N-cycling Genes Research Articles

The Response of Rhizosphere Microbial C and N-Cycling Gene Abundance of Sand-Fixing Shrub to Stand Age Following Desert Restoration.

Rhizosphere microorganisms play a pivotal role in biogeochemical cycles, particularly in relation to carbon (C) and nitrogen (N) cycles. However, the impact of stand age on the composition of rhizosphere microbial communities and the abundance involved in C and N cycling remains largely unexplored in restoration ecosystems dominated by shrubs of temperate deserts. This study focuses on revealing changes in microbial composition and functional genes in the rhizosphere soil of Caragana korshinskii after revegetation, as well as their response mechanisms to changes in environmental factors. The alpha diversity of bacteria tended to increase with stand age, whereas that of fungi decreased. The abundance of denitrification; dissimilatory nitrate reduction to ammonium, nitrification, and ammonium assimilation; and C fixation-related gene levels increased with stand age, whereas those related to the degradation of starch, pectin, hemicellulose, cellulose, and aromatics decreased. The parameters MBC, MBN, and TC were the key factors affecting the bacterial community, whereas the fungal community was regulated by TN, EC, pH, and MBC. Stand age indirectly regulated C and N cycling functions of genes through altered soil properties and microbial community structures. This study presents a novel approach to accurately evaluate the C and N cycling dynamics within ecosystems at various stages of restoration.

Enhancing soil gross nitrogen transformation through regulation of microbial nitrogen-cycling genes by biodegradable microplastics

Microplastics (MPs) in agricultural plastic film mulching system changes microbial functions and nutrient dynamics in soils. However, how biodegradable MPs impact the soil gross nitrogen (N) transformations and crop N uptake remain significantly unknown. In this study, we conducted a paired labeling 15N tracer experiment and microbial N-cycling gene analysis to investigate the dynamics and mechanisms of soil gross N transformation processes in soils amended with conventional (polyethylene, PE) and biodegradable (polybutylene adipate co-terephthalate, PBAT) MPs at concentrations of 0 %, 0.5 %, and 2 % (w/w). The biodegradable MPs-amended soils showed higher gross N mineralization rates (0.5–16 times) and plant N uptake rates (16–32 %) than soils without MPs (CK) and with conventional MPs. The MPs (both PE and PBAT) with high concentration (2 %) increased gross N mineralization rates compared to low concentration (0.5 %). Compare to CK, MPs decreased the soil gross nitrification rates, except for PBAT with 2 % concentration; while PE with 0.5 % concentration and PBAT with 2 % concentration increased but PBAT with 0.5 % concentration decreased the gross N immobilization rates significantly. The results indicated that there were both a concentration effect and a material effect of MPs on soil gross N transformations. Biodegradable MPs increased N-cycling gene abundance by 60–103 %; while there was no difference in the abundance of total N-cycling genes between soils without MPs and with conventional MPs. In summary, biodegradable MPs increased N cycling gene abundance by providing enriched nutrient substrates and enhancing microbial biomass, thereby promoting gross N transformation processes and maize N uptake in short-term. These findings provide insights into the potential consequences associated with the exposure of biodegradable MPs, particularly their impact on soil N cycling processes.

Effects of Vegetation Cover Varying along the Hydrological Gradient on Microbial Community and N-Cycling Gene Abundance in a Plateau Lake Littoral Zone

The lake littoral zone is periodically exposed to water due to water level fluctuations, driving the succession and distribution of littoral vegetation covers, which complexly affect nutrient biogeochemical transformation. However, the combined effects of water level fluctuations and other environmental factors on microbial characteristics and functions at the regional scale remain unclear. In this study, typical vegetation cover types along various water levels were chosen to investigate the effects of water level and vegetation cover on the microbial community and functional genes in the Lake Erhai littoral zone. The results showed that water level fluctuations influenced oxygen and nitrogen compound contents due to oxic–anoxic alternations and intensive material exchange. Meanwhile, vegetation cover affected the organic matter and total nitrogen content through plant residues and root exudation supplying exogenous carbon and nitrogen. Along the hydrological gradient, the high microbial diversity and abundant microbes related to nitrogen cycling were observed in interface sediments. It was attributed to the alternating aerobic–anaerobic environments, which filtered adaptable dominant phyla and genera. The abundances of amoA AOA, nirS, and amx were higher than those of the other genes and were strongly related to flooding days and water content. In conclusion, water level fluctuations and vegetation type jointly affect microbial community structure and nitrogen-related functional genes.

