Ultrasonic-assisted extraction of total flavonoids from Zanthoxylum bungeanum residue and their allelopathic mechanism on Microcystis aeruginosa.

Water eutrophication has emerged as a pressing concern for massive algal blooms, and these harmful blooms can potentially generate harmful toxins, which can detrimentally impact the aquatic environment and human health. Consequently, it is imperative to identify a safe and efficient approach to combat algal blooms to safeguard the ecological safety of water. This study aimed to investigate the procedure for extracting total flavonoids from Z. bungeanum residue and assess its antioxidant properties. The most favorable parameters for extracting total flavonoids from Z. bungeanum residue were a liquid-solid ratio (LSR) of 20 mL/g, a solvent concentration of 60%, an extraction period of 55 min, and an ultrasonic temperature of 80 °C. Meanwhile, the photosynthetic inhibitory mechanism of Z. bungeanum residue extracts against M. aeruginosa was assessed with a particular focus on the concentration-dependent toxicity effect. Z. bungeanum residue extracts damaged the oxygen-evolving complex structure, influenced energy capture and distribution, and inhibited the electron transport of PSII in M. aeruginosa. Furthermore, the enhanced capacity for ROS detoxification enables treated cells to sustain their photosynthetic activity. The findings of this study hold considerable relevance for the ecological management community and offer potential avenues for the practical utilization of resources in controlling algal blooms.

Long-term chemical and organic fertilization induces distinct variations of microbial associations but unanimous elevation of soil multifunctionality.

Intricate microbial associations contribute greatly to the multiple functions (multifunctionality) of natural ecosystems. However, the relationship between microbial associations and soil multifunctionality (SMF) in artificial ecosystems, particularly in agricultural ecosystem with frequent fertilization, remains unclear. In this study, based on a 28-year paddy field experiment, high-throughput sequencing and networks analysis was performed to investigate changes in soil microbial (archaea, bacteria, fungi, and protists) associations and how these changes correlate with SMF under long-term fertilization. Compared to no fertilization (CK), both chemical fertilization with N, P, and K (CF) and chemical fertilization plus rice straw retention (CFR) treatments showed significantly higher soil nutrient content, grain yield, microbial abundance, and SMF. With the exception of archaeal diversity, the CF treatment exhibited the lowest bacterial, fungal, and protist diversity, and the simplest microbial co-occurrence network. In contrast, the CFR treatment had the lowest archaeal diversity, but the highest bacterial, fungal, and protist diversity. Moreover, the CFR treatment exhibited the most complex microbial co-occurrence network with the highest number of nodes, edges, and interkingdom edges. These results highlight that both chemical fertilization with and without straw retention caused high ecosystem multifunctionality while changing microbial association oppositely. Furthermore, these results indicate that rice straw retention contributes to the development of the soil microbiome and ensures the sustainability of high-level ecosystem multifunctionality.

Nitrification inhibitor chlorate and nitrogen substrates differentially affect comammox Nitrospira in a grassland soil.

Introduction: Through the combined use of two nitrification inhibitors, Dicyandiamide (DCD) and chlorate with nitrogen amendment, this study aimed to investigate the contribution of comammox Nitrospira clade B, ammonia oxidizing bacteria (AOB) and archaea (AOA) to nitrification in a high fertility grassland soil, in a 90-day incubation study. Methods: The soil was treated with nitrogen (N) at three levels: 0 mg-N kg-1 soil, 50 mg-N kg-1 soil, and 700 mg-N kg-1 soil, with or without the two nitrification inhibitors. The abundance of comammox Nitrospira, AOA, AOB, and nitrite oxidising bacteria (NOB) was measured using qPCR. The comammox Nitrospira community structure was assessed using Illumina sequencing. Results and Discussion: The results showed that the application of chlorate inhibited the oxidation of both NH4+ and NO2- in all three nitrogen treatments. The application of chlorate significantly reduced the abundance of comammox Nitrospira amoA and nxrB genes across the 90-day experimental period. Chlorate also had a significant effect on the beta diversity (Bray-Curtis dissimilarity) of the comammox Nitrospira clade B community. Whilst AOB grew in response to the N substrate additions and were inhibited by both inhibitors, AOA showed litle or no response to either the N substrate or inhibitor treatments. In contrast, comammox Nitrospira clade B were inhibited by the high ammonium concentrations released from the urine substrates. These results demonstrate the differential and niche responses of the three ammonia oxidising communities to N substrate additions and nitrification inhibitor treatments. Further research is needed to investigate the specificity of the two inhibitors on the different ammonia oxidising communities.

