Application of Bioorganic Fertilizer Significantly Increased Apple Yields and Shaped Bacterial Community Structure in Orchard Soil

Limited dependence on soil nitrogen fixation as subtropical forests develop

Soil nitrogen (N) fixation, driven by microbial reactions, is critical to support the entrance of nitrogen in nutrient poor and pioneer ecosystems. However, how and why N fixation and soil diazotrophs evolve as forests develop remain poorly understood. Here, we used a 60-year forest rewilding chronosequence and found that soil N fixation activity gradually decreased with increasing forest age, experiencing dramatic drops of 64.8% in intermediate stages and 93.0% in the oldest forests. Further analyses revealed loses in diazotrophic diversity and a significant reduction in the abundance of important diazotrophs (e.g., Desulfovibrio and Pseudomonas) as forest develops. This reduction in N fixation, and associated shifts in soil microbes, was driven by acidification and increases in N content during forest succession. Our results provide new insights on the life history of one of the most important groups of soil organisms in terrestrial ecosystems, with consequences for understanding the buildup of nutrients as forest soil develops.

Bacterial community shifts of commercial apples, oranges, and peaches at different harvest points across multiple growing seasons

Assessing the microbes present on tree fruit carpospheres as the fruit enters postharvest processing could have useful applications, as these microbes could have a major influence on spoilage, food safety, verification of packing process controls, or other aspects of processing. The goal of this study was to establish a baseline profile of bacterial communities associated with apple (pome fruit), peach (stone fruit), and Navel orange (citrus fruit) at harvest. We found that commercial peaches had the greatest bacterial richness followed by oranges then apples. Time of harvest significantly changed bacterial diversity in oranges and peaches, but not apples. Shifts in diversity varied by fruit type, where 70% of the variability in beta diversity on the apple carposphere was driven by the gain and loss of species (i.e., nestedness). The peach and orange carposphere bacterial community shifts were driven by nearly an even split between turnover (species replacement) and nestedness. We identified a small core microbiome for apples across and between growing seasons that included only Methylobacteriaceae and Sphingomonadaceae among the samples, while peaches had a larger core microbiome composed of five bacterial families: Bacillaceae, Geodermtophilaceae, Nocardioidaceae, Micrococcaeceae, and Trueperaceae. There was a relatively diverse core microbiome for oranges that shared all the families present on apples and peaches, except for Trueperaceae, but also included an additional nine bacterial families not shared including Oxalobacteraceae, Cytophagaceae, and Comamonadaceae. Overall, our findings illustrate the important temporal dynamics of bacterial communities found on major commercial tree fruit, but also the core bacterial families that constantly remain with both implications being important entering postharvest packing and processing.

Research and experiment on the trenching performance of orchard trenching device

Aiming at the mismatch between the cutter combination of the furrowing device and the operating parameters, and resulting in low quality of furrowing and other problems, the theoretical analysis of the furrowing cutting operation is carried out and the influence law of the furrowing parameters on the trajectory, performance and quality of the furrowing movement is obtained. The influence of trenching parameters on trenching trajectory, performance and quality was obtained. The response surface method was applied to design and carry out field experiments. With the increase of cutter head speed and forward speed, the width and depth of trenching and the thickness of floating soil at the bottom of trenching decreased first and then increased, while the operation power consumption presented the increasing trend gradually. The optimization model of trenching performance quality was constructed to obtain the optimal parameter combination of influencing factors. Field experiments were carried out to verify the optimization results. The optimisation results were verified through field tests, which showed that the average depth of furrowing was 472 mm, the width was 332 mm, the thickness of soil return was 134 mm, and the operating power consumption was 19.95 kW. The results showed that the average depth of furrowing was 472 mm, the width was 332 mm, and the thickness of soil return was 134 mm. The optimization model could meet the operation quality indexes, and provide a theoretical basis for the design of the disc subsection cutting trenching device to select the operation parameter combination required by low power consumption and deep trenching.

Synergistic effects of earthworms and cow manure under reduced chemical fertilization modified microbial community structure to mitigate continuous cropping effects on Chinese flowering cabbage

The substitution of chemical fertilizers with organic fertilizers is a viable strategy to enhance crop yield and soil quality. In this study, the aim was to investigate the changes in soil microorganisms, soil chemical properties, and growth of Chinese flowering cabbage under different fertilization treatments involving earthworms and cow manure. Compared with the control (100% chemical fertilizer), CE (30% reduction in chemical fertilizer + earthworms) and CFE (30% reduction in chemical fertilizer + cow dung + earthworms) treatments at soil pH 8.14 and 8.07, respectively, and CFC (30% reduction in chemical fertilizer + cow manure) and CFE treatments increased soil organic matter (SOM), total nitrogen (TN), available nitrogen (AN), and available potassium (AK) contents. Earthworms and cow manure promoted the abundance of Bacillus and reduced that of the pathogens Plectosphaerella and Gibberella. The mantle test revealed that pH was not correlated with the microbial community. Random forest analysis verified that AN, SOM, and TN were important factors that jointly influenced bacterial and fungal diversity. Overall, the synergistic effect of earthworms and cow manure increased soil fertility and microbial diversity, thereby promoting the growth and development of Chinese flowering cabbage. This study enhanced the understanding of how bioregulation affects the growth and soil quality of Chinese flowering cabbage, and thus provided a guidance for the optimization of fertilization strategies to maximize the yield and quality of Chinese flowering cabbage while reducing environmental risks.

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

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

Bio-organic fertilizer promoted phytoremediation using native plant leymus chinensis in heavy Metal(loid)s contaminated saline soil

Heavy metal(loid)s (HMs) contaminated saline soil appeared around the world, however, remediation regarding these collected from field conditions remains unknown. Native plants cultivation and bio-organic fertilizer (BOF) application were two efficient tools for soil amelioration. Herein, a pot experiment was conducted to examine the feasibility of a native plant (Leymus chinensis) for phytoremediation, and investigate the impacts of lignite based bio-organic fertilizer (LBOF) and manure based bio-organic fertilizer (MBOF) on phytoremediation of the soil contaminated by Pb, Cd, As, Zn, Cu, Ca²⁺, and SO₄^2-. The results demonstrated the effectiveness of L. chinensis and highlighted the positive impacts of BOF according to the improved plant growth, HMs phytostabilization, salt removal, and soil properties. LBOF and MBOF changed soil microbiome to assist phytoremediation in addition to physiological modulation. Having enhanced fungal and bacterial richness respectively, LBOF and MBOF recruited various plant growth promoting rhizobacteria with different functions, and shifted microbial co-occurrence networks and keystone taxa towards these different but beneficial forms. Structural equation models comprehensively reveled the strategy discrepancy of LBOF and MBOF to regulate the plant biomass, HMs uptake, and soil salt. In summary, L. chinensis coupled with BOF, especially LBOF, was a effective strategy to remediate HMs contaminated saline soil.

Tree Root-Associated Microbial Communities Depend on Various Floor Management Systems in an Intensive Apple (Malus × domestica Borkh.) Orchard

Regenerative 3agriculture prioritizes soil health to build up organic soil carbon and nitrogen stocks while supporting the active and diverse soil biota that is a prerequisite for maintaining crop productivity and quality in sustainable food production. This study aimed at unravelling the impact of organic and inorganic soil maintenance systems in a 'Red Jonaprince' apple (Malus × domestica Borkh.) orchard on soil microbiota biodiversity and soil physico-chemical properties. During our study, we compared seven floor management systems in terms of microbial community diversity. Fungal and bacterial communities on all taxonomic levels differed largely between systems that augmented organic matter (organic) and other tested inorganic regimes. The dominant phylum of the soil in all management systems was Ascomycota. The operational taxonomic units (OTUs) within the Ascomycota were largely identified as members of Sordariomycetes, followed by Agaricomycetes, and both dominated in organic systems versus inorganic. The most prominent phyla, Proteobacteria, accounted for 43% of all assigned bacteria OTUs. Gammaproteobacteria, Bacteroidia, and Alphaproteobacteria were predominant in organic samples, while Acidobacteriae, Verrucomicrobiae, and Gemmatimonadetes were more abundant in inorganic mulches.

