In-depth Characterization via Complementing Culture-Independent Approaches of the Microbial Community in an Acidic Hot Spring of the Colombian Andes

Bohorquez, Laura C.; Delgado-Serrano, Luisa; López, Gina; Osorio-Forero, César; Klepac‐Ceraj, Vanja; Kolter, Roberto; Junca, Howard; Baena, Sandra; Zambrano, María Mercedes

doi:10.1007/s00248-011-9943-3

Cited by 106 publications

(95 citation statements)

References 67 publications

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“…Prokaryotic biodiversity was analyzed using pair-end highthroughput sequencing (MiSeq Illumina platform, San Diego, CA, USA) of the regions V5-V6 of the 16S rRNA gene, using the primers 807F and 1050R as previously described (Bohorquez et al, 2012). Libraries for barcoding sequencing were constructed as previously described (Camarinha-Silva et al, 2014).…”

Section: Physiological Characterizationmentioning

confidence: 99%

A robust nitrifying community in a bioreactor at 50 °C opens up the path for thermophilic nitrogen removal

et al. 2016

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The increasing production of nitrogen-containing fertilizers is crucial to meet the global food demand, yet high losses of reactive nitrogen associated with the food production/consumption chain progressively deteriorate the natural environment. Currently, mesophilic nitrogen-removing microbes eliminate nitrogen from wastewaters. Although thermophilic nitrifiers have been separately enriched from natural environments, no bioreactors are described that couple these processes for the treatment of nitrogen in hot wastewaters. Samples from composting facilities were used as inoculum for the batch-wise enrichment of thermophilic nitrifiers (350 days). Subsequently, the enrichments were transferred to a bioreactor to obtain a stable, high-rate nitrifying process (560 days). The community contained up to 17% ammonia-oxidizing archaea (AOAs) closely related to 'Candidatus Nitrososphaera gargensis', and 25% nitrite-oxidizing bacteria (NOBs) related to Nitrospira calida. Incorporation of 13 C-derived bicarbonate into the respective characteristic membrane lipids during nitrification supported their activity as autotrophs. Specific activities up to 198 ± 10 and 894 ± 81 mg N g − 1 VSS per day for AOAs and NOBs were measured, where NOBs were 33% more sensitive to free ammonia. The NOBs were extremely sensitive to free nitrous acid, whereas the AOAs could only be inhibited by high nitrite concentrations, independent of the free nitrous acid concentration. The observed difference in product/substrate inhibition could facilitate the development of NOB inhibition strategies to achieve more cost-effective processes such as deammonification. This study describes the enrichment of autotrophic thermophilic nitrifiers from a nutrient-rich environment and the successful operation of a thermophilic nitrifying bioreactor for the first time, facilitating opportunities for thermophilic nitrogen removal biotechnology.

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Section: Physiological Characterizationmentioning

confidence: 99%

A robust nitrifying community in a bioreactor at 50 °C opens up the path for thermophilic nitrogen removal

et al. 2016

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“…Hypervariable region V5-V6 of the 16S rRNA gene was amplified by using universal primers based on 16S807f and 16S1050r [36]. Resulting PCR products were amplified using sequencing primers for V5-V6 region, the forward primer contains a 6-nt barcode [37] and a 2-nt CA linker [38].…”

Section: Illumina Sequencingmentioning

confidence: 99%

Bacterial Diversity in Bentonites, Engineered Barrier for Deep Geological Disposal of Radioactive Wastes

López-Fernández

Cherkouk²,

Vílchez-Vargas

et al. 2015

Microb Ecol

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The long-term disposal of radioactive wastes in a deep geological repository is the accepted international solution for the treatment and management of these special residues. The microbial community of the selected host rocks and engineered barriers for the deep geological repository may affect the performance and the safety of the radioactive waste disposal. In this work the bacterial population of bentonite formations of Almeria (Spain), selected as reference material for bentonite engineered barriers in the disposal of radioactive wastes, was studied. 16S rRNA gene-based approaches were used to study the bacterial community of the bentonite samples by traditional clone libraries and Illumina-sequencing. By both techniques the bacterial diversity analysis revealed similar results, with phylotypes belonging to 14 different bacterial phyla:

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“…The hypervariable regions of the 16S rRNA gene were amplified using primers 27F and 338R for the V1-V2 region (9) and primers 807F and 1050R (16) for the V5-V6 region. Primers were barcoded and provided with adapters for Illumina sequencing as described previously (9).…”

Section: Methodsmentioning

confidence: 99%

High-Resolution Taxonomic Profiling of the Subgingival Microbiome for Biomarker Discovery and Periodontitis Diagnosis

Szafrański

Wos‐Oxley

Vílchez-Vargas

et al. 2015

Appl Environ Microbiol

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fThe oral microbiome plays a key role for caries, periodontitis, and systemic diseases. A method for rapid, high-resolution, robust taxonomic profiling of subgingival bacterial communities for early detection of periodontitis biomarkers would therefore be a useful tool for individualized medicine. Here, we used Illumina sequencing of the V1-V2 and V5-V6 hypervariable regions of the 16S rRNA gene. A sample stratification pipeline was developed in a pilot study of 19 individuals, 9 of whom had been diagnosed with chronic periodontitis. Five hundred twenty-three operational taxonomic units (OTUs) were obtained from the V1-V2 region and 432 from the V5-V6 region. Key periodontal pathogens like Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia could be identified at the species level with both primer sets. Principal coordinate analysis identified two outliers that were consistently independent of the hypervariable region and method of DNA extraction used. The linear discriminant analysis (LDA) effect size algorithm (LEfSe) identified 80 OTU-level biomarkers of periodontitis and 17 of health. Health-and periodontitis-related clusters of OTUs were identified using a connectivity analysis, and the results confirmed previous studies with several thousands of samples. A machine learning algorithm was developed which was trained on all but one sample and then predicted the diagnosis of the left-out sample (jackknife method). Using a combination of the 10 best biomarkers, 15 of 17 samples were correctly diagnosed. Training the algorithm on time-resolved community profiles might provide a highly sensitive tool to detect the onset of periodontitis.

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In-depth Characterization via Complementing Culture-Independent Approaches of the Microbial Community in an Acidic Hot Spring of the Colombian Andes

Cited by 106 publications

References 67 publications

A robust nitrifying community in a bioreactor at 50 °C opens up the path for thermophilic nitrogen removal

A robust nitrifying community in a bioreactor at 50 °C opens up the path for thermophilic nitrogen removal

Bacterial Diversity in Bentonites, Engineered Barrier for Deep Geological Disposal of Radioactive Wastes

High-Resolution Taxonomic Profiling of the Subgingival Microbiome for Biomarker Discovery and Periodontitis Diagnosis

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