Effects of short-term manure nitrogen input on soil microbial community structure and diversity in a double-cropping paddy field of southern China

Investigation of the Microbial Diversity in the Oryza sativa Cultivation Environment and Artificial Transplantation of Microorganisms to Improve Sustainable Mycobiota

Rice straw is not easy to decompose, it takes a long time to compost, and the anaerobic bacteria involved in the decomposition process produce a large amount of carbon dioxide (CO2), indicating that applications for rice straw need to be developed. Recycling rice straw in agricultural crops is an opportunity to increase the sustainability of grain production. Several studies have shown that the probiotic population gradually decreases in the soil, leading to an increased risk of plant diseases and decreased biomass yield. Because the microorganisms in the soil are related to the growth of plants, when the soil microbial community is imbalanced it seriously affects plant growth. We investigated the feasibility of using composted rice stalks to artificially cultivate microorganisms obtained from the Oryza sativa-planted environment for analyzing the mycobiota and evaluating applications for sustainable agriculture. Microbes obtained from the water-submerged part (group-A) and soil part (group-B) of O. sativa were cultured in an artificial medium, and the microbial diversity was analyzed with internal transcribed spacer sequencing. Paddy field soil was mixed with fermented paddy straw compost, and the microbes obtained from the soil used for O. sativa planting were designated as group-C. The paddy fields transplanted with artificially cultured microbes from group-A were designated as group-D and those from group-B were designated as group-E. We found that fungi and yeasts can be cultured in groups-A and -B. These microbes altered the soil mycobiota in the paddy fields after transplantation in groups-D and -E compared to groups-A and -B. Development in O. sativa post treatment with microbial transplantation was observed in the groups-D and -E compared to group-C. These results showed that artificially cultured microorganisms could be efficiently transplanted into the soil and improve the mycobiota. Phytohormones were involved in improving O. sativa growth and rice yield via the submerged part-derived microbial medium (group-D) or the soil part-derived microbial medium (group-E) treatments. Collectively, these fungi and yeasts may be applied in microbial transplantation via rice straw fermentation to repair soil mycobiota imbalances, facilitating plant growth and sustainable agriculture. These fungi and yeasts may be applied in microbial transplantation to repair soil mycobiota imbalances and sustainable agriculture.

Influence of conditioner and straw on the herbaceous plant-based phytoremediation copper tailings: a field trial at Liujiagou tailings pond, China

A field trial was performed to carry out an enhanced phytoremediation technique for multi-metal contaminated copper tailings by Sudan grass (Sorghum Sudanese), ryegrass (Lolium perenne L.), and Bermuda grass (Cynodon dactylon), using conditioner (TH-LZ01) and straw combination into composite amendments as soil amendments, aimed to obtain the maximum of phytoremediation effect. The results showed that compared with untreated herbaceous plants, the application of conditioner and straw planted with herbaceous plants reduced the pH and conductivity and increased the organic matter and water content of the copper tailings to different degrees. With the addition of conditioner and straw, the DTPA-Cd, DTPA-Cu, DTPA-Pb, and DTPA-Zn contents in the copper tailings showed a decreasing trend compared with the untreated group. The herbaceous plants were promoted to reduce the percentage contents of acid soluble fractions Cd, Cu, Pb, and Zn and to increase the percentage contents of reducible, oxidizable, and residual fractions heavy metals (Cd, Cu, Pb, and Zn) in the copper tailings to different degrees. The contents of Cd, Cu, Pb, and Zn in the underground part of herbaceous plants were higher than those in the aboveground part, and the contents of Cd, Cu, Pb, and Zn in the aboveground part and underground part decreased after adding conditioner and straw, which indicated that the conditioner and straw inhibited the transport of heavy metals in the plant. Furthermore, the principal component analysis showed that the application of conditioner and straw with planting ryegrass had more potential for improving the physicochemical properties of copper tailings and reducing heavy metal toxicity, followed by Bermuda grass and Sudan grass.

