nosZ Communities Research Articles

Fertilizer nitrogen substitution using biochar-loaded ammonium-nitrogen reduces nitrous oxide emissions by regulating nitrous oxide-reducing bacteria

Biochar has been extensively demonstrated as an abundant, cost-effective, and highly efficient adsorbent material for removing ammonium (NH4+) from non-point source-polluted water. The new technology of biochar-loaded NH4+-N (BLN) is urgently needed. However, the underlying mechanisms of BLN in regulating N2O emissions by substituting chemical fertilizer nitrogen (CFN) were poorly understood. Based on the substitution rate of CFN with BLN, a soil column experiment was designed with six treatments: CFN-only (BLN0), 20% BLN plus 80% CFN (BLN20), 40% BLN plus 60% CFN (BLN40), 60% BLN plus 40% CFN (BLN60), 80% BLN plus 20% CFN (BLN80), and BLN only (BLN100). BLN application significantly decreased cumulative N2O emissions by 20.50–40.78% compared to the BLN0 treatment. The optimal ratio of CFN substitution was 66.10%, which was supported by the lowest N2O emissions in the BLN60 treatment. In BLN-treated soil, the abundance of nosZ played a dominant role in N transformation, followed by ammonia-oxidizing bacteria (AOB). Particularly, BLN60 significantly increased nosZ abundance. The high substitution ratio (BLN60–100) promoted N2O reduction by increasing the overall abundance of nosZ-harboring communities, however, low substitution ratio (BLN0–40) promoted it by increasing nosZ cluster Ⅸ abundance and the connectivity of operational taxonomic units within the module. Soil pH and C/N ratio were critical influencing factors to alter the nosZ community structure. These findings highlighted that BLN substitution treatments reduced N2O emissions, while the microbiological mechanism of emission reduction varied with the proportion of substitution. An appropriate substitution ratio (60%) mainly reduced N2O emissions by increasing nosZ abundance.

Soil acidification and ammonia-oxidizing archaeal abundance dominate the contrasting responses of soil N2O emissions to NH4+ and NO3− enrichment in a subtropical plantation

Atmospheric nitrogen (N) deposition markedly increases nitrous oxide (N2O) emissions from subtropical plantation soils. However, the contrasting effects of deposited NH4+ and NO3− on soil N2O emissions and the underlying mechanisms are not well understood. Based on the long-term N fertilization manipulative experiment with two types (NH4Cl and NaNO3) and three levels (0, 40, and 120 kg N ha−1 yr−1), we investigated the response of soil N2O emissions to N addition, as well as the environmental and microbial control on soil N2O emissions using flux observations and molecular biology assays. Nitrogen addition significantly decreased soil pH by 0.30–0.67 units and increased soil N2O emissions by 6- to 21-fold relative to the control; furthermore, the effect of NH4Cl addition was significantly stronger than that of NaNO3 addition. Nitrogen addition significantly increased the abundance of ammonia-oxidizing archaea (AOA), whereas high levels of NH4Cl addition (120 kg N ha−1 yr−1) significantly decreased the abundances of nirS, nirK, and nosZ. In addition, NH4Cl addition decreased the Shannon diversity indices of AOA, nirK, and nosZ communities. Changes in soil N2O flux were positively correlated with changes in soil NO3−-N concentration and AOA abundance, whereas negatively correlated with changes in soil pH. Soil acidification and enhanced AOA-dominated nitrification led to higher soil N2O emissions under NH4Cl addition relative to NaNO3 addition. Overall, the contrasting effects of reduced NH4+ and oxidized NO3− should be incorporated into ecosystem process models to accurately assess the response of N2O emissions from subtropical plantation soils to exogenous N input.

