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Pawlowska TE. Symbioses between fungi and bacteria: from mechanisms to impacts on biodiversity. Curr Opin Microbiol 2024; 80:102496. [PMID: 38875733 DOI: 10.1016/j.mib.2024.102496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 05/20/2024] [Accepted: 05/31/2024] [Indexed: 06/16/2024]
Abstract
Symbiotic interactions between fungi and bacteria range from positive to negative. They are ubiquitous in free-living as well as host-associated microbial communities worldwide. Yet, the impact of fungal-bacterial symbioses on the organization and dynamics of microbial communities is uncertain. There are two reasons for this uncertainty: (1) knowledge gaps in the understanding of the genetic mechanisms underpinning fungal-bacterial symbioses and (2) prevailing interpretations of ecological theory that favor antagonistic interactions as drivers stabilizing biological communities despite the existence of models emphasizing contributions of positive interactions. This review synthesizes information on fungal-bacterial symbioses common in the free-living microbial communities of the soil as well as in host-associated polymicrobial biofilms. The interdomain partnerships are considered in the context of the relevant community ecology models, which are discussed critically.
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Affiliation(s)
- Teresa E Pawlowska
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
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Wang Y, Zhang Y, Yang Z, Fei J, Zhou X, Rong X, Peng J, Luo G. Intercropping improves maize yield and nitrogen uptake by regulating nitrogen transformation and functional microbial abundance in rhizosphere soil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 358:120886. [PMID: 38648726 DOI: 10.1016/j.jenvman.2024.120886] [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: 09/17/2023] [Revised: 04/03/2024] [Accepted: 04/10/2024] [Indexed: 04/25/2024]
Abstract
Intercropping-driven changes in nitrogen (N)-acquiring microbial genomes and functional expression regulate soil N availability and plant N uptake. However, present data seem to be limited to a specific community, obscuring the viewpoint of entire N-acquiring microbiomes and functions. Taking maize intercropped with legumes (peanut and soybean) and non-legumes (gingelly and sweet potato) as models, we studied the effects of intercropping on N transformations and N-acquiring microbiomes in rhizosphere soil across four maize growth stages. Meanwhile, we compiled promising strategies such as random forest analysis and structural equation model for the exploitation of the associations between microbe-driven N dynamics and soil-plant N trade-offs and maize productivity. Compared with monoculture, maize intercropping significantly increased the denitrification rate of rhizosphere soils across four maize growth stages, net N mineralization in the elongation and flowering stages, and the nitrification rate in the seedling and mature stages. The abundance of most N-acquiring microbial populations was influenced significantly by intercropping patterns and maize growth stages. Soil available N components (NH4+-N, NO3--N, and dissolved organic N content) showed a highly direct effect on plant N uptake, which mainly mediated by N transformations (denitrification rate) and N-acquiring populations (amoB, nirK3, and hzsB genes). Overall, the adaptation of N-acquiring microbiomes to changing rhizosphere micro-environments caused by intercropping patterns and maize development could promote soil N transformations and dynamics to meet demand of maize for N nutrient. This would offer another unique perspective to manage the benefits of the highly N-effective and production-effective intercropping ecosystems.
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Affiliation(s)
- Yizhe Wang
- College of Resources, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China
| | - Yuping Zhang
- College of Resources, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China.
| | - Ziyu Yang
- College of Resources, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China
| | - Jiangchi Fei
- College of Resources, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China.
| | - Xuan Zhou
- Institute of Soil and Fertilizer, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Xiangmin Rong
- College of Resources, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
| | - Jianwei Peng
- College of Resources, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
| | - Gongwen Luo
- College of Resources, Hunan Agricultural University, Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China.
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Zhang P, Huguet-Tapia J, Peng Z, Liu S, Obasa K, Block AK, White FF. Genome analysis and hyphal movement characterization of the hitchhiker endohyphal Enterobacter sp. from Rhizoctonia solani. Appl Environ Microbiol 2024; 90:e0224523. [PMID: 38319098 PMCID: PMC10952491 DOI: 10.1128/aem.02245-23] [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: 12/21/2023] [Accepted: 01/05/2024] [Indexed: 02/07/2024] Open
Abstract
Bacterial-fungal interactions are pervasive in the rhizosphere. While an increasing number of endohyphal bacteria have been identified, little is known about their ecology and impact on the associated fungal hosts and the surrounding environment. In this study, we characterized the genome of an Enterobacter sp. Crenshaw (En-Cren), which was isolated from the generalist fungal pathogen Rhizoctonia solani, and examined the genetic potential of the bacterium with regard to the phenotypic traits associated with the fungus. Overall, the En-Cren genome size was typical for members of the genus and was capable of free-living growth. The genome was 4.6 MB in size, and no plasmids were detected. Several prophage regions and genomic islands were identified that harbor unique genes in comparison with phylogenetically closely related Enterobacter spp. Type VI secretion system and cyanate assimilation genes were identified from the bacterium, while some common heavy metal resistance genes were absent. En-Cren contains the key genes for indole-3-acetic acid (IAA) and phenylacetic acid (PAA) biosynthesis, and produces IAA and PAA in vitro, which may impact the ecology or pathogenicity of the fungal pathogen in vivo. En-Cren was observed to move along hyphae of R. solani and on other basidiomycetes and ascomycetes in culture. The bacterial flagellum is essential for hyphal movement, while other pathways and genes may also be involved.IMPORTANCEThe genome characterization and comparative genomics analysis of Enterobacter sp. Crenshaw provided the foundation and resources for a better understanding of the ecology and evolution of this endohyphal bacteria in the rhizosphere. The ability to produce indole-3-acetic acid and phenylacetic acid may provide new angles to study the impact of phytohormones during the plant-pathogen interactions. The hitchhiking behavior of the bacterium on a diverse group of fungi, while inhibiting the growth of some others, revealed new areas of bacterial-fungal signaling and interaction, which have yet to be explored.
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Affiliation(s)
- Peiqi Zhang
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Jose Huguet-Tapia
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Zhao Peng
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- College of Plant Protection, Jilin Agricultural University, Changchun, Jilin, China
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA
| | - Ken Obasa
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- High Plains Plant Disease Diagnostic Lab, Texas A&M AgriLife Extension Service, Amarillo, Texas, USA
| | - Anna K. Block
- Chemistry Research Unit, US Department of Agriculture-Agricultural Research Service, Gainesville, Florida, USA
| | - Frank F. White
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
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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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Liang P, Jiang J, Sun Z, Li Y, Yang C, Zhou Y. Klebsiella michiganensis: a nitrogen-fixing endohyphal bacterium from Ustilago maydis. AMB Express 2023; 13:146. [PMID: 38112810 PMCID: PMC10730499 DOI: 10.1186/s13568-023-01618-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 10/03/2023] [Indexed: 12/21/2023] Open
Abstract
Ustilago maydis is a pathogenic fungus in Basidiomycota causing corn smut disease. A strain of U. maydis YZZF202006 was isolated from the tumor of corn smut collected from Jingzhou city in China. The intracellular bacteria were confirmed inner hyphal of the strain YZZF202006 by PCR amplification and fluorescence in situ hybridization (FISH) and SYTO-9. An endohyphal bacterium YZUMF202001 was isolated from the protoplasts of the strain YZZF202006. It was gram-negative, short rod-shaped with smooth light yellow colony. The endohyphal bacterium was genomic evidenced as Klebsiella michiganensis on the basis of average nucleotide identity (ANI) analysis and the phylogram. Then K. michiganensis was GFP-Labeled and reintroduced into U. maydis, which confirmed the bacterium can live in hyphae of U.maydis. The bacterium can grow on N-free culture media. Its nitrogenase activity was reached av. 646.25 ± 38.61 nmol·mL- 1·h- 1 C2H4 by acetylene reduction assay. A cluster of nitrogen fixation genes (nifJHDKTXENXUSVWZMFLABQ) was found from its genome. The endohyphal K. michiganensis may play an important role to help nitrogen fixation for fungi in the future.
