{"id":37872,"date":"2021-04-16T11:08:42","date_gmt":"2021-04-16T09:08:42","guid":{"rendered":"https:\/\/www.embl.org\/news\/?p=37872"},"modified":"2024-03-22T10:56:23","modified_gmt":"2024-03-22T09:56:23","slug":"using-metagenomic-techniques-to-explore-lichens","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/science\/using-metagenomic-techniques-to-explore-lichens\/","title":{"rendered":"Using metagenomic techniques to explore lichens"},"content":{"rendered":"\n

Researchers from EMBL\u2019s European Bioinformatics Institute (EMBL-EBI), the University of Alberta in Canada, and colleagues have used metagenome analysis to identify yeasts \u2013 single-cell fungi \u2013 found at low abundance within a lichen symbiosis. Their findings suggest that these yeasts might play a role in helping the lichens survive.<\/p>\n\n\n\n

Lichens are unusual organisms. They don\u2019t have roots, stems, or leaves, and each type of lichen is a partnership, or symbiosis, between at least two species, usually a fungus \u2013 such as a yeast \u2013 and an alga. Lichens are essential parts of ecosystems because they help cycle nutrients and provide a home to insects and nesting material for birds. Many lichens are very sensitive to pollution and are of concern to conservationists in industrialised countries.<\/p>\n\n\n\n

Exploring lichen composition is now easier than ever, thanks to modern sequencing technologies and genome analysis tools. This study uses a metagenomics technique to produce genome assemblies for previously unobtainable, low-abundance fungi \u2013 the Basidiomycete yeasts \u2013 found within many wild lichens. Further investigation into the yeast genomes has also helped the researchers to shed light on the important role yeasts play in aiding the survival of lichens in their natural habitat.<\/p>\n\n\n\n

Identifying low-abundance genomes<\/h2>\n\n\n\n

Basidiomycete yeasts have recently been reported as part of many lichen symbioses, but attempts to confirm this using genome sequencing have proven tricky. This is because of the small quantities of these yeasts identified in lichens, and also because they can\u2019t be cultured in a lab. To solve this problem, the researchers used a metagenomics approach to isolate the genomes of the Basidiomycete yeasts.<\/p>\n\n\n\n

\u201cThis study provides a framework for starting to understand the genomics of some of these more complicated biological organisms that form elaborate symbiotic relationships,\u201d says Rob Finn, Team Leader of Microbiome Informatics at EMBL-EBI<\/a>. \u201cUsing metagenomics can help us investigate complex communities, such as lichens, and also ecosystems like soil and ocean water.\u201d<\/p>\n\n\n\n

Once the researchers had acquired what they believed to be the yeast genomes, they used EukCC \u2013 a tool developed at EMBL-EBI for estimating how well eukaryotic genomes have been reconstructed from metagenomic samples \u2013 to confirm with confidence that Basidiomycete yeasts were present in their lichen samples. The yeast genomes obtained from this study are now openly accessible through EMBL-EBI\u2019s European Nucleotide Archive<\/a>.<\/p>\n\n\n\n

\u201cThis study shows that we can determine eukaryotic microbes with confidence using the right tools,\u201d says Paul Saary, PhD student at EMBL-EBI<\/a>. \u201cOur metagenomics approach enabled us to access novel genomes that would otherwise be impossible to put together.\u201d<\/p>\n\n\n\n

The \u201cslurry\u201d method<\/h2>\n\n\n\n

The researchers also developed a method for obtaining the lowly abundant yeast from their lichen samples, to give them enough to work with. This method \u2013 coined the \u201cslurry\u201d method \u2013 works by removing the polysaccharide cement that covers the lichen and makes it difficult to gain access to the yeast.<\/p>\n\n\n\n

\u201cTo enrich a sample in yeast cells, I used a setup similar to a washing machine; I put the lichen in warm water and shook it for a few hours,\u201d says Gulnara Tagirdzhanova, a PhD student at the University of Alberta<\/a>. \u201cThe warm water dissolves the polysaccharides and the yeasts end up in a solution, which I spun down and used the resulting slurry to obtain the yeast we needed.\u201d<\/p>\n\n\n\n