Comparison of N2O-reducing abilities and genome features of two nosZ-containing denitrifying bacteria, Pseudomonas veronii DM15 and Pseudomonas frederiksbergensis DM22.

AIM: The study systematically compared the N2O-reducing functional performances and the genomic features of two N2O-reducing isolates, aimed to screen out effective N2O-reducing bacteria with strong environmental adaption, and explore the possible regulation. METHODS AND RESULTS: Two N2O reducers, namely, Pseudomonas veronii DM15 (DM15) and Pseudomonas frederiksbergensis DM22 (DM22), isolated from paddy soil were selected. Their N2O-reducing abilities, and nosZ gene transcript abundance were determined under different temperatures (20°C, 30°C, 40°C) and oxygen concentrations (0%, 10%, 21%), and the whole genomes were sequenced by Illumina sequencing. The results showed that both DM15 and DM22 exhibited the strongest N2O reducing activity at 30°C and under anaerobic conditions. In comparison, DM15 generally exhibited significantly higher N2O reducing abilities and nosZ gene expression than DM22 under all tested conditions. In addition, DM15 possessed obviously higher expression potentials (codon adaptation index (CAI) value) of nos genes than DM22, and the nos cluster of the former contained a transcriptional regulator gene of dnr, while the latter did not. CONCLUSIONS: The results indicate that DM15 showed obviously stronger N2O-reducing abilities than DM22 under various conditions, which might be closely associated with its dnr transcriptional regulator, and thus promoting the higher transcriptional activities of nos genes. Although anaerobic conditions were the optimal conditions for N2O reduction in both strains, DM15 still reduced a certain amount of N2O even under aerobic conditions.

Mapping Chinese annual gross primary productivity with eddy covariance measurements and machine learning.

Annual gross primary productivity (AGPP) is the basis for grain production and terrestrial carbon sequestration. Mapping regional AGPP from site measurements provides methodological support for analysing AGPP spatiotemporal variations thereby ensures regional food security and mitigates climate change. Based on 641 site-year eddy covariance measuring AGPP from China, we built an AGPP mapping scheme based on its formation and selected the optimal mapping way, which was conducted through analysing the predicting performances of divergent mapping tools, variable combinations, and mapping approaches in predicting observed AGPP variations. The reasonability of the selected optimal scheme was confirmed by assessing the consistency between its generating AGPP and previous products in spatiotemporal variations and total amount. Random forest regression tree explained 85 % of observed AGPP variations, outperforming other machine learning algorithms and classical statistical methods. Variable combinations containing climate, soil, and biological factors showed superior performance to other variable combinations. Mapping AGPP through predicting AGPP per leaf area (PAGPP) explained 86 % of AGPP variations, which was superior to other approaches. The optimal scheme was thus using a random forest regression tree, combining climate, soil, and biological variables, and predicting PAGPP. The optimal scheme generating AGPP of Chinese terrestrial ecosystems decreased from southeast to northwest, which was highly consistent with previous products. The interannual trend and interannual variation of our generating AGPP showed a decreasing trend from east to west and from southeast to northwest, respectively, which was consistent with data-oriented products. The mean total amount of generated AGPP was 7.03 ± 0.45 PgC yr-1 falling into the range of previous works. Considering the consistency between the generated AGPP and previous products, our optimal mapping way was suitable for mapping AGPP from site measurements. Our results provided a methodological support for mapping regional AGPP and other fluxes.

The Contribution of Nitrate Dissimilation to Nitrate Consumption in narG- and napA-Containing Nitrate Reducers with Various Oxygen and Nitrate Supplies.

