Abstract
This research topic focuses on advancing understanding of recent studies on interactions between economic crops and microbiomes. A total of 15 manuscripts were submitted, of which 9 articles were published, including 8 original research articles and 1 mini-review. These studies involve 7 crops-rice, Rheum officinale, citrus, maize, pepper, mango, and Aloe vera-and specifically describe the roles of Botryosphaeria dothidea, Aureobasidium pullulans, and Burkholderia gladioli in economic crops. The articles cover various biological and abiotic stress-related topics, such as plant nitrogen use efficiency, phosphorus solubilization and growth promotion, crop quality improvement, aphid infestation, and pathogen pathogenicity.Bziuk et al. systematically explored the global distribution, ecological functions, and application potential of Aureobasidium pullulans within the frameworks of sustainable agriculture and the "One Health" concept, adopting a fungus with significant application value, from a novel microbiome-based perspective. Using the publicly available GlobalFungi database, the authors generated a macroscale global distribution map of A. pullulans. The analysis revealed a truly global distribution, with significantly higher detection rates in environments closely associated with human activities compared to natural ecosystems, highlighting a strong link to anthropogenic influence.These findings not only confirm the established value of A. pullulans as an effective biocontrol agent but also identity it as a natural core member of the plant microbiome.The results indicate that A. pullulans is not a transient colonizer but a resident symbiotic fungus with significant ecological influence. As a common component of the edible microbiome, A. pullulans may enter the human body through the food chain. Its potentially effects on the gut microbiome and human health was preliminarily explored, elevating its ecological significance to a "One Health" level that integrates plant, environmental, and human health. These findings provide a theoretical foundation for future in-depth development and application of A. pullulans in sustainable agriculture and health-related fields.To explore how soybean green manure with different intercropping durations affects citrus fruit quality by altering soil physicochemical properties and microbial communities in acidified citrus orchards, Deng et al. established field experimental groups with varying intercropping durations. They systematically measured citrus fruit quality indicators and soil physicochemical properties and analyzed the community structures of soil bacteria and fungi using high-throughput sequencing. Through correlation network analysis, they revealed complex associations among intercropping duration, soil parameters, key microbial groups, and fruit quality. Soybean green manure significantly enhanced fruit quality, improved the soil environment, and reshaped the soil microbial community. Intercropping soybean green manure in citrus orchards is an effective ecological agricultural practice. Its core mechanism is the synergistic improvement of fruit quality through dual pathways: enhancement of soil physicochemical properties and regulation of soil microbial communities. This study provides a solid theoretical and practical basis for applying green manure intercropping in acidified orchard soils to support sustainable ecological restoration and improve agricultural production efficiency. and their structure varies significantly among varieties. Rare taxa are the main drivers of community diversity and differentiation, while core taxa are highly conserved across varieties, primarily composed of high-abundance taxa, and occupy central positions in the co-occurrence network, thereby maintaining community stability. Five representative bacterial strains successfully isolated from seeds exhibited various plant growth-promoting characteristics in vitro, including siderophore production, phosphate solubilization, and indole-3-acetic acid synthesis. All strains promoted rice growth, increased nitrogen accumulation, and enhanced NUE. However, their growthpromoting effects were co-regulated by strain identity and nitrogen supply levels.Under low nitrogen conditions, the growth-promoting effects of the strains were pronounced, highlighting their potential for application in nutrient-stressed environments. The endophytic bacterial community within rice seeds co-evolve with the host through strategies of innovation and adaptation driven by rare taxa, and stability and inheritance maintained by core taxa. These natural symbiotic bacterial communities, as microbial allies of the host, enhance host adaptability in low-nitrogen soils through synergistic mechanisms such as nitrogen fixation, regulation of nitrogen metabolism, and production of plant hormones. Future research will focus on multi-dimensional analyses of plant-microbiome interaction networks. Synthetic biology and genome-editing technologies will facilitate the design of customized microbial communities, such as constructing SynComs with nitrogen fixation, phosphorus solubilization, and disease-resistance functions, enabling precise regulation of multiple effects from a single microbial inoculum. Simultaneously, strategies to enhance environmental adaptability are crucial. By utilizing directed evolution and metabolic engineering to modify microbial metabolic pathways, colonization stability under adverse conditions such as salinity, alkalinity, and drought can be improved. Furthermore, interdisciplinary collaboration will accelerate the exploration and industrialization of microbial resources, developing innovative solutions for agricultural carbon neutrality and food security, including living biopesticides based on endophytes and the construction of rhizosphere microbial seed banks.
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Claims 17
Claim · model-written summary
Aureobasidium pullulans shows significantly higher detection rates in environments closely associated with human activities than in natural ecosystems.
Verbatim
t0“economic crops”
e0“with significantly higher detection rates in environments closely associated with human activities compared to natural ecosystems”
Claim · model-written summary
Aureobasidium pullulans is a natural core member of the plant microbiome.
- Taxon
- economic cropst0
- Interactor
- A. pullulans
Aureobasidium pullulanse1symbiont - Outcome
- natural core member of the plant microbiomee1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“economic crops”
e1“These findings not only confirm the established value of A. pullulans as an effective biocontrol agent but also identity it as a natural core member of the plant microbiome”
Claim · model-written summary
Soybean green manure intercropping significantly enhanced citrus fruit quality.
CitrusNot reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e2“affects citrus fruit quality”
e3“Soybean green manure significantly enhanced fruit quality”
Claim · model-written summary
Soybean green manure improved the soil environment of citrus orchards.
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e2“affects citrus fruit quality”
e3“Soybean green manure significantly enhanced fruit quality”
e4“improved the soil environment”
Claim · model-written summary
Soybean green manure reshaped the soil microbial community in citrus orchards.
