Change of soil microbial community under long-term fertilization in a reclaimed sandy agricultural ecosystem

Effects of Deep Tillage on Wheat Regarding Soil Fertility and Rhizosphere Microbial Community

Wheat production is intrinsically linked to global food security. However, wheat cultivation is constrained by the progressive degradation of soil conditions resulting from the continuous application of fertilizers. This study aimed to examine the effects of deep tillage on rhizosphere soil microbial communities and their potential role in improving soil quality, given that the specific mechanisms driving these observed benefits remain unclear. Soil fertility in this research was evaluated through the analysis of various soil parameters, including total nitrogen, total phosphorus, total potassium, available phosphorus, and available potassium, among others. The high-throughput sequencing technique was utilized to examine the rhizosphere microbial community associated with deep tillage wheat. The findings indicated that deep tillage cultivation of wheat led to reduced fertility levels in the 0-20 cm soil layer in comparison with non-deep tillage cultivation. A sequencing analysis indicated that Acidobacteria and Proteobacteria are the dominant bacterial phyla, with Proteobacteria being significantly more abundant in the deep tillage group. The dominant fungal phyla identified were Ascomycota, Mortierellomycota, and Basidiomycota. Among bacterial genera, Arthrobacter, Bacillus, and Nocardioides were predominant, with Arthrobacter showing a significantly higher presence in the deep tillage group. The predominant fungal genera included Mortierella, Alternaria, Schizothecium, and Cladosporium. Deep tillage cultivation has the potential to enhance soil quality and boost crop productivity through the modulation of soil microbial community structure.

Effect of nitrogen reduction by chemical fertilization with green manure (Vicia sativa L.) on soil microbial community, nitrogen metabolism and and yield of Uncaria rhynchophylla by metagenomics

Uncaria rhynchophylla is an important herbal medicine, and the predominant issues affecting its cultivation include a single method of fertilizer application and inappropriate chemical fertilizer application. To reduce the use of inorganic nitrogen fertilization and increase the yield of Uncaria rhynchophylla, field experiments in 2020-2021 were conducted. The experimental treatments included the following categories: S1, no fertilization; S2, application of chemical NPK fertilizer; and S3-S6, application of chemical fertilizers and green manures, featuring nitrogen fertilizers reductions of 0%, 15%, 30%, and 45%, respectively. The results showed that a moderate application of nitrogen fertilizer when combined with green manure, can help alleviate soil acidification and increase urease activity. Specifically, the treatment with green manure provided in a 14.71-66.67% increase in urease activity compared to S2. Metagenomics sequencing results showed a decrease in diversity in S3, S4, S5, and S6 compared to S2, but the application of chemical fertilizer with green manure promoted an increase in the relative abundance of Acidobacteria and Chloroflexi. In addition, the nitrification pathway displayed a progressive augmentation in tandem with the reduction in nitrogen fertilizer and application of green manure, reaching its zenith at S5. Conversely, other nitrogen metabolism pathways showed a decline in correlation with diminishing nitrogen fertilizer dosages. The rest of the treatments showed an increase in yield in comparison to S1, S5 showing significant differences (p < 0.05). In summary, although S2 demonstrate the ability to enhance soil microbial diversity, it is important to consider the long-term ecological impacts, and S5 may be a better choice.

Long-term ecological restoration increased plant diversity and soil total phosphorus content of the alpine flowing sand land in northwest Sichuan, China

The ecological restoration techniques that combine grazing, sand barriers with willows, fertilization, artificial planting, and continuous management are increasingly adopted in the management of flowing sandy land in high-altitude and cold regions. However, few studies have focused on the long-term ecological restoration effects of such technologies. This study systematically compared the vegetation and soil characteristics under different ecological restoration durations (0 (CK), 3 (F1), 14 (F2), 26 (F3), and 46 (F4) years) in the alpine sandy land of northwest Sichuan. The results showed that, with the increase of ecological restoration durations, (1) the aboveground and underground biomass of plants, and species number significantly increased, while the shannon-wiener index, margalef index, and simpson index dramatically decreased; (2) in the early stage of ecological restoration (0-3 yr), Cyperaceae accounted for the main groups, while in the late stage of ecological restoration (14-46 yr), Leguminosae and Forb groups predominated; (3) ecological restoration durations significantly influenced the total phosphorus (TP) content at a soil depth of 0-60 cm, but soil organic carbon and C/P ratio were only significantly impacted at 40-60 cm; (4) the plant and soil characteristics of F1, F2, and F3 treatments were more similar, and CK and F4 treatments were clearly distinguished on PC1 of principal component analysis; (5) there was no significant correlation between Leguminosae groups and environmental factors. Instead, a correlation between total nitrogen (TN) and Forb groups, Gramineae groups, and Cyperaceae groups was revealed. TN was very significantly positively correlated with species diversity and TP. Long-term ecological restoration improved plants biomass, plant species diversity, functional plant groups, and increased soil TP content in the alpine sandy land of northwest Sichuan.

