Organic Farming Improves Soil Microbial Abundance and Diversity under Greenhouse Condition: A Case Study in Shanghai (Eastern China)

Organic amendments modulate the crop yield and rhizospheric bacterial community diversity: a 3-year field study with Cajanus cajan

Excessive use of chemicals to enhance soil nutrient status and crop yield has resulted in a decline in soil health. Organic farming promotes organic amendments, which help to balance the ecosystem. Understanding the dynamic patterns of belowground microbial populations is essential for developing sustainable agricultural systems. Therefore, the study was designed to evaluate the effect of different agri-practices on rhizospheric bacterial diversity and crop yield in an Indian agricultural system. A 3-year field experiment was set up in a randomized block design using Cajanus cajan as a model crop, comparing conventional farming with organic practice (with animal manure and bio-compost as amendments). Plant and rhizospheric soil samples were collected at the harvest stage for assessing various growth attributes, and for characterizing rhizospheric bacterial diversity. Enhanced crop productivity was seen in conventional farming, with a 2.2-fold increase in grain yield over control. However, over the 3 years, an overall positive impact was observed in the bio-compost-based organic amendment, in terms of bacterial abundance, over other treatments. At the harvest stage of the third cropping season, the bacterial diversity in the organic treatments showed little similarity to the initial bacterial community composition of the amendment applied, indicating stabilization along the growth cycles. The study emphasizes the significance of the choice of the amendment for ushering in agricultural sustainability.

Transplantation of soil from organic field confers disease suppressive ability to conducive soil

Organic agriculture is a sustainable method of farming, and confers disease-suppressing abilities to disease-conducive soils via specialized soil microbiomes. This study aimed at transforming a disease-conducive soil from a conventional field into disease-suppressive soil by inoculating soil from an organic field previously established as "disease-suppressive". The effectiveness of the transformed soil was established with the model plant wheat (Triticum aestivum) grown under natural conditions, with regard to its potential in inhibiting fungal phytopathogens, Rhizoctonia solani and Fusarium oxysporum. The conducive soil inoculated with the disease-suppressive soil performed better than the control conducive soil in terms of reduced disease severity in plants, improved soil nutrient content, increased activity of hydrolytic enzymes, and increased abundance of structural and functional microbial markers. The study demonstrates the efficacy of the soil microbiome under long-term organic agriculture in transforming disease-conducive soil into disease-suppressive soils. Such practises are simple and easy to implement, and could greatly improve the sustainability and crop yield in developing countries.

Organic Farming Allows Balanced Fungal and Oomycetes Communities

Conventional and organic farming systems affect soils differently, thereby influencing microbial diversity and composition. Organic farming, which relies on natural processes, biodiversity, and cycles adapted to local conditions, is generally known to improve soil texture and alleviate microbial diversity loss compared with that of conventional farming, which uses synthetic inputs such as chemical fertilisers, pesticides, and herbicides. Although they affect the health and productivity of host plants, the community dynamics of fungi and fungi-like oomycetes (under Chromista) in organic farmland are poorly understood. The present study aimed to determine the differences in the diversity and composition of fungi and oomycetes inhabiting organic and conventional farm soils using culture-based DNA barcoding and culture-independent environmental DNA (eDNA) metabarcoding. Four tomato farms with different farming practices were selected and investigated: mature pure organic (MPO) via non-pesticide and organic fertiliser, mature integrated organic (MIO) via non-pesticide and chemical fertiliser, mature conventional chemical (MCC) via both pesticide and chemical fertiliser, and young conventional chemical (YCC). Culture-based analysis revealed that different genera were dominant on the four farms: Linnemannia in MPO, Mucor in MIO, and Globisporangium in MCC and YCC. eDNA metabarcoding demonstrated that the fungal richness and diversity on the MPO farm were higher than that on other farms. Both conventional farms exhibited simpler fungal and oomycete network structures with lower phylogenetic diversity. Interestingly, a high richness of oomycetes was shown in YCC; in which, Globisporangium, a potential pathogenic group on tomato plants, was abundantly observed. Our findings indicate that organic farming enhances fungal and oomycete diversity, which may provide robust support for maintaining healthy and sustainable agricultural practices. This study contributes to our knowledge on the positive effects of organic farming on crop microbiomes and provides essential information for maintaining biological diversity.

