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Longley R, Robinson A, Liber JA, Bryson AE, Morales DP, LaButti K, Riley R, Mondo SJ, Kuo A, Yoshinaga Y, Daum C, Barry K, Grigoriev IV, Desirò A, Chain PSG, Bonito G. Comparative genomics of Mollicutes-related endobacteria supports a late invasion into Mucoromycota fungi. Commun Biol 2023; 6:948. [PMID: 37723238 PMCID: PMC10507103 DOI: 10.1038/s42003-023-05299-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 08/29/2023] [Indexed: 09/20/2023] Open
Abstract
Diverse members of early-diverging Mucoromycota, including mycorrhizal taxa and soil-associated Mortierellaceae, are known to harbor Mollicutes-related endobacteria (MRE). It has been hypothesized that MRE were acquired by a common ancestor and transmitted vertically. Alternatively, MRE endosymbionts could have invaded after the divergence of Mucoromycota lineages and subsequently spread to new hosts horizontally. To better understand the evolutionary history of MRE symbionts, we generated and analyzed four complete MRE genomes from two Mortierellaceae genera: Linnemannia (MRE-L) and Benniella (MRE-B). These genomes include the smallest known of fungal endosymbionts and showed signals of a tight relationship with hosts including a reduced functional capacity and genes transferred from fungal hosts to MRE. Phylogenetic reconstruction including nine MRE from mycorrhizal fungi revealed that MRE-B genomes are more closely related to MRE from Glomeromycotina than MRE-L from the same host family. We posit that reductions in genome size, GC content, pseudogene content, and repeat content in MRE-L may reflect a longer-term relationship with their fungal hosts. These data indicate Linnemannia and Benniella MRE were likely acquired independently after their fungal hosts diverged from a common ancestor. This work expands upon foundational knowledge on minimal genomes and provides insights into the evolution of bacterial endosymbionts.
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Affiliation(s)
- Reid Longley
- Los Alamos National Laboratory, Los Alamos, NM, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Julian A Liber
- Department of Biology, Duke University, Durham, NC, 27704, USA
| | - Abigail E Bryson
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Kurt LaButti
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Robert Riley
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Stephen J Mondo
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80521, USA
| | - Alan Kuo
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuko Yoshinaga
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Chris Daum
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Alessandro Desirò
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Gregory Bonito
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA.
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Desirò A, Takashima Y, Bonito G, Nishizawa T, Narisawa K, Bonfante P. Investigating Endobacteria that Thrive Within Mucoromycota. Methods Mol Biol 2022; 2605:293-323. [PMID: 36520400 DOI: 10.1007/978-1-0716-2871-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Metagenomics approaches have revealed the importance of Mucoromycota in the evolution and functioning of plant microbiomes. Comprised of three subphyla (Glomeromycotina, Mortierellomycotina, and Mucoromycotina), this early diverging lineage of fungi encompasses species of mycorrhizal fungi, root endophytes, plant pathogens, and many decomposers of plant debris. Interestingly, several taxa of Mucoromycota share a common feature, that is, the presence of endobacteria within their mycelia and spores. The study of these endosymbiotic bacteria is still a challenging task. However, given recent improvements in the sensitivity of culture-free approaches, a deeper understanding of such microbial interactions is now possible and fuels an emerging research field. In this chapter, we report how Mucoromycota, in particular Mortierellomycotina, and their endobacteria can be investigated using a combination of diverse cellular biology, microscopy, and molecular techniques.
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Affiliation(s)
- Alessandro Desirò
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Yusuke Takashima
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Nagano, Japan
| | - Gregory Bonito
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | | | | | - Paola Bonfante
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy.
