51
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Bomble YJ, Lin CY, Amore A, Wei H, Holwerda EK, Ciesielski PN, Donohoe BS, Decker SR, Lynd LR, Himmel ME. Lignocellulose deconstruction in the biosphere. Curr Opin Chem Biol 2017; 41:61-70. [DOI: 10.1016/j.cbpa.2017.10.013] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 12/18/2022]
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52
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Do fungi have an innate immune response? An NLR-based comparison to plant and animal immune systems. PLoS Pathog 2017; 13:e1006578. [PMID: 29073287 PMCID: PMC5658179 DOI: 10.1371/journal.ppat.1006578] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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Swain DM, Yadav SK, Tyagi I, Kumar R, Kumar R, Ghosh S, Das J, Jha G. A prophage tail-like protein is deployed by Burkholderia bacteria to feed on fungi. Nat Commun 2017; 8:404. [PMID: 28864820 PMCID: PMC5581363 DOI: 10.1038/s41467-017-00529-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 07/05/2017] [Indexed: 11/09/2022] Open
Abstract
Some bacteria can feed on fungi, a phenomenon known as mycophagy. Here we show that a prophage tail-like protein (Bg_9562) is essential for mycophagy in Burkholderia gladioli strain NGJ1. The purified protein causes hyphal disintegration and inhibits growth of several fungal species. Disruption of the Bg_9562 gene abolishes mycophagy. Bg_9562 is a potential effector secreted by a type III secretion system (T3SS) and is translocated into fungal mycelia during confrontation. Heterologous expression of Bg_9562 in another bacterial species, Ralstonia solanacearum, confers mycophagous ability in a T3SS-dependent manner. We propose that the ability to feed on fungi conferred by Bg_9562 may help the bacteria to survive in certain ecological niches. Furthermore, considering its broad-spectrum antifungal activity, the protein may be potentially useful in biotechnological applications to control fungal diseases.Some bacteria can feed on live fungi through unclear mechanisms. Here, the authors show that a T3SS-secreted protein, which is homologous to phage tail proteins, allows a Burkholderia gladioli strain to kill and feed on various fungal species.
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Affiliation(s)
- Durga Madhab Swain
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sunil Kumar Yadav
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Isha Tyagi
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rahul Kumar
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rajeev Kumar
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Srayan Ghosh
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Joyati Das
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Gopaljee Jha
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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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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Draft Genome Sequence of Rhizobium sp. Strain TBD182, an Antagonist of the Plant-Pathogenic Fungus Fusarium oxysporum, Isolated from a Novel Hydroponics System Using Organic Fertilizer. GENOME ANNOUNCEMENTS 2017; 5:5/11/e00007-17. [PMID: 28302768 PMCID: PMC5356045 DOI: 10.1128/genomea.00007-17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Rhizobium sp. strain TBD182, isolated from a novel hydroponics system, is an antagonistic bacterium that inhibits the mycelial growth of Fusarium oxysporum but does not eliminate the pathogen. We report the draft genome sequence of TBD182, which may contribute to elucidation of the molecular mechanisms of its fungistatic activity.
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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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57
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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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58
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Nazir R, Mazurier S, Yang P, Lemanceau P, van Elsas JD. The Ecological Role of Type Three Secretion Systems in the Interaction of Bacteria with Fungi in Soil and Related Habitats Is Diverse and Context-Dependent. Front Microbiol 2017; 8:38. [PMID: 28197129 PMCID: PMC5282467 DOI: 10.3389/fmicb.2017.00038] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/06/2017] [Indexed: 12/14/2022] Open
Abstract
Bacteria and fungi constitute important organisms in many ecosystems, in particular terrestrial ones. Both organismal groups contribute significantly to biogeochemical cycling processes. Ecological theory postulates that bacteria capable of receiving benefits from host fungi are likely to evolve efficient association strategies. The purpose of this review is to examine the mechanisms that underpin the bacterial interactions with fungi in soil and other systems, with special focus on the type III secretion system (T3SS). Starting with a brief description of the versatility of the T3SS as an interaction system with diverse eukaryotic hosts, we subsequently examine the recent advances made in our understanding of its contribution to interactions with soil fungi. The analysis used data sets ranging from circumstantial evidence to gene-knockout-based experimental data. The initial finding that the abundance of T3SSs in microbiomes is often enhanced in fungal-affected habitats like the mycosphere and the mycorrhizosphere is now substantiated with in-depth knowledge of the specific systems involved. Different fungal–interactive bacteria, in positive or negative associations with partner fungi, harbor and express T3SSs, with different ecological outcomes. In some particular cases, bacterial T3SSs have been shown to modulate the physiology of its fungal partner, affecting its ecological characteristics and consequently shaping its own habitat. Overall, the analyses of the collective data set revealed that diverse T3SSs have assumed diverse roles in the interactions of bacteria with host fungi, as driven by ecological and evolutionary niche requirements.
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Affiliation(s)
- Rashid Nazir
- Department of Environmental Sciences, COMSATS Institute of Information TechnologyAbbottabad, Pakistan; Department of Soil Environmental Science, Research Centre for Eco-environmental Sciences - Chinese Academy of SciencesBeijing, China
| | - Sylvie Mazurier
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté Dijon, France
| | - Pu Yang
- Department of Microbial Ecology, GELIFES, University of Groningen Groningen, Netherlands
| | - Philippe Lemanceau
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté Dijon, France
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, GELIFES, University of Groningen Groningen, Netherlands
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59
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Viollet A, Pivato B, Mougel C, Cleyet-Marel JC, Gubry-Rangin C, Lemanceau P, Mazurier S. Pseudomonas fluorescens C7R12 type III secretion system impacts mycorrhization of Medicago truncatula and associated microbial communities. MYCORRHIZA 2017; 27:23-33. [PMID: 27549437 DOI: 10.1007/s00572-016-0730-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/11/2016] [Indexed: 05/20/2023]
Abstract
Type three secretion systems (T3SSs) mediate cell-to-cell interactions between Gram-negative bacteria and eukaryotes. We hypothesized that fluorescent pseudomonads harboring T3SS (T3SS+) would be beneficial to arbuscular mycorrhizal symbiosis because non-pathogenic fluorescent pseudomonads have been previously shown to be much more abundant in mycorrhizal than in non-mycorrhizal roots. We tested this hypothesis by comparing mycorrhization and the associated rhizosphere microbial communities of Medicago truncatula grown in a non-sterile soil inoculated with either the T3SS+ mycorrhiza helper bacterium Pseudomonas fluorescens (C7R12) or a T3SS- mutant of the strain. Results showed that the bacterial secretion system was responsible for the promotion of mycorrhization because root colonization by arbuscular mycorrhizal fungi was not promoted by the T3SS- mutant. The observed T3SS-mediated promotion of mycorrhization was associated with changes in the rhizosphere bacterial communities and the increased occurrence of Claroidoglomeraceae within the intraradical arbuscular mycorrhizal fungi. Furthermore, both pseudomonad strains promoted the host-free growth of a model arbuscular mycorrhizal fungus in vitro, suggesting that T3SS-mediated promotion of mycorrhization occurs during plant-fungal interactions rather than during the pre-symbiotic phase of fungal growth. Taken together, these data provide evidence for the involvement of T3SS in promoting arbuscular mycorrhization by a model fluorescent pseudomonad and suggest the implication of interactions between the bacterium and mycorrhizas.
