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Pardo-De la Hoz CJ, Magain N, Lutzoni F, Goward T, Restrepo S, Miadlikowska J. Contrasting Symbiotic Patterns in Two Closely Related Lineages of Trimembered Lichens of the Genus Peltigera. Front Microbiol 2018; 9:2770. [PMID: 30505297 PMCID: PMC6250826 DOI: 10.3389/fmicb.2018.02770] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 10/29/2018] [Indexed: 11/13/2022] Open
Abstract
Species circumscription is key to the characterization of patterns of specificity in symbiotic systems at a macroevolutionary scale. Here, a worldwide phylogenetic framework was used to assess the biodiversity and symbiotic patterns of association among partners in trimembered lichens from the genus Peltigera, section Chloropeltigera. We sequenced six loci of the main fungal partner and performed species discovery and validation analyses to establish putative species boundaries. Single locus phylogenies were used to establish the identity of both photobionts, Nostoc (cyanobacterium) and Coccomyxa (green alga). Distribution and specificity patterns were compared to the closely related clade, section Peltidea, which includes mainly Peltigera species with trimembered thalli. For section Chloropeltigera, eight fungal species (including five newly delimited putative species) were found in association with nine Nostoc phylogroups and two Coccomyxa species. In contrast, eight fungal species (including three newly delimited putative species) in section Peltidea were found in association with only four Nostoc phylogroups and the same two Coccomyxa species as for section Chloropeltigera. This difference in cyanobiont biodiversity between these two sections can potentially be explained by a significantly higher frequency of sexual reproductive structures in species from section Chloropeltigera compared to section Peltidea. Therefore, horizontal transmission of the cyanobiont might be more prevalent in Chloropeltigera species, while vertical transmission might be more common in Peltidea species. All Peltigera species in section Chloropeltigera are generalists in their association with Nostoc compared to more specialized Peltigera species in section Peltidea. Constrained distributions of Peltigera species that associate strictly with one species of green algae (Coccomyxa subellipsoidea) indicate that the availability of the green alga and the specificity of the interaction might be important factors limiting geographic ranges of trimembered Peltigera, in addition to constraints imposed by their interaction with Nostoc partners and by climatic factors.
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Affiliation(s)
- Carlos José Pardo-De la Hoz
- Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
- Department of Biology, Duke University, Durham, NC, United States
| | - Nicolas Magain
- Department of Biology, Duke University, Durham, NC, United States
| | - François Lutzoni
- Department of Biology, Duke University, Durham, NC, United States
| | - Trevor Goward
- UBC Herbarium, Beaty Biodiversity Museum, University of British Columbia, Vancouver, BC, Canada
| | - Silvia Restrepo
- Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
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Vančurová L, Muggia L, Peksa O, Řídká T, Škaloud P. The complexity of symbiotic interactions influences the ecological amplitude of the host: A case study in Stereocaulon (lichenized Ascomycota). Mol Ecol 2018; 27:3016-3033. [PMID: 29900606 DOI: 10.1111/mec.14764] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 06/03/2018] [Accepted: 06/05/2018] [Indexed: 01/21/2023]
Abstract
Symbiosis plays a fundamental role in nature. Lichens are among the best known, globally distributed symbiotic systems whose ecology is shaped by the requirements of all symbionts forming the holobiont. The widespread lichen-forming fungal genus Stereocaulon provides a suitable model to study the ecology of microscopic green algal symbionts (i.e., phycobionts) within the lichen symbiosis. We analysed 282 Stereocaulon specimens, collected in diverse habitats worldwide, using the algal ITS rDNA and actin gene sequences and fungal ITS rDNA sequences. Phylogenetic analyses revealed a great diversity among the predominant phycobionts. The algal genus Asterochloris (Trebouxiophyceae) was recovered in most sampled thalli, but two additional genera, Vulcanochloris and Chloroidium, were also found. We used variation-partitioning analyses to investigate the effects of climatic conditions, substrate/habitat characteristic, spatial distribution and mycobionts on phycobiont distribution. Based on an analogy, we examined the effects of climate, substrate/habitat, spatial distribution and phycobionts on mycobiont distribution. According to our analyses, the distribution of phycobionts is primarily driven by mycobionts and vice versa. Specificity and selectivity of both partners, as well as their ecological requirements and the width of their niches, vary significantly among the species-level lineages. We demonstrated that species-level lineages, which accept more symbiotic partners, have wider climatic niches, overlapping with the niches of their partners. Furthermore, the survival of lichens on substrates with high concentrations of heavy metals appears to be supported by their association with toxicity-tolerant phycobionts. In general, low specificity towards phycobionts allows the host to associate with ecologically diversified algae, thereby broadening its ecological amplitude.