Soil organic carbon stability mediate soil phosphorus in greenhouse vegetable soil by shifting phoD-harboring bacterial communities and keystone taxa

Addition of organic amendments, such as manure and straw, to arable fields as a partial substitute for mineral phosphorus (P), are a sustainable practice in high-efficiency agricultural production. Different organic inputs may induce varied soil organic carbon (OC) stability and phoD harboring microbes, subsequently regulate P behavior, but the underlying mechanisms are poorly understood. A 11-year field experiment examined P forms by ³¹P-nuclear magnetic resonance (NMR), OC chemical composition by ¹³C NMR, and biologically-based P availability methods, phoD bacterial communities, and their co-occurrence in soils amended with chemical P fertilizer (CF), chemical P partly substituted by organic amendments including pig manure (CM), a mixture of pig manure and corn straw (CMS), and corn straw (CS), with equal P input in all treatments. Organic amendments significantly increased soil labile P_i (CaCl₂-P, citrate-P, 2.91-3.26 and 1.16-1.32 times higher than CF) and P_o (enzyme-P, diesters, 4.08-7.47 and 1.71-2.14 times higher than CF) contents and phosphatase activities, while significantly decreased aromaticity (AI) and recalcitrance indexes (RI) of soil C, compared with CF. The keystone genera in manured soils (Alienimomas and Streptomyces) and straw-applied soils (Janthinobacterium and Caulobacter) were significantly correlated with soil enzyme-P, microbial biomass P (MBP), diesters, and citrate-P. Soil AI and RI were significantly correlated with the phoD keystone and soil P species. It suggested that the keystone was impacted by soil OC stability and play a role in regulating P redistribution in amended soils. This study highlights how manure and straw incorporation altered soil OC stability, shaped the phoD harboring community, and enhanced soil P biological processes promoted by the keystone taxa. The partial substitution of mineral P by mixture of manure and straw is effectively promote soil P availability and beneficial for environmental sustainability.

Existence of antibiotic pollutant in agricultural soil: Exploring the correlation between microbiome and pea yield

Due to sewage irrigation, manure fertilizer application or other agricultural activities, antibiotics have been introduced into farmland as an emerging contaminant, existing with other agrochemicals. However, the potential influences of antibiotics on the efficiency of agrochemicals and crops health are still unclear. In this work, the effect of antibiotics on fertilization efficiency and pea yield was evaluated, and the mechanism was explored in view of soil microbiome. Nitrogen utilization and pea yield were decreased by antibiotics. In specific, the weight of seeds decreased 9.5 % by 5 mg/kg antibiotics and decreased 25.1 % by 50 mg/kg antibiotics. For N nutrient in pea, antibiotics resulted in 62.5 %-63.7 % decrease in amino acid content and 8.3 %-35.3 % decrease in inorganic-N content. Further research showed that antibiotics interfered with N cycle in soil, inhibiting urea decomposition and denitrification process by reducing function genes ureC, nirK and norB in soil, thus decreasing N availability. Meanwhile, antibiotics destroyed the enzyme function in N assimilation. This work evaluated the environmental risk of antibiotics from fertilization efficiency and N utilization in crop. Antibiotics could not only affect N cycle, limiting the decomposition of N fertilizer, but also affect N utilization in plants, thus affecting the yield and even the quality of leguminous crops.

Tracking virulence genes and their interaction with antibiotic resistome during manure fertilization

Antibiotic resistance genes, collectively termed as antibiotic resistome, are regarded as emerging contaminants. Antibiotics resistome can be highly variable in different environments, imposing environmental safety concern and public health risk when it is in conjunction with pathogenic bacteria. However, it remains elusive how pathogenic bacteria interact with antibiotic resistome, making it challenging to assess microbial risk. Here, we examined the presence and relative abundance of bacterial virulence genes representing potential pathogens in swine manure, compost, compost-amended soil, and unamended agricultural soil in five suburban areas of Beijing, China. The absolute abundances of virulence genes were marginally significantly (p < 0.100) increased in compost-amended soils than unamended soil, revealing potential health risks in manure fertilization. The composition of potential pathogens differed by sample types and was linked to temperature, antibiotics, and heavy metals. As antibiotics can confer pathogens the resistance to clinic treatment, it was alarming to note that virulence genes tended to co-exist with antibiotic resistance genes, as shown by prevalently positive links among them. Collectively, our results demonstrate that manure fertilization in agriculture might give rise to the development of potentially antibiotic-resistant pathogens, unveiling an environmental health risk that has been frequently overlooked.