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Venice F, Desirò A, Silva G, Salvioli A, Bonfante P. The Mosaic Architecture of NRPS-PKS in the Arbuscular Mycorrhizal Fungus Gigaspora margarita Shows a Domain With Bacterial Signature. Front Microbiol 2020; 11:581313. [PMID: 33329443 PMCID: PMC7732545 DOI: 10.3389/fmicb.2020.581313] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/29/2020] [Indexed: 12/31/2022] Open
Abstract
As obligate biotrophic symbionts, arbuscular mycorrhizal fungi (AMF) live in association with most land plants. Among them, Gigaspora margarita has been deeply investigated because of its peculiar features, i.e., the presence of an intracellular microbiota with endobacteria and viruses. The genome sequencing of this fungus revealed the presence of some hybrid non-ribosomal peptide synthases-polyketide synthases (NRPS-PKS) that have been rarely identified in AMF. The aim of this study is to describe the architecture of these NRPS-PKS sequences and to understand whether they are present in other fungal taxa related to G. margarita. A phylogenetic analysis shows that the ketoacyl synthase (KS) domain of one G. margarita NRPS-PKS clusters with prokaryotic sequences. Since horizontal gene transfer (HGT) has often been advocated as a relevant evolutionary mechanism for the spread of secondary metabolite genes, we hypothesized that a similar event could have interested the KS domain of the PKS module. The bacterial endosymbiont of G. margarita, Candidatus Glomeribacter gigasporarum (CaGg), was the first candidate as a donor, since it possesses a large biosynthetic cluster involving an NRPS-PKS. However, bioinformatics analyses do not confirm the hypothesis of a direct HGT from the endobacterium to the fungal host: indeed, endobacterial and fungal sequences show a different evolution and potentially different donors. Lastly, by amplifying a NRPS-PKS conserved fragment and mining the sequenced AMF genomes, we demonstrate that, irrespective of the presence of CaGg, G. margarita, and some other related Gigasporaceae possess such a sequence.
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Affiliation(s)
- Francesco Venice
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy.,Institute for Sustainable Plant Protection (IPSP)-SS Turin-National Research Council (CNR), Turin, Italy
| | - Alessandro Desirò
- Department of Plant, Soil and Microbial Sciences, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States
| | - Gladstone Silva
- Department of Mycology, Federal University of Pernambuco, Recife, Brazil
| | - Alessandra Salvioli
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
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Vandepol N, Liber J, Desirò A, Na H, Kennedy M, Barry K, Grigoriev IV, Miller AN, O'Donnell K, Stajich JE, Bonito G. Resolving the Mortierellaceae phylogeny through synthesis of multi-gene phylogenetics and phylogenomics. FUNGAL DIVERS 2020; 104:267-289. [PMID: 33364917 PMCID: PMC7751987 DOI: 10.1007/s13225-020-00455-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/25/2020] [Indexed: 12/15/2022]
Abstract
Early efforts to classify Mortierellaceae were based on macro- and micromorphology, but sequencing and phylogenetic studies with ribosomal DNA (rDNA) markers have demonstrated conflicting taxonomic groupings and polyphyletic genera. Although some taxonomic confusion in the family has been clarified, rDNA data alone is unable to resolve higher level phylogenetic relationships within Mortierellaceae. In this study, we applied two parallel approaches to resolve the Mortierellaceae phylogeny: low coverage genome (LCG) sequencing and high-throughput, multiplexed targeted amplicon sequencing to generate sequence data for multi-gene phylogenetics. We then combined our datasets to provide a well-supported genome-based phylogeny having broad sampling depth from the amplicon dataset. Resolving the Mortierellaceae phylogeny into monophyletic groups led to the definition of 14 genera, 7 of which are newly proposed. Low-coverage genome sequencing proved to be a relatively cost-effective means of generating a well-resolved phylogeny. The multi-gene phylogenetics approach enabled much greater sampling depth and breadth than the LCG approach, but was unable to resolve higher-level organization of groups. We present this work to resolve some of the taxonomic confusion and provide a genus-level framework to empower future studies on Mortierellaceae diversity, biology, and evolution.
