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Li H, Wu Q, Yu P, Ni B. Complete genome sequence of Achromobacter sp. strain E1, an endophyte from Zea mays L. cultivar (Zheng dan 958). Microbiol Resour Announc 2024:e0056024. [PMID: 39189723 DOI: 10.1128/mra.00560-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 07/29/2024] [Indexed: 08/28/2024] Open
Abstract
This announcement reports the complete genome sequence of Achromobacter sp. strain E1, which was isolated from the root of maize cultivar (Zheng dan 958) grown in Beijing, China. Achromobacter sp. strain E1 consists of a single, closed genome consisting of 5,975,307 bp, with GC content of 65.86%.
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Affiliation(s)
- Hao Li
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Qingliu Wu
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Pugang Yu
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Bin Ni
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
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Chen X, Liu J, Chen AJ, Wang L, Jiang X, Gong A, Liu W, Wu H. Burkholderia ambifaria H8 as an effective biocontrol strain against maize stalk rot via producing volatile dimethyl disulfide. PEST MANAGEMENT SCIENCE 2024; 80:4125-4136. [PMID: 38578571 DOI: 10.1002/ps.8119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/08/2024] [Accepted: 04/02/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Maize stalk rot (MSR) caused by Fusarium graminearum is the primary factor contributing to the reduction in maize yield and quality. However, this soil-borne disease presents a significant challenge for sustainable control through field management and chemical agents. The screening of novel biocontrol agents can aid in developing innovative and successful strategies for MSR control. RESULTS A total of 407 strains of bacteria were isolated from the rhizosphere soil of a resistant maize inbred line. One strain exhibited significant antagonistic activity in plate and pot experiments, and was identified as Burkholderia ambifaria H8. The strain could significantly inhibit the mycelial growth and spore germination of F. graminearum, induce resistance to stalk rot, and promote plant growth. The volatile compounds produced by strain H8 and its secondary metabolites in the sterile fermentation broth exhibited antagonistic activity. The primary volatile compound produced by strain H8 was identified as dimethyl disulfide (DMDS) using gas chromatography tandem mass spectrometry. Through in vitro antagonistic activity assays and microscopic observation, it was confirmed that DMDS was capable of inhibiting mycelial growth and disrupting the mycelial structure of F. graminearum, suggesting it may be the major active compound for strain H8. The transcriptome data of F. graminearum further indicated that strain H8 and its volatile compounds could alter pathogenic fungi metabolism, influence the related metabolic pathways, and potentially induce cell apoptosis within F. graminearum. CONCLUSION Our results showed that B. ambifaria H8 was capable of producing the volatile substance dimethyl disulfide, which influenced the synthesis and permeability of cell membranes in pathogens. Thus, B. ambifaria H8 was found to be a promising biological control agent against MSR. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Xinyu Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Integrated Pest Management in Crops, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
| | - Jingrong Liu
- College of Life Science, Xinyang Normal University, Xinyang, China
| | - Amanda Juan Chen
- Microbiome Research Center, Moon (Beijing) Biotech Ltd., Beijing, P.R. China
| | - Lin Wang
- Microbiome Research Center, Moon (Beijing) Biotech Ltd., Beijing, P.R. China
| | - Xianzhi Jiang
- Microbiome Research Center, Moon (Beijing) Biotech Ltd., Beijing, P.R. China
| | - Andong Gong
- College of Life Science, Xinyang Normal University, Xinyang, China
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Integrated Pest Management in Crops, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
| | - Hanxiang Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Integrated Pest Management in Crops, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
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Cai Z, Yu T, Tan W, Zhou Q, Liu L, Nian H, Lian T. GmAMT2.1/2.2-dependent ammonium nitrogen and metabolites shape rhizosphere microbiome assembly to mitigate cadmium toxicity. NPJ Biofilms Microbiomes 2024; 10:60. [PMID: 39043687 PMCID: PMC11266425 DOI: 10.1038/s41522-024-00532-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 07/12/2024] [Indexed: 07/25/2024] Open
Abstract
Cadmium (Cd), a heavy metal, is negatively associated with plant growth. AMT (ammonium transporter) genes can confer Cd resistance and enhance nitrogen (N) uptake in soybeans. The potential of AMT genes to alleviate Cd toxicity by modulating rhizosphere microbiota remains unkonwn. Here, the rhizosphere microbial taxonomic and metabolic differences in three genotypes, i.e., double knockout and overexpression lines and wild type, were identified. The results showed that GmAMT2.1/2.2 genes could induce soybean to recruit beneficial microorganisms, such as Tumebacillus, Alicyclobacillus, and Penicillium, by altering metabolites. The bacterial, fungal, and cross-kingdom synthetic microbial communities (SynComs) formed by these microorganisms can help soybean resist Cd toxicity. The mechanisms by which SynComs help soybeans resist Cd stress include reducing Cd content, increasing ammonium (NH4+-N) uptake and regulating specific functional genes in soybeans. Overall, this study provides valuable insights for the developing microbial formulations that enhance Cd resistance in sustainable agriculture.
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Affiliation(s)
- Zhandong Cai
- South China Institute for Soybean Innovation Research, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, 512000, China
| | - Taobing Yu
- South China Institute for Soybean Innovation Research, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Weiyi Tan
- South China Institute for Soybean Innovation Research, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, 512000, China
- Guangdong Provincial Key Laboratory for the Development Biology and Environmental Adaptation of Agricultural Organisms, South China Agricultural University, Guangzhou, Guangdong, China
- Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, China
| | - Qianghua Zhou
- South China Institute for Soybean Innovation Research, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Lingrui Liu
- South China Institute for Soybean Innovation Research, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Hai Nian
- South China Institute for Soybean Innovation Research, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, 512000, China.
- Guangdong Provincial Key Laboratory for the Development Biology and Environmental Adaptation of Agricultural Organisms, South China Agricultural University, Guangzhou, Guangdong, China.
- Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, China.
| | - Tengxiang Lian
- South China Institute for Soybean Innovation Research, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, 512000, China.
- Guangdong Provincial Key Laboratory for the Development Biology and Environmental Adaptation of Agricultural Organisms, South China Agricultural University, Guangzhou, Guangdong, China.
- Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, China.
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Wang HL, Chen ZZ, Koski TM, Zhang B, Wang XF, Zhang RB, Li RQ, Wang SX, Zeng JY, Li HP. Emerald Ash Borer Infestation-Induced Elevated Negative Correlations and Core Genera Shift in the Endophyte Community of Fraxinus bungeana. INSECTS 2024; 15:534. [PMID: 39057267 PMCID: PMC11277034 DOI: 10.3390/insects15070534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/10/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024]
Abstract
Endophytes, prevalent in plants, mediate plant-insect interactions. Nevertheless, our understanding of the key members of endophyte communities involved in inhibiting or assisting EAB infestation remains limited. Employing ITS and 16S rRNA high-throughput sequencing, along with network analysis techniques, we conducted a comprehensive investigation into the reaction of endophytic fungi and bacteria within F. bungeana phloem by comparing EAB-infested and uninfected samples. Our findings reveal that EAB infestation significantly impacts the endophytic communities, altering both their diversity and overall structure. Interestingly, both endophytic fungi and bacteria exhibited distinct patterns in response to the infestation. For instance, in the EAB-infested phloem, the fungi abundance remained unchanged, but diversity decreased significantly. Conversely, bacterial abundance increased, without significant diversity changes. The fungi community structure altered significantly, which was not observed in bacteria. The bacterial composition in the infested phloem underwent significant changes, characterized by a substantial decrease in beneficial species abundance, whereas the fungal composition remained largely unaffected. In network analysis, the endophytes in infested phloem exhibited a modular topology, demonstrating greater complexity due to an augmented number of network nodes, elevated negative correlations, and a core genera shift compared to those observed in healthy phloem. Our findings increase understanding of plant-insect-microorganism relationships, crucial for pest control, considering endophytic roles in plant defense.
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Affiliation(s)
- Hua-Ling Wang
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
- Hebei Urban Forest Health Technology Innovation Center, Hebei Agricultural University, Baoding 071001, China
| | - Zhen-Zhu Chen
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
| | | | - Bin Zhang
- College of Life Sciences, Hebei University, Baoding 071002, China
| | - Xue-Fei Wang
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
| | - Rui-Bo Zhang
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
| | - Ruo-Qi Li
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
| | - Shi-Xian Wang
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
| | - Jian-Yong Zeng
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
- Key Laboratory of Forest Germplasm Resources and Protection of Hebei Province, Hebei Agricultural University, Baoding 071001, China
| | - Hui-Ping Li
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
- Hebei Urban Forest Health Technology Innovation Center, Hebei Agricultural University, Baoding 071001, China
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5
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Xu MQ, Pan F, Peng LH, Yang YS. Advances in the isolation, cultivation, and identification of gut microbes. Mil Med Res 2024; 11:34. [PMID: 38831462 PMCID: PMC11145792 DOI: 10.1186/s40779-024-00534-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 04/17/2024] [Indexed: 06/05/2024] Open
Abstract
The gut microbiome is closely associated with human health and the development of diseases. Isolating, characterizing, and identifying gut microbes are crucial for research on the gut microbiome and essential for advancing our understanding and utilization of it. Although culture-independent approaches have been developed, a pure culture is required for in-depth analysis of disease mechanisms and the development of biotherapy strategies. Currently, microbiome research faces the challenge of expanding the existing database of culturable gut microbiota and rapidly isolating target microorganisms. This review examines the advancements in gut microbe isolation and cultivation techniques, such as culturomics, droplet microfluidics, phenotypic and genomics selection, and membrane diffusion. Furthermore, we evaluate the progress made in technology for identifying gut microbes considering both non-targeted and targeted strategies. The focus of future research in gut microbial culturomics is expected to be on high-throughput, automation, and integration. Advancements in this field may facilitate strain-level investigation into the mechanisms underlying diseases related to gut microbiota.
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Affiliation(s)
- Meng-Qi Xu
- Department of Gastroenterology and Hepatology, the First Medical Center of Chinese, PLA General Hospital, Beijing, 100853, China
- Medical School of Chinese PLA, Beijing, 100853, China
| | - Fei Pan
- Department of Gastroenterology and Hepatology, the First Medical Center of Chinese, PLA General Hospital, Beijing, 100853, China
| | - Li-Hua Peng
- Department of Gastroenterology and Hepatology, the First Medical Center of Chinese, PLA General Hospital, Beijing, 100853, China
| | - Yun-Sheng Yang
- Department of Gastroenterology and Hepatology, the First Medical Center of Chinese, PLA General Hospital, Beijing, 100853, China.
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6
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Bao X, Chong P, He C, Wang X, Zhang F. Mechanism on the promotion of host growth and enhancement of salt tolerance by Bacillaceae isolated from the rhizosphere of Reaumuria soongorica. Front Microbiol 2024; 15:1408622. [PMID: 38881656 PMCID: PMC11176432 DOI: 10.3389/fmicb.2024.1408622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
Salt stress is a major abiotic stress that affects the growth of Reaumuria soongorica and many psammophytes in the desert areas of Northwest China. However, various Plant Growth-Promoting Rhizobacteria (PGPR) have been known to play an important role in promoting plant growth and alleviating the damaging effects of salt stress. In this study, three PGPR strains belonging to Bacillaceae were isolated from the rhizosphere of Reaumuria soongorica by morphological and molecular identification. All isolated strains exhibited capabilities of producing IAA, solubilizing phosphate, and fixing nitrogen, and were able to tolerate high levels of NaCl stress, up to 8-12%. The results of the pot-based experiment showed that salt (400 mM NaCl) stress inhibited Reaumuria soongorica seedlings' growth performance as well as biomass production, but after inoculation with strains P2, S37, and S40, the plant's height significantly increased by 26.87, 17.59, and 13.36%, respectively (p < 0.05), and both aboveground and root fresh weight significantly increased by more than 2 times compared to NaCl treatment. Additionally, inoculation with P2, S37, and S40 strains increased the content of photosynthetic pigments, proline, and soluble protein in Reaumuria soongorica seedlings under NaCl stress, while reducing the content of malondialdehyde and soluble sugars. Metabolomic analysis showed that strain S40 induces Reaumuria soongorica seedling leaves metabolome reprogramming to regulate cell metabolism, including plant hormone signal transduction and phenylalanine, tyrosine, and tryptophan biosynthesis pathways. Under NaCl stress, inoculation with strain S40 upregulated differential metabolites in plant hormone signal transduction pathways including plant hormones such as auxins (IAA), cytokinins, and jasmonic acid. The results indicate that inoculation with Bacillaceae can promote the growth of Reaumuria soongorica seedlings under NaCl stress and enhance salt tolerance by increasing the content of photosynthetic pigments, accumulating osmoregulatory substances, regulating plant hormone levels This study contributes to the enrichment of PGPR strains capable of promoting the growth of desert plants and has significant implications for the psammophytes growth and development in desert regions, as well as the effective utilization and transformation of saline-alkali lands.
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Affiliation(s)
- Xinguang Bao
- College of Forest of Gansu Agriculture University, Lanzhou, China
| | - Peifang Chong
- College of Forest of Gansu Agriculture University, Lanzhou, China
| | - Cai He
- Wuwei Academy of Forestry, Wuwei, China
| | - Xueying Wang
- College of Forest of Gansu Agriculture University, Lanzhou, China
| | - Feng Zhang
- College of Forest of Gansu Agriculture University, Lanzhou, China
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Wu R, Ji P, Hua Y, Li H, Zhang W, Wei Y. Research progress in isolation and identification of rumen probiotics. Front Cell Infect Microbiol 2024; 14:1411482. [PMID: 38836057 PMCID: PMC11148321 DOI: 10.3389/fcimb.2024.1411482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 04/30/2024] [Indexed: 06/06/2024] Open
Abstract
With the increasing research on the exploitation of rumen microbial resources, rumen probiotics have attracted much attention for their positive contributions in promoting nutrient digestion, inhibiting pathogenic bacteria, and improving production performance. In the past two decades, macrogenomics has provided a rich source of new-generation probiotic candidates, but most of these "dark substances" have not been successfully cultured due to the restrictive growth conditions. However, fueled by high-throughput culture and sorting technologies, it is expected that the potential probiotics in the rumen can be exploited on a large scale, and their potential applications in medicine and agriculture can be explored. In this paper, we review and summarize the classical techniques for isolation and identification of rumen probiotics, introduce the development of droplet-based high-throughput cell culture and single-cell sequencing for microbial culture and identification, and finally introduce promising cultureomics techniques. The aim is to provide technical references for the development of related technologies and microbiological research to promote the further development of the field of rumen microbiology research.
