scholarly journals Effect of Dilution Rate on Metabolic Pathway Shift between Aceticlastic and Nonaceticlastic Methanogenesis in Chemostat Cultivation

2004 ◽  
Vol 70 (7) ◽  
pp. 4048-4052 ◽  
Author(s):  
Toru Shigematsu ◽  
Yueqin Tang ◽  
Tsutomu Kobayashi ◽  
Hiromi Kawaguchi ◽  
Shigeru Morimura ◽  
...  
Keyword(s):  
Dilution Rate ◽  
Phylogenetic Analyses ◽  
Gas Chromatography Mass Spectrometry ◽  
High Dilution ◽  
Chemostat Cultivation ◽  
Reductase Gene ◽  
Syntrophic Oxidation ◽  
Hydrogenotrophic Methanogens ◽  
Methyl Coenzyme M Reductase ◽  
Limited Coverage

ABSTRACT Acetate conversion pathways of methanogenic consortia in acetate-fed chemostats at dilution rates of 0.025 and 0.6 day−1 were investigated by using 13C-labeled acetates, followed by gas chromatography-mass spectrometry (GC-MS) analysis of the CH4 and CO2 produced. Nonaceticlastic syntrophic oxidation by acetate-oxidizing syntrophs and hydrogenotrophic methanogens was suggested to occupy a primary pathway (approximately 62 to 90%) in total methanogenesis at the low dilution rate. In contrast, aceticlastic cleavage of acetate by aceticlastic methanogens was suggested to occupy a primary pathway (approximately 95 to 99%) in total methanogenesis at the high dilution rate. Phylogenetic analyses of transcripts of the methyl coenzyme M reductase gene (mcrA) confirmed that a significant number of transcripts of the genera Methanoculleus (hydrogenotrophic methanogens) and Methanosarcina (aceticlastic methanogens) were present in the chemostats at the low and high dilution rates, respectively. The mcrA transcripts of the genus Methanosaeta (aceticlastic methanogens), which dominated the population in a previous study (T. Shigematsu, Y. Tang, H. Kawaguchi, K. Ninomiya, J. Kijima, T. Kobayashi, S. Morimura, and K. Kida, J. Biosci. Bioeng. 96:547-558, 2003), were poorly detected at both dilution rates due to the limited coverage of the primers used. These results demonstrated that the dilution rate could cause a shift in the primary pathway of acetate conversion to methane in acetate-fed chemostats.

scholarly journals Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens

2019 ◽  
Vol 116 (11) ◽  
pp. 5037-5044 ◽  
Author(s):  
Bojk A. Berghuis ◽  
Feiqiao Brian Yu ◽  
Frederik Schulz ◽  
Paul C. Blainey ◽  
Tanja Woyke ◽  
...  
Keyword(s):  
Paradigm Shift ◽  
Carbon Fixation ◽  
Methanogenic Archaea ◽  
Global Carbon Cycle ◽  
Hydrogenotrophic Methanogenesis ◽  
Shared Ancestry ◽  
Hydrogenotrophic Methanogens ◽  
Methyl Coenzyme M Reductase ◽  
Global Carbon ◽  
Insight Into

Methanogenic archaea are major contributors to the global carbon cycle and were long thought to belong exclusively to the euryarchaeal phylum. Discovery of the methanogenesis gene cluster methyl-coenzyme M reductase (Mcr) in the Bathyarchaeota, and thereafter the Verstraetearchaeota, led to a paradigm shift, pushing back the evolutionary origin of methanogenesis to predate that of the Euryarchaeota. The methylotrophic methanogenesis found in the non-Euryarchaota distinguished itself from the predominantly hydrogenotrophic methanogens found in euryarchaeal orders as the former do not couple methanogenesis to carbon fixation through the reductive acetyl-CoA [Wood–Ljungdahl pathway (WLP)], which was interpreted as evidence for independent evolution of the two methanogenesis pathways. Here, we report the discovery of a complete and divergent hydrogenotrophic methanogenesis pathway in a thermophilic order of the Verstraetearchaeota, which we have named Candidatus Methanohydrogenales, as well as the presence of the WLP in the crenarchaeal order Desulfurococcales. Our findings support the ancient origin of hydrogenotrophic methanogenesis, suggest that methylotrophic methanogenesis might be a later adaptation of specific orders, and provide insight into how the transition from hydrogenotrophic to methylotrophic methanogenesis might have occurred.