Effects of continuous cropping on fungal community diversity and soil metabolites in soybean roots

IMPORTANCE

Soybean yield can be affected by soybean soil fungal communities in different tillage patterns. Soybean is an important food crop with great significance worldwide. Continuous cultivation resulted in soil nutrient deficiencies, disordered metabolism of root exudates, fungal pathogen accumulation, and an altered microbial community, which brought a drop in soybean output. In this study, taking the soybean agroecosystem in northeast China, we revealed the microbial ecology and soil metabolites spectrum, especially the diversity and composition of soil fungi and the correlation of pathogenic fungi, and discussed the mechanisms and the measures of alleviating the obstacles.

Competition model explains trends of long-term fertilization in plant communities

Over 40 years ago, Kempton (Biometrics, 35, 1979, 307) reported significant modification to plant community structure following a long-term fertilization experiment. Many researchers have investigated this phenomenon in the years since. Collectively, these studies have shown consistent shifts in rank abundance relationships among species in communities following fertilization. The previous studies indicated that fertilization affects community structure through several critical processes, including trait-based functional response, reordering of species in rank abundance diagram (RAD), and niche dimensionality, although some questions have remained. How does the species reordering driven by the plant responses cause characteristic trends in temporal changes of RAD? Why are those trends ubiquitous in various systems? To answer those questions, we theoretically investigated the effects of fertilization on community structure based on a colonization model (or Levins model) with competition-fecundity trade-offs, which can result in the coexistence of multiple species under competition. The model represents characteristic RAD, which can be an adequate tool to study community composition. Our theoretical model comprehensively represents observed trends in rank abundance relationships following long-term fertilization and suggests that competitive interactions among species are a critical factor in structuring species diversity in plant communities.

A simulated ecological restoration of bare cut slope reveals the dosage and temporal effects of cement on ecosystem multifunctionality in a mountain ecosystem

Cement is a critical building material used in the restorations of bare cut slopes. Yet, how cement affects ecosystem's functions and their undertakers remains elusive. Here, we revealed the dosage and temporal effects of cement on plant and soil traits, extracellular enzymes, greenhouse gas fluxes and microbiome using simulation experiments. The results showed that soil pH increased with the cement content at 1st day but relatively constant values around 7 to 7.5 were detected in the flowing days. The β-1,4-glucosidase, phenol oxidase, leucine aminopeptidase and acid phosphatase showed high activities under high cement content, and they generally increased with the cultivations except for acid phosphatase. CH₄ fluxes at 16th day were less than zero, and they increased to peak around at 37th to 44th days followed by decreasing until reaching to relatively stable fluctuations around 0. Despite of decrease patterns, N₂O fluxes stayed around zero across the temporal gradient except for the maximum around at 30th day in 2%, 5% and 8% cement treatment. Microbial diversity decreased with the cement content, in which there were a recovery trend for bacteria. By integrating above- and belowground ecosystem traits into a multifunctionality index, we identified a potential optimum cement content (11%). PLSPM showed that multifunctionality was affected by the shifts in soil bacterial community, enzyme activity and greenhouse gases while these components were effected by other environmental changes resulted from cement. Our results demonstrate that cement determines multifunctionality through mediating microbial community and activity, providing new insights for designing in situ experiments and ecological restoration strategies for bare cut slopes.

Agricultural management practices influence the soil enzyme activity and bacterial community structure in tea plantations

BACKGROUND

The soil quality and health of the tea plantations are dependent on agriculture management practices, and long-term chemical fertilizer use is implicated in soil decline. Hence, several sustainable practices are used to improve and maintain the soil quality. Here, in this study, changes in soil properties, enzymatic activity, and dysbiosis in bacterial community composition were compared using three agricultural management practices, namely conventional (CA), sustainable (SA), and transformational agriculture (TA) in the tea plantation during 2016 and 2017 period. Soil samples at two-months intervals were collected and analyzed.

