Partial Substation of Organic Fertilizer With Chemical Fertilizer Improves Soil Biochemical Attributes, Rice Yields, and Restores Bacterial Community Diversity in a Paddy Field

Soil Bacterial Diversity and Community Structure of Cotton Rhizosphere under Mulched Drip-Irrigation in Arid and Semi-arid Regions of Northwest China

Xinjiang is situated in an arid and semi-arid region, where abundant heat and sunlight create highly favorable conditions for cotton cultivation. Xinjiang's cotton output accounts for nearly one-quarter of global production. Moreover, the implementation of advanced planting techniques, such as 'dwarfing, high-density, early-maturing' strategies combined with mulched drip irrigation, ensures stable and high yields in this region. Despite these advancements, limited research has focused on the microbial mechanisms in cotton fields employing these advanced planting methods. In this study, high-throughput sequencing technology was utilized to investigate the diversity and composition of bacterial and phoD (Alkaline phosphatases encoding gene) communities in the rhizosphere of cotton grown under different yield levels in Xinjiang Province, China. The Mantel test, redundancy analysis (RDA) and partial least squares path modeling (PLS-PM) were employed to explore the interactions between soil bacterial and phoD communities, their network structures, and environmental factors. The bacterial and phoD communities in the cotton rhizosphere were predominantly composed of nine bacterial phyla (i.e., Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes, Chloroflexi, Bacteroidetes, Rokubacteria, Firmicutes, and Nitrospirae) and five phoD phyla (i.e., Proteobacteria, Actinobacteria, Planctomycetes, Acidobacteria, and Firmicutes), respectively. Alpha diversity analysis indicated that the medium yield cotton field (MYF) exhibited higher bacterial richness and diversity indices compared to low yield (LYF) and high yield (HYF) fields. The symbiotic network analysis of LYF revealed greater values of average degree, number of edges, and modularity, suggesting a more complex network structure in both bacterial and phoD communities. The Mantel test, RDA, and PLS-PM model identified soil pH, electrical conductivity (EC), organic phosphorus (OP), available phosphorus (AP), total nitrogen (TN), microbial biomass carbon (MBC), and clay content as the main driving factors influencing changes in the rhizosphere bacterial community diversity and network structure. These findings provide a theoretical basis for future research aimed at improving soil quality and cotton yield.

Organic-based remediation of heavy metal-contaminated soils in the Taojia river basin affected by long-term non-ferrous mining and logging activities

The upper reaches of the Taojia River have been impacted by unregulated logging linked to non-ferrous metal mining, resulting in significant mineral waste accumulation. Composting has shown promise in reducing heavy metal (HM) contamination in agricultural soils. This study included two segments: the first examined the effects of sheep manure (SM) and chicken manure (CM) with different concentrations on lead (Pb) dynamics in vegetable soils. The second applied the most effective method identified in segment one to assess Pb, cadmium (Cd), zinc (Zn), and copper (Cu) in soil, paddy, and straw in rice fields. Results showed that both compost types increased soil pH to mildly alkaline levels, with SM causing dose-dependent rises (insignificant between 2% and 5%) and CM inducing non-proportional alkalinity. CM compost significantly enhanced soil organic matter (SOM: 0.606-0.660 g/kg) compared to SM (0.414-0.495 g/kg). Total nitrogen (TN) spiked at 2% SM (0.172 g/kg) but plateaued until 10% SM (0.210 g/kg), while CM linearly increased TN with dosage. Total phosphorus (TP) rose proportionally with SM but remained unchanged under CM. For Pb immobilization, 5% SM reduced DTPA-Pb to 11.877 mg/kg, but 10% SM increased it (14.006 mg/kg), whereas 10% CM achieved optimal passivation (11.561 mg/kg). Correlation analyses linked compost dosage to SOM, TP, and available Pb (p < 0.05), with soil pH showing minimal direct influence. In rice fields, 10% CM elevated soil pH (7.10 vs. 6.71), TP, and total Zn/Cu/Pb/Cd but reduced Pb/Cd in paddy and straw. Heavy metal speciation revealed strong inter-state correlations (excluding exchangeable Pb), with soil pH and TP significantly influencing Zn, Cu, and Cd levels. These findings demonstrate CM compost's dual role in improving fertility and mitigating Pb/Cd uptake, though Zn/Cu accumulation risks require careful management.

