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Palomo A, Azevedo D, Touceda-Suárez M, Domingo-Félez C, Mutlu AG, Dechesne A, Wang Y, Zhang T, Smets BF. Efficient management of the nitritation-anammox microbiome through intermittent aeration: absence of the NOB guild and expansion and diversity of the NOx reducing guild suggests a highly reticulated nitrogen cycle. Environ Microbiome 2022; 17:39. [PMID: 35869541 PMCID: PMC9306079 DOI: 10.1186/s40793-022-00432-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
Obtaining efficient autotrophic ammonia removal (aka partial nitritation-anammox, or PNA) requires a balanced microbiome with abundant aerobic and anaerobic ammonia oxidizing bacteria and scarce nitrite oxidizing bacteria. Here, we analyzed the microbiome of an efficient PNA process that was obtained by sequential feeding and periodic aeration. The genomes of the dominant community members were inferred from metagenomes obtained over a 6 month period. Three Brocadia spp. genomes and three Nitrosomonas spp. genomes dominated the autotrophic community; no NOB genomes were retrieved. Two of the Brocadia spp. genomes lacked the genomic potential for nitrite reduction. A diverse set of heterotrophic genomes was retrieved, each with genomic potential for only a fraction of the denitrification pathway. A mutual dependency in amino acid and vitamin synthesis was noted between autotrophic and heterotrophic community members. Our analysis suggests a highly-reticulated nitrogen cycle in the examined PNA microbiome with nitric oxide exchange between the heterotrophs and the anammox guild.
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Affiliation(s)
- Alejandro Palomo
- Microbial Ecology and Technology Lab, Department of Environmental Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Daniela Azevedo
- Microbial Ecology and Technology Lab, Department of Environmental Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - María Touceda-Suárez
- Microbial Ecology and Technology Lab, Department of Environmental Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
- Department of Environmental Science, University of Arizona, Tucson, AZ, USA
| | - Carlos Domingo-Félez
- Microbial Ecology and Technology Lab, Department of Environmental Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - A Gizem Mutlu
- Microbial Ecology and Technology Lab, Department of Environmental Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
- Hydrotech - Veolia Water Technologies, Vellinge, Sweden
| | - Arnaud Dechesne
- Microbial Ecology and Technology Lab, Department of Environmental Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Barth F Smets
- Microbial Ecology and Technology Lab, Department of Environmental Engineering, Technical University of Denmark, Kgs Lyngby, Denmark.
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Riva A, BØrgesen M, Guldmann-Christensen M, Hauge Kyneb M, Voogd K, Andersen C, Epistolio S, Merlo E, Yding Wolff T, Hamilton-Dutoit S, Lorenzen J, Christensen UB, Frattini M. SensiScreen®KRAS exon 2-sensitive simplex and multiplex real-time PCR-based assays for detection of KRAS exon 2 mutations. PLoS One 2017. [PMID: 28636636 PMCID: PMC5479524 DOI: 10.1371/journal.pone.0178027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Activating mutations in codon 12 and codon 13 of the KRAS (Kirsten rat sarcoma viral oncogene homolog) gene are implicated in the development of several human cancer types and influence their clinical evaluation, treatment and prognosis. Numerous different methods for KRAS genotyping are currently available displaying a wide range of sensitivities, time to answer and requirements for laboratory equipment and user skills. Here we present SensiScreen® KRAS exon 2 simplex and multiplex CE IVD assays, that use a novel real-time PCR-based method for KRAS mutation detection based on PentaBase's proprietary DNA analogue technology and designed to work on standard real-time PCR instruments. By means of the included BaseBlocker™ technology, we show that SensiScreen® specifically amplifies the mutated alleles of interest with no or highly subdued amplification of the wild type allele. Furthermore, serial dilutions of mutant DNA in a wild type background demonstrate that all SensiScreen® assays display a limit of detection that falls within the range of 0.25-1%. Finally, in three different colorectal cancer patient populations, SensiScreen® assays confirmed the KRAS genotype previously determined by commonly used methods for KRAS mutation testing, and notably, in two of the populations, SensiScreen® identified additional mutant positive cases not detected by common methods.
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Affiliation(s)
- Alice Riva
- Laboratory of Molecular Pathology, Institute of Pathology, Locarno, Switzerland
| | | | | | | | - Kirsten Voogd
- Laboratory of Research and Development, Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Samantha Epistolio
- Laboratory of Molecular Pathology, Institute of Pathology, Locarno, Switzerland
| | - Elisabetta Merlo
- Laboratory of Molecular Pathology, Institute of Pathology, Locarno, Switzerland
| | - Tine Yding Wolff
- Life Science Division, Danish Technological Institute, Aarhus, Denmark
| | - Stephen Hamilton-Dutoit
- Laboratory of Research and Development, Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Jan Lorenzen
- Life Science Division, Danish Technological Institute, Aarhus, Denmark
| | | | - Milo Frattini
- Laboratory of Molecular Pathology, Institute of Pathology, Locarno, Switzerland
- * E-mail: (UBC); (MF)
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