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Affiliation(s)
- Natalie Vandepol
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing MI 48824, USA
| | - Julian Liber
- Department of Plant Biology, Michigan State University, East Lansing MI 48824, USA
| | - Alessandro Desirò
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing MI 48824, USA
| | - Hyunsoo Na
- Joint Genome Institute, Berkeley, CA 94720, USA
| | | | | | | | - Andrew N Miller
- Illinois Natural History Survey, University of Illinois Urbana-Champaign, Champaign, IL 61820, USA
| | - Kerry O'Donnell
- United States Department of Agriculture, Agricultural Research Service, Peoria, IL 61604, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology & Institute for Integrative Genome Biology, University of California-Riverside, Riverside CA 92521, USA
| | - Gregory Bonito
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing MI 48824, USA
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing MI 48824, USA
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Olivieri E, Epis S, Castelli M, Varotto Boccazzi I, Romeo C, Desirò A, Bazzocchi C, Bandi C, Sassera D. Tissue tropism and metabolic pathways of Midichloria mitochondrii suggest tissue-specific functions in the symbiosis with Ixodes ricinus. Ticks Tick Borne Dis 2019; 10:1070-1077. [PMID: 31176662 DOI: 10.1016/j.ttbdis.2019.05.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/09/2019] [Accepted: 05/31/2019] [Indexed: 12/20/2022]
Abstract
A wide range of arthropod species harbour bacterial endosymbionts in various tissues, many of them playing important roles in the fitness and biology of their hosts. In several cases, many different symbionts have been reported to coexist simultaneously within the same host and synergistic or antagonistic interactions can occur between them. While the associations with endosymbiotic bacteria have been widely studied in many insect species, in ticks such interactions are less investigated. The females and immatures of Ixodes ricinus (Ixodidae), the most common hard tick in Europe, harbour the intracellular endosymbiont "Candidatus Midichloria mitochondrii" with a prevalence up to 100%, suggesting a mutualistic relationship. Considering that the tissue distribution of a symbiont might be indicative of its functional role in the physiology of the host, we investigated M. mitochondrii specific localization pattern and the corresponding abundance in selected organs of I. ricinus females. We paired these experiments with in silico analysis of the metabolic pathways of M. mitochondrii, inferred from the available genome sequence, and additionally compared the presence of these pathways in seven other symbionts commonly harboured by ticks to try to obtain a comparative understanding of their biological effects on the tick hosts. M. mitochondrii was found to be abundant in ovaries and tracheae of unfed I. ricinus, and in ovaries, Malpighian tubules and salivary glands of semi-engorged females. These results, together with the in silico metabolic reconstruction allow to hypothesize that the bacterium could play multiple tissue-specific roles in the host, both enhancing the host fitness (supplying essential nutrients, enhancing the reproductive fitness, helping in the anti-oxidative defence, in the energy production and in the maintenance of homeostasis and water balance) and/or for ensuring its presence in the host population (nutrients acquisition, vertical and horizontal transmission). The ability of M. mitochondrii to colonize different tissues allows to speculate that distinctive sub-populations may display different specializations in accordance with tissue tropism. Our hypotheses should be corroborated with future nutritional and physiological experiments for a better understanding of the mechanisms underlying this symbiotic interaction.
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Affiliation(s)
- Emanuela Olivieri
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Sara Epis
- Department of Biosciences University of Milan, Milan, Italy; Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", University of Milan, 20133, Milan, Italy
| | - Michele Castelli
- Department of Biosciences University of Milan, Milan, Italy; Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", University of Milan, 20133, Milan, Italy
| | - Ilaria Varotto Boccazzi
- Department of Biosciences University of Milan, Milan, Italy; Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", University of Milan, 20133, Milan, Italy
| | - Claudia Romeo
- Department of Veterinary Medicine, Università degli Studi di Milano, via Celoria 10, 20133, Milano, Italy
| | - Alessandro Desirò
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Chiara Bazzocchi
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", University of Milan, 20133, Milan, Italy; Department of Veterinary Medicine, Università degli Studi di Milano, via Celoria 10, 20133, Milano, Italy; Coordinated Research Center "EpiSoMI", University of Milan, 20133, Milan, Italy
| | - Claudio Bandi
- Department of Biosciences University of Milan, Milan, Italy; Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", University of Milan, 20133, Milan, Italy
| | - Davide Sassera
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, 27100, Pavia, Italy.
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Chang Y, Desirò A, Na H, Sandor L, Lipzen A, Clum A, Barry K, Grigoriev IV, Martin FM, Stajich JE, Smith ME, Bonito G, Spatafora JW. Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota. New Phytol 2019; 222:511-525. [PMID: 30485448 DOI: 10.1111/nph.15613] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 10/29/2018] [Indexed: 06/09/2023]
Abstract
Endogonales (Mucoromycotina), composed of Endogonaceae and Densosporaceae, is the only known non-Dikarya order with ectomycorrhizal members. They also form mycorrhizal-like association with some nonspermatophyte plants. It has been recently proposed that Endogonales were among the earliest mycorrhizal partners with land plants. It remains unknown whether Endogonales possess genomes with mycorrhizal-lifestyle signatures and whether Endogonales originated around the same time as land plants did. We sampled sporocarp tissue from four Endogonaceae collections and performed shotgun genome sequencing. After binning the metagenome data, we assembled and annotated the Endogonaceae genomes. We performed comparative analysis on plant-cell-wall-degrading enzymes (PCWDEs) and small secreted proteins (SSPs). We inferred phylogenetic placement of Endogonaceae and estimated the ages of Endogonaceae and Endogonales with expanded taxon sampling. Endogonaceae have large genomes with high repeat content, low diversity of PCWDEs, but without elevated SSP/secretome ratios. Dating analysis estimated that Endogonaceae originated in the Permian-Triassic boundary and Endogonales originated in the mid-late Silurian. Mycoplasma-related endobacterium sequences were identified in three Endogonaceae genomes. Endogonaceae genomes possess typical signatures of mycorrhizal lifestyle. The early origin of Endogonales suggests that the mycorrhizal association between Endogonales and plants might have played an important role during the colonization of land by plants.
