ITS2 metabarcoding analysis complements lichen mycobiome diversity data

Banchi, Elisa; Stanković, D; Fernández-Mendoza, Fernando; Gionechetti, Fabrizia; Pallavicini, Alberto; Muggia, Lucía

doi:10.1007/s11557-018-1415-4

Cited by 39 publications

(39 citation statements)

References 73 publications

(134 reference statements)

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“…For decades, studies dealing with phycobiont diversity in lichen thalli were primarily based on Sanger sequencing. In recent years, metabarcoding analyses have uncovered substantial species diversity associated with lichen symbioses 4 , 68 – 71 because HTS techniques detected a vast number of genotypes that would otherwise have remained undetected using conventional PCR amplifications. In fact, the discovery of phycobiont multiplicity within a single lichen thallus 38 , 39 , 41 , 72 and the exclusive use of Sanger sequencing in the majority of studies led the lichenologist community to consider whether terms such as specificity and selectivity (related to symbiotic association patterns) should be revised under this new perspective.…”

Section: Discussionmentioning

confidence: 99%

Symbiotic microalgal diversity within lichenicolous lichens and crustose hosts on Iberian Peninsula gypsum biocrusts

Moya

Molins

Chiva

et al. 2020

Sci Rep

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This study analyses the interactions among crustose and lichenicolous lichens growing on gypsum biocrusts. The selected community was composed of Acarospora nodulosa , Acarospora placodiiformis , Diploschistes diacapsis , Rhizocarpon malenconianum and Diplotomma rivas-martinezii . These species represent an optimal system for investigating the strategies used to share phycobionts because Acarospora spp . are parasites of D. diacapsis during their first growth stages, while in mature stages, they can develop independently. R. malenconianum is an obligate lichenicolous lichen on D. diacapsis , and D. rivas-martinezii occurs physically close to D. diacapsis . Microalgal diversity was studied by Sanger sequencing and 454-pyrosequencing of the nrITS region, and the microalgae were characterized ultrastructurally. Mycobionts were studied by performing phylogenetic analyses. Mineralogical and macro- and micro-element patterns were analysed to evaluate their influence on the microalgal pool available in the substrate. The intrathalline coexistence of various microalgal lineages was confirmed in all mycobionts. D. diacapsis was confirmed as an algal donor, and the associated lichenicolous lichens acquired their phycobionts in two ways: maintenance of the hosts’ microalgae and algal switching. Fe and Sr were the most abundant microelements in the substrates but no significant relationship was found with the microalgal diversity. The range of associated phycobionts are influenced by thallus morphology.

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Section: Discussionmentioning

confidence: 99%

Symbiotic microalgal diversity within lichenicolous lichens and crustose hosts on Iberian Peninsula gypsum biocrusts

Moya

Molins

Chiva

et al. 2020

Sci Rep

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“…In fact, previous works showed contrasting results when dealing with ITS1 or ITS2. While Blaalid et al 2013obtained similar results when using either ITS1 or ITS2 to perform fungal metabarcoding with environmental data, Banchi et al (2018b) showed discrepancies and biases in the detection of Basidiomycota when ITS1 or ITS2 were used as metabarcode for lichen mycobiomes, and suggested the complementary analysis of both ITS1 and ITS2 to reliably estimate the taxonomic diversity of the samples. In similar studies, Wang et al (2015) concluded conversely that ITS1 provides a better DNA barcode than ITS2 allowing a better species discrimination efficiency, whereas the ITS2 has been specifically selected and preferred to ITS1 in another study to catch fungal diversity in airborne samples (Banchi et al, 2018a).…”

Section: Dna Extraction Amplification and Sequencingmentioning

confidence: 95%

Soil Fungal Communities Investigated by Metabarcoding Within Simulated Forensic Burial Contexts