Impact of two acquisitive plants on N cycle on different soils: The invasive Fallopia japonica does it and so does the native Dactylis glomerata!

Invasive plants may alter ecological and ecosystem processes, including the N-cycle. The Fallopia species complex is a well-studied invasive species whose N-resource acquisition traits define it as an acquisitive species. However, the study of the impacts of invasive plants on the N-cycle never considers the N-acquisition strategy as a reference for choosing another suitable plant control. The purpose of this study is to assess the impacts of an invasive species (Fallopia japonicaFJ) on the N-cycle and to compare with those caused by a native acquisitive species (Dactylis glomerataDG), all compared to unplanted soils. A four-months mesocosm experiment was conducted by growing FJ and DG on nine different soils and measuring their impacts on N-cycle microbial activities (free-living nitrogen fixation FLNF, denitrification DEA, nitrification NEA), on N-mineral forms and on functional N-cycle gene abundance (nifH, AOA, AOB, nirS, nirK) as well as the total bacterial community gene (rRNA 16S). The nine soils differ in microbial enzymatic activities, N-mineral form concentrations, physico-chemical factors, texture, and gene abundances. Plant effects on FLNF, NEA and DEA are only soil dependent and no effect of invasive status was found. In addition, the native plant DG generally affected microbial parameters over a wider range of soils than the invasive plant. Stronger impacts of the native DG on microbial gene abundances were found compared to the invasive FJ. A stronger effect of the invasive plant was found for the soil NO3− concentration, with a significant decrease under the FJ than under the DG. Under both FJ and DG, NH4+ concentrations were not significantly affected. In conclusion, the invasive status in the ecosystem of the two plants studied cannot be explained through their impacts on microbial enzymatic activities and gene abundances of the soil N-cycle and the soil N mineral pools.

Multi-amplicon nitrogen cycling gene standard: An innovative approach for quantifying N-transforming soil microbes in terrestrial ecosystems

Agriculture accounts for nearly three-fourths of all nitrous oxide (N2O) anthropogenic emissions, a potent greenhouse gas (GHG). Improvements in agricultural management practices are critical for improving plant nitrogen (N) use efficiency and reducing N2O emissions. While implementing “climate-smart” management can reduce N2O emissions, building a linkage between these emissions and the N-cycling microbes that drive them will require N-cycling gene assays that are cost-effective, practical, and accessible to climate-smart researchers. In a recent study, a group of researchers demonstrated the suitability of synthetic oligonucleotides to serve as real-time quantitative PCR (qPCR) standards for quantifying microbial genes in soils. While this study is not based on that study, our results complement their findings and offer fresh insights into this novel methodology. Here, we describe an innovative approach that provides precision in the absolute quantification of five N-transforming target genes (AOB amoA, AOA amoA, nirK, nirS, and nosZ) in soils. Similar to the aforementioned study, our method obviates the cost-intensive aspects of traditional qPCR methods for preparing standard curves in soil microbial ecology (e.g., gel purification of PCR products and in-vivo cloning of plasmids) and is capable of being extended to any biochemical system, or environment of interest. Additionally, our qPCR approach provides several advantages: it utilizes a single multi-amplicon synthetic oligonucleotide, requires only a single dilution series and one stock solution to quantify all gene targets, and contains a non-edaphic gene (ZIKV) that can serve as a soil spike to determine DNA extraction efficiency and DNA recovery estimates. Furthermore, our protocol mitigates PCR inhibition from soil-derived substances using a modified DNA extraction protocol and inhibitor-tolerant polymerase. Ultimately, our work aims to reduce the technical burden on non-biologists/biochemists when conducting soil microbiological assays, support the development of climate mediation practices, and advance climate-smart agriculture goals.