Carbon substrate selects for different lineages of N2O reducing communities in soils under anoxic conditions

Agricultural soils are a main source of nitrous oxide (N2O), a potent greenhouse gas and the dominant ozone-depleting substance emitted to the atmosphere. The only known sink of N2O in soil is the microbial reduction of N2O to N2. Carbon (C) availability is a key factor in determining microbial community composition in soil. However, its role in shaping the structure of N2O reducing communities in soil is unexplored. In this study, a microcosm experiment was set up in which two arable soils with contrasting edaphic properties were incubated anaerobically for 83 days with four different C substrates: glucose, acetate, hydroxyethylcellulose (HEC) and mixture of the three. We show that the effect of C addition on the abundance and diversity of clade I and clade II nosZ genes, encoding different variants of the N2O reductase, varies across the different C substrates differently in contrasting soil types, yet still plays an important role in selecting specific taxa of N2O reducers under denitrifying conditions. We observed an increase of betaproteobacterial clade I and II N2O reducing species with addition of HEC, whereas alphaproteobacterial clade I species and clade II species within other Proteobacteria and Bacteriodetes were associated with glucose and acetate. These results show that specific C-substrates select for certain lineages of nitrous oxide reducers and influence patterns of niche partitioning within clades of N2O reducers, whereas other soil factors drive differences between clade I and II nosZ communities.

Bacterial communities in sediments of an urban wetland in Bogota, Colombia

Urban wetlands are biodiversity reservoirs sustained by microbe-mediated processes. In tropical zones, wetland microbial dynamics remain poorly understood. Chemical parameters, heavy metal content, and microbiological community structure were investigated in surface sediments of the Santa Maria del Lago (SML) wetland in Bogota, Colombia. High-throughput sequencing was employed to generate RNAr 16S and nosZ gene sequence data with which bacteria, archaea, and nosZ-type denitrifier community composition and their phylogenetic relationships were investigated. A canonical correspondence analysis was conducted to determine the relationship between assessed environmental variables and microbial community composition. Results showed that the most abundant bacterial phyla were Proteobacteria, Acidobacteria (group GP18), and Aminicenantes; Archaea were represented by the taxa Methanomicrobia and Thermoprotei, and the nosZ community was dominated by Candidatus Competibacter denitrificans. A phylogenetic analysis revealed a high diversity of Operational Taxonomic Units (OTUs), according to 16S rRNA gene sequence data; however, the quantity and diversity of OTUs from the nosZ community were low compared to previous studies. High concentrations of ammonium, phosphorus, organic carbon, Pb, Fe, Zn, Cu, and Cd, were detected in sediments, but they were not strongly related to observed microbial community compositions. In conclusion, in the same polluted SML wetland sediments diverse bacteria and archaea communities were detected, although not nosZ-type denitrifiers.

Assembly of root-associated N2O-reducing communities of annual crops is governed by selection for nosZ clade I over clade II.

The rhizosphere is a hotspot for denitrification. The nitrous oxide (N2O) reductase among denitrifiers and nondenitrifying N2O reducers is the only known N2O sink in the biosphere. We hypothesized that the composition of root-associated N2O-reducing communities when establishing on annual crops depend on soil type and plant species, but that assembly processes are independent of these factors and differ between nosZ clades I and II. Using a pot experiment with barley and sunflower and two soils, we analyzed the abundance, composition, and diversity of soil and root-associated N2O reducing communities by qPCR and amplicon sequencing of nosZ. Clade I was more abundant on roots compared to soil, while clade II showed the opposite. In barley, this pattern coincided with N2O availability, determined as potential N2O production rates, but for sunflower no N2O production was detected in the root compartment. Root and soil nosZ communities differed in composition and phylogeny-based community analyses indicated that assembly of root-associated N2O reducers was driven by the interaction between plant and soil type, with inferred competition being more influential than habitat selection. Selection between clades I and II in the root/soil interface is suggested, which may have functional consequences since most clade I microorganisms can produce N2O.

Response and recovery of nosZ abundant and rare subcommunities to organic amendment and nitrification inhibitor disturbances, with implications for N2O emissions

