Soil Archaea Research Articles

Effects of different irrigation methods on nitrous oxide emissions and ammonia oxidizers microorganisms in greenhouse tomato fields

Agricultural soils are strong sources of the potent greenhouse gas N2O but soil N2O emissions and its microbial mechanism in greenhouse field, especially ammonia-oxidizing microorganisms are unclear. We characterized a potential response in soil N2O production and its influencing factors, such as soil temperature, moisture, pH, and inorganic nitrogen to different irrigation methods named drip irrigation (DI), subsurface irrigation (SI) and furrow irrigation (FI) in a long-term irrigation field in greenhouse. The abundance and metabolic activity of ammonia oxidizing archaea (AOA) and bacteria (AOB) in greenhouse soils were also investigated using amoA gene as a molecular biomarker by quantitative PCR and 13CO2-DNA-stable isotope probing (SIP) methods. Results showed that N2O flux peaks would obviously occur within 1–8 days after each irrigation. The soil N2O flux in FI treatment was significantly higher than that in DI and SI treatments (P < 0.05). Correlation analysis between soil N2O flux and its influencing factors indicated that soil moisture and nitrate nitrogen were substantially affecting soil N2O emissions compared with soil temperature, pH and ammonium nitrogen. The copy numbers of AOA amoA gene in FI treatment were significantly higher than those in DI and SI treatments (P < 0.05), while there is no significant difference of AOB amoA gene among the three treatments. Also, the copy numbers of AOA amoA gene were significantly higher than those of AOB amoA gene. The 13CO2-DNA-SIP and phylogenetic tree results indicated only AOB dominantly involved in Nitrosospira genera was active during the nitrification process in the three irrigation methods. Our findings provided direct evidence that drip irrigation and subsurface irrigation could effectively reduce soil N2O emissions in greenhouse. AOA was dominant in abundance, while AOB played a key role in microbial community under the conditions of this experiment. Future characterization of the mechanisms for ammonia oxidation requires deeper studies in the greenhouse field.

The Variation of Microbial Communities in a Depth Profile of Peat in the Gahai Lake Wetland Natural Conservation Area

ABSTRACTThe Gahai Lake wetland natural conservation area in northwestern China includes peatland that has been accumulating over hundreds of years and is seldom disturbed by industry. Bacteria and archaea in peat soil, which is a reservoir for carbon and water, may influence its ecological function. The objective of this study was to obtain a clearer understanding of peat microbial ecology and its relationship to the environmental conditions of this area. Hence, the microbial community of the peatland ecosystem was investigated by sequencing bacterial and archaeal DNA extracted from samples collected at different peat depths. Results showed that in all samples the dominant bacterial phyla were Proteobacteria (relative abundance 0.39 ± 0.12) and Chloroflexi (0.16 ± 0.09), while the dominant archaeal phyla were Miscellaneous Crenarchaeotic Group (MCG) (0.62 ± 0.21) and Euryarchaeota (0.27 ± 0.16). The diversity and microbial community structure at deeper depths (90 and 120 cm below the peat surface) significantly differ from that at shallower depths (10, 30 and 50 cm deep). In contrast to the shallow layers, the deeper layers became more abundant in the bacterial phyla Chloroflexi, Bacteroidetes, Atribacteria, Aminicenantes, Chlorobi, TA06, Caldiserica and Spirochaetae; and in the archaeal phyla MCG and Miscellaneous Euryarchaeotic Group (MEG). This study revealed a significant shift in microbial community in peat between 50 cm and 90 cm deep, as probably influenced by the oxygen supply at different depths. Furthermore, new insights into the microbial taxa were obtained, thus providing a baseline for future studies of this peat ecosystem.

Ecological drivers of soil microbial diversity and soil biological networks in the Southern Hemisphere.