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Affiliation(s)
| | - Peng Ji
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | | | | | | | - Yanming Wei
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
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Wen X, Xu J, Worrich A, Li X, Yuan X, Ma B, Zou Y, Wang Y, Liao X, Wu Y. Priority establishment of soil bacteria in rhizosphere limited the spread of tetracycline resistance genes from pig manure to soil-plant systems based on synthetic communities approach. ENVIRONMENT INTERNATIONAL 2024; 187:108732. [PMID: 38728817 DOI: 10.1016/j.envint.2024.108732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/02/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024]
Abstract
The spread of antibiotic resistance genes (ARGs) in agroecosystems through the application of animal manure is a global threat to human and environmental health. However, the adaptability and colonization ability of animal manure-derived bacteria determine the spread pathways of ARG in agroecosystems, which have rarely been studied. Here, we performed an invasion experiment by creating a synthetic communities (SynCom) with ten isolates from pig manure and followed its assembly during gnotobiotic cultivation of a soil-Arabidopsis thaliana (A. thaliana) system. We found that Firmicutes in the SynCom were efficiently filtered out in the rhizosphere, thereby limiting the entry of tetracycline resistance genes (TRGs) into the plant. However, Proteobacteria and Actinobacteria in the SynCom were able to establish in all compartments of the soil-plant system thereby spreading TRGs from manure to soil and plant. The presence of native soil bacteria prevented the establishment of manure-borne bacteria and effectively reduced the spread of TRGs. Achromobacter mucicolens and Pantoea septica were the main vectors for the entry of tetA into plants. Furthermore, doxycycline stress promoted the horizontal gene transfer (HGT) of the conjugative resistance plasmid RP4 within the SynCom in A. thaliana by upregulating the expression of HGT-related mRNAs. Therefore, this study provides evidence for the dissemination pathways of ARGs in agricultural systems through the invasion of manure-derived bacteria and HGT by conjugative resistance plasmids and demonstrates that the priority establishment of soil bacteria in the rhizosphere limited the spread of TRGs from pig manure to soil-plant systems.
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Affiliation(s)
- Xin Wen
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Resources and Environment, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan 512005, China; Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig 04318, Germany
| | - Jiaojiao Xu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Resources and Environment, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Anja Worrich
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig 04318, Germany.
| | - Xianghui Li
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Resources and Environment, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xingyun Yuan
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Resources and Environment, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Baohua Ma
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Yongde Zou
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Yan Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Resources and Environment, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xindi Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Resources and Environment, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Yinbao Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Resources and Environment, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong 525000, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
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Zhang J, Zhang H, Luo S, Ye L, Wang C, Wang X, Tian C, Sun Y. Analysis and Functional Prediction of Core Bacteria in the Arabidopsis Rhizosphere Microbiome under Drought Stress. Microorganisms 2024; 12:790. [PMID: 38674734 PMCID: PMC11052302 DOI: 10.3390/microorganisms12040790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/01/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
The effects of global warming, population growth, and economic development are increasing the frequency of extreme weather events, such as drought. Among abiotic stresses, drought has the greatest impact on soil biological activity and crop yields. The rhizosphere microbiota, which represents a second gene pool for plants, may help alleviate the effects of drought on crops. In order to investigate the structure and diversity of the bacterial communities on drought stress, this study analyzed the differences in the bacterial communities by high-throughput sequencing and bioinformatical analyses in the rhizosphere of Arabidopsis thaliana under normal and drought conditions. Based on analysis of α and β diversity, the results showed that drought stress had no significant effect on species diversity between groups, but affected species composition. Difference analysis of the treatments showed that the bacteria with positive responses to drought stress were Burkholderia-Caballeronia-Paraburkholderia (BCP) and Streptomyces. Drought stress reduced the complexity of the rhizosphere bacterial co-occurrence network. Streptomyces was at the core of the network in both the control and drought treatments, whereas the enrichment of BCP under drought conditions was likely due to a decrease in competitors. Functional prediction showed that the core bacteria metabolized a wide range of carbohydrates, such as pentose, glycans, and aromatic compounds. Our results provide a scientific and theoretical basis for the use of rhizosphere microbial communities to alleviate plant drought stress and the further exploration of rhizosphere microbial interactions under drought stress.
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Affiliation(s)
- Jianfeng Zhang
- Key Laboratory of Straw Comprehensive Utilization and Black Soil, Conservation College of Life Science, The Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (H.Z.); (L.Y.); (X.W.)
| | - Hengfei Zhang
- Key Laboratory of Straw Comprehensive Utilization and Black Soil, Conservation College of Life Science, The Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (H.Z.); (L.Y.); (X.W.)
| | - Shouyang Luo
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (S.L.); (C.W.); (C.T.)
| | - Libo Ye
- Key Laboratory of Straw Comprehensive Utilization and Black Soil, Conservation College of Life Science, The Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (H.Z.); (L.Y.); (X.W.)
| | - Changji Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (S.L.); (C.W.); (C.T.)
| | - Xiaonan Wang
- Key Laboratory of Straw Comprehensive Utilization and Black Soil, Conservation College of Life Science, The Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (H.Z.); (L.Y.); (X.W.)
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (S.L.); (C.W.); (C.T.)
| | - Yu Sun
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (S.L.); (C.W.); (C.T.)
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Ji C, Guo J, Ma Y, Xu X, Zang T, Liu S, An Z, Yang M, He X, Zheng W. Application Progress of Culturomics in the Isolated Culture of Rhizobacteria: A Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:7586-7595. [PMID: 38530921 DOI: 10.1021/acs.jafc.3c08885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Comprehending the structure and function of rhizobacteria components and their regulation are crucial for sustainable agricultural management. However, obtaining comprehensive species information for most bacteria in the natural environment, particularly rhizobacteria, presents a challenge using traditional culture methods. To obtain diverse and pure cultures of rhizobacteria, this study primarily reviews the evolution of rhizobacteria culturomics and associated culture methods. Furthermore, it explores new strategies for enhancing the application of culturomics, providing valuable insights into efficiently enriching and isolate target bacterial strains/groups from the environment. The findings will help improve rhizobacteria's culturability and enrich the functional bacterial library.
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Affiliation(s)
- Chao Ji
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Junli Guo
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Ying Ma
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Xiangfu Xu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Tongyu Zang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Sentao Liu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Zhenzhen An
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Min Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Xiahong He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan 650201, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, Yunnan 650224, China
| | - Wenjie Zheng
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan 650201, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, Yunnan 650224, China
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11
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Ouyang Y, Cheng Q, Cheng C, Tang Z, Huang Y, Tan E, Ma S, Lin X, Xie Y, Zhou H. Effects of plants-associated microbiota on cultivation and quality of Chinese herbal medicines. CHINESE HERBAL MEDICINES 2024; 16:190-203. [PMID: 38706825 PMCID: PMC11064599 DOI: 10.1016/j.chmed.2022.12.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/24/2022] [Accepted: 12/29/2022] [Indexed: 02/05/2023] Open
Abstract
Microbial resource influences the life activities of medicinal plants from several perspectives. Endophytes, rhizosphere microorganisms, and other environmental microorganisms play essential roles in medicinal plant growth and development, plant yield, and clinical efficacy. The microbiota can influence the biosynthesis of active compounds in medicinal plants by stimulating specific metabolic pathways. They induce host plants to improve their resistance to environmental stresses by accumulating secondary metabolites. Microorganisms can interact with their host plants to produce long-term, targeted selection results and improve their ability to adapt to the environment. Due to the interdependence and interaction between microorganisms and medicinal plants, Chinese herbal medicines (CHMs) quality is closely related to the associated microorganisms. This review summarizes the relationship between medicinal plants and their associated microorganisms, including their species, distribution, life activities, and metabolites. Microorganisms can aid in quality control, improve the efficacy of medicinal plants, and provide markers for identifying the origin and storage time of CHMs. Therefore, a comprehensive understanding of the relationship between microorganisms and medicinal plants will help to control the quality of CHMs from different perspectives.
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Affiliation(s)
- Yue Ouyang
- Faculty of Chinese Medicine, Macau University of Science and Technology, Macao 999078, China
| | - Qiqing Cheng
- Faculty of Chinese Medicine, Macau University of Science and Technology, Macao 999078, China
- School of Pharmacy, Hubei University of Science and Technology, Xianning 437100, China
| | - Chunsong Cheng
- Key Laboratory of Plant Ex-situ Conservation and Research Center of Resource Plant, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China
| | - Ziyu Tang
- Faculty of Chinese Medicine, Macau University of Science and Technology, Macao 999078, China
| | - Yufeng Huang
- Guangdong Provincial Hospital of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, State Key Laboratory of Dampness Syndrome of Chinese Medicine, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou 510006, China
| | - Eyu Tan
- Guangdong Provincial Hospital of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, State Key Laboratory of Dampness Syndrome of Chinese Medicine, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou 510006, China
- Jiangmen Wuyi Hospital of Traditional Chinese Medicine, Jiangmen 529020, China
- Joint Laboratory for Translational Cancer Research of Chinese Medicine, Ministry of Education, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Shaofeng Ma
- Jiangmen Wuyi Hospital of Traditional Chinese Medicine, Jiangmen 529020, China
| | - Xinheng Lin
- Jiangmen Wuyi Hospital of Traditional Chinese Medicine, Jiangmen 529020, China
| | - Ying Xie
- Guangdong Provincial Hospital of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, State Key Laboratory of Dampness Syndrome of Chinese Medicine, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou 510006, China
- Faculty of Chinese Medicine, Macau University of Science and Technology, Macao 999078, China
| | - Hua Zhou
- Guangdong Provincial Hospital of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, State Key Laboratory of Dampness Syndrome of Chinese Medicine, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou 510006, China
- Faculty of Chinese Medicine, Macau University of Science and Technology, Macao 999078, China
- Joint Laboratory for Translational Cancer Research of Chinese Medicine, Ministry of Education, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
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12
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Gao Y, Peng K, Bai D, Bai XY, Bi Y, Chen A, Chen B, Chen F, Chen J, Chen L, Chen T, Chen W, Cheng X, Cheng Y, Cui J, Dai J, Dai J, Dai Z, Deng Y, Deng YZ, Ding W, Fang Z, Fu W, Gao H, Gu S, Guo X, Guo X, Han D, He L, He Y, Hou HY, Jia B, Jia G, Jiao S, Jin W, Ju F, Ju Z, Kong S, Lan C, Li B, Li D, Li D, Li J, Li M, Li Q, Li Q, Li WJ, Li X, Li X, Li Y, Li YG, Liang Z, Ling N, Liu F, Liu Q, Liu SJ, Lu H, Lu Q, Luo G, Luo H, Luo Y, Lyu H, Ma C, Ma L, Ma T, Ni J, Pang Z, Qiang X, Qin Y, Qu Q, Ran C, Ren S, Shang H, Song L, Sun L, Sun W, Tang L, Tian J, Wang K, Wang M, Wang MK, Wang T, Wang XY, Wang Y, Wang Y, Wang Y, Wei H, Wei H, Wei Z, Wen T, Wu J, Wu L, Wu L, Xi J, Xie B, Xu G, Xu J, Xu S, Xue Q, Yan L, Yang H, Yang J, Yang J, Yang R, Yang Y, Yang YJ, Yao X, Yao Y, Yousuf S, Yu K, Yuan Z, Yuan Z, Zhang D, Zhang T, Zhang W, Zhang Y, Zhang Z, Zhang Z, Zhang ZF, Zhao S, Zhao W, Zheng M, Zheng Z, Zhou X, Zhou Y, Zhou Z, Zhu M, Zhu YG, Chu H, Bai Y, Liu YX. The Microbiome Protocols eBook initiative: Building a bridge to microbiome research. IMETA 2024; 3:e182. [PMID: 38882487 PMCID: PMC11170964 DOI: 10.1002/imt2.182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 06/18/2024]
Abstract
The Microbiome Protocols eBook (MPB) serves as a crucial bridge, filling gaps in microbiome protocols for both wet experiments and data analysis. The first edition, launched in 2020, featured 152 meticulously curated protocols, garnering widespread acclaim. We now extend a sincere invitation to researchers to participate in the upcoming 2nd version of MPB, contributing their valuable protocols to advance microbiome research.