Pyrosequencing and phenotypic microarray to decipher bacterial community variation in Sorghum bicolor (L.) Moench rhizosphere

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Different cultivation practices and climatic conditions play an important role in governing and modulating soil microbial communities.

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This work, investigated the changes in bacterial community composition at taxonomic and functional level in rhizosphere soil of sweet sorghum under extensive cultivation practices at three different field sites of South Africa.

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16S rRNA amplicon sequencing data revealed that at the phylum level, the dominant group was Cyanobacteria with a relative abundance of 63.3%, 71.8% and 81.6% from ASHSOIL1, ASHSOIL2, and ASHSOIL3, respectively.

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Community-level physiological profiling (CLPP) analysis revealed that the metabolic activity of the bacterial community in ASHSOIL3 was the highest, followed by ASHSOIL1 and ASHSOIL2.

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Overall, this study showed that soil pH, nutrient availability and cultivation practices played significant roles in governing the bacterial community composition in sorghum rhizosphere.

Different cultivation practices and climatic conditions play an important role in governing and modulating soil microbial communities as well as soil health. This study investigated, for the first time, keystone microbial taxa inhabiting the rhizosphere of sweet sorghum (Sorghum bicolor) under extensive cultivation practices at three different field sites of South Africa (North West-South (ASHSOIL1); Mpumalanga-West – (ASHSOIL2); and Free State-North West – (ASHSOIL3)). Soil analysis of these sites revealed differences in P, K, Mg, and pH. 16S rRNA amplicon sequencing data revealed that the rhizosphere bacterial microbiome differed significantly both in the structure and composition across the samples. The sequencing data revealed that at the phylum level, the dominant group was Cyanobacteria with a relative abundance of 63.3%, 71.8%, and 81.6% from ASHSOIL1, ASHSOIL2, and ASHSOIL3, respectively. Putative metabolic requirements analyzed by METAGENassist software revealed the ASHSOIL1 sample as the prominent ammonia degrader (21.1%), followed by ASHSOIL3 (17.3%) and ASHSOIL2 (11.1%). The majority of core-microbiome taxa were found to be from Cyanobacteria, Bacteroidetes, and Proteobacteria. Functionally, community-level physiological profiling (CLPP) analysis revealed that the metabolic activity of the bacterial community in ASHSOIL3 was the highest, followed by ASHSOIL1 and ASHSOIL2. This study showed that soil pH and nutrient availability and cultivation practices played significant roles in governing the bacterial community composition in the sorghum rhizosphere across the different sites.

Tools and challenges to exploit microbial communities in agriculture

Plants contain diverse microbial communities. The associated microorganisms confer advantages to the host plant, which include growth promotion, nutrient absorption, stress tolerance, and pathogen and disease resistance. In this review, we explore how agriculture is implementing the use of microbial inoculants (single species or consortia) to improve crop yields, and discuss current strategies to study plant-associated microorganisms and how their diversity varies under unconventional agriculture. It is predicted that microbial inoculation will continue to be used in agriculture.

Isolation and characterization of plant growth promoting rhizobacteria isolated from organically grown high yielding pole type native pea (Pisum sativum L.) variety Dentami of Sikkim, India

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The present research showcases the significant findings pertaining to the assessment and report of the first ever study on the isolation and identification of plant growth promoting rhizobacterial diversity of organic farming pea variety (Dentami) of Sikkim. Proteobacteria dominated the rhizospheric soil whereas the bulk soil was governed by Actinobacteria. Bacillus cereus P8 (66.5 µg ml⁻¹) and Bacillus mycoides PP1 (45.1 µg ml⁻¹) were the highest IAA producer and also showed other plant growth promoting and biocontrol traits, such as phosphorous and potassium solubilization, nitrogen-fixing activity and siderophore production. As, Sikkim is the first state in India to practice organic agriculture farming, hence, such study on the soil microbiology is of immense significance. In these rhizospheric soil, it was dominated by the Proteobacteria and similar bacterial isolates, suggesting that these soil flora might be playing significant roles to enhancing the crop production and soil fertility.

