Impacts and Importance of Ammonia- and Nitrite Oxidation in the Marine Nitrogen Cycle

Nitrification produces the most abundant form of bioavailable nitrogen in the ocean, which is also a major electron acceptor in the oxidation of organic matter. The latter role of nitrate becomes crucial in the absence of oxygen. One major aim of this thesis is to investigate the role of nitrite oxidation in oxygen minimum zone (OMZ) N-cycling. Nitrite oxidation was detected throughout the Namibian OMZ and appears unaffected even by non-detectable oxygen levels. It could recycle up to 100% of reduced nitrate and thereby potentially reduce N-loss. The high abundance of nitrite oxidizing bacteria of the genus Nitrococcus can likely be explained by their versatile metabolism. While Nitrococcus grows chemolithoautotrophically in the presence of oxygen, it gains energy via organoheterotrophic nitrate reduction to nitrite and nitrous oxide in the absence of oxygen. In the oxygenated ocean of the Mauritanian upwelling ammonia- and nitrite oxidizers appeared to be associated with marine aggregates. An alternative source of nitrite was provided by nitrate reduction, which is likely facilitated by oxygen reduced microniches within marine aggregates

Auswirkungen und Bedeutung von Ammoniak- und Nitrit Oxidation im Marinen Stickstoffkreislauf

Nitrification produces the most abundant form of bioavailable nitrogen in the ocean, which is also a major electron acceptor in the oxidation of organic matter. The latter role of nitrate becomes crucial in the absence of oxygen. One major aim of this thesis is to investigate the role of nitrite oxidation in oxygen minimum zone (OMZ) N-cycling. Nitrite oxidation was detected throughout the Namibian OMZ and appears unaffected even by non-detectable oxygen levels. It could recycle up to 100% of reduced nitrate and thereby potentially reduce N-loss. The high abundance of nitrite oxidizing bacteria of the genus Nitrococcus can likely be explained by their versatile metabolism. While Nitrococcus grows chemolithoautotrophically in the presence of oxygen, it gains energy via organoheterotrophic nitrate reduction to nitrite and nitrous oxide in the absence of oxygen. In the oxygenated ocean of the Mauritanian upwelling ammonia- and nitrite oxidizers appeared to be associated with marine aggregates. An alternative source of nitrite was provided by nitrate reduction, which is likely facilitated by oxygen reduced microniches within marine aggregates

Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean

International audienceBiological nitrogen fixation is a major factor contributing to microbial primary productivity in the open ocean. The current view depicts a few cyanobacterial diazotrophs as the most relevant marine nitrogen fixers, whereas heterotrophic diazotrophs are more diverse and considered to have lower impacts on the nitrogen balance. Here, we used 891 Tara Oceans metagenomes to create a manually curated, non-redundant genomic database corresponding to free-living, as well as filamentous, colony-forming, particle-attached and symbiotic bacterial and archaeal populations occurring in the surface of five oceans and two seas. Notably, the database provided the genomic content of eight cyanobacterial diazotrophs including Trichodesmium populations and a newly discovered population similar to Richelia , as well as 40 heterotrophic bacterial diazotrophs organized into three main functional groups that considerably expand the known diversity of abundant marine nitrogen fixers compared to previous genomic surveys. Critically, these 48 populations may account for more than 90% of cells containing known nifH genes and occurring in the sunlit ocean, suggesting that the genomic characterization of the most abundant marine diazotrophs may be nearing completion. The newly identified heterotrophic bacterial diazotrophs are widespread, express their nifH genes in situ , and co-occur under nitrate-depleted conditions in large size fractions where they might form aggregates providing the low-oxygen microenvironments required for nitrogen fixation. Most significantly, we found heterotrophic bacterial diazotrophs to be more abundant than cyanobacterial diazotrophs in most metagenomes from the open oceans and seas. This large-scale environmental genomic survey emphasizes the considerable potential of heterotrophs in the marine nitrogen balance

Community-led, integrated, reproducible multi-omics with anvi'o

International audienceBig data abound in microbiology, but the workflows designed to enable researchers to interpret data can constrain the biological questions that can be asked. Five years after anvi’o was first published, this community-led multi-omics platform is maturing into an open software ecosystem that reduces constraints in ‘omics data analyses