Organic farming significantly improves microbial community structure, network complexity, and functional diversity in the Gannan navel orange orchard

In recent years, improper agricultural management practices have led to the loss of biodiversity and poor fruit quality in orchards. Converting conventional farming to organic farming is an environmentally responsible approach to improving sustainable fruit production. However, questions remain regarding how the microbial community responds to different farming practices in citrus trees. Specifically, this study aims to investigate how organic and conventional farming affect the microbial community structure and functional diversity in the Gannan navel orange orchard using 16S rRNA gene sequencing and Biolog Eco-Plate analysis. The results showed that the soil bacterial diversity (α-diversity index) under organic farming was higher than that under conventional farming. Actinobacteria, Bacteroidetes, and Firmicutes were more abundant in root and fruit compartments under organic farming, indicating that organic farming promotes the enrichment of copiotrophic bacteria (r-strategists). Furthermore, organic farming resulted in a considerable increase in the relative abundance of Burkholderia and Streptomyces in root tissues. Interestingly, organic farming exhibited a more complex bacterial network. Biolog analysis further revealed higher functional diversity of the soil microbial community under organic farming when compared with that under conventional farming. These findings provide evidence that organic farming improves the bacterial community structure and promotes microbial functional diversity in the citrus orchards, contributing to the overall health and production of the citrus crop. Synthetic microbial communities of the organic citrus orchards hold great promise for more efficient environment-friendly orchard management towards sustainable agriculture.

• Publication year

  2025

• Venue

  BMC Microbiology

• Publication date

  2025-08-29

• Fields of study

  Biology, Agricultural and Food Sciences, Medicine, Environmental Science

• Identifiers
  DOI 10.1186/s12866-025-04271-2PMID 40883662PMCID 12395713
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Organic cropping systems balance environmental impacts and agricultural production

  2024cited by this paper
• Grass cover increases soil microbial abundance and diversity and extracellular enzyme activities in orchards: A synthesis across China

  2023cited by this paper
• Organic fertilization drives shifts in microbiome complexity and keystone taxa increase the resistance of microbial mediated functions to biodiversity loss

  2023cited by this paper
• Soil organic carbon sequestration in agricultural long-term field experiments as derived from particulate and mineral-associated organic matter

  2023cited by this paper
• Soil conditions and the plant microbiome boost the accumulation of monoterpenes in the fruit of Citrus reticulata ‘Chachi’

  2023cited by this paper
• Extreme summers impact cropland and grassland soil microbiomes

  2023cited by this paper
• Soil microbial diversity and community composition during conversion from conventional to organic agriculture

  2022cited by this paper
• The phyllosphere microbiome shifts toward combating melanose pathogen

  2022cited by this paper
• Variation of soil bacterial communities in a chronosequence of citrus orchard

  2022cited by this paper
• Mineral and Organic Fertilizers Distinctly Affect Fungal Communities in the Crop Rhizosphere

  2022cited by this paper
• Soil pH: a key edaphic factor regulating distribution and functions of bacterial community along vertical soil profiles in red soil of pomelo orchard

  2022cited by this paper
• Root-secreted bitter triterpene modulates the rhizosphere microbiota to improve plant fitness

  2022cited by this paper
• Differential response of bacterial diversity and community composition to different tree ages of pomelo under red and paddy soils

  2022cited by this paper
• Soil Health and Biodiversity Is Driven by Intensity of Organic Farming in Canada

  2022cited by this paper
• Impact of Application of Abscisic Acid, Benzothiadiazole and Chitosan on Berry Quality Characteristics and Plant Associated Microbial Communities of Vitis vinifera L var. Mouhtaro Plants

  2021cited by this paper
• The Citrus Microbiome: From Structure and Function to Microbiome Engineering and Beyond

  2021cited by this paper
• Comparative Metagenomics Reveals Microbial Signatures of Sugarcane Phyllosphere in Organic Management

  2021influential reference
• Impacts of global change on the phyllosphere microbiome

  2021cited by this paper
• Beyond organic farming - harnessing biodiversity-friendly landscapes.

  2021cited by this paper
• Soil applied Ca, Mg and B altered phyllosphere and rhizosphere bacterial microbiome and reduced Huanglongbing incidence in Gannan Navel Orange.