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Culture-dependent technique was used to assess plant growth promoting rhizobacterial diversity of pole type pea variety (Dentami) of Sikkim.

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The dominant phylum was Proteobacteria (56%) from rhizosphere soil and Actinobacteria (58%) from bulk soil.

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PCA analysis showed that Firmicutes (bulk soil) were positively correlated to SOC, and available K, whereas, Proteobacteria (rhizosphere soil) exhibited a high correlation to pH, and available P.

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Bacillus cereus P8, Arthrobacter woluwensis DP2, Paenarthrobacter nitroguajacolicus UP1, and Bacillus mycoides PP1 showed plant growth promotion and bio-control traits.

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Bacillus cereus P8 (66.5 µg mL⁻¹) and Bacillus mycoides PP1 (45.1 µg mL⁻¹) was thehighest IAA producer.

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Pot experiment confirmed that these isolates can be potential plant growth promoter under the agro-climatic conditions of Sikkim, India.

Organic farming is an eco-friendly and sustainable farming practice that enhances soil fertility and helps in improving soil quality. But with the commencement of more sophisticated advances in agricultural techniques, organic farming has gradually become limited in the world. Culture-dependent plant growth-promoting bacterial isolates were isolated from the bulk and rhizospheric soil, of the native high yielding pole type organic pea (Pisum sativum L.) cultivar Dentami of Dentam, West Sikkim, India. Based on the 16S rRNA gene sequencing identification of these isolates, it was found that from the bulk soil, Actinobacteria (58%) was the dominant phyla followed by Firmicutes (28%), and Proteobacteria (14%). In the rhizospheric soil it was dominated by Proteobacteria (56%), followed by Firmicutes (33%), and Bacteriodetes (11%). A total of 40 bacterial isolates were initially screened for the plant growth-promoting (PGP) activity and out of them only four bacterial isolates i.e., Bacillus cereus P8, Arthrobacter woluwensis DP2, Paenarthrobacter nitroguajacolicus PP3, and Bacillus mycoides PP10 with accession numbers MN589697, MN559516, MN519462 and MN589696 respectively were found to possess higher PGP activity (i.e. phosphorous, potassium solubilization and nitrogen-fixing activity) as compared to the other bacteria present in the soil. Based on the indole-3-acetic acid (IAA) quantitative assay and siderophore production assay, it was found that Bacillus cereus (MN589697) produced the highest IAA (65.5 µg mL⁻¹) and siderophore (71%) when compared with the other isolates. The statistical correlation suggests that pH and available phosphorus were the strongest influencing factors for the distribution of Proteobacteria in the rhizospheric soil. The results indicate that these isolates can be potential plant growth promoter under the agro-climatic conditions of Sikkim, India. To the best of our knowledge the present study is the first report of its kind and showcases significant findings pertaining to the assessment of diversity, isolation and identification of plant growth-promoting rhizobacteria of organic pea grown in Sikkim.

Effects of Abiotic Stress on Soil Microbiome

Rhizospheric organisms have a unique manner of existence since many factors can influence the shape of the microbiome. As we all know, harnessing the interaction between soil microbes and plants is critical for sustainable agriculture and ecosystems. We can achieve sustainable agricultural practice by incorporating plant-microbiome interaction as a positive technology. The contribution of this interaction has piqued the interest of experts, who plan to do more research using beneficial microorganism in order to accomplish this vision. Plants engage in a wide range of interrelationship with soil microorganism, spanning the entire spectrum of ecological potential which can be mutualistic, commensal, neutral, exploitative, or competitive. Mutualistic microorganism found in plant-associated microbial communities assist their host in a number of ways. Many studies have demonstrated that the soil microbiome may provide significant advantages to the host plant. However, various soil conditions (pH, temperature, oxygen, physics-chemistry and moisture), soil environments (drought, submergence, metal toxicity and salinity), plant types/genotype, and agricultural practices may result in distinct microbial composition and characteristics, as well as its mechanism to promote plant development and defence against all these stressors. In this paper, we provide an in-depth overview of how the above factors are able to affect the soil microbial structure and communities and change above and below ground interactions. Future prospects will also be discussed.

