Decoupling function and taxonomy in the global ocean microbiome

Science, Год журнала: 2016, Номер 353(6305), С. 1272 - 1277

Опубликована: Сен. 15, 2016

Microbial metabolism powers biogeochemical cycling in Earth’s ecosystems. The taxonomic composition of microbial communities varies substantially between environments, but the ecological causes this variation remain largely unknown. We analyzed and functional community profiles to determine factors that shape marine bacterial archaeal across global ocean. By classifying >30,000 microorganisms into metabolic groups, we were able disentangle from variation. find environmental conditions strongly influence distribution groups by shaping niches, only weakly within individual groups. Hence, structure constitute complementary roughly independent “axes variation” shaped markedly different processes.

Язык: Английский

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Nitrogen transformations in modern agriculture and the role of biological nitrification inhibition

Nature Plants, Год журнала: 2017, Номер 3(6)

Опубликована: Июнь 6, 2017

Язык: Английский

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Archaea and the human gut: New beginning of an old story

World Journal of Gastroenterology, Год журнала: 2014, Номер 20(43), С. 16062 - 16062

Опубликована: Янв. 1, 2014

Methanogenic archaea are known as human gut inhabitants since more than 30 years ago through the detection of methane in breath and isolation two methanogenic species belonging to order Methanobacteriales, Methanobrevibacter smithii Methanosphaera stadtmanae .During last decade, diversity encountered gastrointestinal tract (GIT) has been extended by sequence identification culturing new strains.Here we provide an updated census archaeal associated with GIT their possible role physiology health.We particularly focus on still poorly characterized 7 th methanogens, Methanomassiliicoccales, aged population.While also largely distributed non-GIT environments, our actual knowledge this novel methanogens mainly revealed inhabitants.They enlarge number final electron acceptors metabolites mono-di-and trimethylamine.Trimethylamine is exclusively a microbiota-derived product nutrients (lecithin, choline, TMAO, L-carnitine) from normal diet, which seems originate diseases, trimethylaminuria (or Fish-Odor Syndrome) cardiovascular disease proatherogenic property its oxidized liver-derived form.This therefore supports interest these use archaebiotics, term coined notion archaea-derived probiotics.

Язык: Английский

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Complete nitrification: insights into the ecophysiology of comammox Nitrospira

Applied Microbiology and Biotechnology, Год журнала: 2018, Номер 103(1), С. 177 - 189

Опубликована: Ноя. 10, 2018

Nitrification, the oxidation of ammonia via nitrite to nitrate, has been considered be a stepwise process mediated by two distinct functional groups microorganisms. The identification complete nitrifying Nitrospira challenged not only paradigm labor division in nitrification, it also raises fundamental questions regarding environmental distribution, diversity, and ecological significance nitrifiers compared canonical Recent genomic physiological surveys identified factors controlling their ecology niche specialization, which thus potentially regulate abundances population dynamics different guilds. This review summarizes recently obtained insights into metabolic differences known discusses these light potential adaptation differentiation between nitrifiers.

Язык: Английский

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Controls and Adaptive Management of Nitrification in Agricultural Soils

Frontiers in Microbiology, Год журнала: 2019, Номер 10

Опубликована: Авг. 30, 2019

Agriculture is responsible for over half of the input reactive nitrogen (N) to terrestrial systems; however improving N availability remains primary management technique increase crop yields in most regions. In majority agricultural soils, ammonium rapidly converted nitrate by nitrification, which increases mobility through soil matrix, strongly influencing retention system. Decreasing nitrification desirable decrease losses and fertilizer use efficiency. We review controlling factors on rate extent soils from temperate regions including substrate supply, environmental conditions, abundance diversity nitrifiers plant microbial interactions with nitrifiers. Approaches include those that control inhibit directly. Strategies timing fertilization coincide rapid update, formulation fertilizers slow release or inhibitors, keeping growing continuously assimilate N, increasing assimilation (immobilization). Another effective strategy directly either synthetic biological inhibitors. Commercial inhibitors are but their complicated a changing climate organic requirements. The nitrifying organisms plants microbes producing promising approach just beginning be critically examined. Climate smart agriculture will need carefully consider optimized seasonal these strategies remain tools.

