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Article: Sequencing genomes from mixed DNA samples - evaluating the metagenome skimming approach in lichenized fungi

Schmitt, Imke / Dal Grande, Francesco

Scientific reports, 7:14881

2017

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 ... ...

Institution	Senckenberg Biodiversität und Klima Forschungszentrum
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.
Keywords	algorithm ; bacteria ; gene prediction ; generation ; genomic analysis ; de-novo assembler ; evolutionary ; extracts ; fungal genomics ; metagenomics ; next-generation sequencing ; single-cell ; population ; raw-materials
Language	English
Document type	Article
Database	Repository for Life Sciences

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Article: Panmixia and dispersal from the Mediterranean Basin to Macaronesian Islands of a macrolichen species

Dal Grande, Francesco / Crespo, Ana / Schmitt, Imke / DIVAKAR, PRADEEP KUMAR

Scientific reports, 7:40879

2017

Abstract: The Mediterranean region, comprising the Mediterranean Basin and the Macaronesian Islands, represents a center of diversification for many organisms. The genetic structure and connectivity of mainland and island microbial populations has been poorly ... ...

Institution	Senckenberg Biodiversität und Klima Forschungszentrum
Abstract	The Mediterranean region, comprising the Mediterranean Basin and the Macaronesian Islands, represents a center of diversification for many organisms. The genetic structure and connectivity of mainland and island microbial populations has been poorly explored, in particular in the case of symbiotic fungi. Here we investigated genetic diversity and spatial structure of the obligate outcrossing lichen-forming fungus Parmelina carporrhizans in the Mediterranean region. Using eight microsatellite and mating-type markers we showed that fungal populations are highly diverse but lack spatial structure. This is likely due to high connectivity and long distance dispersal of fungal spores. Consistent with low levels of linkage disequilibrium and lack of clonality, we detected both mating-type idiomorphs in all populations. Furthermore we showed that the Macaronesian Islands are the result of colonization from the Mediterranean Basin. The unidirectional gene flow, though, seemed not to be sufficient to counterbalance the effects of drift, resulting in comparatively allelic poor peripheral populations. Our study is the first to shed light on the high connectivity and lack of population structure in natural populations of a strictly sexual lichen fungus. Our data further support the view of the Macaronesian Islands as the end of the colonization road for this symbiotic ascomycete.
Keywords	biogeography ; genetic variation ; genetic diversity ; global climate-change ; differentiation ; epiphytic lichen ; lichen-forming fungi ; markers ; systems ; population-structure ; r-package ; transmission
Language	English
Document type	Article
Database	Repository for Life Sciences

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Article: Different diversification histories in tropical and temperate lineages in the ascomycete subfamily Protoparmelioideae (Parmeliaceae)

Singh, Garima / Dal Grande, Francesco / Schnitzler, Jan / Pfenninger, Markus / Schmitt, Imke

MycoKeys, 36:1-19

2018

Abstract: BACKGROUND: Environment and geographic processes affect species’ distributions as well as evolutionary processes, such as clade diversification. Estimating the time of origin and diversification of organisms helps us understand how climate fluctuations ... ...

Institution	Senckenberg Biodiversität und Klima Forschungszentrum
Abstract	BACKGROUND: Environment and geographic processes affect species’ distributions as well as evolutionary processes, such as clade diversification. Estimating the time of origin and diversification of organisms helps us understand how climate fluctuations in the past might have influenced the diversification and present distribution of species. Complementing divergence dating with character evolution could indicate how key innovations have facilitated the diversification of species. METHODS: We estimated the divergence times within the newly recognised subfamily Protoparmelioideae (Ascomycota) using a multilocus dataset to assess the temporal context of diversification events. We reconstructed ancestral habitats and substrate using a species tree generated in *Beast. RESULTS: We found that the diversification in Protoparmelioideae occurred during the Miocene and that the diversification events in the tropical clade Maronina predate those of the extratropical Protoparmelia. Character reconstructions suggest that the ancestor of Protoparmelioideae was most probably a rock-dwelling lichen inhabiting temperate environments. CONCLUSIONS: Major diversification within the subtropical/tropical genus Maronina occurred between the Paleocene and Miocene whereas the diversifications within the montane, arctic/temperate genus Protoparmelia occurred much more recently, i.e. in the Miocene.
Keywords	Diversification pattern ; ancestral state reconstruction ; dating ; extra-tropical ; habitat ; lichenised fungi ; mountain uplifts ; substrate ; parallel evolution
Language	English
Document type	Article
Database	Repository for Life Sciences

