Biogeochemistry of paddy soils

Geoderma, Год журнала: 2010, Номер 157(1-2), С. 1 - 14

Опубликована: Апрель 11, 2010

Язык: Английский

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Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil

Environmental Microbiology, Год журнала: 2009, Номер 11(7), С. 1658 - 1671

Опубликована: Фев. 20, 2009

Agricultural ecosystems annually receive approximately 25% of the global nitrogen input, much which is oxidized at least once by ammonia-oxidizing prokaryotes to complete cycle. Recent discoveries have expanded known from domain Bacteria Archaea. However, in complex soil environment it remains unclear whether ammonia oxidation exclusively or predominantly linked Archaea as implied their exceptionally high abundance. Here we show that rather than functionally dominate an agricultural soil, despite fact archaeal versus bacterial amoA genes are numerically more dominant. In microcosms, was stimulated ammonium and inhibited acetylene, activity change paralleled abundance but not gene copy numbers. Molecular fingerprinting also coupled with patterns. DNA-stable isotope probing demonstrated CO(2) assimilation Our results indicate were important for tested.

Язык: Английский

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Nitrososphaera viennensis , an ammonia oxidizing archaeon from soil

Proceedings of the National Academy of Sciences, Год журнала: 2011, Номер 108(20), С. 8420 - 8425

Опубликована: Апрель 27, 2011

Genes of archaea encoding homologues ammonia monooxygenases have been found on a widespread basis and in large amounts almost all terrestrial marine environments, indicating that oxidizing (AOA) might play major role nitrification Earth. However, only one pure isolate this group from environment has so far obtained, demonstrating archaeal oxidation coupled with autotrophic growth similar to the bacterial counterparts. Here we describe cultivation isolation an AOA soil. It grows or urea as energy source is capable using higher concentrations than isolate, Nitrosopumilus maritimus . Surprisingly, although it able grow chemolithoautotrophically, considerable rates strain are obtained upon addition low pyruvate when grown coculture bacteria. Our findings expand recognized metabolic spectrum help explain controversial results past activity carbon assimilation these globally distributed organisms.

Язык: Английский

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Environmental factors shaping the ecological niches of ammonia-oxidizing archaea

FEMS Microbiology Reviews, Год журнала: 2009, Номер 33(5), С. 855 - 869

Опубликована: Апрель 21, 2009

For more than 100 years it was believed that bacteria were the only group responsible for oxidation of ammonia. However, recently, a new strain archaea bearing putative ammonia monooxygenase subunit A (amoA) gene and able to oxidize isolated from marine aquarium tank. Ammonia-oxidizing (AOA) subsequently discovered in many ecosystems varied characteristics even found as predominant causal organisms some environments. Here, we summarize current knowledge on environmental conditions related presence AOA discuss possible site-related properties. Considering these data, deduct niches based pH, sulfide phosphate levels. It is proposed might be important actors within nitrogen cycle low-nutrient, low-pH, sulfide-containing

Язык: Английский

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Diversity, Physiology, and Niche Differentiation of Ammonia-Oxidizing Archaea

Applied and Environmental Microbiology, Год журнала: 2012, Номер 78(21), С. 7501 - 7510

Опубликована: Авг. 25, 2012

Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, has been suggested have a central part global biogeochemical nitrogen cycle since oxygenation Earth. The cultivation several ammonia-oxidizing archaea (AOA) as well discovery that archaeal monooxygenase (amo)-like gene sequences are nearly ubiquitously distributed in environment and outnumber their bacterial counterparts many habitats fundamentally revised our understanding nitrification. Surprising insights into physiological distinctiveness AOA mirrored by recognition phylogenetic uniqueness these microbes, which fall within novel phylum now known Thaumarchaeota. relative importance nitrification, compared bacteria (AOB), is still under debate. This minireview provides synopsis current knowledge diversity physiology AOA, factors controlling ecology, role carbon cycling potential involvement production greenhouse gas nitrous oxide. It emphasizes activity-based analyses studies formulates priorities for future research.

Язык: Английский

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Ammonia-oxidizing bacteria and archaea grow under contrasting soil nitrogen conditions

FEMS Microbiology Ecology, Год журнала: 2010, Номер 72(3), С. 386 - 394

Опубликована: Март 8, 2010

Nitrification is a key process of the nitrogen (N) cycle in soil with major environmental implications. The recent discovery ammonia-oxidizing archaea (AOA) questions traditional assumption dominant role bacteria (AOB) nitrification. We investigated AOB and AOA growth nitrification rate two different layers three grassland soils treated animal urine substrate inhibitor [dicyandiamide (DCD)]. show that were more abundant topsoils than subsoils, whereas one subsoils. grew substantially when supplied high dose substrate, only Controls without urine-N substrate. amoA gene transcription activity significantly inhibited by DCD. rates much higher subsoils related to abundance, but not abundance. These results suggest prefer N conditions grow: under ammonia (NH3) low NH3 conditions.

