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Title: Evolution of the syntrophic interaction between Desulfovibrio vulgaris and Methanosarcina barkeri: involvement of an ancient horizontal gene transfer

Abstract

The sulfate reducing bacteria Desulfovibrio vulgaris and the methanogenic archaea Methanosarcina barkeri can grow syntrophically on lactate. In this study, three functionally unknown genes of D. vulgaris, DVU2103, DVU2104 and DVU2108, were found to be up-regulated 2-4 fold following the lifestyle shift from syntroph to sulfatereducer; moreover, none of these genes were regulated when D. vulgaris was grown alone in various pure culture conditions. These results suggest that these genes may play roles related to the lifestyle change of D. vulgaris from syntroph to sulfate reducer. This hypothesis is further supported by phylogenomic analyses showing that homologies of these genes were only narrowly present in several groups of bacteria, most of which are restricted to a syntrophic life-style, such as Pelobacter carbinolicus, Syntrophobacter fumaroxidans, Syntrophomonas wolfei and Syntrophus aciditrophicus. Phylogenetic analysis showed that the genes tended to be clustered with archaeal genera, and they were rooted on archaeal species in the phylogenetic trees, suggesting that they originated from an archaeal methanogen and were horizontally transferred to a common ancestor of delta- Proteobacteria, Clostridia and Thermotogae. While lost in most species during evolution, these genes appear to have been retained in bacteria capable of syntrophic relationships, probably due to their providingmore » a selective advantage. In addition, no significant bias in codon and amino acid usages was detected between these genes and the rest of the D. vulgaris genome, suggesting these gene transfers may have occurred early in the evolutionary history so that sufficient time has elapsed to allow an adaptation to the codon and amino acid usages of D. vulgaris. This report provides novel insights into the origin and evolution of bacterial genes involved in the syntrophic lifestyle.« less

Authors:
; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
898620
Report Number(s):
PNNL-SA-51609
TRN: US200706%%233
DOE Contract Number:
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Biochemical and Biophysical Research Communications, 352(1):48-54
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; AMINO ACIDS; BACTERIA; CODONS; DESULFOVIBRIO; GENES; HYPOTHESIS; ORIGIN; SULFATE-REDUCING BACTERIA; SULFATES; TREES; Syntrophy; Horizontal gene transfer involved in microbial syntrophy

