Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes.

BMC Genomics
Patricia C Dos SantosRay Dixon

Abstract

The metabolic capacity for nitrogen fixation is known to be present in several prokaryotic species scattered across taxonomic groups. Experimental detection of nitrogen fixation in microbes requires species-specific conditions, making it difficult to obtain a comprehensive census of this trait. The recent and rapid increase in the availability of microbial genome sequences affords novel opportunities to re-examine the occurrence and distribution of nitrogen fixation genes. The current practice for computational prediction of nitrogen fixation is to use the presence of the nifH and/or nifD genes. Based on a careful comparison of the repertoire of nitrogen fixation genes in known diazotroph species we propose a new criterion for computational prediction of nitrogen fixation: the presence of a minimum set of six genes coding for structural and biosynthetic components, namely NifHDK and NifENB. Using this criterion, we conducted a comprehensive search in fully sequenced genomes and identified 149 diazotrophic species, including 82 known diazotrophs and 67 species not known to fix nitrogen. The taxonomic distribution of nitrogen fixation in Archaea was limited to the Euryarchaeota phylum; within the Bacteria domain we predict that n...Continue Reading

References

Mar 1, 1978·Mikrobiologiia·L A GromovaG I Karavaĭko
Apr 1, 1970·Journal of General Microbiology·M A Riederer-Henderson, P W Wilson
Jan 1, 1993·Journal of Bacteriology·T M Wahlund, M T Madigan
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Feb 24, 2001·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·T KanekoS Tabata
Jan 10, 2002·Journal of Industrial Microbiology & Biotechnology·J S ChenM Kasap
Nov 7, 2002·Archives of Microbiology·John C MeeksFrancis C Wong
Apr 23, 2003·Research in Microbiology·Ilana Berman-FrankPaul Falkowski
Jun 26, 2003·Environmental Microbiology·Jonathan P ZehrGrieg F Steward
Sep 18, 2003·International Journal of Systematic and Evolutionary Microbiology·Peter F DunfieldSvetlana N Dedysh
Aug 1, 1954·Journal of Bacteriology·L PINEH A BARKER
Dec 25, 2003·Molecular Biology and Evolution·Jason RaymondRobert E Blankenship
Nov 17, 2004·International Journal of Systematic and Evolutionary Microbiology·Philippe JourandPhilippe de Lajudie
Apr 5, 2005·Archaea : an International Microbiological Journal·Claudia EhlersRuth A Schmitz
Sep 10, 2005·Applied and Environmental Microbiology·Susan ReslewicDavid C Schwartz
Oct 11, 2005·Nucleic Acids Research·Ross OverbeekVeronika Vonstein
Oct 1, 1987·Applied and Environmental Microbiology·J M Ligon, J P Nakas
Jul 1, 1988·Applied and Environmental Microbiology·A L Lobo, S H Zinder
Mar 1, 2006·Proceedings of the National Academy of Sciences of the United States of America·Víctor GonzálezGuillermo Dávila
Apr 28, 2006·Genome Biology·J Peter W YoungJulian Parkhill
May 24, 2006·Journal of Bioscience and Bioengineering·Hisayoshi TsuihijiMikio Kataoka
Jun 14, 2006·Proceedings of the National Academy of Sciences of the United States of America·Katherina J KechrisAlexander N Glazer
Jul 11, 2006·International Journal of Systematic and Evolutionary Microbiology·Melissa M KendallDavid R Boone
Dec 16, 2006·Science·Mausmi P Mehta, John A Baross
Sep 12, 2007·Bioinformatics·M A LarkinD G Higgins

❮ Previous
Next ❯

Citations

Aug 13, 2013·Journal of Molecular Evolution·Gabriela SotoNicolás Daniel Ayub
Jan 31, 2013·Molecular Plant-microbe Interactions : MPMI·José OlivaresJuan Sanjuán
Sep 10, 2014·Standards in Genomic Sciences·Amy S BiddleJeffrey L Blanchard
Aug 21, 2014·Proceedings of the National Academy of Sciences of the United States of America·Jianguo YangYi-Ping Wang
Feb 22, 2016·Microbial Cell Factories·Xin-Xin LiSan-Feng Chen
Feb 3, 2016·Scientific Reports·Drew MacKellarJürgen Prell
Aug 8, 2015·Environmental Microbiology·Moriya Ohkuma
Jan 29, 2014·Chemical Reviews·Brian M HoffmanLance C Seefeldt
Sep 17, 2015·Journal of Molecular Evolution·Cecilia PascuanNicolas Daniel Ayub
Apr 1, 2014·Current Opinion in Biotechnology·Giles E D Oldroyd, Ray Dixon
Jun 7, 2015·Annual Review of Phytopathology·Erik LimpensRene Geurts
Apr 9, 2015·Environmental Science and Pollution Research International·Ana R LopesOlga C Nunes
Jan 28, 2015·Current Opinion in Biotechnology·Barney A GeddesPhilip Poole
Jul 16, 2014·Plant Science : an International Journal of Experimental Plant Biology·Leonardo Curatti, Luis M Rubio
Oct 22, 2016·Trends in Microbiology·Deniz BombarLasse Riemann
Aug 25, 2016·Scientific Reports·Katsura IgaiMasahiro Umezaki
Nov 4, 2016·Extremophiles : Life Under Extreme Conditions·Xiaoben Jiang, Cristina D Takacs-Vesbach
Jan 26, 2017·World Journal of Microbiology & Biotechnology·Jabir ThajudeenMohamed Hatha Abdulla
Feb 22, 2017·ACS Synthetic Biology·Stefan BurénLuis M Rubio
Mar 18, 2017·International Journal of Systematic and Evolutionary Microbiology·Kelly Nicole Haas, Jeffrey L Blanchard
Mar 5, 2015·Microbes and Environments·Jun-ichi InoueMoriya Ohkuma
Oct 19, 2017·FEMS Microbiology Ecology·Thomas KruseHauke Smidt
Apr 10, 2018·Metallomics : Integrated Biometal Science·Florence MusJohn W Peters
Feb 28, 2018·Journal of Bacteriology·Saroj PoudelEric S Boyd
Dec 19, 2017·Frontiers in Plant Science·Simon ArragainCarlos Echavarri-Erasun

❮ Previous
Next ❯

Datasets Mentioned

BETA
AAT28195.1
AAP99591.1

Software Mentioned

ClustalW
BLAST
FastTree

Related Concepts

Related Feeds

Archaeogenetics

Recent advances in genomic sequencing has led to the discovery of new strains of Archaea and shed light on their evolutionary history. Discover the latest research on Archaeogenetics here.