Язык: Английский

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The rhizosphere zoo: An overview of plant-associated communities of microorganisms, including phages, bacteria, archaea, and fungi, and of some of their structuring factors

Plant and Soil, Год журнала: 2009, Номер 321(1-2), С. 189 - 212

Опубликована: Апрель 27, 2009

Язык: Английский

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Niche specialization of terrestrial archaeal ammonia oxidizers

Proceedings of the National Academy of Sciences, Год журнала: 2011, Номер 108(52), С. 21206 - 21211

Опубликована: Дек. 8, 2011

Soil pH is a major determinant of microbial ecosystem processes and potentially driver evolution, adaptation, diversity ammonia oxidizers, which control soil nitrification. Archaea are components communities contribute significantly to oxidation in some soils. To determine whether drives evolutionary adaptation community structure archaeal sequences amoA, key functional gene oxidation, were examined soils at global, regional, local scales. Globally distributed database clustered into 18 well-supported phylogenetic lineages that dominated specific ranges classified as acidic (pH <5), acido-neutral (5 ≤ <7), or alkalinophilic ≥ 7). patterns reproduced regional scales, amoA fragments amplified from DNA extracted 47 the United Kingdom 3.5-8.7), including pH-gradient formed by seven single site 4.5-7.5). High-throughput sequencing analysis identified an additional, previously undiscovered lineage revealed similar pH-associated distribution most evident for five abundant clusters. Archaeal abundance increased with pH, was only physicochemical characteristic measured influenced structure. These results suggest evolution based on adaptations niche specialization, resulting global have important consequences function nitrogen cycling.

Язык: Английский

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Links between Ammonia Oxidizer Community Structure, Abundance, and Nitrification Potential in Acidic Soils

Applied and Environmental Microbiology, Год журнала: 2011, Номер 77(13), С. 4618 - 4625

Опубликована: Май 14, 2011

Ammonia oxidation is the first and rate-limiting step of nitrification performed by both ammonia-oxidizing archaea (AOA) bacteria (AOB). However, environmental drivers controlling abundance, composition, activity AOA AOB communities are not well characterized, relative importance these two groups in soil still debated. Chinese tea orchard soils provide an excellent system for investigating long-term effects low pH nitrogen fertilization strategies. abundance community composition were therefore investigated adjacent pine forest soils, using quantitative PCR (qPCR), terminal restriction fragment length polymorphism (T-RFLP) sequence analysis respective ammonia monooxygenase (amoA) genes. There was strong evidence that important factor but ratio to amoA gene increased with decreasing soils. In contrast, T-RFLP suggested a key explanatory variable structure, significant relationship between potential observed only AOA. High rates indicated mainly driven acidic Dominant sequences highly all placed within specific clade, one genotype appears be adapted growth Specific populations dominated at particular values N content, suggesting adaptation niches.

Язык: Английский

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AmoA-Targeted Polymerase Chain Reaction Primers for the Specific Detection and Quantification of Comammox Nitrospira in the Environment

Frontiers in Microbiology, Год журнала: 2017, Номер 8

Опубликована: Авг. 4, 2017

Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered be catalyzed by concerted activity ammonia- and nitrite-oxidizing microorganisms. Only recently, complete oxidizers ('comammox'), which oxidize nitrate on their own, were identified in bacterial genus Nitrospira, previously assumed contain only canonical oxidizers. Nitrospira are widespread nature, but for assessments distribution functional importance comammox ecosystems, cultivation-independent tools distinguish from strictly required. Here we developed new PCR primer sets that specifically target amoA genes coding subunit A distinct monooxygenase Nitrospira. While existing primers capture a fraction known diversity, cover as much 95% clade 92% B sequences reference database containing 326 with sequence information at binding sites. Application 13 samples engineered systems (a groundwater well, drinking water treatment wastewater plants) other habitats (rice paddy forest soils, rice rhizosphere, brackish lake sediment freshwater biofilm) detected all revealed considerable diversity most habitats. Excellent specificity was achieved avoiding use highly degenerate preparations using equimolar mixtures oligonucleotides match genes. Quantitative these sensitive specific, enabled efficient quantification gene copy numbers environmental samples. The measured relative abundances compared oxidizers, variable across environments. amoA-targeted enable more encompassing future studies nitrifying microorganisms diverse For example, they may used monitor population dynamics uncultured organisms under changing conditions response altered treatments agricultural ecosystems.

Язык: Английский

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