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Chaudhury R, Chakraborty A, Rahaman F, Sarkar T, Dey S, Das M. Mycorrhization in trees: ecology, physiology, emerging technologies and beyond. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:145-156. [PMID: 38194349 DOI: 10.1111/plb.13613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 11/30/2023] [Indexed: 01/10/2024]
Abstract
Mycorrhization has been an integral part of plants since colonization by the early land plants. Over decades, substantial research has highlighted its potential role in improving nutritional efficiency and growth, development and survival of crop plants. However, the focus of this review is trees. Evidence have been provided to explain ecological and physiological significance of mycorrhization in trees. Advances in recent technologies (e.g., metagenomics, artificial intelligence, machine learning, agricultural drones) may open new windows to apply this knowledge in promoting tree growth in forest ecosystems. Dual mycorrhization relationships in trees and even triple relationships among trees, mycorrhizal fungi and bacteria offer an interesting physiological system to understand how plants interact with other organisms for better survival. Besides, studies indicate additional roles of mycorrhization in learning, memorizing and communication between host trees through a common mycorrhizal network (CMN). Recent observations in trees suggest that mycorrhization may even promote tolerance to multiple abiotic (e.g., drought, salt, heavy metal stress) and biotic (e.g. fungi) stresses. Due to the extent of physiological reliance, local adaptation of trees is heavily impacted by the mycorrhizal community. This knowledge opens the possibility of a non-GMO avenue to promote tree growth and development. Indeed, mycorrhization could impact growth of trees in nurserys and subsequent survival of the inoculated trees in field conditions. Future studies might integrate hyperspectral imaging and drone technologies to identify tree communities that are deficient in nitrogen and spray mycorrhizal spore formulations on them.
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Affiliation(s)
- R Chaudhury
- Department of Life Sciences, Presidency University, Kolkata, India
| | - A Chakraborty
- Department of Life Sciences, Presidency University, Kolkata, India
| | - F Rahaman
- Department of Life Sciences, Presidency University, Kolkata, India
| | - T Sarkar
- Department of Life Sciences, Presidency University, Kolkata, India
| | - S Dey
- Department of Life Sciences, Presidency University, Kolkata, India
| | - M Das
- Department of Life Sciences, Presidency University, Kolkata, India
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2
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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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Yang Z, Dong H, Zhang S, Jiang J, Zhu H, Yang H, Li L. Isolation and identification of mycorrhizal helper bacteria of Vaccinium uliginosum and their interaction with mycorrhizal fungi. Front Microbiol 2023; 14:1180319. [PMID: 37143547 PMCID: PMC10151510 DOI: 10.3389/fmicb.2023.1180319] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 03/28/2023] [Indexed: 05/06/2023] Open
Abstract
Mycorrhizal helper bacteria (MHB) can promote mycorrhizal fungal colonization and form mycorrhizal symbiosis structures. To investigate the effect of interactions between mycorrhizal beneficial microorganisms on the growth of blueberry, 45 strains of bacteria isolated from the rhizosphere soil of Vaccinium uliginosum were screened for potential MHB strains using the dry-plate confrontation assay and the bacterial extracellular metabolite promotion method. The results showed that the growth rate of mycelium of Oidiodendron maius 143, an ericoid mycorrhizal fungal strain, was increased by 33.33 and 77.77% for bacterial strains L6 and LM3, respectively, compared with the control in the dry-plate confrontation assay. In addition, the extracellular metabolites of L6 and LM3 significantly promoted the growth of O. maius 143 mycelium with an average growth rate of 40.9 and 57.1%, respectively, the cell wall-degrading enzyme activities and genes of O. maius 143 was significantly increased. Therefore, L6 and LM3 were preliminarily identified as potential MHB strains. In addition, the co-inoculated treatments significantly increased blueberry growth; increased the nitrate reductase, glutamate dehydrogenase, glutamine synthetase, and glutamate synthase activities in the leaves; and promoted nutrient uptake in blueberry. Based on the physiological, and 16S rDNA gene molecular analyses, we initially identified strain L6 as Paenarthrobacter nicotinovorans and LM3 as Bacillus circulans. Metabolomic analysis revealed that mycelial exudates contain large amounts of sugars, organic acids and amino acids, which can be used as substrates to stimulate the growth of MHB. In conclusion, L6 and LM3 and O. maius 143 promote each other's growth, while co-inoculation of L6 and LM3 with O. maius 143 can promote the growth of blueberry seedlings, providing a theoretical basis for further studies on the mechanism of ericoid mycorrhizal fungi-MHB-blueberry interactions. It laid the technical foundation for the exploitation of biocontrol strain resources and the development of biological fertilizer.
