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Lichen and fungal ecology
Research Guide
What is Lichen and fungal ecology?
Lichen and fungal ecology is the study of how fungi—including lichen-forming fungi and their associated microbial partners—are identified, named, dispersed, and structured into communities across environments, and how these communities interact with substrates, climate, and pollutants.
Lichen and fungal ecology integrates molecular identification, nomenclature, and community-ecological theory to describe fungal diversity and its spatial and environmental patterning. "Towards a unified paradigm for sequence‐based identification of fungi" (2013) established the nuclear ribosomal internal transcribed spacer (ITS) region as the formal fungal barcode and highlighted key challenges in taxonomic assignment from environmental sequences. The provided corpus size for this topic is 99,460 works (5-year growth rate: N/A).
Research Sub-Topics
Lichen Biomonitoring of Air Pollution
Lichens serve as sensitive indicators of atmospheric pollutants like SO2 and heavy metals due to their lack of protective cuticles. Researchers map community changes to assess pollution gradients.
Fungal Sequence-Based Identification
Molecular methods using ITS barcoding and multi-locus phylogenetics identify fungal taxa from environmental samples. Studies standardize protocols amid taxonomic revisions.
Lichen Symbiosis and Functional Traits
Interactions between mycobionts and photobionts drive lichen morphology, physiology, and stress tolerance traits. Researchers explore nutrient exchange and partner specificity.
Soil Fungal Communities and Decomposition
Soil fungi mediate organic matter breakdown, nutrient cycling, and aggregate formation in ecosystems. Metagenomic studies link diversity to soil health and carbon sequestration.
Distance Decay in Fungal Biogeography
Spatial turnover patterns in fungal and lichen distributions follow distance decay, influenced by dispersal and environmental filters. Analyses use spore trap data and refugia modeling.
Why It Matters
Lichen and fungal ecology underpins real-world monitoring, risk assessment, and environmental management because fungi and lichens respond predictably to habitat structure, airborne dispersal, and chemical stressors. For aerobiology and exposure monitoring, Hirst (1952) described "AN AUTOMATIC VOLUMETRIC SPORE TRAP", a suction device that impacts spores onto a Vaseline-coated slide moved at 2 mm/hr, enabling time-resolved estimates of airborne spore content that are directly relevant to plant disease forecasting and indoor/outdoor air-quality surveillance. For pollution and substrate interactions, Ho (2000) in "The kinetics of sorption of divalent metal ions onto sphagnum moss peat" provided a widely cited framework for understanding how biological substrates can bind divalent metal ions, a concept that informs interpretation of contaminant retention in peatland and forest-floor systems where fungi and lichens occur. For biodiversity inventories and reproducible reporting, "International Code of Nomenclature for algae, fungi, and plants" (2018) standardizes names used in conservation lists and monitoring programs, while "Natural vegetation of Oregon and Washington" (1988) provides a vegetation baseline often needed to contextualize lichen and fungal community turnover across habitat types.
Reading Guide
Where to Start
Start with "Towards a unified paradigm for sequence‐based identification of fungi" (2013) because it defines the core marker (ITS) and the main practical obstacles in turning sequences into ecological taxa, which affects nearly every modern fungal and lichen ecology study.
Key Papers Explained
Kõljalg et al. (2013), "Towards a unified paradigm for sequence‐based identification of fungi", provides the molecular identification foundation (ITS as the formal fungal barcode) that underlies most contemporary community surveys. Turland et al. (2018), "International Code of Nomenclature for algae, fungi, and plants", supplies the naming rules needed to keep those molecularly defined taxa stable and comparable across datasets. Nekola and White (1999), "The distance decay of similarity in biogeography and ecology", then offers a general ecological framework for interpreting spatial turnover in the taxa identified and named using the first two resources; Hirst (1952), "AN AUTOMATIC VOLUMETRIC SPORE TRAP", connects dispersal measurement to observed turnover; and Dunn et al. (1982), "Compendium of Soil Fungi", plus "Ainsworth and Bisbys Dictionary of the Fungi" (2008, >21,000 entries) provide practical taxonomic and terminology scaffolding for ecological interpretation.
Paper Timeline
Most-cited paper highlighted in red. Papers ordered chronologically.
Advanced Directions
A current frontier is integrating sequence-based identification with reproducible ecological inference: applying ITS-centered identification principles from "Towards a unified paradigm for sequence‐based identification of fungi" (2013), enforcing stable naming via "International Code of Nomenclature for algae, fungi, and plants" (2018), and then testing dispersal-structured hypotheses using the distance-decay framework of Nekola and White (1999). Another advanced direction is coupling mechanistic environmental chemistry with community change, building conceptually on Ho (2000) to relate substrate binding processes to ecological gradients, while maintaining consistent terminology using "Ainsworth and Bisbys Dictionary of the Fungi" (2008).