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Affiliation(s)
- Yunyun Gao
- Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
| | - Kai Peng
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine Yangzhou University Yangzhou China
| | - Defeng Bai
- Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
| | | | - Yujing Bi
- State Key Laboratory of Pathogen and Biosecurity Beijing Institute of Microbiology and Epidemiology Beijing China
| | - Anqi Chen
- Bio-Protocol Editorial Office China Bio-Protocol Journal Beijing China
| | - Baodong Chen
- Research Center for Eco-Environmental Sciences Chinese Academy of Sciences Beijing China
| | - Feng Chen
- School of Stomatology Peking University Beijing China
| | - Juan Chen
- Institute of Medicinal Plant Development Chinese Academy of Medical Sciences Beijing China
| | - Lei Chen
- Department of Vascular Surgery, Fu Xing Hospital Capital Medical University Beijing China
| | - Tong Chen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica China Academy of Chinese Medical Sciences Beijing China
| | - Wei Chen
- Institute of Hydroecology Ministry of Water Resources & Chinese Academy of Sciences Wuhan China
| | - Xu Cheng
- Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
| | | | - Jie Cui
- The Institute of Infection and Health Research Fudan University Shanghai China
| | - Jingjing Dai
- Department of Medical Laboratory the Affiliated Huaian No.1 Hospital of Nanjing Medical University Huaian China
| | - Junbiao Dai
- Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
| | | | - Ye Deng
- Research Center for Eco-Environmental Sciences Chinese Academy of Sciences Beijing China
| | - Yi-Zhen Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre South China Agricultural University Guangzhou China
| | - Wei Ding
- Ocean University of China Qingdao China
| | - Zhencheng Fang
- Zhujiang Hospital Southern Medical University Guangzhou China
| | - Wei Fu
- Research Center for Eco-Environmental Sciences Chinese Academy of Sciences Beijing China
| | | | - Shaohua Gu
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies Peking University Beijing China
| | - Xue Guo
- Research Center for Eco-Environmental Sciences Chinese Academy of Sciences Beijing China
| | - Xuguang Guo
- Department of Clinical Laboratory Medicine, Guangdong Provincial Key Laboratory of Major Obstetric Diseases; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology The Third Affiliated Hospital of Guangzhou Medical University Guangzhou China
| | - Dongfei Han
- School of Environmental Science and Engineering Suzhou University of Science and Technology Suzhou China
| | - Lele He
- Hunan University Changsha China
| | - Yatao He
- School of Medicine, Model Animal Research Center (MARC) Nanjing University Nanjing China
| | - Hui-Yu Hou
- Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
| | | | - Gengjie Jia
- Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
| | - Shuo Jiao
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences Northwest A&F University Yangling China
| | - Wei Jin
- Nanjing Agricultural University Nanjing China
| | - Feng Ju
- Westlake University Hangzhou China
| | - Zhicheng Ju
- Department of Ocean Science The Hong Kong University of Science and Technology Hong Kong China
| | - Siyuan Kong
- Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
| | - Canhui Lan
- School of Life Science and Technology Wuhan Polytechnic University Wuhan China
- R-Institute Co. Ltd. Beijing China
| | - Bing Li
- Tsinghua Shenzhen International Graduate School Tsinghua University Shenzhen China
| | - Da Li
- Institute of Microbiology Chinese Academy of Sciences Beijing China
| | - Diyan Li
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy Chengdu University Chengdu China
| | | | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study Shenzhen University Shenzhen China
| | - Qi Li
- Institute of Applied Ecology Chinese Academy of Sciences Shenyang China
| | - Qiang Li
- School of Food and Biological Engineering Chengdu University Chengdu China
| | - Wen-Jun Li
- School of Life Sciences Sun Yat-Sen University Guangzhou China
| | - Xiaofang Li
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology Chinese Academy of Sciences Shijiazhuang China
| | - Xuemeng Li
- Guangdong Medical University Dongguan China
| | - Yahui Li
- Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
| | - You-Gui Li
- Zhejiang Academy of Agricultural Sciences Hangzhou China
| | - Zhibin Liang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre South China Agricultural University Guangzhou China
| | - Ning Ling
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Centre for Grassland Microbiome, College of Pastoral Agricultural Science and Technology Lanzhou University Lanzhou China
| | - Fufeng Liu
- College of Biotechnology Tianjin University of Science & Technology Tianjin China
| | - Qing Liu
- Institute of Microbiology Chinese Academy of Sciences Beijing China
| | - Shuang-Jiang Liu
- Institute of Microbiology Chinese Academy of Sciences Beijing China
| | | | - Qi Lu
- Children's Hospital of Chongqing Medical University Chongqing China
| | - Guangwen Luo
- Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
| | - Hao Luo
- Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
| | - Yuheng Luo
- Animal Nutrition Institute Sichuan Agricultural University Chengdu China
| | - Hujie Lyu
- Imperial College of London London UK
| | - Chuang Ma
- Anhui Agricultural University Hefei China
| | - Liyuan Ma
- China University of Geosciences Wuhan China
| | - Tengfei Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Centre for Grassland Microbiome, College of Pastoral Agricultural Science and Technology Lanzhou University Lanzhou China
| | - Jinfeng Ni
- State Key Laboratory of Microbial Technology, Microbial Technology Institute Shandong University Qingdao China
| | - Ziqin Pang
- College of Agriculture Fujian Agriculture and Forestry University Fuzhou China
| | - Xiaojing Qiang
- Institute of Grassland Research Chinese Academy of Agricultural Sciences Hohhot China
| | - Yuan Qin
- Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing China
| | - Qingyue Qu
- Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Chao Ran
- Feed Research Institute Chinese Academy of Agricultural Sciences Beijing China
| | - Shuqiang Ren
- Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
| | - Haitao Shang
- Shenzhen Medical Academy of Research and Translation Shenzhen China
| | | | - Linyang Sun
- Faculty of Biological and Environmental Sciences University of Helsinki Helsinki Finland
| | - Weimin Sun
- Institute of Eco-Environmental and Soil Sciences Guangdong Academy of Sciences Guangzhou China
| | - Liping Tang
- Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Jian Tian
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences Chinese Academy of Agricultural Sciences Beijing China
| | - Kai Wang
- School of Marine Sciences Ningbo University Ningbo China
| | | | - Ming-Ke Wang
- Naval Medical Center of PLA Naval Medical University Shanghai China
| | - Tao Wang
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy Chengdu University Chengdu China
| | - Xiao-Yan Wang
- School of Life Sciences Taizhou University Taizhou China
| | - Yao Wang
- Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
| | - Yiwen Wang
- Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
| | - Youshan Wang
- Institute of Plant Nutrition, Resources and Environment Beijing Academy of Agriculture and Forestry Sciences Beijing China
| | - Hailei Wei
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning Chinese Academy of Agricultural Sciences Beijing China
| | - Hong Wei
- The First Affiliated Hospital Sun Yat-Sen University Guangzhou China
| | - Zhong Wei
- Nanjing Agricultural University Nanjing China
| | - Tao Wen
- Nanjing Agricultural University Nanjing China
| | - Jiqiu Wu
- Department of Genetics, University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Linhuan Wu
- Microbial Resource and Big Data Center, Institute of Microbiology Chinese Academy of Sciences Beijing China
| | - Linkun Wu
- College of JunCao Science and Ecology Fujian Agriculture and Forestry University Fuzhou China
| | - Jiao Xi
- College of Natural Resources and Environment Northwest A&F University Yangling China
| | - Bo Xie
- School of Life Sciences Central China Normal University Wuhan China
| | - Guofang Xu
- Department of Civil and Environmental Engineering National University of Singapore Singapore Singapore
| | - Jun Xu
- Department of Gastroenterology, Clinical Center of Immune-Mediated Digestive Diseases Peking University People's Hospital Beijing China
| | | | - Qing Xue
- Nanjing Agricultural University Nanjing China
| | - Liping Yan
- Beijing Forestry University Beijing China
| | - Haifei Yang
- Qingdao Agriculture University Qingdao China
| | - Jun Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment Chinese Academy of Sciences Xiamen China
| | - Junbo Yang
- Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity Beijing Institute of Microbiology and Epidemiology Beijing China
| | - Yalin Yang
- Feed Research Institute Chinese Academy of Agricultural Sciences Beijing China
| | - Ying-Jie Yang
- Tobacco Research Institute Chinese Academy of Agricultural Sciences Qingdao China
| | - Xiaofang Yao
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture Chinese Academy of Sciences Changsha China
| | - Yanpo Yao
- Agro-Environmental Protection Institute Ministry of Agriculture and Rural Affairs Tianjin China
| | - Salsabeel Yousuf
- Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
| | - Ke Yu
- School of Environment and Energy Peking University Shenzhen Graduate School Shenzhen China
| | | | - Zhilin Yuan
- State Key Laboratory of Tree Genetics and Breeding Chinese Academy of Forestry Beijing China
| | - Dong Zhang
- Beijing Forestry University Beijing China
| | - Tianyuan Zhang
- Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
- Wuhan Benagen Technology Co., Ltd. Wuhan China
| | | | | | | | - Zhen Zhang
- Feed Research Institute Chinese Academy of Agricultural Sciences Beijing China
| | - Zhi-Feng Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) Guangzhou China
| | - Shengguo Zhao
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences Chinese Academy of Agricultural Sciences Beijing China
| | - Wei Zhao
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin China
| | - Maosheng Zheng
- College of Environmental Science and Engineering North China Electric Power University Beijing China
| | - Ziqiang Zheng
- College of Life Science and Technology Wuhan Polytechnic University Wuhan China
| | - Xin Zhou
- Institute of Microbiology Chinese Academy of Sciences Beijing China
| | | | - Zhigang Zhou
- Feed Research Institute Chinese Academy of Agricultural Sciences Beijing China
| | - Mo Zhu
- College of Life Sciences Henan Normal University Xinxiang China
| | - Yong-Guan Zhu
- Institute of Urban Environment Chinese Academy of Sciences Xiamen China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science Chinese Academy of Sciences Nanjing China
| | - Yang Bai
- Peking-Tsinghua Center for Life Sciences, College of Life Sciences Peking University Beijing China
| | - Yong-Xin Liu
- Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
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13
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Luo DL, Huang SY, Ma CY, Zhang XY, Sun K, Zhang W, Dai CC. Seed-borne bacterial synthetic community resists seed pathogenic fungi and promotes plant growth. J Appl Microbiol 2024; 135:lxae073. [PMID: 38520150 DOI: 10.1093/jambio/lxae073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 02/21/2024] [Accepted: 03/21/2024] [Indexed: 03/25/2024]
Abstract
AIMS In this study, the control effects of synthetic microbial communities composed of peanut seed bacteria against seed aflatoxin contamination caused by Aspergillus flavus and root rot by Fusarium oxysporum were evaluated. METHODS AND RESULTS Potentially conserved microbial synthetic communities (C), growth-promoting synthetic communities (S), and combined synthetic communities (CS) of peanut seeds were constructed after 16S rRNA Illumina sequencing, strain isolation, and measurement of plant growth promotion indicators. Three synthetic communities showed resistance to root rot and CS had the best effect after inoculating into peanut seedlings. This was achieved by increased defense enzyme activity and activated salicylic acid (SA)-related, systematically induced resistance in peanuts. In addition, CS also inhibited the reproduction of A. flavus on peanut seeds and the production of aflatoxin. These effects are related to bacterial degradation of toxins and destruction of mycelia. CONCLUSIONS Inoculation with a synthetic community composed of seed bacteria can help host peanuts resist the invasion of seeds by A. flavus and seedlings by F. oxysporum and promote the growth of peanut seedlings.
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Affiliation(s)
- De-Lin Luo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Shi-Yi Huang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Chen-Yu Ma
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Xiang-Yu Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Kai Sun
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Wei Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
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14
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Wang C, Chang J, Tian L, Sun Y, Wang E, Yao Z, Ye L, Zhang H, Pang Y, Tian C. A Synthetic Microbiome Based on Dominant Microbes in Wild Rice Rhizosphere to Promote Sulfur Utilization. RICE (NEW YORK, N.Y.) 2024; 17:18. [PMID: 38429614 PMCID: PMC10907558 DOI: 10.1186/s12284-024-00695-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/14/2024] [Indexed: 03/03/2024]
Abstract
Sulfur (S) is one of the main components of important biomolecules, which has been paid more attention in the anaerobic environment of rice cultivation. In this study, 12 accessions of rice materials, belonging to two Asian rice domestication systems and one African rice domestication system, were used by shotgun metagenomics sequencing to compare the structure and function involved in S cycle of rhizosphere microbiome between wild and cultivated rice. The sulfur cycle functional genes abundances were significantly different between wild and cultivated rice rhizosphere in the processes of sulfate reduction and other sulfur compounds conversion, implicating that wild rice had a stronger mutually-beneficial relationship with rhizosphere microbiome, enhancing sulfur utilization. To assess the effects of sulfate reduction synthetic microbiomes, Comamonadaceae and Rhodospirillaceae, two families containing the genes of two key steps in the dissimilatory sulfate reduction, aprA and dsrA respectively, were isolated from wild rice rhizosphere. Compared with the control group, the dissimilatory sulfate reduction in cultivated rice rhizosphere was significantly improved in the inoculated with different proportions groups. It confirmed that the synthetic microbiome can promote the S-cycling in rice, and suggested that may be feasible to construct the synthetic microbiome step by step based on functional genes to achieve the target functional pathway. In summary, this study reveals the response of rice rhizosphere microbial community structure and function to domestication, and provides a new idea for the construction of synthetic microbiome.
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Affiliation(s)
- Changji Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingjing Chang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Lei Tian
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Yu Sun
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Enze Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zongmu Yao
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Libo Ye
- College of Life Science, Jilin Agricultural University, Jilin, Changchun, China
| | - Hengfei Zhang
- College of Life Science, Jilin Agricultural University, Jilin, Changchun, China
| | - Yingnan Pang
- College of Life Science, Jilin Agricultural University, Jilin, Changchun, China
| | - Chunjie Tian
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China.
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China.
- College of Resources and Environment, Jilin Agricultural University, Changchun, Jilin, China.
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Li J, Luo C, Cai X, Dai Y, Zhang D, Zhang G. Cultivation and characterization of functional-yet-uncultivable phenanthrene degraders by stable-isotope-probing and metagenomic-binning directed cultivation (SIP-MDC). ENVIRONMENT INTERNATIONAL 2024; 185:108555. [PMID: 38458119 DOI: 10.1016/j.envint.2024.108555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/28/2024] [Accepted: 03/02/2024] [Indexed: 03/10/2024]
Abstract
High-throughput identification and cultivation of functional-yet-uncultivable microorganisms is a fundamental goal in environmental microbiology. It remains as a critical challenge due to the lack of routine and effective approaches. Here, we firstly proposed an approach of stable-isotope-probing and metagenomic-binning directed cultivation (SIP-MDC) to isolate and characterize the active phenanthrene degraders from petroleum-contaminated soils. From SIP and metagenome, we assembled 13 high-quality metagenomic bins from 13C-DNA, and successfully obtained the genome of an active PHE degrader Achromobacter (genome-MB) from 13C-DNA metagenomes, which was confirmed by gyrB gene comparison and average nucleotide/amino identity (ANI/AAI), as well as the quantification of PAH dioxygenase and antibiotic resistance genes. Thereinto, we modified the traditional cultivation medium with antibiotics and specific growth factors (e.g., vitamins and metals), and separated an active phenanthrene degrader Achromobacter sp. LJB-25 via directed isolation. Strain LJB-25 could degrade phenanthrene and its identity was confirmed by ANI/AAI values between its genome and genome-MB (>99 %). Our results hinted at the feasibility of SIP-MDC to identify, isolate and cultivate functional-yet-uncultivable microorganisms (active phenanthrene degraders) from their natural habitats. Our findings developed a state-of-the-art SIP-MDC approach, expanded our knowledge on phenanthrene biodegradation mechanisms, and proposed a strategy to mine functional-yet-uncultivable microorganisms.
