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

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.

Type IV secretion system effector sabotages multiple defense systems in a competing bacterium

Effector proteins secreted by bacteria that infect mammalian and plant cells often subdue eukaryotic host cell defenses by simultaneously affecting multiple targets. However, instances when a bacterial effector injected in the competing bacteria sabotage more than a single target have not been reported. Here, we demonstrate that the effector protein, LtaE, translocated by the type IV secretion system from the soil bacterium Lysobacter enzymogenes into the competing bacterium, Pseudomonas protegens, affects several targets, thus disabling the antibacterial defenses of the competitor. One LtaE target is the transcription factor, LuxR1, that regulates biosynthesis of the antimicrobial compound, orfamide A. Another target is the sigma factor, PvdS, required for biosynthesis of another antimicrobial compound, pyoverdine. Deletion of the genes involved in orfamide A and pyoverdine biosynthesis disabled the antibacterial activity of P. protegens, whereas expression of LtaE in P. protegens resulted in the near-complete loss of the antibacterial activity against L. enzymogenes. Mechanistically, LtaE inhibits the assembly of the RNA polymerase complexes with each of these proteins. The ability of LtaE to bind to LuxR1 and PvdS homologs from several Pseudomonas species suggests that it can sabotage defenses of various competitors present in the soil or on plant matter. Our study thus reveals that the multi-target effectors have evolved to subdue cell defenses not only in eukaryotic hosts but also in bacterial competitors.

Soil bacterium manipulates antifungal weapons by sensing intracellular type IVA secretion system effectors of a competitor

Soil beneficial bacteria can effectively inhibit bacterial pathogens by assembling contact-dependent killing weapons, such as the type IVA secretion system (T4ASS). It's not clear whether these antibacterial weapons are involved in biotrophic microbial interactions in soil. Here we showed that an antifungal antibiotic 2,4-DAPG production of the soil bacterium, Pseudomonas protegens can be triggered by another soil bacterium, Lysobacter enzymogenes, via T4ASS by co-culturing on agar plates to mimic cell-to-cell contact. We demonstrated that the induced 2,4-DAPG production of P. protegens is achieved by intracellular detection of the T4ASS effector protein Le1519 translocated from L. enzymogenes. We defined Le1519 as LtaE (Lysobacter T4E triggering antifungal effects), which specifically stimulates the expression of 2,4-DAPG biosynthesis genes in P. protegens, thereby protecting soybean seedlings from infection by the fungus Rhizoctonia solani. We further found that LtaE directly bound to PhlF, a pathway-specific transcriptional repressor of the 2,4-DAPG biosynthesis, then activated the 2,4-DAPG production. Our results highlight a novel pattern of microbial interspecies and interkingdom interactions, providing a unique case for expanding the diversity of soil microbial interactions.

Soil microbial and enzyme activities in different land use systems of the Northwestern Himalayas

Soil microbial activity (SMA) is vital concerning carbon cycling, and its functioning is recognized as the primary factor in modifying soil carbon storage potential. The composition of the microbial community (MC) is significant in sustaining environmental services because the structure and activity of MC also influence nutrient turnover, distribution, and the breakdown rate of soil organic matter. SMA is an essential predictor of soil quality alterations, and microbiome responsiveness is imperative in addressing the escalating sustainability concerns in the Himalayan ecosystem. This study was conducted to evaluate the response of soil microbial and enzyme activities to land conversions in the Northwestern Himalayas (NWH), India. Soil samples were collected from five land use systems (LUSs), including forest, pasture, apple, saffron, and paddy-oilseed, up to a depth of 90 cm. The results revealed a significant difference (p < 0.05) in terms of dehydrogenase (9.97-11.83 TPF µg g-1 day-1), acid phosphatase (22.40-48.43 µg P-NP g-1 h-1), alkaline phosphatase (43.50-61.35 µg P-NP g-1 h-1), arylsulphatase (36.33-48.12 µg P-NP g-1 h-1), fluorescein diacetate hydrolase (12.18-21.59 µg g-1 h-1), bacterial count (67.67-123.33 CFU × 106 g-1), fungal count (19.33-67.00 CFU × 105 g-1), and actinomycetes count (12.00-42.33 CFU × 104 g-1), with the highest and lowest levels in forest soils and paddy-oilseed soils, respectively. Soil enzyme activities and microbial counts followed a pattern: forest > pasture > apple > saffron > paddy-oilseed at all three depths. Paddy-oilseed soils exhibited up to 35% lower enzyme activities than forest soils, implying that land conversion facilitates the depletion of microbiome diversity from surface soils. Additionally, reductions of 49.80% and 62.91% were observed in enzyme activity and microbial counts, respectively, with soil depth (from 0-30 to 60-90 cm). Moreover, the relationship analysis (principal component analysis and correlation) revealed a high and significant (p = 0.05) association between soil microbial and enzyme activities and physicochemical attributes. These results suggest that land conversions need to be restricted to prevent microbiome depletion, reduce the deterioration of natural resources, and ensure the sustainability of soil health.

