Quantitative analysis of methanogenic community dynamics in three anaerobic batch digesters treating different wastewaters

Lee, Changsoo; Kim, Jaai; Hwang, Kwanghyun; O'Flaherty, Vincent; Hwang, Seokhwan

doi:10.1016/j.watres.2008.09.032

Cited by 149 publications

(76 citation statements)

References 30 publications

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“…Although Methanosarcina and Methanosaetaceae are the only aceticlastic methanogens, Methanosaetaceae are obligately aceticlastic, whereas Methanosarcina are also able to produce methane from H 2 /CO 2 and methylated compounds (52). Methanosaetaceae have a lower K s for acetate than Methanosarcina, but as cleavage of acetate yields the least energy for Methanosarcina among its metabolic options (52), members of these two genera may not always directly compete for acetate, and Methanosarcina has been reported to dominate the methanogenic community of anaerobic digesters even when acetate levels are low (26,55). Although both Methanosarcina and Methanosaetaceae were detected in the 20°C acidic peat incubation, Methanosarcina was the only detected aceticlastic methanogen in the 4°C incubation (Table 4).…”

Section: Discussionmentioning

confidence: 99%

mcrA -Targeted Real-Time Quantitative PCR Method To Examine Methanogen Communities

Steinberg

Regan

2009

Appl Environ Microbiol

238

138

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Methanogens are of great importance in carbon cycling and alternative energy production, but quantitation with culture-based methods is time-consuming and biased against methanogen groups that are difficult to cultivate in a laboratory. For these reasons, methanogens are typically studied through culture-independent molecular techniques. We developed a SYBR green I quantitative PCR (qPCR) assay to quantify total numbers of methyl coenzyme M reductase ␣-subunit (mcrA) genes. TaqMan probes were also designed to target nine different phylogenetic groups of methanogens in qPCR assays. Total mcrA and mcrA levels of different methanogen phylogenetic groups were determined from six samples: four samples from anaerobic digesters used to treat either primarily cow or pig manure and two aliquots from an acidic peat sample stored at 4°C or 20°C. Only members of the Methanosaetaceae, Methanosarcina, Methanobacteriaceae, and Methanocorpusculaceae and Fen cluster were detected in the environmental samples. The three samples obtained from cow manure digesters were dominated by members of the genus Methanosarcina, whereas the sample from the pig manure digester contained detectable levels of only members of the Methanobacteriaceae. The acidic peat samples were dominated by both Methanosarcina spp. and members of the Fen cluster. In two of the manure digester samples only one methanogen group was detected, but in both of the acidic peat samples and two of the manure digester samples, multiple methanogen groups were detected. The TaqMan qPCR assays were successfully able to determine the environmental abundance of different phylogenetic groups of methanogens, including several groups with few or no cultivated members.

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Section: Discussionmentioning

confidence: 99%

mcrA -Targeted Real-Time Quantitative PCR Method To Examine Methanogen Communities

Steinberg

Regan

2009

Appl Environ Microbiol

238

138

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“…For the archaeal 16S rRNA gene, an equimolar mixture of the corresponding standard plasmids was used as the template solution for construction of the standard curve (Lee et al 2009;Yu et al 2005). Each primer/probe set had a different dynamic range, i.e., >7 orders of magnitude.…”

Section: Real-time Pcr Analysismentioning

confidence: 99%

Carbon amendment and soil depth affect the distribution and abundance of denitrifiers in agricultural soils

Barrett

Khalil

Jahangir

et al. 2016

Environ Sci Pollut Res

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The nitrite reductase (nirS and nirK) and nitrous oxide reductase-encoding (nosZ) genes of denitrifying populations present in an agricultural grassland soil were quantified using real-time polymerase chain reaction (PCR) assays. Samples from three separate pedological depths at the chosen site were investigated: horizon A (0-10 cm), horizon B (45-55 cm), and horizon C (120-130 cm). The effect of carbon addition (treatment 1, control; treatment 2, glucose-C; treatment 3, dissolved organic carbon (DOC)) on denitrifier gene abundance and N2O and N2 fluxes was determined. In general, denitrifier abundance correlated well with flux measurements; nirS was positively correlated with N2O, and nosZ was positively correlated with N2 (P < 0.03). Denitrifier gene copy concentrations per gram of soil (GCC) varied in response to carbon type amendment (P < 0.01). Denitrifier GCCs were high (ca. 10(7)) and the bac:nirK, bac:nirS, bac:nir (T) , and bac:nosZ ratios were low (ca. 10(-1)/10) in horizon A in all three respective treatments. Glucose-C amendment favored partial denitrification, resulting in higher nir abundance and higher N2O fluxes compared to the control. DOC amendment, by contrast, resulted in relatively higher nosZ abundance and N2 emissions, thus favoring complete denitrification. We also noted soil depth directly affected bacterial, archaeal, and denitrifier abundance, possibly due to changes in soil carbon availability with depth.

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“…These studies have provided substantial insight into the methanogenic populations (Lee et al, 2008b;Steinberg and Regan, 2011), but the interactions between and within functional guilds and their link to reactor performance remain poorly understood. Functional redundancy is thought to be at the core of stable reactor performance, as it ensures the presence of a reservoir of populations able to perform the same ecological function (Briones and Raskin, 2003;Rittmann et al, 2006;Allison and Martiny, 2008;Falk et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters

et al. 2014

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A replicate long-term experiment was conducted using anaerobic digestion (AD) as a model process to determine the relative role of niche and neutral theory on microbial community assembly, and to link community dynamics to system performance. AD is performed by a complex network of microorganisms and process stability relies entirely on the synergistic interactions between populations belonging to different functional guilds. In this study, three independent replicate anaerobic digesters were seeded with the same diverse inoculum, supplied with a model substrate, a-cellulose, and operated for 362 days at a 10-day hydraulic residence time under mesophilic conditions. Selective pressure imposed by the operational conditions and model substrate caused large reproducible changes in community composition including an overall decrease in richness in the first month of operation, followed by synchronised population dynamics that correlated with changes in reactor performance. This included the synchronised emergence and decline of distinct Ruminococcus phylotypes at day 148, and emergence of a Clostridium and Methanosaeta phylotype at day 178, when performance became stable in all reactors. These data suggest that many dynamic functional niches are predictably filled by phylogenetically coherent populations over long time scales. Neutral theory would predict that a complex community with a high degree of recognised functional redundancy would lead to stochastic changes in populations and community divergence over time. We conclude that deterministic processes may play a larger role in microbial community dynamics than currently appreciated, and under controlled conditions it may be possible to reliably predict community structural and functional changes over time.

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Quantitative analysis of methanogenic community dynamics in three anaerobic batch digesters treating different wastewaters

Cited by 149 publications

References 30 publications

mcrA -Targeted Real-Time Quantitative PCR Method To Examine Methanogen Communities

mcrA -Targeted Real-Time Quantitative PCR Method To Examine Methanogen Communities

Carbon amendment and soil depth affect the distribution and abundance of denitrifiers in agricultural soils

Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters

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