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Article: Neoprotoparmelia gen. nov. and Maronina (Lecanorales, Protoparmelioideae): species description and generic delimitation using DNA barcodes and phenotypical characters

Singh, Garima / Aptroot, André / DIVAKAR, PRADEEP KUMAR / Lumbsch, Thorsten / Schmitt, Imke

MycoKeys, 44:19-50

2018

Abstract: Multilocus phylogenetic studies revealed a high level of cryptic diversity within the lichen-forming fungal genus Maronina (Protoparmelioideae, Parmeliaceae). Coalescent-based species delimitation suggested that most of the cryptic molecular lineages ... ...

Institution	Senckenberg Biodiversität und Klima Forschungszentrum
Abstract	Multilocus phylogenetic studies revealed a high level of cryptic diversity within the lichen-forming fungal genus Maronina (Protoparmelioideae, Parmeliaceae). Coalescent-based species delimitation suggested that most of the cryptic molecular lineages warranted recognition as separate species. Here we study the morphology and chemistry of these taxa and formally describe eight new species based on phenotypical and molecular characters. Further, we evaluate the use of ITS rDNA as a DNA barcode for identifying species in this genus. For the first time, we obtained an ITS sequence of Maronina australiensis, the type species of the genus and showed that it is phylogenetically not closely related to species currently placed in Maronina or Protoparmelia. We assembled a dataset of 66 ITS sequences to assess the interspecies genetic distances amongst the twelve Maronina species using ITS as DNA barcode. We found that Maronina and Protoparmelia form a supported monophyletic group whereas M. australiensis is sister to both. We therefore propose a new genus Neoprotoparmelia to accommodate the tropical-subtropical species within Protoparmelioideae, with Neoprotoparmelia corallifera as the type, N. amerisidiata, N. australisidiata, N. brasilisidiata, N. capensis, N. crassa, N. pauli, N. plurisporibadia and N. siamisidiata as new species and N. capitata, N. isidiata, N. multifera, N. orientalis and N. pulchra as new proposed combinations. We provide a key to Neoprotoparmelia and confirm the use of ITS for accurately identifying species in this group.
Keywords	BPP ; ITS ; Parmeliaceae ; lichenised fungi ; new genus ; new species ; taxonomy
Language	English
Document type	Article
Database	Repository for Life Sciences

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Book ; Online ; Thesis: DNA-based analysis of bark associated fungal, algal, and bacterial communities

Dreyling, Lukas [Verfasser] / Schmitt, Imke [Gutachter] / Bässler, Claus [Gutachter]

contributions to understanding the unknown biodiversity of forests

2024

Author's details	Lukas Dreyling ; Gutachter: Imke Schmitt, Claus Bässler
Keywords	Biowissenschaften, Biologie ; Life Science, Biology
Subject code	sg570
Language	English
Publisher	Universitätsbibliothek Johann Christian Senckenberg
Publishing place	Frankfurt am Main
Document type	Book ; Online ; Thesis
Database	Digital theses on the web

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Article ; Online: Biotic interactions outweigh abiotic factors as drivers of bark microbial communities in Central European forests.

Dreyling, Lukas / Penone, Caterina / Schenk, Noëlle Valérie / Schmitt, Imke / Dal Grande, Francesco

ISME communications

2024 Volume 4, Issue 1, Page(s) ycae012

Abstract: Bark surfaces are extensive areas within forest ecosystems, which provide an ideal habitat for microbial communities, through their longevity and seasonal stability. Here we provide a comprehensive account of the bark surface microbiome of living trees ... ...