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Affiliation(s)
- Jibing Li
- State Key Laboratory of Organic Geochemistry and Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry and Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xixi Cai
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yeliang Dai
- State Key Laboratory of Organic Geochemistry and Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Dayi Zhang
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, Jilin University, Changchun 130021, China; College of New Energy and Environment, Jilin University, Changchun 130021, China; Key Laboratory of Regional Environment and Eco-restoration, Ministry of Education, Shenyang University, Shenyang 110044, China.
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry and Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
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Chaudhury R, Chakraborty A, Rahaman F, Sarkar T, Dey S, Das M. Mycorrhization in trees: ecology, physiology, emerging technologies and beyond. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:145-156. [PMID: 38194349 DOI: 10.1111/plb.13613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 11/30/2023] [Indexed: 01/10/2024]
Abstract
Mycorrhization has been an integral part of plants since colonization by the early land plants. Over decades, substantial research has highlighted its potential role in improving nutritional efficiency and growth, development and survival of crop plants. However, the focus of this review is trees. Evidence have been provided to explain ecological and physiological significance of mycorrhization in trees. Advances in recent technologies (e.g., metagenomics, artificial intelligence, machine learning, agricultural drones) may open new windows to apply this knowledge in promoting tree growth in forest ecosystems. Dual mycorrhization relationships in trees and even triple relationships among trees, mycorrhizal fungi and bacteria offer an interesting physiological system to understand how plants interact with other organisms for better survival. Besides, studies indicate additional roles of mycorrhization in learning, memorizing and communication between host trees through a common mycorrhizal network (CMN). Recent observations in trees suggest that mycorrhization may even promote tolerance to multiple abiotic (e.g., drought, salt, heavy metal stress) and biotic (e.g. fungi) stresses. Due to the extent of physiological reliance, local adaptation of trees is heavily impacted by the mycorrhizal community. This knowledge opens the possibility of a non-GMO avenue to promote tree growth and development. Indeed, mycorrhization could impact growth of trees in nurserys and subsequent survival of the inoculated trees in field conditions. Future studies might integrate hyperspectral imaging and drone technologies to identify tree communities that are deficient in nitrogen and spray mycorrhizal spore formulations on them.
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Affiliation(s)
- R Chaudhury
- Department of Life Sciences, Presidency University, Kolkata, India
| | - A Chakraborty
- Department of Life Sciences, Presidency University, Kolkata, India
| | - F Rahaman
- Department of Life Sciences, Presidency University, Kolkata, India
| | - T Sarkar
- Department of Life Sciences, Presidency University, Kolkata, India
| | - S Dey
- Department of Life Sciences, Presidency University, Kolkata, India
| | - M Das
- Department of Life Sciences, Presidency University, Kolkata, India
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17
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An M, Liang R, Lu Y, Li X, Zhao G. Thiopseudomonas acetoxidans sp. nov., an aerobic acetic and butyric acids oxidizer isolated from anaerobic fermentation liquid of food waste. Antonie Van Leeuwenhoek 2024; 117:35. [PMID: 38351143 DOI: 10.1007/s10482-024-01932-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/21/2024] [Indexed: 02/16/2024]
Abstract
A Gram-stain-negative, oxidase-negative, rod-shaped, motile, facultatively anaerobic bacterial strain, designated as CY1220T, was isolated from an anaerobic fermentation liquid of food waste treatment plant. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain CY1220T belongs to the genus Thiopseudomonas, with the highest sequence similarity to Thiopseudomonas alkaliphila B4199T (95.91%), followed by Thiopseudomonas denitrificans X2T (95.56%). The genomic DNA G + C content of strain CY1220T was 48.6 mol%. The average nucleotide identity values and digital DNA-DNA hybridization values between strain CY1220T and the type species of T. alkaliphila and T. denitrificans were in the range of 70.8-71.6% and 19.2-20.0%, respectively, below the thresholds for species delineation. The strain was able to grow utilizing acetic acid and butyric acid (AABA) as the sole carbon source in aerobic conditions. Genomic analysis predicted that the strain could synthesize vitamin B12 and ectoine. The predominant cellular fatty acids were C18:1 ω7c and/or C18:1 ω6c, C16:0, C16:1 ω7c and/or C16:1 ω6c and C12:0. The polar lipids comprised diphosphatidylglycerol, unknown polar lipid, phosphatidylethanolamine, phosphatidylglycerol, and phospholipid. Q-8 (2.1%) and Q-9 (97.9%) were detected as the respiratory quinones. Based on its phenotypic, genotypic and genomic characteristics, strain CY1220T represents a novel species in the genus Thiopseudomonas, for which the name Thiopseudomonas acetoxidans sp. nov. is proposed. The type strain is CY1220T (= GDMCC 1.3503 T = JCM 35747 T).
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Affiliation(s)
- Miaomiao An
- Beijing Key Laboratory of Food Processing and Safety in Forestry, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ruina Liang
- Beijing Key Laboratory of Food Processing and Safety in Forestry, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yanjuan Lu
- Beijing Fairyland Environmental Technology Co., Ltd, Beijing, 100085, China
| | - Xiaoxu Li
- Beijing Fairyland Environmental Technology Co., Ltd, Beijing, 100085, China
| | - Guozhu Zhao
- Beijing Key Laboratory of Food Processing and Safety in Forestry, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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18
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Zhang L, Zhao H, Qin S, Hu C, Shen Y, Qu B, Bai Y, Liu B. Genome-Resolved Metagenomics and Denitrifying Strain Isolation Reveal New Insights into Microbial Denitrification in the Deep Vadose Zone. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:2323-2334. [PMID: 38267389 DOI: 10.1021/acs.est.3c06466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
The heavy use of nitrogen fertilizer in intensive agricultural areas often leads to nitrate accumulation in subsurface soil and nitrate contamination in groundwater, which poses a serious risk to public health. Denitrifying microorganisms in the subsoil convert nitrate to gaseous forms of nitrogen, thereby mitigating the leaching of nitrate into groundwater. Here, we investigated denitrifying microorganisms in the deep vadose zone of a typical intensive agricultural area in China through microcosm enrichment, genome-resolved metagenomic analysis, and denitrifying bacteria isolation. A total of 1000 metagenome-assembled genomes (MAGs) were reconstructed, resulting in 98 high-quality, dereplicated MAGs that contained denitrification genes. Among them, 32 MAGs could not be taxonomically classified at the genus or species level, indicating that a broader spectrum of taxonomic groups is involved in subsoil denitrification than previously recognized. A denitrifier isolate library was constructed by using a strategy combining high-throughput and conventional cultivation techniques. Assessment of the denitrification characteristics of both the MAGs and isolates demonstrated the dominance of truncated denitrification. Functional screening revealed the highest denitrification activity in two complete denitrifiers belonging to the genus Pseudomonas. These findings greatly expand the current knowledge of the composition and function of denitrifying microorganisms in subsoils. The constructed isolate library provided the first pool of subsoil-denitrifying microorganisms that could facilitate the development of microbe-based technologies for nitrate attenuation in groundwater.
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Affiliation(s)
- Linqi Zhang
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Huicheng Zhao
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Shuping Qin
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Chunsheng Hu
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Yanjun Shen
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Baoyuan Qu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Binbin Liu
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
- Xiong'an Institute of Innovation, Chinese Academy of Sciences, Xiong'an 071700, China
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Xiao Y, Cheng P, Zhu X, Xu M, Liu M, Li H, Zhang Y, Yao S. Antimicrobial Agent Functional Gold Nanocluster-Mediated Multichannel Sensor Array for Bacteria Sensing. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:2369-2376. [PMID: 38230676 DOI: 10.1021/acs.langmuir.3c03612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Urinary tract infections (UTIs) have greatly affected human health in recent years. Accurate and rapid diagnosis of UTIs can enable a more effective treatment. Herein, we developed a multichannel sensor array for efficient identification of bacteria based on three antimicrobial agents (vancomycin, lysozyme, and bacitracin) functional gold nanoclusters (AuNCs). In this sensor, the fluorescence intensity of the three AuNCs was quenched to varying degrees by the bacterial species, providing a unique fingerprint for different bacteria. With this sensing platform, seven pathogenic bacteria, different concentrations of the same bacteria, and even bacterial mixtures were successfully differentiated. Furthermore, UTIs can be accurately identified with our sensors in ∼30 min with 100% classification accuracy. The proposed sensing systems offer a rapid, high-throughput, and reliable sensing platform for the diagnosis of UTIs.
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Affiliation(s)
- Yuquan Xiao
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, P.R. China
| | - Pei Cheng
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, P.R. China
| | - Xiaohua Zhu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, P.R. China
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, Henan 476000, P.R. China
| | - Maotian Xu
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, Henan 476000, P.R. China
| | - Meiling Liu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, P.R. China
| | - Haitao Li
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, P.R. China
| | - Youyu Zhang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, P.R. China
| | - Shouzhuo Yao
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, P.R. China
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20
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Yang N, Røder HL, Wicaksono WA, Wassermann B, Russel J, Li X, Nesme J, Berg G, Sørensen SJ, Burmølle M. Interspecific interactions facilitate keystone species in a multispecies biofilm that promotes plant growth. THE ISME JOURNAL 2024; 18:wrae012. [PMID: 38365935 PMCID: PMC10938371 DOI: 10.1093/ismejo/wrae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/04/2024] [Accepted: 01/29/2024] [Indexed: 02/18/2024]
Abstract
Microorganisms colonizing plant roots co-exist in complex, spatially structured multispecies biofilm communities. However, little is known about microbial interactions and the underlying spatial organization within biofilm communities established on plant roots. Here, a well-established four-species biofilm model (Stenotrophomonas rhizophila, Paenibacillus amylolyticus, Microbacterium oxydans, and Xanthomonas retroflexus, termed as SPMX) was applied to Arabidopsis roots to study the impact of multispecies biofilm on plant growth and the community spatial dynamics on the roots. SPMX co-culture notably promoted root development and plant biomass. Co-cultured SPMX increased root colonization and formed multispecies biofilms, structurally different from those formed by monocultures. By combining 16S rRNA gene amplicon sequencing and fluorescence in situ hybridization with confocal laser scanning microscopy, we found that the composition and spatial organization of the four-species biofilm significantly changed over time. Monoculture P. amylolyticus colonized plant roots poorly, but its population and root colonization were highly enhanced when residing in the four-species biofilm. Exclusion of P. amylolyticus from the community reduced overall biofilm production and root colonization of the three species, resulting in the loss of the plant growth-promoting effects. Combined with spatial analysis, this led to identification of P. amylolyticus as a keystone species. Our findings highlight that weak root colonizers may benefit from mutualistic interactions in complex communities and hereby become important keystone species impacting community spatial organization and function. This work expands the knowledge on spatial organization uncovering interspecific interactions in multispecies biofilm communities on plant roots, beneficial for harnessing microbial mutualism promoting plant growth.
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Affiliation(s)
- Nan Yang
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Henriette L Røder
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
- Section for Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Copenhagen 2100, Denmark
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz 8010, Austria
| | - Birgit Wassermann
- Institute of Environmental Biotechnology, Graz University of Technology, Graz 8010, Austria
| | - Jakob Russel
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Xuanji Li
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz 8010, Austria
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Mette Burmølle
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
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21
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Su P, Kang H, Peng Q, Wicaksono WA, Berg G, Liu Z, Ma J, Zhang D, Cernava T, Liu Y. Microbiome homeostasis on rice leaves is regulated by a precursor molecule of lignin biosynthesis. Nat Commun 2024; 15:23. [PMID: 38167850 PMCID: PMC10762202 DOI: 10.1038/s41467-023-44335-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
In terrestrial ecosystems, plant leaves provide the largest biological habitat for highly diverse microbial communities, known as the phyllosphere microbiota. However, the underlying mechanisms of host-driven assembly of these ubiquitous communities remain largely elusive. Here, we conduct a large-scale and in-depth assessment of the rice phyllosphere microbiome aimed at identifying specific host-microbe links. A genome-wide association study reveals a strong association between the plant genotype and members of four bacterial orders, Pseudomonadales, Burkholderiales, Enterobacterales and Xanthomonadales. Some of the associations are specific to a distinct host genomic locus, pathway or even gene. The compound 4-hydroxycinnamic acid (4-HCA) is identified as the main driver for enrichment of bacteria belonging to Pseudomonadales. 4-HCA can be synthesized by the host plant's OsPAL02 from the phenylpropanoid biosynthesis pathway. A knockout mutant of OsPAL02 results in reduced Pseudomonadales abundance, dysbiosis of the phyllosphere microbiota and consequently higher susceptibility of rice plants to disease. Our study provides a direct link between a specific plant metabolite and rice phyllosphere homeostasis opening possibilities for new breeding strategies.
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Affiliation(s)
- Pin Su
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Houxiang Kang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qianze Peng
- National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya City, Sanya, 572024, China
- College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, 14469, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, 14476, Germany
| | - Zhuoxin Liu
- Longping Branch, College of Biology, Hunan University, Changsha, 410082, China
| | - Jiejia Ma
- Longping Branch, College of Biology, Hunan University, Changsha, 410082, China
| | - Deyong Zhang
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
- National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya City, Sanya, 572024, China.
- College of Tropical Crops, Hainan University, Haikou, 570228, China.
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria.
