Abundance Of Ammonia Oxidizers Research Articles

Abundance and community composition of ammonia oxidizers in rhizosphere sediment of two submerged macrophytes

ABSTRACTAmmonium oxidation is both the first and a rate-limiting step in the nitrification process that can be catalysed by ammonia-oxidizing archaea (AOA) or ammonia-oxidizing bacteria (AOB). In this study, the abundance and community composition of AOA and AOB in the rhizosphere sediments of two submerged macrophytes (Ceratophyllum demersum and Potamogeton malainus) were investigated. Physicochemical parameters, including pH, total nitrogen, total phosphorus, ammonia nitrogen, nitrate and organic matter, were measured. The number of copies of both the archaeal and bacterial amoA gene was quantified by real-time PCR and clone libraries were constructed for both AOA and AOB. The abundance of archaeal amoA gene ranged from 3.83 × 106 to 4.23 × 106 copies per gram of dry sediment and no significant difference was found among the three treatment groups (one control group and two submerged macrophyte groups). The abundance of bacterial amoA gene ranged from 2.68 × 106 to 8.05 × 107 copies per gram of dry sediment. Bulk sediment maintained significantly higher copy numbers of bacterial amoA gene than those of C. demersum rhizosphere sediment. The diversity of archaeal amoA gene was higher in the rhizosphere sediment of C. demersum; however, the diversity of bacterial amoA gene was relatively lower in rhizosphere sediment of both macrophytes.

Land-use change drives abundance and community structure alterations of thaumarchaeal ammonia oxidizers in tropical rainforest soils in Rondônia, Brazil

The Amazon Rainforest plays major roles in global carbon and nitrogen cycling. Despite this region’s immense importance, deforestation and pasture creation are still occurring at alarming rates. In this study, we investigated the effects of land-use change on aerobic ammonia-oxidizers in primary rainforest, young and old pasture, and secondary forest in Rondônia, Brazil. Forest-to-pasture conversion decreased soil nitrate, phosphorus, and exchangeable acidity contents that recovered to pre-disturbance levels as pastures aged or were abandoned and formed secondary forest. The ammonia-oxidizing community, numerically dominated by thaumarchaea, shifted due to land-use change, both in terms of gene abundance and community structure. However, thaumarchaeal ammonia monooxygenase gene abundances did not correlate with any measured soil physicochemial parameters. Phylogenetic analyses showed that community structural changes in ammonia-oxidizing thaumarchaea are driven by a shift away from primary rainforest, old pasture, and secondary forest clusters to separate clusters for young pasture. Additionally, the nearly complete disappearance in young pasture, old pasture, and secondary forest sites of a thaumarchaeal genus, the Nitrosotalea, indicates that land-use change can have long lasting effects on large portions of the thaumarchaeal community. The results of this study can be used as a conceptual foundation for determining how ammonia-oxidizers become altered by land-use change in South American tropical forests.

Organic Nitrogen-Driven Stimulation of Arbuscular Mycorrhizal Fungal Hyphae Correlates with Abundance of Ammonia Oxidizers.

