DNA extraction from low-biomass carbonate rock: An improved method with reduced contamination and the low-biomass contaminant database

Barton, Hazel A.; Taylor, Nicholas M.; Lubbers, Brad; Pemberton, Adin

doi:10.1016/j.mimet.2005.10.005

Cited by 129 publications

(124 citation statements)

References 20 publications

Supporting

Mentioning

120

Contrasting

Order By: Relevance

“…This suggests that the urine deposition at the Wee site led to a dramatic increase in population size. This increase in numbers also matches the detection limits of our assay (Barton et al, 2006;Lavoie, 1995).…”

Section: Discussionsupporting

confidence: 85%

“…While DNA was readily obtained from the Wee samples, three independent attempts were unable to isolate DNA from the CTL sample. This suggests that the total number of microorganisms in the CTL sample was below the detection limit of this assay (,10 4 cells g 21 ; Barton et al, 2006). A clone library of 136 bacterial phylotypes was generated from the Wee sample DNA via PCR amplification; however, no amplifiable PCR products were obtained using archaeal-specific primers after numerous attempts (data not shown).…”

Section: Resultsmentioning

confidence: 96%

“…Negative control isolations were carried out in parallel to measure any contamination of the final samples. DNA was extracted from either 0.5 mL of liquid culture or 0.5 g of sediment using our previously described protocol (Barton et al, 2006). Community 16S ribosomal RNA gene sequence libraries for Bacteria were prepared from extracted DNA by amplification using the universal forward primer 8F (59 -AGA GTT TGA TCC Figure 2.…”

Section: Sample Collection and Molecular Techniquesmentioning

confidence: 99%

See 2 more Smart Citations

Human urine in Lechuguilla Cave: the microbiological impact and potential for bioremediation

Johnston¹,

Muench²,

Banks³

et al. 2012

JCKS

View full text Add to dashboard Cite

During extended exploration trips in caves, it is sometimes not possible to remove all excreted urine due to its volume and weight. Excess urine can be particularly problematic in dry caves where, without dilution, urine introduces a significant source of nitrogen into these otherwise nitrogen-limited environments. It was the aim of this study to determine the impact that human urine could have on cave microbiota over an extended period of time. To do this, we examined the microbial community structure of a heavily impacted site in Lechuguilla Cave, USA. Using a molecular phylogenetic approach we generated a 136-member 16S rRNA clone library that demonstrated representatives of the Alpha-Beta-and Gammaproteobacteria, the Bacteroidetes, Firmicutes, Actinobacteria and Deinococcus-Thermus group at this site. The structure of the microbial community at the impacted site suggests that it is colonized by endemic cave species rather than human commensal organisms, while metabolic inference suggests that these organisms are taking advantage of both the nitrogenous and organic compounds in urine for growth. The intrinsic nature of such metabolic activity in the cave environment was confirmed by examining non-impacted sites using cultivation, which demonstrated that endemic species express both the capacity to degrade urine and to reduce urea to nitrogen gas. Our results differ from those of previous studies by implying a more resilient nature of the microbial ecosystem in caves to invasion by exogenous (commensal) species, while suggesting that endemic microbial species may be able to mitigate the impact of excess nitrogen in the cave through bioremediation.

show abstract

Section: Discussionsupporting

confidence: 85%

Section: Resultsmentioning

confidence: 96%

Section: Sample Collection and Molecular Techniquesmentioning

confidence: 99%

See 1 more Smart Citation

Human urine in Lechuguilla Cave: the microbiological impact and potential for bioremediation

Johnston¹,

Muench²,

Banks³

et al. 2012

JCKS

View full text Add to dashboard Cite

show abstract

“…These data were confirmed by quantitative PCR with primers specific for SFB genes (Fig 3C). The presence of the Methylobacterium genus has been associated with contamination in samples with low biomass (Barton et al, 2006;Salter et al, 2014 Figure 3. Development of antinuclear antibodies in lymphotoxin-deficient mice is influenced by gut microbiota.…”

Section: Resultsmentioning

confidence: 99%

Commensal microbiota influence systemic autoimmune responses

et al. 2015

View full text Add to dashboard Cite

Antinuclear antibodies are a hallmark feature of generalized autoimmune diseases, including systemic lupus erythematosus and systemic sclerosis. However, the processes underlying the loss of tolerance against nuclear self-constituents remain largely unresolved. Using mice deficient in lymphotoxin and Hox11, we report that approximately 25% of mice lacking secondary lymphoid organs spontaneously develop specific antinuclear antibodies. Interestingly, we find this phenotype is not caused by a defect in central tolerance. Rather, cell-specific deletion and in vivo lymphotoxin blockade link these systemic autoimmune responses to the formation of gut-associated lymphoid tissue in the neonatal period of life. We further demonstrate antinuclear antibody production is influenced by the presence of commensal gut flora, in particular increased colonization with segmented filamentous bacteria, and IL-17 receptor signaling. Together, these data indicate that neonatal colonization of gut microbiota influences generalized autoimmunity in adult life.

show abstract

“…To overcome such limitations, investigators can employ a number of different techniques to relate identified microbial phylotypes to environmental metabolic activities, including the use of isotopic probing and quantitative mRNA and metagenomic analyses (43). Such techniques are technically challenging and often difficult in the context of low-biomass environments (12). In this paper we evaluated the utility of attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy to examine microbial metabolic products on carbonate rock surfaces in low-biomass environments.…”

mentioning

confidence: 99%

Use of Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy To Identify Microbial Metabolic Products on Carbonate Mineral Surfaces

Bullen¹,

Oehrle²,

Bennett

et al. 2008

Appl Environ Microbiol

View full text Add to dashboard Cite

This paper demonstrates the use of attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy to detect microbial metabolic products on carbonate mineral surfaces. By creating an ATR-FTIR spectral database for specific organic acids using ATR-FTIR spectroscopy we were able to distinguish metabolic acids on calcite surfaces following Escherichia coli growth. The production of these acids by E. coli was verified using high-performance liquid chromatography with refractive index detection. The development of this technique has allowed us to identify microbial metabolic products on carbonate surfaces in nutrientlimited cave environments.Molecular phylogenetic analysis using the 16S rRNA gene sequence has revolutionized microbiology, allowing investigators to create comparative and evolutionary phylogenies for microbial species (49, 50). Phylogenetic placement also allows metabolic inference for the activity of previously uncultivated species within the environment, dramatically changing our understanding of microbial ecology and the role of microbial species within the biosphere (3, 36, 41). While metabolic inference is a valuable tool for estimating metabolic activity, specific metabolic responses to environmental conditions are harder to estimate, even for closely related species (1,24). To overcome such limitations, investigators can employ a number of different techniques to relate identified microbial phylotypes to environmental metabolic activities, including the use of isotopic probing and quantitative mRNA and metagenomic analyses (43).

show abstract

DNA extraction from low-biomass carbonate rock: An improved method with reduced contamination and the low-biomass contaminant database

Cited by 129 publications

References 20 publications

Human urine in Lechuguilla Cave: the microbiological impact and potential for bioremediation

Human urine in Lechuguilla Cave: the microbiological impact and potential for bioremediation

Commensal microbiota influence systemic autoimmune responses

Use of Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy To Identify Microbial Metabolic Products on Carbonate Mineral Surfaces

Contact Info

Product

Resources

About