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The Genus Pelobacter

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The Genus Pelobacter s Genu Pelobacter The Genus Pelobacter BERNHARD SCHINK The genus Pelobacter was proposed as a taxonomic entity Viable counts using the characteristic substrates consisting of strictly anaerobic, Gram-negative, nonspore- gallic acid, acetoin, polyethylene glycol, and forming, rod-shaped bacteria that use only a very limited acetylene showed that there were approximately number of substrates. The members of the genus are all 100 cells/ml of each of the Pelobacter species in unable to ferment sugars and therefore cannot be grouped sediment and up to 2,500 cells/ml in sewage with any other genus in the family Bacteroidaceae (Krieg and Holt, 1984). The genus comprises five different species, P. sludge. Since their substrate ranges are compa- acidigallici (Schink and Pfennig, 1982), P. venetianus (Schink rably small, their ecological niche in such sedi- and Sti eb, 1983), P. carbinolicus (Schink, 1984), P. propioni- ments can be understood rather well in most cus (Schink, 1984), and P. acetylenicus (Schink, 1985), which cases. P. acidigallici is restricted to the utilization all are based on 3–5 described strains. of trihydroxybenzenoids, which are probably its Comparisons of the various Pelobacter species by DNA- only energy source in its natural habitat. P. vene- DNA hybridization experiments revealed that the genus is tianus, P. carbinolicus, P. propionicus, and P. rather inhomogenous; therefore, a reorganization may per- acetylenicus were enriched and isolated with haps be necessary in the future (J. P. Touzel and B. Schink, polyethylene glycol, 2,3-butanediol, and acety- unpublished observations). Whereas the species P. vene- lene, respectively, but the ecological importance tianus, P. carbinolicus, and P. acetylenicus form a homoge- nous cluster, P. acidigallici and P. propionicus appear to be of these substrates in the respective environ- only distantly related to the others. These findings are con- ments is questionable. Since all these species can sistent to some extent with the fermentation patterns of these also ferment ethanol, either in syntrophic coop- species (see below). Comparison of three Pelobacter species eration with hydrogen scavengers or in pure cul- with other anaerobes on the basis of 16S rRNA structure ture, it appears more probable that degradation analysis supports this view. Whereas P. venetianus and P. of this important fermentation intermediate is carbinolicus exhibit a rather high similarity, with an SAB of their predominant function in these environ- 0.70, P. acidigallici is related to both at an SAB of only 0.53 ments. P. carbinolicus has been identified as (Stackebrandt et al., 1989). It is interesting to note that these the dominant ethanol-degrading bacterium in three Pelobacter strains did not show any resemblance to digesting industrial sewage sludge (Dubourguier other fermenting Gram-negative strict anaerobes; instead, 6 7 they appeared to be highly related to several strains of sulfur- et al., 1986), and high numbers (10 –10 cells/ml) reducing anaerobes, namely, Desulfuromonas succinoxidans, of syntrophically ethanol-oxidizing anaerobes D. acetexigens, and D. acetoxidans, to which they are even were detected also in other sewage sludges more closely related than P. acidigallici is to the other two (Schink et al., 1985) and in freshwater creek sed- Pelobacter species. Since Pelobacter species and the obli- iments (Eichler and Schink, 1985). Pelobacter gately sulfur-respiring bacteria are quite diverse metaboli- has to compete for ethanol with certain homo- cally and the latter are supposed to have derived directly acetogenic bacteria, e.g., Clostridium aceticum from phototrophic ancestors, it has been suggested that the (Wieringa, 1940) or Acetobacterium carbinoli- genus Pelobacter represents a group of fermenting bacteria cum (Eichler and Schink, 1984), which appear to that developed a fermentative metabolism as a “secondary” be at least as successful in freshwater sediments evolutionary event and that they are separate from the first fermentative bacteria (Stackebrandt et al., 1989). (Schink et al., 1985), especially if the sediment is slightly acidic (Schink et al., 1985) or the temper- ature is low (Conrad et al., 1989). The ecological importance of ethanol fermentation to propi- Habitat onate by P. propionicus has been elucidated by enumerations and by tracer experiments (Schink All Pelobacter strains have been isolated so far et al., 1985). These studies revealed that up to from marine or freshwater sediments. The name 20% of the total ethanol turnover can go through Pelobacter was based on this origin (Greek pelos propionate and that bacteria forming propionate meaning mud, sediment). Enrichments from from ethanol contribute significantly