Influence of temperature on the composition and activity of denitrifying soil communities

Conservation tillage: a way to improve yield and soil properties and decrease global warming potential in spring wheat agroecosystems

Climate change is one of the main challenges, and it poses a tough challenge to the agriculture industry globally. Additionally, greenhouse gas (GHG) emissions are the main contributor to climate change; however, croplands are a prominent source of GHG emissions. Yet this complex challenge can be mitigated through climate-smart agricultural practices. Conservation tillage is commonly known to preserve soil and mitigate environmental change by reducing GHG emissions. Nonetheless, there is still a paucity of information on the influences of conservation tillage on wheat yield, soil properties, and GHG flux, particularly in the semi-arid Dingxi belt. Hence, in order to fill this gap, different tillage systems, namely conventional tillage (CT) control, straw incorporation with conventional tillage (CTS), no-tillage (NT), and stubble return with no-tillage (NTS), were laid at Dingxi, Gansu province of China, under a randomized complete block design with three replications to examine their impacts on yield, soil properties, and GHG fluxes. Results depicted that different conservative tillage systems (CTS, NTS, and NT) significantly (p < 0.05) increased the plant height, number of spikes per plant, seed number per meter square, root yield, aboveground biomass yield, thousand-grain weight, grain yield, and dry matter yield compared with CT. Moreover, these conservation tillage systems notably improved the soil properties (soil gravimetric water content, water-filled pore space, water storage, porosity, aggregates, saturated hydraulic conductivity, organic carbon, light fraction organic carbon, carbon storage, microbial biomass carbon, total nitrogen, available nitrogen storage, microbial biomass nitrogen, total phosphorous, available phosphorous, total potassium, available potassium, microbial counts, urease, alkaline phosphatase, invertase, cellulase, and catalase) while decreasing the soil temperature and bulk density over CT. However, CTS, NTS, and NT had non-significant effects on ECe, pH, and stoichiometric properties (C:N ratio, C:P ratio, and N:P ratio). Additionally, conservation-based tillage regimes NTS, NT, and CTS significantly (p < 0.05) reduced the emission and net global warming potential of greenhouse gases (carbon dioxide, methane, and nitrous oxide) by 23.44, 19.57, and 16.54%, respectively, and decreased the greenhouse gas intensity by 23.20, 29.96, and 18.72%, respectively, over CT. We conclude that NTS is the best approach to increasing yield, soil and water conservation, resilience, and mitigation of agroecosystem capacity.

Multi-experiment assessment of soil nitrous oxide emissions in sugarcane

Soil nitrous oxide (N2O) fluxes comprise a significant part of the greenhouse gas emissions of agricultural products but are spatially and temporally variable, due to complex interactions between climate, soil and management variables. This study aimed to identify the main factors that affect N2O emissions under sugarcane, using a multi-site database from field experiments. Greenhouse gas fluxes, soil, climate, and management data were obtained from 13 field trials spanning the 2011-2017 period. We conducted exploratory, descriptive and inferential data analyses in experiments with varying fertiliser and stillage (vinasse) type and rate, and crop residue rates. The most relevant period of high N2O fluxes was the first 46 days after fertiliser application. The results indicate a strong positive correlation of cumulative N2O with nitrogen (N) fertiliser rate, soil fungi community (18S rRNA gene), soil ammonium (NH4+) and nitrate (NO3-); and a moderate negative correlation with amoA genes of ammonia-oxidising archaea (AOA) and soil organic matter content. The regression analysis revealed that easily routinely measured climate and management-related variables explained over 50% of the variation in cumulative N2O emissions, and that additional soil chemical and physical parameters improved the regression fit with an R2 = 0.65. Cross-wavelet analysis indicated significant correlations of N2O fluxes with rainfall and air temperature up to 64 days, associated with temporal lags of 2 to 4 days in some experiments, and presenting a good environmental control over fluxes in general. The nitrogen fertiliser mean emission factors ranged from 0.03 to 1.17% of N applied, with urea and ammonium nitrate plus vinasse producing high emissions, while ammonium sulphate, ammonium nitrate without vinasse, calcium nitrate, and mitigation alternatives (nitrification inhibitors and timing of vinasse application) producing low N2O-EFs. Measurements from multiple sites spanning several cropping seasons were useful for exploring the influence of environmental and management-related variables on soil N2O emissions in sugarcane production, providing support for global warming mitigation strategies, nitrogen management policies, and increased agricultural input efficiency.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10705-023-10321-w.