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Affiliation(s)
- Ying Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Alessandro Desirò
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Hyunsoo Na
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Laura Sandor
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Francis M Martin
- Institut national de la recherche agronomique, Laboratoire d'excellence ARBRE, Centre INRA-Grand Est, Unité mixte de recherche Inra-Université de Lorraine "Interactions Arbres/Microorganismes", 54280, Champenoux, France
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - Gregory Bonito
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
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Desirò A, Hao Z, Liber JA, Benucci GMN, Lowry D, Roberson R, Bonito G. Mycoplasma-related endobacteria within Mortierellomycotina fungi: diversity, distribution and functional insights into their lifestyle. ISME J 2018; 12:1743-1757. [PMID: 29476142 DOI: 10.1038/s41396-018-0053-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 12/22/2017] [Accepted: 01/10/2018] [Indexed: 11/09/2022]
Abstract
Bacterial interactions with animals and plants have been examined for over a century; by contrast, the study of bacterial-fungal interactions has received less attention. Bacteria interact with fungi in diverse ways, and endobacteria that reside inside fungal cells represent the most intimate interaction. The most significant bacterial endosymbionts that have been studied are associated with Mucoromycota and include two main groups: Burkholderia-related and Mycoplasma-related endobacteria (MRE). Examples of Burkholderia-related endobacteria have been reported in the three Mucoromycota subphyla. By contrast, MRE have only been identified in Glomeromycotina and Mucoromycotina. This study aims to understand whether MRE dwell in Mortierellomycotina and, if so, to determine their impact on the fungal host. We carried out a large-scale screening of 394 Mortierellomycotina strains and employed a combination of microscopy, molecular phylogeny, next-generation sequencing and qPCR. We detected MRE in 12 strains. These endosymbionts represent novel bacterial phylotypes and show evidence of recombination. Their presence in Mortierellomycotina demonstrates that MRE occur within fungi across Mucoromycota and they may have lived in their common ancestor. We cured the fungus of its endosymbionts with antibiotics and observed improved biomass production in isogenic lines lacking MRE, demonstrating that these endobacteria impose some fitness costs to their fungal host. Here we provided the first functional insights into the lifestyle of MRE. Our findings indicate that MRE may be antagonistic to their fungal hosts, and adapted to a non-lethal parasitic lifestyle in the mycelium of Mucoromycota. However, context-dependent adaptive benefits to their host at minimal cost cannot not be excluded. Finally, we conclude that Mortierellomycotina represent attractive model organisms for exploring interactions between MRE and fungi.
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Affiliation(s)
- Alessandro Desirò
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA.
