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Blázquez M, Ortiz-Álvarez R, Gasulla F, Pérez-Vargas I, Pérez-Ortega S. Bacterial communities associated with an island radiation of lichen-forming fungi. PLoS One 2024; 19:e0298599. [PMID: 38498492 PMCID: PMC10947700 DOI: 10.1371/journal.pone.0298599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/28/2024] [Indexed: 03/20/2024] Open
Abstract
Evolutionary radiations are one of the most striking processes biologists have studied in islands. A radiation is often sparked by the appearance of ecological opportunity, which can originate in processes like trophic niche segregation or the evolution of key innovations. Another recently proposed mechanism is facilitation mediated by the bacterial communities associated with the radiating species. Here we explore the role of the bacterial communities in a radiation of lichen-forming fungi endemic to Macaronesia. Bacterial diversity was quantified by high throughput sequencing of the V1-V2 hyper-variable region of 172 specimens. We characterized the taxonomic and phylogenetic diversity of the bacterial communities associated with the different species, tested for compositional differences between these communities, carried out a functional prediction, explored the relative importance of different factors in bacterial community structure, searched for phylosymbiosis and tried to identify the origin of this pattern. The species of the radiation differed in the composition of their bacterial communities, which were mostly comprised of Alphaproteobacteria and Acidobacteriia, but not in the functionality of those communities. A phylosimbiotic pattern was detected, but it was probably caused by environmental filtering. These findings are congruent with the combined effect of secondary chemistry and mycobiont identity being the main driver of bacterial community structure. Altogether, our results suggest that the associated bacterial communities are not the radiation's main driver. There is one possible exception, however, a species that has an abnormally diverse core microbiome and whose bacterial communities could be subject to a specific environmental filter at the functional level.
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Affiliation(s)
| | | | - Francisco Gasulla
- Department of Life Sciences, Universidad de Alcalá, Alcalá de Henares, Spain
| | - Israel Pérez-Vargas
- Department of Botany, Ecology and Plant Physiology, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
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2
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Ramírez N, Sigurbjörnsdóttir MA, Monteil C, Berge O, Heiðmarsson S, Jackson RW, Morris C, Vilhelmsson O. Pseudomonas syringae isolated in lichens for the first time: Unveiling Peltigera genus as the exclusive host. Environ Microbiol 2023; 25:3502-3511. [PMID: 37658725 DOI: 10.1111/1462-2920.16490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 08/01/2023] [Indexed: 09/03/2023]
Abstract
Pseudomonas syringae is a bacterial complex that is widespread through a range of environments, typically associated with plants where it can be pathogenic, but also found in non-plant environments such as clouds, precipitation, and surface waters. Understanding its distribution within the environment, and the habitats it occupies, is important for examining its evolution and understanding behaviours. After a recent study found P. syringae living among a range of vascular plant species in Iceland, we questioned whether lichens could harbour P. syringae. Sixteen different species of lichens were sampled all over Iceland, but only one lichen genus, Peltigera, was found to consistently harbour P. syringae. Phylogenetic analyses of P. syringae from 10 sampling points where lichen, tracheophyte, and/or moss were simultaneously collected showed significant differences between sampling points, but not between different plants and lichens from the same point. Furthermore, while there were similarities in the P. syringae population in tracheophytes and Peltigera, the densities in Peltigera thalli were lower than in moss and tracheophyte samples. This discovery suggests P. syringae strains can localize and survive in organisms beyond higher plants, and thus reveals opportunities for studying their influence on P. syringae evolution.
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Affiliation(s)
- Natalia Ramírez
- Department of Natural Resource Sciences, University of Akureyri, Akureyri, Iceland
| | | | - Cecile Monteil
- INRA, UR0407 Pathologie Vegétale, Montfavet Cedex, France
| | - Odile Berge
- INRA, UR0407 Pathologie Vegétale, Montfavet Cedex, France
| | | | - Robert W Jackson
- School of Biosciences and Birmingham Institute of Forest Research, University of Birmingham, Birmingham, UK
| | - Cindy Morris
- INRA, UR0407 Pathologie Vegétale, Montfavet Cedex, France
| | - Oddur Vilhelmsson
- Department of Natural Resource Sciences, University of Akureyri, Akureyri, Iceland
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3
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Llamas A, Leon-Miranda E, Tejada-Jimenez M. Microalgal and Nitrogen-Fixing Bacterial Consortia: From Interaction to Biotechnological Potential. PLANTS (BASEL, SWITZERLAND) 2023; 12:2476. [PMID: 37447037 DOI: 10.3390/plants12132476] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/15/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023]
Abstract
Microalgae are used in various biotechnological processes, such as biofuel production due to their high biomass yields, agriculture as biofertilizers, production of high-value-added products, decontamination of wastewater, or as biological models for carbon sequestration. The number of these biotechnological applications is increasing, and as such, any advances that contribute to reducing costs and increasing economic profitability can have a significant impact. Nitrogen fixing organisms, often called diazotroph, also have great biotechnological potential, mainly in agriculture as an alternative to chemical fertilizers. Microbial consortia typically perform more complex tasks than monocultures and can execute functions that are challenging or even impossible for individual strains or species. Interestingly, microalgae and diazotrophic organisms are capable to embrace different types of symbiotic associations. Certain corals and lichens exhibit this symbiotic relationship in nature, which enhances their fitness. However, this relationship can also be artificially created in laboratory conditions with the objective of enhancing some of the biotechnological processes that each organism carries out independently. As a result, the utilization of microalgae and diazotrophic organisms in consortia is garnering significant interest as a potential alternative for reducing production costs and increasing yields of microalgae biomass, as well as for producing derived products and serving biotechnological purposes. This review makes an effort to examine the associations of microalgae and diazotrophic organisms, with the aim of highlighting the potential of these associations in improving various biotechnological processes.
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Affiliation(s)
- Angel Llamas
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain
| | - Esperanza Leon-Miranda
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain
| | - Manuel Tejada-Jimenez
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain
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4
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García-Breijo FJ, Molins A, Reig-Armiñana J, Barreno E. The Tripartite Lichen Ricasolia virens: Involvement of Cyanobacteria and Bacteria in Its Morphogenesis. Microorganisms 2023; 11:1517. [PMID: 37375019 DOI: 10.3390/microorganisms11061517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Ricasolia virens is an epiphytic lichen-forming fungus mainly distributed in Western Europe and Macaronesia in well-structured forests with ecological continuity that lack eutrophication. It is considered to be threatened or extinct in many territories in Europe (IUCN). Despite its biological and ecological relevance, studies on this taxon are scarce. The thalli are tripartite, and the mycobiont has a simultaneous symbiotic relationship with cyanobacteria and green microalgae, which represent interesting models to analyse the strategies and adaptations resulting from the interactions of lichen symbionts. The present study was designed to contribute to a better understanding of this taxon, which has shown a clear decline over the last century. The symbionts were identified by molecular analysis. The phycobiont is Symbiochloris reticulata, and the cyanobionts (Nostoc) are embedded in internal cephalodia. Light, transmission electron and low-temperature scanning microscopy techniques were used to investigate the thallus anatomy, ultrastructure of microalgae and ontogeny of pycnidia and cephalodia. The thalli are very similar to its closest relative, Ricasolia quercizans. The cellular ultrastructure of S. reticulata by TEM is provided. Non-photosynthetic bacteria located outside the upper cortex are introduced through migratory channels into the subcortical zone by the splitting of fungal hyphae. Cephalodia were very abundant, but never as external photosymbiodemes.
