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A rapid, sensitive, low-cost assay for detecting hydrogenotrophic methanogens in anaerobic digesters using loop-mediated isothermal amplification

A rapid, sensitive, low-cost assay for detecting hydrogenotrophic methanogens in anaerobic digesters using loop-mediated isothermal amplification
A rapid, sensitive, low-cost assay for detecting hydrogenotrophic methanogens in anaerobic digesters using loop-mediated isothermal amplification
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.
Anaerobic digestion, Hydrogenotrophic methanogens, Loop-mediated isothermal amplification, Metagenomes
Alessi, Anna
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Tao, Bing
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Zhang, Wei
e896f9bd-f169-4c5a-a465-cadf5d5a96a3
Zhang, Yue
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Heaven, Sonia
f25f74b6-97bd-4a18-b33b-a63084718571
Banks, Charles
5c6c8c4b-5b25-4e37-9058-50fa8d2e926f
Chong, James
4e4ecdde-b11e-4efa-b40b-73f0c6f62160
Alessi, Anna
b8c92e5e-a720-42cb-8ef8-b978a9f1ee9c
Tao, Bing
a016d442-8190-4f19-b71b-d3f7e4ce357f
Zhang, Wei
e896f9bd-f169-4c5a-a465-cadf5d5a96a3
Zhang, Yue
69b11d32-d555-46e4-a333-88eee4628ae7
Heaven, Sonia
f25f74b6-97bd-4a18-b33b-a63084718571
Banks, Charles
5c6c8c4b-5b25-4e37-9058-50fa8d2e926f
Chong, James
4e4ecdde-b11e-4efa-b40b-73f0c6f62160

Alessi, Anna, Tao, Bing, Zhang, Wei, Zhang, Yue, Heaven, Sonia, Banks, Charles and Chong, James (2020) A rapid, sensitive, low-cost assay for detecting hydrogenotrophic methanogens in anaerobic digesters using loop-mediated isothermal amplification. Microorganisms, 8 (5), [740]. (doi:10.3390/microorganisms8050740).

Record type: Article

Abstract

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.

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Alessi et al 2020 accepted version 1 - Accepted Manuscript
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More information

Accepted/In Press date: 13 May 2020
e-pub ahead of print date: 15 May 2020
Published date: 15 May 2020
Keywords: Anaerobic digestion, Hydrogenotrophic methanogens, Loop-mediated isothermal amplification, Metagenomes

Identifiers

Local EPrints ID: 441047
URI: http://eprints.soton.ac.uk/id/eprint/441047
PURE UUID: b5c9bff7-8aa7-4806-b7f1-e75be7bc608b
ORCID for Yue Zhang: ORCID iD orcid.org/0000-0002-5068-2260
ORCID for Sonia Heaven: ORCID iD orcid.org/0000-0001-7798-4683

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Date deposited: 28 May 2020 16:57
Last modified: 18 Feb 2021 17:00

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