Nitrate reducers containing narG or napA play an important role in the nitrogen cycle, but little is known about their functional differentiations in relation to environmental changes. In this study, three types of nitrate reducers in the genus Pseudomonas, including strains containing narG (G type), napA (A type) and both narG and napA (GA type), were selected to explore their functional performances under varied nitrate and oxygen concentrations. Their growth characteristics, nitrate consumption, and dissimilatory nitrate-reducing activity were investigated. Growth and nitrate consumption of all three types of strains were generally promoted with increasing oxygen and nitrate concentrations. However, their dissimilatory nitrate-reducing activities were restricted by oxygen supply. When supplied with 0.25 mM KNO3, A-type strains showed a higher growth rate but lower activity of dissimilatory nitrate reduction (DNR) than G-type strains, regardless of oxygen concentration. However, when nitrate concentration increased to 0.75 mM or 5 mM, G-type strains displayed stronger capability of nitrate consumption and DNR than A-type strains under anaerobic conditions, whereas under oxygenated conditions, A-type strains exhibited higher growth and nitrate consumption but weaker DNR than G-type strains. The GA-type strains appeared similar to G type under anaerobic conditions but performed more similarly to A type in aerobic environments. In summary, the nitrate consumption of narG-containing nitrate reducers is mainly caused by DNR in both anaerobic and aerobic environments, while the large proportion of nitrate consumption in A-type nitrate reducers under the aerobic condition is attributed to the assimilation by cell growth. IMPORTANCE Nitrate reducers containing narG or napA are ubiquitous, but little is known about their functional performance in various environments. Our study provides an important clue that the nitrate consumption of narG-containing strains is mainly caused by dissimilatory reduction in the environments, while that of napA-containing nitrate reducers under anaerobic conditions is ascribed to nitrate dissimilation but under the aerobic condition is attributed to the assimilation by cell growth. This finding broadens the understanding of aerobic nitrate reduction in the nitrogen cycle and highlights the important role of narG-containing bacteria in nitrate reduction under aerobic conditions.

Comammox Nitrospira Clade B is the most abundant complete ammonia oxidizer in a dairy pasture soil and inhibited by dicyandiamide and high ammonium concentrations.

The recent discovery of comammox Nitrospira, a complete ammonia oxidizer, capable of completing the nitrification on their own has presented tremendous challenges to our understanding of the nitrification process. There are two divergent clades of comammox Nitrospira, Clade A and B. However, their population abundance, community structure and role in ammonia and nitrite oxidation are poorly understood. We conducted a 94-day microcosm study using a grazed dairy pasture soil amended with urea fertilizers, synthetic cow urine, and the nitrification inhibitor, dicyandiamide (DCD), to investigate the growth and community structure of comammox Nitrospira spp. We discovered that comammox Nitrospira Clade B was two orders of magnitude more abundant than Clade A in this fertile dairy pasture soil and the most abundant subcluster was a distinctive phylogenetic uncultured subcluster Clade B2. We found that comammox Nitrospira Clade B might not play a major role in nitrite oxidation compared to the role of canonical Nitrospira nitrite-oxidizers, however, comammox Nitrospira Clade B is active in nitrification and the growth of comammox Nitrospira Clade B was inhibited by a high ammonium concentration (700 kg synthetic urine-N ha-1) and the nitrification inhibitor DCD. We concluded that comammox Nitrospira Clade B: (1) was the most abundant comammox in the dairy pasture soil; (2) had a low tolerance to ammonium and can be inhibited by DCD; and (3) was not the dominant nitrite-oxidizer in the soil. This is the first study discovering a new subcluster of comammox Nitrospira Clade B2 from an agricultural soil.

Generalist Taxa Shape Fungal Community Structure in Cropping Ecosystems.

Fungi regulate nutrient cycling, decomposition, symbiosis, and pathogenicity in cropland soils. However, the relative importance of generalist and specialist taxa in structuring soil fungal community remains largely unresolved. We hypothesized that generalist fungi, which are adaptable to various environmental conditions, could potentially dominate the community and become the basis for fungal coexisting networks in cropping systems. In this study, we identified the generalist and habitat specialist fungi in cropland soils across a 2,200 kms environmental gradient, including three bioclimatic regions (subtropical, warm temperate, and temperate). A few fungal taxa in our database were classified as generalist taxa (~1%). These generalists accounted for >35% of the relative abundance of all fungal populations, and most of them are Ascomycota and potentially pathotrophic. Compared to the specialist taxa (5-17% of all phylotypes in three regions), generalists had a higher degree of connectivity and were often identified as hub within the network. Structural equation modeling provided further evidence that after accounting for spatial and climatic/edaphic factors, generalists had larger contributions to the fungal coexistence pattern than habitat specialists. Taken together, our study provided evidence that generalist taxa are crucial components for fungal community structure. The knowledge of generalists can provide important implication for understanding the ecological preference of fungal groups in cropland systems.