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Affiliation(s)
- Francisco J García-Breijo
- Departamento de Ecosistemas Agroforestales, ETSIAMN, Universitat Politècnica de València, Camino de Vera s/n, 46022 València, Spain
| | - Arantzazu Molins
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva (ICBiBE), Botánica, Universitat de València, C/Dr. Moliner, 50, 46100 Burjassot, Spain
- Instituto de Investigaciones Agroambientales y de Economía del Agua (INAGEA), Departamento de Biología, Universitat de les Illes Balears (UIB), Ctra. Valldemossa Km.7., 07122 Palma de Malllorca, Spain
| | - José Reig-Armiñana
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva (ICBiBE), Botánica, Universitat de València, C/Dr. Moliner, 50, 46100 Burjassot, Spain
| | - Eva Barreno
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva (ICBiBE), Botánica, Universitat de València, C/Dr. Moliner, 50, 46100 Burjassot, Spain
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5
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He Z, Naganuma T. Chronicle of Research into Lichen-Associated Bacteria. Microorganisms 2022; 10:2111. [PMID: 36363703 PMCID: PMC9698887 DOI: 10.3390/microorganisms10112111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/30/2022] [Accepted: 10/21/2022] [Indexed: 02/12/2024] Open
Abstract
Lichens are mutually symbiotic systems consisting of fungal and algal symbionts. While diverse lichen-forming fungal species are known, limited species of algae form lichens. Plasticity in the combination of fungal and algal species with different eco-physiological properties may contribute to the worldwide distribution of lichens, even in extreme habitats. Lichens have been studied systematically for more than 200 years; however, plasticity in fungal-algal/cyanobacterial symbiotic combinations is still unclear. In addition, the association between non-cyanobacterial bacteria and lichens has attracted attention in recent years. The types, diversity, and functions of lichen-associated bacteria have been studied using both culture-based and culture-independent methods. This review summarizes the history of systematic research on lichens and lichen-associated bacteria and provides insights into the current status of research in this field.
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Affiliation(s)
| | - Takeshi Naganuma
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima 739-8528, Japan
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Valim HF, Dal Grande F, Otte J, Singh G, Merges D, Schmitt I. Identification and expression of functionally conserved circadian clock genes in lichen-forming fungi. Sci Rep 2022; 12:15884. [PMID: 36151124 PMCID: PMC9508176 DOI: 10.1038/s41598-022-19646-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: 03/28/2022] [Accepted: 08/31/2022] [Indexed: 12/02/2022] Open
Abstract
Lichen-forming fungi establish stable symbioses with green algae or cyanobacteria. Many species have broad distributions, both in geographic and ecological space, making them ideal subjects to study organism-environment interactions. However, little is known about the specific mechanisms that contribute to environmental adaptation in lichen-forming fungi. The circadian clock provides a well-described mechanism that contributes to regional adaptation across a variety of species, including fungi. Here, we identify the putative circadian clock components in phylogenetically divergent lichen-forming fungi. The core circadian genes (frq, wc-1, wc-2, frh) are present across the Fungi, including 31 lichen-forming species, and their evolutionary trajectories mirror overall fungal evolution. Comparative analyses of the clock genes indicate conserved domain architecture among lichen- and non-lichen-forming taxa. We used RT-qPCR to examine the core circadian loop of two unrelated lichen-forming fungi, Umbilicaria pustulata (Lecanoromycetes) and Dermatocarpon miniatum (Eurotiomycetes), to determine that the putative frq gene is activated in a light-dependent manner similar to the model fungus Neurospora crassa. Together, these results demonstrate that lichen-forming fungi retain functional light-responsive mechanisms, including a functioning circadian clock. Our findings provide a stepping stone into investigating the circadian clock in the lichen symbiosis, e.g. its role in adaptation, and in synchronizing the symbiotic interaction.
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Affiliation(s)
- Henrique F Valim
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany. .,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Department of Biology, University of Padua, Via U. Bassi 58/B, Padua, Italy
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Garima Singh
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Department of Biology, University of Padua, Via U. Bassi 58/B, Padua, Italy
| | - Dominik Merges
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, P.O. Box 7070, 750 07, Uppsala, Sweden
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany. .,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany. .,Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue-Straße 13, 60438, Frankfurt am Main, Germany.
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7
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Srimani S, Schmidt CX, Gómez-Serranillos MP, Oster H, Divakar PK. Modulation of Cellular Circadian Rhythms by Secondary Metabolites of Lichens. Front Cell Neurosci 2022; 16:907308. [PMID: 35813500 PMCID: PMC9260025 DOI: 10.3389/fncel.2022.907308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/20/2022] [Indexed: 12/14/2022] Open
Abstract
Background Most mammalian cells harbor molecular circadian clocks that synchronize physiological functions with the 24-h day-night cycle. Disruption of circadian rhythms, through genetic or environmental changes, promotes the development of disorders like obesity, cardiovascular diseases, and cancer. At the cellular level, circadian, mitotic, and redox cycles are functionally coupled. Evernic (EA) and usnic acid (UA), two lichen secondary metabolites, show various pharmacological activities including anti-oxidative, anti-inflammatory, and neuroprotective action. All these effects have likewise been associated with a functional circadian clock. Hypothesis/Purpose To test, if the lichen compounds EA and UA modulate circadian clock function at the cellular level. Methods We used three different cell lines and two circadian luminescence reporter systems for evaluating dose- and time-dependent effects of EA/UA treatment on cellular clock regulation at high temporal resolution. Output parameters studied were circadian luminescence rhythm period, amplitude, phase, and dampening rate. Results Both compounds had marked effects on clock rhythm amplitudes and dampening independent of cell type, with UA generally showing a higher efficiency than EA. Only in fibroblast cells, significant effects on clock period were observed for UA treated cells showing shorter and EA treated cells showing longer period lengths. Transient treatment of mouse embryonic fibroblasts at different phases had only minor clock resetting effects for both compounds. Conclusion Secondary metabolites of lichen alter cellular circadian clocks through amplitude reduction and increased rhythm dampening.