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Affiliation(s)
- Zhiyu Yang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Hui Dong
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Sai Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Jing Jiang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Haifeng Zhu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Hongyi Yang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
- *Correspondence: Hongyi Yang,
| | - Lili Li
- Institute of Forestry Science of Heilongjiang Province, Harbin, China
- Lili Li,
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Zeng Q, Man X, Lebreton A, Dai Y, Martin FM. The bacterial and fungal microbiomes of ectomycorrhizal roots from stone oaks and Yunnan pines in the subtropical forests of the Ailao Mountains of Yunnan. Front Microbiol 2022; 13:916337. [PMID: 35966686 PMCID: PMC9372452 DOI: 10.3389/fmicb.2022.916337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 07/11/2022] [Indexed: 12/02/2022] Open
Abstract
Ectomycorrhizal (ECM) symbioses play an important role in tree biology and forest ecology. However, little is known on the composition of bacterial and fungal communities associated to ECM roots. In the present study, we surveyed the bacterial and fungal microbiome of ECM roots from stone oaks (Lithocarpus spp.) and Yunnan pines (Pinus yunnanensis) in the subtropical forests of the Ailao Mountains (Yunnan, China). The bacterial community was dominated by species pertaining to Rhizobiales and Acidobacteriales, whereas the fungal community was mainly composed of species belonging to the Russulales and Thelephorales. While the bacterial microbiome hosted by ECM roots from stone oaks and Yunnan pines was very similar, the mycobiome of these host trees was strikingly distinct. The microbial networks for bacterial and fungal communities showed a higher complexity in Lithocarpus ECM roots compared to Pinus ECM roots, but their modularity was higher in Pinus ECM roots. Seasonality also significantly influenced the fungal diversity and their co-occurrence network complexity. Our findings thus suggest that the community structure of fungi establishing and colonizing ECM roots can be influenced by the local soil/host tree environment and seasonality. These results expand our knowledge of the ECM root microbiome and its diversity in subtropical forest ecosystems.
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Affiliation(s)
- Qingchao Zeng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
| | - Xiaowu Man
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Forestry, Beijing Forestry University, Beijing, China
| | - Annie Lebreton
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE, Grand Est-Nancy, Champenoux, France
| | - Yucheng Dai
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
- *Correspondence: Yucheng Dai,
| | - Francis M. Martin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE, Grand Est-Nancy, Champenoux, France
- Francis M. Martin,
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Mycelial Growth-promoting Potential of Extracellular Metabolites of Paraburkholderia spp. Isolated from Rhizopogon roseolus Sporocarp. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.2.43] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study aimed to investigate the effect of potential metabolite(s) produced by Paraburkholderia spp. isolated from the Rhizopogon roseolus (shouro mushroom) sporocarp on the mycelial growth of R. roseolus. For this purpose, we selected two molecularly identified bacteria: P. fungorum GIB024 and P. caledonica KN1. Direct confrontation assay at three different distances, a pour plate method that sampled bacterial spent broth either with and without agitation at 25 °C, and an indirect confrontation assay was carried out in order to assess the R. roseolus growth-promoting ability of Paraburkholderia spp. These assessments were carried out in a 1:5 diluted Melin-Norkran-modified medium with glucose (hs-dMMN) and without glucose (ls-dMMN). GIB024 promoted the growth of R. roseolus in ls-dMMN in short distance, whereas KN1 inhibited the growth of the fungus in that condition. In hs-dMMN, both bacteria have neutral or slightly promotion effect toward R. roseolus. We determined from the spent broth analysis that Paraburkholderia spp. that grew axenically under static conditions had a more pronounced mycelial growth-promoting effect on R. roseolus than under agitation conditions. We also found that high concentration of spent broth resulted in a decrease in mycelial growth-promoting ability. Volatile metabolite(s) produced by both bacteria did not promote the mycelial growth of R. roseolus. In conclusion, Paraburkholderia spp. exhibited a species- and nutrient (sugar)-dependent ability to promote the mycelial growth of R. roseolus, and the bacterial soluble metabolite(s) play a crucial role in their growth-promoting ability.
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Bai HY, Zhang AY, Mei Y, Xu M, Lu XL, Dai CC, Jia Y. Effects of ectomycorrhizal fungus bolete identity on the community assemblages of endofungal bacteria. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:852-861. [PMID: 34494716 DOI: 10.1111/1758-2229.13007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Ectomycorrhiza-associated bacteria, especially endofungal bacterial microbiota (EBM) in the fruiting body, play important roles in driving the establishment and function of ectomycorrhizae. However, the influence of ectomycorrhizal fungus bolete identity on their EBM is still unclear. We analysed the EBM of three different bolete fruiting body species on Thousand Island Lake, including Tylopilus felleus, Tylopilus areolatus and Boletus queletii, and compared them with their corresponding mycosphere soil bacterial microbiota by high-throughput sequencing. The EBM was classified into Bacillus, Pseudomonas, Burkholderia and Stenotrophomonas genera. Proteobacteria, Bacteroidetes and Acidobacteria were predominant in the EBM of bolete fruiting bodies as well as their mycosphere soil, while Firmicutes was significantly higher in the EBM. Moreover, the core microbiome (342 operational taxonomic units) of the EBM was shared among the three bolete fungal species. The relative abundances of gene families related to cell cycle control and nucleotide, coenzyme and lipid metabolism were significantly higher in the EBM than in the corresponding mycosphere soil bacterial microbiota, but there was no difference among the three different boletes. The results suggested that the host identity of ectomycorrhizal fungus boletes could affect the EBM, which might be mainly due to the selection of host fungi for the different functional EBM needed.
