High quality draft genome sequence of Meganema perideroedes str. Gr1T and a proposal for its reclassification to the family Meganemaceae fam. nov.
© McIlroy et al.; licensee BioMed Central. 2015
Received: 21 May 2014
Accepted: 27 November 2014
Published: 27 February 2015
Meganema perideroedes Gr1T is a filamentous bacterium isolated from an activated sludge wastewater treatment plant where it is implicated in poor sludge settleability (bulking). M. perideroedes is the sole described species of the genus Meganema and of the proposed novel family “Meganemaceae”. Here we describe the features of the type strain Gr1T along with its annotated genome sequence. The 3,409,949 bp long draft genome consists of 22 scaffolds with 3,033 protein-coding and 59 RNA genes and is a part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes KMG project. Notably, genome annotation indicated the potential for facultative methylotrophy. However, the ability to utilize methanol as a carbon source could not be empirically demonstrated for the type strain or for in situ Meganema spp. strains.
KeywordsActivated sludge Bulking Facultative methylotroph Filamentous Meganema Meganemaceae Wastewater
Classification and features
M. perideroedes Gr1T was initially reported to be affiliated with the Methylobacterium/Xanthobacter group based on the common major fatty acid C18:1 ω7c , which presumably led to its later classification to the family Methylobacteriaceae in ‘The All-Species Living Tree Project Database’ (release LTPs111) . However, in The Prokaryotes Manual 4 th Edition, this classification was suggested to be erroneous . The need for reclassification was primarily based on the lack of 16S rRNA gene relatedness of the M. perideroedes and other members of the Methylobacteriaceae family (see Figure 1), which was originally transcribed based solely on 16S rRNA based phylogeny . Kelly and others  noted that M. perideroedes had no closely related species (none > 90% 16S rRNA gene similarity), with no phenotypic traits that specifically associate it with other described bacterial families. As such, the authors suggested that Meganema be classified as a novel family, designated “Meganemaceae”, within the order Rhizobiales, or alternatively transferred to the family Caulobacteraceae within the order Caulobacterales based on Greengenes taxonomy . However, the latest release of the Greengenes taxonomy (October 2012) no longer classifies Meganema as such, and phylogenetic analysis does not appear to support its inclusion in either the Methylobacteriaceae or Caulobacteriaceae families (Figure 1). Therefore, we propose that the genus be classified to the novel family “Meganemaceae”.
Classification and general features of M. perideroedes Gr1 T 
Evidence code a
Species M. perideroedes
Type strain Gr1
Irregular disc-shaped in filaments
pH range; Optimum
Sample collection time
The main respiratory quinone is Q-10 and the fatty acid profile is dominated by C18:1ω7c (86.4%) with smaller amounts of C18:0 (3.8%), C16:0 (2.9%), summed feature 2 (C14:0 3-OH, C16:1 iso I)(2.4%), C18:0 3-OH (2.3%) and C19:0 10-methyl (1.1%) .
Genome sequencing and annotation
Genome project history
Level 2: High-Quality Draft
Illumina Std. shotgun library
Illumina HiSeq 2000,
Velvet v. 1.1.04; ALLPATHS v. r41043
Gene calling method
Genbank Date of Release
December 12, 2013
Tree of Life, GEBA-KMG
Source material identifier
Growth conditions and genomic DNA preparation
M. perideroedes Gr1T, DSM 15528, was grown in R2A medium (DSMZ medium 830) at 25°C . DNA was isolated from 0.5-1.0 g of cell paste using Jetflex DNA purification kit (GENOMED 600100) following the standard protocol provided by the manufacturer but modified by an incubation time of 60 min, incubation on ice overnight on a shaker, the use of an additional 50 μl proteinase K, and the addition of 100 μl protein precipitation buffer. DNA is available through the DNA Bank Network .