Large fraction of mineral nutrients in natural soil environments is recycled from complex and heterogeneously distributed organic sources. These sources are explored by both roots and associated mycorrhizal fungi. However, the mechanisms behind the responses of arbuscular mycorrhizal (AM) hyphal networks to soil organic patches of different qualities remain little understood. Therefore, we conducted a multiple-choice experiment examining hyphal responses to different soil patches within the root-free zone by two AM fungal species (Rhizophagus irregularis and Claroideoglomus claroideum) associated with Medicago truncatula, a legume forming nitrogen-fixing root nodules. Hyphal colonization of the patches was assessed microscopically and by quantitative real-time PCR (qPCR) using AM taxon-specific markers, and the prokaryotic and fungal communities in the patches (pooled per organic amendment treatment) were profiled by 454-amplicon sequencing. Specific qPCR markers were then designed and used to quantify the abundance of prokaryotic taxa showing the strongest correlation with the pattern of AM hyphal proliferation in the organic patches as per the 454-sequencing. The hyphal density of both AM fungi increased due to nitrogen (N)-containing organic amendments (i.e., chitin, DNA, albumin, and clover biomass), while no responses as compared to the non-amended soil patch were recorded for cellulose, phytate, or inorganic phosphate amendments. Abundances of several prokaryotes, including Nitrosospira sp. (an ammonium oxidizer) and an unknown prokaryote with affiliation to Acanthamoeba endosymbiont, which were frequently recorded in the 454-sequencing profiles, correlated positively with the hyphal responses of R. irregularis to the soil amendments. Strong correlation between abundance of these two prokaryotes and the hyphal responses to organic soil amendments by both AM fungi was then confirmed by qPCR analyses using all individual replicate patch samples. Further research is warranted to ascertain the causality of these correlations and particularly which direct roles (if any) do these prokaryotes play in the observed AM hyphal responses to organic N amendment, organic N utilization by the AM fungus and its (N-unlimited) host plant. Further, possible trophic dependencies between the different players in the AM hyphosphere needs to be elucidated upon decomposing the organic N sources.

Irrigation water salinity and N fertilization: Effects on ammonia oxidizer abundance, enzyme activity and cotton growth in a drip irrigated cotton field

Use of saline water in irrigated agriculture has become an important means for alleviating water scarcity in arid and semi-arid regions. The objective of this field experiment was to evaluate the effects of irrigation water salinity and N fertilization on soil physicochemical and biological properties related to nitrification and denitrification. A 3×2 factorial design was used with three levels of irrigation water salinity (0.35, 4.61 and 8.04 dS m−1) and two N rates (0 and 360 kg N ha−1). The results indicated that irrigation water salinity and N fertilization had significant effects on many soil physicochemical properties including water content, salinity, pH, NH4-N concentration, and NO3-N concentration. The abundance (i.e., gene copy number) of ammonia-oxidizing archaea (AOA) was greater than that of ammonia-oxidizing bacteria (AOB) in all treatments. Irrigation water salinity had no significant effect on the abundance of AOA or AOB in unfertilized plots. However, saline irrigation water (i.e., the 4.61 and 8.04 dS m−1 treatments) reduced AOA abundance, AOB abundance and potential nitrification rate in N fertilized plots. Regardless of N application rate, saline irrigation water increased urease activity but reduced the activities of both nitrate reductase and nitrite reductase. Irrigation with saline irrigation water significantly reduced cotton biomass, N uptake and yield. Nitrogen application exacerbated the negative effect of saline water. These results suggest that brackish water and saline water irrigation could significantly reduce both the abundance of ammonia oxidizers and potential nitrification rates. The AOA may play a more important role than AOB in nitrification in desert soil.

Effects of different fertilizers on the abundance and community structure of ammonia oxidizers in a yellow clay soil.

Yellow clay paddy soil (Oxisols) is a typical soil with low productivity in southern China. Nitrification inhibitors and slow release fertilizers have been used to improve nitrogen fertilizer utilization and reduce environmental impaction of the paddy soil. However, their effects on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in paddy soil have rarely been investigated. In the present work, we compared the influences of several slow release fertilizers and nitrification inhibitors on the community structure and activities of the ammonia oxidizers in yellow clay soil. The abundances and community compositions of AOA and AOB were determined with qPCR, terminal restriction fragment length polymorphism (T-RFLP), and clone library approaches. Our results indicated that the potential nitrification rate (PNR) of the soil was significantly related to the abundances of both AOA and AOB. Nitrogen fertilizer application stimulated the growth of AOA and AOB, and the combinations of nitrapyrin with urea (NPU) and urea-formaldehyde (UF) inhibited the growth of AOA and AOB, respectively. Compared with other treatments, the applications of NPU and UF also led to significant shifts in the community compositions of AOA and AOB, respectively. NPU showed an inhibitory effect on AOA T-RF 166bp that belonged to Nitrosotalea. UF had a negative effect on AOB T-RF 62bp that was assigned to Nitrosospira. These results suggested that NPU inhibited PNR and increased nitrogen use efficiency (NUE) by inhibiting the growth of AOA and altering AOA community. UF showed no effect on NUE but decreased AOB abundance and shifted AOB community.