The ecological drivers of soil biodiversity in the Southern Hemisphere remain underexplored. Here, in a continental survey comprising 647 sites, across 58 degrees of latitude between tropical Australia and Antarctica, we evaluated the major ecological patterns in soil biodiversity and relative abundance of ecological clusters within a co-occurrence network of soil bacteria, archaea and eukaryotes. Six major ecological clusters (modules) of co-occurring soil taxa were identified. These clusters exhibited strong shifts in their relative abundances with increasing distance from the equator. Temperature was the major environmental driver of the relative abundance of ecological clusters when Australia and Antarctica are analyzed together. Temperature, aridity, soil properties and vegetation types were the major drivers of the relative abundance of different ecological clusters within Australia. Our data supports significant reductions in the diversity of bacteria, archaea and eukaryotes in Antarctica vs. Australia linked to strong reductions in temperature. However, we only detected small latitudinal variations in soil biodiversity within Australia. Different environmental drivers regulate the diversity of soil archaea (temperature and soil carbon), bacteria (aridity, vegetation attributes and pH) and eukaryotes (vegetation type and soil carbon) across Australia. Together, our findings provide new insights into the mechanisms driving soil biodiversity in the Southern Hemisphere.

Oxygenated derivative is more influential than unsubstituted polycyclic aromatic hydrocarbon on ammonia-oxidizing archaea in an acidic soil

Oxygenated polycyclic aromatic hydrocarbons (PAHs) often co-occur with their parent compounds and may be chemically more reactive due to increased hydrophilicity and polarity. However, the influences of oxygenated PAH on soil functions and involved microbes, for example, nitrification and ammonia-oxidizing microorganisms, are largely unknown. Benz(a)anthracene (BaA) and benz(a)anthracene-7,12-dione (BaAD) were selected to represent unsubstituted and oxygenated PAHs, respectively. A microcosm experiment was performed with an acidic agricultural soil following the ISO 14238 method. Each microcosm was spiked with varied concentration (1, 10, and 100 mg kg−1) of either pollutants, with the unamended as the control. Ammonium was added to all microcosms to stimulate soil nitrification. After 28 days of incubation, abundance and composition of both bacterial and archaeal amoA genes were determined using quantitative PCR and denaturing gradient gel electrophoresis (DGGE). In addition, the growth inhibition of an ammonia-oxidizing Thaumarchaeota by both PAHs were examined. Neither BaA nor BaAD suppressed soil nitrate production and reduced the abundance of ammonia-oxidizing archaea. DGGE analysis of archaeal amoA genes revealed the enrichment of a few I.1b Thaumarchaeota in the ammonium fertilized control treatment; however, no such succession was observed in all BaAD and in 100 mg kg−1 BaA microcosms. Ammonia-oxidizing bacteria appeared to be less responsive to the ammonium fertilization and PAH stress. The cultivation experiment indicated the growth of the archaeal enrichment YT7-2 was more sensitive to BaAD than to BaA. These findings indicate inhibitory potency of BaAD to soil ammonia-oxidizing I.1b Thaumarchaeota, thus implicating potential ecological risks of the widely occurred oxygenated PAHs.

Ammonia Oxidizing Archaea and Bacteria in East Asian Paddy Soils—A Mini Review

Ammonia oxidation is crucial in nitrogen removal and global nitrogen dynamics since it is the first step of the nitrification process. In this review, we focus on the distribution and community structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in East Asian paddy soils with variable soil properties. The available East Asian paddy soil data shows that the ammonium concentration and pH ranges from 0.4 to 370 mg/kg and 5.1 to 8.2, respectively. Our meta-analysis suggest that AOA specific gene sequences are generally more abundant than those of AOB in both acidic and alkaline paddy soils, where Nitrosophaera and Nitrosospira amoA clusters mainly dominate the microbial community, respectively. In addition, the contribution of ammonia oxidizers to the nitrification process has been demonstrated using DNA-SIP (DNA-based stable-isotope probing); the results of these studies indicate that pH is the most important factor in niche separation of AOA and AOB under a variety of edaphic conditions. Finally, we discuss a number of other environmental variables that affect the abundance, distribution, and activity of AOA and AOB in East Asian paddy soils.

