Direct Methane Oxidation by Copper- and Iron-Dependent Methane Monooxygenases

Chemical Reviews, Journal Year: 2024, Volume and Issue: 124(3), P. 1288 - 1320

Published: Feb. 2, 2024

Methane is a potent greenhouse gas that contributes significantly to climate change and primarily regulated in Nature by methanotrophic bacteria, which consume methane as their source of energy carbon, first oxidizing it methanol. The direct oxidation methanol chemically difficult transformation, accomplished methanotrophs complex monooxygenase (MMO) enzyme systems. These enzymes use iron or copper metallocofactors have been the subject detailed investigation. While structure, function, active site architecture copper-dependent particulate (pMMO) investigated extensively, its putative quaternary interactions, regulation, requisite cofactors, mechanism remain enigmatic. iron-dependent soluble (sMMO) has characterized biochemically, structurally, spectroscopically, and, for most part, mechanistically. Here, we review history MMO research, focusing on recent developments providing an outlook future directions field. Engineered biological catalysis systems bioinspired synthetic catalysts may continue emerge along with deeper understanding molecular mechanisms oxidation. Harnessing power these will necessitate combined efforts biochemistry, structural biology, inorganic chemistry, microbiology, computational engineering.

Language: Английский

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Nitrification and beyond: metabolic versatility of ammonia oxidising archaea

The ISME Journal, Journal Year: 2023, Volume and Issue: 17(9), P. 1358 - 1368

Published: July 14, 2023

Ammonia oxidising archaea are among the most abundant living organisms on Earth and key microbial players in global nitrogen cycle. They carry out oxidation of ammonia to nitrite, their activity is relevant for both food security climate change. Since discovery nearly 20 years ago, major insights have been gained into carbon metabolism, growth preferences mechanisms adaptation environment, as well diversity, abundance environment. Despite significant strides forward through cultivation novel omics-based approaches, there still many knowledge gaps metabolism which enable them adapt microorganisms typically considered metabolically streamlined highly specialised. Here we review physiology archaea, with focus aspects metabolic versatility regulation, discuss these traits context nitrifier ecology.

Language: Английский

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Enzyme-Induced Reactive Oxygen Species Trigger Oxidative Degradation of Sulfamethoxazole within a Methanotrophic Biofilm

Water Research, Journal Year: 2024, Volume and Issue: 253, P. 121330 - 121330

Published: Feb. 17, 2024

Language: Английский

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Membraneless channels sieve cations in ammonia-oxidizing marine archaea

Nature, Journal Year: 2024, Volume and Issue: 630(8015), P. 230 - 236

Published: May 29, 2024

Abstract Nitrosopumilus maritimus is an ammonia-oxidizing archaeon that crucial to the global nitrogen cycle 1,2 . A critical step for oxidation entrapment of ammonium ions from a dilute marine environment at cell surface and their subsequent channelling membrane N. Here we elucidate structure molecular machinery responsible this process, comprising layer (S-layer), using electron cryotomography subtomogram averaging cells. We supplemented our in situ ammonium-binding S-layer array with single-particle cryomicroscopy structure, revealing detailed features immunoglobulin-rich glycan-decorated S-layer. Biochemical analyses showed strong binding by surface, which was lost after disassembly. Sensitive bioinformatic identified similar S-layers many archaea, conserved sequence structural characteristics. Moreover, simulations determination ammonium-enriched specimens enabled us examine cation-binding properties S-layer, how it concentrates on its cell-facing side, effectively acting as multichannel sieve membrane. This study illuminates biogeochemically essential process channelling, common microorganisms are fundamental cycle.

Language: Английский

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Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments

The ISME Journal, Journal Year: 2024, Volume and Issue: 18(1)

Published: Jan. 1, 2024

Abstract Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant on Earth, widely distributed in marine, terrestrial, geothermal ecosystems. However, genomic diversity, biogeography, evolutionary process of AOA populations subsurface environments vastly understudied compared to those marine soil systems. Here, we report a novel order Candidatus (Ca.) Nitrosomirales which forms sister lineage thermophilic Ca. Nitrosocaldales. Metagenomic 16S rRNA gene-read mapping demonstrates presence various groundwater their widespread distribution across range geothermal, habitats. Terrestrial show genetic capacity using formate as source reductant nitrate an alternative electron acceptor. appear have acquired key metabolic genes operons from other mesophilic via horizontal gene transfer, including encoding urease, nitrite reductase, V-type ATPase. The additional versatility conferred by functions may facilitated radiation into variety subsurface, environments. We also provide evidence that each four orders spans both terrestrial habitats, suggests more complex history for major lineages than previously proposed. Together, these findings establish robust phylogenomic framework new insights ecology adaptation this globally functional guild.

