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Bai G, Xie Y, Gao X, Xiao C, Yong T, Huang L, Cai M, Liu Y, Hu H, Chen S. Selective impact of three homogenous polysaccharides with different structural characteristics from Grifola frondosa on human gut microbial composition and the structure-activity relationship. Int J Biol Macromol 2024; 269:132143. [PMID: 38729493 DOI: 10.1016/j.ijbiomac.2024.132143] [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: 12/26/2023] [Revised: 04/08/2024] [Accepted: 05/05/2024] [Indexed: 05/12/2024]
Abstract
Natural polysaccharides interact with gut microbes to enhance human well-being. Grifola frondosa is a polysaccharides-rich edible and medicinal mushroom. The prebiotic potential of G. frondosa polysaccharides has been explored in recent years, however, the relationship between their various structural features and prebiotic activities is poorly understood. In this study, three homogenous polysaccharides GFP10, GFP21 and GFP22 having different molecular weights (Mw), monosaccharide compositions and glycosidic linkages were purified from G. frondosa, and their effects on intestinal microbial composition were compared. GFP10 was a fucomannogalactan with an Mw of 23.0 kDa, and it selectively inhibited Enterobacter, while GFP21 was a fucomannogalactoglucan with an Mw of 18.6 kDa, and it stimulated Catenibacterium. GFP22 was a 4.9 kDa mannoglucan that selectively inhibited Klebsiella and boosted Bifidobacterium, Catenibacterium and Phascolarctobacterium, and prominently promoted the production of short-chain fatty acids (SCFAs). The selective modulation of gut microbiota by polysaccharides was structure-dependent. A relatively lower Mw and a high proportion of glycosidic linkages like T-Glcp, 1,3-Glcp, 1,3,6-Glcp and 1,4-Glcp might be more easily utilized to produce SCFAs and beneficial for the proliferation of Catenibacterium and Phascolarctobacterium. This research provided a valuable resource for further exploring the structure-activity relationship and prebiotic activity of G. frondosa polysaccharides.
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Affiliation(s)
- Guangjian Bai
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, China
| | - Yizhen Xie
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, China; Guangdong Yuewei Edible Fungi Co., Ltd, China
| | - Xiong Gao
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, China
| | - Chun Xiao
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, China
| | - Tianqiao Yong
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, China
| | - Longhua Huang
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, China
| | - Manjun Cai
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, China
| | - Yuanchao Liu
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, China
| | - Huiping Hu
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, China.
| | - Shaodan Chen
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, China.
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Hirpara KR, Hinsu AT, Kothari RK. Metagenomic evaluation of peanut rhizosphere microbiome from the farms of Saurashtra regions of Gujarat, India. Sci Rep 2024; 14:10525. [PMID: 38720057 PMCID: PMC11079051 DOI: 10.1038/s41598-024-61343-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 05/05/2024] [Indexed: 05/12/2024] Open
Abstract
The narrow zone of soil around the plant roots with maximum microbial activity termed as rhizosphere. Rhizospheric bacteria promote the plant growth directly or indirectly by providing the nutrients and producing antimicrobial compounds. In this study, the rhizospheric microbiota of peanut plants was characterized from different farms using an Illumina-based partial 16S rRNA gene sequencing to evaluate microbial diversity and identify the core microbiome through culture-independent (CI) approach. Further, all rhizospheric bacteria that could grow on various nutrient media were identified, and the diversity of those microbes through culture-dependent method (CD) was then directly compared with their CI counterparts. The microbial population profiles showed a significant correlation with organic carbon and concentration of phosphate, manganese, and potassium in the rhizospheric soil. Genera like Sphingomicrobium, Actinoplanes, Aureimonas _A, Chryseobacterium, members from Sphingomonadaceae, Burkholderiaceae, Pseudomonadaceae, Enterobacteriaceae family, and Bacilli class were found in the core microbiome of peanut plants. As expected, the current study demonstrated more bacterial diversity in the CI method. However, a higher number of sequence variants were exclusively present in the CD approach compared to the number of sequence variants shared between both approaches. These CD-exclusive variants belonged to organisms that are more typically found in soil. Overall, this study portrayed the changes in the rhizospheric microbiota of peanuts in different rhizospheric soil and environmental conditions and gave an idea about core microbiome of peanut plant and comparative bacterial diversity identified through both approaches.
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Affiliation(s)
- Krunal R Hirpara
- Department of Biosciences, Saurashtra University, Rajkot, Gujarat, 360005, India
| | - Ankit T Hinsu
- Department of Biosciences, Saurashtra University, Rajkot, Gujarat, 360005, India
- Royal Veterinary College, London, AL9 7TA, UK
| | - Ramesh K Kothari
- Department of Biosciences, Saurashtra University, Rajkot, Gujarat, 360005, India.
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Wang N, Chen S, Xie Y, Liu X, Xi Z, Li J, Xue C, Deng R, Min W, Kang R, Xie L. The Sanbi Decoction alleviates intervertebral disc degeneration in rats through intestinal flora and serum metabolic homeostasis modulation. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 127:155480. [PMID: 38484462 DOI: 10.1016/j.phymed.2024.155480] [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: 11/13/2023] [Revised: 01/29/2024] [Accepted: 02/23/2024] [Indexed: 03/26/2024]
Abstract
BACKGROUND Intervertebral disc degeneration (IVDD) is an essential cause of low back pain (LBP), the incidence of which has risen in recent years and is progressively younger, but treatment options are limited, placing a serious economic burden on society. Sanbi decoction (SBD) is an important classical formula for the treatment of IVDD, which can significantly improve patients' symptoms and is a promising alternative therapy. PURPOSE The aim of this study is to investigate the safety and efficacy of SBD in the treatment of IVDD and to explore the underlying mechanisms by using an integrated analytical approach of microbiomics and serum metabolomics, as well as by using molecular biology. METHODS A rat IVDD puncture model was established and treated by gavage with different concentrations of SBD, and clean faeces, serum, liver, kidney, and intervertebral disc (IVD) were collected after 4 weeks. We assessed the safety by liver and kidney weighing, functional tests and tissue staining, the expression of tumor necrosis factor-alpha (TNF-ɑ), interleukin 1β (IL-1β) and interleukin 6 (IL-6) inflammatory factors in serum was detected by ELISA kits, and X-ray test, magnetic resonance imaging (MRI) examination, immunohistochemistry (IHC), western blotting (WB), hematoxylin-eosin (HE) staining and safranin O-fast green (SO/FG) staining were used to assess the efficacy. Finally, we performed 16S rRNA sequencing analysis on the faeces of different groups and untargeted metabolomics on serum and analyzed the association between them. RESULTS SBD can effectively reduce the inflammatory response, regulate the metabolic balance of extracellular matrix (ECM), improve symptoms, and restore IVD function. In addition, SBD can significantly improve the diversity of intestinal flora and maintain the balance. At the phylum level, SBD greatly increased the relative abundance of Patescibacteria and Actinobacteriota and decreased the relative abundance of Bacteroidota. At the genus level, SBD significantly increased the relative abundance of Clostridia_UCG-014, Enterorhabdus, and Adlercreutzia, and decreased the relative abundance of Ruminococcaceae_UCG-005 (p < 0.05). Untargeted metabolomics indicated that SBD significantly improved serum metabolites and altered serum expression of 4alpha-phorbol 12,13-didecanoate (4alphaPDD), euscaphic acid (EA), alpha-muricholic acid (α-MCA), 5-hydroxyindoleacetic acid (5-HIAA), and kynurenine (Kyn) (p < 0.05), and the metabolic pathways were mainly lipid metabolism and amino acid metabolism. CONCLUSIONS This study demonstrated that SBD can extensively regulate intestinal flora and serum metabolic homeostasis to reduce inflammatory response, inhibit the degradation of ECM, restore IVD height and water content to achieve apparent therapeutic effect for IVDD.
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Affiliation(s)
- Nan Wang
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province, 210028, China
| | - Shuang Chen
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province, 210028, China
| | - Yimin Xie
- Department of Orthopedics, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province 210029, China
| | - Xin Liu
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province, 210028, China
| | - Zhipeng Xi
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province, 210028, China
| | - Jingchi Li
- The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, Sichuan Province, 646000, China
| | - Congyang Xue
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province, 210028, China
| | - Rongrong Deng
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province, 210028, China
| | - Wen Min
- Department of Orthopedics, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province 210029, China.
| | - Ran Kang
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province, 210028, China.
| | - Lin Xie
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province, 210028, China.
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Abdullaeva Y, Ratering S, Rosado-Porto D, Ambika Manirajan B, Glatt A, Schnell S, Cardinale M. Domestication caused taxonomical and functional shifts in the wheat rhizosphere microbiota, and weakened the natural bacterial biocontrol against fungal pathogens. Microbiol Res 2024; 281:127601. [PMID: 38218094 DOI: 10.1016/j.micres.2024.127601] [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: 11/12/2023] [Revised: 12/14/2023] [Accepted: 01/02/2024] [Indexed: 01/15/2024]
Abstract
Modern crops might have lost some of their functional traits, required for interacting with beneficial microbes, as a result of the genotypic/phenotypic modifications that occurred during domestication. Here, we studied the bacterial and fungal microbiota in the rhizosphere of two cultivated wheat species (Triticum aestivum and T. durum) and their respective ancestors (Aegilops tauschii and T. dicoccoides), in three experimental fields, by using metabarcoding of 16S rRNA genes and ITS2, coupled with co-occurrence network analysis. Moreover, the abundance of bacterial genes involved in N- and P-cycles was estimated by quantitative PCR, and urease, alkaline phosphatase and phosphomonoesterase activities were assessed by enzymatic tests. The relationships between microbiota and environmental metadata were tested by correlation analysis. The assemblage of core microbiota was affected by both site and plant species. No significant differences in the abundance of potential fungal pathogens between wild and cultivated wheat species were found; however, co-occurrence analysis showed more bacterial-fungal negative correlations in the wild species. Concerning functions, the nitrogen denitrification nirS gene was consistently more abundant in the rhizosphere of A. tauschii than T. aestivum. Urease activity was higher in the rhizosphere of each wild wheat species in at least two of the research locations. Several microbiota members, including potentially beneficial taxa such as Lysobacter and new taxa such as Blastocatellaceae, were found to be strongly correlated to rhizospheric soil metadata. Our results showed that a functional microbiome shift occurred as a result of wheat domestication. Notably, these changes also included the reduction of the natural biocontrol potential of rhizosphere-associated bacteria against pathogenic fungi, suggesting that domestication disrupted the equilibrium of plant-microbe relationships that had been established during million years of co-evolution.
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Affiliation(s)
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | - David Rosado-Porto
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | | | - Andrea Glatt
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany.
| | - Massimiliano Cardinale
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany; Department of Biological and Environmental Sciences and Technologies - DiSTeBA, University of Salento, Lecce, Italy.
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Yang Y, Xu N, Zhang Z, Lei C, Chen B, Qin G, Qiu D, Lu T, Qian H. Deciphering Microbial Community and Nitrogen Fixation in the Legume Rhizosphere. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5659-5670. [PMID: 38442360 DOI: 10.1021/acs.jafc.3c09160] [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: 03/07/2024]
Abstract
Nitrogen is the most limiting factor in crop production. Legumes establish a symbiotic relationship with rhizobia and enhance nitrogen fixation. We analyzed 1,624 rhizosphere 16S rRNA gene samples and 113 rhizosphere metagenomic samples from three typical legumes and three non-legumes. The rhizosphere microbial community of the legumes had low diversity and was enriched with nitrogen-cycling bacteria (Sphingomonadaceae, Xanthobacteraceae, Rhizobiaceae, and Bacillaceae). Furthermore, the rhizosphere microbiota of legumes exhibited a high abundance of nitrogen-fixing genes, reflecting a stronger nitrogen-fixing potential, and Streptomycetaceae and Nocardioidaceae were the predominant nitrogen-fixing bacteria. We also identified helper bacteria and confirmed through metadata analysis and a pot experiment that the synthesis of riboflavin by helper bacteria is the key factor in promoting nitrogen fixation. Our study emphasizes that the construction of synthetic communities of nitrogen-fixing bacteria and helper bacteria is crucial for the development of efficient nitrogen-fixing microbial fertilizers.
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Affiliation(s)
- Yaohui Yang
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, P. R. China
| | - Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, P. R. China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, P. R. China
| | - Chaotang Lei
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, P. R. China
| | - Bingfeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, P. R. China
| | - Guoyan Qin
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, P. R. China
| | - Danyan Qiu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, P. R. China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, P. R. China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, P. R. China
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Qu L, Ma X, Wang F. The roles of gut microbiome and metabolites associated with skin photoaging in mice by intestinal flora sequencing and metabolomics. Life Sci 2024; 341:122487. [PMID: 38316265 DOI: 10.1016/j.lfs.2024.122487] [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: 11/15/2023] [Revised: 01/03/2024] [Accepted: 02/02/2024] [Indexed: 02/07/2024]
Abstract
Photoaging of skin, a chronic disease, can produce the appearance changes and cancer lesions of skin. Therefore, it is of great significance to investigate the mechanisms and explore effective methods to treat the disorder. Gut microbiota and intestinal metabolisms have critical roles in a variety of diseases. However, their roles on photoaging of skin were not well tested. In the present work, the results showed that compared with control group, the levels of MDA, SOD and CAT associated with oxidative stress, the levels of COL I, CER, and HA associated with skin function, and the mRNA levels of IL-1β, IL-6, TNF-α associated with inflammation after long-term exposure to ultraviolet radiation in mice were significantly changed. Skin pathological tissue was also seriously damaged. The protein levels of AQP3 and FLG were significantly decreased. Ultraviolet exposure also promoted skin photoaging by activating TNFR1/TRAF2-mediated MAPK pathway, in which the protein levels of P38/P-P38, c-FOS/P-c-FOS, MMP1, TNFR1 and TRAF2 were significantly increased in model mice compared with control group. In fecal microbiota transplantation (FMT) experiment, we found that the intestinal microbiome of control mice alleviated skin photoaging via adjusting the protein levels of P38/P-P38, c-FOS/P-c-FOS, MMP1, TNFR1 and TRAF2. 16S rRNA sequencing found that 1639 intestinal bacteria were found, in which 15 bacteria including norank_f_Ruminococcaceae, Lachnospirac -eae_NK4A136_group, Lachnoclostridium, etc., were significantly different at the genus level. Untargeted GC-TOF/MS and UHPLC-MS/MS metabolomics showed 72 and 188 metabolites including taurine, ornithine, L-arginine, L-histidine, sucrose with significant differences compared with control group. Then, amino acid targeting assay showed 10 amino acids including L-ornithine, L-arginine and L-citrulline with higher levels in control group compared with model group. In addition, we also found that the variation of Lachnoclostridium abundance may regulate L-arginine metabolism to affect skin photoaging. Some intestinal bacteria and metabolites including amino acids may be closely related to skin photoaging, which should provide new methods to treat skin photoaging in the future.