Plant species diversity affects soil-atmosphere fluxes of methane and nitrous oxide.

Plant diversity effects on ecosystem functioning can potentially interact with global climate by altering fluxes of the radiatively active trace gases nitrous oxide (N2O) and methane (CH4). We studied the effects of grassland species richness (1-16) in combination with application of fertilizer (nitrogen:phosphorus:potassium=100:43.6:83kgha(-1)a(-1)) on N2O and CH4 fluxes in a long-term field experiment. Soil N2O emissions, measured over 2years using static chambers, decreased with species richness unless fertilizer was added. N2O emissions increased with fertilization and the fraction of legumes in plant communities. Soil CH4 uptake, a process driven by methanotrophic bacteria, decreased with plant species numbers, irrespective of fertilization. Using structural equation models, we related trace gas fluxes to soil moisture, soil inorganic N concentrations, nitrifying and denitrifying enzyme activity, and the abundance of ammonia oxidizers, nitrite oxidizers, and denitrifiers (quantified by real-time PCR of gene fragments amplified from microbial DNA in soil). These analyses indicated that plant species richness increased soil moisture, which in turn increased N cycling-related activities. Enhanced N cycling increased N2O emission and soil CH4 uptake, with the latter possibly caused by removal of inhibitory ammonium by nitrification. The moisture-related indirect effects were surpassed by direct, moisture-independent effects opposite in direction. Microbial gene abundances responded positively to fertilizer but not to plant species richness. The response patterns we found were statistically robust and highlight the potential of plant biodiversity to interact with climatic change through mechanisms unrelated to carbon storage and associated carbon dioxide removal.

Nitrification and its influence on biogeochemical cycles from the equatorial Pacific to the Arctic Ocean.

We examined nitrification in the euphotic zone, its impact on the nitrogen cycles, and the controlling factors along a 7500 km transect from the equatorial Pacific Ocean to the Arctic Ocean. Ammonia oxidation occurred in the euphotic zone at most of the stations. The gene and transcript abundances for ammonia oxidation indicated that the shallow clade archaea were the major ammonia oxidizers throughout the study regions. Ammonia oxidation accounted for up to 87.4% (average 55.6%) of the rate of nitrate assimilation in the subtropical oligotrophic region. However, in the shallow Bering and Chukchi sea shelves (bottom ⩽67 m), the percentage was small (0–4.74%) because ammonia oxidation and the abundance of ammonia oxidizers were low, the light environment being one possible explanation for the low activity. With the exception of the shallow bottom stations, depth-integrated ammonia oxidation was positively correlated with depth-integrated primary production. Ammonia oxidation was low in the high-nutrient low-chlorophyll subarctic region and high in the Bering Sea Green Belt, and primary production in both was influenced by micronutrient supply. An ammonium kinetics experiment demonstrated that ammonia oxidation did not increase significantly with the addition of 31–1560 nm ammonium at most stations except in the Bering Sea Green Belt. Thus, the relationship between ammonia oxidation and primary production does not simply indicate that ammonia oxidation increased with ammonium supply through decomposition of organic matter produced by primary production but that ammonia oxidation might also be controlled by micronutrient availability as with primary production.

Geographic Distribution of Archaeal Ammonia Oxidizing Ecotypes in the Atlantic Ocean.

