A comparison of methods for total community DNA preservation and extraction from various thermal environments

Mitchell, Kendra; Takacs-Vesbach, Cristina

doi:10.1007/s10295-008-0393-y

Cited by 83 publications

(62 citation statements)

References 39 publications

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“…Sediment samples were taken using 50 ml falcon tubes, preserved in sucrose lysis buffer and kept at −20°C until further use. DNA used for the metagenomic library was extracted from ∼500 mg of sediment using cetyltrimethyl ammonium bromide (CTAB)/phenol/chloroform method 33 .…”

Section: Methodsmentioning

confidence: 99%

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea

Baker¹,

et al. 2016

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The subsurface biosphere is largely unexplored and contains a broad diversity of uncultured microbes1. Despite being one of the few prokaryotic lineages that is cosmopolitan in both the terrestrial and marine subsurface2–4, the physiological and ecological roles of SAGMEG (South-African Gold Mine Miscellaneous Euryarchaeal Group) Archaea are unknown. Here, we report the metabolic capabilities of this enigmatic group as inferred from genomic reconstructions. Four high-quality (63–90% complete) genomes were obtained from White Oak River estuary and Yellowstone National Park hot spring sediment metagenomes. Phylogenomic analyses place SAGMEG Archaea as a deeply rooting sister clade of the Thermococci, leading us to propose the name Hadesarchaea for this new Archaeal class. With an estimated genome size of around 1.5 Mbp, the genomes of Hadesarchaea are distinctly streamlined, yet metabolically versatile. They share several physiological mechanisms with strict anaerobic Euryarchaeota. Several metabolic characteristics make them successful in the subsurface, including genes involved in CO and H2 oxidation (or H2 production), with potential coupling to nitrite reduction to ammonia (DNRA). This first glimpse into the metabolic capabilities of these cosmopolitan Archaea suggests they are mediating key geochemical processes and are specialized for survival in the subsurface biosphere.

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Section: Methodsmentioning

confidence: 99%

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea

Baker¹,

et al. 2016

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“…Sterile 3-mm tungsten carbide beads (Qiagen) were used to lyse the tissue samples in a TissueLyser II (Qiagen) and create a homogenous mixture. For extraction, we followed the cetyltrimethylammonium bromide (CTAB) buffer method as previously described (22). DNA pellets were then resuspended in 30 l of DNase-and RNase-free molecular-biology-grade water.…”

Section: Methodsmentioning

confidence: 99%

Topographical Mapping of the Rainbow Trout (Oncorhynchus mykiss) Microbiome Reveals a Diverse Bacterial Community with Antifungal Properties in the Skin