Response of soil microbial community diversity to continuous cucumber cropping in facilities along the Yellow River irrigation area

Cucumber is an important cash crop; however, continuous cropping obstacles readily occur within the intensive production processes of facility horticulture. This study aimed to determine the effects of continuous cropping on soil quality and the microbial community in the rhizosphere soil of cucumbers. Rhizosphere soil of cucumber planted continuously for 4, 8, and 12 years was investigated, and soil that was not continuously planted was used as the control. Soil physicochemical properties, enzyme activity, microbial diversity, and richness were determined. The results showed that with the increase in continuous cropping years (0, 4, 8, and 12 years), soil total salt content continuously increased, while the pH value significantly decreased. Compared with the control, soil organic matter, alkali-hydrolyzed nitrogen, available phosphorus, available potassium, and nitrate nitrogen contents increased significantly after 4 and 8 years of continuous cropping. Spearman correlation analysis showed that pH was negatively correlated with sucrase or sucrose and available phosphorus was positively correlated with alkaline phosphatase. Compared with the control, the diversity and abundance of bacterial and fungal communities in cucumber rhizosphere soil decreased after 4 and 12 years of continuous cropping. Continuous cropping led to a significant increase in the richness of the dominant phylum of cucumber rhizosphere soil. Principal coordinates analysis showed that, compared with the control, the soil microbial community structure was significantly separated after 4, 8, and 12 years of continuous cropping, and the microbial community structure was most similar after 4 and 8 years of continuous cropping. In addition, redundancy analysis showed that pH was the main driver of soil microbial dominance. In conclusion, continuous cropping of cucumber along the Yellow River irrigation area has led to the deterioration of soil nutrients and microbial communities in that region. This experiment provides a theoretical foundation for addressing the challenges associated with continuous cropping in cucumber cultivation.

Effects of peach branch organic fertilizer on the soil microbial community in peach orachards

Peach branches is a by-product of peach industry. Making peach branch waste into peach branch organic fertilizer (PBOF) is a promising strategy of ecological utilization. In this study, the effects of PBOF on the yield and quality of peach fruit, chemical properties of bulk soil, and soil bacterial communities were investigated in a peach orchard. The results showed that the yield and sugar/acid ratio of two high-level PBOF treatments (SDH.4 and SKR.4) was higher than no fertilization treatment (CK), but there was no significant difference compared to the commercial organic fertilizer treatment (SYT.4). Moreover, the three fertilizer treatments increased soil nutrients such as soil organic matter (SOM) and available potassium (AK), compared to CK. Furthermore, PBOF increased the relative abundance of beneficial bacteria, and enhanced the soil bacterial co-occurrence pattern and the potential function of bacterial communities to degrade exogenous compounds. In addition, thanks to the local policy of encouraging the use of PBOF, the use cost of PBOF is lower than commercial organic fertilizer, which is conducive to the development of ecological agriculture.

Moderate organic fertilizer substitution for partial chemical fertilizer improved soil microbial carbon source utilization and bacterial community composition in rain-fed wheat fields: current year

Organic fertilizers can partially replace chemical fertilizers to improve agricultural production and reduce negative environmental impacts. To study the effect of organic fertilizer on soil microbial carbon source utilization and bacterial community composition in the field of rain-fed wheat, we conducted a field experiment from 2016 to 2017 in a completely randomized block design with four treatments: the control with 100% NPK compound fertilizer (N: P₂O₅: K₂O = 20:10:10) of 750 kg/ha (CK), a combination of 60% NPK compound fertilizer with organic fertilizer of 150 kg/ha (FO1), 300 kg/ha (FO2), and 450 kg/ha (FO3), respectively. We investigated the yield, soil property, the utilization of 31 carbon sources by soil microbes, soil bacterial community composition, and function prediction at the maturation stage. The results showed that (1) compared with CK, organic fertilizer substitution treatments improved ear number per hectare (13%-26%), grain numbers per spike (8%-14%), 1000-grain weight (7%-9%), and yield (3%-7%). Organic fertilizer substitution treatments increased the total nitrogen, available nitrogen, available phosphorus, and soil organic matter contents by 26%, 102%, 12%, and 26%, respectively, compared with CK treatments. Organic fertilizer substitution treatments significantly advanced the partial productivity of fertilizers. (2) Carbohydrates and amino acids were found to be the most sensitive carbon sources for soil microorganisms in different treatments. Particularly for FO3 treatment, the utilization of β-Methyl D-Glucoside, L-Asparagine acid, and glycogen by soil microorganisms was higher than other treatments and positively correlated with soil nutrients and wheat yield. (3) Compared with CK, organic fertilizer substitution treatments increased the relative abundance of Proteobacteria, Acidobacteria, and Gemmatimonadetes and decreased the relative abundance of Actinobacteria and Firmicutes. Interestingly, FO3 treatment improved the relative abundance of Nitrosovibrio, Kaistobacter, Balneimonas, Skermanella, Pseudomonas, and Burkholderia belonging to Proteobacteria and significantly boosted the relative abundance of function gene K02433 [the aspartyl-tRNA (Asn)/glutamyl-tRNA (Gln)]. Based on the abovementioned findings, we suggest FO3 as the most appropriate organic substitution method in rain-fed wheat fields.

