Soil amendment alters soil physicochemical properties and bacterial community structure of a replanted apple orchard

Changes in soil organic carbon components and microbial community following spent mushroom substrate application

While spent mushroom substrate (SMS) has shown promise in increasing soil organic carbon (SOC) and improving soil quality, research on the interplay between SOC components and microbial community following the application of diverse SMS types remains scant. A laboratory soil incubation experiment was conducted with application of two types of SMSs from cultivation of Pleurotus eryngii (PE) and Agaricus bisporus (AB), each at three application rates (3, 5.5, and 8%). Advanced techniques, including solid-state 13C nuclear magnetic resonance (NMR) and high-throughput sequencing, were employed to investigate on SOC fractions and chemical structure, microbial community composition and functionality. Compared to SMS-AB, SMS-PE application increased the relative abundances of carbohydrate carbon and O-alkyl C in SOC. In addition, SMS-PE application increased the relative abundance of the bacterial phylum Proteobacteria and those of the fungal phyla Basidiomycota and Ascomycota. The relative abundances of cellulose-degrading bacterial (e.g., Flavisolibacter and Agromyces) and fungal genera (e.g., Myceliophthora, Thermomyces, and Conocybe) were increased as well. The application of SMS-AB increased the aromaticity index of SOC, the relative abundance of aromatic C, and the contents of humic acid and heavy fraction organic carbon. In addition, SMS-AB application significantly increased the relative abundances of the bacterial phyla Firmicutes and Actinobacteria. Notably, the genera Actinomadura, Ilumatobacter, and Bacillus, which were positively correlated with humic acid, experienced an increase in relative abundance. Functional prediction revealed that SMS-PE application elevated carbohydrate metabolism and reduced the prevalence of fungal pathogens, particularly Fusarium. The application of high-rate SMS-AB (8%) enhanced bacterial amino acid metabolism and the relative abundances of plant pathogenic fungi. Our research provides strategies for utilizing SMS to enrich soil organic carbon and fortify soil health, facilitating the achievement of sustainable soil management.

Response of bacterial community metabolites to bacterial wilt caused by Ralstonia solanacearum: a multi-omics analysis

The soil microbial community plays a critical role in promoting robust plant growth and serves as an effective defence mechanism against root pathogens. Current research has focused on unravelling the compositions and functions of diverse microbial taxa in plant rhizospheres invaded by Ralstonia solanacearum, however, the specific mechanisms by which key microbial groups with distinct functions exert their effects remain unclear. In this study, we employed a combination of amplicon sequencing and metabolomics analysis to investigate the principal metabolic mechanisms of key microbial taxa in plant rhizosphere soil. Compared to the healthy tobacco rhizosphere samples, the bacterial diversity and co-occurrence network of the diseased tobacco rhizosphere soil were significantly reduced. Notably, certain genera, including Gaiella, Rhodoplanes, and MND1 (Nitrosomonadaceae), were found to be significantly more abundant in the rhizosphere of healthy plants than in that of diseased plants. Eight environmental factors, including exchangeable magnesium, available phosphorus, and pH, were found to be crucial factors influencing the composition of the microbial community. Ralstonia displayed negative correlations with pH, exchangeable magnesium, and cation exchange flux, but showed a positive correlation with available iron. Furthermore, metabolomic analysis revealed that the metabolic pathways related to the synthesis of various antibacterial compounds were significantly enriched in the healthy group. The correlation analysis results indicate that the bacterial genera Polycyclovorans, Lysobacter, Pseudomonas, and Nitrosospira may participate in the synthesis of antibacterial compounds. Collectively, our findings contribute to a more in-depth understanding of disease resistance mechanisms within healthy microbial communities and provide a theoretical foundation for the development of targeted strategies using beneficial microorganisms to suppress disease occurrence.

Differential Gene Expression Patterns in Peach Roots under Non-Uniform Soil Conditions in Response to Organic Matter

Organic matter (OM) amendments are often encouraged in sustainable agriculture programs but can create heterogeneous soil environments when applied to perennial crops such as peaches (Prunus persica (L.) Batsch). To better understand the responses of peach roots to non-uniform soil conditions, transcriptomic analysis was performed in a split-root study using uniform soil (the same soil type for all roots) or non-uniform soil (different soil types for each half of the root system) from either (1) autoclaved sand (S), (2) autoclaved sand with autoclaved compost (A), or (3) autoclaved sand with compost which included inherent biological soil life (B). Each uniform soil type (S, A, and B) was grouped and compared by uniform and non-uniform soil comparisons for a total of nine treatments. Comparisons revealed peach roots had differentially expressed genes (DEGs) and gene ontology terms between soil groups, with the S and B groups having a range of 106-411 DEGs and the A group having a range of 19-94 DEGs. Additionally, six modules were identified and correlated (p > 0.69) for six of the nine treatment combinations. This study broadly highlights the complexity of how OM and biological life in the rhizosphere interact with immediate and distant roots and sheds light on how non-homogenous soil conditions can influence peach root gene expression.

