Exploring the influence of climatic variables on mycobiome composition and community diversity in lichens: insights from structural equation modeling analysis

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Abstract

Background

Lichens are symbiotic organisms composed of a fungus and a photosynthetic partner, which are key ecological bioindicators due to their sensitivity to environmental changes. The endolichenic fungi (ELF) living inside lichen thalli, are an important but understudied component of playing crucial ecological roles such as nutrient cycling and protection against environmental stressors. Therefore ELF community investigation is vital for fostering sustainable ecosystems and leveraging their ecological benefits. Deciphering the intricate relationships between ELF and their lichen hosts, alongside the influence of environmental factors on these communities, presents a significant challenge in pinpointing the underlying drivers of community structure and diversity.

Results

Our research demonstrated that locational factors were the main drivers of the ELF community structure, rather than host haplotype. Several climatic factors affected the diversity of the ELF community and contributed to the prevalence of different types of fungal residents within the ELF community. A decrease in isothermality was associated with a greater prevalence of pathotrophic and saprotrophic fungi within the ELF community, resulting in an overall increase in community diversity. By conducting a structural equation modeling analysis, we identified a robust link between climatic variables, fungal trophic mode abundance, and the species diversity of the ELF community.

Conclusion

This study’s discoveries emphasize the significance of examining climate-related factors when investigating ELF’s structure and function. The connection between fungi and climate is intricate and complex, and can be influenced by various other factors. Investigating the potential for ELF to adapt to changing climatic conditions, as well as the potential effects of changes in ELF communities on lichen function, would be valuable research areas. We anticipate that our research results will establish a basis for numerous future ELF research projects and have a significant impact on the field.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40793-023-00535-4.

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Most cited references 64

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DADA2: High resolution sample inference from Illumina amplicon data

Benjamin J. Callahan, Paul McMurdie, Michael Rosen … (2016)

We present DADA2, a software package that models and corrects Illumina-sequenced amplicon errors. DADA2 infers sample sequences exactly, without coarse-graining into OTUs, and resolves differences of as little as one nucleotide. In several mock communities DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.

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MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

Sudhir Kumar, Glen Stecher, Koichiro Tamura (2016)

We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.

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Is Open Access

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Alexandros Stamatakis (2014)

Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.

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Author and article information

Contributors

Jae-Seoun Hur: jshur1@scnu.ac.kr

Journal

Journal ID (nlm-ta): Environ Microbiome

Journal ID (iso-abbrev): Environ Microbiome

Title: Environmental Microbiome

Publisher: BioMed Central (London )

ISSN (Electronic): 2524-6372

Publication date (Electronic): 27 October 2023

Publication date PMC-release: 27 October 2023

Publication date Collection: 2023

Volume: 18

Electronic Location Identifier: 79

Affiliations

[1 ]Korean Lichen Research Institute, Sunchon National University, ( https://ror.org/043jqrs76) 255 Jungang-ro, Suncheon, 57922 South Korea

[2 ]Department of Biology and Chemistry, Changwon National University, ( https://ror.org/04ts4qa58) 20 Changwondaehak-ro, Changwon, 51140 South Korea

Article

Publisher ID: 535

DOI: 10.1186/s40793-023-00535-4

PMC ID: 10612307

PubMed ID: 37891696

SO-VID: 18852d7b-23e6-4354-a25a-6fa7b4eda30c

License:

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

History

Date received : 20 July 2023

Date accepted : 24 October 2023

Funding

Funded by: National Research Foundation of Korea

Award ID: NRF-2020R1I1A2073283

Custom metadata

Keywords: lichen,endolichenic fungi,community feature,host haplotype,geographical distance,climatic variables,isothermality

Data availability:

Keywords: lichen, endolichenic fungi, community feature, host haplotype, geographical distance, climatic variables, isothermality

Exploring the influence of climatic variables on mycobiome composition and community diversity in lichens: insights from structural equation modeling analysis

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Abstract

Background

Results

Conclusion

Supplementary Information

Related collections

Fracture and Structural Integrity

Most cited references 64

DADA2: High resolution sample inference from Illumina amplicon data

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

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