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Puginier C, Libourel C, Otte J, Skaloud P, Haon M, Grisel S, Petersen M, Berrin JG, Delaux PM, Dal Grande F, Keller J. Phylogenomics reveals the evolutionary origins of lichenization in chlorophyte algae. Nat Commun 2024; 15:4452. [PMID: 38789482 PMCID: PMC11126685 DOI: 10.1038/s41467-024-48787-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Mutualistic symbioses have contributed to major transitions in the evolution of life. Here, we investigate the evolutionary history and the molecular innovations at the origin of lichens, which are a symbiosis established between fungi and green algae or cyanobacteria. We de novo sequence the genomes or transcriptomes of 12 lichen algal symbiont (LAS) and closely related non-symbiotic algae (NSA) to improve the genomic coverage of Chlorophyte algae. We then perform ancestral state reconstruction and comparative phylogenomics. We identify at least three independent gains of the ability to engage in the lichen symbiosis, one in Trebouxiophyceae and two in Ulvophyceae, confirming the convergent evolution of the lichen symbioses. A carbohydrate-active enzyme from the glycoside hydrolase 8 (GH8) family was identified as a top candidate for the molecular-mechanism underlying lichen symbiosis in Trebouxiophyceae. This GH8 was acquired in lichenizing Trebouxiophyceae by horizontal gene transfer, concomitantly with the ability to associate with lichens fungal symbionts (LFS) and is able to degrade polysaccharides found in the cell wall of LFS. These findings indicate that a combination of gene family expansion and horizontal gene transfer provided the basis for lichenization to evolve in chlorophyte algae.
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Affiliation(s)
- Camille Puginier
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP, Toulouse, 31320, Castanet-Tolosan, France
| | - Cyril Libourel
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP, Toulouse, 31320, Castanet-Tolosan, France
| | - Juergen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Pavel Skaloud
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-12800, Praha 2, Czech Republic
| | - Mireille Haon
- INRAE, Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques (BBF), 13009, Marseille, France
- INRAE, Aix Marseille Université, 3PE Platform, 13009, Marseille, France
| | - Sacha Grisel
- INRAE, Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques (BBF), 13009, Marseille, France
- INRAE, Aix Marseille Université, 3PE Platform, 13009, Marseille, France
| | - Malte Petersen
- High Performance Computing & Analytics Lab, University of Bonn, Friedrich-Hirzebruch-Allee 8, 53115, Bonn, Germany
| | - Jean-Guy Berrin
- INRAE, Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques (BBF), 13009, Marseille, France
- INRAE, Aix Marseille Université, 3PE Platform, 13009, Marseille, France
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP, Toulouse, 31320, Castanet-Tolosan, France.
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
- Department of Biology, University of Padova, Padua, Italy.
| | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP, Toulouse, 31320, Castanet-Tolosan, France.
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany.
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Ingham CS, Engl T, Matarrita-Carranza B, Vogler P, Huettel B, Wielsch N, Svatoš A, Kaltenpoth M. Host hydrocarbons protect symbiont transmission from a radical host defense. Proc Natl Acad Sci U S A 2023; 120:e2302721120. [PMID: 37487102 PMCID: PMC10400980 DOI: 10.1073/pnas.2302721120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 06/06/2023] [Indexed: 07/26/2023] Open
Abstract
Symbioses with microbes play a pivotal role in the evolutionary success of insects, and can lead to intimate host-symbiont associations. However, how the host maintains a stable symbiosis with its beneficial partners while keeping antagonistic microbes in check remains incompletely understood. Here, we uncover a mechanism by which a host protects its symbiont from the host's own broad-range antimicrobial defense during transmission. Beewolves, a group of solitary digger wasps (Hymenoptera: Crabronidae), provide their brood cells with symbiotic Streptomyces bacteria that are later transferred to the cocoon and protect the offspring from opportunistic pathogens by producing antibiotics. In the brood cell, however, the symbiont-containing secretion is exposed to a toxic burst of nitric oxide (NO) released by the beewolf egg, which effectively kills antagonistic microorganisms. How the symbiont survives this lethal NO burst remained unknown. Here, we report that upon NO exposure in vitro, the symbionts mount a global stress response, but this is insufficient to ensure survival at brood cell-level NO concentrations. Instead, in vivo bioassays demonstrate that the host's antennal gland secretion (AGS) surrounding the symbionts in the brood cell provides an effective diffusion barrier against NO. This physicochemical protection can be reconstituted in vitro by beewolf hydrocarbon extracts and synthetic hydrocarbons, indicating that the host-derived long-chain alkenes and alkanes in the AGS are responsible for shielding the symbionts from NO. Our results reveal how host adaptations can protect a symbiont from host-generated oxidative and nitrosative stress during transmission, thereby efficiently balancing pathogen defense and mutualism maintenance.
