New FeFe-hydrogenase genes identified in a metagenomic fosmid library from a municipal wastewater treatment plant as revealed by high-throughput sequencing

Geizecler T, Wibberg D, Schlüter A, Oliveira VM (2015)
Research in Microbiology 166(1): 9-19.

Journal Article | Published | English

No fulltext has been uploaded

Abstract
A fosmid metagenomic library was constructed with total community DNA obtained from a municipal wastewater treatment plant (MWWTP), with the aim of identifying new FeFe-hydrogenase genes encoding the enzymes most important for hydrogen metabolism. The dataset generated by pyrosequencing of a fosmid library was mined to identify environmental gene tags (EGTs) assigned to FeFe-hydrogenase. The majority of EGTs representing FeFe-hydrogenase genes were affiliated with the class Clostridia, suggesting that this group is the main hydrogen producer in the MWWTP analyzed. Based on assembled sequences, three FeFe-hydrogenase genes were predicted based on detection of the L2 motif (MPCxxKicxE) in the encoded gene product, confirming true FeFe-hydrogenase sequences. These sequences were used to design specific primers to detect fosmids encoding FeFe-hydrogenase genes predicted from the dataset. Three identified fosmids were completely sequenced. The cloned genomic fragments within these fosmids are closely related to members of the Spirochaetaceae, Bacteroidales and Firmicutes, and their FeFe-hydrogenase sequences are characterized by the structure type M3, which is common to clostridial enzymes. FeFe-hydrogenase sequences found in this study represent hitherto undetected sequences, indicating the high genetic diversity regarding these enzymes in MWWTP. Results suggest that MWWTP have to be considered as reservoirs for new FeFe-hydrogenase genes. (C) 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.
Publishing Year
ISSN
PUB-ID

Cite this

Geizecler T, Wibberg D, Schlüter A, Oliveira VM. New FeFe-hydrogenase genes identified in a metagenomic fosmid library from a municipal wastewater treatment plant as revealed by high-throughput sequencing. Research in Microbiology. 2015;166(1):9-19.
Geizecler, T., Wibberg, D., Schlüter, A., & Oliveira, V. M. (2015). New FeFe-hydrogenase genes identified in a metagenomic fosmid library from a municipal wastewater treatment plant as revealed by high-throughput sequencing. Research in Microbiology, 166(1), 9-19.
Geizecler, T., Wibberg, D., Schlüter, A., and Oliveira, V. M. (2015). New FeFe-hydrogenase genes identified in a metagenomic fosmid library from a municipal wastewater treatment plant as revealed by high-throughput sequencing. Research in Microbiology 166, 9-19.
Geizecler, T., et al., 2015. New FeFe-hydrogenase genes identified in a metagenomic fosmid library from a municipal wastewater treatment plant as revealed by high-throughput sequencing. Research in Microbiology, 166(1), p 9-19.
T. Geizecler, et al., “New FeFe-hydrogenase genes identified in a metagenomic fosmid library from a municipal wastewater treatment plant as revealed by high-throughput sequencing”, Research in Microbiology, vol. 166, 2015, pp. 9-19.
Geizecler, T., Wibberg, D., Schlüter, A., Oliveira, V.M.: New FeFe-hydrogenase genes identified in a metagenomic fosmid library from a municipal wastewater treatment plant as revealed by high-throughput sequencing. Research in Microbiology. 166, 9-19 (2015).
Geizecler, Tomazetto, Wibberg, Daniel, Schlüter, Andreas, and Oliveira, Valeria M. “New FeFe-hydrogenase genes identified in a metagenomic fosmid library from a municipal wastewater treatment plant as revealed by high-throughput sequencing”. Research in Microbiology 166.1 (2015): 9-19.
This data publication is cited in the following publications:
This publication cites the following data publications:

1 Citation in Europe PMC

Data provided by Europe PubMed Central.

Metagenomics reveals the high polycyclic aromatic hydrocarbon-degradation potential of abundant uncultured bacteria from chronically polluted subantarctic and temperate coastal marine environments.
Loviso CL, Lozada M, Guibert LM, Musumeci MA, Sarango Cardenas S, Kuin RV, Marcos MS, Dionisi HM., J. Appl. Microbiol. 119(2), 2015
PMID: 25968322

38 References

Data provided by Europe PubMed Central.

The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology.
Schluter A, Bekel T, Diaz NN, Dondrup M, Eichenlaub R, Gartemann KH, Krahn I, Krause L, Kromeke H, Kruse O, Mussgnug JH, Neuweger H, Niehaus K, Puhler A, Runte KJ, Szczepanowski R, Tauch A, Tilker A, Viehover P, Goesmann A., J. Biotechnol. 136(1-2), 2008
PMID: 18597880
The genome of Syntrophomonas wolfei: new insights into syntrophic metabolism and biohydrogen production.
Sieber JR, Sims DR, Han C, Kim E, Lykidis A, Lapidus AL, McDonnald E, Rohlin L, Culley DE, Gunsalus R, McInerney MJ., Environ. Microbiol. 12(8), 2010
PMID: 21966920
Monitoring the bacterial community dynamics in a petroleum refinery wastewater membrane bioreactor fed with a high phenolic load.
Silva CC, Viero AF, Dias AC, Andreote FD, Jesus EC, De Paula SO, Torres AP, Santiago VM, Oliveira VM., J. Microbiol. Biotechnol. 20(1), 2010
PMID: 20134229
MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S., Mol. Biol. Evol. 28(10), 2011
PMID: 21546353
Oliveira VM investigation of the FeFe-hydrogenase gene diversity combined with phylogenetic microbial community analysis of an anaerobic domestic sewage sludge
Tomazetto, W J Microbiol Biotechnol 29(), 2013
Classification and phylogeny of hydrogenases.
Vignais PM, Billoud B, Meyer J., FEMS Microbiol. Rev. 25(4), 2001
PMID: 11524134
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.
Wang Q, Garrity GM, Tiedje JM, Cole JR., Appl. Environ. Microbiol. 73(16), 2007
PMID: 17586664
Characterization of a biogas-producing microbial community by short-read next generation DNA sequencing.
Wirth R, Kovacs E, Maroti G, Bagi Z, Rakhely G, Kovacs KL., Biotechnol Biofuels 5(), 2012
PMID: 22673110
Metagenomic analysis of sludge from full-scale anaerobic digesters operated in municipal wastewater treatment plants.
Yang Y, Yu K, Xia Y, Lau FT, Tang DT, Fung WC, Fang HH, Zhang T., Appl. Microbiol. Biotechnol. 98(12), 2014
PMID: 24633414
MetaSAMS-A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets
Zakrzewski, J Biotechnol 167(), 2012
Comprehensive phylogenetic diversity of [FeFe]-hydrogenase genes in termite gut microbiota.
Zheng H, Bodington D, Zhang C, Miyanaga K, Tanji Y, Hongoh Y, Xing XH., Microbes Environ. 28(4), 2013
PMID: 24240187

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 25446611
PubMed | Europe PMC

Search this title in

Google Scholar