Technologies for the selection, culture and metabolic profiling of unique Rhizosphere Microorganisms for natural product discovery

Saliya Gurusinghe, Tabin Brooks, Russell Barrow, Xiaocheng Zhu, Agasthya Thotagamuwa, Paul Dennis, Vadakattu Gupta, Thiru Vanniasinkam, Leslie A. Weston

Research output: Contribution to journalArticle

2 Downloads (Pure)

Abstract

Small molecule discovery has benefitted from the development of technologies that have aided in the culture and identification of soil microorganisms and the subsequent analysis of their respective metabolomes. We report herein on the use of both culture dependent and independent approaches for evaluation of soil microbial diversity in the rhizosphere of canola, a crop known to support a diverse microbiome, including plant growth promoting rhizobacteria. Initial screening of rhizosphere soils showed that microbial diversity, particularly bacterial, was greatest at crop maturity; therefore organismal recovery was attempted with soil collected at canola harvest. Two standard media (Mueller Hinton and gellan gum) were evaluated following inoculation with soil aqueous suspensions and compared with a novel “rhizochip” prototype buried in a living canola crop rhizosphere for microbial culture in situ. Following successful recovery and identification of 375 rhizosphere microbiota of interest from all culture methods, isolates were identified by Sanger sequencing and/or characterization using morphological and biochemical traits. Three bacterial isolates of interest were randomly selected as case studies for intensive metabolic profiling. After successful culture in liquid media and solvent extraction, individual extracts were subjected to evaluation by UHPLC-DAD-QToF-MS, resulting in the rapid characterization of metabolites of interest from cultures of two isolates. After evaluation of key molecular features, unique or unusual bacterial metabolites were annotated and are reported herein.
Original languageEnglish
Pages (from-to)1-20
Number of pages20
JournalMolecules
Volume24
DOIs
Publication statusPublished - 21 May 2019

Fingerprint

Rhizosphere
microorganisms
Biological Products
Microorganisms
soils
Soil
Technology
crops
Soils
Crops
products
metabolites
Microbiota
Metabolites
recovery
Recovery
solvent extraction
sequencing
Metabolome
evaluation

Grant Number

  • UCS 00020

Cite this

@article{0e7a6e02747b4268a2ef80de7caa1bce,
title = "Technologies for the selection, culture and metabolic profiling of unique Rhizosphere Microorganisms for natural product discovery",
abstract = "Small molecule discovery has benefitted from the development of technologies that have aided in the culture and identification of soil microorganisms and the subsequent analysis of their respective metabolomes. We report herein on the use of both culture dependent and independent approaches for evaluation of soil microbial diversity in the rhizosphere of canola, a crop known to support a diverse microbiome, including plant growth promoting rhizobacteria. Initial screening of rhizosphere soils showed that microbial diversity, particularly bacterial, was greatest at crop maturity; therefore organismal recovery was attempted with soil collected at canola harvest. Two standard media (Mueller Hinton and gellan gum) were evaluated following inoculation with soil aqueous suspensions and compared with a novel “rhizochip” prototype buried in a living canola crop rhizosphere for microbial culture in situ. Following successful recovery and identification of 375 rhizosphere microbiota of interest from all culture methods, isolates were identified by Sanger sequencing and/or characterization using morphological and biochemical traits. Three bacterial isolates of interest were randomly selected as case studies for intensive metabolic profiling. After successful culture in liquid media and solvent extraction, individual extracts were subjected to evaluation by UHPLC-DAD-QToF-MS, resulting in the rapid characterization of metabolites of interest from cultures of two isolates. After evaluation of key molecular features, unique or unusual bacterial metabolites were annotated and are reported herein.",
keywords = "rhizosphere, soil microbiota, Brassica napus, rhizochip, natural products, LC-DAD-QToF-MS, chemicl diversity, allelochemicals, in situ isolation, Next generation sequencing",
author = "Saliya Gurusinghe and Tabin Brooks and Russell Barrow and Xiaocheng Zhu and Agasthya Thotagamuwa and Paul Dennis and Vadakattu Gupta and Thiru Vanniasinkam and Weston, {Leslie A.}",
year = "2019",
month = "5",
day = "21",
doi = "10.3390/molecules24101955",
language = "English",
volume = "24",
pages = "1--20",
journal = "Molecules",
issn = "1420-3049",
publisher = "Multidisciplinary Digital Publishing Institute (MDPI)",

