Nitrosospira sp. Govern Nitrous Oxide Emissions in a Tropical Soil Amended With Residues of Bioenergy Crop

AOB Nitrosospira cluster 3a.2 (D11) dominates N2O emissions in fertilised agricultural soils

Ammonia-oxidation process directly contribute to soil nitrous oxide (N2O) emissions in agricultural soils. However, taxonomy of the key nitrifiers (within ammonia oxidising bacteria (AOB), archaea (AOA) and complete ammonia oxidisers (comammox Nitrospira)) responsible for substantial N2O emissions in agricultural soils is unknown, as is their regulation by soil biotic and abiotic factors. In this study, cumulative N2O emissions, nitrification rates, abundance and community structure of nitrifiers were investigated in 16 agricultural soils from major crop production regions of China using microcosm experiments with amended nitrogen (N) supplemented or not with a nitrification inhibitor (nitrapyrin). Key nitrifier groups involved in N2O emissions were identified by comparative analyses of the different treatments, combining sequencing and random forest analyses. Soil cumulative N2O emissions significantly increased with soil pH in all agricultural soils. However, they decreased with soil organic carbon (SOC) in alkaline soils. Nitrapyrin significantly inhibited soil cumulative N2O emissions and AOB growth, with a significant inhibition of the AOB Nitrosospira cluster 3a.2 (D11) abundance. One Nitrosospira multiformis-like OTU phylotype (OTU34), which was classified within the AOB Nitrosospira cluster 3a.2 (D11), had the greatest importance on cumulative N2O emissions and its growth significantly depended on soil pH and SOC contents, with higher growth at high pH and low SOC conditions. Collectively, our results demonstrate that alkaline soils with low SOC contents have high N2O emissions, which were mainly driven by AOB Nitrosospira cluster 3a.2 (D11). Nitrapyrin can efficiently reduce nitrification-related N2O emissions by inhibiting the activity of AOB Nitrosospira cluster 3a.2 (D11). This study advances our understanding of key nitrifiers responsible for high N2O emissions in agricultural soils and their controlling factors, and provides vital knowledge for N2O emission mitigation in agricultural ecosystems.

Moderate precipitation reduction enhances nitrogen cycling and soil nitrous oxide emissions in a semi-arid grassland

The ongoing climate change is predicted to induce more weather extremes such as frequent drought and high-intensity precipitation events, causing more severe drying-rewetting cycles in soil. However, it remains largely unknown how these changes will affect soil nitrogen (N)-cycling microbes and the emissions of potent greenhouse gas nitrous oxide (N₂ O). Utilizing a field precipitation manipulation in a semi-arid grassland on the Loess Plateau, we examined how precipitation reduction (ca. -30%) influenced soil N₂ O and carbon dioxide (CO₂ ) emissions in field, and in a complementary lab-incubation with simulated drying-rewetting cycles. Results obtained showed that precipitation reduction stimulated plant root turnover and N-cycling processes, enhancing soil N₂ O and CO₂ emissions in field, particularly after each rainfall event. Also, high-resolution isotopic analyses revealed that field soil N₂ O emissions primarily originated from nitrification process. The incubation experiment further showed that in field soils under precipitation reduction, drying-rewetting stimulated N mineralization and ammonia-oxidizing bacteria in favor of genera Nitrosospira and Nitrosovibrio, increasing nitrification and N₂ O emissions. These findings suggest that moderate precipitation reduction, accompanied with changes in drying-rewetting cycles under future precipitation scenarios, may enhance N cycling processes and soil N₂ O emissions in semi-arid ecosystems, feeding positively back to the ongoing climate change.

Incorporating straw into intensively farmed cropland soil can reduce N2O emission via inhibition of nitrification and denitrification pathways