Effect of fertilization combination on cucumber quality and soil microbial community

Due to the lack of scientific guidance on the usage of fertilizer, the overuse of chemical and organic fertilizer is commonly witnessed all over the world, which causes soil degradation and leads to environmental pollution. The effect of fertilizer strategies on soil properties, cucumber nutrients, and microbial community was investigated in this study with the aim to explore an optimized and enhanced fertilizer strategy. There were five fertilizer strategies conducted including CK (no fertilizer), M (cow dung manure only), NPK (chemical fertilizer only), NPKM (chemical fertilizer combined with manure), and DNPKM (30%-reducing chemical fertilizer combined with manure). It was found that different fertilizer strategies significantly affected the soil organic matter and nutrient levels and cucumber production and nutrient contents of the experimental field. Different fertilizer strategies showed dramatic effects on the alpha- and beta-diversity of soil microbial communities. Moreover, NPKM and DNPKM groups could significantly improve the bacterial abundance and fungal diversity. In addition, the structure of microbial communities was significantly changed in the presence of manure, chemical fertilizer, and their combination. Optimized combination of NPK with M improved the abundance of aerobic, biofilm formation-related, and Gram-negative bacteria and suppressed the anaerobic and Gram-positive bacteria. The presence of saprotrophs fungi was enhanced by all fertilizer strategies, especially the plethora of Gymnoascus. The combination of manure with chemical fertilizer could improve the availability of nutrients, and therefore reduce the adverse effects and potential risks induced by excessive fertilizer application. In conclusion, the new fertilization approach can not only meet the growth requirements of cucumber after reduced fertilization, but also protect soil health, which provides a new candidate for the eco-friendly technology to satisfy the topic of carbon neutrality.

Effects of sweet potato intercropping in banana orchard on soil microbial population diversity

Purpose

This study was purposely designed to understand the effects of intercropping banana and sweet potato on soil microbial community. The research question addressed was what were the differences in population number, population diversity and dominant population of soil microorganisms between interplant bananas with sweet potatoes and banana monoculture.

Methods

The Illumina MiSeq high-throughput sequencing technology was used to detect and analyse the population composition and structure of soil microorganisms in banana field.

Results

The results showed that from May to September, the number of soil bacterial population in intercropping sweet potato was 5.54-28.67% higher than that in monoculture, and the richness and diversity of the population were significantly or extremely significantly higher than that in monoculture. The number of dominant bacterial population was less than that in monoculture, and the relative abundance of non dominant population was 10.58 - 58.81% higher than that in monoculture. The number, abundance and diversity of soil fungal populations in intercropping were higher than those in monoculture.

Conclusions

The intercropping of banana and sweet potato has a significant effect on regulating the composition structure of soil microbial population and improving the abundance and diversity of microbial population. There has a great significance to improve the micro ecological environment of banana root soil and promote the stable and sustainable development of banana industry.