Mediative Mechanism of Freezing/Thawing on Greenhouse Gas Emissions in an Inland Saline-Alkaline Wetland: a Metagenomic Analysis

Inland saline-alkaline wetlands distributed in the mid-high latitude have repeatedly experienced freezing and thawing. However, the response of greenhouse gas (GHG) emission and microbially-mediated carbon and nitrogen cycle to freezing and thawing remains unclear. We monitored the GHG flux in an inland saline-alkaline wetland and found that, compared with the growth period, the average CO2 flux decreased from 171.99 to 76.61-80.71 mg/(m2‧h), the average CH4 flux decreased from 10.72 to 1.96-3.94 mg/(m2‧h), and the average N2O flux decreased from 56.17 to - 27.14 to - 20.70 μg/(m2‧h). Freezing and thawing significantly decreased the relative abundance of functional genes involved in carbon and nitrogen cycles. The aceticlastic methanogenic pathway was the main methanogenic pathway, whereas the Candidatus Methylomirabilis oxyfera was the most abundant methane oxidizer in the wetland. Ammonia-oxidizing archaea and denitrifier belonging to proteobacteria was the major microbial N2O source, while bacteria within clade II nosZ was the major microbial N2O sink. Freezing and thawing reduced the relative abundance of these genes, leading to a decrease in GHG flux.

Effects of different land use patterns on soil properties and N2O emissions on a semi-arid Loess Plateau of Central Gansu

Nitrous oxide (N2O) is one of the significant greenhouse gases in the atmosphere. Different land use patterns are the sink or source of N2O, which plays a vigorous role in controlling N2O emissions. Yet, how different land use patterns affect soil N2O emissions in the Loess Plateau of Central Gansu is still not clear. Therefore; in order to fill this gap, six different land use patterns, including Picea asperata (PA), Hippophae rhamnoides (HR), Medicago sativa (MS), No-tillage wheat field (NT) and Conventional tillage wheat field (T) were studied. The objective of this study was to examine the impact of different land use patterns on soil properties and N2O emission flux. Our results showed that compared with other treatments, Picea asperata woodland increased the soil bulk density, organic matter and soil water content, total nitrogen accumulation and microbial biomass nitrogen whilst reduced the soil pH. The wheat field is more favorable to accumulating soil nitrate nitrogen and ammonium nitrogen. Moreover, soil N2O emission rates followed the trend of T&gt;NT&gt;HR&gt;GL&gt;MS&gt;PA. In addition, soil physicochemical properties were closely related to N2O emission flux and soil temperature was the most significant factor affecting N2O emission. General, Picea asperata woodland could significantly increased soil nutrient and reduce N2O emissions. We suggest that more forest land should be selected as the optimal site for nitrogen fixation and emission reduction for sustainable development of the terrestrial ecosystem on the Loess Plateau in Central Gansu.

Effects of biochar addition on nitrous oxide emission during soil freeze–thaw cycles

Biochar applied to soil can reduce nitrous oxide (N2O) emissions produced by freeze–thaw processes. Nonetheless, how biochar modification affects N2O emissions during freeze–thaw cycles is not completely clear. In our research, during freeze–thaw cycles, microcosm experiments were conducted to investigate the effects of maize straw biochar (MB) or rice straw biochar (RB) addition on soil N2O emissions under different water conditions. The N2O emissions peaked at the initial stage of thawing in all the soils, and the total N2O emissions were considerably greater in the flooded soils than in the nonflooded soils. Compared with the soils without biochar addition, RB and MB amendments inhibited N2O emissions by 69 and 67%, respectively. Moreover, after biochar addition, the abundance of AOB amoA genes decreased by 9–13%. Biochar addition significantly decreased the content of microbial biomass nitrogen (MBN) in flooded soil during thawing, which was significantly correlated with N2O emissions and nitrification and denitrification communities. The PLS-PM further revealed that biochar can inhibit the production and emission of soil N2O by reducing soil MBN during soil thawing. In addition, soil moisture directly significantly affects N2O emissions and indirectly affects N2O emissions through its influence on soil physicochemical properties. Our results revealed the important function of biochar in decreasing the emission of N2O in flooded soil during freeze–thaw cycles.