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Yong Liu
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
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22
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Yu J, Zheng Y, Song C, Chen S. New insights into the roles of fungi and bacteria in the development of medicinal plant. J Adv Res 2023:S2090-1232(23)00394-6. [PMID: 38092299 DOI: 10.1016/j.jare.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 01/02/2024] Open
Abstract
BACKGROUND The interaction between microorganisms and medicinal plants is a popular topic. Previous studies consistently reported that microorganisms were mainly considered pathogens or contaminants. However, with the development of microbial detection technology, it has been demonstrated that fungi and bacteria affect beneficially the medicinal plant production chain. AIM OF REVIEW Microorganisms greatly affect medicinal plants, with microbial biosynthesis a high regarded topic in medicinal plant-microbial interactions. However, it lacks a systematic review discussing this relationship. Current microbial detection technologies also have certain advantages and disadvantages, it is essential to compare the characteristics of various technologies. KEY SCIENTIFIC CONCEPTS OF REVIEW This review first illustrates the role of fungi and bacteria in various medicinal plant production procedures, discusses the development of microbial detection and identification technologies in recent years, and concludes with microbial biosynthesis of natural products. The relationship between fungi, bacteria, and medicinal plants is discussed comprehensively. We also propose a future research model and direction for further studies.
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Affiliation(s)
- Jingsheng Yu
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu 611137 China; Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700 China
| | - Yixuan Zheng
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu 611137 China
| | - Chi Song
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu 611137 China
| | - Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu 611137 China; Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700 China.
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23
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Guo S, Ma W, Tang Y, Chen L, Wang Y, Cui Y, Liang J, Li L, Zhuang J, Gu J, Li M, Fang H, Lin X, Shih C, Labandeira CC, Ren D. A new method for examining the co-occurrence network of fossil assemblages. Commun Biol 2023; 6:1102. [PMID: 37907587 PMCID: PMC10618518 DOI: 10.1038/s42003-023-05417-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 10/04/2023] [Indexed: 11/02/2023] Open
Abstract
Currently, studies of ancient faunal community networks have been based mostly on uniformitarian and functional morphological evidence. As an important source of data, taphonomic evidence offers the opportunity to provide a broader scope for understanding palaeoecology. However, palaeoecological research methods based on taphonomic evidence are relatively rare, especially for body fossils in lacustrine sediments. Such fossil communities are not only affected by complex transportation and selective destruction in the sedimentation process, they also are strongly affected by time averaging. Historically, it has been believed that it is difficult to study lacustrine entombed fauna by a small-scale quadrat survey. Herein, we developed a software, the TaphonomeAnalyst, to study the associational network of lacustrine entombed fauna, or taphocoenosis. TaphonomeAnalyst allows researchers to easily perform exploratory analyses on common abundance profiles from taphocoenosis data. The dataset for these investigations resulted from fieldwork of the latest Middle Jurassic Jiulongshan Formation near Daohugou Village, in Ningcheng County of Inner Mongolia, China, spotlighting the core assemblage of the Yanliao Fauna. Our data included 27,000 fossil specimens of animals from this deposit, the Yanliao Fauna, whose analyses reveal sedimentary environments, taphonomic conditions, and co-occurrence networks of this highly studied assemblage, providing empirically robust and statistically significant evidence for multiple Yanliao habitats.
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Affiliation(s)
- Shilong Guo
- College of Life Sciences, Capital Normal University, Beijing, 100048, PR China
| | - Wang Ma
- Department of Bioinformatics, Freshwind Biotechnology (Tianjin) Limited Company, Tianjin, 300301, PR China
| | - Yunyu Tang
- College of Life Sciences, Capital Normal University, Beijing, 100048, PR China
| | - Liang Chen
- College of Life Sciences, Capital Normal University, Beijing, 100048, PR China
| | - Ying Wang
- Beijing Museum of Natural History, Beijing, 100050, PR China
| | - Yingying Cui
- College of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Junhui Liang
- Tianjin Natural History Museum, Tianjin, 300203, PR China
| | - Longfeng Li
- Institute of Vertebrate Paleontology, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Jialiang Zhuang
- College of Life Sciences, Capital Normal University, Beijing, 100048, PR China
| | - Junjie Gu
- College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Mengfei Li
- College of Life Sciences, Capital Normal University, Beijing, 100048, PR China
| | - Hui Fang
- Institute of Paleontology, Hebei GEO University, Shijiazhuang, 050031, PR China
| | - Xiaodan Lin
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, School of Plant Protection, Hainan University, Haikou, 570228, PR China
| | - Chungkun Shih
- College of Life Sciences, Capital Normal University, Beijing, 100048, PR China
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Conrad C Labandeira
- College of Life Sciences, Capital Normal University, Beijing, 100048, PR China
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
- Department of Entomology, University of Maryland, College Park, MD, 20742, USA
| | - Dong Ren
- College of Life Sciences, Capital Normal University, Beijing, 100048, PR China.
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24
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Gao Y, Li D, Liu YX. Microbiome research outlook: past, present, and future. Protein Cell 2023; 14:709-712. [PMID: 37219087 PMCID: PMC10599639 DOI: 10.1093/procel/pwad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 05/24/2023] Open
Affiliation(s)
- Yunyun Gao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Danyi Li
- R-Institute Co. Ltd., Beijing 100011, China
| | - Yong-Xin Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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Guo B, Zhang H, Liu Y, Chen J, Li J. Drought-resistant trait of different crop genotypes determines assembly patterns of soil and phyllosphere microbial communities. Microbiol Spectr 2023; 11:e0006823. [PMID: 37754752 PMCID: PMC10581042 DOI: 10.1128/spectrum.00068-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 08/04/2023] [Indexed: 09/28/2023] Open
Abstract
Crop microbiomes are widely recognized to play a role in crop stress resistance, but the ecological processes that shape crop microbiomes under water stress are unclear. Therefore, we investigated the bacterial communities of two oat (Avena sativa) and two wheat (Triticum aestivum) genotypes under different water stress conditions. Our results show that the microbial assemblage was determined by the crop compartment niche. Host selection pressure on the bacterial community increased progressively from soil to epiphyte to endophyte pathways, leading to a decrease in bacterial community diversity and network complexity. Source tracing shows that soil is the primary source of crop microbial communities and that bulk soil is the main potential source of crop microbiota. It filters gradually through the different compartment niches of the crop. We found that the phyla Actinobacteria, Proteobacteria, Gemmatimonadota, and Myxococcota were significantly enriched in bacterial communities associated with crop-resistance enzyme activity. Crop genotype influenced the composition of the rhizosphere soil microbial community, and the composition of the phylloplane microbial community was affected by water stress. IMPORTANCE In this paper, we investigated the assembly of the plant microbiome in response to water stress. We found that the determinant of microbiome assembly under water stress was the host type and that microbial communities were progressively filtered and enriched as they moved from soil to epiphyte to endophyte communities, with the main potential source being bulk soil. We also screened for bacterial communities that were significantly associated with crop enzyme activity. Our research provides insights into the manipulation of microbes in response to crop resistance to water stress.
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Affiliation(s)
- Baobei Guo
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
- Pomology Institute, Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Hong Zhang
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Yong Liu
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Jianwen Chen
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Junjian Li
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
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Yang Z, Lian Z, Liu L, Fang B, Li W, Jiao J. Cultivation strategies for prokaryotes from extreme environments. IMETA 2023; 2:e123. [PMID: 38867929 PMCID: PMC10989778 DOI: 10.1002/imt2.123] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 05/28/2023] [Indexed: 06/14/2024]
Abstract
The great majority of microorganisms are as-yet-uncultivated, mostly found in extreme environments. High-throughput sequencing provides data-rich genomes from single-cell and metagenomic techniques, which has enabled researchers to obtain a glimpse of the unexpected genetic diversity of "microbial dark matter." However, cultivating microorganisms from extreme environments remains essential for dissecting and utilizing the functions of extremophiles. Here, we provide a straightforward protocol for efficiently isolating prokaryotic microorganisms from different extreme habitats (thermal, xeric, saline, alkaline, acidic, and cryogenic environments), which was established through previous successful work and our long-term experience in extremophile resource mining. We propose common processes for extremophile isolation at first and then summarize multiple cultivation strategies for recovering prokaryotic microorganisms from extreme environments and meanwhile provide specific isolation tips that are always overlooked but important. Furthermore, we propose the use of multi-omics-guided microbial cultivation approaches for culturing these as-yet-uncultivated microorganisms and two examples are provided to introduce how these approaches work. In summary, the protocol allows researchers to significantly improve the isolation efficiency of pure cultures and novel taxa, which therefore paves the way for the protection and utilization of microbial resources from extreme environments.
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Affiliation(s)
- Zi‐Wen Yang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Zheng‐Han Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Bao‐Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqiChina
| | - Wen‐Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqiChina
| | - Jian‐Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
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Badr AA, Fouad WM. Comparative study of multiple approaches for identifying cultivable microalgae population diversity from freshwater samples. PLoS One 2023; 18:e0285913. [PMID: 37418475 PMCID: PMC10328328 DOI: 10.1371/journal.pone.0285913] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 05/03/2023] [Indexed: 07/09/2023] Open
Abstract
The vast diversity of microalgae imposes the challenge of identifying them through the most common and economical identification method, morphological identification, or through using the more recent molecular-level identification tools. Here we report an approach combining enrichment and metagenomic molecular techniques to enhance microalgae identification and identify microalgae diversity from environmental water samples. From this perspective, we aimed to identify the most suitable culturing media and molecular approach (using different primer sets and reference databases) for detecting microalgae diversity. Using this approach, we have analyzed three water samples collected from the River Nile on several enrichment media. A total of 37 microalgae were identified morphologically to the genus level. While sequencing the three-primer sets (16S rRNA V1-V3 and V4-V5 and 18S rRNA V4 region) and aligning them to three reference databases (GG, SILVA, and PR2), a total of 87 microalgae were identified to the genus level. The highest eukaryotic microalgae diversity was identified using the 18S rRNA V4 region and alignment to the SILVA database (43 genera). The two 16S rRNA regions sequenced added to the eukaryotic microalgae identification, 26 eukaryotic microalgae. Cyanobacteria were identified through the two sequenced 16S rRNA regions. Alignment to the SILVA database served to identify 14 cyanobacteria to the genera level, followed by Greengenes, 11 cyanobacteria genera. Our multiple-media, primer, and reference database approach revealed a high microalgae diversity that would have been overlooked if a single approach had been used over the other.
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Affiliation(s)
- Amal A. Badr
- Biotechnology Graduate Program, School of Sciences and Engineering, The American University in Cairo, New Cairo, Egypt
| | - Walid M. Fouad
- Biotechnology Graduate Program, School of Sciences and Engineering, The American University in Cairo, New Cairo, Egypt
- Department of Biology, School of Sciences and Engineering, The American University in Cairo, New Cairo, Egypt
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Liu L, Cheng L, Liu K, Yu T, Liu Q, Gong Z, Cai Z, Liu J, Zhao X, Nian H, Ma Q, Lian T. Transgenic soybean of GsMYB10 shapes rhizosphere microbes to promote resistance to aluminum (Al) toxicity. JOURNAL OF HAZARDOUS MATERIALS 2023; 455:131621. [PMID: 37187122 DOI: 10.1016/j.jhazmat.2023.131621] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/27/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023]
Abstract
Plant resistance genes could affect rhizosphere microbiota, which in turn enhanced plant resistance to stresses. Our previous study found that overexpression of the GsMYB10 gene led to enhanced tolerance of soybean plants to aluminum (Al) toxicity. However, whether GsMYB10 gene could regulate rhizosphere microbiota to mitigate Al toxicity remains unclear. Here, we analyzed the rhizosphere microbiomes of HC6 soybean (WT) and transgenic soybean (trans-GsMYB10) at three Al concentrations, and constructed three different synthetic microbial communities (SynComs), including bacterial, fungal and cross-kingdom (bacteria and fungi) SynComs to verify their role in improving Al tolerance of soybean. Trans-GsMYB10 shaped the rhizosphere microbial communities and harbored some beneficial microbes, such as Bacillus, Aspergillus and Talaromyces under Al toxicity. Fungal and cross-kingdom SynComs showed a more effective role than the bacterial one in resistance to Al stress, and these SynComs helped soybean resist Al toxicity via affecting some functional genes that involved cell wall biosynthesis and organic acid transport etc. Overall, this study reveals the mechanism of soybean functional genes regulating the synergistic resistance of rhizosphere microbiota and plants to Al toxicity, and also highlights the possibility of focusing on the rhizobial microbial community as a potential molecular breeding target to produce crops.
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Affiliation(s)
- Lingrui Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Lang Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Kun Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Taobing Yu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Qi Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zhihui Gong
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zhandong Cai
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Junjie Liu
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Xueqiang Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.
| | - Qibin Ma
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.
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Liu Q, Cheng L, Nian H, Jin J, Lian T. Linking plant functional genes to rhizosphere microbes: a review. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:902-917. [PMID: 36271765 PMCID: PMC10106864 DOI: 10.1111/pbi.13950] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/09/2022] [Accepted: 10/16/2022] [Indexed: 05/04/2023]
Abstract
The importance of rhizomicrobiome in plant development, nutrition acquisition and stress tolerance is unquestionable. Relevant plant genes corresponding to the above functions also regulate rhizomicrobiome construction. Deciphering the molecular regulatory network of plant-microbe interactions could substantially contribute to improving crop yield and quality. Here, the plant gene-related nutrient uptake, biotic and abiotic stress resistance, which may influence the composition and function of microbial communities, are discussed in this review. In turn, the influence of microbes on the expression of functional plant genes, and thereby plant growth and immunity, is also reviewed. Moreover, we have specifically paid attention to techniques and methods used to link plant functional genes and rhizomicrobiome. Finally, we propose to further explore the molecular mechanisms and signalling pathways of microbe-host gene interactions, which could potentially be used for managing plant health in agricultural systems.
