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Vishal V, Das T, Lal S, Rahaman S. Endophytic bacterial diversity in the latex-bearing caulosphere of Hevea brasiliensis Müll. Arg. Braz J Microbiol 2024; 55:2473-2481. [PMID: 38789907 PMCID: PMC11405552 DOI: 10.1007/s42770-024-01373-3] [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: 05/29/2023] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
Rubber trees are a commercial cash crop, and the milky latex or polyisoprene they produce is the natural source of rubber. Little is known about the bacterial populations found in active zone of latex-bearing caulosphere. We employed a tailored cloud microbial bioinformatic approach for the identification and potential hypothetical ecological roles of an uncultured endophytic hidden bacterial community in the active zone of the latex-bearing caulosphere of Hevea brasiliensis. Small pieces of slivers were collected from healthy plant from the village: Belonia, South Tripura, rubber plantation in Northeastern India. These uncultured bacteria were identified using the V3-V4 hypervariable amplicon region of the 16 S rDNA gene. A total of 209,586 contigs have been generated. EasyMAP Version 1.0, a cloud-based microbial bioinformatics tool with an integrated QIIME2 pipeline, was used to analyze contigs. We detected 15 phyla and 91 OTUs (operational taxonomic units). Proteobacteria (73.5%) was the most enriched phylum, followed by Firmicutes (13.8%), Bacteroidetes (5.2%), and Actinobacteria (3.2%). Ammonia oxidizers, sulfate reducers, dehalogenation, chitin degradation, nitrite reducers, and aromatic hydrocarbon degraders were the most prevalent functional categories in the active zones of caulosphere. Furthermore, Gammaproteobacteria (49.2%) and Erwinia (29.19%) were the most abundant classes and genera of endophytic bacterial communities. Thus, the presence of a substantial amount of phosphate-solubilizing Gammaproteobacteria (PSB) may stimulate growth, increase plant resilience, suppress disease, and aid in the rubber and sugar breakdown. This is the first report of microbial endophytes associated with Hevea caulosphere.
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Affiliation(s)
- Vineet Vishal
- Department of Botany, Bangabasi Evening College, Kolkata, West Bengal, 700009, India
- Department of Botany, Dr. Shyama Prasad Mukherjee University, Ranchi, Jharkhand, 834008, India
| | - Tandra Das
- Department of Botany, Narasinha Dutta College, Howrah, West Bengal, 711101, India
| | - Shalini Lal
- Department of Botany, Dr. Shyama Prasad Mukherjee University, Ranchi, Jharkhand, 834008, India
| | - Sabdar Rahaman
- Department of Botany, Bangabasi Evening College, Kolkata, West Bengal, 700009, India.
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Fang Y, Xiao X, Lin J, Lin Q, Wang J, Liu K, Li Z, Xing J, Liu Z, Wang B, Qi Y, Long X, Zeng X, Hu Y, Qi J, Qin Y, Yang J, Zhang Y, Zhang S, Ye D, Zhang J, Liu J, Tang C. Pan-genome and phylogenomic analyses highlight Hevea species delineation and rubber trait evolution. Nat Commun 2024; 15:7232. [PMID: 39174505 PMCID: PMC11341782 DOI: 10.1038/s41467-024-51031-3] [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: 11/30/2023] [Accepted: 07/28/2024] [Indexed: 08/24/2024] Open
Abstract
The para rubber tree (Hevea brasiliensis) is the world's sole commercial source of natural rubber, a vital industrial raw material. However, the narrow genetic diversity of this crop poses challenges for rubber breeding. Here, we generate high-quality de novo genome assemblies for three H. brasiliensis cultivars, two H. brasiliensis wild accessions, and three other Hevea species (H. nitida, H. pauciflora, and H. benthamiana). Through analyzing genomes of 94 Hevea accessions, we identify five distinct lineages that do not align with their previous species delineations. We discover multiple accessions with hybrid origins between these lineages, indicating incomplete reproductive isolation between them. Only two out of four wild lineages have been introduced to commercial rubber cultivars. Furthermore, we reveal that the rubber production traits emerged following the development of a large REF/SRPP gene cluster and its functional specialization in rubber-producing laticifers within this genus. These findings would enhance rubber breeding and benefit research communities.