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Affiliation(s)
- Amandine Viollet
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Barbara Pivato
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Christophe Mougel
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 21000, Dijon, France
- INRA, UMR1349 IGEPP, 35653, Le Rheu, France
| | - Jean-Claude Cleyet-Marel
- INRA, UMR 113 'Laboratoire des Symbioses Tropicales et Méditerranéennes', Campus International de Baillarguet, TA-A82/J, 34398, Montpellier Cedex 5, France
| | - Cécile Gubry-Rangin
- INRA, UMR 113 'Laboratoire des Symbioses Tropicales et Méditerranéennes', Campus International de Baillarguet, TA-A82/J, 34398, Montpellier Cedex 5, France
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | - Philippe Lemanceau
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Sylvie Mazurier
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 21000, Dijon, France.
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60
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Lipid metabolic changes in an early divergent fungus govern the establishment of a mutualistic symbiosis with endobacteria. Proc Natl Acad Sci U S A 2016; 113:15102-15107. [PMID: 27956601 PMCID: PMC5206550 DOI: 10.1073/pnas.1615148113] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The recent accumulation of newly discovered fungal-bacterial mutualisms challenges the paradigm that fungi and bacteria are natural antagonists. To understand the mechanisms that govern the establishment and maintenance over evolutionary time of mutualisms between fungi and bacteria, we studied a symbiosis of the fungus Rhizopus microsporus (Mucoromycotina) and its Burkholderia endobacteria. We found that nonhost R. microsporus, as well as other mucoralean fungi, interact antagonistically with endobacteria derived from the host and are not invaded by them. Comparison of gene expression profiles of host and nonhost fungi during interaction with endobacteria revealed dramatic changes in expression of lipid metabolic genes in the host. Analysis of the host lipidome confirmed that symbiosis establishment was accompanied by specific changes in the fungal lipid profile. Diacylglycerol kinase (DGK) activity was important for these lipid metabolic changes, as its inhibition altered the fungal lipid profile and caused a shift in the host-bacterial interaction into an antagonism. We conclude that adjustments in host lipid metabolism during symbiosis establishment, mediated by DGKs, are required for the mutualistic outcome of the Rhizopus-Burkholderia symbiosis. In addition, the neutral and phospholipid profiles of R. microsporus provide important insights into lipid metabolism in an understudied group of oleaginous Mucoromycotina. Lastly, our study revealed that the DGKs involved in the symbiosis form a previously uncharacterized clade of DGK domain proteins.
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61
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Haack FS, Poehlein A, Kröger C, Voigt CA, Piepenbring M, Bode HB, Daniel R, Schäfer W, Streit WR. Molecular Keys to the Janthinobacterium and Duganella spp. Interaction with the Plant Pathogen Fusarium graminearum. Front Microbiol 2016; 7:1668. [PMID: 27833590 PMCID: PMC5080296 DOI: 10.3389/fmicb.2016.01668] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 10/05/2016] [Indexed: 11/18/2022] Open
Abstract
Janthinobacterium and Duganella are well-known for their antifungal effects. Surprisingly, almost nothing is known on molecular aspects involved in the close bacterium-fungus interaction. To better understand this interaction, we established the genomes of 11 Janthinobacterium and Duganella isolates in combination with phylogenetic and functional analyses of all publicly available genomes. Thereby, we identified a core and pan genome of 1058 and 23,628 genes. All strains encoded secondary metabolite gene clusters and chitinases, both possibly involved in fungal growth suppression. All but one strain carried a single gene cluster involved in the biosynthesis of alpha-hydroxyketone-like autoinducer molecules, designated JAI-1. Genome-wide RNA-seq studies employing the background of two isolates and the corresponding JAI-1 deficient strains identified a set of 45 QS-regulated genes in both isolates. Most regulated genes are characterized by a conserved sequence motif within the promoter region. Among the most strongly regulated genes were secondary metabolite and type VI secretion system gene clusters. Most intriguing, co-incubation studies of J. sp. HH102 or its corresponding JAI-1 synthase deletion mutant with the plant pathogen Fusarium graminearum provided first evidence of a QS-dependent interaction with this pathogen.
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Affiliation(s)
- Frederike S Haack
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg Hamburg, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Goettingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Germany
| | - Cathrin Kröger
- Department of Molecular Phytopathology, Biocenter Klein Flottbek, University of Hamburg Hamburg, Germany
| | - Christian A Voigt
- Department of Phytopathology and Biochemistry, Biocenter Klein Flottbek, University of Hamburg Hamburg, Germany
| | - Meike Piepenbring
- Department of Mycology, Goethe University Frankfurt Frankfurt am Main, Germany
| | - Helge B Bode
- Merck-Stiftungsprofessur für Molekulare Biotechnologie Fachbereich Biowissenschaften and Buchmann Institute for Molecular Life Sciences, Goethe Universität Frankfurt Frankfurt am Main, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Goettingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Germany
| | - Wilhelm Schäfer
- Department of Molecular Phytopathology, Biocenter Klein Flottbek, University of Hamburg Hamburg, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg Hamburg, Germany
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62
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Johnston SR, Boddy L, Weightman AJ. Bacteria in decomposing wood and their interactions with wood-decay fungi. FEMS Microbiol Ecol 2016; 92:fiw179. [PMID: 27559028 DOI: 10.1093/femsec/fiw179] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2016] [Indexed: 01/02/2023] Open
Abstract
The fungal community within dead wood has received considerable study, but far less attention has been paid to bacteria in the same habitat. Bacteria have long been known to inhabit decomposing wood, but much remains underexplored about their identity and ecology. Bacteria within the dead wood environment must interact with wood-decay fungi, but again, very little is known about the form this takes; there are indications of both antagonistic and beneficial interactions within this fungal microbiome. Fungi are hypothesised to play an important role in shaping bacterial communities in wood, and conversely, bacteria may affect wood-decay fungi in a variety of ways. This minireview considers what is currently known about bacteria in wood and their interactions with fungi, and proposes possible associations based on examples from other habitats. It aims to identify key knowledge gaps and pressing questions for future research.
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Affiliation(s)
- Sarah R Johnston
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Lynne Boddy
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Andrew J Weightman
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
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63
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Haq IU, Calixto RODR, Yang P, Dos Santos GMP, Barreto-Bergter E, van Elsas JD. Chemotaxis and adherence to fungal surfaces are key components of the behavioral response of Burkholderia terrae BS001 to two selected soil fungi. FEMS Microbiol Ecol 2016; 92:fiw164. [PMID: 27495244 DOI: 10.1093/femsec/fiw164] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2016] [Indexed: 01/27/2023] Open
Abstract
Burkholderia terrae BS001 has previously been proposed to be a 'generalist' associate of soil fungi, but its strategies of interaction have been largely ignored. Here, we studied the chemotactic behavior of B. terrae BS001 towards Lyophyllum sp. strain Karsten and Trichoderma asperellum 302 and the role of fungal surface molecules in their physical interaction with the bacteria. To assess the involvement of the type 3 secretion system (T3SS), wild-type strain BS001 and T3SS mutant strain BS001-ΔsctD were used in the experiments. First, the two fungi showed divergent behavior when confronted with B. terrae BS001 on soil extract agar medium. Lyophyllum sp. strain Karsten revealed slow growth towards the bacterium, whereas T. asperellum 302 grew avidly over it. Both on soil extract and M9 agar, B. terrae BS001 and BS001-ΔsctD moved chemotactically towards the hyphae of both fungi, with a stronger response to Lyophyllum sp. strain Karsten than to T. asperellum 302. The presence of a progressively increasing glycerol level in the M9 agar enhanced the level of movement. Different oxalic acid concentrations exerted varied effects, with a significantly raised chemotactic response at lower, and a subdued response at higher concentrations. Testing of the adherence of B. terrae BS001 and BS001-ΔsctD to Lyophyllum sp. strain Karsten and to cell envelope-extracted ceramide monohexosides (CMHs) revealed that CMHs in both conidia and hyphae could bind strain BS001 cells. As BS001-ΔsctD adhered significantly less to the CMHs than BS001, the T3SS was presumed to have a role in the interaction. In contrast, such avid adherence was not detected with T. asperellum 302. Thus, B. terrae BS001 shows a behavior characterized by swimming towards Lyophyllum sp. strain Karsten and T. asperellum 302 and attachment to the CMH moiety in the cell envelope, in particular of the former.
