pH-driven shifts in overall and transcriptionally active denitrifiers control gaseous product stoichiometry in growth experiments with extracted bacteria from soil

Nitrous oxide respiration in acidophilic methanotrophs

Aerobic methanotrophic bacteria are considered strict aerobes but are often highly abundant in hypoxic and even anoxic environments. Despite possessing denitrification genes, it remains to be verified whether denitrification contributes to their growth. Here, we show that acidophilic methanotrophs can respire nitrous oxide (N2O) and grow anaerobically on diverse non-methane substrates, including methanol, C-C substrates, and hydrogen. We study two strains that possess N2O reductase genes: Methylocella tundrae T4 and Methylacidiphilum caldifontis IT6. We show that N2O respiration supports growth of Methylacidiphilum caldifontis at an extremely acidic pH of 2.0, exceeding the known physiological pH limits for microbial N2O consumption. Methylocella tundrae simultaneously consumes N2O and CH4 in suboxic conditions, indicating robustness of its N2O reductase activity in the presence of O2. Furthermore, in O2-limiting conditions, the amount of CH4 oxidized per O2 reduced increases when N2O is added, indicating that Methylocella tundrae can direct more O2 towards methane monooxygenase. Thus, our results demonstrate that some methanotrophs can respire N2O independently or simultaneously with O2, which may facilitate their growth and survival in dynamic environments. Such metabolic capability enables these bacteria to simultaneously reduce the release of the key greenhouse gases CO2, CH4, and N2O.

Molecular and Dual-Isotopic Profiling of the Microbial Controls on Nitrogen Leaching in Agricultural Soils under Managed Aquifer Recharge

Nitrate (NO₃^-) leaching is a serious health and ecological concern in global agroecosystems, particularly those under the application of agricultural-managed aquifer recharge (Ag-MAR); however, there is an absence of information on microbial controls affecting NO₃^- leaching outcomes. We combine natural dual isotopes of NO₃^- (¹⁵N/¹⁴N and ¹⁸O/¹⁶O) with metagenomics, quantitative polymerase chain reaction (PCR), and a threshold indicator taxa analysis (TITAN) to investigate the activities, taxon profiles, and environmental controls of soil microbiome associated with NO₃^- leaching at different depths from Californian vineyards under Ag-MAR application. The isotopic signatures demonstrated a significant priming effect (P < 0.01) of Ag-MAR on denitrification activities in the topsoil (0-10 cm), with a 12-25-fold increase of ¹⁵N-NO₃^- and ¹⁸O-NO₃^- after the first 24 h of flooding, followed by a sharp decrease in the enrichment of both isotopes with ∼80% decline in denitrification activities thereafter. In contrast, deeper soils (60-100 cm) showed minimal or no denitrification activities over the course of Ag-MAR application, thus resulting in 10-20-fold of residual NO₃^- being leached. Metagenomic profiling and laboratory microcosm demonstrated that both nitrifying and denitrifying groups, responsible for controlling NO₃^- leaching, decreased in abundance and potential activity rates with soil depth. TITAN suggested that Nitrosocosmicus and Bradyrhizobium, as the major nitrifier and denitrifier, had the highest and lowest tipping points with regard to the NO₃^- changes (P < 0.05), respectively. Overall, our study provides new insight into specific depth limitations of microbial controls on soil NO₃^- leaching in agroecosystems.

Nitrate determines the bacterial habitat specialization and impacts microbial functions in a subsurface karst cave

Karst caves are usually considered as natural laboratories to study pristine microbiomes in subsurface biosphere. However, effects of the increasingly detected nitrate in underground karst ecosystem due to the acid rain impact on microbiota and their functions in subsurface karst caves have remained largely unknown. In this study, samples of weathered rocks and sediments were collected from the Chang Cave, Hubei province and subjected to high-throughput sequencing of 16S rRNA genes. The results showed that nitrate significantly impacted bacterial compositions, interactions, and functions in different habitats. Bacterial communities clustered according to their habitats with distinguished indicator groups identified for each individual habitat. Nitrate shaped the overall bacterial communities across two habitats with a contribution of 27.2%, whereas the pH and TOC, respectively, structured bacterial communities in weathered rocks and sediments. Alpha and beta diversities of bacterial communities increased with nitrate concentration in both habitats, with nitrate directly affecting alpha diversity in sediments, but indirectly on weathered rocks by lowering pH. Nitrate impacted more on bacterial communities in weathered rocks at the genus level than in sediments because more genera significantly correlated with nitrate concentration in weathered rocks. Diverse keystone taxa involved in nitrogen cycling were identified in the co-occurrence networks such as nitrate reducers, ammonium-oxidizers, and N₂-fixers. Tax4Fun2 analysis further confirmed the dominance of genes involved in nitrogen cycling. Genes of methane metabolism and carbon fixation were also dominant. The dominance of dissimilatory and assimilatory nitrate reduction in nitrogen cycling substantiated nitrate impact on bacterial functions. Our results for the first time revealed the impact of nitrate on subsurface karst ecosystem in terms of bacterial compositions, interactions, and functions, providing an important reference for further deciphering the disturbance of human activities on the subsurface biosphere.

