Comparison of innovative molecular approaches and standard spore assays for assessment of surface cleanliness - PubMed (original) (raw)

Comparative Study

. 2011 Aug;77(15):5438-44.

doi: 10.1128/AEM.00192-11. Epub 2011 Jun 7.

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Comparative Study

Comparison of innovative molecular approaches and standard spore assays for assessment of surface cleanliness

Moogega Cooper et al. Appl Environ Microbiol. 2011 Aug.

Abstract

A bacterial spore assay and a molecular DNA microarray method were compared for their ability to assess relative cleanliness in the context of bacterial abundance and diversity on spacecraft surfaces. Colony counts derived from the NASA standard spore assay were extremely low for spacecraft surfaces. However, the PhyloChip generation 3 (G3) DNA microarray resolved the genetic signatures of a highly diverse suite of microorganisms in the very same sample set. Samples completely devoid of cultivable spores were shown to harbor the DNA of more than 100 distinct microbial phylotypes. Furthermore, samples with higher numbers of cultivable spores did not necessarily give rise to a greater microbial diversity upon analysis with the DNA microarray. The findings of this study clearly demonstrated that there is not a statistically significant correlation between the cultivable spore counts obtained from a sample and the degree of bacterial diversity present. Based on these results, it can be stated that validated state-of-the-art molecular techniques, such as DNA microarrays, can be utilized in parallel with classical culture-based methods to further describe the cleanliness of spacecraft surfaces.

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Figures

Fig. 1.

Fig. 1.

PhyloChip analysis of hybridization intensity differences between the three spore abundance categories. (a) Hybridization intensity difference of category B (1 to 50 spores) compared to category A (0 spores). (b) Hybridization intensity difference of category C (>50 spores) compared to category B. Bars above the zero line represent bacteria that increased in abundance relative to category A and category B bacteria for panels a and b, respectively; bars below the zero line represent those bacterial DNAs that declined in abundance.

Fig. 2.

Fig. 2.

NMDS analysis based on log2 transformation·1 × 103 hybridization intensity of OTUs reveals that the spore categorical groupings are from similar community structures, as they greatly overlap. x axis, dimension 1; y axis, dimension 2.

Fig. 3.

Fig. 3.

(a) Comparison of subfamily richness and spore counts grouped by the spore abundance categories and based on the NASA standard spore assay. The results show that there is no strong correlation between sample category and subfamily count. (b) Calculated cell density based on 16S rRNA gene copies compared to spore counts and total hybridization intensity. The average number of 16S rRNA gene copies is 3.6 per cell (17, 22, 32). Gene copies correlate similarly to hybridization intensities but show no correlation to spore counts.

Fig. 4.

Fig. 4.

Overall microbial diversity grouped by taxa. Numbers of subfamilies and OTUs detected per taxon are given in the parentheses. Percentages lower than 2% are not displayed.

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