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Affiliation(s)
- Irshad Ul Haq
- Microbial Ecology, Groningen Institute of Evolutionary Life Sciences (GELIFES), Nijenborgh 7, 9747 AG, University of Groningen, The Netherlands
| | - Renata Oliveira da Rocha Calixto
- Microbial Ecology, Groningen Institute of Evolutionary Life Sciences (GELIFES), Nijenborgh 7, 9747 AG, University of Groningen, The Netherlands Departamento de Microbiologia Geral, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, UFRJ, 21941-902, Rio de Janeiro, Brazil
| | - Pu Yang
- Microbial Ecology, Groningen Institute of Evolutionary Life Sciences (GELIFES), Nijenborgh 7, 9747 AG, University of Groningen, The Netherlands
| | - Giulia Maria Pires Dos Santos
- Departamento de Microbiologia Geral, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, UFRJ, 21941-902, Rio de Janeiro, Brazil
| | - Eliana Barreto-Bergter
- Departamento de Microbiologia Geral, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, UFRJ, 21941-902, Rio de Janeiro, Brazil
| | - Jan Dirk van Elsas
- Microbial Ecology, Groningen Institute of Evolutionary Life Sciences (GELIFES), Nijenborgh 7, 9747 AG, University of Groningen, The Netherlands
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64
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Schulz-Bohm K, Tyc O, de Boer W, Peereboom N, Debets F, Zaagman N, Janssens TKS, Garbeva P. Fungus-associated bacteriome in charge of their host behavior. Fungal Genet Biol 2016; 102:38-48. [PMID: 27486066 DOI: 10.1016/j.fgb.2016.07.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 07/19/2016] [Accepted: 07/28/2016] [Indexed: 11/18/2022]
Abstract
Bacterial-fungal interactions are widespread in nature and there is a growing number of studies reporting distinct fungus-associated bacteria. However, little is known so far about how shifts in the fungus-associated bacteriome will affect the fungal host's lifestyle. In the present study, we describe for the first time the bacterial community associated with the saprotrophic fungus Mucor hiemalis, commonly found in soil and rhizosphere. Two broad-spectrum antibiotics that strongly altered the bacterial community associated with the fungus were applied. Our results revealed that the antibiotic treatment did not significantly reduce the amount of bacteria associated to the fungus but rather changed the community composition by shifting from initially dominating Alpha-Proteobacteria to dominance of Gamma-Proteobacteria. A novel approach was applied for the isolation of fungal-associated bacteria which also revealed differences between bacterial isolates obtained from the original and the antibiotic-treated M. hiemalis. The shift in the composition of the fungal-associated bacterial community led to significantly reduced fungal growth, changes in fungal morphology, behavior and secondary-metabolites production. Furthermore, our results showed that the antibiotic-treated isolate was more attractive and susceptible to mycophagous bacteria as compared to the original isolate. Overall, our study highlights the importance of the fungus-associated bacteriome for the host's lifestyle and interactions and indicate that isolation with antibacterials is not sufficient to eradicate the associated bacteria.
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Affiliation(s)
- Kristin Schulz-Bohm
- Department Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, PO Box 50, 6700 AB Wageningen, Netherlands; Department of Soil Quality, Wageningen University & Research Centre (WUR), PO Box 47, 6700 AA Wageningen, Netherlands
| | - Olaf Tyc
- Department Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, PO Box 50, 6700 AB Wageningen, Netherlands; Department of Soil Quality, Wageningen University & Research Centre (WUR), PO Box 47, 6700 AA Wageningen, Netherlands
| | - Wietse de Boer
- Department Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, PO Box 50, 6700 AB Wageningen, Netherlands; Department of Soil Quality, Wageningen University & Research Centre (WUR), PO Box 47, 6700 AA Wageningen, Netherlands
| | - Nils Peereboom
- Department Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, PO Box 50, 6700 AB Wageningen, Netherlands; Laboratory of Genetics, Wageningen University & Research Centre (WUR), PO Box 16, 6700 AA Wageningen, Netherlands
| | - Fons Debets
- Laboratory of Genetics, Wageningen University & Research Centre (WUR), PO Box 16, 6700 AA Wageningen, Netherlands
| | - Niels Zaagman
- MicroLife Solutions b.v., Science Park 406, 1098 XH Amsterdam, Netherlands
| | | | - Paolina Garbeva
- Department Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, PO Box 50, 6700 AB Wageningen, Netherlands.
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65
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Arendt KR, Hockett KL, Araldi-Brondolo SJ, Baltrus DA, Arnold AE. Isolation of Endohyphal Bacteria from Foliar Ascomycota and In Vitro Establishment of Their Symbiotic Associations. Appl Environ Microbiol 2016; 82:2943-2949. [PMID: 26969692 PMCID: PMC4959084 DOI: 10.1128/aem.00452-16] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 03/03/2016] [Indexed: 12/16/2022] Open
Abstract
Endohyphal bacteria (EHB) can influence fungal phenotypes and shape the outcomes of plant-fungal interactions. Previous work has suggested that EHB form facultative associations with many foliar fungi in the Ascomycota. These bacteria can be isolated in culture, and fungi can be cured of EHB using antibiotics. Here, we present methods for successfully introducing EHB into axenic mycelia of strains representing two classes of Ascomycota. We first establish in vitro conditions favoring reintroduction of two strains of EHB (Luteibacter sp.) into axenic cultures of their original fungal hosts, focusing on fungi isolated from healthy plant tissue as endophytes: Microdiplodia sp. (Dothideomycetes) and Pestalotiopsis sp. (Sordariomycetes). We then demonstrate that these EHB can be introduced into a novel fungal host under the same conditions, successfully transferring EHB between fungi representing different classes. Finally, we manipulate conditions to optimize reintroduction in a focal EHB-fungal association. We show that EHB infections were initiated and maintained more often under low-nutrient culture conditions and when EHB and fungal hyphae were washed with MgCl2 prior to reassociation. Our study provides new methods for experimental assessment of the effects of EHB on fungal phenotypes and shows how the identity of the fungal host and growth conditions can define the establishment of these widespread and important symbioses.