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Affiliation(s)
- Hong-Yan Bai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Ai-Yue Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Yan Mei
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Man Xu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Xiao-Lin Lu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Yong Jia
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
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Ścigaczewska A, Boruta T, Bizukojć M. Quantitative Morphological Analysis of Filamentous Microorganisms in Cocultures and Monocultures: Aspergillus terreus and Streptomyces rimosus Warfare in Bioreactors. Biomolecules 2021; 11:1740. [PMID: 34827738 PMCID: PMC8615777 DOI: 10.3390/biom11111740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/15/2021] [Accepted: 11/19/2021] [Indexed: 11/25/2022] Open
Abstract
The aim of this study was to quantitatively characterize the morphology of the filamentous microorganisms Aspergillus terreus ATCC 20542 and Streptomyces rimosus ATCC 10970, cocultivated in stirred tank bioreactors, and to characterize their mutual influence with the use of quantitative image analysis. Three distinct coculture initiation strategies were applied: preculture versus preculture, spores versus spores and preculture versus preculture with time delay for one of the species. Bioreactor cocultures were accompanied by parallel monoculture controls. The results recorded for the mono- and cocultures were compared in order to investigate the effect of cocultivation on the morphological evolution of A. terreus and S. rimosus. Morphology-related observations were also confronted with the analysis of secondary metabolism. The morphology of the two studied filamentous species strictly depended on the applied coculture initiation strategy. In the cocultures initiated by the simultaneous inoculation, S. rimosus gained domination or advance over A. terreus. The latter microorganism dominated only in these experiments in which S. rimosus was introduced with a delay.
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Affiliation(s)
- Anna Ścigaczewska
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, ul. Wolczanska 213, 90-924 Lodz, Poland; (T.B.); (M.B.)
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Methods for Studying Bacterial–Fungal Interactions in the Microenvironments of Soil. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11199182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Due to their small size, microorganisms directly experience only a tiny portion of the environmental heterogeneity manifested in the soil. The microscale variations in soil properties constrain the distribution of fungi and bacteria, and the extent to which they can interact with each other, thereby directly influencing their behavior and ecological roles. Thus, to obtain a realistic understanding of bacterial–fungal interactions, the spatiotemporal complexity of their microenvironments must be accounted for. The objective of this review is to further raise awareness of this important aspect and to discuss an overview of possible methodologies, some of easier applicability than others, that can be implemented in the experimental design in this field of research. The experimental design can be rationalized in three different scales, namely reconstructing the physicochemical complexity of the soil matrix, identifying and locating fungi and bacteria to depict their physical interactions, and, lastly, analyzing their molecular environment to describe their activity. In the long term, only relevant experimental data at the cell-to-cell level can provide the base for any solid theory or model that may serve for accurate functional prediction at the ecosystem level. The way to this level of application is still long, but we should all start small.
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Xu M, Bai HY, Fu WQ, Sun K, Wang HW, Xu DL, Dai CC, Jia Y. Endophytic bacteria promote the quality of Lyophyllum decastes by improving non-volatile taste components of mycelia. Food Chem 2020; 336:127672. [PMID: 32771899 DOI: 10.1016/j.foodchem.2020.127672] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 07/14/2020] [Accepted: 07/23/2020] [Indexed: 11/29/2022]
Abstract
Endophytic bacteria are always related to the host different traits, including the secondary metabolites production. However, the effect and mechanism of endophytic bacteria in the mushrooms fruit body on mycelia are still not clear. In this study, we investigated the effect of endophytic bacterial metabolites on the quality of Lyophyllum decastes mycelia. Soluble sugars, starch, protein, free amino acids, 5'-Nucleotides, EUC, and organic acids contents of mycelia were analyzed. We found that endophytic bacterial metabolites significantly increased the contents of soluble sugars, starch, protein, free amino acids, organic acids, and EUC. The present study thus suggests that endophytic bacteria could promote the quality of Lyophyllum decastes by improving non-volatile taste components of mycelia.
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Affiliation(s)
- Man Xu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; Nanjing Institute of Environmental Science, Ministry of Ecology and Environmental of China, Nanjing 210042, China
| | - Hong-Yan Bai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Wan-Qiu Fu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Kai Sun
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Hong-Wei Wang
- Nanjing Institute of Environmental Science, Ministry of Ecology and Environmental of China, Nanjing 210042, China
| | - De-Lei Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yong Jia
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
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Obase K. Effects of bacterial strains isolated from the ectomycorrhizal roots of Laccaria parva on sporocarp production by the fungus in vitro. MYCOSCIENCE 2020. [DOI: 10.1016/j.myc.2019.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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11
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Rodríguez-Gutiérrez I, Ramírez-Martínez D, Garibay-Orijel R, Jacob-Cervantes V, Pérez-Moreno J, Ortega-Larrocea MDP, Arellano-Torres E. Sympatric species develop more efficient ectomycorrhizae in the Pinus-Laccaria symbiosis. REV MEX BIODIVERS 2019. [DOI: 10.22201/ib.20078706e.2019.90.2868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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12
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Uehling JK, Entler MR, Meredith HR, Millet LJ, Timm CM, Aufrecht JA, Bonito GM, Engle NL, Labbé JL, Doktycz MJ, Retterer ST, Spatafora JW, Stajich JE, Tschaplinski TJ, Vilgalys RJ. Microfluidics and Metabolomics Reveal Symbiotic Bacterial-Fungal Interactions Between Mortierella elongata and Burkholderia Include Metabolite Exchange. Front Microbiol 2019; 10:2163. [PMID: 31632357 PMCID: PMC6779839 DOI: 10.3389/fmicb.2019.02163] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/03/2019] [Indexed: 01/12/2023] Open
Abstract
We identified two poplar (Populus sp.)-associated microbes, the fungus, Mortierella elongata strain AG77, and the bacterium, Burkholderia strain BT03, that mutually promote each other’s growth. Using culture assays in concert with a novel microfluidic device to generate time-lapse videos, we found growth specific media differing in pH and pre-conditioned by microbial growth led to increased fungal and bacterial growth rates. Coupling microfluidics and comparative metabolomics data results indicated that observed microbial growth stimulation involves metabolic exchange during two ordered events. The first is an emission of fungal metabolites, including organic acids used or modified by bacteria. A second signal of unknown nature is produced by bacteria which increases fungal growth rates. We find this symbiosis is initiated in part by metabolic exchange involving fungal organic acids.
