Andrew R. Babbin

• PhD
• PostDoc Position at Massachusetts Institute of Technology

Nitrous oxide (N2O) is a potent greenhouse gas emitted by oceanic and terrestrial sources, and its biogeochemical cycle is influenced by both natural processes and anthropogenic activities. Current atmospheric N2O monitoring networks, including tall-tower and flask measurements, often overlook major marine hotspots, such as the eastern tropical Pac...

Microorganisms in marine oxygen minimum zones (OMZs) drive globally impactful biogeochemical processes. One such process is multistep denitrification (NO 3 – →NO 2 – →NO→N 2 O→N 2 ), which dominates OMZ bioavailable nitrogen (N) loss and nitrous oxide (N 2 O) production. Denitrification-derived N loss is typically measured and modeled as a single s...

Nitrous oxide (N2O) is a potent greenhouse gas emitted by oceanic and terrestrial sources, with its biogeochemical cycle influenced by both natural processes and anthropogenic activities. Current atmospheric N2O monitoring networks, including tall-tower and flask measurements, often overlook major marine hotspots, such as the eastern tropical Pacif...

Nitrite is a ubiquitous compound found across aquatic systems and an intermediate in both the oxidative and reductive metabolisms transforming fixed nitrogen in the environment. Yet, the abiotic cycling of nitrite is often overlooked in favor of biologically mediated reactions. Here we quantify the apparent acid dissociation constant (pKa) between...

Microorganisms in marine oxygen minimum zones (OMZs) drive globally impactful biogeochemical processes. One such process is the multi-step denitrification, the dominant pathway for bioavailable nitrogen (N) loss and nitrous oxide (N2O) production. Denitrification-derived N loss is typically measured and modeled as a single step, but observations re...

Anammox bacteria inhabiting oxygen-deficient zones (ODZs) are a major functional group mediating fixed nitrogen loss in the global ocean. However, many basic questions regarding the diversity, broad metabolisms, origin, and adaptive mechanisms of ODZ anammox bacteria remain unaddressed. Here we report two novel metagenome-assembled genomes of anamm...

Nitrite-oxidizing bacteria (NOB) are important nitrifiers whose activity regulates the availability of nitrite and dictates the magnitude of nitrogen loss in ecosystems. In oxic marine sediments, ammonia-oxidizing archaea (AOA) and NOB together catalyze the oxidation of ammonium to nitrate, but the abundance ratios of AOA to canonical NOB in some c...

Most microbial life on Earth is found in localized microenvironments that collectively exert a crucial role in maintaining ecosystem health and influencing global biogeochemical cycles. In many habitats such as biofilms in aquatic systems, bacterial flocs in activated sludge, periphyton mats, or particles sinking in the ocean, these microenvironmen...

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 r...

Anammox bacteria inhabiting oxygen deficient zones (ODZs) are a major functional group mediating fixed nitrogen loss and thus exerting a critical control on the nitrogen budget in the global ocean. However, the diversity, origin, and broad metabolisms of ODZ anammox bacteria remain unknown. Here we report two novel metagenome-assembled genomes of S...

Archaea belonging to the DPANN superphylum have been found within 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 interac...

Nitrite-oxidizing bacteria (NOB) are important nitrifiers whose activity regulates the availability of nitrite and links reduced ammonium and oxidized nitrate in ecosystems. In oxic marine sediments, ammonia-oxidizing archaea (AOA) and NOB together catalyze the oxidation of ammonium to nitrate, but the observed abundance ratios of AOA to canonical...

Most microbial life on Earth is found in localized microenvironments that collectively exert a crucial role in maintaining ecosystem health and influencing global biogeochemical cycles. In many habitats such as biofilms in aquatic systems, bacterial flocs in activated sludge, periphyton mats, or particles sinking in the ocean, these microenvironmen...

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 l...

Bacteria specialized in anaerobic ammonium oxidation (anammox) are widespread in many anoxic habitats and form an important functional guild in the global nitrogen cycle by consuming bio-available nitrogen for energy rather than biomass production. Due to their slow growth rates, cultivation-independent approaches have been used to decipher their d...

Oxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially mediated pathway proceeding stepwise from NO3- to N2. This process may be performed entirely by complete denitrifiers capable of all four enzymatic steps, but many organisms possess only partial denitrifica...

Oxygen minimum zones (OMZs), due to their large volumes of perennially deoxygenated waters, are critical regions for understanding how the interplay between anaerobic and aerobic nitrogen (N) cycling microbial pathways affects the marine N budget. Here, we present a suite of measurements of the most significant OMZ N cycling rates, which all involv...