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Affiliation(s)
- Kayla R Arendt
- School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Kevin L Hockett
- School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | | | - David A Baltrus
- School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - A Elizabeth Arnold
- School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
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66
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Spraker JE, Sanchez LM, Lowe TM, Dorrestein PC, Keller NP. Ralstonia solanacearum lipopeptide induces chlamydospore development in fungi and facilitates bacterial entry into fungal tissues. ISME JOURNAL 2016; 10:2317-30. [PMID: 26943626 PMCID: PMC4989320 DOI: 10.1038/ismej.2016.32] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 01/21/2016] [Accepted: 01/23/2016] [Indexed: 01/14/2023]
Abstract
Ralstonia solanacearum is a globally distributed soil-borne plant pathogenic bacterium, which shares a broad ecological range with many plant- and soil-associated fungi. We sought to determine if R. solanacearum chemical communication directs symbiotic development of polymicrobial consortia. R. solanacearum produced a diffusible metabolite that induced conserved morphological differentiation in 34 species of fungi across three diverse taxa (Ascomycetes, Basidiomycetes and Zygomycetes). Fungi exposed to this metabolite formed chlamydospores, survival structures with thickened cell walls. Some chlamydospores internally harbored R. solanacearum, indicating a newly described endofungal lifestyle for this important plant pathogen. Using imaging mass spectrometry and peptidogenomics, we identified an undescribed lipopeptide, ralsolamycin, produced by an R. solanacearum non-ribosomal peptide synthetase-polyketide synthase hybrid. Inactivation of the hybrid non-ribosomal peptide synthetase-polyketide synthase gene, rmyA, abolished ralsolamycin synthesis. R. solanacearum mutants lacking ralsolamycin no longer induced chlamydospore development in fungal coculture and invaded fungal hyphae less well than wild-type. We propose that ralsolamycin contributes to the invasion of fungal hyphae and that the formation of chlamydospores may provide not only a specific niche for bacterial colonization but also enhanced survival for the partnering fungus.
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Affiliation(s)
- Joseph E Spraker
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Laura M Sanchez
- Departments of Pharmacology, Chemistry and Biochemistry, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, La Jolla, CA, USA
| | - Tiffany M Lowe
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Pieter C Dorrestein
- Departments of Pharmacology, Chemistry and Biochemistry, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, La Jolla, CA, USA.,Collaborative Mass Spectrometry Innovation Center, University of California-San Diego, La Jolla, CA, USA
| | - Nancy P Keller
- Departments of Bacteriology, Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
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67
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Helfrich EJN, Piel J. Biosynthesis of polyketides by trans-AT polyketide synthases. Nat Prod Rep 2016; 33:231-316. [DOI: 10.1039/c5np00125k] [Citation(s) in RCA: 230] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This review discusses the biosynthesis of natural products that are generated bytrans-AT polyketide synthases, a family of catalytically versatile enzymes that represents one of the major group of proteins involved in the production of bioactive polyketides.
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Affiliation(s)
- Eric J. N. Helfrich
- Institute of Microbiology
- Eidgenössische Technische Hochschule (ETH) Zurich
- 8093 Zurich
- Switzerland
| | - Jörn Piel
- Institute of Microbiology
- Eidgenössische Technische Hochschule (ETH) Zurich
- 8093 Zurich
- Switzerland
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68
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Dolatabadi S, Scherlach K, Figge M, Hertweck C, Dijksterhuis J, Menken SBJ, de Hoog GS. Food preparation with mucoralean fungi: A potential biosafety issue? Fungal Biol 2015; 120:393-401. [PMID: 26895868 DOI: 10.1016/j.funbio.2015.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 11/26/2015] [Accepted: 12/01/2015] [Indexed: 02/04/2023]
Abstract
Mucorales have been used for production of fermented food in Asia and Africa since time immemorial. Particularly Rhizopus species are rapidly growing, active producers of lipases and proteases and occur naturally during the first stages of soybean fermentation. Two biosafety issues have been raised in recent literature: (1) pathogenicity, Rhizopus species being prevalent opportunists causing erosive infections in severely compromised patients, and (2) toxicity, strains harbouring endosymbiotic Burkholderia producing toxic secondary metabolites. At the molecular level, based on different gene markers, species identity was found between strains used for food processing and clinical strains. In this study, we screened for bacterial symbionts in 64 Rhizopus strains by light microscopy, 16S rRNA sequencing, and HPLC. Seven strains (11 %) carried bacteria identified as Burkholderia rhizoxinica and Burkholderia endofungorum, and an unknown Burkholderia species. The Burkholderia isolates proved to be able to produce toxic rhizoxins. Strains with endosymbionts originated from food, soil, and a clinical source, and thus their presence could not be linked to particular habitats. The presence of Burkholderia in Rhizopus producing toxins could not be excluded as a potential risk for human health. In contrast, given the type of diseases caused by Rhizopus species, we regard the practical risk of infection via the food industry as negligible.
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Affiliation(s)
- Somayeh Dolatabadi
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands; Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands; Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran.
| | - Kirstin Scherlach
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany
| | - Marian Figge
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany
| | | | - Steph B J Menken
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - G Sybren de Hoog
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands; Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands; Peking University Health Science Center, Research Center for Medical Mycology, Beijing, China; Chang Zheng Hospital, Second Military Medical University, Shanghai, China; Basic Pathology Department, Federal University of Paraná State, Curitiba, Paraná, Brazil; King Abdulaziz University, Jeddah, Saudi Arabia
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69
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Netzker T, Fischer J, Weber J, Mattern DJ, König CC, Valiante V, Schroeckh V, Brakhage AA. Microbial communication leading to the activation of silent fungal secondary metabolite gene clusters. Front Microbiol 2015; 6:299. [PMID: 25941517 PMCID: PMC4403501 DOI: 10.3389/fmicb.2015.00299] [Citation(s) in RCA: 212] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 03/26/2015] [Indexed: 11/22/2022] Open
Abstract
Microorganisms form diverse multispecies communities in various ecosystems. The high abundance of fungal and bacterial species in these consortia results in specific communication between the microorganisms. A key role in this communication is played by secondary metabolites (SMs), which are also called natural products. Recently, it was shown that interspecies “talk” between microorganisms represents a physiological trigger to activate silent gene clusters leading to the formation of novel SMs by the involved species. This review focuses on mixed microbial cultivation, mainly between bacteria and fungi, with a special emphasis on the induced formation of fungal SMs in co-cultures. In addition, the role of chromatin remodeling in the induction is examined, and methodical perspectives for the analysis of natural products are presented. As an example for an intermicrobial interaction elucidated at the molecular level, we discuss the specific interaction between the filamentous fungi Aspergillus nidulans and Aspergillus fumigatus with the soil bacterium Streptomyces rapamycinicus, which provides an excellent model system to enlighten molecular concepts behind regulatory mechanisms and will pave the way to a novel avenue of drug discovery through targeted activation of silent SM gene clusters through co-cultivations of microorganisms.