Long-term rice-crab coculturing leads to changes in soil microbial communities

Purpose

In order to investigate the effects of a rice-crab coculture mode and its duration on the richness and diversity of the soil microbial community.

Method

Soil from long-term rice-crab coculture mode (MY), newly established rice-crab coculture mode (OY) and rice monoculture mode (N) were used to measured soil physicochemical properties, enzyme activity and 16S and ITS soil microbial communities.

Results

The results revealed that in terms of mode, the MBC, MBN and CAT of OY were significantly greater than those of N by 10.75, 23.47 and 30.71% (p < 0.05), respectively. The richness and diversity of the soil microbial communities changed little, and there was no difference in the main species. In terms of duration, the OM, SC and PPO contents of MY were significantly greater than those of OY by 21.96, 41.89 and 11.52% (p < 0.05), respectively. The soil fungi changed significantly, and the main species were Mortierella and Pseudeurotium in genus level. The soil physicochemical properties and soil enzymes explained 93.38 and 93.66%, respectively, of the variation in the soil microbial community, and OM and DHA were the main factors influencing the change in soil biodiversity.

Conclusion

Our results suggested that long-term rice-crab coculture mode altered the richness and diversity of the soil microbial community and soil carbon sequestration.

Increased stability of a subtropic bamboo forest soil bacterial communities through integration of water and fertilizer management compared to conventional management

BACKGROUND

Conventional management (CM), substantial fertilization and flooding irrigation, has led to soil acidification, the decrease in soil bacterial diversity in bamboo forests. Integration of water and fertilizer management (IWF) can effectively improve the efficiency of water and fertilizer use, but its effect on soil environment, especially on microbial community, is still unclear.

METHODS

Here, we used next-generation high-throughput sequencing to compare soil properties and bacterial communities through different fertilization and irrigation methods under IWF and CM.

RESULTS

Compared to the control group, CM significantly reduced soil pH and bacterial diversity, while IWF improved soil nutrition status, increased soil bacterial diversity and soil pH to a level similar to the control group. Compared with CM, IWF also improved the relative abundance of beneficial bacteria and copiotrophic bacteria community in the soil, and the bacterial community in IWF was similar to CK. The structure of the bacterial community was also significantly correlated with soil organic matter, total nitrogen, hydrolyzable nitrogen, and available potassium, while soil bacterial diversity was mainly associated with soil hydrolyzable nitrogen.

CONCLUSIONS

IWF can play an important role in preventing soil acidification, the loss of soil bacterial diversity, and improving the structure of the bacterial community under specific conditions.

Vermicompost Supply Enhances Fragrant-Rice Yield by Improving Soil Fertility and Eukaryotic Microbial Community Composition under Environmental Stress Conditions