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Affiliation(s)
- Liping Qu
- Yunnan Botanee Bio-technology Group Co., Ltd., Kunming 650106, China; Yunnan Characteristic Plant Extraction Laboratory, Yunnan Yunke Characteristic Plant Extraction Laboratory Co., Ltd., Kunming 650106, China; Innovation Materials Research and Development Center, Botanee Research Institute, Shanghai Jiyan Biomedical Development Co., Ltd., Shanghai 201702, China
| | - Xiao Ma
- Yunnan Botanee Bio-technology Group Co., Ltd., Kunming 650106, China; Yunnan Characteristic Plant Extraction Laboratory, Yunnan Yunke Characteristic Plant Extraction Laboratory Co., Ltd., Kunming 650106, China
| | - Feifei Wang
- Yunnan Botanee Bio-technology Group Co., Ltd., Kunming 650106, China; Yunnan Characteristic Plant Extraction Laboratory, Yunnan Yunke Characteristic Plant Extraction Laboratory Co., Ltd., Kunming 650106, China; Innovation Materials Research and Development Center, Botanee Research Institute, Shanghai Jiyan Biomedical Development Co., Ltd., Shanghai 201702, China.
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Soldan R, Fusi M, Cardinale M, Homma F, Santos LG, Wenzl P, Bach-Pages M, Bitocchi E, Chacon Sanchez MI, Daffonchio D, Preston GM. Consistent effects of independent domestication events on the plant microbiota. Curr Biol 2024; 34:557-567.e4. [PMID: 38232731 DOI: 10.1016/j.cub.2023.12.056] [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: 08/23/2022] [Revised: 12/01/2023] [Accepted: 12/18/2023] [Indexed: 01/19/2024]
Abstract
The effect of plant domestication on plant-microbe interactions remains difficult to prove. In this study, we provide evidence of a domestication effect on the composition and abundance of the plant microbiota. We focused on the genus Phaseolus, which underwent four independent domestication events within two species (P. vulgaris and P. lunatus), providing multiple replicates of a process spanning thousands of years. We targeted Phaseolus seeds to identify a link between domesticated traits and bacterial community composition as Phaseolus seeds have been subject to large and consistent phenotypic changes during these independent domestication events. The seed bacterial communities of representative plant accessions from subpopulations descended from each domestication event were analyzed under controlled and field conditions. The results showed that independent domestication events led to similar seed bacterial community signatures in independently domesticated plant populations, which could be partially explained by selection for common domesticated plant phenotypes. Our results therefore provide evidence of a consistent effect of plant domestication on seed microbial community composition and abundance and offer avenues for applying knowledge of the impact of plant domestication on the plant microbiota to improve microbial applications in agriculture.
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Affiliation(s)
| | - Marco Fusi
- Center for Conservation and Restoration Science, Edinburgh Napier University, Edinburgh, UK
| | - Massimiliano Cardinale
- University of Salento, Department of Biological and Environmental Sciences and Technologies, Lecce, Italy
| | - Felix Homma
- University of Oxford, Department of Biology, Oxford, UK
| | - Luis Guillermo Santos
- The Alliance Biodiversity International and the International Center for Tropical Agriculture (CIAT), Palmira, Colombia
| | - Peter Wenzl
- The Alliance Biodiversity International and the International Center for Tropical Agriculture (CIAT), Palmira, Colombia
| | | | - Elena Bitocchi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Maria Isabel Chacon Sanchez
- Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Daniele Daffonchio
- Red Sea Research Center (RSRC), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Gail M Preston
- University of Oxford, Department of Biology, Oxford, UK.
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Liu S, Imad S, Hussain S, Xiao S, Yu X, Cao H. Sex, health status and habitat alter the community composition and assembly processes of symbiotic bacteria in captive frogs. BMC Microbiol 2024; 24:34. [PMID: 38262927 PMCID: PMC10804495 DOI: 10.1186/s12866-023-03150-y] [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: 06/28/2023] [Accepted: 12/11/2023] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND Frogs are critical economic animals essential to agricultural ecosystem equilibrium. However, Meningitis-like Infectious Disease (MID) often affects them in agricultural settings. While frog-associated microbiota contribute to elemental cycling and immunity, the effects of frog sex and health on gut bacteria remain understudied, and the relationship between frog habitat and soil microbes is unclear. We aimed to determine how frog sex, health status and habitat influence symbiotic bacteria and community assembly mechanism to provide guidance for sustainable frog farming and conservation. RESULTS We employed 16S rRNA sequencing to investigate gut microbiota differences in relation to frog sex and health status. We also compared symbiotic communities in frog-aggregation, native and soybean soil on the farm. Results showed that gut bacterial β-diversity and taxonomy were markedly influenced by frog sex and health. Healthy frogs had more robust gut bacterial metabolism than frogs infected with MID. Cooccurrence network analysis revealed that healthy female frogs had more complex microbial network structure than males; however, diseased males showed the greatest network complexity. The assembly mechanism of gut bacteria in male frogs was dominated by deterministic processes, whereas in female frogs it was dominated by stochastic processes. Among symbiotic bacteria in frog habitat soils, deterministic processes predominantly shaped the community assembly of soybean soil. In particular, soybean soil was enriched in pathogens and nitrogen functions, whereas frog-aggregation soil was markedly increased in sulphur respiration and hydrocarbon degradation. CONCLUSION Our study reveals that sex mainly alters the interaction network and assembly mechanism of frog intestinal bacteria; MID infection significantly inhibits the metabolic functions of intestinal bacteria. Furthermore, diverse frog habitat soils could shape more symbiotic bacteria to benefit frog farming. Our findings provide new horizons for symbiotic bacteria among frogs, which could contribute to sustainable agriculture and ecological balance.
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Affiliation(s)
- Senlin Liu
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, Jiangsu, 210095, People's Republic of China
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, UK
| | - Sewar Imad
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Sarfraz Hussain
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, Jiangsu, 210095, People's Republic of China
| | | | - Xiaowei Yu
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Hui Cao
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, Jiangsu, 210095, People's Republic of China.
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Escudero-Martinez C, Bulgarelli D. Engineering the Crop Microbiota Through Host Genetics. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:257-277. [PMID: 37196364 DOI: 10.1146/annurev-phyto-021621-121447] [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] [Indexed: 05/19/2023]
Abstract
The microbiota populating the plant-soil continuum defines an untapped resource for sustainable crop production. The host plant is a driver for the taxonomic composition and function of these microbial communities. In this review, we illustrate how the host genetic determinants of the microbiota have been shaped by plant domestication and crop diversification. We discuss how the heritable component of microbiota recruitment may represent, at least partially, a selection for microbial functions underpinning the growth, development, and health of their host plants and how the magnitude of this heritability is influenced by the environment. We illustrate how host-microbiota interactions can be treated as an external quantitative trait and review recent studies associating crop genetics with microbiota-based quantitative traits. We also explore the results of reductionist approaches, including synthetic microbial communities, to establish causal relationships between microbiota and plant phenotypes. Lastly, we propose strategies to integrate microbiota manipulation into crop selection programs. Although a detailed understanding of when and how heritability for microbiota composition can be deployed for breeding purposes is still lacking, we argue that advances in crop genomics are likely to accelerate wider applications of plant-microbiota interactions in agriculture.
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Affiliation(s)
| | - Davide Bulgarelli
- Plant Sciences, School of Life Sciences, University of Dundee, Dundee, United Kingdom; ,
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López JL, Fourie A, Poppeliers SWM, Pappas N, Sánchez-Gil JJ, de Jonge R, Dutilh BE. Growth rate is a dominant factor predicting the rhizosphere effect. THE ISME JOURNAL 2023; 17:1396-1405. [PMID: 37322285 PMCID: PMC10432406 DOI: 10.1038/s41396-023-01453-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023]
Abstract
The root microbiome is shaped by plant root activity, which selects specific microbial taxa from the surrounding soil. This influence on the microorganisms and soil chemistry in the immediate vicinity of the roots has been referred to as the rhizosphere effect. Understanding the traits that make bacteria successful in the rhizosphere is critical for developing sustainable agriculture solutions. In this study, we compared the growth rate potential, a complex trait that can be predicted from bacterial genome sequences, to functional traits encoded by proteins. We analyzed 84 paired rhizosphere- and soil-derived 16S rRNA gene amplicon datasets from 18 different plants and soil types, performed differential abundance analysis, and estimated growth rates for each bacterial genus. We found that bacteria with higher growth rate potential consistently dominated the rhizosphere, and this trend was confirmed in different bacterial phyla using genome sequences of 3270 bacterial isolates and 6707 metagenome-assembled genomes (MAGs) from 1121 plant- and soil-associated metagenomes. We then identified which functional traits were enriched in MAGs according to their niche or growth rate status. We found that predicted growth rate potential was the main feature for differentiating rhizosphere and soil bacteria in machine learning models, and we then analyzed the features that were important for achieving faster growth rates, which makes bacteria more competitive in the rhizosphere. As growth rate potential can be predicted from genomic data, this work has implications for understanding bacterial community assembly in the rhizosphere, where many uncultivated bacteria reside.
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Affiliation(s)
- José L López
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, The Netherlands
- Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales, Bariloche, Rio Negro, Argentina
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Arista Fourie
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, The Netherlands
| | - Sanne W M Poppeliers
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht, The Netherlands
| | - Nikolaos Pappas
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, The Netherlands
| | - Juan J Sánchez-Gil
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht, The Netherlands
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht, The Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, The Netherlands.
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany.
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11
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Brandl MT, Mammel MK, Simko I, Richter TKS, Gebru ST, Leonard SR. Weather factors, soil microbiome, and bacteria-fungi interactions as drivers of the epiphytic phyllosphere communities of romaine lettuce. Food Microbiol 2023; 113:104260. [PMID: 37098420 DOI: 10.1016/j.fm.2023.104260] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/16/2023] [Accepted: 03/07/2023] [Indexed: 03/16/2023]
Abstract
Lettuce is associated with seasonal outbreaks of Shiga toxin-producing Escherichia coli (STEC) infections. Little is known about how various biotic and abiotic factors affect the lettuce microbiome, which in turn impacts STEC colonization. We characterized the lettuce phyllosphere and surface soil bacterial, fungal, and oomycete communities at harvest in late-spring and -fall in California using metagenomics. Harvest season and field type, but not cultivar, significantly influenced the microbiome composition of leaves and surface soil near plants. Phyllosphere and soil microbiome compositions were correlated with specific weather factors. The relative abundance of Enterobacteriaceae, but not E. coli, was enriched on leaves (5.2%) compared to soil (0.4%) and correlated positively with minimum air temperature and wind speed. Co-occurrence networks revealed seasonal trends in fungi-bacteria interactions on leaves. These associations represented 39%-44% of the correlations between species. All significant E. coli co-occurrences with fungi were positive, while all negative associations were with bacteria. A large proportion of the leaf bacterial species was shared with those in soil, indicating microbiome transmission from the soil surface to the canopy. Our findings provide new insight into factors that shape lettuce microbial communities and the microbial context of foodborne pathogen immigration events in the lettuce phyllosphere.
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Affiliation(s)
- Maria T Brandl
- Produce Safety and Microbiology Research Unit, US Department of Agriculture, Agricultural Research Service, Albany, CA, USA
| | - Mark K Mammel
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Ivan Simko
- Crop Improvement and Protection Research Unit, US Department of Agriculture, Agricultural Research Service, Salinas, CA, USA
| | - Taylor K S Richter
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Solomon T Gebru
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Susan R Leonard
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA.
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12
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da Silva JL, Mendes LW, Rocha SMB, Antunes JEL, Oliveira LMDS, Melo VMM, Oliveira FAS, Pereira APDA, Costa GDN, da Silva VB, Gomes RLF, de Alcantara Neto F, Lopes ACDA, Araujo ASF. Domestication of Lima Bean (Phaseolus lunatus) Changes the Microbial Communities in the Rhizosphere. MICROBIAL ECOLOGY 2023; 85:1423-1433. [PMID: 35525854 DOI: 10.1007/s00248-022-02028-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/26/2022] [Indexed: 05/10/2023]
Abstract
Plants modulate the soil microbiota and select a specific microbial community in the rhizosphere. However, plant domestication reduces genetic diversity, changes plant physiology, and could have an impact on the associated microbiome assembly. Here, we used 16S rRNA gene sequencing to assess the microbial community in the bulk soil and rhizosphere of wild, semi-domesticated, and domesticated genotypes of lima bean (Phaseolus lunatus), to investigate the effect of plant domestication on microbial community assembly. In general, rhizosphere communities were more diverse than bulk soil, but no differences were found among genotypes. Our results showed that the microbial community's structure was different from wild and semi-domesticated as compared to domesticated genotypes. The community similarity decreased 57.67% from wild to domesticated genotypes. In general, the most abundant phyla were Actinobacteria (21.9%), Proteobacteria (20.7%), Acidobacteria (14%), and Firmicutes (9.7%). Comparing the different genotypes, the analysis showed that Firmicutes (Bacillus) was abundant in the rhizosphere of the wild genotypes, while Acidobacteria dominated semi-domesticated plants, and Proteobacteria (including rhizobia) was enriched in domesticated P. lunatus rhizosphere. The domestication process also affected the microbial community network, in which the complexity of connections decreased from wild to domesticated genotypes in the rhizosphere. Together, our work showed that the domestication of P. lunatus shaped rhizosphere microbial communities from taxonomic to a functional level, changing the abundance of specific microbial groups and decreasing the complexity of interactions among them.
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Affiliation(s)
- Josieli Lima da Silva
- Plant Genetic Resource Group, Agricultural Science Center, Federal University of Piauí, Teresina, PI, Brazil
| | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, SP, Brazil
| | - Sandra Mara Barbosa Rocha
- Soil Microbial Ecology Group, Agricultural Science Center, Federal University of Piauí, Teresina, PI, Brazil
| | | | | | - Vania Maria Maciel Melo
- Laboratório de Ecologia Microbiana E Biotecnologia, Federal University of Ceará, Fortaleza, CE, Brazil
| | | | | | - Gérson do Nascimento Costa
- Plant Genetic Resource Group, Agricultural Science Center, Federal University of Piauí, Teresina, PI, Brazil
| | - Veronica Brito da Silva
- Plant Genetic Resource Group, Agricultural Science Center, Federal University of Piauí, Teresina, PI, Brazil
| | - Regina Lucia Ferreira Gomes
- Plant Genetic Resource Group, Agricultural Science Center, Federal University of Piauí, Teresina, PI, Brazil
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13
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Hu S, He R, Zeng J, Zhao D, Wang S, He F, Yu Z, Wu QL. Lower Compositional Variation and Higher Network Complexity of Rhizosphere Bacterial Community in Constructed Wetland Compared to Natural Wetland. MICROBIAL ECOLOGY 2023; 85:965-979. [PMID: 35641581 DOI: 10.1007/s00248-022-02040-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 05/09/2022] [Indexed: 05/04/2023]
Abstract
Macrophyte rhizosphere microbes, as crucial components of the wetland ecosystem, play an important role in maintaining the function and stability of natural and constructed wetlands. Distinct environmental conditions and management practices between natural and constructed wetlands would affect macrophytes rhizosphere microbial communities and their associated functions. Nevertheless, the understanding of the diversity, composition, and co-occurrence patterns of the rhizosphere bacterial communities in natural and constructed wetlands remains unclear. Here, we used 16S rRNA gene high-throughput sequencing to characterize the bacterial community of the rhizosphere and bulk sediments of macrophyte Phragmites australis in representative natural and constructed wetlands. We observed higher alpha diversity of the bacterial community in the constructed wetland than that of the natural wetland. Additionally, the similarity of bacterial community composition between rhizosphere and bulk sediments in the constructed wetland was increased compared to that of the natural wetland. We also found that plants recruit specific taxa with adaptive functions in the rhizosphere of different wetland types. Rhizosphere samples of the natural wetland significantly enriched the functional bacterial groups that mainly related to nutrient cycling and plant-growth-promoting, while those of the constructed wetland-enriched bacterial taxa with potentials for biodegradation. Co-occurrence network analysis showed that the interactions among rhizosphere bacterial taxa in the constructed wetland were more complex than those of the natural wetland. This study broadens our understanding of the distinct selection processes of the macrophytes rhizosphere-associated microbes and the co-occurrence network patterns in different wetland types. Furthermore, our findings emphasize the importance of plant-microbe interactions in wetlands and further suggest P. australis rhizosphere enriched diverse functional bacteria that might enhance the wetland performance through biodegradation, nutrient cycling, and supporting plant growth.
