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Nag M, Pallavi J, Chakraborty S, Roychoudhury T, Mondal S, Ghosh A, Saha C, Banerjee M, Seal A. Bacterial endosymbionts of a nitrogen-fixing yeast Rhodotorula mucilaginosa JGTA-S1 - insights into a yet unknown micro-ecosystem. Mol Omics 2024. [PMID: 39263696 DOI: 10.1039/d3mo00273j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Rhodotorula mucilaginosa JGTA-S1 is a yeast strain capable of fixing nitrogen and improving nitrogen nutrition in rice plants because of its nitrogen-fixing endobacteria, namely Stutzerimonas (Pseudomonas) stutzeri and Bradyrhizobium sp. To gain a deeper understanding of yeast endosymbionts, we conducted a whole-genome shotgun metagenomic analysis of JGTA-S1 cells grown under conditions of nitrogen sufficiency and deficiency. Our results showed that the endosymbiont population varied depending on the nitrogen regime. Upon mechanical disruption of yeast cells, we obtained endosymbionts in culturable form viz. Bacillus velezensis and Staphylococcus sp. under nitrogen-replete conditions and Lysinibacillus telephonicus., Brevibacillus sp., and Niallia circulans under nitrogen-depleted conditions. S. stutzeri and Bradyrhizobium sp. the previously reported endosymbionts remained unculturable. The culturable endosymbionts Staphylococcus sp. and Bacillus velezensis appear to possess genes for dissimilatory nitrate reduction (DNRA), an alternative pathway for ammonia synthesis. However, our findings suggest that these endosymbionts are facultative as they survive outside the host. The fitness of the yeast was not affected by curing of these microbes. Curing the yeast diazotrophic endosymbionts took a toll on its fitness. Our results also showed that the populations of S. stutzeri and B. velezensis increased significantly under nitrogen-depleted conditions compared to nitrogen-sufficient conditions. The importance of DNRA and nitrogen fixation is also reflected in the metagenomic reads of JGTA-S1.
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Affiliation(s)
- Mayurakshi Nag
- Department of Biotechnology and Dr B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata - 700019, India.
| | - Janardhan Pallavi
- Center for Innovation in Molecular and Pharmaceutical Sciences (CIMPS), Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India
| | - Sandipan Chakraborty
- Center for Innovation in Molecular and Pharmaceutical Sciences (CIMPS), Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India
| | - Trina Roychoudhury
- Department of Biotechnology and Dr B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata - 700019, India.
| | - Sangita Mondal
- Department of Biological Sciences Bose Institute, Unified Academic Campus, EN 80. Sector V, Bidhan Nagar, Kolkata - 700091, India
| | - Abhrajyoti Ghosh
- Department of Biological Sciences Bose Institute, Unified Academic Campus, EN 80. Sector V, Bidhan Nagar, Kolkata - 700091, India
| | - Chinmay Saha
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Manidipa Banerjee
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Anindita Seal
- Department of Biotechnology and Dr B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata - 700019, India.
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Nag M, Seal A. Draft genome announcement of Bacillus velezensis TSB6.1 isolated as a culturable endosymbiont of a nitrogen-fixing endophytic yeast Rhodotorula mucilaginosa JGTA-S1. Microbiol Resour Announc 2024; 13:e0120223. [PMID: 38864644 PMCID: PMC11256793 DOI: 10.1128/mra.01202-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 05/09/2024] [Indexed: 06/13/2024] Open
Abstract
We here report the genome of Bacillus velezensis TSB6.1 isolated as a culturable endosymbiont of an endophytic yeast Rhodotorula mucilaginosa JGTA-S1. TSB6.1 has a genome size of approximately 4.50 Mb, with 4,597 genes, 45.54% GC content, 3 rRNAs, and 73 tRNAs.
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Affiliation(s)
- Mayurakshi Nag
- Department of Biotechnology and Dr B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, West Bengal, India
| | - Anindita Seal
- Department of Biotechnology and Dr B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, West Bengal, India
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Vighnesh L, Jagadeeshwari U, Sasikala C, Venkata Ramana C. Metagenome-assembled genome of Zalaria obscura strain JY119. Microbiol Resour Announc 2024; 13:e0078623. [PMID: 38682769 PMCID: PMC11237627 DOI: 10.1128/mra.00786-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 04/09/2024] [Indexed: 05/01/2024] Open
Abstract
Here, we report a 22.1-Mbp genome sequence of microcolonial fungi, Zalaria obscura, isolated from a pine tree bark. The microbiome of the new fungi is predicted to be largely associated with Acidobacteriota. The genome sequence of Zalaria obscura will help us in understanding the unusual relationship with Acidobacteriota member(s).