Clarifying the mechanisms underpinning the responses of abundant and rare taxa of the nitrous oxide reductase (nosZ) gene to fertilization disturbances is beneficial for understanding the relationships between N2O reduction and the nosZ community. Here, we compared the species richness, composition, and abundance of rare and abundant nosZ taxa and their community resistance and resilience within 85 days after different fertilization disturbances, i.e., chemical N anole (CF), chemical N + cattle manure (CM), and cattle manure + nitrification inhibitor nitrapyrin (CP). Our results showed that CM and CP disturbances significantly increased the species richness and α-diversity of the whole nosZ community (P < 0.05), which was mainly attributed to the changes in rare taxa rather than in the abundant taxa. The Bray–Curtis dissimilarity of community composition (average 0.56) of nosZ rare taxa was significantly greater than that of abundant taxa (average 0.26) after disturbances. The rare subcommunity was sensitive to CM and CP disturbances but was resistant to CF disturbance. The α-diversity and abundance of the nosZ community almost recovered at 85 days after disturbance, more so under CM amendment, while its community composition hardly recovered. The nosZ co-occurrence networks indicated that CM and CP disturbances substantially increased the strength of the connections and degrees and strengthened the co-occurrence relationships among modules compared to the CF disturbance. Furthermore, our results confirmed that the resistance or resilience of rare subcommunity compositions contributed more to the mitigation of N2O caused by CM and CF disturbances, and these were mainly derived by edaphic factors, including SOC, NO3−, pH, and CEC. Our findings suggested that rare taxa played a dominant role in mediating the resistance and resilience of nosZ communities in agro-soil under environmental disturbances and could significantly influence N2O emissions.

Recovery of Soil-Denitrifying Community along a Chronosequence of Sand-Fixation Forest in a Semi-Arid Desertified Grassland

Revegetation on moving sand dunes is a widely used approach for restoring the degraded sandy land in northeastern China. The development of sand-fixation forest might improve the structures of soil microbial communities and affect soil N cycle. In the present study, the diversities of nitrite (nirS and nirK) and nitrous oxide (nosZ) reductase genes were investigated under a chronosequence of Caragana microphylla sand-fixation shrub forest (9- and 19-year), adjacent non-vegetated shifting sand-dune, and a natural forest dominated by C. microphylla. The dominant compositions and gene abundance were analyzed by a clone library technique and quantitative polymerase chain reaction, respectively. The compositions and dominant taxa of nirK, nirS, and nosZ communities under forest soil were all similar to those in the shifting sand-dune. However, the three gene abundances all linearly increased across forest age. Clones associated with known denitrifiers carrying nosZ, nirK, or nirS genes, such as members of Pseudomonas, Mesorhizobium, Rhizobium, Rhodopseudomonas, Azospirillum, and Cupriavidus, were detected. These denitrifiers were found to be abundant in soil and dominant in soil denitrification. Soil pH, total N, and available N affected the denitrifying communities by altering the relative abundance of dominant taxa. Overall, although soil attributes and forest age had no significant effects on the dominant constituents of nirK, nirS, and nosZ communities, revegetation on shifting sand-dunes facilitated the quantitative restoration of soil denitrifiers due to the increase in soil nutrients.

Influence of Season, Occupancy Pattern, and Technology on Structure and Composition of Nitrifying and Denitrifying Bacterial Communities in Advanced Nitrogen-Removal Onsite Wastewater Treatment Systems

Advanced onsite wastewater treatment systems (OWTS) use biological nitrogen removal (BNR) to mitigate the threat that N-rich wastewater poses to coastal waterbodies and groundwater. These systems lower the N concentration of effluent via sequential microbial nitrification and denitrification. We used high-throughput sequencing to evaluate the structure and composition of nitrifying and denitrifying bacterial communities in advanced N-removal OWTS, targeting the genes encoding ammonia monooxygenase (amoA) and nitrous oxide reductase (nosZ) present in effluent from 44 advanced systems. We used QIIME2 and the phyloseq package in R to examine differences in taxonomy and alpha and beta diversity as a function of advanced OWTS technology, occupancy pattern (seasonal vs. year-round use), and season (June vs. September). Richness and Shannon’s diversity index for amoA were significantly influenced by season, whereas technology influenced nosZ diversity significantly. Season also had a strong influence on differences in beta diversity among amoA communities, and had less influence on nosZ communities, whereas technology had a stronger influence on nosZ communities. Nitrosospira and Nitrosomonas were the main genera of nitrifiers in advanced N-removal OWTS, and the predominant genera of denitrifiers included Zoogloea, Thauera, and Acidovorax. Differences in taxonomy for each gene generally mirrored those observed in diversity patterns, highlighting the possible importance of season and technology in shaping communities of amoA and nosZ, respectively. Knowledge gained from this study may be useful in understanding the connections between microbial communities and OWTS performance and may help manage systems in a way that maximizes N removal.

Habitat diversity and type govern potential nitrogen loss by denitrification in coastal sediments and differences in ecosystem-level diversities of disparate N2O reducing communities.