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Affiliation(s)
- Qi Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Lang Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Jian Jin
- Northeast Institute of Geography and AgroecologyChinese Academy of SciencesHarbinChina
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioscienceLa Trobe UniversityBundooraVictoriaAustralia
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
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30
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Feng Z, Sun H, Qin Y, Zhou Y, Zhu H, Yao Q. A synthetic community of siderophore-producing bacteria increases soil selenium bioavailability and plant uptake through regulation of the soil microbiome. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:162076. [PMID: 36758687 DOI: 10.1016/j.scitotenv.2023.162076] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Dietary selenium (Se) is an effective strategy to meet Se requirement of human body, and Se biofortification in crops in seleniferous soils with selenobacteria represents an eco-friendly biotechnique. In this study, we tested the effectiveness of siderophore-producing bacterial (SPB) synthetic communities (SynComs) in promoting plant Se uptake in a subtropical seleniferous soil where the fixation of Se by ferric-oxides is severe. The results indicated that SPB SynComs drastically elevated soil bioavailable Se content by up to 68.7 %, and significantly increased plant Se concentration and uptake by up to 83.1 % and 92.2 %, respectively. Seven out of ten SPB isolates in the SynComs were enriched in soils after 120 days of inoculation. Additionally, variation partitioning analysis (VPA) revealed that the contribution of soil bacterial community (up to 42.8 %) to the increased plant Se uptake was much greater than that of soil bioavailable Se (up to 5.1 %), suggesting a direct pathway other than the pathway of mobilizing Se. The relative abundances of some operational taxonomic units (OTUs) showed significantly positive relationship with plant Se status but not with soil Se status, which supports the results of VPA. Network analysis indicates that some inoculated SPB isolates promoted plant Se uptake by regulating the native bacterial taxa. Taken together, this study demonstrates that SPB can be used in Se biofortification in crops, especially in subtropical soils.
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Affiliation(s)
- Zengwei Feng
- College of Horticulture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Hui Sun
- College of Horticulture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Yongqiang Qin
- College of Horticulture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, South China Agricultural University, Guangzhou 510642, China
| | - Yang Zhou
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Qing Yao
- College of Horticulture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, South China Agricultural University, Guangzhou 510642, China.
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Liu S, Yu Z, Zhong H, Zheng N, Huws S, Wang J, Zhao S. Functional gene-guided enrichment plus in situ microsphere cultivation enables isolation of new crucial ureolytic bacteria from the rumen of cattle. MICROBIOME 2023; 11:76. [PMID: 37060083 PMCID: PMC10105427 DOI: 10.1186/s40168-023-01510-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/05/2023] [Indexed: 05/12/2023]
Abstract
BACKGROUND Ruminants can utilize urea as a dietary nitrogen source owing to their ability to recycle urea-N back to the rumen where numerous ureolytic bacteria hydrolyze urea into ammonia, which is used by numerous bacteria as their nitrogen source. Rumen ureolytic bacteria are the key microbes making ruminants the only type of animals independent of pre-formed amino acids for survival, thus having attracted much research interest. Sequencing-based studies have helped gain new insights into ruminal ureolytic bacterial diversity, but only a limited number of ureolytic bacteria have been isolated into pure cultures or studied, hindering the understanding of ureolytic bacteria with respect to their metabolism, physiology, and ecology, all of which are required to effectively improve urea-N utilization efficiency. RESULTS We established and used an integrated approach, which include urease gene (ureC) guided enrichment plus in situ agarose microsphere embedding and cultivation under rumen-simulating conditions, to isolate ureolytic bacteria from the rumen microbiome. We optimized the dilutions of the rumen microbiome during the enrichment, single-cell embedding, and then in situ cultivation of microsphere-embedded bacteria using dialysis bags placed in rumen fluid. Metabonomic analysis revealed that the dialysis bags had a fermentation profile very similar to the simulated rumen fermentation. In total, we isolated 404 unique strains of bacteria, of which 52 strains were selected for genomic sequencing. Genomic analyses revealed that 28 strains, which were classified into 12 species, contained urease genes. All these ureolytic bacteria represent new species ever identified in the rumen and represented the most abundant ureolytic species. Compared to all the previously isolated ruminal ureolytic species combined, the newly isolated ureolytic bacteria increased the number of genotypically and phenotypically characterized ureolytic species by 34.38% and 45.83%, respectively. These isolated strains have unique genes compared to the known ureolytic strains of the same species indicating their new metabolic functions, especially in energy and nitrogen metabolism. All the ureolytic species were ubiquitous in the rumen of six different species of ruminants and were correlated to dietary urea metabolism in the rumen and milk protein production. We discovered five different organizations of urease gene clusters among the new isolates, and they had varied approaches to hydrolyze urea. The key amino acid residues of the UreC protein that potentially plays critical regulatory roles in urease activation were also identified. CONCLUSIONS We established an integrated methodology for the efficient isolation of ureolytic bacteria, which expanded the biological resource of crucial ureolytic bacteria from the rumen. These isolates play a vital role in the incorporation of dietary nitrogen into bacterial biomass and hence contribute to ruminant growth and productivity. Moreover, this methodology can enable efficient isolation and cultivation of other bacteria of interest in the environment and help bridge the knowledge gap between genotypes and phenotypes of uncultured bacteria. Video abstract.
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Affiliation(s)
- Sijia Liu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road Haidian, Beijing,, 100193, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Huiyue Zhong
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road Haidian, Beijing,, 100193, China
| | - Nan Zheng
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road Haidian, Beijing,, 100193, China
| | - Sharon Huws
- School of Biological Sciences and Institute for Global Food Security, 19 Chlorine Gardens, Queen's University Belfast, Belfast, UK
| | - Jiaqi Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road Haidian, Beijing,, 100193, China.
| | - Shengguo Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road Haidian, Beijing,, 100193, China.
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Wang Z, Hu X, Solanki MK, Pang F. A Synthetic Microbial Community of Plant Core Microbiome Can Be a Potential Biocontrol Tool. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:5030-5041. [PMID: 36946724 DOI: 10.1021/acs.jafc.2c08017] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Microbes are accepted as the foremost drivers of the rhizosphere ecology that influences plant health in direct or indirect ways. In recent years, the rapid development of gene sequencing technology has greatly facilitated the study of plant microbiome structure and function, and various plant-associated microbiomes have been categorized. Additionally, there is growing research interest in plant-disease-related microbes, and some specific microflora beneficial to plant health have been identified. This Review discusses the plant-associated microbiome's biological control pathways and functions to modulate plant defense against pathogens. How do plant microbiomes enhance plant resistance? How does the plant core microbiome-associated synthetic microbial community (SynCom) improve plant health? This Review further points out the primary need to develop smart agriculture practices using SynComs against plant diseases. Finally, this Review provides ideas for future opportunities in plant disease control and mining new microbial resources.
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Affiliation(s)
- Zhen Wang
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin, Guangxi 537000, China
| | - Xiaohu Hu
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin, Guangxi 537000, China
| | - Manoj Kumar Solanki
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice 40-701, Poland
| | - Fei Pang
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin, Guangxi 537000, China
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An MM, Shen L, Liang RN, Lu YJ, Zhao GZ. Alcanivorax quisquiliarum sp. nov., isolated from anaerobic fermentation liquid of food waste by high-throughput cultivation. Int J Syst Evol Microbiol 2023; 73. [PMID: 37093733 DOI: 10.1099/ijsem.0.005764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
Strain CY1518T was isolated from an anaerobic fermentation liquid of food waste treatment plant in Beijing, PR China, and characterized to assess its taxonomy. Cells of CY1518T were Gram-stain-negative, oxidase-negative, catalase-positive and ellipsoidal. Growth occurred at 20-42 °C (optimum, 37 °C), pH 6.0-10.0 (optimum, pH 8) and with 0-6.0 % (w/v) NaCl (optimum, 1.5%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CY1518T belongs to the genus Alcanivorax, with the highest sequence similarity to Alcanivorax pacificus W11-5T (95.97 %), followed by Alcanivorax indicus SW127T (95.08%). The similarity between strain CY1518T and other strains of Alcanivorax was less than 95 %. The genomic DNA G+C content of strain CY1518T was 60.88 mol%. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between strain CY1518T and the closely related taxa A. pacificus W11-5T and A. indicus SW127T were 77.61, 78.03 and 21.2 % and 74.15, 70.02 and 19.3%, respectively. The strain was able to use d-serine, Tween 40 and some organic acid compounds for growth. The polar lipids comprised aminophospholipid, diphosphatidylglycerol, glycolipid, an unknown polar lipid, phosphatidylethanolamine, phosphatidylglycerol and phospholipid. The principal fatty acids (>5 %) were C19 : 0 cyclo ω8c (36.3%), C16 : 0 (32.3%), C12 : 0 3-OH (8.3%) and C12 : 0 (7.6%). Based on its phenotypic, genotypic and genomic characteristics, strain CY1518T represents a novel species in the genus Alcanivorax, for which the name Alcanivorax quisquiliarum sp. nov. is proposed. The type strain is CY1518T (=GDMCC 1.2918T=JCM 35120T).
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Affiliation(s)
- Miao-Miao An
- Beijing Key Laboratory of Food Processing and Safety in Forestry, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Lei Shen
- Beijing Key Laboratory of Food Processing and Safety in Forestry, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
- College of Life Sciences, Langfang Normal University, Langfang 065000, PR China
| | - Rui-Na Liang
- Beijing Key Laboratory of Food Processing and Safety in Forestry, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Yan-Juan Lu
- Beijing Fairyland Environmental Technology Co., Ltd, Beijing 100085, PR China
| | - Guo-Zhu Zhao
- Beijing Key Laboratory of Food Processing and Safety in Forestry, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
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Athanasopoulou K, Adamopoulos PG, Scorilas A. Unveiling the Human Gastrointestinal Tract Microbiome: The Past, Present, and Future of Metagenomics. Biomedicines 2023; 11:biomedicines11030827. [PMID: 36979806 PMCID: PMC10045138 DOI: 10.3390/biomedicines11030827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/26/2023] [Accepted: 03/08/2023] [Indexed: 03/30/2023] Open
Abstract
Over 1014 symbiotic microorganisms are present in a healthy human body and are responsible for the synthesis of vital vitamins and amino acids, mediating cellular pathways and supporting immunity. However, the deregulation of microbial dynamics can provoke diverse human diseases such as diabetes, human cancers, cardiovascular diseases, and neurological disorders. The human gastrointestinal tract constitutes a hospitable environment in which a plethora of microbes, including diverse species of archaea, bacteria, fungi, and microeukaryotes as well as viruses, inhabit. In particular, the gut microbiome is the largest microbiome community in the human body and has drawn for decades the attention of scientists for its significance in medical microbiology. Revolutions in sequencing techniques, including 16S rRNA and ITS amplicon sequencing and whole genome sequencing, facilitate the detection of microbiomes and have opened new vistas in the study of human microbiota. Especially, the flourishing fields of metagenomics and metatranscriptomics aim to detect all genomes and transcriptomes that are retrieved from environmental and human samples. The present review highlights the complexity of the gastrointestinal tract microbiome and deciphers its implication not only in cellular homeostasis but also in human diseases. Finally, a thorough description of the widely used microbiome detection methods is discussed.
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Affiliation(s)
- Konstantina Athanasopoulou
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Panagiotis G Adamopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
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35
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Liu Y, Chen L, Ma T, Li X, Zheng M, Zhou X, Chen L, Qian X, Xi J, Lu H, Cao H, Ma X, Bian B, Zhang P, Wu J, Gan R, Jia B, Sun L, Ju Z, Gao Y, Wen T, Chen T. EasyAmplicon: An easy-to-use, open-source, reproducible, and community-based pipeline for amplicon data analysis in microbiome research. IMETA 2023; 2:e83. [PMID: 38868346 PMCID: PMC10989771 DOI: 10.1002/imt2.83] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/01/2023] [Accepted: 01/10/2023] [Indexed: 06/14/2024]
Abstract
It is difficult for beginners to learn and use amplicon analysis software because there are so many software tools to choose from, and all of them need multiple steps of operation. Herein, we provide a cross-platform, open-source, and community-supported analysis pipeline EasyAmplicon. EasyAmplicon has most of the modules needed for an amplicon analysis, including data quality control, merging of paired-end reads, dereplication, clustering or denoising, chimera detection, generation of feature tables, taxonomic diversity analysis, compositional analysis, biomarker discovery, and publication-quality visualization. EasyAmplicon includes more than 30 cross-platform modules and R packages commonly used in the field. All steps of the pipeline are integrated into RStudio, which reduces learning costs, keeps the flexibility of the analysis process, and facilitates personalized analysis. The pipeline is maintained and updated by the authors and editors of WeChat official account "Meta-genome." Our team will regularly release the latest tutorials both in Chinese and English, read the feedback from users, and provide help to them in the WeChat account and GitHub. The pipeline can be deployed on various platforms, and the installation time is less than half an hour. On an ordinary laptop, the whole analysis process for dozens of samples can be completed within 3 h. The pipeline is available at GitHub (https://github.com/YongxinLiu/EasyAmplicon) and Gitee (https://gitee.com/YongxinLiu/EasyAmplicon).
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Affiliation(s)
- Yong‐Xin Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdongChina
| | - Lei Chen
- Department of Vascular Surgery, Fu Xing HospitalCapital Medical UniversityBeijingChina
| | - Tengfei Ma
- State Key Laboratory of Grassland Agro‐ecosystems, Centre for Grassland Microbiome, College of Pastoral Agricultural Science and TechnologyLanzhou UniversityLanzhouGansuChina
| | - Xiaofang Li
- Centre for Agricultural Resources Research, Institute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuangChina
| | - Maosheng Zheng
- College of Environmental Science and EngineeringNorth China Electric Power UniversityBeijingChina
| | - Xin Zhou
- Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Liang Chen
- Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Xubo Qian
- Department of Pediatrics, Affiliated Jinhua HospitalZhejiang University School of MedicineJinhuaZhejiangChina
| | - Jiao Xi
- College of Natural Resources and EnvironmentNorthwest A&F UniversityYanglingShaanxiChina
| | - Hongye Lu
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Clinical Research Center for Oral Diseases of Zhejiang Province, School of Stomatology, Zhejiang University School of MedicineStomatology HospitalHangzhouZhejiangChina
| | - Huiluo Cao
- Department of MicrobiologyUniversity of Hong KongHong KongChina
| | - Xiaoya Ma
- Center of Excellence in Fungal ResearchMae Fah Luang UniversityChiang RaiThailand
| | - Bian Bian
- Graduate School of Frontier SciencesUniversity of TokyoChibaJapan
| | - Pengfan Zhang
- Department of Plant‐Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
| | - Jiqiu Wu
- APC Microbiome InstituteUniversity College CorkCorkIreland
- Department of Genetics, University Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
| | - Ren‐You Gan
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for ScienceTechnology and Research (A*STAR)SingaporeSingapore
| | - Baolei Jia
- Department of Life ScienceChung‐Ang UniversitySeoulRepublic of Korea
| | - Linyang Sun
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdongChina
| | - Zhicheng Ju
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdongChina
| | - Yunyun Gao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdongChina
| | - Tao Wen
- The Key Laboratory of Plant Immunity Jiangsu Provincial Key Lab for Organic Solid Waste Utilization Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic‐Based FertilizersNanjing Agricultural UniversityNanjingChina
| | - Tong Chen
- National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
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36
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Lyu F, Han F, Ge C, Mao W, Chen L, Hu H, Chen G, Lang Q, Fang C. OmicStudio: A composable bioinformatics cloud platform with real-time feedback that can generate high-quality graphs for publication. IMETA 2023; 2:e85. [PMID: 38868333 PMCID: PMC10989813 DOI: 10.1002/imt2.85] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 01/06/2023] [Accepted: 01/12/2023] [Indexed: 06/14/2024]
Abstract
OmicStudio focuses on speed, quality together with flexibility. Generally, OmicStudio can not only meet the users' demand of ordinary bioinformatics data analysis, statistics, and visualization, but also provides them freedom of data mining beyond developer's framework. Additionally, unlimited to developer's aesthetics, users can get more elegant graphs through customizing. Available online https://www.omicstudio.cn.