Not reportedComparatorDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e2“affects citrus fruit quality”
e3“Soybean green manure significantly enhanced fruit quality”
e5“reshaped the soil microbial community”
Claim · model-written summary
Improved citrus fruit quality under soybean green manure works through soil physicochemical properties and soil microbial communities.
- Outcome
- fruit qualitye6
- Qualifier
- dual pathways: enhancement of soil physicochemical properties and regulation of soil microbial communitiese6
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e2“affects citrus fruit quality”
e6“Its core mechanism is the synergistic improvement of fruit quality through dual pathways: enhancement of soil physicochemical properties and regulation of soil microbial communities”
Claim · model-written summary
The structure of the endophytic bacterial community in rice seeds varies significantly among varieties.
- Taxon
- rice
Oryza sativae7 - Outcome
- their structuree0
- Qualifier
- varies significantly among varietiese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e7“The endophytic bacterial community within rice seeds co-evolve with the host”
e0“and their structure varies significantly among varieties”
Claim · model-written summary
Rare taxa are the main drivers of community diversity and differentiation of rice seed endophytes.
- Taxon
- riceOryza sativae7
- Outcome
- community diversity and differentiatione1
- Qualifier
- Rare taxa are the main driverse1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e7“The endophytic bacterial community within rice seeds co-evolve with the host”
e1“Rare taxa are the main drivers of community diversity and differentiation”
Claim · model-written summary
Core taxa of rice seed endophytes are highly conserved across varieties.
- Taxon
- riceOryza sativae7
- Outcome
- core taxae2
- Qualifier
- highly conserved across varietiese2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e7“The endophytic bacterial community within rice seeds co-evolve with the host”
e2“while core taxa are highly conserved across varieties”
Claim · model-written summary
Core taxa of rice seed endophytes occupy central positions in the co-occurrence network.
- Taxon
- riceOryza sativae7
- Outcome
- occupy central positions in the co-occurrence networke3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e7“The endophytic bacterial community within rice seeds co-evolve with the host”
e3“occupy central positions in the co-occurrence network”
Claim · model-written summary
Five bacterial strains isolated from rice seeds showed plant growth-promoting characteristics in vitro.
- Taxon
- riceOryza sativae7
- Interactor
- bacterial strainse4symbiont
- Outcome
- plant growth-promoting characteristics in vitroe4
- Qualifier
- siderophore production, phosphate solubilization, and indole-3-acetic acid synthesise5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e7“The endophytic bacterial community within rice seeds co-evolve with the host”
e4“Five representative bacterial strains successfully isolated from seeds exhibited various plant growth-promoting characteristics in vitro”
e5“including siderophore production, phosphate solubilization, and indole-3-acetic acid synthesis”
Claim · model-written summary
All strains promoted rice growth.
- Taxon
- riceOryza sativae7
- Treatment
- All strainse6
- Interactor
- strainse6symbiont
- Outcome
- rice growthe6
- Direction
- promotede6
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e7“The endophytic bacterial community within rice seeds co-evolve with the host”
e6“All strains promoted rice growth, increased nitrogen accumulation, and enhanced NUE”
Claim · model-written summary
All strains increased nitrogen accumulation in rice.
- Taxon
- riceOryza sativae7
- Treatment
- All strainse6
- Interactor
- strainse6symbiont
- Outcome
- nitrogen accumulatione6
- Direction
- increasede6
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e7“The endophytic bacterial community within rice seeds co-evolve with the host”
e6“All strains promoted rice growth, increased nitrogen accumulation, and enhanced NUE”
Claim · model-written summary
All strains enhanced nitrogen use efficiency in rice.
- Taxon
- riceOryza sativae7
- Treatment
- All strainse6
- Interactor
- strainse6symbiont
- Outcome
- NUEe6
- Direction
- enhancede6
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e7“The endophytic bacterial community within rice seeds co-evolve with the host”
e6“All strains promoted rice growth, increased nitrogen accumulation, and enhanced NUE”
Claim · model-written summary
The growth-promoting effects of the strains in rice are co-regulated by strain identity and nitrogen supply levels.
- Taxon
- riceOryza sativae7
- Treatment
- nitrogen supply levelse6
- Outcome
- promoting effectse6
- Qualifier
- co-regulated by strain identity and nitrogen supply levelse6
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e7“The endophytic bacterial community within rice seeds co-evolve with the host”
e6“However, their growthpromoting effects were co-regulated by strain identity and nitrogen supply levels”
Claim · model-written summary
Under low nitrogen conditions, the growth-promoting effects of the strains in rice were pronounced.
- Taxon
- riceOryza sativae7
- Treatment
- low nitrogen conditionse6
- Outcome
- growth-promoting effectse6
- Direction
- pronouncede6
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e7“The endophytic bacterial community within rice seeds co-evolve with the host”
e6“Under low nitrogen conditions, the growth-promoting effects of the strains were pronounced”
Claim · model-written summary
Natural symbiotic bacterial communities enhance rice adaptability in low-nitrogen soils through nitrogen fixation, regulation of nitrogen metabolism and production of plant hormones.
- Taxon
- riceOryza sativae7
- Interactor
- natural symbiotic bacterial communitiese6symbiont
- Outcome
- host adaptability in low-nitrogen soilse6
- Qualifier
- synergistic mechanisms such as nitrogen fixation, regulation of nitrogen metabolism, and production of plant hormonese6
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e7“The endophytic bacterial community within rice seeds co-evolve with the host”
e6“These natural symbiotic bacterial communities, as microbial allies of the host, enhance host adaptability in low-nitrogen soils through synergistic mechanisms such as nitrogen fixation, regulation of nitrogen metabolism, and production of plant hormones”