Spatial pattern of functional genes abundance reveals the importance of PhoD gene harboring bacterial community for maintaining plant growth in the tropical forest of Southwestern China

The concept of microbial functional genes has added a new dimension to microbial ecology research by improving the model of microbial community-ecosystem functions relationship. However, our knowledge vis-à-vis fine-scale spatial distribution pattern of functional genes and their probable impact on plant community in the hyper-diverse tropical forest ecosystem is very limited. Here, we investigated the spatial pattern of functional genes abundance (NirK, AOA, AOB, and PhoD), identified key influencing factors, and distinguished the key functional group supporting the plant community in a tropical rainforest located in Xishuangbanna. In total, 200 soil samples and vegetation data of ~4800 individuals of plants across a 1 ha study area were collected. Our results detected higher spatial variability with a maximum magnitude of abundance for PhoD gene (4.53 × 10⁷ copies) followed by NirK (2.71 × 10⁶ copies), AOA (1.97 × 10⁶ copies), and AOB (7.38 × 10⁴ copies). A strong spatial dependence was observed for PhoD and NirK over the distance of 17 and 18 m, respectively. Interestingly, the N:P stoichiometry played a critical role in structuring the spatial pattern of the most abundant PhoD gene. The significant positive and negative relationship of PhoD with N:P ratio and available phosphorus, respectively, indicated that the P-limiting environment was a driving factor for recruitment of PhoD gene community. The structural equation modeling ascertained the direct positive impact of PhoD on plant biomass and high demand of available P by plants suggesting that the organic phosphorus mineralization process is essential to maintain plant productivity by re-establishing the availability of the most limiting P nutrient. Our preliminary study improves our understanding of how microbial functional genes-environment associations could be used for monitoring soil health and its overall impact on ecosystem multifunctionality. Finally, we intend to conduct the study at a large spatial scale for achieving a holistic view.

Co-composting of cattle manure with biochar and elemental sulphur and its effects on manure quality, plant biomass and microbiological characteristics of post-harvest soil

Improvement of manure by co-composting with other materials is beneficial to the quality of the amended soil. Therefore, the manure was supplied with either biochar, elemental sulphur or both prior to fermentation in 50 L barrels for a period of eight weeks. The manure products were subsequently analyzed and used as fertilizers in a short-term pot experiment with barley fodder (Hordeum vulgare L.). The experiment was carried out under controlled conditions in a growth chamber for 12 weeks. The sulphur-enriched manure showed the lowest manure pH and highest ammonium content. The co-fermentation of biochar and sulphur led to the highest sulphur content and an abundance of ammonium-oxidizing bacteria in manure. The biochar+sulphur-enriched manure led to the highest dry aboveground plant biomass in the amended soil, whose value was 98% higher compared to the unamended control, 38% higher compared to the variant with biochar-enriched manure and 23% higher compared to the manure-amended variant. Amendment of the sulphur-enriched manure types led to the highest enzyme activities and soil respirations (basal, substrate-induced). This innovative approach to improve the quality of organic fertilizers utilizes treated agricultural waste (biochar) and a biotechnological residual product (elementary sulphur from biogas desulphurization) and hence contributes to the circular economy.

Urea fertilization and grass species alter microbial nitrogen cycling capacity and activity in a C4 native grassland

Soil microbial transformation of nitrogen (N) in nutrient-limited native C₄ grasslands can be affected by N fertilization rate and C₄ grass species. Here, we report in situ dynamics of the population size (gene copy abundances) and activity (transcript copy abundances) of five functional genes involved in soil N cycling (nifH, bacterial amoA, nirK, nirS, and nosZ) in a field experiment with two C₄ grass species (switchgrass (Panicum virgatum) and big bluestem (Andropogon gerardii)) under three N fertilization rates (0, 67, and 202 kg N ha^-1). Diazotroph (nifH) abundance and activity were not affected by N fertilization rate nor grass species. However, moderate and high N fertilization promoted population size and activity of ammonia oxidizing bacteria (AOB, quantified via amoA genes and transcripts) and nitrification potential. Moderate N fertilization increased abundances of nitrite-reducing bacterial genes (nirK and nirS) under switchgrass but decreased these genes under big bluestem. The activity of nitrous oxide reducing bacteria (nosZ transcripts) was also promoted by moderate N fertilization. In general, high N fertilization had a negative effect on N-cycling populations compared to moderate N addition. Compared to big bluestem, the soils planted with switchgrass had a greater population size of AOB and nitrite reducers. The significant interaction effects of sampling season, grass species, and N fertilization rate on N-cycling microbial community at genetic-level rather than transcriptional-level suggested the activity of N-cycling microbial communities may be driven by more complex environmental factors in native C₄ grass systems, such as climatic and edaphic factors.