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Affiliation(s)
- Fengye Lyu
- Operation DepartmentLC‐Bio Technology Co., Ltd.HangzhouChina
| | - Feiran Han
- Operation DepartmentLC‐Bio Technology Co., Ltd.HangzhouChina
| | - Changli Ge
- Operation DepartmentLC‐Bio Technology Co., Ltd.HangzhouChina
| | - Weikang Mao
- Operation DepartmentLC‐Bio Technology Co., Ltd.HangzhouChina
| | - Li Chen
- Operation DepartmentLC‐Bio Technology Co., Ltd.HangzhouChina
| | - Huipeng Hu
- Operation DepartmentLC‐Bio Technology Co., Ltd.HangzhouChina
| | - Guoguo Chen
- Operation DepartmentLC‐Bio Technology Co., Ltd.HangzhouChina
| | - Qiulei Lang
- Operation DepartmentLC‐Bio Technology Co., Ltd.HangzhouChina
| | - Chao Fang
- Operation DepartmentLC‐Bio Technology Co., Ltd.HangzhouChina
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37
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Nguyen BT, Dumack K, Trivedi P, Islam Z, Hu H. Plant associated protists-Untapped promising candidates for agrifood tools. Environ Microbiol 2023; 25:229-240. [PMID: 36482161 PMCID: PMC10108267 DOI: 10.1111/1462-2920.16303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
The importance of host-associated microorganisms and their biotic interactions for plant health and performance has been increasingly acknowledged. Protists, main predators and regulators of bacteria and fungi, are abundant and ubiquitous eukaryotes in terrestrial ecosystems. Protists are considered to benefit plant health and performance, but the community structure and functions of plant-associated protists remain surprisingly underexplored. Harnessing plant-associated protists and other microbes can potentially enhance plant health and productivity and sustain healthy food and agriculture systems. In this review, we summarize the knowledge of multifunctionality of protists and their interactions with other microbes in plant hosts, and propose a future framework to study plant-associated protists and utilize protists as agrifood tools for benefiting agricultural production.
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Affiliation(s)
- Bao‐Anh Thi Nguyen
- School of Agriculture and Food, Faculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVictoriaAustralia
| | - Kenneth Dumack
- Terrestrial EcologyInstitute of Zoology, University of CologneKölnGermany
| | - Pankaj Trivedi
- Microbiome Network and Department of Agricultural BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Zahra Islam
- School of Agriculture and Food, Faculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVictoriaAustralia
- ARC Hub for Smart FertilisersThe University of MelbourneParkvilleVictoriaAustralia
| | - Hang‐Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVictoriaAustralia
- ARC Hub for Smart FertilisersThe University of MelbourneParkvilleVictoriaAustralia
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38
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Zhang YL, Guo XJ, Huang X, Guo RJ, Lu XH, Li SD, Zhang H. The Co-Association of Enterobacteriaceae and Pseudomonas with Specific Resistant Cucumber against Fusarium Wilt Disease. BIOLOGY 2023; 12:biology12020143. [PMID: 36829422 PMCID: PMC9952826 DOI: 10.3390/biology12020143] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 01/10/2023] [Indexed: 01/18/2023]
Abstract
The root microbiota contributes to the plant's defense against stresses and pathogens. However, the co-association pattern of functional bacteria that improves plant resistance has not been interpreted clearly. Using Illumina high-throughput sequencing technology, the root bacterial community profiles of six cucumber cultivars with different resistance in response to the causative agent of cucumber Fusarium wilt (CFW), Fusarium oxysporum f. sp. cucumerinum (Foc), were analyzed. The principal coordinate analysis indicated that the interactions of the cultivars and pathogens drove the cucumber root bacterial communities (p = 0.001). The resistance-specific differential genera across the cultivars were identified, including Massilia in the resistant cultivars, unclassified Enterobacteriaceae in resistant CL11 and JY409, Pseudomonas in JY409, Cronobacter in moderately resistant ZN106, and unclassified Rhizobiaceae and Streptomyces in susceptible ZN6. The predominant root bacterium Massilia accounted for the relative abundance of up to 28.08-61.55%, but dramatically declined to 9.36% in Foc-inoculated susceptible ZN6. Pseudomonas ASV103 and ASV48 of Pseudomonadaceae and Cronobacter ASV162 of Enterobacteriaceae were consistently differential across the cultivars at the phylum, genus, and ASV levels. Using the culture-based method, antagonistic strains of Enterobacteriaceae with a high proportion of 51% were isolated. Furthermore, the bacterial complexes of Pantoea dispersa E318 + Pseudomonas koreensis Ps213 and Cronobacter spp. C1 + C7 reduced the disease index of CFW by 77.2% and 60.0% in the pot experiment, respectively. This study reveals the co-association of specific root bacteria with host plants and reveals insight into the suppressing mechanism of resistant cultivars against CFW disease by regulating the root microbiota.
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Affiliation(s)
- Yu-Lu Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiao-Jing Guo
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xin Huang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Rong-Jun Guo
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence:
| | - Xiao-Hong Lu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shi-Dong Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hao Zhang
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
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39
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Cross Cultivation on Homologous/Heterologous Plant-Based Culture Media Empowers Host-Specific and Real Time In Vitro Signature of Plant Microbiota. DIVERSITY 2022. [DOI: 10.3390/d15010046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Alliances of microbiota with plants are masked by the inability of in vitro cultivation of their bulk. Pure cultures piled in international centers originated from dissimilar environments/hosts. Reporting that plant root/leaf-based culture media support the organ-specific growth of microbiota, it was of interest to further investigate if a plant-based medium prepared from homologous (maize) supports specific/adapted microbiota compared to another prepared from heterologous plants (sunflower). The culture-independent community of maize phyllosphere was compared to communities cross-cultivated on plant broth-based media: CFU counts and taxa prevalence (PCR-DGGE; Illumina MiSeq amplicon sequencing). Similar to total maize phyllospheric microbiota, culture-dependent communities were overwhelmed by Proteobacteria (>94.3–98.3%); followed by Firmicutes (>1.3–3.7%), Bacteroidetes (>0.01–1.58%) and Actinobacteria (>0.06–0.34%). Differential in vitro growth on homologous versus heterologous plant-media enriched/restricted various taxa. In contrast, homologous cultivation over represented members of Proteobacteria (ca. > 98.0%), mainly Pseudomonadaceae and Moraxellaceae; heterologous cultivation and R2A enriched Firmicutes (ca. > 3.0%). The present strategy simulates/fingerprints the chemical composition of host plants to expand the culturomics of plant microbiota, advance real-time in vitro cultivation and lab-keeping of compatible plant microbiota, and identify preferential pairing of plant-microbe partners toward future synthetic community (SynComs) research and use in agriculture.
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40
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Zhou X, Wang J, Liu F, Liang J, Zhao P, Tsui CKM, Cai L. Cross-kingdom synthetic microbiota supports tomato suppression of Fusarium wilt disease. Nat Commun 2022; 13:7890. [PMID: 36550095 PMCID: PMC9780251 DOI: 10.1038/s41467-022-35452-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
The role of rhizosphere microbiota in the resistance of tomato plant against soil-borne Fusarium wilt disease (FWD) remains unclear. Here, we showed that the FWD incidence was significantly negatively correlated with the diversity of both rhizosphere bacterial and fungal communities. Using the microbiological culturomic approach, we selected 205 unique strains to construct different synthetic communities (SynComs), which were inoculated into germ-free tomato seedlings, and their roles in suppressing FWD were monitored using omics approach. Cross-kingdom (fungi and bacteria) SynComs were most effective in suppressing FWD than those of Fungal or Bacterial SynComs alone. This effect was underpinned by a combination of molecular mechanisms related to plant immunity and microbial interactions contributed by the bacterial and fungal communities. This study provides new insight into the dynamics of microbiota in pathogen suppression and host immunity interactions. Also, the formulation and manipulation of SynComs for functional complementation constitute a beneficial strategy in controlling soil-borne disease.
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Affiliation(s)
- Xin Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
- University of Chinese Academy of Sciences, 100101, Beijing, P. R. China
| | - Jinting Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
- University of Chinese Academy of Sciences, 100101, Beijing, P. R. China
| | - Fang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Junmin Liang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Peng Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Clement K M Tsui
- Faculty of Medicine, University of British Columbia, Vancouver, Canada
- National Centre for Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Pathology, Sidra Medicine, Doha, Qatar
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China.
- University of Chinese Academy of Sciences, 100101, Beijing, P. R. China.
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41
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Zhan C, Matsumoto H, Liu Y, Wang M. Pathways to engineering the phyllosphere microbiome for sustainable crop production. NATURE FOOD 2022; 3:997-1004. [PMID: 37118297 DOI: 10.1038/s43016-022-00636-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/12/2022] [Indexed: 04/30/2023]
Abstract
Current disease resistance breeding, which is largely dependent on the exploitation of resistance genes in host plants, faces the serious challenges of rapidly evolving phytopathogens. The phyllosphere is the largest biological surface on Earth and an untapped reservoir of functional microbiomes. The phyllosphere microbiome has the potential to defend against plant diseases. However, the mechanisms of how the microbiota assemble and function in the phyllosphere remain largely elusive, and this restricts the exploitation of the targeted beneficial microbes in the field. Here we review the endogenous and exogenous cues impacting microbiota assembly in the phyllosphere and how the phyllosphere microbiota in turn facilitate the disease resistance of host plants. We further construct a holistic framework by integrating of holo-omics, genetic manipulation, culture-dependent characterization and emerging artificial intelligence techniques, such as deep learning, to engineer the phyllosphere microbiome for sustainable crop production.
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Affiliation(s)
- Chengfang Zhan
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Haruna Matsumoto
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yufei Liu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Mengcen Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China.
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Global Education Program for AgriScience Frontiers, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan.
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42
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Li H, Zhao HM, Purchase D, Chen XW. Editorial: Microbial communities and functions contribute to plant performance under various stresses. Front Microbiol 2022; 13:992909. [DOI: 10.3389/fmicb.2022.992909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/25/2022] [Indexed: 11/09/2022] Open
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43
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Gonçalves AC, Sánchez-Juanes F, Meirinho S, Silva LR, Alves G, Flores-Félix JD. Insight into the Taxonomic and Functional Diversity of Bacterial Communities Inhabiting Blueberries in Portugal. Microorganisms 2022; 10:2193. [PMID: 36363783 PMCID: PMC9695653 DOI: 10.3390/microorganisms10112193] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 10/15/2023] Open
Abstract
Vaccinium myrtillus is a dwarf shrub of the Ericaceae family with a Palearctic distribution, associated with temperate and cold humid climates. It is widespread on the European continent; on the Iberian Peninsula it is located on Atlantic climate mountains and glacial relicts. In Portugal, we find scattered and interesting populations; however, the majority of them are threatened by climate change and wildfires. Given that, the objective of this study is to determine the rhizospheric and root bacterial communities of this plant in the southernmost regions, and, consequently, its potential range and ability to be used as a biofertilizer. In this work, metabarcoding of 16S rRNA gene showed that the endophytic bacterial diversity is dependent on the plant and selected by it according to the observed alpha and beta diversity. Moreover, a culturomic approach allowed 142 different strains to be isolated, some of them being putative new species. Additionally, some strains belonging to the genera Bacillus, Paenibacillus, Pseudomonas, Paraburkholderia, and Caballeronia showed significant potential to be applied as multifunctional biofertilizers since they present good plant growth-promoting (PGP) mechanisms, high colonization capacities, and an increase in vegetative parameters in blueberry and tomato plants.
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Affiliation(s)
- Ana C. Gonçalves
- CICS–UBI—Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal
- CIBIT—Coimbra Institute for Biomedical Imaging and Translational Research, University of Coimbra, 3000-540 Coimbra, Portugal
| | - Fernando Sánchez-Juanes
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Universidad de Salamanca, CSIC, 37007 Salamanca, Spain
- Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Sara Meirinho
- CICS–UBI—Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal
| | - Luís R. Silva
- CICS–UBI—Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal
- CPIRN-UDI/IPG—Center of Potential and Innovation of Natural Resources, Research Unit for Inland Development (UDI), Polytechnic Institute of Guarda, 6300-559 Guarda, Portugal
| | - Gilberto Alves
- CICS–UBI—Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal
| | - José David Flores-Félix
- CICS–UBI—Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal
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44
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Jiang MZ, Zhu HZ, Zhou N, Liu C, Jiang CY, Wang Y, Liu SJ. Droplet microfluidics-based high-throughput bacterial cultivation for validation of taxon pairs in microbial co-occurrence networks. Sci Rep 2022; 12:18145. [PMID: 36307549 PMCID: PMC9616874 DOI: 10.1038/s41598-022-23000-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 10/21/2022] [Indexed: 12/31/2022] Open
Abstract
Co-occurrence networks inferred from the abundance data of microbial communities are widely applied to predict microbial interactions. However, the high workloads of bacterial isolation and the complexity of the networks themselves constrained experimental demonstrations of the predicted microbial associations and interactions. Here, we integrate droplet microfluidics and bar-coding logistics for high-throughput bacterial isolation and cultivation from environmental samples, and experimentally investigate the relationships between taxon pairs inferred from microbial co-occurrence networks. We collected Potamogeton perfoliatus plants (including roots) and associated sediments from Beijing Olympic Park wetland. Droplets of series diluted homogenates of wetland samples were inoculated into 126 96-well plates containing R2A and TSB media. After 10 days of cultivation, 65 plates with > 30% wells showed microbial growth were selected for the inference of microbial co-occurrence networks. We cultivated 129 bacterial isolates belonging to 15 species that could represent the zero-level OTUs (Zotus) in the inferred co-occurrence networks. The co-cultivations of bacterial isolates corresponding to the prevalent Zotus pairs in networks were performed on agar plates and in broth. Results suggested that positively associated Zotu pairs in the co-occurrence network implied complicated relations including neutralism, competition, and mutualism, depending on bacterial isolate combination and cultivation time.