Nanopesticide risk assessment based on microbiome profiling - Community structure and functional potential as biomarkers in captan@ZnO35-45 nm and captan@SiO220-30 nm treated orchard soil

Nanoformulation should minimise the usage of pesticides and limit their environmental footprint. The risk assessment of two nanopesticides with fungicide captan as an active organic substance and ZnO35-45 nm or SiO220-30 nm as nanocarriers was evaluated using the non-target soil microorganisms as biomarkers. The first time for that kind of nanopesticides next-generation sequencing (NGS) of bacterial 16 S rRNA and fungal ITS region and metagenomics functional predictions (PICRUST2) was made to study structural and functional biodiversity. During a 100-day microcosm study in soil with pesticide application history, the effect of nanopesticides was compared to pure captan and both nanocarriers. Nanoagrochemicals affected microbial composition, especially Acidobacteria-6 class, and alpha diversity, but the observed effect was generally more substantial for pure captan. As for beta diversity, the negative impact was detected only in response to captan and still observed on day 100. Fungal community in the orchard soil showed only a decrease in phylogenetic diversity in captan set-up since day 30. PICRUST2 analysis confirmed several times lower impact of nanopesticides considering the abundance of functional pathways and genes encoding enzymes. Furthermore, the overall data indicated that using SiO220-30 nm as a nanocarrier speeds up a recovery process compared to ZnO35-45 nm.

Effects of partial substitution of chemical fertilizer with organic manure on the activity of enzyme and soil bacterial communities in the mountain red soil

Introduction

The partial substitution of chemical fertilizer with organic manure takes on a critical significance to enhancing soil quality and boosting sustainable agricultural development. However, rare research has studied the effects of partial substitution of chemical fertilizer with organic manure on soil bacterial community diversity and enzyme activity in maize field in the mountain red soil region of Yunnan.

Methods

In this study, four treatments were set up in which chemical fertilizer (the application rates of N, P2O5 and K2O were 240, 75 and 75 kg·ha-1, respectively) was substituted by 10% (M10), 20% (M20), 30% (M30) and 40% (M40) of organic manure with equal nitrogen, as well as two control treatments of single application of chemical fertilizer (M0) and no fertilization (CK). The maize (Zea mays L.) crop was sown as a test crop in May 2018. The effects of partial substitution of chemical fertilizer with organic manure on soil physicochemical properties, soil bacterial community diversity and enzyme activity were studied.

Results

The activities of Cellulase (CBH), Invertase (INV) and β-glucosidase (BG) increased with the increase of organic manure substitution ratio. The activities of β-1,4-N-acetylglucosaminidase (NAG), Urease (URE), and leucine aminopeptidase (LAP) also had the same trend, but the highest activities were 159.92 mg·g-1·h-1, 66.82 mg·g-1·h-1 and 143.90 mg·g-1·h-1 at 30% substitution ratio. Compared with CK and M0 treatments, Shannon index increased notably by 82.91%-116.74% and 92.42%-128.01%, respectively, at the organic manure substitution ratio ranging from 10% to 40%. Chao1 and ACE index increased significantly at the organic manure substitution ratio ranging from 10% to 30%. Proteobacteria was the dominant phylum in all treatments, the relative abundance of Proteobacteria decreased as the organic manure substitution ratio increased. Redundancy analysis showed that microbial biomass C was the main factor affecting the bacterial community composition under partial replacement of chemical fertilizer treatment, while Actinobacteria was the main factor affecting the enzyme activity. In addition, the maize yield of M30 and M40 treatments was significantly higher than that of CK and M0-M20 treatments, and the yield of M30 treatment was the highest, reaching 7652.89 kg·ha-1.

Conclusion

Therefore, the partial substitution of chemical fertilizer with organic manure can improve soil biological characteristics, while increasing bacterial community diversity and soil enzyme activity. Therefore, a thirty percent organic manure substitution was determined as the optimal substitution ratio for maize farmland in the mountain red soil area of Yunnan, China.

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.

Effects of a Nanonetwork-Structured Soil Conditioner on Microbial Community Structure

Fertilizer application can increase yields, but nutrient runoff may cause environmental pollution and affect soil quality. A network-structured nanocomposite used as a soil conditioner is beneficial to crops and soil. However, the relationship between the soil conditioner and soil microbes is unclear. We evaluated the soil conditioner's impact on nutrient loss, pepper growth, soil improvement, and, especially, microbial community structure. High-throughput sequencing was applied to study the microbial communities. The microbial community structures of the soil conditioner treatment and the CK were significantly different, including in diversity and richness. The predominant bacterial phyla were Pseudomonadota, Actinomycetota, and Bacteroidota. Acidobacteriota and Chloroflexi were found in significantly higher numbers in the soil conditioner treatment. Ascomycota was the dominant fungal phylum. The Mortierellomycota phylum was found in significantly lower numbers in the CK. The bacteria and fungi at the genus level were positively correlated with the available K, available N, and pH, but were negatively correlated with the available P. Our results showed that the loss of nutrients controlled by the soil conditioner increased available N, which improved soil properties. Therefore, the microorganisms in the improved soil were changed. This study provides a correlation between improvements in microorganisms and the network-structured soil conditioner, which can promote plant growth and soil improvement.