Long-term partial replacement of mineral fertilizer with in situ crop residues ensures continued rice yields and soil fertility: A case study of a 27-year field experiment in subtropical China.

High yields and environment-related issues because of over-fertilization in rice (Oryza sativa L.) production is a major concern in China. Partial replacement of mineral fertilizer (MF) with organic matter is considered a win-win approach for resource-saving and environmentally friendly rice production. Here, we examined the effects of reduced MF and in situ crop residue on the rice yield and soil fertility in the long term. A 27-year field experiment (a randomized block design with three replicates) in subtropical China was conducted to test the feasibility of the substitution in a double rice paddy ecosystem. The treatments were CT (no fertilizer application considered as control), NPK (mineral fertilizer N, P, and K), and RFC (reduced MF and in situ crop residue to supplement the reduced NPK dose). The crop residue included half of the rice straw and green manure contents, which were retained in situ in the RFC treatment. The RFC maintained the same rice yield and soil fertility levels as NPK. In general, soil organic carbon (SOC) and total nitrogen (TN) content in RFC increased by 10.3% -20.8%, and 7.5% -28.0%, respectively, than that in NPK from the 5th to the 25th years. There was no significant difference in the content and net accumulation of SOC, TN, and TP and soil available nutrients between the RFC and NPK treatments after 25 years. The average annual yields were 9690 and 9872 kg ha-1 for the NPK and RFC treatments, respectively. There was no difference in the yield of the first, second, and annual rice crops between RFC and NPK in most years (six of the fifty-four seasons showed a significant difference). RFC increased the partial factor productivity (PFP), agronomic efficiency (AE) of MF, and yield stability (CV) (p < 0.05). Positive nutrient balance and a reduced loss of nutrients are evident reasons for achieving better indicators (PFP, AE, and CV) for nutrient compensation and organic nutrient utilization in the RFC treatment. The partial replacement of MF with in situ crop residue retention, is a simple and efficient way to maintain the soil fertility and rice yield as NPK in southern China.

[Consumption Capacity of N2O in Paddy Soil and the Response Mechanism of nosZ-I-containing Communities].

The long-term flooding anaerobic environment in paddy soils is conducive to denitrification, which is one of the most important reasons for N2O emissions. N2O can be transformed to nitrogen gas (N2) by bacteria and archaea containing nitrous oxide reductase (N2OR) encoded by the nosZ gene, which is the only known biological pathway of N2O consumption in soil. nosZ-I is known to be typical in denitrifying bacteria, which is one of the clades of the nosZ gene and is mainly possessed a Tat signal peptide motif. Although many researchers have studied N2O emission characteristics of paddy soil, the capacity of N2O consumption and the response mechanism of related functional microorganisms in paddy fields is not yet clear. To verify the effect of exogenous N2O on N2O consumption and nosZ-I gene, a pot trial experiment was performed under anaerobic conditions. We collected intact soil cores from flooding paddy fields at a 0-5 cm depth, and exogenous N2O gas was input through the bottom of flooding paddy soil cores. Meanwhile, a control treatment (CK) with no additional N2O gas was also performed. The dynamic characteristics of the added exogenous N2O concentration through the intact soil cores, the content of inorganic nitrogen, and DOC were systematically monitored. In addition, the change in the nosZ-I population diversity and community composition were investigated by high-throughput sequencing approaches, with the purpose of revealing the N2O uptake ability of flooded paddy soil and the response mechanism of the nosZ-I population. The results showed that 97.39% of exogenous N2O diffused into the soil cores, and only 0.72%-7.75% of exogenous N2O escaped from the soil surface. The N2O released in the headspace of soil cores could continue being absorbed and consumed by the flooding soil column. In addition, 67.10% of the N2O escaped to the headspace was consumed in exogenous N2O treatment after 192 h of incubation, which was higher than that in CK treatment, and the N2O consumption rate increased by 144.2% than that in CK treatment. Meanwhile, the consumption of NH4+-N, NO3--N, and DOC consumed during exogenous N2O addition treatment was 19.65%, 16.29%, and 8.41% higher than that in CK treatment, respectively. However, the diversity of the nosZ-I gene community had no significant difference; the community composition of nosZ-I-containing bacteria changed significantly after 192 h when exogenous N2O was input. The abundances of OTU5004, OTU5065, OTU960, and OTU1282 (Proteobacteria) significantly increased, which were the dominant bacterial strain of nosZ-I gene on the OTU level. Compared with the initial sample and CK, the abundance of the OTU5004 strain increased by 7.3% and 4.63%, and the abundance of the OTU5265 strain (Azoarcus sp.) increased by 0.33% and 0.15%, respectively. The result indicated that the flooding paddy soil column at the soil layer of 0-5 cm has a strong N2O absorption and consumption ability. In summary, compared with CK, the addition of exogenous N2O significantly accelerated the N2O consumption rate, improved the consumption potential of flooding paddy soil column, promoted carbon and nitrogen conversion, and changed nosZ-I community composition. These results would provide a new reference for reducing atmospheric N2O emissions.