Straw incorporation (SI) combined with N fertilizer has been shown to affect soil N₂O emission and N-related functional microbes in agriculture. However, the responses of N₂O emission, community structure of nitrifiers and denitrifiers and related microbial functional genes to straw management strategies in the winter wheat season in China remain unclear. Here, we conducted a two-season experiment in a winter wheat field in Ningjing County, northern China, to examine four treatments: no fertilizer with (N0S1) and without maize straw (N0S0); N fertilizer with (N1S1) and without maize straw (N1S0), and their effects on N₂O emissions, soil chemical parameters, crop yield, as well as the dynamics of nitrifying and denitrifying microbial communities. We found that seasonal N₂O emissions decreased by 7.1-11.1% (p < 0.05) in N1S1 as compared to N1S0, without significant difference between N0S1 and N0S0. In combination with N fertilization, SI increased the yield by 2.6-4.3%, altered the microbial community composition, increased Shannon and ACE indexes, and decreased the abundance of AOA (9.2%), AOB (32.2%; p < 0.05), nirS (35.2%; p < 0.05), nirK (21.6%; p < 0.05) and nosZ (19.2%). However, in the absence of N fertilizer, SI promoted the major genera of Nitrosavbrio (AOB), unclassifiied_Gammaproteobacteria, Rhodanobacter (nirS), Sinorhizobium (nirK), which strongly correlated positively with N₂O emissions. Thereby, a negative interaction effect between SI and N fertilizer on AOB and nirS emphasized that SI could offset the increase of N₂O emission caused by fertilization. Soil moisture and NO₃^- concentration were the major factors affecting N-related microbial community structure. Our study reveals that SI suppressed N₂O emission significantly and simultaneously decreased the abundance of N-related functional genes and altered denitrifying bacterial community composition. We conclude that SI helps to enhance yield and alleviate fertilizer-induced environmental costs in intensively farmed fields in northern China.

Isotopic assessment of soil N2O emission from a sub-tropical agricultural soil under varying N-inputs

Nitrogen fertilizers result in high crop productivity but also enhance the emission of N₂O, an environmentally harmful greenhouse gas. Only approximately a half of the applied nitrogen is utilized by crops and the rest is either vaporized, leached, or lost as NO, N₂O and N₂ via soil microbial activity. Thus, improving the nitrogen use efficiency of cropping systems has become a global concern. Factors such as types and rates of fertilizer application, soil texture, moisture level, pH, and microbial activity/diversity play important roles in N₂O production. Here, we report the results of N₂O production from a set of chamber experiments on an acidic sandy-loam agricultural soil under varying levels of an inorganic N-fertilizer, urea. Stable isotope technique was employed to determine the effect of increasing N-fertilizer levels on N₂O emissions and identify the microbial processes involved in fertilizer N-transformation that give rise to N₂O. We monitored the isotopic changes in both substrate (ammonium and nitrate) and the product N₂O during the entire course of the incubation experiments. Peak N₂O emissions of 122 ± 98 μg N₂O-N m^-2 h^-1, 338 ± 49 μg N₂O-N m^-2 h^-1 and 739 ± 296 μg N₂O-N m^-2 h^-1 were observed for urea application rate of 40, 80, and 120 μg N g^-1. The duration of emissions also increased with urea levels. The concentration and isotopic compositions of the substrates and product showed time-bound variation. Combining the observations of isotopic effects in δ¹⁵N, δ¹⁸O, and ¹⁵N site preference, we inferred co-occurrence of several microbial N₂O production pathways with nitrification and/or fungal denitrification as the dominant processes responsible for N₂O emissions. Besides this, dominant signatures of bacterial denitrification were observed in a second N₂O emission pulse in intermediate urea-N levels. Signature of N₂O consumption by reduction could be traced during declining emissions in treatment with high urea level.

Soil metabolomics and bacterial functional traits revealed the responses of rhizosphere soil bacterial community to long-term continuous cropping of Tibetan barley

Continuous cropping often leads to an unbalanced soil microbial community, which in turn negatively affects soil functions. However, systematic research of how these effects impact the bacterial composition, microbial functional traits, and soil metabolites is lacking. In the present study, the rhizosphere soil samples of Tibetan barley continuously monocropped for 2 (CCY02), 5 (CCY05), and 10 (CCY10) years were collected. By utilizing 16S high-throughput sequencing, untargeted metabolomes, and quantitative microbial element cycling smart chips, we examined the bacterial community structure, soil metabolites, and bacterial functional gene abundances, respectively. We found that bacterial richness (based on Chao1 and Phylogenetic Diversity [PD] indices) was significantly higher in CCY02 and CCY10 than in CCY05. As per principal component analysis (PCA), samples from the continuous monocropping year tended to share more similar species compositions and soil metabolites, and exhibited distinct patterns over time. The results of the Procrustes analysis indicated that alterations in the soil metabolic profiles and bacterial functional genes after long-term continuous cropping were mainly mediated by soil microbial communities (P < 0.05). Moreover, 14 genera mainly contributed to the sample dissimilarities. Of these, five genera were identified as the dominant shared taxa, including Blastococcus, Nocardioides, Sphingomonas, Bacillus, and Solirubrobacter. The continuous cropping of Tibetan barley significantly increased the abundances of genes related to C-degradation (F = 9.25, P = 0.01) and P-cycling (F = 5.35, P = 0.03). N-cycling significantly negatively correlated with bacterial diversity (r =  - 0.71, P = 0.01). The co-occurrence network analysis revealed that nine hub genera correlated with most of the functional genes and a hub taxon, Desulfuromonadales, mainly co-occurred with the metabolites via both negative and positive correlations. Collectively, our findings indicated that continuous cropping significantly altered the bacterial community structure, functioning of rhizosphere soils, and soil metabolites, thereby providing a comprehensive understanding of the effects of the long-term continuous cropping of Tibetan barley.