In marine ecosystems, Thaumarchaeota are most likely the major ammonia oxidizers. While ammonia concentrations vary by about two orders of magnitude in the oceanic water column, archaeal ammonia oxidizers (AOA) vary by only one order of magnitude from surface to bathypelagic waters. Thus, the question arises whether the key enzyme responsible for ammonia oxidation, ammonia monooxygenase (amo), exhibits different affinities to ammonia along the oceanic water column and consequently, whether there are different ecotypes of AOA present in the oceanic water column. We determined the abundance and phylogeny of AOA based on their amoA gene. Two ecotypes of AOA exhibited a distribution pattern reflecting the reported availability of ammonia and the physico-chemical conditions throughout the Atlantic, and from epi- to bathypelagic waters. The distinction between these two ecotypes was not only detectable at the nucleotide level. Consistent changes were also detected at the amino acid level. These changes include substitutions of polar to hydrophobic amino acid, and glycine substitutions that could have an effect on the configuration of the amo protein and thus, on its activity. Although we cannot identify the specific effect, the ratio of non-synonymous to synonymous substitutions (dN/dS) between the two ecotypes indicates a strong positive selection between them. Consequently, our results point to a certain degree of environmental selection on these two ecotypes that have led to their niche specialization.

Relationships between ammonia-oxidizing communities, soil methane uptake and nitrous oxide fluxes in a subtropical plantation soil with nitrogen enrichment

Ammonia-oxidizers play an essential role in nitrogen (N) transformation and nitrous oxide (N2O) emission in forest soils. It remains unclear if ammonia-oxidizers affect interaction between methane (CH4) uptake and N2O emission. Our specific goal was to test the impacts of changes in ammonia-oxidizing communities elicited by N enrichment on soil CH4 uptake and N2O emission. Based on a field experiment, two-forms (NH4Cl and NaNO3) and two levels (40 and 120 kg N ha−1 yr−1) of N were applied in the subtropical plantation forest of southern China. Soil CH4 and N2O fluxes, the abundance and structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities were measured using static chamber-gas chromatography, quantitative PCR (qPCR), and terminal-restriction fragment length polymorphism (T-RFLP). Nitrogen addition tended to inhibit soil CH4 uptake, but significantly promoted soil N2O emission; moreover, these impacts were more significant with NH4+−N than with NO3−−N addition. NH4Cl addition significantly changed ammonia-oxidizer abundance with an increase in AOA and a decrease in AOB. Nitrogen additions significantly decreased the relative abundance of 329 bp and 421 bp of archaeal amoA gene. Negative relationships occurred between soil CH4 uptake and AOA abundance and between soil CH4 uptake and AOA/AOB ratio; however, a positive relationship was found between soil N2O emission and AOA abundance. These results indicate that a shift in abundance and composition of ammonia-oxidizing communities is closely linked to changes in soil CH4 uptake and N2O emission under N enrichment. Furthermore, AOA communities play a contrasting role from AOB communities for regulating the fluctuation between soil CH4 and N2O fluxes.

Short-term impact of soybean management on ammonia oxidizers in a Brazilian savanna under restoration as revealed by coupling different techniques

Interactions between soil characteristics and soil microbiota influence soil ecosystem processes such as nitrification however, their complexity makes interpretation difficult. Furthermore, the impact of soil management systems on abundance and activity of soil microbial community is poorly understood, especially in the Neotropics. To investigate these interactions, the effects of tillage, inorganic fertilization, and plant cover on the abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were assessed by quantification of the marker gene (amoA) during different stages of soybean cultivation in a site under restoration from gravel extraction in the Central Brazilian Savanna (Cerrado). Results of molecular analysis and classic and isotope techniques showed that levels of organic C and NH4 +–N were higher in the soybean field during fallow than in an adjacent undisturbed field (Campo sujo). Ammonia oxidizer abundance and nitrification rates were also higher in the agricultural soil than in the undisturbed site, with the lowest ammonium/nitrate ratio in tilled soil. Soil δ15N was lower in the undisturbed soil than the agricultural soil. Both AOA and AOB were more abundant during soybean crop transitional stages, and this increase positively correlated with soil pH, particularly for AOB abundance, in tilled soil and within the soybean rhizosphere. The results suggest that AOB have more copiotrophic characteristics than AOA and are better able to change available ammonium in the soil. The combination of standard soil ecological methods and modern molecular analysis show the short-term modification of ammonia oxidizer abundance and soil N dynamics in a managed system within the Cerrado biome.