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Affiliation(s)
- Chantal Selina Ingham
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University Mainz, Mainz55128, Germany
| | - Tobias Engl
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University Mainz, Mainz55128, Germany
- Department of Insect Symbiosis, Max-Planck-Institute for Chemical Ecology, Jena07745, Germany
| | | | - Paul Vogler
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University Mainz, Mainz55128, Germany
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
| | - Natalie Wielsch
- Research Group Mass Spectrometry/Proteomics, Max-Planck-Institute for Chemical Ecology, Jena07745, Germany
| | - Aleš Svatoš
- Research Group Mass Spectrometry/Proteomics, Max-Planck-Institute for Chemical Ecology, Jena07745, Germany
| | - Martin Kaltenpoth
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University Mainz, Mainz55128, Germany
- Department of Insect Symbiosis, Max-Planck-Institute for Chemical Ecology, Jena07745, Germany
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Ganesan R, Wierz JC, Kaltenpoth M, Flórez LV. How It All Begins: Bacterial Factors Mediating the Colonization of Invertebrate Hosts by Beneficial Symbionts. Microbiol Mol Biol Rev 2022; 86:e0012621. [PMID: 36301103 PMCID: PMC9769632 DOI: 10.1128/mmbr.00126-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Beneficial associations with bacteria are widespread across animals, spanning a range of symbiont localizations, transmission routes, and functions. While some of these associations have evolved into obligate relationships with permanent symbiont localization within the host, the majority require colonization of every host generation from the environment or via maternal provisions. Across the broad diversity of host species and tissue types that beneficial bacteria can colonize, there are some highly specialized strategies for establishment yet also some common patterns in the molecular basis of colonization. This review focuses on the mechanisms underlying the early stage of beneficial bacterium-invertebrate associations, from initial contact to the establishment of the symbionts in a specific location of the host's body. We first reflect on general selective pressures that can drive the transition from a free-living to a host-associated lifestyle in bacteria. We then cover bacterial molecular factors for colonization in symbioses from both model and nonmodel invertebrate systems where these have been studied, including terrestrial and aquatic host taxa. Finally, we discuss how interactions between multiple colonizing bacteria and priority effects can influence colonization. Taking the bacterial perspective, we emphasize the importance of developing new experimentally tractable systems to derive general insights into the ecological factors and molecular adaptations underlying the origin and establishment of beneficial symbioses in animals.
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Affiliation(s)
- Ramya Ganesan
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Jürgen C. Wierz
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Martin Kaltenpoth
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Laura V. Flórez
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
- Department of Plant and Environmental Sciences, Section for Organismal Biology, University of Copenhagen, Copenhagen, Denmark
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Chong SL, Tan JL, Ngeow YF. The resistomes of Mycobacteroides abscessus complex and their possible acquisition from horizontal gene transfer. BMC Genomics 2022; 23:715. [PMID: 36261788 PMCID: PMC9583574 DOI: 10.1186/s12864-022-08941-7] [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] [Received: 07/14/2022] [Accepted: 10/14/2022] [Indexed: 11/19/2022] Open
Abstract
Background Mycobacteroides abscessus complex (MABC), an emerging pathogen, causes human infections resistant to multiple antibiotics. In this study, the genome data of 1,581 MABC strains were downloaded from NCBI database for phylogenetic relatedness inference, resistance profile identification and the estimation of evolutionary pressure on resistance genes in silico. Results From genes associated with resistance to 28 antibiotic classes, 395 putative proteins (ARPs) were identified, based on the information in two antibiotic resistance databases (CARD and ARG-ANNOT). The ARPs most frequently identified in MABC were those associated with resistance to multiple antibiotic classes, beta-lactams and aminoglycosides. After excluding ARPs that had undergone recombination, two ARPs were predicted to be under diversifying selection and 202 under purifying selection. This wide occurrence of purifying selection suggested that the diversity of commonly shared ARPs in MABC have been reduced to achieve stability. The unequal distribution of ARPs in members of the MABC could be due to horizontal gene transfer or ARPs pseudogenization events. Most (81.5%) of the ARPs were observed in the accessory genome and 72.2% ARPs were highly homologous to proteins associated with mobile genetic elements such as plasmids, prophages and viruses. On the other hand, with TBLASTN search, only 18 of the ARPs were identified as pseudogenes. Conclusion Altogether, our results suggested an important role of horizontal gene transfer in shaping the resistome of MABC. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08941-7.