A review on nirS-type and nirK-type denitrifiers via a scientometric approach coupled with case studies

The denitrification process plays an important role in improving water quality and is a source/sink of nitrous oxide to the atmosphere. The second important rate-limiting step of the denitrification process is catalyzed by two enzymes with different structures and unrelated evolutionary relationships, namely, the Cu-type nitrite reductase encoded by the nirK gene and the cytochrome cd1-type nitrite reductase encoded by the nirS gene. Although some relevant reviews have been published on denitrifiers, most of these reviews do not include statistical analysis, and do not compare the nirS and nirK communities in-depth. However, a systematic study of the nirS-type and nirK-type denitrifying communities and their response to environmental factors in different ecosystems is needed. In this review, a scientometric approach combined with case studies was used to study the nirS-type and nirK-type denitrifiers. The scientometric approach demonstrated that Pseudomonas, Paracoccus, and Thauera are the most frequently mentioned nirS-type denitrifiers, while Pseudomonas and Bradyrhizobium are the top two most frequently mentioned nirK-type denitrifiers. Among various environmental factors, the concentrations of nitrite, nitrate and carbon sources were widely reported factors that can influence the abundance and structure of nirS-type and nirK-type denitrifying communities. Case studies indicated that Bradyrhizobium was the major genus detected by high-throughput sequencing in both nirS and nirK-type denitrifiers in soil systems. nirS-type denitrifiers are more sensitive to the soil type, soil moisture, pH, and rhizosphere effect than nirK. To clarify the relationships between denitrifying communities and environmental factors, the DNA stable isotope probe combined with metagenomic sequencing is needed for new denitrifier detections.

Effects of Land-Use Type and Flooding on the Soil Microbial Community and Functional Genes in Reservoir Riparian Zones

Ecological processes (e.g., nutrient cycling) in riparian zones are often affected by land-use type and flooding. The extent to which land-use types and flooding conditions affect soil microorganisms and their ecological functions in riparian zones is not well known. By using high-throughput sequencing and quantitative PCR (q-PCR), we tested the effects of three land-use types (i.e., forest, wetland, and grassland) and two flooding conditions (i.e., landward locations and waterward locations within the land-use types) on soil microbial communities and microbial functional genes in the riparian zones of a reservoir. Land-use type but not flooding significantly affected soil microbial community composition at the phylum level, while both land-use type and flooding significantly affected the orders Nitrosotaleales and Nitrososphaerales. Alpha diversity was higher in the wetland and forest regardless of flooding conditions. Functional gene abundance differed among the three land-use types. Archaeal amoA (AOA) and nirS genes were more abundant in the wetland than in the grassland or forest. Bacterial amoA (AOB), nirK, nirS, and nosZ genes were more abundant in the waterward location than in the landward location but only in the wetland. Soil pH, moisture, and concentrations of soil organic matter and total soil nitrogen were significantly associated with the composition of archaeal and bacterial communities as well as with their gene abundance. This study revealed that soil microorganisms putatively involved in nitrogen cycling in riparian zones were more affected by land-use type than flooding.

The Presence of Denitrifiers In Bacterial Communities of Urban Stormwater Best Management Practices (BMPs)

Stormwater best management practices (BMPs) are engineered structures that attempt to mitigate the impacts of stormwater, which can include nitrogen inputs from the surrounding drainage area. The goal of this study was to assess bacterial community composition in different types of stormwater BMP soils to establish whether a particular BMP type harbors more denitrification potential. Soil sampling took place over the summer of 2015 following precipitation events. Soils were sampled from four bioretention facilities, four dry ponds, four surface sand filters, and one dry swale. 16S rRNA gene analysis of extracted DNA and RNA amplicons indicated high bacterial diversity in the soils of all BMP types sampled. An abundance of denitrifiers was also indicated in the extracted DNA using presence/absence of nirS, nirK, and nosZ denitrification genes. BMP soil bacterial communities were impacted by the surrounding soil physiochemistry. Based on the identification of a metabolically-active community of denitrifiers, this study has indicated that denitrification could potentially occur under appropriate conditions in all types of BMP sampled, including surface sand filters that are often viewed as providing low potential for denitrification. The carbon content of incoming stormwater could be providing bacterial communities with denitrification conditions. The findings of this study are especially relevant for land managers in watersheds with legacy nitrogen from former agricultural land use.