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.

The effects of cultivation patterns and nitrogen levels on fertility and bacterial community characteristics of surface and subsurface soil

The cropping system affects the physicochemical property and microbial community of paddy soil. Previous research mostly focused on the study of soil 0-20 cm underground. However, there may be difference in the laws of nutrient and microorganism distribution at different depths of arable soil. In surface (0-10 cm) and subsurface (10-20 cm) soil, a comparative analysis including soil nutrients, enzymes, and bacterial diversity was carried out between the organic and conventional cultivation patterns, low and high nitrogen levels. Analysis results suggested that under the organic farming pattern, the contents of total nitrogen (TN), alkali-hydrolyzable nitrogen (AN), available phosphorus (AP), and soil organic matter (SOM) as well as alkaline phosphatase and sucrose activity increased in surface soil, but the SOM concentration and urease activity decreased in subsurface soil. A moderate reduction of nitrogen applied to soil could enhance soil enzyme activity. It was demonstrated by α diversity indices that high nitrogen levels remarkably undermined soil bacterial richness and diversity. Venn diagrams and NMDS analysis manifested great difference in bacterial communities and an apparent clustering tendency under different treatment conditions. Species composition analysis indicated that the total relative abundance of Proteobacteria, Acidobacteria, and Chloroflexi retained stable in paddy soil. LEfSe results revealed that a low nitrogen organic treatment could elevate the relative abundance of Acidobacteria in surface soil and Nitrosomonadaceae in subsurface soil, thereby tremendously optimizing the community structure. Moreover, Spearman's correlation analysis was also performed, which proved the significant correlation of diversity with enzyme activity and AN concentration. Additionally, redundancy analysis disclosed that the Acidobacteria abundance in surface soil and Proteobacteria abundance in subsurface soil exerted conspicuous influence on environmental factors and the microbial community structure. According to the findings of this study, it was believed that reasonable nitrogen application together with an organic agriculture cultivation system could effectively improve soil fertility in Gaoyou City, Jiangsu Province, China.

Predicting the Postmortem Interval Based on Gravesoil Microbiome Data and a Random Forest Model

The estimation of a postmortem interval (PMI) is particularly important for forensic investigations. The aim of this study was to assess the succession of bacterial communities associated with the decomposition of mouse cadavers and determine the most important biomarker taxa for estimating PMIs. High-throughput sequencing was used to investigate the bacterial communities of gravesoil samples with different PMIs, and a random forest model was used to identify biomarker taxa. Redundancy analysis was used to determine the significance of environmental factors that were related to bacterial communities. Our data showed that the relative abundance of Proteobacteria, Bacteroidetes and Firmicutes showed an increasing trend during decomposition, but that of Acidobacteria, Actinobacteria and Chloroflexi decreased. At the genus level, Pseudomonas was the most abundant bacterial group, showing a trend similar to that of Proteobacteria. Soil temperature, total nitrogen, NH₄⁺-N and NO₃^--N levels were significantly related to the relative abundance of bacterial communities. Random forest models could predict PMIs with a mean absolute error of 1.27 days within 36 days of decomposition and identified 18 important biomarker taxa, such as Sphingobacterium, Solirubrobacter and Pseudomonas. Our results highlighted that microbiome data combined with machine learning algorithms could provide accurate models for predicting PMIs in forensic science and provide a better understanding of decomposition processes.

Organomineral fertilizer application enhances Perilla frutescens nutritional quality and rhizosphere microbial community stability in karst mountain soils

Introduction

Applications of organomineral fertilizer (OMF) are important measures for developing organic agriculture in karst mountain areas. However, the influence of OMF on the structure and function of soil microbial diversity and their relationship with crop yield and quality are still unclear.

Methods

Based on soil science, crop science, and high-throughput sequencing methods, we investigated the changes of rhizosphere soil microbial communities of Perilla frutescens under different fertilization measures. Then, the relationship between P. frutescens yield and quality with soil quality was analyzed.

Results

The results showed that the addition of OMF increased the amount of total carbon and total potassium in soil. OF, especially OMF, improved P. frutescens yield and quality (e.g., panicle number per plant, main panicle length, and unsaturated fatty acid contents). Both OF and OMF treatments significantly increased the enrichment of beneficial microorganism (e.g., Bacillus, Actinomadura, Candidatus_Solibacter, Iamia, Pseudallescheria, and Cladorrhinum). The symbiotic network analysis demonstrated that OMF strengthened the connection among the soil microbial communities, and the community composition became more stable. Redundancy analysis and structural equation modeling showed that the soil pH, available phosphorus, and available potassium were significantly correlated with soil microbial community diversity and P. frutescens yield and quality.

Discussion

Our study confirmed that OMF could replace CF or common OF to improve soil fertility, crop yield and quality in karst mountain soils.

Bioorganic fertilizer promotes pakchoi growth and shapes the soil microbial structure

As a functional probiotic, Bacillus subtilis can promote crop growth and improve nutrient utilization by various mechanisms, so it has been made into bioorganic fertilizer as a replacement for chemical fertilizer. However, the effects of B. subtilis bioorganic fertilizer application on the yield and quality of commercial crops of Brassica chinensis L., the soil physicochemical properties and the microflora have not been clarified. In this study, pot experiments were conducted using Brassica chinensis L. plants with four fertilization treatments: control without fertilization (CK), chemical fertilizer (CF), organic fertilizer (OF), and bioorganic fertilizer containing B. subtilis (BF). After 30 days of pot experiment, the results showed that BF efficiently improved plant height and biomass (1.20- and 1.93-fold, respectively); as well as significantly increasing soil available potassium and pH value. Using high-throughput sequencing, we examined the bacterial and fungal communities in the soil, and found that their diversity was remarkablely reduced in the BF treatment compared to CK group. A principal coordinate analysis also showed a clear separation of bacterial and fungal communities in the BF and CK groups. After application of B. subtilis bioorganic fertilizer, some beneficial bacteria (such as Bacillus and Ammoniphilus) and fungi (Trichoderma and Mortierella) were enriched. A network analysis indicated that bacteria were the dominant soil microbes and the presence of B. subtilis stimulated the colonization of beneficial microbial communities. In addition, predictive functional profiling demonstrated that the application of bioorganic fertilizer enhanced the function of mineral element metabolism and absorption and increased the relative abundance of saprotrophs. Overall, the application of bioorganic fertilizer effectively changed the soil microflora, improved the soil available potassium and pH value, and boosted the yield of Brassica chinensis L. This work has valuable implications for promoting the safe planting of facility vegetables and the sustainable development of green agriculture.

Effects of Trichoderma harzianum biofertilizer on growth, yield, and quality of Bupleurum chinense

The use of chemical fertilizers and pesticides led to a decline in the quality and yield of Bupleurum chinense. The aim of this study was to determine the effects of Trichoderma harzianum biofertilizer on the growth, yield, and quality of radix bupleuri and microbial responses. The results showed that T. harzianum biofertilizer promoted the growth of B. chinense and increased the yield and quality of radix bupleuri. In addition, it increased the contents of NH4 +-N, NO3 --N, available K, and available P and increased the activities of sucrase and catalase in the rhizosphere soil. High-throughput analysis showed that the dominant bacteria in the rhizosphere were Proteobacteria (28%), Acidobacteria (23%), and Actinobacteria (17%), whereas the dominant fungi were Ascomycota (49%), Zygomycota (30%), and Basidiomycota (6%). After the application of T. harzianum biofertilizer, the abundance of Proteobacteria and Actinobacteria (relative to total bacteria) and Ascomycota and Basidiomycota (relative to total fungi) increased, but the relative abundance of Acidobacteria decreased. Canonical correlation analysis (CCA) showed that the relative abundance of Pseudarthrobacter, Streptomyces, Rhizobium, Nocardioides, Minimedusa, and Chaetomium were positively correlated with NO3 --N, NH4 +-N, available K, available P, sucrase, and catalase in microbial communities, whereas Aeromicrobium and Mortierella were positively correlated with soil organic matter and urease. These results suggest that T. harzianum biofertilizer could significantly improve the yield and quality of radix bupleuri by changing the structure of soil microbial flora and soil enzyme activity. Therefore, it could be recommended for commercial scale production of Bupleurum.