Язык: Английский

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Nitrososphaera viennensis gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon from soil and a member of the archaeal phylum Thaumarchaeota

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Год журнала: 2014, Номер 64(Pt_8), С. 2738 - 2752

Опубликована: Июнь 7, 2014

A mesophilic, neutrophilic and aerobic, ammonia-oxidizing archaeon, strain EN76 T , was isolated from garden soil in Vienna (Austria). Cells were irregular cocci with a diameter of 0.6–0.9 µm possessed archaella archaeal pili as cell appendages. Electron microscopy also indicated clearly discernible areas high low electron density, well tubule-like structures. Strain had an S-layer p3 symmetry, so far only reported for members the Sulfolobales . Crenarchaeol major core lipid. The organism gained energy by oxidizing ammonia to nitrite aerobically, thereby fixing CO 2 but growth depended on addition small amounts organic acids. optimal temperature 42 °C pH 7.5, ammonium pyruvate concentrations 2.6 1 mM, respectively. genome DNA G+C content 52.7 mol%. Phylogenetic analyses 16S rRNA genes showed that is affiliated recently proposed phylum Thaumarchaeota sharing 85 % gene sequence identity closest cultivated relative ‘ Candidatus Nitrosopumilus maritimus’ SCM1, marine maximum 81 phyla Crenarchaeota Euryarchaeota any other (e.g. Korarchaeota ’ Aigarchaeota ’). We propose name Nitrososphaera viennensis gen. nov., sp. nov. accommodate type ( = DSM 26422 JMC 19564 ) Additionally, we family Nitrososphaeraceae fam. order Nitrososphaerales ord. class Nitrososphaeria classis

Язык: Английский

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Effects of long-term application of chemical and organic fertilizers on the abundance of microbial communities involved in the nitrogen cycle

Applied Soil Ecology, Год журнала: 2015, Номер 95, С. 171 - 178

Опубликована: Июль 14, 2015

Язык: Английский

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Meta-analysis reveals ammonia-oxidizing bacteria respond more strongly to nitrogen addition than ammonia-oxidizing archaea

Soil Biology and Biochemistry, Год журнала: 2016, Номер 99, С. 158 - 166

Опубликована: Май 24, 2016

Язык: Английский

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Freshwater Recirculating Aquaculture System Operations Drive Biofilter Bacterial Community Shifts around a Stable Nitrifying Consortium of Ammonia-Oxidizing Archaea and Comammox Nitrospira

Frontiers in Microbiology, Год журнала: 2017, Номер 8

Опубликована: Янв. 30, 2017

Recirculating aquaculture systems (RAS) are unique engineered ecosystems that minimize environmental perturbation by reducing nutrient pollution discharge. RAS typically employ a biofilter to control ammonia levels produced as byproduct of fish protein catabolism. Nitrosomonas (ammonia-oxidizing), Nitrospira, and Nitrobacter (nitrite-oxidizing) species thought be the primary nitrifiers present in biofilters. We explored this assertion characterizing bacterial archaeal community commercial scale freshwater has been operation for >15 years. found harbored diverse array taxa (>1000 genus-level taxon assignments) dominated Chitinophagaceae (~12%) Acidobacteria (~9%). The exhibited significant composition shifts with changes depth conjunction operational across rearing cycle. Archaea also were abundant, comprised solely low diversity assemblage Thaumarchaeota (>95%), ammonia-oxidizing archaea (AOA) from presence AOA monooxygenase genes. at all depths time points. However, their abundance was >3 orders magnitude less than depth-time variability not observed AOA. Phylogenetic analysis nitrite oxidoreductase beta subunit (nxrB) gene indicated two distinct Nitrospira populations present, while detected. Subsequent identification alpha genes phylogenetic placement quantification nxrB genotypes suggests complete (comammox) nitrite-oxidizing co-exist relatively equivalent stable abundances system. It appears biofilters harbor complex microbial communities whose can affected directly typical system operations supporting multiple oxidation lifestyles within nitrifying consortium.

Язык: Английский

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Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system

The ISME Journal, Год журнала: 2017, Номер 11(5), С. 1142 - 1157

Опубликована: Фев. 14, 2017

Thaumarchaeota have been detected in several industrial and municipal wastewater treatment plants (WWTPs), despite the fact that ammonia-oxidizing archaea (AOA) are thought to be adapted low ammonia environments. However, activity, physiology metabolism of WWTP-associated AOA remain poorly understood. We report cultivation complete genome sequence Candidatus Nitrosocosmicus exaquare, a novel representative from WWTP Guelph, Ontario (Canada). In enrichment culture, Ca. N. exaquare oxidizes nitrite stoichiometrically, is mesophilic, tolerates at least 15 mm ammonium chloride or sodium nitrite. Microautoradiography (MAR) for cultures demonstrates assimilates bicarbonate association with oxidation. using inorganic carbon, activity greatly stimulated culture by addition organic compounds, especially malate succinate. cells coccoid diameter ~1-2 μm. Phylogenetically, belongs Nitrososphaera sister cluster within Group I.1b Thaumarchaeota, lineage which includes most other reported sequences WWTPs. The 2.99 Mbp encodes pathways oxidation, fixation, urea transport breakdown. addition, this key genes dealing oxidative stress, including peroxidase catalase. Incubations biofilm demonstrate partial inhibition 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO), suggesting exaquare-like may contribute nitrification situ. CARD-FISH-MAR showed no incorporation Thaumarchaeaota, incorporate non-bicarbonate carbon sources rely on an alternative yet unknown metabolism.

Язык: Английский

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