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Affiliation(s)
- Soumi Srimani
- Institute of Neurobiology, Center of Brain, Behavior & Metabolism (CBBM), University of Lübeck, Lübeck, Germany
- Department of Pharmacology, Pharmacognosy and Botany, Faculty of Pharmacy, Complutense University of Madrid, Madrid, Spain
| | - Cosima Xenia Schmidt
- Institute of Neurobiology, Center of Brain, Behavior & Metabolism (CBBM), University of Lübeck, Lübeck, Germany
| | - Maria Pilar Gómez-Serranillos
- Department of Pharmacology, Pharmacognosy and Botany, Faculty of Pharmacy, Complutense University of Madrid, Madrid, Spain
| | - Henrik Oster
- Institute of Neurobiology, Center of Brain, Behavior & Metabolism (CBBM), University of Lübeck, Lübeck, Germany
| | - Pradeep K. Divakar
- Department of Pharmacology, Pharmacognosy and Botany, Faculty of Pharmacy, Complutense University of Madrid, Madrid, Spain
- *Correspondence: Pradeep K. Divakar
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Chavarria-Pizarro T, Resl P, Kuhl-Nagel T, Janjic A, Fernandez Mendoza F, Werth S. Antibiotic-Induced Treatments Reveal Stress-Responsive Gene Expression in the Endangered Lichen Lobaria pulmonaria. J Fungi (Basel) 2022; 8:jof8060625. [PMID: 35736108 PMCID: PMC9225190 DOI: 10.3390/jof8060625] [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: 05/16/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/30/2022] Open
Abstract
Antibiotics are primarily found in the environment due to human activity, which has been reported to influence the structure of biotic communities and the ecological functions of soil and water ecosystems. Nonetheless, their effects in other terrestrial ecosystems have not been well studied. As a result of oxidative stress in organisms exposed to high levels of antibiotics, genotoxicity can lead to DNA damage and, potentially, cell death. In addition, in symbiotic organisms, removal of the associated microbiome by antibiotic treatment has been observed to have a big impact on the host, e.g., corals. The lung lichen Lobaria pulmonaria has more than 800 associated bacterial species, a microbiome which has been hypothesized to increase the lichen's fitness. We artificially exposed samples of L. pulmonaria to antibiotics and a stepwise temperature increase to determine the relative effects of antibiotic treatments vs. temperature on the mycobiont and photobiont gene expression and the viability and on the community structure of the lichen-associated bacteria. We found that the mycobiont and photobiont highly reacted to different antibiotics, independently of temperature exposure. We did not find major differences in bacterial community composition or alpha diversity between antibiotic treatments and controls. For these reasons, the upregulation of stress-related genes in antibiotic-treated samples could be caused by genotoxicity in L. pulmonaria and its photobiont caused by exposure to antibiotics, and the observed stress responses are reactions of the symbiotic partners to reduce damage to their cells. Our study is of great interest for the community of researchers studying symbiotic organisms as it represents one of the first steps to understanding gene expression in an endangered lichen in response to exposure to toxic environments, along with dynamics in its associated bacterial communities.
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Affiliation(s)
- Tania Chavarria-Pizarro
- Systematics, Biodiversity and Evolution of Plants, Faculty of Biology, LMU Munich, Menzingerstraße 67, 80638 Munich, Germany;
- Correspondence: (T.C.-P.); (S.W.)
| | - Philipp Resl
- Systematics, Biodiversity and Evolution of Plants, Faculty of Biology, LMU Munich, Menzingerstraße 67, 80638 Munich, Germany;
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria;
| | - Theresa Kuhl-Nagel
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute for Network Biology (INET), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany;
| | - Aleksandar Janjic
- Anthropology and Human Genomics, Faculty of Biology, LMU Munich, Großhaderner Straße 2-4, 82152 Planegg-Martinsried, Germany;
| | | | - Silke Werth
- Systematics, Biodiversity and Evolution of Plants, Faculty of Biology, LMU Munich, Menzingerstraße 67, 80638 Munich, Germany;
- Correspondence: (T.C.-P.); (S.W.)
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9
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Snelders NC, Rovenich H, Thomma BPHJ. Microbiota manipulation through the secretion of effector proteins is fundamental to the wealth of lifestyles in the fungal kingdom. FEMS Microbiol Rev 2022; 46:6590816. [PMID: 35604874 PMCID: PMC9438471 DOI: 10.1093/femsre/fuac022] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Fungi are well-known decomposers of organic matter that thrive in virtually any environment on earth where they encounter wealths of other microbes. Some fungi evolved symbiotic lifestyles, including pathogens and mutualists, that have mostly been studied in binary interactions with their hosts. However, we now appreciate that such interactions are greatly influenced by the ecological context in which they take place. While establishing their symbioses, fungi not only interact with their hosts, but also with the host-associated microbiota. Thus, they target the host and its associated microbiota as a single holobiont. Recent studies have shown that fungal pathogens manipulate the host microbiota by means of secreted effector proteins with selective antimicrobial activity to stimulate disease development. In this review we discuss the ecological contexts in which such effector-mediated microbiota manipulation is relevant for the fungal lifestyle and argue that this is not only relevant for pathogens of plants and animals, but beneficial in virtually any niche where fungi occur. Moreover, we reason that effector-mediated microbiota manipulation likely evolved already in fungal ancestors that encountered microbial competition long before symbiosis with land plants and mammalian animals evolved. Thus, we claim that effector-mediated microbiota manipulation is fundamental to fungal biology.
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Affiliation(s)
- Nick C Snelders
- Institute for Plant Sciences, University of Cologne, Cologne, Germany.,Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Hanna Rovenich
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Bart P H J Thomma
- Institute for Plant Sciences, University of Cologne, Cologne, Germany.,Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, CologneGermany
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10
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Fungal-derived compounds and mycogenic nanoparticles with antimycobacterial activity: a review. SN APPLIED SCIENCES 2022. [DOI: 10.1007/s42452-022-05010-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
AbstractTuberculosis (TB) is a persistent lung infection caused by Mycobacterium tuberculosis. The disease is characterized by high mortality rates of over 1 million per year. Unfortunately, the potency and effectiveness of currently used anti-TB drugs is gradually decreasing due to the constant development of persistence and resistance by M. tuberculosis. The adverse side effects associated with current anti-TB drugs, along with anti-TB drug resistance, present an opportunity to bio-prospect novel potent anti-TB drugs from unique sources. Fundamentally, fungi are a rich source of bioactive secondary metabolites with valuable therapeutic potential. Enhancing the potency and effectiveness of fungal-based anti-TB drug leads by chemical synthesis and/or modification with nanomaterials, may result in the discovery of novel anti-TB drugs. In this review, the antimycobacterial activity of fungal-derived compounds and mycogenic nanoparticles are summarized. Numerous fungal-derived compounds as well as some mycogenic nanoparticles that exhibit strong antimycobacterial activity that is comparable to that of approved drugs, were found. If fully explored, fungi holds the promise to become key drivers in the generation of lead compounds in TB-drug discovery initiatives.
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11
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Xu H, Wang L, Feng X, Gong X. Core taxa and photobiont-microbial interaction within the lichen Heterodermia obscurata (Physcsiaceae, Heterodermia). Symbiosis 2022. [DOI: 10.1007/s13199-022-00832-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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12
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Lin W, Chen L, Tan Z, Deng Z, Liu H. Application of filamentous fungi in microalgae-based wastewater remediation for biomass harvesting and utilization: From mechanisms to practical application. ALGAL RES 2022. [DOI: 10.1016/j.algal.2021.102614] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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13
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Kyriatzi A, Tzivras G, Pirintsos S, Kotzabasis K. Biotechnology under extreme conditions: Lichens after extreme UVB radiation and extreme temperatures produce large amounts of hydrogen. J Biotechnol 2021; 342:128-138. [PMID: 34743006 DOI: 10.1016/j.jbiotec.2021.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/04/2021] [Accepted: 10/29/2021] [Indexed: 10/19/2022]
Abstract
The present study demonstrates biotechnological applications of the lichen Pleurosticta acetabulum, specifically the production of large amounts of hydrogen even after the lichen exposure to extreme conditions such as a) extreme UVB radiation (1.7 mW/cm2 = 1000 J m-2 min-1) over different time periods (4, 20 & 70 h) and b) combined exposure of the lichen to high intensity UVB radiation and extreme low (-196 °C) or extreme high temperatures (+70 °C). The results highlight that the extremophilic and polyextremophilic behavior of lichens both in dehydrated and in regenerated form, under extreme conditions not necessarily recorded on earth, is compatible with their biotechnological uses. The lichen viability was measured using fluorescence induction techniques (OJIP-test), which record changes in the molecular structure and function of the photosynthetic mechanism, while its ability to produce molecular hydrogen was measured through thermal conductivity gas chromatography (GC-TCD) analysis. Hydrogen is a promising fuel for the future. The exciting result of a lichen micro-ecosystem is its ability to expel its moisture and remain in an inactive state, protecting itself from extreme conditions and maintaining its ability to high yield hydrogen production in a closed system, with the sole addition of water and without the need for additional energy. Our results expand the potential use of lichens for future biotechnological applications in extreme Earth environments, but also in environments on other planets, such as Mars, thus paving the way for astrobiotechnological applications.