Heavy-metal contamination in agricultural soil, particularly of cadmium (Cd), poses serious threats to soil biodiversity, rice production, and food safety. Soil microbes improve soil fertility by regulating soil organic matter production, plant nutrient accumulation, and pollutant transformation. Addressing the impact of Cd toxicity on soil fungal community composition, soil health, and rice yield is urgently required for sustainable rice production. Vermicompost (VC) is an organic fertilizer that alleviates the toxic effects of Cd on soil microbial biodiversity and functionality and improves crop productivity sustainably. In the present study, we examined the effects of different doses of VC (i.e., 0, 3, and 6 tons ha-1) and levels of Cd stress (i.e., 0 and 25 mg Cd kg-1) on soil biochemical attributes, soil fungal community composition, and fragrant-rice grain yield. The results showed that the Cd toxicity significantly reduced soil fertility, eukaryotic microbial community composition and rice grain yield. However, the VC addition alleviated the Cd toxicity and significantly improved the soil fungal community; additionally, it enhanced the relative abundance of Ascomycota, Chlorophyta, Ciliophora, Basidiomycota, and Glomeromycta in Cd-contaminated soils. Moreover, the VC addition enhanced the soil's chemical attributes, including soil pH, soil organic carbon (SOC), available nitrogen (AN), total nitrogen (TN), and microbial biomass C and N, compared to non-VC treated soil under Cd toxicity conditions. Similarly, the VC application significantly increased rice grain yield and decreased the Cd uptake in rice. One possible explanation for the reduced Cd uptake in plants is that VC amendments influence the soil's biological properties, which ultimately reduces soil Cd bioavailability and subsequently influences the Cd uptake and accumulation in rice plants. RDA analysis determined that the leading fungal species were highly related to soil environmental attributes and microbial biomass C and N production. However, the relative abundance levels of Ascomycota, Basidiomycota, and Glomeromycta were strongly associated with soil environmental variables. Thus, the outcomes of this study reveal that the use of VC in Cd-contaminated soils could be useful for sustainable rice production and safe utilization of Cd-polluted soil.

Bacterial and fungal communities regulated directly and indirectly by tobacco-rape rotation promote tobacco production

Tobacco continuous cropping is prevalent in intensive tobacco agriculture but often leads to microbial community imbalance, soil nutrient deficiency, and decreased crop productivity. While the tobacco-rape rotation has demonstrated significant benefits in increasing tobacco yield. Microorganisms play a crucial role in soil nutrient cycling and crop productivity. However, the internal mechanism of tobacco-rape rotation affecting tobacco yield through microbe-soil interaction is still unclear. In this study, two treatments, tobacco continuous cropping (TC) and tobacco-rape rotation (TR) were used to investigate how planting systems affect soil microbial diversity and community structure, and whether these changes subsequently affect crop yields. The results showed that compared with TC, TR significantly increased the Shannon index, Chao1 index, ACE index of bacteria and fungi, indicating increased microbial α-diversity. On the one hand, TR may directly affect the bacterial and fungal community structure due to the specificity of root morphology and root exudates in rape. Compared with TC, TR significantly increased the proportion of beneficial bacterial and fungal taxa while significantly reduced soil-borne pathogens. Additionally, TR enhanced the scale and complexity of microbial co-occurrence networks, promoting potential synergies between bacterial OTUs. On the other hand, TR indirectly changed microbial community composition by improving soil chemical properties and changing microbial life history strategies. Compared with TC, TR significantly increased the relative abundance of copiotrophs while reduced oligotrophs. Notably, TR significantly increased tobacco yield by 39.6% compared with TC. The relationships among yield, microbial community and soil chemical properties indicated that planting systems had the greatest total effect on tobacco yield, and the microbial community, particularly bacteria, had the greatest direct effect on tobacco yield. Our findings highlighted the potential of tobacco-rape rotation to increase yield by both directly and indirectly optimizing microbial community structure.

Substation of vermicompost mitigates Cd toxicity, improves rice yields and restores bacterial community in a Cd-contaminated soil in Southern China