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Affiliation(s)
- Pengyu Liang
- Department of Plant Protection, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Jianwei Jiang
- Department of Plant Protection, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Zhengxiang Sun
- Department of Plant Protection, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Yanyan Li
- Tobacco Research Institute of Hubei Province, Wuhan, 430000, China
| | - Chunlei Yang
- Tobacco Research Institute of Hubei Province, Wuhan, 430000, China.
| | - Yi Zhou
- Department of Plant Protection, College of Agriculture, Yangtze University, Jingzhou, 434025, China.
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Li Y, Lei S, Cheng Z, Jin L, Zhang T, Liang LM, Cheng L, Zhang Q, Xu X, Lan C, Lu C, Mo M, Zhang KQ, Xu J, Tian B. Microbiota and functional analyses of nitrogen-fixing bacteria in root-knot nematode parasitism of plants. MICROBIOME 2023; 11:48. [PMID: 36895023 PMCID: PMC9999639 DOI: 10.1186/s40168-023-01484-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Root-knot nematodes (RKN) are among the most important root-damaging plant-parasitic nematodes, causing severe crop losses worldwide. The plant rhizosphere and root endosphere contain rich and diverse bacterial communities. However, little is known about how RKN and root bacteria interact to impact parasitism and plant health. Determining the keystone microbial taxa and their functional contributions to plant health and RKN development is important for understanding RKN parasitism and developing efficient biological control strategies in agriculture. RESULTS The analyses of rhizosphere and root endosphere microbiota of plants with and without RKN showed that host species, developmental stage, ecological niche, and nematode parasitism, as well as most of their interactions, contributed significantly to variations in root-associated microbiota. Compared with healthy tomato plants at different developmental stages, significant enrichments of bacteria belonging to Rhizobiales, Betaproteobacteriales, and Rhodobacterales were observed in the endophytic microbiota of nematode-parasitized root samples. Functional pathways related to bacterial pathogenesis and biological nitrogen fixation were significantly enriched in nematode-parasitized plants. In addition, we observed significant enrichments of the nifH gene and NifH protein, the key gene/enzyme involved in biological nitrogen fixation, within nematode-parasitized roots, consistent with a potential functional contribution of nitrogen-fixing bacteria to nematode parasitism. Data from a further assay showed that soil nitrogen amendment could reduce both endophytic nitrogen-fixing bacteria and RKN prevalence and galling in tomato plants. CONCLUSIONS Results demonstrated that (1) community variation and assembly of root endophytic microbiota were significantly affected by RKN parasitism; (2) a taxonomic and functional association was found for endophytic nitrogen-fixing bacteria and nematode parasitism; and (3) the change of nitrogen-fixing bacterial communities through the addition of nitrogen fertilizers could affect the occurrence of RKN. Our results provide new insights into interactions among endophytic microbiota, RKN, and plants, contributing to the potential development of novel management strategies against RKN. Video Abstract.
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Affiliation(s)
- Ye Li
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, 350108, China
| | - Shaonan Lei
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, 350108, China
| | - Zhiqiang Cheng
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, 350108, China
| | - Lingyue Jin
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, 350108, China
| | - Ting Zhang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, 350108, China
| | - Lian-Ming Liang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, China
| | - Linjie Cheng
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, 350108, China
| | - Qinyi Zhang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, 350108, China
| | - Xiaohong Xu
- Library, Fujian Normal University, Fuzhou, 350108, Fujian, China
| | - Canhua Lan
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, 350108, China
| | - Chaojun Lu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, China
| | - Minghe Mo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, China
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON, L8S 4K1, Canada.
| | - Baoyu Tian
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, 350108, China.
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Fang L, Zheng X, Sun Z, Li Y, Deng J, Zhou YI. Characterization of a Plant Growth-Promoting Endohyphal Bacillus subtilis in Fusarium acuminatum from Spiranthes sinensis. Pol J Microbiol 2023; 72:29-37. [PMID: 36929887 DOI: 10.33073/pjm-2023-007] [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: 11/10/2022] [Accepted: 02/03/2023] [Indexed: 03/18/2023] Open
Abstract
Successful seed germination and seedling growth in orchids require an association with mycorrhizal fungi. An endophytic Fusarium fungal strain YZU 172038 exhibiting plant growth-promoting (PGP) ability was isolated from the roots of Spiranthes sinensis (Orchidaceae). The harboring endohyphal bacteria were detected in the hypha by SYTO-9 fluorescent nucleic acid staining, fluorescence in situ hybridization (FISH), and PCR amplification of the 16S rDNA gene's region. Consequently, one endohyphal bacterium (EHB) - a strain YZSR384 was isolated and identified as Bacillus subtilis based on morphology, phylogenetic analysis, and genomic information. The results indicated that the strain YZSR384 could significantly promote the growth of rice roots and shoots similar to its host fungus. Its indole acetic acid (IAA) production reached a maximum of 23.361 μg/ml on the sixth day after inoculation. The genome annotation revealed several genes involved in PGP traits, including the clusters of genes encoding the IAA (trpABCDEFS), the siderophores (entABCE), and the dissolving phosphate (pstABCS and phoABDHPR). As an EHB, B. subtilis was first isolated from endophytic Fusarium acuminatum from S. sinensis.
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Affiliation(s)
- Lan Fang
- 1College of Agriculture, Yangtze University, Jingzhou, China
| | - Xiao Zheng
- 1College of Agriculture, Yangtze University, Jingzhou, China
| | - Zhengxiang Sun
- 1College of Agriculture, Yangtze University, Jingzhou, China
| | - Yanyan Li
- 2Tobacco Research Institute of Hubei Province, Wuhan, China
| | - Jianxin Deng
- 1College of Agriculture, Yangtze University, Jingzhou, China
| | - Y I Zhou
- 1College of Agriculture, Yangtze University, Jingzhou, China
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Ma T, Zhang Y, Yan C, Zhang C. Phenotypic and Genomic Difference among Four Botryosphaeria Pathogens in Chinese Hickory Trunk Canker. J Fungi (Basel) 2023; 9:204. [PMID: 36836318 PMCID: PMC9963396 DOI: 10.3390/jof9020204] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/25/2023] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
Abstract
Botryosphaeria species are amongst the most widespread and important canker and dieback pathogens of trees worldwide, with B. dothidea as one of the most common Botryosphaeria species. However, the information related to the widespread incidence and aggressiveness of B. dothidea among various Botryosphaeria species causing trunk cankers is still poorly investigated. In this study, the metabolic phenotypic diversity and genomic differences of four Chinese hickory canker-related Botryosphaeria pathogens, including B. dothidea, B. qingyuanensis, B. fabicerciana, and B. corticis, were systematically studied to address the competitive fitness of B. dothidea. Large-scale screening of physiologic traits using a phenotypic MicroArray/OmniLog system (PMs) found B. dothidea has a broader spectrum of nitrogen source and greater tolerance toward osmotic pressure (sodium benzoate) and alkali stress among Botryosphaeria species. Moreover, the annotation of B. dothidea species-specific genomic information via a comparative genomics analysis found 143 B. dothidea species-specific genes that not only provides crucial cues in the prediction of B. dothidea species-specific function but also give a basis for the development of a B. dothidea molecular identification method. A species-specific primer set Bd_11F/Bd_11R has been designed based on the sequence of B. dothidea species-specific gene jg11 for the accurate identification of B. dothidea in disease diagnoses. Overall, this study deepens the understanding in the widespread incidence and aggressiveness of B. dothidea among various Botryosphaeria species, providing valuable clues to assist in trunk cankers management.