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Affiliation(s)
- Anastasia Kyriatzi
- Department of Biology, University of Crete, Voutes University Campus, GR-70013 Heraklion, Crete, Greece
| | - Gerasimos Tzivras
- Department of Biology, University of Crete, Voutes University Campus, GR-70013 Heraklion, Crete, Greece
| | - Stergios Pirintsos
- Department of Biology, University of Crete, Voutes University Campus, GR-70013 Heraklion, Crete, Greece; Botanical Garden, University of Crete, Gallos University Campus, GR-74100 Rethymnon, Crete, Greece
| | - Kiriakos Kotzabasis
- Department of Biology, University of Crete, Voutes University Campus, GR-70013 Heraklion, Crete, Greece; Botanical Garden, University of Crete, Gallos University Campus, GR-74100 Rethymnon, Crete, Greece.
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15
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Tang J, Fu J, Wang Y, Li B, Li Y, Yang Q, Cui X, Hong J, Li X, Chen Y, Xue W, Zhu F. ANPELA: analysis and performance assessment of the label-free quantification workflow for metaproteomic studies. Brief Bioinform 2021; 21:621-636. [PMID: 30649171 PMCID: PMC7299298 DOI: 10.1093/bib/bby127] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/19/2018] [Accepted: 12/06/2018] [Indexed: 12/13/2022] Open
Abstract
Label-free quantification (LFQ) with a specific and sequentially integrated workflow of acquisition technique, quantification tool and processing method has emerged as the popular technique employed in metaproteomic research to provide a comprehensive landscape of the adaptive response of microbes to external stimuli and their interactions with other organisms or host cells. The performance of a specific LFQ workflow is highly dependent on the studied data. Hence, it is essential to discover the most appropriate one for a specific data set. However, it is challenging to perform such discovery due to the large number of possible workflows and the multifaceted nature of the evaluation criteria. Herein, a web server ANPELA (https://idrblab.org/anpela/) was developed and validated as the first tool enabling performance assessment of whole LFQ workflow (collective assessment by five well-established criteria with distinct underlying theories), and it enabled the identification of the optimal LFQ workflow(s) by a comprehensive performance ranking. ANPELA not only automatically detects the diverse formats of data generated by all quantification tools but also provides the most complete set of processing methods among the available web servers and stand-alone tools. Systematic validation using metaproteomic benchmarks revealed ANPELA's capabilities in 1 discovering well-performing workflow(s), (2) enabling assessment from multiple perspectives and (3) validating LFQ accuracy using spiked proteins. ANPELA has a unique ability to evaluate the performance of whole LFQ workflow and enables the discovery of the optimal LFQs by the comprehensive performance ranking of all 560 workflows. Therefore, it has great potential for applications in metaproteomic and other studies requiring LFQ techniques, as many features are shared among proteomic studies.
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Affiliation(s)
- Jing Tang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Jianbo Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yunxia Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Bo Li
- School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Yinghong Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Qingxia Yang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Xuejiao Cui
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Jiajun Hong
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xiaofeng Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Yuzong Chen
- Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | - Weiwei Xue
- School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
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16
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Leiva D, Fernández-Mendoza F, Acevedo J, Carú M, Grube M, Orlando J. The Bacterial Community of the Foliose Macro-lichen Peltigera frigida Is More than a Mere Extension of the Microbiota of the Subjacent Substrate. MICROBIAL ECOLOGY 2021; 81:965-976. [PMID: 33404820 DOI: 10.1007/s00248-020-01662-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
Lichens host highly diverse microbial communities, with bacteria being one of the most explored groups in terms of their diversity and functioning. These bacteria could partly originate from symbiotic propagules developed by many lichens and, perhaps more commonly and depending on environmental conditions, from different sources of the surroundings. Using the narrowly distributed species Peltigera frigida as an object of study, we propose that bacterial communities in these lichens are different from those in their subjacent substrates, even if some taxa might be shared. Ten terricolous P. frigida lichens and their substrates were sampled from forested sites in the Coyhaique National Reserve, located in an understudied region in Chile. The mycobiont identity was confirmed using partial 28S and ITS sequences. Besides, 16S fragments revealed that mycobionts were associated with the same cyanobacterial haplotype. From both lichens and substrates, Illumina 16S amplicon sequencing was performed using primers that exclude cyanobacteria. In lichens, Proteobacteria was the most abundant phylum (37%), whereas soil substrates were dominated by Acidobacteriota (39%). At lower taxonomic levels, several bacterial groups differed in relative abundance among P. frigida lichens and their substrates, some of them being highly abundant in lichens but almost absent in substrates, like Sphingomonas (8% vs 0.2%), and others enriched in lichens, as an unassigned genus of Chitinophagaceae (10% vs 2%). These results reinforce the idea that lichens would carry some components of their microbiome when propagating, but they also could acquire part of their bacterial community from the substrates.
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Affiliation(s)
- Diego Leiva
- Faculty of Sciences, Department of Ecological Sciences, Universidad de Chile, Santiago, Chile
- Institute of Biology, University of Graz, Graz, Austria
| | | | - José Acevedo
- Faculty of Sciences, Department of Ecological Sciences, Universidad de Chile, Santiago, Chile
| | - Margarita Carú
- Faculty of Sciences, Department of Ecological Sciences, Universidad de Chile, Santiago, Chile
| | - Martin Grube
- Institute of Biology, University of Graz, Graz, Austria
| | - Julieta Orlando
- Faculty of Sciences, Department of Ecological Sciences, Universidad de Chile, Santiago, Chile.
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17
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Grimm M, Grube M, Schiefelbein U, Zühlke D, Bernhardt J, Riedel K. The Lichens' Microbiota, Still a Mystery? Front Microbiol 2021; 12:623839. [PMID: 33859626 PMCID: PMC8042158 DOI: 10.3389/fmicb.2021.623839] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/10/2021] [Indexed: 01/03/2023] Open
Abstract
Lichens represent self-supporting symbioses, which occur in a wide range of terrestrial habitats and which contribute significantly to mineral cycling and energy flow at a global scale. Lichens usually grow much slower than higher plants. Nevertheless, lichens can contribute substantially to biomass production. This review focuses on the lichen symbiosis in general and especially on the model species Lobaria pulmonaria L. Hoffm., which is a large foliose lichen that occurs worldwide on tree trunks in undisturbed forests with long ecological continuity. In comparison to many other lichens, L. pulmonaria is less tolerant to desiccation and highly sensitive to air pollution. The name-giving mycobiont (belonging to the Ascomycota), provides a protective layer covering a layer of the green-algal photobiont (Dictyochloropsis reticulata) and interspersed cyanobacterial cell clusters (Nostoc spec.). Recently performed metaproteome analyses confirm the partition of functions in lichen partnerships. The ample functional diversity of the mycobiont contrasts the predominant function of the photobiont in production (and secretion) of energy-rich carbohydrates, and the cyanobiont's contribution by nitrogen fixation. In addition, high throughput and state-of-the-art metagenomics and community fingerprinting, metatranscriptomics, and MS-based metaproteomics identify the bacterial community present on L. pulmonaria as a surprisingly abundant and structurally integrated element of the lichen symbiosis. Comparative metaproteome analyses of lichens from different sampling sites suggest the presence of a relatively stable core microbiome and a sampling site-specific portion of the microbiome. Moreover, these studies indicate how the microbiota may contribute to the symbiotic system, to improve its health, growth and fitness.