Cadmium (Cd) contamination in agricultural soil is a global concern for soil health and food sustainability because it can cause Cd accumulation in cereal grains. An in-situ stabilizing technology (using organic amendments) has been widely used for Cd remediation in arable lands. Therefore, the current study examined the influence of vermicompost (VC) on soil biochemical traits, bacterial community diversity and composition, Cd uptake and accumulation in rice plants and grain yield in a Cd-contaminated soil during the late growing season in 2022. Different doses of VC (i.e., V1 = 0 t ha-1, V2 = 3 t ha-1 and V3 = 6 t ha-1) and two concentrations of Cd (i.e., Cd1 = 0 and Cd2 = 50 mg Cd Kg-1 were used. We performed high-throughput sequencing of 16S ribosomal RNA gene amplicons to characterize soil bacterial communities. The addition of VC considerably affected the diversity and composition of the soil bacterial community; and increased the relative abundance of phyla Chloroflexi, Proteobacteria, Acidobacteriota, Plantomycetota, Gemmatimonadota, Patescibacteria and Firmicute. In addition, VC application, particularly High VC treatment, exhibited the highest bacterial diversity and richness (i.e., Simpson, Shannon, ACE, and Chao 1 indexes) of all treatments. Similarly, the VC application increased the soil chemical traits, including soil pH, soil organic carbon (SOC), available nitrogen (AN), total nitrogen (TN), total potassium (TK), total phosphorous (TP) and enzyme activities (i.e., acid phosphatase, catalase, urease and invertase) compared to non-VC treated soil under Cd stress. The average increase in SOC, TN, AN, TK and TP were 5.75%, 41.15%, 18.51%, 12.31%, 25.45% and 29.67%, respectively, in the High VC treatment (Pos-Cd + VC3) compared with Cd stressed soil. Redundancy analysis revealed that the leading bacterial phyla were associated with SOC, AN, TN, TP and pH, although the relative abundance of Firmicutes, Proteobacteria, Bacteroidata, and Acidobacteria on a phylum basis and Actinobacteria, Gammaproteobacteria and Myxococcia on a class basis, were highly correlated with soil environmental factors. Moreover, the VC application counteracted the adverse effects of Cd on plants and significantly reduced the Cd uptake and accumulation in rice organs, such as roots, stem + leaves and grain under Cd stress conditions. Similarly, applying VC significantly increased the fragrant rice grain yield and yield traits under Cd toxicity. The correlation analysis showed that the increased soil quantities traits were crucial in obtaining high rice grain yield. Generally, the findings of this research demonstrate that the application of VC in paddy fields could be useful for growers in Southern China by sustainably enhancing soil functionality and crop production.

Distillers' grains organic fertilizer alters soil bacterial composition and co-occurrence patterns in a tobacco-growing field

In recent years, numerous studies have indicated that the combination of organic and inorganic fertilizers can effectively improve soil fertility and soil productivity. Distillers' grain (DG), the primary by-product of Chinese spirits production, has a high utilization value for producing organic fertilizer. We investigated the effects of distillers' grain organic fertilizer (DGOF) on soil chemical properties and microbial community composition, as well as the effects of chemical properties on the abundance of keystone species. The results indicated that the application of DGOF significantly increased tobacco yield by 14.8% and mainly affected the composition rather than the alpha diversity of the bacterial community. Ten amplicon sequence variants (ASVs) were identified as keystone species in the bacterial communities, and most of their relative abundance was influenced by the DGOF addition through affecting soil chemical properties. Our results elucidated the alterations in soil chemical properties and microbial community composition resulting from DGOF application, which is of great importance to better understand the relationship between DGOF and soil microorganisms in the flue-cured tobacco cultivation field.

Microbial community composition in the dung of five sympatric European herbivore species

