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Comparison of Actinobacteria communities from human-impacted and pristine karst caves
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  • Andrea BURESOVA,
  • Jan Kopecky,
  • Marketa SAGOVA-MARECKOVA,
  • Lise Alonso,
  • Florian VAUTRIN,
  • Yvan Moenne-Loccoz,
  • Veronica RODRIGUEZ NAVA
Andrea BURESOVA
Université Claude Bernard Lyon 1

Corresponding Author:andrea.buresova@seznam.cz

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Jan Kopecky
Crop Research Institute
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Marketa SAGOVA-MARECKOVA
Crop Research Institute
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Lise Alonso
Universite Claude Bernard Lyon 1
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Florian VAUTRIN
Université Claude Bernard Lyon 1
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Yvan Moenne-Loccoz
Universite Claude Bernard Lyon 1
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Veronica RODRIGUEZ NAVA
Universite Claude Bernard Lyon 1
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Abstract

Actinobacteria are important cave inhabitants, but knowledge of how anthropization and anthropization-related visual marks affect this community on cave walls is lacking. We compared Actinobacteria communities among four French limestone caves (Mouflon, Reille, Rouffignac, Lascaux) ranging from pristine to anthropized, and within Lascaux Cave between marked (wall visual marks) and unmarked areas in different rooms (Sas-1, Passage, Apse, Diaclase). In addition to the 16S rRNA gene marker, 441 bp fragments of the hsp65 gene were used and an hsp65-related taxonomic database was constructed for identification of Actinobacteria to the species level by Illumina-MiSeq analysis. The hsp65 marker revealed higher resolution for species and higher richness (99% OTU cutoff) versus 16S rRNA gene; however, more taxa were identified at higher taxonomic ranks. Actinobacteria communities varied between Mouflon and Reille caves (both pristine), and Rouffignac and Lascaux (both anthropized). Rouffignac displayed high diversity of Nocardia, suggesting human inputs, and Lascaux exhibited high Mycobacterium relative abundance, whereas Gaiellales were typical in pristine caves and the Diaclase (least affected area of Lascaux Cave). Within Lascaux, Pseudonocardiaceae dominated on unmarked walls and Streptomycetaceae (especially Streptomyces mirabilis) on marked walls, indicating a possible role in mark formation. A new taxonomic database (https://zenodo.org/record/5576074) was developed. Although not all Actinobacteria species were represented, the use of the hsp65 marker enabled species-level variations of the Actinobacteria community to be documented based on the extent of anthropogenic pressure. This approach proved effective when comparing different limestone caves or specific conditions within one cave.
24 Jun 2021Submitted to MicrobiologyOpen
25 Jun 2021Submission Checks Completed
25 Jun 2021Assigned to Editor
30 Jun 2021Reviewer(s) Assigned
15 Jul 2021Review(s) Completed, Editorial Evaluation Pending
16 Jul 2021Editorial Decision: Revise Minor
07 Nov 20211st Revision Received
08 Nov 2021Submission Checks Completed
08 Nov 2021Assigned to Editor
09 Nov 2021Review(s) Completed, Editorial Evaluation Pending
10 Nov 2021Reviewer(s) Assigned
25 Nov 2021Editorial Decision: Revise Minor
30 Jan 20222nd Revision Received
31 Jan 2022Submission Checks Completed
31 Jan 2022Assigned to Editor
31 Jan 2022Review(s) Completed, Editorial Evaluation Pending
31 Jan 2022Reviewer(s) Assigned
15 Feb 2022Editorial Decision: Revise Minor
01 Mar 20223rd Revision Received
02 Mar 2022Submission Checks Completed
02 Mar 2022Assigned to Editor
05 Mar 2022Review(s) Completed, Editorial Evaluation Pending
10 Mar 2022Editorial Decision: Accept