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Affiliation(s)
- Maria Grimm
- Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Martin Grube
- Institute of Plant Sciences, Karl-Franzens-University Graz, Graz, Austria
| | | | - Daniela Zühlke
- Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Jörg Bernhardt
- Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, University Greifswald, Greifswald, Germany
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18
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Mikolasch A, Berzhanova R, Omirbekova A, Reinhard A, Zühlke D, Meister M, Mukasheva T, Riedel K, Urich T, Schauer F. Moniliella spathulata, an oil-degrading yeast, which promotes growth of barley in oil-polluted soil. Appl Microbiol Biotechnol 2021; 105:401-415. [PMID: 33219393 PMCID: PMC7778628 DOI: 10.1007/s00253-020-11011-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 11/26/2022]
Abstract
The yeast strain Moniliella spathulata SBUG-Y 2180 was isolated from oil-contaminated soil at the Tengiz oil field in the Atyrau region of Kazakhstan on the basis of its unique ability to use crude oil and its components as the sole carbon and energy source. This yeast used a large number of hydrocarbons as substrates (more than 150), including n-alkanes with chain lengths ranging from C10 to C32, monomethyl- and monoethyl-substituted alkanes (C9-C23), and n-alkylcyclo alkanes with alkyl chain lengths from 3 to 24 carbon atoms as well as substituted monoaromatic and diaromatic hydrocarbons. Metabolism of this huge range of hydrocarbon substrates produced a very large number of aliphatic, alicyclic, and aromatic acids. Fifty-one of these were identified by GC/MS analyses. This is the first report of the degradation and formation of such a large number of compounds by a yeast. Inoculation of barley seeds with M. spathulata SBUG-Y 2180 had a positive effect on shoot and root development of plants grown in oil-contaminated sand, pointing toward potential applications of the yeast in bioremediation of polluted soils. KEY POINTS: • Moniliella spathulata an oil-degrading yeast • Increase of the growth of barley.
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Affiliation(s)
- Annett Mikolasch
- Institute of Microbiology, University Greifswald, Felix-Hausdorff-Straße 8, 17489, Greifswald, Germany.
| | - Ramza Berzhanova
- Department of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave 71, Almaty, Kazakhstan, 050040
| | - Anel Omirbekova
- Department of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave 71, Almaty, Kazakhstan, 050040
| | - Anne Reinhard
- Institute of Microbiology, University Greifswald, Felix-Hausdorff-Straße 8, 17489, Greifswald, Germany
| | - Daniele Zühlke
- Institute of Microbiology, University Greifswald, Felix-Hausdorff-Straße 8, 17489, Greifswald, Germany
| | - Mareike Meister
- Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Str. 2, 17489, Greifswald, Germany
| | - Togzhan Mukasheva
- Department of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave 71, Almaty, Kazakhstan, 050040
| | - Katharina Riedel
- Institute of Microbiology, University Greifswald, Felix-Hausdorff-Straße 8, 17489, Greifswald, Germany
| | - Tim Urich
- Institute of Microbiology, University Greifswald, Felix-Hausdorff-Straße 8, 17489, Greifswald, Germany
| | - Frieder Schauer
- Institute of Microbiology, University Greifswald, Felix-Hausdorff-Straße 8, 17489, Greifswald, Germany
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19
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Muggia L, Ametrano CG, Sterflinger K, Tesei D. An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota. Life (Basel) 2020; 10:E356. [PMID: 33348904 PMCID: PMC7765829 DOI: 10.3390/life10120356] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 12/26/2022] Open
Abstract
Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi.
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Affiliation(s)
- Lucia Muggia
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Claudio G. Ametrano
- Grainger Bioinformatics Center, Department of Science and Education, The Field Museum, Chicago, IL 60605, USA;
| | - Katja Sterflinger
- Academy of Fine Arts Vienna, Institute of Natual Sciences and Technology in the Arts, 1090 Vienna, Austria;
| | - Donatella Tesei
- Department of Biotechnology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria;
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20
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Ullah J, Khanum Z, Khan IA, Khalid AN, Musharraf SG, Ali A. Metaproteomics reveals the structural and functional diversity of Dermatocarpon miniatum (L.) W. Mann. Microbiota. Fungal Biol 2020; 125:32-38. [PMID: 33317774 DOI: 10.1016/j.funbio.2020.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/02/2020] [Accepted: 10/04/2020] [Indexed: 12/30/2022]
Abstract
Metaproteomics is a strategy to understand the taxonomy, functionality and metabolic pathways of the microbial communities. The relationship among the symbiotic microbiota in the entire lichen thallus, Dermatocarpon miniatum, was evaluated using the metaproteomic approach. Proteomic profiling using one-dimensional SDS-PAGE followed by LC-MS/MS analysis resulted in a total of 138 identified proteins via Mascot search against UniRef100 and Swiss-Prot databases. In addition to the fungal and algal partners, D. miniatum proteome encompasses proteins from prokaryotes, which is a multifarious community mainly dominated by cyanobacteria and proteobacteria. While proteins assigned to fungus were the most abundant (55 %), followed by protists (16 %), bacterial (13 %), plant (11 %), and viral (1 %) origin, whereas 4 % remained undefined. Various proteins were assigned to the different lichen symbionts by using Gene Ontology (GO) terms, e.g. fungal proteins involved in the oxidation-reduction process, protein folding and glycolytic process, while protists and bacterial proteins were involved in photosynthetic electron transport in photosystem II (PS II), ATP synthesis coupled proton transport, and carbon fixation. The presence of bacterial communities extended the traditional concept of fungal-algal lichen symbiotic interaction.
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Affiliation(s)
- Junaid Ullah
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Zainab Khanum
- Jamil Ur Rahman Center for Genome Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Ishtiaq Ahmad Khan
- Jamil Ur Rahman Center for Genome Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | | | - Syed Ghulam Musharraf
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan; Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
| | - Arslan Ali
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
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21
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Schiebenhoefer H, Schallert K, Renard BY, Trappe K, Schmid E, Benndorf D, Riedel K, Muth T, Fuchs S. A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane. Nat Protoc 2020; 15:3212-3239. [PMID: 32859984 DOI: 10.1038/s41596-020-0368-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 05/29/2020] [Indexed: 12/14/2022]
Abstract
Metaproteomics, the study of the collective protein composition of multi-organism systems, provides deep insights into the biodiversity of microbial communities and the complex functional interplay between microbes and their hosts or environment. Thus, metaproteomics has become an indispensable tool in various fields such as microbiology and related medical applications. The computational challenges in the analysis of corresponding datasets differ from those of pure-culture proteomics, e.g., due to the higher complexity of the samples and the larger reference databases demanding specific computing pipelines. Corresponding data analyses usually consist of numerous manual steps that must be closely synchronized. With MetaProteomeAnalyzer and Prophane, we have established two open-source software solutions specifically developed and optimized for metaproteomics. Among other features, peptide-spectrum matching is improved by combining different search engines and, compared to similar tools, metaproteome annotation benefits from the most comprehensive set of available databases (such as NCBI, UniProt, EggNOG, PFAM, and CAZy). The workflow described in this protocol combines both tools and leads the user through the entire data analysis process, including protein database creation, database search, protein grouping and annotation, and results visualization. To the best of our knowledge, this protocol presents the most comprehensive, detailed and flexible guide to metaproteomics data analysis to date. While beginners are provided with robust, easy-to-use, state-of-the-art data analysis in a reasonable time (a few hours, depending on, among other factors, the protein database size and the number of identified peptides and inferred proteins), advanced users benefit from the flexibility and adaptability of the workflow.