Genome sequencing and assembly
The draft genome sequence was generated using the Illumina technology . An Illumina Standard shotgun library was constructed and sequenced using the Illumina HiSeq 2000 platform which generated 14,100,926 reads totaling 2,115.1 Mbp. All general aspects of library construction and sequencing performed at the JGI can be found at . All raw Illumina sequence data was passed through DUK, a filtering program developed at JGI, which removes known Illumina sequencing and library preparation artifacts (Mingkun L, Copeland A, Han J. DUK. 2011, in preparation). The following steps were then performed for assembly: (1) filtered Illumina reads were assembled using Velvet , (2) 1–3 kbp simulated paired end reads were created from Velvet contigs using wgsim , (3) Illumina reads were assembled with simulated read pairs using Allpaths–LG . Parameters for assembly steps were: 1) Velvet (velveth: 63 –shortPaired and velvetg: −very clean yes –export-Filtered yes –min contig lgth 500 –scaffolding no –cov cutoff 10) 2) wgsim (−e 0 –1 100 –2 100 –r 0 –R 0 –X 0) 3) Allpaths–LG (PrepareAllpathsInputs: PHRED 64 = 1 PLOIDY = 1 FRAG COVERAGE = 125 JUMP COVERAGE = 25 LONG JUMP COV = 50, RunAllpathsLG: THREADS = 8 RUN = std shredpairs TARGETS = standard VAPI WARN ONLY = True OVERWRITE = True). The final draft assembly contained 22 contigs in 22 scaffolds. The total size of the genome is 3.4 Mbp and the final assembly is based on 368.8 Mbp of Illumina data, which provides an average 108.2 × coverage of the genome.
Genes were identified using Prodigal  as part of the DOE-JGI genome annotation pipeline , followed by a round of manual curation using the JGI GenePRIMP pipeline . The predicted CDSs were translated and used to search the NCBI non-redundant database, UniProt, TIGR-Fam, Pfam, PRIAM, KEGG, COG, and InterPro database. These data sources were combined to assert a product description for each predicted protein. Additional gene prediction analysis and functional annotation was performed within the IMG-ER platform . Pathway assessment for genomic insights also utilized the ‘MicroScope’ pipeline .
% of total
Genome size (bp)
DNA coding (bp)
DNA G + C (bp)
Genes in internal clusters
Genes with function prediction
Genes assigned to COGs
Genes assigned Pfam domains
Genes with signal peptides
Genes with transmembrane helices
Number of genes associated with the 25 general COG functional categories
Translation, ribosomal structure and biogenesis
RNA processing and modification
Replication, recombination and repair
Chromatin structure and dynamics
Cell cycle control, cell division, chromosome partitioning
Signal transduction mechanisms
Cell wall/membrane/envelope biogenesis
Intracellular trafficking, secretion, and vesicular transport
Posttranslational modification, protein turnover, chaperones
Energy production and conversion
Carbohydrate transport and metabolism
Amino acid transport and metabolism
Nucleotide transport and metabolism
Coenzyme transport and metabolism
Lipid transport and metabolism
Inorganic ion transport and metabolism
Secondary metabolites biosynthesis, transport and catabolism
General function prediction only
Not in COGs
Insights from the genome sequence
Analysis of the genome of M. perideroedes Gr1T indicates the potential for storage of polyphosphate, PHAs and glycogen, with the former two polymers supported by selective stains in axenic culture and in situ strains in activated sludge [1,9]. Storage of such polymers is common in Bacteria, and shown to be key to the metabolic strategies of several activated sludge organisms, such as the PAO and GAO phenotypes . The PAO utilize aerobically stored polyphosphate to energize anaerobic carbon uptake. Whilst Meganema spp. appear to be able to store polyphosphates, they are unable to assimilate carbon anaerobically . This may in part be due to the absence of the low affinity phosphate Pit transport gene, suggested to be key to the use of polyphosphate for energizing anaerobic carbon uptake in the PAO [38,39]. Distribution of Meganema spp. appears somewhat restricted to industrial WWTPs, without the anaerobic tanks implemented in EBPR plants. Thus the ability to assimilate PHA likely provides advantage during intermittent periods of carbon starvation or under the unbalanced growth conditions (i.e. high COD to N:P ratio) that often characterize industrial waste streams. Such an explanation was suggested for members of the alphaproteobacterial genus Amaricoccus, which also assimilate relatively high PHA reserves and only appear in high abundance in aerated systems treating industrial wastes [40-42].