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Affiliation(s)
- Siwen Hu
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Rujia He
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China
| | - Shuren Wang
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Fei He
- Ministry of Ecology and Environment, Nanjing Institute of Environmental Sciences, Nanjing, China
| | - Zhongbo Yu
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
- Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China
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14
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Artificial Cultivation Changes Foliar Endophytic Fungal Community of the Ornamental Plant Lirianthe delavayi. Microorganisms 2023; 11:microorganisms11030775. [PMID: 36985348 PMCID: PMC10059682 DOI: 10.3390/microorganisms11030775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/10/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023] Open
Abstract
Many wild ornamental plant species have been introduced to improve the landscape of cities; however, until now, no study has been performed to explore the composition and function of foliar endophytes associated with cultivated rare plants in cities after their introduction. In this study, we collected the leaves of the healthy ornamental plant Lirianthe delavayi from wild and artificially cultivated habitats in Yunnan and compared their diversity, species composition, and functional predictions of their foliar endophytic fungal community based on high-throughput sequencing technology. In total, 3125 ASVs of fungi were obtained. The alpha diversity indices of wild L. delavayi populations are similar to those of cultivated samples; however, the species compositions of endophytic fungal ASVs were significantly varied in the two habitats. The dominant phylum is Ascomycota, accounting for more than 90% of foliar endophytes in both populations; relatively, artificial cultivation trends to increase the frequency of common phytopathogens of L. delavayi, such as Alternaria, Erysiphe. The relative abundance of 55 functional predictions is different between wild and cultivated L. delavayi leaves (p < 0.05); in particular, chromosome, purine metabolism, and peptidases are significantly increased in wild samples, while flagellar assembly, bacterial chemotaxis, and fatty acid metabolism are significantly enhanced in cultivated samples. Our results indicated that artificial cultivation can greatly change the foliar endophytic fungal community of L. delavayi, which is valuable for understanding the influence of the domestication process on the foliar fungal community associated with rare ornamental plants in urban environments.
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15
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Zhang Y, Cao B, Pan Y, Tao S, Zhang N. Metabolite-Mediated Responses of Phyllosphere Microbiota to Rust Infection in Two Malus Species. Microbiol Spectr 2023; 11:e0383122. [PMID: 36916990 PMCID: PMC10101083 DOI: 10.1128/spectrum.03831-22] [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: 09/22/2022] [Accepted: 02/24/2023] [Indexed: 03/15/2023] Open
Abstract
Plants recruit beneficial microbes to enhance their ability to fight pathogens. However, the current understanding of microbial recruitment is largely limited to belowground systems (root exudates and the rhizosphere). It remains unclear whether the changes in leaf metabolites induced by infectious pathogens can actively recruit beneficial microbes to mitigate the growth of foliar pathogens. In this study, we integrated microbiome and metabolomic analyses to systematically explore the dynamics of phyllosphere fungal and bacterial communities and key leaf metabolites in two crabapple species (Malus sp. "Flame" and Malus sp. "Kelsey") at six stages following infection with Gymnosporangium yamadae. Our results showed that the phyllosphere microbiome changed during lesion expansion, as highlighted by a reduction in bacterial alpha-diversity and an increase in fungal alpha-diversity; a decreasing and then an increasing complexity of the microbial co-occurrence network was observed in Kelsey and a decreasing complexity occurred in Flame. In addition, nucleotide sugars, diarylheptanoids, and carboxylic acids with aromatic rings were more abundant in early stages of collection, which positively regulated the abundance of bacterial orders Pseudomonadales (in Kelsey), Acidimicrobiales, Bacillales, and Flavobacteriales (in Flame). In addition, metabolites such as flavonoids, lignin precursors, terpenoids, coumarins, and quaternary ammonium salts enriched with the expansion of lesions had a positive regulatory effect on fungal families Rhynchogastremataceae and Golubeviaceae (in Flame) and the bacterial order Actinomycetales (in Kelsey). Our findings highlight that plants may also influence phyllosphere microorganisms by adjusting leaf metabolites in response to biotic stress. IMPORTANCE Our findings demonstrate the response patterns of bacterial and fungal communities in the Malus phyllosphere to rust fungus G. yamadae infection, and they also reveal how the phyllosphere microbiome changes with the expansion of lesions. We identified several metabolites whose relative abundance varied significantly with lesion expansion. Using a framework for assessing the role of leaf metabolites in shaping the phyllosphere microbiome of the two Malus species, we identified several specific metabolites that have profoundly selective effects on the microbial community. In conclusion, our study provides new evidence of the ecological niche of the phyllosphere in supporting the "cry for help" strategy for plants.
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Affiliation(s)
- Yunxia Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, People’s Republic of China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People’s Republic of China
| | - Bin Cao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Yumei Pan
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, People’s Republic of China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People’s Republic of China
| | - Siqi Tao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, People’s Republic of China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People’s Republic of China
| | - Naili Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, People’s Republic of China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People’s Republic of China
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16
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Rapeseed Domestication Affects the Diversity of Rhizosphere Microbiota. Microorganisms 2023; 11:microorganisms11030724. [PMID: 36985297 PMCID: PMC10056747 DOI: 10.3390/microorganisms11030724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/04/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
Rhizosphere microbiota is important for plant growth and health. Domestication is a process to select suitable plants to satisfy the needs of humans, which may have great impacts on the interaction between the host and its rhizosphere microbiota. Rapeseed (Brassica napus) is an important oilseed crop derived from the hybridization between Brassica rapa and Brassica oleracea ~7500 years ago. However, variations in rhizosphere microbiota along with rapeseed domestication remain poorly understood. Here, we characterized the composition and structure of the rhizosphere microbiota among diverse rapeseed accessions, including ten B. napus, two B. rapa, and three B. oleracea accessions through bacterial 16S rRNA gene sequencing. B. napus exhibited a higher Shannon index and different bacterial relative abundance compared with its wild relatives in rhizosphere microbiota. Moreover, artificial synthetic B. napus lines G3D001 and No.2127 showed significantly different rhizosphere microbiota diversity and composition from other B. napus accessions and their ancestors. The core rhizosphere microbiota of B. napus and its wild relatives was also described. FAPROTAX annotation predicted that the synthetic B. napus lines had more abundant pathways related to nitrogen metabolism, and the co-occurrence network results demonstrated that Rhodoplanes acted as hub nodes to promote nitrogen metabolism in the synthetic B. napus lines. This study provides new insights into the impacts of rapeseed domestication on the diversity and community structure of rhizosphere microbiota, which may highlight the contribution of rhizosphere microbiota to plant health.
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Rong L, Wang Y, Meidl P, Wang L, Sun H. Microplastics affect soybean rhizosphere microbial composition and function during vegetative and reproductive stages. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 252:114577. [PMID: 36709538 DOI: 10.1016/j.ecoenv.2023.114577] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/08/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Microplastics (MPs) are emerging contaminants in agricultural soil, whereas their effects on the rhizosphere microbial ecosystems and biogeochemical nitrogen cycles during plant growth remain unknown. Here, a 70-day greenhouse experiment was carried out with black and fluvo-aquic soil to evaluate the influence of polyamide (PA), polyethylene (PE), polyester (PES), and polyvinyl chloride (PVC) MPs on the bacterial communities and functions in the soybean rhizosphere. The PA treatment consistently affected the rhizobacterial alpha diversity in the fluvo-aquic soil at soybean vegetative and reproductive growth stages, whereas the PE, PES, and PVC treatments had a short-term effect on the bacterial alpha diversity. At two growth stages, 6 and 23 biomarkers were consistently abundant in the PA treatment in the black soil and fluvo-aquic soil, respectively, and order Rhizobiales was found to be a biomarker for PA MPs contamination in both soils. Additionally, PA treatment decreased bacterial network complexity and tightness, whereas the effects of the PE, PES, and PVC on bacterial co-occurrence patterns varied depending on the soil types. Furthermore, PES and PVC treatments inhibited ammonification processes in the soybean rhizosphere, and PE could temporarily inhibit ammonia oxidation and denitrification processes according to the variations of N-cycling gene abundances. These effects on soil N-cycling also varied with soil types and soybean growth stages. This study provides profound information for understanding of MPs residues on the assembly of the soybean rhizosphere communities and function during plant development.
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Affiliation(s)
- Lili Rong
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, 38 Tongyan Road, Jinnan District, 300350 Tianjin, China
| | - Yu Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, 38 Tongyan Road, Jinnan District, 300350 Tianjin, China.
| | - Peter Meidl
- Institute of Biology, Freie Universität Berlin, 14195 Berlin, Germany; Berlin-Brandenburg Institute of Advanced Biodiversity Research, 14195 Berlin, Germany
| | - Lei Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, 38 Tongyan Road, Jinnan District, 300350 Tianjin, China
| | - Hongwen Sun
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, 38 Tongyan Road, Jinnan District, 300350 Tianjin, China.
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Zhang Y, Cheng Z, Li Q, Dai Q, Hu J. Responses of rhizosphere bacterial communities in newly reclaimed mudflat paddies to rice genotype and nitrogen fertilizer rate. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:38761-38774. [PMID: 36586025 DOI: 10.1007/s11356-022-25020-2] [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: 07/25/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
The rhizosphere microbiome plays a vital role in crop growth and adaptation. However, the effects of rice genotype, nitrogen (N) fertilization, and their interactions on the rhizosphere bacterial communities in low fertility soil remain poorly understood. In this study, a two-factor field experiment was performed in newly reclaimed mudflat paddies characterized by poor fertility to analyze bacterial communities in the rhizosphere of Yongyou 2640 (japonica/indica hybrid rice, JIH) and Huaidao No.5 (japonica conventional rice, JC) under different N fertilizer rates. Results showed that genotype, followed by N fertilizer rate, was the primary factor affecting rhizobacteria diversity. Rhizobacteria diversity was higher in JIH than in JC and that of JIH and JC did not significantly change overall as N fertilizer rates but increased and decreased at N fertilizer rates of over 300 kg N ha-1, respectively. The inconsistent response was probably attributed to the difference in the increase of ammonium and/or nitrate in the rhizosphere of JIH and JC. Genotype explained approximately 26% of the variation in rhizosphere bacterial communities. Rhizosphere bacterial communities with N fertilizer rates of over 300 kg N ha-1 were more dissimilar to those without N fertilization relative to those with N fertilizer rates of below 300 kg N ha-1, which was mainly attributed to changes in the concentration of ammonium and/or nitrate. The relative abundances of some potential beneficial genera such as Salinimicrobium, Salegentibacter, Gillisia, and Anaerolinea in the rhizosphere of JC and Salegentibacter, Lysobacter, Nocardioides, and Pontibacter in the rhizosphere of JIH were increased under N fertilizer rates of less than 300 kg N ha-1 and positively correlated with rice yields, which indicate that changes in bacterial communities caused by N fertilization might be strongly associated with the improvement of rice yield. Overall, rhizosphere bacterial communities were more sensitive to genotype in newly reclaimed mudflat paddies and showed a consistent response to N fertilizer rates.
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Affiliation(s)
- Yang Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, China
- Key Laboratory of Arable Land Quality Monitoring and Evaluation, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou, 225127, China
| | - Zhandou Cheng
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, China
| | - Qing Li
- Jiangsu Key Laboratory of Crop Genetic and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, 225009, China
| | - Qigen Dai
- Jiangsu Key Laboratory of Crop Genetic and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, 225009, China.
| | - Jian Hu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, China
- Key Laboratory of Arable Land Quality Monitoring and Evaluation, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou, 225127, China
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Xavier GR, Jesus EDC, Dias A, Coelho MRR, Molina YC, Rumjanek NG. Contribution of Biofertilizers to Pulse Crops: From Single-Strain Inoculants to New Technologies Based on Microbiomes Strategies. PLANTS (BASEL, SWITZERLAND) 2023; 12:954. [PMID: 36840302 PMCID: PMC9962295 DOI: 10.3390/plants12040954] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Pulses provide distinct health benefits due to their low fat content and high protein and fiber contents. Their grain production reaches approximately 93,210 × 103 tons per year. Pulses benefit from the symbiosis with atmospheric N2-fixing bacteria, which increases productivity and reduces the need for N fertilizers, thus contributing to mitigation of environmental impact mitigation. Additionally, the root region harbors a rich microbial community with multiple traits related to plant growth promotion, such as nutrient increase and tolerance enhancement to abiotic or biotic stresses. We reviewed the eight most common pulses accounting for almost 90% of world production: common beans, chickpeas, peas, cowpeas, mung beans, lentils, broad beans, and pigeon peas. We focused on updated information considering both single-rhizobial inoculation and co-inoculation with plant growth-promoting rhizobacteria. We found approximately 80 microbial taxa with PGPR traits, mainly Bacillus sp., B. subtilis, Pseudomonas sp., P. fluorescens, and arbuscular mycorrhizal fungi, and that contributed to improve plant growth and yield under different conditions. In addition, new data on root, nodule, rhizosphere, and seed microbiomes point to strategies that can be used to design new generations of biofertilizers, highlighting the importance of microorganisms for productive pulse systems.