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Affiliation(s)
- Lucie Vančurová
- Faculty of Science, Department of Botany, Charles University, Prague 2, Czech Republic
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Ondřej Peksa
- The West Bohemian Museum in Pilsen, Plzeň, Czech Republic
| | - Tereza Řídká
- Faculty of Science, Department of Botany, Charles University, Prague 2, Czech Republic
| | - Pavel Škaloud
- Faculty of Science, Department of Botany, Charles University, Prague 2, Czech Republic
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Paul F, Otte J, Schmitt I, Dal Grande F. Comparing Sanger sequencing and high-throughput metabarcoding for inferring photobiont diversity in lichens. Sci Rep 2018; 8:8624. [PMID: 29872090 PMCID: PMC5988838 DOI: 10.1038/s41598-018-26947-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/22/2018] [Indexed: 11/26/2022] Open
Abstract
The implementation of HTS (high-throughput sequencing) approaches is rapidly changing our understanding of the lichen symbiosis, by uncovering high bacterial and fungal diversity, which is often host-specific. Recently, HTS methods revealed the presence of multiple photobionts inside a single thallus in several lichen species. This differs from Sanger technology, which typically yields a single, unambiguous algal sequence per individual. Here we compared HTS and Sanger methods for estimating the diversity of green algal symbionts within lichen thalli using 240 lichen individuals belonging to two species of lichen-forming fungi. According to HTS data, Sanger technology consistently yielded the most abundant photobiont sequence in the sample. However, if the second most abundant photobiont exceeded 30% of the total HTS reads in a sample, Sanger sequencing generally failed. Our results suggest that most lichen individuals in the two analyzed species, Lasallia hispanica and L. pustulata, indeed contain a single, predominant green algal photobiont. We conclude that Sanger sequencing is a valid approach to detect the dominant photobionts in lichen individuals and populations. We discuss which research areas in lichen ecology and evolution will continue to benefit from Sanger sequencing, and which areas will profit from HTS approaches to assessing symbiont diversity.
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Affiliation(s)
- Fiona Paul
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
- Departamento de Farmacología, Farmacognosia y Botánica, Universidad Complutense de Madrid, 28040, Madrid, Spain.
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Onuț-Brännström I, Benjamin M, Scofield DG, Heiðmarsson S, Andersson MGI, Lindström ES, Johannesson H. Sharing of photobionts in sympatric populations of Thamnolia and Cetraria lichens: evidence from high-throughput sequencing. Sci Rep 2018. [PMID: 29535321 PMCID: PMC5849601 DOI: 10.1038/s41598-018-22470-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In this study, we explored the diversity of green algal symbionts (photobionts) in sympatric populations of the cosmopolitan lichen-forming fungi Thamnolia and Cetraria. We sequenced with both Sanger and Ion Torrent High-Throughput Sequencing technologies the photobiont ITS-region of 30 lichen thalli from two islands: Iceland and Öland. While Sanger recovered just one photobiont genotype from each thallus, the Ion Torrent data recovered 10-18 OTUs for each pool of 5 lichen thalli, suggesting that individual lichens can contain heterogeneous photobiont populations. Both methods showed evidence for photobiont sharing between Thamnolia and Cetraria on Iceland. In contrast, our data suggest that on Öland the two mycobionts associate with distinct photobiont communities, with few shared OTUs revealed by Ion Torrent sequencing. Furthermore, by comparing our sequences with public data, we identified closely related photobionts from geographically distant localities. Taken together, we suggest that the photobiont composition in Thamnolia and Cetraria results from both photobiont-mycobiont codispersal and local acquisition during mycobiont establishment and/or lichen growth. We hypothesize that this is a successful strategy for lichens to be flexible in the use of the most adapted photobiont for the environment.
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Affiliation(s)
- Ioana Onuț-Brännström
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Mitchell Benjamin
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Douglas G Scofield
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.,Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX), Uppsala University, Uppsala, Sweden
| | - Starri Heiðmarsson
- Icelandic Institute of Natural History, Akureyri Division, Borgir Nordurslod, Iceland
| | - Martin G I Andersson
- Limnology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Eva S Lindström
- Limnology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Hanna Johannesson
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.
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Meiser A, Otte J, Schmitt I, Grande FD. Sequencing genomes from mixed DNA samples - evaluating the metagenome skimming approach in lichenized fungi. Sci Rep 2017; 7:14881. [PMID: 29097759 PMCID: PMC5668418 DOI: 10.1038/s41598-017-14576-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 10/12/2017] [Indexed: 01/07/2023] Open
Abstract
The metagenome skimming approach, i.e. low coverage shotgun sequencing of multi-species assemblages and subsequent reconstruction of individual genomes, is increasingly used for in-depth genomic characterization of ecological communities. This approach is a promising tool for reconstructing genomes of facultative symbionts, such as lichen-forming fungi, from metagenomic reads. However, no study has so far tested accuracy and completeness of assemblies based on metagenomic sequences compared to assemblies based on pure culture strains of lichenized fungi. Here we assembled the genomes of Evernia prunastri and Pseudevernia furfuracea based on metagenomic sequences derived from whole lichen thalli. We extracted fungal contigs using two different taxonomic binning methods, and performed gene prediction on the fungal contig subsets. We then assessed quality and completeness of the metagenome-based assemblies using genome assemblies as reference which are based on pure culture strains of the two fungal species. Our comparison showed that we were able to reconstruct fungal genomes from uncultured lichen thalli, and also cover most of the gene space (86-90%). Metagenome skimming will facilitate genome mining, comparative (phylo)genomics, and population genetics of lichen-forming fungi by circumventing the time-consuming, sometimes unfeasible, step of aposymbiotic cultivation.
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Affiliation(s)
- Anjuli Meiser
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue Str. 13, D-60438, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, D-60486, Frankfurt, Germany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, D-60486, Frankfurt, Germany
| | - Imke Schmitt
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue Str. 13, D-60438, Frankfurt, Germany.
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, D-60486, Frankfurt, Germany.
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, D-60486, Frankfurt, Germany.
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