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Affiliation(s)
- Jessie K Uehling
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States.,Department of Biology, Duke University, Durham, NC, United States
| | - Matthew R Entler
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Hannah R Meredith
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States.,Department of Biomedical Engineering, Duke University, Durham, NC, United States
| | - Larry J Millet
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,The Bredesen Center, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Collin M Timm
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jayde A Aufrecht
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Gregory M Bonito
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Nancy L Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jessy L Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Genome Science & Technology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Genome Science & Technology, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Scott T Retterer
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
| | | | - Rytas J Vilgalys
- Department of Biology, Duke University, Durham, NC, United States
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13
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de Novais CB, Giovannetti M, de Faria SM, Sbrana C. Two herbicides, two fungicides and spore-associated bacteria affect Funneliformis mosseae extraradical mycelium structural traits and viability. MYCORRHIZA 2019; 29:341-349. [PMID: 31190279 DOI: 10.1007/s00572-019-00901-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/28/2019] [Indexed: 06/09/2023]
Abstract
The extraradical mycelium (ERM) produced by arbuscular mycorrhizal fungi is fundamental for the maintenance of biological fertility in agricultural soils, representing an important inoculum source, together with spores and mycorrhizal root fragments. Its viability and structural traits, such as density, extent and interconnectedness, which are positively correlated with the growth and nutrition of host plants, may be affected by different agronomic practices, including the use of pesticides and by different mycorrhizospheric communities. This work, carried out using a whole-plant experimental model system, showed that structural traits of ERM, such as length and density, were strongly decreased by the herbicides dicamba and glufosinolate and the fungicides benomyl and fenhexamid, while anastomosis frequency and hyphal branching were differentially modulated by singly inoculated mycorrhizospheric bacteria, depending on their identity.
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Affiliation(s)
- Candido Barreto de Novais
- Department of Agriculture, Food and Environment, University of Pisa, 56126, Pisa, PI, Italy
- Forestry Institute, Federal Rural University of Rio de Janeiro, Seropédica, Brazil
| | - Manuela Giovannetti
- Department of Agriculture, Food and Environment, University of Pisa, 56126, Pisa, PI, Italy
| | - Sergio Miana de Faria
- Brazilian Agricultural Research Corporation - Embrapa Agrobiologia, Seropédica, Brazil
| | - Cristiana Sbrana
- CNR-Institute of Agricultural Biology and Biotechnology UOS Pisa, Pisa, Italy.
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14
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Obase K. Extending the hyphal area of the ectomycorrhizal fungus Laccaria parva co-cultured with ectomycorrhizosphere bacteria on nutrient agar plate. MYCOSCIENCE 2019. [DOI: 10.1016/j.myc.2018.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Bahram M, Vanderpool D, Pent M, Hiltunen M, Ryberg M. The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:155-166. [PMID: 29327481 DOI: 10.1111/1758-2229.12612] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/19/2017] [Accepted: 01/04/2018] [Indexed: 06/07/2023]
Abstract
Recent advances in molecular methods have increased our understanding of various fungal symbioses. However, little is known about genomic and microbiome features of most uncultured symbiotic fungal clades. Here, we analysed the genome and microbiome of Inocybaceae (Agaricales, Basidiomycota), a largely uncultured ectomycorrhizal clade known to form symbiotic associations with a wide variety of plant species. We used metagenomic sequencing and assembly of dikaryotic fruiting-body tissues from Inocybe terrigena (Fr.) Kuyper, to classify fungal and bacterial genomic sequences, and obtained a nearly complete fungal genome containing 93% of core eukaryotic genes. Comparative genomics reveals that I. terrigena is more similar to ectomycorrhizal and brown rot fungi than to white rot fungi. The reduction in lignin degradation capacity has been independent from and significantly faster than in closely related ectomycorrhizal clades supporting that ectomycorrhizal symbiosis evolved independently in Inocybe. The microbiome of I. terrigena fruiting-bodies includes bacteria with known symbiotic functions in other fungal and non-fungal host environments, suggesting potential symbiotic functions of these bacteria in fungal tissues regardless of habitat conditions. Our study demonstrates the usefulness of direct metagenomics analysis of fruiting-body tissues for characterizing fungal genomes and microbiome.