Effects of combined application of nitrogen fertilizer and biochar on the nitrification and ammonia oxidizers in an intensive vegetable soil

Soil amended with single biochar or nitrogen (N) fertilizer has frequently been reported to alter soil nitrification process due to its impact on soil properties. However, little is known about the dynamic response of nitrification and ammonia-oxidizers to the combined application of biochar and N fertilizer in intensive vegetable soil. In this study, an incubation experiment was designed to evaluate the effects of biochar and N fertilizer application on soil nitrification, abundance and community shifts of ammonia-oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) in Hangzhou greenhouse vegetable soil. Results showed that single application of biochar had no significant effect on soil net nitrification rates and ammonia-oxidizers. Conversely, the application of only N fertilizer and N fertilizer + biochar significantly increased net nitrification rate and the abundance of AOB rather than AOA, and only AOB abundance was significantly correlated with soil net nitrification rate. Moreover, the combined application of N fertilizer and biochar had greater effect on AOB communities than that of the only N fertilizers, and the relative abundance of 156 bp T-RF (Nitrosospira cluster 3c) decreased but 60 bp T-RF (Nitrosospira cluster 3a and cluster 0) increased to become a single predominant group. Phylogenetic analysis indicated that all the AOB sequences were grouped into Nitrosospira cluster, and most of AOA sequences were clustered within group 1.1b. We concluded that soil nitrification was stimulated by the combined application of N fertilizer and biochar via enhancing the abundance and shifting the community composition of AOB rather than AOA in intensive vegetable soil.

Effect of Conservational and Conventional Tillage Systems on Functional Soil Archaea Diversity in Wheat-Pea Rotation Field

Soil borne archaea in agricultural systems is crucial for cycling of nutrient such as Nitrogen, Carbon and Sulphur. The objective of the study was to assess the effect of different tillage systems on functional archaea diversity in a 15 years cereal-legume rotation field using Illumina sequencing platform for archaea 16S rRNA gene. The treatments in the study included conventional tillage with stubble removed (T), no-till with stubble removed (NT), conventional tillage with stubble incorporated (TS) and no-till with stubble retained (NTS). The results showed that the dominant soil archaea phyla was Crenarchaeota (&gt; 96%), followed by Euryarchaeota with a lower abundance of &lt; 3% and then Parvarchaeota and other bacteria phyla made up &lt; 1% across the treatments and depths. The treatment means were ranked as NT &gt; NTS &gt; TS &gt; T for 16S rRNA number of OTUs, Shannon and Simpson indices calculated for the 0-10cm soil depth. Analysis of factor effect revealed that tillage but not stubble retention or their interaction significantly influenced (P &lt; 0.01 and P &lt; 0.05) 16S rRNA diversity. Non metric Multidimensional Scaling (NMDS) analysis clearly grouped the microbial communities according to depths. Linear Discriminant Analysis Effect Size (LEfSe) identified Crenarchaeota and Thaumarchaeota (to genus level) as significantly enriched clades in 0-10 cm depth of T while Euryarchaeota and Thermoplasmata were significantly enriched in TS. The conservational tillage systems (NT and NTS) promoted even distribution of archaea diversity while conventional tillage systems (T and TS) enriched the archaea communities identified in the study.

Ecological niche differentiation of ammonia-oxidising archaea and bacteria in acidic soils due to land use change

Nitrification can be driven by either ammonia-oxidising bacteria (AOB) or ammonia-oxidising archaea (AOA) and is a central process in the nitrogen cycle. However, to date, it is not clear how the ecological niche differentiation of AOB and AOA are affected by land use and management changes in strongly acidic soils in subtropical China. In this study, three different land-use acidic soils – forest, upland, and paddy soils – were collected and a DNA Stable-Isotope Probing experiment performed to determine the relative contributions of AOA and AOB to ammonia oxidation in these soils. The results showed that AOA, but not AOB, amoA genes were detected in 13C-labelled DNA in the forest and paddy soils; however, only AOB amoA genes were detected in 13C-labelled DNA in the upland agricultural soils. The growth and activity of AOA and AOB in the different land-use soils provided direct evidence for the shift in roles for AOA and AOB in ammonia oxidation. AOA played the predominant role in ammonia oxidation in acidic forest and paddy soils. However, AOB, not AOA, mainly regulated the ammonia oxidation in acidic upland agricultural soils. Phylogenetic analysis indicated that AOA members within the marine Group1.1a-associated lineage dominated nitrification in the forest and paddy soils. Ammonia oxidation in the upland soil was catalysed by Nitrosospira cluster 3-like AOB. The moisture condition was likely the main reason inducing the ecological niche differentiation between upland and paddy soils; and AOA was more suitable for growth in the flooded, low oxygen conditions.