Spinach (Spinacia oleracea) as green manure modifies the soil nutrients and microbiota structure for enhanced pepper productivity

Spinach has been suggested as a potential rotation crop for increasing crop yield by enhancing beneficial fungal microbes in continuous monocropping. However, no research on the use of spinach as a green manure has been reported. Thus, we tested the effects of spinach and Korean mustard cultivars (green and red mustards) (10 g pot ^-1) as green manure on soil chemical properties, pepper productivity, and soil microbiome of long-year pepper-monocropped soil. Spinach improved the soil nutrition (e.g., pH, SOM, TN, NH₄⁺, and K), weed suppression, and pepper growth. Spinach had by far the highest fruit yield, over 100% pepper fruit yield increment over the mustard green manures and control. Our study showed that the major influencing factors to cause a shift in both bacterial and fungal community assemblies were soil pH, TC TN, and K. Following green manure amendment Bacillota, especially Clostridium, Bacillus and Sedimentibacter, were enriched, whereas Chloroflexi and Acidobacteriota were reduced. In addition, spinach highly reduced the abundance of Leotiomycetes and Fusarium but enriched Papiliotrema. FAPROTAX and FUNGuild analysis revealed that predicted functional profiles of bacterial and fungal communities in spinach-amended soil were changed. Spinach-treated soil was differentially abundant in function related to hydrocarbon degradation and functional guilds of symbiotrophs and ectomycorrhizal. This study contributes significantly to our understanding of how the soil fertility and soil microbiome alteration via spinach green manure application as a pre-plant soil treatment might help alleviate continuous cropping obstacles.

Soil amendment with cow dung modifies the soil nutrition and microbiota to reduce the ginseng replanting problem

Ginseng is a profitable crop worldwide; however, the ginseng replanting problem (GRP) is a major threat to its production. Soil amendment is a non-chemical method that is gaining popularity for alleviating continuous cropping obstacles, such as GRP. However, the impact of soil amendment with either cow dung or canola on GRP reduction and the associated soil microbiota remains unclear. In the present study, we evaluated the effect of soil amendment with cow dung, canola seed powder, and without amendment (control), on the survival of ginseng seedling transplants, the soil bacterial and fungal communities, and their associated metabolic functions. The results showed that cow dung increased ginseng seedling survival rate by 100 percent and had a remarkable positive effect on ginseng plant growth compared to control, whereas canola did not. Cow dung improved soil nutritional status in terms of pH, electrical conductivity, NO 3 - , total carbon, total phosphorus, and available phosphorus. The amplicon sequencing results using Illumina MiSeq showed that canola had the strongest negative effect in reducing soil bacterial and fungal diversity. On the other hand, cow dung stimulated beneficial soil microbes, including Bacillus, Rhodanobacter, Streptomyces, and Chaetomium, while suppressing Acidobacteriota. Community-level physiological profiling analysis using Biolog Ecoplates containing 31 different carbon sources showed that cow dung soil had a different metabolic activity with higher utilization rates of carbohydrates and polymer carbon sources, mainly Tween 40 and beta-methyl-d-glucoside. These carbon sources were most highly associated with Bacillota. Furthermore, predicted ecological function analyses of bacterial and fungal communities showed that cow dung had a higher predicted function of fermentation and fewer functions related to plant pathogens and fungal parasites, signifying its potential to enhance soil suppressiveness. Co-occurrence network analysis based on random matrix theory (RMT) revealed that cow dung transformed the soil microbial network into a highly connected and complex network. This study is the first to report the alleviation of GRP using cow dung as a soil amendment, and the study contributes significantly to our understanding of how the soil microbiota and metabolic alterations via cow dung can aid in GRP alleviation.

Is foliar spectrum predictive of belowground bacterial diversity? A case study in a peach orchard

Rhizosphere bacteria can have wide-ranging effects on their host plants, influencing plant biochemical and structural characteristics, and overall productivity. The implications of plant-microbe interactions provides an opportunity to interfere agriculture ecosystem with exogenous regulation of soil microbial community. Therefore, how to efficiently predict soil bacterial community at low cost is becoming a practical demand. Here, we hypothesize that foliar spectral traits can predict the diversity of bacterial community in orchard ecosystem. We tested this hypothesis by studying the ecological linkages between foliar spectral traits and soil bacterial community in a peach orchard in Yanqing, Beijing in 2020. Foliar spectral indexes were strongly correlated with alpha bacterial diversity and abundant genera that can promote soil nutrient conversion and utilization, such as Blastococcus, Solirubrobacter, and Sphingomonas at fruit mature stage. Certain unidentified or relative abundance <1% genera were also associated with foliar spectral traits. We selected specific indicators (photochemical reflectance index, normalized difference vegetable index, greenness index, and optimized soil-adjusted vegetation index) of foliar spectral indexes, alpha and beta diversities of bacterial community, and quantified the relations between foliar spectral traits and belowground bacterial community via SEM. The results of this study indicated that foliar spectral traits could powerfully predict belowground bacterial diversity. Characterizing plant attributes with easy-accessed foliar spectral indexes provides a new thinking in untangling the complex plant-microbe relationship, which could better cope with the decreased functional attributes (physiological, ecological, and productive traits) in orchard ecosystem.