| | - Zhen Hao
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Julian A Liber
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | | | - David Lowry
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Robert Roberson
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Gregory Bonito
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
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Desirò A, Rimington WR, Jacob A, Pol NV, Smith ME, Trappe JM, Bidartondo MI, Bonito G. Multigene phylogeny of Endogonales, an early diverging lineage of fungi associated with plants. IMA Fungus 2017; 8:245-257. [PMID: 29242774 PMCID: PMC5729711 DOI: 10.5598/imafungus.2017.08.02.03] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 09/27/2017] [Indexed: 12/25/2022] Open
Abstract
Endogonales is a lineage of early diverging fungi within Mucoromycota. Many species in this order produce small sporophores (“sporocarps”) containing a large number of zygospores, and many species form symbioses with plants. However, due to limited collections, subtle morphological differentiation, difficulties in growing these organisms in vitro, and idiosyncrasies in their rDNA that make PCR amplification difficult, the systematics and character evolution of these fungi have been challenging to resolve. To overcome these challenges we generated a multigene phylogeny of Endogonales using sporophores collected over the past three decades from four continents. Our results show that Endogonales harbour significant undescribed diversity and form two deeply divergent and well-supported phylogenetic clades, which we delimit as the families Endogonaceae and Densosporaceae fam. nov. The family Densosporaceae consists of the genus Densospora,Sphaerocreas pubescens, and many diverse lineages known only from environmental DNA sequences of plant-endosymbiotic fungi. Within Endogonaceae there are two clades. One corresponds to Endogone and includes the type species, E. pisiformis. Species of Endogone are characterized by above- and below-ground sporophores, a hollow and infolded sporophore form, a loose zygosporangial hyphal mantle, homogeneous gametangia, and an enigmatic trophic mode with no evidence of ectomycorrhizal association for most species. For the other clade we introduce a new generic name, Jimgerdemannia gen. nov. Members of that genus (J. flammicorona and J. lactiflua species complexes, and an undescribed species) are characterized by hypogeous sporophores with a solid gleba, a well-developed zygosporangial hyphal mantle, heterogeneous gametangia, and an ectomycorrhizal trophic mode. Future studies on Densosporaceae and Endogonaceae will be important for understanding fungal innovations including evolution of macroscopic sporophores and symbioses with plants.
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Affiliation(s)
- Alessandro Desirò
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | | | - Alison Jacob
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Natalie Vande Pol
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - James M Trappe
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USA
| | - Martin I Bidartondo
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.,Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK
| | - Gregory Bonito
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
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Berruti A, Desirò A, Visentin S, Zecca O, Bonfante P. ITS fungal barcoding primers versus 18S AMF-specific primers reveal similar AMF-based diversity patterns in roots and soils of three mountain vineyards. Environ Microbiol Rep 2017; 9:658-667. [PMID: 28799720 DOI: 10.1111/1758-2229.12574] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 05/17/2017] [Accepted: 08/03/2017] [Indexed: 05/26/2023]
Abstract
ITS primers commonly used to describe soil fungi are flawed for AMF although it is unknown the extent to which they distort the interpretation of community patterns. Here, we focus on how the use of a specific ITS2 fungal barcoding primer pair biased for AMF changes the interpretation of AMF community patterns from three mountain vineyards compared to a novel AMF-specific approach on the 18S. We found that although discrepancies were present in the taxonomic composition of the two resulting datasets, the estimation of diversity patterns among AMF communities was similar and resulted in both primer systems being able to correctly assess the community-structuring effect of location, compartment (root vs. soil) and environment. Both methodologies made it possible to detect the same alpha-diversity trend among the locations under study but not between root and soil transects. We show that the ITS2 primer system for fungal barcoding provides a good estimate of both AMF community structure and relation to environmental variables. However, this primer system does not fit in with cross-compartment surveys (roots vs. soil) as it can underestimate AMF diversity in soil samples. When specifically focusing on AMF, the 18S primer system resulted in wide coverage and marginal non-target amplification.
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Affiliation(s)
- Andrea Berruti
- Department of Life Sciences and System Biology, University of Torino, viale Mattioli 25, Torino 10125, Italy
- Institute for Sustainable Plant Protection, UOS Torino - National Research Council, viale Mattioli 25, Torino 10125, Italy
| | - Alessandro Desirò
- Department of Life Sciences and System Biology, University of Torino, viale Mattioli 25, Torino 10125, Italy
| | - Stefano Visentin
- Department of Life Sciences and System Biology, University of Torino, viale Mattioli 25, Torino 10125, Italy
| | - Odoardo Zecca
- Institut Agricole Re´gional, strada la Rochere 1, Aosta 11100, Italy
| | - Paola Bonfante
- Department of Life Sciences and System Biology, University of Torino, viale Mattioli 25, Torino 10125, Italy
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Torres-Cruz TJ, Billingsley Tobias TL, Almatruk M, Hesse CN, Kuske CR, Desirò A, Benucci GMN, Bonito G, Stajich JE, Dunlap C, Arnold AE, Porras-Alfaro A. Bifiguratus adelaidae, gen. et sp. nov., a new member of Mucoromycotina in endophytic and soil-dwelling habitats. Mycologia 2017; 109:363-378. [PMID: 28876195 DOI: 10.1080/00275514.2017.1364958] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Illumina amplicon sequencing of soil in a temperate pine forest in the southeastern United States detected an abundant, nitrogen (N)-responsive fungal genotype of unknown phylogenetic affiliation. Two isolates with ribosomal sequences consistent with that genotype were subsequently obtained. Examination of records in GenBank revealed that a genetically similar fungus had been isolated previously as an endophyte of moss in a pine forest in the southwestern United States. The three isolates were characterized using morphological, genomic, and multilocus molecular data (18S, internal transcribed spacer [ITS], and 28S rRNA sequences). Phylogenetic and maximum likelihood phylogenomic reconstructions revealed that the taxon represents a novel lineage in Mucoromycotina, only preceded by Calcarisporiella, the earliest diverging lineage in the subphylum. Sequences for the novel taxon are frequently detected in environmental sequencing studies, and it is currently part of UNITE's dynamic list of most wanted fungi. The fungus is dimorphic, grows best at room temperature, and is associated with a wide variety of bacteria. Here, a new monotypic genus, Bifiguratus, is proposed, typified by Bifiguratus adelaidae.