Zinc application promotes nitrogen transformation in rice rhizosphere soil by modifying microbial communities and gene expression levels

Application of Zn fertilizers to agricultural field is a simple and effective way for farmers to manage Zn deficient stress in soils to avoid yield lose. Although a synergistic effect of Zn on N transformation in soil has been reported, the mechanism is not fully understood yet. In this study, we planted rice in soils with different combinations of Zn and N supply, and analyzed the plant growth and N uptake, the N transformation, microbial communities, enzyme activities and gene expression levels in rhizosphere soil to reveal the underlying mechanism. Results showed that Zn application promoted the rice growth and N uptake, increased the soil alkali-hydrolyzed N and NH₄⁺, but decreased NO₃^- and inhibited NH₃ volatilization from the rhizosphere soil under optimal N condition. Zn supply significantly increased the relative abundances of Sphingomonas, Gaiella, subgroup_6, and Gemmatimonas, but decreased nitrosifying bacteria Ellin6067; while increased saprophytic fungi Schizothecium and Mortierella, but decreased pathogenic fungi Gaeumannomyces, Acremonium, Curvularia, and Fusarium in the rhizosphere soil under optimal N condition. Meanwhile, Zn application elevated the activities of protease, cellulase and dehydrogenase, and up-regulated the expression levels of napA, nirS, cnorB, and qnorB genes involved in the denitrification process in rice rhizosphere soil under optimal N condition. These results indicated Zn application could facilitate the soil N transformation and improved its availability by modifying both bacterial and fungal communities, and altering the soil enzyme activities and functional gene expression levels, ultimately promoted the N uptake and biomass of rice plant. However, this synergistic effect of Zn on rice growth, N uptake and soil N transformation strongly depended on the external N conditions, as no significant changes were observed under high N condition. Our results indicated that Zn co-fertilized with appropriate application of N is a useful strategy to improve the N bioavailability in rice rhizosphere soil and enhance the N uptake in rice plant.

Effects of organic fertilization on functional microbial communities associated with greenhouse gas emissions in paddy soils

Soil microbial communities play a key role in the biochemical processes and nutrient cycles of the soil ecosystem and their byproducts, including greenhouse gases (GHGs). Organic fertilization influences bacterial soil biodiversity and is an essential emission source of GHGs in paddy soil ecosystems. However, the impact of organic fertilization on the functional microorganisms associated with the GHGs methane and nitrous oxide remains unknown. We conducted paddy soil field experiments under three different treatments (no fertilization, base fertilization, and organic fertilization) to investigate the contribution of organic fertilization to soil nutrients and the functional microorganisms associated with GHG emissions. We found that organic fertilization effectively increased the soil organic matter (P < 0.001), soil organic carbon (P < 0.001), and total nitrogen (P < 0.05) as well as the richness (operational taxonomic units and abundance-based coverage estimators) of the methanogenic communities. Correlation analyses showed that methanogenic communities that were present in abundance were more vulnerable to perturbations in soil properties compared to nitrifying bacterial communities. Partial least squares path model analyses elucidated that organic fertilization directly affected both methanogenic communities and nitrifying bacterial communities (P < 0.05), thereby accelerating methane emissions. Strong co-occurrence networks were observed within the soil-dominant phyla Acidobacteria, Bacteroidetes, and Proteobacteria. Our findings highlight the impact of organic fertilization on soil nutrients and functional microorganisms and guide mitigating GHG emissions from paddy soil agroecosystems.

Short-term application of chicken manure under different nitrogen rates alters structure and co-occurrence pattern but not diversity of soil microbial community in wheat field

