Diversity and Taxonomy of Methanogens

Boone, David R.; Whitman, William B.; Rouvière, Pierre E.

doi:10.1007/978-1-4615-2391-8_2

Cited by 307 publications

(250 citation statements)

References 151 publications

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“…Only strain AK-4 grew on methanol as the catabolic substrate. This is the first report of methyltrophic methanogens that can not grow on methanol, although Methanohalobium evestigatum can grow on low concentrations of methanol (Boone et al, 1993). None of the strains could catabolize acetate, dimethylsulfide, formate or hydrogen.…”

Section: Growth Characteristicsmentioning

confidence: 81%

Isolation and characterization of methylotrophic methanogens from anoxic marine sediments in Skan Bay, Alaska: description of Methanococcoides alaskense sp. nov., and emended description of Methanosarcina baltica

Singh

Kendall

Liu

et al. 2005

International Journal of Systematic and Evolutionary Microbiology

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105

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Three novel strains of methylotrophic methanogens were isolated from Skan Bay, Alaska, by using anaerobic cultivation techniques. The water was 65 m deep at the sampling site. Strains AK-4 (=OCM 774), AK-5 T (=OCM 775 T =DSM 17273 T ) and AK-9 (=OCM 793) were isolated from the sulfate-reducing zone of the sediments. Each of the strains was a non-motile coccus and occurred singly. Cells grew with trimethylamine as a catabolic substrate and strain AK-4 could also catabolize methanol. Yeast extract and trypticase peptones were not required for growth, but their addition to the culture medium slightly stimulated growth. Each of the strains grew at temperatures of 5-28 6C; they were slight halophiles and grew fastest in the neutral pH range. Analysis of the 16S rRNA gene sequences indicated that strain AK-4 was most closely related to Methanosarcina baltica. DNA-DNA hybridization studies showed 88 % relatedness, suggesting that strain AK-4 represents a novel strain within this species. Strains AK-5 T and AK-9 had identical 16S rRNA gene sequences that were most closely related to the sequence of Methanococcoides burtonii (99?8 % sequence similarity). DNA-DNA hybridization studies showed that strains AK-5 T and AK-9 are members of the same species (88 % relatedness value), but strain AK-5 T had a DNA-DNA relatedness value of only 55 % to Methanococcoides burtonii. This indicates that strains AK-5 T and AK-9 should be considered as members of a novel species in the genus Methanococcoides. We propose the name Methanococcoides alaskense sp. nov., with strain AK-5 T (=OCM 775 T =DSM 17273 T ) as the type strain.In the marine environment, sulfate reduction is the dominant microbial process in the upper sediment layers. Generally, when sulfate is present, sulfate reduction is the major catabolic process and methanogenesis is limited. Because of their higher affinity for hydrogen and acetate, sulfate-reducing bacteria out-compete methanogens for these important substrates (King et al., 1983;King, 1984;Oremland & Taylor, 1978). As a result, methanogenesis becomes a dominant process only in deeper sediments in which the sulfate ions have been exhausted. The limited methane production that occurs together with sulfate reduction is due to the activity of methylotrophic methanogens (King, 1984;Oremland & Taylor, 1978;Oremland & Polcin, 1982).Methanogens that belong to the family Methanosarcinaceae are characterized as having the broadest substrate range of methanogens; many can grow by reducing CO 2 with H 2 or by the splitting of acetate and all can grow by dismutating methyl compounds (Kendall & Boone, 2004). The family Methanosarcinaceae includes eight genera: Methanosarcina, Methanolobus, Methanococcoides, Methanohalobium, Methanohalophilus, Methanosalsum, Methanomethylovorans and Methanimicrococcus. The only described species of Methanimicrococcus, Methanimicrococcus blatticola, is unique among the Methanosarcinaceae because it reduces methylated compounds only in the presence of H 2 (Sprenger et al., 2000). The GenBank/EMB...

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Section: Growth Characteristicsmentioning

confidence: 81%

Isolation and characterization of methylotrophic methanogens from anoxic marine sediments in Skan Bay, Alaska: description of Methanococcoides alaskense sp. nov., and emended description of Methanosarcina baltica

Singh

Kendall

Liu

et al. 2005

International Journal of Systematic and Evolutionary Microbiology

Self Cite

105

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“…It is striking that although coenzyme F 420 is present in all characterized methanogens, DFTR homologs were limited to the most phylogenetically deeply rooted group euryarchaeal class of Methanococci (Figs. 8 and 9), which utilize primarily hydrogen as energy source (51,71), carry limited numbers (2-4) of Trx homologs, and lack NTR and FTR. The more ancient members of this group, the Methanocaldococcus species live in the early Earth environment of deep-sea hydrothermal vents (51,52).…”