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Affiliation(s)
- Henning Schiebenhoefer
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
- Hasso Plattner Institute, Faculty for Digital Engineering, University of Potsdam, Potsdam, Germany
| | - Kay Schallert
- Bioprocess Engineering, Otto von Guericke University, Magdeburg, Germany
| | - Bernhard Y Renard
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
- Hasso Plattner Institute, Faculty for Digital Engineering, University of Potsdam, Potsdam, Germany
| | - Kathrin Trappe
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Emanuel Schmid
- ID Computational & Data Science Support, Eidgenössische Technische Hochschule, Zurich, Switzerland
| | - Dirk Benndorf
- Bioprocess Engineering, Otto von Guericke University, Magdeburg, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Katharina Riedel
- Center for Functional Genomics of Microbes (CFGM), Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Thilo Muth
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
- Section S.3 eScience, Federal Institute for Materials Research and Testing (BAM), Berlin, Germany
| | - Stephan Fuchs
- Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany.
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22
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Spribille T, Tagirdzhanova G, Goyette S, Tuovinen V, Case R, Zandberg WF. 3D biofilms: in search of the polysaccharides holding together lichen symbioses. FEMS Microbiol Lett 2020; 367:5731805. [PMID: 32037451 PMCID: PMC7164778 DOI: 10.1093/femsle/fnaa023] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 02/07/2020] [Indexed: 12/14/2022] Open
Abstract
Stable, long-term interactions between fungi and algae or cyanobacteria, collectively known as lichens, have repeatedly evolved complex architectures with little resemblance to their component parts. Lacking any central scaffold, the shapes they assume are casts of secreted polymers that cement cells into place, determine the angle of phototropic exposure and regulate water relations. A growing body of evidence suggests that many lichen extracellular polymer matrices harbor unicellular, non-photosynthesizing organisms (UNPOs) not traditionally recognized as lichen symbionts. Understanding organismal input and uptake in this layer is key to interpreting the role UNPOs play in lichen biology. Here, we review both polysaccharide composition determined from whole, pulverized lichens and UNPOs reported from lichens to date. Most reported polysaccharides are thought to be structural cell wall components. The composition of the extracellular matrix is not definitively known. Several lines of evidence suggest some acidic polysaccharides have evaded detection in routine analysis of neutral sugars and may be involved in the extracellular matrix. UNPOs reported from lichens include diverse bacteria and yeasts for which secreted polysaccharides play important biological roles. We conclude by proposing testable hypotheses on the role that symbiont give-and-take in this layer could play in determining or modifying lichen symbiotic outcomes.
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Affiliation(s)
- Toby Spribille
- Department of Biological Sciences, CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Gulnara Tagirdzhanova
- Department of Biological Sciences, CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Spencer Goyette
- Department of Biological Sciences, CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Veera Tuovinen
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Rebecca Case
- Department of Biological Sciences, CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Wesley F Zandberg
- Department of Chemistry, University of British Columbia, Okanagan Campus, 3427 University Way, Kelowna, BC V1V 1V7, Canada
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23
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Chinchilla D, Bruisson S, Meyer S, Zühlke D, Hirschfeld C, Joller C, L'Haridon F, Mène-Saffrané L, Riedel K, Weisskopf L. A sulfur-containing volatile emitted by potato-associated bacteria confers protection against late blight through direct anti-oomycete activity. Sci Rep 2019; 9:18778. [PMID: 31889050 PMCID: PMC6937334 DOI: 10.1038/s41598-019-55218-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 11/12/2019] [Indexed: 12/14/2022] Open
Abstract
Plant diseases are a major cause for yield losses and new strategies to control them without harming the environment are urgently needed. Plant-associated bacteria contribute to their host’s health in diverse ways, among which the emission of disease-inhibiting volatile organic compounds (VOCs). We have previously reported that VOCs emitted by potato-associated bacteria caused strong in vitro growth inhibition of the late blight causing agent Phytophthora infestans. This work focuses on sulfur-containing VOCs (sVOCs) and demonstrates the high in planta protective potential of S-methyl methane thiosulfonate (MMTS), which fully prevented late blight disease in potato leaves and plantlets without phytotoxic effects, in contrast to other sVOCs. Short exposure times were sufficient to protect plants against infection. We further showed that MMTS’s protective activity was not mediated by the plant immune system but lied in its anti-oomycete activity. Using quantitative proteomics, we determined that different sVOCs caused specific proteome changes in P. infestans, indicating perturbations in sulfur metabolism, protein translation and redox balance. This work brings new perspectives for plant protection against the devastating Irish Famine pathogen, while opening new research avenues on the role of sVOCs in the interaction between plants and their microbiome.
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Affiliation(s)
- Delphine Chinchilla
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700, Fribourg, Switzerland
| | - Sébastien Bruisson
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700, Fribourg, Switzerland
| | - Silvan Meyer
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700, Fribourg, Switzerland
| | - Daniela Zühlke
- Department of Microbial Physiology and Molecular Biology, University of Greifswald, Felix-Hausdorff-Strasse 8, D-17489, Greifswald, Germany
| | - Claudia Hirschfeld
- Department of Microbial Proteomics, University of Greifswald, Felix-Hausdorff-Strasse 8, D-17489, Greifswald, Germany
| | - Charlotte Joller
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700, Fribourg, Switzerland
| | - Floriane L'Haridon
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700, Fribourg, Switzerland
| | - Laurent Mène-Saffrané
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700, Fribourg, Switzerland
| | - Katharina Riedel
- Department of Microbial Physiology and Molecular Biology, University of Greifswald, Felix-Hausdorff-Strasse 8, D-17489, Greifswald, Germany
| | - Laure Weisskopf
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700, Fribourg, Switzerland.
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24
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Lee SJ, Morse D, Hijri M. Holobiont chronobiology: mycorrhiza may be a key to linking aboveground and underground rhythms. MYCORRHIZA 2019; 29:403-412. [PMID: 31190278 DOI: 10.1007/s00572-019-00903-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/05/2019] [Indexed: 06/09/2023]
Abstract
Circadian clocks are nearly ubiquitous timing mechanisms that can orchestrate rhythmic behavior and gene expression in a wide range of organisms. Clock mechanisms are becoming well understood in fungal, animal, and plant model systems, yet many of these organisms are surrounded by a complex and diverse microbiota which should be taken into account when examining their biology. Of particular interest are the symbiotic relationships between organisms that have coevolved over time, forming a unit called a holobiont. Several studies have now shown linkages between the circadian rhythms of symbiotic partners. Interrelated regulation of holobiont circadian rhythms seems thus important to coordinate shifts in activity over the day for all the partners. Therefore, we suggest that the classical view of "chronobiological individuals" should include "a holobiont" rather than an organism. Unfortunately, mechanisms that may regulate interspecies temporal acclimation and the evolution of the circadian clock in holobionts are far from being understood. For the plant holobiont, our understanding is particularly limited. In this case, the holobiont encompasses two different ecosystems, one above and the other below the ground, with the two potentially receiving timing information from different synchronizing signals (Zeitgebers). The arbuscular mycorrhizal (AM) symbiosis, formed by plant roots and fungi, is one of the oldest and most widespread associations between organisms. By mediating the nutritional flux between the plant and the many microbes in the soil, AM symbiosis constitutes the backbone of the plant holobiont. Even though the importance of the AM symbiosis has been well recognized in agricultural and environmental sciences, its circadian chronobiology remains almost completely unknown. We have begun to study the circadian clock of arbuscular mycorrhizal fungi, and we compile and here discuss the available information on the subject. We propose that analyzing the interrelated temporal organization of the AM symbiosis and determining its underlying mechanisms will advance our understanding of the role and coordination of circadian clocks in holobionts in general.