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Affiliation(s)
- Mohammad Bahram
- Department of Organismal Biology, Evolutionary Biology Centre Uppsala University, Norbyvägen 18D, Uppsala, 75236 Sweden
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, Tartu, 51005 Estonia
| | - Dan Vanderpool
- Division of Biological Sciences, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
| | - Mari Pent
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, Tartu, 51005 Estonia
| | - Markus Hiltunen
- Department of Organismal Biology, Evolutionary Biology Centre Uppsala University, Norbyvägen 18D, Uppsala, 75236 Sweden
| | - Martin Ryberg
- Department of Organismal Biology, Evolutionary Biology Centre Uppsala University, Norbyvägen 18D, Uppsala, 75236 Sweden
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16
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Looney BP, Meidl P, Piatek MJ, Miettinen O, Martin FM, Matheny PB, Labbé JL. Russulaceae: a new genomic dataset to study ecosystem function and evolutionary diversification of ectomycorrhizal fungi with their tree associates. THE NEW PHYTOLOGIST 2018; 218:54-65. [PMID: 29381218 DOI: 10.1111/nph.15001] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 12/13/2017] [Indexed: 05/05/2023]
Abstract
The family Russulaceae is considered an iconic lineage of mostly mushroom-forming basidiomycetes due to their importance as edible mushrooms in many parts of the world, and their ubiquity as ectomycorrhizal symbionts in both temperate and tropical forested biomes. Although much research has been focused on this group, a comprehensive or cohesive synthesis by which to understand the functional diversity of the group has yet to develop. Interest in ectomycorrhizal fungi, of which Russulaceae is a key lineage, is prodigious due to the important roles they play as plant root mutualists in ecosystem functioning, global carbon sequestration, and a potential role in technology development toward environmental sustainability. As one of the most species-diverse ectomycorrhizal lineages, the Russulaceae has recently been the focus of a dense sampling and genome sequencing initiative with the Joint Genome Institute aimed at untangling their functional roles and testing whether functional niche specialization exists for independent lineages of ectomycorrhizal fungi. Here we present a review of important studies on this group to contextualize what we know about its members' evolutionary history and ecosystem functions, as well as to generate hypotheses establishing the Russulaceae as a valuable experimental system.
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Affiliation(s)
- Brian P Looney
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
- INRA Université de Lorraine, UMR Interactions Arbres-Microorganismes, Laboratoire d'excellence ARBRE, 54280 Champenoux, France
| | - Peter Meidl
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Marek J Piatek
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Otto Miettinen
- Finnish Museum of Natural History, University of Helsinki, Helsinki 00170, Finland
| | - Francis M Martin
- INRA Université de Lorraine, UMR Interactions Arbres-Microorganismes, Laboratoire d'excellence ARBRE, 54280 Champenoux, France
| | - P Brandon Matheny
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Jessy L 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
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17
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Microbial communities in the native habitats of Agaricus sinodeliciosus from Xinjiang Province revealed by amplicon sequencing. Sci Rep 2017; 7:15719. [PMID: 29146962 PMCID: PMC5691072 DOI: 10.1038/s41598-017-16082-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 11/07/2017] [Indexed: 11/22/2022] Open
Abstract
Agaricus sinodeliciosus is an edible species described from China and has been successfully cultivated. However, no studies have yet reported the influence factors implicated in the process of fructification. To better know abiotic and biotic factors, physiochemical characteristics and microbial communities were investigated in five different soil samples collected in the native habitats of specimens from northern Xinjiang, southern Xinjiang, and Zhejiang Province, respectively. There are major differences in texture and morphology among different specimens of A. sinodeliciosus from Xinjiang Province. A. sinodeliciosus from southern Xinjiang was the largest. Concentrations of DOC and TN and C/N ratio are not the main reason for the differences. Microbial communities were analyzed to find out mushroom growth promoting microbes (MGPM), which may lead to the differences. Functional microbes were picked out and can be divided into two categories. Microbes in the first category may belong to MGPM. There may be symbiotic relationships between microbes in the second category and A. sinodeliciosus. Certain analyses of microbial communities support the hypothesis that interactions between microbes and mushrooms would be implicated in morphological variation of the collected mushrooms. Redundancy analysis results indicate that high DOC/NH4+-N ratio and NH4+-N concentration can improve the yield of A. sinodeliciosus.
