Effects of 30 Years of Crop Rotation and Tillage on Bacterial and Archaeal Ammonia Oxidizers

Soil microbial nitrogen-cycling gene abundances in response to crop diversification: A meta-analysis

Single planting structure has a significant impact on the maintenance of nitrogen in managed ecosystems. Although the effect of crop diversity on soil nitrogen-cycling microbes is mainly related to the influence of environmental factors, there is a lack of quantitative research. This study aims to determine the effect of diversified cropping mode on the abundance of functional genes in the soil nitrogen cycle based on the quantitative integration of a meta-analysis database containing 189 observation data pairs. The results show that the soil nifH (nitrogenase coding gene), nirS and nirK (nitrite reductase coding gene), and narG (nitrate reductase coding gene) abundances are positively affected by the diversity of plant species, whereas the amoA (ammonia monooxygenase coding gene) and nosZ (nitrous oxide reductase coding gene) show no response. Diversification duration and ecosystem type are important factors that regulate soil nitrogen fixation and nitrification gene abundances. Denitrification genes are mainly affected by categorical variables such as the planting pattern, soil layer, application species, duration, and soil texture. Among them, the long-term continuous diversification is mainly manifested in the reduction of soil nifH and increase of nirK abundances. Soil organic carbon and nitrogen linearly affect the responses of nifH, amoA, nirS, and nirK. Therefore, to maintain the soil ecological function, diversity of planting patterns needs to be applied flexibly by regulating the abundance of nitrogen-cycling genes. Our study draws conclusions in order to provide theoretical references for the sustainability of nitrogen and improvement of management measures in the process of terrestrial managed ecosystem diversification.

Effects of Rotations With Legume on Soil Functional Microbial Communities Involved in Phosphorus Transformation

Including legumes in the cereal cropping could improve the crop yield and the uptake of nitrogen (N) and phosphorus (P) of subsequent cereals. The effects of legume-cereal crop rotations on the soil microbial community have been studied in recent years, the impact on soil functional genes especially involved in P cycling is raising great concerns. The metagenomic approach was used to investigate the impacts of crop rotation managements of soybean-wheat (SW) and maize-wheat (MW) lasting 2 and 7years on soil microbial communities and genes involved in P transformation in a field experiment. Results indicated that SW rotation increased the relative abundances of Firmicutes and Bacteroidetes, reduced Actinobacteria, Verrucomicrobia, and Chloroflexi compared to MW rotation. gcd, phoR, phoD, and ppx predominated in genes involved in P transformation in both rotations. Genes of gcd, ppa, and ugpABCE showed higher abundances in SW rotation than in MW rotation, whereas gadAC and pstS showed less abundances. Proteobacteria, Acidobacteria, and Gemmatimonadetes played predominant roles in microbial P cycling. Our study provides a novel insight into crop P, which requires strategy and help to understand the mechanism of improving crop nutrient uptake and productivity in different rotations.

Effects of short-term soil tillage practice on activity and community structure of ammonia-oxidizing bacteria and archaea under the double-cropping rice field

AIMS

The potential nitrification activity (PNA), population size and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in paddy soil from a short-term (5 years) tillage field experiment conducted at tillering stage of late rice were investigated using the shaken slurry method and quantitative real-time polymerase chain reaction.

METHODS AND RESULTS

The experiment included four tillage treatments: conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), no-tillage with crop residue returning (NT) and rotary tillage with all crop residues removed as a control (RTO). The results showed that PNA in paddy soil of CT, RT and NT treatments was higher than that of RTO treatment, and the abundance of AOA and AOB was much higher in paddy soil of CT, RT and NT treatments than RTO treatment. Meanwhile, PNA and the abundance of AOB and AOA in paddy soil were greatly enhanced by combined application of tillage and crop residue, whereas PNA and the abundance of AOB and AOA in paddy soil were decreased by combined application of no-tillage and crop residue. Moreover, PNA was closely correlated with the abundance and community structure of AOB rather than AOA. The results also showed that PNA and the population sizes of AOB and AOA in crop incorporation treatments were higher than that of crop residue removed treatment. Cluster and redundancy analyses indicated that crop residue effect played a more important role in shaping AOA community structure compared to short-term tillage management.

CONCLUSIONS

The results indicated that AOB rather than AOA functionally dominated ammonia oxidation in the double-cropping rice paddy soil, the activities of AOB and AOA were increased and the community structure was also changed under the combination of conventional tillage, rotary tillage and crop residue condition.

SIGNIFICANCE AND IMPACT OF STUDY

The activity and community structure of AOB and AOA, which were affected by the combination of tillage and crop residue managements, play an important role in cycling of nitrogen.