Changes in litter input exert divergent effects on the soil microbial community and function in stands of different densities

Soil microbial communities influence soil biogeochemical cycling by affecting the production of extracellular enzymes and the release of carbon dioxide. Changes in litter input or stand density due to thinning can affect soil microbial communities and their function by altering soil biochemical properties. However, it is unclear how or to what extent different amounts of litter input affect soil microbial communities and their function in forest stands with different densities. Therefore, we simulated litter removal, 50 % litter reduction, normal litter input, and double litter increase under field conditions by applying different amounts of litter to soils with different stand densities in the laboratory. We then measured soil biochemical properties, microbial communities, enzyme activity, and respiration rate. Our results revealed that the responses of soil dissolved organic carbon and total nitrogen to litter input were more pronounced in the high-density forest stand with poor soil than in the low-density forest stand with nutrient-rich soil, which was mainly reflected in that the addition of litter significantly decreased the concentration of dissolved organic carbon while increasing the content of total nitrogen in the soil of the high-density forest stand. In comparison to the soil carbon component, the nitrogen component of the soil was more affected by stand density. The responses of soil fungal and bacterial communities to leaf litter treatment varied with stand density, as reflected primarily in changes in the relative abundances of Ascomycota, unclassified_K_fungi, and Proteobacteria, and changes in the relative abundances of their functional groups (ectomycorrhizal fungi, saprophytic fungi, pathogens, parasites, and bacteria involved in the nitrogen cycle). Soil fungal community responses to changes in litter input are more sensitive in the high-density forest with nutrient-poor soil than in the low-density forest stand. Furthermore, litter input inhibited the activities of soil β-glucuronidase, N-acetyl-β-d-glucosaminidase, and acid phosphatase more strongly in the low-density forest stand. Litter manipulation primarily affected enzymatic activity in the high-density forest stand by changing the diversity and composition of the soil fungal community. However, in the low-density forest stand, litter treatment affected soil enzyme activity, primarily through changes in soil bacterial and fungal community composition, as well as soil respiration through changes in bacterial richness (Chao 1) and community composition. We conclude that how the change in litter input impacts the soil microbial community and its function, or the magnitude of the effects, is largely dependent on soil quality. Relationships among soil variables, microbial communities, and function differ between stand densities. Our study contributes to an enhanced understanding of the impact of changes in litter input due to climate change or anthropogenic activities on soil biogeochemical cycles and can also guide rationally formulating forest management approaches to improve microbial function under climate change.

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.

WGCNA analysis revealing molecular mechanism that bio-organic fertilizer improves pear fruit quality by increasing sucrose accumulation and reducing citric acid metabolism

It's been long known that the application of organic fertilizer (OF) and bio-organic fertilizer (BF) which containing beneficial microorganisms to pear trees can both significantly improve fruit quality and yield. In order to reveal the mechanism of BF and OF regulating fruit growth and quality in pear, the effects of BF and OF on the photosynthetic characteristics and the accumulation of major sugars and organic acids of the pear fruit were quantified compared with chemical fertilizer (CF). Additionally, the molecular mechanisms regulating pear fruit development and quality were studied through transcriptome analysis. The three treatments were conducted based on the same amounts of nitrogen supply. The results showed that compared with CF, BF and OF treatments increased the fruit yield, and also significantly improved the photosynthesis efficiency in pear. BF and OF both significantly increased the sucrose content but significantly decreased the fructose and glucose content within the pear fruit. The amount of malic acid was significantly higher in OF treatment. Compared with CF and OF, BF significantly increased the sugar-acid ratio and thus improved the fruit quality. Transcriptome analysis and weighted correlation network analysis (WGCNA) revealed that the sugar metabolism of fruits applied with the BF was enhanced compared with those applied with CF or OF. More specifically, the expression of SDH (Sorbitol dehydrogenase) was higher in BF, which converts sorbitol into fructose. For both of the OF and BF, the transcript abundance of sugar transporter genes was significantly increased, such as SOT (Sorbitol transporter), SUT14 (Sugar transport 14), UDP-GLUT4 (UDP-glucose transporter 4), UDP-SUT (UDP-sugar transporter), SUC4 (Sucrose transport 4), SUT7 (Sugar transporter 7), SWEET10 and SWEET15 (Bidirectional sugar transporter), which ensures sugar transportation. The genes involved in organic acid metabolism showed decreased transcripts abundance in both BF and OF treatments, such as VAP (Vesicle-associated protein) and cyACO (Cytosolic aconitase), which reduce the conversion from succinate to citric acid, and decrease the conversion from citric acid to malic acid in the TCA cycle (Tricarboxylic Acid cycle) through Pept6 (Oligopeptide transporter). In conclusion, the application of BF and OF improved fruit quality by regulating the expression of sugar and organic acid metabolism-related genes and thus altering the sugar acid metabolism. Both BF and OF promote sucrose accumulation and citric acid degradation in fruits, which may be an important reason for improving pear fruit quality. The possible mechanism of bio-organic fertilizer to improve fruit quality was discussed.

Spatio-temporal variation in the root-associated microbiota of orchard-grown apple trees

BACKGROUND

The root-associated microbiome has been of keen research interest especially in the last decade due to the large potential for increasing overall plant performance in agricultural systems. Studies about spatio-temporal variation of the root-associated microbiome focused so far primarily on community-compositional changes of annual plants, while little is known about their perennial counterparts. The aim of this work was to get deep insight into the spatial patterns and temporal dynamics of the root associated microbiota of apple trees.

RESULTS

The bacterial community structure in rhizospheric soil and endospheric root material from orchard-grown apple trees was characterized based on 16S rRNA gene amplicon sequencing. At the small scale, the rhizosphere and endosphere bacterial communities shifted gradually with increasing root size diameter (PERMANOVA R²-values up to 0.359). At the larger scale, bulk soil heterogeneity introduced variation between tree individuals, especially in the rhizosphere microbiota, while the presence of a root pathogen was contributing to tree-to-tree variation in the endosphere microbiota. Moreover, the communities of both compartments underwent seasonal changes and displayed year-to-year variation (PERMANOVA R²-values of 0.454 and 0.371, respectively).

CONCLUSIONS

The apple tree root-associated microbiota can be spatially heterogeneous at field scale due to soil heterogeneities, which particularly influence the microbiota in the rhizosphere soil, resulting in tree-to-tree variation. The presence of pathogens can contribute to this variation, though primarily in the endosphere microbiota. Smaller-scale spatial heterogeneity is observed in the rhizosphere and endosphere microbiota related to root diameter, likely influenced by root traits and processes such as rhizodeposition. The microbiota is also subject to temporal variation, including seasonal effects and annual variation. As a consequence, responses of the tree root microbiota to further environmental cues should be considered in the context of this spatio-temporal variation.

Organic mulch can suppress litchi downy blight through modification of soil microbial community structure and functional potentials

BACKGROUND

Organic mulch is an important management practice in agricultural production to improve soil quality, control crop pests and diseases and increase the biodiversity of soil microecosystem. However, the information about soil microbial diversity and composition in litchi plantation response to organic mulch and its attribution to litchi downy blight severity was limited. This study aimed to investigate the effect of organic mulch on litchi downy blight, and evaluate the biodiversity and antimicrobial potential of soil microbial community of litchi plantation soils under organic mulch.

RESULTS

Organic mulch could significantly suppress the disease incidence in the litchi plantation, and with a reduction of 37.74% to 85.66%. As a result of high-throughput 16S rRNA and ITS rDNA gene illumine sequencing, significantly higher bacterial and fungal community diversity indexes were found in organic mulch soils, the relative abundance of norank f norank o Vicinamibacterales, norank f Vicinamibacteraceae, norank f Xanthobacteraceae, Unclassified c sordariomycetes, Aspergillus and Thermomyces were significant more than that in control soils. Isolation and analysis of antagonistic microorganism showed that 29 antagonistic bacteria strains and 37 antagonistic fungi strains were unique for mulching soils.