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Affiliation(s)
| | | | - Anelise Dias
- Departamento de Fitotecnia, Instituto de Agronomia, Universidade Federal Rural do Rio de Janeiro, UFRRJ, Rodovia BR-465, Km 7, Seropédica 23890-000, RJ, Brazil
| | | | - Yulimar Castro Molina
- Programa de Pós-graduação em Microbiologia Agrícola, Universidade Federal de Lavras, UFLA, Trevo Rotatório Professor Edmir Sá Santos, Lavras 37203-202, MG, Brazil
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Rai S, Omar AF, Rehan M, Al-Turki A, Sagar A, Ilyas N, Sayyed RZ, Hasanuzzaman M. Crop microbiome: their role and advances in molecular and omic techniques for the sustenance of agriculture. PLANTA 2022; 257:27. [PMID: 36583789 DOI: 10.1007/s00425-022-04052-5] [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: 04/11/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
This review is an effort to provide in-depth knowledge of microbe's interaction and its role in crop microbiome using combination of advanced molecular and OMICS technology to translate this information for the sustenance of agriculture. Increasing population, climate change and exhaustive agricultural practices either influenced nutrient inputs of soil or generating biological and physico-chemical deterioration of the soils and affecting the agricultural productivity and agro-ecosystems. Alarming concerns toward food security and crop production claim for renewed attention in microbe-based farming practices. Microbes are omnipresent (soil, water, and air) and their close association with plants would help to accomplish sustainable agriculture goals. In the last few decades, the search for beneficial microbes in crop production, soil fertilization, disease management, and plant growth promotion is the thirst for eco-friendly agriculture. The crop microbiome opens new paths to utilize beneficial microbes and manage pathogenic microbes through integrated advanced biotechnology. The crop microbiome helps plants acquire nutrients, growth, resilience against phytopathogens, and tolerance to abiotic stresses, such as heat, drought, and salinity. Despite the emergent functionality of the crop microbiome as a complicated constituent of the plant fitness, our understanding of how the functionality of microbiome influenced by numerous factors including genotype of host, climatic conditions, mobilization of minerals, soil composition, nutrient availability, interaction between nexus of microbes, and interactions with other external microbiomes is partially understood. However, the structure, composition, dynamics, and functional contribution of such cultured and uncultured crop microbiome are least explored. The advanced biotechnological approaches are efficient tools for acquiring the information required to investigate the microbiome and extract data to develop high yield producing and resistant variety crops. This knowledge fills the fundamental gap between the theoretical concepts and the operational use of these advanced tools in crop microbiome studies. Here, we review (1) structure and composition of crop microbiome, (2) microbiome-mediated role associated with crops fitness, (3) Molecular and -omics techniques for exploration of crop microbiome, and (4) current approaches and future prospectives of crop microbiome and its exploitation for sustainable agriculture. Recent -omic approaches are influential tool for mapping, monitoring, modeling, and management of crops microbiome. Identification of crop microbiome, using system biology and rhizho-engineering, can help to develop future bioformulations for disease management, reclamation of stressed agro-ecosystems, and improved productivity of crops. Nano-system approaches combined with triggering molecules of crop microbiome can help in designing of nano-biofertilizers and nano-biopesticides. This combination has numerous merits over the traditional bioinoculants. They stimulate various defense mechanisms in plants facing stress conditions; provide bioavailability of nutrients in the soil, helps mitigate stress conditions; and enhance chances of crops establishment.
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Affiliation(s)
- Shalini Rai
- Department of Biotechnology, SHEPA, Varanasi, India.
| | - Ayman F Omar
- Department of Plant Production and Protection, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, 51452, Saudi Arabia.
- Department of Plant Pathology, Plant Pathology and Biotechnology Laboratory and EPCRS Excellence Center, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh, 33516, Egypt.
| | - Medhat Rehan
- Department of Plant Production and Protection, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, 51452, Saudi Arabia
- Department of Genetics, College of Agriculture, Kafrelsheikh University, Kafr El-Sheikh, 33516, Egypt
| | - Ahmad Al-Turki
- Department of Plant Production and Protection, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, 51452, Saudi Arabia
| | - Alka Sagar
- Department of Microbiology, MIET, Meerut, India
| | - Noshin Ilyas
- Department of Botany, PMAS Arid Agriculture University, Rawalpindi, 46300, Pakistan
| | - R Z Sayyed
- Asian PGPR Society, Auburn Venture, Auburn, AL, USA.
| | - Mirza Hasanuzzaman
- Department of Agronomy, Faculty of Agriculture, Sher-E-Bangla Agricultural University (SAU), Sher-E-Bangla Nagar, Dhaka, 1207, Bangladesh
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Lang M, Li H, Lakshmanan P, Chen Y, Chen X. phoD-harboring bacterial community composition dominates organic P mineralization under long-term P fertilization in acid purple soil. Front Microbiol 2022; 13:1045919. [PMID: 36504812 PMCID: PMC9730253 DOI: 10.3389/fmicb.2022.1045919] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/03/2022] [Indexed: 11/25/2022] Open
Abstract
Introduction A better understanding of the regulatory role of microorganisms on soil phosphorous (P) mobilization is critical for developing sustainable fertilization practices and reducing P resource scarcity. The phoD genes regulate soil organic P (Po) mobilization. Methods Based on the long-term P application experiments in acid purple soil of maize system in Southwest China (started in 2010), the experiment included five P levels: 0, 16, 33, 49, and 65.5 kg P hm-2 (P0, P16, P33, P49, and P65.5, respectively). The molecular speciation of organic P in soil was determined by 31P-nuclear magnetic resonance (NMR), high-throughput sequencing technology, and real-time qPCR were used to analyze the bacterial community and abundance of phoD-harboring bacterial genes, exploring the bacterial community and abundance characteristics of phoD gene and its relationship with the forms of Po and alkaline phosphatase (ALP) activity in the soil. Results The results showed that the orthophosphate monoesters (OM) were the main Po speciation and varied by P fertilization in acid purple soil. ALP activity decreased as P fertilization increased. Co-occurrence network analysis identified the overall network under five P fertilizations. The keystone taxon base on the network showed that Collimonas, Roseateles, Mesorhizobium, and Cellulomonas positively correlated with both OM and Po. The random forest showed that Cellulomonas, Roseateles, and Rhodoplanes were the key predictors for ALP activity. The keystone taxon was a more important predictor than the dominant taxon for ALP, OM, and Po. The structural equation model (SEM) showed that soil organic matter (SOM), available P (AP), and OM were the main factors influencing the ALP by reshaping phoD-harboring bacteria alpha diversity, community composition, and phoD abundance. Discussion The phoD-harboring bacterial community composition especially the keystone taxon rather than alpha diversity and abundance dominated the ALP activity, which could promote P utilization over an intensive agroecosystem. These findings improve the understanding of how long-term gradient fertilization influences the community composition and function of P-solubilizing microorganisms in acid purple soil.
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Affiliation(s)
- Ming Lang
- College of Resources and Environment, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing, China
| | - Haoming Li
- College of Resources and Environment, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Prakash Lakshmanan
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing, China
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Yuanxue Chen
- College of Resource Sciences, Sichuan Agricultural University, Chengdu, China
| | - Xinping Chen
- College of Resources and Environment, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing, China
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22
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Pantigoso HA, Newberger D, Vivanco JM. The rhizosphere microbiome: Plant-microbial interactions for resource acquisition. J Appl Microbiol 2022; 133:2864-2876. [PMID: 36648151 PMCID: PMC9796772 DOI: 10.1111/jam.15686] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 06/16/2022] [Accepted: 06/22/2022] [Indexed: 01/21/2023]
Abstract
While horticulture tools and methods have been extensively developed to improve the management of crops, systems to harness the rhizosphere microbiome to benefit plant crops are still in development. Plants and microbes have been coevolving for several millennia, conferring fitness advantages that expand the plant's own genetic potential. These beneficial associations allow the plants to cope with abiotic stresses such as nutrient deficiency across a wide range of soils and growing conditions. Plants achieve these benefits by selectively recruiting microbes using root exudates, positively impacting their nutrition, health and overall productivity. Advanced knowledge of the interplay between root exudates and microbiome alteration in response to plant nutrient status, and the underlying mechanisms there of, will allow the development of technologies to increase crop yield. This review summarizes current knowledge and perspectives on plant-microbial interactions for resource acquisition and discusses promising advances for manipulating rhizosphere microbiomes and root exudation.
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Affiliation(s)
- Hugo A. Pantigoso
- Center for Root and Rhizosphere Biology, Department of Horticulture and Landscape ArchitectureColorado State UniversityFort CollinsColorado80523‐1173United States
| | - Derek Newberger
- Center for Root and Rhizosphere Biology, Department of Horticulture and Landscape ArchitectureColorado State UniversityFort CollinsColorado80523‐1173United States
| | - Jorge M. Vivanco
- Center for Root and Rhizosphere Biology, Department of Horticulture and Landscape ArchitectureColorado State UniversityFort CollinsColorado80523‐1173United States
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Zhang H, Yang H, Zhang X, Sun J, Dong L, Han H, Chen Z. Bama Pig Manure Organic Fertilizer Regulates the Watermelon Rhizosphere Bacterial Community to Inhibit the Occurrence of Fusarium Wilt Under Continuous Cropping Conditions. Curr Microbiol 2022; 79:364. [PMID: 36253496 DOI: 10.1007/s00284-022-03056-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 09/23/2022] [Indexed: 12/01/2022]
Abstract
Fusarium wilt caused by Fusarium oxysporum f. sp. niveum is an important manifestation of continuous cropping barrier, which causes the quality and yield of watermelon to decline. In early stage of this study, the organic fertilizer fermented by Bama pig manure applied in soil was proved to significantly inhibit the occurrence of disease by improving the structure of soil microbial community. However, the mechanism was not clear. The high-throughput sequencing technology, combined with network and PICRUSt2 function analysis was used to investigate it. MiSeq sequencing showed that the bacterial community of organic fertilizer treated soil was composed of 34 phyla and 768 genera, the number of genera was higher than that of sterile water treated soil. Fertilization significantly increased the diversity and changed the composition of bacterial community based on alpha, beta diversity, and ANOSIM/Adonis analysis. LEfSe species difference and network analysis showed that fertilization improved the relative abundance of bacteria with biological control or plant growth promotion characteristics in soil, such as Sphingomonas, Halobacillus, Nocardioides, and enhanced the interaction between rhizosphere bacteria, made the network structure more complex. PICRUSt2 also revealed fertilization promoted the bacterial function, such as metabolism and genetic information processing. These results showed that the pig manure organic fertilizer might reduce the occurrence of Fusarium wilt by regulating bacterial community, interaction, and functional metabolism in watermelon rhizosphere soil.
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Affiliation(s)
- Hao Zhang
- School of Life Science and Agricultural Engineering, Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Henan Province Artemisiae Argyi Development and Utilization Engineering Technology Research Center, Innovation Center of Water Security for Water Source Region of Mid-Route Project of South-North Water Diversion of Henan Province, Nanyang Normal University, Nanyang, 473061, People's Republic of China
| | - Huiying Yang
- School of Life Science and Agricultural Engineering, Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Henan Province Artemisiae Argyi Development and Utilization Engineering Technology Research Center, Innovation Center of Water Security for Water Source Region of Mid-Route Project of South-North Water Diversion of Henan Province, Nanyang Normal University, Nanyang, 473061, People's Republic of China
| | - Xin Zhang
- School of Life Science and Agricultural Engineering, Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Henan Province Artemisiae Argyi Development and Utilization Engineering Technology Research Center, Innovation Center of Water Security for Water Source Region of Mid-Route Project of South-North Water Diversion of Henan Province, Nanyang Normal University, Nanyang, 473061, People's Republic of China
| | - Jie Sun
- School of Life Science and Agricultural Engineering, Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Henan Province Artemisiae Argyi Development and Utilization Engineering Technology Research Center, Innovation Center of Water Security for Water Source Region of Mid-Route Project of South-North Water Diversion of Henan Province, Nanyang Normal University, Nanyang, 473061, People's Republic of China
| | - Lianzheng Dong
- School of Life Science and Agricultural Engineering, Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Henan Province Artemisiae Argyi Development and Utilization Engineering Technology Research Center, Innovation Center of Water Security for Water Source Region of Mid-Route Project of South-North Water Diversion of Henan Province, Nanyang Normal University, Nanyang, 473061, People's Republic of China
| | - Hui Han
- School of Life Science and Agricultural Engineering, Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Henan Province Artemisiae Argyi Development and Utilization Engineering Technology Research Center, Innovation Center of Water Security for Water Source Region of Mid-Route Project of South-North Water Diversion of Henan Province, Nanyang Normal University, Nanyang, 473061, People's Republic of China
| | - Zhaojin Chen
- School of Water Resources and Environmental Engineering, Nanyang Normal University, Nanyang, 473061, People's Republic of China.
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Chang J, van Veen JA, Tian C, Kuramae EE. A review on the impact of domestication of the rhizosphere of grain crops and a perspective on the potential role of the rhizosphere microbial community for sustainable rice crop production. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156706. [PMID: 35724776 DOI: 10.1016/j.scitotenv.2022.156706] [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: 01/22/2022] [Revised: 06/10/2022] [Accepted: 06/11/2022] [Indexed: 06/15/2023]
Abstract
The rhizosphere-associated microbiome impacts plant performance and tolerance to abiotic and biotic stresses. Despite increasing recognition of the enormous functional role of the rhizomicrobiome on the survival of wild plant species growing under harsh environmental conditions, such as nutrient, water, temperature, and pathogen stresses, the utilization of the rhizosphere microbial community in domesticated rice production systems has been limited. Better insight into how this role of the rhizomicrobiome for the performance and survival of wild plants has been changed during domestication and development of present domesticated crops, may help to assess the potential of the rhizomicrobial community to improve the sustainable production of these crops. Here, we review the current knowledge of the effect of domestication on the microbial rhizosphere community of rice and other crops by comparing its diversity, structure, and function in wild versus domesticated species. We also examine the existing information on the impact of the plant on their physico-chemical environment. We propose that a holobiont approach should be explored in future studies by combining detailed analysis of the dynamics of the physicochemical microenvironment surrounding roots to systematically investigate the microenvironment-plant-rhizomicrobe interactions during rice domestication, and suggest focusing on the use of beneficial microbes (arbuscular mycorrhizal fungi and Nitrogen fixers), denitrifiers and methane consumers to improve the sustainable production of rice.
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Affiliation(s)
- Jingjing Chang
- 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; Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, 6708 PB Wageningen, the Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, 6708 PB Wageningen, the Netherlands
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, 6708 PB Wageningen, the Netherlands; Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, the Netherlands.
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25
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Zhang J, Liu P, Nie B, Liu X, Zhang Z, He R, Dong W, Ji W. Effects of genotype and ecological environment on the community structure and function of symbiotic bacteria in rhizosphere of ginseng. BMC Microbiol 2022; 22:235. [PMID: 36192685 PMCID: PMC9531419 DOI: 10.1186/s12866-022-02649-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 09/07/2022] [Indexed: 11/11/2022] Open
Abstract
Background Ginseng, an important traditional Chinese medicine and a new resource food, has two production modes: farmland ginseng and forestland ginseng. Ginseng faces many problems such as high soil bulk density, easy hardening, low nutrient content, reduced porosity and increased soil acidification because of continuous cropping. Increasing studies indicate that plant rhizosphere symbiotic bacteria have an important effect on plant growth and development. We speculate that differences in microbial community may play an important role in promoting ginseng growth, development and health. To reveal the differences between farmland and forestland ginseng cultivation, and to address problems associated with continuous ginseng cropping, we investigated the effects of differences in plant rhizosphere symbiotic bacterial communities in promoting ginseng growth, development, and health. Result In the present study, the microbial communities in the rhizosphere of different genotypes and ecological environments were analyzed using the high-throughput sequencing platform Illumina, phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt), and other technologies. The organic matter, total nitrogen, available nitrogen, and available phosphorus contents in forestland soil were significantly different from those in farmland. The bacterial communities of ginseng in forestland, farmland, and greenhouse environments have specific dominant groups at the phylum and genus levels. There were differences in the gene functions of ginseng root-related bacterial communities between forestland and farmland. There were significant differences in the abundance distribution of rhizosphere bacteria among the different genotypes at the phylum and genus levels. Conclusions There is a close relationship between the ecological environment and bacterial population structure, and the ecological environment of forestland is more conducive to the formation of rich rhizosphere bacterial populations; additionally, the genetic diversity is richer than that of farmland. The rhizosphere bacterial community structure of ginseng was influenced by genotype, and there was a correlation between the distance between ginseng genotypes and the stratified clustering of its rhizosphere bacterial community structure.