  2021cited by this paper
• Linking the Phyllosphere Microbiome to Plant Health.

  2020cited by this paper
• Distinct microbial communities among different tissues of citrus tree Citrus reticulata cv. Chachiensis

  2020cited by this paper
• Dramatic loss of inorganic carbon by nitrogen‐induced soil acidification in Chinese croplands

  2020cited by this paper
• Innovative management programme reduces environmental impacts in Chinese vegetable production

  2020cited by this paper
• Soil Fertility, Microbial Biomass, and Microbial Functional Diversity Responses to Four Years Fertilization in an Apple Orchard in North China

  2020cited by this paper
• Spatial variation of the soil bacterial community in major apple producing regions of China

  2020cited by this paper
• Host selection shapes crop microbiome assembly and network complexity.

  2020cited by this paper
• Plant–microbiome interactions: from community assembly to plant health

  2020cited by this paper
• Organic management promotes natural pest control through altered plant resistance to insects

  2020cited by this paper
• National food production stabilized by crop diversity

  2019cited by this paper
• The Citrus Huanglongbing Crisis and Potential Solutions.

  2019cited by this paper
• Biodiversity and yield under different land-use types in orchard/vineyard landscapes: A meta-analysis

  2019cited by this paper
• Using enzyme activities and soil microbial diversity to understand the effects of fluoxastrobin on microorganisms in fluvo-aquic soil.

  2019cited by this paper
• Deciphering bacterial community variation during soil and leaf treatments with biologicals and biofertilizers to control huanglongbing in citrus trees

  2019cited by this paper
• Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

  2019influential reference
• Sustainability in global agriculture driven by organic farming

  2019cited by this paper
• Predicting perturbation patterns from the topology of biological networks

  2018cited by this paper
• Pursuing sustainable productivity with millions of smallholder farmers

  2018cited by this paper
• Fertilizer N application rate impacts plant-soil feedback in a sanqi production system.

  2018cited by this paper
• Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

  2018cited by this paper
• Studies of Microbiota Dynamics Reveals Association of “Candidatus Liberibacter Asiaticus” Infection with Citrus (Citrus sinensis) Decline in South of Iran

  2018cited by this paper
• Soil bacterial networks are less stable under drought than fungal networks

  2018cited by this paper
• Transcriptome sequencing and ITRAQ reveal the detoxification mechanism of Bacillus GJ1, a potential biocontrol agent for Huanglongbing

  2018cited by this paper
• Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming

  2018cited by this paper
• Effects of agricultural management on phyllosphere fungal diversity in vineyards and the association with adjacent native forests

  2018cited by this paper
• The structure and function of the global citrus rhizosphere microbiome

  2018influential reference
• Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots

  2018influential reference
• Response of the soil microbial community to different fertilizer inputs in a wheat-maize rotation on a calcareous soil

  2018cited by this paper
• Organic Agriculture, Food Security, and the Environment

  2018cited by this paper
• Influence of red mud on soil microbial communities: Application and comprehensive evaluation of the Biolog EcoPlate approach as a tool in soil microbiological studies.

  2017cited by this paper
• The influence of fertiliser and pesticide emissions model on life cycle assessment of agricultural products: The case of Danish and Italian barley.

  2017cited by this paper
• Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees

  2017cited by this paper
• Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System

  2017cited by this paper
• Defining the Core Citrus Leaf- and Root-Associated Microbiota: Factors Associated with Community Structure and Implications for Managing Huanglongbing (Citrus Greening) Disease

  2017cited by this paper
• Soil networks become more connected and take up more carbon as nature restoration progresses

  2017cited by this paper
• Characterization of Antimicrobial-Producing Beneficial Bacteria Isolated from Huanglongbing Escape Citrus Trees

  2017cited by this paper
• Functional diversity and dominant populations of bacteria in banana plantation soils as influenced by long-term organic and conventional farming

  2017cited by this paper
• Variation of functional diversity of soil microbial community in sub-humid tropical rice-rice cropping system under long-term organic and inorganic fertilization

  2017cited by this paper
• Organic farming increases richness of fungal taxa in the wheat phyllosphere

  2017cited by this paper
• Organic farming enhances soil microbial abundance and activity—A meta-analysis and meta-regression

  2017cited by this paper
• Root order-dependent seasonal dynamics in the carbon and nitrogen chemistry of poplar fine roots