Controlled nitrogen transformation in chemo-amended urea improves nitrogen use efficiency and productivity of wheat grown on alkaline calcareous soil

Low wheat production is linked to soil degradation, low organic matter, temperature variation, and nutrient depletion in soils of semiarid regions. Nitrogen is mostly applied as urea to meet crop requirements; however, excessive N application may pollute the environment and contaminate groundwater. The current studies explored possible ways for decreasing N losses (NH₃ volatilization and NO₃ leaching) and improving N availability for wheat production in alkaline soil. The ZnO was coated on urea (1% Zn coating) to get zinc-coated urea (ZnU), and both urea and ZnU were incubated in laboratory at recommended rate (RR), i.e., 150 kg N ha^-1 and 80% (N of RR), after further coating with inhibitors [N-(n-butyl) thiophosphoric triamide (NBPT) at 1% of urea and 4-amino-1,2,4-triazole (ATC) at 2% of urea], thus creating six treatments. The results showed higher NH₃-N loss at day 4 and thereafter a decreasing trend reaching to minimum at day 14. The cumulative NH₃-N volatilization from urea alone was found higher (28.99%), except ATC treatments producing statistically similar losses due to restriction in nitrification process. In greenhouse, the treatments were tested in wheat cultivars (Faisalabad 2008 and Lasani) for crop growth, nutrient (N, P, K, and Zn) uptake, and yield parameters, where 80% of RR treatment, i.e., NBPT + ZnU₈₀, was found at par with full RR as commercial products, especially comparable to ZnU (at RR) that produced the highest chlorophyll (53.65unit value), net leaf photosynthetic rate (19.64 μmol CO₂ m^-2 s^-1), plant biomass (208.13 g/pot), grain yield (63.65 g/pot), and nutrient (NPK and Zn) accumulation in grain of Fsd-2008 cultivar. In field trial, NBPT + ZnU₈₀ also outperformed and produced the highest physiological efficiency (PE), agronomic efficiency (AE), and nitrogen recovery efficiency (REN); the treatment also found statistically similar with ZnU (at RR) that produced the maximum plant height (95.4 cm), plant biomass (11.58 t/ha), grain yield (4.69 t/ha), and 1000-grain weight (42.55 g). The relative NO₃ leaching was found lower in 80% N treatments, yet leaching was not significant from either treatment at the three stages of crop growth. Overall, current studies revealed the effectiveness of NBPT-amended urea (followed by ZnU) with 20% saving of N inputs through higher N availability for plant uptake that could benefit growers as well as conserve environment.

Ecological Role of Bacteria Involved in the Biogeochemical Cycles of Mangroves Based on Functional Genes Detected through GeoChip 5.0