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18
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Marupakula S, Mahmood S, Jernberg J, Nallanchakravarthula S, Fahad ZA, Finlay RD. Bacterial microbiomes of individual ectomycorrhizal Pinus sylvestris roots are shaped by soil horizon and differentially sensitive to nitrogen addition. Environ Microbiol 2017; 19:4736-4753. [PMID: 28967195 DOI: 10.1111/1462-2920.13939] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 08/29/2017] [Accepted: 09/19/2017] [Indexed: 12/31/2022]
Abstract
Plant roots select non-random communities of fungi and bacteria from the surrounding soil that have effects on their health and growth, but we know little about the factors influencing their composition. We profiled bacterial microbiomes associated with individual ectomycorrhizal Pinus sylvestris roots colonized by different fungi and analyzed differences in microbiome structure related to soils from distinct podzol horizons and effects of short-term additions of N, a growth-limiting nutrient commonly applied as a fertilizer, but known to influence patterns of carbon allocation to roots. Ectomycorrhizal roots growing in soil from different horizons harboured distinct bacterial communities. The fungi colonizing individual roots had a strong effect on the associated bacterial communities. Even closely related species within the same ectomycorrhizal genus had distinct bacterial microbiomes in unfertilized soil, but fertilization removed this specificity. Effects of N were rapid and context dependent, being influenced by both soil type and the particular ectomycorrhizal fungi involved. Fungal community composition changed in soil from all horizons, but bacteria only responded strongly to N in soil from the B horizon where community structure was different and bacterial diversity was significantly reduced, possibly reflecting changed carbon allocation patterns.
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Affiliation(s)
- Srisailam Marupakula
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Shahid Mahmood
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Johanna Jernberg
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Srivathsa Nallanchakravarthula
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Zaenab A Fahad
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Roger D Finlay
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
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19
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Pangesti N, Vandenbrande S, Pineda A, Dicke M, Raaijmakers JM, Van Loon JJA. Antagonism between two root-associated beneficial Pseudomonas strains does not affect plant growth promotion and induced resistance against a leaf-chewing herbivore. FEMS Microbiol Ecol 2017; 93:3071447. [PMID: 28334335 DOI: 10.1093/femsec/fix038] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 03/13/2017] [Indexed: 02/05/2023] Open
Abstract
Plant growth-promoting microbes residing on the roots may cooperate or compete, thereby affecting their collective benefit to the host plant. Pseudomonas simiae WCS417r (formerly known as P. fluorescens WCS417r) and Pseudomonas fluorescens SS101 are well known for their ability to induce systemic resistance in Arabidopsis. Here, we evaluate how these species interact on the roots of Arabidopsis thaliana Col-0 and how their co-inoculation affects plant defense to the leaf-chewing herbivore Mamestra brassicae and plant growth promotion. WCS417r and SS101, applied individually to root tips or at two different positions along the roots, established similar population densities on Arabidopsis roots. When co-inoculated at the same position on the roots, however, WCS417r established significantly higher population densities than SS101. Both upon single inoculation and co-inoculation, the two pseudomonads induced the same level of induced systemic resistance against the caterpillar M. brassicae and the same increase in plant biomass. These results suggest that combined inoculation of both Pseudomonas strains does not significantly modify the plant's defensive capacity compared to individual inoculation, resulting in a similar effect on performance of the generalist herbivore M. brassicae.
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Affiliation(s)
- Nurmi Pangesti
- Laboratory of Entomology, Wageningen University, PO Box 16, 6700 AA Wageningen, The Netherlands
| | - Simon Vandenbrande
- Laboratory of Entomology, Wageningen University, PO Box 16, 6700 AA Wageningen, The Netherlands
| | - Ana Pineda
- Laboratory of Entomology, Wageningen University, PO Box 16, 6700 AA Wageningen, The Netherlands
| | - Marcel Dicke
- Laboratory of Entomology, Wageningen University, PO Box 16, 6700 AA Wageningen, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700 AB Wageningen, The Netherlands
| | - Joop J A Van Loon
- Laboratory of Entomology, Wageningen University, PO Box 16, 6700 AA Wageningen, The Netherlands
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20
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Deveau A, Gross H, Palin B, Mehnaz S, Schnepf M, Leblond P, Dorrestein PC, Aigle B. Role of secondary metabolites in the interaction between Pseudomonas fluorescens and soil microorganisms under iron-limited conditions. FEMS Microbiol Ecol 2016; 92:fiw107. [PMID: 27199346 PMCID: PMC5975829 DOI: 10.1093/femsec/fiw107] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/15/2016] [Accepted: 05/15/2016] [Indexed: 01/18/2023] Open
Abstract
Microorganisms can be versatile in their interactions with each other, being variously beneficial, neutral or antagonistic in their effect. Although this versatility has been observed among many microorganisms and in many environments, little is known regarding the mechanisms leading to these changes in behavior. In the present work, we analyzed the mechanism by which the soil bacterium Pseudomonas fluorescens BBc6R8 shifts from stimulating the growth of the ectomycorrhizal fungus Laccaria bicolor S238N to killing the fungus. We show that among the three secondary metabolites produced by the bacterial strain-the siderophores enantio-pyochelin and pyoverdine, and the biosurfactant viscosin-the siderophores are mainly responsible for the antagonistic activity of the bacterium under iron-limited conditions. While the bacterial strain continues to produce beneficial factors, their effects are overridden by the action of their siderophores. This antagonistic activity of the strain P. fluorescens BBC6R8 in iron-depleted environments is not restricted to its influence on L. bicolor, since it was also seen to inhibit the growth of the actinomycete Streptomyces ambofaciens ATCC23877. We show that the strain P. fluorescens BBc6R8 uses different strategies to acquire iron, depending on certain biotic and abiotic factors.