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Affiliation(s)
| | | | | | - Chuanqing Zhang
- Department of Plant Pathology, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
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Cui P, Kong K, Yao Y, Huang Z, Shi S, Liu P, Huang Y, Abbas N, Yu L, Zhang Y. Community composition, bacterial symbionts, antibacterial and antioxidant activities of honeybee-associated fungi. BMC Microbiol 2022; 22:168. [PMID: 35761187 PMCID: PMC9235140 DOI: 10.1186/s12866-022-02580-4] [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: 03/22/2022] [Accepted: 06/02/2022] [Indexed: 11/25/2022] Open
Abstract
Background Fungi associated with insects represent one potentially rich source for the discovery of novel metabolites. However, a comprehensive understanding of the fungal communities of Apis mellifera ligustica remains elusive. Results Here, we investigated the phylogenetic diversity and community composition of honeybee-associated fungi using combination of culture-dependent and culture-independent approaches. A total of forty-five fungi were isolated and purified from the Apis mellifera ligustica, royal jelly, and honeycomb, which belonged to four classes and eleven different genera. Furthermore, 28 bacterial 16S rRNA gene sequences were obtained by PCR from the fungal metagenome. High-throughput sequencing analyses revealed that the fungal communities were more diverse, a total of 62 fungal genera were detected in the honeybee gut by culture-independent method, whereas only 4 genera were isolated by culture-dependent method. Similarly, 247 fungal genera were detected in the honeycomb, whereas only 4 genera were isolated. In addition, we assessed the antibacterial and antioxidant activities of fungal isolates. Most fungal crude extracts obtained from the cultivation supernatant exhibited antioxidant activities. Only two fungal crude extracts displayed moderate activity against Escherichia coli and Staphylococcus aureus. Chemical analysis of Chaetomium subaffine MFFC22 led to the discovery of three known compounds, including cochliodinol (1), emodin (2), chrysophanol (3). Among them, cochliodinol (1) showed intense DPPH radical scavenging activity with the 50% inhibitory concentration (IC50) of 3.06 μg/mL, which was comparable to that of the positive ascorbic acid (IC50 = 2.25 μg/mL). Compound 2 displayed weak inhibitory activities against Micrococcus tetragenus and S. aureus. Conclusions This research provided a fundamental clue for the complex interactions among honeybees, fungi, bacterial symbionts, and the effects on the honeybee. Furthermore, the diversity of honeybee-associated fungi had great potential in finding the resource of new species and antioxidants. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02580-4.
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Zhou Y, Wang H, Xu S, Liu K, Qi H, Wang M, Chen X, Berg G, Ma Z, Cernava T, Chen Y. Bacterial-fungal interactions under agricultural settings: from physical to chemical interactions. STRESS BIOLOGY 2022; 2:22. [PMID: 37676347 PMCID: PMC10442017 DOI: 10.1007/s44154-022-00046-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/17/2022] [Indexed: 09/08/2023]
Abstract
Bacteria and fungi are dominant members of environmental microbiomes. Various bacterial-fungal interactions (BFIs) and their mutual regulation are important factors for ecosystem functioning and health. Such interactions can be highly dynamic, and often require spatiotemporally resolved assessments to understand the interplay which ranges from antagonism to mutualism. Many of these interactions are still poorly understood, especially in terms of the underlying chemical and molecular interplay, which is crucial for inter-kingdom communication and interference. BFIs are highly relevant under agricultural settings; they can be determinative for crop health. Advancing our knowledge related to mechanisms underpinning the interactions between bacteria and fungi will provide an extended basis for biological control of pests and pathogens in agriculture. Moreover, it will facilitate a better understanding of complex microbial community networks that commonly occur in nature. This will allow us to determine factors that are crucial for community assembly under different environmental conditions and pave the way for constructing synthetic communities for various biotechnological applications. Here, we summarize the current advances in the field of BFIs with an emphasis on agriculture.
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Affiliation(s)
- Yaqi Zhou
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Hongkai Wang
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Sunde Xu
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Kai Liu
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Hao Qi
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Mengcen Wang
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Xiaoyulong Chen
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, 550025, China
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, 8010, Graz, Austria
- Leibniz-Institute for Agricultural Engineering and Bioeconomy, Potsdam, Germany
- University of Potsdam, Potsdam, Germany
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, 8010, Graz, Austria.
| | - Yun Chen
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.
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11
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Cheng S, Jiang JW, Tan LT, Deng JX, Liang PY, Su H, Sun ZX, Zhou Y. Plant Growth-Promoting Ability of Mycorrhizal Fusarium Strain KB-3 Enhanced by Its IAA Producing Endohyphal Bacterium, Klebsiella aerogenes. Front Microbiol 2022; 13:855399. [PMID: 35495715 PMCID: PMC9051524 DOI: 10.3389/fmicb.2022.855399] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 03/15/2022] [Indexed: 11/29/2022] Open
Abstract
Fusarium oxysporum KB-3 had been reported as a mycorrhizal fungus of Bletilla striata, which can promote the seed germination and vegetative growth. Endohyphal bacteria were demonstrated in the hyphae of the KB-3 by 16S rDNA PCR amplification and SYTO-9 fluorescent nucleic acid staining. A strain Klebsiella aerogenes KE-1 was isolated and identified based on the multilocus sequence analysis. The endohyphal bacterium was successfully removed from the wild strain KB-3 (KB-3−), and GFP-labeled KE-1 was also transferred to the cured strain KB-3− (KB-3+). The production of indole-3-acetic acid (IAA) in the culturing broths of strains of KE-1, KB-3, KB-3−, and KB-3+ was examined by HPLC. Their IAA productions were estimated using Salkowski colorimetric technique. The highest concentrations of IAA were 76.9 (at 48 h after inoculation), 31.4, 9.6, and 19.4 μg/ml (at 60 h after inoculation), respectively. Similarly, the three fungal cultural broths exhibited plant promoting abilities on the tomato root and stem growth. The results indicated that the ability of mycorrhizal Fusarium strain KB-3 to promote plant growth was enhanced because its endohyphal bacterium, Klebsiella aerogenes KE-1, produced a certain amount of IAA.
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12
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Khanal S, Schroeder L, Nava-Mercado OA, Mendoza H, Perlin MH. Role for nitrate assimilatory genes in virulence of Ustilago maydis. Fungal Biol 2021; 125:764-775. [PMID: 34537172 DOI: 10.1016/j.funbio.2021.04.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 04/14/2021] [Accepted: 04/28/2021] [Indexed: 11/16/2022]
Abstract
Ustilago maydis can utilize nitrate as a sole source of nitrogen. This process is initiated by transporting nitrate from the extracellular environment into the cell by a nitrate transporter and followed by a two-step reduction of nitrate to ammonium via nitrate reductase and nitrite reductase enzymes, respectively. Here, we characterize the genes encoding nitrate transporter, um03849 and nitrite reductase, um03848 in U. maydis based on their roles in mating and virulence. The deletion mutants for um03848, um03849 or both genes were constructed in mating compatible haploid strains 1/2 and 2/9. In addition, CRISPR-Cas9 gene editing technique was used for um03849 gene to create INDEL mutations in U. maydis mating strains. For all the mutants, phenotypes such as growth ability, mating efficiency and pathogenesis were examined. The growth of all the mutants was diminished when grown in a medium with nitrate as the source of nitrogen. Although no clear effects on haploid filamentation or mating were observed for either single mutant, double Δum03848 Δum03849 mutants showed reduction in mating, but increased filamentation on low ammonium, particularly in the 1/2 background. With respect to pathogenesis on the host, all the mutants showed reduced degrees of disease symptoms. Further, when the deletion mutants were paired with wild type of opposite mating-type, reduced virulence was observed, in a manner specific to the genetic background of the mutant's progenitor. This background specific reduction of plant pathogenicity was correlated with differential expression of genes for the mating program in U. maydis.
