Unlocking bacterial potential to reduce farmland N2O emissions

Nature, Год журнала: 2024, Номер 630(8016), С. 421 - 428

Опубликована: Май 29, 2024

Abstract Farmed soils contribute substantially to global warming by emitting N 2 O (ref. 1 ), and mitigation has proved difficult . Several microbial nitrogen transformations produce O, but the only biological sink for is enzyme NosZ, catalysing reduction of 3 ). Although strengthening NosZ activity in would reduce emissions, such bioengineering soil microbiota considered challenging 4,5 However, we have developed a technology achieve this, using organic waste as substrate vector O-respiring bacteria selected their capacity thrive 6–8 Here analysed biokinetics our most promising bacterium, Cloacibacterium sp. CB-01, its survival effect on emissions field experiments. Fertilization with from biogas production, which CB-01 had grown aerobically about 6 × 10 9 cells per millilitre, reduced 50–95%, depending type. The strong long-lasting ascribed tenacity soil, rather than biokinetic parameters, were inferior those other strains bacteria. Scaling data up European level, find that national anthropogenic could be 5–20%, more if including wastes. This opens an avenue cost-effective options are lacking at present.

Язык: Английский

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Partitioning of the denitrification pathway and other nitrite metabolisms within global oxygen deficient zones

ISME Communications, Год журнала: 2023, Номер 3(1)

Опубликована: Июль 20, 2023

Abstract Oxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially mediated pathway proceeding stepwise from NO3− to N2. This process may be performed entirely by complete denitrifiers capable all four enzymatic steps, but many organisms possess only partial denitrification pathways, either producing or consuming key intermediates such as the greenhouse gas N2O. Metagenomics and marker gene surveys have revealed diversity genes within ODZs, whether these co-occur identities denitrifying taxa remain open questions. We assemble genomes metagenomes spanning ETNP Arabian Sea, map metagenome-assembled (MAGs) 56 three major ODZs reveal predominance denitrifiers, particularly single-step denitrifiers. find niche differentiation among nitrogen-cycling organisms, with communities performing each transformation distinct in taxonomic identity motility traits. Our collection 962 MAGs presents largest pelagic ODZ microorganisms reveals clearer picture cycling community this environment.

Язык: Английский

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New insights into the structure, microbial diversity and ecology of yellow biofilms in a Paleolithic rock art cave (Pindal Cave, Asturias, Spain)

The Science of The Total Environment, Год журнала: 2023, Номер 897, С. 165218 - 165218

Опубликована: Июль 6, 2023

In the absence of sunlight, caves harbor a great diversity microbial colonies to extensive biofilms with different sizes and colors visible naked eye. One most widespread types biofilm are those yellow hues that can constitute serious problem for conservation cultural heritage in many caves, such as Pindal Cave (Asturias, Spain). This cave, declared World Heritage Site by UNESCO its Paleolithic parietal art, shows high degree development represents real threat painted engraved figures. study aims to: 1) identify structures characteristic taxa composing biofilms, 2) seek linked microbiome reservoir primarily contributing their growth; 3) seed light on driving vectors contribute formation determine subsequent proliferation spatial distribution. To achieve this goal, we used amplicon-based massive sequencing, combination other techniques microscopy, situ hybridization environmental monitoring, compare communities drip waters, cave sediments exterior soil. The results revealed related phylum Actinomycetota bacteria represented genera wb1-P19, Crossiella, Nitrospira, Arenimonas. Our findings suggest serve potential reservoirs colonization sites these develop into under favorable substrate conditions, particular affinity speleothems rugged-surfaced rocks found condensation-prone areas. presents an exhaustive which could be procedure identification similar design effective strategies valuable heritage.

Язык: Английский

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Community‐scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing

Microbial Biotechnology, Год журнала: 2024, Номер 17(1)

Опубликована: Янв. 1, 2024

Abstract Building models is essential for understanding the functions and dynamics of microbial communities. Metabolic built on genome‐scale metabolic network reconstructions (GENREs) are especially relevant as a means to decipher complex interactions occurring among species. Model reconstruction increasingly relies metagenomics, which permits direct characterisation naturally communities that may contain organisms cannot be isolated or cultured. In this review, we provide an overview field modelling its increasing reliance synergy with metagenomics bioinformatics. We survey assigning reconstructing networks from (meta‐)genomes, present variety mathematical fundamentals foster dynamics. emphasise scaling model construction large communities, two important bottlenecks in applicability these models. give current state art metagenome sequencing bioinformatics analysis, focusing genomes Metagenomics benefits tremendously third‐generation sequencing, discuss opportunities long‐read strain‐level eukaryotic metagenomics. aim at providing algorithmic support, together tool application resources, permit bridging gap between modelling.