Effects of conservation tillage strategies on soil physicochemical indicators and N2O emission under spring wheat monocropping system conditions

As one of the important greenhouse gas, nitrous oxide (N₂O) has attracted much attention globally under climate change context. Agricultural practices are the main sources of greenhouse gas emissions. Nevertheless, scarcity of literature is available on the effects of different tillage measures on soil N₂O emission under spring wheat (Triticum aestivum L.) ecosystem in the semi-arid area of the Loess Plateau. The main objective of the experimental study was to explore the influence of conservation tillage techniques on soil physicochemical properties, nitrous oxide emission and yield in the Northern semi-arid Dingxi region of China. Four treatments viz., conventional tillage (CT), no tillage (NT), straw mulch with conventional tillage (TS) and stubble-return with no-till (NTS) were evaluated under randomized complete block design with three replications. Our results depicted that compared with conventional tillage, bulk density and water content of topsoil was increased and soil pH value was reduced under conservation tillage techniques. Conservation tillage NT, TS and NTS increased organic carbon, TN, MBN and NH₄⁺-N and reduced the accumulation of NO₃^–N. Additionally, although the N₂O emission under NT, TS and NTS was 8.95, 41.90 and 21.05% respectively higher than under T treatment, the corresponding wheat yield was 15.40, 31.97 and 63.21% higher than T treatment. Moreover, correlation analysis showed that soil moisture and temperature were the most significant factors affecting soil N₂O emission. The NTS treatment pointedly increased crop yield without significantly increasing soil N₂O emission. Consequently, based on economic and environmental benefits and considering N₂O emission and crop yield, we suggest that NTS technique is the best conservation tillage strategy in the semi-arid environmental zone of the Loess Plateau of Dingxi China.

Management Strategies to Mitigate N2O Emissions in Agriculture

The concentration of greenhouse gases (GHGs) in the atmosphere has been increasing since the beginning of the industrial revolution. Nitrous oxide (N2O) is one of the mightiest GHGs, and agriculture is one of the main sources of N2O emissions. In this paper, we reviewed the mechanisms triggering N2O emissions and the role of agricultural practices in their mitigation. The amount of N2O produced from the soil through the combined processes of nitrification and denitrification is profoundly influenced by temperature, moisture, carbon, nitrogen and oxygen contents. These factors can be manipulated to a significant extent through field management practices, influencing N2O emission. The relationships between N2O occurrence and factors regulating it are an important premise for devising mitigation strategies. Here, we evaluated various options in the literature and found that N2O emissions can be effectively reduced by intervening on time and through the method of N supply (30–40%, with peaks up to 80%), tillage and irrigation practices (both in non-univocal way), use of amendments, such as biochar and lime (up to 80%), use of slow-release fertilizers and/or nitrification inhibitors (up to 50%), plant treatment with arbuscular mycorrhizal fungi (up to 75%), appropriate crop rotations and schemes (up to 50%), and integrated nutrient management (in a non-univocal way). In conclusion, acting on N supply (fertilizer type, dose, time, method, etc.) is the most straightforward way to achieve significant N2O reductions without compromising crop yields. However, tuning the rest of crop management (tillage, irrigation, rotation, etc.) to principles of good agricultural practices is also advisable, as it can fetch significant N2O abatement vs. the risk of unexpected rise, which can be incurred by unwary management.

Warming Shapes nirS- and nosZ-Type Denitrifier Communities and Stimulates N2O Emission in Acidic Paddy Soil

Warming strongly stimulates soil nitrous oxide (N2O) emission, contributing to the global warming trend. Submerged paddy soils exhibit huge N2O emission potential; however, the N2O emission pathway and underlying mechanisms for warming are not clearly understood. We conducted an incubation experiment using 15N to investigate the dynamics of N2O emission at controlled temperatures (5, 15, 25, and 35°C) in 125% water-filled pore space. The community structures of nitrifiers and denitrifiers were determined via high-throughput sequencing of functional genes. Our results showed that elevated temperature sharply enhanced soil N2O emission from submerged paddy soil. Denitrification was the main contributor, accounting for more than 90% of total N2O emission at all treatment temperatures. N2O flux was coordinatively regulated by nirK-, nirS-, and nosZ-containing denitrifiers but not ammonia-oxidizing archaea or ammonia-oxidizing bacteria. The nirS-containing denitrifiers were more sensitive to temperature shifts, especially at a lower temperature range (5 to 25°C), and showed a stronger correlation with N2O flux than that of nirK-containing denitrifiers. In contrast, nosZ-containing denitrifiers exhibited substantial variation at higher temperatures (15 to 35°C), thereby playing an important role in N2O consumption. Certain taxa of nirS- and nosZ-containing denitrifiers regulated N2O flux, including nirS-containing denitrifiers affiliated with Rhodanobacter and Cupriavidus as well as nosZ-containing denitrifiers affiliated with Azoarcus and Azospirillum. Together, these findings suggest that elevated temperature can significantly increase N2O emission from denitrification in submerged paddy soils by shifting the overall community structures and enriching some indigenous taxa of nirS- and nosZ-containing denitrifiers. IMPORTANCE The interdependence between global warming and greenhouse gas N2O has always been the hot spot. However, information on factors contributing to N2O and temperature-dependent community structure changes is scarce. This study demonstrated high-temperature-induced N2O emission from submerged paddy soils, mainly via stimulating denitrification. Further, we speculate that key functional denitrifiers drive N2O emission. This study showed that denitrifiers were more sensitive to temperature rise than nitrifiers, and the temperature sensitivity differed among denitrifier communities. N2O-consuming denitrifiers (nosZ-containing denitrifiers) were more sensitive at a higher temperature range than N2O-producing denitrifiers (nirS-containing denitrifiers). This study's findings help predict N2O fluxes under different degrees of warming and develop strategies to mitigate N2O emissions from paddy fields based on microbial community regulation.