Divergent Changes in Bacterial Functionality as Affected by Root-Zone Ecological Restoration in an Aged Peach Orchard

Soil restoration is a crucial approach to improving plant productivity in orchards with soil degradation, yield reduction, and fruit quality declination in China. A self-invented root-zone ecological restoration practice (RERP) with soil conditioner, or organic fertilizer, was employed in a degraded peach orchard in Beijing in 2020 to investigate the consequent impacts on soil bacterial composition and functionality at soil depths of 0–20 cm and 20–40 cm. Bacterial diversity was sensitive to RERP, especially in subsurface soil. RERP with soil conditioner significantly increased bacterial diversity, and affected abundances of certain genera, such as a significantly increased amount of Bacillus in surface soil and Blastococcus, Microvirga, Nocardioides, and Sphingomonas in subsurface soil. It also significantly affected abundances of bacterial functions related to metabolism in subsurface soil, particularly those with low abundance such as decreased transcription abundance and increased amino acid metabolism abundance. Soil bacterial functions were observably affected by bacterial diversity and composition, particularly in the deep soil layer. RERP affected bacterial functionality via responses of soil bacteria and bacteria-mediated alterations to the changed soil property. Correlation analysis between soil properties, bacterial taxonomy, and bacterial functions revealed that RERP affected bacterial functionality by altering the soil microenvironment with ample nutrients and water supply in root zone. Consequently, shifted bacterial functionality could have a potential in orchard ecosystem services in view of fruit yield and quality. Taken together, RERP had notably positive impacts on soil bacterial diversity and functions, and a prospect of increased plant productivity in the degrade orchard ecosystem.

Inoculation of Prickly Pear Litter with Microbial Agents Promotes the Efficiency in Aerobic Composting

Prickly pear (Rosa roxburghii Tratt), a shrub mainly distributed in South China, is an economically essential plant for helping the local people out of poverty. To efficiently provide sufficient nutrients to the plant in the soil for the ecological cultivation of prickly pear, we studied the aerobic composting of a prickly pear litter with three agents, including AC (Bacillus natto, Bacillus sp., Actinomycetes sp., Saccharomyces sp., Trichoderma sp., Azotobacter sp., and Lactobacillus sp.), BC (Bacillus subtilis, Lactobacillaceae sp., Bacillus licheniformis, Saccharomyces sp., and Enterococcus faecalis), and CC (Bacillus sp., Actinomycetes sp., Lactobacillaceae sp., Saccharomyces sp., and Trichoderma sp.) and a control without microbial agents. The results show that the physicochemical and microbial traits of three resultant prickly pear composts were different after the inoculation with AC, BC, or CC. The pH values of three composts ranged from 8.0 to 8.5, and their conductivity values were between 1.6 and 1.9 mS/cm. The seed germination index of all three composts exceeded 70%. The contents of volatile solids and organic matter of the three composts both decreased significantly. The BC maximally increased the total N (18%) of the compost, whereas the CC maximally increased the total P (48%) and total K (38%) contents. Contents of available P and available K of the three composts increased significantly, and the available N content in compost after BC inoculation increased by 16%. The physicochemical features showed that three composts were non-hazardous to plants, and the microbial agents improved nutrient availability. The richness, Chao1, and Shannon index in the bacterial communities of three composts increased significantly. At the phylum level, Proteobacteria, Bacteroidetes, and Firmicutes bacterium became dominant in the three composts, whereas at the family level, Microscillaceae and A4b (phylum Chloroflexi) became the dominant groups. Abundant cellulose-degrading bacteria existed at the dominant phylum level, which promoted fiber degradation in composts. Organic matter and the available N content regulated the composting bacterium. The inoculants enhanced the efficiency of composting: agents B and C were more suitable exogenous inoculants for the composting of a prickly pear litter.

Application of ammonium to a N limited arable soil enriches a succession of bacteria typically found in the rhizosphere