Changes in Soil Microbial Activity, Bacterial Community Composition and Function in a Long-Term Continuous Soybean Cropping System After Corn Insertion and Fertilization

Corn-soybean rotation and fertilization are common practices improving soil fertility and crop yield. Their effects on bacterial community have been extensively studied, yet, few comprehensive studies about the microbial activity, bacterial community and functional groups in a long-term continuous soybean cropping system after corn insertion and fertilization. The effects of corn insertions (Sm: no corn insertion, CS: 3 cycles of corn-soybean rotations and CCS: 2 cycles of corn-corn-soybean rotations) with two fertilization regimes (No fertilization and NPK) on bacterial community and microbial activity were investigated in a long-term field experiment. The bacterial communities among treatments were evaluated using high-throughput sequencing then bacterial functions were predicted based on the FaProTax database. Soil respiration and extracellular enzyme activities were used to assess soil microbial activity. Soil bacterial community structure was significantly altered by corn insertions (p < 0.01) and fertilization (p < 0.01), whereas bacterial functional structure was only affected by corn insertion (p < 0.01). The activities of four enzymes (invertase, β-glucosidase, β-xylosidase, and β-D-1,4-cellobiohydrolase) involved in soil C cycling were enhanced by NPK fertilizer, and were also enhanced by corn insertions except for the invertase and β-xylosidase under NPK fertilization. NPK fertilizer significantly improved soil microbial activity except for soil metabolic quotient (qCO₂) and the microbial quotient under corn insertions. Corn insertions also significantly improved soil microbial activity except for the ratio of soil induced respiration (SIR) to basal respiration (BR) under fertilization and the qCO₂ was decreased by corn insertions. These activity parameters were highly correlated with the soil functional capability of aromatic compound degradation, which was the main predictors of bacterial functional structure. In general, the combination of soil microbial activity, bacterial community and corresponding functional analysis provided comprehensive insights into compositional and functional adaptations to corn insertions and fertilization.

Straw mulching and nitrogen application altered ammonia oxidizers communities and improved soil quality in the alkaline purple soil of southwest China

Microbe-mediated ammonia oxidation is a key process in soil nitrogen cycle. However, the effect of maize straw mulching on the ammonia oxidizers in the alkaline purple soil remains largely unknown. A three-year positioning experiment was designed as follows: straw mulching measures as the main-plot treatment and three kinds of nitrogen application as the sub-plot treatment. We found the contents of soil organic carbon (SOC), total nitrogen (TN), available potassium (AK), available nitrogen (AN), available phosphorus (AP), and NH₄⁺-N were increased after straw mulching and nitrogen application in alkaline purple soil, so did the amoA genes abundance of ammonia-oxidizing archaeal (AOA) and bacterial (AOB). Terminal restriction fragment length polymorphism (T-RFLP) analysis revealed that Thaumarchaeote (448-bp T-RF) was dominated the AOA communities, whereas Nitrosospira sp (111-bp T-RF) dominated the AOB communities. The community compositions of both AOA and AOB were altered by straw mulching and nitrogen application in alkaline purple soil, however, the AOB communities was more responsive than AOA communities to the straw mulching and nitrogen application. Further analysis indicated that SOC and AP were the main factors affecting the abundance and community compositions of AOA and AOB in alkaline purple soil. The present study reported that straw mulching and nitrogen strategies differently shape the soil ammonia oxidizers community structure and abundance, which should be considered when evaluating agricultural management strategies regarding their sustainability and soil quality.

Assessing the impacts of diversified crop rotation systems on yields and nitrous oxide emissions in Canada using the DNDC model

Process-based models are effective tools for assessing the sustainability of agricultural productivity and environmental health under various management practices and rotation systems. The objectives of this study were to (1) calibrate and evaluate the DeNitrification-DeComposition (DNDC) model using measurements of yields, nitrogen (N) uptake, soil inorganic N, soil temperature, soil moisture and nitrous oxide (N₂O) emissions under long-term fertilized continuous corn (CC) and corn-oats-alfalfa-alfalfa (COAA) rotation systems in southwest Ontario from 1959 to 2015, Canada, and (2) explore the impacts of four diverse rotation systems (CC, COAA, corn-soybean-corn-soybean (CSCS) and corn-soybean-winter wheat (CSW)) on corn yields and annual N₂O emissions under long-term climate variability. DNDC demonstrated "good" performance in simulating corn, oats and alfalfa yield (normalized root mean square error (nRMSE) < 20%, Nash-Sutcliffe efficiency (NSE) > 0.5 and index of agreement (d) > 0.8). The model provided "fair" to "good" simulations for corn N uptake and soil inorganic N (NSE > 0.2 and d > 0.8), and also daily soil temperature and soil moisture (nRMSE <30% and d > 0.7) for both calibration and validation periods. The model demonstrated "good" performance in estimating daily and cumulative N₂O emissions from both the continuous and rotational corn, whereas it produced "poor" to "good" predictions for N₂O emissions from the rotational oats and alfalfa crops, however, the emissions from these crops were very low and the relative magnitude of these emissions between all crops investigated were well predicted. The lowest N₂O emissions were from COAA followed by CSCS, CSW then CC. The highest corn yields were from COAA, followed by CSW, CSCS, then CC. This study highlights how modelling approaches can help improve the understanding of the impacts of diversified rotations on crop production and greenhouse gas emissions and contribute towards developing policies aimed at improving the sustainability and resiliency of cropping systems.

