Dataset Information

A Defined Medium for Cultivation and Exometabolite Profiling of Soil Bacteria.

ABSTRACT: Exometabolomics is an approach to assess how microorganisms alter, or react to their environments through the depletion and production of metabolites. It allows the examination of how soil microbes transform the small molecule metabolites within their environment, which can be used to study resource competition and cross-feeding. This approach is most powerful when used with defined media that enable tracking of all metabolites. However, microbial growth media have traditionally been developed for the isolation and growth of microorganisms but not metabolite utilization profiling through Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS). Here, we describe the construction of a defined medium, the Northen Lab Defined Medium (NLDM), that not only supports the growth of diverse soil bacteria but also is defined and therefore suited for exometabolomic experiments. Metabolites included in NLDM were selected based on their presence in R2A medium and soil, elemental stoichiometry requirements, as well as knowledge of metabolite usage by different bacteria. We found that NLDM supported the growth of 108 of the 110 phylogenetically diverse (spanning 36 different families) soil bacterial isolates tested and all of its metabolites were trackable through LC-MS/MS analysis. These results demonstrate the viability and utility of the constructed NLDM medium for growing and characterizing diverse microbial isolates and communities.

SUBMITTER: de Raad M

PROVIDER: S-EPMC9174792 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Publications

A Defined Medium for Cultivation and Exometabolite Profiling of Soil Bacteria.

de Raad Markus M Li Yifan V YV Kuehl Jennifer V JV Andeer Peter F PF Kosina Suzanne M SM Hendrickson Andrew A Saichek Nicholas R NR Golini Amber N AN Han La Zhen Z Wang Ying Y Bowen Benjamin P BP Deutschbauer Adam M AM Arkin Adam P AP Chakraborty Romy R Northen Trent R TR

Frontiers in microbiology 20220525

Exometabolomics is an approach to assess how microorganisms alter, or react to their environments through the depletion and production of metabolites. It allows the examination of how soil microbes transform the small molecule metabolites within their environment, which can be used to study resource competition and cross-feeding. This approach is most powerful when used with defined media that enable tracking of all metabolites. However, microbial growth media have traditionally been developed f ...[more]

PMID: 35694313

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Project description:Rotational shifting cultivation (RSC) in Northern Thailand serves the dual purpose of ensuring food security and meeting economic goals through maize cultivation. However, the research question remains: Does the dynamics of soil bacterial communities differ between maize monoculture and RSC fields with continuous fallow throughout the season? Therefore, the objective of this study was to investigate and compare the variation of soil bacterial communities in maize monoculture and fallow RSC fields. A continuous 5-year fallow field (undisturbed soil; CF-5Y) and a continuous 5-year maize cultivation field (M-5Y) in Mae Chaem District, Chiang Mai Province, Northern Thailand, were selected due to their similarities in microclimate, topography, and the 5-year duration of different field activities. Over the span of a year, we collected soil samples from the surface layer (0-2 cm depth) at both sites. These collections occurred at 3-month intervals, starting from March 2022 (summer season) and followed by June (rainy season), September (rainy season), December (winter season), and March 2023 (summer season). Soil bacterial diversity and composition were analyzed using 16S rRNA gene-based metagenomic analysis. The results found that undisturbed soil over a 5-year period exhibited more stability in the richness and diversity of bacteria across seasons compared with M-5Y. Notably, fertilizer application and tillage practices in M-5Y can enhance both the diversity and richness of soil bacteria. In terms of bacterial abundance, Proteobacteria prevailed in CF-5Y, while Actinobacteria dominated in M-5Y. At the genus level, Candidatus Udaeobacter dominated during the summer and winter seasons in both CF-5Y and M-5Y sites. Interestingly, during the rainy season, the dominant genus shifted to Bacillus in both CF-5Y and M-5Y fields. The soil bacterial community in M-5Y was strongly influenced by organic matter (OM) and organic carbon (OC). In contrast, in CF-5Y, there was no correlation between soil properties and the soil bacterial community, likely due to the lower variation in soil properties across seasons. β-Glucosidase was the dominant enzyme in both CF-5Y and M-5Y sites, and it showed a positive correlation with OM and OC. Further studies should continue to investigate soil bacteria dynamics, considering the changes in land management practices.

Dataset Information

A Defined Medium for Cultivation and Exometabolite Profiling of Soil Bacteria.

Publications

A Defined Medium for Cultivation and Exometabolite Profiling of Soil Bacteria.

Similar Datasets

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