Nitrification Activity and Autotrophic Nitrifiers in Long-term Fertilized Acidic Upland Soils

Soil microcosm incubation, molecular ecology techniques including denaturing gradient gel electrophoresis and Illumina MiSeq high-throughput sequencing, and bioinformatics analysis were carried out to investigate the effect of long-term fertilization with chemical fertilizers (NPK) and organic manure (OM) on soil nitrification activity and the autotrophic nitrifying communities in acidic upland soils. No fertilization soil (CK) was the control. Relationships between soil nitrification activities, autotrophic nitrifying communities, and soil characteristics were further evaluated. Long-term fertilization significantly increased the soil organic carbon and inorganic nitrogen contents. Fertilization with organic manure significantly increased soil pH and total nitrogen contents, but decreased soil C/N. Autotrophic nitrification dominated soil nitrification, and accounted for 73.60%-85.32% of total nitrification. Fertilization significantly increased soil autotrophic nitrification activity and the highest value was observed in the OM soil. During the microcosm incubation, the absolute abundances of amoA genes and the relative abundances of 16S rRNA genes of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the OM soil significantly increased. The relative abundances of 16S rRNA genes of the AOA greatly increased in both CK and NPK soils. These results suggested the remarkable activity of AOA in the three soils (the predominant population was Nitrososphaera,>99.30%) and implied that AOB was active in the OM soil (the predominant population was Nitrosospira,>99.99%). We also found the activity of nitrite-oxidizing bacteria (NOB) in the OM soil, and the predominant population was Nitrospira (>96.69%). Stepwise regression analysis demonstrated that soil autotrophic nitrification activity was significantly affected by soil total nitrogen content, whereas the abundances of archaeal and bacterial amoA genes were significantly affected by soil organic carbon content and soil pH, respectively. We also found significant positive correlation between the relative abundance of Nitrososphaera and soil nitrate content and a negative correlation between the relative abundance of Nitrosospira and Nitrospira with soil C/N. Overall, our results showed that long-term fertilization greatly increased soil nitrification activity and altered the autotrophic nitrifying communities in acidic upland soils. Soil autotrophic nitrification activity was significantly stimulated by soil total nitrogen content. The Nitrososphaera group played a critical role in nitrification of acidic upland soils. The increased soil pH and decreased soil C/N stimulated the growth of Nitrosospira.

Elevational diversity and distribution of ammonia-oxidizing archaea community in meadow soils on the Tibetan Plateau.

Unraveling elevational diversity patterns of plants and animals has long been attracting scientific interests. However, whether soil microorganisms exhibit similar elevational patterns remains largely less explored, especially for functional microbial communities, such as ammonia oxidizers. Here, we investigated the diversity and distribution pattern of ammonia-oxidizing archaea (AOA) in meadow soils along an elevation gradient from 4400m to the grassline at 5100m on the Tibetan Plateau using terminal restriction fragment length polymorphism (T-RFLP) and sequencing methods by targeting amoA gene. Increasing elevations led to lower soil temperature and pH, but higher nutrients and water content. The results showed that AOA diversity and evenness monotonically increased with elevation, while richness was relatively stable. The increase of diversity and evenness was attributed to the growth inhibition of warm-adapted AOA phylotypes by lower temperature and the growth facilitation of cold-adapted AOA phylotypes by richer nutrients at higher elevations. Low temperature thus played an important role in the AOA growth and niche separation. The AOA community variation was explained by the combined effect of all soil properties (32.6%), and 8.1% of the total variation was individually explained by soil pH. The total AOA abundance decreased, whereas soil potential nitrification rate (PNR) increased with increasing elevations. Soil PNR positively correlated with the abundance of cold-adapted AOA phylotypes. Our findings suggest that low temperature plays an important role in AOA elevational diversity pattern and niche separation, rising the negative effects of warming on AOA diversity and soil nitrification process in the Tibetan region.

