Next Article in Journal
Escherichia coli Isolated from Cases of Colibacillosis in Russian Poultry Farms (Perm Krai): Sensitivity to Antibiotics and Bacteriocins
Next Article in Special Issue
Microbial Consortiums of Hydrogenotrophic Methanogenic Mixed Cultures in Lab-Scale Ex-Situ Biogas Upgrading Systems under Different Conditions of Temperature, pH and CO
Previous Article in Journal
Phenotypic and Genotypic Characterization of Veterinary Vibrio cincinnatiensis Isolates
Previous Article in Special Issue
A Modular Metagenomics Pipeline Allowing for the Inclusion of Prior Knowledge Using the Example of Anaerobic Digestion
Open AccessArticle

A Rapid, Sensitive, Low-Cost Assay for Detecting Hydrogenotrophic Methanogens in Anaerobic Digesters Using Loop-Mediated Isothermal Amplification

1
Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
2
Biorenewables Development Centre Ltd., 1 Hassacarr Close, Chessingham Park, Dunnington, York YO19 5SN, UK
3
Water and Environmental Engineering Group, Faculty of Engineering and Physical Sciences, University of Southampton, University Road, Southampton SO17 1BJ, UK
*
Author to whom correspondence should be addressed.
Microorganisms 2020, 8(5), 740; https://doi.org/10.3390/microorganisms8050740
Received: 16 April 2020 / Revised: 11 May 2020 / Accepted: 13 May 2020 / Published: 15 May 2020
(This article belongs to the Special Issue Anaerobic Digestion)
Understanding how the presence, absence, and abundance of different microbial genera supply specific metabolic functions for anaerobic digestion (AD) and how these impact on gas production is critical for a long-term understanding and optimization of the AD process. The strictly anaerobic methanogenic archaea are essential for methane production within AD microbial communities. Methanogens are a phylogenetically diverse group that can be classified into three metabolically distinct lineages based on the substrates they use to produce methane. While process optimization based on physicochemical parameters is well established in AD, measurements that could allow manipulation of the underlying microbial community are seldom used as they tend to be non-specific, expensive, or time-consuming, or a combination of all three. Loop-mediated isothermal amplification (LAMP) assays combine a simple, rapid, low-cost detection technique with high sensitivity and specificity. Here, we describe the optimization of LAMP assays for the detection of four different genera of hydrogenotrophic methanogens: Methanoculleus, Methanothermobacter, Methanococcus, and Methanobrevibacter spp. By targeting archaeal elongation factor 2 (aEF2), these LAMP assays provide a rapid, low-cost, presence/absence indication of hydrogenotrophic methanogens that could be used as a real-time measure of process conditions. The assays were shown to be sensitive to 1 pg of DNA from most tested methanogen species, providing a route to a quantitative measure through simple serial dilution of samples. The LAMP assays described here offer a simple, fast, and affordable method for the specific detection of four different genera of hydrogenotrophic methanogens. Our results indicate that this approach could be developed into a quantitative measure that could provide rapid, low-cost insight into the functioning and optimization of AD and related systems. View Full-Text
Keywords: hydrogenotrophic methanogens; anaerobic digestion; loop-mediated isothermal amplification; metagenomes hydrogenotrophic methanogens; anaerobic digestion; loop-mediated isothermal amplification; metagenomes
Show Figures

Figure 1

MDPI and ACS Style

Alessi, A.M.; Tao, B.; Zhang, W.; Zhang, Y.; Heaven, S.; Banks, C.J.; Chong, J.P.J. A Rapid, Sensitive, Low-Cost Assay for Detecting Hydrogenotrophic Methanogens in Anaerobic Digesters Using Loop-Mediated Isothermal Amplification. Microorganisms 2020, 8, 740.

Show more citation formats Show less citations formats
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Search more from Scilit
 
Search
Back to TopTop