Journal: Microorganisms

Article Title: Lampenflora in a Show Cave in the Great Basin Is Distinct from Communities on Naturally Lit Rock Surfaces in Nearby Wild Caves

doi: 10.3390/microorganisms9061188

Figure Lengend Snippet: Summary of amplicon-sequencing diversity at lit surfaces in eight caves in Great Basin National Park. The number Illumina reads are reported for each cave—partial 16S amplicons targeting bacteria, partial 23S amplicons targeting photoautotrophs, and ITS2 amplicons targeting fungi. The number of operational taxonomic units (OTU) represented by >4 reads/OTU are reported for major organismal groups in each cave. The total number of “lampenflora” (cyanobacteria + green algae + bryophytes) OTUs is summarized for each cave, as is the total number of OTUs from each cave.

Article Snippet: We note that there was no evidence from fungal ITS2 amplicons, suggesting the presence of Pseudogymnoascus desctructans —the psychrophilic fungus that causes white-nose syndrome in bats [ ]—in Great Basin National Park.

Techniques: Amplicon Sequencing, Bacteria, Algae

Journal: Microorganisms

Article Title: Lampenflora in a Show Cave in the Great Basin Is Distinct from Communities on Naturally Lit Rock Surfaces in Nearby Wild Caves

doi: 10.3390/microorganisms9061188

Figure Lengend Snippet: Overview of photoautotroph diversity at eight caves in Great Basin National Park inferred from environmental DNA metabarcoding of partial 23S amplicons. OTUs were broadly assigned to one of five broad groups—“algae”, “bryophytes”, “cyanobacteria”, “diatoms”, and “vascular plants” based on phylogenetic reconstructions of the alignment of the 23S fragment and BLAST comparisons. Bar plot depicts the relative proportion of reads assigned to cyanobacteria, algae, bryophytes, diatoms, and vascular plants—each column represents a sampled cave (see ). In “algae”, “cyanobacteria”, and “diatoms”, additional groupings were reported that coincided with well-supported monophyletic clades. The proportion of reads assigned to each group is reported for each cave. The show cave with artificial lighting, Lehman Cave, was represented by two composite samples: “LEHM 1” collected in May 2019 from 10 sites within the cave; and “LEHM 2” collected from five sites within the cave in November 2019.

Article Snippet: We note that there was no evidence from fungal ITS2 amplicons, suggesting the presence of Pseudogymnoascus desctructans —the psychrophilic fungus that causes white-nose syndrome in bats [ ]—in Great Basin National Park.

Techniques: Algae

Journal: Microorganisms

Article Title: Lampenflora in a Show Cave in the Great Basin Is Distinct from Communities on Naturally Lit Rock Surfaces in Nearby Wild Caves

doi: 10.3390/microorganisms9061188

Figure Lengend Snippet: Overview of bacterial diversity at eight caves in Great Basin National Park inferred from environmental DNA metabarcoding of partial 16S amplicons. Bar plot depicts the relative proportion of reads assigned to different taxonomic ranks—each column represents a sampled cave (see ). ( A ) The proportion of 16S reads assigned to phylum-level groups, inferred using the FROGS pipeline, for each cave. ( B ) The proportion of 16S reads assigned to class-level groups, inferred using the FROGS pipeline, for each cave. ( C ) The proportion of 16S reads assigned to order-level groups, inferred using the FROGS pipeline, for each cave. The show cave with artificial lighting, Lehman Caves, was represented by two composite samples: “LEHM 1” collected in May 2019 from 10 sites within the cave; and ‘LEHM 2′ collected from five sites within the cave in November 2019. Note: in panel ( C ), the color pattern repeats starting with the order “Micropepsales” and the repeat is indicated with a white asterisk in each stacked bar plot.

Article Snippet: We note that there was no evidence from fungal ITS2 amplicons, suggesting the presence of Pseudogymnoascus desctructans —the psychrophilic fungus that causes white-nose syndrome in bats [ ]—in Great Basin National Park.

Techniques:

Journal: Microorganisms

Article Title: Lampenflora in a Show Cave in the Great Basin Is Distinct from Communities on Naturally Lit Rock Surfaces in Nearby Wild Caves

doi: 10.3390/microorganisms9061188

Figure Lengend Snippet: Overview of fungal diversity at eight caves in Great Basin National Park inferred from environmental DNA metabarcoding of ITS amplicons. Bar plot depicts the relative proportion of reads assigned to different taxonomic ranks—each column represents a sampled cave (see ). ( A ) The proportion of ITS reads assigned to phylum-level groups, inferred using the PIPITS pipeline, for each cave. ( B ) Class-level assignments for ascomycete OTUs; all non-ascomycete reads are excluded (see panel ( A )), and the relative abundance of remaining ascomycete classes were adjusted proportionally. ( C ) Class-level assignments for basidiomycete OTUs; all non-basidiomycete reads are excluded (see panel ( A )), and the relative abundance of remaining basidiomycete classes were adjusted proportionally.

Article Snippet: We note that there was no evidence from fungal ITS2 amplicons, suggesting the presence of Pseudogymnoascus desctructans —the psychrophilic fungus that causes white-nose syndrome in bats [ ]—in Great Basin National Park.

Techniques:

Journal: eLife

Article Title: Processing of the ribosomal ubiquitin-like fusion protein FUBI-eS30/FAU is required for 40S maturation and depends on USP36

doi: 10.7554/eLife.70560

Figure Lengend Snippet: .

Article Snippet: Sequence-based reagent , Cy3-5'ITS1 , Microsynth ( ) DOI: 10.1038/sj.emboj.7600752 , , 5'-CCTCGCCCTCCGGGCTCCGTTAATGATC-3' See Materials and methods, Fluorescence in situ hybridization.

Techniques: Cell Culture, Recombinant, Molecular Cloning, Sequencing, Northern Blot, Fluorescence, In Situ Hybridization, Negative Control