Citation Formats

Scholten, Johannes C., Culley, David E., Brockman, Fred J., Wu, Gang, and Zhang, Weiwen. Evolution of the syntrophic interaction between Desulfovibrio vulgaris and Methanosarcina barkeri: involvement of an ancient horizontal gene transfer. United States: N. p., 2007. Web. doi:10.1016/j.bbrc.2006.10.164.
Scholten, Johannes C., Culley, David E., Brockman, Fred J., Wu, Gang, & Zhang, Weiwen. Evolution of the syntrophic interaction between Desulfovibrio vulgaris and Methanosarcina barkeri: involvement of an ancient horizontal gene transfer. United States. doi:10.1016/j.bbrc.2006.10.164.
Scholten, Johannes C., Culley, David E., Brockman, Fred J., Wu, Gang, and Zhang, Weiwen. Fri . "Evolution of the syntrophic interaction between Desulfovibrio vulgaris and Methanosarcina barkeri: involvement of an ancient horizontal gene transfer". United States. doi:10.1016/j.bbrc.2006.10.164.
@article{osti_898620,
title = {Evolution of the syntrophic interaction between Desulfovibrio vulgaris and Methanosarcina barkeri: involvement of an ancient horizontal gene transfer},
author = {Scholten, Johannes C. and Culley, David E. and Brockman, Fred J. and Wu, Gang and Zhang, Weiwen},
abstractNote = {The sulfate reducing bacteria Desulfovibrio vulgaris and the methanogenic archaea Methanosarcina barkeri can grow syntrophically on lactate. In this study, three functionally unknown genes of D. vulgaris, DVU2103, DVU2104 and DVU2108, were found to be up-regulated 2-4 fold following the lifestyle shift from syntroph to sulfatereducer; moreover, none of these genes were regulated when D. vulgaris was grown alone in various pure culture conditions. These results suggest that these genes may play roles related to the lifestyle change of D. vulgaris from syntroph to sulfate reducer. This hypothesis is further supported by phylogenomic analyses showing that homologies of these genes were only narrowly present in several groups of bacteria, most of which are restricted to a syntrophic life-style, such as Pelobacter carbinolicus, Syntrophobacter fumaroxidans, Syntrophomonas wolfei and Syntrophus aciditrophicus. Phylogenetic analysis showed that the genes tended to be clustered with archaeal genera, and they were rooted on archaeal species in the phylogenetic trees, suggesting that they originated from an archaeal methanogen and were horizontally transferred to a common ancestor of delta- Proteobacteria, Clostridia and Thermotogae. While lost in most species during evolution, these genes appear to have been retained in bacteria capable of syntrophic relationships, probably due to their providing a selective advantage. In addition, no significant bias in codon and amino acid usages was detected between these genes and the rest of the D. vulgaris genome, suggesting these gene transfers may have occurred early in the evolutionary history so that sufficient time has elapsed to allow an adaptation to the codon and amino acid usages of D. vulgaris. This report provides novel insights into the origin and evolution of bacterial genes involved in the syntrophic lifestyle.},
doi = {10.1016/j.bbrc.2006.10.164},
journal = {Biochemical and Biophysical Research Communications, 352(1):48-54},
number = ,
volume = ,
place = {United States},
year = {Fri Jan 05 00:00:00 EST 2007},
month = {Fri Jan 05 00:00:00 EST 2007}
}
  • Abstract Desulfovibrio vulgaris is a metabolically flexible microorganism. It can use sulfate as electron acceptor to catabolize a variety of substrates, or in the absence of sulfate can utilize organic acids and alcohols by forming a syntrophic association with hydrogen scavenging partner to relieve inhibition by hydrogen. These alternativemetabolic types increase the chance of survival for D. vulgaris in environments where one of the potential external electron acceptors becomes depleted. In this work, whole-genome D. vulgaris microarrays were used to determine relative transcript levels as D. vulgaris shifted its metabolism from syntroph in a lactate-oxidizing dual-culture with Methanosarcina barkeri tomore » a sulfidogenic metabolism. Syntrophic dual-cultures were grown in two independent chemostats and perturbation was introduced after six volume changes with the addition of sulfate. The results showed that 132 genes were differentially expressed in D. vulgaris 2 hours after addition of sulfate. Functional analyses suggested that genes involved in cell envelope and energy metabolism were the most regulated when comparing syntrophic and sulfidogenic metabolism. Up-regulation was observed for genes encoding ATPase and the membrane-integrated energy conserving hydrogenase (Ech) when cells shifted to a sulfidogenic metabolism. A five-gene cluster encoding several lipo- and membrane-bound proteins was down-regulated when cells were shifted to a sulfidogenic metabolism. Interestingly, this gene cluster has orthologs found only in another syntrophic bacterium Syntrophobacter fumaroxidans and four recently sequenced Desulfovibrio strains. This study also identified several novel c-type cytochrome encoding genes which may be involved in the sulfidogenic metabolism.« less
