Yan Zheng

Bio: Yan Zheng is an academic researcher from Zhengzhou University of Light Industry. The author has contributed to research in topics: Stable-isotope probing & Anaerobic oxidation of methane. The author has an hindex of 5, co-authored 7 publications receiving 241 citations. Previous affiliations of Yan Zheng include Chinese Academy of Sciences.

Conventional methanotrophs are responsible for atmospheric methane oxidation in paddy soils.

Abstract: Soils serve as the biological sink of the potent greenhouse gas methane with exceptionally low concentrations of ∼1.84 p.p.m.v. in the atmosphere. The as-yet-uncultivated methane-consuming bacteria have long been proposed to be responsible for this 'high-affinity' methane oxidation (HAMO). Here we show an emerging HAMO activity arising from conventional methanotrophs in paddy soil. HAMO activity was quickly induced during the low-affinity oxidation of high-concentration methane. Activity was lost gradually over 2 weeks, but could be repeatedly regained by flush-feeding the soil with elevated methane. The induction of HAMO activity occurred only after the rapid growth of methanotrophic populations, and a metatranscriptome-wide association study suggests that the concurrent high- and low-affinity methane oxidation was catalysed by known methanotrophs rather than by the proposed novel atmospheric methane oxidizers. These results provide evidence of atmospheric methane uptake in periodically drained ecosystems that are typically considered to be a source of atmospheric methane.

Competitive interactions between methane- and ammonia-oxidizing bacteria modulate carbon and nitrogen cycling in paddy soil

Abstract: . Pure culture studies have demonstrated that methanotrophs and ammonia oxidizers can both carry out the oxidation of methane and ammonia. However, the expected interactions resulting from these similarities are poorly understood, especially in complex, natural environments. Using DNA-based stable isotope probing and pyrosequencing of 16S rRNA and functional genes, we report on biogeochemical and molecular evidence for growth stimulation of methanotrophic communities by ammonium fertilization, and that methane modulates nitrogen cycling by competitive inhibition of nitrifying communities in a rice paddy soil. Pairwise comparison between microcosms amended with CH4, CH4+Urea, and Urea indicated that urea fertilization stimulated methane oxidation activity 6-fold during a 19-day incubation period, while ammonia oxidation activity was significantly suppressed in the presence of CH4. Pyrosequencing of the total 16S rRNA genes revealed that urea amendment resulted in rapid growth of Methylosarcina-like MOB, and nitrifying communities appeared to be partially inhibited by methane. High-throughput sequencing of the 13C-labeled DNA further revealed that methane amendment resulted in clear growth of Methylosarcina-related MOB while methane plus urea led to an equal increase in Methylosarcina and Methylobacter-related type Ia MOB, indicating the differential growth requirements of representatives of these genera. An increase in 13C assimilation by microorganisms related to methanol oxidizers clearly indicated carbon transfer from methane oxidation to other soil microbes, which was enhanced by urea addition. The active growth of type Ia methanotrops was significantly stimulated by urea amendment, and the pronounced growth of methanol-oxidizing bacteria occurred in CH4-treated microcosms only upon urea amendment. Methane addition partially inhibited the growth of Nitrosospira and Nitrosomonas in urea-amended microcosms, as well as growth of nitrite-oxidizing bacteria. These results suggest that type I methanotrophs can outcompete type II methane oxidizers in nitrogen-rich environments, rendering the interactions among methane and ammonia oxidizers more complicated than previously appreciated.

Active ammonia oxidizers in an acidic soil are phylogenetically closely related to neutrophilic archaeon.

Abstract: All cultivated ammonia-oxidizing archaea (AOA) within the Nitrososphaeracluster (former soil group 1.1b) are neutrophilic. Molecular surveys also indicate the existence of Nitrososphaera-like phylotypes in acidic soil, but their ecological roles are poorly understood. In this study, we present molecular evidence for the chemolithoautotrophic growth of Nitrososphaera-like AOA in an acidic soil with pH 4.92 using DNA-based stable isotope probing (SIP). Soil microcosm incubations demonstrated that nitrification was stimulated by urea fertilization and accompanied by a significant increase in the abundance of AOA rather than ammonia-oxidizing bacteria (AOB). Real-time PCR analysis of amoAgenes as a function of the buoyant density of the DNA gradient following the ultracentrifugation of the total DNA extracted from SIP microcosms indicated a substantial growth of soil AOA during nitrification. Pyrosequencing of the total 16S rRNA genes in the “heavy” DNA fractions suggested that archaeal communities were labeled to a much greater extent than soil AOB. Acetylene inhibition further showed that 13 CO2assimilation by nitrifying communities depended solely on ammonia oxidation activity, suggesting a chemolithoautotrophic lifestyle. Phylogenetic analysis of both 13 C-labeledamoAand 16S rRNA genes revealed that most of the active AOA were phylogenetically closely related to the neutrophilic strains Nitrososphaera viennensis EN76 and JG1 within the Nitrososphaera cluster. Our results provide strong evidence for the adaptive growth of Nitrososphaera-like AOA in acidic soil, suggesting a greater metabolic versatility of soil AOA than previously appreciated.

