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Working Draft Genome Sequence of the Mesophilic Acetate Oxidizing Manzoor et al. Standards in Genomic Sciences (2015) 10:99 DOI 10.1186/s40793-015-0092-z SHORT GENOME REPORT Open Access Working draft genome sequence of the mesophilic acetate oxidizing bacterium Syntrophaceticus schinkii strain Sp3 Shahid Manzoor1,3, Bettina Müller2*, Adnan Niazi1, Anna Schnürer2 and Erik Bongcam-Rudloff1 Abstract Syntrophaceticus schinkii strain Sp3 is a mesophilic syntrophic acetate oxidizing bacterium, belonging to the Clostridia class within the phylum Firmicutes, originally isolated from a mesophilic methanogenic digester. It has been shown to oxidize acetate in co-cultivation with hydrogenotrophic methanogens forming methane. The draft genome shows a total size of 3,196,921 bp, encoding 3,688 open reading frames, which includes 3,445 predicted protein-encoding genes and 55 RNA genes. Here, we are presenting assembly and annotation features as well as basic genomic properties of the type strain Sp3. Keywords: Syntrophic acetate oxidizing bacteria, Acetogens, Syntrophy, Methanogens, Hydrogen producer, Methane production Introduction [2] and Thermotoga lettingae [8] currently renamed to During anaerobic degradation of organic material, acet- Pseudothermotoga lettingae have been isolated and charac- ate is formed as a main fermentation product, which is terized. Among those, two complete genome sequences of further converted to methane. Two mechanisms for me- T. phaeum [9], “T. acetatoxydans” [10] and one draft gen- thane formation from acetate have been described: The ome sequence of C. ultunense [11] have been published, first one is carried out by aceticlastic methanogens con- the later two by this working group. Here, we are present- verting acetate to methane and CO2 under low ammonia ing the draft genome sequence of the third mesophilic conditions [1]. The second mechanism, dominating under SAOB Syntrophaceticus schinkii strain Sp3. To date, high ammonia conditions, occurs in two steps, and is per- strain Sp3 is the only isolated and characterized repre- formed by acetate-oxidizing bacteria oxidizing acetate to sentative of the species S. schinkii and was recovered H2 (formate) and CO2 and a methanogenic partner using from an up flow anaerobic filter treating wastewater the hydrogen (formate) to reduce CO2 to methane [2–4]. from a fishmeal factory [6]. This process was character- −1 + Most fascinating on this syntrophic relationship is, that ized by high ammonium concentration (6.4 g l NH4). − the overall reaction operates with a ΔG°´ of -36 kJ x mol 1 S. schinkii shows the least narrow substrate spectrum close to the thermodynamic equilibrium. compared to all known SAOB, when growing heterotro- The number of isolated and characterized SAOB is phically [6]. The main end product formed is acetate, what restricted most likely due to their considerable differ- allocates the species to the physiological group of ences in substrate utilization abilities and cultivation acetogens. requirements. To date three mesophilic SAOB, namely Since the recovery of S. schinkii we found it at high Clostridium ultunense [5], Syntrophaceticus schinkii [6], abundance in all mesophilic large scale and lab scale bio- “Tepidanaerobacter acetatoxydans” [7] and two gas producing process we have investigated so far. Gen- thermophilic SAOB, namely Thermacetogenium phaeum ome analysis and comparative genomics might help us to understand general features of syntrophy in particular * Correspondence: [email protected] 2Department of Microbiology, Swedish University of Agricultural Sciences, BioCenter, Uppsala SE 750 07, Sweden Full list of author information is available at the end of the article © 2015 Manzoor et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Manzoor et al. Standards in Genomic Sciences (2015) 10:99 Page 2 of 8 Organism information Classification and features Syntrophaceticus schinkii Sp3 (Fig. 1) is an obligate an- aerobic, endospores forming bacterium, whose cells were found to be Gram variable with changing shapes dependent on the growth condition (Table 1, [6]). No flagella have been observed under any condition tested. It can grow up to 0.6 M NH4Cl in pure culture between 25 °C and 40 °C. A more detailed physiological descrip- tion can be found in Westerholm et al. [6]. Minimum Information about the Genome Sequence (MIGS) of S. schinkii strain Sp3 is provided in Table 1 and Table S1 (Additional file 1). Phylogentic analysis of the