CONCLUSIONS

Thus, we believe that organic mulch has a positive regulatory effect on the litchi downy blight and the soil microbial communities, and so, is more suitable for litchi plantation.

Organic amendments alleviate early defoliation and increase fruit yield by altering assembly patterns and of microbial communities and enzymatic activities in sandy pear (Pyrus pyrifolia)

Severe early defoliation has become an important factor restricting the development of the pear industry in southern China. However, the assembly patterns of microbial communities and their functional activities in response to the application of bioorganic fertilizer (BIO) or humic acid (HA) in southern China’s pear orchards remain poorly understood, particularly the impact on the early defoliation of the trees. We conducted a 3-year field experiment (2017–2019) in an 18-year-old ‘Cuiguan’ pear orchard. Four fertilization schemes were tested: local custom fertilization as control (CK), CK plus HA (CK-HA), BIO, and BIO plus HA (BIO-HA). Results showed that BIO and BIO-HA application decreased the early defoliation rate by 50–60%, and increased pear yield by 40% compared with the CK and CK-HA treatments. The BIO and BIO-HA application significantly improved soil pH, available nutrient content, total enzyme activity and ecosystem multifunctionality, and also changed the structure of soil bacterial and fungal communities. The genus Acidothermus was positively correlated with the early defoliation rate, while the genus Rhodanobacter was negatively correlated. Additionally, random forest models revealed that the early defoliation rate could be best explained by soil pH, ammonium content, available phosphorus, and total enzyme activity. In conclusion, application of BIO or BIO mixed with HA could have assembled distinct microbial communities and increased total enzyme activity, leading to significant improvement of soil physicochemical traits. The increased availability of soil nutrient thus changed leaf nutrient concentrations and alleviated the early defoliation rate of pear trees in acid red soil in southern China.

Effect of Two Kinds of Fertilizers on Growth and Rhizosphere Soil Properties of Bayberry with Decline Disease

Decline disease causes severe damage to bayberry. However, the cause of this disease remains unclear. Interestingly, our previous studies found that the disease severity is related with the level of soil fertilizer. This study aims to explore the effect and mechanism of compound fertilizer (CF) and bio-organic fertilizer (OF) in this disease by investigating the vegetative growth, fruit characters, soil property, rhizosphere microflora and metabolites. Results indicated that compared with the disease control, CF and OF exhibited differential effect in plant healthy and soil quality, together with the increase in relative abundance of Burkholderia and Mortierella, and the reduction in that of Rhizomicrobium and Acidibacter, Trichoderma, and Cladophialophora reduced. The relative abundance of Geminibasidium were increased by CF (251.79%) but reduced by OF (13.99%). In general, the composition of bacterial and fungal communities in rhizosphere soil was affected significantly at genus level by exchangeable calcium, available phosphorus, and exchangeable magnesium, while the former two variables had a greater influence in bacterial communities than fungal communities. Analysis of GC-MS metabonomics indicated that compared to the disease control, CF and OF significantly changed the contents of 31 and 45 metabolites, respectively, while both fertilizers changed C5-branched dibasic acid, galactose, and pyrimidine metabolic pathway. Furthermore, a significant correlation was observed at the phylum, order and genus levels between microbial groups and secondary metabolites of bayberry rhizosphere soil. In summary, the results provide a new way for rejuvenation of this diseased bayberry trees.

Earthworm activity optimized the rhizosphere bacterial community structure and further alleviated the yield loss in continuous cropping lily (Lilium lancifolium Thunb.)

The soil microbial community plays a vital role in the biogeochemical cycles of bioelements and maintaining healthy soil conditions in agricultural ecosystems. However, how the soil microbial community responds to mitigation measures for continuous cropping obstacles remains largely unknown. Here we examined the impact of quicklime (QL), chemical fungicide (CF), inoculation with earthworm (IE), and a biocontrol agent (BA) on the soil microbial community structure, and the effects toward alleviating crop yield decline in lily. High-throughput sequencing of the 16S rRNA gene from the lily rhizosphere after 3 years of continuous cropping was performed using the Illumina MiSeq platform. The results showed that Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Chloroflexi and Gemmatimonadetes were the dominant bacterial phyla, with a total relative abundance of 86.15-91.59%. On the other hand, Betaproteobacteriales, Rhizobiales, Myxococcales, Gemmatimonadales, Xanthomonadales, and Micropepsales were the dominant orders with a relative abundance of 28.23-37.89%. The hydrogen ion concentration (pH) and available phosphorus (AP) were the key factors affecting the structure and diversity of the bacterial community. The yield of continuous cropping lily with using similar treatments decreased yearly for the leaf blight, but that of IE was significantly (p < 0.05) higher than with the other treatments in the same year, which were 17.9%, 18.54%, and 15.69% higher than that of blank control (CK) over 3 years. In addition, IE significantly (p < 0.05) increased organic matter (OM), available nitrogen (AN), AP, and available potassium (AK) content in the lily rhizosphere soil, optimized the structure and diversity of the rhizosphere bacterial community, and increased the abundance of several beneficial bacterial taxa, including Rhizobiales, Myxococcales, Streptomycetales and Pseudomonadales. Therefore, enriching the number of earthworms in fields could effectively optimize the bacterial community structure of the lily rhizosphere soil, promote the circulation and release in soil nutrients and consequently alleviate the loss of continuous cropping lily yield.

The Damage Caused by Decline Disease in Bayberry Plants through Changes in Soil Properties, Rhizosphere Microbial Community Structure and Metabolites

Decline disease causes serious damage and rapid death in bayberry, an important fruit tree in south China, but the cause of this disease remains unclear. The aim of this study was to investigate soil quality, microbial community structure and metabolites of rhizosphere soil samples from healthy and diseased trees. The results revealed a significant difference between healthy and diseased bayberry in soil properties, microbial community structure and metabolites. Indeed, the decline disease caused a 78.24% and 78.98% increase in Rhizomicrobium and Cladophialophora, but a 28.60%, 57.18%, 38.84% and 68.25% reduction in Acidothermus, Mortierella, Trichoderma and Geminibasidium, respectively, compared with healthy trees, based on 16S and ITS amplicon sequencing of soil microflora. Furthermore, redundancy discriminant analysis of microbial communities and soil properties indicated that the main variables of bacterial and fungal communities included pH, organic matter, magnesium, available phosphorus, nitrogen and calcium, which exhibited a greater influence in bacterial communities than in fungal communities. In addition, there was a high correlation between the changes in microbial community structure and secondary metabolites. Indeed, GC-MS metabolomics analysis showed that the healthy and diseased samples differed over six metabolic pathways, including thiamine metabolism, phenylalanine-tyrosine-tryptophan biosynthesis, valine-leucine-isoleucine biosynthesis, phenylalanine metabolism, fatty acid biosynthesis and fatty acid metabolism, where the diseased samples showed a 234.67% and 1007.80% increase in palatinitol and cytidine, respectively, and a 17.37-8.74% reduction in the other 40 metabolites compared to the healthy samples. Overall, these results revealed significant changes caused by decline disease in the chemical properties, microbiota and secondary metabolites of the rhizosphere soils, which provide new insights for understanding the cause of this bayberry disease.

The Impacts of Field Management on Soil and Tea Root Microbiomes

Due to the importance of microbes in soil health and crop production, manipulation of microbiomes provides a new strategy for improving crop growth and agricultural ecosystems. Current understanding is limited regarding the responses of soil and crop endophytic microbiomes to field management and microbiome programming. In this study, we investigated soil and tea root bacterial communities under conventional and organic cropping systems using 16S rRNA gene sequencing. A significant difference in soil and root bacterial community structure was observed under different field managements, leading to 43% and 35% variance, respectively. We also identified field management-sensitive species both in soils and tea roots that have great potential as bioindicators for bacterial microbiome manipulation. Moreover, through functional profile predictions of microbiomes, xenobiotics degradation in soil bacterial communities is enriched in organic farms, suggesting that biodegradation capabilities are enhanced under organic cropping systems. Our results demonstrate the effects of field management on both soil and tea root bacterial microbiomes and provide new insights into the reprogramming of microbial structures.

