Free access
9 November 2012

Genome Sequence of “Candidatus Microthrix parvicella” Bio17-1, a Long-Chain-Fatty-Acid-Accumulating Filamentous Actinobacterium from a Biological Wastewater Treatment Plant


Candidatus Microthrix” bacteria are deeply branching filamentous actinobacteria which occur at the water-air interface of biological wastewater treatment plants, where they are often responsible for foaming and bulking. Here, we report the first draft genome sequence of a strain from this genus: “Candidatus Microthrix parvicella” strain Bio17-1.


Actinobacteria of the genus “Candidatus Microthrix” are commonly found in biological wastewater treatment plants, where they are considered notorious in causing solid-liquid separation problems and foaming (see reference 14 for a recent review). On culture media they grow meagerly, yet they seem to have an in situ competitive advantage mediated by their avid uptake of long-chain fatty acids, which are accumulated as neutral lipids under anaerobic conditions and converted into phospholipids for cell division under aerobic conditions (1, 13).
Here, we present the draft genome sequence of “Candidatus Microthrix parvicella” Bio17-1, a strain isolated from a Dutch wastewater treatment plant serving fish industries (10). First, two sequencing libraries were prepared from genomic DNA with mean insert lengths of 350 bp (paired ends) or 2,750 bp (mated pairs) and sequenced on an Illumina Genome Analyzer II. Raw 100-bp reads were error corrected with Quake (8). A total of 5.84 × 106 paired-end and 1.12 × 106 single-end reads with a minimum mean quality value of 30 and a minimum length of 70 bp were used for assemblies. Second, 24,031 single molecule, real-time (SMRT) sequence reads were obtained on a Pacific Biosciences PacBio RS using C1 chemistry. Error correction yielded 2,625 reads (232 to 1,984 bp).
Using the Illumina sequence reads, two preliminary assemblies were obtained with Velvet (17) and Edena (7) and merged with the minimus2 utility (16). The resulting 27 contigs were scaffolded with SSPACE (3), and gaps were filled with GapFiller (4). Additional assemblies were obtained using SOAPdenovo (11) (kmer values between 65 and 81, steps of 2) and CABOG (12). Error-corrected PacBio reads (9) were mapped onto the preliminary assemblies. Draft contigs were broken where discrepancies among assemblies or PacBio reads suggested misassemblies. Conversely, contigs were joined where contig ends overlapped with perfect identity for at least 500 bp. Manual curation of the assemblies was performed using Consed (5). Automatic annotation and draft metabolic reconstruction were performed by the RAST server (2). CRISPR loci were identified using CRISPRFinder (6).
The draft assembly consists of 4,202,850 bp, arranged in 13/16 scaffolds/contigs, with a mean GC content of 66.4%. Automated annotation identified 4,063 coding sequences, in addition to 1 rRNA operon and 46 tRNAs covering all amino acids. A complete pentose phosphate pathway and tricarboxylic acid (TCA) cycle are encoded in the genome. As previously hypothesized for “Candidatus Microthrix parvicella” strain RN1 (15), a nitrate reductase is encoded by the genome, but no nitrite reductase appears to be present. The strain is also predicted to be a prototroph for all amino acids, to be able to polymerize/depolymerize polyhydroxybutyrate, to accumulate polyphosphate, and to translate several selenoproteins. No genes are annotated that are related to photosynthesis. The assembly contains one CRISPR locus with 88 spacers.
Candidatus Microthrix parvicella” Bio17-1's ability to process and accumulate excessive amounts of fatty acids is highlighted by its gene content: the genome encodes 28 homologs of long-chain fatty acid–acyl coenzyme A (acyl-CoA) ligase and 17 of enoyl-CoA hydratase. The genetic inventory of “Candidatus Microthrix parvicella” makes it of particular interest for future wastewater treatment strategies based around the comprehensive reclamation of nutrients and chemical energy-rich biomolecules.

Nucleotide sequence accession numbers.

The genome sequence of “Candidatus Microthrix parvicella” strain Bio17-1 has been deposited at DDBJ/EMBL/GenBank under accession number AMPG00000000; the version described in this paper is the first version, AMPG01000000. A provisional annotation is available upon request. Raw sequence reads were deposited in the Sequence Read Archive under accession number SRA058866.


