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

---

The host-associated archaeome

Nature Reviews Microbiology, Journal Year: 2020, Volume and Issue: 18(11), P. 622 - 636

Published: July 20, 2020

Language: Английский

---

Microalgae, Seaweeds and Aquatic Bacteria, Archaea, and Yeasts: Sources of Carotenoids with Potential Antioxidant and Anti-Inflammatory Health-Promoting Actions in the Sustainability Era

Marine Drugs, Journal Year: 2023, Volume and Issue: 21(6), P. 340 - 340

Published: June 1, 2023

Carotenoids are a large group of health-promoting compounds used in many industrial sectors, such as foods, feeds, pharmaceuticals, cosmetics, nutraceuticals, and colorants. Considering the global population growth environmental challenges, it is essential to find new sustainable sources carotenoids beyond those obtained from agriculture. This review focuses on potential use marine archaea, bacteria, algae, yeast biological factories carotenoids. A wide variety carotenoids, including novel ones, were identified these organisms. The role organisms their actions have also been discussed. Marine great capacity synthesize which can be renewable manner without depleting natural resources. Thus, concluded that they represent key source could help Europe achieve its Green Deal Recovery Plan. Additionally, lack standards, clinical studies, toxicity analysis reduces traditional Therefore, further research processing organisms, biosynthetic pathways, extraction procedures, examination content needed increase carotenoid productivity, document safety, decrease costs for implementation.

Language: Английский

---

Metagenomic probing toward an atlas of the taxonomic and metabolic foundations of the global ocean genome

Frontiers in Science, Journal Year: 2024, Volume and Issue: 1

Published: Jan. 16, 2024

The global ocean genome (the pool of genes in marine organisms and the functional information they encode) is a major, untapped resource for science society with growing range biotechnology applications sectors such as biomedicine, energy, food. Shotgun sequencing metagenomics can now be used to catalog diversity microbial life explore its potential, but has been limited by sample coverage, access suitable platforms, computational capacity. Here we provide novel synthesis based on analysis 2,102 sampled metagenomes, gene assembly annotation via KAUST Metagenome Analysis Platform (KMAP) Global Ocean Gene Catalog 1.0 containing 308.6 million clusters. Taxonomically, report distribution across tree different basins depth zone biomes. Functionally, map relationship protein families biogeochemical processes, including major metabolic pathways that process three elements play fundamental roles cycles are relevant climate change. These data extend our understanding complex, dynamic nature microbiome capabilities. Further research critical importance both unlock potential understand predict effects human-induced changes, pollution hypothesis-driven should target under-sampled deep sea benthic communities using enhanced metagenomic methods, better ecosystem functioning. Investment necessary capacity essential, intellectual property frameworks.

Language: Английский

---

Linking metagenomics to aquatic microbial ecology and biogeochemical cycles

Limnology and Oceanography, Journal Year: 2019, Volume and Issue: 65(S1)

Published: Nov. 20, 2019

Abstract Microbial communities are essential components of aquatic ecosystems through their contribution to food web dynamics and biogeochemical processes. Aquatic microbial diversity is immense a general challenge understand how metabolism interactions single organisms shape community ecosystem‐scale transformations. Metagenomic approaches have developed rapidly, proven be powerful in linking In this review, we provide an overview metagenomic approaches, followed by discussion on some recent insights they provided, including those special issue. These include the discovery new taxa metabolisms microbiomes, into assembly functional ecology as well evolutionary processes shaping genomes influence human activities microbiomes. Given that metagenomics can now considered mature technology where data generation descriptive analyses relatively routine informative, then discuss metagenomic‐enabled research avenues further link integration well‐designed ecological experiments, use inform validate metabolic models, pressing need for ecologically relevant model simple systems better interpret taxonomic information integrated metagenomes. will contribute more mechanistic predictive understanding links between cycles. Owing rapid climate change impacts ecosystems, urgency such has never been greater.