Microbial interactions govern marine biogeochemistry. These interactions are generally considered to rely on exchange of organic molecules. Here we report on a novel inorganic route of microbial communication, showing that algal-bacterial interactions between Phaeobacter inhibens bacteria and Gephyrocapsa huxleyi algae are mediated through inorgani...

By consuming ammonium and nitrite, anammox bacteria form an important functional guild in nitrogen cycling in many environments, including marine sediments. However, their distribution and impact on the important substrate nitrite has not been well characterized. Here we combined biogeochemical, microbiological, and genomic approaches to study anam...

Oxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially-mediated pathway proceeding stepwise from NO 3 ⁻ to N 2 . This process may be performed entirely by complete denitrifiers capable of all four steps, but many organisms possess only partial denitrification p...

Particulate organic carbon settling through the marine water column is a key process that regulates 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 trans...

Oxygen minimum zones (OMZs), due to their large volumes of perennially deoxygenated waters, are critical regions for understanding how the interplay between anaerobic and aerobic nitrogen (N) cycling microbial pathways affects the marine N budget. Here we present a suite of measurements of the most significant OMZ N cycling rates, which all involve...

The Eastern Tropical North Pacific (ETNP), like the other marine oxygen deficient zones (ODZs), is characterized by an anoxic water column, nitrite accumulation at the anoxic core, and fixed nitrogen loss via nitrite reduction to N2O and N2 gases. Here, we constrain the relative contribution of biogeochemical processes to observable features such a...

Oceanic emissions of nitrous oxide (N2O) account for roughly one-third of all natural sources to the atmosphere. Hot-spots of N2O outgassing occur over oxygen minimum zones (OMZs), where the presence of steep oxygen gradients surrounding anoxic waters leads to enhanced N2O production from both nitrification and denitrification. However, the relativ...

Sinking marine particles drive the biological gravitational pump that naturally sequesters carbon dioxide from the atmosphere. Ubiquitous throughout the ocean, these particles are largely composed of phytoplankton that aggregate together or are repackaged by zooplankton into pellets that sink to the deep. Despite their small size, the compartmental...

Oxygen deficient zones (ODZs) are important biogeochemical provinces of the global oceans wherein standing dissolved oxygen concentrations decrease to nanomolar levels. Despite their confinement, these regions are disproportionally important to the ocean's role in modulating Earth's climate through the interactions between the marine nitrogen cycle...

Denitrifying microbes sequentially reduce nitrate (NO 3 – ) to nitrite (NO 2 – ), NO, N 2 O, and N 2 through enzymes encoded by nar , nir , nor , and nos . Some denitrifiers maintain the whole four-gene pathway, but others possess partial pathways. Partial denitrifiers may evolve through metabolic specialization whereas complete denitrifiers may ad...

Heterotrophic denitrification enables facultative anaerobes to continue growing even when limited by oxygen (O 2 ) availability. Particles in particular provide physical matrices characterized by reduced O 2 permeability even in well-oxygenated bulk conditions, creating microenvironments where microbial denitrifiers may proliferate. Whereas numeric...

Coral reef health depends on an intricate relationship among the coral animal, photosynthetic algae, and a complex microbial community. The holobiont can impact the nutrient balance of their hosts amid an otherwise oligotrophic environment, including by cycling physiologically important nitrogen compounds. Here we use ¹⁵ N-tracer experiments to pro...

Emissions of ice-nucleating particles (INPs) from sea spray can impact climate and precipitation by changing cloud formation, precipitation, and albedo. However, the relationship between seawater biogeochemistry and the ice nucleation activity of sea spray aerosols remains unclarified. Here, we demonstrate a link between the biological productivity...

Nitrous oxide (N2O) is a powerful greenhouse gas and ozone depleting substance, but its natural sources, especially marine emissions, are poorly constrained. Localized high concentrations have been observed in the oxygen minimum zones (OMZs) of the tropical Pacific but the impacts of El Niño cycles on this key source region are unknown. Here we sho...

Emissions of ice nucleating particles from sea spray can impact climate and precipitation by changing cloud formation, precipitation, and albedo. However, the relationship between seawater biogeochemistry and the ice nucleation activity of sea spray aerosols remains unclarified. Here, we demonstrate a link between the biological productivity in sea...

The diversity of nitrogen-based dissimilatory metabolisms in anoxic waters continues to increase with additional studies to the marine oxygen deficient zones (ODZs). Although the microbial oxidation of nitrite (NO2–) has been known for over a century, studies of the pathways and microbes involved have generally proceeded under the assumption that n...