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.

Nitrogen inhibitors improve soil ecosystem multifunctionality by enhancing soil quality and alleviating microbial nitrogen limitation

Soil quality (SQI) is a comprehensive indicator reflecting the agricultural productivity of soil, and soil ecosystem multifunctionality (performing multiple functions simultaneously; EMF) can reflect complex biogeochemical processes. However, the effects of enhanced efficiency nitrogen fertilizers (EENFs; urease inhibitors (NBPT), nitrification inhibitors (DCD), and coated controlled-release urea (RCN)) application on the SQI and soil EMF and their relationships are still unclear. Therefore, we conducted a field experiment to study the effects of different EENFs on the SQI, enzyme stoichiometry and soil EMF in semiarid areas of Northwest China (Gansu, Ningxia, Shaanxi, Shanxi). Across the four study sites, DCD and NBPT increased SQI by 7.61-16.80 % and 2.61 %-23.20 % compared to mineral fertilizer, respectively. N fertilizer application (N200 and EENFs) alleviated microbial N limitation, and EENFs alleviated microbial N and C limitations to a greater extent in Gansu and Shanxi. Moreover, nitrogen inhibitors (Nis; DCD and NBPT) improved the soil EMF to a greater extent than N200 and RCN, DCD increased by 205.82-340.00 % and 145.00-215.47 % in Gansu and Shanxi, respectively; NBPT increased by 332.75-778.59 % and 364.44-929.62 % in Ningxia and Shanxi, respectively. A random forest model showed that the microbial biomass carbon (MBC), microbial biomass nitrogen (MBN) and soil water content (SWC) of the SQI factors were the main driving forces of soil EMF. Moreover, SQI improvement could alleviate microbial C and N limitations and promote the improvement of soil EMF. It is worth noting that soil EMF was mainly affected by microbial N limitation rather than C limitation. Overall, NIs application is an effective way to improve the SQI and soil EMF in the semiarid region of Northwest China.

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.

Effect and mechanism of the improvement of coastal silt soil by application of organic fertilizer and gravel combined with Sesbania cannabina cultivation

Jiangsu Province of China has a large area of coastal silt soil (CSS) with poor permeability, high salinity, and poor nutrients, which brings great difficulties to the development and utilization of coastal zones, so that needs to be improved as a matter of urgency. In this study, river-sand, serpentine, and organic fertilizer were used as additives in CSS, and Sesbania cannabina, a salt-tolerant cash crop, was planted in these differently treated soils. Through high-throughput sequencing, analysis of soil physico-chemical properties, and detection of plant growth status, the rhizosphere bacterial diversity of S. cannabina growing in CSS under different treatments and their environmental impact factors were studied, while exploring the effect and mechanism of organic fertilizer combined with gravel as a CSS modifier. The results implied that single application of organic fertilizer could significantly increase the fertility levels of total nitrogen (TN), total organic carbon (TOC) and Avail. P in CSS; then, the application of organic fertilizer with river-sand significantly reduced salt content and alkalinity of soil; meanwhile, in the treatment of single application of organic fertilizer and application of organic fertilizer combined with river-sand, the rhizosphere of S. cannabina enriched the bacterial communities of organic matter degradation and utilization to varying degrees. The soil moisture content and indicators related to saline-alkali soil (including total salt, electrical conductivity (EC), exchangeable sodium percentage (ESP), Avail. Na and Avail. K, etc.) were further reduced significantly by the application of organic fertilizer combined with river-sand and serpentine. The method has greatly improved the growth conditions of S. cannabina and promoted the positive development of its rhizosphere bacterial community. Among them, in the treatment of organic fertilizer combined with river-sand and serpentine, a variety of plant growth-promoting rhizobacteria (PGPR, such as Sphingomonas, Ensifer, and Rhodobacter) and nitrogen-cycle-related bacteria (such as nitrate-reduction-related bacteria, nitrogen-fixing bacteria like Ensifer, and purple non-sulfur photosynthetic bacteria like Rhodobacter) were enriched in the rhizosphere of S. cannabina; moreover, the mutual association and robustness of bacterial co-occurrence networks have been significantly enhanced. The results provide a theoretical basis and reference model for the improvement of coastal saline-alkali silt soil.