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Affiliation(s)
- Terry J Torres-Cruz
- a Department of Biological Sciences , Western Illinois University , Macomb , Illinois 61455
| | | | - Maryam Almatruk
- a Department of Biological Sciences , Western Illinois University , Macomb , Illinois 61455
| | - Cedar N Hesse
- b Bioscience Division, Los Alamos National Laboratory , Los Alamos , New Mexico 87545
| | - Cheryl R Kuske
- b Bioscience Division, Los Alamos National Laboratory , Los Alamos , New Mexico 87545
| | - Alessandro Desirò
- c Department of Plant, Soil and Microbial Sciences , Michigan State University , East Lansing , Michigan 48824
| | - Gian Maria Niccolò Benucci
- c Department of Plant, Soil and Microbial Sciences , Michigan State University , East Lansing , Michigan 48824
| | - Gregory Bonito
- c Department of Plant, Soil and Microbial Sciences , Michigan State University , East Lansing , Michigan 48824
| | - Jason E Stajich
- d Department of Plant Pathology and Microbiology , University of California , Riverside , California 92521
| | - Christopher Dunlap
- e National Center for Agricultural Utilization Research, Agricultural Research Service , U.S. Department of Agriculture , Peoria , Illinois 61604
| | - A Elizabeth Arnold
- f School of Plant Sciences and Department of Ecology and Evolutionary Biology, The University of Arizona , Tucson , Arizona 85721
| | - Andrea Porras-Alfaro
- a Department of Biological Sciences , Western Illinois University , Macomb , Illinois 61455
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11
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Naito M, Desirò A, González JB, Tao G, Morton JB, Bonfante P, Pawlowska TE. 'Candidatus Moeniiplasma glomeromycotorum', an endobacterium of arbuscular mycorrhizal fungi. Int J Syst Evol Microbiol 2017; 67:1177-1184. [PMID: 28073398 DOI: 10.1099/ijsem.0.001785] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF, subphylum Glomeromycotina) are symbionts of most terrestrial plants. They commonly harbour endobacteria of a largely unknown biology, referred to as MRE (Mollicutes/mycoplasma-related endobacteria). Here, we propose to accommodate MRE in the novel genus 'Candidatus Moeniiplasma.' Phylogeny reconstructions based on the 16S rRNA gene sequences cluster 'Ca.Moeniiplasma' with representatives of the class Mollicutes, whereas phylogenies derived from amino acid sequences of 19 genes indicate that it is a discrete lineage sharing ancestry with the members of the family Mycoplasmataceae. Cells of 'Ca.Moeniiplasma' reside directly in the host cytoplasm and have not yet been cultivated. They are coccoid, ~500 nm in diameter, with an electron-dense layer outside the plasma membrane. However, the draft genomes of 'Ca.Moeniiplasma' suggest that this structure is not a Gram-positive cell wall. The evolution of 'Ca.Moeniiplasma' appears to be driven by an ultrarapid rate of mutation accumulation related to the loss of DNA repair mechanisms. Moreover, molecular evolution patterns suggest that, in addition to vertical transmission, 'Ca.Moeniiplasma' is able to transmit horizontally among distinct Glomeromycotina host lineages and exchange genes. On the basis of these unique lifestyle features, the new species 'Candidatus Moeniiplasma glomeromycotorum' is proposed.