Manure application is an effective way to improve the utilization efficiency of organic resources and alleviate the adverse effects of long-term application of chemical fertilizers. However, the impact of applying manure under different nitrogen rates on soil microbial community in wheat field remains unclear. Treatments with and without chicken manure application under three nitrogen rates (N 135, 180 and 225 kg⋅hm-2) were set in wheat field. Soil organic carbon, available nutrients, and abundance, diversity, structure and co-occurrence pattern of soil microbial community at wheat maturity were investigated. Compared with no manure application, chicken manure application increased the soil organic carbon and available phosphorus, while the effects on soil mineral nitrogen and available potassium varied with different nitrogen rates. Chicken manure application significantly increased soil bacterial abundance under the nitrogen fertilization of 135 and 225 kg⋅hm-2, increased soil fungal abundance under the nitrogen fertilization of 135 kg⋅hm-2, but decreased soil fungal abundance under the nitrogen fertilization of 180 and 225 kg⋅hm-2 (P < 0.05). There was no significant difference in alpha diversity indices of soil microbial communities between treatments with and without chicken manure application under different nitrogen rates (P > 0.05). Chicken manure application and its interaction with nitrogen rate significantly changed soil bacterial and fungal community structures (P < 0.05). There were significantly different taxa of soil microbial communities between treatments with and without chicken manure application. Chicken manure application reduced the ecological network complexity of soil bacterial community and increased that of soil fungal community. In summary, the responses of soil available nutrients and microbial abundance to applying chicken manure varied with different nitrogen rates. One growing season application of chicken manure was sufficient to alter the soil microbial community structure, composition and co-occurrence pattern, whereas not significantly affected soil microbial community diversity.

Application of Manure Rather Than Plant-Origin Organic Fertilizers Alters the Fungal Community in Continuous Cropping Tobacco Soil

Continuous cropping leads to the development of serious fungal diseases in tobacco plants and depleted yield of tobacco (Nicotiana tabacum), which can be mitigated by organic fertilization. Yet, we know little about how organic fertilizers affect the fungal community of continuous cropping tobacco soil. In this study, we investigated the soil fungal community after 11 years of tobacco planting with chemical fertilization (CF) or chemical fertilization combined with organic fertilizers obtained from plant or animal origin, including oil cake (CFO), straw (CFS), and farmyard fertilizer (CFM). The predominant phyla of Ascomycota (70%) and Mortierellomycota (15%) were identified in all the treatments. A significantly higher proportion of Pyrenochaetopsis and lower relative abundance of Sordariomycetes were observed in the CFM group compared to the controls. Compared to CF and non-fertilized control (CK), CFO and CFS led to higher species richness (P < 0.05), while CFM led to a less uniform fungal community, indicated by lower Shannon and higher Simpson diversity indices (P < 0.05). Pearson's correlation and redundancy analysis suggested that fertilizations primarily influenced the fungal community by altering the soil nutrient conditions, among which soil organic carbon and total phosphorus significantly correlated with the fungal diversity and community composition (P < 0.05). Notably, FUNGuild annotation suggested that while other treatments showed no significant effect on the fungal trophic modes, CFM strongly increased the abundance of saprotrophic fungi by more than 30% (P < 0.05), thus preventing the prevalence of potential pathotypes and symbionts. The results suggest that the type of organic fertilizers is essential to the long-term effects of organic application on the fungal community, and the animal-origin manure seems to be a better choice than plant-origin materials in continuous cropping tobacco fields.

Impact of long-term tillage management on utilization of microbial carbon sources in rhizosphere and non-rhizosphere soils under a double-cropping rice paddy field

In order to reveal the mechanism of microbial carbon (C) sequestration in paddy soil under different tillage management and to provide an important theoretical basis for perfecting the mechanism of C sequestration in paddy soil. C can indicate changes of soil nutrient content and soil microbial community, but more research is needed to study how C sources utilization characteristics respond to different tillage management under a double-cropping rice (Oryza sativa L.) paddy field in southern China. Hence, the impact of long-term (2005-2018) tillage management on utilization of microbial carbon sources in rhizosphere and non-rhizosphere soils under a double-cropping rice paddy field was studied by using 18O-H2O method in this study. The tillage treatments were included: (1) moldboard plow with all crop residue removed as a control (CT), (2) moldboard plow with all crop residue incorporated (CTS), (3) no-tillage with all crop residue retained on the soil surface (NTS), and (4) rotary tillage with all crop residue incorporated (RTS). The results indicated that Richness, Shannon, and McIntosh indices were increased by application of crop residue management, compared with treatment without crop residue, and soil microbial growth rate, soil microbial biomass C content, and soil microbial basal respiration with CT treatment were significantly lower (p < 0.05) than that of NTS, RTS, and CTS treatments. And the soil C utilization efficiency in rhizosphere soil with NTS, RTS, and CTS treatments was significantly lower (p < 0.05) than that of CT treatment. Compared with CT and CTS treatments, the metabolic capacity of soil microorganisms to exogenous C sources with NTS and RTS treatments was increased, and the different types of exogenous C sources were showed as following: complex compounds < carbohydrate < amino acid < carboxylic acids. The redundancy analysis results showed that utilization characteristics of soil microorganisms to exogenous C sources were significantly changed under tillage and crop residue incorporated conditions. Hence, this result indicated that characteristics of soil C sources utilization were significantly increased combined applied with tillage and crop residue incorporated management.

