Culturomics of Bacteria from Radon-Saturated Water of the World’s Oldest Radium Mine

Kapinusova, Gabriela; Jani, Kunal; Smrhova, Tereza; Pajer, Petr; Jarosova, Irena; Šuman, Jáchym; Strejcek, Michal; Uhlík, Ondřej

doi:10.1128/spectrum.01995-22

Cited by 7 publications

(13 citation statements)

References 129 publications

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“…Finally, another potential difficulty was considered: the presence of the same organism in multiple isolates in the same multiplex set of six samples. Indeed, many culturomics projects have to deal with dereplication of isolates to avoid wasting time characterizing the same biological object several times . To test this scenario, two types of mixtures were created: four sets with at least one organism repeated in two distant fractions and three with the same organism repeated in neighboring fractions.…”

Section: Discussionmentioning

confidence: 99%

“…Indeed, many culturomics projects have to deal with dereplication of isolates to avoid wasting time characterizing the same biological object several times. 33 To test this scenario, two types of mixtures were created: four sets with at least one organism repeated in two distant fractions and three with the same organism repeated in neighboring fractions. Once again, this worst-case scenario did not affect the identification, and the patterns detected were correctly assigned to the initial samples.…”

Section: ■ Discussionmentioning

confidence: 99%

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A Simplified Label-Free Method for Proteotyping Sets of Six Isolates in a Single Liquid Chromatography-High-Resolution Tandem Mass Spectrometry Analysis

Chabas,

Armengaud,

Alpha-Bazin

2024

J. Proteome Res.

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Clinical diagnostics and microbiology require high-throughput identification of microorganisms. Sample multiplexing prior to detection is an attractive means to reduce analysis costs and time-to-result. Recent studies have demonstrated the discriminative power of tandem mass spectrometrybased proteotyping. This technology can rapidly identify the most likely taxonomical position of any microorganism, even uncharacterized organisms. Here, we present a simplified label-free multiplexing method to proteotype isolates by tandem mass spectrometry that can identify six microorganisms in a single 20 min analytical run. The strategy involves the production of peptide fractions with distinct hydrophobicity profiles using spin column fractionation. Assemblages of different fractions can then be analyzed using mass spectrometry. Results are subsequently interpreted based on the hydrophobic characteristics of the peptides detected, which make it possible to link each taxon identified to the initial sample. The methodology was tested on 32 distinct sets of six organisms including several worstscenario assemblages−with differences in sample quantities or the presence of the same organisms in multiple fractions−and proved to be robust. These results pave the way for the deployment of tandem mass spectrometry-based proteotyping in microbiology laboratories.

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Section: Discussionmentioning

confidence: 99%

Section: ■ Discussionmentioning

confidence: 99%

A Simplified Label-Free Method for Proteotyping Sets of Six Isolates in a Single Liquid Chromatography-High-Resolution Tandem Mass Spectrometry Analysis

Chabas,

Armengaud,

Alpha-Bazin

2024

J. Proteome Res.

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“…In the future, the microbial exploration of plant endosphere environments should stay in the spotlight, not only as cultivation-dependent studies but also as studies focused on community construction and plant–microbe co-culture. Cultivation-dependent studies mainly include culturomics and cultivation improvements (Kapinusova et al, 2022 ), which are necessary to largely obtain microorganisms that have specific functions. On the one hand, the collected microorganisms can be used to elucidate their ecological roles and biosynthesize their own secondary metabolites.…”

Section: Discussionmentioning

confidence: 99%

Enriching the endophytic bacterial microbiota of Ginkgo roots

et al. 2023

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Bacterial endophytes of Ginkgo roots take part in the secondary metabolic processes of the fossil tree and contribute to plant growth, nutrient uptake, and systemic resistance. However, the diversity of bacterial endophytes in Ginkgo roots is highly underestimated due to the lack of successful isolates and enrichment collections. The resulting culture collection contains 455 unique bacterial isolates representing 8 classes, 20 orders, 42 families, and 67 genera from five phyla: Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Deinococcus-Thermus, using simply modified media (a mixed medium without any additional carbon sources [MM)] and two other mixed media with separately added starch [GM] and supplemented glucose [MSM]). A series of plant growth-promoting endophytes had multiple representatives within the culture collection. Moreover, we investigated the impact of refilling carbon sources on enrichment outcomes. Approximately 77% of the natural community of root-associated endophytes were predicted to have successfully cultivated the possibility based on a comparison of the 16S rRNA gene sequences between the enrichment collections and the Ginkgo root endophyte community. The rare or recalcitrant taxa in the root endosphere were mainly associated with Actinobacteria, Alphaproteobacteria, Blastocatellia, and Ktedonobacteria. By contrast, more operational taxonomic units (OTUs) (0.6% in the root endosphere) became significantly enriched in MM than in GM and MSM. We further found that the bacterial taxa of the root endosphere had strong metabolisms with the representative of aerobic chemoheterotrophy, while the functions of the enrichment collections were represented by the sulfur metabolism. In addition, the co-occurrence network analysis suggested that the substrate supplement could significantly impact bacterial interactions within the enrichment collections. Our results support the fact that it is better to use the enrichment to assess the cultivable potential and the interspecies interaction as well as to increase the detection/isolation of certain bacterial taxa. Taken together, this study will deepen our knowledge of the indoor endophytic culture and provide important insights into the substrate-driven enrichment.

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“…Aquatic environments offer the advantage of using the water directly from the source as part of the cultivation media. Applying this strategy, Kapinusova et al (2022) isolated over 100 bacterial species, including several novel species of Alphaproteobacteria , Betaproteobacteria , Flavobacteriia, and even a member of a novel genus of Thermoleophilia ( Kapinusova et al, 2022 ). A similar strategy combined with a prolonged incubation time was used for the culturomics of the world-renowed thermal springs of Karlovy Vary ( Smrhova et al, 2022 ) and led to the acquisition of several thermotolerant strains of the Bacillota phylum and isolation of novel microorganisms of Bacilli , Gammaproteobacteria , and Actinomycetia classes.…”

Section: A Helping Hand From the Environment – Physical And Chemical ...mentioning

confidence: 99%

Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons

2023

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In terms of the number and diversity of living units, the prokaryotic empire is the most represented form of life on Earth, and yet it is still to a significant degree shrouded in darkness. This microbial “dark matter” hides a great deal of potential in terms of phylogenetically or metabolically diverse microorganisms, and thus it is important to acquire them in pure culture. However, do we know what microorganisms really need for their growth, and what the obstacles are to the cultivation of previously unidentified taxa? Here we review common and sometimes unexpected requirements of environmental microorganisms, especially soil-harbored bacteria, needed for their replication and cultivation. These requirements include resuscitation stimuli, physical and chemical factors aiding cultivation, growth factors, and co-cultivation in a laboratory and natural microbial neighborhood.

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Culturomics of Bacteria from Radon-Saturated Water of the World’s Oldest Radium Mine

Cited by 7 publications

References 129 publications

A Simplified Label-Free Method for Proteotyping Sets of Six Isolates in a Single Liquid Chromatography-High-Resolution Tandem Mass Spectrometry Analysis

A Simplified Label-Free Method for Proteotyping Sets of Six Isolates in a Single Liquid Chromatography-High-Resolution Tandem Mass Spectrometry Analysis

Enriching the endophytic bacterial microbiota of Ginkgo roots

Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons

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