  2017cited by this paper
• Research priorities for harnessing plant microbiomes in sustainable agriculture

  2017cited by this paper
• Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation

  2016cited by this paper
• Networking in the Plant Microbiome

  2016cited by this paper
• Effects of organic–inorganic compound fertilizer with reduced chemical fertilizer application on crop yields, soil biological activity and bacterial community structure in a rice–wheat cropping system

  2016cited by this paper
• Thirty four years of nitrogen fertilization decreases fungal diversity and alters fungal community composition in black soil in northeast China

  2016cited by this paper
• Organic agriculture in the twenty-first century

  2016cited by this paper
• Changes in soil physicochemical and microbial properties along elevation gradients in two forest soils

  2016cited by this paper
• Effect of biochar on the growth of Poncirus trifoliata (L.) Raf. seedlings in Gannan acidic red soil

  2016cited by this paper
• Organic Farming, Soil Health, and Food Quality: Considering Possible Links

  2016cited by this paper
• Significant alteration of soil bacterial communities and organic carbon decomposition by different long-term fertilization management conditions of extremely low-productivity arable soil in South China.

  2016cited by this paper
• DADA2: High resolution sample inference from Illumina amplicon data

  2016cited by this paper
• Financial competitiveness of organic agriculture on a global scale

  2015cited by this paper
• Bacterial diversity in soils subjected to long-term chemical fertilization can be more stably maintained with the addition of livestock manure than wheat straw

  2015cited by this paper
• The Application of the Biolog EcoPlate Approach in Ecotoxicological Evaluation of Dairy Sewage Sludge

  2014cited by this paper
• Biodiversity conservation in agriculture requires a multi-scale approach

  2014cited by this paper
• Distinct soil microbial diversity under long-term organic and conventional farming

  2014influential reference
• Enhanced nitrogen deposition over China

  2013cited by this paper
• Bacterial Communities Associated with the Surfaces of Fresh Fruits and Vegetables

  2013cited by this paper
• Effects of actinobacteria on plant disease suppression and growth promotion

  2013cited by this paper
• Effects of actinobacteria on plant disease suppression and growth promotion

  2013cited by this paper
• Beyond the Venn diagram: the hunt for a core microbiome.

  2012cited by this paper
• Soil microbial biomass and organic matter fractions during transition from conventional to organic farming systems

  2012cited by this paper
• Environmental Impact of Different Agricultural Management Practices: Conventional vs. Organic Agriculture

  2011cited by this paper
• Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere

  2011cited by this paper
• The impact of ice melting on bacterioplankton in the Arctic Ocean

  2010cited by this paper
• Linear and nonlinear multivariate regressions for determination sugar content of intact Gannan navel orange by Vis-NIR diffuse reflectance spectroscopy

  2010cited by this paper
• Significant Acidification in Major Chinese Croplands

  2010cited by this paper
• Impact of organic and conventional management on the phyllosphere microbial ecology of an apple crop.

  2009cited by this paper
• Fast UniFrac: Facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data

  2009influential reference
• Culturable Fungi of Stored ‘Golden Delicious’ Apple Fruits: A One-Season Comparison Study of Organic and Integrated Production Systems in Switzerland

  2008cited by this paper
• Agricultural sustainability: concepts, principles and evidence

  2008cited by this paper
• Response of soil microbial biomass and community structures to conventional and organic farming systems under identical crop rotations.

  2007cited by this paper
• Toward an ecological classification of soil bacteria.

  2007cited by this paper
• Ecological networks and their fragility

  2006cited by this paper
• The igraph software package for complex network research

  2006cited by this paper
• Arbuscular mycorrhizal fungi and organic farming

  2006cited by this paper
• Organic and Conventional Farming Systems: Environmental and Economic Issues.

  2005cited by this paper
• The effects of organic agriculture on biodiversity and abundance: a meta‐analysis

  2005cited by this paper
• The use of colony development for the characterization of bacterial communities in soil and on roots

  2004cited by this paper

• Do soil microbes regulate citrus fruit quality through soil nutrient availability?

  2026cites this paper
• Mg-enriched nutrient management enhances phyllosphere bacterial diversity, community structure, and functional traits in pomelo orchards

  2025cites this paper