Effect of the conversion of conventional pasture to intensive silvopastoral systems on edaphic bacterial and ammonia oxidizer communities in Colombia

Colombia, as well as many tropical countries, has experienced severe deforestation in the last decades, and millions of acres of native forest areas (F) have been replaced by conventional monoculture pastures (CP), contributing to ecological and soil degradation. In response, multi-canopy intensive silvopastoral systems (ISS), which includes herbs, shrubs and trees, have been developed to provide local fodder sources for livestock while reducing the need for external inputs with a goal to conserve landscapes and improve soil quality. However, there is limited information on the temporal responsiveness of ISS to deliver ecosystem services as reflected in soil microbial properties. Therefore, the objective of this study was to examine the shifts of total and ammonia-oxidizing bacteria (AOB) communities along an ISS chronosequence (ranging from 3 to 15 years since establishment), in comparison to CP and native F and investigate P. juliflora trees as a resource island relative to soil microbial properties. Denaturing gradient gel electrophoresis (DGGE) fingerprints of 16S rRNA gene (total bacteria) as well as amoA gene (ammonia-oxidizing bacteria) (AOB) indicated that soil bacterial communities varied between the land uses, with higher similarities between F and ISS communities, in comparison to CP. The abundance and nitrification potential of ammonia oxidizers were significantly higher in CP and lower in F. In addition, the bacterial communities across ISS chronosequence were more similar between older (ISS-12) and intermediate (ISS-8) systems in comparison with youngest systems (ISS-3). Finally, the canopy of P. juliflora tree did not have an impact on structure of total bacterial community; though, it did have an effect on the structure of AOB communities. Our study suggests that ISS might restore some of the ecosystem services offered by soil microbial communities.

Factors influencing nitrification rates and the abundance and transcriptional activity of ammonia‐oxidizing microorganisms in the dark northeast P acific O cean

Pelagic marine Thaumarchaea play a primary role in ammonia oxidation, an integral part of nitrification and the nitrogen cycle. This study examines how physicochemical and biological variables influence rates of nitrification and the distribution, abundance and activity of ammonia oxidizers throughout the dark northeast Pacific Ocean. Nitrification rates are highest near the epipelagic-upper mesopelagic transition and decrease with depth according to a Martin-like power function, suggestive of a coupling to the organic matter flux. In contrast, archaeal and bacterial ammonia monooxygenase (amoA) gene abundance remains fairly constant throughout the upper mesopelagic. Density-based composites reveal nitrification to be highest in the upper pycnocline, within the nitrate:silica and ammonium maxima, while ammonia-oxidizing archaea (AOA) abundances are highest in the lower pycnocline. Water column group A (WCA) and B (WCB) AOA amoA genes are present throughout the dark ocean but have no relationship to nitrification rates. WCA comprise the majority of the AOA community above 200 m and WCB comprise the majority of it below 500 m, largely because WCA abundances decrease precipitously from 200 m to 500 m. WCA and WCB amoA genes are actively transcribed throughout the dark ocean, irrespective of conditions. Thaumarchaeal urease (ureC) genes are also present throughout, implying a widespread capacity for mixotrophy; however, unlike amoA, their expression is not detectable. Together, the results support a strong linkage between organic matter flux and nitrification rates, identify density as an important control over AOA distributions, and suggest that WCA and WCB distributions are influenced by the availability of their preferred substrates in the dark ocean.

