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A field experiment was conducted in northeast China to examine the response of nitrogen cycling enzymes, that is, protease, N‐acetyl‐β‐D‐glucosaminidase (NAG), amidase, urease, and peptidase, as well soil organic nitrogen (SON) fractions and their relationships to RT (no maize residue application), NT (no tillage with maize residues placed on the surface), TT (plow maize residues into the soil at 0–35 cm depth in the first year, 0–20 cm in the second year, and 0–15 cm in the third year), and PT (plow maize residues into soil at 0–35 cm depth). The results have shown that NT significantly enhanced the activities of protease and NAG at 0–10 cm soil depth in comparison with other treatments. NT and TT significantly enhanced the activities of protease compared to RT and PT at 10–20 cm soil depth. TT significantly enhanced the activities of NAG in comparison with RT at 10–20 cm soil depth. TT and PT significantly enhanced the activities of NAG and peptidase compared to RT and NT at 20–35 cm soil depth. PT significantly increased the activities of protease in comparison with RT at 20–35 cm soil depth. NT, TT, and PT significantly enhanced the activities of peptidase compared to RT at 10–20 cm soil depth. NT significantly increased the concentration of hydrolyzable NH4+‐N$$ {\\mathrm{NH}}_4^{+}\\hbox{-} \\mathrm{N} $$ in comparison with other treatments at 0–10 cm soil depth. PT significantly enhanced the concentration of hydrolyzable NH4+‐N$$ {\\mathrm{NH}}_4^{+}\\hbox{-} \\mathrm{N} $$ and amino acid N compared to other treatments at 20–35 cm soil depth. Redundancy analysis showed that protease played a crucial role in the cycling of SON under RT and NT, whereas peptidase and NAG played a significant role in the cycling of SON under TT and PT, respectively. This study provided a comprehensive understanding of crop residue return methods for regulating soil N cycling. To deepen our understanding of soil nitrogen cycling under different crop residue managements in northeast China, we conducted a field experiment with different maize residue incorporation methods and examined nitrogen cycling enzymes and organic nitrogen fractions, besides, the correlations between nitrogen cycling enzymes and organic nitrogen fractions were also explored. The results indicates that soil nitrogen cycling under different crop residue managements were regulated by different nitrogen cycling enzymes.

ABSTRACT Nutrient inputs influence the sustainability of bioenergy crop production through contemporary (shortly after addition) and legacy effects (persisting over years) on microbial nitrogen (N) and carbon cycling, which contribute to greenhouse gas emissions. However, the relative importance of contemporary and legacy effects and how that could vary by crop functional types is poorly understood. Considering its rhizomatous roots and perennial growth, we hypothesized that Miscanthus × giganteus (M×g) would be more sensitive to legacy N fertilization and the historical context of its environment than an annual crop like maize. To test this hypothesis, we examined the effects of legacy and contemporary N inputs on nitrous oxide (N2O) and carbon dioxide (CO2) emissions, as well as key N cycling genes in soils where M×g and maize were grown. A 150‐day soil incubation experiment was conducted using soils from a long‐term M×g and maize fertility experiment with three historic N fertilization rates (0, 112, and 336 kg N ha−1 year−1) and a contemporary amendment (60 mg N kg−1) with negative control (0 mg N kg−1). We observed significant increases in cumulative N2O emissions in Mxg soils relative to maize soils, particularly at higher legacy fertilization rates, while contemporary N had no significant effect. Bacterial amoA gene abundance, which plays a significant role in nitrification in nutrient‐rich soils, also increased with higher legacy fertilization rates in M×g soils but was unaffected by the contemporary N. In maize soils, legacy and contemporary N did not significantly affect N2O emissions, but cumulative CO2 emissions and amoA gene abundance significantly increased. The abundances of norB genes were not significantly influenced by either legacy fertilization or contemporary N amendments in either soil. Our findings demonstrate the greater importance of fertilization history over contemporary N in mediating soil N2O emissions, particularly for perennial bioenergy crops. This study investigates how legacy and contemporary nitrogen (N) inputs influence soil greenhouse gas emissions and microbial dynamics in miscanthus and maize‐cultivated soils. Through a 150‐day incubation, significant increases in cumulative N2O emissions were observed in M×g soils compared to maize soils, particularly at higher legacy fertilization rates, while contemporary N had no significant effect. Furthermore, legacy N had a dominant impact on shaping N2O and CO2 emissions, as well as microbial responses. These findings indicate that these legacy effects are important to consider for sustainable bioenergy production.

Floodplains are critical ecosystems where terrestrial and riverine systems meet. Floodplain sediments experience many, sometimes dramatic, changes in moisture and oxygen concentrations because of changes in water table height, flooding, and drought, leading to active microbial cycling of contaminants and nutrients. Nitrogen is one such nutrient that is not only essential for the building blocks of life but can also be used as an energy source by some microorganisms. Microorganisms that oxidize ammonia and nitrite are a crucial part of the nitrogen cycle and can lead to eventual nitrogen loss from a system. Investigating the genes present in microorganisms responsible for nitrification in a dynamic floodplain suggests that organic nitrogen—from decaying plants or potentially other sources, such as fertilizers, grazing livestock feces, or contaminants (e.g., pesticides, pharmaceuticals)—is an important nitrogen source to these microorganisms. This study identifies genes not previously described in nitrifying microorganisms, expanding their potential metabolic substrates.