Patterns and Drivers of nirK-Type and nirS-Type Denitrifier Community Assembly along an Elevation Gradient

nirK-type and nirS-type denitrifier communities mediate the conversion of nitrite to nitric oxide, which is the key step in denitrification. Results of previous studies have indicated that nirK-type and nirS-type denitrifiers may occupy different niches; however, the mechanisms and drivers of their responses to environmental changes within community assembly are poorly understood. In this study, we evaluated the distribution and assembly of nirK-type and nirS-type denitrifier communities along an elevation gradient from 1,800 to 4,100 m at Mount Gongga, China. Results showed that elevational patterns of alpha diversity in nirK-type and nirS-type denitrifier communities followed hump-backed patterns along the elevation gradient. However, nirK-type denitrifier communities formed two distinct clusters that were primarily separated by elevation, whereas nirS-type denitrifier communities formed three distinct clusters that were primarily separated by forest type along the elevation gradient. Moreover, deterministic processes were dominant in governing the assemblages of nirK-type and nirS-type denitrifiers. Soil pH was a key factor influencing the alpha and beta diversity of the nirK-type denitrifier communities, whereas plant richness was a primary variable influencing nirS-type denitrifiers. Additionally, our work revealed that soil denitrification potential was mainly explained by the variation in the beta diversity of denitrifier communities rather than the alpha diversity of denitrifier communities or denitrifier abundances over a large elevation gradient, and nirK-type denitrifiers played more important roles in soil denitrification. These results may contribute to predicting the consequences of global changes on denitrifier communities and their ecological services. IMPORTANCE Mount Gongga is the highest peak in the Hengduan Mountain region and is located at the southeastern fringe of the Tibetan Plateau, Sichuan Province, southwest China. As a transitional zone between the Tibetan Plateau and Sichuan Basin, Gongga Mountain features particularly diverse topography, geology, climate, and biodiversity and is a globally significant hot spot of biodiversity. In this contribution, we comprehensively describe the diversity and assembly of denitrifier communities along an elevation gradient on Gongga Mountain. Our findings established for the first time that the distribution patterns of beta diversity and driving factors differed between nirK-type and nirS-type denitrifier communities, and deterministic processes were dominant in shaping communities of denitrifiers. Moreover, the beta diversity of denitrifier communities rather than alpha diversity or denitrifier abundance played an important role in explaining denitrification potential, and the beta diversity of nirK-type denitrifier communities was more important than nirS-type denitrifier communities in soil denitrification. This work provides crucial insights into the spatial distribution of denitrifier communities and their ecological function and increases our understanding of the mechanisms underlying spatial distribution of community assembly along large elevation gradients.

Effect of pH on the denitrification proteome of the soil bacterium Paracoccus denitrificans PD1222

Denitrification is a respiratory process by which nitrate is reduced to dinitrogen. Incomplete denitrification results in the emission of the greenhouse gas nitrous oxide and this is potentiated in acidic soils, which display reduced denitrification rates and high N2O/N2 ratios compared to alkaline soils. In this work, impact of pH on the proteome of the soil denitrifying bacterium Paracoccus denitrificans PD1222 was analysed with nitrate as sole energy and nitrogen source under anaerobic conditions at pH ranging from 6.5 to 7.5. Quantitative proteomic analysis revealed that the highest difference in protein representation was observed when the proteome at pH 6.5 was compared to the reference proteome at pH 7.2. However, this difference in the extracellular pH was not enough to produce modification of intracellular pH, which was maintained at 6.5 ± 0.1. The biosynthetic pathways of several cofactors relevant for denitrification and nitrogen assimilation like cobalamin, riboflavin, molybdopterin and nicotinamide were negatively affected at pH 6.5. In addition, peptide representation of reductases involved in nitrate assimilation and denitrification were reduced at pH 6.5. Data highlight the strong negative impact of pH on NosZ synthesis and intracellular copper content, thus impairing active NosZ assembly and, in turn, leading to elevated nitrous oxide emissions.

Denitrification using permeable reactive barriers with organic substrate or zero-valent iron fillers: controlling mechanisms, challenges, and future perspectives

Nitrate as a diffusive agricultural contaminant has been causing substantial groundwater quality deterioration worldwide. In situ groundwater remediation techniques using permeable reactive barriers (PRBs) have attracted increasing interest. Particularly, PRBs based on biological denitrification, using the organic substrate as a biostimulator, and chemical nitrate reduction, using zero-valent iron (ZVI) as a reductant, are two major PRB approaches for groundwater denitrification. This review paper analyzed the published studies over the past 10 years (2010-2020) using laboratory, modeling, and field-scale approaches to explore the performance and mechanisms of these two types of PRBs. Important factors affecting the denitrification efficiencies as well as the influential mechanisms were discussed. Several research gaps have been identified and further research needs are discussed in the end.

