Syntrophy in Methanogenic Degradation
2018-11-05, Müller, Nicolai, Timmers, Peer, Plugge, Caroline M., Stams, Alfons J. M., Schink, Bernhard
This chapter deals with microbial communities of bacteria and archaea which closely cooperate in methanogenic degradation and perform metabolic functions in this community that neither one of them could carry out alone. The methanogenic degradation of fatty acids, alcohols, most aromatic compounds, amino acids, and others is performed in partnership between fermenting bacteria and methanogenic Archaea. The energy available in these processes is very small, attributing only fractions of an ATP unit per reaction run to every partner. The biochemical strategies taken include in most cases reactions of substrate-level phosphorylation combined with various kinds of reversed electron transport systems in which part of the gained ATP is reinvested into thermodynamically unfavorable electron transport processes. Altogether, these systems represent fascinating examples of energy efficiency at the lowermost energy level that allows microbial life.
Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes
2015-11-01, Garrity, George M., Whitman, William B., Schink, Bernhard, Trujillo, Martha E., Rosselló-Móra, Ramon, Sutcliffe, Iain, da Costa, Milton S., Oren, Aharon, Rainey, Fred A.
The International Code of Nomenclature of Prokaryotes covers the nomenclature of prokaryotes up to the rank of class. We propose here modifying the Code to include the rank of phylum so that names of phyla that fulfil the rules of the Code will obtain standing in the nomenclature.
Activation of Acetone and Other Simple Ketones in Anaerobic Bacteria
2016-03-10, Heider, Johann, Schühle, Karola, Frey, Jasmin, Schink, Bernhard
Acetone and other ketones are activated for subsequent degradation through carboxylation by many nitrate-reducing, phototrophic, and obligately aerobic bacteria. Acetone carboxylation leads to acetoacetate, which is subsequently activated to a thioester and degraded via thiolysis. Two different types of acetone carboxylases have been described, which require either 2 or 4 ATP equivalents as an energy supply for the carboxylation reaction. Both enzymes appear to combine acetone enolphosphate with carbonic phosphate to form acetoacetate. A similar but more complex enzyme is known to carboxylate the aromatic ketone acetophenone, a metabolic intermediate in anaerobic ethylbenzene metabolism in denitrifying bacteria, with simultaneous hydrolysis of 2 ATP to 2 ADP. Obligately anaerobic sulfate-reducing bacteria activate acetone to a four-carbon compound as well, but via a different process than bicarbonate- or CO2-dependent carboxylation. The present evidence indicates that either carbon monoxide or a formyl residue is used as a cosubstrate, and that the overall ATP expenditure of this pathway is substantially lower than in the known acetone carboxylase reactions.
Formation of names of genera of prokaryotes that end on -oides or -opsis : A proposal for addenda to Rule 65(2) and Appendix 9 of the International Code of Nomenclature of Prokaryotes
2016, Oren, Aharon, Schink, Bernhard
In view of the current confusion about the correct gender of genus names ending on -oides, and possible confusion in the future for genus names ending on -opsis, we propose non-retroactive addenda to Rule 65(2) and Appendix 9 of the International Code of Nomenclature of Prokaryotes so that new genera to be formed by adding the ending -oides to the stem of an existing genus name or another (Neo-) Latin word must be treated as neuter and genus names ending on -opsis are to be treated as feminine.
Methanogens : Syntrophic Metabolism
2018-03-14, Sieber, Jessica R., McInerney, Michael J., Müller, Nicolai, Schink, Bernhard, Gunsalus, Rob P., Plugge, Caroline M.
Syntrophy is a mutualistic interaction in which two metabolically different types of microorganisms are linked by the need to keep metabolites exchanged between the two partners at low concentrations to make the overall metabolism of both organisms feasible. In most cases, the cooperation is based on the transfer of hydrogen, formate, or acetate from fermentative bacteria to methanogens to make the degradation of electron-rich substrates thermodynamically favorable. Syntrophic metabolism proceeds at very low Gibbs’ free energy changes, close to the minimum free energy change needed to conserve energy biologically, which is the energy needed to transport one proton across the cytoplasmic membrane. Pathways for syntrophic degradation of fatty acids predict the net synthesis of about one-third of an ATP per round of catabolism. Syntrophic metabolism entails critical oxidation-reduction reactions in which H2 or formate production would be thermodynamically unfavorable unless energy is invested. Molecular insights into the membrane processes involved in ion translocation and reverse electron transport revealed that syntrophs harbor multiple systems for reverse electron transfer. While much evidence supports the interspecies transfer of H2 and formate, other mechanisms of interspecies electron transfer exist including cysteine cycling and possibly direct interspecies electron transfer as electric current via conductive pili or (semi)conductive minerals.
2016, Schink, Bernhard, Rahalkar, Monali
Me.thy.lo.so'ma. N.L. neut. n. methylum, the methyl group; Gr. neut. n. soma, body; N.L. neut. n. Methylosoma methyl-using body. Proteobacteria / Gammaproteobacteria / Methylococcales / Methylococcaceae The genus Methylosoma belongs to the Gammaproteobacteria and consists so far of only one species, M. difficile. Cells are microaerobic and use only methane or methanol as substrate. Only a particulate methane monooxygenase was found. Closest phylogenetic relatives are the genera Methyloglobulus and Methylovulum. DNA G + C content (mol%): 49.9 (HPLC determination).
Proposal to change Recommendation 12c of the International Code of Nomenclature of Prokaryotes
2015-11-01, Oren, Aharon, Garrity, George M., Schink, Bernhard
We propose changing Recommendation 12c of the International Code of Nomenclature of Prokaryotes to clarify the ways species and subspecies can be named to honour persons.