A critical assessment on the short-term response of microbial relative composition in a mine tailings soil amended with biochar and manure compost

Phytomanagement of tailings requires the use of soil conditioners to favour plant establishment, but their benefits on soil microbial composition need to be assessed. The goal of this work was to evaluate the effect of two organic amendments, manure compost and biochar, on soil bacterial and fungal composition at metallic mine tailings. The addition of compost caused stronger effects in most of soil parameters and microbial composition than biochar, especially at the initial stage of the experiment. However, the higher dependence on labile organic carbon for some bacterial groups at the treatments containing compost determined their decay along time (Flavobacteriales, Sphingobacteriales) and the appearance of other taxa more dependent on recalcitrant organic matter (Xanthomonadales, Myxococcales). Biochar favoured bacterial decomposers (Actinomycetales) specialised in high lignin and other recalcitrant carbon compounds. Unlike bacteria, only a few fungal orders increased their relative abundances in the treatments containing compost (Sordariales and Microascales) while the rest showed a decrease or remained unaltered. The mix biochar-compost may result the best option to support a more diverse microbial population in terms of soil functionality that is able to decompose both labile and recalcitrant carbon compounds. This may favour the resilience of the system against environmental stressors.

Long-term effects of liquid swine manure land surface application in an apple orchard field on soil bacterial community and heavy metal contents in apple (Malus pumila Mill.)

This study investigated the impact of liquid swine manure (LSM) land surface application in an apple orchard on soil health and copper (Cu) and zinc (Zn) in soil and apple. Three apple plots were selected, among which two for LSM application for 5 (AY5) and 11 (AY11) years with different application rates, a long-term inorganic fertilizer application plot as the control treatment (AY0). The soil and apple samples were collected for analysis of soil physicochemical properties, bacterial diversity and abundance, and the contents of Cu and Zn in soil and apple. Results showed that the LSM application significantly increased the concentration of soil nutrients with the highest in AY5, which has a high application rate of LSM. After 5 or 11 years applied, the content of total nitrogen (TN) in AY5 and AY11 increased by 125.2% and 96.7%, total phosphorus (TP) increased by 167.6% and 148.6%, and soil organic matter (SOM) increased by 180.7% and 120.6%, respectively. The AY5 treatment significantly lowered OTUs and decreased Shannon index trend with a negative correlation between soil organic matter and Shannon index. The six predominant bacterial phyla in different treatments were similar, but the LSM application significantly increased the abundance of Chloroflexi and Firmicutes. However, the abundance of Actinobacteria and Acidobacteria significantly decreased in AY5 as compared to control treatment, followed by a significant positive correlation between the abundance of Acidobacteria and soil pH. Besides, LSM application significantly increased the contents of soil Cu, Zn, and apple Zn. Overall, the results illustrated that appropriate application rate of LSM can effectively improve apple orchard soil quality and bacterial community structure, but it will increase the risk of heavy metal accumulation in soil and apples.

Long-term cover crops improved soil phosphorus availability in a rain-fed apple orchard

The objective of this present study was to understand the distribution patterns of various forms of soil phosphorus (P) and the biotic and abiotic factors affecting the soil P fractions under long-term cover crops. Here, we investigated the characteristics of soil P forms, community structure of P-solubilizing bacteria (using 16S rRNA) and the related enzyme activity under clean tillage (CT), 14 years of white clover (WC, Trifolium repens L.) and orchard grass (OG, Dactylis glomerata L.) cover crops in a rain-fed apple orchard on the Weibei Loess Plateau, China. Relative to CT treatment, long-term cover crops enhanced the bioavailability of soil P by increasing the contents of total phosphorus (TP), microbial phosphorus (MBP), organic phosphorus (Po) and certain forms of inorganic phosphorus (e.g. Al-P, Ca₂-P, Ca₈-P and Fe-P) in the surface soil, in addition, WC treatment also increase the available P (AP) contents in the topsoil. A redundant analysis (RDA) showed that soil organic matter (SOM), NH₄⁺-N and pH were the key environmental factors affecting the morphological changes of soil P. In addition, the effects of long-term cover crops on soil P forms were mainly concentrated in the topsoil, and the WC treatment had a greater impact on soil P composition than the OG treatment. Interestingly, long-term cover crops effectively increased the abundances of P-solubilizing bacteria, such as Streptomyces, Sphingomonas, Nocardioides and Haliangium, and enhanced the alkaline phosphatase (ALP) activity. Overall, long-term cover crops were an effective strategy to activate soil P as they improve the soil environment.

Palmitic acid mediated change of rhizosphere and alleviation of Fusarium wilt disease in watermelon

Palmitic acid (PA) in root exudates or decaying residues can reduce the incidence of soil-borne diseases and promote the growth of some crop plants. However, the effects of PA on soil-borne pathogens and microbial communities are poorly understood. Here, we investigate the effects of PA on overall watermelon microbial communities and the populations of Fusarium oxysporum f.sp. niveum (Fon). The effects of PA on the mycelial growth and spore production of Fon were tested in vitro, while its effects on Fon, total bacteria and total fungi populations, and microbial communities were evaluated in a pot experiment. The results revealed that all test concentrations of PA inhibited Fon mycelia growth and spore production. The pot experiment showed that 0.5 mM and 1 mM PA reduced Fon but increased total bacteria populations, and 0.5 mM and 1 mM PA 0.5 mM and 1 mM PA promoted the change to a soil type of bacteria soil. Meanwhile, 0.5 mM PA and 1 mM PA altered the community composition of the rhizosphere microorganisms and reduced the relative abundance of two bacterial operational taxonomic units (OTUs) and the two fungal OTUs that were significantly (p < 0.01) related with disease severity and increased that of four bacterial OTUs and the two fungal that were highly significantly (p < 0.01) negatively correlated with the disease severity. These results suggest that application of PA decreased the populations of Fon, changed the rhizosphere microbial composition, reduced the disease severity of Fusarium wilt, and promoted the growth of watermelon.

Long-Term Manure Application Changes Bacterial Communities in Rice Rhizosphere and Arsenic Speciation in Rice Grains

Bioavailability and speciation of arsenic (As) are impacted by fertilization and bacteria in the rice rhizosphere. In this study, we investigated the effects of long-term manure application on As bioavailability, microbial community structure, and functional genes in a rice paddy field. The results showed that manure application did not affect total As in the soil but increased soluble As forms by 19%, increasing arsenite (As(III)) accumulation in rice grains and roots by 34 and 64% compared to a control. A real-time quantitative polymerase chain reaction (qPCR) and high-throughput sequencing analysis demonstrated that manure application increased the relative abundance of Rhizobium, Burkholderia, Sphingobium, and Sphingomonas containing arsenate reductase genes (arsC) in the rhizosphere soil, consistent with the 529% increase in arsC, which may have promoted arsenate (As(V)) reduction and increased As availability in pore water. In addition, manure application significantly altered the iron (Fe)-plaque microbial community structure and diversity. The microbes, particularly, Bradyrhizobium, Burkholderia, and Ralstonia, were mostly associated with As, Fe, and sulfur (S) cycles. This result was consistent with changes in the functional genes related to As, Fe, and S transformation. Although manure application promoted As(V) reduction (arsC) in Fe-plaque by 682%, it inhibited Fe and S reduction by decreasing Fe^III reduction bacteria (Geobacteraceae) and the sulfate-reducing gene (dsrA) abundance. Further, manure application changed the composition of the microbial community that contained the arsC gene. In short, caution needs to be excised even in the soil with a low As concentration as manure application increased As(III) accumulation in rice grains.