Enumeration of Chemoorganotrophic Carbonyl Sulfide (COS)-degrading Microorganisms by the Most Probable Number Method

Carbonyl sulfide (COS) is the most abundant sulfur compound in the atmosphere, and, thus, is important in the global sulfur cycle. Soil is a major sink of atmospheric COS and the numerical distribution of soil microorganisms that degrade COS is indispensable for estimating the COS-degrading potential of soil. However, difficulties are associated with counting COS-degrading microorganisms using culture-dependent approaches, such as the most probable number (MPN) method, because of the chemical hydrolysis of COS by water. We herein developed a two-step MPN method for COS-degrading microorganisms: the first step for chemoorganotrophic growth that supported a sufficient number of cells for COS degradation in the second step. Our new MPN analysis of various environmental samples revealed that the cell density of COS-degrading microorganisms in forest soils ranged between 10⁶ and 10⁸ MPN (g dry soil)^–1, which was markedly higher than those in volcanic deposit and water samples, and strongly correlated with the rate of COS degradation in environmental samples. Numerically dominant COS degraders that were isolated from the MPN-positive culture were related to bacteria in the orders Bacillales and Actinomycetales. The present results provide numerical evidence for the ubiquity of COS-degrading microbes in natural environments.

Understanding the Dependence of Micropollutant Biotransformation Rates on Short-Term Temperature Shifts

Temperature is a key factor that influences chemical biotransformation potential and rates, on which exposure and fate models rely to predict the environmental (micro)pollutant fate. Arrhenius-based models are currently implemented in environmental exposure assessment to adapt biotransformation rates to actual temperatures, assuming validity in the 0-30 °C range. However, evidence on how temperature shifts affect the physicochemical and microbial features in biological systems is scarce, questioning the validity of the existing modeling approaches. In this work, laboratory-scale batch assays were designed to investigate how a mixed microbial community responds to short-term temperature shifts, and how this impacts its ability to biotransform a range of structurally diverse micropollutants. Our results revealed three distinct kinetic responses at temperatures above 20 °C, mostly deviating from the classic Arrhenius-type behavior. Micropollutants with similar temperature responses appeared to undergo mostly similar initial biotransformation reactions, with substitution-type reactions maintaining Arrhenius-type behavior up to higher temperatures than oxidation-type reactions. Above 20 °C, the microbial community also showed marked shifts in both composition and activity, which mostly correlated with the observed deviations from Arrhenius-type behavior, with compositional changes becoming a more relevant factor in biotransformations catalyzed by more specific enzymes (e.g., oxidation reactions). Our findings underline the need to re-examine and further develop current environmental fate models by integrating biological aspects, to improve accuracy in predicting the environmental fate of micropollutants.

Global nitrogen input on wetland ecosystem: The driving mechanism of soil labile carbon and nitrogen on greenhouse gas emissions

Greenhouse gas emissions from wetlands are significantly promoted by global nitrogen input for changing the rate of soil carbon and nitrogen cycling, and are substantially affected by soil labile carbon and nitrogen conversely. However, the driving mechanism by which soil labile carbon and nitrogen affect greenhouse gas emissions from wetland ecosystems under global nitrogen input is not well understood. Working out the driving factor of nitrogen input on greenhouse gas emissions from wetlands is critical to reducing global warming from nitrogen input. Thus, we synthesized 72 published studies (2144 paired observations) of greenhouse gas fluxes and soil labile compounds of carbon and nitrogen (ammonium, nitrate, dissolved organic carbon, soil microbial biomass nitrogen and carbon), to understand the effects of labile carbon and nitrogen on greenhouse gas emissions under global nitrogen input. Across the data set, nitrogen input significantly promoted carbon dioxide, methane and nitrous oxide emissions from wetlands. In particular, at lower nitrogen rates (<100 kg ha^-1·yr^-1) and with added ammonium compounds, freshwater wetland significantly promoted carbon dioxide and methane emissions. Peatland was the largest nitrous oxide source under these conditions. This meta-analysis also revealed that nitrogen input stimulated dissolved organic carbon, ammonium, nitrate, microbial biomass carbon and microbial biomass nitrogen accumulation in the wetland ecosystem. The variation-partitioning analysis and structural equation model were used to analyze the relationship between the greenhouse gas and labile carbon and nitrogen further. These results revealed that dissolved organic carbon (DOC) is the primary factor driving greenhouse gas emission from wetlands under global nitrogen input, whereas microbial biomass carbon (MBC) more directly affects greenhouse gas emission than other labile carbon and nitrogen.