Having access to these genomes has also given the researchers an insight into the role the yeast may play within the lichen symbiosis. Genetic evidence suggests that the yeast may be involved in both nutrient scavenging and secreting the polysaccharide that surrounds the lichen. These potential functions are currently being investigated experimentally.<\/p>\n\n\n\n

\u201cThis study opens the door to accessing and interrogating different lichen systems from many different ecosystems in a way that wasn’t possible before,\u201d says Toby Spribille, Assistant Professor at the University of Alberta<\/a>. \u201cIt’s the innovation here that has paved the way for us to be able to study many other systems using these same methods.\u201d<\/p>\n\n\n\n

This post was originally published on EMBL-EBI News<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

Researchers have used a metagenomics approach to piece together the genomes of yeasts found in wild lichens.<\/p>\n","protected":false},"author":77,"featured_media":37874,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[2,17591],"tags":[28,1702,36,684,780,88,5736],"embl_taxonomy":[2906,13366],"class_list":["post-37872","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-science","category-science-technology","tag-bioinformatics","tag-ecosystem","tag-embl-ebi","tag-environment","tag-finn","tag-metagenomics","tag-planetary-biology","embl_taxonomy-embl-ebi","embl_taxonomy-planetary-biology"],"acf":{"featured":true,"show_featured_image":false,"color":"#007B53","link_color":"#fff","article_intro":"

Researchers have used a metagenomics approach to piece together the genomes of yeasts found in wild lichens<\/p>\n","related_links":[{"link_description":"Microbiomes help predict the future of the Atlantic","link_url":"https:\/\/www.embl.org\/news\/science\/atlanteco-launch\/"},{"link_description":"Unparalleled inventory of the human gut ecosystem","link_url":"https:\/\/www.embl.org\/news\/science\/inventory-of-the-human-gut-ecosystem\/"},{"link_description":"Almost 2000 unknown gut bacteria discovered","link_url":"https:\/\/www.embl.org\/news\/science\/almost-2000-unknown-bacteria-discovered-in-the-human-gut\/"}],"article_sources":[{"source_description":"

Tagirdzhanova, G., et al<\/em>. Predicted input of uncultured fungal symbionts to a lichen symbiosis from metagenome-assembled genomes. Genome Biology and Evolution<\/em>. Published on 9 March 2021. DOI: 10.1093\/gbe\/evab047<\/p>\n","source_link_url":"https:\/\/academic.oup.com\/gbe\/article\/13\/4\/evab047\/6163286"},{"source_description":"

Saary, P., et al<\/em>. Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC. Genome Biology<\/em>. Published on 10 September 2020; DOI: 10.1186\/s13059-020-02155-4<\/p>\n","source_link_url":"https:\/\/genomebiology.biomedcentral.com\/articles\/10.1186\/s13059-020-02155-4"},{"source_description":"

The EukCC code is available through Github<\/p>\n","source_link_url":"https:\/\/github.com\/Finn-Lab\/EukCC"},{"source_description":"

Learn more about the \u201cslurry\u201d method in Gulnara\u2019s blog post<\/p>\n","source_link_url":"https:\/\/metalichen.github.io\/posts\/2021\/03\/blog-post-1\/"}],"in_this_article":false,"youtube_url":"","mp4_url":"","video_caption":"","press_contact":"None","translations":false,"vf_locked":false},"embl_taxonomy_terms":[{"uuid":"a:3:{i:0;s:36:\"b14d3f13-5670-44fb-8970-e54dfd9c921a\";i:1;s:36:\"89e00fee-87f4-482e-a801-4c3548bb6a58\";i:2;s:36:\"a99d1a7c-ca83-4c00-ab61-d082d3e41ce3\";}","parents":[],"name":["EMBL-EBI"],"slug":"embl-ebi","description":"Where > All EMBL sites > EMBL-EBI"},{"uuid":"a:3:{i:0;s:36:\"302cfdf7-365b-462a-be65-82c7b783ebf7\";i:1;s:36:\"e6ac6e6e-6386-48ff-9a0b-618e391d09bb\";i:2;s:36:\"a2c8c382-f6fa-4fac-a3d6-4da05ea5ef74\";}","parents":[],"name":["Planetary Biology"],"slug":"planetary-biology","description":"What > Research > Planetary Biology"}],"yoast_head":"\nUsing metagenomic techniques to explore lichens | EMBL<\/title>\n<meta name=\"description\" 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