High quality draft genome sequence of Meganema perideroedes str. Gr1T and a proposal for its reclassification to the family Meganemaceae fam. nov.

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.

[1]  S. Rossetti,et al.  Synthesis of intracellular storage polymers by Amaricoccus kaplicensis, a tetrad forming bacterium present in activated sludge , 2001, Journal of applied microbiology.

[2]  Stefan Engelen,et al.  MicroScope: a platform for microbial genome annotation and comparative genomics , 2009, Database J. Biol. Databases Curation.

[3]  I-Min A. Chen,et al.  The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata , 2007, Nucleic Acids Res..

[4]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[5]  J. Nielsen,et al.  Microautoradiographic Study of Rhodocyclus-Related Polyphosphate-Accumulating Bacteria in Full-Scale Enhanced Biological Phosphorus Removal Plants , 2004, Applied and Environmental Microbiology.

[6]  K. Schleifer,et al.  Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses. , 2010, Systematic and applied microbiology.

[7]  Aaron Marc Saunders,et al.  ‘Candidatus Competibacter’-lineage genomes retrieved from metagenomes reveal functional metabolic diversity , 2013, The ISME Journal.

[8]  D. Dionisi,et al.  Storage of biodegradable polymers by an enriched microbial community in a sequencing batch reactor operated at high organic load rate , 2005 .

[9]  E. Geldreich,et al.  A new medium for the enumeration and subculture of bacteria from potable water , 1985, Applied and environmental microbiology.

[10]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[11]  R. Amann,et al.  Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations , 1990, Applied and environmental microbiology.

[12]  J. Nielsen,et al.  Ecophysiology of the filamentous Alphaproteobacterium Meganema perideroedes in activated sludge. , 2005, FEMS microbiology ecology.

[13]  D. Dionisi,et al.  Enrichment of activated sludge in a sequencing batch reactor for polyhydroxyalkanoate production. , 2006, Water science and technology : a journal of the International Association on Water Pollution Research.

[14]  Simon J McIlroy,et al.  In situ profiling of microbial communities in full-scale aerobic sequencing batch reactors treating winery waste in australia. , 2011, Environmental science & technology.

[15]  W. Liesack,et al.  Methylotrophic Autotrophy in Beijerinckia mobilis , 2005, Journal of bacteriology.

[16]  Natalia N. Ivanova,et al.  The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes , 2009, Standards in genomic sciences.

[17]  K. Schleifer,et al.  ARB: a software environment for sequence data. , 2004, Nucleic acids research.

[18]  G. Garrity,et al.  Alphaproteobacteria class. nov. , 2015 .

[19]  Thomas S. Brettin,et al.  The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation , 2012, PloS one.

[20]  K. Schleifer,et al.  The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set. , 1999, Systematic and applied microbiology.

[21]  J. Nielsen,et al.  Meganema perideroedes gen. nov., sp. nov., a filamentous alphaproteobacterium from activated sludge. , 2006, International journal of systematic and evolutionary microbiology.

[22]  Chris F. Taylor,et al.  The minimum information about a genome sequence (MIGS) specification , 2008, Nature Biotechnology.

[23]  G. Zanaroli,et al.  Feed frequency in a sequencing batch reactor strongly affects the production of polyhydroxyalkanoates (PHAs) from volatile fatty acids. , 2014, New biotechnology.

[24]  Natalia Ivanova,et al.  Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities , 2006, Nature Biotechnology.

[25]  Miriam L. Land,et al.  Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .

[26]  H. Klenk,et al.  En route to a genome-based classification of Archaea and Bacteria? , 2010, Systematic and applied microbiology.

[27]  Per Halkjær Nielsen,et al.  High and stable substrate specificities of microorganisms in enhanced biological phosphorus removal plants. , 2013, Environmental microbiology.

[28]  O. Kandler,et al.  Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[29]  S. Rossetti,et al.  Filamentous Alphaproteobacteria associated with bulking in industrial wastewater treatment plants. , 2004, Systematic and applied microbiology.

[30]  G. Garrity,et al.  Class I. Alphaproteobacteria class. nov. , 2005 .

[31]  S. Bennett Solexa Ltd. , 2004, Pharmacogenomics.

[32]  Anton Güntsch,et al.  The DNA bank network: the start from a german initiative. , 2011, Biopreservation and biobanking.

[33]  E. Delong,et al.  The Prokaryotes : Alphaproteobacteria and Betaproteobacteria , 2014 .

[34]  M. Lidstrom,et al.  7 Aerobic Methylotrophic Prokaryotes , 2013 .

[35]  I-Min A. Chen,et al.  The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata , 2011, Nucleic Acids Res..

[36]  I-Min A. Chen,et al.  IMG ER: a system for microbial genome annotation expert review and curation , 2009, Bioinform..

[37]  D. Dionisi,et al.  Effect of the applied organic load rate on biodegradable polymer production by mixed microbial cultures in a sequencing batch reactor. , 2006, Biotechnology and bioengineering.

[38]  H. Klenk,et al.  Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects , 2013, Standards in genomic sciences.

[39]  Natalia N. Ivanova,et al.  GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes , 2010, Nature Methods.

[40]  D. Dionisi,et al.  Exploiting olive oil mill effluents as a renewable resource for production of biodegradable polymers through a combined anaerobic-aerobic process , 2009 .

[41]  C. Anthony,et al.  The Biochemistry of Methylotrophs , 1982 .

[42]  George Garrity,et al.  Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project , 2014, Standards in Genomic Sciences.

[43]  T. Williams,et al.  The nutrition of Thiothrix, type 021N, Beggiatoa and Leucothrix strains , 1989 .

[44]  Natalia N. Ivanova,et al.  A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea , 2009, Nature.

[45]  J. Nielsen,et al.  Advances in microscopy: microautoradiography of single cells. , 2005, Methods in enzymology.

[46]  Motoharu Onuki,et al.  The microbiology of biological phosphorus removal in activated sludge systems. , 2003, FEMS microbiology reviews.