The 'oxygen' in oxygen minimum zones

Depth-dependent microbial metagenomes sampled in the northeastern Indian Ocean

The northeastern Indian Ocean exhibits distinct hydrographic characteristics influenced by various local and remote forces. Variations in these driving factors may alter the physiochemical properties of seawater, such as dissolved oxygen levels, and affect the diversity and function of microbial communities. How the microbial communities change across water depths spanning a dissolved oxygen gradient has not been well understood. Here we employed both 16S rDNA amplicon and metagenomic sequencing approaches to study the microbial communities collected from different water depths along the E87 transect in the northeastern Indian Ocean. Samples were collected from the surface, Deep Chlorophyll Maximum (DCM), Oxygen Minimum Zone (OMZ), and bathypelagic layers. Proteobacteria were prevalent throughout the water columns, while Thermoproteota were found to be abundant in the aphotic layers. A total of 675 non-redundant metagenome-assembled genomes (MAGs) were constructed, spanning 21 bacterial and 5 archaeal phyla. The community structure and genomic information provided by this dataset offer valuable resources for the analysis of microbial biogeography and metabolism in the northeastern Indian Ocean.

Collaborative metabolisms of urea and cyanate degradation in marine anammox bacterial culture

Anammox process greatly contributes to nitrogen loss occurring in oceanic oxygen minimum zones (OMZs), where the availability of NH4+ is scarce as compared with NO2-. Remineralization of organic nitrogen compounds including urea and cyanate (OCN-) into NH4+ has been believed as an NH4+ source of the anammox process in oxygen minimum zones. However, urea- or OCN-- dependent anammox has not been well examined due to the lack of marine anammox bacterial culture. In the present study, urea and OCN- degradation in a marine anammox bacterial consortium were investigated based on 15N-tracer experiments and metagenomic analysis. Although a marine anammox bacterium, Candidatus Scalindua sp., itself was incapable of urea and OCN- degradation, urea was anoxically decomposed to NH4+ by the coexisting ureolytic bacteria (Rhizobiaceae, Nitrosomonadaceae, and/or Thalassopiraceae bacteria), whereas OCN- was abiotically degraded to NH4+. The produced NH4+ was subsequently utilized in the anammox process. The activity of the urea degradation increased under microaerobic condition (ca. 32-42 μM dissolved O2, DO), and the contribution of the anammox process to the total nitrogen loss also increased up to 33.3% at 32 μM DO. Urea-dependent anammox activities were further examined in a fluid thioglycolate media with a vertical gradient of O2 concentration, and the active collaborative metabolism of the urea degradation and anammox was detected at the lower oxycline (21 μM DO).

Genome-centered metagenomics illuminates adaptations of core members to a partial Nitritation-Anammox bioreactor under periodic microaeration

The partial nitritation-anaerobic ammonium oxidation (anammox; PN-A) process has been considered a sustainable method for wastewater ammonium removal, with recent attempts to treat low-strength wastewater. However, how microbes adapt to the alternate microaerobic-anoxic operation of the process when treating low ammonium concentrations remains poorly understood. In this study, we applied a metagenomic approach to determine the genomic contents of core members in a PN-A reactor treating inorganic ammonium wastewater at loading as low as 0.0192 kg-N/m³/day. The metabolic traits of metagenome-assembled genomes from 18 core species were analyzed. Taxonomically diverse ammonia oxidizers, including two Nitrosomonas species, a comammox Nitrospira species, a novel Chloroflexota-related species, and two anammox bacteria, Ca. Brocadia and Ca. Jettenia, accounted for the PN-A reactions. The characteristics of a series of genes encoding class II ribonucleotide reductase, high-affinity bd-type terminal oxidase, and diverse antioxidant enzymes revealed that comammox Nitrospira has a superior adaptation ability over the competitors, which may confer the privileged partnership with anammox bacteria in the PN-A reactor. This finding is supported by the long-term monitoring experiment, showing the predominance of the comammox Nitrospira in the ammonia-oxidizing community. Metagenomic analysis of seven heterotrophs suggested that nitrate reduction is a common capability in potentially using endogenous carbohydrates and peptides to enhance nitrogen removals. The prevalence of class II ribonucleotide reductase and antioxidant enzymes genes may grant the adaptation to cyclically microaerobic/anoxic environments. The predominant heterotroph is affiliated with Chloroflexota; its genome encodes complete pathways for synthesizing vitamin B6 and methionine. By contrast, other than the two growth factors, Nitrospira and anammox bacteria are complementary to produce various vitamins and amino acids. Besides, the novel Chloroflexota-related ammonia oxidizer lacks corresponding genes for detoxifying the reactive oxygen species and thus requires the aid of co-existing members to alleviate oxidative stress. The analysis results forecast the exchanges of substrates and nutrients as well as the collective alleviation of oxidative stress among the core populations. The new findings of the genomic features and predicted microbial interplay shed light on microbial adaptation to intermittent microaeration specific to the PN-A reactor, which may aid in improving its application to low-strength ammonium wastewater.

The 'oxygen' in oxygen minimum zones

Aerobic processes require oxygen, and anaerobic processes are typically hindered by it. In many places in the global ocean, oxygen is completely removed at mid-water depths forming anoxic oxygen minimum zones (A-OMZs). Within the oxygen gradients linking oxygenated waters with A-OMZs, there is a transition from aerobic to anaerobic microbial processes. This transition is not sharp and there is an overlap between processes using oxygen and those using other electron acceptors. This review will focus on the oxygen control of aerobic and anaerobic metabolisms and will explore how this overlap impacts both the carbon and nitrogen cycles in A-OMZ environments. We will discuss new findings on non-phototrophic microbial processes that produce oxygen, and we focus on how oxygen impacts the loss of fixed nitrogen (as N₂ ) from A-OMZ waters. There are both physiological and environmental controls on the activities of microbial processes responsible for N₂ loss, and the environmental controls are active at extremely low levels of oxygen. Understanding how these controls function will be critical to understanding and predicting how fixed-nitrogen loss in the oceans will respond to future global warming.