Nitrogen functional profiles of microbiomes in diverse agricultural and forest soils and its driver at continental scale in China

Functional characteristics of microbiomes are good predictors of nitrogen (N) biogeochemistry, but soil microbial N-functional profiles under different land use practices and their dominant drivers at continental scale remain unclear. For this study, we selected soils having a broad range of edaphic factors across different land use practices and soil types in China and used metagenomic sequencing to investigate N-functional profiles of microbiomes. The N-pathway frequencies were highest in paddy soils, and the composition of N-cycling genes in paddy soils significantly diverged from upland and forest soils. Differential abundance analysis showed that genes associated with nitrogen dissimilatory pathways exhibited enrichment in paddy soils, whereas those linked to assimilatory pathways were enriched in forest soils. Aggregated boosted tree analysis revealed that the frequencies of N-pathways and relative abundances of N-cycling genes were mainly explained by soil moisture and pH. Partial Mantel and redundancy analysis consistently showed that N-functional composition correlated strongest with moisture and pH. Overall, our results demonstrated that soil moisture and pH were vital drivers of microbial N-functional profiles, providing novel evidence for soil moisture and pH’s role in driving whole nitrogen cycling. Considering the large fluctuations in moisture over time, soil pH, with minor seasonality, could be used as indicators to reflect microbial N-functional profiles at the continental scale.

Disinfectant-induced ammonia oxidation disruption in microbial N-cycling process in aquatic ecosystem after the COVID-19 outbreak

Anthropogenic activities significantly impact the elemental cycles in aquatic ecosystems, with the N-cycling playing a critical role in potential nutrient turnover and substance cycling. We hypothesized that measures to prevent COVID-19 transmission profoundly altered the nitrogen cycle in riverine ecosystems. To investigate this, we re-analyzed metagenomic data and identified 60 N-cycling genes and 21 host metagenomes from four urban reaches (one upstream city, Wuhan, and two downstream cities) along the Yangtze River. Our analyses revealed a marked decrease in the abundance of bacterial ammonia monooxygenase genes, as well as in the host, ammonia-oxidizing autotrophic Nitrosomonas, followed by a substantial recovery post-pandemic. We posited that discharge of sodium hypochlorite (NaOCl) disinfectant may be a primary factor in the reduction of N-cycling process. To test this hypothesis, we exposed pure cultures of Nitrosomonas europaea to NaOCl to explore the microbial stress response. Results indicated that NaOCl exposure rapidly compromised the cell structure and inhibited ammonia oxidation of N. europaea, likely due to oxidative stress damage and reduced expression of nitrogen metabolism-related ammonia monooxygenase. Using the functional tagging technique, we determined that NaOCl directly destroyed the ammonia monooxygenase protein and DNA structure. This study highlights the negative impacts of chlorine disinfectants on the function of aquatic ecosystems and elucidates potential mechanisms of action.

Biodegradable film mulching increases soil microbial network complexity and decreases nitrogen-cycling gene abundance

Biodegradable plastic films have emerged as a substitute for conventional plastic films. Nevertheless, responses of plant-associated microbiomes to the application of biodegradable film mulching at field scale have received little attention. A field experiment was conducted to assess the influence of different film mulching treatments on various microbial attributes and nitrogen (N) cycling functional genes in bulk and rhizosphere soils. Biodegradable film mulching raised the bacterial Shannon index in bulk soils but not in rhizosphere soils. Biodegradable film mulching has led to an increase in the complexity and connectivity of microbial networks, as well as an enhancement in the positive association among microorganisms owing to raised soil nutrients and increased crop biomass. In biodegradable film-treated soils, both bacterial and fungal communities were primarily influenced by stochastic processes associated with dispersal limitation. Moreover, conventional plastic film mulching increased denitrification, anammox, N fixation, and dissimilatory nitrate-reduction (DNRA) gene abundance in bulk soils. In rhizosphere soils, biodegradable film mulching reduced nitrification, denitrification, anammox, N fixation, and DNRA gene abundance. Furthermore, keystone genera (e.g., Nitrosospira, Truepera, Adhaeribacter, Opitutus, and Fusarium) were affected by edaphic variables, contributing to decreased N-cycling gene abundance in biodegradable film-treated soils. Collectively, biodegradable film mulching transformed soil microbiome assembly and functional adaptation, and soil nutrient availability and plant biomass were the critical factors influencing the microbial community. These findings present a novel perspective on the diverse impacts of biodegradable and conventional film mulching on soil microbiome and N-cycling processes.