Ammonia-oxidizing archaea and bacteria responding differently to fertilizer type and irrigation frequency as revealed by Illumina Miseq sequencing

Ammonia oxidation, the first and rate-limiting step of nitrification, can be strongly influenced by agricultural practices, but little is known about the effects of fertilization and irrigation combination on ammonia oxidizers in agricultural soils. This study was designed to reveal how fertilizer type and irrigation frequency affect the ammonia-oxidizing archaea (AOA) and bacteria (AOB) communities in a northern Chinese wheat-maize rotation soil. Soil samples were collected from a long-term field experiment under different fertilization and irrigation regimes located in Wuqiao Experimental Station of China Agricultural University in June 2016. The abundance, diversity, and composition of AOA and AOB in the soils were investigated by using real-time PCR and Illumina Miseq sequencing approaches. The abundance of AOA was higher in the irrigated treatments, but lower in the treatments without irrigation, than that of AOB. The AOA abundance was positively correlated with soil moisture, pH, and NO3 −-N, while the AOB abundance was positively correlated with TN and NO3 −-N. Soil potential nitrification activity (PNA) was significantly positively correlated with the AOB abundance. Both fertilizer type and irrigation frequency significantly affected Shannon, ACE, and Chao1 indices of the AOB community, while only irrigation frequency had a significant impact on Shannon index of the AOA community. PCoA analysis results indicated that irrigation frequency greatly affected the AOA community structure, while fertilizer type played a more important role in affecting the AOB community structure. Mantel test and correlation heatmap analysis results indicated that soil moisture, pH, and NH4 +-N were significantly correlated to the AOA community structure, and TN and SOC were significantly correlated to the AOB community structure. This study demonstrated that irrigation frequency greatly influenced the AOA community, while fertilizer type had a stronger effect on the AOB community. It was AOB but not AOA played a more important role in soil nitrification. Moreover, soil moisture, pH, and TN were the main determinants in driving the AOA community and TN and SOC were the main factors in influencing the AOB community.

Response of ammonia-oxidizing archaea and bacteria in calcareous soil to mineral and organic fertilizer application and their relative contribution to nitrification

Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) co-exist in soils. However, little is known about the effects of fertilization on the AOA and AOB communities and their relative contribution to soil nitrification. The objective of this field study was to determine the effects of four years of mineral and organic fertilizer (i.e., either cattle manure or biofertilizer) application on AOB and AOA in calcareous soil. The combined application of mineral and organic fertilizer (especially cattle manure) significantly increased the species richness (Chao1 and Ace) and α-diversity (Shannon index) of AOB (P < 0.05) but not AOA (P = 0.102). The AOA/AOB ratios were 1.64 and 1.19 in the unfertilized and the mineral fertilizer treatments, respectively. In contrast, the AOA/AOB rations were <1.0 in treatments with both mineral and organic fertilizer. These findings indicated that organic fertilizer increased AOB comparatively to AOA. Fertilizer addition was associated with significant shifts in the community structure of AOB (P < 0.01) but had little effect on AOA. Soil potential nitrification rate were greatly increased by the application of either mineral fertilizer or mineral plus organic fertilizer (P < 0.05). Moreover, potential nitrification rate were positively correlated with AOB abundance (P < 0.001) but not AOA abundance (P = 0.223). Variations in AOB community structure were closely associated with fertilizer-induced changes in soil pH, NH4+ and SOC, whereas AOA community structure was only significantly correlated with SOC (P = 0.040). Our findings suggest (i) that AOB is more sensitive than AOA to different fertilization regimes and (ii) that AOB contribute more than AOA to nitrification in this fertilized calcareous field soil.

Ammonia oxidizer populations vary with nitrogen cycling across a tropical montane mean annual temperature gradient.