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Affiliation(s)
- Mizue Naito
- Graduate Field of Microbiology, Cornell University, Ithaca, NY, USA
| | - Alessandro Desirò
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy.,Present address: Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Jonathan B González
- School of Integrative Plant Science, Plant Pathology & Plant-Microbe Biology, Cornell University, Ithaca, NY, USA
| | - Gang Tao
- School of Integrative Plant Science, Plant Pathology & Plant-Microbe Biology, Cornell University, Ithaca, NY, USA.,Present address: Guizhou Academy of Agricultural Sciences, Guizhou Institute of Plant Protection, Guiyang 550006, PR China
| | - Joseph B Morton
- Division of Plant & Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Teresa E Pawlowska
- School of Integrative Plant Science, Plant Pathology & Plant-Microbe Biology, Cornell University, Ithaca, NY, USA
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12
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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: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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Abstract
The study of the so-called unculturable bacteria is still considered a challenging task. However, given recent improvements in the sensitivity of culture-free approaches, the identification and characterization of such microbes in complex biological samples is now possible. In this chapter we report how endobacteria thriving inside arbuscular mycorrhizal fungi (AMF), which are themselves obligate biotrophs of plants, can be studied using a combination of in vitro culture, molecular biology, and microscopy techniques.
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Affiliation(s)
- Alessandro Desirò
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, Turin, 48824, Italy.
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 10125, USA.
| | - Alessandra Salvioli
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, Turin, 48824, Italy
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, Turin, 48824, Italy
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14
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Desirò A, Faccio A, Kaech A, Bidartondo MI, Bonfante P. Endogone, one of the oldest plant-associated fungi, host unique Mollicutes-related endobacteria. New Phytol 2015; 205:1464-1472. [PMID: 25345989 DOI: 10.1111/nph.13136] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 09/29/2014] [Indexed: 05/16/2023]
Abstract
Glomeromycota have been considered the most ancient group of fungi capable of positively interacting with plants for many years. Recently, other basal fungi, the Endogone Mucoromycotina fungi, have been identified as novel plant symbionts, challenging the paradigm of Glomeromycota as the unique ancestral symbionts of land plants. Glomeromycota are known to host endobacteria and recent evidences show that also some Mucoromycotina contain endobacteria. In order to examine similarities between basal groups of plant-associated fungi, we tested whether Endogone contained endobacteria. Twenty-nine Endogone were investigated in order to identify Mollicutes-related endobacteria (Mre). Fruiting bodies were processed for transmission electron microscopy and molecularly investigated using fungal and Mre-specific primers. We demonstrate that Mre are present inside 13 out of 29 Endogone: endobacteria are directly embedded in the fungal cytoplasm and their 16S rDNA sequences cluster together with the ones retrieved from Glomeromycota, forming, however, a separate new clade. Our findings provide new insights on the evolutionary relations between Glomeromycota, Mucoromycotina and endobacteria, raising new questions on the role of these still enigmatic microbes in the ecology, evolution and diversification of their fungal hosts during the history of plant-fungal symbiosis.