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.

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.

Soil Rehabilitation Promotes Resilient Microbiome with Enriched Keystone Taxa than Agricultural Infestation in Barren Soils on the Loess Plateau

Drylands provide crucial ecosystem and economic services across the globe. In barren drylands, keystone taxa drive microbial structure and functioning in soil environments. In the current study, the Chinese Loess plateau’s agricultural (AL) and twenty-year-old rehabilitated lands (RL) provided a unique opportunity to investigate land-use-mediated effects on barren soil keystone bacterial and fungal taxa. Therefore, soils from eighteen sites were collected for metagenomic sequencing of bacteria specific 16S rRNA and fungi specific ITS2 regions, respectively, and to conduct molecular ecological networks and construct microbial OTU-based correlation matrices. In RL soils we found a more complex bacterial network represented by a higher number of nodes and links, with a link percentage of 77%, and a lower number of nodes and links for OTU-based fungal networks compared to the AL soils. A higher number of keystone taxa was observed in the RL (66) than in the AL (49) soils, and microbial network connectivity was positively influenced by soil total nitrogen and microbial biomass carbon contents. Our results indicate that plant restoration and the reduced human interventions in RL soils could guide the development of a better-connected microbial network and ensure sufficient nutrient circulation in barren soils on the Loess plateau.

Impacts of Agriculture on the Environment and Soil Microbial Biodiversity

Agriculture represents an important mechanism in terms of reducing plant, animal, and microbial biodiversity and altering the environment. The pressure to cope with the increasing food demands of the human population has intensified the environmental impact, and alternative ways to produce food are required in order to minimize the decrease in biodiversity. Conventional agricultural practices, such as floods and irrigation systems; the removal of undesired vegetation by fires, tilling, and plowing; the use of herbicides, fertilizers, and pesticides; and the intensification of these practices over the last 50 years, have led to one of the most important environmental threats—a major loss of biodiversity. In this study, we review the impact that agriculture and its intensification have had on the environment and biodiversity since its invention. Moreover, we demonstrate how these impacts could be reduced through the use of microorganisms as biostimulants.

Expatiating the impact of anthropogenic aspects and climatic factors on long-term soil monitoring and management

This article is an extensive collection of scientific literature related to the impact of fertilizers on soil microbial and enzymatic activity. Due to the significance of technology in quantitative and qualitative evaluation of agricultural production, this is a basic problem for the present and future of mankind, where the scientific data being of utmost importance related to the topic. The comparison, including pedo-enzymological evaluation of minerals along with organic fertilization, highlights significant differences between mineral and organic fertilizers, confirming the superiority of complex mineral-organic fertilization. Enzymatic indicators that describe and define the soil quality resulted from enzymatic activities value and provide valuable information regarding the soil fertility status. Moreover, soil enzyme responds to soil management as well as to environmental pollutants. Changes of environmental conditions and pollutants like heavy metals and other toxic substances result in a shift in the biological activity of the soil. These changes can destabilize the soil system and cause a decrease in the nutrient pools. To ensure the improvement of fertilization techniques, the properties of nanoparticles are exploited that can efficiently release nutrients to plant cells. Numerous researches were performed in order to follow the long-term effects of incorporating nanofertilizers into the soil, obtaining an exhaustive overview of this new technology over the development of sustainable agriculture.