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Affiliation(s)
- Jiyue Zhang
- College of Integration Science, Yanbian University, Yanji, Jilin Province, 133002, China
| | - Pin Liu
- College of Agriculture, Yanbian University, Yanji, Jilin Province, 133002, China
| | - Botao Nie
- College of Agriculture, Yanbian University, Yanji, Jilin Province, 133002, China
| | - Xinxin Liu
- College of Agriculture, Yanbian University, Yanji, Jilin Province, 133002, China
| | - Zhen Zhang
- College of Agriculture, Yanbian University, Yanji, Jilin Province, 133002, China
| | - Runlong He
- College of Agriculture, Yanbian University, Yanji, Jilin Province, 133002, China
| | - Weiwei Dong
- College of Integration Science, Yanbian University, Yanji, Jilin Province, 133002, China. .,College of Agriculture, Yanbian University, Yanji, Jilin Province, 133002, China.
| | - Wenxiu Ji
- College of Integration Science, Yanbian University, Yanji, Jilin Province, 133002, China. .,College of Agriculture, Yanbian University, Yanji, Jilin Province, 133002, China.
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26
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Shen Z, Thomashow LS, Ou Y, Tao C, Wang J, Xiong W, Liu H, Li R, Shen Q, Kowalchuk GA. Shared Core Microbiome and Functionality of Key Taxa Suppressive to Banana Fusarium Wilt. Research (Wash D C) 2022; 2022:9818073. [PMID: 36204250 PMCID: PMC9513836 DOI: 10.34133/2022/9818073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/22/2022] [Indexed: 11/08/2022] Open
Abstract
Microbial contributions to natural soil suppressiveness have been reported for a range of plant pathogens and cropping systems. To disentangle the mechanisms underlying suppression of banana Panama disease caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc4), we used amplicon sequencing to analyze the composition of the soil microbiome from six separate locations, each comprised of paired orchards, one potentially suppressive and one conducive to the disease. Functional potentials of the microbiomes from one site were further examined by shotgun metagenomic sequencing after soil suppressiveness was confirmed by greenhouse experiments. Potential key antagonists involved in disease suppression were also isolated, and their activities were validated by a combination of microcosm and pot experiments. We found that potentially suppressive soils shared a common core community with relatively low levels of F. oxysporum and relatively high proportions of Myxococcales, Pseudomonadales, and Xanthomonadales, with five genera, Anaeromyxobacter, Kofleria, Plesiocystis, Pseudomonas, and Rhodanobacter being significantly enriched. Further, Pseudomonas was identified as a potential key taxon linked to pathogen suppression. Metagenomic analysis showed that, compared to the conducive soil, the microbiome in the disease suppressive soil displayed a significantly greater incidence of genes related to quorum sensing, biofilm formation, and synthesis of antimicrobial compounds potentially active against Foc4. We also recovered a higher frequency of antagonistic Pseudomonas isolates from disease suppressive experimental field sites, and their protective effects against banana Fusarium wilt disease were demonstrated under greenhouse conditions. Despite differences in location and soil conditions, separately located suppressive soils shared common characteristics, including enrichment of Myxococcales, Pseudomonadales, and Xanthomonadales, and enrichment of specific Pseudomonas populations with antagonistic activity against the pathogen. Moreover, changes in functional capacity toward an increase in quorum sensing, biofilm formation, and antimicrobial compound synthesizing involve in disease suppression.
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Affiliation(s)
- Zongzhuan Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, China
| | - Linda S. Thomashow
- U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, USA
| | - Yannan Ou
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
| | - Chengyuan Tao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
| | - Jiabao Wang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, China
| | - Wu Xiong
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
| | - Hongjun Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, China
| | - George A. Kowalchuk
- Ecology and Biodiversity Group, Institute of Environmental Biology, Department of Biology, Utrecht University, 3584 CH Utrecht, Netherlands
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Characterization of Microbial Communities and Naturally Occurring Radionuclides in Soilless Growth Media Amended with Different Concentrations of Biochar. Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol2030051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Biochar, derived from the pyrolysis of plant materials has the potential to enhance plant growth in soilless media. Howevetar, little is known about the impact of biochar amendments to soilless growth media, microbial community composition, and fate of chemical constituents in the media. In this study, different concentrations of biochar were added to soilless media and microbial composition, and chemical constituents were analyzed using metagenomics and gamma spectroscopy techniques, respectively. Across treatments, carboxyl-C, phenolic-C, and aromatic-C were the main carbon sources that influenced microbial community composition. Flavobacterium (39.7%), was the predominantly bacteria genus, followed by Acidibacter (12.2%), Terrimonas (10.1%), Cytophaga (7.5%), Ferruginibacter (6.0%), Lacunisphaera (5.9%), Cellvibrio (5.8%), Opitutus (4.8%), Mucilaginibacter (4.0%) and Bryobacter (4.0%). Negative relationships were found between Cytophaga and 226Ra (r = −0.84, p = 0.0047), 40K (r = −0.82, p = 0.0069) and 137Cs (r = −0.93, p = 0.0002). Similarly, Mucilaginibacter was negatively correlated with 226Ra (r = −0.83, p = 0.0054) and 137Cs (r = −0.87, p = 0.0021). Overall, the data suggest that high % biochar amended samples have high radioactivity concentration levels. Some microorganisms have less presence in high radioactivity concentration levels.
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28
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Johnston-Monje D, Gutiérrez JP, Becerra Lopez-Lavalle LA. Stochastic Inoculum, Biotic Filtering and Species-Specific Seed Transmission Shape the Rare Microbiome of Plants. Life (Basel) 2022; 12:life12091372. [PMID: 36143410 PMCID: PMC9506401 DOI: 10.3390/life12091372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
A plant’s health and productivity is influenced by its associated microbes. Although the common/core microbiome is often thought to be the most influential, significant numbers of rare or uncommon microbes (e.g., specialized endosymbionts) may also play an important role in the health and productivity of certain plants in certain environments. To help identify rare/specialized bacteria and fungi in the most important angiosperm plants, we contrasted microbiomes of the seeds, spermospheres, shoots, roots and rhizospheres of Arabidopsis, Brachypodium, maize, wheat, sugarcane, rice, tomato, coffee, common bean, cassava, soybean, switchgrass, sunflower, Brachiaria, barley, sorghum and pea. Plants were grown inside sealed jars on sterile sand or farm soil. Seeds and spermospheres contained some uncommon bacteria and many fungi, suggesting at least some of the rare microbiome is vertically transmitted. About 95% and 86% of fungal and bacterial diversity inside plants was uncommon; however, judging by read abundance, uncommon fungal cells are about half of the mycobiome, while uncommon bacterial cells make up less than 11% of the microbiome. Uncommon-seed-transmitted microbiomes consisted mostly of Proteobacteria, Firmicutes, Bacteriodetes, Ascomycetes and Basidiomycetes, which most heavily colonized shoots, to a lesser extent roots, and least of all, rhizospheres. Soil served as a more diverse source of rare microbes than seeds, replacing or excluding the majority of the uncommon-seed-transmitted microbiome. With the rarest microbes, their colonization pattern could either be the result of stringent biotic filtering by most plants, or uneven/stochastic inoculum distribution in seeds or soil. Several strong plant–microbe associations were observed, such as seed transmission to shoots, roots and/or rhizospheres of Sarocladium zeae (maize), Penicillium (pea and Phaseolus), and Curvularia (sugarcane), while robust bacterial colonization from cassava field soil occurred with the cyanobacteria Leptolyngbya into Arabidopsis and Panicum roots, and Streptomyces into cassava roots. Some abundant microbes such as Sakaguchia in rice shoots or Vermispora in Arabidopsis roots appeared in no other samples, suggesting that they were infrequent, stochastically deposited propagules from either soil or seed (impossible to know based on the available data). Future experiments with culturing and cross-inoculation of these microbes between plants may help us better understand host preferences and their role in plant productivity, perhaps leading to their use in crop microbiome engineering and enhancement of agricultural production.
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Affiliation(s)
- David Johnston-Monje
- Max Planck Tandem Group in Plant Microbial Ecology, Universidad del Valle, Cali 76001, Colombia
- International Center for Tropical Agriculture (CIAT), Cali 763537, Colombia
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Correspondence: ; Tel.: +57-315-545-6227
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Xu G, Geng S, Cao W, Zuo R, Teng Y, Ding A, Fan F, Dou J. Vertical distribution characteristics and interactions of polycyclic aromatic compounds and bacterial communities in contaminated soil in oil storage tank areas. CHEMOSPHERE 2022; 301:134695. [PMID: 35472616 DOI: 10.1016/j.chemosphere.2022.134695] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 04/03/2022] [Accepted: 04/20/2022] [Indexed: 06/14/2023]
Abstract
Polycyclic aromatic compound (PAC) contamination in soil as a result of oil spills is a serious issue because of the huge global demand for fossil energy. This study assessed the vertical variation in polycyclic aromatic hydrocarbons (PAHs), derivatives of PAHs (dPAHs) and bacterial community structure in deep soil with long-term contamination by oil spillage. Our results suggest that the content of total PACs ranged from 1196.6 μg/kg to 14980.9 μg/kg and decreased with depth at all sites. PAHs were the most abundant PACs, with a mean concentration of 6640.7 μg/kg, followed by oxygenated PAHs (mean 156.3 μg/kg) and nitrated PAHs (mean 33.4 μg/kg). PAHs are mainly low molecular weight PACs such as naphthalene, fluorene and phenanthrene, while derivatives of PAHs are all low molecular weight PACs and mainly oxygenated PAHs. Low molecular weight PAHs were an important source of dPAHs under specific conditions. The bacterial community structure showed higher bacterial diversity and lower bacterial richness in shallow soil (2-6 m in depth) than in deep soil (8-10 m in depth). Spearman's analysis confirmed that dramatic bacterial community shifts are a response to contamination. At the genus level, the presence of PACs highly selected for Pseudomonas, belonging to Proteobacteria. Moreover, functional predictions based on Tax4Fun revealed that soil with long-term contamination had a strong potential for PAC degradation. In addition, statistical analysis showed that oxidation-reduction potential (Eh) was closely related to variations of bacterial community composition and function. Finally, Ramlibacter, Pseudomonas, Pseudonocardia, c_MB-A2-108, f_Amb-16S-1323, and Qipengyuania were identified by cooccurrence network analysis as keystone taxa contributing to the maintenance of bacterial ecological function. Together, our results provide evidence of tight bacterial effects of PAHs and dPAHs and a more complete understanding of the fate of PACs in deep contaminated soils.
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Affiliation(s)
- Guangming Xu
- Engineering Research Center of Ministry of Education on Groundwater Pollution Control and Remediation, College of Water Sciences, Beijing Normal University, Beijing, 100875, PR China
| | - Shuying Geng
- Engineering Research Center of Ministry of Education on Groundwater Pollution Control and Remediation, College of Water Sciences, Beijing Normal University, Beijing, 100875, PR China
| | - Wei Cao
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Tianjin, 300384, PR China
| | - Rui Zuo
- Engineering Research Center of Ministry of Education on Groundwater Pollution Control and Remediation, College of Water Sciences, Beijing Normal University, Beijing, 100875, PR China
| | - Yanguo Teng
- Engineering Research Center of Ministry of Education on Groundwater Pollution Control and Remediation, College of Water Sciences, Beijing Normal University, Beijing, 100875, PR China
| | - Aizhong Ding
- Engineering Research Center of Ministry of Education on Groundwater Pollution Control and Remediation, College of Water Sciences, Beijing Normal University, Beijing, 100875, PR China
| | - Fuqiang Fan
- Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai, 519087, PR China
| | - Junfeng Dou
- Engineering Research Center of Ministry of Education on Groundwater Pollution Control and Remediation, College of Water Sciences, Beijing Normal University, Beijing, 100875, PR China.
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Deng R, Ma P, Li B, Wu Y, Yang X. Development of allergic asthma and changes of intestinal microbiota in mice under high humidity and/or carbon black nanoparticles. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 241:113786. [PMID: 35738102 DOI: 10.1016/j.ecoenv.2022.113786] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/02/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
In respiratory diseases, the induction of allergic asthma is one of the hottest issues of international concern. The adjuvant effect of air pollutants including nanoparticles (NPs) has be pointed out to facilitate the occurrence and development of allergic asthma. This work studied the development of allergic asthma upon exposures of carbon black nanoparticles (CB NPs, 30-50 nm) and/or high environmental humidity (90% relative humidity). The mechanisms involved were investigated from perspectives of the activation of oxidative stress and transient receptor potential vanilloid 1 (TRPV1) pathways and the alteration in intestinal microbiota. Both high humidity and CB NPs aggravated the airway hyperreactivity, remodeling, and inflammation in Balb/c mice sensitized by ovalbumin. The co-exposure of these two risk factors exhibited adjuvant effect on the development of asthma likely through activating oxidative stress pathway and TRPV1 pathway and then facilitating type I hypersensitivity. Additionally, exposures of high humidity and/or CB NPs reduced the richness of intestinal microbes, altered microbial community composition, and weakened corresponding biological functions, which may interact with the development of asthma. The findings will add new toxicological knowledge to the health risk assessment and management of co-exposures of NPs and other risk factors in the environment.