Gross N2O Production Process, Not Consumption, Determines the Temperature Sensitivity of Net N2O Emission in Arable Soil Subject to Different Long-Term Fertilization Practices

Chronic amendment of agricultural soil with synthetic nitrogen fertilization and/or livestock manure has been demonstrated to enhance the feedback intensity of net N₂O emission to temperature variation (i.e., temperature sensitivity, TS). Yet few studies have explored the relevance of changes in underlying gross N₂O production and consumption processes toward explaining this phenomenon, in particular for the latter. Furthermore, the microbe-based mechanisms associated with the variation of N₂O consumption process remain largely unexplored. To address this knowledge gap, a temperature- (15, 25, and 35°C) and moisture-controlled (50% water holding capacity) microcosm incubation experiment was established using an arable soil subject to long-term addition of synthetic fertilizer (NPK), a mixture of synthetic fertilizer with livestock manure (MNPK), or with no fertilizer treatment (CT). Over the incubation time period, the C₂H₂ inhibition method was adopted to monitor reaction rates of gross N₂O production and consumption; the population sizes and community structures of nosZI- and nosZII-N₂O reducers were analyzed using quantitative PCR (Q-PCR) and terminal restriction fragment length polymorphism (T-RFLP). The results indicated that only NPK significantly increased the TS of net N₂O emission, and gross N₂O consumption process consistently occurred under all treatment combinations (temperature and fertilization) at each sampling time point. The responses of gross N₂O production and consumption processes to temperature elevation exhibited fertilization- and sampling time-dependent pattern, and the higher net N₂O production TS in the NPK treatment was underlain by its higher TS of gross production process and insensitivity of gross consumption process to temperature. The size and structure of nosZII-N₂O reducers, as well as the community structure of nosZI-N₂O reducers, were positively correlated with variation of gross N₂O production and consumption rates across all fertilization regimes. NosZII-N₂O reducer abundance was less responsive to temperature change, and its community structure less susceptible to fertilization, as compared with nosZI-N₂O reducers. Overall, our results demonstrate that the TS of the gross N₂O production process, not gross consumption, is the key step regulating the TS of net N₂O production, and both nosZI- and nosZII-N₂O clades are likely active N₂O reducers in the tested soil.

Bradyrhizobium as the Only Rhizobial Inhabitant of Mung Bean (Vigna radiata) Nodules in Tropical Soils: A Strategy Based on Microbiome for Improving Biological Nitrogen Fixation Using Bio-Products

The mung bean has a great potential under tropical conditions given its high content of grain protein. Additionally, its ability to benefit from biological nitrogen fixation (BNF) through association with native rhizobia inhabiting nodule microbiome provides most of the nitrogen independence on fertilizers. Soil microbial communities which are influenced by biogeographical factors and soil properties, represent a source of rhizobacteria capable of stimulating plant growth. The objective of this study is to support selection of beneficial bacteria that form positive interactions with mung bean plants cultivated in tropical soils, as part of a seed inoculation program for increasing grain yield based on the BNF and other mechanisms. Two mung bean genotypes (Camaleão and Esmeralda) were cultivated in 10 soil samples. Nodule microbiome was characterized by next-generation sequencing using Illumina MiSeq 16S rRNA. More than 99% of nodule sequences showed similarity with Bradyrhizobium genus, the only rhizobial present in nodules in our study. Higher bacterial diversity of soil samples collected in agribusiness areas (MW_MT-I, II or III) was associated with Esmeralda genotype, while an organic agroecosystem soil sample (SE_RJ-V) showed the highest bacterial diversity independent of genotype. Furthermore, OTUs close to Bradyrhizobium elkanii have dominated in all soil samples, except in the sample from the organic agroecosystem, where just B. japonicum was present. Bacterial community of mung bean nodules is mainly influenced by soil pH, K, Ca, and P. Besides a difference on nodule colonization by OTU sequences close to the Pseudomonas genus regarding the two genotypes was detected too. Although representing a small rate, around 0.1% of the total, Pseudomonas OTUs were only retrieved from nodules of Esmeralda genotype, suggesting a different trait regarding specificity between macro- and micro-symbionts. The microbiome analysis will guide the next steps in the development of an inoculant for mung bean aiming to promote plant growth and grain yield, composed either by an efficient Bradyrhizobium strain on its own or co-inoculated with a Pseudomonas strain. Considering the results achieved, the assessment of microbial ecology parameters is a potent coadjuvant capable to accelerate the inoculant development process and to improve the benefits to the crop by soil microorganisms.

