet the mechanisms promoting the onset of denitrification, a metabolism that arises once oxygen is limiting, remain to be established. Here we show experimentally that slow sinking aggregates composed of marine diatoms—important primary producers for global carbon export—support active denitrification even among bulk oxygenated water typically thought to exclude anaerobic metabolisms. Denitrification occurs at anoxic microsites distributed throughout a particle and within microns of a particle’s boundary, and fluorescence-reporting bacteria show nitrite can be released into the water column due to segregated dissimilatory reduction of nitrate and nitrite. Examining intact and broken diatoms as organic sources, we show slowly leaking cells promote more bacterial growth, allow particles to have lower oxygen, and generally support greater denitrification. 

The end of Dennard scaling and the slowing of Moore’s Law has put the energy use of datacenters on an unsustainable path. Datacenters are already a significant fraction of worldwide electricity use, with application demand scaling at a rapid rate. We argue that substantial reductions in the carbon intensity of datacenter computing are possible with a software-centric approach: by making energy and carbon visible to application developers on a fine-grained basis, by modifying system APIs to make it possible to make informed trade offs between performance and carbon emissions, and by raising the level of application programming to allow for flexible use of more energy efficient means of compute and storage.We also lay out a research agenda for systems software to reduce the carbon footprint of datacenter computing. 

Abstract Particulate organic carbon settling through the marine water column is a key process that regulates the global climate by sequestering atmospheric carbon. The initial colonization of marine particles by heterotrophic bacteria represents the first step in recycling this carbon back to inorganic constituents—setting the magnitude of vertical carbon transport to the abyss. Here, we demonstrate experimentally using millifluidic devices that, although bacterial motility is essential for effective colonization of a particle leaking organic nutrients into the water column, chemotaxis specifically benefits at intermediate and higher settling velocities to navigate the particle boundary layer during the brief window of opportunity provided by a passing particle. We develop an individual-based model that simulates the encounter and attachment of bacterial cells with leaking marine particles to systematically evaluate the role of different parameters associated with bacterial run-and-tumble motility. We further use this model to explore the role of particle microstructure on the colonization efficiency of bacteria with different motility traits. We find that the porous microstructure facilitates additional colonization by chemotactic and motile bacteria, and fundamentally alters the way nonmotile cells interact with particles due to streamlines intersecting with the particle surface. 

Microsecond I/O will make data serialization a major bottleneck for datacenter applications. Serialization is fundamentally about data movement: serialization libraries coalesce and flatten in-memory data structures into a single transmittable buffer. CPU-based serialization approaches will hit a performance limit due to data movement overheads and be unable to keep up with modern networks. We observe that widely deployed NICs possess scatter-gather capabilities that can be re-purposed to accelerate serialization's core task of coalescing and flattening in-memory data structures. It is possible to build a completely zero-copy, zero-allocation serialization library with commodity NICs. Doing so introduces many research challenges, including using the hardware capabilities efficiently for a wide variety of non-uniform data structures, making application memory available for zero-copy I/O, and ensuring memory safety.