Crop residue management and tillage are known to affect the soil bacterial community, but when and which bacterial groups are enriched by application of ammonium in soil under different agricultural practices from a semi-arid ecosystem is still poorly understood. Soil was sampled from a long-term agronomic experiment with conventional tilled beds and crop residue retention (CT treatment), permanent beds with crop residue burned (PBB treatment) or retained (PBC) left unfertilized or fertilized with 300 kg urea-N ha⁻¹ and cultivated with wheat (Triticum durum L.)/maize (Zea mays L.) rotation. Soil samples, fertilized or unfertilized, were amended or not (control) with a solution of (NH₄)₂SO₄ (300 kg N ha⁻¹) and were incubated aerobically at 25 ± 2 °C for 56 days, while CO₂ emission, mineral N and the bacterial community were monitored. Application of NH₄⁺ significantly increased the C mineralization independent of tillage-residue management or N fertilizer. Oxidation of NH₄⁺ and NO₂⁻ was faster in the fertilized soil than in the unfertilized soil. The relative abundance of Nitrosovibrio, the sole ammonium oxidizer detected, was higher in the fertilized than in the unfertilized soil; and similarly, that of Nitrospira, the sole nitrite oxidizer. Application of NH₄⁺ enriched Pseudomonas, Flavisolibacter, Enterobacter and Pseudoxanthomonas in the first week and Rheinheimera, Acinetobacter and Achromobacter between day 7 and 28. The application of ammonium to a soil cultivated with wheat and maize enriched a sequence of bacterial genera characterized as rhizospheric and/or endophytic independent of the application of urea, retention or burning of the crop residue, or tillage.

Soil pH: a key edaphic factor regulating distribution and functions of bacterial community along vertical soil profiles in red soil of pomelo orchard

Background

Soil microbes exist throughout the soil profile and those inhabiting topsoil (0–20 cm) are believed to play a key role in nutrients cycling. However, the majority of the soil microbiology studies have exclusively focused on the distribution of soil microbial communities in the topsoil, and it remains poorly understood through the subsurface soil profile (i.e., 20–40 and 40–60 cm). Here, we examined how the bacterial community composition and functional diversity changes under intensive fertilization across vertical soil profiles [(0–20 cm (RS1), 20–40 cm (RS2), and 40–60 cm (RS3)] in the red soil of pomelo orchard, Pinghe County, Fujian, China.

Results

Bacterial community composition was determined by 16S rRNA gene sequencing and interlinked with edaphic factors, including soil pH, available phosphorous (AP), available nitrogen (AN), and available potassium (AK) to investigate the key edaphic factors that shape the soil bacterial community along with different soil profiles. The most dominant bacterial taxa were Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Crenarchaeota, and Bacteriodetes. Bacterial richness and diversity was highest in RS1 and declined with increasing soil depth. The distinct distribution patterns of the bacterial community were found across the different soil profiles. Besides, soil pH exhibited a strong influence (pH ˃AP ˃AN) on the bacterial communities under all soil depths. The relative abundance of Proteobacteria, Actinobacteria, Crenarchaeota, and Firmicutes was negatively correlated with soil pH, while Acidobacteria, Chloroflexi, Bacteriodetes, Planctomycetes, and Gemmatimonadetes were positively correlated with soil pH. Co-occurrence network analysis revealed that network topological features were weakened with increasing soil depth, indicating a more stable bacterial community in the RS1. Bacterial functions were estimated using FAPROTAX and the relative abundance of functional bacterial community related to metabolic processes, including C-cycle, N-cycle, and energy production was significantly higher in RS1 compared to RS2 and RS3, and soil pH had a significant effect on these functional microbes.

Conclusions

This study provided the valuable findings regarding the structure and functions of bacterial communities in red soil of pomelo orchards, and highlighted the importance of soil depth and pH in shaping the soil bacterial population, their spatial distribution and ecological functioning. These results suggest the alleviation of soil acidification by adopting integrated management practices to preserve the soil microbial communities for better ecological functioning.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02452-x.

Effects of Bacillus amyloliquefaciens QSB-6 on the Growth of Replanted Apple Trees and the Soil Microbial Environment

Apple replant disease (ARD), caused largely by soil-borne fungal pathogens, has seriously hindered the development of the apple industry. The use of antagonistic microorganisms has been confirmed as a low-cost and environmentally friendly means of controlling ARD. In the present study, we assessed the effects of Bacillus amyloliquefaciens QSB-6 on the growth of replanted apple saplings and the soil microbial environment under field conditions, thus providing a theoretical basis for the successful use of microbial biocontrol agents. Four treatments were implemented in three apple orchards: untreated replant soil (CK1), methyl bromide fumigation (CK2), blank carrier treatment (T1), and QSB-6 bacterial fertilizer treatment (T2). The plant height, ground diameter, and branch length of apple saplings treated with T2 in three replanted apple orchards were significantly higher than that of the CK1 treatment. Compared with the other treatments, T2 significantly increased the number of soil bacteria, the proportion of actinomycetes, and the activities of soil enzymes. By contrast, compared with the CK1 treatments, the phenolic acid content, the number of fungi, and the abundance of Fusarium oxysporum, Fusarium moniliforme, Fusarium proliferatum, and Fusarium solani in the soil were significantly reduced. PCoA and cluster analysis showed that soil inoculation with strain QSB-6 significantly decreased the Mcintosh and Brillouin index of soil fungi and increased the diversity of soil bacteria in T2 relative to CK1. The soil bacterial community structure in T2 was different from the other treatments, and the soil fungal communities of T2 and CK2 were similar. In summary, QSB-6 bacterial fertilizer shows promise as a potential bio-inoculum for the control of ARD.