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Affiliation(s)
- Aurélie Deveau
- INRA, Interactions Arbres-Microorganismes, UMR1136, Université de Lorraine, F-54280 Champenoux, France
| | - Harald Gross
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Béatrice Palin
- INRA, Interactions Arbres-Microorganismes, UMR1136, Université de Lorraine, F-54280 Champenoux, France
| | - Samina Mehnaz
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany Department of Biological Sciences, Forman Christian College, Ferozepur Road, Lahore 54600, Pakistan
| | - Max Schnepf
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Pierre Leblond
- Dynamique des Génomes et Adaptation Microbienne, UMR1128, Université de Lorraine, Faculté des Sciences et Technologies-Campus Aiguillettes, Vandœuvre-lès-Nancy, F-54506, France
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA 92093, USA
| | - Bertrand Aigle
- Dynamique des Génomes et Adaptation Microbienne, UMR1128, Université de Lorraine, Faculté des Sciences et Technologies-Campus Aiguillettes, Vandœuvre-lès-Nancy, F-54506, France
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21
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Marupakula S, Mahmood S, Finlay RD. Analysis of single root tip microbiomes suggests that distinctive bacterial communities are selected by Pinus sylvestris roots colonized by different ectomycorrhizal fungi. Environ Microbiol 2015; 18:1470-83. [PMID: 26521936 DOI: 10.1111/1462-2920.13102] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 10/19/2015] [Accepted: 10/21/2015] [Indexed: 11/30/2022]
Abstract
Symbiotic ectomycorrhizal tree roots represent an important niche for interaction with bacteria since the fungi colonizing them have a large surface area and receive a direct supply of photosynthetically derived carbon. We examined individual root tips of Pinus sylvestris at defined time points between 5 days and 24 weeks, identified the dominant fungi colonizing each root tip using Sanger sequencing and the bacterial communities colonizing individual root tips by 454 pyrosequencing. Bacterial colonization was extremely dynamic with statistically significant variation in time and increasing species richness until week 16 (3477 operational taxonomic units). Bacterial community structure of roots colonized by Russula sp. 6 GJ-2013b, Piloderma spp., Meliniomyces variabilis and Paxillus involutus differed significantly at weeks 8 and 16 but diversity declined and significant differences were no longer apparent at week 24. The most common genera were Burkholderia, Sphingopyxsis, Dyella, Pseudomonas, Acinetobacter, Actinospica, Aquaspirillum, Acidobacter Gp1, Sphingomonas, Terriglobus, Enhydrobacter, Herbaspirillum and Bradyrhizobium. Many genera had high initial abundance at week 8, declining with time but Dyella and Terriglobus increased in abundance at later time points. In roots colonized by Piloderma spp. several other bacterial genera, such as Actinospica, Bradyrhizobium, Acidobacter Gp1 and Rhizomicrobium appeared to increase in abundance at later sampling points.
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Affiliation(s)
- Srisailam Marupakula
- Uppsala BioCenter, Department of Forest Mycology & Plant Pathology, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Shahid Mahmood
- Uppsala BioCenter, Department of Forest Mycology & Plant Pathology, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Roger D Finlay
- Uppsala BioCenter, Department of Forest Mycology & Plant Pathology, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
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22
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Deveau A, Barret M, Diedhiou AG, Leveau J, de Boer W, Martin F, Sarniguet A, Frey-Klett P. Pairwise transcriptomic analysis of the interactions between the ectomycorrhizal fungus Laccaria bicolor S238N and three beneficial, neutral and antagonistic soil bacteria. MICROBIAL ECOLOGY 2015; 69:146-59. [PMID: 25085516 DOI: 10.1007/s00248-014-0445-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 06/09/2014] [Indexed: 05/21/2023]
Abstract
Ectomycorrhizal fungi are surrounded by bacterial communities with which they interact physically and metabolically during their life cycle. These bacteria can have positive or negative effects on the formation and the functioning of ectomycorrhizae. However, relatively little is known about the mechanisms by which ectomycorrhizal fungi and associated bacteria interact. To understand how ectomycorrhizal fungi perceive their biotic environment and the mechanisms supporting interactions between ectomycorrhizal fungi and soil bacteria, we analysed the pairwise transcriptomic responses of the ectomycorrhizal fungus Laccaria bicolor (Basidiomycota: Agaricales) when confronted with beneficial, neutral or detrimental soil bacteria. Comparative analyses of the three transcriptomes indicated that the fungus reacted differently to each bacterial strain. Similarly, each bacterial strain produced a specific and distinct response to the presence of the fungus. Despite these differences in responses observed at the gene level, we found common classes of genes linked to cell-cell interaction, stress response and metabolic processes to be involved in the interaction of the four microorganisms.
