Journal Article
- Comparative analysis of bacterial diversity in the rhizosphere of tomato by culture-dependent and -independent approaches
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Shin Ae Lee , Jiyoung Park , Bora Chu , Jeong Myeong Kim , Jae-Ho Joa , Mee Kyung Sang , Jaekyeong Song , Hang-Yeon Weon
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J. Microbiol. 2016;54(12):823-831. Published online November 26, 2016
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DOI: https://doi.org/10.1007/s12275-016-6410-3
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Abstract
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The microbiome in the rhizosphere–the region surrounding
plant roots–plays a key role in plant growth and health,
enhancing nutrient availability and protecting plants from
biotic and abiotic stresses. To assess bacterial diversity in the
tomato rhizosphere, we performed two contrasting approaches:
culture-dependent and -independent. In the culturedependent
approach, two culture media (Reasoner’s 2A agar
and soil extract agar) were supplemented with 12 antibiotics
for isolating diverse bacteria from the tomato rhizosphere
by inhibiting predominant bacteria. A total of 689 bacterial
isolates were clustered into 164 operational taxonomic units
(OTUs) at 97% sequence similarity, and these were found to
belong to five bacterial phyla (Proteobacteria, Actinobacteria,
Bacteroidetes, Acidobacteria, and Firmicutes). Of these, 122
OTUs were retrieved from the antibiotic-containing media,
and 80 OTUs were recovered by one specific antibiotic-containing
medium. In the culture-independent approach, we
conducted Illumina MiSeq amplicon sequencing of the 16S
rRNA gene and obtained 19,215 high-quality sequences, which
clustered into 478 OTUs belonging to 16 phyla. Among the
total OTUs from the MiSeq dataset, 22% were recovered in
the culture collection, whereas 41% of OTUs in the culture
collection were not captured by MiSeq sequencing. These
results
showed that antibiotics were effective in isolating
various taxa that were not readily isolated on antibiotic-free
media, and that both contrasting approaches provided complementary
information to characterize bacterial diversity
in the tomato rhizosphere.
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Research Support, Non-U.S. Gov't
- Isolation and Characterization of Marine Pigmented Bacteria from Norwegian Coastal Waters and Screening for Carotenoids with UVA-Blue Light Absorbing Properties
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Marit H. Stafsnes , Kjell D Josefsen , Geir Kildahl-Andersen , Svein Valla , Trond E. Ellingsen , Per Bruheim
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DOI: https://doi.org/10.1007/s12275-009-0118-6
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Abstract
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Microbial culture collections are important resources for isolation of natural compounds with novel properties. In this study, a culture collection of around 1,500 pigmented heterotrophic bacteria was established. The bacteria were isolated from the sea surface microlayer at different sampling sites along the mid-part of the Norwegian coast. The bacterial isolates produced pigments of various coloration (e.g. golden, yellow, red, pink and orange). Methanol extracts of sixteen isolates were characterized with LC-Diodearray-TOF mass spectrometry analysis. The number of pigments per isolate varied considerably, and a tentative identification of the pigments was performed based on UV-absorbance profile and molecular formula
assignation based on the accurate mass determination. The LC-MS analyses evealed that most of the pigments probably were carotenoids. Furthermore, we developed a high throughput LC-MS method for characterization and screening of a larger sub-fraction (300 isolates) of the culture collection. The aim was to screen and identify bacterial isolates producing carotenoids that absorb light in the UVA-Blue light. Six of the bacterial strains were selected for detailed investigation, including 16s rRNA sequencing, preparative HPLC for purification of major carotenoids and subsequent structural elucidation with NMR. Among the identified
carotenoids were zeaxanthin, nostoxanthin and sarcinaxanthin, some with novel glycosylation patterns.