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Affiliation(s)
- Tina Netzker
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena , Jena, Germany
| | - Juliane Fischer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena , Jena, Germany
| | - Jakob Weber
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena , Jena, Germany
| | - Derek J Mattern
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena , Jena, Germany
| | - Claudia C König
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena , Jena, Germany
| | - Vito Valiante
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany
| | - Volker Schroeckh
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena , Jena, Germany
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70
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Horn F, Üzüm Z, Möbius N, Guthke R, Linde J, Hertweck C. Draft Genome Sequences of Symbiotic and Nonsymbiotic Rhizopus microsporus Strains CBS 344.29 and ATCC 62417. GENOME ANNOUNCEMENTS 2015; 3:e01370-14. [PMID: 25614557 PMCID: PMC4319578 DOI: 10.1128/genomea.01370-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 12/09/2014] [Indexed: 12/13/2022]
Abstract
Specific Rhizopus microsporus pathovars harbor bacterial endosymbionts (Burkholderia rhizoxinica) for the production of a phytotoxin. Here, we present the draft genome sequences of two R. microsporus strains, one symbiotic (ATCC 62417), and one endosymbiont-free (CBS 344.29). The gene predictions were supported by RNA sequencing (RNA-seq) data. The functional annotation sets the basis for comparative analyses.
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Affiliation(s)
- Fabian Horn
- Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Zerrin Üzüm
- Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Nadine Möbius
- Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Reinhard Guthke
- Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Jörg Linde
- Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Christian Hertweck
- Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
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71
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Uzum Z, Silipo A, Lackner G, De Felice A, Molinaro A, Hertweck C. Structure, Genetics and Function of an Exopolysaccharide Produced by a Bacterium Living within Fungal Hyphae. Chembiochem 2014; 16:387-92. [DOI: 10.1002/cbic.201402488] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Indexed: 11/08/2022]
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72
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Draft Genome Sequence of the Betaproteobacterial Endosymbiont Associated with the Fungus Mortierella elongata FMR23-6. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01272-14. [PMID: 25502669 PMCID: PMC4263831 DOI: 10.1128/genomea.01272-14] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The fungus Mortierella elongata FMR23-6 harbors an endobacterium inside its mycelium. Attempts to isolate the endobacterium from the fungus were not yet successful, but a highly purified bacterial fraction was prepared. Here, we report the draft genome sequence of the endobacterium.
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73
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Haq IU, Zhang M, Yang P, van Elsas JD. The interactions of bacteria with fungi in soil: emerging concepts. ADVANCES IN APPLIED MICROBIOLOGY 2014; 89:185-215. [PMID: 25131403 DOI: 10.1016/b978-0-12-800259-9.00005-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this chapter, we review the existing literature on bacterial-fungal interactions in soil, exploring the role fungi may play for soil bacteria as providers of hospitable niches. A focus is placed on the mycosphere, i.e., the narrow zone of influence of fungal hyphae on the external soil milieu, in which hypha-associated bacterial cells dwell. Evidence is brought forward for the contention that the hyphae of both mycorrhizal and saprotrophic fungi serve as providers of ecological opportunities in a grossly carbon-limited soil, as a result of their release of carbonaceous compounds next to the provision of a colonizable surface. Soil bacteria of particular nature are postulated to have adapted to such selection pressures, evolving to the extent that they acquired capabilities that allow them to thrive in the novel habitat created by the emerging fungal hyphae. The mechanisms involved in the interactions and the modes of genetic adaptation of the mycosphere dwellers are discussed, with an emphasis on one key mycosphere-adapted bacterium, Burkholderia terrae BS001. In this discussion, we interrogate the positive interactions between soil fungi and bacteria, and refrain from considering negative interactions.
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Affiliation(s)
- Irshad Ul Haq
- Department of Microbial Ecology, Center for Ecological and Evolutionary Studies (CEES), University of Groningen, Groningen, The Netherlands
| | - Miaozhi Zhang
- Department of Microbial Ecology, Center for Ecological and Evolutionary Studies (CEES), University of Groningen, Groningen, The Netherlands
| | - Pu Yang
- Department of Microbial Ecology, Center for Ecological and Evolutionary Studies (CEES), University of Groningen, Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Center for Ecological and Evolutionary Studies (CEES), University of Groningen, Groningen, The Netherlands.
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74
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Requena N, Fischer R. Breaking down walls to live in harmony. eLife 2014; 3:e04603. [PMID: 25268072 PMCID: PMC4179302 DOI: 10.7554/elife.04603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Some of the proteins and enzymes that allow bacteria to enter living fungal cells and cause rice seedling blight have been identified.
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Affiliation(s)
- Natalia Requena
- Natalia Requena is in the Department of Molecular Phytopathology, Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Reinhard Fischer
- Reinhard Fischer is in the Department of Microbiology, Institute for Applied Biosciences, Karlsruhe Institute of Technology, Karlsruhe, Germany
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75
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Moebius N, Üzüm Z, Dijksterhuis J, Lackner G, Hertweck C. Active invasion of bacteria into living fungal cells. eLife 2014; 3:e03007. [PMID: 25182414 PMCID: PMC4166002 DOI: 10.7554/elife.03007] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 08/29/2014] [Indexed: 12/12/2022] Open
Abstract
The rice seedling blight fungus Rhizopus microsporus and its endosymbiont Burkholderia rhizoxinica form an unusual, highly specific alliance to produce the highly potent antimitotic phytotoxin rhizoxin. Yet, it has remained a riddle how bacteria invade the fungal cells. Genome mining for potential symbiosis factors and functional analyses revealed that a type 2 secretion system (T2SS) of the bacterial endosymbiont is required for the formation of the endosymbiosis. Comparative proteome analyses show that the T2SS releases chitinolytic enzymes (chitinase, chitosanase) and chitin-binding proteins. The genes responsible for chitinolytic proteins and T2SS components are highly expressed during infection. Through targeted gene knock-outs, sporulation assays and microscopic investigations we found that chitinase is essential for bacteria to enter hyphae. Unprecedented snapshots of the traceless bacterial intrusion were obtained using cryo-electron microscopy. Beyond unveiling the pivotal role of chitinolytic enzymes in the active invasion of a fungus by bacteria, these findings grant unprecedented insight into the fungal cell wall penetration and symbiosis formation.
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Affiliation(s)
- Nadine Moebius
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Zerrin Üzüm
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | | | - Gerald Lackner
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
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76
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Haq IU, Graupner K, Nazir R, van Elsas JD. The genome of the fungal-interactive soil bacterium Burkholderia terrae BS001-a plethora of outstanding interactive capabilities unveiled. Genome Biol Evol 2014; 6:1652-68. [PMID: 24923325 PMCID: PMC4122924 DOI: 10.1093/gbe/evu126] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Burkholderia terrae strain BS001, obtained as an inhabitant of the mycosphere of Laccaria proxima (a close relative of Lyophyllum sp. strain Karsten), actively interacts with Lyophyllum sp. strain Karsten. We here summarize the remarkable ecological behavior of B. terrae BS001 in the mycosphere and add key data to this. Moreover, we extensively analyze the approximately 11.5-Mb five-replicon genome of B. terrae BS001 and highlight its remarkable features. Seventy-nine regions of genomic plasticity (RGP), that is, 16.48% of the total genome size, were found. One 70.42-kb RGP, RGP76, revealed a typical conjugal element structure, including a full type 4 secretion system. Comparative analyses across 24 related Burkholderia genomes revealed that 95.66% of the total BS001 genome belongs to the variable part, whereas the remaining 4.34% constitutes the core genome. Genes for biofilm formation and several secretion systems, under which a type 3 secretion system (T3SS), were found, which is consistent with the hypothesis that T3SSs play a role in the interaction with Lyophyllum sp. strain Karsten. The high number of predicted metabolic pathways and membrane transporters suggested that strain BS001 can take up and utilize a range of sugars, amino acids and organic acids. In particular, a unique glycerol uptake system was found. The BS001 genome further contains genetic systems for the degradation of complex organic compounds. Moreover, gene clusters encoding nonribosomal peptide synthetases (NRPS) and hybrid polyketide synthases/NRPS were found, highlighting the potential role of secondary metabolites in the ecology of strain BS001. The patchwork of genetic features observed in the genome is consistent with the notion that 1) horizontal gene transfer is a main driver of B. terrae BS001 adaptation and 2) the organism is very flexible in its ecological behavior in soil.