}

TY - JOUR

T1 - Technologies for the selection, culture and metabolic profiling of unique Rhizosphere Microorganisms for natural product discovery

AU - Gurusinghe, Saliya

AU - Brooks, Tabin

AU - Barrow, Russell

AU - Zhu, Xiaocheng

AU - Thotagamuwa, Agasthya

AU - Dennis, Paul

AU - Gupta, Vadakattu

AU - Vanniasinkam, Thiru

AU - Weston, Leslie A.

PY - 2019/5/21

Y1 - 2019/5/21

N2 - Small molecule discovery has benefitted from the development of technologies that have aided in the culture and identification of soil microorganisms and the subsequent analysis of their respective metabolomes. We report herein on the use of both culture dependent and independent approaches for evaluation of soil microbial diversity in the rhizosphere of canola, a crop known to support a diverse microbiome, including plant growth promoting rhizobacteria. Initial screening of rhizosphere soils showed that microbial diversity, particularly bacterial, was greatest at crop maturity; therefore organismal recovery was attempted with soil collected at canola harvest. Two standard media (Mueller Hinton and gellan gum) were evaluated following inoculation with soil aqueous suspensions and compared with a novel “rhizochip” prototype buried in a living canola crop rhizosphere for microbial culture in situ. Following successful recovery and identification of 375 rhizosphere microbiota of interest from all culture methods, isolates were identified by Sanger sequencing and/or characterization using morphological and biochemical traits. Three bacterial isolates of interest were randomly selected as case studies for intensive metabolic profiling. After successful culture in liquid media and solvent extraction, individual extracts were subjected to evaluation by UHPLC-DAD-QToF-MS, resulting in the rapid characterization of metabolites of interest from cultures of two isolates. After evaluation of key molecular features, unique or unusual bacterial metabolites were annotated and are reported herein.

AB - Small molecule discovery has benefitted from the development of technologies that have aided in the culture and identification of soil microorganisms and the subsequent analysis of their respective metabolomes. We report herein on the use of both culture dependent and independent approaches for evaluation of soil microbial diversity in the rhizosphere of canola, a crop known to support a diverse microbiome, including plant growth promoting rhizobacteria. Initial screening of rhizosphere soils showed that microbial diversity, particularly bacterial, was greatest at crop maturity; therefore organismal recovery was attempted with soil collected at canola harvest. Two standard media (Mueller Hinton and gellan gum) were evaluated following inoculation with soil aqueous suspensions and compared with a novel “rhizochip” prototype buried in a living canola crop rhizosphere for microbial culture in situ. Following successful recovery and identification of 375 rhizosphere microbiota of interest from all culture methods, isolates were identified by Sanger sequencing and/or characterization using morphological and biochemical traits. Three bacterial isolates of interest were randomly selected as case studies for intensive metabolic profiling. After successful culture in liquid media and solvent extraction, individual extracts were subjected to evaluation by UHPLC-DAD-QToF-MS, resulting in the rapid characterization of metabolites of interest from cultures of two isolates. After evaluation of key molecular features, unique or unusual bacterial metabolites were annotated and are reported herein.

KW - rhizosphere

KW - soil microbiota

KW - Brassica napus

KW - rhizochip

KW - natural products

KW - LC-DAD-QToF-MS

KW - chemicl diversity

KW - allelochemicals

KW - in situ isolation

KW - Next generation sequencing

U2 - 10.3390/molecules24101955

DO - 10.3390/molecules24101955

M3 - Article

C2 - 31117282

VL - 24

SP - 1

EP - 20

JO - Molecules

JF - Molecules

SN - 1420-3049

ER -