Elucidating the effect of biofertilizers on bacterial diversity in maize rhizosphere soil

This study was conducted to investigate the effect of biofertilizers on the structure and diversity of the rhizosphere bacterial community of maize. Different biofertilizers were applied to maize. The physical and chemical properties of rhizosphere soil samples were analyzed and the rhizosphere bacteria were analyzed by 16S amplicon sequencing. The results showed that treatment with Bacillus licheniformis and B. amyloliquefaciens as biofertilizers increased the soil organic matter (SOM), total nitrogen, total phosphorus (TP), available phosphorus (AP), and available potassium (AK) contents, indicating that the plant growth-promoting rhizobacteria in the biofertilizers might help the host plant to produce root exudates that, in return, recruit beneficial communities due to available sugars, amino acids, organic acids, vitamins, and polymers. The rhizosphere of maize treated with B. subtilis biofertilizer had the highest diversity and richness. However, the rhizosphere treated with the combined bacterial strains had the lowest diversity and richness, which might be due to the directional increase of the abundance of some bacteria with special functions, but the decrease of the overall bacterial community diversity in the soil. The dominant bacterial phyla were Proteobacteria (32.2%–34.6%), Acidobacteria (15.0%–21.0%), Actinobacteria (13.1%–17.2%), and Gemmatimonadetes (9.0%–10.8%), and the dominant bacterial species were Aciditerrimonas ferrireducens JCM 15389 (4.3%–5.2%), Gemmatimonas aurantiaca (3.2%–4.1%), and Pyrinomonas methylaliphatogenes (2.1%–4.8%). The significantly enriched bacterial functions were associated with amino acid metabolism, sugar metabolism, and energy metabolism pathways. The results of a redundancy analysis showed that SOM, TP, and AK were the main factors affecting the microbial community structure in the maize rhizosphere. In conclusion, the application of biofertilizers increased the diversity and richness of the bacterial community in the maize rhizosphere soil. However, combined strain treatment was failed and not an ideal strategy due to the lowest abundance and diversity.

Effects of Living Cover on the Soil Microbial Communities and Ecosystem Functions of Hazelnut Orchards

Living cover is an important management measure for orchards in China, and has certain influences on soil properties, microorganisms, and the micro-ecological environment. However, there are few studies on the effects of living cover on the soil changes in hazelnut orchards. In this study, we compared the soils of living cover treatments with Vulpia myuros and the soils of no cover treatments, and analyzed the observed changes in soil properties, microorganisms, and microbial functions by using high-throughput ITS rDNA and 16S rRNA gene Illumina sequencing. The results demonstrated that the total organic carbon content in the 20-40 cm deep soils under the living cover treatments increased by 32.87 and 14.82% in May and July, respectively, compared with those under the no cover treatments. The living cover treatment with V. myuros also significantly increased the contents of total phosphorus (TP), total nitrogen (TN), available phosphorus (AP), and available potassium (AK) in the soil samples. Moreover, the influence of seasons was not as significant as that of soil depth. The living cover treatment also significantly improved the soil enzyme activity levels. The results demonstrated that Ascomycota, Mortierellomycota and Basidiomycota were the dominant fungal phyla in all samples, while Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes, and Chloroflexi were the dominant bacterial phyla, but the different treatments impacted the compositions of fungal and bacterial communities. Principal component analysis (PCA) showed that living cover with V. myuros significantly changed the soil fungal community structures whereas the bacterial community structures may be more sensitive to seasonal changes. At the microbial functional level, the living cover treatment increased the fungal operational taxonomic units (OTUs) of symbiotrophs and decreased that of pathotrophs. According to this study, we believe that the application of a living cover with V. myuros has a favorable regulating influence on soil properties, microbial communities and microbial function. This treatment can also reduce the use of herbicides, reduce the cost of orchard management, and store more carbon underground to achieve sustainable intensification of production in hazelnut orchards, so it can be considered as a management measure for hazelnut orchards.