Mangroves provide a variety of ecosystem services and contribute greatly to the global biogeochemical cycle. Microorganisms play important roles in biogeochemical cycles and maintain the dynamic balance of mangroves. However, the roles of bacteria in the biogeochemical cycles of mangroves and their ecological distribution and functions remain largely uncharacterized. This study thus sought to analyze and compare the ecological distributions and potential roles of bacteria in typical mangroves using 16S rRNA gene amplicon sequencing and GeoChip. Interestingly, the bacterial community compositions were largely similar in the studied mangroves, including Shenzhen, Yunxiao, Zhanjiang, Hainan, Hongkong, Fangchenggang, and Beihai mangroves. Moreover, gamma-proteobacterium_uncultured and Woeseia were the most abundant microorganisms in the mangroves. Furthermore, most of the bacterial communities were significantly correlated with phosphorus levels (P < 0.05; −0.93 < R < 0.93), suggesting that this nutrient is a vital driver of bacterial community composition. Additionally, GeoChip analysis indicated that the functional genes amyA, narG, dsrA, and ppx were highly abundant in the studied mangroves, suggesting that carbon degradation, denitrification, sulfite reduction, and polyphosphate degradation are crucial processes in typical mangroves. Moreover, several genera were found to synergistically participate in biogeochemical cycles in mangroves. For instance, Neisseria, Ruegeria, Rhodococcus, Desulfotomaculum, and Gordonia were synergistically involved in the carbon, nitrogen, and sulfur cycles, whereas Neisseria and Treponema were synergistically involved in the nitrogen cycle and the sulfur cycle. Taken together, our findings provide novel insights into the ecological roles of bacteria in the biogeochemical cycles of mangroves.

IMPORTANCE Bacteria have important functions in biogeochemical cycles, but studies on their function in an important ecosystem, mangroves, are still limited. Here, we investigated the ecological role of bacteria involved in biogeochemical cycles in seven representative mangroves of southern China. Furthermore, various functional genes from bacteria involved in biogeochemical cycles were identified by GeoChip 5.0. The functional genes associated with the carbon cycle (particularly carbon degradation) were the most abundant, suggesting that carbon degradation is the most active process in mangroves. Additionally, some high-abundance bacterial populations were found to synergistically mediate key biogeochemical cycles in the mangroves, including Neisseria, Pseudomonas, Treponema, Desulfotomaculum, and Nitrosospira. In a word, our study gives novel insights into the function of bacteria in biogeochemical cycles in mangroves.

Ammonia-oxidizing bacterial communities are affected by nitrogen fertilization and grass species in native C4 grassland soils

Background

Fertilizer addition can contribute to nitrogen (N) losses from soil by affecting microbial populations responsible for nitrification. However, the effects of N fertilization on ammonia oxidizing bacteria under C₄ perennial grasses in nutrient-poor grasslands are not well studied.

Methods

In this study, a field experiment was used to assess the effects of N fertilization rate (0, 67, and 202 kg N ha⁻¹) and grass species (switchgrass (Panicum virgatum) and big bluestem (Andropogon gerardii)) on ammonia-oxidizing bacterial (AOB) communities in C₄ grassland soils using quantitative PCR, quantitative reverse transcription-PCR, and high-throughput amplicon sequencing of amoA genes.

Results

Nitrosospira were dominant AOB in the C₄ grassland soil throughout the growing season. N fertilization rate had a stronger influence on AOB community composition than C₄ grass species. Elevated N fertilizer application increased the abundance, activity, and alpha-diversity of AOB communities as well as nitrification potential, nitrous oxide (N₂O) emission and soil acidity. The abundance and species richness of AOB were higher under switchgrass compared to big bluestem. Soil pH, nitrate, nitrification potential, and N₂O emission were significantly related to the variability in AOB community structures (p < 0.05).

Di-(2-ethylhexyl) phthalate (DEHP) exposure suppressed the community diversity and abundance of ammonia-oxidizers and mitigated N2O emissions in an alkaline soil

Phthalic acid esters (PAEs) pollution has become an increasing issue worldwide, but little is known about its effects on ammonia-oxidizers and nitrous oxide (N₂O) in the soil environment. Here, a 50-day soil microcosm experiment was conducted using low and high doses bis (2-Ethylhexyl) phthalate (DEHP) to estimate the effect of DEHP exposure on soil N₂O emissions and the nitrifying community in calcareous soil. The results showed that DEHP exposure at 10 and 100 mg kg^-1 doses significantly reduced N₂O by 67.5% and 73.6%, respectively, relative to the DEHP absent treatment. The microbial biomass carbon and nitrogen (MBC and MBN) were consistently and significantly decreased with DEHP exposure at 5, 22, and 50 days after incubation, especially with high-dose. The bipartite association networks showed that DEHP exposure changed the compositions of both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities. Moreover, the AOA and AOB amoA gene abundances were significantly decreased by DEHP addition to the soil (P < 0.05). Random forest modeling showed that the AOB Shannon index and pH were the most important biotic and abiotic factors affecting N₂O emissions in the soil with DEHP exposure, respectively. Partial least squares path modeling (PLS-PM) demonstrated that the reduction of N₂O emissions due to DEHP exposure was mainly ascribed to the changes of the AOB community. The results from this study highlight the toxicity of DEHP on the ammonia oxidizers, and its mitigating effect on N₂O emissions in the soil where ammonia-oxidation is largely driven by AOB.