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Affiliation(s)
- Rui Deng
- School of Civil Engineering, Chongqing University, Chongqing 400045, China.
| | - Ping Ma
- Xianning Engineering Research Center for Healthy Environment, Xianning Medical College, Hubei University of Science and Technology, Xianning 437100, China
| | - Baizhan Li
- School of Civil Engineering, Chongqing University, Chongqing 400045, China
| | - Yang Wu
- Xianning Engineering Research Center for Healthy Environment, Xianning Medical College, Hubei University of Science and Technology, Xianning 437100, China
| | - Xu Yang
- Xianning Engineering Research Center for Healthy Environment, Xianning Medical College, Hubei University of Science and Technology, Xianning 437100, China; Institute of Eastern-Himalaya Biodiversity Research, Dali university, Dali 671003, China
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Rhizosphere Microbial Communities and Geochemical Constraining Mechanism of Antimony Mine Waste-Adapted Plants in Southwestern China. Microorganisms 2022; 10:microorganisms10081507. [PMID: 35893564 PMCID: PMC9330434 DOI: 10.3390/microorganisms10081507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 02/04/2023] Open
Abstract
Antimony (Sb) and arsenic (As) are two hazardous metalloid elements, and the biogeochemical cycle of Sb and As can be better understood by studying plant rhizosphere microorganisms associated with Sb mine waste. In the current study, samples of three types of mine waste—Sb mine tailing, waste rocks, and smelting slag—and associated rhizosphere microorganisms of adapted plants were collected from Qinglong Sb mine, southwest China. 16S rRNA was sequenced and used to study the composition of the mine waste microbial community. The most abundant phylum in all samples was Proteobacteria, followed by Bacteroidota, Acidobacteriota, and Actinobacteriota. The community composition varied among different mine waste types. Gammaproteobacteria was the most abundant microorganism in tailings, Actinobacteria was mainly distributed in waste rock, and Saccharimonadia, Acidobacteriae, and Ktedonobacteria were mainly present in slag. At the family level, the vast majority of Hydrogenophilaceae were found in tailings, Ktedonobacteraceae, Chthoniobacteraceae, and Acidobacteriaceae (Subgroup 1) were mostly found in slag, and Pseudomonadaceae and Micrococcaceae were mainly found in waste rock. Actinobacteriota and Arthrobacter are important taxa for reducing heavy metal(loid) mobility, vegetation restoration, and self-sustaining ecosystem construction on antimony mine waste. The high concentrations of Sb and As reduce microbial diversity.
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Medina-Paz F, Herrera-Estrella L, Heil M. All Set before Flowering: A 16S Gene Amplicon-Based Analysis of the Root Microbiome Recruited by Common Bean ( Phaseolus vulgaris) in Its Centre of Domestication. PLANTS (BASEL, SWITZERLAND) 2022; 11:1631. [PMID: 35807585 PMCID: PMC9269403 DOI: 10.3390/plants11131631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 04/18/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Plant roots recruit most prokaryotic members of their root microbiota from the locally available inoculum, but knowledge on the contribution of native microorganisms to the root microbiota of crops in native versus non-native areas remains scarce. We grew common bean (Phaseolus vulgaris) at a field site in its centre of domestication to characterise rhizosphere and endosphere bacterial communities at the vegetative, flowering, and pod filling stage. 16S r RNA gene amplicon sequencing of ten samples yielded 9,401,757 reads, of which 8,344,070 were assigned to 17,352 operational taxonomic units (OTUs). Rhizosphere communities were four times more diverse than in the endosphere and dominated by Actinobacteria, Bacteroidetes, Crenarchaeota, and Proteobacteria (endosphere: 99% Proteobacteria). We also detected high abundances of Gemmatimonadetes (6%), Chloroflexi (4%), and the archaeal phylum Thaumarchaeota (Candidatus Nitrososphaera: 11.5%): taxa less frequently reported from common bean rhizosphere. Among 154 OTUs with different abundances between vegetative and flowering stage, we detected increased read numbers of Chryseobacterium in the endosphere and a 40-fold increase in the abundances of OTUs classified as Rhizobium and Aeromonas (equivalent to 1.5% and over 6% of all reads in the rhizosphere). Our results indicate that bean recruits specific taxa into its microbiome when growing 'at home'.
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Affiliation(s)
- Francisco Medina-Paz
- Laboratorio de Ecología de Plantas, Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados (CINVESTAV)—Unidad Irapuato, Irapuato 36824, GTO, Mexico;
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados (CINVESTAV)—Unidad de Genómica Avanzada, Irapuato 36824, GTO, Mexico; or
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX 79424, USA
| | - Martin Heil
- Laboratorio de Ecología de Plantas, Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados (CINVESTAV)—Unidad Irapuato, Irapuato 36824, GTO, Mexico;
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Escudero-Martinez C, Coulter M, Alegria Terrazas R, Foito A, Kapadia R, Pietrangelo L, Maver M, Sharma R, Aprile A, Morris J, Hedley PE, Maurer A, Pillen K, Naclerio G, Mimmo T, Barton GJ, Waugh R, Abbott J, Bulgarelli D. Identifying plant genes shaping microbiota composition in the barley rhizosphere. Nat Commun 2022; 13:3443. [PMID: 35710760 PMCID: PMC9203816 DOI: 10.1038/s41467-022-31022-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/30/2022] [Indexed: 12/13/2022] Open
Abstract
A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere, the interface between roots and soil. Here, we use metagenomics information as an external quantitative phenotype to map the host genetic determinants of the rhizosphere microbiota in wild and domesticated genotypes of barley, the fourth most cultivated cereal globally. We identify a small number of loci with a major effect on the composition of rhizosphere communities. One of those, designated the QRMC-3HS, emerges as a major determinant of microbiota composition. We subject soil-grown sibling lines harbouring contrasting alleles at QRMC-3HS and hosting contrasting microbiotas to comparative root RNA-seq profiling. This allows us to identify three primary candidate genes, including a Nucleotide-Binding-Leucine-Rich-Repeat (NLR) gene in a region of structural variation of the barley genome. Our results provide insights into the footprint of crop improvement on the plant’s capacity of shaping rhizosphere microbes. A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere. Here, the authors report QTLs and the associated candidate genes underlying rhizosphere microbiome composition in barley.
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Affiliation(s)
| | - Max Coulter
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK.,University of Dundee, Computational Biology, School of Life Sciences, Dundee, UK
| | - Rodrigo Alegria Terrazas
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK.,Mohammed VI Polytechnic University, Agrobiosciences Program, Plant & Soil Microbiome Subprogram, Bengurir, Morocco
| | | | - Rumana Kapadia
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK
| | - Laura Pietrangelo
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK.,Department of Biosciences and Territory, University of Molise, Campobasso, Italy
| | - Mauro Maver
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK.,Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy.,Competence Centre for Plant Health, Free University of Bozen-Bolzano, Bolzano, Italy
| | | | - Alessio Aprile
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK.,Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | | | | | - Andreas Maurer
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University, Halle-Wittenberg, Germany
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University, Halle-Wittenberg, Germany
| | - Gino Naclerio
- Department of Biosciences and Territory, University of Molise, Campobasso, Italy
| | - Tanja Mimmo
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy.,Competence Centre for Plant Health, Free University of Bozen-Bolzano, Bolzano, Italy
| | - Geoffrey J Barton
- University of Dundee, Computational Biology, School of Life Sciences, Dundee, UK
| | - Robbie Waugh
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK.,The James Hutton Institute, Invergowrie, UK
| | - James Abbott
- University of Dundee, Computational Biology, School of Life Sciences, Dundee, UK
| | - Davide Bulgarelli
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK.
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Chang F, Jia F, Guan M, Jia Q, Sun Y, Li Z. Responses of Soil Rare and Abundant Sub-Communities and Physicochemical Properties after Application of Different Chinese Herb Residue Soil Amendments. J Microbiol Biotechnol 2022; 32:564-574. [PMID: 35354763 PMCID: PMC9628873 DOI: 10.4014/jmb.2202.02029] [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: 02/21/2022] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 12/15/2022]
Abstract
Microbial diversity in the soil is responsive to changes in soil composition. However, the impact of soil amendments on the diversity and structure of rare and abundant sub-communities in agricultural systems is poorly understood. We investigated the effects of different Chinese herb residue (CHR) soil amendments and cropping systems on bacterial rare and abundant sub-communities. Our results showed that the bacterial diversity and structure of these sub-communities in soil had a specific distribution under the application of different soil amendments. The CHR soil amendments with high nitrogen and organic matter additives significantly increased the relative abundance and stability of rare taxa, which increased the structural and functional redundancy of soil bacterial communities. Rare and abundant sub-communities also showed different preferences in terms of bacterial community composition, as the former was enriched with Bacteroidetes while the latter had more Alphaproteobacteria and Betaproteobacteria. All applications of soil amendments significantly improved soil quality of newly created farmlands in whole maize cropping system. Rare sub-communitiy genera Niastella and Ohtaekwangia were enriched during the maize cropping process, and Nitrososphaera was enriched under the application of simple amendment group soil. Thus, Chinese medicine residue soil amendments with appropriate additives could affect soil rare and abundant sub-communities and enhance physicochemical properties. These findings suggest that applying soil composite amendments based on CHR in the field could improve soil microbial diversity, microbial redundancy, and soil fertility for sustainable agriculture on the Loess Plateau.
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Affiliation(s)
- Fan Chang
- College of Life Science, Shaanxi Normal University, Xi’an 710062, P.R. China,Shaanxi Institute of Microbiology, Xi’an 710043, P.R. China
| | - Fengan Jia
- Shaanxi Institute of Microbiology, Xi’an 710043, P.R. China
| | - Min Guan
- Shaanxi Agricultural Machinery Research Institute, Xianyang 712000, P.R. China
| | - Qingan Jia
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an 710072, P.R. China
| | - Yan Sun
- College of Life Science, Shaanxi Normal University, Xi’an 710062, P.R. China,Corresponding authors Y. Sun Phone: +8615353554537 E-mail:
| | - Zhi Li
- College of Life Science, Shaanxi Normal University, Xi’an 710062, P.R. China,
Z. Li Phone: +8613572900787 E-mail:
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35
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Tao S, Zhang Y, Tian C, Duplessis S, Zhang N. Elevated Ozone Concentration and Nitrogen Addition Increase Poplar Rust Severity by Shifting the Phyllosphere Microbial Community. J Fungi (Basel) 2022; 8:jof8050523. [PMID: 35628778 PMCID: PMC9148057 DOI: 10.3390/jof8050523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/16/2022] [Accepted: 05/16/2022] [Indexed: 12/04/2022] Open
Abstract
Tropospheric ozone and nitrogen deposition are two major environmental pollutants. A great deal of research has focused on the negative impacts of elevated O3 and the complementary effect of soil N addition on the physiological properties of trees. However, it has been overlooked how elevated O3 and N addition affect tree immunity in face of pathogen infection, as well as of the important roles of phyllosphere microbiome community in host–pathogen–environment interplay. Here, we examined the effects of elevated O3 and soil N addition on poplar leaf rust [Melampsora larici-populina] severity of two susceptible hybrid poplars [clone ‘107’: Populus euramericana cv. ‘74/76’; clone ‘546’: P. deltoides Í P. cathayana] in Free-Air-Controlled-Environment plots, in addition, the link between Mlp-susceptibility and changes in microbial community was determined using Miseq amplicon sequencing. Rust severity of clone ‘107’ significantly increased under elevated O3 or N addition only; however, the negative impact of elevated O3 could be significantly mitigated when accompanied by N addition, likewise, this trade-off was reflected in its phyllosphere microbial α-diversity responding to elevated O3 and N addition. However, rust severity of clone ‘546’ did not differ significantly in the cases of elevated O3 and N addition. Mlp infection altered microbial community composition and increased its sensitivity to elevated O3, as determined by the markedly different abundance of taxa. Elevated O3 and N addition reduced the complexity of microbial community, which may explain the increased severity of poplar rust. These findings suggest that poplars require a changing phyllosphere microbial associations to optimize plant immunity in response to environmental changes.
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Affiliation(s)
- Siqi Tao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China; (S.T.); (Y.Z.); (C.T.)
| | - Yunxia Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China; (S.T.); (Y.Z.); (C.T.)
| | - Chengming Tian
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China; (S.T.); (Y.Z.); (C.T.)
| | | | - Naili Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China; (S.T.); (Y.Z.); (C.T.)
- Correspondence:
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Bintarti AF, Kearns PJ, Sulesky-Grieb A, Shade A. Abiotic Treatment to Common Bean Plants Results in an Altered Endophytic Seed Microbiome. Microbiol Spectr 2022; 10:e0021021. [PMID: 35377190 PMCID: PMC9045313 DOI: 10.1128/spectrum.00210-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 03/10/2022] [Indexed: 11/30/2022] Open
Abstract
There has been a growing interest in the seed microbiome due to its important role as an end and starting point of plant microbiome assembly that can have consequences for plant health. However, the effect of abiotic conditions on the seed microbial community remains unknown. We performed a pilot study in a controlled growth chamber to investigate how the endophytic seed microbiome of the common bean (Phaseolus vulgaris L. [var. Red Hawk]) was altered under abiotic treatments relevant for crop management with changing climate. Bean plants were subjected to one of three treatments: 66% water withholding to simulate mild drought, 50% Hoagland nutrient solution to simulate fertilization, or control with sufficient water and baseline nutrition. We performed 16S rRNA gene amplicon sequencing and Internal Transcribed Spacer 1 (ITS1) amplicon sequencing of the endophytic DNA to assess seed bacterial/archaeal and fungal community structure, respectively. We found that variability in the seed microbiome structure was high, while α-diversity was low, with tens of taxa present. Water withholding and nutrient addition significantly altered the seed microbiome structure for bacterial/archaeal communities compared to the control, and each treatment resulted in a distinct microbiome structure. Conversely, there were no statistically supported differences in the fungal microbiome across treatments. These promising results suggest that further investigation is needed to better understand abiotic or stress-induced changes in the seed microbiome, the mechanisms that drive those changes, and their implications for the health and stress responses of the next plant generation. IMPORTANCE Seed microbiome members initiate the assembly of plant-associated microbial communities, but the environmental drivers of endophytic seed microbiome composition are unclear. Here, we exposed plants to short-term drought and fertilizer treatments during early vegetative growth and quantified the microbiome composition of the seeds that were ultimately produced. We found that seeds produced by plants stressed by water limitation or receiving nutrient addition had statistically different endophytic bacterial/archaeal microbiome compositions from each other and from seeds produced by control plants. This work suggests that the abiotic experience of a parental plant can influence the composition of its seed microbiome, with unknown consequences for the next plant generation.
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Affiliation(s)
- A. Fina Bintarti
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
- The Plant Resilience Institute, Michigan State University, East Lansing, Michigan, USA
| | - Patrick J. Kearns
- The Plant Resilience Institute, Michigan State University, East Lansing, Michigan, USA
| | - Abby Sulesky-Grieb
- The Plant Resilience Institute, Michigan State University, East Lansing, Michigan, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Ashley Shade
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
- The Plant Resilience Institute, Michigan State University, East Lansing, Michigan, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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Xiao J, Chen SY, Sun Y, Yang SD, He Y. Differences of rhizospheric and endophytic bacteria are recruited by different watermelon phenotypes relating to rind colors formation. Sci Rep 2022; 12:6360. [PMID: 35428856 PMCID: PMC9012882 DOI: 10.1038/s41598-022-10533-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 03/28/2022] [Indexed: 11/09/2022] Open
Abstract
To elucidate the biological mechanism of yellow rind formation on watermelon, the characteristics of soil bacterial community structure in rhizosphere and endophytic bacteria in stem of yellow rind watermelon were analyzed. Based on high-throughput sequencing technology, plant stem and rhizosphere soil samples, which collected from yellow and green rind watermelons were used in this paper, respectively. The structural characteristics of the endophytic bacteria in stems and soil bacterial communities in rhizospheres of yellow and green rind watermelons were comparative studied. Firstly, significant different proportions of some dominant bacteria and abundances could be detected between yellow and rind watermelons. Meanwhile, although different abundances of endophytic bacteria could be found, but no significant differences were observed between yellow and green rind watermelons. Moreover, Gemmatimonadota, Myxococcota, WPS-2, norank_f_Gemmatimonadaceae and Bradyrhizobium were the soil dominant bacterial genera in rhizosphere of green rind watermelon. All above results suggest that differences of rhizospheric and endophytic bacteria are exactly recruited as "workers" by different watermelon phenotypes relating to rind color formations.