Large-scale patterns of soil antibiotic resistome in Chinese croplands.

Soil is a vital reservoir of antibiotic resistance genes (ARGs), but we still know little about their distribution in cropland soils and the main driving forces. Here we performed an investigation for ARGs patterns in 105 cropland soils (planted with maize, peanut or soybean) along a 2, 200 km transect in China using high-throughput quantitative PCR approaches. Totally, 204 ARGs were detected, with a higher diversity found in central China than that in northeast and south China. The most abundant (top 50%) and highly shared (present in >50% samples) ARGs regarded as core resistome were dominated by multidrug resistance genes such as oprJ, acrA-05 and acrA-04. Regressive analyses revealed that the relative abundance of total ARGs and core resistome both had significant relationships with mobile genetic elements (MGEs). Anthropogenic factors including the consumption of plastic films and soil properties including heavy metals showed good correlations with the diversity of ARGs. Structural equation modelling analysis further explained that anthropogenic factors were the main forces shaping the ARGs patterns. These findings highlight the importance of human activities in shaping soil antibiotic resistome in the croplands, providing potential management strategies to mitigate the dissemination of ARGs to humans via food chain.

[Impact of Dicyandiamide (DCD) and 3,4-Dimethylpyrazole Phosphate (DMPP) on Ammonia-oxidizing Bacteria and Archaea in a Vegetable Planting Soil].

Nitrification inhibitors (NIs) dicyandiamide (DCD) and 3,4-dimethylpyrazole phosphate (DMPP) showed significant effects in the inhibition of nitrification and the improvement of the utilization efficiency of nitrogen fertilizer in agricultural soils. However, the effects of different NIs on ammonia-oxidizing bacteria (AOB) and archaea (AOA) is still unclear. To verify the inhibitory effect of DCD and DMPP on AOB and AOA, a pot experiment was performed, including Urea, Urea+DCD, and Urea+DMPP treatments. The dynamics of NH4+-N and NO3--N and nitrification potential among different treatments were measured. In addition, real-time PCR and high-throughput sequencing approaches were applied to investigate the changes in the AOB and AOA population abundance and composition. The results revealed that the concentrations of NH4+-N in Urea+DCD and Urea+DMPP treatments were 213% and 675% higher than that in the CK treatment, respectively. However, the concentrations of NO3--N and the nitrification potentials were 13.3% and 37.2%, and 20.4% and 82.4% lower than that in CK treatment, respectively; Furthermore, the copy numbers of the bacterial and archaeal amoA gene were 51.2% and 56.5%, and 6.0% and 27.0% lower than that in the CK treatment, respectively. However, the diversity indexes of AOB and AOA communities, including evenness and richness, exhibited no significant differences after addition of DCD and DMPP. The nork-environmental-samples, unclassified-Nitrosomonadaceae, unclassified-Bacteria, and Nitrosospira, were the predominant genera of the AOB community. The no rank-Crenarchaeota, no rank-environmental-samples and Nitrososphaera were the predominant groups in the AOA community. Summarily, application of DCD and DMPP significantly delayed the transformation of NH4+-N, decreased the formation of NO3--N, inhibited the abundance and changed the composition of AOB and AOA communities. DMPP had a stronger inhibitory effect on nitrification, and on AOB and AOA than DCD. Therefore, compared with DCD, DMPP had a better application prospect regarding the improvement of the nitrogen utilization efficiency in vegetable soil.