Functional gene approaches have been used to better understand the roles of microbes in driving forest soil nitrogen (N) cycling rates and bioavailability. Ammonia oxidation is a rate limiting step in nitrification, and is a key area for understanding environmental constraints on N availability in forests. We studied how increasing temperature affects the role of ammonia oxidizing archaea (AOA) and bacteria (AOB) in soil N cycling and availability by using a highly constrained natural mean annual temperature (MAT) elevation gradient in a tropical montane wet forest. We found that net nitrate (NO3- ) bioavailability is positively related to MAT (r2 =0.79, P=0.0033), and AOA DNA abundance is positively related to both NO3- availability (r2 =0.34, P=0.0071) and MAT (r2 =0.34, P<0.001). In contrast, AOB DNA was only detected in some soils across the gradient. We identified three distinct phylotypes within the AOA which differed from one another in abundance and relative gene expression. In addition, one AOA phylotype increased in abundance with MAT, while others did not. We conclude that MAT is the primary driver of ecosystem N availability across this gradient, and AOA population size and structure appear to mediate the relationship between the nitrification and N bioavailability. These findings hold important implications for nutrient limitation in forests and feedbacks to primary production under changing climate.

3-1-7 Response of active community of methanogenic archaea in paddy field soil to a management of paddy-upland rotation

3-1-7 Response of active community of methanogenic archaea in paddy field soil to a management of paddy-upland rotation

C and N stocks are not impacted by land use change from Brazilian Savanna (Cerrado) to agriculture despite changes in soil fertility and microbial abundances

AbstractCentral Brazil is the region with the most dynamic agriculture expansion worldwide, where tropical forests and Cerrado (Brazilian savanna) are converted to pastures and crop fields. Following deforestation, agricultural practices, such as fertilization, tillage and crop rotations, alter soil parameters and affect microbial abundances and the C and N cycles. The objective of this study was to compare changes in soil fertility, stocks of soil C and N, microbial biomass, and abundance of bacteria, fungi and archaea in Cerrado soils following land use change to crops (soybean/corn/cotton) and pasture (the perennial forage grass Brachiaria brizantha A. Rich.). Agriculture increased soil fertility and conserved soil C and N since their absolute concentration values were highest in agriculture soils and the C and N stocks adjusted by soil density were similar to the native vegetation soils. At the same time, agriculture changed the microbial abundances (decrease of microbial biomass C and N, increase of archaea, and reduction of bacteria and fungi at the crop sites), and N dynamics (increase of soil ammonium and nitrate concentrations). Even if these changes can be beneficial for food and agricultural commodities production, all these soil alterations should be further investigated due to their possible unknown effects on biosphere–hydrosphere–atmosphere exchange processes such as greenhouse gases emissions and nitrate leaching.

農耕地土壌における細菌,真核生物および古細菌のrDNA存在比の推定 : 古細菌rDNA存在比に及ぼす土壌環境要因の解析

農耕地土壌における細菌,真核生物および古細菌のrDNA存在比の推定 : 古細菌rDNA存在比に及ぼす土壌環境要因の解析

DNA-based stable isotope probing identifies formate-metabolizing methanogenic archaea in paddy soil

Paddy methane (CH4) production is biologically dominated by methanogenic archaea that metabolize a variety of organic and/or inorganic carbon sources. Though formate is easily dissimilated into H2/CO2, formate-metabolizing methanogenic archaea are distinct from CO2-utilizing methanogen taxa. The identity of formate-metabolizing methanogenic archaea in paddy soil remains elusive. In this investigation, molecular approaches based on stable isotope probing (SIP) technique were conducted to identify the formate-metabolizing methanogenic archaea in paddy soil. CH4 emission monitor, real-time quantitative PCR (qPCR) and Denaturing Gradient Gel Electrophoresis (DGGE) analyses consistently indicated that some methanogenic archaea metabolized 13C-labeled formate in microcosm and accounted for a large portion of formate-metabolizing archaea in anoxic paddy soil. Phylogenetic identification further found that this guild was affiliated to Methanobacteriaceae. Taken together Methanobacteriaceae could be the dominant formate-metabolizing methanogenic archaea and play an important role in the CH4 production in paddy soil. These findings would extend the extant knowledge on paddy methanogenic archaea and microbial-driven paddy CH4 emission.