Taxonomic and Functional Diversity of Rhizosphere Microbiome Recruited From Compost Synergistically Determined by Plant Species and Compost

Compost is frequently served as the first reservoir for plants to recruit rhizosphere microbiome when used as growing substrate in the seedling nursery. In the present study, recruitment of rhizosphere microbiome from two composts by tomato, pepper, or maize was addressed by shotgun metagenomics and 16S rRNA amplicon sequencing. The 16S rRNA amplicon sequencing analysis showed that 41% of variation in the rhizosphere bacterial community was explained by compost, in contrast to 23% by plant species. Proteobacterial genera were commonly recruited by all three plant species with specific selections for Ralstonia by tomato and Enterobacteria by maize. These findings were confirmed by analysis of 16S rRNA retrieved from the shotgun metagenomics library. Approximately 70% of functional gene clusters differed more than sevenfold in abundance between rhizosphere and compost. Functional groups associated with the sensing and up-taking of C3 and C4 carboxylic acids, amino acids, monosaccharide, production of antimicrobial substances, and antibiotic resistance were over-represented in the rhizosphere. In summary, compost and plant species synergistically shaped the composition of the rhizosphere microbiome and selected for functional traits associated with the competition on root exudates.

Insight to bacteria community response of organic management in apple orchard-bagasse fertilizer combined with biochar

Based on the sustainable development practice-zero growth in chemical fertilizer application, this article used bagasse organic fertilizer and rice husk derived biochar to investigate the response of soil bacterial community in apple orchard. Aimed at realize the soil quality improvement and biomass resource recovery to contribute agricultural and environmental sustainability. The co-trophic Proteobacteria was predominant in all the treatments (29-36 %) and enriched in non-nitrifying Alphaproteobacteria (9-11 %) and ammonia oxidant Betaproteobacteria (8-10 %), especially richest in bagasse fertilizer combine biochar treated soil. In addition, bacterial community variation was assessed by alpha and beta diversity, four treatments dispersed distribution and richer abundance observed in combined apply bagasse fertilizer and biochar treatment (3909.22 observed-species) than single application (3729.88 and 3646.58 observed-species). Biochar as microbial carrier combined organic fertilizer were established synergistic interaction and favorable to organic matter availability during sustainable agriculture. Finally, integrated biochar-bagasse fertilizer was richer than single organic or biochar fertilization in improving soil bacterial diversity, notably by promoting the metabolism of copiotrophic bacteria, nutrient cycling, plant growth and disease inhibit-related bacteria.

Clean technology for biochar and organic waste recycling, and utilization in apple orchard

Present study evaluated the utilization of clean technology for biochar combined with organic fertilizer in apple orchard aspect of soil organic carbon fractions and microbial community. Four treatments were performed with control (CK), rice husk biochar alone (B), bagasse fermented organic fertilizer alone (O) and biochar combined with organic fertilizer (BO). The results demonstrated that utilization of organic fertilizer integrated with biochar were obviously enhanced the total and active fractions organic carbon in the top-soil (0-20 cm), enriched the bacterial community diversity and the richest abundance presented in BO treatment with 4253 operational taxonomic unit. The visualization illustrated the superior bacterial community was affiliated with Proteobacteria (35.14%), Actinobacteria (21.34%), Acidobacteria (16.82%) and Firmicutes (14.70%). Additionally, redundancy analysis suggested the strong interaction between microorganisms and organic carbon fractions. Overall, the application of biochar combine with organic fertilizer was favorable approach in apple orchard management, attributed to the influence of essential factors by improve organic carbon and bacterial diversity especially conductive to the profitable strain proliferation.

Microbiota Diversity Change as Quality Indicator of Soils Exposed to Intensive Periurban Agriculture

In Argentina, periurban agriculture is performed by farmers with inadequate training in the use of pesticides and chemical fertilizers, developing horticulture with serious soil deterioration. The aim of this work was to monitor bacterial diversity of a horticultural soil (S) and a reference soil (R) as quality index for the design of future restoration strategies. As crops changed together with the agrochemical applications, sample collection was before harvest for strawberries, post-harvest for red peppers, pre-harvest broccoli crop and of a resting soil in treatment with poultry litter as a fertilizing amendment. Bacterial diversity was analysed by the use of high throughput sequencing of the V1-V3 region of the 16S rRNA gene. Analysis of R soils seemed relatively constant in time, enriched in Alphaproteobacteria and Acidobacteria consistent with a reference to soil health. The effect of the intensive use of S soils was proved by differences in Chloroflexi, Bacteroidetes and Proteobacteria relative abundances. The main evidence of the alteration of S soils was the increase in Bacteroidetes and Betaproteobacteria. A weak recuperation trend of S soil microbiota was registered during a post-harvest inactive period. A strong influence of the soil use routine-consisting in high crop rotation and short time-rest cycles-on microbial community structure was verified. These results indicate the microbiota perturbation, caused by the intense use of periurban agriculture soils and will contribute for further actions to improve environment quality.