The Soil Nutrient Environment Determines the Strategy by Which Bacillus velezensis HN03 Suppresses Fusarium wilt in Banana Plants

Biological control agents (BCAs) are considered as one of the most important strategies for controlling Fusarium wilt, and bioorganic fertilizer, in particular, has been extensively investigated. However, little is known regarding how a biocontrol microorganism affects the suppression mechanisms when combined with different amendments. In this study, a pot experiment was performed using banana plants to investigate the different mechanisms by which the biocontrol bacterium Bacillus velezensis HN03 (isolated from our laboratory) and amendments suppress Fusarium wilt. The incidence of banana wilt was decreased under HN03 and was reduced further when HN03 was combined with compost, particularly wormcast. In the suppression of Fusarium wilt, HN03 was found to influence the soil environment in various ways. HN03 increased the peroxidase level, which improves plant defense, and was highest when combined with wormcast, being 69 times higher than when combined with cow dung compost. The high accumulation of Mg and P in the "HN03 + wormcast" and Zn and Mn in the "HN03 + cow dung" treatments was negatively correlated with disease incidence. Furthermore, HN03 re-established the microbial community destroyed by the pathogen and further increased the level of suppression in the wormcast. HN03 also enhanced the functional traits of the soil, including defensive mechanism-related traits, and these traits were further enhanced by the combination of HN03 + wormcast.

Metagenomic Analysis Exploring Taxonomic and Functional Diversity of Soil Microbial Communities in Sugarcane Fields Applied with Organic Fertilizer

Organic fertilizers are critically important to soil fertility, microbial communities, and sustainable agricultural strategies. We compared the effect of two fertilizer groups (organic+chemical fertilizer: OM, chemical fertilizer: CK) on sugarcane growth, by observing the difference in microbial communities and functions, soil nutrient status, and agronomic characters of sugarcane. The results showed that the sugar content and yield of sugarcane increased significantly under organic fertilizer treatment. We believe that the increased soil nutrient status and soil microorganisms are the reasons for this phenomenon. In addition, redundancy analysis (RDA) shows that the soil nutrient condition has a major impact on the soil microbial community. In comparison with CK, the species richness of Acidobacteria, Proteobacteria, Chloroflexi, and Gemmatimonadetes as well as the functional abundance of nucleotide metabolism and energy metabolism increased significantly in the OM field. Moreover, compared with CK, genes related to the absorption and biosynthesis of sulfate were more prominent in OM. Therefore, consecutive organic fertilizer application could be an effective method in reference to sustainable production of sugarcane.

Spatial variation of the soil bacterial community in major apple producing regions of China

AIMS

In China, apple production areas are largely from the coastal to inland areas and across varied climate zones. However, the relationship among soil micro-organisms, environmental factors and fruit quality has not been clearly confirmed in orchards. Here we attempted to identify the variation of soil bacteria in the main apple producing regions and reveal the relationship among climatic factor, soil properties, soil bacterial community and fruit quality.

METHODS AND RESULTS

Sixty soil samples were collected from six main apple producing areas in China. We examined the soil bacteria using bacterial 16S rRNA gene amplicon profiling. The results show that the soil bacterial diversity of apple orchards varied from the Bohai Bay Region to the Loess Plateau Region. Proteobacteria, Acidobacteria and Actinobacteria were the predominant taxa at the phylum level for all six areas. In the Bohai Bay and the Loess Plateau region, which are the two largest apple producing areas, Proteobacteria and Actinobacteria had the highest relative abundance, respectively. Furthermore, soil bacterial diversity showed positive correlation with the mean annual temperature (MAT), soil organic matter (SOM) and pH. Excluding a direct effect on the apple fruit quality, MAT exerted an indirect influence through soil SOM and pH to alter the relative abundance of dominant taxa and shift the bacterial diversity, which affects the apple fruit titratable acids and soluble solids.

CONCLUSIONS

Geographic variables underlie apple orchard soil bacterial communities vary according to spatial scale. Environmental factors exert an indirect effect on apple fruit quality via shaping soil bacterial community.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides a list of bacteria associated with environmental factors and the ecological attributes of their interactions in apple orchards, which will improve our ability to promote soil bacterial functional capabilities in order to reduce the fertilizer input and enhance the fruit quality.

How Do Soil Bacterial Diversity and Community Composition Respond under Recommended and Conventional Nitrogen Fertilization Regimes?

Shifts in soil bacterial diversity and community composition are suggested to be induced by elevated input of nitrogen (N) fertilization with implications for soil quality, and consequently production. In this study, we evaluated the impacts of recommended fertilization (RF) and conventional fertilization (CF) on soil chemical properties, crop yield, bacterial diversity, and community composition from two long-term experiments conducted in fluvo-aquic soil and black soil of China. Each site comprised of four treatments, i.e., RF N−, RF N+, CF N−, CF N+. No N fertilization was indicated by N− and N fertilization was indicated by N+. Across both sites, N fertilization significantly increased crop yield compared with no N fertilization and RF successfully enhanced crop yield over CF. Interestingly, the RF maintained bacterial diversity, while CF depressed bacterial diversity in the two soils. Microbial taxa performing important ecological roles such as order Rhodospirillales and Bacillales were significantly enhanced in the RF approach, while Rhizobiales declined under CF. Furthermore, the results of partial least square path modeling revealed that soil available phosphorus (AP) negatively affected bacterial diversity while it positively affected bacterial community structure in fluvo-aquic soils. In contrast, soil pH was positively linked with both bacterial diversity and community structure in black soil. Overall, our study demonstrated that RF is an environmentally friendly approach which not only maintained above ground plant productivity, but also preserved belowground microbial populations and important soil variables regulating bacterial communities varied in different soil types.

Increased organic fertilizer application and reduced chemical fertilizer application affect the soil properties and bacterial communities of grape rhizosphere soil

Increasing organic fertilizer application can improve the sustainability of soil productivity, but the effects of increased organic fertilizer application with reduced chemical fertilizer application over different time periods on chemical properties and bacterial community of grape rhizosphere soil in an arid region are not clear. In this study, three years of fixed-point field tests were used to compare the effects of various fertilization treatments on the soil properties and bacterial community in the grape rhizosphere. The results showed that (1) T1 and T2 significantly increased SOM, AN, AP and AK contents in grape rhizosphere soil. TN, TP and TK contents in grape leaves of T2 were the highest of those in five fertilization treatments. (2) The abundances of Proteobacteria and Bacteroidetes phyla and especially of Arthrobacter, Pseudomonas, Nitrosopira and Bacillus genera were higher in T2 than in the other samples. (3) SOM, AP and AN contents in soil were the main factors affecting soil bacterial community and mineral element contents in grape leaves and roots according to an RDA analysis. In summary, the application of organic fertilizer with reduced chemical fertilizer for two years had the greatest impact on the soil properties and bacterial community of the grape rhizosphere soil.

Apple endophyte community is shaped by tissue type, cultivar and site and has members with biocontrol potential against Neonectria ditissima

AIMS

This research aimed to identify factors influencing endophyte community structure in apple shoots and the bioactivity of cultured representatives against the fungal pathogen Neonectria ditissima.

METHODS AND RESULTS

The endophyte community in leaves and stems of the apple cultivars 'Royal Gala' and 'Braeburn' were analysed by a cultivation-independent method (PCR-DGGE) which showed that tissue type, cultivar and site were determinant factors, with the endophyte taxa in 'Royal Gala' more variable than that in 'Braeburn', with leaf endophyte communities typically differing from stems in both cultivars. Seasonal (spring vs autumn) and regional (Nelson vs Hawke's Bay) variations were not obvious in woody stems. A collection of 783 bacterial and 87 fungal endophytes were recovered from leaves and stems of 'Royal Gala', 'Braeburn', 'Scilate' and/or 'Scifresh' from Nelson (nine sites) and Hawke's Bay (five sites) in spring and from Nelson (three sites) in autumn. A dual culture plating assay was used to test their ability to inhibit the mycelial growth of N. ditissima. Thirteen bacterial (mean of percent inhibition ≥20%) and 17 fungal isolates were antagonistic towards N. ditissima. These isolates belonged to the bacterial genera Bacillus and Pseudomonas, and fungal genera Chaetomium, Epicoccum, Biscogniauxia, Penicillium, Diaporthe, Phlyctema and two unidentified fungal isolates.

CONCLUSIONS

Endophyte communities in apple shoots were determined by tissue type, cultivar and site. Endophytic bacterial and fungal isolates inhibiting N. ditissima growth in vitro were found.

SIGNIFICANCE AND IMPACT OF THE STUDY

These results provided new evidence of factors influencing apple endophyte community in New Zealand. Endophytes with potential to reduce N. ditissima infection were identified, with the potential to be developed into a biocontrol strategy for European canker.