ABSTRACTIn coastal sediments, excess nitrogen is removed primarily by denitrification. However, losses in habitat diversity may reduce the functional diversity of microbial communities that drive this important filter function. We examined how habitat type and habitat diversity affects denitrification and the abundance and diversity of denitrifying and N2O reducing communities in illuminated shallow-water sediments. In a mesocosm experiment, cores from four habitats were incubated in different combinations, representing ecosystems with different habitat diversities. We hypothesized that habitat diversity promotes the diversity of N2O reducing communities and genetic potential for denitrification, thereby influencing denitrification rates. We also hypothesized that this will depend on the identity of the habitats. Habitat diversity positively affected ecosystem-level diversity of clade II N2O reducing communities, however neither clade I nosZ communities nor denitrification activity were affected. The composition of N2O reducing communities was determined by habitat type, and functional gene abundances indicated that silty mud and sandy sediments had higher genetic potentials for denitrification and N2O reduction than cyanobacterial mat and Ruppia maritima meadow sediments. These results indicate that loss of habitat diversity and specific habitats could have negative impacts on denitrification and N2O reduction, which underpin the capacity for nitrogen removal in coastal ecosystems.

Structure of greenhouse gas-consuming microbial communities in surface soils of a nitrogen-removing experimental drainfield

Septic systems represent a source of greenhouse gases generated by microbial processes as wastewater constituents are degraded. Both aerobic and anerobic wastewater transformation processes can generate nitrous oxide and methane, both of which are potent greenhouse gases (GHGs). To understand how microbial communities in the surface soils above shallow drainfields contribute to methane and nitrous oxide consumption, we measured greenhouse gas surface flux and below-ground concentrations and compared them to the microbial communities present using functional genes pmoA and nosZ. These genes encode portions of particulate methane monooxygenase and nitrous oxide reductase, respectively, serving as a potential sink for the respective greenhouse gases. We assessed the surface soils above three drainfields served by a single household: an experimental layered passive N-reducing drainfield, a control conventional drainfield, and a reserve drainfield not in use but otherwise identical to the control. We found that neither GHG flux, below-ground concentration or soil properties varied among drainfield types, nor did methane oxidizing and nitrous oxide reducing communities vary by drainfield type. We found differences in pmoA and nosZ communities based on depth from the soil surface, and differences in nosZ communities based on whether the sample came from the rhizosphere or surrounding bulk soils. Type I methanotrophs (Gammaproteobacteria) were more abundant in the upper and middle portions of the soil above the drainfield. In general, we found no relationship in community composition for either gene based on GHG flux or below-ground concentration or soil properties (bulk density, organic matter, above-ground biomass). This is the first study to assess these communities in the surface soils above an experimental working drainfield, and more research is needed to understand the dynamics of greenhouse gas production and consumption in these systems.

Nitrifying and Denitrifying Microbial Communities in Centralized and Decentralized Biological Nitrogen Removing Wastewater Treatment Systems

Biological nitrogen removal (BNR) in centralized and decentralized wastewater treatment systems is assumed to be driven by the same microbial processes and to have communities with a similar composition and structure. There is, however, little information to support these assumptions, which may impact the effectiveness of decentralized systems. We used high-throughput sequencing to compare the structure and composition of the nitrifying and denitrifying bacterial communities of nine onsite wastewater treatment systems (OWTS) and one wastewater treatment plant (WTP) by targeting the genes coding for ammonia monooxygenase (amoA) and nitrous oxide reductase (nosZ). The amoA diversity was similar between the WTP and OWTS, but nosZ diversity was generally higher for the WTP. Beta diversity analyses showed the WTP and OWTS promoted distinct amoA and nosZ communities, although there is a core group of N-transforming bacteria common across scales of BNR treatment. Our results suggest that advanced N-removal OWTS have microbial communities that are sufficiently distinct from those of WTP with BNR, which may warrant different management approaches.