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Affiliation(s)
- Aurélie Deveau
- Interactions Arbres - Microorganismes, INRA UMR1136, 54280, Champenoux, France,
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23
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Yang RH, Wang XL, Su JH, Li Y, Jiang SP, Gu F, Yao YJ. Bacterial diversity in native habitats of the medicinal fungus Ophiocordyceps sinensis on Tibetan Plateau as determined using Illumina sequencing data. FEMS Microbiol Lett 2014; 362:fnu044. [PMID: 25743069 DOI: 10.1093/femsle/fnu044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ophiocordyceps sinensis is one of the most well-known traditional Chinese medicinal fungi. In this study, bacterial diversity in the soils of native habitats of O. sinensis was investigated using Illumina sequencing data. A total of 525,000 sequences of V6-16S rRNA were analyzed. The number of OTUs from each sample ranged from 13,858 to 15,978 at 97% sequence similarity cut-off. The results demonstrated that the deep sequencing approach provides improved access to rare genotypes. Richness indices and Shannon's diversity index did not differ significantly between samples collected from locations where O. sinensis was present (Os1-3) and not present (NOs1-3). Classified bacterial sequences were grouped into 23 phyla including Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, etc. The Venn diagram revealed that 7183 OTUs belonging to 14 phyla were shared by Os, NOs and MP (mycelial pellicle wrapping the sclerotium of O. sinensis) samples, possibly representing a core microbiome existing in native habitats of O. sinensis, and that 863 belonging to 12 phyla were shared by Os and MP samples, possibly related to the occurrence of O. sinensis. Overall, the results revealed a high bacterial diversity in the soil samples and the relationships between the bacterial diversity and O. sinensis merit further investigation.
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Affiliation(s)
- Rui-Heng Yang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China ITPB-IMCAS Key Joint Laboratory of Alpine Fungi, Lhasa 850001, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Liang Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China ITPB-IMCAS Key Joint Laboratory of Alpine Fungi, Lhasa 850001, China
| | - Jin-He Su
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China ITPB-IMCAS Key Joint Laboratory of Alpine Fungi, Lhasa 850001, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Si-Ping Jiang
- ITPB-IMCAS Key Joint Laboratory of Alpine Fungi, Lhasa 850001, China Tibet Plateau Institute of Biology, Lhasa 850001, China
| | - Fei Gu
- Institute of Animal Science, Aba Academy of Science and Technology, Wenchuan 623000, China
| | - Yi-Jian Yao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China ITPB-IMCAS Key Joint Laboratory of Alpine Fungi, Lhasa 850001, China
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24
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Labbé JL, Weston DJ, Dunkirk N, Pelletier DA, Tuskan GA. Newly identified helper bacteria stimulate ectomycorrhizal formation in Populus. FRONTIERS IN PLANT SCIENCE 2014; 5:579. [PMID: 25386184 PMCID: PMC4208408 DOI: 10.3389/fpls.2014.00579] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 10/08/2014] [Indexed: 05/24/2023]
Abstract
Mycorrhiza helper bacteria (MHB) are known to increase host root colonization by mycorrhizal fungi but the molecular mechanisms and potential tripartite interactions are poorly understood. Through an effort to study Populus microbiome, we isolated 21 Pseudomonas strains from native Populus deltoides roots. These bacterial isolates were characterized and screened for MHB effectiveness on the Populus-Laccaria system. Two additional Pseudomonas strains (i.e., Pf-5 and BBc6R8) from existing collections were included for comparative purposes. We analyzed the effect of co-cultivation of these 23 individual Pseudomonas strains on Laccaria bicolor "S238N" growth rate, mycelial architecture and transcriptional changes. Nineteen of the 23 Pseudomonas strains tested had positive effects on L. bicolor S238N growth, as well as on mycelial architecture, with strains GM41 and GM18 having the most significant effect. Four of seven L. bicolor reporter genes, Tra1, Tectonin2, Gcn5, and Cipc1, thought to be regulated during the interaction with MHB strain BBc6R8, were induced or repressed, while interacting with Pseudomonas strains GM17, GM33, GM41, GM48, Pf-5, and BBc6R8. Strain GM41 promoted the highest roots colonization across three Populus species but most notably in P. deltoides, which is otherwise poorly colonized by L. bicolor. Here we report novel MHB strains isolated from native Populus that improve L. bicolor root colonization on Populus. This tripartite relationship could be exploited for Populus species/genotypes nursery production as a means of improving establishment and survival in marginal lands.
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Affiliation(s)
- Jessy L. Labbé
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
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25
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Kemen E. Microbe-microbe interactions determine oomycete and fungal host colonization. CURRENT OPINION IN PLANT BIOLOGY 2014; 20:75-81. [PMID: 24845577 DOI: 10.1016/j.pbi.2014.04.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 03/22/2014] [Accepted: 04/24/2014] [Indexed: 05/03/2023]
Abstract
Microbial organisms sharing habitats aim for maximum fitness that they can only reach by collaboration. Developing stable networks within communities are crucial and can be achieved by exchanging common goods and genes that benefit the community. Only recently was it shown that horizontal gene transfer is not only common between prokaryotes but also into eukaryotic organisms such as fungi and oomycetes benefiting communal stability. Eukaryotic plant symbionts and pathogens coevolve with the plant microbiome and can acquire the ability to communicate or even collaborate, facilitating communal host colonization. Understanding communal infection will lead to a mechanistic understanding in how new hosts can be colonized under natural conditions and how we can counteract.
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Affiliation(s)
- Eric Kemen
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, Cologne 50829, Germany.
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