scholarly journals Phylogenetic and Structural Comparisons of the Three Types of Methyl Coenzyme M Reductase from Methanococcales and Methanobacteriales

2017 ◽  
Vol 199 (16) ◽  
Author(s):  
Tristan Wagner ◽  
Carl-Eric Wegner ◽  
Jörg Kahnt ◽  
Ulrich Ermler ◽  
Seigo Shima
Keyword(s):  
Active Site ◽  
Phylogenetic Analyses ◽  
Methanogenic Archaea ◽  
Methane Formation ◽  
Type I ◽  
Type Ii ◽  
Coenzyme M ◽  
Content Type ◽  
Type Iii ◽  
Methyl Coenzyme M Reductase

ABSTRACT The phylogenetically diverse family of methanogenic archaea universally use methyl coenzyme M reductase (MCR) for catalyzing the final methane-forming reaction step of the methanogenic energy metabolism. Some methanogens of the orders Methanobacteriales and Methanococcales contain two isoenzymes. Comprehensive phylogenetic analyses on the basis of all three subunits grouped MCRs from Methanobacteriales and Methanococcales into three distinct types: (i) MCRs from Methanobacteriales, (ii) MCRs from Methanobacteriales and Methanococcales, and (iii) MCRs from Methanococcales. The first and second types contain MCR isoenzymes I and II from Methanothermobacter marburgensis, respectively; therefore, they were designated MCR type I and type II and accordingly; the third one was designated MCR type III. For comparison with the known MCR type I and type II structures, we determined the structure of MCR type III from Methanotorris formicicus and Methanothermococcus thermolithotrophicus. As predicted, the three MCR types revealed highly similar overall structures and virtually identical active site architectures reflecting the chemically challenging mechanism of methane formation. Pronounced differences were found at the protein surface with respect to loop geometries and electrostatic properties, which also involve the entrance of the active-site funnel. In addition, the C-terminal end of the γ-subunit is prolonged by an extra helix after helix γ8 in MCR type II and type III, which is, however, differently arranged in the two MCR types. MCR types I, II, and III share most of the posttranslational modifications which appear to fine-tune the enzymatic catalysis. Interestingly, MCR type III lacks the methyl-cysteine but possesses in subunit α of M. formicicus a 6-hydroxy-tryptophan, which thus far has been found only in the α-amanitin toxin peptide but not in proteins. IMPORTANCE Methyl coenzyme M reductase (MCR) represents a prime target for the mitigation of methane releases. Phylogenetic analyses of MCRs suggested several distinct sequence clusters; those from Methanobacteriales and Methanococcales were subdivided into three types: MCR type I from Methanobacteriales, MCR type II from Methanobacteriales and Methanococcales, and the newly designated MCR type III exclusively from Methanococcales. We determined the first X-ray structures for an MCR type III. Detailed analyses revealed substantial differences between the three types only in the peripheral region. The subtle modifications identified and electrostatic profiles suggested enhanced substrate binding for MCR type III. In addition, MCR type III from Methanotorris formicicus contains 6-hydroxy-tryptophan, a new posttranslational modification that thus far has been found only in the α-amanitin toxin.

scholarly journals Diversification of methanogens into hyperalkaline serpentinizing environments through adaptations to minimize oxidant limitation

2020 ◽  
Author(s):  
Elizabeth M. Fones ◽  
Daniel R. Colman ◽  
Emily A. Kraus ◽  
Ramunas Stepanauskas ◽  
Alexis S. Templeton ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Relative Abundance ◽  
Hydrogen Oxidation ◽  
Phylogenetic Analyses ◽  
Gene Content ◽  
Type I ◽  
Type Ii ◽  
Sultanate Of Oman ◽  
Methane Generation ◽  
Hydrogenotrophic Methanogens