et al. 2020

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Decomposition of animal bodies in the burial environment plays a key role in the biochemistry of the soil, altering the balance of the local microbial populations present before the introduction of the carcass. Despite the growing number of studies on decomposition and soil bacterial populations, less is known on its effects on fungal communities. Shifts in the fungal populations at different post-mortem intervals (PMIs) could provide insights for PMI estimation and clarify the role that specific fungal taxa have at specific decomposition stages. In this study, we buried pig carcasses over a period of 1-to 6-months, and we sampled the soil in contact with each carcass at different PMIs. We performed metabarcoding analysis of the mycobiome targeting both the internal transcribed spacer (ITS) 1 and 2, to elucidate which one was more suitable for this purpose. Our results showed a decrease in the fungal taxonomic richness associated with increasing PMIs, and the alteration of the soil fungal signature even after 6 months post-burial, showing the inability of soil communities to restore their original composition within this timeframe. The results highlighted taxonomic trends associated with specific PMIs, such as the increase of the Mortierellomycota after 4and 6-months and of Ascomycota particularly after 2 months, and the decrease of Basidiomycota from the first to the last time point. We have found a limited number of taxa specifically associated with the carrion and not present in the control soil, showing that the major contributors to the recorded changes are originated from the soil and were not introduced by the carrion. As this is the first study conducted on burial graves, it sets the baseline for additional studies to investigate the role of fungal communities on prolonged decomposition periods and to identify fungal biomarkers to improve the accuracy of PMI prediction for forensic applications.

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“…With the dominance of Ascomycota and Basidiomycota in LAF and Alphaproteobacteria in bacterial communities across diverse lichen species, lichen-associated microbial compositions are known to be largely influenced by various environmental factors Bates et al, 2011;Cardinale et al, 2012;Hodkinson et al, 2012;U'Ren et al, 2012;Beck et al, 2014;Park et al, 2015Park et al, , 2016Wang et al, 2016). For example, lichenassociated fungal communities varied according to the host species (Beck et al, 2014;Park et al, 2015;Fernández-Mendoza et al, 2017;Banchi et al, 2018), climate conditions (U'Ren et al, 2012), seasonal changes of environmental conditions (Beck et al, 2014), geographic location, and altitude (Wang et al, 2016). Bacterial compositions in lichens were influenced by host species (Bates et al, 2011), age and sun exposure (Cardinale et al, 2012), substrate type and growth form (Park et al, 2016), and photoautotrophic symbiont and geography (Hodkinson et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Microbiome in Cladonia squamosa Is Vertically Stratified According to Microclimatic Conditions

et al. 2020

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Lichens are miniature ecosystems that contain fungi, microalgae, and bacteria. It is generally accepted that symbiosis between mycobiont and photobiont and microbial contribution to the ecosystem support the wide distribution of lichens in terrestrial ecosystems, including polar areas. The composition of symbiotic components can be affected by subtle microenvironmental differences within a thallus, as well as large-scale climate differences. In this study, we investigated fine-scale profiles of algal, fungal, and bacterial compositions through horizontal and vertical positions of the Antarctic lichen Cladonia squamosa colonies by next-generation sequencing of the nuclear large subunit rRNA gene (nucLSU) of eukaryotes and the 16S rRNA gene of bacteria. Apical parts of thalli were exposed to strong light, low moisture, and high variability of temperature compared with basal parts. Microbial diversity increased from apical parts to basal parts of thalli. Asterochloris erici was the major photobiont in apical positions of thalli, but other microalgal operational taxonomic units (OTUs) of Trebouxiophyceae and Ulvophyceae were major microalgal components in basal positions. Photochemical responses of algal components from apical and basal parts of thalli were quite different under variable temperature and humidity conditions. Several fungal OTUs that belonged to Arthoniomycetes and Lecanoromycetes, and diverse bacterial OTUs that belonged to Alphaproteobacteria, Acidobacteria_Gp1, and candidate division WPS-2 showed a clear distribution pattern according to their vertical positions within thalli. The overall lichen microbiome was significantly differentiated by the vertical position within a thallus. These results imply that different microclimate are formed at different lichen thallus parts, which can affect microbial compositions and physiological responses according to positions within the thalli.

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ITS2 metabarcoding analysis complements lichen mycobiome diversity data

Cited by 39 publications

References 73 publications

Symbiotic microalgal diversity within lichenicolous lichens and crustose hosts on Iberian Peninsula gypsum biocrusts

Symbiotic microalgal diversity within lichenicolous lichens and crustose hosts on Iberian Peninsula gypsum biocrusts

Soil Fungal Communities Investigated by Metabarcoding Within Simulated Forensic Burial Contexts

Microbiome in Cladonia squamosa Is Vertically Stratified According to Microclimatic Conditions

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