Response of Soil N2O Emissions to Soil Microbe and Enzyme Activities with Aeration at Two Irrigation Levels in Greenhouse Tomato (Lycopersicon esculentum Mill.) Fields

Aerated irrigation is proven to increase soil N2O emissions; however, the mechanisms of N2O release are still unknown. A field experiment for two consecutive greenhouse tomato-growing seasons, from August 2016 to July 2017, was carried out to examine (1) the differences of aeration and irrigation on soil N2O emissions with a static chamber GC technique, and on soil physical and biotic parameters, and (2) the response of soil N2O emissions to soil physical and biotic parameters. Two irrigation levels were included: 60% (low irrigation) and 100% (high irrigation) of the full irrigation amount. Each irrigation level contained aeration and control, totaling four treatments. During the two growing seasons, soil N2O emissions with aeration were 4.5% higher than the control (p > 0.05). Soil N2O emissions under the high irrigation were 13.8% greater than under the low irrigation, and the difference was significant in 2017 (p < 0.05). Aeration and irrigation had positive effects on the mean soil nitrifier abundance and mean soil urease activity, and the impact of irrigation on urease was significant in 2016 (p = 0.001). In addition, aeration negatively influenced the mean soil denitrifier abundance, while irrigation positively influenced the mean soil denitrifier abundance. Regression analysis showed that the soil water-filled pore space, temperature, and denitrifier abundance were primary factors influencing soil N2O fluxes. This study provides a further understanding of the processes affecting soil N2O emissions and N dynamics, which may assist in developing mitigation strategies to reduce N2O emissions.

Distinct distribution patterns of proteobacterial nirK- and nirS-type denitrifiers in the Yellow River estuary, China

Denitrification is considered to be the critical process in removing reactive nitrogen in estuarine ecosystems. In the present study, the abundance, diversity, and community structure of nirK- and nirS-type denitrifiers were compared in sediments from the Yellow River estuary. Quantitative polymerase chain reaction showed that the 2 types of denitrifiers exhibited different distribution patterns among the samples, indicating their distinct habitat preference. Phylogenetic analysis revealed that most of the sequences from clusters I, III, IV, and V for nirK-type denitrifiers were dominant and were distributed at sites where dissolved oxygen (DO) was lower, and the sequences in the other clusters were dominant at sites with higher DO. However, there was no spatially heterogeneous distribution for the nirS-type denitrifier community. Canonical correlation analysis and correlation analysis demonstrated that the community structure of nirK was more responsive to environmental factors than was that of nirS. Inversely, the abundance and α-diversity targeting nirS gene could be more easily influenced by environmental parameters. These findings can extend our current knowledge about the distribution patterns of denitrifying bacteria and provide a basic theoretical reference for the dynamics of denitrifying communities in estuarine ecosystem of China.

Response of Spatial Patterns of Denitrifying Bacteria Communities to Water Properties in the Stream Inlets at Dianchi Lake, China

Streams are an important sink for anthropogenic N owing to their hydrological connections with terrestrial systems, but main factors influencing the community structure and abundance of denitrifiers in stream water remain unclear. To elucidate the potential impact of varying water properties of different streams on denitrifiers, the abundance and community of three denitrifying genes coding for nitrite (nirK, nirS) and nitrous oxide (nosZ) reductase were investigated in 11 streams inlets at the north part of Dianchi Lake. The DGGE results showed the significant pairwise differences in community structure of nirK, nirS, and nosZ genes among different streams. The results of redundancy analysis (RDA) confirmed that nitrogen and phosphorus concentrations, pH, and temperature in waters were the main environmental factors leading to a significant alteration in the community structure of denitrifiers among different streams. The denitrifying community size was assessed by quantitative PCR (qPCR) of the nirS, nirK, and nosZ genes. The abundance of nirK, nirS, and nosZ was positively associated with concentrations of total N (TN) and PO4 (3-) (p < 0.001). The difference in spatial patterns between nirK and nirS community diversity, in combination with the spatial distribution of the nirS/nirK ratio, indicated the occurrence of habitat selection for these two types of denitrifiers in the different streams. The results indicated that the varying of N species and PO4 (3-) together with pH and temperature would be the main factors shaping the community structure of denitrifiers. Meanwhile, the levels of N in water, together with PO4 (3-), tend to affect the abundance of denitrifiers.

