Isolation and co-culturing of symbionts in the genus Usnea

Rafat, Arash; Ridgway, Hayley J.; Cruickshank, Robert; Buckley, Hannah L.

doi:10.1007/s13199-015-0343-1

Cited by 12 publications

(24 citation statements)

References 28 publications

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“…We assume that the more recently deposited sequences are currently in the process of being published in peer-reviewed studies. The bulk of the unidentified depositions originated from studies on mycobiont-photobiont associations of New Zealand Usnea (Rafat 2014;Buckley et al 2014;Rafat et al 2015).…”

Section: Categorymentioning

confidence: 99%

“…For 112 accessions, the identification given with the accession in GenBank did not match the identification in the corresponding original publication (Table S1). In 24 cases of accessions labeled Usnea sp., precise identifications were provided in the actual papers (Shen et al 2012;Buckley et al 2014;Rafat et al 2015), but not updated in the GenBank accessions. In six instances, the label Usnea sp.…”

Section: Categorymentioning

confidence: 99%

“…S1). Most of the samples were not identified (Buckley et al 2014), but the few identified specimens (Rafat et al 2015) include two names also associated with subgenus Neuropogon by Walker (1985), namely U. inermis Motyka and U. torulosa (Müll. Arg.…”

Section: Metadata Diversitymentioning

confidence: 99%

“…Broader DNA barcoding studies also included data on Usnea or in part focused on the latter, particularly in New Zealand (Kelly et al 2011), but also Switzerland (Mark et al 2016b), Norway (Marthinsen et al 2019), and Cameroon (Orock et al 2012). A large amount of ITS data was generated for analyses of mycobiont-photobiont associations of Usnea lichens and their corresponding ecology and morphology in New Zealand and Antarctica (Rafat 2014;Buckley et al 2014;Cao et al 2015Cao et al , 2018Park et al 2015;Rafat et al 2015). Another broad study in the Northern Hemisphere focused on genetic variation in Dolichousnea longissima (Ach.)…”

Section: Introductionmentioning

confidence: 99%

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Two decades of DNA barcoding in the genus Usnea (Parmeliaceae): how useful and reliable is the ITS?

Lücking¹,

Nadel²,

Araújo³

et al. 2020

Plant and Fungal Systematics

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We present an exhaustive analysis of the ITS barcoding marker in the genus Usnea s.lat., separated into Dolichousnea, Eumitria, and Usnea including the subgenus Neuropogon, analyzing 1,751 accessions. We found only a few low-quality accessions, whereas information on voucher specimens and accuracy and precision of identifications was of subpar quality for many accessions. We provide an updated voucher table, alignment and phylogenetic tree to facilitate DNA barcoding of Usnea, either locally or through curated databases such as UNITE. Taxonomic and geographic coverage was moderate: while Dolichousnea and subgenus Neuropogon were well-represented among ITS data, sampling for Eumitria and Usnea s.str. was sparse and biased towards certain lineages and geographic regions, such as Antarctica, Europe, and South America. North America, Africa, Asia and Oceania were undersampled. A peculiar situation arose with New Zealand, represented by a large amount of ITS accessions from across both major islands, but most of them left unidentified. The species pair Usnea antarctica vs. U. aurantiacoatra was the most sampled clade, including numerous ITS accessions from taxonomic and ecological studies. However, published analyses of highly resolved microsatellite and RADseq markers showed that ITS was not able to properly resolve the two species present in this complex. While lack of resolution appears to be an issue with ITS in recently evolving species complexes, we did not find evidence for gene duplication (paralogs) or hybridization for this marker. Comparison with other markers demonstrated that particularly IGS and RPB1 are useful to complement ITS-based phylogenies. Both IGS and RPB1 provided better backbone resolution and support than ITS; while IGS also showed better resolution and support at species level, RPB1 was less resolved and delineated for larger species complexes. The nuLSU was of limited use, providing neither resolution nor backbone support. The other three commonly employed protein-coding markers, TUB2, RPB2, and MCM7, showed variable evidence of possible gene duplication and paralog formation, particularly in the MCM7, and these markers should be used with care, especially in multimarker coalescence approaches. A substantial challenge was provided by difficult morphospecies that did not form coherent clades with ITS or other markers, suggesting various levels of cryptic speciation, the most notorious example being the U. cornuta complex. In these cases, the available data suggest that multimarker approaches using ITS, IGS and RPB1 help to assess distinct lineages. Overall, ITS was found to be a good first approximation to assess species delimitation and recognition in Usnea s.lat., as long as the data are carefully analyzed, and reference sequences are critically assessed and not taken at face value. In difficult groups, we recommend IGS as a secondary barcode marker, with the option to employ more resource-intensive approaches, such as RADseq, in species complexes involving so-called species pairs or other cases of disparate morphology not reflected in the ITS or IGS. Attempts should be made to close taxonomic and geographic gaps especially for the latter two markers, in particular in Eumitria and Usnea s.str. and in the highly diverse areas of North America and Central America, Africa, Asia, and Oceania.

