Searching for bacteria in sticky situations: Methods for investigating bacterial survival at solid-air interfaces involving Wyoming MX-80 bentonite

Pashang, Rosha; Laursen, Andrew E.

doi:10.1016/j.clay.2020.105487

“…Higher 16S rRNA gene copy numbers compared to culturable abundance estimations may be due to multiple 16S rRNA gene copies per genome or detection of “relic” DNA within samples. Most culturable aerobic heterotroph abundances ranged from 10 2 to 10 4 colony forming units per gram dry weight (CFU/gdw), which is within the range previously reported for bentonite clays (10 2 –10 5 CFU/g; 15 , 17 , 24 , 26 ). Eleven samples contained average aerobic heterotroph abundances below the limit of plate count quantification (i.e., 2500 CFU/gdw, based on 25 colonies per plate minimum).…”

Section: Resultssupporting

confidence: 82%

“…The 10 –1 dilution was prepared in a 50-mL conical tube by slowly adding 2 g of clay to 18 mL of PBS while vortexing continuously, followed immediately by continuous gentle agitation for 30 min at room temperature. The agitation time was necessary to allow the clay to suspend and swell evenly, which has been shown to result in greater homogeneity of the clay-PBS solution and a higher efficiency of cell removal from clay interfaces 26 . Remaining dilutions were prepared by transferring 1 mL of the previous dilution into 9 mL of PBS.…”

Section: Methodsmentioning

confidence: 99%

Fifteen shades of clay: distinct microbial community profiles obtained from bentonite samples by cultivation and direct nucleic acid extraction

Vachon

¹

,

Engel

²

,

Beaver

³

et al. 2021

Sci Rep

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Characterizing the microbiology of swelling bentonite clays can help predict the long-term behaviour of deep geological repositories (DGRs), which are proposed as a solution for the management of used nuclear fuel worldwide. Such swelling clays represent an important component of several proposed engineered barrier system designs and, although cultivation-based assessments of bentonite clay are routinely conducted, direct nucleic acid detection from these materials has been difficult due to technical challenges. In this study, we generated direct comparisons of microbial abundance and diversity captured by cultivation and direct nucleic acid analyses using 15 reference bentonite clay samples. Regardless of clay starting material, the corresponding profiles from cultivation-based approaches were consistently associated with phylogenetically similar sulfate-reducing bacteria, denitrifiers, aerobic heterotrophs, and fermenters, demonstrating that any DGR-associated growth may be consistent, regardless of the specific bentonite clay starting material selected for its construction. Furthermore, dominant nucleic acid sequences in the as-received clay microbial profiles did not correspond with the bacteria that were enriched or isolated in culture. Few core taxa were shared among cultivation and direct nucleic acid analysis profiles, yet those in common were primarily affiliated with Streptomyces, Micrococcaceae, Bacillus, and Desulfosporosinus genera. These putative desiccation-resistant bacteria associated with diverse bentonite clay samples can serve as targets for experiments that evaluate microbial viability and growth within DGR-relevant conditions. Our data will be important for global nuclear waste management organizations, demonstrating that identifying appropriate design conditions with suitable clay swelling properties will prevent growth of the same subset of clay-associated bacteria, regardless of clay origin or processing conditions.

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From individual response to population ecology: Environmental factors restricting survival of vegetative bacteria at solid-air interfaces

Pashang

¹

,

Gilbride

²

2021

Science of The Total Environment

2

0

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Fifteen shades of clay: distinct microbial community profiles obtained from bentonite samples by cultivation and direct nucleic acid extraction

Vachon

¹

,

Engel

²

,

Beaver

³

et al. 2021

Preprint

0

View full text Add to dashboard Cite

Characterizing the microbiology of swelling bentonite clays can help predict the long-term behaviour of deep geological repositories (DGRs), which are proposed as a solution for the management of used nuclear fuel worldwide. Such swelling clays represent an important component of several proposed engineered barrier system designs and, although cultivation-based assessments of bentonite clay are routinely conducted, direct nucleic acid detection from these materials has been difficult due to technical challenges. In this study, we generated direct comparisons of microbial abundance and diversity captured by cultivation and direct nucleic acid analyses using 15 reference bentonite clay samples. Regardless of clay starting material, the corresponding profiles from cultivation-based approaches were consistently associated with phylogenetically similar sulfate-reducing bacteria, denitrifiers, aerobic heterotrophs, and fermenters, demonstrating that any DGR-associated growth may be consistent, regardless of the specific bentonite clay starting material selected for its construction. Furthermore, dominant nucleic acid sequences in the as-received clay microbial profiles did not correspond with the bacteria that were enriched or isolated in culture. Few core taxa were shared among cultivation and direct nucleic acid analysis profiles, yet those in common were primarily affiliated with Streptomyces, Micrococcaceae, Bacillus, and Desulfosporosinus genera. These putative desiccation-resistant bacteria associated with diverse bentonite clay samples can serve as targets for experiments that evaluate microbial viability and growth within DGR-relevant conditions. Our data will be important for global nuclear waste management organizations, demonstrating that identifying appropriate design conditions with suitable clay swelling properties will prevent growth of the same subset of clay-associated bacteria, regardless of clay origin or processing conditions.

show abstract

Searching for bacteria in sticky situations: Methods for investigating bacterial survival at solid-air interfaces involving Wyoming MX-80 bentonite

Cited by 3 publications

References 52 publications

Fifteen shades of clay: distinct microbial community profiles obtained from bentonite samples by cultivation and direct nucleic acid extraction

Fifteen shades of clay: distinct microbial community profiles obtained from bentonite samples by cultivation and direct nucleic acid extraction

From individual response to population ecology: Environmental factors restricting survival of vegetative bacteria at solid-air interfaces

Fifteen shades of clay: distinct microbial community profiles obtained from bentonite samples by cultivation and direct nucleic acid extraction

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