RESULTS

The results of the enzyme activities revealed that acid phosphatase, arylsulfatase, β-glucosidase, and urease activities differed considerably among the soils representing the three management practices. Combining the redundancy and multiple regression analysis, the change in the arylsulfatase activity was explained by soil pH as a significant predictor in the SA soils. The soil bacterial community was predominated by the phyla Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, and Bacteroidetes in the soil throughout the sampling period. Higher Alpha diversity scores indicated increased bacterial abundance and diversity in the SA soils. A significant relationship between bacterial richness indices (SOBS, Chao and ACE) and soil pH, K and, P was observed in the SA soils. The diversity indices namely Shannon and Simpson also showed variations, suggesting the shift in the diversity of less abundant and more common species. Furthermore, the agricultural management practices, soil pH fluctuation, and the extractable elements had a greater influence on bacterial structure than that of temporal change.

CONCLUSIONS

Based on the cross-over analysis of the bacterial composition, enzymatic activity, and soil properties, the relationship between bacterial composition and biologically-driven ecological processes can be identified as indicators of sustainability for the tea plantation.

Soil structure, nutrient status and water holding capacity shape Uruguayan grassland prokaryotic communities

Soil microbial communities play critical roles in maintaining natural ecosystems such as the Campos biome grasslands of southern South America. These grasslands are characterized by a high diversity of soils, low available phosphorus (P) and limited water holding capacity. This work aimed to describe prokaryotic communities associated with different soil types and to examine the relationship among these soil communities, the parent material and the soil nutrient status. Five Uruguayan soils with different parent material and nutrient status, under natural grasslands, were compared. The structure and diversity of prokaryotic communities were characterized by sequencing 16S rRNA gene amplicons. Proteobacteria, Actinobacteria, Firmicutes,Verrucomicrobia, Acidobacteria, Planctomycetes and Chloroflexi were the predominant phyla. Ordination based on several distance measures was able to discriminate clearly between communities associated with different soil types. Edge-PCA phylogeny-sensitive ordination and differential relative abundance analyses identified Archaea and the bacterial phyla Firmicutes, Acidobacteria, Actinobacteria and Verrucomicrobia as those with significant differences among soil types. Canonical analysis of principal coordinates identified porosity, clay content, available P, soil organic carbon and water holding capacity as the main variables contributing to determine the characteristic prokaryotic communities of each soil type.

Soil N availability drives the shifts of enzyme activity and microbial phosphorus limitation in the artificial soil on cut slope in southwestern China

The construction of highways in the subalpine mountains generates many cut slopes. Currently, the restoration of cut slope mainly focuses on the aboveground landscapes and slope stability. Yet, it remains elusive about the belowground ecosystem functions at the early stage of restoration. In this study, we evaluated the belowground ecosystem functions of cut slopes that had been restored approximately 3 years using soil enzymatic activities, microbial biomass, and stoichiometry as the proxies. The results indicated that the phenol oxidase activity was higher in cut slopes, while the activities of β-1,4-glucosidase, β-1,4-N-acetylglucosaminidase, leucine aminopeptidase, and acid phosphatase were lower in cut slope soils compared with natural soils. Soil nitrogen availabilities (total and/or ammonium nitrogen) showed high negative correlations with the phenol oxidase activity and positive correlations with the activities of almost all other enzymes. These results suggested that soil nitrogen was the key factor in driving the shifts of enzymatic activities across two types of soils. Moreover, we found the imbalance of soil nutrients in cut slope soils, especially the carbon vs. nitrogen and the nitrogen vs. phosphorus. By applying the vector analysis, we found that the vector A values were more than 45° in all samples, suggesting that microbial phosphorus limitation occurred in both cut slope and natural soils. These findings suggested that maintaining the balance of soil nutrient supplies is important to the recovery of the below-ground ecosystem functions at the early restoration stage of cut slopes. This study provided new insights into designing the ecological restoration strategies for cut slopes by considering the belowground ecosystem functions.

Efficiency of Wheat Straw Biochar in Combination with Compost and Biogas Slurry for Enhancing Nutritional Status and Productivity of Soil and Plant

In the present study, we investigated the impact of different combinations of wheat straw biochar, compost and biogas slurry on maize growth, physiology, and nutritional status in less productive soils. The experiment was performed as a completely randomized block design in a greenhouse pot experiment. The compost and biogas slurry were applied with and without biochar. The results revealed that a combination of biochar, compost, and biogas slurry enhanced the cation exchange capacity (31%), carbon (83%), phosphorus (67%) and potassium (81%) contents in the soil. Likewise, a significant increase in soil microbial biomass carbon (15%) and nitrogen (37%) was noticed with the combined use of all organic amendments. Moreover, the combined application of biochar, compost and biogas slurry enhanced soil urease and β-glucosidase activity up to 96% and 67% over control respectively. In addition, plant height, chlorophyll content, water use efficiency and 1000-grain weight were also enhanced up to 54%, 90%, 53% and 21% respectively, with the combined use of all amendments. Here, biochar addition helped to reduce the nutrient losses of compost and biogas slurry as well. It is concluded that biochar application in combination with compost and biogas slurry could be a more sustainable, environment-friendly and cost-effective approach, particularly for less fertile soils.