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Affiliation(s)
- Lakshmanan Vighnesh
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Uppada Jagadeeshwari
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
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Zheng H, Chen T, Li W, Hong J, Xu J, Yu Z. Endosymbiotic bacteria within the nematode-trapping fungus Arthrobotrys musiformis and their potential roles in nitrogen cycling. Front Microbiol 2024; 15:1349447. [PMID: 38348183 PMCID: PMC10860758 DOI: 10.3389/fmicb.2024.1349447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/10/2024] [Indexed: 02/15/2024] Open
Abstract
Endosymbiotic bacteria (ESB) have important effects on their hosts, contributing to its growth, reproduction and biological functions. Although the effects of exogenous bacteria on the trap formation of nematode-trapping fungi (NTF) have been revealed, the effects of ESB on NTF remain unknown. In this study, we investigated the species diversity of ESB in the NTF Arthrobotrys musiformis using high-throughput sequencing and culture-dependent approaches, and compared bacterial profiles to assess the effects of strain source and culture media on A. musiformis. PICRUSt2 and FAPROTAX were used to predict bacterial function. Our study revealed that bacterial communities in A. musiformis displayed high diversity and heterogeneity, with Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria as the dominant phyla. The ESB between A. musiformis groups isolated from different habitats and cultured in the same medium were more similar to each other than the other groups isolated from the same habitat but cultured in different media. Function analysis predicted a broad and diverse functional repertoire of ESB in A. musiformis, and unveiled that ESB have the potential to function in five modules of the nitrogen metabolism. We isolated nitrogen-fixing and denitrifying bacteria from the ESB and demonstrated their effects on trap formation of A. musiformis. Among seven bacteria that we tested, three bacterial species Bacillus licheniformis, Achromobacter xylosoxidans and Stenotrophomonas maltophilia were found to be efficient in inducing trap formation. In conclusion, this study revealed extensive ESB diversity within NTF and demonstrated that these bacteria likely play important roles in nitrogen cycling, including nematode trap formation.
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Affiliation(s)
- Hua Zheng
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Tong Chen
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Wenjie Li
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Jianan Hong
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Zefen Yu
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, China
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Cappelli A, Damiani C, Capone A, Bozic J, Mensah P, Clementi E, Spaccapelo R, Favia G, Ricci I. Tripartite interactions comprising yeast-endobacteria systems in the gut of vector mosquitoes. Front Microbiol 2023; 14:1157299. [PMID: 37396392 PMCID: PMC10311912 DOI: 10.3389/fmicb.2023.1157299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
It is shown that bacteria use yeast as a niche for survival in stressful conditions, therefore yeasts may act as temporary or permanent bacterial reservoirs. Endobacteria colonise the fungal vacuole of various osmotolerant yeasts which survive and multiply in sugar-rich sources such as plant nectars. Nectar-associated yeasts are present even in the digestive system of insects and often establish mutualistic symbioses with both hosts. Research on insect microbial symbioses is increasing but bacterial-fungal interactions are yet unexplored. Here, we have focused on the endobacteria of Wickerhamomyces anomalus (formerly Pichia anomala and Candida pelliculosa), an osmotolerant yeast associated with sugar sources and the insect gut. Symbiotic strains of W. anomalus influence larval development and contribute digestive processes in adults, in addition to exerting wide antimicrobial properties for host defence in diverse insects including mosquitoes. Antiplasmodial effects of W. anomalus have been shown in the gut of the female malaria vector mosquito Anopheles stephensi. This discovery highlights the potential of utilizing yeast as a promising tool for symbiotic control of mosquito-borne diseases. In the present study, we have carried out a large Next Generation Sequencing (NGS) metagenomics analysis including W. anomalus strains associated with vector mosquitoes Anopheles, Aedes and Culex, which has highlighted wide and heterogeneous EB communities in yeast. Furthermore, we have disclosed a Matryoshka-like association in the gut of A stephensi that comprises different EB in the strain of W. anomalus WaF17.12. Our investigations started with the localization of fast-moving bacteria-like bodies within the yeast vacuole of WaF17.12. Additional microscopy analyses have validated the presence of alive intravacuolar bacteria and 16S rDNA libraries from WaF17.12 have identified a few bacterial targets. Some of these EB have been isolated and tested for lytic properties and capability to re-infect the yeast cell. Moreover, a selective competence to enter yeast cell has been shown comparing different bacteria. We suggested possible tripartite interactions among EB, W. anomalus and the host, opening new knowledge on the vector biology.
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Affiliation(s)
- Alessia Cappelli
- School of Biosciences and Veterinary Medicine, University of Camerino, CIRM Italian Malaria Network, Camerino, Italy
| | - Claudia Damiani
- School of Biosciences and Veterinary Medicine, University of Camerino, CIRM Italian Malaria Network, Camerino, Italy
| | - Aida Capone
- School of Biosciences and Veterinary Medicine, University of Camerino, CIRM Italian Malaria Network, Camerino, Italy
| | - Jovana Bozic
- Center for Infectious Disease Dynamics and Huck Institutes of the Life Sciences, Department of Entomology, Penn State University, University Park, PA, United States
| | - Priscilla Mensah
- School of Biosciences and Veterinary Medicine, University of Camerino, CIRM Italian Malaria Network, Camerino, Italy
| | - Emanuela Clementi
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Roberta Spaccapelo
- Department of Medicine and Surgery, University of Perugia, CIRM Italian Malaria Network, Functional Genomic Center (C.U.R.Ge.F), Perugia, Italy
| | - Guido Favia
- School of Biosciences and Veterinary Medicine, University of Camerino, CIRM Italian Malaria Network, Camerino, Italy
| | - Irene Ricci
- School of Biosciences and Veterinary Medicine, University of Camerino, CIRM Italian Malaria Network, Camerino, Italy
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