Language: Английский

---

Ammonia‐oxidizing archaea release a suite of organic compounds potentially fueling prokaryotic heterotrophy in the ocean

Environmental Microbiology, Journal Year: 2019, Volume and Issue: 21(11), P. 4062 - 4075

Published: July 23, 2019

Summary Ammonia‐oxidizing archaea (AOA) constitute a considerable fraction of microbial biomass in the global ocean, comprising 20%–40% ocean's prokaryotic plankton. However, it remains enigmatic to what extent these chemolithoautotrophic release dissolved organic carbon (DOC). A combination targeted and untargeted metabolomics was used characterize exometabolomes three model AOA strains Nitrosopumilus genus. Our results indicate that marine exude suite compounds with potentially varying reactivities, dominated by nitrogen‐containing compounds. significant released matter (DOM) consists labile compounds, which typically limit heterotrophic activity open ocean waters, including amino acids, thymidine B vitamins. Amino acid rates corresponded ammonia oxidation predominantly hydrophobic as result passive diffusion. Despite low contribution DOC (~0.08%–1.05%) demand, physiologically relevant metabolites could be crucial for microbes are auxotrophic some members globally abundant ubiquitous SAR11 clade.

Language: Английский

---

A comparative metagenomic study reveals microbial diversity and their role in the biogeochemical cycling of Pangong lake

The Science of The Total Environment, Journal Year: 2020, Volume and Issue: 731, P. 139074 - 139074

Published: April 29, 2020

Language: Английский

---

Phosphonate production by marine microbes: Exploring new sources and potential function

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(11)

Published: March 7, 2022

Significance Phosphonates are a class of phosphorus metabolites characterized by highly stable C-P bond. accumulate to high concentrations in seawater, fuel large fraction marine methane production, and serve as source microbes inhabiting nutrient-limited regions the oligotrophic ocean. Here, we show that 15% all bacterioplankton surface ocean have genes phosphonate synthesis most belong abundant groups Prochlorococcus SAR11. Genomic chemical evidence suggests phosphonates incorporated into cell-surface phosphonoglycoproteins may act mitigate cell mortality grazing viral lysis. These results underscore global biogeochemical impact relatively rare but expressed traits numerically bacteria.

Language: Английский

---

Archaeal lipids trace ecology and evolution of marine ammonia-oxidizing archaea

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(31)

Published: July 29, 2022

Archaeal membrane lipids are widely used for paleotemperature reconstructions, yet these molecular fossils also bear rich information about ecology and evolution of marine ammonia-oxidizing archaea (AOA). Here we identified thermal nonthermal behaviors archaeal glycerol dialkyl tetraethers (GDGTs) by comparing the GDGT-based temperature index (TEX86) to ratio GDGTs with two three cyclopentane rings (GDGT-2/GDGT-3). Thermal-dependent biosynthesis should increase TEX86 decrease GDGT-2/GDGT-3 when ambient increases. This presumed temperature-dependent (PTD) trend is observed in derived from cultures thermophilic mesophilic AOA. The distribution suspended particulate matter (SPM) sediments collected above pycnocline-shallow water samples-also follows PTD trend. These similar GDGT distributions between AOA shallow environmental samples reflect ecotypes While there currently no deep clades, SPM sediment exhibit behavior deviating presence increases distorts temperature-controlled correlation TEX86. We then Gaussian mixture models statistically characterize diagnostic patterns modern paleo-GDGT records infer Mid-Mesozoic present. Long-term trends suggest a suppression today's during Mesozoic-early Cenozoic greenhouse climates. Our analysis provides invaluable insights into evolutionary timeline expansion niches associated major oceanographic climate changes.

Language: Английский

---

Prokaryotic Life in the Deep Ocean's Water Column

Annual Review of Marine Science, Journal Year: 2022, Volume and Issue: 15(1), P. 461 - 483

Published: July 14, 2022

The oceanic waters below a depth of 200 m represent, in terms volume, the largest habitat biosphere, harboring approximately 70% prokaryotic biomass water column. These are characterized by low temperature, increasing hydrostatic pressure, and decreasing organic matter supply with depth. Recent methodological advances microbial oceanography have refined our view ecology prokaryotes dark ocean. Here, we review ocean, present data on distribution heterotrophic chemolithoautotrophic production major basins, highlight phylogenetic functional diversity this part We describe connectivity surface deep-water molecular adaptations piezophilic to high pressure. also knowledge gaps ocean's their role biogeochemical cycles biosphere.

Language: Английский

---