The Status of Soil Microbiome as Affected by the Application of Phosphorus Biofertilizer: Fertilizer Enriched with Beneficial Bacterial Strains

Regarding the unfavourable changes in agroecosystems resulting from the excessive application of mineral fertilizers, biopreparations containing live microorganisms are gaining increasing attention. We assumed that the application of phosphorus mineral fertilizer enriched with strains of beneficial microorganisms contribute to favourable changes in enzymatic activity and in the genetic and functional diversity of microbial populations inhabiting degraded soils. Therefore, in field experiments conditions, the effects of phosphorus fertilizer enriched with bacterial strains on the status of soil microbiome in two chemically degraded soil types (Brunic Arenosol - BA and Abruptic Luvisol - AL) were investigated. The field experiments included treatments with an optimal dose of phosphorus fertilizer (without microorganisms - FC), optimal dose of phosphorus fertilizer enriched with microorganisms including Paenibacillus polymyxa strain CHT114AB, Bacillus amyloliquefaciens strain AF75BB and Bacillus sp. strain CZP4/4 (FA100) and a dose of phosphorus fertilizer reduced by 40% and enriched with the above-mentioned bacteria (FA60). The analyzes performed included: the determination of the activity of the soil enzymes (protease, urease, acid phosphomonoesterase, β-glucosidase), the assessment of the functional diversity of microorganisms with the application of BIOLOGTM plates and the characterization of the genetic diversity of bacteria, archaea and fungi with multiplex terminal restriction fragment length polymorphism and next generation sequencing. The obtained results indicated that the application of phosphorus fertilizer enriched with microorganisms improved enzymatic activity, and the genetic and functional diversity of the soil microbial communities, however these effects were dependent on the soil type.

Microbial Communities in Soils and Endosphere of Solanum tuberosum L. and their Response to Long-Term Fertilization

An understanding of how fertilization influences endophytes is crucial for sustainable agriculture, since the manipulation of the plant microbiome could affect plant fitness and productivity. This study was focused on the response of microbial communities in the soil and tubers to the regular application of manure (MF; 330 kg N/ha), sewage sludge (SF; 330 and SF3x; 990 kg N/ha), and chemical fertilizer (NPK; 330-90-300 kg N-P-K/ha). Unfertilized soil was used as a control (CF), and the experiment was set up at two distinct sites. All fertilization treatments significantly altered the prokaryotic and fungal communities in soil, whereas the influence of fertilization on the community of endophytes differed for each site. At the site with cambisol, prokaryotic and fungal endophytes were significantly shifted by MF and SF3 treatments. At the site with chernozem, neither the prokaryotic nor fungal endophytic communities were significantly associated with fertilization treatments. Fertilization significantly increased the relative abundance of the plant-beneficial bacteria Stenotrophomonas, Sphingomonas and the arbuscular mycorrhizal fungi. In tubers, the relative abundance of Fusarium was lower in MF-treated soil compared to CF. Although fertilization treatments clearly influenced the soil and endophytic community structure, we did not find any indication of human pathogens being transmitted into tubers via organic fertilizers.

Long-term fertilization alters soil properties and fungal community composition in fluvo-aquic soil of the North China Plain

Different fertilization regimes can substantially influence soil fungal community composition, yet fewer studies try to control for the effects of nitrogen input. Here, we investigated the impact of fertilization with equal nitrogen upon soil properties and soil fungal diversity and community composition in the North China Plain in a long-term field experiment. Long-term (32 years) fertilization regimes were applied with equal amounts of nitrogen: no chemical fertilizer or organic manure; chemical fertilization only; organic manure fertilization only, and; combination of 1/2 chemical fertilizer and 1/2 organic manure. Then we investigated the influence of these four fertilization regimes to soil properties, fungal diversity and community composition. The results showed that applying organic manure significantly influenced soil properties. Illumina MiSeq sequencing and its analysis revealed that organic manure fertilization significantly changed soil fungal alpha diversity, but chemical fertilization did not. Although soil fungal community composition did not differ significantly among all the fertilization regimes at the phylum and class levels, they did show differences in the abundance of dominant fungi. Yet at the genus level, soil fungal community composition, abundance, and beta diversity was affected by all fertilization regimes. Application of organic manure also reduced the abundance of soil-born fungal pathogens such as Fusarium. Our results suggest that long-term application of organic manure could markedly improve soil properties, altering soil fungal community composition and its diversity. Moreover, organic manure fertilization could limit soil-born fungal diseases, to further contribute to soil ecosystem sustainability.