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Affiliation(s)
- Shay Lee Chong
- Faculty of Information Science and Technology, Multimedia University, Jalan Ayer Keroh Lama, Bukit Beruang, 75450, Melaka, Malaysia
| | - Joon Liang Tan
- Faculty of Information Science and Technology, Multimedia University, Jalan Ayer Keroh Lama, Bukit Beruang, 75450, Melaka, Malaysia.
| | - Yun Fong Ngeow
- Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Bandar Sungai Long, 43000, Kajang, Selangor, Malaysia.,Center for Research On Communincable Diseases, Universiti Tunku Abdul Rahman, Bandar Sungai Long, 43000, Kajang, Selangor, Malaysia
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Lajoie G, Parfrey LW. Beyond specialization: re-examining routes of host influence on symbiont evolution. Trends Ecol Evol 2022; 37:590-598. [PMID: 35466020 DOI: 10.1016/j.tree.2022.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 03/15/2022] [Accepted: 03/20/2022] [Indexed: 11/17/2022]
Abstract
Our understanding of host influence on microbial evolution has focused on symbiont specialization and the genomic streamlining that often accompanies it. However, a vast diversity of symbiotic lineages facultatively interact with hosts or associate with multiple hosts. Yet, there are no clear expectations for how host association influences the niche of these symbionts or their evolution. Here, we discuss how weak or variable selection on microbial symbiotic associations, horizontal transmission, and low costs of adaptation to novel host habitats are predicted to promote the expansion or maintenance of microbial niches. This broad perspective will aid in developing better and more general predictions for evolution in microbial symbioses.
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Affiliation(s)
- Geneviève Lajoie
- Botany Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC, Canada, V6T 1Z4.
| | - Laura Wegener Parfrey
- Botany Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC, Canada, V6T 1Z4
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Fronk DC, Sachs JL. Symbiotic organs: the nexus of host-microbe evolution. Trends Ecol Evol 2022; 37:599-610. [PMID: 35393155 DOI: 10.1016/j.tree.2022.02.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/14/2022] [Accepted: 02/28/2022] [Indexed: 02/07/2023]
Abstract
Diverse plants and animals have evolved specialized structures to filter and house beneficial microbes. These symbiotic organs form crucial points of exchange between host and symbiont, are often shaped by both partners, and exhibit features that facilitate a suite of microbial services. While symbiotic organs exhibit varied function, morphology, and developmental plasticity, they share core features linked to the evolutionary maintenance of beneficial symbiosis. Moreover, these organs can have a significant role in altering the demographic forces that shape microbial genomes, driving population bottlenecks and horizontal gene transfer (HGT). To advance our understanding of these 'joint phenotypes' across varied systems, future research must consider the emergent forces that can shape symbiotic organs, including fitness feedbacks and conflicts between interacting genomes.
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Affiliation(s)
- David C Fronk
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA
| | - Joel L Sachs
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA; Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA; Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA.
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Alajlani MM. Characterization of subtilosin gene in wild type Bacillus spp. and possible physiological role. Sci Rep 2022; 12:10521. [PMID: 35732659 PMCID: PMC9217942 DOI: 10.1038/s41598-022-13804-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/27/2022] [Indexed: 11/09/2022] Open
Abstract
In a designed study to screen for antimicrobial exhibiting bacteria using molecular aspects, Bacillus species were considered to investigate antibiotic biosynthesis genes. 28 bacterial strains and 3 induced mutants were screened for the presence of subtilosin gene (sbo) and subtilosin through PCR and Mass spectrometry respectively. Sbo gene was detected in 16 out of 28 Bacillus strains. The results from gene sequences deliberated by multiple sequence alignments revealed high-level homology to the sequences of the sbo-alb gene locus of B. subtilis 168 and the other limited reported strains. Hence, this report provided additional strains to support the idea of subtilosin gene predominance amongst Bacillus strains isolated from environment and to find different species containing homologous genes, furthermore the utilization of its conserved region as a means of identifying Bacillus spp. that produce subtilosin. This is the first report to confirm the detection of subtilosin production from B. amyloliquefaciens.
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Affiliation(s)
- Muaaz Mutaz Alajlani
- Department of Pharmaceutical Biology/Pharmacognosy, Institute of Pharmacy, University of Halle-Wittenberg, Hoher Weg 8, 06120, Halle (Saale), Germany.