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Affiliation(s)
- Sunita Khanal
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, USA
| | - Luke Schroeder
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, USA
| | | | - Hector Mendoza
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, USA
| | - Michael H Perlin
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, USA.
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13
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Pérez-Rodríguez F, González-Prieto JM, Vera-Núñez JA, Ruiz-Medrano R, Peña-Cabriales JJ, Ruiz-Herrera J. Wide distribution of the Ustilago maydis-bacterium endosymbiosis in naturally infected maize plants. PLANT SIGNALING & BEHAVIOR 2021; 16:1855016. [PMID: 33356903 PMCID: PMC7849723 DOI: 10.1080/15592324.2020.1855016] [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: 08/27/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 06/12/2023]
Abstract
We have previously described that laboratory strains of Ustilago maydis, a fungal pathogen of maize and its ancestor teosinte, harbor an intracellular bacterium that enables the fungus to fix nitrogen. However, it is not clear whether other strains isolated from nature also harbor endosymbiotic bacteria, and whether these fix nitrogen for its host. In the present study, we isolated U. maydis strains from naturally infected maize. All the isolated strains harbored intracellular bacteria as determined by PCR amplification of the 16S rRNA gene, and some of them showed capacity to fix nitrogen. That these are truly bacterial endosymbionts were shown by the fact that, after thorough treatments with CuSO4 followed by serial incubations with antibiotics, the aforementioned bacterial gene was still amplified in treated fungi. In all, these data support the notion that U. maydis-bacterium endosymbiosis is a general phenomenon in this species.
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Affiliation(s)
- Fernando Pérez-Rodríguez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Irapuato, Irapuato Gto, México
| | | | - José Antonio Vera-Núñez
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Irapuato, Irapuato Gto, México
| | - Roberto Ruiz-Medrano
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Zacatenco, Ciudad de México, México
| | - Juan José Peña-Cabriales
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Irapuato, Irapuato Gto, México
| | - José Ruiz-Herrera
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Irapuato, Irapuato Gto, México
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14
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Bastías DA, Johnson LJ, Card SD. Symbiotic bacteria of plant-associated fungi: friends or foes? CURRENT OPINION IN PLANT BIOLOGY 2020; 56:1-8. [PMID: 31786411 DOI: 10.1016/j.pbi.2019.10.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/21/2019] [Accepted: 10/30/2019] [Indexed: 06/10/2023]
Abstract
Many bacteria form symbiotic associations with plant-associated fungi. The effects of these symbionts on host fitness usually depend on symbiont or host genotypes and environmental conditions. However, bacterial endosymbionts, that is those living within fungal cells, may positively regulate host performance as their survival is often heavily dependent on host fitness. Contrary to this, bacteria that establish ectosymbiotic associations with fungi, that is those located on the hyphal surface or in close vicinity to fungal mycelia, may not have an apparent net effect on fungal performance due to the low level of fitness dependency on their host. Our analysis supports the hypothesis that endosymbiotic bacteria of fungi are beneficial symbionts, and that effects of ectosymbiotic bacteria on fungal performance depends on the bacterial type involved in the interaction (e.g. helper versus pathogen of fungi). Ecological scenarios, where the presence of beneficial bacterial endosymbionts of fungi could be compromised, are also discussed.
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Affiliation(s)
- Daniel A Bastías
- Forage Science, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand.
| | - Linda J Johnson
- Forage Science, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Stuart D Card
- Forage Science, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
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15
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Reyes-Hernández SJ, Zamora-Briseño JA, Cerqueda-García D, Castaño E, Rodríguez-Zapata LC. Alterations in the sap-associated microbiota of Carica papaya in response to drought stress. Symbiosis 2020. [DOI: 10.1007/s13199-020-00682-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Ruiz-Herrera J, Pérez-Rodríguez F, Velez-Haro J. The signaling mechanisms involved in the dimorphic phenomenon of the Basidiomycota fungus Ustilago maydis. Int Microbiol 2020; 23:121-126. [PMID: 31915950 DOI: 10.1007/s10123-019-00100-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 09/02/2019] [Accepted: 09/12/2019] [Indexed: 12/24/2022]
Abstract
In the present manuscript, we describe the mechanisms involved in the yeast-to-hypha dimorphic transition of the plant pathogenic Basidiomycota fungus Ustilago maydis. During its life cycle, U. maydis presents two stages: one in the form of haploid saprophytic yeasts that divide by budding and the other that is the product of the mating of sexually compatible yeast cells (sporidia), in the form of mycelial dikaryons that invade the plant host. The occurrence of the involved dimorphic transition is controlled by the two mating loci a and b. In addition, the dimorphic event can be obtained in vitro by different stimuli: change in the pH of the growth medium, use of different carbon sources, and by nitrogen depletion. The presence of other factors and mechanisms may affect this phenomenon; among these, we may cite the PKA and MAPK signal transduction pathways, polyamines, and factors that affect the structure of the nucleosomes. Some of these factors and conditions may affect all these dimorphic events, or they may be specific for only one or more but not all the processes involved. The conclusion reached by these experiments is that U. maydis has constituted a useful model for the analysis of the mechanisms involved in cell differentiation of fungi in general.
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Affiliation(s)
- José Ruiz-Herrera
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, Km. 9.4 Carretera Irapuato-León, Irapuato, Gto., Mexico.
| | - Fernando Pérez-Rodríguez
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, Km. 9.4 Carretera Irapuato-León, Irapuato, Gto., Mexico
| | - John Velez-Haro
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, Km. 9.4 Carretera Irapuato-León, Irapuato, Gto., Mexico.,Instituto Tecnológico de Celaya, Celaya, Gto., Mexico
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17
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Fungal Epigenetic Engineering. Fungal Biol 2020. [DOI: 10.1007/978-3-030-41870-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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18
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Sen D, Paul K, Saha C, Mukherjee G, Nag M, Ghosh S, Das A, Seal A, Tripathy S. A unique life-strategy of an endophytic yeast Rhodotorula mucilaginosa JGTA-S1-a comparative genomics viewpoint. DNA Res 2019; 26:131-146. [PMID: 30615101 PMCID: PMC6476726 DOI: 10.1093/dnares/dsy044] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 12/05/2018] [Indexed: 01/30/2023] Open
Abstract
Endophytic yeasts of genus Rhodotorula are gaining importance for their ability to improve plant growth. The nature of their interaction with plants, however, remains unknown. Rhodotorula mucilaginosa JGTA-S1 was isolated as an endophyte of Typha angustifolia and promoted growth in the host. To investigate the life-strategy of the yeast from a genomics perspective, we used Illumina and Oxford Nanopore reads to generate a high-quality annotated draft assembly of JGTA-S1 and compared its genome to three other Rhodotorula yeasts and the close relative Rhodosporidium toruloides. JGTA-S1 is a haploid yeast possessing several genes potentially facilitating its endophytic lifestyle such as those responsible for solubilizing phosphate and producing phytohormones. An intact mating-locus in JGTA-S1 raised the possibility of a yet unknown sexual reproductive cycle in Rhodotorula yeasts. Additionally, JGTA-S1 had functional anti-freezing genes and was also unique in lacking a functional nitrate-assimilation pathway—a feature that is associated with obligate biotrophs. Nitrogen-fixing endobacteria were found within JGTA-S1 that may circumvent this defective N-metabolism. JGTA-S1 genome data coupled with experimental evidence give us an insight into the nature of its beneficial interaction with plants.