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Affiliation(s)
- Irshad Ul Haq
- Department of Microbial Ecology, Center for Ecological and Evolutionary Studies (CEES), University of Groningen, The Netherlands
| | - Katharina Graupner
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Rashid Nazir
- Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Center for Ecological and Evolutionary Studies (CEES), University of Groningen, The Netherlands
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Scherlach K, Graupner K, Hertweck C. Molecular Bacteria-Fungi Interactions: Effects on Environment, Food, and Medicine. Annu Rev Microbiol 2013; 67:375-97. [DOI: 10.1146/annurev-micro-092412-155702] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kirstin Scherlach
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany;
| | - Katharina Graupner
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany;
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany;
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78
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Bondarev V, Richter M, Romano S, Piel J, Schwedt A, Schulz-Vogt HN. The genus Pseudovibrio contains metabolically versatile bacteria adapted for symbiosis. Environ Microbiol 2013; 15:2095-113. [PMID: 23601235 PMCID: PMC3806328 DOI: 10.1111/1462-2920.12123] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 03/08/2013] [Accepted: 03/19/2013] [Indexed: 11/28/2022]
Abstract
The majority of strains belonging to the genus Pseudovibrio have been isolated from marine invertebrates such as tunicates, corals and particularly sponges, but the physiology of these bacteria is poorly understood. In this study, we analyse for the first time the genomes of two Pseudovibrio strains – FO-BEG1 and JE062. The strain FO-BEG1 is a required symbiont of a cultivated Beggiatoa strain, a sulfide-oxidizing, autotrophic bacterium, which was initially isolated from a coral. Strain JE062 was isolated from a sponge. The presented data show that both strains are generalistic bacteria capable of importing and oxidizing a wide range of organic and inorganic compounds to meet their carbon, nitrogen, phosphorous and energy requirements under both, oxic and anoxic conditions. Several physiological traits encoded in the analysed genomes were verified in laboratory experiments with both isolates. Besides the versatile metabolic abilities of both Pseudovibrio strains, our study reveals a number of open reading frames and gene clusters in the genomes that seem to be involved in symbiont–host interactions. Both Pseudovibrio strains have the genomic potential to attach to host cells, interact with the eukaryotic cell machinery, produce secondary metabolites and supply the host with cofactors.
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Affiliation(s)
- Vladimir Bondarev
- Max Planck Institute for Marine Microbiology, Ecophysiology Group, Celsiusstr. 1, 28359 Bremen, Germany
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79
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Nazir R, Warmink JA, Voordes DC, van de Bovenkamp HH, van Elsas JD. Inhibition of mushroom formation and induction of glycerol release-ecological strategies of Burkholderia terrae BS001 to create a hospitable niche at the fungus Lyophyllum sp. strain Karsten. MICROBIAL ECOLOGY 2013; 65:245-54. [PMID: 22915155 DOI: 10.1007/s00248-012-0100-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 07/25/2012] [Indexed: 05/21/2023]
Abstract
We investigated the ecological strategies exerted by the soil bacterium Burkholderia terrae BS001 at the hyphae of the soil saprotrophic fungus Lyophyllum sp. strain Karsten. Recently, this bacterium has been reported to form biofilms around, and to comigrate with, growing hyphae of Lyophyllum sp. strain Karsten. In addition, it was found to be able to utilize fungal metabolites. Here, we extend this work to shed some light on the interactions between the bacterial and fungal partner which allow ecological success for the former. In standing liquid microcosms inoculated with Lyophyllum sp. strain Karsten, we detected, upon prolonged incubation, the formation of a mycelial mat at the liquid-air interface. From this mat, primordia were formed after 4-6 weeks, which eventually resulted in mushrooms. However, upon addition of strain BS001 to the bulk liquid, mushroom formation from the fungal mat was clearly inhibited, as evidenced by (1) the formation of significantly lower numbers of primordia and (2) a delay of the onset of primordia formation. Moreover and importantly, the presence of strain BS001 caused the fungus to secrete large amounts of exudates at the mycelial mat, whereas such exudation was absent from control (uninoculated) or Escherichia coli K12- or Variovorax paradoxus BS64-inoculated microcosms. In the exudates, glycerol was the main carbonaceous component, and this compound could be easily utilized by strain BS001. Thus, in different experimental set-ups with the fungal partner, strain BS001 was shown to grow in the fungal exudates on the mat. The two fungal-interactive phenotypes were specific for B. terrae strain BS001, as the other bacteria used in our study, i.e. E. coli K12 and V. paradoxus BS64, did not exhibit any of these phenomena.
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Affiliation(s)
- Rashid Nazir
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Linneausborg, Nijenborgh 7, 9747 Groningen, Netherlands.
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80
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Complete genome sequence of the endophytic bacterium Burkholderia sp. strain KJ006. J Bacteriol 2012; 194:4432-3. [PMID: 22843575 DOI: 10.1128/jb.00821-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Endophytes live inside plant tissues without causing any harm and may even benefit plants. Here, we provide the high-quality genome sequence of Burkholderia sp. strain KJ006, an endophytic bacterium of rice with antifungal activity. The 6.6-Mb genome, consisting of three chromosomes and a single plasmid, contains genes related to plant growth promotion or degradation of aromatic compounds.
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81
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Abby SS, Rocha EPC. The non-flagellar type III secretion system evolved from the bacterial flagellum and diversified into host-cell adapted systems. PLoS Genet 2012; 8:e1002983. [PMID: 23028376 PMCID: PMC3459982 DOI: 10.1371/journal.pgen.1002983] [Citation(s) in RCA: 202] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 08/09/2012] [Indexed: 12/20/2022] Open
Abstract
Type 3 secretion systems (T3SSs) are essential components of two complex bacterial machineries: the flagellum, which drives cell motility, and the non-flagellar T3SS (NF-T3SS), which delivers effectors into eukaryotic cells. Yet the origin, specialization, and diversification of these machineries remained unclear. We developed computational tools to identify homologous components of the two systems and to discriminate between them. Our analysis of >1,000 genomes identified 921 T3SSs, including 222 NF-T3SSs. Phylogenomic and comparative analyses of these systems argue that the NF-T3SS arose from an exaptation of the flagellum, i.e. the recruitment of part of the flagellum structure for the evolution of the new protein delivery function. This reconstructed chronology of the exaptation process proceeded in at least two steps. An intermediate ancestral form of NF-T3SS, whose descendants still exist in Myxococcales, lacked elements that are essential for motility and included a subset of NF-T3SS features. We argue that this ancestral version was involved in protein translocation. A second major step in the evolution of NF-T3SSs occurred via recruitment of secretins to the NF-T3SS, an event that occurred at least three times from different systems. In rhizobiales, a partial homologous gene replacement of the secretin resulted in two genes of complementary function. Acquisition of a secretin was followed by the rapid adaptation of the resulting NF-T3SSs to multiple, distinct eukaryotic cell envelopes where they became key in parasitic and mutualistic associations between prokaryotes and eukaryotes. Our work elucidates major steps of the evolutionary scenario leading to extant NF-T3SSs. It demonstrates how molecular evolution can convert one complex molecular machine into a second, equally complex machine by successive deletions, innovations, and recruitment from other molecular systems.