The dung microbiome is a complex system that is highly influenced by species and diet. This study characterized the dung bacterial and fungal communities of five herbivore species inhabiting the National Park Zuid-Kennemerland, the Netherlands. The five selected herbivore species were rabbit (Oryctolagus cuniculus L.), cow (Bos taurus L.), horse (Equus ferus caballus L.), fallow deer (Dama dama L.), and European bison (Bison bonasus L.). We explored the effects of distinct digestive physiology (ruminants vs. non-ruminants) and diverse dietary preferences on the microbial community composition of herbivore dung. Firmicutes and Bacteroidetes were dominant bacterial phyla in the dung of all five herbivore species, and Ascomycota was the predominant fungal phylum. Verrucomicrobiota and Mucoromycota were more present in horse dung and Proteobacteria were more abundant in rabbit dung than the three ruminant dung types. There were few significant differences in the microbial community structure among the three ruminant dung types. The alpha and beta diversity of dung microbial communities significantly differed between ruminants and non-ruminants, especially in bacterial communities. Based on MetaCyc pathways, we found that the primary functions of bacteria in herbivore dung were focused on biosynthesis, various super pathways, and degradation, with a few differences between ruminant and non-ruminant dung. FUNGuild analysis showed that horse dung had more saprotrophic fungi, while the fungi in fallow deer dung had more symbiotrophic properties, with the fungal functions of bison, cow, and rabbit dung somewhere in between. There was also a correlation between microbial community and nutrient composition of the substrate in herbivore dung. Understanding the dung microbial community composition of these herbivore species can enrich the database of mammalian gut microbiomes for studying the mechanisms of microbial community variation while preparing for exploring a new perspective to study the impact of herbivores on ecosystems through dung deposition.

Effect of different fertilization strategies on the yield, quality of Euryales Semen and soil microbial community

Introduction

Euryales Semen, a medicinal herb widely utilized in Asia, faces a critical constraint in its production, primarily attributed to fertilizer utilization. Understanding the impact of different fertilization schemes on Euryales Semen (ES) planting and exploring the supporting mechanism are crucial for achieving high yield and sustainable development of the ES planting industry.

Methods

In this study, a field plot experiment was conducted to evaluate the effects of four different fertilization treatments on the yield and quality of ES using morphological characteristics and metabolomic changes. These treatments included a control group and three groups with different organic fertilizer to chemical fertilizer ratios (3:7, 5:5, and 7:3). The results of this study revealed the mechanisms underlying the effect of the different treatments on the yield and quality of Euryales Semen. These insights were achieved through analyses of soil physicochemical properties, soil enzyme activity, and soil microbial structure.

Results

We found that the quality and yield of ES were the best at a ratio of organic fertilizer to chemical fertilizer of 7:3. The optimality of this treatment was reflected in the yield, soil available nitrogen, soil available phosphorus, and soil enzyme activity of ES. This ratio also increased soil microbial diversity, resulting in an increase and decrease in Proteobacteria and Firmicutes abundances, respectively. In addition, linear discriminant analysis showed that Chloroflexi, Gammaproteobacteria, and Hypocreales-incertae-sedis were significantly enriched in the ratio of organic fertilizer to chemical fertilizer of 7:3. Variance partitioning analysis showed that the soil properties, enzyme activities, and their interactions cumulatively can explain 90.80% of the differences in Euryales Semen yield and metabolome. In general, blending organic and chemical fertilizers at a 7:3 ratio can enhance soil fertility, boost Euryales Semen yield and quality, and bring forth conditions that are agriculturally beneficial to microbial (bacteria and fungi) dynamics.

Discussion

This study initially revealed the scientific connotation of the effects of different fertilization patterns on the planting of Euryales Semen and laid a theoretical foundation for the study of green planting patterns of Euryales Semen with high quality and yield.

Effects of organic fertilizers on yield, soil physico-chemical property, soil microbial community diversity and structure of Brassica rapa var. Chinensis