Soil dependence of biochar composts in mitigating greenhouse gas emissions: An overlooked biophysical mechanism

Biochar-manure co-compost (BM) has garnered considerable attention as a promising soil amendment for improving nutrient retention and mitigating the emission of greenhouse gases (GHGs). However, its efficacy often varies largely from one soil to another. By comparing soil CO2 and N2O effluxes, solution chemistry, enzyme activities, and the abundances of N-cycle genes between BM and manure compost (M) across three soils of different texture classes through microcosm incubations, we aimed to develop biophysical mechanics to untangle the soil-dependent efficacy of BM in mediating soil carbon and nitrogen transformation processes. Compared to M addition, BM addition significantly reduced soil CO2 and N2O emissions, but its effectiveness was soil texture-dependent, being strongest for CO2 and N2O in fine-textured clay loam and coarse-textured sand, respectively. Such soil texture-dependent effects of BM versus M were also observed in soil enzyme activities and gene copy numbers of ammonia-oxidizing bacteria and denitrifiers. Our datasets suggest that BM interacted strongly with soil texture to modulate the pore scale-based diffusion of oxygen, thereby creating divergence in the aeration status among soils. Sequentially, soil phenol oxidase activity was greater in BM than in M under more aerobic conditions but no difference between BM and M in oxygen-limited soils. The balance between oxygen depletion due to microbial respiration of organic amendments and oxygen diffusion through soil/biochar pores also shaped the activities of nitrifying and denitrifying prokaryotes differently between coarse- and fine-textured soils. This logic model well-explained the magnitude of change in soil-dependent CO2 and N2O emissions from organic amendments. The knowledge gained in this work will likely have profound practical ramifications for optimizing BM efficacy in mitigating the GHGs emission.

N-cycle gene abundance determination of N mineralization rate following re-afforestation in the Loess Plateau of China

N-cycle gene abundance determination of N mineralization rate following re-afforestation in the Loess Plateau of China

Nitrous oxide emissions and N-cycling gene abundances in a drip-fertigated (surface versus subsurface) maize crop with different N sources

Surface drip fertigation has demonstrated promising results regarding the mitigation of nitrous oxide (N2O) emissions. The use of subsurface irrigation may offer the possibility of reducing these emissions further due to the modification of the soil moisture profile and N allocation, both of which affect the biochemical processes leading to N2O fluxes. However, the mitigation potential of subsurface irrigation combined with different mineral nitrogen (N) fertilizers (ammonium or nitrate-based, use of nitrification inhibitors) still needs to be evaluated. To respond to this need, a 2-year field experiment was set up in central Spain to test two different drip-fertigation systems (surface and subsurface at 30 cm depth) and four N fertilization treatments (control, calcium nitrate, and ammonium sulfate with or without the nitrification inhibitor 3,4-dimethylpyrazole phosphate, DMPP) in an irrigated maize (Zea mays L.) crop. Nitrous oxide emissions, mineral N concentrations (ammonium, NH4+, and nitrate, NO3−), and abundance of key N genes involved in nitrification and denitrification processes were measured in two soil layers (0–20 and 20–40 cm). Regardless of the irrigation system, ammonium sulfate gave the highest cumulative N2O losses in both campaigns, while calcium nitrate and the use of DMPP were the most effective strategies to abate N2O fluxes in the first and second years, respectively. Differences between irrigation systems were not statistically significant for cumulative N2O emissions, despite the clear effect on topsoil mineral N (higher NH4+ and NO3− concentrations in surface and subsurface drip, respectively). Nitrous oxide emissions were positively correlated with soil NH4+ concentrations. Gene abundances were not a trustworthy predictor of N2O losses in the 1st year, although a clear inhibitory effect of fertilization on microbial communities (i.e., ammonia oxidizers, nitrite reducers, and N2O reducers) was observed during this campaign. During the second year, nitrifying and denitrifying genes were affected by irrigation (with higher abundances in the 20–40 cm layer in subsurface than in surface drip) and by the addition of DMPP (which had a detrimental effect on gene abundances in both irrigation systems that disappeared after the fertigation period). In conclusion, the use of DMPP or calcium nitrate instead of ammonium sulfate may enhance the chances for an additional mitigation in both surface and subsurface irrigation systems.