Linking soil bacterial diversity to satellite-derived vegetation productivity: a case study in arid and semi-arid desert areas

Increasing studies have begun to focus on biodiversity-productivity relationships for soil microorganisms through molecular ecology methods. However, most of these studies involve controlled experiments, and whether the relationship remains at large spatial scales is still largely unknown. To unravel this issue, archived desert soils from long-term experiments were analysed using high-throughput sequencing, and satellite-derived vegetation datasets were acquired to quantify productivity. Most of the abundant genera were significantly different between low- and high-productivity conditions, and soil bacterial communities were strongly impacted by productivity. Soil bacterial biodiversity, including observed operational taxonomic units and the Chao1, Shannon, and Faith's PD indexes, increased rapidly with productivity at low levels and then reached a relatively stable state, and similar phenomena were observed at multiple taxonomic ranks and for most of the dominant groups. Furthermore, we discovered that the mechanisms resulting in the observed relationship might be ecosystem resource availability in large-scale regions and species competition in local regions. Collectively, these results enhance our understanding of the linkage between belowground microorganisms and aboveground vegetation in arid and semi-arid areas and confirm the potential value of satellite-derived datasets in research on soil microbial diversity at large spatial scales.

Genetic and Morphological Diversity of Indigenous Bradyrhizobium Nodulating Soybean in Organic and Conventional Family Farming Systems

Organic farming systems are gaining popularity as agronomically and environmentally sound soil management strategies with potential to enhance soil microbial diversity and fertility, environmental quality and sustainable crop production. This work aimed at understanding the effect of organic and conventional farming on the diversity of soybean nodulating bradyrhizobia species. Field trapping of indigenous soybean Bradyrhizobium was done by planting promiscuous soybeans varieties SB16 and SC squire as well as non-promiscuous Gazelle in three organic and three conventional farms in Tharaka-Nithi County of Kenya. After 45 days of growth, 108 nodule isolates were obtained from the soybean nodules and placed into 13 groups based on their morphological characteristics. Genetic diversity was done by polymerase chain reaction (PCR) targeting 16S rDNA gene using universal primers P5-R and P3-F and sequencing was carried out using the same primer. High morphological and genetic diversity of the nodule isolates was observed in organic farms as opposed to conventional farms. There was little or no genetic differentiation between the nodule isolates from the different farms with the highest molecular variation (91.12%) being partitioned within populations as opposed to among populations (8.88%). All the isolates were identified as bradyrhizobia with close evolutionary ties with Bradyrhizobium japonicum and Bradyrhizobium yuanminense. Organic farming systems favor the proliferation of bradyrhizobia species and therefore a suitable environmentally friendly alternative for enhancing soybean production.

Distinct Root Microbial Communities in Nature Farming Rice Harbor Bacterial Strains With Plant Growth-Promoting Traits

A nature farming system is an ecological farming practice that entails cultivating crops without using chemical fertilizers and pesticides. To understand the diversity and functions of root microbiomes associated with nature farming systems, we compared the root microbial community of rice under nature farming conditions with those under conventional farming conditions. High-throughput amplicon analysis demonstrated a higher abundance and greater diversity of the root microbiome under unfertilized nature farming conditions than under conventional conditions. The application of chemical fertilizers reduced the microbial diversity and abundance of some beneficial taxa important for plant growth and health. Subsequently, we isolated and identified 46 endo- and epiphytic bacteria from rice roots grown under nature farming conditions and examined their plant growth-promoting activity. Six potential isolates were selected for plant growth assessment in insoluble P- and K-containing media. Most of the isolates promoted rice growth, and Pseudomonas koreensis AEPR1 was able to enhance rice growth significantly in both insoluble P- and K-containing media. Our data indicated that nature farming systems create a distinct root microbiome that is comparatively more diverse and supports plant growth under low-input cultivation practices than under conventional practices. The potential isolates could be exploited as sources with potential applications in sustainable agriculture.

