Yaping Yin , Raja Asad Ali Khan , Liping Li , Yinggu Wu , Chun Li , Yuejian Li , Sen Ren , Jing Zhang , Weiwei Wang , Runmao Lin , Manman Zhang , Xiaojun Liu , Jumei Hou , Genyun Liang
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These samples were analyzed to study the interrelationships between different cultivation modes and crop rhizosphere microorganisms.</div></div><div><h3>Results</h3><div>The results revealed significant regional differences in microbial communities due to microhabitat (rhizosphere and bulk soil) and geographic location. Common bacteria such as <em>Pseudomonas</em>, <em>Sphingomonas</em>, <em>Lysobacter</em> and <em>Rhodanobacter</em> were the most abundant and showed strong correlations with several other bacteria through co-occurrence networking. In addition, <em>Flavobacterium</em> sp. and <em>Bacillus</em> sp. were identified as keystone species for the rhizobia community structure. Synthetic microbial communities and pot experiments confirmed that these two keystone species could enrich the soil microbime and promote cucumber growth. <em>Flavobacterium</em> sp. may promote cucumber growth by regulating the rhizosphere microbial community while <em>Bacillus</em> sp. may influence cucumber growth by stabilizing the rhizosphere microbial biomass, further enhancing nutrient cycling efficiency and improving system stability, which in turn affected the agroecosystem.</div></div><div><h3>Conclusions</h3><div>Our study demonstrates that specific keystone species are important in shaping the cucumber rhizosphere microbiome and plant growth. These results provide insights into agroecosystem-microbe interrelationships and provide a potential basis for optimizing agricultural management strategies.</div></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"90 ","pages":"Pages 134-144"},"PeriodicalIF":4.9000,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"The diversity and keystone species of cucumber rhizosphere microbiome: Unveiling their role in driving cucumber growth and microbial communities\",\"authors\":\"Yaping Yin , Raja Asad Ali Khan , Liping Li , Yinggu Wu , Chun Li , Yuejian Li , Sen Ren , Jing Zhang , Weiwei Wang , Runmao Lin , Manman Zhang , Xiaojun Liu , Jumei Hou , Genyun Liang\",\"doi\":\"10.1016/j.nbt.2025.09.007\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>Background</h3><div>Studying the interrelationship between agroecosystems and the microbiome is essential in achieving sustainable agricultural development. In particular, the relationship between the rhizosphere microbiome and crops is critical to the health and stability of agroecosystems. This study evaluated the diversity and keystone species of the cucumber rhizosphere microbiome and investigated their contributing role in cucumber growth and microbial community regulation. A total of 108 soil samples were collected from the rhizosphere and bulk soil of cucumber crops in different locations and under different cultivation modes in a high-yield area. These samples were analyzed to study the interrelationships between different cultivation modes and crop rhizosphere microorganisms.</div></div><div><h3>Results</h3><div>The results revealed significant regional differences in microbial communities due to microhabitat (rhizosphere and bulk soil) and geographic location. Common bacteria such as <em>Pseudomonas</em>, <em>Sphingomonas</em>, <em>Lysobacter</em> and <em>Rhodanobacter</em> were the most abundant and showed strong correlations with several other bacteria through co-occurrence networking. In addition, <em>Flavobacterium</em> sp. and <em>Bacillus</em> sp. were identified as keystone species for the rhizobia community structure. Synthetic microbial communities and pot experiments confirmed that these two keystone species could enrich the soil microbime and promote cucumber growth. <em>Flavobacterium</em> sp. may promote cucumber growth by regulating the rhizosphere microbial community while <em>Bacillus</em> sp. may influence cucumber growth by stabilizing the rhizosphere microbial biomass, further enhancing nutrient cycling efficiency and improving system stability, which in turn affected the agroecosystem.</div></div><div><h3>Conclusions</h3><div>Our study demonstrates that specific keystone species are important in shaping the cucumber rhizosphere microbiome and plant growth. These results provide insights into agroecosystem-microbe interrelationships and provide a potential basis for optimizing agricultural management strategies.</div></div>\",\"PeriodicalId\":19190,\"journal\":{\"name\":\"New biotechnology\",\"volume\":\"90 \",\"pages\":\"Pages 134-144\"},\"PeriodicalIF\":4.9000,\"publicationDate\":\"2025-09-24\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"New biotechnology\",\"FirstCategoryId\":\"5\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S1871678425000950\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"BIOCHEMICAL RESEARCH METHODS\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"New biotechnology","FirstCategoryId":"5","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1871678425000950","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
The diversity and keystone species of cucumber rhizosphere microbiome: Unveiling their role in driving cucumber growth and microbial communities
Background
Studying the interrelationship between agroecosystems and the microbiome is essential in achieving sustainable agricultural development. In particular, the relationship between the rhizosphere microbiome and crops is critical to the health and stability of agroecosystems. This study evaluated the diversity and keystone species of the cucumber rhizosphere microbiome and investigated their contributing role in cucumber growth and microbial community regulation. A total of 108 soil samples were collected from the rhizosphere and bulk soil of cucumber crops in different locations and under different cultivation modes in a high-yield area. These samples were analyzed to study the interrelationships between different cultivation modes and crop rhizosphere microorganisms.
Results
The results revealed significant regional differences in microbial communities due to microhabitat (rhizosphere and bulk soil) and geographic location. Common bacteria such as Pseudomonas, Sphingomonas, Lysobacter and Rhodanobacter were the most abundant and showed strong correlations with several other bacteria through co-occurrence networking. In addition, Flavobacterium sp. and Bacillus sp. were identified as keystone species for the rhizobia community structure. Synthetic microbial communities and pot experiments confirmed that these two keystone species could enrich the soil microbime and promote cucumber growth. Flavobacterium sp. may promote cucumber growth by regulating the rhizosphere microbial community while Bacillus sp. may influence cucumber growth by stabilizing the rhizosphere microbial biomass, further enhancing nutrient cycling efficiency and improving system stability, which in turn affected the agroecosystem.
Conclusions
Our study demonstrates that specific keystone species are important in shaping the cucumber rhizosphere microbiome and plant growth. These results provide insights into agroecosystem-microbe interrelationships and provide a potential basis for optimizing agricultural management strategies.
期刊介绍:
New Biotechnology is the official journal of the European Federation of Biotechnology (EFB) and is published bimonthly. It covers both the science of biotechnology and its surrounding political, business and financial milieu. The journal publishes peer-reviewed basic research papers, authoritative reviews, feature articles and opinions in all areas of biotechnology. It reflects the full diversity of current biotechnology science, particularly those advances in research and practice that open opportunities for exploitation of knowledge, commercially or otherwise, together with news, discussion and comment on broader issues of general interest and concern. The outlook is fully international.
The scope of the journal includes the research, industrial and commercial aspects of biotechnology, in areas such as: Healthcare and Pharmaceuticals; Food and Agriculture; Biofuels; Genetic Engineering and Molecular Biology; Genomics and Synthetic Biology; Nanotechnology; Environment and Biodiversity; Biocatalysis; Bioremediation; Process engineering.