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1. Novel metagenome-assembled genomes involved in the nitrogen cycle from a Pacific oxygen minimum zone

   https://doi.org/10.1038/s43705-021-00030-2  

   Sun, Xin; Ward, Bess B. (December 2021, ISME Communications)

   null (Ed.)

   Abstract Oxygen minimum zones (OMZs) are unique marine regions where broad redox gradients stimulate biogeochemical cycles. Despite the important and unique role of OMZ microbes in these cycles, they are less characterized than microbes from the oxic ocean. Here we recovered 39 high- and medium-quality metagenome-assembled genomes (MAGs) from the Eastern Tropical South Pacific OMZ. More than half of these MAGs were not represented at the species level among 2631 MAGs from global marine datasets. OMZ MAGs were dominated by denitrifiers catalyzing nitrogen loss and especially MAGs with partial denitrification metabolism. A novel bacterial genome with nitrate-reducing potential could only be assigned to the phylum level. A Marine-Group II archaeon was found to be a versatile denitrifier, with the potential capability to respire multiple nitrogen compounds including N 2 O. The newly discovered denitrifying MAGs will improve our understanding of microbial adaptation strategies and the evolution of denitrification in the tree of life. 

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2. Potential for microbial denitrification coupled with methanol oxidation found in abundant MAGs in Antarctic Peninsula sediments

   https://doi.org/10.1093/femsle/fnaf050  

   Howland, Katie E; Nygaard, Hannah J; Steen, Andrew D; Halanych, Kenneth M; Mahon, Andrew R; Learman, Deric R (January 2025, FEMS Microbiology Letters)

   Abstract Denitrification accounts for a substantial nitrogen loss from environmental systems, shifting microbial composition and impacting other biogeochemical cycles. In Antarctica, rising temperatures cause increased organic matter deposition in marine sediments, which can significantly alter microbially mediated denitrification. To examine the genetic potential of microorganisms driving N-cycling in these sediments, benthic sediment cores were collected at two sites in the Weddell Sea, Antarctica. DNA was extracted from multiple depths at each site, resulting in the reconstruction of 75 high-quality metagenome-assembled genomes (MAGs). Forty-seven of these MAGs contained reductases involved in denitrification. MAGs belonging to the genus Methyloceanibacter were the most abundant MAGs at both sites and all depths, except depth 3–6 cmbsf at one site, where they were not identified. The abundance of these Methyloceanibacter MAGs suggests the potential for nitrate-driven methanol oxidation at both sites. MAGs belonging to Beggiatoaceae and Sedimenticolaceae were found to have the genetic potential to produce intermediates in denitrification and the complete pathway for dissimilatory nitrate reduction to ammonia. MAGs within Acidimicrobiia and Dadabacteria had the potential to complete the final denitrification step. Based on MAGs, Antarctic peninsula sediment communities have the potential for complete denitrification and dissimilatory nitrate reduction to ammonia via a consortium. 

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3. Potential for microbial denitrification coupled with methanol oxidation found in abundant MAGs in Antarctic Peninsula sediments

   Howland, KE; Nygaard, HJ; Steen, AD; Halanych, KM; Mahon, AR; Learman, DR (May 2025, FEMS microbiology letters)

   Denitrification accounts for a substantial nitrogen loss from environmental systems, shifting microbial composition and impacting other biogeochemical cycles. In Antarctica, rising temperatures cause increased organic matter deposition in marine sediments, which can significantly alter microbially mediated denitrification. To examine the genetic potential of microorganisms driving N-cycling in these sediments, benthic sediment cores were collected at two sites in the Weddell Sea, Antarctica. DNA was extracted from multiple depths at each site, resulting in the reconstruction of 75 high-quality metagenome-assembled genomes (MAGs). Forty-seven of these MAGs contained reductases involved in denitrification. MAGs belonging to the genus Methyloceanibacter were the most abundant MAGs at both sites and all depths, except depth 3–6 cmbsf at one site, where they were not identified. The abundance of these Methyloceanibacter MAGs suggests the potential for nitrate-driven methanol oxidation at both sites. MAGs belonging to Beggiatoaceae and Sedimenticolaceae were found to have the genetic potential to produce intermediates in denitrification and the complete pathway for dissimilatory nitrate reduction to ammonia. MAGs within Acidimicrobiia and Dadabacteria had the potential to complete the final denitrification step. Based on MAGs, Antarctic peninsula sediment communities have the potential for complete denitrification and dissimilatory nitrate reduction to ammonia via a consortium. 

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4. Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen-deficient zones with diverse metabolic potential

   https://doi.org/10.1128/mbio.02918-23  

   Zhang, Irene H.; Borer, Benedict; Zhao, Rui; Wilbert, Steven; Newman, Dianne K.; Babbin, Andrew R. (March 2024, mBio)

   Giovannoni, Stephen J. (Ed.)

   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. 

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5. Nitrous oxide reduction by two partial denitrifying bacteria requires denitrification intermediates that cannot be respired

   https://doi.org/10.1128/aem.01741-23  

   LaSarre, Breah; Morlen, Ryan; Neumann, Gina C; Harwood, Caroline S; McKinlay, James B (January 2024, Applied and Environmental Microbiology)

   Bose, Arpita (Ed.)

   ABSTRACT Denitrification is a form of anaerobic respiration wherein nitrate (NO₃⁻) is sequentially reduced via nitrite (NO₂⁻), nitric oxide, and nitrous oxide (N₂O) to dinitrogen gas (N₂) by four reductase enzymes. Partial denitrifying bacteria possess only one or some of these four reductases and use them as independent respiratory modules. However, it is unclear if partial denitrifiers sense and respond to denitrification intermediates outside of their reductase repertoire. Here, we tested the denitrifying capabilities of two purple nonsulfur bacteria,Rhodopseudomonas palustrisCGA0092 andRhodobacter capsulatusSB1003. Each had denitrifying capabilities that matched their genome annotation; CGA0092 reduced NO₂⁻to N₂, and SB1003 reduced N₂O to N₂. For each bacterium, N₂O reduction could be used both for electron balance during growth on electron-rich organic compounds in light and for energy transformation via respiration in darkness. However, N₂O reduction required supplementation with a denitrification intermediate, including those for which there was no associated denitrification enzyme. For CGA0092, NO₃⁻served as a stable, non-catalyzable molecule that was sufficient to activate N₂O reduction. Using a β-galactosidase reporter, we found that NO₃⁻acted, at least in part, by stimulating N₂O reductase gene expression. In SB1003, NO₂⁻but not NO₃⁻activated N₂O reduction, but NO₂⁻was slowly removed, likely by a promiscuous enzyme activity. Our findings reveal that partial denitrifiers can still be subject to regulation by denitrification intermediates that they cannot use. IMPORTANCEDenitrification is a form of microbial respiration wherein nitrate is converted via several nitrogen oxide intermediates into harmless dinitrogen gas. Partial denitrifying bacteria, which individually have some but not all denitrifying enzymes, can achieve complete denitrification as a community by cross-feeding nitrogen oxide intermediates. However, the last intermediate, nitrous oxide (N2O), is a potent greenhouse gas that often escapes, motivating efforts to understand and improve the efficiency of denitrification. Here, we found that at least some partial denitrifying N2O reducers can sense and respond to nitrogen oxide intermediates that they cannot otherwise use. The regulatory effects of nitrogen oxides on partial denitrifiers are thus an important consideration in understanding and applying denitrifying bacterial communities to combat greenhouse gas emissions. 

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