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Affiliation(s)
- Sophie S Abby
- Département Génomes et Génétique, Institut Pasteur, Microbial Evolutionary Genomics, Paris, France.
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82
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Scherlach K, Busch B, Lackner G, Paszkowski U, Hertweck C. Symbiotic Cooperation in the Biosynthesis of a Phytotoxin. Angew Chem Int Ed Engl 2012; 51:9615-8. [DOI: 10.1002/anie.201204540] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Indexed: 01/08/2023]
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83
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Scherlach K, Busch B, Lackner G, Paszkowski U, Hertweck C. Symbiotic Cooperation in the Biosynthesis of a Phytotoxin. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201204540] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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84
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Production of the Quorum-Sensing Molecules N-Acylhomoserine Lactones by Endobacteria Associated with Mortierella alpina A-178. Chembiochem 2012; 13:1776-84. [DOI: 10.1002/cbic.201200263] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Indexed: 12/19/2022]
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85
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Kusari S, Hertweck C, Spiteller M. Chemical Ecology of Endophytic Fungi: Origins of Secondary Metabolites. ACTA ACUST UNITED AC 2012; 19:792-8. [DOI: 10.1016/j.chembiol.2012.06.004] [Citation(s) in RCA: 456] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 05/08/2012] [Accepted: 06/04/2012] [Indexed: 11/26/2022]
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86
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Carlier AL, Eberl L. The eroded genome of a Psychotria leaf symbiont: hypotheses about lifestyle and interactions with its plant host. Environ Microbiol 2012; 14:2757-69. [PMID: 22548823 DOI: 10.1111/j.1462-2920.2012.02763.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Several plant species of the genus Psychotria (Rubiaceae) harbour Burkholderia sp. bacteria within specialized leaf nodules. The bacteria are transmitted vertically between plant generations and have not yet been cultured outside of their host. This symbiosis is also generally described as obligatory because plants devoid of symbionts fail to develop into mature individuals. We sequenced for the first time the genome of the symbiont of Psychotria kirkii in order to shed some light on the nature of their symbiotic relationship. We found that the 4 Mb genome of Candidatus Burkholderia kirkii (B. kirkii) is small for a Burkholderia species and displays features consistent with ongoing genome erosion such as large proportions of pseudogenes and transposable elements. Reductive genome evolution affected a wide array of functional categories that may hinder the ability of the symbiont to be free-living. The genome does not encode functions commonly found in plant symbionts such as nitrogen fixation or plant hormone metabolism. Instead, a collection of genes for secondary metabolites' synthesis is located on the 140 kb plasmid of B. kirkii and suggests that leaf nodule symbiosis benefits the host by providing protection against herbivores or pathogens.
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Affiliation(s)
- Aurelien L Carlier
- Institute of Plant Biology, University of Zurich, CH-8008 Zurich, Switzerland.
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87
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Ghignone S, Salvioli A, Anca I, Lumini E, Ortu G, Petiti L, Cruveiller S, Bianciotto V, Piffanelli P, Lanfranco L, Bonfante P. The genome of the obligate endobacterium of an AM fungus reveals an interphylum network of nutritional interactions. THE ISME JOURNAL 2012; 6:136-45. [PMID: 21866182 PMCID: PMC3246228 DOI: 10.1038/ismej.2011.110] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 07/11/2011] [Accepted: 07/11/2011] [Indexed: 11/08/2022]
Abstract
As obligate symbionts of most land plants, arbuscular mycorrhizal fungi (AMF) have a crucial role in ecosystems, but to date, in the absence of genomic data, their adaptive biology remains elusive. In addition, endobacteria are found in their cytoplasm, the role of which is unknown. In order to investigate the function of the Gram-negative Candidatus Glomeribacter gigasporarum, an endobacterium of the AMF Gigaspora margarita, we sequenced its genome, leading to an ∼1.72-Mb assembly. Phylogenetic analyses placed Ca. G. gigasporarum in the Burkholderiaceae whereas metabolic network analyses clustered it with insect endobacteria. This positioning of Ca. G. gigasporarum among different bacterial classes reveals that it has undergone convergent evolution to adapt itself to intracellular lifestyle. The genome annotation of this mycorrhizal-fungal endobacterium has revealed an unexpected genetic mosaic where typical determinants of symbiotic, pathogenic and free-living bacteria are integrated in a reduced genome. Ca. G. gigasporarum is an aerobic microbe that depends on its host for carbon, phosphorus and nitrogen supply; it also expresses type II and type III secretion systems and synthesizes vitamin B12, antibiotics- and toxin-resistance molecules, which may contribute to the fungal host's ecological fitness. Ca. G. gigasporarum has an extreme dependence on its host for nutrients and energy, whereas the fungal host is itself an obligate biotroph that relies on a photosynthetic plant. Our work represents the first step towards unraveling a complex network of interphylum interactions, which is expected to have a previously unrecognized ecological impact.
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Affiliation(s)
| | | | - Iulia Anca
- Dipartimento di Biologia Vegetale and IPP-CNR, Torino, Italy
| | - Erica Lumini
- Dipartimento di Biologia Vegetale and IPP-CNR, Torino, Italy
| | - Giuseppe Ortu
- Dipartimento di Biologia Vegetale and IPP-CNR, Torino, Italy
| | - Luca Petiti
- Dipartimento di Biologia Vegetale and IPP-CNR, Torino, Italy
| | | | | | | | - Luisa Lanfranco
- Dipartimento di Biologia Vegetale and IPP-CNR, Torino, Italy
| | - Paola Bonfante
- Dipartimento di Biologia Vegetale and IPP-CNR, Torino, Italy
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88
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Frey-Klett P, Burlinson P, Deveau A, Barret M, Tarkka M, Sarniguet A. Bacterial-fungal interactions: hyphens between agricultural, clinical, environmental, and food microbiologists. Microbiol Mol Biol Rev 2011; 75:583-609. [PMID: 22126995 PMCID: PMC3232736 DOI: 10.1128/mmbr.00020-11] [Citation(s) in RCA: 461] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Bacteria and fungi can form a range of physical associations that depend on various modes of molecular communication for their development and functioning. These bacterial-fungal interactions often result in changes to the pathogenicity or the nutritional influence of one or both partners toward plants or animals (including humans). They can also result in unique contributions to biogeochemical cycles and biotechnological processes. Thus, the interactions between bacteria and fungi are of central importance to numerous biological questions in agriculture, forestry, environmental science, food production, and medicine. Here we present a structured review of bacterial-fungal interactions, illustrated by examples sourced from many diverse scientific fields. We consider the general and specific properties of these interactions, providing a global perspective across this emerging multidisciplinary research area. We show that in many cases, parallels can be drawn between different scenarios in which bacterial-fungal interactions are important. Finally, we discuss how new avenues of investigation may enhance our ability to combat, manipulate, or exploit bacterial-fungal complexes for the economic and practical benefit of humanity as well as reshape our current understanding of bacterial and fungal ecology.