The amount of chemical fertilizer for vegetables is on the high level in China. The use of organic fertilizers to meet the nutrient requirement of crops will be an inevitable practice in sustainable agriculture. In this study, we compared the effects of pig manure fertilizer, rabbit manure fertilizer and chemical fertilizer on yield, quality of Brassica rapa var. Chinensis, soil physico-chemical properties and microbial community by using two consecutive seasons of three fertilizers in a pot experiment. The results were as follows: (1) In the first season, the fresh yield of Brassica rapa var. Chinensis applying chemical fertilizer was significantly (p ≤ 5%) higher than those of applying the pig manure and rabbit manure fertilizer, and the results were the opposite in the second season. The total soluble sugar concentration of fresh Brassica rapa var. Chinensis applying rabbit manure fertilizer was significantly (p ≤ 5%) higher than those of applying pig manure fertilizer and chemical fertilizer in the first season, and the NO₃-N content of fresh Brassica rapa var. Chinensis on the contrary. (2) The organic fertilizer increased the concentration of total nitrogen, total phosphorus and organic carbon in soil in both two seasons. Rabbit manure fertilizer increased the soil pH and EC and significantly (p ≤ 5%) reduced the soil NO₃-N content. (3) The pig manure and rabbit manure fertilizer significantly (p ≤ 5%) increased the diversity and abundance of soil bacterial of Brassica rapa var. Chinensis, but had no significant effect on soil fungi. Pearson correlation analysis showed that soil TN, TP, organic carbon content and EC were significantly correlated with soil bacterial α - diversity. There were significant differences (p ≤ 5%) in the bacterial community structures between three treatments in two seasons, and significant differences (p ≤ 5%) in the fungal community structures between fertilizer treatments while not between two seasons. Pig manure and rabbit manure fertilizer decreased the relative abundance of soil Acidobacteria and Crenarchaeota, rabbit manure fertilizer significantly increased the abundance of Actinobacteria in the second season. Distance-based redundancy analysis (dbRDA) showed that soil EC, TN, and organic carbon content were key physico-chemical factors in determining bacterial community structure in Brassica rapa var. Chinensis soil, and soil NO₃-N, EC, SOC concentration and soil pH in the fungal community structure.

Combined Application of Manure and Chemical Fertilizers Alters Soil Environmental Variables and Improves Soil Fungal Community Composition and Rice Grain Yield

Soil microorganisms play vital roles in energy flow and soil nutrient cycling and, thus, are important for crop production. A detailed understanding of the complex responses of microbial communities to diverse organic manure and chemical fertilizers (CFs) is crucial for agroecosystem sustainability. However, little is known about the response of soil fungal communities and soil nutrients to manure and CFs, especially under double-rice cropping systems. In this study, we investigated the effects of the application of combined manure and CFs to various fertilization strategies, such as no N fertilizer (Neg-CF); 100% chemical fertilizer (Pos-CF); 60% cattle manure (CM) + 40% CF (high-CM); 30% CM + 70% CF (low-CM); 60% poultry manure (PM) + 40% CF (high-PM), and 30% PM + 70% CF (low-PM) on soil fungal communities' structure and diversity, soil environmental variables, and rice yield. Results showed that synthetic fertilizer plus manure addition significantly increased the soil fertility and rice grain yield compared to sole CFs' application. Moreover, the addition of manure significantly changed the soil fungal community structure and increased the relative abundance of fungi such as phyla Ascomycota, Basidiomycota, Mortierellomycota, and Rozellomycota. The relative abundances dramatically differed at each taxonomic level, especially between manured and non-manured regimes. Principal coordinates analysis (PCoA) exhibited greater impacts of the addition of manure amendments than CFs on fungal community distributions. Redundancy analysis showed that the dominant fungal phyla were positively correlated with soil pH, soil organic C (SOC), total N, and microbial biomass C, and the fungal community structure was strongly affected by SOC. Network analysis explored positive relationships between microorganisms and could increase their adaptability in relevant environments. In addition, the structural equation model (SEM) shows the relationship between microbial biomass, soil nutrients, and rice grain yield. The SEM showed that soil nutrient contents and their availability directly affect rice grain yield, while soil fungi indirectly affect grain yield through microbial biomass production and nutrient levels. Our results suggest that manure application combined with CFs altered soil biochemical traits and soil fungal community structure and counteracted some of the adverse effects of the synthetic fertilizer. Overall, the findings of this research suggest that the integrated application of CF and manure is a better approach for improving soil health and rice yield.