Effect of chemical fertilization and green manure on the abundance and community structure of ammonia oxidizers in a paddy soil

Ammonia oxidization is a critical step in the soil N cycle and can be affected by the fertilization regimes. Chinese milk-vetch (Astragalus sinicus L., MV) is a major green manure of rice (Oryza sativa L.) fields in southern China, which is recommended as an important agronomic practice to improve soil fertility. Soil chemical properties, abundance and community structures of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in a MV-rice rotation field under different fertilization regimes were investigated. The field experiment included six treatments: control, without MV and chemical fertilizer (CK); 100% chemical fertilizer (NPK); 18 000 kg MV ha-1 plus 100% chemical fertilizer (NPKM1); 18 000 kg MV ha-1 plus 40% chemical fertilizer (NPKM2); 18 000 kg MV ha-1 alone (MV); and 18 000 kg MV ha-1 plus 40% chemical fertilizer plus straw (NPKMS). Results showed that NPKMS treatment could improve the soil fertility greatly although the application of 60% chemical fertilizer. The abundance of AOB only in the MV treatment had significant difference with the control; AOA were more abundant than AOB in all corresponding treatments. The NPKMS treatment had the highest AOA abundance (1.19 x 108 amoA gene copies g-1) and the lowest abundance was recorded in the CK treatment (3.21 x 107 amoA gene copies g-1). The abundance of AOA was significantly positively related to total N, available N, NH4+-N, and NO3--N. The community structure of AOA exhibited little variation among different fertilization regimes, whereas the community structure of AOB was highly responsive. Phylogenetic analysis showed that all AOB sequences were affiliated with Nitrosospira or Nitrosomonas and all AOA denaturing gradient gel electrophoresis (DGGE) bands belonged to the soil and sediment lineage. These findings could be fundamental to improve our understanding of AOB and AOA in the N cycle in the paddy soil.

Macrophyte landscape modulates lake ecosystem-level nitrogen losses through tightly coupled plant-microbe interactions

Root functional diversity of submerged vegetation exerts a major effect on nitrogen (N) cycling in lake sediments. This fact, however, is neglected in current N-balance models because the links between the engineering role of plants and in situ microbial N cycling are poorly understood. We hypothesized that macrophyte species with high root oxygen loss (ROL) capacity promote the highest denitrification because of a higher abundance of ammonia oxidizers and tighter coupling between nitrifiers and denitrifier communities. We sampled five small ultraoligotrophic shallow lakes with abundant macrophyte cover including sediments dominated either by Isoetes spp. (high ROL), mixed communities of natopotamids (low ROL), and unvegetated sandy sediments. At each site, we quantified denitrification (DNT) rates and proxies for the abundance of denitrifiers (nirS and nirK genes), and both ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) and the diversity of nirS-harboring bacteria. Vegetated sediments showed significantly higher abundances of N-cycling genes than bare sediments. Plant communities dominated by Isoetes generated sediments with higher redox and NO3− concentrations and significantly higher DNT rates than natopotamids-dominated landscapes. Accordingly, increasing DNT rates were observed along the gradient from low ROL plants-bare sediments-high ROL plants. Significantly higher abundance of the archaeal amoA gene was recorded in sediments colonized by high ROL plants unveiling a key biogeochemical role for AOA in coupling macrophyte landscape and ecosystem denitrification.

Nitrogen losses, uptake and abundance of ammonia oxidizers in soil under mineral and organo-mineral fertilization regimes.