Papers at a Glance
| # | Paper | Year | Venue | Citations | Open Access |
|---|---|---|---|---|---|
| 1 | Towards a unified paradigm for sequence‐based identification o... | 2013 | Molecular Ecology | 3.5K | ✓ |
| 2 | The kinetics of sorption of divalent metal ions onto sphagnum ... | 2000 | Water Research | 2.9K | ✕ |
| 3 | Compendium of Soil Fungi | 1982 | Taxon | 2.8K | ✕ |
| 4 | International Code of Nomenclature for algae, fungi, and plants | 2018 | Regnum vegetabile | 2.5K | ✓ |
| 5 | Glossary of pollen and spore terminology | 2006 | Review of Palaeobotany... | 2.5K | ✕ |
| 6 | Ainsworth and Bisbys Dictionary of the Fungi | 2008 | CABI eBooks | 2.2K | ✕ |
| 7 | Molecular evidence for glacial refugia of mountain plants in t... | 2005 | Molecular Ecology | 2.1K | ✕ |
| 8 | Natural vegetation of Oregon and Washington | 1988 | — | 1.9K | ✕ |
| 9 | The distance decay of similarity in biogeography and ecology | 1999 | Journal of Biogeography | 1.9K | ✕ |
| 10 | AN AUTOMATIC VOLUMETRIC SPORE TRAP | 1952 | Annals of Applied Biology | 1.8K | ✕ |
In the News
The lichen secondary metabolite lichesterinic acid exhibits antibiofilm activity against fungal pathogens
Lichens are symbiotic associations between fungi (typically ascomycetes) and photosynthetic partners (algae or cyanobacteria). They are known to produce diverse secondary metabolites, most of which...
Complexity of the lichen symbiosis revealed by metagenome and transcriptome analysis of Xanthoria parietina
characterize a lichen symbiosis and identify processes involved in symbiosis maintenance and development. As a model, we used Xanthoria parietina —a widespread lichen that has served as a model sys...
A reference metagenome sequence of the lichen Cladonia rangiformis
provides the first chromosome-scale genomic framework for a lichen holobiont, offering a foundational resource for future research into metagenomics, symbiosis, and microbial ecology in lichens.
Mapping cellular dynamics with the lichen cell atlas
Her work generating the data was supported by EMBL-EBI and the Wellcome Sanger Institute. She is currently collaborating with Nick Talbot’s group at the Sainsbury Laboratory, generating single-cell...
'A precarious position': almost 3000 species at risk of ...
Environmental body says modest investment and changes can help preserve long list of animals, fungi and lichen
Code & Tools
## Repository files navigation # Lichen Microbiomes Pipeline for the analysis of Lichen microbiomes
Lichens are complex symbiotic assemblies of microorganisms. On the 28th of March 2022 we received 22 selected metagenome assembled genomes (MAGs) r...
This repository contains the analysis pipeline used in the publication: **Large differences in carbohydrate degradation and transport potential amo...
Scripts used in the analysis for the "Predicted input of uncultured fungal symbionts to a lichen symbiosis from metagenome-assembled genomes" paper...
MicroEcoTools is an R package developed for microbial ecologists to apply ecological frameworks to microbial community data. This package helps ana...
Recent Preprints
Mycobiomes of Six Lichen Species from the Russian Subarctic: A Culture-Independent Analysis and Cultivation Study
Lichens are defined as holobionts, whose thalli are known to contain a significant diversity of bacteria, fungi, protozoa, and viruses. Research into the presence of these organisms in lichens rema...
New records of lichen species found in the National Forest ...
information obtained from ongoing nationwide surveys. Keywords forest diversity forest health lichenized fungi taxonomy Cited by (0) Peer review under responsibility of National Science Museum of K...
Surprising Uses of Lichens that Improve Human Life
Lichens essential oil Alternative sources of medicine VOLUME: 3 ISSUE: 2 - FEBRUARY, 2022 BIOLOGY GROUP MICROBIOLOGY VIROLOGY BIOLOGY Lichens are rich in nutrients and in biologically active comp...
Journal of Fungi
*Journal of Fungi*is an international, peer-reviewed ,open access journal of mycology published monthly online by MDPI. The Medical Mycological Society of the Americas (MMSA) and Spanish Phytopatho...
Semilichen, an unjustly neglected symbiotic system between green biofilms and true lichens
Symbiotic systems of photosynthetic microorganisms and fungi are widespread in terrestrial biomes and lichens are probably the most advanced and complex. Conversely, the least complex systems are “...