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Section: Categorymentioning

confidence: 99%

Section: Categorymentioning

confidence: 99%

Section: Metadata Diversitymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Two decades of DNA barcoding in the genus Usnea (Parmeliaceae): how useful and reliable is the ITS?

Lücking¹,

Nadel²,

Araújo³

et al. 2020

Plant and Fungal Systematics

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show abstract

“…Taxonomic profiling revealed Cyanobacteria as abundant members of all microbiomes. In fact, Cyanobacteria were present in Cladonia, Hypotrachyna and Usnea, which are considered to be chlorolichens (46)(47)(48)(49), that is to say, lichens with a green alga as its major or unique photobiont (50).…”

Section: Discussionmentioning

confidence: 99%

The microbiomes of seven lichen genera reveal host specificity, a reduced core community and potential as source of antimicrobials

Sierra

Danko

Sandoval

et al. 2019

Preprint

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The High Andean Paramo ecosystem is a unique neotropical mountain biome considered a diversity and evolutionary hotspot. Lichens, which are complex symbiotic structures that contain diverse commensal microbial communities, are prevalent in Paramos. There they play vital roles in soil formation and mineral fixation. In this study we analyzed the microbiomes of seven lichen genera in two Colombian Paramos using 16S rRNA gene analyses and provide the first description of the bacterial communities associated with Cora and Hypotrachyna lichens. Paramo lichen microbiomes were diverse, and in some cases were distinguished based on the identity of the lichen host. The majority of the lichen-associated microorganisms were not present in all lichens sampled and could be considered transient or specialists.We also uncovered sixteen shared taxa that suggest a core lichen microbiome among this diverse group of lichens, broadening our concept of these symbiotic structures. Additionally, we identified strains producing compounds active against clinically relevant pathogens. These results indicate that lichen microbiomes from the Paramo ecosystem are diverse and host-specific but share a taxonomic core and can be a source of new bacterial taxa and antimicrobials.Lichens represent some of the oldest and most diverse symbioses on Earth (16). Lichens consist of a photobiont (cyanobacterium/alga) and a mycobiont (fungus), which together form a unique structure called the thallus (17). Lichens play a vital role in ecosystems as they are essential in soil formation, naked soil colonization, and nutrient uptake and release for plants (18,19). Lichens can colonize a wide range of substrates, from natural surfaces to man-made materials such as plastic, rubber, metals and glass (20). They can also tolerate extreme environmental conditions and offer a niche for diverse microorganisms (21,22). The diversity of these lichen-associated microbial communities is not yet well characterized, and has only recently been investigated using high-throughput techniques (23, 24). These studies indicate substantial microbial and functional diversity (24-26) that has been suggested to help protect the thalli against pathogens through the production of antimicrobials (27,28). The process of community establishment within lichens is poorly understood and has been proposed to be driven either by the photobiont (29) or by geography and habitat (30).Recent studies have described the microbial communities associated with lichens using cultureindependent strategies (24, 25). However, comparisons between studies are hindered by differences in sampling methods, data analyses, and poor or complete lack of lichen description. Given the complexity of the lichen symbiotic structures, with recent evidence indicating that some lichens may be composed of multiple bacteria and more than one fungus (26), it is important to study lichen microbiomes in order to understand their ecological role in the symbiosis.A large and unexplored diversity of lichens is located in the Par...

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The Potential of Pioneer Lichens in Terraforming Mars

Armstrong¹

2021

Terraforming Mars

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Isolation and co-culturing of symbionts in the genus Usnea

Cited by 12 publications

References 28 publications

Two decades of DNA barcoding in the genus Usnea (Parmeliaceae): how useful and reliable is the ITS?

Two decades of DNA barcoding in the genus Usnea (Parmeliaceae): how useful and reliable is the ITS?

The microbiomes of seven lichen genera reveal host specificity, a reduced core community and potential as source of antimicrobials

The Potential of Pioneer Lichens in Terraforming Mars

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