Abstract
Despite significant technological advancements in the field of microbial ecology, cultivation and subsequent isolation of the vast majority of environmental microorganisms continues to pose challenges. Isolation of the environmental microbiomes is prerequisite to better understand a myriad of ecosystem services they provide, such as bioremediation of contaminants. Towards this end, in this culturomics study, we evaluated the colonization of soil bacterial and fungal communities within diffusion chambers (DC) and microbial traps (MT) established using uraniferous soils collected from a historically contaminated soil from Aiken, USA. Microbial assemblages were compared between the DC and MT relative to the native soils using amplicon based metagenomic and bioinformatic analysis. The overall rationale of this study is that DC and MT growth chambers provide the optimum conditions under which desired microbiota, identified in a previous study to serve as the “core” microbiomes, will proliferate, leading to their successful isolation. Specifically, the core microbiomes consisted of assemblages of bacteria (Burkholderia spp.) and fungi (Penicillium spp.), respectively. The findings from this study further supported previous data such that the abundance and diversity of the desired “core” microbiomes significantly increased as a function of enrichments over three consecutive generations of DC and MT, respectively. Metagenomic analysis of the DC/MT generations also revealed that enrichment and stable populations of the desired “core” bacterial and fungal microbiomes develop within the first 20 days of incubation and the practice of subsequent transfers for second and third generations, as is standard in previous studies, may be unnecessary. As a cost and time cutting measure, this study recommends running the DC/MT chambers for only a 20-day time period, as opposed to previous studies, which were run for months. In summation, it was concluded that, using the diffusion chamber-based enrichment techniques, growth of desired microbiota possessing environmentally relevant functions can be achieved in a much shorter time frame than has been previously shown.
Highlights
Despite the tremendous progress in microbial ecology techniques, cultivation of the soil microbiomes still remains challenging and, less than 1% of the total soil microbiome is amenable to cultivation under standard laboratory conditions [1]
When metagenomics was coupled to study the enrichment of soil-borne microbiota in diffusion chambers (DC), this approach emerged as a holistic assessment of the bacterial and fungal assemblages colonizing the chambers
In a recent study, we showed the microbial diversity in DC and microbial traps (MT) (Microbial Trap) experiments to be dominated by Proteobacterial phyla and Burkholderia genus [12]
Summary
Despite the tremendous progress in microbial ecology techniques, cultivation of the soil microbiomes still remains challenging and, less than 1% of the total soil microbiome is amenable to cultivation under standard laboratory conditions [1]. In our previous study on the evaluation of the DC and MT techniques to enrich and isolate U-resistant fungal microbiota from the uranium-rich SRS soils, a predominance of Ascomycota phylum, with Penicillium as the most dominant genus, was demonstrated [18]. These dominant bacterial and fungal strains were isolated and found to possess environmentally beneficial traits of U bioremediation. As a cost and time cutting measure, this study recommends running the DC/MT chambers for only a 20-day time period, as opposed to previous studies that were run for months
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