Co-association of Two nir Denitrifiers Under the Influence of Emergent Macrophytes

Diverse microorganisms perform similar metabolic process in biogeochemical cycles, whereas they are found of highly genomic differentiation. Biotic interactions should be considered in any community survey of these functional groups, as they contribute to community assembly and ultimately alter ecosystem properties. Current knowledge has mainly been achieved based on functional community characterized by a single gene using co-occurrence network analysis. Biotic interactions between functionally equivalent microorganisms, however, have received much less attention. Herein, we propose the nirK- and nirS-type denitrifier communities represented by these two nitrite reductase (nir)-encoding genes, as model communities to investigate the potential interactions of two nir denitrifiers. We evaluated co-occurrence patterns and co-association network structures of nir denitrifier community from an emergent macrophyte-dominated riparian zone of highly active denitrification in Lake Taihu, China. We found a more segregated pattern in combined nir communities than in individual communities. Network analyses revealed a modularized structure of associating nir denitrifiers. An increased proportion of negative associations among combined communities relative to those of individual communities indicated potential interspecific competition between nirK and nirS denitrifiers. pH and NH₄⁺-N were the most important factors driving co-occurrence and mutual exclusion between nirK and nirS denitrifiers. We also showed the topological importance of nirK denitrifiers acting as module hubs for constructing entire association networks. We revealed previously unexplored co-association relationships between nirK and nirS denitrifiers, which were previously neglected in network analyses of individual communities. Using nir denitrifier community as a model, these findings would be helpful for us to understand the biotic interactions and mechanisms underlying how functional groups co-exist in performing biogeochemical cycles.

The distribution of functional N-cycle related genes and ammonia and nitrate nitrogen in soil profiles fertilized with mineral and organic N fertilizer

Nitrogen transformation in soil is a complex process and the soil microbial population can regulate the potential for N mineralization, nitrification and denitrification. Here we show that agricultural soils under standard agricultural N-management are consistently characterized by a high presence of gene copies for some of the key biological activities related to the N-cycle. This led to a strong NO₃^- reduction (75%) passing from the soil surface (15.38 ± 11.36 g N-NO₃ kg^-1 on average) to the 1 m deep layer (3.92 ± 4.42 g N-NO₃ kg^-1 on average), and ensured low nitrate presence in the deepest layer. Under these circumstances the other soil properties play a minor role in reducing soil nitrate presence in soil. However, with excessive N fertilization, the abundance of bacterial gene copies is not sufficient to explain N leaching in soil and other factors, i.e. soil texture and rainfall, become more important in controlling these aspects.

Performance of sulfur-based autotrophic denitrification and denitrifiers for wastewater treatment under acidic conditions

Autotrophic denitrification under acidic conditions using sulfide (S^2-), elemental sulfur (S⁰), and thiosulfate (S₂O₃^2-) as electron donors are evaluated. Results from batch and column experiments show that when different S species were supplied, different pH conditions and denitrifier communities were required for denitrification to occur. Nitrate and nitrite were removed via autotrophic denitrification at pH ranging from 4 to 8, when S^2- or S₂O₃^2- was the electron donor, while with S⁰ denitrification was only observed at pH > 6. When S^2- was used as electron donor, it was converted to S⁰, and S⁰ was not used while S^2- was available. When addition of S^2- was discontinued, or S^2- depleted, S⁰ that had accumulated was used as electron donor for denitrification. These findings demonstrate that sulfur-based autotrophic denitrification can proceed under acidic conditions, but that the addition of appropriate S species and the presence of an effective denitrifier community are required.

Mitigation of N2O emissions from urine treated acidic soils by liming

Nitrous oxide (N₂O) is a devastating greenhouse gas mainly released from soils to the atmosphere. Pasture soils, particularly acidic in nature, are large contributors of atmospheric N₂O through deposition of urine-N. Devising strategies for reducing N₂O emissions in acidic soils are the utmost need of the time. Therefore, the present study was carried out to investigate the possible efficacy of dolomite application to reduce N₂O emissions from urine treated acidic soil. Application of urine to soil enlarged the production of NH₄⁺-N, NO₃^--N, microbial biomass C (MBC) and dissolved organic C (DOC), resulting in higher N₂O emissions as compared to the control (soil only). The highest N₂O emission rate (1.35 μg N₂O-N kg^-1 h^-1) and cumulative flux (408 μg N₂O-N kg^-1) occurred in urine only treated soil. Dolomite addition, especially higher application dose, greatly reduced N₂O emissions through improved soil pH. The results suggest that increasing pH of acidic soils is a good applicable approach for reducing N₂O emissions from urine-treated soils.

Variable response of nirK and nirS containing denitrifier communities to long-term pH manipulation and cultivation

Denitrification is a key process responsible for the majority of soil nitrous oxide (N2O) emissions but the influences of pH and cultivation on the soil denitrifier community remain poorly understood. We hypothesised that the abundance and community structure of the total bacterial community and bacterial denitrifiers would be pH sensitive and that nirK and nirS containing denitrifiers would differ in their responses to change in pH and cultivation. We investigated the effect of long-term pH-adjusted soils (ranging from pH 4.2 to 6.6) under different lengths of grass cultivation (one, two and three years of ley grass) on the general bacterial and denitrifier functional communities using 16S rRNA, nirK and nirS genes as markers. Denitrifier abundance increased with pH, and at pH below 4.7 there was a greater loss in nirS abundance per unit drop in pH than soils above this threshold pH. All community structures responded to changes in soil pH, while cultivation only influenced the community structure of nirK. These differences in denitrifier responses highlight the importance of considering both nirK and nirS gene markers for estimating denitrifier activity. Identifying such thresholds in response of the microbial community to changes in pH is essential to understanding impacts of management or environmental change.