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Affiliation(s)
- Jian Xiao
- Guangxi Key Laboratory of Subtropical Bio-resource Conservation and Utilization, Agricultural College, Guangxi University, Nanning, 530004, Guangxi, People's Republic of China
| | - Si-Yu Chen
- Guangxi Key Laboratory of Subtropical Bio-resource Conservation and Utilization, Agricultural College, Guangxi University, Nanning, 530004, Guangxi, People's Republic of China
| | - Yan Sun
- Guangxi Key Laboratory of Subtropical Bio-resource Conservation and Utilization, Agricultural College, Guangxi University, Nanning, 530004, Guangxi, People's Republic of China
| | - Shang-Dong Yang
- Guangxi Key Laboratory of Subtropical Bio-resource Conservation and Utilization, Agricultural College, Guangxi University, Nanning, 530004, Guangxi, People's Republic of China.
| | - Yi He
- Horticultural Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, People's Republic of China.
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Díaz-Cruz GA, Cassone BJ. Changes in the phyllosphere and rhizosphere microbial communities of soybean in the presence of pathogens. FEMS Microbiol Ecol 2022; 98:fiac022. [PMID: 35195242 DOI: 10.1093/femsec/fiac022] [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: 11/02/2021] [Revised: 01/20/2022] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Soybean (Glycine max L.) is host to an array of foliar- and root-infecting pathogens that can cause significant yield losses. To provide insights into the roles of microorganisms in disease development, we evaluated the bacterial and fungal communities associated with the soybean rhizosphere and phyllosphere. For this, leaf and soil samples of healthy, Phytophthora sojae-infected and Septoria glycines-infected plants were sampled at three stages during the production cycle, and then subjected to 16S and Internal Transcribed Spacer (ITS) amplicon sequencing. The results indicated that biotic stresses did not have a significant impact on species richness and evenness regardless of growth stage. However, the structure and composition of soybean microbial communities were dramatically altered by biotic stresses, particularly for the fungal phyllosphere. Additionally, we cataloged a variety of microbial genera that were altered by biotic stresses and their associations with other genera, which could serve as biological indicators for disease development. In terms of soybean development, the rhizosphere and phyllosphere had distinct microbial communities, with the fungal phyllosphere most influenced by growth stage. Overall, this study characterized the phyllosphere and rhizosphere microbial communities of soybean, and described the impact of pathogen infection and plant development in shaping these bacterial and fungal communities.
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Affiliation(s)
- Gustavo A Díaz-Cruz
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
- Department of Biology, Brandon University, Brandon, MB, R7A 6A9, Canada
| | - Bryan J Cassone
- Department of Biology, Brandon University, Brandon, MB, R7A 6A9, Canada
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Abstract
Coffee is one of the most important commodities in the global market. Of the 130 species of Coffea, only Coffea arabica and Coffea canephora are actually cultivated on a large scale. Despite the economic and social importance of coffee, little research has been done on the coffee tree microbiome. To assess the structure and function of the rhizosphere microbiome, we performed a deep shotgun metagenomic sequencing of the rhizospheres of five different species, C. arabica, C. canephora, Coffea stenophylla, Coffea racemosa, and Coffea liberica. Our findings indicated that C. arabica and C. stenophylla have different microbiomes, while no differences were detected between the other Coffea species. The core rhizosphere microbiome comprises genera such as Streptomyces, Mycobacterium, Bradyrhizobium, Burkholderia, Sphingomonas, Penicillium, Trichoderma, and Rhizophagus, several of which are potential plant-beneficial microbes. Streptomyces and mycorrhizal fungi dominate the microbial communities. The concentration of sucrose in the rhizosphere seems to influence fungal communities, and the concentration of caffeine/theobromine has little effect on the microbiome. We also detected a possible relationship between drought tolerance in Coffea and known growth-promoting microorganisms. The results provide important information to guide future studies of the coffee tree microbiome to improve plant production and health. IMPORTANCE The microbiome has been identified as a fundamental factor for the maintenance of plant health, helping plants to fight diseases and the deleterious effects of abiotic stresses. Despite this, in-depth studies of the microbiome have been limited to a few species, generally with a short life cycle, and perennial species have mostly been neglected. The coffee tree microbiome, on the other hand, has gained interest in recent years as Coffea trees are perennial tropical species of enormous importance, especially for developing countries. A better understanding of the microorganisms associated with coffee trees can help to mitigate the deleterious effects of climate change on the crop, improving plant health and making the system more sustainable.
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Zhang C, Liu S, Hussain S, Li L, Baiome BA, Xiao S, Cao H. Fe(II) Addition Drives Soil Bacterial Co-Ocurrence Patterns and Functions Mediated by Anaerobic and Chemoautotrophic Taxa. Microorganisms 2022; 10:microorganisms10030547. [PMID: 35336122 PMCID: PMC8950066 DOI: 10.3390/microorganisms10030547] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/04/2022] [Accepted: 02/05/2022] [Indexed: 12/10/2022] Open
Abstract
Iron is among the most abundant elements in the soil of paddy fields, and its valence state and partitioning can be transformed by flooding and drainage alternations. However, little is known about the function of soil microbes that interact with Fe(II). In this study, sandy and loamy soils originating from rice fields were treated with Fe(II) at low and high concentrations. The findings demonstrate that additional Fe(II) has various effects on the soil’s microbial community structure and metabolic pathways. We conclude that Fe(II) at high concentrations reduced bacterial abundance and diversity in two textured paddy soils, yet the abundance in loamy soils was higher than it was in sandy soil. Additionally, in environments with high Fe(II) levels, the relative abundance of both anaerobic and chemoautotrophic bacteria increased. The Fe(II) concentration was positively correlated with total reduced substances but negatively correlated with redox potential and pH. Co-occurrence networks revealed that Fe(II) significantly promoted interactions with the most anaerobic and chemoautotrophic bacteria. In addition, adding Fe(II) greatly increased the number of more complex bacterial networks, and an increase in the number of mutually beneficial taxa occurred. We found that Fe(II) promoted the methane pathway, the Calvin cycle, and nitrate reduction to small but significant extents. These pathways involve the growth and interrelation of autotrophic and anaerobic bacteria. These results suggest that changes in the bacterial community structure occur in many dry–wet alternating environments.
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Affiliation(s)
- Chenyang Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, College of Life Sciences, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, China; (C.Z.); (S.L.); (S.H.); (L.L.); (B.A.B.)
| | - Senlin Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, College of Life Sciences, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, China; (C.Z.); (S.L.); (S.H.); (L.L.); (B.A.B.)
- Wellington Research Group, School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Sarfraz Hussain
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, College of Life Sciences, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, China; (C.Z.); (S.L.); (S.H.); (L.L.); (B.A.B.)
| | - Lifeng Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, College of Life Sciences, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, China; (C.Z.); (S.L.); (S.H.); (L.L.); (B.A.B.)
| | - Baiome Abdelmaguid Baiome
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, College of Life Sciences, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, China; (C.Z.); (S.L.); (S.H.); (L.L.); (B.A.B.)
| | - Shuiqing Xiao
- School of Intercultural Studies, Jiangxi Normal University, Nanchang 330022, China;
| | - Hui Cao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, College of Life Sciences, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, China; (C.Z.); (S.L.); (S.H.); (L.L.); (B.A.B.)
- Correspondence: ; Tel./Fax: +86-025-8439-6753
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Genetically related genotypes of cowpea present similar bacterial community in the rhizosphere. Sci Rep 2022; 12:3472. [PMID: 35236879 PMCID: PMC8891268 DOI: 10.1038/s41598-022-06860-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 02/08/2022] [Indexed: 12/31/2022] Open
Abstract
Plant breeding reduces the genetic diversity of plants and could influence the composition, structure, and diversity of the rhizosphere microbiome, selecting more homogeneous and specialized microbes. In this study, we used 16S rRNA sequencing to assess the bacterial community in the rhizosphere of different lines and modern cowpea cultivars, to investigate the effect of cowpea breeding on bacterial community assembly. Thus, two African lines (IT85F-2687 and IT82D-60) and two Brazilian cultivars (BRS-Guariba and BRS-Tumucumaque) of cowpea were assessed to verify if the generation advance and genetic breeding influence the bacterial community in the rhizosphere. No significant differences were found in the structure, richness, and diversity of bacterial community structure between the rhizosphere of the different cowpea genotypes, and only slight differences were found at the OTU level. The complexity of the co-occurrence network decreased from African lines to Brazilian cultivars. Regarding functional prediction, the core functions were significantly altered according to the genotypes. In general, African lines presented a more abundance of groups related to chemoheterotrophy, while the rhizosphere of the modern cultivars decreased functions related to cellulolysis. This study showed that the genetic breeding process affects the dynamics of the rhizosphere community, decreasing the complexity of interaction in one cultivar. As these cowpea genotypes are genetically related, it could suggest a new hypothesis of how genetic breeding of similar genotypes could influence the rhizosphere microbiome.
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Zhou Q, He R, Zhao D, Zeng J, Yu Z, Wu QL. Contrasting Patterns of the Resident and Active Rhizosphere Bacterial Communities of Phragmites Australis. MICROBIAL ECOLOGY 2022; 83:314-327. [PMID: 33956174 DOI: 10.1007/s00248-021-01767-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
Rhizosphere microbes play a key role in maintaining plant health and regulating biogeochemical cycles. The active bacterial community (ABC) in rhizosphere, as a small fraction of the rhizosphere resident bacterial community (RBC), has the potential to actively participate in nutrient cycling processes at the root-sediment interface. Here, we investigated the ABC and RBC within the rhizosphere of Phragmites australis (P. australis) subjected to different environmental conditions (i.e., seasons and flooding conditions) in Lake Taihu, China. Our results indicated that RBC exhibited significantly higher alpha diversity as well as lower beta diversity than ABC. The active ratios of 16S rRNA to 16S rDNA (also RNA/DNA) of the bacterial communities in summer and winter suggested a lower proportion of potential active taxa in the rhizosphere bacterial community during summer. Network analysis showed that negative correlations in each network were observed to dominate the species correlations between the rhizosphere and bulk sediment bacterial communities. Our results revealed that niche differentiation and seasonal variation played crucial roles in driving the assembly of ABC and RBC associated with the rhizospheres of P. australis. These findings broaden our knowledge about how rhizosphere bacterial communities respond to environmental variations through changing their diversity and composition.
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Affiliation(s)
- Qi Zhou
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
| | - Rujia He
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China.
| | - Zhongbo Yu
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China
- Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, 100039, China
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Ma X, Chao L, Li J, Ding Z, Wang S, Li F, Bao Y. The Distribution and Turnover of Bacterial Communities in the Root Zone of Seven Stipa Species Across an Arid and Semi-arid Steppe. Front Microbiol 2022; 12:782621. [PMID: 35003012 PMCID: PMC8741278 DOI: 10.3389/fmicb.2021.782621] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/26/2021] [Indexed: 11/23/2022] Open
Abstract
The bacterial communities of the root-zone soil are capable of regulating vital biogeochemical cycles and the succession of plant growth. Stipa as grassland constructive species is restricted by the difference features of east–west humidity and north–south heat, which shows the population substituting distribution. The distribution, turnover, and potential driving factors and ecological significance of the root-zone bacterial community along broad spatial gradients of Stipa taxa transition remain unclear. This paper investigated seven Stipa species root-zone soils based on high-throughput sequencing combined with the measurements of multiple environmental parameters in arid and semi-arid steppe. The communities of soil bacteria in root zone had considerable turnover, and some regular variations in structure along the Stipa taxa transition are largely determined by climatic factors, vegetation coverage, and pH at a regional scale. Bacterial communities had a clear Stipa population specificity, but they were more strongly affected by the main annual precipitation, which resulted in a biogeographical distribution pattern along precipitation gradient, among which Actinobacteria, Acidobacteria, Proteobacteria, and Chloroflexi were the phyla that were most abundant. During the transformation of Stipa taxa from east to west, the trend of diversity shown by bacterial community in the root zone decreased first, and then increased sharply at S. breviflora, which was followed by continuous decreasing toward northwest afterwards. However, the richness and evenness showed an opposite trend, and α diversity had close association with altitude and pH. There would be specific and different bacterial taxa interactions in different Stipa species, in which S. krylovii had the simplest and most stable interaction network with the strongest resistance to the environment and S. breviflora had most complex and erratic. Moreover, the bacterial community was mainly affected by dispersal limitation at a certain period. These results are conducive to the prediction of sustainable ecosystem services and protection of microbial resources in a semi-arid grassland ecosystem.
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Affiliation(s)
- Xiaodan Ma
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.,State Key Laboratory of Reproductive Regulatory and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
| | - Lumeng Chao
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.,State Key Laboratory of Reproductive Regulatory and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
| | - Jingpeng Li
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.,State Key Laboratory of Reproductive Regulatory and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
| | - Zhiying Ding
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.,State Key Laboratory of Reproductive Regulatory and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
| | - Siyu Wang
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.,State Key Laboratory of Reproductive Regulatory and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
| | - Fansheng Li
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.,State Key Laboratory of Reproductive Regulatory and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
| | - Yuying Bao
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.,State Key Laboratory of Reproductive Regulatory and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
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Tian L, Chang J, Shi S, Ji L, Zhang J, Sun Y, Li X, Li X, Xie H, Cai Y, Chen D, Wang J, van Veen JA, Kuramae EE, Tran LSP, Tian C. Comparison of methane metabolism in the rhizomicrobiomes of wild and related cultivated rice accessions reveals a strong impact of crop domestication. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 803:150131. [PMID: 34788940 DOI: 10.1016/j.scitotenv.2021.150131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 06/28/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
Microbial communities from rhizosphere (rhizomicrobiomes) have been significantly impacted by domestication as evidenced by a comparison of the rhizomicrobiomes of wild and related cultivated rice accessions. While there have been many published studies focusing on the structure of the rhizomicrobiome, studies comparing the functional traits of the microbial communities in the rhizospheres of wild rice and cultivated rice accessions are not yet available. In this study, we used metagenomic data from experimental rice plots to analyze the potential functional traits of the microbial communities in the rhizospheres of wild rice accessions originated from Africa and Asia in comparison with their related cultivated rice accessions. The functional potential of rhizosphere microbial communities involved in alanine, aspartate and glutamate metabolism, methane metabolism, carbon fixation pathways, citrate cycle (TCA cycle), pyruvate metabolism and lipopolysaccharide biosynthesis pathways were found to be enriched in the rhizomicrobiomes of wild rice accessions. Notably, methane metabolism in the rhizomicrobiomes of wild and cultivated rice accessions clearly differed. Key enzymes involved in methane production and utilization were overrepresented in the rhizomicrobiome samples obtained from wild rice accessions, suggesting that the rhizomicrobiomes of wild rice maintain a different ecological balance for methane production and utilization compared with those of the related cultivated rice accessions. A novel assessment of the impact of rice domestication on the primary metabolic pathways associated with microbial taxa in the rhizomicrobiomes was performed. Results indicated a strong impact of rice domestication on methane metabolism; a process that represents a critical function of the rhizosphere microbial community of rice. The findings of this study provide important information for future breeding of rice varieties with reduced methane emission during cultivation for sustainable agriculture.