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Affiliation(s)
- P Frey-Klett
- INRA, UMR1136 Interactions Arbres-Microorganismes, 54280 Champenoux, France.
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89
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Silipo A, Leone MR, Lanzetta R, Parrilli M, Lackner G, Busch B, Hertweck C, Molinaro A. Structural characterization of two lipopolysaccharide O-antigens produced by the endofungal bacterium Burkholderia sp. HKI-402 (B4). Carbohydr Res 2011; 347:95-8. [PMID: 22115719 DOI: 10.1016/j.carres.2011.10.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Revised: 10/21/2011] [Accepted: 10/25/2011] [Indexed: 12/22/2022]
Abstract
Two different polysaccharides were isolated and identified from the lipopolysaccharide fraction of endofungal bacterium Burkholderia sp. HKI-402 (B4). The complete structure was elucidated by chemical analysis and 2D NMR spectroscopy as the following:
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Affiliation(s)
- Alba Silipo
- Dipartimento di Chimica Organica e Biochimica, Università di Napoli Federico II, via Cintia 4, 80126 Napoli, Italy
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90
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Bacteria-induced natural product formation in the fungus Aspergillus nidulans requires Saga/Ada-mediated histone acetylation. Proc Natl Acad Sci U S A 2011; 108:14282-7. [PMID: 21825172 DOI: 10.1073/pnas.1103523108] [Citation(s) in RCA: 234] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Sequence analyses of fungal genomes have revealed that the potential of fungi to produce secondary metabolites is greatly underestimated. In fact, most gene clusters coding for the biosynthesis of antibiotics, toxins, or pigments are silent under standard laboratory conditions. Hence, it is one of the major challenges in microbiology to uncover the mechanisms required for pathway activation. Recently, we discovered that intimate physical interaction of the important model fungus Aspergillus nidulans with the soil-dwelling bacterium Streptomyces rapamycinicus specifically activated silent fungal secondary metabolism genes, resulting in the production of the archetypal polyketide orsellinic acid and its derivatives. Here, we report that the streptomycete triggers modification of fungal histones. Deletion analysis of 36 of 40 acetyltransferases, including histone acetyltransferases (HATs) of A. nidulans, demonstrated that the Saga/Ada complex containing the HAT GcnE and the AdaB protein is required for induction of the orsellinic acid gene cluster by the bacterium. We also showed that Saga/Ada plays a major role for specific induction of other biosynthesis gene clusters, such as sterigmatocystin, terrequinone, and penicillin. Chromatin immunoprecipitation showed that the Saga/Ada-dependent increase of histone 3 acetylation at lysine 9 and 14 occurs during interaction of fungus and bacterium. Furthermore, the production of secondary metabolites in A. nidulans is accompanied by a global increase in H3K14 acetylation. Increased H3K9 acetylation, however, was only found within gene clusters. This report provides previously undescribed evidence of Saga/Ada dependent histone acetylation triggered by prokaryotes.
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91
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92
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Lackner G, Moebius N, Partida-Martinez LP, Boland S, Hertweck C. Evolution of an endofungal lifestyle: Deductions from the Burkholderia rhizoxinica genome. BMC Genomics 2011; 12:210. [PMID: 21539752 PMCID: PMC3102044 DOI: 10.1186/1471-2164-12-210] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Accepted: 05/04/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Burkholderia rhizoxinica is an intracellular symbiont of the phytopathogenic zygomycete Rhizopus microsporus, the causative agent of rice seedling blight. The endosymbiont produces the antimitotic macrolide rhizoxin for its host. It is vertically transmitted within vegetative spores and is essential for spore formation of the fungus. To shed light on the evolution and genetic potential of this model organism, we analysed the whole genome of B. rhizoxinica HKI 0454 - a type strain of endofungal Burkholderia species. RESULTS The genome consists of a structurally conserved chromosome and two plasmids. Compared to free-living Burkholderia species, the genome is smaller in size and harbors less transcriptional regulator genes. Instead, we observed accumulation of transposons over the genome. Prediction of primary metabolic pathways and transporters suggests that endosymbionts consume host metabolites like citrate, but might deliver some amino acids and cofactors to the host. The rhizoxin biosynthesis gene cluster shows evolutionary traces of horizontal gene transfer. Furthermore, we analysed gene clusters coding for nonribosomal peptide synthetases (NRPS). Notably, B. rhizoxinica lacks common genes which are dedicated to quorum sensing systems, but is equipped with a large number of virulence-related factors and putative type III effectors. CONCLUSIONS B. rhizoxinica is the first endofungal bacterium, whose genome has been sequenced. Here, we present models of evolution, metabolism and tools for host-symbiont interaction of the endofungal bacterium deduced from whole genome analyses. Genome size and structure suggest that B. rhizoxinica is in an early phase of adaptation to the intracellular lifestyle (genome in transition). By analysis of tranporters and metabolic pathways we predict how metabolites might be exchanged between the symbiont and its host. Gene clusters for biosynthesis of secondary metabolites represent novel targets for genomic mining of cryptic natural products. In silico analyses of virulence-associated genes, secreted proteins and effectors might inspire future studies on molecular mechanisms underlying bacterial-fungal interaction.
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Affiliation(s)
- Gerald Lackner
- Leibniz Institute for Natural Product Research and Infection Biology (HKI), Department of Biomolecular Chemistry, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Nadine Moebius
- Leibniz Institute for Natural Product Research and Infection Biology (HKI), Department of Biomolecular Chemistry, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Laila P Partida-Martinez
- Leibniz Institute for Natural Product Research and Infection Biology (HKI), Department of Biomolecular Chemistry, Beutenbergstr. 11a, 07745 Jena, Germany
- Departamento de Ingeniería Genética, CINVESTAV-Irapuato, Km. 9.6 Libramiento Norte, CP 36821 Irapuato, Guanajuato, México
| | - Sebastian Boland
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology (HKI), Department of Biomolecular Chemistry, Beutenbergstr. 11a, 07745 Jena, Germany
- Friedrich Schiller University, 07743 Jena, Germany
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93
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Complete genome sequence of Burkholderia rhizoxinica, an Endosymbiont of Rhizopus microsporus. J Bacteriol 2010; 193:783-4. [PMID: 21131495 DOI: 10.1128/jb.01318-10] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Burkholderia rhizoxinica is an intracellular symbiont of the phytopathogenic fungus Rhizopus microsporus. The vertically transmitted endosymbiont not only delivers the antimitotic macrolide rhizoxin to its host but is also essential for vegetative spore formation of the fungus. To shed light on the genetic equipment of this model organism, we sequenced the whole genome of B. rhizoxinica HKI 0454, thus providing the first genomic insight into an intracellular mutualist of a fungal species. The 3.75-Mb genome consists of a chromosome and two strain-specific plasmids. The primary metabolism appears to be specialized for the uptake of fungal metabolites. Besides the rhizoxin biosynthesis gene cluster, there are 14 loci coding for nonribosomal peptide synthetase (NRPS) assembly lines, which represent novel targets for genomic mining of cryptic natural products. Furthermore, the endosymbionts are equipped with a repertoire of virulence-related factors, which can now be studied to elucidate molecular mechanisms underlying bacterial-fungal interaction.
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94
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A helping hand. Nat Rev Microbiol 2010; 8:758. [PMID: 21080561 DOI: 10.1038/nrmicro2466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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