The Potential of Switchgrass and Miscanthus to Enhance Soil Organic Carbon Sequestration—Predicted by DayCent Model

Warm season perennial C4 grasses (WSGs), switchgrass (Panicum virgatum L.) and miscanthus species (Miscanthus spp.), have been reported to positively influence short-term (15–20 years) soil organic carbon (SOC). In this study, the DayCent model was used to predict changes in long-term SOC stocks under WSGs for moderate (Representative Concentration Pathway (RCP) 4.5) and high (RCP 8.5) warming climate change scenarios in southern Ontario, Canada, and to determine how long the enhanced SOC stock will last when WSGs are converted back to annual crop rotation. The model predicted that a consistent corn–corn–soybean–winter wheat (CCSW) rotation prevented SOC from depletion over the 21st century. Under WSGs, the model predicted high rates of SOC sequestration during the first 20–30 years which then tended to stabilize after 50–60 years. However, the rate of SOC sequestration over 90 years for RCP 4.5 was 0.26 and 0.94 Mg C ha−1 yr−1 for switchgrass and miscanthus, respectively. If 40-year stands of WSGs are converted back to CCSW, the model predicted SOC decline to the previous level in 40–50 years. DayCent predicted that under RCP 8.5 scenario in the second half of the 21st century and in the future, there will be a reduction in SOC stocks, especially under miscanthus stands.

Acidification in corn monocultures favor fungi, ammonia oxidizing bacteria, and nirK-denitrifier groups

Agricultural practices of no-till and crop rotations are critical to counteract the detrimental effects of monocultures and tillage operations on ecosystem services related to soil health such as microbial N cycling. The present study explored the main steps of the microbial N cycle, using targeted gene abundance as a proxy, and concerning soil properties, following 19 and 20 years of crop monocultures and rotations of corn (Zea mays L.), and soybean [Glycine max (L.) Merr.], either under no-till or chisel tillage. Real-time quantitative polymerase chain reaction (qPCR) was implemented to estimate phylogenetic groups and functional genes related to the microbial N cycle: nifH (N₂ fixation), amoA (nitrification) and nirK, nirS, and nosZ (denitrification). Our results indicate that long-term crop rotation and tillage decisions affect soil health as it relates to soil properties and microbial parameters. No-till management increased soil organic matter (SOM), decreased soil pH, and increased copy numbers of AOB (ammonia oxidizing bacteria). Crop rotations with more corn increased SOM, reduced soil pH, reduced AOA (ammonia oxidizing archaea) copy numbers, and increased AOB and fungal ITS copy numbers. NirK denitrifier groups were also enhanced under continuous corn. Altogether, the more corn years included in a crop rotation multiplies the amount of N needed to sustain yield levels, thereby intensifying the N cycle in these systems, potentially leading to acidification, enhanced bacterial nitrification, and creating an environment primed for N losses and increased N₂O emissions.

The Structure and Diversity of Nitrogen Functional Groups from Different Cropping Systems in Yellow River Delta

The Yellow River Delta (YRD) region is an important production base in Shandong Province. It encompasses an array of diversified crop systems, including the corn-wheat rotation system (Wheat-Corn), soybean-corn rotation system (Soybean-Corn), fruits or vegetables system (Fruit), cotton system (Cotton) and rice system (Rice). In this study, the communities of ammonia oxidizer-, denitrifier- and nitrogen (N)-fixing bacteria in those cropping systems were investigated by Illumina Miseq sequencing. We found that Rice soil exhibited significantly higher diversity indices of investigated N-cycling microbial communities than other crop soils, possibly due to its high soil water content. Wheat-Corn soils had higher abundances of nitrification gene amoA and denitrification genes nirK and nirS, and exhibited higher soil potential nitrification rate (PNR), compared with Soybean-Corn, Cotton and Fruit soils. Consistently, redundancy analysis (RDA) showed that soil water content (SWC), electrical conductivity (EC), and total nitrogen (TN) were the most important influencing factors of the diversity and structure of the investigated N-cycling microbial.