Ecological and physiological implications of nitrogen oxide reduction pathways on greenhouse gas emissions in agroecosystems

Microbial reductive pathways of nitrogen (N) oxides are highly relevant to net emissions of greenhouse gases (GHG) from agroecosystems. Several biotic and abiotic N-oxide reductive pathways influence the N budget and net GHG production in soil. This review summarizes the recent findings of N-oxide reduction pathways and their implications to GHG emissions in agroecosystems and proposes several mitigation strategies. Denitrification is the primary N-oxide reductive pathway that results in direct N2O emissions and fixed N losses, which add to the net carbon footprint. We highlight how dissimilatory nitrate reduction to ammonium (DNRA), an alternative N-oxide reduction pathway, may be used to reduce N2O production and N losses via denitrification. Implications of nosZ abundance and diversity and expressed N2O reductase activity to soil N2O emissions are reviewed with focus on the role of the N2O-reducers as an important N2O sink. Non-prokaryotic N2O sources, e.g. fungal denitrification, codenitrification and chemodenitrification, are also summarized to emphasize their potential significance as modulators of soil N2O emissions. Through the extensive review of these recent scientific advancements, this study posits opportunities for GHG mitigation through manipulation of microbial N-oxide reductive pathways in soil.

Rapid increases in soil pH solubilise organic matter, dramatically increase denitrification potential and strongly stimulate microorganisms from the Firmicutes phylum

Rapid and transient changes in pH frequently occur in soil, impacting dissolved organic matter (DOM) and other chemical attributes such as redox and oxygen conditions. Although we have detailed knowledge on microbial adaptation to long-term pH changes, little is known about the response of soil microbial communities to rapid pH change, nor how excess DOM might affect key aspects of microbial N processing. We used potassium hydroxide (KOH) to induce a range of soil pH changes likely to be observed after livestock urine or urea fertilizer application to soil. We also focus on nitrate reductive processes by incubating microcosms under anaerobic conditions for up to 48 h. Soil pH was elevated from 4.7 to 6.7, 8.3 or 8.8, and up to 240-fold higher DOM was mobilized by KOH compared to the controls. This increased microbial metabolism but there was no correlation between DOM concentrations and CO₂ respiration nor N-metabolism rates. Microbial communities became dominated by Firmicutes bacteria within 16 h, while few changes were observed in the fungal communities. Changes in N-biogeochemistry were rapid and denitrification enzyme activity (DEA) increased up to 25-fold with the highest rates occurring in microcosms at pH 8.3 that had been incubated for 24-hour prior to measuring DEA. Nitrous oxide reductase was inactive in the pH 4.7 controls but at pH 8.3 the reduction rates exceeded 3,000 ng N₂-N g^-1 h^-1 in the presence of native DOM. Evidence for dissimilatory nitrate reduction to ammonium and/or organic matter mineralisation was observed with ammonium increasing to concentrations up to 10 times the original native soil concentrations while significant concentrations of nitrate were utilised. Pure isolates from the microcosms were dominated by Bacillus spp. and exhibited varying nitrate reductive potential.

How Rainforest Conversion to Agricultural Systems in Sumatra (Indonesia) Affects Active Soil Bacterial Communities

Palm oil production in Indonesia increased constantly over the last decades, which led to massive deforestation, especially on Sumatra island. The ongoing conversion of rainforest to agricultural systems results in high biodiversity loss. Here, we present the first RNA-based study on the effects of rainforest transformation to rubber and oil palm plantations in Indonesia for the active soil bacterial communities. For this purpose, bacterial communities of three different converted systems (jungle rubber, rubber plantation, and oil palm plantation) were studied in two landscapes with rainforest as reference by RT-PCR amplicon-based analysis of 16S rRNA gene transcripts. Active soil bacterial communities were dominated by Frankiales (Actinobacteria), subgroup 2 of the Acidobacteria and Alphaproteobacteria (mainly Rhizobiales and Rhodospirillales). Community composition differed significantly between the converted land use systems and rainforest reference sites. Alphaproteobacteria decreased significantly in oil palm samples compared to rainforest samples. In contrast, relative abundances of taxa within the Acidobacteria increased. Most important abiotic drivers for shaping soil bacterial communities were pH, calcium concentration, base saturation and C:N ratio. Indicator species analysis showed distinct association patterns for the analyzed land use systems. Nitrogen-fixing taxa including members of Rhizobiales and Rhodospirillales were associated with rainforest soils while nitrifiers and heat-resistant taxa including members of Actinobacteria were associated with oil palm soils. Predicted metabolic profiles revealed that the relative abundances of genes associated with fixation of nitrogen significantly decreased in plantation soils. Furthermore, predicted gene abundances regarding motility, competition or gene transfer ability indicated rainforest conversion-induced changes as well.