Oceanic oxygen deficient zones (ODZs) influence global biogeochemical cycles in a variety of ways, most notably by acting as a sink for fixed nitrogen (Codispoti et al. 2001). Optimum multiparameter analysis of data from two cruises in the Eastern Tropical North Pacific (ETNP) was implemented to develop a water mass analysis for the large ODZ in th...

A key challenge in origins-of-life studies is estimating the abundances of species relevant to the chemical pathways proposed to have contributed to the emergence of life on early Earth. Dissolved nitrogen oxide anions (NO ⁻x ), in particular nitrate (NO ⁻3 ) and nitrite (NO ⁻2 ), have been invoked in diverse origins-of-life chemistry, from the oli...

A key challenge in origins-of-life studies is estimating the abundances of species relevant to the chemical pathways proposed to have contributed to the emergence of life on early Earth. Dissolved nitrogen oxide anions (NO$_{X}^{-}$), in particular nitrate (NO$_{3}^{-}$) and nitrite (NO$_{2}^{-}$), have been invoked in diverse origins-of-life chemi...

The Eastern Tropical South Pacific is one of the three major oxygen deficient zones (ODZs) in the global ocean and is responsible for approximately one third of marine water column nitrogen loss. It is the best studied of the ODZs and, like the others, features a broad nitrite maximum across the low oxygen layer. How the microbial processes that pr...

Marine oxygen deficient zones (ODZs) have long been identified as sites of fixed nitrogen (N) loss. However, the mechanisms and rates of N loss processes have been debated, and traditional methods for measuring these rates are labor-intensive and may miss hot spots in spatially and temporally variable environments. Here, we estimate rates of hetero...

Coastal marine sediments, as locations of substantial fixed nitrogen loss, are very important to the nitrogen budget and to the primary productivity of the oceans. Coastal sediment systems are also highly dynamic and subject to periodic natural and anthropogenic organic substrate additions. The response to organic matter by the microbial community...

The Eastern Tropical South Pacific oxygen minimum zone (ETSP-OMZ) is a site of intense nitrous oxide (N2O) flux to the atmosphere. This flux results from production of N2O by nitrification and denitrification, but the contribution of the two processes is unknown. The rates of these pathways and their distributions were measured directly using 15N t...

Nitrous oxide (N2O) is a powerful greenhouse gas and a major cause of stratospheric ozone depletion, yet its sources and sinks remain poorly quantified in the oceans. We used isotope tracers to directly measure N2O reduction rates in the eastern tropical North Pacific. Because of incomplete denitrification, N2O cycling rates are an order of magnitu...

Nitrous oxide (N2O) is important to Earth's climate because it is a strong absorber of radiation and an important ozone depletion agent. Increasing anthropogenic nitrogen input into the marine environment, especially to coastal waters, has led to increasing N2O emissions. Identifying the nitrogen compounds that serve as substrates for N2O productio...

Significance Nitrogen, the limiting nutrient for primary production across much of the ocean, is converted to biologically inactive N 2 by denitrification and anaerobic ammonium oxidation (anammox) in anoxic waters. Anammox requires an active source of ammonium, which can be provided by concurrent denitrification. However, anammox has been observed...

Connecting molecular information directly to microbial transformation rates remains a challenge, despite the availability of molecular methods to investigate microbial biogeochemistry. By combining information on gene abundance and expression for key genes with quantitative modeling of nitrogen fluxes, we can begin to understand the scales on which...

Understanding N Loss Biologically available nitrogen (N) is essential for marine plants, and shortage of N limits photosynthesis. Marine N can be removed by denitrification and anaerobic ammonia oxidation (anammox) processes, but what controls the balance between these two pathways? Babbin et al. (p. 406 , published online 10 April) tested the effe...

The flux of fixed nitrogen into the marine environment is increasing as a direct result of anthropogenic nitrogen loading, but the controls on the mechanisms responsible for the removal of this increased supply are not well constrained. The fate of fixed nitrogen via mineralization and nitrogen loss processes was investigated by simulating a settli...

Nitrification rates, as well as the relationships between rates and ammonia oxidizer abundance (both archaeal and bacterial), were investigated in the Arabian Sea. Ammonia oxidation rates were measured directly using 15N-NH4+stable isotope additions in gas-impermeable, trace metal clean trilaminate bags (500 mL) at in situ temperature. Tracer incub...

Molecular methods for the investigation of biogeochemical processes, including denitrification, are being developed at an astonishing rate, but it remains difficult to use the molecular information to understand the regulation and variation in biogeochemical transformation rates. By combining information on gene abundance and expression for nirS, a...