Язык: Английский

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High-resolution spatial patterns and drivers of terrestrial ecosystem carbon dioxide, methane, and nitrous oxide fluxes in the tundra

Biogeosciences, Год журнала: 2024, Номер 21(2), С. 335 - 355

Опубликована: Янв. 19, 2024

Abstract. Arctic terrestrial greenhouse gas (GHG) fluxes of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) play an important role in the global GHG budget. However, these are rarely studied simultaneously, our understanding conditions controlling them across spatial gradients is limited. Here, we explore magnitudes drivers fine-scale during peak growing season (July) sub-Arctic Finland. We measured chamber-derived soil temperature, moisture, organic nitrogen stocks, pH, carbon-to-nitrogen (C/N) ratio, dissolved content, vascular plant biomass, vegetation type from 101 plots scattered a heterogeneous tundra landscape (5 km2). used field data together with high-resolution remote sensing to develop machine learning models for predicting (i.e., upscaling) daytime at 2 m resolution. Our results show that this region was on average net sink season. Although suggest driven by CO2 uptake, it also revealed small but widespread CH4 uptake upland types, almost surpassing high wetland emissions scale. Average N2O were negligible. controlled primarily annual temperature biomass (both increase sink) type, moisture (increases emissions) C/N (lower increases source). These demonstrate potential resolution modeling Arctic. They reveal dominant dry soils might significant regional

Язык: Английский

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Genome-Resolved Metagenomics and Denitrifying Strain Isolation Reveal New Insights into Microbial Denitrification in the Deep Vadose Zone

Environmental Science & Technology, Год журнала: 2024, Номер 58(5), С. 2323 - 2334

Опубликована: Янв. 24, 2024

The heavy use of nitrogen fertilizer in intensive agricultural areas often leads to nitrate accumulation subsurface soil and contamination groundwater, which poses a serious risk public health. Denitrifying microorganisms the subsoil convert gaseous forms nitrogen, thereby mitigating leaching into groundwater. Here, we investigated denitrifying deep vadose zone typical area China through microcosm enrichment, genome-resolved metagenomic analysis, bacteria isolation. A total 1000 metagenome-assembled genomes (MAGs) were reconstructed, resulting 98 high-quality, dereplicated MAGs that contained denitrification genes. Among them, 32 could not be taxonomically classified at genus or species level, indicating broader spectrum taxonomic groups is involved than previously recognized. denitrifier isolate library was constructed by using strategy combining high-throughput conventional cultivation techniques. Assessment characteristics both isolates demonstrated dominance truncated denitrification. Functional screening revealed highest activity two complete denitrifiers belonging Pseudomonas. These findings greatly expand current knowledge composition function subsoils. provided first pool subsoil-denitrifying facilitate development microbe-based technologies for attenuation

Язык: Английский

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The activity and functions of soil microbial communities in the Finnish sub-Arctic vary across vegetation types

FEMS Microbiology Ecology, Год журнала: 2022, Номер 98(8)

Опубликована: Июль 1, 2022

Due to climate change, increased microbial activity in high-latitude soils may lead higher greenhouse gas (GHG) emissions. However, GHG production and consumption mechanisms tundra are not thoroughly understood. To investigate how the diversity functional potential of bacterial archaeal communities vary across vegetation types soil layers, we analyzed 116 metatranscriptomes from 73 sites Finnish sub-Arctic. Meadow were characterized by pH lower organic matter (SOM) carbon/nitrogen ratio. By contrast, dwarf shrub-dominated ecosystems had SOM pH. Although Actinobacteria, Acidobacteria, Alphaproteobacteria Planctomycetes dominant all communities, there significant differences at genus level between types; plant polymer-degrading groups more active than meadows. Given that climate-change scenarios predict expansion shrubs high latitudes, our results indicate harbor decomposers litter, which affect rate carbon turnover soils. Additionally, transcripts methanotrophs detected mineral layer soils, moderate methane fluxes. This study provides new insights into possible shifts due change.

Язык: Английский

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Novel diversity of polar Cyanobacteria revealed by genome-resolved metagenomics

Microbial Genomics, Год журнала: 2023, Номер 9(7)

Опубликована: Июль 7, 2023

Benthic microbial mats dominated by Cyanobacteria are important features of polar lakes. Although culture-independent studies have provided insights into the diversity Cyanobacteria, only a handful genomes been sequenced to date. Here, we applied genome-resolved metagenomics approach data obtained from Arctic, sub-Antarctic and Antarctic mats. We recovered 37 metagenome-assembled (MAGs) representing 17 distinct species, most which distantly related that so far. These include (i) lineages common in such as filamentous taxa

Язык: Английский

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Microbial Ecology of Permafrost Soils: Populations, Processes, and Perspectives

Permafrost and Periglacial Processes, Год журнала: 2025, Номер unknown

Опубликована: Янв. 13, 2025

ABSTRACT Permafrost microbial research has flourished in the past decades, due part to improvements sampling and molecular techniques, but also increased focus on permafrost greenhouse gas feedback climate change other ecological processes high latitude alpine soils. microorganisms are adapted these extreme environments remain active at low temperatures when resources limited. They an important component of global elemental cycles as they regulate organic matter turnover production, particularly thaws. Here we review microbiology literature coupled with exploration its historical aspects, a particular new understanding advanced by biology techniques. We further identify knowledge gaps ways forward improve our contributions ecosystem biogeochemistry permafrost‐affected systems.

Язык: Английский

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Effects of decabromodiphenyl ethane (DBDPE) exposure on soil microbial community: Nitrogen cycle, microbial defense and repair and antibiotic resistance genes transfer

Journal of Environmental Management, Год журнала: 2025, Номер 376, С. 124503 - 124503

Опубликована: Фев. 15, 2025

Язык: Английский

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