Ammonia Oxidizing Prokaryotes Respond Differently to Fertilization and Termination Methods in Common Oat's Rhizosphere

Cover crops (CC) have demonstrated beneficial effects on several soil properties yet questions remain regarding their effects on soil microbial communities. Among them, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) have a key role for N cycling in soil and their responses in the rhizosphere of terminated CC deserve further investigation. A greenhouse experiment was established to assess N fertilization (with or without N) and termination methods (glyphosate, mowing, and untreated control) of common oat (Avena sativa L.) as potential drivers of AOA and AOB responses in the rhizosphere. The abundance of amoA genes was determined by quantitative real-time PCR (qPCR), the community structure was assessed with Illumina amplicon sequencing of these genes, while the function was assessed from potential nitrification activity (PNA). While N fertilization had no influence on AOA, the termination method significantly increased amoA gene copies of AOA in mowed plants relative to glyphosate termination or the untreated control (1.76 and 1.49-fold change, respectively), and shifted AOA community structure (PERMANOVA, p<0.05). Ordination methods indicated a separation between AOA communities from control and glyphosate-terminated plants relative to mowed plants for both UniFrac and Aitchison distance. Converserly, N fertilization significantly increased AOB abundance in the rhizosphere of mowed and control plants, yet not in glyphosate-treated plants. Analyses of community structure showed that AOB changed only in response to N fertilization and not to the termination method. In line with these results, significantly higher PNA values were measured in all fertilized samples, regardless of the termination methods. Overall, the results of this study indicated that bacterial and archaeal nitrifiers have contrasting responses to fertlization and plant termination methods. While AOA were responsive to the termination method, AOB were more sensitive to N additions, although, the stimulative effect of N fertilization on amoA_AOB abundance was dependent on the termination method.

Maize-Brachiaria intercropping: A strategy to supply recycled N to maize and reduce soil N2O emissions?

Nitrogen use in agriculture directly impacts food security, global warming, and environmental degradation. Forage grasses intercropped with maize produce feed for animals and or mulch for no-till systems. Forage grasses may exude nitrification inhibitors. It was hypothesized that brachiaria intercropping increases N recycling and maize grain yield and reduces nitrous oxide (N₂O) emissions from soil under maize cropping. A field experiment was set up in December 2016 to test three cropping system (maize monocropped, maize intercropped with Brachiaria brizantha or with B. humidicola) and two N rates (0 or 150 kg ha^-1). The grasses were sown with maize, but B. humidicola did not germinate well in the first year. B. brizantha developed slowly during the maize cycle because of shading but expanded after maize was harvested. The experiment was repeated in 2017/2018 when B. humidicola was replanted. N₂O and carbon dioxide (CO₂) emissions, maize grain yield and N content were measured during the two seasons. After the first maize harvest, the above- and below-ground biomass, C and N content of B. brizantha grown during fall-winter, and the biological nitrification inhibition potential of B. brizantha were evaluated. Maize yield responded to N fertilization (5.1 vs. 9.8 t ha^-1) but not to brachiaria intercropping. B. brizantha recycled approximately 140 kg N ha^-1 and left 12 t dry matter ha^-1 for the second maize crop. However, the 2017/18 maize yields were not affected by the N recycled by B. brizantha, whereas N₂O emissions were higher in the plots with brachiaria, suggesting that part of the recycled N was released too early after desiccation. Brachiarias showed no evidence of causing nitrification inhibition. The strategy of intercropping brachiarias did not increase maize yield, although it added C and recycled N in the system.