Liming reduces N2O emissions from Mediterranean soil after-rewetting and affects the size, structure and transcription of microbial communities

In Mediterranean regions, the accumulation of nitrogenous substrates in soil during summer fallow period has been linked to pulses of N2O emissions upon soil rewetting. Although the mechanisms of N2O emission after soil rewetting have been previously studied, potential mitigation of agronomic practices on N2O pulses is still poorly understood. We studied the N2O emissions after rewetting of degraded soils managed by no-tillage (NT) and conventional tillage (CT), both with or without lime application under laboratory conditions. The soil was rewetted to 50 and 100% of field capacity (FC) and the N2O fluxes, size, structure and gene transcription of the microbial communities involved in the N2O emissions were evaluated. Liming reduced the cumulative N2O emission by more than 70 and 65% respect to the unamended soil after soil rewetting to 50% and 100% of FC, respectively, whereas no significant effect of tillage on N2O emission was observed. Liming strongly influenced the size and structure of ammonia oxidizing bacteria (AOB) and denitrifier communities, increased the transcription of the nirK after soil rewetting, while transcription of genes encoding nitrification enzymes was undetectable. Tillage slightly affected the nitrifier and denitrifier communities, with CT increasing the size of nosZ community. The results indicated that the N2O pulse after soil rewetting was caused by denitrification rather than nitrification. In addition, the increase of nirK transcription suggested that the mitigation of N2O emissions observed in limed soils was due to changes in the denitrification process, possibly with a higher or more efficient reduction of N2O to N2. This study showed the potentials of NT and liming management to mitigate the N2O emission from degraded Mediterranean soils after soil rewetting due to changes in the efficiency of the denitrification process. Our results also showed the usefulness of coupling determinations of gas emission, microbial community structure and gene transcription to clarify the underlying mechanisms of N2O emissions from soil.

Insight into the microbiology of nitrogen cycle in the dairy manure composting process revealed by combining high-throughput sequencing and quantitative PCR

Nitrogen cycling during composting process is not yet fully understood. This study explored the key genes involved in nitrogen cycling during dairy manure composting process using high-throughput sequencing and quantitative PCR technologies. Results showed that nitrogen fixation occurred mainly during the thermophilic and cooling phases, and significantly enhanced the nitrogen content of compost. Thermoclostridium stercorarium was the main diazotroph. Ammonia oxidation occurred during the maturation phase and Nitrosomonas sp. was the most abundant ammonia oxidizing bacteria. Denitrification contributed to the greatest nitrogen loss during the composting process. The nirK community was dominated by Luteimonas sp. and Achromobacter sp., while the nirS community was dominated by Alcaligenes faecalis and Pseudomonas stutzeri. The nosZ community varied in a succession of Halomonas ilicicola, Pseudomonas flexibili and Labrenzia alba dominated communities according to different composting phases. Based on these results, nitrogen cycling models for different phases of the dairy manure composting process were established.

The Structure and Species Co-Occurrence Networks of Soil Denitrifying Bacterial Communities Differ Between A Coniferous and A Broadleaved Forests.

Acacia mangium (AM) and Pinus massoniana (PM) are widely planted in tropical regions, whereas their effects on soil microbial communities remain unclear. We did a comprehensive investigation of soil denitrifying bacterial communities in AM and PM monoculture plantations in Southern China based on the high throughput sequencing data of their functional genes: nirK, nirS, and nosZ. The average abundance of nosZ (1.3 × 107) was significantly higher than nirS (5.6 × 106) and nirK (4.9 × 105). Shannon estimator revealed a markedly higher α-diversity of nirS and nosZ communities in PM than in AM plantations. The AM and PM plantations were dominated by different nirS and nosZ taxa belonging to proteobacteria, actinobacteria, thermoleophilia, chloroflexia, and acidobacteria, while the dominant nirK taxa were mainly categorized into proteobacteria in both types of plantations. The structure of nirS and nosZ communities shifted substantially from AM to PM plantations with changes in soil moisture, NH4+, and microbial biomass nitrogen content. The species co-occurrence network of nirK community was better organized in a more modular manner compared to nirS and nosZ communities, and the network keystone species mostly occurred in PM plantations. These results indicated a highly species corporation of nirK community in response to environmental changes, especially in PM plantations. AM and PM plantations can form different soil denitrifying microbial communities via altering soil physicochemical properties, which may further affect soil N transformations.