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Affiliation(s)
- Diya Sen
- Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India
| | - Karnelia Paul
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, India
| | - Chinmay Saha
- Department of Endocrinology & Metabolism, Institute of Post Graduate Medical Education & Research and SSKM Hospital, Kolkata, West Bengal, India
| | - Gairik Mukherjee
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, India
| | - Mayurakshi Nag
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, India
| | - Samrat Ghosh
- Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research, New Delhi, India
| | - Abhishek Das
- Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research, New Delhi, India
| | - Anindita Seal
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, India
| | - Sucheta Tripathy
- Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research, New Delhi, India
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19
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Soberanes-Gutiérrez CV, Vázquez-Carrada M, López-Villegas EO, Vega-Arreguín JC, Villa-Tanaca L, Ruiz-Herrera J. Autophagosomes accumulation in the vacuoles of the fungus Ustilago maydis and the role of proteases in their digestion. FEMS Microbiol Lett 2019; 366:5513442. [DOI: 10.1093/femsle/fnz108] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 06/06/2019] [Indexed: 01/08/2023] Open
Affiliation(s)
- Cinthia V Soberanes-Gutiérrez
- Laboratorio de Ciencias Agrogenómicas, de la Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México. 37684, León Guanajuato, México
| | - Melissa Vázquez-Carrada
- Departamento de Microbiología de la Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional. 11340, Ciudad de México, México
| | - Edgar O López-Villegas
- Departamento de Microbiología de la Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional. 11340, Ciudad de México, México
| | - Julio C Vega-Arreguín
- Laboratorio de Ciencias Agrogenómicas, de la Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México. 37684, León Guanajuato, México
| | - Lourdes Villa-Tanaca
- Departamento de Microbiología de la Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional. 11340, Ciudad de México, México
| | - José Ruiz-Herrera
- Departamento de Ingeniería Genética del Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Irapuato. 36821, Irapuato Guanajuato, México
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20
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Wu X, Xie Y, Qiao J, Chai S, Chen L. Rhizobacteria Strain from a Hypersaline Environment Promotes Plant Growth of Kengyilia thoroldiana. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719020127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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21
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Arora P, Riyaz-Ul-Hassan S. Endohyphal bacteria; the prokaryotic modulators of host fungal biology. FUNGAL BIOL REV 2019. [DOI: 10.1016/j.fbr.2018.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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22
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Deveau A, Bonito G, Uehling J, Paoletti M, Becker M, Bindschedler S, Hacquard S, Hervé V, Labbé J, Lastovetsky OA, Mieszkin S, Millet LJ, Vajna B, Junier P, Bonfante P, Krom BP, Olsson S, van Elsas JD, Wick LY. Bacterial-fungal interactions: ecology, mechanisms and challenges. FEMS Microbiol Rev 2018; 42:335-352. [PMID: 29471481 DOI: 10.1093/femsre/fuy008] [Citation(s) in RCA: 321] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 02/16/2018] [Indexed: 12/14/2022] Open
Abstract
Fungi and bacteria are found living together in a wide variety of environments. Their interactions are significant drivers of many ecosystem functions and are important for the health of plants and animals. A large number of fungal and bacterial families engage in complex interactions that lead to critical behavioural shifts of the microorganisms ranging from mutualism to antagonism. The importance of bacterial-fungal interactions (BFI) in environmental science, medicine and biotechnology has led to the emergence of a dynamic and multidisciplinary research field that combines highly diverse approaches including molecular biology, genomics, geochemistry, chemical and microbial ecology, biophysics and ecological modelling. In this review, we discuss recent advances that underscore the roles of BFI across relevant habitats and ecosystems. A particular focus is placed on the understanding of BFI within complex microbial communities and in regard of the metaorganism concept. We also discuss recent discoveries that clarify the (molecular) mechanisms involved in bacterial-fungal relationships, and the contribution of new technologies to decipher generic principles of BFI in terms of physical associations and molecular dialogues. Finally, we discuss future directions for research in order to stimulate synergy within the BFI research area and to resolve outstanding questions.
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Affiliation(s)
- Aurélie Deveau
- Université de Lorraine, INRA, UMR IAM, 54280 Champenoux, France
| | - Gregory Bonito
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Jessie Uehling
- Biology Department, Duke University, Box 90338, Durham, NC 27705, USA.,Plant and Microbial Biology, University of California, Berkeley, CA 94703, USA
| | - Mathieu Paoletti
- Institut de Biologie et Génétique Cellulaire, UMR 5095 CNRS et Université de Bordeaux, 1 rue Camille Saint-Saëns, 33077 Bordeaux cedex, France
| | - Matthias Becker
- IGZ, Leibniz-Institute of Vegetable and Ornamental Crops, 14979 Großbeeren, Germany
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
| | - Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Vincent Hervé
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland.,Laboratory of Biogeosciences, Institute of Earth Surface Dynamics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Jessy Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Olga A Lastovetsky
- Graduate Field of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Sophie Mieszkin
- Université de Lorraine, INRA, UMR IAM, 54280 Champenoux, France
| | - Larry J Millet
- Joint Institute for Biological Science, University of Tennessee, and the Biosciences Division of Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Balázs Vajna
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
| | - Paola Bonfante
- Department of Life Science and Systems Biology, University of Torino, 10125 Torino, Italy
| | - Bastiaan P Krom
- Department of Preventive Dentistry, Academic Centre for Dentistry, G. Mahlerlaan 3004, 1081 LA, Amsterdam, The Netherlands
| | - Stefan Olsson
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University (FAFU), Fuzhou 350002, China
| | - Jan Dirk van Elsas
- Microbial Ecology group, GELIFES, University of Groningen, 9747 Groningen, The Netherlands
| | - Lukas Y Wick
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraße 15, 04318 Leipzig, Germany
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23
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Shaffer JP, Zalamea PC, Sarmiento C, Gallery RE, Dalling JW, Davis AS, Baltrus DA, Arnold AE. Context-dependent and variable effects of endohyphal bacteria on interactions between fungi and seeds. FUNGAL ECOL 2018. [DOI: 10.1016/j.funeco.2018.08.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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24
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Unveiling Concealed Functions of Endosymbiotic Bacteria Harbored in the Ascomycete Stachylidium bicolor. Appl Environ Microbiol 2018; 84:AEM.00660-18. [PMID: 29858203 DOI: 10.1128/aem.00660-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/23/2018] [Indexed: 02/07/2023] Open
Abstract
Among the plethora of unusual secondary metabolites isolated from Stachylidium bicolor are the tetrapeptidic endolides A and B. Both tetrapeptides contain 3-(3-furyl)-alanine residues, previously proposed to originate from bacterial metabolism. Inspired by this observation, we aimed to identify the presence of endosymbiotic bacteria in S. bicolor and to discover the true producer of the endolides. The endobacterium Burkholderia contaminans was initially detected by 16S rRNA gene amplicon sequencing from the fungal metagenome and was subsequently isolated. It was confirmed that the tetrapeptides were produced by the axenic B. contaminans only when in latency. Fungal colonies unable to produce conidia and the tetrapeptides were isolated and confirmed to be free of B. contaminans A second endosymbiont identified as related to Sphingomonas leidyi was also isolated. In situ imaging of the mycelium supported an endosymbiotic relationship between S. bicolor and the two endobacteria. Besides the technical novelty, our in situ analyses revealed that the two endobacteria are compartmentalized in defined fungal cells, prevailing mostly in latency when in symbiosis. Within the emerging field of intracellular bacterial symbioses, fungi are the least studied eukaryotic hosts. Our study further supports the Fungi as a valuable model for understanding endobacterial symbioses in eukaryotes.IMPORTANCE The discovery of two bacterial endosymbionts harbored in Stachylidium bicolor mycelium, Burkholderia contaminans and Sphingomonas leidyi, is described here. Production of tetrapeptides inside the mycelium is ensured by B. contaminans, and fungal sporulation is influenced by the endosymbionts. Here, we illustrate the bacterial endosymbiotic origin of secondary metabolites in an Ascomycota host.