[Differential Responses of Rhizospheric nirK- and nirS-type Denitrifier Communities to Different Phosphorus Levels in Paddy Soil].

Phosphorus is an essential life element, which can affect the activities and functions of denitrifiers. Both nirK and nirS genes can code nitrite reductase; however, it remains unclear whether nirK- and nirS-containing denitrifers respond differentially to changes in the availability of phosphorus in paddy soil. In this study, P-deficient paddy soil was used to grow rice plants. Three phosphorus levels established by applying P fertilizer at a rate of 0 mg·kg-1 (CK), 15 mg·kg-1 (P1), and 30 mg·kg-1(P2), respectively. The abundance and community structure of nirK- and nirS- containing denitrifers were determined using quantitative PCR and high-throughput sequencing techniques. Results indicated that nirK- and nirS-containing communities responded differentially to changes in the P levels. The nirS-containing communities are more sensitive to the changes in P in both rhizosphere and bulk soil samples. In addition, the abundance of nirS genes was 2-3 times higher in the P2 treatment than in the CK treatment. Furthermore, the nirS community structure is also clearly differed from the CK treatment. However, P addition only induced partial modification of the community structure and abundance of nirK-containing denitrifiers. Moreover, compared to the bulk soil with each phosphorus level, the nirS community structure in the rhizosphere soil changed significantly; however, only the P2 treatment induced significant increases in the abundance of the nirS gene. In contrast, no significant differences in the abundance and composition of nirK-containing denitrifers were detected between rhizosphere and bulk soils under different phosphorus levels. Collectively, application of phosphate fertilizer in P-deficient paddy soil could significantly increase the abundance of nirK- and nirS-containing denitrifiers, changing their community structures, with nirS-type showing a greater sensitivity than nirK-type denitrifiers. In comparison, the denitrifying communities in the rhizosphere were more sensitive to variable P levels than that in the bulk soil. Compared to bulk soils, rice growth shifted the community structure of nirS- and nirK-containing denitrifiers in rhizosphere soils at each level of P, but failed to induce significant changes in their abundance (except for P2) that could cause a significant increase in nirS abundance. These results could provide a theoretical basis for exploring the effects of fertilization on soil denitrification.

Multiple factors drive the abundance and diversity of the diazotrophic community in typical farmland soils of China.

Biological nitrogen fixation plays an important role in nitrogen cycling by transferring atmospheric N2 to plant-available N in the soil. However, the diazotrophic activity and distribution in different types of soils remain to be further explored. In this study, 152 upland soils were sampled to examine the diazotrophic abundance, nitrogenase activity, diversity and community composition by quantitative polymerase chain reaction, acetylene reduction assay and the MiSeq sequencing of nifH genes, respectively. The results showed that diazotrophic abundance and nitrogenase activity varied among the three soil types. The diazotrophic community was mainly dominated by Bradyrhizobium, Azospirillum, Myxobacter, Desulfovibrio and Methylobacterium. The symbiotic diazotroph Bradyrhizobium was widely distributed among soils, while the distribution of free-living diazotrophs showed large variation and was greatly affected by multiple factors. Crop type and soil properties directly affected the diazotrophic ɑ-diversity, while soil properties, climatic factors and spatial distance together influenced the diazotrophic community. Network structures were completely different among all three types of soils, with most complex interactions observed in the Red soil. These findings suggest that diazotrophs have various activities and distributions in the three soil types, which played different roles in nitrogen input in agricultural soil in China, being driven by multiple environmental factors.

Demonstration of Chemical Distinction among Soil Humic Fractions Using Quantitative Solid-State 13C NMR.

Humic substances (HS) are vital to soil fertility and carbon sequestration. Using multiple cross-polarization/magic-angle spinning (multiCP/MAS) NMR combined with dipolar dephasing, we quantitatively characterized humic fractions, i.e., fulvic acid (FA), humic acid (HA), and humin (HM), isolated from two representative soils (upland and paddy soils) in China under six long-term (>20 years) fertilizer treatments. Results indicate that each humic fraction showed chemical distinction between the upland and paddy soils, especially with much greater aromaticity of upland HMs than of paddy HMs. Fertilizer treatment exerted greater influence on chemical natures of upland HS than of paddy HS, although the effect was less than that of soil type. Organic manure application especially decreased the percentages of aromatic C in the upland HAs and HMs compared with the control. We concluded that humic fractions responded in chemical nature to environmental conditions, i.e., soil type/cropping system/soil aeration and fertilizer treatments.