A laboratory incubation experiment and greenhouse studies investigated the impact of organo-mineral (OM) fertilization as an alternative practice to conventional mineral (M) fertilization on nitrogen (N) uptake and losses in perennial ryegrass (Lolium perenne) as well as on soil microbial biomass and ammonia oxidizers. While no significant difference in plant productivity and ammonia emissions between treatments could be detected, an increase in soil total N content and an average 17.9% decrease in nitrates leached were observed in OM fertilization compared with M fertilization. The microbial community responded differentially to treatments, suggesting that the organic matter fraction of the OM fertilizer might have influenced N immobilization in the microbial biomass in the short-medium term. Furthermore, nitrate contents in fertilized soils were significantly related to bacterial but not archaeal amoA gene copies, whereas in non-fertilized soils a significant relationship between soil nitrates and archaeal but not bacterial amoA copies was found. The application of OM fertilizer to soil maintained sufficient productivity and in turn increased N use efficiency and noticeably reduced N losses. Furthermore, in this experiment, ammonia-oxidizing bacteria drove nitrification when an N source was added to the soil, whereas ammonia-oxidizing archaea were responsible for ammonia oxidation in non-fertilized soil. © 2015 Society of Chemical Industry.

The effect of human settlement on the abundance and community structure of ammonia oxidizers in tropical stream sediments.

Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are a diverse and functionally important group in the nitrogen cycle. Nevertheless, AOA and AOB communities driving this process remain uncharacterized in tropical freshwater sediment. Here, the effect of human settlement on the AOA and AOB diversity and abundance have been assessed by phylogenetic and quantitative PCR analyses, using archaeal and bacterial amoA and 16S rRNA genes. Overall, each environment contained specific clades of amoA and 16S rRNA genes sequences, suggesting that selective pressures lead to AOA and AOB inhabiting distinct ecological niches. Human settlement activities, as derived from increased metal and mineral nitrogen contents, appear to cause a response among the AOB community, with Nitrosomonas taking advantage over Nitrosospira in impacted environments. We also observed a dominance of AOB over AOA in mining-impacted sediments, suggesting that AOB might be the primary drivers of ammonia oxidation in these sediments. In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them. Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH. These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms.

Activity, abundance and structure of ammonia-oxidizing microorganisms in plateau soils

Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can be involved in biotransformation of ammonia to nitrite in soil ecosystems. However, the distribution of AOA and AOB in plateau soils and influential factors remain largely unclear. In the present study, the activity, abundance and structure of ammonia oxidizers in different soils on the Yunnan Plateau were assessed using potential nitrification rates (PNRs), quantitative PCR assay and clone library analysis, respectively. Wide variation was found in both AOA and AOB communities in plateau soils. PNRs showed a significant positive correlation with AOB abundance. Both were determined by the ratio of organic carbon to nitrogen (C/N) and total phosphorous (TP). AOB could play a more important role in ammonia oxidation. AOB community diversity was likely affected by soil total nitrogen (TN) and total organic carbon (TOC) and was usually higher than AOA community diversity. Moreover, Nitrososphaera- and Nitrosospira-like organisms, respectively, were the dominant AOA and AOB in plateau soils. AOA community structure was likely shaped by TP and C/N, while AOB community structure was determined by pH.

Linkage of N2O emissions to the abundance of soil ammonia oxidizers and denitrifiers in purple soil under long-term fertilization

Microbial nitrification and denitrification are responsible for the majority of soil nitrous (N2O) emissions. In this study, N2O emissions were measured and the abundance of ammonium oxidizers and denitrifiers were quantified in purple soil in a long-term fertilization experiment to explore their relationships. The average N2O fluxes and abundance of the amoAgene in ammonia-oxidizing bacteria during the observed dry season were highest when treated with mixed nitrogen, phosphorus and potassium fertilizer (NPK) and a single N treatment (N) using NH4HCO3as the sole N source; lower values were obtained using organic manure with pig slurry and added NPK at a ratio of 40%:60% (OMNPK),organic manure with pig slurry (OM) and returning crop straw residue plus synthetic NH4HCO3fertilizer at a ratio of 15%:85% (SRNPK). The lowest N2O fluxes were observed in the treatment that used crop straw residue(SR) and in the control with no fertilizer (CK). Soil NH4+provides the substrate for nitrification generating N2O as a byproduct. The N2O flux was significantly correlated with the abundance of the amoA gene in ammonia-oxidizing bacteria (r = 0.984, p < 0.001), which was the main driver of nitrification. During the wet season, soil nitrate (NO3−) and soil organic matter (SOC) were found positively correlated with N2O emissions (r = 0.774, p = 0.041 and r = 0.827, p = 0.015, respectively). The nirS gene showed a similar trend with N2O fluxes. These results show the relationship between the abundance of soil microbes and N2O emissions and suggest that N2O emissions during the dry season were due to nitrification, whereas in wet season, denitrification might dominate N2O emission.