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25
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Hassani MA, Durán P, Hacquard S. Microbial interactions within the plant holobiont. MICROBIOME 2018; 6:58. [PMID: 29587885 PMCID: PMC5870681 DOI: 10.1186/s40168-018-0445-0] [Citation(s) in RCA: 492] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 03/13/2018] [Indexed: 05/09/2023]
Abstract
Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often referred to as a "holobiont." Selective pressure acting on holobiont components has likely shaped plant-associated microbial communities and selected for host-adapted microorganisms that impact plant fitness. However, the high microbial densities detected on plant tissues, together with the fast generation time of microbes and their more ancient origin compared to their host, suggest that microbe-microbe interactions are also important selective forces sculpting complex microbial assemblages in the phyllosphere, rhizosphere, and plant endosphere compartments. Reductionist approaches conducted under laboratory conditions have been critical to decipher the strategies used by specific microbes to cooperate and compete within or outside plant tissues. Nonetheless, our understanding of these microbial interactions in shaping more complex plant-associated microbial communities, along with their relevance for host health in a more natural context, remains sparse. Using examples obtained from reductionist and community-level approaches, we discuss the fundamental role of microbe-microbe interactions (prokaryotes and micro-eukaryotes) for microbial community structure and plant health. We provide a conceptual framework illustrating that interactions among microbiota members are critical for the establishment and the maintenance of host-microbial homeostasis.
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Affiliation(s)
- M Amine Hassani
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Environmental Genomics, Christian-Albrechts University of Kiel, 24118, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Paloma Durán
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
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26
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Sharmin D, Guo Y, Nishizawa T, Ohshima S, Sato Y, Takashima Y, Narisawa K, Ohta H. Comparative Genomic Insights into Endofungal Lifestyles of Two Bacterial Endosymbionts, Mycoavidus cysteinexigens and Burkholderia rhizoxinica. Microbes Environ 2018. [PMID: 29540638 PMCID: PMC5877345 DOI: 10.1264/jsme2.me17138] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Endohyphal bacteria (EHB), dwelling within fungal hyphae, markedly affect the growth and metabolic potential of their hosts. To date, two EHB belonging to the family Burkholderiaceae have been isolated and characterized as new taxa, Burkholderia rhizoxinica (HKI 454T) and Mycoavidus cysteinexigens (B1-EBT), in Japan. Metagenome sequencing was recently reported for Mortierella elongata AG77 together with its endosymbiont M. cysteinexigens (Mc-AG77) from a soil/litter sample in the USA. In the present study, we elucidated the complete genome sequence of B1-EBT and compared it with those of Mc-AG77 and HKI 454T. The genomes of B1-EBT and Mc-AG77 contained a higher level of prophage sequences and were markedly smaller than that of HKI 454T. Although the B1-EBT and Mc-AG77 genomes lacked the chitinolytic enzyme genes responsible for invasion into fungal cells, they contained several predicted toxin-antitoxin systems including an insecticidal toxin complex and PIN domain imposing an addiction-like mechanism essential for endohyphal growth control during host colonization. Despite the different host fungi, the alignment of amino acid sequences showed that the HKI 454T genome consisted of 1,265 (32.6%) and 1,221 (31.5%) orthologous coding sequences (CDSs) with those of B1-EBT and Mc-AG77, respectively. This comparative study of three phylogenetically associated endosymbionts has provided insights into their origin and evolution, and suggests the later bacterial invasion and adaptation of B1-EBT to its host metabolism.
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Affiliation(s)
- Dilruba Sharmin
- Ibaraki University College of Agriculture, Department of Bioresource Science
| | - Yong Guo
- Ibaraki University College of Agriculture, Department of Bioresource Science
| | - Tomoyasu Nishizawa
- Ibaraki University College of Agriculture, Department of Bioresource Science.,United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology
| | - Shoko Ohshima
- Ibaraki University College of Agriculture, Department of Bioresource Science
| | - Yoshinori Sato
- Center for Conservation and Restoration Techniques, Tokyo National Research Institute for Cultural Properties
| | - Yusuke Takashima
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology
| | - Kazuhiko Narisawa
- Ibaraki University College of Agriculture, Department of Bioresource Science.,United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology
| | - Hiroyuki Ohta
- Ibaraki University College of Agriculture, Department of Bioresource Science.,United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology
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27
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Lipid droplets accumulation and other biochemical changes induced in the fungal pathogen Ustilago maydis under nitrogen-starvation. Arch Microbiol 2017; 199:1195-1209. [PMID: 28550409 DOI: 10.1007/s00203-017-1388-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 04/28/2017] [Accepted: 05/16/2017] [Indexed: 10/19/2022]
Abstract
In many organisms, the growth under nitrogen-deprivation or a poor nitrogen source impacts on the carbon flow distribution and causes accumulation of neutral lipids, which are stored as lipid droplets (LDs). Efforts are in progress to find the mechanism of LDs synthesis and degradation, and new organisms capable of accumulating large amounts of lipids for biotechnological applications. In this context, when Ustilago maydis was cultured in the absence of a nitrogen source, there was a large accumulation of lipid bodies containing mainly triacylglycerols. The most abundant fatty acids in lipid bodies at the stationary phase were palmitic, linoleic, and oleic acids, and they were synthesized de novo by the fatty-acid synthase. In regard to the production of NADPH for the synthesis of fatty acids, the cytosolic NADP+-dependent isocitrate dehydrogenase and the glucose-6-phosphate and 6-phosphogluconate dehydrogenases couple showed the highest specific activities, with a lower activity of the malic enzyme. The ATP-citrate lyase activity was not detected in any of the culture conditions, which points to a different mechanism for the transfer of acetyl-CoA into the cytosol. Protein and RNA contents decreased when U. maydis was grown without a nitrogen source. Due to the significant accumulation of triacylglycerols and the particular composition of fatty acids, U. maydis can be considered an alternative model for biotechnological applications.
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28
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Sánchez-Arreguin JA, Hernandez-Oñate MA, León-Ramirez CG, Ruiz-Herrera J. Transcriptional analysis of the adaptation of Ustilago maydis during growth under nitrogen fixation conditions. J Basic Microbiol 2017; 57:597-604. [PMID: 28429489 DOI: 10.1002/jobm.201600660] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/04/2017] [Indexed: 01/13/2023]
Abstract
Regulation of genes involved in nitrogen metabolism likely plays a role in the ability of fungi to exploit and survive under different environmental situations. To learn about the mechanism of adaptation of the biotrophic fungus Ustilago maydis from a medium containing a source of fixed nitrogen, to a medium depending on the ability to fix N2 by its bacterial endosymbiont, we explored gene expression profiles using RNA-Seq analyses under these two conditions. The differentially expressed (DE) fungal genes were analyzed, identifying 90 genes that were regulated 24 h after shifting the fungus to media lacking ammonium nitrate as a nitrogen source. From these, mRNA levels were increased for 49 genes, whereas 41 were down-regulated. The functional description associated to the regulated genes revealed that nine key pathways were represented, including, secondary metabolism, the metabolism of nitrogen, amino acid, fatty acid, amino sugar and nucleotide sugar, purine, peroxisome, and the regulation of actin cytoskeleton. These results suggest that the interplay of U. maydis with its N2 fixing bacterial endosymbiont is a flexible process that may be active during the adaptation of the fungus to the different nitrogen sources.