Conversion of upland to paddy field specifically alters the community structure of archaeal ammonia oxidizers in an acid soil

Abstract: The function of ammonia-oxidizing archaea (AOA) and bacteria (AOB) depends on the major energy-generating compounds (i.e., ammonia and oxygen). The diversification of AOA and AOB communities along ecological gradients of substrate availability in a complex environment have been much debated but rarely tested. In this study, two ecosystems of maize and rice crops under different fertilization regimes were selected to investigate the community diversification of soil AOA and AOB upon conversion of an upland field to a paddy field and long-term field fertilization in an acid soil. Real-time quantitative polymerase chain reaction of ammonia monooxygenase ( amoA ) genes demonstrated that the abundance of AOA was significantly stimulated after conversion of upland to paddy soils for more than 100 yr, whereas a slight decline in AOB numbers was observed. Denaturing gradient gel electrophoresis fingerprints of amoA genes further revealed remarkable changes in the community compositions of AOA after conversion of aerobic upland to flooded paddy field. Sequencing analysis revealed that upland soil was dominated by AOA within the soil group 1.1b lineage, whereas the marine group 1.1a-associated lineage predominated in AOA communities in paddy soils. Irrespective of whether the soil was upland or paddy soil, long-term field fertilization led to increased abundance of amoA genes in AOA and AOB compared with control treatments (no fertilization), whereas archaeal amoA gene abundances outnumbered their bacterial counterparts in all samples. Phylogenetic analyses of amoA genes showed that Nitrosospira cluster-3-like AOB dominated bacterial ammonia oxidizers in both paddy and upland soils, regardless of fertilization treatment. The results of this study suggest that the marine group 1.1a-associated AOA will be better adapted to the flooded paddy field than AOA ecotypes of the soil group 1.1b lineage, and indicate that long-term flooding is the dominant selective force driving the community diversification of AOA populations in the acid soil tested.

Stable isotope probing of active methane oxidizers in rice field soils from cold regions

Abstract: DNA-based stable isotope probing (DNA-SIP) was employed to establish direct link between methane oxidation activity and the taxonomic identity of active methanotrophs in three rice field soils from Jian-San-Jiang (one baijiang origin soil, JB and one meadow origin soil, JM) and Qing-An (meadow origin soil, QA) districts in Northeastern China. Following microcosm incubation under 1% v/v13CH4 condition, soil organic 13C atom percent significantly increased from background 1.08 to 1.21% in average, indicating the biomass synthesis supported by methanotrophy. Real-time PCR analysis of methanotroph-specific biomarker pmoA genes of the buoyant density for DNA gradient, following the ultracentrifugation of the total DNA extracted from SIP microcosms, indicated an enrichment of methanotroph genomes in 13C-labeled DNA. It suggested propagation of microbial methane oxidizers in soils. High-throughput sequencing of 16S rRNA and pmoA genes from 13C-labeled DNA further revealed a diverse guild of both type I and II methanotrophs in all three soils. Specifically, Methylobacter-affiliated type I methanotrophs dominated the methanotrophic activity in JB and JM soils, whereas Methylocystis-affiliated type II methanotrophs dominated QA soil. This implied the physiological diversification of soil methanotrophs that might be due to constant environmental fluctuations in paddies.

Nitrification and nitrifiers in acidic soils

Abstract: Nitrification, as a crucial step in nitrogen cycling and plant nutrition, is a biologically mediated process responsible for enormous losses of nitrogen fertilizer and a contributor to environmental pollution. The recent progress in our understanding of nitrification and nitrifiers, specifically in acidic soils, is discussed and reviewed. At one time it was assumed that rates of nitrification are relatively low in acidic soils. However, more recent studies have demonstrated nitrification down to pH 3.0 and that the rate of nitrification can equal, or even exceed, that found in neutral soils. Studies on acidic forest soils in Europe noted that they have a high potential for nitrate production. Furthermore, using the 15N isotope-dilution technique it was shown that net nitrification measurements can markedly underestimate gross nitrification in these natural and highly organic systems. Using selective inhibitors it has been demonstrated that heterotrophic nitrifiers can contribute to nitrification. While heterotrophic nitrification can be performed by a wide range of bacteria and fungi, inhibitor studies point to fungi to be mainly responsible. Autotrophic ammonia-oxidizing bacteria (AOB), such as Nitrosomonas and Nitrosospira, have been known for some considerable time but have generally found to be inactive in acidic conditions. The discovery of ammonia monooxygenase in uncultured archaea that were functionally active at low pH pointed to an autotrophic microbial group (ammonia oxidizing archaea, AOA) that might be adapted to low substrate (ammonia) concentrations and responsible for nitrification in the wider range of acidic grassland and cultivated soils. Obligately acidophilic AOA have more recently been cultivated while stable isotope probing has been used to confirm the dominance of AOA over AOB in acidic soils. Detailed molecular studies using both 16S rRNA and amoA (ammonia monooxygenase sub-unit A) gene sequencing are continuing to expand our appreciation of the diversity of both AOB and AOA and how this varies over different pH ranges and in different ecosystems. Similar work is being directed towards nitrite oxidizing bacteria (NOB) but to date we do not fully know the role of pH in controlling NOB activity. Such understanding of nitrification and nitrifiers will help develop new effective nitrification inhibitors and aid the management of nitrogen cycling in acidic soils.

Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes.

Abstract: Ammonia-oxidising archaea (AOA) are ubiquitous and abundant in nature and play a major role in nitrogen cycling. AOA have been studied intensively based on the amoA gene (encoding ammonia monooxygenase subunit A), making it the most sequenced functional marker gene. Here, based on extensive phylogenetic and meta-data analyses of 33,378 curated archaeal amoA sequences, we define a highly resolved taxonomy and uncover global environmental patterns that challenge many earlier generalisations. Particularly, we show: (i) the global frequency of AOA is extremely uneven, with few clades dominating AOA diversity in most ecosystems; (ii) characterised AOA do not represent most predominant clades in nature, including soils and oceans; (iii) the functional role of the most prevalent environmental AOA clade remains unclear; and (iv) AOA harbour molecular signatures that possibly reflect phenotypic traits. Our work synthesises information from a decade of research and provides the first integrative framework to study AOA in a global context.

Conventional methanotrophs are responsible for atmospheric methane oxidation in paddy soils.

Abstract: Soils serve as the biological sink of the potent greenhouse gas methane with exceptionally low concentrations of ∼1.84 p.p.m.v. in the atmosphere. The as-yet-uncultivated methane-consuming bacteria have long been proposed to be responsible for this 'high-affinity' methane oxidation (HAMO). Here we show an emerging HAMO activity arising from conventional methanotrophs in paddy soil. HAMO activity was quickly induced during the low-affinity oxidation of high-concentration methane. Activity was lost gradually over 2 weeks, but could be repeatedly regained by flush-feeding the soil with elevated methane. The induction of HAMO activity occurred only after the rapid growth of methanotrophic populations, and a metatranscriptome-wide association study suggests that the concurrent high- and low-affinity methane oxidation was catalysed by known methanotrophs rather than by the proposed novel atmospheric methane oxidizers. These results provide evidence of atmospheric methane uptake in periodically drained ecosystems that are typically considered to be a source of atmospheric methane.

pH regulates key players of nitrification in paddy soils

Abstract: Increasing lines of evidence have suggested the functional importance of ammonia-oxidizing archaea (AOA) rather than bacteria (AOB) for nitrification in upland soils with low pH. However, it remains unclear whether niche specialization of AOA and AOB occurs in rice paddy wetlands constrained by oxygen availability. Using DNA-based stable isotope probing, we conclude that AOA dominated nitrification activity in acidic paddy soils (pH 5.6) while AOB dominated in alkaline soils (pH 8.2). Nitrification activity was stimulated by urea fertilization and accompanied by a significant increase of AOA in acid soils and AOB in alkaline soils. DNA-based stable isotope probing indicated significant assimilation of 13 CO 2 for AOA only in acidic paddy soil, while AOB was the solely responsible for ammonia oxidation in the alkaline paddy soil. Phylogenetic analysis further indicated that AOA members within the soil group 1.1b lineage dominated nitrification in acid soils. Ammonia oxidation in the alkaline soil was catalyzed by Nitrosospira cluster 3-like AOB, suggesting that the physiological diversity of AOA is more complicated than previously thought, and soil pH plays important roles in shaping the community structures of ammonia oxidizers in paddy field.

Ammonia oxidation: Ecology, physiology, biochemistry and why they must all come together.

Abstract: Ammonia oxidation is a fundamental core process in the global biogeochemical nitrogen cycle. Oxidation of ammonia (NH3) to nitrite (NO2 −) is the first and rate-limiting step in nitrification and is carried out by distinct groups of microorganisms. Ammonia oxidation is essential for nutrient turnover in most terrestrial, aquatic and engineered ecosystems and plays a major role, both directly and indirectly, in greenhouse gas production and environmental damage. Although ammonia oxidation has been studied for over a century, this research field has been galvanised in the past decade by the surprising discoveries of novel ammonia oxidising microorganisms. This review reflects on the ammonia oxidation research to date and discusses the major gaps remaining in our knowledge of the biology of ammonia oxidation.