Microbial communities play critical roles in the Earth’s biosphere by mediating various biogeochemical cycles of essential elements and maintaining ecosystem stability and multi-functioning through the functional genes they carry. However, recovering the key functional genes from such complex communities remains challenging. Both advantages and limitations exist for different technologies. In this study, using the amo gene family as an example, we show that targeted assembly enables accurate and rapid recovery of high-quality amo sequences from shotgun metagenomes, consuming minimal computational resources and running time. Compared to conventional full-assembly approaches, the amo sequences recovered by targeted assembly are found with more operons, higher (phylo)genetic diversity, and fewer chimeras. This study provides an efficient alternative route for recovering microbial functional genes, particularly when computational resources are limited.

This study aimed to assess the influences of short-term straw return combined with nitrogen (N) fertilizer on crop yield, soil properties, the bacterial community, and soil nitrogen cycling gene abundance in a rice–rapeseed planting system. A two-year field experiment was conducted in a paddy field from 2019 to 2021. There were four treatments in the experiment: −N−S, no N applied with no straw return; −N+S, no N applied with straw return; +N−S, N applied with no straw return; and +N+S, N applied with straw return. The results showed that short-term straw return combined with N fertilizer could increase crop yield and N use efficiency. N fertilizer application had a positive effect on Gemmatimonadota and Desulfobacterota abundance. Straw returning had a positive effect on Desulfobacterota and Proteobacteria abundance. N fertilization significantly increased the abundance of amoA-AOA, amoA-AOB, and nxrB in agricultural soils. Straw return and N fertilization were not conducive to denitrification. We conclude that short-term straw return combined with N fertilizer in rice-growing areas not only increase crop yield and improve crop N uptake but also increase SOM, total N, and NH4+ and improve the soil microbial activity and N use efficiency.

Agricultural soils contaminated with heavy metals poison crops and disturb the normal functioning of rhizosphere microbial communities. Different crops and rhizosphere microbial communities exhibit different heavy metal resistance mechanisms. Here, indoor pot studies were used to assess the mechanisms of grain and soil rhizosphere microbial communities on chromium (Cr) stress. Millet grain variety ‘Jingu 21’ ( Setaria italica ) and soil samples were collected prior to control (CK), 6 hours after (Cr_6h), and 6 days following (Cr_6d) Cr stress. Transcriptomic analysis, high-throughput sequencing and quantitative polymerase chain reaction (qPCR) were used for sample determination and data analysis. Cr stress inhibited the expression of genes related to cell division, and photosynthesis in grain plants while stimulating the expression of genes related to DNA replication and repair, in addition to plant defense systems resist Cr stress. In response to chromium stress, rhizosphere soil bacterial and fungal community compositions and diversity changed significantly ( p  < 0.05). Both bacterial and fungal co-occurrence networks primarily comprised positively correlated edges that would serve to increase community stability. However, bacterial community networks were larger than fungal community networks and were more tightly connected and less modular than fungal networks. The abundances of C/N functional genes exhibited increasing trends with increased Cr exposure. Overall, these results suggest that Cr stress primarily prevented cereal seedlings from completing photosynthesis, cell division, and proliferation while simultaneously triggering plant defense mechanisms to resist the toxic effects of Cr. Soil bacterial and fungal populations exhibited diverse response traits, community-assembly mechanisms, and increased expression of functional genes related to carbon and nitrogen cycling, all of which are likely related to microbial survival during Cr stress. This study provides new insights into resistance mechanisms, microbial community structures, and mechanisms of C/N functional genes responses in cereal plants to heavy metal contaminated agricultural soils. Portions of this text were previously published as part of a preprint ( https://www.researchsquare.com/article/rs-2891904/v1 ).

Reforestation is effective in restoring ecosystem functions and enhancing ecosystem services of degraded land. The three most commonly employed reforestation methods of natural reforestation, artificial reforestation with native Masson pine, and introduced slash pine plantations were equally successful in biomass yield in southern China. However, it is not known whether soil ecosystem functions, such as nitrogen (N) cycling, are also successfully restored. Here, we employed a functional microarray to illustrate soil N‐cycling. The composition of N‐cycling genes in soils varied significantly with reforestation method and varied with constructive species identity and plant diversity. Artificial reforestation had less superior organization of N‐cycling genes than natural reforestation, as indicated by the less diverse and less stable pathways to perform the biogeochemical N‐cycling processes. Besides, artificial reforestation had lower functional potential (abundance of ammonification, denitrification, assimilatory, and dissimilatory nitrate reduction to ammonium genes) in soils than natural method. Evaluations of the abundance and interactions of N‐cycling genes in soils showed that plantations, especially artificial reforestation with slash pine plantations, possessed a smaller range of ecosystem functions that provide a less diverse array of N‐related substrates and nutrients to microbial communities compared with natural restoration. This might lead to a lower independence of N‐cycling, which indicated a higher risk of N release in plantations. The unfavorable N‐cycling conditions in plantations were corroborated by the lower contents of available N, ammonium N, and nitrate N. These findings demonstrate that reforestation methods could have broad regional and possibly global implications for N‐cycling.