A novel finding with analysis of the Gr1T genome was the apparent potential for methylotrophic growth. Putative genes for a methanol dehydrogenase (EC. 126.96.36.199), the formaldehyde oxidation pathway (glutathione-dependent), and a formate dehydrogenase (EC 188.8.131.52), were collocated on a putative operon in the genome. These together catalyze the oxidation of methanol to carbon dioxide via formaldehyde . Analysis of potential assimilatory pathways for C1 compounds  revealed that key genes were missing for the described serine and ribulose monophosphate pathways, but present for the CBB cycle. Therefore, methanol may be assimilated, via oxidation to CO2, through the CBB carbon fixation pathway. Such a phenotype, sometimes referred to as “pseudomethylotrophy” or “autotrophic methylotrophy” , has previously been demonstrated for other related members of the order Rhizobiales [43,45]. Given the annotated potential for facultative methylotrophy, experimental validation of the ability was assessed in pure culture and for in situ community strains present in an environmental sample (for details see Additional file 1). Attempts to grow strain Gr1T on media with methanol as the sole carbon source were unsuccessful. More comprehensive experimental work is required to assess the ability for, and nature of, methylotrophic growth of the Gr1T strain. Methanol assimilation was also not detected for probe-defined in situ strains of the genus in the Grindsted WWTP (Additional file 1). The same negative result was obtained for formate assimilation in previous FISH-MAR investigations of the genus . Thus, the ability for methylotrophy is yet to be empirically demonstrated for the genus and the importance of methanol metabolism remains to be resolved. In the case of the activated sludge environment, utilisation of other carbon sources in situ, including stored PHA, would be more energetically favorable. Methanol and/or formate oxidation to CO2 may supplement energy derived from other sources, or may not be important substrates for these organisms in activated sludge. This is consistent with previous observations that microorganisms in environmental systems are demonstrated to have more specialized physiologies and niches despite metabolic potentials for more diverse activities .
Putative denitrification genes were not located in the genome, supporting axenic characterisation of the Gr1 strain, which was unable to grow with nitrate as electron acceptor . In situ strains of the genus have been demonstrated to assimilate some substrates anoxically in the presence of nitrate or nitrite, indicating an ability for denitrification . Thus, members of the genus appear to vary in their potential for denitrification. The capacity to fix atmospheric nitrogen is common for other methylotrophic bacteria , but the absence of a nitrogenase (EC 184.108.40.206) indicates that this is not the case for M. perideroedes Gr1 T .
Description of Meganemaceae fam. nov.
Meganemaceae (Me.ga.nem.a'ce.ae. N.L. neut. n. Meganema, type genus of the family; suff. -aceae ending denoting a family; N.L. fem. pl. n. Meganemaceae, the family of Meganema).
Filamentous morphology with irregular disc shaped cells. Cells stain Gram-negative and, Nile Blue and Neisser positive. The major quinone is Q-10. Fatty acid profiles are dominated by C18:1ω7c; characteristic hydroxy acids are C14:0 3-OH and C18:0 3-OH. Meganemaceae belongs to the order Rhizobiales and the type genus is Meganema.
The draft genome sequence of M. perideroedes Gr1T is 3.4 Mbp, consisting of 22 scaffolds with 3,033 protein-coding genes. The annotated ability of the organism for facultative methylotrophy could not be demonstrated in either pure culture or for in situ strains. Further work is required to elucidate the role of these pathways for the organism, and why they are maintained in the genome. The genome sequence presented here provides a resource for more detailed investigations of this biotechnologically important organism. Based on 16S rRNA gene analysis we formally propose the novel family Meganemaceae to include the genus Meganema.
Chemical oxygen demand
Enhanced biological phosphorus removal
Fluorescence in situ hybridization
Glycogen accumulating organism
Integrated Microbial Genomes-Expert Review
Minimal information about a genome sequence
Polyphosphate accumulating organism
Wastewater treatment plant
The authors gratefully acknowledge the assistance of J Ildal and M Stevenson at the Center for Microbial Communities for technical assistance, Anja Frühling for growing M. perideroedes cultures and Evelyne-Marie Brambilla for DNA extraction and quality control (both at the DSMZ). We also acknowledge the LABGeM team at Genoscope for providing access to their automated annotation pipeline as well as for database maintenance and technical assistance. This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344. A.L. was supported in part by Russian Ministry of Science Mega-grant no.11.G34.31.0068 (PI. Dr Stephen J O'Brien).
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