  • When grown in the absence of added sulfate, cocultures of Desulfovibrio desulfuricans or Desulfovibrio vulgaris with Methanobrevibacter smithii (Methanobacterium ruminantium), which uses H2 and CO2 for methanogenesis, degraded lactate, with the production of acetate and CH4. When D. desulfuricans or D. vulgaris was grown in the absence of added sulfate in coculture with Methanosarcina barkeri (type strain), which uses both H2-CO2 and acetate for methanogenesis, lactate was stoichiometrically degraded to CH4 and presumably to CO2. During the first 12 days of incubation of the D. desulfuricans-M. barkeri coculture, lactate was completely degraded, with almost stoichiometric production of acetate and CH4.more » Later, acetate was degraded to CH4 and presumably to CO2. In experiments in which 20 mM acetate and 0 to 20 mM lactate were added to D. desulfuricans-M. barkeri cocultures, no detectable degradation of acetate occurred until the lactate was catabolized. The ultimate rate of acetate utilization for methanogenesis was greater for those cocultures receiving the highest levels of lactate. A small amount of H2 was detected in cocultures which contained D. desulfuricans and M. barkeri until after all lactate was degraded. The addition of H2, but not of lactate, to the growth medium inhibited acetate degradation by pure cultures of M. barkeri. Pure cultures of M. barkeri produced CH4 from acetate at a rate equivalent to that observed for cocultures containing M. barkeri. Inocula of M. barkeri grown with H2-CO2 as the methanogenic substrate produced CH4 from acetate at a rate equivalent to that observed for acetate-grown inocula when grown in a rumen fluid-vitamin-based medium but not when grown in a yeast extract-based medium. The results suggest that H2 produced by the Desulfovibrio species during growth with lactate inhibited acetate degradation by M. barkeri. (Refs. 26).« less
  • A bacterial consortium capable of sucrose degradation primarily to CH/sub 4/ and CO/sub 2/ was constructed, with acetate as the key methanogenic precursor. In addition, the effect of agar immobilization on the activity of the consortium was determined. The primary fermentative organism, Escherichia coli, produced acetate, formate, H/sub 2/, and CO/sub 2/ (known substrates for methanogens), as well as ethanol and lactate, compounds that are not substrates for methanogens. Oxidation of the nonmethanogenic substrates, lactate and ethanol, to acetate was mediated by the addition of Acetobacterium woodii and Desulfovibrio vulgaris. The methanogenic stage was accomplished by the addition of themore » acetophilic methanogen Methanosarcina barkeri and the hydrogenophilic methanogen Methanobacterium formicicum. Results of studies with low substrate concentrations (0.05 to 0.2% (wt/vol)), a growth-limiting medium, and the five-component consortium indicated efficient conversion (40%) of sucrose carbon to CH/sub 4/. Significant decreases in yields of CH/sub 4/ and rates of CH/sub 4/ production were observed if any component of the consortium was omitted. Approximately 70% of the CH/sub 4/ generated occurred via acetate. Agar-immobilized cells of the consortium exhibited yields of CH/sub 4/ and rates of CH/sub 4/ production from sucrose similar to those of nonimmobilized cells. The rate of CH/sub 4/ production decreased by 25% when cysteine was omitted from reaction conditions and by 40% when the immobilized consortium was stored for 1 week at 4/sup 0/C.« less
  • Microbial formate production and consumption during syntrophic conversion of ethanol or lactate to methane was examined in purified flocs and digestor contents obtained from a whey-processing digestor. Formate production by digestor contents or purified digestor flocs was dependent on CO/sub 2/ and either ethanol or lactate but not H/sub 2/ gas as an electron donor. Floc preparations accumulated fourfold-higher levels of formate (40 ..mu..M) than digestor contents, and the free flora was the primary site for formate cleavage to CO/sub 2/ and H/sub 2/ (90 ..mu..M formate per h). Inhibition of methanogenesis by CHCl/sub 3/ resulted in formate accumulation andmore » suppression of syntrophic ethanol oxidation. H/sub 2/ gas was an insignificant intermediary metabolite of syntrophic ethanol conversion by flocs, and it exogenous addition neither stimulated methanogenes nor inhibited the initial rate of ethanol oxidation. These results demonstrated that >90% of the syntrophic ethanol conversion to methane by mixed cultures containing primarily Desulfovibrio vulgaris and Methanobacterium formicicum was mediated via interspecies formate transfer and the <10% was mediated via interspecies H/sub 2/ transfer. The results are discussed in relation to biochemical thermodynamics. A model is presented which describes the dynamics of a bicarbonate-formate electron shuttle mechanism for control of carbon and electron flow during syntrophic methanogenesis and provides a novel mechanism for energy conservation by syntrophic acetogens.« less
  • The fermentation of cellulose by monocultures of Acetivibrio cellulolyticus and cocultures of A. cellulolyticus-Methanosarcina barkeri, A. cellulolyticus-Desulfovibrio sp., and A. cellulolyticus-M. barkeri-Desulfovibrio sp. was studied. The monoculture produced ethanol, acetate, H, and CO. More acetate and less ethanol was formed by the cocultures than by the monoculture. Acetate was utilized by M. barkeri in coculture with A. cellulolyticus after a lag period, whereas ethanol was metabolized by the sulfate reducer only under conditions of low H partial pressure, i.e., when cocultured with A. cellulolyticus-M. barkeri or when grown together with the methanogen. Only the 3-component culture carried out the rapidmore » conversion of cellulose to CO2 and CH4. Furthermore, this culture hydrolyzed the most cellulose-85% of that initially present. This amount was increased to 90% by increasing the population of M. barkeri in the triculture. CH4 production was also increased, and a quicker fermentation rate was achieved.« less