Contrasting potential impact patterns of unique and shared microbial species on nitrous oxide emissions in grassland soil on the Tibetan Plateau

Microbial nitrogen transformation processes in grasslands are important nitrous oxide (N2O) sources on the Tibetan Plateau. Different microorganisms carrying various functional nitrogen (N) cycling genes colonize different soil types and have varying impacts on N2O emissions. However, the role of specific microbial components such as unique and shared microbial species, in N2O flux in alpine grassland soils remains understudied. Thus, we combined gas chromatography-based static opaque chamber methods with metagenomic sequencing to investigate the role of unique and shared microbial species carrying N-cycling genes in N2O emissions from two alpine grassland types on the Tibetan Plateau. Our results showed that the N2O flux in the alpine meadows (9.48 × 10−9 g m−2 h−1) was higher than that in the alpine steppes (4.21 × 10−9 g m−2 h−1). Furthermore, our study revealed a significant negative correlation between the abundance of unique microbial species and the N2O flux in alpine steppes. In contrast, the abundance of shared microbial species was significantly and positively correlated with N2O flux. The unique microbial species in the phyla Chloroflexi and Actinobacteria carried the ureC, nasA and nirB genes, which could consume nitrogen substrates in forms other than producing N2O, which could explain the N2O reduction seen in the alpine steppes. In addition, the higher abundance of shared microbial species in the phyla Proteobacteria, Actinobacteria, Thaumarchaeota and Acidobacteria carried genes encoding denitrification pathways (nirK, narG, and norB) could interpret the higher N2O emissions in the alpine meadows. In addition, our study revealed that the soil substrate contents (e.g., soil organic carbon and total nitrogen) and soil environment factors (e.g., soil pH and soil moisture) were potentially important drivers of N2O emissions in soil via their regulation of the composition of unique and shared microbial communities carrying N-cycling genes. Collectively, our results suggested that identifying the unique and shared microbial species carrying different N-cycling genes could provide potential biological strategies for mitigating N2O emissions in alpine grasslands, such as blocking the growth of shared microbial species. Future management practices for mitigating N2O emissions in alpine grassland should also focus on adopting appropriate nutrient management strategies, such as balanced fertilization, to prevent excessive nutrient. Our findings provide insights for further elucidating the different potential regulatory effects of unique and shared microbial species on emissions under the control of the soil environment in different types of grasslands on the Tibetan Plateau.

Responses of bacterial communities and nitrogen-cycling microbiomes to the conversion from cereals to legumes in the rice-based system

Legumes are gaining popularity in rice-centric agroecosystems to boost yield, improve sustainability, and enhance soil fertility. However, their effects on soil nitrogen(N)-transforming networks, and predominant drivers governing microbial communities shift remain largely opaque. Here, we investigated soil bacterial community composition and N-cycling genes after converting to legume rotations in a 7-year field experiment for both rice and winter cropping seasons. Two conventional rice-based systems, rice-wheat (RW) and rice-rape (RRa), and four rice-legume rotations, rice-milk vetch (RM), rice-fava bean (RF), rice-milk vetch-rice-fava bean after continuous rice-milk vetch (RMF), and rice-fava bean-rice-milk vetch following continuous rice-fava bean (RFM) were constructed. Results showed that legume integration imposed greater impacts on soil biogeochemistry properties and bacterial communities in winter versus rice seasons. Integration of legume into rice-based cropping systems elicited significant alterations in soil water content, CEC, pH, total N content (TN), microbial biomass N, and dissolved organic carbon. Taxa including Acidobacteria (RFM), Rokubacteria (RMF), and Chloroflexi (RM) related to decomposition potentials were altered. Shift in soil bacterial community were attributed to alterations in environmental factors including soil pH, CEC, and TN. Legume mulching during rice seasons significantly reduced potential for assimilatory nitrite reduction (RM). Legume cultivation, on the other hand, suppressed the processes of N fixation (RFM), nitrate and nitrite reduction (RF and RFM) during winter seasons, potentially decreasing N leaching and N2O emissions. This study demonstrates strategic legume integration can reshape soil N cycling to improve agricultural sustainability.