Variation in N2O emission and N2O related microbial functional genes in straw- and biochar-amended and non-amended soils

Reducing mineral fertilizer application is an important management practice for mitigating nitrous oxide (N2O) emissions. Crop straw and biochar are two farmer-friendly residues that can be used for reducing the application of mineral fertilizers. However, different effect of straw- and biochar-amended and non-amended soils on N2O emissions is not well understood. Here, we conducted a mesocosm experiment in a vegetable field in Southwestern China using four treatments: control (CT, no addition), solely mineral fertilizers at the recommended dosage (F), maize straw with mineral fertilizers (SF), and biochar with mineral fertilizers (BF), based on the same total nitrogen, phosphorus and potassium contents. Soil N2O fluxes, cumulative N2O emission, soil chemical parameters, the abundance of N2O related microbial functional genes (amoA, nirS, nirK and nosZ) and microbial community structure were monitored and analyzed. Compared to F, the SF treatment increased the cumulative N2O emission. However, no significant difference was observed in cumulative N2O emission between F and BF treatments. Covariation in cumulative N2O emission and soil dissolved organic nitrogen (DON) content indicated that heterotrophic ammonia oxidation fueled by soil DON might be the driving force for N2O production. Compared to F, both SF and BF treatments increased the amoA gene copy numbers of ammonia oxidizing bacteria (AOB) but reduced those of ammonia oxidizing archaea (AOA); nirS and nosZ gene copy numbers were also reduced under SF and BF treatments. Compared to SF, the diversity of nirK and nosZ communities under the BF treatment was increased, whereas the diversity of nirS community was decreased. Lower cumulative N2O emission under BF than that under SF may be attributed to lower N2O production from heterotrophic ammonia oxidation fueled by soil DON and increased N2O consumption mediated by nosZ-harboring denitrifiers.

Response of greenhouse gas emissions and microbial community dynamics to temperature variation during partial nitrification

This study investigated the greenhouse gas emission characteristics and microbial community dynamics with the variation of temperature during partial nitrification. Low temperature weakened nitrite accumulation, and partial nitrification would shift to complete nitrification easily at 15 °C. Based on CO2 equivalents (CO2-eq), partial nitrification process released 2.7 g of greenhouse gases per gMLSS per cycle, and N2O accounted for more than 98% of the total CO2-eq emission. The total CO2-eq emission amount at 35 °C was 45.6% and 153.4% higher than that at 25 °C and 15 °C, respectively. During partial nitrification, the microbial community diversity greatly declined compared with seed sludge. However, the diversity was enhanced at low temperature. The abundance of Betaproteobacteria at class level increased greatly during partial nitrification. Proteobacteria abundance declined while Nitrospira raised at low temperature. The nosZ community abundance was not affected by temperature, although N2O emission was varied with the operating temperature.

Temperature determines the diversity and structure of N2O‐reducing microbial assemblages

Abstract Micro‐organisms harbouring the nosZ gene convert N2O to N2 and play a critical role in reducing global N2O emissions. As higher denitrifier diversity can result in higher denitrification rates, here we aimed to understand the diversity, composition and spatial structure of N2O‐reducing microbial assemblages in forest soils across a large latitudinal and temperature gradient. We sequenced nosZ gene amplicons of 126 soil samples from six forests with mean annual soil temperatures (MAST) ranging from 3.7 to 25.3°C and tested predictions of the metabolic theory of ecology (MTE) and metabolic‐niche theory (MNT). As predicted, α‐diversity of nosZ communities increased with increasing MAST, within‐site β‐diversity decreased and two (pH and soil moisture) of the three niche widths examined were larger with increasing MAST. We calculated β‐nearest taxon distance and Raup–Crick metric to quantify the relative influence of the assembly processes determining nosZ assemblage structure. Environmental selection was the primary process driving assemblage structure in all six forests. Homogenizing dispersal was also important at one site, which could be explained by the site's much lower variability in soil chemistry. We used canonical correspondence analysis and multiple regression on matrices to examine relationships between nosZ communities and environmental factors, and found that temperature and spatial distance were significant predictors of nosZ assemblage structure. Overall our results support both theories (MTE and MNT) tested, showing that higher temperatures are correlated with higher local diversity, wider niche breadths and lower within‐site turnover rates. A plain language summary is available for this article.

