Drops join to make a stream: high‐throughput nanoscale cultivation to grasp the lettuce root microbiome

Summary Root endospheres house complex and diverse bacterial communities, of which many strains have not been cultivated yet by means of the currently available isolation techniques. The Prospector® (General Automation Lab Technologies, San Carlos, CA, USA), an automated and high‐throughput bacteria...

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Bibliographic Details
Published in:Environmental microbiology reports 2022-02, Vol.14 (1), p.60-69
Main Authors: Persyn, Antoine, Mueller, André, Goormachtig, Sofie
Format: Article
Language:English
Subjects:
Automation
Bacteria
Cultivation
Cultivation techniques
Culture collections
Culture Media
Hand Strength
Lactuca
Lettuce
Microbiomes
Microbiota
Plant growth
Rivers
Sequences
Species extinction
Species richness
Strains (organisms)
Temperature
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Summary:Summary Root endospheres house complex and diverse bacterial communities, of which many strains have not been cultivated yet by means of the currently available isolation techniques. The Prospector® (General Automation Lab Technologies, San Carlos, CA, USA), an automated and high‐throughput bacterial cultivation system, was applied to analyse the root endomicrobiome of lettuce (Lactuca sativa L.). By using deep sequencing, we compared the results obtained with the Prospector and the traditional solid medium culturing and extinction methods. We found that the species richness did not differ and that the amount of previously uncultured bacteria did not increase, but that the bacterial diversity isolated by the three methods varied. In addition, the tryptic soy broth and King's B media provided a lower, but different, diversity of bacteria than that of Reasoner's 2A (R2A) medium when used within the Prospector system and the number of unique bacterial strains did not weigh up against those isolated with the R2A medium. Thus, to cultivate as broad a variety of bacteria as possible, divergent isolation techniques should be used in parallel. Thanks to its speed and limited manual requirements, the Prospector is a valuable system to enlarge root microbiome culture collections.
ISSN:1758-2229
1758-2229
DOI:10.1111/1758-2229.13014