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Alajlani MM. Characterization of subtilosin gene in wild type Bacillus spp. and possible physiological role. Sci Rep 2022; 12:10521. [DOI: https:/doi.org/10.1038/s41598-022-13804-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/27/2022] [Indexed: 08/08/2023] Open
Abstract
AbstractIn a designed study to screen for antimicrobial exhibiting bacteria using molecular aspects, Bacillus species were considered to investigate antibiotic biosynthesis genes. 28 bacterial strains and 3 induced mutants were screened for the presence of subtilosin gene (sbo) and subtilosin through PCR and Mass spectrometry respectively. Sbo gene was detected in 16 out of 28 Bacillus strains. The results from gene sequences deliberated by multiple sequence alignments revealed high-level homology to the sequences of the sbo-alb gene locus of B. subtilis 168 and the other limited reported strains. Hence, this report provided additional strains to support the idea of subtilosin gene predominance amongst Bacillus strains isolated from environment and to find different species containing homologous genes, furthermore the utilization of its conserved region as a means of identifying Bacillus spp. that produce subtilosin. This is the first report to confirm the detection of subtilosin production from B. amyloliquefaciens.
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Santos-Aberturas J, Vior NM. Beyond Soil-Dwelling Actinobacteria: Fantastic Antibiotics and Where to Find Them. Antibiotics (Basel) 2022; 11:195. [PMID: 35203798 PMCID: PMC8868522 DOI: 10.3390/antibiotics11020195] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/27/2022] [Accepted: 01/29/2022] [Indexed: 12/10/2022] Open
Abstract
Bacterial secondary metabolites represent an invaluable source of bioactive molecules for the pharmaceutical and agrochemical industries. Although screening campaigns for the discovery of new compounds have traditionally been strongly biased towards the study of soil-dwelling Actinobacteria, the current antibiotic resistance and discovery crisis has brought a considerable amount of attention to the study of previously neglected bacterial sources of secondary metabolites. The development and application of new screening, sequencing, genetic manipulation, cultivation and bioinformatic techniques have revealed several other groups of bacteria as producers of striking chemical novelty. Biosynthetic machineries evolved from independent taxonomic origins and under completely different ecological requirements and selective pressures are responsible for these structural innovations. In this review, we summarize the most important discoveries related to secondary metabolites from alternative bacterial sources, trying to provide the reader with a broad perspective on how technical novelties have facilitated the access to the bacterial metabolic dark matter.
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Affiliation(s)
| | - Natalia M. Vior
- Department of Molecular Microbiology, John Innes Centre, Norwich NR7 4UH, UK
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Goettler W, Kaltenpoth M, McDonald S, Strohm E. Comparative Morphology of the Symbiont Cultivation Glands in the Antennae of Female Digger Wasps of the Genus Philanthus (Hymenoptera: Crabronidae). Front Physiol 2022; 13:815494. [PMID: 35153837 PMCID: PMC8826713 DOI: 10.3389/fphys.2022.815494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/04/2022] [Indexed: 11/13/2022] Open
Abstract
Females of the solitary digger wasp tribe Philanthini, called the beewolves (Hymenoptera, Crabronidae), cultivate strains of symbiotic bacteria that belong to the genus Streptomyces in unique and highly specialized glands in their antennae. The glands consist of large reservoirs that are surrounded by numerous gland cell complexes (class III). The symbionts are cultivated inside the reservoirs and are probably provisioned with nutrients secreted from the surrounding glands and/or sequestered from the hemolymph. The wasp female delivers the bacteria into the subterranean brood cell prior to oviposition. Fully grown larvae take up the bacteria and apply them to their cocoon. There the bacteria produce several antibiotics that protect the wasp offspring against fungus infestation. Hitherto Streptomyces bacteria were detected in the antennae of 38 species of the Philanthini. However, a detailed morphological analysis of the antennal glands is only available for a few species. In order to shed light on the evolutionary history of the association between beewolf wasps and bacteria, we investigated the morphology of the antennal glands of another 14 Philanthus species from the Palearctic, Paleotropic, and Nearctic. We generated 3D-models of the glands based on serial semithin sections and/or micro-CT (μCT). Despite broad similarities in number and structure of antennal glands, the results revealed interspecific differences with regard to overall shape, complexity, and relative size of the reservoirs as well as the number of the surrounding gland cell units. Mapping the morphology of all species studied so far on the phylogeny (that parallels geographical distribution) revealed that related species share similarities in gland morphology, but there are notable differences between lineages. In particular, compared to the North American species the European and African species possess more complex gland structures with a higher number of gland cells. We discuss morphological, ecological, and physiological aspects and provide scenarios for the evolution of the antennal glands of the Philanthini as symbiont cultivation organs.
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Affiliation(s)
- Wolfgang Goettler
- Department of Zoology, University of Regensburg, Regensburg, Germany
| | - Martin Kaltenpoth
- Department of Zoology, University of Regensburg, Regensburg, Germany
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Samuel McDonald
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Erhard Strohm
- Department of Zoology, University of Regensburg, Regensburg, Germany
- *Correspondence: Erhard Strohm,
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