This project received financial support from the Integrated Biobank of Luxembourg with funds from the Luxembourg Ministry of Higher Education and Research, from an ATTRACT program grant to P.W. (ATTRACT/A09/03), and from an Aide à la Formation Recherche (AFR) grant to E.E.L.M. (PRD-2011-1/SR), all funded by the Luxembourg National Research Fund (FNR). We also thank the Luxembourg Centre for Systems Biomedicine and the University of Luxembourg for support of N.P.


Andreasen K and Nielsen PH. 1998. In situ characterization of substrate uptake by Microthrix parvicella using microautoradiography. Water Sci. Technol. 37:19–26.
Aziz RK et al. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75.
Boetzer M, Henkel CV, Jansen HJ, Butler D, and Pirovano W. 2011. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27:578–579.
Boetzer M and Pirovano W. 2012. Toward almost closed genomes with GapFiller. Genome Biol. 13:R56.
Gordon D, Abajian C, and Green P. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8:195–202.
Grissa I and Vergnaud G. 2007. CRISPRFinder: a Web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 35:W52–7.
Hernandez D, François P, Farinelli L, Østerås M, and Schrenzel J. 2008. De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res. 18:802–809.
Kelley DR, Schatz MC, and Salzberg SL. 2010. Quake: quality-aware detection and correction of sequencing errors. Genome Biol. 11:R116.
Koren S et al. 2012. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat. Biotechnol. 30:693–700.
Levantesi C et al. 2006. Phylogeny, physiology and distribution of “Candidatus Microthrix calida,” a new Microthrix species isolated from industrial activated sludge wastewater treatment plants. Environ. Microbiol. 8:1552–1563.
Li R et al. 2010. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20:265–272.
Miller JR et al. 2008. Aggressive assembly of pyrosequencing reads with mates. Bioinformatics 24:2818–2824.
Nielsen PH, Roslev P, Dueholm TE, and Nielsen JL. 2002. Microthrix parvicella, a specialized lipid consumer in anaerobic-aerobic activated sludge plants. Water Sci. Technol. 46:73–80.
Rossetti S, Tomei MC, Nielsen PH, and Tandoi V. 2005. “Microthrix parvicella,” a filamentous bacterium causing bulking and foaming in activated sludge systems: a review of current knowledge. FEMS Microbiol. Rev. 29:49–64.
Tandoi V, Rossetti S, Blackall L, and Majone M. 1998. Some physiological properties of an Italian isolate of Microthrix parvicella. Water Sci. Technol. 37:1–8.
Treangen TJ, Sommer DD, Angly FE, Koren S, and Pop M. 2011. Next generation sequence assembly with AMOS. Curr. Protoc. Bioinformatics 33:11.8.1–11.8.18.
Zerbino DR and Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821–829.

Information & Contributors


Published In

cover image Journal of Bacteriology
Journal of Bacteriology
Volume 194Number 231 December 2012
Pages: 6670 - 6671
PubMed: 23144412


Received: 21 September 2012
Accepted: 28 September 2012
Published online: 9 November 2012


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Emilie E. L. Muller
Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
Nicolás Pinel
Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
Institute for Systems Biology, Seattle, Washington, USA
John D. Gillece
TGen North, Flagstaff, Arizona, USA
James M. Schupp
TGen North, Flagstaff, Arizona, USA
Lance B. Price
TGen North, Flagstaff, Arizona, USA
David M. Engelthaler
TGen North, Flagstaff, Arizona, USA
Caterina Levantesi
Water Research Institute, CNR, Monterotondo, Italy
Valter Tandoi
Water Research Institute, CNR, Monterotondo, Italy
Khai Luong
Pacific Biosciences, Menlo Park, California, USA
Nitin S. Baliga
Institute for Systems Biology, Seattle, Washington, USA
Jonas Korlach
Pacific Biosciences, Menlo Park, California, USA
Paul S. Keim
TGen North, Flagstaff, Arizona, USA
Northern Arizona University, Flagstaff, Arizona, USA
Paul Wilmes
Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg


Address correspondence to Paul Wilmes, [email protected].
E.E.L.M. and N.P. contributed equally to this work.

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