Water Properties Influencing the Abundance and Diversity of Denitrifiers on Eichhornia crassipes Roots: A Comparative Study from Different Effluents around Dianchi Lake, China

To evaluate effects of environmental conditions on the abundance and communities of three denitrifying genes coding for nitrite (nirK, nirS) reductase and nitrous oxide (nosZ) reductase on the roots of Eichhornia crassipes from 11 rivers flowing into the northern part of Dianchi Lake. The results showed that the abundance and community composition of denitrifying genes on E. crassipes root varied with different rivers. The nirK gene copies abundance was always greater than that of nirS gene on the roots of E. crassipes, suggesting that the surface of E. crassipes roots growth in Dianchi Lake was more suitable for the growth of nirK-type denitrifying bacteria. The DGGE results showed significant differences in diversity of denitrifying genes on the roots of E. crassipes among the 11 rivers. Using redundancy analysis (RDA), the correlations of denitrifying microbial community compositions with environmental factors revealed that water temperature (T), dissolved oxygen (DO), and pH were relatively important environmental factors to modifying the community structure of the denitrifying genes attached to the root of E. crassipes. The results indicated that the specific environmental conditions related to different source of rivers would have a stronger impact on the development of denitrifier communities on E. crassipes roots.

Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils

Increasing temperatures have been shown to impact soil biogeochemical processes, although the corresponding changes to the underlying microbial functional communities are not well understood. Alterations in the nitrogen (N) cycling functional component are particularly important as N availability can affect microbial decomposition rates of soil organic matter and influence plant productivity. To assess changes in the microbial component responsible for these changes, the composition of the N-fixing (nifH), and denitrifying (nirS, nirK, nosZ) soil microbial communities was assessed by targeted pyrosequencing of functional genes involved in N cycling in two major biomes where the experimental effect of climate warming is under investigation, a tallgrass prairie in Oklahoma (OK) and the active layer above permafrost in Alaska (AK). Raw reads were processed for quality, translated with frameshift correction, and a total of 313,842 amino acid sequences were clustered and linked to a nearest neighbor using reference datasets. The number of OTUs recovered ranged from 231 (NifH) to 862 (NirK). The N functional microbial communities of the prairie, which had experienced a decade of experimental warming were the most affected with changes in the richness and/or overall structure of NifH, NirS, NirK and NosZ. In contrast, the AK permafrost communities, which had experienced only 1 year of warming, showed decreased richness and a structural change only with the nirK-harboring bacterial community. A highly divergent nirK-harboring bacterial community was identified in the permafrost soils, suggesting much novelty, while other N functional communities exhibited similar relatedness to the reference databases, regardless of site. Prairie and permafrost soils also harbored highly divergent communities due mostly to differing major populations.

N2O production, a widespread trait in fungi

N₂O is a powerful greenhouse gas contributing both to global warming and ozone depletion. While fungi have been identified as a putative source of N₂O, little is known about their production of this greenhouse gas. Here we investigated the N₂O-producing ability of a collection of 207 fungal isolates. Seventy strains producing N₂O in pure culture were identified. They were mostly species from the order Hypocreales order—particularly Fusarium oxysporum and Trichoderma spp.—and to a lesser extent species from the orders Eurotiales, Sordariales, and Chaetosphaeriales. The N₂O ¹⁵N site preference (SP) values of the fungal strains ranged from 15.8‰ to 36.7‰, and we observed a significant taxa effect, with Penicillium strains displaying lower SP values than the other fungal genera. Inoculation of 15 N₂O-producing strains into pre-sterilized arable, forest and grassland soils confirmed the ability of the strains to produce N₂O in soil with a significant strain-by-soil effect. The copper-containing nitrite reductase gene (nirK) was amplified from 45 N₂O-producing strains, and its genetic variability showed a strong congruence with the ITS phylogeny, indicating vertical inheritance of this trait. Taken together, this comprehensive set of findings should enhance our knowledge of fungi as a source of N₂O in the environment.

Genome analysis coupled with physiological studies reveals a diverse nitrogen metabolism in Methylocystis sp. strain SC2

BACKGROUND

Methylocystis sp. strain SC2 can adapt to a wide range of methane concentrations. This is due to the presence of two isozymes of particulate methane monooxygenase exhibiting different methane oxidation kinetics. To gain insight into the underlying genetic information, its genome was sequenced and found to comprise a 3.77 Mb chromosome and two large plasmids.