Different effects of soil bacterial communities affected by biocontrol agent YH-07 on tomato Fusarium wilt inhibition

The model plant tomato was used to verify the effect and mechanism of a novel discovered strain YH-07 which is a potential agent for biological control of soil borne disease named tomato Fusarium wilt.

Modification of Rhizosphere Bacterial Community Structure and Functional Potentials to Control Pseudostellaria heterophylla Replant Disease

Replant disease caused by negative plant-soil feedback commonly occurs in a Pseudostellaria heterophylla monoculture regime. Here, barcoded pyrosequencing of 16S ribosomal DNA amplicons combined with phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis was applied to study the shifts in soil bacterial community structure and functional potentials in the rhizosphere of P. heterophylla under consecutive monoculture and different soil amendments (i.e., bio-organic fertilizer application [MF] and paddy-upland rotation [PR]). The results showed that the yield of tuberous roots decreased under P. heterophylla consecutive monoculture and then increased after MF and PR treatments, which was consistent with the changes in soil bacterial diversity. Both principal coordinate analysis and the unweighted pair-group method with arithmetic means cluster analysis showed the distinct difference in bacterial community structure between the consecutively monocultured soil (relatively unhealthy soil) and other relatively healthy soils (i.e., newly planted soil, MF, and PR). Furthermore, taxonomic analysis showed that consecutive monoculture of P. heterophylla significantly decreased the relative abundances of the families Burkholderiaceae and Acidobacteriaceae (subgroup 1), whereas it increased the population density of families Xanthomonadaceae, Phyllobacteriaceae, Sphingobacteriaceae, and Alcaligenaceae, and Fusarium oxysporum. In contrast, the MF and PR treatments recovered the soil microbiome and decreased F. oxysporum abundance through the different ways; for example, the introduction of beneficial microorganisms (in MF) or the switching between anaerobic and aerobic conditions (in PR). In addition, PICRUSt analysis revealed the higher abundances of membrane transport, cell motility, and DNA repair in the consecutively monocultured soil, which might contribute to the root colonization and survival for certain bacterial pathogens under monoculture. These findings highlight the close association between replant disease of P. heterophylla and the variations in structure and potential functions of rhizosphere bacterial community.

Effects of soil properties, heavy metals, and PBDEs on microbial community of e-waste contaminated soil

Heavy metals and polybrominated diphenyl ethers (PBDEs) are ubiquitous pollutants at electronic waste (e-waste) contaminated sites, their individual impacts on soil microbial community has attracted wide attention, however, limited research is available on the combined effects of heavy metals and PBDEs on microbial community of e-waste contaminated. Therefore, combined effects of heavy metals and PBDEs on the microbial community in the e-waste contaminated soil were investigated in this study. Samples were collected from Ziya e-waste recycling area in Tianjin, northern China, and the soil microbial communities were then analyzed by the high-throughput MiSeq 16S rRNA sequencing to assess the effects of soil properties, heavy metals, and PBDEs on the soil microbial community. Candidatus Nitrososphaera, Steroidobacter and Kaistobacter were the dominant microbial species in the soils. Similar microbial metabolic functions, including amino acid metabolism, carbohydrate metabolism and membrane transport, were found in all soil samples. Redundancy analysis and variation partition analysis revealed that the microbial community was mainly influenced by PBDEs (including BDE 183, BDE 99, BDE 100 and BDE 154) in horizontal soil samples. However, TN, biomass, BDE 100, BDE 99 and BDE 66 were the major drivers shaping the microbial community in vertical soil samples.

Deciphering microbial diversity associated with Fusarium wilt-diseased and disease-free banana rhizosphere soil

Background

Fusarium wilt of banana (Musa spp.) caused by the fungal pathogen Fusarium oxysporum f. sp. cubense (Foc) is a typical soilborne disease, that severely devastates the banana industry worldwide, and soil microbial diversity is closely related to the spread of Fusarium wilt. To understand the relationship between microbial species and Fusarium wilt, it is important to understand the microbial diversity of the Fusarium wilt-diseased and disease-free soils from banana fields.

Results

Based on sequencing analysis of the bacterial 16S rRNA genes and fungal internal transcribed spacer (ITS) sequences, Foc abundance, fungal or bacterial richness and diversity were higher in the diseased soils than in the disease-free soils. Although Ascomycota and Zygomycota were the most abundant fungi phyla in all soil samples, Ascomycota abundance was significantly reduced in the disease-free soils. Mortierella (36.64%) was predominant in the disease-free soils. Regarding bacterial phyla, Proteobacteria, Acidobacteria, Chloroflexi, Firmicutes, Actinobacteria, Gemmatimonadetes, Bacteroidetes, Nitrospirae, Verrucomicrobia and Planctomycetes were dominant phyla in all soil samples. In particular, Firmicutes contributed 16.20% of the total abundance of disease-free soils. At the bacterial genus level, Bacillus, Lactococcus and Pseudomonas were abundant in disease-free soils with abundances of 8.20, 5.81 and 2.71%, respectively; lower abundances, of 4.12, 2.35 and 1.36%, respectively, were found in diseased soils. The distribution characteristics of fungal and bacterial genera may contribute to the abundance decrease of Foc in the disease-free soils.

Conclusion

Unique distributions of bacteria and fungi were observed in the diseased and disease-free soil samples from banana fields. These specific genera are useful for constructing a healthy microbial community structure of soil.

Soil Organic Carbon Content and Microbial Functional Diversity Were Lower in Monospecific Chinese Hickory Stands than in Natural Chinese Hickory–Broad-Leaved Mixed Forests

To assess the effects of long-term intensive management on soil carbon cycle and microbial functional diversity, we sampled soil in Chinese hickory (Carya cathayensis Sarg.) stands managed intensively for 5, 10, 15, and 20 years, and in reference Chinese hickory–broad-leaved mixed forest (NMF) stands. We analyzed soil total organic carbon (TOC), microbial biomass carbon (MBC), and water-soluble organic carbon (WSOC) contents, applied 13C-nuclear magnetic resonance analysis for structural analysis, and determined microbial carbon source usage. TOC, MBC, and WSOC contents and the MBC to TOC ratios were lower in the intensively managed stands than in the NMF stands. The organic carbon pool in the stands managed intensively for twenty years was more stable, indicating that the easily degraded compounds had been decomposed. Diversity and evenness in carbon source usage by the microbial communities were lower in the stands managed intensively for 15 and 20 years. Based on carbon source usage, the longer the management time, the less similar the samples from the monospecific Chinese hickory stands were with the NMF samples, indicating that the microbial community compositions became more different with increased management time. The results call for changes in the management of the hickory stands to increase the soil carbon content and restore microbial diversity.

Soil acidification amendments change the rhizosphere bacterial community of tobacco in a bacterial wilt affected field

Application of soil amendments has been wildly used to increase soil pH and control bacterial wilt. However, little is known about causal shifts in the rhizosphere microbial community of crops, especially when the field naturally harbors the disease of bacterial wilt to tobacco for many years due to long-term continuous cropping and soil acidification. In this study, biochar (CP), lime (LM), oyster shell powder (OS) and no soil amendment additions (Control; CK) were assessed for their abilities to improve the soil acidification, change the composition of rhizosphere soil bacterial communities and thus control tobacco bacterial wilt. The results showed that oyster shell powder significantly increased soil pH by 0.77 and reduced the incidence of tobacco bacterial wilt by 36.67% compared to the control. The Illumina sequencing -based community analysis showed that soil amendment applications affected the composition of rhizosphere bacterial community and increased the richness and diversity. In contrast, the richness and diversity correlated negatively to disease incidence. Using LEfSe analyses, 11 taxa were found to be closely related with disease suppression, in which Saccharibacteria, Aeromicrobium, and Pseudoxanthomonas could be potential indicators of disease suppression. Our results suggested that the suppression of bacterial wilt after the application of soil amendments (especially oyster shell powder) was attributed to the improved soil pH and increased bacterial richness and diversity.