Differentiations of determinants for the community compositions of bacteria, fungi, and nitrogen fixers in various steppes.

Different types of steppes could provide heterogeneous habitat environments for underground microorganisms, but much less is known about how soil microbes fit the distinct habitats and what are the underlying mechanisms in shaping their community patterns.We simultaneously examined the community compositions and structures of soil bacteria, fungi, and diazotrophs across desert, typical, and meadow steppes in Inner Mongolia using high-throughput sequencing.The results showed that soil bacteria, fungi, and diazotrophs exhibited different distribution patterns across steppe types. Although different steppes displayed obvious differences in climate conditions, plant traits, and soil properties, most of bacterial species were shared by all the steppes while only a few species were unique, indicating that the soil bacterial compositions were hardly influenced by the steppe types. Nevertheless, the habitat heterogeneity could cause shifts in the relative abundance of some bacterial groups, which resulted in significant changes in the community structure of soil bacteria across steppes. However, the fungal community compositions and structures were similar in typical and meadow steppes but that in desert steppe were significantly different. Whereas, the community compositions and structures of diazotrophs were strongly related to the steppe types. In this study, the similar parent material backgrounds of the steppe soils might be the important factor in shaping the homologous bacterial compositions. However, the variations in soil fertility, soil water repellency, and plant species across steppes would be the major driving forces in regulating the compositions and structures of fungal communities, while the diazotrophic communities would be more closely related to the changes in plant traits and soil fertility among steppes.Our results provided evidence of habitat specificity for different microbial groups and their underlying drivers.

Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils.

BACKGROUND: Agricultural food production is at the base of food and fodder, with fertilization having fundamentally and continuously increased crop yield over the last decades. The performance of crops is intimately tied to their microbiome as they together form holobionts. The importance of the microbiome for plant performance is, however, notoriously ignored in agricultural systems as fertilization disconnects the dependency of plants for often plant-beneficial microbial processes. Moreover, we lack a holistic understanding of how fertilization regimes affect the soil microbiome. Here, we examined the effect of a 2-year fertilization regime (no nitrogen fertilization control, nitrogen fertilization, and nitrogen fertilization plus straw amendment) on entire soil microbiomes (bacteria, fungi, and protist) in three common agricultural soil types cropped with maize in two seasons. RESULTS: We found that the application of nitrogen fertilizers more strongly affected protist than bacterial and fungal communities. Nitrogen fertilization indirectly reduced protist diversity through changing abiotic properties and bacterial and fungal communities which differed between soil types and sampling seasons. Nitrogen fertilizer plus straw amendment had greater effects on soil physicochemical properties and microbiome diversity than nitrogen addition alone. Moreover, nitrogen fertilization, even more together with straw, increased soil microbiome network complexity, suggesting that the application of nitrogen fertilizers tightened soil microbiomes interactions. CONCLUSIONS: Together, our results suggest that protists are the most susceptible microbiome component to the application of nitrogen fertilizers. As protist communities also exhibit the strongest seasonal dynamics, they serve as the most sensitive bioindicators of soil changes. Changes in protist communities might have long-term effects if some of the key protist hubs that govern microbiome complexities as top microbiome predators are altered. This study serves as the stepping stone to promote protists as promising agents in targeted microbiome engineering to help in reducing the dependency on exogenous unsustainably high fertilization and pesticide applications.

Remarkable N2O emissions by draining fallow paddy soil and close link to the ammonium-oxidizing archaea communities.