Organic amendments exacerbate the effects of silver nanoparticles on microbial biomass and community composition of a semiarid soil

Increased utilization of silver nanoparticles (AgNPs) can result in an accumulation of these particles in the environment. The potential detrimental effects of AgNPs in soil may be associated with the low fertility of soils in semiarid regions that are usually subjected to restoration through the application of organic amendments. Microbial communities are responsible for fundamental processes related to soil fertility, yet the potential impacts of low and realistic AgNPs concentrations on soil microorganisms are still unknown. We studied the effects of realistic citrate-stabilized AgNPs concentrations (0.015 and 1.5 μg kg^-1) at two exposure times (7 and 30 days) on a sandy clay loam Mediterranean soil unamended (SU) and amended with compost (SA). We assessed soil microbial biomass (microbial fatty acids), soil enzyme activities (urease, β-glucosidase, and alkaline phosphatase), and composition of the microbial community (bacterial 16S rRNA gene and fungal ITS2 sequencing) in a microcosm experiment. In the SA, the two concentrations of AgNPs significantly decreased the bacterial biomass after 7 days of incubation. At 30 days of incubation, only a significant decrease in the Gram+ was observed at the highest AgNPs concentration. In contrast, in the SU, there was a significant increase in bacterial biomass after 30 days of incubation at the lowest AgNPs concentration. Overall, we found that fungal biomass was more resistant to AgNPs than bacterial biomass, in both SA and SU. Further, the AgNPs changed the composition of the soil bacterial community in SA, the relative abundance of some bacterial taxa in SA and SU, and fungal richness in SU at 30 days of incubation. However, AgNPs did not affect the activity of extracellular enzymes. This study demonstrates that the exposure time and organic amendments modulate the effects of realistic concentrations of AgNPs in the biomass and composition of the microbial community of a Mediterranean soil.

Comparative study of neighboring Holm oak and olive trees-belowground microbial communities subjected to different soil management

It is well-known that different plant species, and even plant varieties, promote different assemblages of the microbial communities associated with them. Here, we investigate how microbial communities (bacteria and fungi) undergo changes within the influence of woody plants (two olive cultivars, one tolerant and another susceptible to the soilborne fungal pathogen Verticillium dahliae, plus wild Holm oak) grown in the same soil but with different management (agricultural versus native). By the use of metabarcoding sequencing we determined that the native Holm oak trees rhizosphere bacterial communities were different from its bulk soil, with differences in some genera like Gp4, Gp6 and Solirubrobacter. Moreover, the agricultural management used in the olive orchard led to belowground microbiota differences with respect to the natural conditions both in bulk soils and rhizospheres. Indeed, Gemmatimonas and Fusarium were more abundant in olive orchard soils. However, agricultural management removed the differences in the microbial communities between the two olive cultivars, and these differences were minor respect to the olive bulk soil. According to our results, and at least under the agronomical conditions here examined, the composition and structure of the rhizospheric microbial communities do not seem to play a major role in olive tolerance to V. dahliae.

Community-level genetic profiles of actinomycetales in long-term biowaste-amended soils

Actinomycetales is an order of actinobacteria that have an important role in the decomposition of organic matter. Their abundance and distribution can reflect a good level of soil fertility as well as biological activity. In this research study, actinomycetal diversity in soil was investigated under various field treatments with biowastes. Initially, unvegetated agricultural soil plots of 4 m² had been annually amended with increasing rates of municipal solid waste compost (MSWC at 40, 80 and 120 t ha^-1 year^-1) and farmyard manure (FM at 40 and 120 t ha^-1 year^-1) for eight consecutive years. Control consisted of unamended soil and all treatments were distributed in four randomized complete blocks. At the end of the experimental period, total DNA was extracted from fresh topsoil samples (0-20 cm) then nested PCR-DGGE sequencing method was applied to assess the long-term effect of treatments on the diversity of actinomycetes. Analytical outcomes revealed the presence of ten actinomycetal families with Streptomycetaceae, Pseudonocardiaceae and Nocardioidaceae being the most dominant regardless to changes in experimental conditions. Besides, the long-term accumulation of both biowastes in soil affected the diversity of actinomycetal communities in different ways including contribution, stimulation or inhibition. Interestingly, soil treated with MSWC at an equivalent rate of 40 t ha^-1 year^-1 was likely to provide optimal growth conditions for major identified genera because it showed the highest actinomycetal diversity as compared to the rest of the treatments.

Rapid elimination of foodborne and environmental fungal contaminants by benzo analogs

BACKGROUND

Contamination of food or the environment by fungi, especially those resistant to conventional fungicides or drugs, represents a hazard to human health. The objective of this study is to identify safe, natural antifungal agents that can remove fungal pathogens or contaminants rapidly from food and / or environmental sources.

