Exploring microbial diversity in volcanic environments: A review of methods in DNA extraction

Herrera, Aude; Cockell, Charles S.

doi:10.1016/j.mimet.2007.04.005

Cited by 85 publications

(69 citation statements)

References 60 publications

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“…To avoid contamination, the rocks were collected aseptically and stored in sterile plastic bags (Whirlpak; Fisher Scientific) at Ϫ80°C. For DNA extraction, three of the collected rocks were crushed, as previously described (24). The powdered rock was ground in a sterile pestle and mortar containing liquid nitrogen.…”

Section: Methodsmentioning

confidence: 99%

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Isolation of Novel Extreme-Tolerant Cyanobacteria from a Rock-Dwelling Microbial Community by Using Exposure to Low Earth Orbit

Olsson-Francis

Torre

Cockell

2010

Appl Environ Microbiol

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Many cyanobacteria are known to tolerate environmental extremes. Motivated by an interest in selecting cyanobacteria for applications in space, we launched rocks from a limestone cliff in Beer, Devon, United Kingdom, containing an epilithic and endolithic rock-dwelling community of cyanobacteria into low Earth orbit (LEO) at a height of approximately 300 kilometers. The community was exposed for 10 days to isolate cyanobacteria that can survive exposure to the extreme radiation and desiccating conditions associated with space. Culture-independent (16S rRNA) and culture-dependent methods showed that the cyanobacterial community was composed of Pleurocapsales, Oscillatoriales, and Chroococcales. A single cyanobacterium, a previously uncharacterized extremophile, was isolated after exposure to LEO. We were able to isolate the cyanobacterium from the limestone cliff after exposing the rock-dwelling community to desiccation and vacuum (0.7 ؋ 10 ؊3 kPa) in the laboratory. The ability of the organism to survive the conditions in space may be linked to the formation of dense colonies. These experiments show how extreme environmental conditions, including space, can be used to select for novel microorganisms. Furthermore, it improves our knowledge of environmental tolerances of extremophilic rock-dwelling cyanobacteria.

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Section: Methodsmentioning

confidence: 99%

“…The purified product was ligated at 4°C with the pCR4-TOPO vector. Chemical transformation was conducted with OneShot TOP10 chemically competent Escherichia coli from the TOPO-TA cloning kit (Invitrogen, Paisley, United Kingdom), as previously described (24).…”

Section: Methodsmentioning

confidence: 99%

Isolation of Novel Extreme-Tolerant Cyanobacteria from a Rock-Dwelling Microbial Community by Using Exposure to Low Earth Orbit

Olsson-Francis

Torre

Cockell

2010

Appl Environ Microbiol

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“…For DNA extraction, three of the collected rocks were crushed, as previously described (Herrera and Cockell, 2007). The powdered rock was grounded in a sterile pestle and mortar containing liquid nitrogen.…”

Section: Molecular Analysismentioning

confidence: 99%

Exposure of phototrophs to 548 days in low Earth orbit: microbial selection pressures in outer space and on early earth

Cockell

Rettberg²,

Rabbow³

et al. 2011

The ISME Journal

115

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An epilithic microbial community was launched into low Earth orbit, and exposed to conditions in outer space for 548 days on the European Space Agency EXPOSE-E facility outside the International Space Station. The natural phototroph biofilm was augmented with akinetes of Anabaena cylindrica and vegetative cells of Nostoc commune and Chroococcidiopsis. In space-exposed dark controls, two algae (Chlorella and Rosenvingiella spp.), a cyanobacterium (Gloeocapsa sp.) and two bacteria associated with the natural community survived. Of the augmented organisms, cells of A. cylindrica and Chroococcidiopsis survived, but no cells of N. commune. Only cells of Chroococcidiopsis were cultured from samples exposed to the unattenuated extraterrestrial ultraviolet (UV) spectrum (4110 nm or 200 nm). Raman spectroscopy and bright-field microscopy showed that under these conditions the surface cells were bleached and their carotenoids were destroyed, although cell morphology was preserved. These experiments demonstrate that outer space can act as a selection pressure on the composition of microbial communities. The results obtained from samples exposed to 4200 nm UV (simulating the putative worst-case UV exposure on the early Earth) demonstrate the potential for epilithic colonization of land masses during that time, but that UV radiation on anoxic planets can act as a strong selection pressure on surface-dwelling organisms. Finally, these experiments have yielded new phototrophic organisms of potential use in biomass and oxygen production in space exploration.