Fallow paddies experience natural flooding and draining water status due to rainfall and evaporation, which could induce considerable nitrous oxide (N2O) emissions and need to be studied specially. In this study, intact soil columns were collected from a fallow paddy field and the flooding-draining process was simulated in a microcosm experiment. The results showed that both N2O concentrations in the soil and N2O emission rates were negligible during flooding period, which were greatly elevated by draining the fallow paddy soil. The remarkable N2O concentrations in the soil and N2O emission/h during draining both had significant relationships with the Arch-amoA gene (P < 0.01) but not the Bac-amoA, narG, nirK, nirS, and nosZ genes, indicating that the ammonium-oxidizing archaea (AOA) might be the important players in soil N2O net production and emissions after draining. Moreover, we observed that N2O concentrations in the upper soil layers (0-10 cm) were not significantly different from that in the 10-20 cm layer under draining condition (P > 0.05). However, the number of AOA and the nitrification substrate (NH4+-N) in the 0-10 cm layer were significantly higher than in the 10-20 cm layer (P < 0.01), indicating N2O production in the 0-10 cm layer might be higher than the measured concentration and would contribute considerably to N2O emissions as shorter distance of gas diffusion to the soil surface.

Characterization of Fungal nirK-Containing Communities and N2O Emission From Fungal Denitrification in Arable Soils.

Fungal denitrifiers play important roles in soil nitrogen cycling, but we have very limited knowledge about their distribution and functions in ecosystems. In this study, three types of arable soils were collected across different climate zones in China, including quaternary red clay soils, alluvial soils, and black soils. The composition and abundance of fungal nirK-containing denitrifiers was determined by MiSeq high-throughput sequencing and qPCR, respectively. Furthermore, a substrate-induced inhibition approach was used to explore N2O emissions from fungal denitrification. The results showed that the arable soils contained a wide range of nirK-containing fungal denitrifiers, with four orders and eight genera. Additionally, approximately 57.30% of operational taxonomic unit (OTUs) belonged to unclassified nirK-containing fungi. Hypocreales was the most predominant order, with approximately 40.51% of the total number of OTUs, followed by Sordariales, Eurotiales, and Mucorales. It was further indicated that 53% of fungal nirK OTUs were shared by the three types of soils (common), and this group of fungi comprised about 98% of the total relative abundance of the nirK-containing population, indicating that the distribution of fungal nirK-containing denitrifiers was quite homogenous among the soil types. These common OTUs were determined by multiple soil characteristics, while the composition of unique OTUs was manipulated by the specific properties of each soil type. Furthermore, fungal N2O emissions were significantly and positively correlated with fungal nirK abundance in the soils, whereas it was not clearly related to fungal nirK compositions. In conclusion, although the arable soils hosted diverse nirK-containing fungal denitrifiers, fungal nirK compositions were highly homogenous among the soil types, which could be a consequence of enduring agricultural practices. The abundance of fungal nirK-containing denitrifiers, rather than their composition, may play more significant roles in relation to N2O emission from fungal denitrification.

Effect of controlled-release fertilizer on N2O emissions and tea yield from a tea field in subtropical central China.

Tea (Camellia sinensis L.), a perennial leaf-harvested crop, favors warm/humid climate and acidic/well-drained soils, and demands high nitrogen (N) fertilizer inputs which lead to significant emissions of N2O. Potential mitigation options should be adopted to improve N use efficiency (NUE) and reduce environmental pollution in tea field system. A 3-year field experiment was carried out in a tea field in southern China from January 2014 to December 2016 to investigate the effect of controlled-release fertilizer (CRF) application on N2O emissions in tea field system. Three practices, namely conventional treatment (CON, 105 kg N-oilcake ha-1 year-1 + 345 kg N-urea ha-1 year-1), treatment with a half amount of the N fertilizer (CRF50%, 105 kg N-oilcake ha-1 year-1 + 120 kg N CRF ha-1 year-1) and full amount of N fertilizer (CRF100%, 105 kg N-oilcake ha-1 year-1 + 345 kg N CRF ha-1 year-1) were used. Compared with the CON, our results showed that CRF50% reduced the N2O emissions by 26.2% (p > 0.05) and increased the tea yield by 31.3% (p > 0.05), while CRF100% significantly increased the N2O emissions by 96.7% (p < 0.05) and decreased the tea yield by 6.77% (p > 0.05). Overall, yield-scaled N2O emissions of tea were reduced by 44.5% (p > 0.05) under CRF50% and significantly increased by 100% (p < 0.05) under CRF100%, compared with CON. Based on the gross margin analysis, CRF50% obtained the highest net economic profit. Our findings suggest that reducing N input of CRF (CRF50%) is necessary and feasible for adoption in the current tea plantation system.