Spent mushroom substrate as a substitute for chemical fertilizer changes N-cycling genes and reduces N2O emission in different textured soils

Spent mushroom substrate as a substitute for chemical fertilizer changes N-cycling genes and reduces N2O emission in different textured soils

Nitrogen-cycling genes in oyster reefs and surrounding sediments: Relationships with environmental factors and respective nitrogen rates

To investigate nitrogen (N) cycling in oyster reef habitats along the East coast of Australia, we assessed N-cycling gene abundances in oyster shell biofilms and surrounding sediments, and explored their correlation with environmental factors and respective N rates. We found higher abundances of the denitrification gene nosZII in oyster shell biofilms, while there were not significant differences in the denitrification genes nirS and nirK between oyster biofilms and sediments. Additionally, oyster shell biofilms had a lower (nirS + nirK)/nosZII ratio, indicating a greater capacity for N removal and limited nitrous oxide release compared to sediments. Abundance of nirS, nirK, and dissimilatory nitrate reduction to ammonium (nrfA) genes in sediments decreased with increasing content of organic material, suggesting the influence of large-scale environmental conditions. N-cycling gene abundances did not relate to N rates, emphasising the importance of investigating microbial genes to enhance our understanding of the N cycle in oyster reef habitats.

Excessive manure application stimulates nitrogen cycling but only weakly promotes crop yields in an acidic Ultisol: Results from a 20-year field experiment

Population growth and growing demand for livestock products produce large amounts of manure, which can be harnessed to maintain soil sustainability and crop productivity. However, the impacts of excessive manure application on crop yields, nitrogen (N)-cycling processes and microorganisms remain unknown. Here, we explored the effects of 20-year of excessive rates (18 and 27 Mg ha–1 yr–1) of pig manure application on peanut crop yields, soil nutrient contents, N-cycling processes and the abundance of N-cycling microorganisms in an acidic Ultisol in summer and winter, compared with none and a regular rate (9 Mg ha–1 yr–1) of pig manure application. Long-term excessive pig manure application, especially at the high-rate, significantly increased soil nutrient contents, the abundance of N-cycling functional genes, potential nitrification and denitrification activity, while it had a weaker effect on peanut yield and plant biomass. Compared with manure application, seasonality had a much weaker effect on N-cycling gene abundance. Random forest analysis showed that available phosphorus (AP) content was the primary predictor for N-cycling gene abundance, with significant and positive associations with all tested N-cycling genes. Our study clearly illustrated that excessive manure application would increase N-cycling gene abundance and potential N loss with relatively weak promotion of crop yields, providing significant implications for sustainable agriculture in the acidic Ultisols.

Earthworm effect on rhizosphere N-cycle microbial genes depends on soil properties

Earthworms are known to improve plant growth in a soil-dependent way, notably via modifications of the rhizosphere microbiota and its functions. We tested the hypothesis that earthworms influence the abundance of microbial genes involved in N cycle according to the type of soil. In three soils with contrasting texture, we quantified five N-cycling genes in different microsites (bulk, rhizosphere or earthworm casts) of microcosms containing (i) neither plants nor eathworms, (ii) plants, (iii) earthworms, (iv) both plant and earthworms. In the presence of earthworms, rhizophere was enriched in nifH (N2 fixation) and depressed in nosZ or narG (denitrification) in sandy soil, suggesting a shift in N balance towards immobilization; rhizosphere was enriched in nifH but also nosZ and narG in loamy soil; no effect was detected in clayey soil. The pattern of gene abundance across the different soils and microsites suggests that earthworms could favor microorganisms with a potential beneficial effect on plants specifically in sandy soils.

Cropping rotation improved the bacterial diversity and N-cycling genes in tobacco fields through a 19-year long-term experiment