Latest Developments
Recent developments in lichen and fungal ecology research include the discovery that lichens were already widespread over 410 million years ago, with fossil evidence showing fungi-algae alliances that contributed to terrestrial life (Phys.org, 2025). Additionally, studies have revealed the high diversity and complexity of lichen-associated fungi, including the identification of new fungal lineages within the order Chaetothyriales, and extensive characterization of their microbial communities across different species and environments (ScienceDirect, 2024; ScienceDirect, 2025; PLOS Biology, 2024).
Sources
Frequently Asked Questions
What is the standard DNA barcode used for sequence-based identification of fungi in ecological studies?
"Towards a unified paradigm for sequence‐based identification of fungi" (2013) stated that the nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and is commonly used to explore fungal diversity in environmental samples. The same paper emphasized that satisfactory taxonomic assignment from environmental sequences can be challenging, making reference frameworks and careful annotation essential.
How are fungal and lichen names standardized so ecological datasets remain comparable across studies?
"International Code of Nomenclature for algae, fungi, and plants" (2018) defines the rules governing scientific naming for these groups and records revisions decided at an International Botanical Congress. Using the Code allows ecological checklists, monitoring reports, and sequence reference databases to align on the same accepted names.
How can researchers measure airborne fungal spores for ecological or applied monitoring?
Hirst (1952) in "AN AUTOMATIC VOLUMETRIC SPORE TRAP" described a suction trap that directs spores into the wind and impacts them onto a Vaseline-coated microscope slide moved at 2 mm/hr. The design enables estimates of spore content of the air with higher efficiency than earlier traps, supporting quantitative aeromycology.
Which ecological pattern links community similarity to geographic distance in fungal and lichen biogeography?
Nekola and White (1999) in "The distance decay of similarity in biogeography and ecology" framed distance decay as a quantitative technique for describing how similarity changes with distance in biological communities. This perspective is directly applicable to fungal and lichen datasets when testing whether dispersal limitation, habitat turnover, or rarity contributes to spatial structuring.
Which reference works are commonly used to support identification and terminology in fungal ecology?
"Ainsworth and Bisbys Dictionary of the Fungi" (2008) reports that it contains more than 21,000 entries, providing a standardized source for generic names and descriptive terms used by mycologists. For soil-focused ecological work, Dunn et al. (1982) published "Compendium of Soil Fungi", a highly cited reference used to support identification and interpretation of soil fungal assemblages.
Which baseline resources help connect lichen and fungal communities to habitat context in the Pacific Northwest?
Franklin and Dyrness (1988) in "Natural vegetation of Oregon and Washington" compiled a regional vegetation synthesis that can be used to stratify sampling and interpret community differences among forest and non-forest habitat types. Such vegetation baselines help separate effects of substrate and stand type from purely spatial effects when analyzing fungal and lichen community data.
Open Research Questions
- ? How can ITS-based workflows reduce taxonomic assignment uncertainty in environmental sequencing while remaining consistent with the constraints described in "Towards a unified paradigm for sequence‐based identification of fungi" (2013)?
- ? Which sampling designs and statistical models best separate distance decay from environmental turnover when applying the framework of "The distance decay of similarity in biogeography and ecology" (1999) to fungal and lichen communities?
- ? How can time-resolved aerobiological sampling using the approach in "AN AUTOMATIC VOLUMETRIC SPORE TRAP" (1952) be integrated with modern community datasets to link spore flux to observed colonization and turnover?
- ? How should ecological datasets handle name changes and synonymy over time to remain interoperable with "International Code of Nomenclature for algae, fungi, and plants" (2018) while preserving historical records?
- ? What mechanistic links connect substrate sorption behavior described in "The kinetics of sorption of divalent metal ions onto sphagnum moss peat" (2000) to observed shifts in fungal or lichen community composition across contaminated gradients?
Recent Trends
Within the provided materials, the clearest quantified signal is the scale of the literature: 99,460 works are associated with lichen and fungal ecology (5-year growth rate: N/A).
Methodologically, the most-cited molecular standardization work remains "Towards a unified paradigm for sequence‐based identification of fungi" (2013; 3,536 citations), indicating sustained reliance on ITS-based identification in ecological studies.
Foundational infrastructure for comparability—"International Code of Nomenclature for algae, fungi, and plants" (2018; 2,481 citations) and "Ainsworth and Bisbys Dictionary of the Fungi" (2008; more than 21,000 entries; 2,183 citations)—continues to be central for ensuring that ecological conclusions are linked to stable names and consistent terminology.
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