Section: Discussionmentioning

confidence: 99%

A Novel F420-dependent Thioredoxin Reductase Gated by Low Potential FAD

Susanti¹,

Loganathan²,

Mukhopadhyay

2016

Journal of Biological Chemistry

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A recent report suggested that the thioredoxin-dependent metabolic regulation, which is widespread in all domains of life, existed in methanogenic archaea about 3.5 billion years ago. We now show that the respective electron delivery enzyme (thioredoxin reductase, TrxR), although structurally similar to flavincontaining NADPH-dependent TrxRs (NTR), lacked an NADPH-binding site and was dependent on reduced coenzyme F 420 (F 420 H 2 ), a stronger reductant with a mid-point redox potential (E 0 ) of ؊360 mV; E 0 of NAD(P)H is ؊320 mV. Because F 420 is a deazaflavin, this enzyme was named deazaflavin-dependent flavin-containing thioredoxin reductase (DFTR). It transferred electrons from F 420 H 2 to thioredoxin via proteinbound flavin; K m values for thioredoxin and F 420 H 2 were 6.3 and 28.6 M, respectively. The E 0 of DFTR-bound flavin was approximately ؊389 mV, making electron transfer from NAD(P)H or F 420 H 2 to flavin endergonic. However, under high partial pressures of hydrogen prevailing on early Earth and present day deep-sea volcanoes, the potential for the F 420 /F 420 H 2 pair could be as low as ؊425 mV, making DFTR efficient. The presence of DFTR exclusively in ancient methanogens and mostly in the early Earth environment of deep-sea volcanoes and DFTR's characteristics suggest that the enzyme developed on early Earth and gave rise to NTR. A phylogenetic analysis revealed six more novel-type TrxR groups and suggested that the broader flavin-containing disulfide oxidoreductase family is more diverse than previously considered. The unprecedented structural similarities between an F 420 -dependent enzyme (DFTR) and an NADPH-dependent enzyme (NTR) brought new thoughts to investigations on F 420 systems involved in microbial pathogenesis and antibiotic production.

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“…Methanogens of the families Methanosarcinaceae, Methanobacteriaceae and Methanomicrobiaceae were previously detected in the E. eugeniae gut contents (Depkat-Jakob et al, 2012), and the detection of mcrA sequences related to these taxa (Figure 4b) suggest that these taxa are linked to methanogenesis in the alimentary canal. Members of Methanosarcinaceae are acetoclastic, that is, can convert acetate to CO 2 and CH 4 (Boone et al, 1993;Hedderich and Whitman, 2006). However, mcrA sequences related to the genus Methanosarcina were not detected in 'heavy' fractions of [ 13 C]-glucose treatments in which acetate accumulated (Figure 3).…”

Section: Discussionmentioning

confidence: 99%

Methanogenic food web in the gut contents of methane-emitting earthworm Eudrilus eugeniae from Brazil

et al. 2015

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The anoxic saccharide-rich conditions of the earthworm gut provide an ideal transient habitat for ingested microbes capable of anaerobiosis. It was recently discovered that the earthworm Eudrilus eugeniae from Brazil can emit methane (CH 4 ) and that ingested methanogens might be associated with this emission. The objective of this study was to resolve trophic interactions of bacteria and methanogens in the methanogenic food web in the gut contents of E. eugeniae. RNA-based stable isotope probing of bacterial 16S rRNA as well as mcrA and mrtA (the alpha subunit of methyl-CoM reductase and its isoenzyme, respectively) of methanogens was performed with [ 13 C]-glucose as a model saccharide in the gut contents. Concomitant fermentations were augmented by the rapid consumption of glucose, yielding numerous products, including molecular hydrogen (H 2 ), carbon dioxide (CO 2 ), formate, acetate, ethanol, lactate, succinate and propionate. Aeromonadaceaeaffiliated facultative aerobes, and obligate anaerobes affiliated to Lachnospiraceae, Veillonellaceae and Ruminococcaceae were associated with the diverse fermentations. Methanogenesis was ongoing during incubations, and 13 C-labeling of CH 4 verified that supplemental [ 13 C]-glucose derived carbon was dissimilated to CH 4 . Hydrogenotrophic methanogens affiliated with Methanobacteriaceae and Methanoregulaceae were linked to methanogenesis, and acetogens related to Peptostreptoccocaceae were likewise found to be participants in the methanogenic food web. H 2 rather than acetate stimulated methanogenesis in the methanogenic gut content enrichments, and acetogens appeared to dissimilate supplemental H 2 to acetate in methanogenic enrichments. These findings provide insight on the processes and associated taxa potentially linked to methanogenesis and the turnover of organic carbon in the alimentary canal of methane-emitting E. eugeniae.

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Diversity and Taxonomy of Methanogens

Cited by 307 publications

References 151 publications

Isolation and characterization of methylotrophic methanogens from anoxic marine sediments in Skan Bay, Alaska: description of Methanococcoides alaskense sp. nov., and emended description of Methanosarcina baltica

Isolation and characterization of methylotrophic methanogens from anoxic marine sediments in Skan Bay, Alaska: description of Methanococcoides alaskense sp. nov., and emended description of Methanosarcina baltica

A Novel F420-dependent Thioredoxin Reductase Gated by Low Potential FAD

Methanogenic food web in the gut contents of methane-emitting earthworm Eudrilus eugeniae from Brazil

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