Diversity of microbial communities and genes involved in nitrous oxide emissions in Antarctic soils impacted by marine animals as revealed by metagenomics and 100 metagenome-assembled genomes

Antarctic soils generally have low temperatures and limited availability of liquid water and nutrients. However, animals can increase the nutrient availability of ice-free areas by transferring nutrients from marine to terrestrial ecosystems, mainly through their excreta. In this study, we employed shotgun metagenomics and population genome binning techniques to study the diversity of microbial communities in Antarctic soils impacted by marine pinnipeds and birds relative to soils with no evident animal presence. We obtained ~285,000 16S rRNA gene-carrying metagenomic reads representing ~60 phyla and 100 metagenome-assembled genomes (MAGs) representing eight phyla. Only nine of these 100 MAGs represented previously described species, revealing that these soils harbor extensive novel diversity. Proteobacteria, Actinobacteria, and Bacteroidetes were the most abundant phyla in all samples, with Rhodanobacter being one of the most abundant genera in the bird-impacted soils. Further, the relative abundance of genes related to denitrification was at least double in soils impacted by birds than soils without animal influence. These results advance our understanding of the microbial populations and their genes involved in nitrous oxide emissions in ice-free coastal Antarctic soils impacted by marine animals and reveal novel microbial diversity associated with these ecosystems.

Revealing the community and metabolic potential of active methanotrophs by targeted metagenomics in the Zoige wetland of the Tibetan Plateau

The Zoige wetland of the Tibetan Plateau is one of the largest alpine wetlands in the world and a major emission source of methane. Methane oxidation by methanotrophs can counteract the global warming effect of methane released in the wetlands. Understanding methanotroph activity, diversity and metabolism at the molecular level can guide the isolation of the uncultured microorganisms and inform strategy-making decisions and policies to counteract global warming in this unique ecosystem. Here we applied DNA stable isotope probing using ¹³ C-labelled methane to label the genomes of active methanotrophs, examine the methane oxidation potential and recover metagenome-assembled genomes (MAGs) of active methanotrophs. We found that gammaproteobacteria of type I methanotrophs are responsible for methane oxidation in the wetland. We recovered two phylogenetically novel methanotroph MAGs distantly related to extant Methylobacter and Methylovulum. They belong to type I methanotrophs of gammaproteobacteria, contain both mxaF and xoxF types of methanol dehydrogenase coding genes, and participate in methane oxidation via H₄ MPT and RuMP pathways. Overall, the community structure of active methanotrophs and their methanotrophic pathways revealed by DNA-SIP metagenomics and retrieved methanotroph MAGs highlight the importance of methanotrophs in suppressing methane emission in the wetland under the scenario of global warming.

Plastic film mulching affects N2O emission and ammonia oxidizers in drip irrigated potato soil in northwest China

In soil, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are regarded as key factors mediating nitrous oxide (N₂O) production and emission. However, there are scarce reports about the effect of film mulching on ammonia oxidizers, and the biological nitrification process of N₂O emission is unclear. This study was based on potato field experiments under different mulching films, including polyethylene mulching film (PM), transparent degradable mulching film (TDM), black degradable mulching film (BDM), and bare land (CK). AOB and AOA abundances were estimated using real-time PCR, and their diversity and community structure were measured using high-throughput sequencing. Result revealed that the total N₂O emission from CK was 12.32%-41.03% higher than that from film mulching soil. Under film mulching, according to total N₂O emission from soil and N₂O concentration in soil treatments were ordered as PM > BDM > TDM, and N₂O production was closely correlated with copy numbers of the amoA gene. BDM significantly increased the number of amoA-AOB gene copies (P < 0.01), and PM significantly increased the those of amoA-AOA (P < 0.01). BDM and TDM increased AOB operational taxonomic units (OTUs), Chao1, Simpson, and Shannon indices, while PM increased the AOA OTUs and Chao1 index. Variations in AOA abundance and diversity were closely related to soil mineral N and temperature changes induced by polyethylene film mulching (P < 0.05), whereas AOB showed no significant association with soil properties. Meanwhile, we did not find a distinct treatment effect on AOB community structure. Our findings indicate that (i) degradable film mulching increased AOB abundance and diversity and N₂O concentration, but obviously reduced N₂O emissions, and (ii) AOA were more sensitive than AOB to polyethylene mulching film.

Methods to Identify Soil Microbial Bioindicators of Sustainable Management of Bioenergy Crops

Here we describe a suite of methods to identify potential taxonomic and functional soil microbial indicators of soil quality and plant health in biofuel crops in various areas and land types. This approach draws on tools to assess microbial diversity, greenhouse gas fluxes, and soil physicochemical properties in bioenergy cropping systems. Integrative statistical models are then used to identify potential microbial indicators for sustainable management of bioenergy crops.