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Affiliation(s)
- Soon-Jae Lee
- Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - David Morse
- Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada.
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25
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Villa F, Cappitelli F. The Ecology of Subaerial Biofilms in Dry and Inhospitable Terrestrial Environments. Microorganisms 2019; 7:microorganisms7100380. [PMID: 31547498 PMCID: PMC6843906 DOI: 10.3390/microorganisms7100380] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/17/2019] [Accepted: 09/20/2019] [Indexed: 11/23/2022] Open
Abstract
The ecological relationship between minerals and microorganisms arguably represents one of the most important associations in dry terrestrial environments, since it strongly influences major biochemical cycles and regulates the productivity and stability of the Earth’s food webs. Despite being inhospitable ecosystems, mineral substrata exposed to air harbor form complex and self-sustaining communities called subaerial biofilms (SABs). Using life on air-exposed minerals as a model and taking inspiration from the mechanisms of some microorganisms that have adapted to inhospitable conditions, we illustrate the ecology of SABs inhabiting natural and built environments. Finally, we advocate the need for the convergence between the experimental and theoretical approaches that might be used to characterize and simulate the development of SABs on mineral substrates and SABs’ broader impacts on the dry terrestrial environment.
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Affiliation(s)
- Federica Villa
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy.
| | - Francesca Cappitelli
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy.
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26
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Pfaff F, Hägglund S, Zoli M, Blaise-Boisseau S, Laloy E, Koethe S, Zühlke D, Riedel K, Zientara S, Bakkali-Kassimi L, Valarcher JF, Höper D, Beer M, Eschbaumer M. Proteogenomics Uncovers Critical Elements of Host Response in Bovine Soft Palate Epithelial Cells Following In Vitro Infection with Foot-And-Mouth Disease Virus. Viruses 2019; 11:E53. [PMID: 30642035 PMCID: PMC6356718 DOI: 10.3390/v11010053] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/08/2019] [Accepted: 01/11/2019] [Indexed: 12/21/2022] Open
Abstract
Foot-and-mouth disease (FMD) is the most devastating disease of cloven-hoofed livestock, with a crippling economic burden in endemic areas and immense costs associated with outbreaks in free countries. Foot-and-mouth disease virus (FMDV), a picornavirus, will spread rapidly in naïve populations, reaching morbidity rates of up to 100% in cattle. Even after recovery, over 50% of cattle remain subclinically infected and infectious virus can be recovered from the nasopharynx. The pathogen and host factors that contribute to FMDV persistence are currently not understood. Using for the first time primary bovine soft palate multilayers in combination with proteogenomics, we analyzed the transcriptional responses during acute and persistent FMDV infection. During the acute phase viral RNA and protein was detectable in large quantities and in response hundreds of interferon-stimulated genes (ISG) were overexpressed, mediating antiviral activity and apoptosis. Although the number of pro-apoptotic ISGs and the extent of their regulation decreased during persistence, some ISGs with antiviral activity were still highly expressed at that stage. This indicates a long-lasting but ultimately ineffective stimulation of ISGs during FMDV persistence. Furthermore, downregulation of relevant genes suggests an interference with the extracellular matrix that may contribute to the skewed virus-host equilibrium in soft palate epithelial cells.
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Affiliation(s)
- Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald, Germany.
| | - Sara Hägglund
- Swedish University of Agricultural Sciences, Host-pathogen interaction group, Division of Ruminant Medicine, 75007 Uppsala, Sweden.
| | - Martina Zoli
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald, Germany.
| | - Sandra Blaise-Boisseau
- Laboratoire de Santé Animale de Maisons-Alfort, UMR 1161 virologie, INRA, Ecole Nationale Vétérinaire d'Alfort, ANSES, Université Paris-Est, 94700 Maisons-Alfort, France.
| | - Eve Laloy
- Laboratoire de Santé Animale de Maisons-Alfort, UMR 1161 virologie, INRA, Ecole Nationale Vétérinaire d'Alfort, ANSES, Université Paris-Est, 94700 Maisons-Alfort, France.
- Biopôle EnvA, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, 94700 Maisons-Alfort, France.
| | - Susanne Koethe
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald, Germany.
| | - Daniela Zühlke
- Institute of Microbiology, Department for Microbial Physiology and Molecular Biology, University of Greifswald, 17489 Greifswald, Germany.
| | - Katharina Riedel
- Institute of Microbiology, Department for Microbial Physiology and Molecular Biology, University of Greifswald, 17489 Greifswald, Germany.
| | - Stephan Zientara
- Laboratoire de Santé Animale de Maisons-Alfort, UMR 1161 virologie, INRA, Ecole Nationale Vétérinaire d'Alfort, ANSES, Université Paris-Est, 94700 Maisons-Alfort, France.
| | - Labib Bakkali-Kassimi
- Laboratoire de Santé Animale de Maisons-Alfort, UMR 1161 virologie, INRA, Ecole Nationale Vétérinaire d'Alfort, ANSES, Université Paris-Est, 94700 Maisons-Alfort, France.
| | - Jean-François Valarcher
- Swedish University of Agricultural Sciences, Host-pathogen interaction group, Division of Ruminant Medicine, 75007 Uppsala, Sweden.
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald, Germany.
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald, Germany.
| | - Michael Eschbaumer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald, Germany.
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Cernava T, Vasfiu Q, Erlacher A, Aschenbrenner IA, Francesconi K, Grube M, Berg G. Adaptions of Lichen Microbiota Functioning Under Persistent Exposure to Arsenic Contamination. Front Microbiol 2018; 9:2959. [PMID: 30555453 PMCID: PMC6283889 DOI: 10.3389/fmicb.2018.02959] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/16/2018] [Indexed: 11/13/2022] Open
Abstract
Host-associated microbiota play an important role in the health and persistence of more complex organisms. In this study, metagenomic analyses were used to reveal microbial community adaptations in three lichen samples as a response to different arsenic concentrations at the sampling sites. Elevated arsenic concentrations at a former mining site expanded the spectrum and number of relevant functions in the lichen-associated microorganisms. Apparent changes affected the abundance of numerous detoxification-related genes, they were substantially enhanced in arsenic-polluted samples. Complementary quantifications of the arsenite S-adenosylmethionine methyltransferase (arsM) gene showed that its abundance is not strictly responding to the environmental arsenic concentrations. The analyzed samples contained rather low numbers of the arsM gene with a maximum of 202 gene copies μl-1 in total community DNA extracts. In addition, bacterial isolates were screened for the presence of arsM. Positive isolates were exposed to different As(III) and As(V) concentrations and tolerated up to 30 mM inorganic arsenic in fluid media, while no substantial biotransformations were observed. Obtained data deepens our understanding related to adaptions of whole microbial communities to adverse environmental conditions. Moreover, this study provides the first evidence that the integrity of bacteria in the lichen holobiont is maintained by acquisition of specific resistances.