Effects of partially saturated conditions on the metabolically active microbiome and on nitrogen removal in vertical subsurface flow constructed wetlands

Nitrogen dynamics and its association to metabolically active microbial populations were assessed in two vertical subsurface vertical flow (VF) wetlands treating urban wastewater. These VF wetlands were operated in parallel with unsaturated (UVF) and partially saturated (SVF) configurations. The SVF wetland exhibited almost 2-fold higher total nitrogen removal rate (5 g TN m^-2 d^-1) in relation to the UVF wetland (3 g TN m^-2 d^-1), as well as a low NO_x-N accumulation (1 mg L^-1 vs. 26 mg L^-1 in SVF and UVF wetland effluents, respectively). After 6 months of operation, ammonia oxidizing prokaryotes (AOP) and nitrite oxidizing bacteria (NOB) displayed an important role in both wetlands. Oxygen availability and ammonia limiting conditions promoted shifts on the metabolically active nitrifying community within 'nitrification aggregates' of wetland biofilms. Ammonia oxidizing archaea (AOA) and Nitrospira spp. overcame ammonia oxidizing bacteria (AOB) in the oxic layers of both wetlands. Microbial quantitative and diversity assessments revealed a positive correlation between Nitrobacter and AOA, whereas Nitrospira resulted negatively correlated with Nitrobacter and AOB populations. The denitrifying gene expression was enhanced mainly in the bottom layer of the SVF wetland, in concomitance with the depletion of NO_x-N from wastewater. Functional gene expression of nitrifying and denitrifying populations combined with the active microbiome diversity brought new insights on the microbial nitrogen-cycling occurring within VF wetland biofilms under different operational conditions.

Linking Nitrogen Load to the Structure and Function of Wetland Soil and Rhizosphere Microbial Communities

Microorganisms living within the rhizospheres of wetland plants significantly contribute to greenhouse gas emissions. Understanding how microbes produce these gases under conditions that have been imposed by human activities (i.e., nitrogen pollution) is important to the development of future management strategies. Our results illustrate that within the rhizosphere of the wetland plant Juncus acutiflorus, physiological differences associated with nitrogen availability can influence microbial activity linked to greenhouse gas production. By pairing taxonomic information and environmental conditions like nitrogen availability with functional outputs of a system such as greenhouse gas fluxes, we present a framework to link certain taxa to both nitrogen load and greenhouse gas production. We view this type of combined information as essential in moving forward in our understanding of complex systems such as rhizosphere microbial communities.

Wetland ecosystems are important reservoirs of biodiversity and significantly contribute to emissions of the greenhouse gases CO₂, N₂O, and CH₄. High anthropogenic nitrogen (N) inputs from agriculture and fossil fuel combustion have been recognized as a severe threat to biodiversity and ecosystem functioning, such as control of greenhouse gas emissions. Therefore, it is important to understand how increased N input into pristine wetlands affects the composition and activity of microorganisms, especially in interaction with dominant wetland plants. In a series of incubations analyzed over 90 days, we disentangled the effects of N fertilization on the microbial community in bulk soil and the rhizosphere of Juncus acutiflorus, a common and abundant graminoid wetland plant. We observed an increase in greenhouse gas emissions when N is increased in incubations with J. acutiflorus, changing the system from a greenhouse gas sink to a source. Using 16S rRNA gene amplicon sequencing, we determined that the bacterial orders Opitutales, subgroup 6 Acidobacteria, and Sphingobacteriales significantly responded to high N availability. Based on metagenomic data, we hypothesize that these groups are contributing to the increased greenhouse gas emissions. These results indicated that increased N input leads to shifts in microbial activity within the rhizosphere, altering N cycling dynamics. Our study provides a framework for connecting environmental conditions of wetland bulk and rhizosphere soil to the structure and metabolic output of microbial communities.

IMPORTANCE Microorganisms living within the rhizospheres of wetland plants significantly contribute to greenhouse gas emissions. Understanding how microbes produce these gases under conditions that have been imposed by human activities (i.e., nitrogen pollution) is important to the development of future management strategies. Our results illustrate that within the rhizosphere of the wetland plant Juncus acutiflorus, physiological differences associated with nitrogen availability can influence microbial activity linked to greenhouse gas production. By pairing taxonomic information and environmental conditions like nitrogen availability with functional outputs of a system such as greenhouse gas fluxes, we present a framework to link certain taxa to both nitrogen load and greenhouse gas production. We view this type of combined information as essential in moving forward in our understanding of complex systems such as rhizosphere microbial communities.