Elucidating the role of earthworms in N2O emission and production pathway during vermicomposting of sewage sludge and rice straw

Vermicomposting is a sustainable option for the recycling of biodegradable organic waste. However, it also produces nitrous oxide (N₂O), which is a highly potent greenhouse gas. In this study, the N₂O stable isotope and functional genes for nitrogen cycling were determined to investigate the sources of N₂O during vermicomposting. The results showed that vermicomposting promoted the organic degradation and nitrogen nitrification, and the presence of earthworms increased the emission of N₂O during vermicomposting compared to that during the control treatment with no earthworms. The site preference analysis of N₂O stable isotope showed that both nitrification and denitrification were present during the early stages of vermicomposting, while nitrification was the dominant contributor to N₂O production in the later stages. Moreover, earthworms increased the gene copies of amoA, and stimulated the nitrifying bacteria, and hence, increased the N₂O emission via nitrification. In addition, the activity of earthworms reduced the gene number of nosZ during vermicomposting, while the denitrification was the main source of N₂O in the earthworm gut, as the conditions inside the gut inhibited nosZ. Overall, nitrification was the major pathway (55.8-88.7 %) for N₂O production, which was promoted by the introduction of earthworms through nitrification.

Nitrifying Microbes in the Rhizosphere of Perennial Grasses are Modified by Biological Nitrification Inhibition

Soil nitrification (microbial oxidation of ammonium to nitrate) can lead to nitrogen leaching and environmental pollution. A number of plant species are able to suppress soil nitrifiers by exuding inhibitors from roots, a process called biological nitrification inhibition (BNI). However, the BNI activity of perennial grasses in the nutrient-poor soils of Australia and the effects of BNI activity on nitrifying microbes in the rhizosphere microbiome have not been well studied. Here we evaluated the BNI capacity of bermudagrass (Cynodon dactylon L.), St. Augustinegrass (Stenotaphrum secundatum (Walt.) Kuntze), saltwater couch (Sporobolus virginicus), seashore paspalum (Paspalum vaginatum Swartz.), and kikuyu grass (Pennisetum clandestinum) compared with the known positive control, koronivia grass (Brachiaria humidicola). The microbial communities were analysed by sequencing 16S rRNA genes. St. Augustinegrass and bermudagrass showed high BNI activity, about 80 to 90% of koronivia grass. All the three grasses with stronger BNI capacities suppressed the populations of Nitrospira in the rhizosphere, a bacteria genus with a nitrite-oxidizing function, but not all of the potential ammonia-oxidizing archaea. The rhizosphere of saltwater couch and seashore paspalum exerted a weak recruitment effect on the soil microbiome. Our results demonstrate that BNI activity of perennial grasses played a vital role in modulating nitrification-associated microbial populations.

Biological Nitrification Inhibition (BNI): Phenotyping of a Core Germplasm Collection of the Tropical Forage Grass Megathyrsus maximus Under Greenhouse Conditions

Modern intensively managed pastures that receive large external nitrogen (N) inputs account for high N losses in form of nitrate (NO₃ ^-) leaching and emissions of the potent greenhouse gas nitrous oxide (N₂O). The natural plant capacity to shape the soil N cycle through exudation of organic compounds can be exploited to favor N retention without affecting productivity. In this study, we estimated the relationship between biological nitrification inhibition (BNI), N₂O emissions and plant productivity for 119 germplasm accessions of Guineagrass (Megathyrsus maximus), an important tropical forage crop for livestock production. This relation was tested in a greenhouse experiment measuring BNI as (i) rates of soil nitrification; (ii) abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA); and (iii) the capacity of root tissue extracts to inhibit nitrification in vitro. We then measured N₂O emissions, aboveground biomass and forage nutrition quality parameters. Reductions on nitrification activity ranging between 30 and 70% were found across the germplasm collection of M. maximus. Accessions with low nitrification rates showed a lower abundance of AOB as well as a reduction in N₂O emissions compared to accessions of high nitrification rates. The BNI capacity was not correlated to N uptake of plants, suggesting that there may be intraspecific variation in the exploitation of different N sources in this grass species. A group of accessions (cluster) with the most desirable agronomic and environmental traits among the collection was identified for further field validation. These results provide evidence of the ability of M. maximus to suppress soil nitrification and N₂O emissions and their relationship with productivity and forage quality, pointing a way to develop N conservative improved forage grasses for tropical livestock production.