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

Compost amendment reportedly improved apple tree growth in replant soils. However, its effects should be evaluated at different soil depths and locations. This study investigated the impact of soil improvement with compost on soil physicochemical properties and bacterial community structure of a replanted apple orchard in comparison with the original orchard without compost improvement. The V1-V3 region of the bacterial 16S rRNA gene was subjected to high-throughput 454 pyrosequencing, and data were analyzed using the Mothur pipeline. The results showed that the soil improvement benefited tree growth and fruit quality during the study period. The compost amendment markedly increased tree height and stem diameter by a range of 6.1%-21.0% and 4.0%-14.0%, respectively. Fruit yield (9.5%), average weight (9.6%), and soluble solid content (5.6%) were also increased by compost amendment compared to those of the unimproved treatment. The pH, organic matter, and available N, P, and K contents were significantly increased by 5.7%-21.9%, 0.2%-62.9%, 9.3%-29.3%, 36.7%-64.5%, and 17.2%-100.3% in the compost improved soil. The pyrosequencing data showed that the soil improvement changed the bacterial community structure at all soil depths (0-20 cm and 20-40 cm) and locations (in-row and inter-row) considered; e.g., the relative abundance of Proteobacteria (20.2%), Bacteroidetes (2.5%), and Cyanobacteria (1.0%) was increased while that of Chloroflexi (5.5%), Acidobacteria (5.2%), Nitrospirae (4.5%), Gemmatimonadetes (3.8%), and Actinobacteria (1.8%) was decreased. The relative abundance of some dominant genera Burkholderia (2.3%), Pseudomonas (1.0%), and Paenibacillus (0.5%) were enhanced in the compost improved soil. Moreover, other dominant genera such as Nitrospira (6.4%), Gemmatimonas (2.2%), and Phenylobacterium (0.3%) were reduced by the application of compost. Our results indicate that soil improvement benefits the growth of tree and fruit quality, and is likely mediated by increased soil pH, organic matter, and available nutrient contents and beneficial bacterial community composition.

Influence of high-carbon basal fertiliser on the structure and composition of a soil microbial community under tobacco cultivation

Soil microorganisms play a crucial role in cycling soil nutrients and providing organic nutrients for plant growth and development. Fertilisation balances soil fertility and quality, and affects soil microbial communities. Fertilisation is a frontier subject in agricultural and environmental sciences. Here we showed that the application of high-carbon basal fertiliser treatment could improve the tobacco yield and quality when compared to chemical fertiliser, high-carbon basal fertiliser and mixed high-carbon chemical fertiliser. The potential reason is that different fertiliser treatments influence soil fertility, such as nitrogen, phosphorus, and other contents, besides soil organic matter. Further experiments revealed that populations of bacteria, fungi and actinomycetes fluctuated during tobacco development under different fertilisation treatments. Then we performed high-throughput sequencing of the 16S rRNA gene, and the results showed that the fertilisation treatments had significant effects on the microbial community, particularly within the finer taxonomic divisions or non-dominant taxa. Moreover, proteobacteria and fungal genera had significantly different relative abundances during tobacco growth under various tobacco developmental stages and fertilisation treatments. These results indicated that mixed high-carbon chemical fertiliser could improve soil fertility by influencing the soil microorganism, and that the fertilisation treatments impacted on the structure and composition of the microbial community, and especially the diversity of non-dominant taxa. However, more studies are needed to confirm their reliability.

Cropping systems affect paddy soil organic carbon and total nitrogen stocks (in rice-garlic and rice-fava systems) in temperate region of southern China

The accumulation of soil organic carbon (SOC) in agricultural soils is critical to food security and climate change. However, there is still limited information on the dynamic trend of SOC sequestration following changes in cropping systems. Paddy soils, typical of temperate region of southern China, have a large potential for carbon (C) sequestration and nitrogen (N) fixation. It is of great importance to study the impacts of changes in cropping systems on stocks of SOC and total nitrogen (TN) in paddy soils. A six-year field experiment was conducted to clarify the dynamics of SOC and TN stocks in the paddy topsoil (0-20cm) when crop rotation of rice (Oryza sativa L.) -garlic (Allium sativum) (RG) was changed to rice-fava (Vicia faba L.) (RF), and to examine how the dynamics were affected by two N management strategies. The results showed that SOC stocks increased by 24.9% in the no N (control) treatment and by 18.9% in the treatment applied with conventional rate of N (CON), when RG was changed to RF. Correspondingly, TN stocks increased by 8.5% in the control but decreased by 2.6% in the CON. Compared with RG, RF was more conducive to increase the contents of soil microbial biomass C and N. Moreover, changing the cropping system from RG to RF increased the year-round N use efficiency from 21.6% to 34.4% and reduced soil N surplus in the CON treatment from 547kg/ha to 93kg/ha. In conclusion, changes in the cropping system from RG to RF could markedly increase SOC stocks, improve N utilization, reduce soil N surplus, and thus reduce the risk of N loss in the paddy soil. Overall, this study showed the potential of paddy agro-ecological systems to store C and maintain N stocks in the temperate regions.

Vertical distribution of microbial communities in soils contaminated by chromium and perfluoroalkyl substances

Both Bacteria and Archaea are important players in soil biogeochemical cycles. Both chromium (Cr) and perfluoroalkyl substances (PFASs) are widely present in soil environment. However, the depth-related distribution of microbial community in soils contaminated by Cr or/and PFASs remains unknown. Hence, the present study applied quantitative PCR assay and Illumina MiSeq sequencing to investigate the vertical variations of archaeal and bacterial communities in soils (0.5-12.5m depth) contaminated by chrome plating waste and the potential effects of Cr and PFASs. Both bacterial and archaeal communities displayed the remarkable depth-related changes of abundance (2.16×10⁷-5.05×10⁹ and 4.95×10⁵-2.56×10⁸ 16S rRNA gene copies per gram dry soil respectively for Bacteria and Archaea), diversity (bacterial and archaeal Shannon diversity indices of 5.06-6.34 and 2.91-4.61, respectively) and structure. However, at each soil depth, bacterial community had higher abundance, richness and diversity than archaeal community. Soil bacterial communities were mainly composed of Proteobacteria, Chloroflexi, Actinobacteria and Firmicutes, and archaeal communities were dominated by Thaumarchaeota and unclassified Archaea. Moreover, microbial abundance and richness increased with increasing perfluorohexane sulfonate (PFHxS) content. Microbial abundance was correlated to total Cr, and archaeal richness was correlated to total Cr and Cr(IV). In addition, total Cr might be a key determinant of soil microbial community structure.

Long-Term Application of Bioorganic Fertilizers Improved Soil Biochemical Properties and Microbial Communities of an Apple Orchard Soil

Soil biochemical properties and microbial communities are usually considered as important indicators of soil health because of their association with plant nutrition. In this study, we investigated the impact of long-term application of bioorganic fertilizer (BOF) on soil biochemical properties and microbial communities in the apple orchard soil of the Loess Plateau. The experiment included three treatments: (1) control without fertilization (CK); (2) chemical fertilizer application (CF); and (3) bioorganic fertilizer application (BOF). The high throughput sequencing was used to examine the bacterial and fungal communities in apple orchard soil. The results showed that the BOF treatment significantly increased the apple yield during the experimental time (2009-2015). The application of BOF significantly increased the activities of catalase and invertase compared to those in CK and CF treatments. The high throughput sequencing data showed that the application of BOF changed the microbial community composition of all soil depths considered (0-20 cm, 20-40 cm, and 40-60 cm), e.g., the relative abundance of bio-control bacteria (Xanthomonadales, Lysobacter, Pseudomonas, and Bacillus), Proteobacteria, Bacteroidetes, Ohtaekwangia, Ilyonectria, and Lecanicillium was increased while that of Acidobacteria, Chloroflexi, Gp4, Gp6 and Sphaerobacter was decreased. The increase in apple yield after the application of BOF might be due to increase in organic matter, total nitrogen and catalase and invertase activities of soil and change in the bacterial community composition by enriching Bacillus, Pseudomonas, Lysobacter, and Ohtaekwangia. These results further enhance the understanding on how BOFs alter soil microbial community composition to stimulate soil productivity.