10.5061/DRYAD.MKKWH70VG
Oberhofer, Martina
0000-0001-7371-2496
University of Vienna
Hess, Jaqueline
University of Vienna
Leutgeb, Marlene
University of Vienna
Gössnitzer, Florian
International Atomic Energy Agency
Rattei, Thomas
University of Vienna
Wawrosch, Christoph
University of Vienna
Zotchev, Sergey B.
University of Vienna
Data from: Exploring actinobacteria associated with rhizosphere and
endosphere of the native Alpine medicinal plant Leontopodium nivale
Subspecies alpinum
Dryad
dataset
2019
University of Vienna
https://ror.org/03prydq77
2019-10-31T00:00:00Z
2019-10-31T00:00:00Z
en
741889 bytes
4
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
The rhizosphere of plants is enriched in nutrients facilitating growth of
microorganisms, some of which are recruited as endophytes. Endophytes,
especially Actinobacteria, are known to produce a plethora of bioactive
compounds. We hypothesized that Leontopodium nivale subsp. alpinum
(Edelweiss), a rare alpine medicinal plant, may serve as yet untapped
source for uncommon Actinobacteria associated with this plant. Rhizosphere
soil of native Alpine plants was used, after physical and chemical
pretreatments, for isolating Actinobacteria. Isolates were selected based
on morphology and identified by 16S rRNA gene-based barcoding. Resulting
77 Actinobacteria isolates represented the genera Actinokineospora,
Kitasatospora, Asanoa, Microbacterium, Micromonospora, Micrococcus,
Mycobacterium, Nocardia, and Streptomyces. In parallel, Edelweiss plants
from the same location were surface-sterilized, separated into leaves,
roots, rhizomes, and inflorescence and pooled within tissues before
genomic DNA extraction. Metagenomic 16S rRNA gene amplicons confirmed
large numbers of actinobacterial operational taxonomic units (OTUs)
descending in diversity from roots to rhizomes, leaves and inflorescences.
These metagenomic data, when queried with isolate sequences, revealed an
overlap between the two datasets, suggesting recruitment of soil bacteria
by the plant. Moreover, this study uncovered a profound diversity of
uncultured Actinobacteria from Rubrobacteridae, Thermoleophilales,
Acidimicrobiales and unclassified Actinobacteria specifically in
belowground tissues, which may be exploited by a targeted isolation
approach in the future.
Fig.1.fas Sanger sequence alignment of all experimental sequences (prefix
-RLA) of Actinobacteria other than the genus Streptomyces with their
Genbank accession numbers, closest matches in Genbank Blast search and
type strains (T) of closest matches from rhizosphere isolates
of Leontopodium nivalesubsp. alpinum. Alignments were performed with MEGA
version 7.0.18 using ClustalW algorithms (Kumar et al., 2016).
Fig.1.newick Maximum composite likelihood analysis (MCL) of Actinobacteria
isolates from the rhizosphere of Leontopodium nivalesubsp. alpinumbased on
Tamura and Nei (1993) model with Gamma distribution and invariate sites
using Mega software version 7.0.18 (Kumar et al., 2016). The phylogenetic
tree contains experimental sequences (RLA) with their Genbank accession
numbers, their closest matches in Genbank Blast search and respectively
closest type strains (T). The tree is drawn to scale with branch length
representing the substitutions per site. Bootstrap support values were
calculated with 1000 replicates. Isolates identify by the prefix -RLA
followed by an individual isolate number and Genbank accession numbers in
brackets. Fig.2.fas Sanger sequences alignment of all experimental
sequences (prefix -RLA) of the genus Streptomyces with their Genbank
accession numbers, closest matches in Genbank Blast search and type
strains (T) of closest matches from rhizosphere isolates of Leontopodium
nivalesubsp. alpinum. Alignments were performed with MEGA version 7.0.18
using ClustalW algorithms (Kumar et al., 2016). Fig.2.newick MCL
clustering of Streptomycesisolates from Edelweiss rhizosphere.
Phylogenetic tree reconstruction was performed with Tamura (1992) as best
fitting evolutionary model with invariant sites and Gamma
distribution using Mega software version 7.0.18 (Kumar et al.,
2016).Further specifications of the phylogeny are congruent to Figure 1.
Supplem.Fig.S1.fas Alignment of curated metagenomic sequence data of
Actinobacteria endophytes from Leontopodium nivalesubsp. alpinumresulting
from Illumina HiSeq2500. Amplicons were acquired with the primers 357F and
806R and entailed the V3 and V4 region of 16S rDNA as paired end reads of
250 bases. Sequences were processed according to the Mothur MiSeq SOP by
using mothur 1.39.5 (Schloss et al.,2009; Kozich et al.,2013). The full
analysis script is available on GitHub
(https://github.com/JackyHess/Leontopodium_metagen).
Supplem.Fig.S1.RAxML ML analysis sequences of Actinobacterial endophyte
metagenome of Edelweiss. Phylogenetic relationships include endophytes
from all host plant tissues.Data are clustered into operational taxonomic
units (OTUs) with an identity cutoff of 97% and taxonomic assignments are
based on RDB classifier and Silva database (Wang et al., 2007).
The submitted data contain the alignments of sequences used for Fig. 1, 2
and Supplem. Fig. S1 in the format of .fas. Moreover, the submission
entails the tree files in in the format of .newick (Fig. 1, 2) and .RAxML
(Suppl. Fig S1).