AbstractMetagenome assembled genomes (MAGs) and single amplified genomes (SAGs) affiliated with two distinct Methanobacterium lineages were recovered from subsurface fracture waters of the Samail Ophiolite, Sultanate of Oman. Lineage Type I was abundant in waters with circumneutral pH, whereas lineage Type II was abundant in hydrogen rich, hyperalkaline waters. Type I encoded proteins to couple hydrogen oxidation to CO2 reduction, typical of hydrogenotrophic methanogens. Surprisingly, Type II, which branched from the Type I lineage, lacked homologs of two key oxidative [NiFe]-hydrogenases. These functions were presumably replaced by formate dehydrogenases that oxidize formate to yield reductant and cytoplasmic CO2 via a pathway that was unique among characterized Methanobacteria, allowing cells to overcome CO2/oxidant limitation in high pH waters. This prediction was supported by microcosm-based radiotracer experiments that showed significant biological methane generation from formate, but not bicarbonate, in waters where the Type II lineage was detected in highest relative abundance. Phylogenetic analyses and variability in gene content suggested that recent and ongoing diversification of the Type II lineage was enabled by gene transfer, loss, and transposition. These data indicate that selection imposed by CO2/oxidant availability drove recent methanogen diversification into hyperalkaline waters that are heavily impacted by serpentinization.

Evolution of Fusarium graminearum A3/5 grown in a series of glucose-limited chemostat cultures at a high dilution rate

1995 ◽  
Vol 99 (2) ◽  
pp. 173-178 ◽  
Author(s):  
Marilyn G. Wiebe ◽  
Geoffrey D. Robson ◽  
Stephen G. Oliver ◽  
Anthony P.J. Trinci
Keyword(s):  
Dilution Rate ◽  
Fusarium Graminearum ◽  
High Dilution ◽  
Chemostat Cultures ◽  
High Dilution Rate

scholarly journals Chemostat Production of Plantaricin C ByLactobacillus plantarum LL441

1998 ◽  
Vol 64 (9) ◽  
pp. 3512-3514 ◽  
Author(s):  
J. M. Bruno Bárcena ◽  
F. Siñeriz ◽  
D. González de Llano ◽  
Ana Rodríguez ◽  
Juan E. Suárez
Keyword(s):  
Carbon Source ◽  
Dilution Rate ◽  
Lactobacillus Plantarum ◽  
Carbon Sources ◽  
High Dilution

ABSTRACT Plantaricin C, a bacteriocin synthesized by Lactobacillus plantarum LL441, was optimally produced in chemostats kept at pH 5.0, 30°C, 150 rpm, and a dilution rate of 0.05 h−1 when glucose was used as carbon source and a dilution rate of 0.10 to 0.12 h−1 when sucrose or fructose was used instead. Production was abolished at high dilution rates, i.e., when the cells grew rapidly in all carbon sources.

scholarly journals Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Zheng-Shuang Hua ◽  
Yu-Lin Wang ◽  
Paul N. Evans ◽  
Yan-Ni Qu ◽  
Kian Mau Goh ◽  
...  
Keyword(s):  
Hot Springs ◽  
Ammonia Oxidation ◽  
Hot Spring ◽  
Phylogenetic Analyses ◽  
Optimal Growth ◽  
Ancestral State ◽  
Coenzyme M ◽  
Key Enzyme ◽  
Vertical Evolution ◽  
Methyl Coenzyme M Reductase

Abstract Several recent studies have shown the presence of genes for the key enzyme associated with archaeal methane/alkane metabolism, methyl-coenzyme M reductase (Mcr), in metagenome-assembled genomes (MAGs) divergent to existing archaeal lineages. Here, we study the mcr-containing archaeal MAGs from several hot springs, which reveal further expansion in the diversity of archaeal organisms performing methane/alkane metabolism. Significantly, an MAG basal to organisms from the phylum Thaumarchaeota that contains mcr genes, but not those for ammonia oxidation or aerobic metabolism, is identified. Together, our phylogenetic analyses and ancestral state reconstructions suggest a mostly vertical evolution of mcrABG genes among methanogens and methanotrophs, along with frequent horizontal gene transfer of mcr genes between alkanotrophs. Analysis of all mcr-containing archaeal MAGs/genomes suggests a hydrothermal origin for these microorganisms based on optimal growth temperature predictions. These results also suggest methane/alkane oxidation or methanogenesis at high temperature likely existed in a common archaeal ancestor.

scholarly journals Occurrence and expression of novel methyl-coenzyme M reductase gene (mcrA) variants in hot spring sediments

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Luke J. McKay ◽  
Roland Hatzenpichler ◽  
William P. Inskeep ◽  
Matthew W. Fields
Keyword(s):  
Hot Spring ◽  
Coenzyme M ◽  
Reductase Gene ◽  
Methyl Coenzyme M Reductase
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