Soil microorganisms play crucial roles in various processes within the soil ecosystem, such as nutrient cycling, organic matter decomposition, and maintenance of soil structure. However, their responses to fertilization and different cropping systems in tobacco soils remain poorly understood. In this study, we conducted a 19-year-long field experiment on rice-tobacco rotation cropping (R) and continuous tobacco cropping (C), with three fertilization treatments: no fertilizer (NF), chemical NPK fertilizer (NPK), and composted pig manure (OM). The composition, co-occurrence patterns, N-cycling genes (nifH, AOA-amoA, AOB-amoA, nirS, nirK, and nosZ) of the bacterial communities as well as the soil properties were analyzed in the soils after tobacco was harvested. The pH and available potassium (AK) in the rotation cropping soil were significantly lower than those in continuous cropping soil, while the α-diversity index, and the abundance of nifH, nirS, nirK, and nosZ genes were opposite. The phyla Chloroflexi, Desulfobacterota, MBNT15, and Nitrospinota, as well as number of low-abundance genera, were significantly enriched in rice-tobacco rotation cropping. Partial least squares path model (PLSPM) indicated that cropping systems had a greater influence on the variations in bacterial communities compared to fertilization practices. These findings enhance our understanding of the significance of land management and fertilization in shaping the soil bacteria of tobacco. The rice-tobacco rotation cropping system demonstrated greater benefits to soil microorganisms and N-cycling genes compared to continuous cropping system.

Carbon and nitrogen fractions are more important than bacterial composition for carbon and nitrogen mineralization considering parent material and fertilization

Microorganisms and organic carbon (C) pool composition are vital in regulating soil organic matter mineralization. However, our understanding of how parent materials and fertilizers affect this process is still limited. In this two-year study, the changes of cumulative soil organic C and nitrogen (N) mineralization and C and N pools (total, labile, and recalcitrant), C- and N-cycling enzymes, bacterial composition, and C- and N-cycling gene and their interactions were analyzed for soils developed on loess and river alluvium. These soils were under rice-rape seed rotation, and no fertilization (Control), NPK (NPK), and NPK plus organic manure (NPKM) were applied; treatments were arranged into a completely randomized design. Soil organic C mineralization was influenced by soil parent material and fertilization, whereas no interactive effects were found for soil N mineralization. The river alluvium promoted 2.24 times higher C and 1.27 times higher N mineralization than loess; fertilization intensified C and N mineralization in 1.70 and 1.22 times only in loess. Soil C and N fractions were influenced by the parent material, with 1.39 and 1.10 times higher effects found in soils formed on river alluvium. NPKM increased the content of total organic C in 1.31 times, labile C in 1.24 times, recalcitrant C in 1.34 times, total N in 1.21 times, and recalcitrant N in 1.17 times in loess soil. Similarly, in river alluvium soil, the increases were 1.41、1.21、1.53、1.23 and 1.28 times. Fertilization with NPKM increased C- and N-cycling enzyme activities in both soils. Parent material and fertilization shifted bacterial composition by changing pH, subsequently influencing N-cycling genes. However, only parent material affected C-cycling genes. Thus, C and N fractions play a direct role in the mineralization process of soil organic C, while bacteria indirectly influenced the C mineralization processes by promoting the enzyme activities.

Long-term maintenance rate fertilisation increases soil bacterial-archaeal community diversity in the subsoil and N-cycling potentials in a humid crop season

Among agronomical practices, fertilisation greatly influences soil microbial diversity and functionality and severely disturbs the global nitrogen (N) cycle. In this study, we assessed the effect of 16 years of mineral fertilisation (NPS) on soil bacterial-archaeal communities in a no-tillage experiment in a humid climate season. We used 16S rRNA amplicon sequencing and functional prediction of marker genes involved in the N cycle at two soil depths (0–5 and 5–10 cm). Samples were taken after soybean harvest in a wheat/soybean-maize crop sequence. At both soil depths, fertilisation increased the abundance of Proteobacteria while reducing the abundance of Verrucomicrobiota. Indicator species analyses revealed that MB-A2–108 (Actinobacteriota) and Nitrososphaeraceae (Archaea) were indicators of the low fertiliser rates at 0–5 cm. Instead, Rokubacteriales (Methylomirabilota) and Nitrolancea (Chloroflexi) were indicators of low and high rates, respectively, at 5–10 cm. Biological N–fixation genes (nifA, nifV nifHD1, and nifHD2) showed an inconsistent response depending on the soil depth. Yet, the high abundance of nifA revealed the presence of N-fixing microorganisms even at high levels of N fertilisation. The predominance of genes involved in the dissimilatory (nirB and nirK) and assimilatory (nirA) reduction of nitrate was steadily found at higher fertilisation. Given that the predecessor crop was a legume that did not receive N, our results revealed the substantial legacy of long-term N inputs on soil bacterial-archaeal diversity and N-cycling genes that might have been umpired by the current humid conditions.