Methane uptake in tropical soybean–wheat agroecosystem under different fertilizer regimes

Methane (CH4) consumption in the rhizosphere of soybean and wheat was evaluated under different fertilizer management practice in a tropical vertisol. The soybean (Glycine max L.) and wheat (Triticum aestivum L.) were grown with inorganic, organic, and both (integrated) fertilizer regimes. Cattle dung manure (CDM), poultry manure (PM) and vermicompost (VC) were used as organic fertilizers. Apparent rate constant (k) of CH4 consumption (CH4 consumed g−1 soil d−1) and other soil parameters including pH, EC, bulk density (BD), organic C (OC), available N (AN), mean weight diameter (MWD) of soil aggregates, and water-soluble aggregates (WSA) were estimated. Parameters like crop biomass, and grain yield were estimated after harvesting of the crops. Abundance of methanotrophs, heterotrophs and ammonia oxidizers were estimated after the end of CH4 consumption. CH4 consumption was analyzed under 60 and 100 % moisture-holding capacity (MHC). CH4 consumption rate k varied from 0.34 to 0.58 in wheat and 0.08–0.59 in soybean. Rate k was in the order of organic > integrated > inorganic irrespective of the crop. Half-life t 1/2 (in day) of CH4 varied from 1.19 to 1.74 in wheat and 1.53–2.82 in the soybean. One-way analysis of variance (ANOVA) and Pearson’s correlation revealed significant relation (p < 0.0001) among the variables. The regression model fitted k linearly (p < 0.05) with the variables. Principal component analysis (PCA) explained 76.06 and 18.17 % of variation by the first two components. Result highlighted that organic farming can significantly decrease global atmospheric CH4 budget in addition to improving soil physical and biological properties.

Water availability and abundance of microbial groups are key determinants of greenhouse gas fluxes in a dryland forest ecosystem

Forests are considered key biomes that could contribute to minimising global warming as they sequester carbon (C) and contribute to mitigate emissions of the potent greenhouse gases (GHG) including nitrous oxide (N2O), methane (CH4) and carbon dioxide (CO2). Management practices are prevalent in forestry, particularly in dryland ecosystems, known to be water and nitrogen (N) limited. Irrigation and fertilisation are thus routinely applied to increase the yield of forest products. However, the contribution of forest management practices to current GHG budgets and consequently to soil net global warming potential (GWP) is still largely unaccounted for, particularly in dryland ecosystems. We quantified the long-term effect (six years) of irrigation and fertilisation and the impact of land-use change, from grassland to a Eucalyptus plantation on N2O, CH4 and CO2 emissions and soil net GWP, within a dryland ecosystem. To identify biotic and abiotic drivers of GHG emissions, we explored the relationship of N2O, CH4 and CO2 fluxes with soil abiotic characteristics and abundance of ammonia-oxidizers, N2O-reducing bacteria, methanotrophs and total soil bacteria. Our results show that GHG emissions, particularly N2O and CO2 are constrained by water availability and both N2O and CH4 are constrained by N availability in the soil. We also provide evidence of functional microbial groups being key players in driving GHG emissions. Our findings illustrate that GHG emission budgets can be affected by forest management practices and provide a better mechanistic understanding for future mitigation options.