Language: Английский

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Enhancing agroecosystem nitrogen management: microbial insights for improved nitrification inhibition

Trends in Microbiology, Journal Year: 2023, Volume and Issue: 32(6), P. 590 - 601

Published: Nov. 15, 2023

Language: Английский

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Metabolic potential of Nitrososphaera-associated clades

The ISME Journal, Journal Year: 2024, Volume and Issue: 18(1)

Published: Jan. 1, 2024

Soil ammonia-oxidizing archaea (AOA) play a crucial role in converting ammonia to nitrite, thereby mobilizing reactive nitrogen species into their soluble form, with significant impact on losses from terrestrial soils. Yet, our knowledge regarding diversity and functions remains limited. In this study, we reconstructed 97 high-quality AOA metagenome-assembled genomes (MAGs) 180 soil samples collected Central Germany during 2014-2019 summers. These MAGs were affiliated the order Nitrososphaerales clustered four family-level clades (NS-α/γ/δ/ε). Among these MAGs, 75 belonged most abundant but least understood δ-clade. Within δ-clade, amoA genes three neutral soils showed 99.5% similarity fosmid clone 54d9, which has served as representative of δ-clade for past two decades since even today no cultivated representatives are available. Seventy-two constituted distinct δ sub-clade, abundance expression activity more than twice that other slightly acidic Unlike less (α, γ, ε), δ-MAGs possessed multiple highly expressed intracellular extracellular carbohydrate-active enzymes responsible carbohydrate binding (CBM32) degradation (GH5), along involved oxidation. Together, results suggest metabolic versatility uncultured potential mixotrophic or chemolithoheterotrophic lifestyle among 54d9-like AOA.

Language: Английский

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Metagenomics and plant-microbe symbioses: Microbial community dynamics, functional roles in carbon sequestration, nitrogen transformation, sulfur and phosphorus mobilization for sustainable soil health

Biotechnology Advances, Journal Year: 2025, Volume and Issue: 82, P. 108580 - 108580

Published: April 15, 2025

Language: Английский

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Novel hot spring Thermoproteota support vertical inheritance of ammonia oxidation and carbon fixation in Nitrososphaeria

Access Microbiology, Journal Year: 2025, Volume and Issue: 7(4)

Published: April 1, 2025

Aerobic ammonia oxidation is crucial to the nitrogen cycle and only known be performed by a small number of bacterial lineages [ammonia-oxidizing bacteria (AOB)] single lineage archaea belonging Nitrososphaeria class Thermoproteota Archaea (AOA)]. Most cultivated AOA originate from marine or soil environments, but this may capture limited subset full diversity clade. Here, we describe several genomes metagenomic sequencing hot spring microbial mat, representing poorly characterized basal that important for understanding early evolution archaeal oxidation. These include novel genus most closely related Nitrososphaera as well species genera Nitrosotenuis, Nitrosotalea. Furthermore, distributions phylogenetic relationships key metabolic genes support history vertical inheritance carbon fixation last common ancestor crown group AOA.

Language: Английский

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Species-specific relationships between deep sea sponges and their symbiotic Nitrosopumilaceae

The ISME Journal, Journal Year: 2023, Volume and Issue: 17(9), P. 1517 - 1519

Published: May 31, 2023

Sponges thrive in the deep, dark and nutrient-depleted ocean may rely on microbial symbionts for carbon acquisition energy generation. However, these symbiotic relationships remain largely unexplored. In this study, we analyze microbiome of deep-sea sponges show that ammonia-oxidizing archaea (AOA) family Nitrosopumilaceae make up at least 75% communities Aphrocallistes sp., Farrea sp. Paratimea sp.. Given known autotrophic metabolism AOAs, implies sponge holobionts can have capacity primary production deep-sea. We also specific AOA lineages are highly towards their hosts, hinting an unprecedent vertical transmission sponges. Our results ecology evolution is distinct from shallow-water counterparts.

Language: Английский

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