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

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

Potential Benefits and Risks for Soil Health Derived From the Use of Organic Amendments in Agriculture

The use of organic amendments in agriculture is a common practice due to their potential to increase crop productivity and enhance soil health. Indeed, organic amendments of different origin and composition (e.g., animal slurry, manure, compost, sewage sludge, etc.) can supply valuable nutrients to the soil, as well as increase its organic matter content, with concomitant benefits for soil health. However, the application of organic amendments to agricultural soil entails a variety of risks for environmental and human health. Organic amendments often contain a range of pollutants, including heavy metals, persistent organic pollutants, potential human pathogens, and emerging pollutants. Regarding emerging pollutants, the presence of antibiotic residues, antibiotic-resistant bacteria, and antibiotic-resistance genes in agricultural amendments is currently a matter of much concern, due to the concomitant risks for human health. Similarly, currently, the introduction of microplastics to agricultural soil, via the application of organic amendments (mainly, sewage sludge), is a topic of much relevance, owing to its magnitude and potential adverse effects for environmental health. There is, currently, much interest in the development of efficient strategies to mitigate the risks associated to the application of organic amendments to agricultural soil, while benefiting from their numerous advantages.

Constructal Macroscale Thermodynamic Model of Spherical Urban Greenhouse Form with Double Thermal Envelope within Heat Currents

Urban agriculture is becoming a timely environmental friendly practice to strengthen cities’ resilience to climate change. However, there is a lack of academic literature regarding the thermodynamic potential of interior urban agriculture. Furthermore, there is always a need to develop, from scratch, an updated methodological approach that aims to assist architects of conceiving such specific thermodynamically complex interior environments. In this paper, urban space is identified as a ‘flow system’, and Bejan’s constructal law of generation of flow structure is used to morph and discover the system flow architecture that offers greater global performance (greater access to what flows). More precisely, a macroscale thermodynamic model of spherical urban greenhouse form with double thermal envelope has been developed while the methodological approach resulted in the definition of a decisional flowchart that can be reproduced by other researchers. On the basis of this macroscale constructal model, the present paper proposes reduced models that link thermodynamic and geometric parameters in an accurate manner and can be used at early design stages for pedagogic and qualitative optimization purposes, integrating urban farming to architectural programming.

Natural Farming Improves Soil Quality and Alters Microbial Diversity in a Cabbage Field in Japan

Natural farming (NF), an environmentally friendly agricultural practice similar to organic farming, was developed in Japan. Unlike conventional farming, little is known about the influence of NF on soil microbial communities, especially the surface soil. We therefore compared the effect of seven years’ conventional practice (CP), conventional practice without chemicals (CF), and NF on soil properties and microbial community structure at two soil depths (0–10, 10–20 cm) in an experimental cabbage field. Both soil depth and agricultural practice significantly influenced edaphic measures and microbial community structure. NF improved bulk density, pH, electrical conductivity, urease activity, and nitrate reductase activity in topsoil; similar trends were observed in deeper soil. Pyrosequencing demonstrated that the use of pesticides in conventional farming (CP) led to lower microbial abundance and diversity in topsoil than CF. Similarly, NF increased microbial abundance compared to CP. However, distinct taxa were present in the topsoil, but not deeper soil, in each treatment. CP-enriched microbial genera may be related to plant pathogens (e.g., Erwinia and Brenneria) and xenobiotic degraders (e.g., Sphingobacterium and Comamonas). The microbial community structure of NF was distinct to CP/CF, with enrichment of Pedomicrobium and Solirubrobacter, which may prefer stable soil conditions. Network analysis of dominant genera confirmed the more stable, complex microbial network structure of the 0–10 cm than 10–20 cm layer. Flavisolibacter/Candidatus Solibacter and Candidatus Nitrososphaera/Leuconostoc are potentially fundamental taxa in the 0–10 cm and 10–20 cm layer networks, respectively. Overall, we show that NF positively affects soil quality and microbial community composition within sustainable farming systems.