to the total sewage sludges led to similar isolates as well. ethanol-metabolizing microbial community. It has to be concluded that bacteria of the This chapter was taken unchanged from the second edition. metabolic types represented by the various Pelo- 6 bacter species make up a significant part of the ment solution, e.g., SL 10 (Widdel et al., 1983); d) 0.5 ml anaerobic microbial population in sediments and of 10-fold concentrated, filter-sterilized vitamin solution sewage sludge. No Pelobacter-like bacteria have (Pfennig, 1978); and e) adequate amounts of sterile 1 M so far been isolated from the rumen. The numer- HC1 or 1 M Na2 CO3 to adjust the pH to 7.1–7.3. ically predominant, syntrophically ethanol- The complete medium is dispensed into either screw- cap bottles or screw-cap tubes which are filled completely oxidizing Pelobacter species represent new to the top, leaving a lentil-sized air bubble for pressure isolates of the metabolic type of the S-strain in equilibration. Enrichment cultures usually produce gas the mixed culture “Methanobacillus omelianskii” in the first enrichment stages and are better cultivated (Bryant et al., 1967). These Pelobocter species in half-filled serum bottles (50–100 ml volume) under have become accessible to pure culture growth a headspace of nitrogen: carbon dioxide mixture in our laboratory by the use of unusual substrates (90%:10%). that all can be converted easily into acetalde- This mineral medium is amended with the respective hyde, the key intermediate in the energy metab- organic substrates for enrichment and cultivation of pure olism of these bacteria (see next section). cultures. The vitamin mixture is not really needed by all strains. Isolation Selective Enrichment Growth Media All enrichment cultures were set up in our labo- ratory at 27–30∞C in 50-ml fluid cultures inocu- All Pelobacter strains have been enriched and lated with about 5 ml of sediment or sludge. isolated in a carbonate-buffered, sulfide-reduced Smaller inocula may also lead to isolation of the mineral medium that contained only one organic same bacteria, but this has not been evaluated in energy and carbon source. Since they grow with our lab. P. acidigallici can be selectively enriched substrates that yield 2-carbon intermediates with either one of its growth substrates (see exclusively, they have to form pyruvate and sug- Table 1) at 5–10 mM concentration. For enrich- ars via reductive carboxylation of acetyl coen- ment of P. venetianus,either polyethylene glycol zyme A and need carbon dioxide for this (mol wt 106–20,000; 0.1% w/v) or methoxyetha- reaction. Use of a bicarbonate-buffered medium nol (10 mM; Tanaka and Pfennig, 1988) is recom- is therefore recommended for enrichment, isola- mended. In this medium, 10 mM 2,3-butanediol tion, and maintenance. Three different versions enriches for P. carbinolicus from marine sedi- of this medium are described below for the iso- ments and for P. propionicus from freshwater lation of Pelobacter from freshwater, estuarine, sediments. P. acetylenicus is successfully enriched and marine sediment, respectively (after Widdel with mineral medium under the above- and Pfennig, 1981; Schink and Pfennig, 1982): mentioned nitrogen: carbon dioxide atmosphere containing 5–10% acetylene in addition. Pelobacter Growth Media Dissolve in 1 liter of distilled water: Autoclave the complete mineral medium in a vessel Isolation equipped with 1) a filter inlet to allow flushing of the headspace with sterile oxygen-free gas; 2) screw-cap After 3–4 transfers in liquid medium, a homoge- inlets for addition of thermally unstable additives after neous microbial population should have become autoclaving; 3) a silicon tubing connection from the bot- established in liquid enrichment cultures. Purifi- tom of the vessel out to a dispensing tap (if possible with cation of Pelobacter species is most easily done a protecting bell) for sterile dispensing of the medium (do by serial dilution in agar deep cultures (“agar not use latex tubing; it releases compounds which are shakes”; Pfennig, 1978). Roll tubes have not highly toxic to many anaerobes); and 4) a stirring bar. been used and are not necessary since these bac- After autoclaving, connect the vessel with the still-hot teria neither consume nor produce insoluble gas- medium to a line of oxygen-free nitrogen/carbon dioxide mixture (90%: 10%) at low pressure (<100 mbar), flush eous compounds. P. acetylenicus can be easily the headspace and cool it under this atmosphere to room purified with 10 mM acetoin as substrate. Other temperature, perhaps with the help of a cooling water procedures (streaking on agar plates in an anoxic bath. glove box or on agar surfaces in flat agar bottles) The mineral medium is amended with the following have not been tried yet, but there is no reason additions
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