How To Look, Where To Look

Bull, A. T.

doi:10.1128/9781555817770.ch7

Cited by 6 publications

(4 citation statements)

References 67 publications

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“…Deserts have often been overlooked in the search for bioactive, natural products, and the focus on the Atacama Desert is very recent in this regard. The success of bioprospecting is dependent upon a number of critical elements, particularly chemical, environmental, and taxonomic space from which we have argued that there is a high probability of isolating novel organisms that present novel chemistry from extreme environments (11,62).…”

Section: Biotechnology Developmentsmentioning

confidence: 99%

The Atacama Desert: Technical Resources and the Growing Importance of Novel Microbial Diversity

Bull

Asenjo

Goodfellow

et al. 2016

Annu. Rev. Microbiol.

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120

104

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The Atacama Desert of northern Chile is the oldest and most arid nonpolar environment on Earth. It is a coastal desert covering approximately 180,000 km(2), and together with the greater Atacama region it comprises a dramatically wide range of ecological niches. Long known and exploited for its mineral resources, the Atacama Desert harbors a rich microbial diversity that has only recently been discovered; the great majority of it has not yet been recovered in culture or even taxonomically identified. This review traces the progress of microbiology research in the Atacama and dispels the popular view that this region is virtually devoid of life. We examine reasons for such research activity and demonstrate that microbial life is the latest recognized and least explored resource in this inspiring biome.

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Section: Biotechnology Developmentsmentioning

confidence: 99%

The Atacama Desert: Technical Resources and the Growing Importance of Novel Microbial Diversity

Bull

Asenjo

Goodfellow

et al. 2016

Annu. Rev. Microbiol.

Self Cite

120

104

View full text Add to dashboard Cite

show abstract

“…Despite the fact that molecular studies describe to a great extent the taxonomic and genetic diversity of the key players in their environments, they have failed to culture living organisms that can be potentially important sources of information for biotechnological, pharmaceutical and even taxonomic purposes. Culturing techniques may satisfy the needs of many microbiologists, as exemplified very well by the statement of Steve Giovannoni that "Nothing beats actually having the organism in culture" [7].…”

Section: Introductionmentioning

confidence: 99%

Diversity of extremely halophilic cultivable prokaryotes in Mediterranean, Atlantic and Pacific solar salterns: Evidence that unexplored sites constitute sources of cultivable novelty

Viver

Cifuentes

Díaz

et al. 2015

Systematic and Applied Microbiology

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“…The presence of multiple 16S rDNA copies and possible intragenomic heterogeneity can be, therefore, a limiting factor for both correct identification and counting of operational taxonomic units (OTUs) in biodiversity studies of both culturable and unculturable bacteria (Coenye and Vandamme, 2003;Pei et al, 2010;Chen et al, 2015). Although culturable microbes represent only 0.1-5% of the estimated total microbial diversity of any given environment (Bull, 2004), the levels of 16S rDNA intragenomic variation in a culturable population may provide a glance of what can occur in the whole community. Knowing such variation is useful in studies on microbial ecology and diversity, to prevent overestimation of this latter parameter (Sun et al, 2013) and to provide correction factors to compensate it.…”

Section: Introductionmentioning

confidence: 99%

Peer Review #1 of "First-tier detection of intragenomic 16S rRNA gene variation in culturable endophytic bacteria from cacao seeds (v0.1)"

2019

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Background. Intragenomic variability in 16S rDNA is a limiting factor for taxonomic and diversity characterization of Bacteria, and studies on its occurrence in natural/environmental populations are scarce. In this work, direct DNA amplicon sequencing coupled with frequent-cutter restriction analysis allowed detection of intragenomic 16S rDNA variation in culturable endophytic bacteria from cacao seeds in a fast and attractive manner. Methods. Total genomic DNA from 65 bacterial strains was extracted and the 16S rDNA hyper variable V5-V9 regions were amplified for enzyme digestion and direct Sanger-type sequencing. The resulting electropherograms were visually inspected and compared to the corresponding AluI-restriction profiles, as well as to complete genome sequences in databases. Restriction analysis were employed to substitute the need of amplicon cloning and re-sequencing. A specifically improved polyacrylamide-gradient electrophoresis allowed to resolve 5-bp differences in restriction fragment sizes. Chi-square analysis on 2 x 2 contingency table tested for the independence between the 'number of AluI bands' and 'type of eletropherogram'. Results. Two types of electropherograms were obtained: unique template, with single peaks per base (clean chromatograms), and heterogeneous template, with various levels of multiple peaks per base (mixed chromatograms). Statistics revealed significant interaction between number of restriction fragments and type of electropherogram for the same amplicons: clean or mixed ones associated to ≤ 5 or ≥ 6 bands, respectively. The mixed-template pattern combined with the AluI-restriction profiles indicated a high proportion of 49% of the culturable endophytes from a tropical environment showing evidence of intragenomic 16S rDNA heterogeneity. Conclusion. The approach presented here was useful for a rapid, first-tier detection of intragenomic variation in culturable isolates, which can be applied in studies of other natural populations; a preliminary view of intragenomic heterogeneity levels can complement culture-dependent and-independent methods. Consequences of these findings in taxonomic and diversity studies in complex bacterial communities are discussed.

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How To Look, Where To Look

Cited by 6 publications

References 67 publications

The Atacama Desert: Technical Resources and the Growing Importance of Novel Microbial Diversity

The Atacama Desert: Technical Resources and the Growing Importance of Novel Microbial Diversity

Diversity of extremely halophilic cultivable prokaryotes in Mediterranean, Atlantic and Pacific solar salterns: Evidence that unexplored sites constitute sources of cultivable novelty

Peer Review #1 of "First-tier detection of intragenomic 16S rRNA gene variation in culturable endophytic bacteria from cacao seeds (v0.1)"

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