Effects of organic matter addition on chronically hydrocarbon-contaminated soil

Soil is the recipient of organic pollutants as a consequence of anthropogenic activities. Hydrocarbons are contaminants that pose a risk to human and environmental health. Bioremediation of aging contaminated soils is a challenge due to the low biodegradability of contaminants as a result of their interaction with the soil matrix. The aim of this work was to evaluate the effect of both composting and the addition of mature compost on a soil chronically contaminated with hydrocarbons, focusing mainly on the recovery of soil functions and transformations of the soil matrix as well as microbial community shifts. The initial pollution level was 214 ppm of polycyclic aromatic hydrocarbons (PAHs) and 2500 ppm of aliphatic hydrocarbons (AHs). Composting and compost addition produced changes on soil matrix that promoted the release of PAHs (5.7 and 15 % respectively) but not the net PAH elimination. Interestingly, composting stimulated AHs elimination (about 24 %). The lack of PAHs elimination could be attributed to the insufficient PAHs content to stimulate the microbial degrading capacity, and the preferential consumption of easily absorbed C sources by the bacterial community. Despite the low PAH catabolic potential of the aging soil, metabolic shift was driven by the addition of organic matter, which could be monitored by the ratio of Proteobacteria to Actinobacteria combined with E₄/E₆ ratio. Regarding the quality of the soil, the nutrients provided by the exogenous organic matter contributed to the recovery of the global functions and species diversity of the soil along with the reduction of phytotoxicity.

Beneficial Effects of Mixing Kentucky Bluegrass With Red Fescue via Plant-Soil Interactions in Black Soil of Northeast China

Continuous monoculture of cool-season turfgrass causes soil degradation, and visual turf quality decline is a major concern in black soil regions of Northeast China. Turf mixtures can enhance turfgrass resistance to biotic and abiotic stresses and increase soil microbial diversity. Understanding mechanism by plant-soil interactions and changes of black soil microbial communities in turf mixture is beneficial to restoring the degradation of urbanized black soils and maintaining sustainable development of urban landscape ecology. In this study, based on the previous research of different sowing models, two schemes of turf monoculture and mixture were conducted in field plots during 2016-2018 in a black soil of Heilongjiang province of Northeast China. The mixture turf was established by mixing 50% Kentucky bluegrass "Midnight" (Poa pratensis L.) with 50% Red fescue "Frigg" (Festuca rubra L.); and the monoculture turf was established by sowing with pure Kentucky bluegrass. Turf performance, soil physiochemical properties, and microbial composition from rhizosphere were investigated. Soil microbial communities and abundance were analyzed by Illumina MiSeq sequencing and quantitative PCR methods. Results showed that turfgrass quality, turfgrass biomass, soil organic matter (SOM), urease, alkaline phosphatase, invertase, and catalase activities increased in PF mixture, but disease percentage and soil pH decreased. The microbial diversity was also significantly enhanced under turf mixture model. The microbial community compositions were significantly different between the two schemes. Turf mixtures obviously increased the abundances of Beauveria, Lysobacter, Chryseolinea, and Gemmatimonas spp., while remarkably reduced the abundances of Myrothecium and Epicoccum spp. Redundancy analysis showed that the compositions of bacteria and fungi were related to edaphic parameters, such as SOM, pH, and enzyme activities. Since the increasing of turf quality, biomass, and disease resistance were highly correlated with the changes of soil physiochemical parameters and microbial communities in turf mixture, which suggested that turf mixture with two species (i.e., Kentucky blue grass and Red fescue) changed soil microbial communities and enhanced visual turfgrass qualities through positive plant-soil interactions by soil biota.

Improving yield and quality of vegetable grown in PAEs-contaminated soils by using novel bioorganic fertilizer

Phthalate acid esters (PAEs) are ubiquitous pollutants in agricultural soils. Application of bioorganic fertilizer (BOF) containing beneficial microbes represents a promising approach to improve the yield and quality of crops grown in contaminated soils. In the present study, a novel multifunctional bioorganic fertilizer N-BOF was developed by using compost of sewage sludge and agricultural waste and inoculating with PAEs-degrading B. megaterium YJB3 and phosphate solubilizing B. megaterium YLYP1. Its feasibility of improving the yield and quality of vegetable grown in PAEs (including DBP and DEHP) contaminated soil was evaluated by pot experiments. The N-BOF could effectively promote plant growth, with biomass increasing by 4-66.9% and 19-110% compared to chemical (CF) and no fertilizer (CK), respectively. The concentrations of DBP and DEHP in shoots of chemically fertilised vegetable ranged 1.23-3.12 mg/kg (dry weight, DW) and 1.63-3.89 mg/kg (DW), respectively. Their concentrations were significantly decreased (p < 0.05) when N-BOF was applied (1%, 2%, 5% amendment), especially at higher application rate ranging 0.11-0.3 mg/kg (DW) and 0.16-0.32 mg/kg (DW), respectively. Meanwhile, vegetable quality attributes were also significantly improved when 2% N-BOF was applied, with increase in the contents of vitamin C, vitamin B1, total protein, and starch, and decrease in the contents of nitrite and nitrate. In this case, the human health risk from consumption of the vegetable grown in PAEs-contaminated soil could be significantly reduced. Thus, our study is expected to provide an efficient way of high-value utilization of organic substrates by producing low-cost but high quality N-BOF. Future studies on the effects of N-BOF in terms of fertilizer regimes on yield and quality of the vegetable are needed, and further field studies for assessing the long-term efficacy and reliability of this promising N-BOF are also warranted.