Peat substrate amended with chitin modulates the N-cycle, siderophore and chitinase responses in the lettuce rhizobiome

Chitin is a valuable peat substrate amendment by increasing lettuce growth and reducing the survival of the zoonotic pathogen Salmonella enterica on lettuce leaves. The production of chitin-catabolic enzymes (chitinases) play a crucial role and are mediated through the microbial community. A higher abundance of plant-growth promoting microorganisms and genera involved in N and chitin metabolism are present in a chitin-enriched substrate. In this study, we hypothesize that chitin addition to peat substrate stimulates the microbial chitinase production. The degradation of chitin leads to nutrient release and the production of small chitin oligomers that are related to plant growth promotion and activation of the plant's defense response. First a shotgun metagenomics approach was used to decipher the potential rhizosphere microbial functions then the nutritional content of the peat substrate was measured. Our results show that chitin addition increases chitin-catabolic enzymes, bacterial ammonium oxidizing and siderophore genes. Lettuce growth promotion can be explained by a cascade degradation of chitin to N-acetylglucosamine and eventually ammonium. The occurrence of increased ammonium oxidizing bacteria, Nitrosospira, and amoA genes results in an elevated concentration of plant-available nitrate. In addition, the increase in chitinase and siderophore genes may have stimulated the plant's systemic resistance.

Bacterial community composition and diversity of two different forms of an organic residue of bioenergy crop

The use of residue of sugarcane ethanol industry named vinasse in fertirrigation is an established and widespread practice in Brazil. Both non-concentrated vinasse (NCV) and concentrated vinasse (CV) are used in fertirrigation, particularly to replace the potassium fertilizer. Although studies on the chemical and organic composition of vinasse and their impact on nitrous oxide emissions when applied in soil have been carried out, no studies have evaluated the microbial community composition and diversity in different forms of vinasse. We assessed the bacterial community composition of NCV and CV by non-culturable and culturable approaches. The non-culturable bacterial community was assessed by next generation sequencing of the 16S rRNA gene and culturable community by isolation of bacterial strains and molecular and biochemical characterization. Additionally, we assessed in the bacterial strains the presence of genes of nitrogen cycle nitrification and denitrification pathways. The microbial community based on 16S rRNA sequences of NCV was overrepresented by Bacilli and Negativicutes while CV was mainly represented by Bacilli class. The isolated strains from the two types of vinasse belong to class Bacilli, similar to Lysinibacillus, encode for nirK gene related to denitrification pathway. This study highlights the bacterial microbial composition particularly in CV what residue is currently recycled and recommended as a sustainable practice in sugarcane cultivation in the tropics.

Nitrification inhibitors effectively target N2 O-producing Nitrosospira spp. in tropical soil

The nitrification inhibitors (NIs) 3,4-dimethylpyrazole (DMPP) and dicyandiamide (DCD) can effectively reduce N2 O emissions; however, which species are targeted and the effect of these NIs on the microbial nitrifier community is still unclear. Here, we identified the ammonia oxidizing bacteria (AOB) species linked to N2 O emissions and evaluated the effects of urea and urea with DCD and DMPP on the nitrifying community in a 258 day field experiment under sugarcane. Using an amoA AOB amplicon sequencing approach and mining a previous dataset of 16S rRNA sequences, we characterized the most likely N2 O-producing AOB as a Nitrosospira spp. and identified Nitrosospira (AOB), Nitrososphaera (archaeal ammonia oxidizer) and Nitrospira (nitrite-oxidizer) as the most abundant, present nitrifiers. The fertilizer treatments had no effect on the alpha and beta diversities of the AOB communities. Interestingly, we found three clusters of co-varying variables with nitrifier operational taxonomic units (OTUs): the N2 O-producing AOB Nitrosospira with N2 O, NO3 - , NH4 + , water-filled pore space (WFPS) and pH; AOA Nitrososphaera with NO3 - , NH4 + and pH; and AOA Nitrososphaera and NOB Nitrospira with NH4 + , which suggests different drivers. These results support the co-occurrence of non-N2 O-producing Nitrososphaera and Nitrospira in the unfertilized soils and the promotion of N2 O-producing Nitrosospira under urea fertilization. Further, we suggest that DMPP is a more effective NI than DCD in tropical soil under sugarcane.