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Affiliation(s)
- Min-Zhi Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, People's Republic of China
| | - Hai-Zhen Zhu
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Nan Zhou
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Chang Liu
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Yulin Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, People's Republic of China.
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, People's Republic of China.
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
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45
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Jia Y, Li X, Xu F, Liu Z, Fu Y, Xu X, Yang J, Zhang S, Shen C. Single-cell-level microfluidics assisted with resuscitation-promoting factor technology (SMART) to isolate novel biphenyl-degrading bacteria from typical soils in eastern China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 311:119864. [PMID: 35952991 DOI: 10.1016/j.envpol.2022.119864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 06/15/2023]
Abstract
Soil microorganisms represent one of the largest biodiversity reservoirs. However, most low-abundance, slow-growing or dormant microorganisms in soils are difficult to capture with traditional enrichment culture methods. These types of microorganisms represent a valuable "microbial seed bank". To better exploit and utilize this "microbial dark matter", we developed a novel strategy that integrates single-cell-level isolation with microfluidics technology and culture with resuscitation-promoting factor (Rpf) to isolate biphenyl-degrading bacteria from four typical soils (paddy soil, red soil, alluvial soil and black soil) in eastern China. Multitudinous bacteria were successfully isolated and cultured; some of the identified clades have not been previously linked to biphenyl biodegradation, such as Actinotalea, Curtobacterium and Rothia. Soil microcosmic experiments validated that some bacteria are responsible for biphenyl degradation in soil. In addition, genomic sequencing and Illumina MiSeq sequencing of 16S rRNA genes indicated that exogenous Rpf mainly promotes the recovery and growth of bacteria containing endogenous Rpf-encoding genes. In summary, this study provides a novel strategy for capturing target functional microorganisms in soils, indicates potential bioresources for the bioremediation of contaminated soils, and enhances our current understanding of the mechanisms involved in the response to exogenous Rpf.
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Affiliation(s)
- Yangyang Jia
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xinyi Li
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Fengjun Xu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zefan Liu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yulong Fu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xin Xu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jiawen Yang
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Jialan Environmental Technology Co., LTD, Hangzhou, 311051, China
| | - Shuai Zhang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Chaofeng Shen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
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Afridi MS, Fakhar A, Kumar A, Ali S, Medeiros FHV, Muneer MA, Ali H, Saleem M. Harnessing microbial multitrophic interactions for rhizosphere microbiome engineering. Microbiol Res 2022; 265:127199. [PMID: 36137486 DOI: 10.1016/j.micres.2022.127199] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 07/02/2022] [Accepted: 09/13/2022] [Indexed: 10/14/2022]
Abstract
The rhizosphere is a narrow and dynamic region of plant root-soil interfaces, and it's considered one of the most intricate and functionally active ecosystems on the Earth, which boosts plant health and alleviates the impact of biotic and abiotic stresses. Improving the key functions of the microbiome via engineering the rhizosphere microbiome is an emerging tool for improving plant growth, resilience, and soil-borne diseases. Recently, the advent of omics tools, gene-editing techniques, and sequencing technology has allowed us to unravel the entangled webs of plant-microbes interactions, enhancing plant fitness and tolerance to biotic and abiotic challenges. Plants secrete signaling compounds with low molecular weight into the rhizosphere, that engage various species to generate a massive deep complex array. The underlying principle governing the multitrophic interactions of the rhizosphere microbiome is yet unknown, however, some efforts have been made for disease management and agricultural sustainability. This review discussed the intra- and inter- microbe-microbe and microbe-animal interactions and their multifunctional roles in rhizosphere microbiome engineering for plant health and soil-borne disease management. Simultaneously, it investigates the significant impact of immunity utilizing PGPR and cover crop strategy in increasing rhizosphere microbiome functions for plant development and protection using omics techniques. The ecological engineering of rhizosphere plant interactions could be used as a potential alternative technology for plant growth improvement, sustainable disease control management, and increased production of economically significant crops.
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Affiliation(s)
- Muhammad Siddique Afridi
- Department of Plant Pathology, Federal University of Lavras, CP3037, 37200-900 Lavras, MG, Brazil.
| | - Ali Fakhar
- Division of Applied Science, Gyeongsang National University, South Korea
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, MP, India
| | - Sher Ali
- NMR Lab, Department of Chemistry, Federal University of Paraná, Curitiba 81530-900, PR, Brazil
| | - Flavio H V Medeiros
- Department of Plant Pathology, Federal University of Lavras, CP3037, 37200-900 Lavras, MG, Brazil
| | - Muhammad Atif Muneer
- International Magnesium Institute, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hina Ali
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Muhammad Saleem
- Department of Biological Sciences, Alabama State University, Montgomery, AL 36104, USA
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Schultz J, Modolon F, Rosado AS, Voolstra CR, Sweet M, Peixoto RS. Methods and Strategies to Uncover Coral-Associated Microbial Dark Matter. mSystems 2022; 7:e0036722. [PMID: 35862824 PMCID: PMC9426423 DOI: 10.1128/msystems.00367-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The vast majority of environmental microbes have not yet been cultured, and most of the knowledge on coral-associated microbes (CAMs) has been generated from amplicon sequencing and metagenomes. However, exploring cultured CAMs is key for a detailed and comprehensive characterization of the roles of these microbes in shaping coral health and, ultimately, for their biotechnological use as, for example, coral probiotics and other natural products. Here, the strategies and technologies that have been used to access cultured CAMs are presented, while advantages and disadvantages associated with each of these strategies are discussed. We highlight the existing gaps and potential improvements in culture-dependent methodologies, indicating several possible alternatives (including culturomics and in situ diffusion devices) that could be applied to retrieve the CAM "dark matter" (i.e., the currently undescribed CAMs). This study provides the most comprehensive synthesis of the methodologies used to recover the cultured coral microbiome to date and draws suggestions for the development of the next generation of CAM culturomics.
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Affiliation(s)
- Júnia Schultz
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Flúvio Modolon
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre S. Rosado
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | | | - Michael Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, UK
| | - Raquel S. Peixoto
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Deng X, Zhang N, Li Y, Zhu C, Qu B, Liu H, Li R, Bai Y, Shen Q, Falcao Salles J. Bio-organic soil amendment promotes the suppression of Ralstonia solanacearum by inducing changes in the functionality and composition of rhizosphere bacterial communities. THE NEW PHYTOLOGIST 2022; 235:1558-1574. [PMID: 35569105 DOI: 10.1111/nph.18221] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Stimulating the development of soil suppressiveness against certain pathogens represents a sustainable solution toward reducing pesticide use in agriculture. However, understanding the dynamics of suppressiveness and the mechanisms leading to pathogen control remain largely elusive. Here, we investigated the mechanisms used by the rhizosphere microbiome induces bacterial wilt disease suppression in a long-term field experiment where continuous application of bio-organic fertilizers (BFs) triggered disease suppressiveness when compared to chemical fertilizer application. We further demonstrated in a glasshouse experiment that the suppressiveness of the rhizosphere bacterial communities was triggered mainly by changes in community composition rather than only by the abundance of the introduced biocontrol strain. Metagenomics approaches revealed that members of the families Sphingomonadaceae and Xanthomonadaceae with the ability to produce secondary metabolites were enriched in the BF plant rhizosphere but only upon pathogen invasion. We experimentally validated this observation by inoculating bacterial isolates belonging to the families Sphingomonadaceae and Xanthomonadaceae into conducive soil, which led to a significant reduction in pathogen abundance and increase in nonribosomal peptide synthetase gene abundance. We conclude that priming of the soil microbiome with BF amendment fostered reactive bacterial communities in the rhizosphere of tomato plants in response to biotic disturbance.
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Affiliation(s)
- Xuhui Deng
- Jiangsu Provincial Key Laboratory of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Microbial Ecology Cluster, Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, 9747AG, the Netherlands
| | - Na Zhang
- Jiangsu Provincial Key Laboratory of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yuchan Li
- Jiangsu Provincial Key Laboratory of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Chengzhi Zhu
- Jiangsu Provincial Key Laboratory of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Baoyuan Qu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
| | - Hongjun Liu
- Jiangsu Provincial Key Laboratory of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Rong Li
- Jiangsu Provincial Key Laboratory of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Qirong Shen
- Jiangsu Provincial Key Laboratory of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Joana Falcao Salles
- Microbial Ecology Cluster, Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, 9747AG, the Netherlands
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Wang H, Zhou L, Qin J, Chen J, Stewart C, Sun Y, Huang H, Xu L, Li L, Han J, Li F. One-Component Multichannel Sensor Array for Rapid Identification of Bacteria. Anal Chem 2022; 94:10291-10298. [PMID: 35802909 DOI: 10.1021/acs.analchem.2c02236] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial infections routinely cause serious problems to public health. To mitigate the impact of bacterial infections, sensing systems are urgently required for the detection and subsequent epidemiological control of pathogenic organisms. Most conventional approaches are time-consuming and highly instrument- and professional operator-dependent. Here, we developed a novel one-component multichannel array constructed with complex systems made from three modified polyethyleneimine as well as negatively charged graphene oxide, which provided an information-rich multimode response to successfully identify 10 bacteria within minutes via electrostatic interactions and hydrophobic interactions. Furthermore, the concentration of bacteria (from OD600 = 0.025 to 1) and the ratio of mixed bacteria were successfully achieved with our smart sensing system. Our designed sensor array also exhibited huge potential in biological samples, such as in urine (OD600 = 0.125, 94% accuracy). The way to construct a sensor array with minimal sensor element with abundant signal outputs tremendously saves cost and time, providing a powerful tool for the diagnosis and assessment of bacterial infections in the clinic.
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Affiliation(s)
- Hao Wang
- State Key Laboratory of Natural Medicines and National R&D Center for Chinese Herbal Medicine Processing, Department of Food Quality and Safety, College of Engineering, China Pharmaceutical University, Nanjing 211109, China
| | - Lingjia Zhou
- State Key Laboratory of Natural Medicines and National R&D Center for Chinese Herbal Medicine Processing, Department of Food Quality and Safety, College of Engineering, China Pharmaceutical University, Nanjing 211109, China
| | - Jiaojiao Qin
- State Key Laboratory of Natural Medicines and National R&D Center for Chinese Herbal Medicine Processing, Department of Food Quality and Safety, College of Engineering, China Pharmaceutical University, Nanjing 211109, China
| | - Jiahao Chen
- State Key Laboratory of Natural Medicines and National R&D Center for Chinese Herbal Medicine Processing, Department of Food Quality and Safety, College of Engineering, China Pharmaceutical University, Nanjing 211109, China
| | - Callum Stewart
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Stockholm 17177, Sweden
| | - Yimin Sun
- School of Pharmacy, China Pharmaceutical University, Nanjing 211109, China
| | - Hui Huang
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Stockholm 17177, Sweden
| | - Lian Xu
- State Key Laboratory of Natural Medicines and National R&D Center for Chinese Herbal Medicine Processing, Department of Food Quality and Safety, College of Engineering, China Pharmaceutical University, Nanjing 211109, China
| | - Linxian Li
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Stockholm 17177, Sweden
| | - Jinsong Han
- State Key Laboratory of Natural Medicines and National R&D Center for Chinese Herbal Medicine Processing, Department of Food Quality and Safety, College of Engineering, China Pharmaceutical University, Nanjing 211109, China
| | - Fei Li
- State Key Laboratory of Natural Medicines and National R&D Center for Chinese Herbal Medicine Processing, Department of Food Quality and Safety, College of Engineering, China Pharmaceutical University, Nanjing 211109, China
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50
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Fusarium fruiting body microbiome member Pantoea agglomerans inhibits fungal pathogenesis by targeting lipid rafts. Nat Microbiol 2022; 7:831-843. [PMID: 35618775 DOI: 10.1038/s41564-022-01131-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 04/22/2022] [Indexed: 12/13/2022]
Abstract
Plant-pathogenic fungi form intimate interactions with their associated bacterial microbiota during their entire life cycle. However, little is known about the structure, functions and interaction mechanisms of bacterial communities associated with fungal fruiting bodies (perithecia). Here we examined the bacterial microbiome of perithecia formed by Fusarium graminearum, the major pathogenic fungus causing Fusarium head blight in cereals. A total of 111 shared bacterial taxa were identified in the microbiome of 65 perithecium samples collected from 13 geographic locations. Within a representative culture collection, 113 isolates exhibited antagonistic activity against F. graminearum, with Pantoea agglomerans ZJU23 being the most efficient in reducing fungal growth and infectivity. Herbicolin A was identified as the key antifungal compound secreted by ZJU23. Genetic and chemical approaches led to the discovery of its biosynthetic gene cluster. Herbicolin A showed potent in vitro and in planta efficacy towards various fungal pathogens and fungicide-resistant isolates, and exerted a fungus-specific mode of action by directly binding and disrupting ergosterol-containing lipid rafts. Furthermore, herbicolin A exhibited substantially higher activity (between 5- and 141-fold higher) against the human opportunistic fungal pathogens Aspergillus fumigatus and Candida albicans in comparison with the clinically used fungicides amphotericin B and fluconazole. Its mode of action, which is distinct from that of other antifungal drugs, and its efficacy make herbicolin A a promising antifungal drug to combat devastating fungal pathogens, both in agricultural and clinical settings.
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