PCR-based DGGE fingerprinting and identification of methanogens detected in three different types of UASB granules

Keyser, M.; Witthuhn, R. Corli; Lamprecht, Corné; Coetzee, Martin Petrus Albertus; Britz, T. J.

doi:10.1016/j.syapm.2005.06.003

Cited by 62 publications

(33 citation statements)

References 21 publications

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“…The biotic component, in casu the microbial community, can be investigated by molecular tools (Emanuelsson et al 2005;McMahon et al 2007). Up to now, a series of different tools were applied to evaluate the biotic dynamics based on molecular fingerprints: appearance or disappearance of discrete bands (Keyser et al 2006), the Dice index (Eichner et al 1999), nonmetric multi-dimensional scaling (van Hannen et al 1999), principal component analysis (Boon et al 2002) and moving window analysis (Wittebolle et al 2005). However, many environmental engineers described stability almost entirely in terms of processes and functions, often failing to take into account the community component (Briones and Raskin 2003).…”

Section: Introductionmentioning

confidence: 99%

High reproducibility of ammonia-oxidizing bacterial communities in parallel sequential batch reactors

Wittebolle

Vooren

Verstraete

et al. 2009

Journal of Applied Microbiology

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Aims: To investigate whether the ammonia‐oxidizing bacterial (AOB) communities of replicate nitrifying bioreactors (i) co‐evolve or diverge over time and (ii) are stable or dynamic during periods of complete nitrification. Methods and Results: Three sequential batch reactors (SBR) were inoculated with sludge from a municipal wastewater treatment plant, fed with ammonium‐enriched tap water and operated in parallel for 134 days. Polymerase chain reaction‐denaturing gradient gel electrophoresis (PCR‐DGGE) demonstrated co‐evolvement of the AOB communities over time. During start‐up, temporary decreases in nitrification were noticed, and the AOB community rate of change values (Δt(week)) were medium to high (12–22%). During the adjacent period of complete nitrification, low AOB community dynamics were observed (Δt(week) < 5%). Further pragmatic processing of the DGGE profiles revealed a high range‐weighted richness and a medium functional organization of the AOB communities. Conclusions: After a start‐up period, high functional stability and low dynamics of the AOB communities were observed. Deterministic rather than stochastic driving forces led to AOB community co‐evolvement in the replicate SBR. Significance and Impact of the Study: Replicates in identical set‐ups are reproducible, and pragmatic processing of DGGE patterns is a straightforward tool to score and compare the functionality of the bacterial communities.

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Section: Introductionmentioning

confidence: 99%

High reproducibility of ammonia-oxidizing bacterial communities in parallel sequential batch reactors

Wittebolle

Vooren

Verstraete

et al. 2009

Journal of Applied Microbiology

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“…These primers amplify the region between base pair 341 and 534 of the rRNA gene of E. coli (Muyzer et al, 1993), yielding 200 base pair (bp) fragments. The primers were selected on the basis of previous successful PCRbased DGGE analyses (Garbers et al, 2004;Keyser et al, 2006). PCR reactions contained ~30 ng (5 µl) of the template DNA, 1 µl of each primer (0.5 µM), 1 U Taq polymerase (ABGene, supplied by Southern Cross Biotechnology, Cape Town, South Africa), 2 µl dNTPs (200 µM) (Promega), 5 µl of the 10 x PCR buffer and 3 µl MgCl2 (2.5 mM) (ABGene, Southern Cross Biotechnology) in a total reaction volume of 50 µl.…”

Section: Dna Extraction and Pcr-based Dgge Analysismentioning

confidence: 99%

PCR-based DGGE Identification of Bacteria Present in Pasteurised South African Fruit Juices

Duvenage

Gouws

Witthuhn

2016

SAJEV

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The contamination of pasteurised fruit juice products by thermophilic acidophilic bacteria (TAB) has become a concern for producers. The aim of this study was to identify the bacteria present in South African fruit juices before and after pasteurisation, using polymerase chain reaction (PCR)-based denaturing gradient gel electrophoresis (DGGE). Alicyclobacillus acidoterrestris was found to be present in apple, pear, white grape and aloe vera juice. White grape juice was found to contain Alicyclobacillus pomorum, while two uncultured bacteria in the orange, apple, mango and pear juices were presumptively identified as members of the genus Bacillus, and one uncultured bacteria was identified as being closely related to Alcaligenes faecalis. The results emphasise the need for rapid and accurate detection of TAB in food products.

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“…In particular, two-stage anaerobic digestion physically separates stages of digestion into separate reactors, allowing much better control over the anaerobic digestion process (Dinsdale et al 1996;Dugba and Zhang 1999;Shin et al 2010;Varel et al 1988;Vergara-Fernandez et al 2008;Yu et al 2002). Furthermore, molecular research underway is providing new insights into the microbial communities associated with the anaerobic digestion process and aim to understand the impact of internal environmental conditions and change within the digester community (Keyser et al 2006;Shin et al 2010;Supaphol et al 2011). For example, new molecular methods in the anaerobic digestion process (such as "poly chain reaction denaturing gel gradient electrophoresis" and "real time poly chain reaction") are under investigation to improve metabolic pathways within the digester and the abundance and species composition of bacterial populations (Patil et al 2010a, b;Shin et al 2010;Skilman et al 2009;Supaphol et al 2011;Ziganshin et al 2011).…”

Section: The Future Prospects Of Anaerobic Digestion In Microalgae Prmentioning

confidence: 99%

Biomass and Biofuels from Microalgae

Moheimani¹,

McHenry²,

Boer³

et al. 2015

Biofuel and Biorefinery Technologies

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PCR-based DGGE fingerprinting and identification of methanogens detected in three different types of UASB granules

Cited by 62 publications

References 21 publications

High reproducibility of ammonia-oxidizing bacterial communities in parallel sequential batch reactors

High reproducibility of ammonia-oxidizing bacterial communities in parallel sequential batch reactors

PCR-based DGGE Identification of Bacteria Present in Pasteurised South African Fruit Juices

Biomass and Biofuels from Microalgae

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