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Affiliation(s)
- Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Qerimane Vasfiu
- Institute of Chemistry, NAWI Graz, University of Graz, Graz, Austria
| | - Armin Erlacher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | | | - Kevin Francesconi
- Institute of Chemistry, NAWI Graz, University of Graz, Graz, Austria
| | - Martin Grube
- Institute of Biology, University of Graz, Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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Almendras K, García J, Carú M, Orlando J. Nitrogen-Fixing Bacteria Associated with Peltigera Cyanolichens and Cladonia Chlorolichens. Molecules 2018; 23:E3077. [PMID: 30477264 PMCID: PMC6320784 DOI: 10.3390/molecules23123077] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/15/2018] [Accepted: 11/21/2018] [Indexed: 11/16/2022] Open
Abstract
Lichens have been extensively studied and described; however, recent evidence suggests that members of the bacterial community associated with them could contribute new functions to the symbiotic interaction. In this work, we compare the nitrogen-fixing guild associated with bipartite terricolous lichens with different types of photobiont: Peltigera cyanolichens and Cladonia chlorolichens. Since cyanobacteria contribute nitrogen to the symbiosis, we propose that chlorolichens have more diverse bacteria with the ability to fix nitrogen compared to cyanolichens. In addition, since part of these bacteria could be recruited from the substrate where lichens grow, we propose that thalli and substrates share some bacteria in common. The structure of the nitrogen-fixing guild in the lichen and substrate bacterial communities of both lichens was determined by terminal restriction fragment length polymorphism (TRFLP) of the nifH gene. Multivariate analyses showed that the nitrogen-fixing bacteria associated with both types of lichen were distinguishable from those present in their substrates. Likewise, the structure of the nitrogen-fixing bacteria present in the cyanolichens was different from that of chlorolichens. Finally, the diversity of this bacterial guild calculated using the Shannon index confirms the hypothesis that chlorolichens have a higher diversity of nitrogen-fixing bacteria than cyanolichens.
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Affiliation(s)
- Katerin Almendras
- Laboratory of Microbial Ecology, Department of Ecological Sciences, Faculty of Sciences, Universidad de Chile, Santiago 7800003, Chile.
| | - Jaime García
- Laboratory of Microbial Ecology, Department of Ecological Sciences, Faculty of Sciences, Universidad de Chile, Santiago 7800003, Chile.
| | - Margarita Carú
- Laboratory of Microbial Ecology, Department of Ecological Sciences, Faculty of Sciences, Universidad de Chile, Santiago 7800003, Chile.
| | - Julieta Orlando
- Laboratory of Microbial Ecology, Department of Ecological Sciences, Faculty of Sciences, Universidad de Chile, Santiago 7800003, Chile.
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29
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Cernava T, Aschenbrenner IA, Soh J, Sensen CW, Grube M, Berg G. Plasticity of a holobiont: desiccation induces fasting-like metabolism within the lichen microbiota. ISME JOURNAL 2018; 13:547-556. [PMID: 30310167 PMCID: PMC6331575 DOI: 10.1038/s41396-018-0286-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/31/2018] [Accepted: 09/08/2018] [Indexed: 01/08/2023]
Abstract
The role of host-associated microbiota in enduring dehydration and drought is largely unknown. We have used lichens to study this increasingly important problem because they are the organisms that are optimally adapted to reoccurring hydration/dehydration cycles, and they host a defined and persistent bacterial community. The analysis of metatranscriptomic datasets from bacterial communities of the lung lichen (Lobaria pulmonaria (L.) Hoffm.), sampled under representative hydration stages, revealed significant structural shifts and functional specialization to host conditions. The hydrated samples showed upregulated transcription of transport systems, tRNA modification and various porins (Omp2b by Rhizobiales), whereas the desiccated samples showed different functions related to stress adaption prominently. Carbohydrate metabolism was activated under both conditions. Under dry conditions, upregulation of a specialized ketone metabolism indicated a switch to lipid-based nutrition. Several bacterial lineages were involved in a functional transition that was reminiscent of a 'fasting metaorganism'. Similar functional adaptions were assigned to taxonomically unrelated groups, indicating hydration-related specialization of the microbiota. We were able to show that host-associated bacterial communities are well adapted to dehydration by stress protection and changes of the metabolism. Moreover, our results indicate an intense interplay in holobiont functioning under drought stress.
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Affiliation(s)
- Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
| | - Ines Aline Aschenbrenner
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
| | - Jung Soh
- Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Christoph W Sensen
- Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria.,BioTechMed Graz, Mozartgasse 12/II, 8010, Graz, Austria
| | - Martin Grube
- Institute of Plant Sciences, University of Graz, Holteigasse 6, 8010, Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria. .,BioTechMed Graz, Mozartgasse 12/II, 8010, Graz, Austria.
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West NJ, Parrot D, Fayet C, Grube M, Tomasi S, Suzuki MT. Marine cyanolichens from different littoral zones are associated with distinct bacterial communities. PeerJ 2018; 6:e5208. [PMID: 30038864 PMCID: PMC6054067 DOI: 10.7717/peerj.5208] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/20/2018] [Indexed: 11/20/2022] Open
Abstract
The microbial diversity and function of terrestrial lichens have been well studied, but knowledge about the non-photosynthetic bacteria associated with marine lichens is still scarce. 16S rRNA gene Illumina sequencing was used to assess the culture-independent bacterial diversity in the strictly marine cyanolichen species Lichina pygmaea and Lichina confinis, and the maritime chlorolichen species Xanthoria aureola which occupy different areas on the littoral zone. Inland terrestrial cyanolichens from Austria were also analysed as for the marine lichens to examine further the impact of habitat/lichen species on the associated bacterial communities. The L. confinis and L. pygmaea communities were significantly different from those of the maritime Xanthoria aureola lichen found higher up on the littoral zone and these latter communities were more similar to those of the inland terrestrial lichens. The strictly marine lichens were dominated by the Bacteroidetes phylum accounting for 50% of the sequences, whereas Alphaproteobacteria, notably Sphingomonas, dominated the maritime and the inland terrestrial lichens. Bacterial communities associated with the two Lichina species were significantly different sharing only 33 core OTUs, half of which were affiliated to the Bacteroidetes genera Rubricoccus, Tunicatimonas and Lewinella, suggesting an important role of these species in the marine Lichina lichen symbiosis. Marine cyanolichens showed a higher abundance of OTUs likely affiliated to moderately thermophilic and/or radiation resistant bacteria belonging to the Phyla Chloroflexi, Thermi, and the families Rhodothermaceae and Rubrobacteraceae when compared to those of inland terrestrial lichens. This most likely reflects the exposed and highly variable conditions to which they are subjected daily.
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Affiliation(s)
- Nyree J. West
- Observatoire Océanologique de Banyuls sur mer, Sorbonne Université, CNRS, Banyuls sur mer, France
| | - Delphine Parrot
- Univ Rennes, CNRS, ISCR—UMR 6226, Rennes, France
- Current address: GEOMAR Helmholtz Centre for Ocean Research Kiel, Research Unit Marine Natural Products Chemistry, GEOMAR Centre for Marine Biotechnology, Kiel, Germany
| | - Claire Fayet
- Observatoire Océanologique de Banyuls sur mer, Sorbonne Université, CNRS, Banyuls sur mer, France
| | - Martin Grube
- Institute of Plant Sciences, University of Graz, Graz, Austria
| | | | - Marcelino T. Suzuki
- Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Sorbonne Université, CNRS, Banyuls sur mer, France
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