Soil properties impacting denitrifier community size, structure, and activity in New Zealand dairy-grazed pasture

Abstract. Denitrification is an anaerobic respiration process that is the primary contributor of the nitrous oxide (N2O) produced from grassland soils. Our objective was to gain insight into the relationships between denitrifier community size, structure, and activity for a range of pasture soils. We collected 10 dairy pasture soils with contrasting soil textures, drainage classes, management strategies (effluent irrigation or non-irrigation), and geographic locations in New Zealand, and measured their physicochemical characteristics. We measured denitrifier abundance by quantitative polymerase chain reaction (qPCR) and assessed denitrifier diversity and community structure by terminal restriction fragment length polymorphism (T-RFLP) of the nitrite reductase (nirS, nirK) and N2O reductase (nosZ) genes. We quantified denitrifier enzyme activity (DEA) using an acetylene inhibition technique. We investigated whether varied soil conditions lead to different denitrifier communities in soils, and if so, whether they are associated with different denitrification activities and are likely to generate different N2O emissions. Differences in the physicochemical characteristics of the soils were driven mainly by soil mineralogy and the management practices of the farms. We found that nirS and nirK communities were strongly structured along gradients of soil water and phosphorus (P) contents. By contrast, the size and structure of the nosZ community was unrelated to any of the measured soil characteristics. In soils with high water content, the richnesses and abundances of nirS, nirK, and nosZ genes were all significantly positively correlated with DEA. Our data suggest that management strategies to limit N2O emissions through denitrification are likely to be most important for dairy farms on fertile or allophanic soils during wetter periods. Finally, our data suggest that new techniques that would selectively target nirS denitrifiers may be the most effective for limiting N2O emissions through denitrification across a wide range of soil types.

Community Composition of Nitrous Oxide Consuming Bacteria in the Oxygen Minimum Zone of the Eastern Tropical South Pacific.

The ozone-depleting and greenhouse gas, nitrous oxide (N2O), is mainly consumed by the microbially mediated anaerobic process, denitrification. N2O consumption is the last step in canonical denitrification, and is also the least O2 tolerant step. Community composition of total and active N2O consuming bacteria was analyzed based on total (DNA) and transcriptionally active (RNA) nitrous oxide reductase (nosZ) genes using a functional gene microarray. The total and active nosZ communities were dominated by a limited number of nosZ archetypes, affiliated with bacteria from marine, soil and marsh environments. In addition to nosZ genes related to those of known marine denitrifiers, atypical nosZ genes, related to those of soil bacteria that do not possess a complete denitrification pathway, were also detected, especially in surface waters. The community composition of the total nosZ assemblage was significantly different from the active assemblage. The community composition of the total nosZ assemblage was significantly different between coastal and off-shore stations. The low oxygen assemblages from both stations were similar to each other, while the higher oxygen assemblages were more variable. Community composition of the active nosZ assemblage was also significantly different between stations, and varied with N2O concentration but not O2. Notably, nosZ assemblages were not only present but also active in oxygenated seawater: the abundance of total and active nosZ bacteria from oxygenated surface water (indicated by nosZ gene copy number) was similar to or even larger than in anoxic waters, implying the potential for N2O consumption even in the oxygenated surface water.

Interactive effects of multiple climate change factors on ammonia oxidizers and denitrifiers in a temperate steppe.

Global climate change could have profound effects on belowground microbial communities and subsequently affect soil biogeochemical processes. The interactive effects of multiple co-occurring climate change factors on microbially mediated processes are not well understood. A four-factorial field experiment with elevated CO2, watering, nitrogen (N) addition and night warming was conducted in a temperate steppe of northern China. Real-time polymerase chain reaction and terminal-restriction fragment length polymorphism, combined with clone library techniques, were applied to examine the effects of those climate change factors on N-related microbial abundance and community composition. Only the abundance of ammonia-oxidizing bacteria significantly increased by nitrogen addition and decreased by watering. The interactions of watering × warming on the bacterial amoA community and warming × nitrogen addition on the nosZ community were found. Redundancy analysis indicated that the ammonia-oxidizing archaeal community was affected by total N and total carbon, while the community of bacterial amoA and nosZ were significantly affected by soil pH. According to a structural equation modeling analysis, climate change influenced net primary production indirectly by altering microbial abundance and activities. These results indicated that microbial responses to the combination of chronic global change tend to be smaller than expected from single-factor global change manipulations.