PRINCIPAL FINDINGS

We report important features of the strain SC2 genome. Its sequence is compared with those of seven other methanotroph genomes, comprising members of the Alphaproteobacteria, Gammaproteobacteria, and Verrucomicrobia. While the pan-genome of all eight methanotroph genomes totals 19,358 CDS, only 154 CDS are shared. The number of core genes increased with phylogenetic relatedness: 328 CDS for proteobacterial methanotrophs and 1,853 CDS for the three alphaproteobacterial Methylocystaceae members, Methylocystis sp. strain SC2 and strain Rockwell, and Methylosinus trichosporium OB3b. The comparative study was coupled with physiological experiments to verify that strain SC2 has diverse nitrogen metabolism capabilities. In correspondence to a full complement of 34 genes involved in N2 fixation, strain SC2 was found to grow with atmospheric N2 as the sole nitrogen source, preferably at low oxygen concentrations. Denitrification-mediated accumulation of 0.7 nmol (30)N2/hr/mg dry weight of cells under anoxic conditions was detected by tracer analysis. N2 production is related to the activities of plasmid-borne nitric oxide and nitrous oxide reductases.

CONCLUSIONS/PERSPECTIVES

Presence of a complete denitrification pathway in strain SC2, including the plasmid-encoded nosRZDFYX operon, is unique among known methanotrophs. However, the exact ecophysiological role of this pathway still needs to be elucidated. Detoxification of toxic nitrogen compounds and energy conservation under oxygen-limiting conditions are among the possible roles. Relevant features that may stimulate further research are, for example, absence of CRISPR/Cas systems in strain SC2, high number of iron acquisition systems in strain OB3b, and large number of transposases in strain Rockwell.

A meta-analysis of experimental warming effects on terrestrial nitrogen pools and dynamics

Global warming may have profound effects on terrestrial ecosystems. However, a comprehensive evaluation of the effects of warming on ecosystem nitrogen (N) pools and dynamics is not available. Here, we compiled data of 528 observations from 51 papers and carried out a meta-analysis of experimental warming effects on 13 variables related to terrestrial N pools and dynamics. We found that, on average, net N mineralization and net nitrification rate were increased by 52.2 and 32.2%, respectively, under experimental warming treatment. N pools were also increased by warming, although the magnitude of this increase was less than that of N fluxes. Soil microbial N and N immobilization were not changed by warming, probably because microbes are limited by carbon sources. Grassland and shrubland/heathland were less responsive to warming than forest, probably because the reduction of soil moisture by warming offset the temperature effect in these areas. Soil heating cable and all-day treatment appeared to be the most effective method on N cycling among all treatment methods. Results of this meta-analysis are useful for better understanding the response of N cycling to global warming and the underlying mechanism of warming effects on plants and ecosystem functions.

Short-term effects of temperature on the abundance and diversity of magnetotactic cocci

Temperature is one of the most important climate factors that can regulate the activity and growth of organisms. However, it is so far unclear how temperature influences the abundance and community composition of magnetotactic bacteria (MTB) that mineralize intracellular magnetite and/or greigite magnetosomes and play significant roles in the global iron cycling and sediment magnetization. To address this specific problem, in this study we have assessed the impact of temperature on freshwater magnetotactic cocci through laboratory microcosm simulations. Microcosms containing MTB were exposed to four constant temperatures ranging from 9°C to 37°C. After 10 days and 28 days of incubation, no significant differences in abundance were detected in microcosms at 9°C, 15°C, and 26°C (Student's t-test, P > 0.05); however, microcosms exposed to 37°C exhibited a significant decrease of magnetotactic cocci abundance (P < 0.05). Dendrogram analysis of community-amplified ribosomal DNA restriction analysis (community ARDRA) banding patterns distinguished the 37°C samples from samples at lower temperatures regardless of incubation periods. Furthermore, clone library analysis revealed that most of the operational taxonomic units (OTUs) detected in samples from 9°C to 26°C were absent from the 37°C microcosms, whereas six OTUs were exclusively detected in the 37°C samples. Community compositions from four incubation temperatures were further compared using statistical phylogenetic methods (UniFrac and LIBSHUFF), which revealed that the 37°C samples harbored phylogenetically distinct MTB communities compared to those found in 9°C, 15°C, and 26°C samples. Taken together, our results indicate that elevated temperature can influence the abundance and diversity of dominant members of magnetotactic cocci. This linkage further infers that the abundance and diversity of MTB (e.g., based on the fossil magnetosomes) may be useful in reconstruction of paleotemperature.