Effect of Pennisetum giganteum z.x.lin mixed nitrogen-fixing bacterial fertilizer on the growth, quality, soil fertility and bacterial community of pakchoi (Brassica chinensis L.)

Biofertilizer plays a significant role in crop cultivation that had reduced its inorganic fertilizer use. The effects of inorganic fertilizer reduction combined with Pennisetum giganteum z.x.lin mixed nitrogen-fixing biofertilizer on the growth, quality, soil nutrients and diversity of the soil bacterial community in the rhizosphere soil of pakchoi were studied. The experiment composed of 6 treatments, including CK (no fertilization), DL (10% inorganic fertilizer reduction combined with Pennisetum giganteum z.x.lin mixed nitrogen-fixing biofertilizer), ZL (25% inorganic fertilizer reduction combined with Pennisetum giganteum z.x.lin mixed nitrogen-fixing biofertilizer), SL (50% inorganic fertilizer reduction combined with Pennisetum giganteum z.x.lin mixed nitrogen-fixing biofertilizer), FHF (100% inorganic fertilizer) and JZ (100% inorganic fertilizer combined with sterilized Pennisetum giganteum z.x.lin mixed nitrogen-fixing biofertilizer). Compared with conventional fertilization, the 25% reduction in chemical fertilizer applied with the Pennisetum giganteum mixed nitrogen-fixing biofertilizer resulted in higher plant height, plant weight, chlorophyll content, soluble protein content, soluble sugar content, vitamin C content, alkali hydrolyzed nitrogen content, available phosphorus content, available potassium content and organic matter content in pakchoi, and these variables increased by 11.81%, 8.54%, 7.37%, 16.88%, 17.05%, 23.70%, 24.24%, 36.56%, 21.09% and 19.72%, respectively. In addition, the 25% reduction in chemical fertilizer applied with the Pennisetum giganteum mixed nitrogen-fixing biofertilizer also had the lowest nitrate content, which was 53.86% lower than that with conventional fertilization. Different fertilizer treatments had a significant effect on the soil bacterial community structure. Compared with conventional fertilization, the coapplication of Pennisetum giganteum z.x.lin mixed nitrogen-fixing biofertilizer and inorganic fertilizer significantly increased the relative abundance of Proteobacteria and Actinobacteria in the soil. The results of the redundancy analysis (RDA) showed that soil organic matter, alkali-hydrolyzed nitrogen, available phosphorus, available potassium, pH and water content had a specific impact on the soil bacterial community. Among the factors, soil water content was the main factor affecting the soil bacterial community, followed by soil organic matter, soil pH, available potassium, soil available phosphorus and soil alkali-hydrolyzed nitrogen.

Manure application increased denitrifying gene abundance in a drip-irrigated cotton field

Application of inorganic nitrogen (N) fertilizer and manure can increase nitrous oxide (N₂O) emissions. We tested the hypothesis that increased N₂O flux from soils amended with manure reflects a change in bacterial community structure and, specifically, an increase in the number of denitrifiers. To test this hypothesis, a field experiment was conducted in a drip-irrigated cotton field in an arid region of northwestern China. Treatments included plots that were not amended (Control), and plots amended with urea (Urea), animal manure (Manure) and a 50/50 mix of urea and manure (U+M). Manure was broadcast-incorporated into the soil before seeding while urea was split-applied with drip irrigation (fertigation) over the growing season. The addition treatments did not, as assessed by nextgen sequencing of PCR-amplicons generated from rRNA genes in soil, affect the alpha diversity of bacterial communities but did change the beta diversity. Compared to the Control, the addition of manure (U+M and Manure) significantly increased the abundance of genes associated with nitrate reduction (narG) and denitrfication (nirK and nosZ). Manure addition (U+M and Manure) did not affect the nitrifying enzyme activity (NEA) of soil but resulted in 39–59 times greater denitrifying enzyme activity (DEA). In contrast, urea application had no impact on the abundances of nitrifier and denitrifier genes, DEA and NEA; likely due to a limitation of C availability. DEA was highly correlated (r = 0.70–0.84, P < 0.01) with the abundance of genes narG, nirK and nosZ. An increase in the abundance of these functional genes was further correlated with soil NO₃⁻, dissolved organic carbon, total C, and total N concentrations, and soil C:N ratio. These results demonstrated a positive relationship between the abundances of denitrifying functional genes (narG, nirK and nosZ) and denitrification potential, suggesting that manure application increased N₂O emission by increasing denitrification and the population of bacteria that mediated that process.