Bioavailability of Sulfur from Waste Obtained during Biogas Desulfurization and the Effect of Sulfur on Soil Acidity and Biological Activity

Sulfur deficiency has been recognized as a limiting factor for crop production in many regions of the world. A 120-day incubation experiment was conducted to assess the effect of the applied waste elemental sulfur on sulfur bioavailability in soil. Four doses of sulfur were applied: 10, 20, 30 and 60 mg S kg−1 dry matter (d.m.) of soil. In order to assess the effect of soil pH adjustment on sulfur oxidation, the research was conducted on two sets of soil samples: one set of soil samples had natural pH, and the second one was limed before sulfur application. Application of waste sulfur slightly affected the soil pH, and increased the content of available sulfur in soil proportionally to sulfur dose. A beneficial effect of waste sulfur application on soil dehydrogenase and catalase activity was found. Liming reduced soil acidity, and significantly increased sulfate content and soil enzymatic activity. Waste elemental sulfur may be an alternative source of sulfur, supplementing the deficiencies of this element in soils. The described way of sulfur waste reuse corresponds with the increasingly common approach to create waste-free technologies in all economy.

Mulching practices alter the bacterial-fungal community and network in favor of soil quality in a semiarid orchard system

The study aimed to investigate how mulching practices can improve soil quality by altering microbial community composition and the interrelations among its members. The experiment was conducted for 7 years (from 2012 to 2018) in an apple (Malus domestica cv. Fuji) orchard located on the Loess Plateau, China. Four treatments were applied: conventional tillage (CT), intercrop ryegrass (Lolium perenne L.) cover (RE), inter-row cornstalk mulch (CS), and black ground fabric mulch (BF). The results indicated that compared to CT treatment, all the three mulching practices significantly increased soil moisture content. The RE and CS treatments improved soil organic matter content by 11.8% and 36.5%, respectively, and CS treatment also increased available nitrogen content in soil by 42.0% compared with CT treatment. The soil environmental heterogeneity under different mulching practices shaped the microbial community structure and the dominant populations. All the mulching practices significantly increased the operational taxonomic unit (OTU) abundance and alpha diversity of fungi, and positively affected bacterial richness. Network analyses showed that the microbial structure was significantly affected by soil water and microbial biomass nitrogen. Interestingly, based on network correlation analysis among microorganisms, the BF treatment reduced competition between bacteria, whereas RE treatment increased their cooperation, however, the CS treatment not only promoted cooperation between fungi, but also increased correlations between fungi and bacteria. Finally, our results indicated that mulching practices not only increased the diversity of microorganisms and abundance of dominant species, but also promoted the interrelations among microorganisms in favor of soil quality.

Insight to shape of soil microbiome during the ternary cropping system of Gastradia elata

Background

The ternary cropping system of Gastradia elata depends on a symbiotic relationship with the mycorrhizal fungi Armillaria mellea, which decays wood to assimilate nutrition for the growth of G. elata. The composition of microbe flora as key determinants of rhizoshere and mycorrhizoshere soil fertility and health was investigated to understand how G. elata and A. mellea impacted on its composition. The next generation pyrosequencing analysis was applied to assess the shift of structure of microbial community in rhizoshere of G. elata and mycorrhizoshere of A. mellea compared to the control sample under agriculture process.