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Affiliation(s)
- José Alejandro Sánchez-Arreguin
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México.,Facultad de Ciencias Biológicas, Laboratorio de Micología y Fitopatología, Unidad de Manipulación Genética, Universidad Autónoma de Nuevo León, San Nicolas de Los Garza, Nuevo León, México
| | - Miguel Angel Hernandez-Oñate
- Cátedras-CONACYT-Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Sonora, México
| | - Claudia Geraldine León-Ramirez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - José Ruiz-Herrera
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
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29
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Partida‐Martínez LP. The fungal holobiont: Evidence from early diverging fungi. Environ Microbiol 2017; 19:2919-2923. [DOI: 10.1111/1462-2920.13731] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 03/11/2017] [Indexed: 01/02/2023]
Affiliation(s)
- Laila P. Partida‐Martínez
- Departamento de Ingeniería GenéticaCentro de Investigación y de Estudios Avanzados del IPNIrapuato 36821, Gto México
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30
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Shaffer JP, U'Ren JM, Gallery RE, Baltrus DA, Arnold AE. An Endohyphal Bacterium ( Chitinophaga, Bacteroidetes) Alters Carbon Source Use by Fusarium keratoplasticum ( F. solani Species Complex, Nectriaceae). Front Microbiol 2017; 8:350. [PMID: 28382021 PMCID: PMC5361657 DOI: 10.3389/fmicb.2017.00350] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 02/20/2017] [Indexed: 01/12/2023] Open
Abstract
Bacterial endosymbionts occur in diverse fungi, including members of many lineages of Ascomycota that inhabit living plants. These endosymbiotic bacteria (endohyphal bacteria, EHB) often can be removed from living fungi by antibiotic treatment, providing an opportunity to assess their effects on functional traits of their fungal hosts. We examined the effects of an endohyphal bacterium (Chitinophaga sp., Bacteroidetes) on substrate use by its host, a seed-associated strain of the fungus Fusarium keratoplasticum, by comparing growth between naturally infected and cured fungal strains across 95 carbon sources with a Biolog® phenotypic microarray. Across the majority of substrates (62%), the strain harboring the bacterium significantly outperformed the cured strain as measured by respiration and hyphal density. These substrates included many that are important for plant- and seed-fungus interactions, such as D-trehalose, myo-inositol, and sucrose, highlighting the potential influence of EHB on the breadth and efficiency of substrate use by an important Fusarium species. Cases in which the cured strain outperformed the strain harboring the bacterium were observed in only 5% of substrates. We propose that additive or synergistic substrate use by the fungus-bacterium pair enhances fungal growth in this association. More generally, alteration of the breadth or efficiency of substrate use by dispensable EHB may change fungal niches in short timeframes, potentially shaping fungal ecology and the outcomes of fungal-host interactions.
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Affiliation(s)
| | - Jana M U'Ren
- School of Plant Sciences, University of ArizonaTucson, AZ, USA; Department of Agricultural and Biosystems Engineering, University of ArizonaTucson, AZ, USA
| | - Rachel E Gallery
- School of Natural Resources and the Environment, University of ArizonaTucson, AZ, USA; Department of Ecology and Evolutionary Biology, University of ArizonaTucson, AZ, USA
| | - David A Baltrus
- School of Plant Sciences, University of Arizona Tucson, AZ, USA
| | - A Elizabeth Arnold
- School of Plant Sciences, University of ArizonaTucson, AZ, USA; Department of Ecology and Evolutionary Biology, University of ArizonaTucson, AZ, USA
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31
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Baltrus DA, Dougherty K, Arendt KR, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Ngan CY, Daum C, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Woyke T, Arnold AE. Absence of genome reduction in diverse, facultative endohyphal bacteria. Microb Genom 2017; 3:e000101. [PMID: 28348879 PMCID: PMC5361626 DOI: 10.1099/mgen.0.000101] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 12/04/2016] [Indexed: 01/03/2023] Open
Abstract
Fungi interact closely with bacteria, both on the surfaces of the hyphae and within their living tissues (i.e. endohyphal bacteria, EHB). These EHB can be obligate or facultative symbionts and can mediate diverse phenotypic traits in their hosts. Although EHB have been observed in many lineages of fungi, it remains unclear how widespread and general these associations are, and whether there are unifying ecological and genomic features can be found across EHB strains as a whole. We cultured 11 bacterial strains after they emerged from the hyphae of diverse Ascomycota that were isolated as foliar endophytes of cupressaceous trees, and generated nearly complete genome sequences for all. Unlike the genomes of largely obligate EHB, the genomes of these facultative EHB resembled those of closely related strains isolated from environmental sources. Although all analysed genomes encoded structures that could be used to interact with eukaryotic hosts, pathways previously implicated in maintenance and establishment of EHB symbiosis were not universally present across all strains. Independent isolation of two nearly identical pairs of strains from different classes of fungi, coupled with recent experimental evidence, suggests horizontal transfer of EHB across endophytic hosts. Given the potential for EHB to influence fungal phenotypes, these genomes could shed light on the mechanisms of plant growth promotion or stress mitigation by fungal endophytes during the symbiotic phase, as well as degradation of plant material during the saprotrophic phase. As such, these findings contribute to the illumination of a new dimension of functional biodiversity in fungi.
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Affiliation(s)
- David A Baltrus
- 1School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Kevin Dougherty
- 1School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Kayla R Arendt
- 1School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | | | - Alicia Clum
- 2Joint Genome Institute, Walnut Creek, CA, USA
| | | | | | | | | | | | - T B K Reddy
- 2Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Chris Daum
- 2Joint Genome Institute, Walnut Creek, CA, USA
| | | | | | | | | | - Tanja Woyke
- 2Joint Genome Institute, Walnut Creek, CA, USA
| | - A Elizabeth Arnold
- 1School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.,3Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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32
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Uehling J, Gryganskyi A, Hameed K, Tschaplinski T, Misztal PK, Wu S, Desirò A, Vande Pol N, Du Z, Zienkiewicz A, Zienkiewicz K, Morin E, Tisserant E, Splivallo R, Hainaut M, Henrissat B, Ohm R, Kuo A, Yan J, Lipzen A, Nolan M, LaButti K, Barry K, Goldstein AH, Labbé J, Schadt C, Tuskan G, Grigoriev I, Martin F, Vilgalys R, Bonito G. Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens. Environ Microbiol 2017; 19:2964-2983. [PMID: 28076891 DOI: 10.1111/1462-2920.13669] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 01/05/2017] [Accepted: 01/07/2017] [Indexed: 12/13/2022]
Abstract
Endosymbiosis of bacteria by eukaryotes is a defining feature of cellular evolution. In addition to well-known bacterial origins for mitochondria and chloroplasts, multiple origins of bacterial endosymbiosis are known within the cells of diverse animals, plants and fungi. Early-diverging lineages of terrestrial fungi harbor endosymbiotic bacteria belonging to the Burkholderiaceae. We sequenced the metagenome of the soil-inhabiting fungus Mortierella elongata and assembled the complete circular chromosome of its endosymbiont, Mycoavidus cysteinexigens, which we place within a lineage of endofungal symbionts that are sister clade to Burkholderia. The genome of M. elongata strain AG77 features a core set of primary metabolic pathways for degradation of simple carbohydrates and lipid biosynthesis, while the M. cysteinexigens (AG77) genome is reduced in size and function. Experiments using antibiotics to cure the endobacterium from the host demonstrate that the fungal host metabolism is highly modulated by presence/absence of M. cysteinexigens. Independent comparative phylogenomic analyses of fungal and bacterial genomes are consistent with an ancient origin for M. elongata - M. cysteinexigens symbiosis, most likely over 350 million years ago and concomitant with the terrestrialization of Earth and diversification of land fungi and plants.
