Nitrous oxide production by ammonia oxidizers: Physiological diversity, niche differentiation and potential mitigation strategies

Global Change Biology, Journal Year: 2019, Volume and Issue: 26(1), P. 103 - 118

Published: Oct. 22, 2019

Abstract Oxidation of ammonia to nitrite by bacteria and archaea is responsible for global emissions nitrous oxide directly indirectly through provision and, after further oxidation, nitrate denitrifiers. Their contributions increasing N 2 O are greatest in terrestrial environments, due the dramatic continuing increases use ammonia‐based fertilizers, which have been driven requirement increased food production, but also provide a source energy oxidizers (AO), leading an imbalance nitrogen cycle. Direct production AO results from several metabolic processes, sometimes combined with abiotic reactions. Physiological characteristics, including mechanisms vary within between ammonia‐oxidizing (AOA) (AOB) comammox yield AOB higher than other two groups. There strong evidence niche differentiation AOA respect environmental conditions natural engineered environments. In particular, favored low soil pH are, respectively, rates ammonium supply, equivalent application slow‐release fertilizer, or high addition concentrations inorganic urea. These differences potential better fertilization strategies that could both increase fertilizer efficiency reduce agricultural soils. This article reviews research on biochemistry, physiology ecology discusses consequences communities subjected different practices ways this knowledge, coupled improved methods characterizing communities, might lead mitigation emissions.

Language: Английский

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Accurate and complete genomes from metagenomes

Genome Research, Journal Year: 2020, Volume and Issue: 30(3), P. 315 - 333

Published: March 1, 2020

Genomes are an integral component of the biological information about organism; thus, more complete genome, informative it is. Historically, bacterial and archaeal genomes were reconstructed from pure (monoclonal) cultures, first reported sequences manually curated to completion. However, bottleneck imposed by requirement for isolates precluded genomic insights vast majority microbial life. Shotgun sequencing communities, referred initially as community genomics subsequently genome-resolved metagenomics, can circumvent this limitation obtaining metagenome-assembled (MAGs); but gaps, local assembly errors, chimeras, contamination fragments other limit value these genomes. Here, we discuss genome curation improve and, in some cases, achieve (circularized, no gaps) MAGs (CMAGs). To date, few CMAGs have been generated, although notably very complex systems such soil sediment. Through analysis 7000 published isolate genomes, verify cumulative GC skew combination with metrics establish sequence accuracy. The identified potential misassemblies reference isolated bacteria repeat that likely gave rise them. We methods could be implemented bioinformatic approaches ensure metabolic evolutionary analyses based on high-quality

Language: Английский

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Global Nitrogen Cycle: Critical Enzymes, Organisms, and Processes for Nitrogen Budgets and Dynamics

Chemical Reviews, Journal Year: 2020, Volume and Issue: 120(12), P. 5308 - 5351

Published: June 12, 2020

Nitrogen (N) is used in many of life's fundamental biomolecules, and it also a participant environmental redox chemistry. Biogeochemical processes control the amount form N available to organisms ("fixed" N). These interacting result acting as proximate limiting nutrient most surface environments. Here, we review global biogeochemical cycle its anthropogenic perturbation. We introduce important reservoirs affecting environment, focusing on ocean, which cycling more generalizable than terrestrial systems, are heterogeneous. Particular attention given that create destroy fixed because these comprise input/output budget, universal availability. discuss preindustrial budgets for marine systems their modern-day alteration by inputs from human activities. summarize evidence indicating simultaneous roles required biomass constituent an intermediate lead stabilizing feedbacks tend blunt impact perturbations at larger spatiotemporal scales, particularly systems. As feedbacks, "N problem" distinct "carbon dioxide being local less global, immediate persistent.

Language: Английский

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Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes

Nature Biotechnology, Journal Year: 2019, Volume and Issue: 37(8), P. 937 - 944

Published: July 29, 2019

Language: Английский

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Comparative genomics sheds light on niche differentiation and the evolutionary history of comammox Nitrospira

The ISME Journal, Journal Year: 2018, Volume and Issue: 12(7), P. 1779 - 1793

Published: March 1, 2018

Language: Английский

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