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“…For example, the extremely halophilic bacterium Limimonas halophila was isolated from the mud of hypersaline Lake Aran-Bidgol in Iran (Amoozegar et al 2013), while Salinibacter iranicus and Salinibacter luteus were isolated from Aran-Bidgol salt lake in Iran (Makhdoumi-Kakhki et al 2012). Moreover, volcanic environments (mud, groundwater, aquifers, soil and lakes in craters) have attracted a great deal of attention from many research groups worldwide owing to their microbial diversity and distribution of indigenous species (Herrera & Cockell 2007). This is because the geochemistry of active volcanoes changes frequently, especially in lakes of craters (Mapelli et al 2015) and their related streams and springs.…”

Section: Introductionmentioning

confidence: 99%

“…The typical conditions in these surrounding areas are extreme as they have high temperatures, high concentrations of dissolved metals/minerals and developing patterns of biominerals (Glamoclija et al 2004), low pH (Löhr et al 2006). Therefore, screening for new novel species from these volcanic sites has resulted in development of new methods for DNA extraction and isolation (Herrera & Cockell 2007). For example, Cupriavidus pinatubonensis and Cupriavidus laharis are novel isolates from volcanic mudflow deposits from Mt.…”

Section: Introductionmentioning

confidence: 99%

Niche for high abundant extremophilic microbial communities in an ancient crater

Albokari

Al-Najjar

Mashhour

et al. 2017

International Journal of Astrobiology

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Al Wahbah Crater, located in a remote area in western Saudi Arabia as part of The Harrat extinct volcanic chain, is 2 km wide with a depth of 250 m. It is registered by the General Commission for Tourism and National Heritage as an ancient and archaeological site. The crater is subjected to extreme environmental conditions as its bottom is rarely subjected to rainfall and mudflows. Because of high temperature, high evaporation rates and extremely limited rainfall, the crater leaves behind dried thick white sodium phosphate crystals. Here, we studied the chemical composition and the microbial community composition using 16S rRNA pyrosequencing in different vertical layers (2, 20, 40, 60, 80 and 100 cm) of the crater sediment. Total sodium concentrations were 28 000-46 700 ppm and calcium levels were 31 400-56 500 ppm. In addition, samples were very sulphuric, with sulphate and sulphite levels exceeding 2157 ppm and 5.54 ppm, respectively. Ferric ions concentrations were <0.2 ppm, while nitrate, ammonium and nitrite levels were <2 ppm, 1.5 ppm and 0.05 ppm, respectively. Archaea dominated the surface and the bottom, while bacteria were most common at 20-60 cm. Extremely halophilic archaea and bacteria including Halorhabdus spp. Halorubrum spp., Salinibacter iranicus and Halorhodospira halophila were identified in all samples. Moreover, the relative abundance of Halanaerobiaceae accounted for 22% of the species in the top of the crater. S. iranicus and species belonging to Halorhabdus and Halorubrum that were identified between 60 and 100 cm could be considered as extreme organisms.

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Exploring microbial diversity in volcanic environments: A review of methods in DNA extraction

Cited by 85 publications

References 60 publications

Isolation of Novel Extreme-Tolerant Cyanobacteria from a Rock-Dwelling Microbial Community by Using Exposure to Low Earth Orbit

Isolation of Novel Extreme-Tolerant Cyanobacteria from a Rock-Dwelling Microbial Community by Using Exposure to Low Earth Orbit

Exposure of phototrophs to 548 days in low Earth orbit: microbial selection pressures in outer space and on early earth

Niche for high abundant extremophilic microbial communities in an ancient crater

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