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Affiliation(s)
- J Uehling
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - A Gryganskyi
- LF Lambert Spawn Company Coatesville, PA, 19320, USA
| | - K Hameed
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - T Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - P K Misztal
- University of California Berkeley, Berkeley, CA, 94720, USA
| | - S Wu
- Arizona State University Tempe, AZ, 85281, USA
| | - A Desirò
- Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - N Vande Pol
- Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Z Du
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| | - A Zienkiewicz
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| | - K Zienkiewicz
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA.,Department of Plant Biochemistry, Georg-August University, Göttingen, 37073, Germany
| | - E Morin
- Institut National de la Recherche Agronomique, UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'excellence ARBRE, INRA-Nancy, Champenoux, 54280, France
| | - E Tisserant
- Institut National de la Recherche Agronomique, UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'excellence ARBRE, INRA-Nancy, Champenoux, 54280, France
| | - R Splivallo
- Goethe University Frankfurt, Institute for Molecular Biosciences, 60438 Frankfurt, Germany Integrative Fungal Research Cluster (IPF), Frankfurt, 60325, Germany
| | - M Hainaut
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, 13288, France
| | - B Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, 13288, France
| | - R Ohm
- Microbiology, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - A Kuo
- Department of Energy, Joint Genome Institute, Oakland, CA, 94598, USA
| | - J Yan
- Department of Energy, Joint Genome Institute, Oakland, CA, 94598, USA
| | - A Lipzen
- Department of Energy, Joint Genome Institute, Oakland, CA, 94598, USA
| | - M Nolan
- Department of Energy, Joint Genome Institute, Oakland, CA, 94598, USA
| | - K LaButti
- Department of Energy, Joint Genome Institute, Oakland, CA, 94598, USA
| | - K Barry
- Department of Energy, Joint Genome Institute, Oakland, CA, 94598, USA
| | - A H Goldstein
- University of California Berkeley, Berkeley, CA, 94720, USA
| | - J Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - C Schadt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - G Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - I Grigoriev
- Department of Energy, Joint Genome Institute, Oakland, CA, 94598, USA
| | - F Martin
- Institut National de la Recherche Agronomique, UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'excellence ARBRE, INRA-Nancy, Champenoux, 54280, France
| | - R Vilgalys
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - G Bonito
- Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
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33
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Vannini C, Carpentieri A, Salvioli A, Novero M, Marsoni M, Testa L, de Pinto MC, Amoresano A, Ortolani F, Bracale M, Bonfante P. An interdomain network: the endobacterium of a mycorrhizal fungus promotes antioxidative responses in both fungal and plant hosts. THE NEW PHYTOLOGIST 2016; 211:265-275. [PMID: 26914272 DOI: 10.1111/nph.13895] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 01/12/2016] [Indexed: 06/05/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are obligate plant biotrophs that may contain endobacteria in their cytoplasm. Genome sequencing of Candidatus Glomeribacter gigasporarum revealed a reduced genome and dependence on the fungal host. RNA-seq analysis of the AMF Gigaspora margarita in the presence and absence of the endobacterium indicated that endobacteria have an important role in the fungal pre-symbiotic phase by enhancing fungal bioenergetic capacity. To improve the understanding of fungal-endobacterial interactions, iTRAQ (isobaric tags for relative and absolute quantification) quantitative proteomics was used to identify differentially expressed proteins in G. margarita germinating spores with endobacteria (B+), without endobacteria in the cured line (B-) and after application of the synthetic strigolactone GR24. Proteomic, transcriptomic and biochemical data identified several fungal and bacterial proteins involved in interspecies interactions. Endobacteria influenced fungal growth, calcium signalling and metabolism. The greatest effects were on fungal primary metabolism and respiration, which was 50% higher in B+ than in B-. A shift towards pentose phosphate metabolism was detected in B-. Quantification of carbonylated proteins indicated that the B- line had higher oxidative stress levels, which were also observed in two host plants. This study shows that endobacteria generate a complex interdomain network that affects AMF and fungal-plant interactions.
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Affiliation(s)
- Candida Vannini
- Department of Biotechnology and Life Science, Università dell'Insubria, via J.H. Dunant 3, I-21100, Varese, Italy
| | - Andrea Carpentieri
- Department of Chemical Sciences, Università di Napoli 'Federico II', via Cintia 4, I-80126, Napoli, Italy
| | - Alessandra Salvioli
- Department of Life Sciences and Systems Biology, Università di Torino, viale Mattioli 25, I-10125, Torino, Italy
| | - Mara Novero
- Department of Life Sciences and Systems Biology, Università di Torino, viale Mattioli 25, I-10125, Torino, Italy
| | - Milena Marsoni
- Department of Biotechnology and Life Science, Università dell'Insubria, via J.H. Dunant 3, I-21100, Varese, Italy
| | - Lorenzo Testa
- Department of Biotechnology and Life Science, Università dell'Insubria, via J.H. Dunant 3, I-21100, Varese, Italy
| | - Maria Concetta de Pinto
- Department of Biology, Università di Bari 'Aldo Moro', via E. Orabona 4, I-70125, Bari, Italy
| | - Angela Amoresano
- Department of Chemical Sciences, Università di Napoli 'Federico II', via Cintia 4, I-80126, Napoli, Italy
| | - Francesca Ortolani
- Department of Biotechnology and Life Science, Università dell'Insubria, via J.H. Dunant 3, I-21100, Varese, Italy
| | - Marcella Bracale
- Department of Biotechnology and Life Science, Università dell'Insubria, via J.H. Dunant 3, I-21100, Varese, Italy
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, Università di Torino, viale Mattioli 25, I-10125, Torino, Italy
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34
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Toomer KH, Chen X, Naito M, Mondo SJ, den Bakker HC, VanKuren NW, Lekberg Y, Morton JB, Pawlowska TE. Molecular evolution patterns reveal life history features of mycoplasma-related endobacteria associated with arbuscular mycorrhizal fungi. Mol Ecol 2015; 24:3485-500. [DOI: 10.1111/mec.13250] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 05/01/2015] [Accepted: 05/22/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Kevin H. Toomer
- School of Integrative Plant Science, Plant Pathology & Plant Microbe-Biology; Cornell University; Ithaca NY 14853 USA
| | - Xiuhua Chen
- School of Integrative Plant Science, Plant Pathology & Plant Microbe-Biology; Cornell University; Ithaca NY 14853 USA
- State Key Laboratory of Agricultural Microbiology; Huazhong Agricultural University; Wuhan 430070 China
| | - Mizue Naito
- School of Integrative Plant Science, Plant Pathology & Plant Microbe-Biology; Cornell University; Ithaca NY 14853 USA
| | - Stephen J. Mondo
- School of Integrative Plant Science, Plant Pathology & Plant Microbe-Biology; Cornell University; Ithaca NY 14853 USA
| | - Henk C. den Bakker
- School of Integrative Plant Science, Plant Pathology & Plant Microbe-Biology; Cornell University; Ithaca NY 14853 USA
| | - Nicholas W. VanKuren
- School of Integrative Plant Science, Plant Pathology & Plant Microbe-Biology; Cornell University; Ithaca NY 14853 USA
| | - Ylva Lekberg
- MPG Ranch; Missoula MT 59802 USA
- Department of Ecosystem and Conservation Sciences; University of Montana; Missoula MT 59812 USA
| | - Joseph B. Morton
- Division of Plant & Soil Sciences; West Virginia University; Morgantown WV 26506 USA
| | - Teresa E. Pawlowska
- School of Integrative Plant Science, Plant Pathology & Plant Microbe-Biology; Cornell University; Ithaca NY 14853 USA
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