Responses of soil nitrous oxide production and abundances and composition of associated microbial communities to nitrogen and water amendment

Soil moisture and nitrogen (N) are two important factors influencing N2O emissions and the growth of microorganisms. Here, we carried out a microcosm experiment to evaluate effects of soil moisture level and N fertilizer type on N2O emissions and abundances and composition of associated microbial communities in the two typical arable soils. The abundances and community composition of functional microbes involved in nitrification and denitrification were determined via quantitative PCR (qPCR) and terminal restriction length fragment polymorphism (T-RFLP), respectively. Results showed that N2O production was higher at 90% water-filled pore (WFPS) than at 50% WFPS. The N2O emissions in the two soils amended with ammonium were higher than those amended with nitrate, especially at relatively high moisture level. In both soils, increased soil moisture stimulated the growth of ammonia-oxidizing bacteria (AOB) and nitrite reducer (nirK). Ammonium fertilizer treatment increased the population size of AOB and nirK genes in the alluvial soil, while reduced the abundances of ammonia-oxidizing archaea (AOA) and denitrifiers (nirK and nosZ) in the red soil. Nitrate addition had a negative effect on AOA abundance in the red soil. Total N2O emissions were positively correlated to AOB abundance, but not to other functional genes in the two soils. Changed soil moisture significantly affected AOA rather than AOB community composition in both soils. The way and extent of N fertilizers impacted on nitrifier and denitrifier community composition varied with N form and soil type. These results indicate that N2O emissions and the succession of nitrifying and denitrifying communities are selectively affected by soil moisture and N fertilizer form in the two contrasting types of soil.

Convergence and contrast in the community structure of Bacteria, Fungi and Archaea along a tropical elevation-climate gradient.

Changes in species richness along climatological gradients have been instrumental in developing theories about the general drivers of biodiversity. Previous studies on microbial communities along climate gradients on mountainsides have revealed positive, negative and neutral richness trends. We examined changes in richness and composition of Fungi, Bacteria and Archaea in soil along a 50-1000 m elevation, 280-3280 mm/yr precipitation gradient in Hawai'i. Soil properties and their drivers are exceptionally well understood along this gradient. All three microbial groups responded strongly to the gradient, with community ordinations being similar along axes of environmental conditions (pH, rainfall) and resource availability (nitrogen, phosphorus). However, the form of the richness-climate relationship varied between Fungi (positive linear), Bacteria (unimodal) and Archaea (negative linear). These differences were related to resource-ecology and limiting conditions for each group, with fungal richness increasing most strongly with soil carbon, ammonia-oxidizing Archaea increasing with nitrogen mineralization rate, and Bacteria increasing with both carbon and pH. Reponses to the gradient became increasingly variable at finer taxonomic scales and within any taxonomic group most individual OTUs occurred in narrow climate-elevation ranges. These results show that microbial responses to climate gradients are heterogeneous due to complexity of underlying environmental changes and the diverse ecologies of microbial taxa.

Abundance and diversity of ammonia-oxidizing archaea and bacteria in the rhizosphere soil of three plants in the Ebinur Lake wetland

Ammonia oxidation is carried out by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). The Ebinur Lake wetland is the best example of a temperate arid zone wetland ecosystem in China. Soil samples were collected from rhizosphere and non-rhizosphere soil containing Halocnemum strobilaceum (samples H and H'), Phragmites australis (samples R and R'), and Karelinia caspia (samples K and K') to study the relationship between environmental factors and the community structure of AOB and AOA. Phylogenetic analysis showed that the AOA sequences belonged to the Nitrosopumilus and Nitrososphaera clusters. AOB were grouped into Nitrosospira sp. and Nitrosomonas sp. Quantitative polymerase chain reaction results showed that the AOA abundance ranged from 2.09 × 104 to 2.94 × 105 gene copies/g soil. The highest number of AOA was detected in sample K, followed by samples R and H. AOB abundance varied between 2.91 × 105 and 1.05 × 106 gene copies/g soil, which was higher than that of AOA. Redundancy analysis indicated that electrical conductivity, pH, and NH4+-N might influence the community structure of AOA and AOB. AOB might play a more crucial role than AOA in ammonia oxidation based on AOB's higher diversity and abundance in the Ebinur Lake wetland in Xinjiang.