Lowrey

Woodhams

Tacchi

et al. 2015

Appl Environ Microbiol

209

239

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The mucosal surfaces of wild and farmed aquatic vertebrates face the threat of many aquatic pathogens, including fungi. These surfaces are colonized by diverse symbiotic bacterial communities that may contribute to fight infection. Whereas the gut microbiome of teleosts has been extensively studied using pyrosequencing, this tool has rarely been employed to study the compositions of the bacterial communities present on other teleost mucosal surfaces. Here we provide a topographical map of the mucosal microbiome of an aquatic vertebrate, the rainbow trout (Oncorhynchus mykiss). Using 16S rRNA pyrosequencing, we revealed novel bacterial diversity at each of the five body sites sampled and showed that body site is a strong predictor of community composition. The skin exhibited the highest diversity, followed by the olfactory organ, gills, and gut. Flectobacillus was highly represented within skin and gill communities. Principal coordinate analysis and plots revealed clustering of external sites apart from internal sites. A highly diverse community was present within the epithelium, as demonstrated by confocal microscopy and pyrosequencing. Using in vitro assays, we demonstrated that two Arthrobacter sp. skin isolates, a Psychrobacter sp. strain, and a combined skin aerobic bacterial sample inhibit the growth of Saprolegnia australis and Mucor hiemalis, two important aquatic fungal pathogens. These results underscore the importance of symbiotic bacterial communities of fish and their potential role for the control of aquatic fungal diseases.T he mucosal surfaces of vertebrate animals are at the interface between the environment and the animal host. Mucosal epithelia form important mechanical and chemical barriers that prevent pathogen invasion but permit colonization by symbiotic microorganisms, the microbiota. The microbiota is crucial for the development, homeostasis, and immune function of an animal's mucosal epithelia (1, 2, 3).The associations between metazoans and commensal microorganisms are among the most ancient and successful associations found in nature (4, 5). The microbial communities of different organisms, such as plants, corals, annelids, gastropods, insects, and many vertebrates, are being characterized. In the particular case of vertebrates, mucosal surfaces have undergone drastic changes over the course of evolution due to the transition of vertebrate animals from water to land. These evolutionary pressures especially affected some mucosal barriers, such as the skin. While the skin of fish is a living cell layer that secretes a mucous layer and has imbricated scales for protection (6), amphibians have a cornified layer of skin that has developed into a more uniform epidermis (6). Finally, in birds and mammals, the presence of feathers, scales, hair, sweat glands, coats, or the leather-like thickening of the dermis represents unique adaptations to terrestrial environments. All these structures and appendages, in turn, provide unique niches within the skin for microbial colonization (6, 7).All verte...

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“…Soils (0.7 g) from each of the 36 samples were extracted with the cetyltrimethylammonium bromide (CTAB) method adapted by Mitchell and Takacs-Vesbach (44). Bar-coded amplicon pyrosequencing of 16S rRNA genes was performed as described previously (17,45,46) using universal V6 bacterial primers 939F (5=-TTG ACG GGG GCC CGC ACA AG-3=) and 1492R (5=-GTT TAC CTT GTT ACG ACT T-3=) on a Roche 454 FLX instrument using Roche titanium reagents and titanium procedures at the Research and Testing Laboratory, Lubbock, TX.…”

Section: Methodsmentioning

confidence: 99%

Soil Microbial Responses to Increased Moisture and Organic Resources along a Salinity Gradient in a Polar Desert

Horn

Okie

Buelow³

et al. 2014

Appl Environ Microbiol

Self Cite

178

102

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dMicrobial communities in extreme environments often have low diversity and specialized physiologies suggesting a limited resistance to change. The McMurdo Dry Valleys (MDV) are a microbially dominated, extreme ecosystem currently undergoing climate change-induced disturbances, including the melting of massive buried ice, cutting through of permafrost by streams, and warming events. These processes are increasing moisture across the landscape, altering conditions for soil communities by mobilizing nutrients and salts and stimulating autotrophic carbon inputs to soils. The goal of this study was to determine the effects of resource addition (water/organic matter) on the composition and function of microbial communities in the MDV along a natural salinity gradient representing an additional gradient of stress in an already extreme environment. Soil respiration and the activity of carbon-acquiring extracellular enzymes increased significantly (P < 0.05) with the addition of resources at the low-and moderate-salinity sites but not the high-salinity site. The bacterial community composition was altered, with an increase in Proteobacteria and Firmicutes with water and organic matter additions at the low-and moderate-salinity sites and a near dominance of Firmicutes at the high-salinity site. Principal coordinate analyses of all samples using a phylogenetically informed distance matrix (UniFrac) demonstrated discrete clustering among sites (analysis of similarity [ANOSIM], P < 0.05 and R > 0.40) and among most treatments within sites. The results from this experimental work suggest that microbial communities in this environment will undergo rapid change in response to the altered resources resulting from climate change impacts occurring in this region.

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A comparison of methods for total community DNA preservation and extraction from various thermal environments

Cited by 83 publications

References 39 publications

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea

Topographical Mapping of the Rainbow Trout (Oncorhynchus mykiss) Microbiome Reveals a Diverse Bacterial Community with Antifungal Properties in the Skin

Soil Microbial Responses to Increased Moisture and Organic Resources along a Salinity Gradient in a Polar Desert

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