Dimethyl pyrazol-based nitrification inhibitors effect on nitrifying and denitrifying bacteria to mitigate N2O emission

Nitrous oxide (N2O) emissions have been increasing as a result of intensive nitrogen (N) fertilisation. Soil nitrification and denitrification are the main sources of N2O, and the use of ammonium-based fertilisers combined with nitrification inhibitors (NIs) could be useful in mitigating N2O emissions from agricultural systems. In this work we looked at the N2O mitigation capacity of two dimethylpyrazol-based NIs, 3,4-dimethylpyrazole phosphate (DMPP) and 2-(N-3,4-dimethyl-1H-pyrazol-1-yl) succinic acid isomeric mixture (DMPSA), on soil nitrifying and denitrifying microbial populations under two contrasting soil water contents (40% and 80% soil water filled pore space; WFPS). Our results show that DMPP and DMPSA are equally efficient at reducing N2O emissions under 40% WFPS conditions by inhibiting bacterial ammonia oxidation. In contrast, at 80% WFPS DMPSA was less efficient than DMPP at reducing N2O emissions. Interestingly, at 80% WFPS, where lowered oxygen availability limits nitrification, both DMPP and DMPSA not only inhibited nitrification but also stimulated N2O reduction to molecular nitrogen (N2) via nitrous oxide reductase activity (Nos activity). Therefore, in this work we observed that DMP-based NIs stimulated the reduction of N2O to N2 by nitrous oxide reductase during the denitrification process.

pH Control Enables Simultaneous Enhancement of Nitrogen Retention and N2O Reduction in Shewanella loihica Strain PV-4

pH has been recognized as one of the key environmental parameters with significant impacts on the nitrogen cycle in the environment. In this study, the effects of pH on NO₃^-/NO₂^- fate and N₂O emission were examined with Shewanella loihica strain PV-4, an organism with complete denitrification and respiratory ammonification pathways. Strain PV-4 was incubated at varying pH with lactate as the electron donor and NO₃^-/NO₂^- and N₂O as the electron acceptors. When incubated with NO₃^- and N₂O at pH 6.0, transient accumulation of N₂O was observed and no significant NH₄⁺ production was observed. At pH 7.0 and 8.0, strain PV-4 served as a N₂O sink, as N₂O concentration decreased consistently without accumulation. Respiratory ammonification was upregulated in the experiments performed at these higher pH values. When NO₂^- was used in place of NO₃^-, neither growth nor NO₂^- reduction was observed at pH 6.0. NH₄⁺ was the exclusive product from NO₂^- reduction at both pH 7.0 and 8.0 and neither production nor consumption of N₂O was observed, suggesting that NO₂^- regulation superseded pH effects on the nitrogen-oxide dissimilation reactions. When NO₃^- was the electron acceptor, nirK transcription was significantly upregulated upon cultivation at pH 6.0, while nrfA transcription was significantly upregulated at pH 8.0. The highest level of nosZ transcription was observed at pH 6.0 and the lowest at pH 8.0. With NO₂^- as the electron acceptor, transcription profiles of nirK, nrfA, and nosZ were statistically indistinguishable between pH 7.0 and 8.0. The transcriptions of nirK and nosZ were severely downregulated regardless of pH. These observations suggested that the kinetic imbalance between N₂O production and consumption, but neither decrease in expression nor activity of NosZ, was the major cause of N₂O accumulation at pH 6.0. The findings also suggest that simultaneous enhancement of nitrogen retention and N₂O emission reduction may be feasible through pH modulation, but only in environments where C:N or NO₂^-:NO₃^- ratio does not exhibit overarching control over the NO₃^-/NO₂^- reduction pathways.

Phylogenetic and functional potential links pH and N2O emissions in pasture soils

Denitrification is mediated by microbial, and physicochemical, processes leading to nitrogen loss via N₂O and N₂ emissions. Soil pH regulates the reduction of N₂O to N₂, however, it can also affect microbial community composition and functional potential. Here we simultaneously test the link between pH, community composition, and the N₂O emission ratio (N₂O/(NO + N₂O + N₂)) in 13 temperate pasture soils. Physicochemical analysis, gas kinetics, 16S rRNA amplicon sequencing, metagenomic and quantitative PCR (of denitrifier genes: nirS, nirK, nosZI and nosZII) analysis were carried out to characterize each soil. We found strong evidence linking pH to both N₂O emission ratio and community changes. Soil pH was negatively associated with N₂O emission ratio, while being positively associated with both community diversity and total denitrification gene (nir & nos) abundance. Abundance of nosZII was positively linked to pH, and negatively linked to N₂O emissions. Our results confirm that pH imposes a general selective pressure on the entire community and that this results in changes in emission potential. Our data also support the general model that with increased microbial diversity efficiency increases, demonstrated in this study with lowered N₂O emission ratio through more efficient conversion of N₂O to N₂.