Effect of Nitrogen Addition on Soil Microbial Functional Gene Abundance and Community Diversity in Permafrost Peatland

Nitrogen is the limiting nutrient for plant growth in peatland ecosystems. Nitrogen addition significantly affects the plant biomass, diversity and community structure in peatlands. However, the response of belowground microbe to nitrogen addition in peatland ecosystems remains largely unknown. In this study, we performed long-term nitrogen addition experiments in a permafrost peatland in the northwest slope of the Great Xing'an Mountains. The four nitrogen addition treatments applied in this study were 0 g N·m-2·year-1 (CK), 6 g N·m-2·year-1 (N1), 12 g N·m-2·year-1 (N2), and 24 g N·m-2·year-1 (N3). Effects of nitrogen addition over a period of nine growing seasons on the soil microbial abundance and community diversity in permafrost peatland were analyzed. The results showed that the abundances of soil bacteria, fungi, archaea, nitrogen-cycling genes (nifH and b-amoA), and mcrA increased in N1, N2, and N3 treatments compared to CK. This indicated that nitrogen addition promoted microbial decomposition of soil organic matter, nitrogen fixation, ammonia oxidation, nitrification, and methane production. Moreover, nitrogen addition altered the microbial community composition. At the phylum level, the relative abundance of Proteobacteria increased significantly in the N2 treatment. However, the relative abundances of Actinobacteria and Verrucifera in the N2 treatment and Patescibacteria in the N1 treatment decreased significantly. The heatmap showed that the dominant order composition of soil bacteria in N1, N2, and N3 treatments and the CK treatment were different, and the dominant order composition of soil fungi in CK and N3 treatments were different. The N1 treatment showed a significant increase in the Ace and Chao indices of bacteria and Simpson index of fungi. The outcomes of this study suggest that nitrogen addition altered the soil microbial abundance, community structure, and diversity, affecting the soil microbial carbon and nitrogen cycling in permafrost peatland. The results are helpful to understand the microbial mediation on ecological processes in response to N addition.

Manure derived nutrients alter microbial community composition and increase the presence of potential pathogens in freshwater sediment

AIM

To determine the impact of an acute, pulse disturbance of nutrients from manure on freshwater sediment microbiomes in an experimental system.

METHODS AND RESULTS

A controlled freshwater mesocosm experiment was designed to compare the effect of disturbance from nutrients derived from sterile manure (SM), disturbance from equivalent concentrations of laboratory-derived nutrients, and a nondisturbed control on freshwater sediment microbial community composition and function using 16S rRNA amplicon sequencing. Sediment microbiomes impacted by nutrients from SM showed no sign of compositional recovery after 28 days but those impacted by laboratory-derived chemicals lead to a new steady-state (p < 0.05). Carbon and nitrate sources within disturbed mesocosms were the primary drivers of altered microbial community composition. Additionally, multiple potential pathogens (based on exact sequence matching at the species level) were enriched in mesocosms treated with SM.

CONCLUSIONS

Nutrient disturbance from SM, in the absence of the manure microbial community, alters the microbiome of sediments without recovery after 28 days and enriches potential pathogens.

SIGNIFICANCE AND IMPACT OF THE STUDY

These results suggest manure land application practices should be re-evaluated to account for impact of nutrient disturbance on environmental microbiomes in addition to the impact of the manure microbial community.