RESULTS

Fifteen antifungal compounds (nine benzo derivatives as candidates; six conventional fungicides as references) were investigated. Three benzo analogs, namely octyl gallate (OG), trans-cinnamaldehyde (CA), and 2-hydroxy-5-methoxybenzaldehyde (2H5M), at 1 g L^-1 (3.54 mmol), 1 mL L^-1 (7.21 mmol), 1 mL L^-1 (5.39 mmol), respectively, achieved ≥99.9% fungal death after 0.5, 2.5 or 24 h of treatments, respectively, in in vitro phosphate-buffered saline (PBS) bioassay. However, when OG, CA, and 2H5M were examined in commercial food matrices, organic apple, or grape juices, only CA maintained a similar level of antifungal activity, compared with a PBS bioassay. trans-Cinnamaldehyde showed higher antifungal activity at pH 3.5, equivalent to that of commercial fruit juices, than at pH 5.6. In soil sample tests, the application of 1 mL L^-1 (7.21 mmol) CA to conventional maize / tomato soil samples (pH 6.8) for 2.5 h resulted in ≥99.9% fungal death, indicating CA could also eliminate fungal contaminants in soil. While the conventional fungicide thiabendazole exerted antifungal activity comparable to CA, thiabendazole enhanced the production of carcinogenic aflatoxins by Aspergillus flavus, an undesirable side effect.

CONCLUSION

trans-Cinnamaldehyde could be developed as a potent antifungal agent in food processing or soil sanitation by reducing the time / cost necessary for fungal removal. Published 2020. This article is a U.S. Government work and is in the public domain in the USA.

Rhizospheric Organic Acids as Biostimulants: Monitoring Feedbacks on Soil Microorganisms and Biochemical Properties

The biostimulant potential of three different organic acids (OAs) present in the rhizosphere, specifically lactic, oxalic, and citric acids, have been studied. The results showed a rapid and complete metabolism of these three acids with soil microorganisms using them as a source of carbon and energy. Biostimulation was confirmed by soil biochemical studies which showed an increase in enzymatic activities, such as dehydrogenase and phosphatase, lactic and citric acids being those that produced the greatest biostimulation. With regard to microbiota composition, amplicon sequencing of the 16S rRNA gene showed changes in the structure of soil microbial communities. Applying OAs produced a decrease in richness and diversity indices, inducing specific changes in the structure of the microbiological communities. Applying lactic acid induced rapid changes in microbiota composition at both phylum and family taxonomic levels, favoring the proliferation of microorganisms involved in its degradation and soil fertility, such as the genus Bacillus and the family Micrococcaceae. Once the lactic acid was degraded, the biodiversity tended to return to similar phyla, but specific distinctive families and genera remained, leaving a pattern of induction of taxa described as plant growth-promoting bacteria (PGPB), such as the Sinorhizobium and Lysobacter genera, and the Pseudomonaceae family. Similar behavior was found with citric acid, which favored the proliferation and dominance of microorganisms of the Clostridiaceae family, involved in its degradation, as well as microorganisms of both the Micrococcaceae and Pseudomonadaceae families which were found on day 7, leaving a similar pattern of induction as that found after the mineralization of lactic acid. On the other hand, oxalic acid induced long-lasting changes in the bacterial community composition. This was characterized by an increase in the proportion of the Burkholderiales order, which includes microorganisms involved in the degradation of this acid and microorganisms described as PGPB. This study presents evidence supporting the use of OAs as potential soil fertility inducers, due both to their effects in enhancing the dominance of taxa described as PGPB and to their stimulating soil microbial activity.

Streptomyces pactum combined with manure compost alters soil fertility and enzymatic activities, enhancing phytoextraction of potentially toxic metals (PTMs) in a smelter-contaminated soil

The effect of manure compost alone and combined with Streptomyces pactum (Act12) applied in the smelter-contaminated soil was investigated. The soil fertility, enzymatic activities, potentially toxic metals (PTMs) solubility, and phytoremediation efficiency of potherb mustard (Brassica juncea, Coss.) were assessed. Results showed that the application of compost reduced the soil pH, while significantly increased the soil electrical conductivity (EC) (7.0 folds), available phosphorus (AP) (10.8 folds), available potassium (AK) (2.81 folds), dissolved organic carbon (DOC) (5.22 folds), organic matter (OM) (4.93 folds), together with soil enzymatic activities viz. urease (UR) (4.39 folds), dehydrogenase (DEH) (45.0 folds) and alkaline phosphatase (ALP) (123.9 folds) in comparison with control. The inoculation of Act12 increased AP, AK, DOC, OM and UR values, but reduced EC, DEH and ALP values compared to corresponding lone compost amendment. Additionally, Act12 solubilized PTMs (Cd and Zn) in the soil, and accordingly enhanced the PTMs uptake in the plant. The phytoextraction indices viz. biological concentration factor (BCF), translocation factor (TF) and metal extraction amount (MEA) indicated that compost and Act12 had a synergistic role in enhancing the phytoremediation efficiency, among which MEA values of Cd and Zn maximally increased by 9.64 and 11.4 folds, respectively, compared to control. Redundancy analysis (RDA) indicated that phytoextraction indices correlated well with soil parameters. Our results suggested that manure compost associated with Act12 is a potential strengthening strategy in phytoremediation of PTMs contaminated soil.