Abstract	Bark surfaces are extensive areas within forest ecosystems, which provide an ideal habitat for microbial communities, through their longevity and seasonal stability. Here we provide a comprehensive account of the bark surface microbiome of living trees in Central European forests, and identify drivers of diversity and community composition. We examine algal, fungal, and bacterial communities and their interactions using metabarcoding on samples from over 750 trees collected in the Biodiversity Exploratories in northern, central, and southern Germany. We show that mutual biotic influence is more important than the abiotic environment with regard to community composition, whereas abiotic conditions and geography are more important for alpha diversity. Important abiotic factors are the relative humidity and light availability, which decrease the algal and bacterial alpha diversity but strongly increase fungal alpha diversity. In addition, temperature is important in shaping the microbial community, with higher temperature leading to homogeneous communities of dominant fungi, but high turnover in bacterial communities. Changes in the community dissimilarity of one organismal group occur in close relation to changes in the other two, suggesting that there are close interactions between the three major groups of the bark surface microbial communities, which may be linked to beneficial exchange. To understand the functioning of the forest microbiome as a whole, we need to further investigate the functionality of interactions within the bark surface microbiome and combine these results with findings from other forest habitats such as soil or canopy.
Language	English
Publishing date	2024-01-25
Publishing country	England
Document type	Journal Article
ISSN	2730-6151
ISSN (online)	2730-6151
DOI	10.1093/ismeco/ycae012
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Article ; Online: Circadian clock- and temperature-associated genes contribute to overall genomic differentiation along elevation in lichenized fungi.

Valim, Henrique F / Grande, Francesco Dal / Wong, Edgar L Y / Schmitt, Imke

Molecular ecology

2023 Volume 33, Issue 4, Page(s) e17252

Abstract: Circadian regulation is linked to local environmental adaptation, and many species with broad climatic niches display variation in circadian genes. Here, we hypothesize that lichenizing fungi occupying different climate zones tune their metabolism to ... ...

Abstract	Circadian regulation is linked to local environmental adaptation, and many species with broad climatic niches display variation in circadian genes. Here, we hypothesize that lichenizing fungi occupying different climate zones tune their metabolism to local environmental conditions with the help of their circadian systems. We study two species of the genus Umbilicaria occupying similar climatic niches (Mediterranean and the cold temperate) in different continents. Using homology to Neurospora crassa genes, we identify gene sets associated with circadian rhythms (11 core, 39 peripheral genes) as well as temperature response (37 genes). Nucleotide diversity of these genes is significantly correlated with mean annual temperature, minimum temperature of the coldest month and mean temperature of the coldest quarter. Furthermore, we identify altitudinal clines in allele frequencies in several non-synonymous substitutions in core clock components, for example, white collar-like, frh-like and various ccg-like genes. A dN/dS approach revealed a few significant peripheral clock- and temperature-associated genes (e.g. ras-1-like, gna-1-like) that may play a role in fine-tuning the circadian clock and temperature-response machinery. An analysis of allele frequency changes demonstrated the strongest evidence for differentiation above the genomic background in the clock-associated genes in U. pustulata. These results highlight the likely relevance of the circadian clock in environmental adaptation, particularly frost tolerance, of lichens. Whether or not the fungal clock modulates the symbiotic interaction within the lichen consortium remains to be investigated. We corroborate the finding of genetic variation in clock components along altitude-not only latitude-as has been reported in other species.
MeSH term(s)	Circadian Clocks/genetics ; Temperature ; Circadian Rhythm/genetics ; Neurospora crassa/genetics ; Genomics ; Fungal Proteins/genetics ; Fungal Proteins/metabolism
Chemical Substances	Fungal Proteins
Language	English
Publishing date	2023-12-26
Publishing country	England
Document type	Journal Article
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.17252
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Article ; Online: Genome mining as a biotechnological tool for the discovery of novel biosynthetic genes in lichens.

Singh, Garima / Dal Grande, Francesco / Schmitt, Imke

Frontiers in fungal biology

2022 Volume 3, Page(s) 993171

Abstract: Natural products (NPs) and their derivatives are a major contributor to modern medicine. Historically, microorganisms such as bacteria and fungi have been instrumental in generating drugs and lead compounds because of the ease of culturing and ... ...