Biochar application to legume-based mixed cropping systems may enhance soil microbial diversity and nitrogen (N)-cycling function. This study was conducted to elucidate the effect of biochar application on soil microbial diversity and N-cycling function with a particular focus on legume species. Therefore, we performed a pot experiment consisting of three legume species intercropped with maize: cowpea, velvet bean, and common bean. In addition, one of three fertilizers was applied to each crop: biochar made of chicken manure (CM), a chemical fertilizer, or no fertilizer. Amplicon sequencing for the prokaryotic community and functional prediction with Tax4Fun2 were conducted. Under the CM, Simpson’s diversity index was higher in soils with common beans than those in other legume treatments. On the other hand, N-cycling genes for ammonia oxidation and nitrite reductase (NO-forming) were more abundant in velvet bean/maize treatment, and this is possibly due to the increased abundance of Thaumarchaeota (6.7%), Chloroflexi (12%), and Planctomycetes (11%). Cowpea/maize treatment had the lowest prokaryotes abundances among legume treatments. Our results suggest that the choice of legume species is important for soil microbial diversity and N-cycling functions in CM applied mixed cropping systems.

Management practices may influence dryland soil N cycling. We evaluated the effects of tillage, crop rotation, and cultural practice on dryland crop biomass (stems and leaves) N, surface residue N, and soil N fractions at the 0–20 cm depth in a Williams loam from 2004 to 2008 in eastern Montana, USA. Treatments were two tillage practices (no-tillage [NT] and conventional tillage [CT]), two crop rotations (continuous spring wheat [ Triticum aestivum L.] [CW] and spring wheat-barley [ Hordeum vulgaris L.] hay-corn [ Zea mays L.]-pea [ Pisum sativum L.] [W-B-C-P]), and two cultural practices (regular [conventional seed rates and plant spacing, conventional planting date, broadcast N fertilization, and reduced stubble height] and ecological [variable seed rates and plant spacing, delayed planting, banded N fertilization, and increased stubble height]). Nitrogen fractions were soil total N (STN), particulate organic N (PON), microbial biomass N (MBN), potential N mineralization (PNM), NH 4 –N, and NO 3 –N. Crop biomass N was 30 % greater in W-B-C-P than in CW in 2005. Surface residue N was 30–34 % greater in NT with the regular and ecological practices than in CT with the regular practice. The STN, PON, and MBN at 10–20 and 0–20 cm were 5–41 % greater in NT or CW with the regular practice than in CT or CW with the ecological practice. The PNM at 5–10 cm was 22 % greater in the regular than in the ecological practice. The NH 4 –N and NO 3 –N contents at 10–20 and 0–20 cm were greater in CT with W-B-C-P and the regular practice than with most other treatments in 2007. Surface residue and soil N fractions, except PNM and NO 3 –N, declined from autumn 2007 to spring 2008. In 2008, NT with W-B-C-P and the regular practice gained 400 kg N ha −1 compared with a loss of 221 kg N ha −1 to a gain of 219 kg N ha −1 in other treatments. No-tillage with the regular cultural practice increased surface residue and soil N storage but conventional tillage with diversified crop rotation and the regular practice increased soil N availability. Because of continuous N mineralization, surface residue and soil N storage decreased without influencing N availability from autumn to the following spring.

Nitrogen is the major nutrient limiting plant growth in terrestrial ecosystems, and the transformation of inert nitrogen to forms that can be assimilated by plants is mediated by soil micro‐organisms. The last decade has witnessed many significant advances in our understanding of plant–microbe interactions with evidence that plants have evolved multiple strategies to cope with nitrogen limitation by shaping and recruiting nitrogen‐cycling microbial communities. However, most studies have typically focused on the impact of plants on only one, or relatively few, processes within the nitrogen cycle. This review synthesizes recent advances in our understanding of the various routes by which plants influence the availability of nitrogen via an array of interactions with different guilds of nitrogen‐cycling micro‐organisms. We also propose a plant trait‐based framework for linking plant nitrogen acquisition strategies to the activities of nitrogen‐cycling microbial guilds. In doing so, we provide a more comprehensive picture of the ecological relationships between plants and nitrogen‐cycling micro‐organisms in terrestrial ecosystems. Finally, we identify previously overlooked processes within the nitrogen cycle that could be targeted in future research and be of interest for plant health or for improving plant nitrogen acquisition, while minimizing nitrogen inputs and losses in sustainable agricultural systems. A plain language summary is available for this article. Plain Language Summary