Results

The root-associated microbe floras were significantly impacted by rhizocompartments (including rhizoshere and mycorrhizoshere) and agriculture process. Cropping process of G. elata enhanced the richness and diversity of the microbial community in rhizoshere and mycorrhizoshere soil. Furthermore, planting process of G. elata significantly reduced the abundance of phyla Basidiomycota, Firmicutes and Actinobacteria, while increased the abundance of phyla Ascomycota, Chloroflexi, Proteobacteria, Planctomycetes, and Gemmatimonadetes in rhizoshere and mycorrhizoshere. Besides, A. mellea and G. elata significantly enriched several members of saprophytoic and pathogenic fungus (i.e., Exophiala, Leptodontidium, Cosmospora, Cercophora, Metarhizium, Ilyonectria, and Sporothrix), which will enhance the possibility of G. elata disease incidence. At the same time, the ternary cropping system significantly deterred several members of beneficial ectomycorrhizal fungus (i.e., Russula, Sebacina, and Amanita), which will reduce the ability to protect G. elata from diseases.

Conclusions

In the ternary cropping system of G. elata, A. mellea and G. elata lead to imbalance of microbial community in rhizoshere and mycorrhizoshere soil, suggested that further studies on maintaining the balance of microbial community in A. mellea mycorrhizosphere and G. elata rhizosphere soil under field conditions may provide a promising avenue for high yield and high quality G. elata.

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.

Discussion paper: Sustainable increase of crop production through improved technical strategies, breeding and adapted management - A European perspective

During the next decade it will be necessary to develop novel combinations of management strategies to sustainably increase crop production and soil resilience. Improving agricultural productivity, while conserving and enhancing biotic and abiotic resources, is an essential requirement to increase global food production on a sustainable basis. The role of farmers in increasing agricultural productivity growth sustainably will be crucial. Farmers are at the center of any process of change involving natural resources and for this reason they need to be encouraged and guided, through appropriate incentives and governance practices, to conserve natural ecosystems and their biodiversity, and minimize the negative impact agriculture can have on the environment. Farmers and stakeholders need to revise traditional approaches not as productive as the modern approaches but more friendly with natural and environmental ecosystems values as well as emerging novel tools and approaches addressing precise farming, organic amendments, lowered water consumption, integrated pest control and beneficial plant-microbe interactions. While practical solutions are developing, science based recommendations for crop rotations, breeding and harvest/postharvest strategies leading to environmentally sound and pollinator friendly production and better life in rural areas have to be provided.

Response of bacterial communities in rubber plantations to different fertilizer treatments

In the present study, the effects of chemical fertilizer (CF) and organic fertilizer plus chemical fertilizer application (OF-CF) on natural rubber yield, soil properties, and soil bacterial community were systematically investigated in rubber plantations. The rubber dry yield was 26.3% more in the OF treatment group than in the CF treatment group. The contents of total nitrogen (TN), available nitrogen (AN), available phosphorus (AP), and available potassium (AK) as well as soil organic matter (SOM) and pH value were higher following OF-CF treatment. Using Illumina sequencing, a total of 927 operational taxonomic units (OTUs) were obtained following CF treatment, while 955 OTUs were obtained after OF-CF treatment. Relative abundance analysis showed the relative abundances of four phyla (Acidobacteria, Proteobacteria, Actinobacteria, Gemmatimonadetes) were different between the two treatment groups. Correlation analysis revealed Acidobacteria, Bacteroidetes, Thaumarchaeota, Elusimicrobia, Verrucomicrobia were the key taxa that determined the soil properties. Additionally, five OTUs (OTU_506, OTU_391, OTU_189, OTU_278, OTU_1057) were thought to be related to the biodegradation of natural rubber. Taken together, these results improve our understanding of the OF-mediated improvement in soil fertility and contribute to the identification of rubber-degrading bacteria in rubber plantations.

A Rhizosphere-Derived Consortium of Bacillus subtilis and Trichoderma harzianum Suppresses Common Scab of Potato and Increases Yield

The ability of a rhizosphere-derived microbial product (composed of a consortium of a strain of Bacillus subtilis and a strain of Trichoderma harzianum) to suppress common scab disease in potato caused by Streptomyces spp. was examined over a two-year period. Relative to the condition in which 0 kg·ha^-1 of the designated microbial product was applied (control), the disease index decreased by 30.6%-46.1%, and yield increased by 23.0%-32.2% in treatments in which 225 or 300 kg·ha^-1 of the microbial product was administered, respectively. The bacterial communities present in the rhizosphere were assessed at an early stage of tuber formation, a time at which tubers are susceptible to common scab. Potato plants in which soils were treated with 225 or 300 kg·ha^-1 of the microbial product harbored rhizospheric microbiota with lower α-diversity and an increased relative abundance of taxa representing the beneficial bacteria. In summary, a select microbial product composed of a consortium of Bacillus subtilis and Trichoderma harzianum effectively suppressed common scab disease and increased tuber yield by establishing a high relative abundance of beneficial bacteria in the rhizosphere.