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Affiliation(s)
- Lei Tian
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Jingjing Chang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, the Netherlands; Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, the Netherlands
| | - Shaohua Shi
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Li Ji
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianfeng Zhang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Yu Sun
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Xiaojie Li
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Xiujun Li
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Hongwei Xie
- Jiangxi Super-rice Research and Development Center, National Engineering Laboratory for Rice, Nanchang, China
| | - Yaohui Cai
- Jiangxi Super-rice Research and Development Center, National Engineering Laboratory for Rice, Nanchang, China
| | - Dazhou Chen
- Jiangxi Super-rice Research and Development Center, National Engineering Laboratory for Rice, Nanchang, China
| | - Jilin Wang
- Jiangxi Super-rice Research and Development Center, National Engineering Laboratory for Rice, Nanchang, China
| | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, the Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, the Netherlands; Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, the Netherlands.
| | - Lam-Son Phan Tran
- Institute of Research and Development, Duy Tan University, Da Nang 550000, Viet Nam; Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, TX 79409, USA.
| | - Chunjie Tian
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China.
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Bacterial communities in the rhizosphere of biofortified BRS pontal and conventional carioca bean (Phaseolus vulgaris) plants. Arch Microbiol 2021; 204:14. [PMID: 34894275 DOI: 10.1007/s00203-021-02620-z] [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: 10/22/2021] [Revised: 10/22/2021] [Accepted: 11/30/2021] [Indexed: 10/19/2022]
Abstract
The current knowledge of bean plants microbiome is far from being complete. Unraveling the complexity of the bacterial communities within common bean cultivars that may significantly contribute to plant health, growth and protection against soil pathogens, represents a major challenge. In this study, the richness and composition of the bacterial communities from bean plant rhizospheres and control bulk soils were analyzed by high-throughput sequencing and comparative analyses. From the classified sequences, Proteobacteria represented the most abundant phylum (42-66%), followed by Acidobacteria (12-36%) and Actinobacteria (11-18%), Bacterial community structures were different between bulk soil and rhizosphere samples. Comparing the bean cultivars, the biofortified cultivar presented high number of sequences affiliated to the genera Burkholderia and Rhodanobacter. Interestingly, despite the presence of stable and persistent core bacterial taxa associated with the common bean varieties, our analysis suggested that the biofortified common bean cultivar could select and maintain differential abundances of microbial groups in the rhizosphere environment.
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de Almeida JR, Bonatelli ML, Batista BD, Teixeira-Silva NS, Mondin M, Dos Santos RC, Bento JMS, de Almeida Hayashibara CA, Azevedo JL, Quecine MC. Bacillus thuringiensis RZ2MS9, a tropical plant growth-promoting rhizobacterium, colonizes maize endophytically and alters the plant's production of volatile organic compounds during co-inoculation with Azospirillum brasilense Ab-V5. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:812-821. [PMID: 34433236 DOI: 10.1111/1758-2229.13004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
The beneficial features of Bacillus thuringiensis (Bt) are not limited to its role as an insecticide; it is also able to promote plant growth interacting with plants and other plant growth-promoting rhizobacterium (PGPR). The PGPR Bt strain RZ2MS9 is a multi-trait maize growth promoter. We obtained a stable mutant of RZ2MS9 labelled with green fluorescent protein (RZ2MS9-GFP). We demonstrated that the Bt RZ2MS9-GFP successfully colonizes maize's roots and leaves endophytically. We evaluated whether RZ2MS9 has an additive effect on plant growth promotion when co-inoculated with Azospirillum brasilense Ab-V5. The two strains combined enhanced maize's roots and shoots dry weight around 50% and 80%, respectively, when compared to the non-inoculated control. However, non-differences were observed comparing RZ2MS9 alone and when co-inoculated with Ab-V5, In addition, we used co-inoculation experiments in glass chambers to analyse the plant's volatile organic compounds (VOCs) production during the maize-RZ2MS9 and maize-RZ2MS9-Ab-V5 interaction. We found that the single and co-inoculation altered maize's VOCs emission profile, with an increase in the production of indoles in the co-inoculation. Collectively, these results increase our knowledge about the interaction between the Bt and maize, and provide a new possibility of combined application with the commercial inoculant A. brasilense Ab-V5.
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Affiliation(s)
- Jaqueline Raquel de Almeida
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, ESALQ, University of São Paulo, Piracicaba, SP, Brazil
| | - Maria Letícia Bonatelli
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, ESALQ, University of São Paulo, Piracicaba, SP, Brazil
| | - Bruna Durante Batista
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, ESALQ, University of São Paulo, Piracicaba, SP, Brazil
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Natalia Sousa Teixeira-Silva
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, ESALQ, University of São Paulo, Piracicaba, SP, Brazil
| | - Mateus Mondin
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, ESALQ, University of São Paulo, Piracicaba, SP, Brazil
| | - Rafaela Cristina Dos Santos
- Department of Entomology, "Luiz de Queiroz" College of Agriculture, ESALQ, University of São Paulo, Piracicaba, SP, Brazil
| | - José Maurício Simões Bento
- Department of Entomology, "Luiz de Queiroz" College of Agriculture, ESALQ, University of São Paulo, Piracicaba, SP, Brazil
| | | | - João Lúcio Azevedo
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, ESALQ, University of São Paulo, Piracicaba, SP, Brazil
| | - Maria Carolina Quecine
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, ESALQ, University of São Paulo, Piracicaba, SP, Brazil
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Johnston-Monje D, Gutiérrez JP, Lopez-Lavalle LAB. Seed-Transmitted Bacteria and Fungi Dominate Juvenile Plant Microbiomes. Front Microbiol 2021; 12:737616. [PMID: 34745040 PMCID: PMC8569520 DOI: 10.3389/fmicb.2021.737616] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
Plant microbiomes play an important role in agricultural productivity, but there is still much to learn about their provenance, diversity, and organization. In order to study the role of vertical transmission in establishing the bacterial and fungal populations of juvenile plants, we used high-throughput sequencing to survey the microbiomes of seeds, spermospheres, rhizospheres, roots, and shoots of the monocot crops maize (B73), rice (Nipponbare), switchgrass (Alamo), Brachiaria decumbens, wheat, sugarcane, barley, and sorghum; the dicot crops tomato (Heinz 1706), coffee (Geisha), common bean (G19833), cassava, soybean, pea, and sunflower; and the model plants Arabidopsis thaliana (Columbia-0) and Brachypodium distachyon (Bd21). Unsterilized seeds were planted in either sterile sand or farm soil inside hermetically sealed jars, and after as much as 60 days of growth, DNA was extracted to allow for amplicon sequence-based profiling of the bacterial and fungal populations that developed. Seeds of most plants were dominated by Proteobacteria and Ascomycetes, with all containing operational taxonomic units (OTUs) belonging to Pantoea and Enterobacter. All spermospheres also contained DNA belonging to Pseudomonas, Bacillus, and Fusarium. Despite having only seeds as a source of inoculum, all plants grown on sterile sand in sealed jars nevertheless developed rhizospheres, endospheres, and phyllospheres dominated by shared Proteobacteria and diverse fungi. Compared to sterile sand-grown seedlings, growth on soil added new microbial diversity to the plant, especially to rhizospheres; however, all 63 seed-transmitted bacterial OTUs were still present, and the most abundant bacteria (Pantoea, Enterobacter, Pseudomonas, Klebsiella, and Massilia) were the same dominant seed-transmitted microbes observed in sterile sand-grown plants. While most plant mycobiome diversity was observed to come from soil, judging by read abundance, the dominant fungi (Fusarium and Alternaria) were also vertically transmitted. Seed-transmitted fungi and bacteria appear to make up the majority of juvenile crop plant microbial populations by abundance, and based on occupancy, there seems to be a pan-angiosperm seed-transmitted core bacterial microbiome. Further study of these seed-transmitted microbes will be important to understand their role in plant growth and health, as well as their fate during the plant life cycle and may lead to innovations for agricultural inoculant development.
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Affiliation(s)
- David Johnston-Monje
- MaxPlanck Tandem Group in Plant Microbial Ecology, Universidad del Valle, Cali, Colombia.,International Center for Tropical Agriculture, Palmira, Colombia.,Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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Ambardar S, Bhagat N, Vakhlu J, Gowda M. Diversity of Rhizo-Bacteriome of Crocus sativus Grown at Various Geographical Locations and Cataloging of Putative PGPRs. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.644230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Earlier plant growth promoting rhizo-bacteria (PGPRs) were isolated from the plants, by cultivation based techniques and the interaction was mostly thought to be bilateral. The routine bilateral study, with no information on the associated microbiome, could be one of the reasons for the limited success of PGPRs in the field conditions. Keeping in view the role of PGPRs in rhizo-bacteriome on the growth and production of plant, the present study was aimed at studying the diversity of the rhizo-bacteriome of saffron grown across three geographical locations namely Kashmir, Kishtwar and Bengaluru. Variation in the rhizo-bacteriome of saffron growing across 10 different sites from 3 geographical locations was studied using 16S rDNA amplicon metagenomic sequencing. 16 bacterial phyla, 261 genera and 73 bacterial species were cataloged from all the rhizosphere samples. Proteobacteria was a dominant phylum in all the rhizosphere samples. Rhizo-bacteriome of saffron grown in Kishtwar was found to be significantly different from the rhizo-bacteriome of saffron grown in Kashmir and Bengaluru. Interestingly, the rhizo-bacteriome of saffron grown in Bengaluru was very similar to the saffron grown in Kashmir, thereby indicating that the rhizo-bacteriome in saffron is “plant driven” as the corm sown in Bengaluru were from Kashmir. Despite variation in rhizo-bacteriome, core rhizo-bacteriome in saffron was identified that was represented by 53 genera and eight bacterial species belonging to 11 phyla irrespective of their geographical distribution. In addition, 21 PGPRs were reported for the first time from the saffron rhizosphere. The high yielding saffron field Wuyan was found to have the highest number of PGPRs; this indicates that the presence of PGPR is important for yield enhancement than diversity. The two PGPR Rhizobium leguminosarum and Luteibacter rhizovicinus were reported from all the locations except Kishtwar that had escaped isolation in our previous attempts using cultivation based techniques. It is being proposed instead of going for random isolation and screening for PGPRs from plant rhizosphere, an alternate strategy using metagenomic cataloging of the rhizo-bacteriome community and cultivation of the dominant PGPR should be undertaken. This strategy will help in the selection of dominant PGPRs, specific to the plant in question.
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Zhang Z, Li J, Zhang Z, Liu Y, Wei Y. Tomato Endophytic Bacteria Composition and Mechanism of Suppressiveness of Wilt Disease ( Fusarium oxysporum). Front Microbiol 2021; 12:731764. [PMID: 34721330 PMCID: PMC8555416 DOI: 10.3389/fmicb.2021.731764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/16/2021] [Indexed: 11/13/2022] Open
Abstract
Tomato wilt disease, caused by the Fusarium oxysporum is an ever-increasing threat for agricultural production, and unreasonable fertilization and pesticide abuse caused environmental challenge. Increasing evidence suggested that microbiomes or those associated with crops, played key roles on plant health. Plant disease dynamics were affected by multiple biotic and abiotic factors including phytopathogen population density, the genetic type of the pathogen and the host, in particular, the composition and assembly of the host-associated microbiome. However, it was unclear how pathogen invasion interaction and correlate with endophytic bacterial communities in natural field conditions. To study this, we sampled temporally the tomato plants that were exposed to F. oxysporum invasions over one crop season. High-throughput sequencing were performed to explore the correlation between agricultural practice, pathogen invasion, and endophytic microbiota communities. Results showed that pathogen invasion had clear effect on the endophytic and a strong link between increased pathogen densities and reduced abundance of Bacillus sp., which are crucial taxonomy for suppressiveness to F. oxysporum in vitro and in greenhouse condition. In summary, monitoring the dynamics of endophytic bacteria communities and densities of pathogen could thus open new avenue for more accurate disease diagnostics and high-efficiency screening antagonisms methods in the future, and our results will broaden the agricultural view of beneficial microbiota as biological control agents against plant pathogen.
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Affiliation(s)
- Zeyu Zhang
- College of Resources and Environmental Science, China Agricultural University, Beijing, China
| | - Ji Li
- College of Resources and Environmental Science, China Agricultural University, Beijing, China
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Xianyang, China
| | - Youzhou Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences (JAAS), Nanjing, China
| | - Yuquan Wei
- College of Resources and Environmental Science, China Agricultural University, Beijing, China
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Liu S, Khan MH, Yuan Z, Hussain S, Cao H, Liu Y. Response of soil microbiome structure and its network profiles to four soil amendments in monocropping strawberry greenhouse. PLoS One 2021; 16:e0245180. [PMID: 34587178 PMCID: PMC8480769 DOI: 10.1371/journal.pone.0245180] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 09/01/2021] [Indexed: 01/03/2023] Open
Abstract
With the constant surge of strawberry cultivation and human demand, widespread concern has been expressed about the severe soil and plant health problems caused by continuous strawberry cropping, particularly monocropping in greenhouses. Effective microorganisms (EM) and Bacillus subtilis (BS) have been extensively commercialized as biological control agents (BCAs) to promote plant growth and yield enhancement. However, their effects on soil microbes are obscure. To regulate the microbial community in continuous cropping strawberry soils, we developed four soil amendments based on these two BCAs by adding low and high contents of compost. The amplicon sequencing of bacterial and fungal ribosomal markers was applied to study the response of the soil microbiome structure. We noticed a sharp increase in bacterial diversity after adding EM-treated high compost and BS-treated low compost, while there was no significant change in fungal diversity among treatments. Through taxonomic classification and FUNGuild analysis, we found that the application of soil amendments resulted in a significant decline in the relative abundance of fungal plant pathogens (Rhizopus, Penicillium and Fusarium) in the soils; accordingly, the metabolic functions of a range of detrimental fungi were inhibited. Correlation analysis indicated that soil microbial community was indirectly driven by soil physicochemical properties. Co-occurrence networks revealed that soil amendments contributed to the connectivity of bacterial network, and EM-treated with high compost was the most complex and balanced. Collectively, EM-treated high compost and BS-treated low compost can well regulate the microbial community structure and thus maintain soil health.
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Affiliation(s)
- Senlin Liu
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, Nanjing Agricultural University, Nanjing, P. R. China
| | - Muzammil Hassan Khan
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, Nanjing Agricultural University, Nanjing, P. R. China
| | - Zhongyuan Yuan
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, Nanjing Agricultural University, Nanjing, P. R. China
| | - Sarfraz Hussain
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, Nanjing Agricultural University, Nanjing, P. R. China
| | - Hui Cao
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, Nanjing Agricultural University, Nanjing, P. R. China
- * E-mail: (HC); (YL)
| | - Yabo Liu
- Zhenjiang Institute of Agricultural Sciences, Jurong, China
- * E-mail: (HC); (YL)
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