Abstract	Natural products (NPs) and their derivatives are a major contributor to modern medicine. Historically, microorganisms such as bacteria and fungi have been instrumental in generating drugs and lead compounds because of the ease of culturing and genetically manipulating them. However, the ever-increasing demand for novel drugs highlights the need to bioprospect previously unexplored taxa for their biosynthetic potential. Next-generation sequencing technologies have expanded the range of organisms that can be explored for their biosynthetic content, as these technologies can provide a glimpse of an organism's entire biosynthetic landscape, without the need for cultivation. The entirety of biosynthetic genes can be compared to the genes of known function to identify the gene clusters potentially coding for novel products. In this study, we mine the genomes of nine lichen-forming fungal species of the genus
Language	English
Publishing date	2022-10-03
Publishing country	Switzerland
Document type	Journal Article
ISSN	2673-6128
ISSN (online)	2673-6128
DOI	10.3389/ffunb.2022.993171
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Article ; Online: Fungal Host Affects Photosynthesis in a Lichen Holobiont.

Schulz, Meike / Schmitt, Imke / Weber, Daniel / Dal Grande, Francesco

Journal of fungi (Basel, Switzerland)

2022 Volume 8, Issue 12

Abstract: Corals and lichens are iconic examples of photosynthetic holobionts, i.e., ecological and evolutionary units resulting from the tightly integrated association of algae and prokaryotic microbiota with animal or fungal hosts, respectively. While the role ... ...

Abstract	Corals and lichens are iconic examples of photosynthetic holobionts, i.e., ecological and evolutionary units resulting from the tightly integrated association of algae and prokaryotic microbiota with animal or fungal hosts, respectively. While the role of the coral host in modulating photosynthesis has been clarified to a large extent in coral holobionts, the role of the fungal host in this regard is far less understood. Here, we address this question by taking advantage of the recent discovery of highly specific fungal-algal pairings corresponding to climatically adapted ecotypes of the lichen-forming genus
Language	English
Publishing date	2022-11-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2784229-0
ISSN	2309-608X ; 2309-608X
ISSN (online)	2309-608X
ISSN	2309-608X
DOI	10.3390/jof8121267
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Article ; Online: Lichen holobionts show compositional structure along elevation.

Rolshausen, Gregor / Dal Grande, Francesco / Otte, Jürgen / Schmitt, Imke

Molecular ecology

2022 Volume 32, Issue 23, Page(s) 6619–6630

Abstract: Holobionts are dynamic ecosystems that may respond to abiotic drivers with compositional changes. Uncovering elevational diversity patterns within these microecosystems can further our understanding of community-environment interactions. Here, we assess ... ...

Abstract	Holobionts are dynamic ecosystems that may respond to abiotic drivers with compositional changes. Uncovering elevational diversity patterns within these microecosystems can further our understanding of community-environment interactions. Here, we assess how the major components of lichen holobionts-fungal hosts, green algal symbionts, and the bacterial community-collectively respond to an elevational gradient. We analyse populations of two lichen symbioses, Umbilicaria pustulata and U. hispanica, along an elevational gradient spanning 2100 altitudinal metres and covering three major biomes. Our study shows (i) discontinuous genomic variation in fungal hosts with one abrupt genomic differentiation within each of the two host species, (ii) altitudinally structured bacterial communities with pronounced turnover within and between hosts, and (iii) altitude-specific presence of algal symbionts. Alpha diversity of bacterial communities decreased with increasing elevation. A marked turnover in holobiont diversity occurred across two altitudinal belts: at 11°C-13°C average annual temperature (here: 800-1200 m a.s.l.), and at 7°C-9°C average annual temperature (here: 1500-1800 m a.s.l.). The two observed zones mark a clustering of distribution limits and community shifts. The three ensuing altitudinal classes, that is, the most frequent combinations of species in holobionts, approximately correspond to the Mediterranean, cool-temperate, and alpine climate zones. We conclude that multitrophic microecosystems, such as lichen holobionts, respond with concerted compositional changes to climatic factors that also structure communities of macroorganisms, for example, vascular plants.
MeSH term(s)	Lichens/genetics ; Lichens/microbiology ; Ecosystem ; Environment ; Altitude ; Bacteria/genetics
Language	English
Publishing date	2022-04-22
Publishing country	England
Document type	Journal Article
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.16471
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