Ten years of application of sewage sludge on tropical soil. A balance sheet on agricultural crops and environmental quality

Sewage sludge (SS) has been used in agriculture on a large scale in Europe. In tropical climate conditions, due to rapid organic matter degradation, SS can provide toxic elements that can cause damage to the environment. We evaluated an area that received doses of SS for 10 years compared to mineral fertilization. The biogeochemical parameters (amylase, cellulase, invertase and dehydrogenase activity, carbon microbial biomass, basal respiration, metabolic quotient, soluble carbohydrates, total carbohydrates and glucose) and maize agronomic performance were evaluated. There was no increase of organic matter in the area due to the SS application. However, the application of SS for 10 consecutive years influenced the biogeochemical parameters evaluated in a similar way to the area that received mineral fertilizer. The SS proved efficient in completely replacing P fertilization and micronutrients. SS can also partially replace N fertilization without reducing maize productivity.

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.

MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health

Plant roots nurture a tremendous diversity of microbes via exudation of photosynthetically fixed carbon sources. In turn, probiotic members of the root microbiome promote plant growth and protect the host plant against pathogens and pests. In the Arabidopsis thaliana-Pseudomonas simiae WCS417 model system the root-specific transcription factor MYB72 and the MYB72-controlled β-glucosidase BGLU42 emerged as important regulators of beneficial rhizobacteria-induced systemic resistance (ISR) and iron-uptake responses. MYB72 regulates the biosynthesis of iron-mobilizing fluorescent phenolic compounds, after which BGLU42 activity is required for their excretion into the rhizosphere. Metabolite fingerprinting revealed the antimicrobial coumarin scopoletin as a dominant metabolite that is produced in the roots and excreted into the rhizosphere in a MYB72- and BGLU42-dependent manner. Shotgun-metagenome sequencing of root-associated microbiota of Col-0, myb72, and the scopoletin biosynthesis mutant f6'h1 showed that scopoletin selectively impacts the assembly of the microbial community in the rhizosphere. We show that scopoletin selectively inhibits the soil-borne fungal pathogens Fusarium oxysporum and Verticillium dahliae, while the growth-promoting and ISR-inducing rhizobacteria P. simiae WCS417 and Pseudomonas capeferrum WCS358 are highly tolerant of the antimicrobial effect of scopoletin. Collectively, our results demonstrate a role for coumarins in microbiome assembly and point to a scenario in which plants and probiotic rhizobacteria join forces to trigger MYB72/BGLU42-dependent scopolin production and scopoletin excretion, resulting in improved niche establishment for the microbial partner and growth and immunity benefits for the host plant.

Antifungal activity of the bioactive substance from Bacillus atrophaeus strain HAB-5 and its toxicity assessment on Danio rerio

The prevalence of pathogen inhibitors bacteria has motivate the study for antimicrobial compounds. Bioactive fungicide have always received considerable attention. A bacterial isolated strain HAB-5 showed antifungal activity against plant fungi. Based on morphological, physiological, biochemical and 16SrDNA sequence analysis, the strain was identified to be a Bacillus atrophaeus. This strain possessed a broad spectrum antifungal activity against various plant pathogenic fungi. Extraction of antifungal substance was performed and the crude extract had potent antifungal ability and showed great potential for swelling and inhibiting spore germination. This antifungal displayed heat stability and active in a wide pH range 5.0-10.0. Moreover no reduction was found in its activity after enzyme treatment. The toxicity test was evaluated in Danio rerio. The acute toxicity test indicated that the 24, 48, 72, 96h LC₅₀ values of UMTLS to the zebrafish were 14.4, 13.8, 13.4, and 12.9%, respectively. Based on the results obtained in this study, antifungal substance was not toxic to zebra. Analyses of disease suppression showed that HAB-5 was effective to reduce the incidence of anthracnose symptoms on mango fruits, also prevent disease infection and protect tobacco seedling from Phytophtora nicotianae. The bioactive substance from Bacillus atrophaeus HAB-5 could be a candidate in the generation of new antifungal agents in crop.