single 16S rRNA gene copy affiliates S. schinkii strain Sp3 to the Clostridia class Fig. 1 Image. Phase-contrast micrograph of Syntrophaceticus schinkii strain Sp3 within the phylum Firmicutes. The RDP Classifier ([12] 2015-08-05) confirmed further the affiliation to Thermo- anaerobacteraceae as published by [6] in 2011 (Table 1). energy conservation and electron transfer mechanisms The comparison of the 16S rRNA gene sequence with the during syntrophic acetate oxidation. latest available databases from GenBank (2015-08-05) using The present study summarizes genome sequencing, NCBI BLAST [13] under default settings identified the assembly and annotation as well as general genomic thermophilic SAOB T. phaeum (NR_074723.1) as the clos- properties of the Syntrophaceticus schinkii strain Sp3 est characterized relative sharing 92.12 % identity (Fig. 2). S. genome. schinkii is only distantly related to the characterized meso- philic SAOB C. ultunense ( 82.54 % identity), and “T. Fig. 2 Phylogentic tree. Phylogenetic tree highlighting the relationship of Syntrophaceticus schinkii Sp3 relative to known SAOB, acetogens, and other syntrophic operating bacteria. The 16S rRNA-based alignment was carried out using MUSCLE [32] and the phylogenetic tree was inferred from 1,521 aligned characteristics of the 16S rRNA gene sequence using the maximum-likelihood (ML) algorithm [33] with MEGA 6.06 [34, 35]. Bootstrap analysis [36] with 100 replicates was performed to assess the support of the clusters Manzoor et al. Standards in Genomic Sciences (2015) 10:99 Page 3 of 8 Table 1 Classification and general features of Syntrophaceticus schinkii strain Sp3 according to the “minimum information about a Genome Sequence” (MIGS) specification [22] MIGS ID Property Term Evidence codea Classification Domain Bacteria TAS [23, 24] Phylum Firmicutes TAS [25] Class Clostridia TAS [26, 27] Order Thermoanaerobacterales TAS [26] (p132), [28] Family Thermoanaerobacteraceae TAS [26] (p132), [29] Genus Syntrophaceticus TAS [6, 30] Species Syntrophaceticus schinki TAS [6, 30] Strain Sp3 TAS [6] Gram stain Variable TAS [6] Cell shape Variable b TAS [6] Motility Non motile TAS [6] Sporulation Terminal endospores TAS [6] Temperature range Mesophilic TAS [6] Optimum temperature 37–40 °C TAS [6] Carbon source Heterotroph TAS [6] Energy source Chemoheterotroph TAS [6] MIGS-6 Habitat Anaerobic sludge TAS [6] MIGS-6.3 Salinity Up to 0.6 M NH4Cl TAS [6] MIGS-22 Oxygen Obligate anaerob TAS [6] MIGS-15 Biotic relationship Syntrophy (beneficial) TAS [6] MIGS-14 Pathogenicity Not reported NAS MIGS-4 Geographic location Spain NAS MIGS-5 Sample collection time 1992 NAS MIGS-4.1 Latitude 42.851329 NAS MIGS-4.2 Longitude −8.475933 NAS MIGS-4.3 Depth Not reported NAS MIGS-4.4 Altitude Not reported NAS aEvidence codes—TAS Traceable Author Statement (i.e., a direct report exists in the literature), NAS Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). Evidence codes are from the Gene Ontology project [31]. b Shape of cells varies between cocci and straight or slightly curved rods depend on NH4Cl concentration [6] acetatoxydans” (84.1 % identity) and the thermophilic P. on the basis of environmental relevance to issues in global lettingae (79.64 %). Although S. schinkii has been physiolo- carbon cycling, alternative energy production, and bio- gically affiliated to the group of acetogens, Fig. 2 illustrates a chemical importance. Table 2 contains the summary of pro- distant relationship to this group, as represented by e.g. the ject information. model acetogen Moorella thermoacetica (89.15 % identity). Genome sequencing information Growth conditions and genomic DNA preparation Genome project history Since isolation by our research group, the strain has been Syntrophaceticus schinkii strain Sp3 was sequenced and kept in liquid cultures and a live culture and medium have annotated by the SLU-Global Bioinformatics Centre at been sent to DSMZ, (DSM21860). For DNA isolation batch the Swedish University of Agricultural Sciences, Uppsala, cultures were grown in basal medium supplemented with Sweden. The genome project is deposited in the Ge- 20 mM betaine as described by Westerholm et al. [6]. Cells nomes OnLine Database [14] with GOLD id Gi0035837 weregrownfor4weeksat37°Cwithoutshakingandhar- and the working draft genome is deposited in the Euro- vested at 5000 × g. DNA was isolated using the Blood & pean Nucleotide Archive database with accession num- Tissue Kit from Qiagen (Hilden,
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