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Affiliation(s)
- Alessandro Desirò
- Department of Life Sciences and Systems Biology, University of Turin, Turin, 10125, Italy
| | - Antonella Faccio
- Institute for Sustainable Plant Protection, UOS Turin, National Research Council, Turin, Italy
| | - Andres Kaech
- Center for Microscopy and Image Analysis, University of Zurich, Zurich, Switzerland
| | | | - Paola Bonfante
- Department of Life Sciences and Systems Biology, University of Turin, Turin, 10125, Italy
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15
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Desirò A, Salvioli A, Ngonkeu EL, Mondo SJ, Epis S, Faccio A, Kaech A, Pawlowska TE, Bonfante P. Detection of a novel intracellular microbiome hosted in arbuscular mycorrhizal fungi. ISME J 2014; 8:257-70. [PMID: 24008325 PMCID: PMC3906812 DOI: 10.1038/ismej.2013.151] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 07/17/2013] [Accepted: 07/22/2013] [Indexed: 12/27/2022]
Abstract
Arbuscular mycorrhizal fungi (AMF) are important members of the plant microbiome. They are obligate biotrophs that colonize the roots of most land plants and enhance host nutrient acquisition. Many AMF themselves harbor endobacteria in their hyphae and spores. Two types of endobacteria are known in Glomeromycota: rod-shaped Gram-negative Candidatus Glomeribacter gigasporarum, CaGg, limited in distribution to members of the Gigasporaceae family, and coccoid Mollicutes-related endobacteria, Mre, widely distributed across different lineages of AMF. The goal of the present study is to investigate the patterns of distribution and coexistence of the two endosymbionts, CaGg and Mre, in spore samples of several strains of Gigaspora margarita. Based on previous observations, we hypothesized that some AMF could host populations of both endobacteria. To test this hypothesis, we performed an extensive investigation of both endosymbionts in G. margarita spores sampled from Cameroonian soils as well as in the Japanese G. margarita MAFF520054 isolate using different approaches (molecular phylotyping, electron microscopy, fluorescence in situ hybridization and quantitative real-time PCR). We found that a single AMF host can harbour both types of endobacteria, with Mre population being more abundant, variable and prone to recombination than the CaGg one. Both endosymbionts seem to retain their genetic and lifestyle peculiarities regardless of whether they colonize the host alone or together. These findings show for the first time that fungi support an intracellular bacterial microbiome, in which distinct types of endobacteria coexist in a single cell.
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Affiliation(s)
- Alessandro Desirò
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Alessandra Salvioli
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Eddy L Ngonkeu
- Institute of Agronomic Research for Development (IRAD), Yaoundé, Cameroon
| | - Stephen J Mondo
- Department of Plant Pathology and Plant Microbe-Biology, Cornell University, Ithaca, NY, USA
| | - Sara Epis
- Department of Veterinary Science and Public Health, University of Milano, Milano, Italy
| | | | - Andres Kaech
- Center for Microscopy and Image Analysis, University of Zurich, Zurich, Switzerland
| | - Teresa E Pawlowska
- Department of Plant Pathology and Plant Microbe-Biology, Cornell University, Ithaca, NY, USA
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
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16
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Abstract
Hornworts are considered the sister group to vascular plants, but their fungal associations remain largely unexplored. The ancestral symbiotic condition for all plants is, nonetheless, widely assumed to be arbuscular mycorrhizal with Glomeromycota fungi. Owing to a recent report of other fungi in some non-vascular plants, here we investigate the fungi associated with diverse hornworts worldwide, using electron microscopy and molecular phylogenetics. We found that both Glomeromycota and Mucoromycotina fungi can form symbioses with most hornworts, often simultaneously. This discovery indicates that ancient terrestrial plants relied on a wider and more versatile symbiotic repertoire than previously thought, and it highlights the so far unappreciated ecological and evolutionary role of Mucoromycotina fungi.
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Affiliation(s)
- Alessandro Desirò
- Department of Life Sciences and Systems Biology, University of Turin, Viale P.A. Mattioli 25, 10125, Turin, Italy.
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17
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Desirò A, Naumann M, Epis S, Novero M, Bandi C, Genre A, Bonfante P. Mollicutes-related endobacteria thrive inside liverwort-associated arbuscular mycorrhizal fungi. Environ Microbiol 2012; 15:822-36. [PMID: 22830931 DOI: 10.1111/j.1462-2920.2012.02833.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Arbuscular mycorrhizal fungi (AMF) can host Gram-positive endobacteria (BLOs) in their cytoplasm. These have been identified as Mollicutes-related microbes based on an inventory of AMF spores from fungal collections. Bacteria-like organisms (BLOs) of unknown identity have also been reported in the cytoplasm of AMF associated with liverworts, the earliest-diverged extant lineage of land plants. A combination of morphological, molecular and phylogenetic analyses revealed that three samples of two liverwort species (Conocephalum conicum and Lunularia cruciata) growing spontaneously in a botanical garden harboured AMF belonging to Glomerales, and these, in turn, hosted coccoid BLOs. 16S rDNA sequences from these BLOs clustered with the Mollicutes sequences identified from the spore collections but revealed the presence of novel phylotypes. Electron microscopy and fluorescence in situ hybridization (FISH) confirmed the presence of BLOs inside the cytoplasm of AMF hyphae colonizing the liverwort thalli. The high genetic variability of BLOs in liverwort-AMF associations thriving in the same ecological niche raises questions about the mechanisms underlying such diversity.
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Affiliation(s)
- Alessandro Desirò
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
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