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Affiliation(s)
- Yongjun Fang
- National Key Laboratory for Tropical Crop Breeding, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, China
| | - Xiaohu Xiao
- National Key Laboratory for Tropical Crop Breeding, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, China
| | - Jishan Lin
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China
| | - Qiang Lin
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jiang Wang
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China
- Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC, Haikou, China
| | - Kaiye Liu
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China
- Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC, Haikou, China
| | - Zhonghua Li
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China
- Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC, Haikou, China
| | - Jianfeng Xing
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China
| | - Zhenglin Liu
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China
| | - Baiyu Wang
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Yiying Qi
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiangyu Long
- National Key Laboratory for Tropical Crop Breeding, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, China
| | - Xia Zeng
- National Key Laboratory for Tropical Crop Breeding, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, China
| | - Yanshi Hu
- National Key Laboratory for Tropical Crop Breeding, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, China
| | - Jiyan Qi
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China
- Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC, Haikou, China
| | - Yunxia Qin
- National Key Laboratory for Tropical Crop Breeding, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, China
| | - Jianghua Yang
- National Key Laboratory for Tropical Crop Breeding, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, China
| | - Yi Zhang
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China
- Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC, Haikou, China
| | - Shengmin Zhang
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China
- Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC, Haikou, China
| | - De Ye
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China
- Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC, Haikou, China
| | - Jisen Zhang
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, China.
| | - Chaorong Tang
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, China.
- Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC, Haikou, China.
- Yunnan Institute of Tropical Crops, Xishuangbanna, China.
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Malacrinò A, Bennett AE. Soil microbiota and herbivory drive the assembly of tomato plant-associated microbial communities through different mechanisms. Commun Biol 2024; 7:564. [PMID: 38740889 DOI: 10.1038/s42003-024-06259-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/26/2024] [Indexed: 05/16/2024] Open
Abstract
Plant-associated microbial communities are key to shaping many aspects of plant biology. In this study, we tested whether soil microbial communities and herbivory influence the bacterial community of tomato plants and whether their influence in different plant compartments is driven by microbial spillover between compartments or whether plants are involved in mediating this effect. We grew our plants in soils hosting three different microbial communities and covered (or not) the soil surface to prevent (or allow) passive microbial spillover between compartments, and we exposed them (or not) to herbivory by Manduca sexta. Here we show that the soil-driven effect on aboveground compartments is consistently detected regardless of soil coverage, whereas soil cover influences the herbivore-driven effect on belowground microbiota. Together, our results suggest that the soil microbiota influences aboveground plant and insect microbial communities via changes in plant metabolism and physiology or by sharing microorganisms via xylem sap. In contrast, herbivores influence the belowground plant microbiota via a combination of microbial spillover and changes in plant metabolism. These results demonstrate the important role of plants in linking aboveground and belowground microbiota, and can foster further research on soil microbiota manipulation for sustainable pest management.
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Affiliation(s)
- Antonino Malacrinò
- Dept. of Agriculture, Università degli Studi Mediterranea di Reggio Calabria, Reggio Calabria, Italy.
| | - Alison E Bennett
- Dept. of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
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Malacrinò A, Böttner L, Nouere S, Huber M, Schäfer M, Xu S. Induced responses contribute to rapid adaptation of Spirodela polyrhiza to herbivory by Lymnaea stagnalis. Commun Biol 2024; 7:81. [PMID: 38200287 PMCID: PMC10781955 DOI: 10.1038/s42003-023-05706-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
Herbivory-induced responses in plants are typical examples of phenotypic plasticity, and their evolution is thought to be driven by herbivory. However, direct evidence of the role of induced responses in plant adaptive evolution to herbivores is scarce. Here, we experimentally evolve populations of an aquatic plant (Spirodela polyrhiza, giant duckweed) and its native herbivore (Lymnaea stagnalis, freshwater snail), testing whether herbivory drives rapid adaptive evolution in plant populations using a combination of bioassays, pool-sequencing, metabolite analyses, and amplicon metagenomics. We show that snail herbivory drove rapid phenotypic changes, increased herbivory resistance, and altered genotype frequencies in the plant populations. Additional bioassays suggest that evolutionary changes of induced responses contributed to the rapid increase of plant resistance to herbivory. This study provides direct evidence that herbivory-induced responses in plants can be subjected to selection and have an adaptive role by increasing resistance to herbivores.
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Affiliation(s)
- Antonino Malacrinò
- Department of Agriculture, Università degli Studi Mediterranea di Reggio Calabria, Reggio Calabria, Italy.
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.
| | - Laura Böttner
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Institute for Plant Biology and Biotechnology, University of Münster, Münster, Germany
| | - Sara Nouere
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Meret Huber
- Institute for Plant Biology and Biotechnology, University of Münster, Münster, Germany
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Martin Schäfer
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Shuqing Xu
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany.
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