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The Evolutionary History of Nitrogen Fixation, as Assessed by NifD

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Abstract

The evolutionary history of nitrogen fixation has been vigorously debated for almost two decades. Previous phylogenetic analyses of nitrogen fixation genes (nif) have shown support for either evolution by vertical descent or lateral transfer, depending on the specific nif gene examined and the method of analyses used. The debate centers on the placement and monophyly of the cyanobacteria, proteobacteria, and Gram-positive bacteria (actinobacteria and firmicutes). Some analyses place the cyanobacteria and actinobacteria within the proteobacteria, which suggests that the nif genes have been laterally transferred since this topology is incongruent with ribosomal phylogenies, the standard marker for comparison. Other nif analyses resolve and support the monophyly of the cyanobacteria, proteobacteria, and actinobacteria, supporting vertical descent. We have revisited these conflicting scenarios by analyzing nifD from an increased number of cyanobacteria, proteobacteria, and Gram-positive bacteria. Parsimony analyses of amino acid sequences and maximum likelihood analysis of nucleic acid sequences support the monophyly of the cyanobacteria and actinobacteria but not the proteobacteria, lending support for vertical descent. However, distance analysis of nucleic acid sequences placed the actinobacteria within the proteobacteria, supporting lateral transfer. We discuss evidence for both vertical descent and lateral transfer of nitrogen fixation.

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Acknowledgements

This research was partially funded by the National Science Foundation–POWRE Grant 9973340 to S.R.B., Miami University Committee on Faculty Research Grant to S.R.B, Ohio Sea Grant Development to S.R.B. and L.E.W., and Ohio Board of Regents Academic Challenge Grant to B.J.H. We also acknowledge the help of Chris Wood and The Center for Functional Genomics and Bioinformatics at Miami University, Eric Stahlberg with the Ohio Super Computer, and Dr. Guillermo Orti for providing advice on the analyses. This paper represents, in part, the senior author’s master’s thesis.

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  1. Department of Botany, Miami University, Oxford, OH 45056, USA

    Brian J. Henson, Linda E. Watson & Susan R. Barnum

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  1. Brian J. Henson
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  2. Linda E. Watson
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  3. Susan R. Barnum
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Correspondence to Susan R. Barnum.

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Henson, B.J., Watson, L.E. & Barnum, S.R. The Evolutionary History of Nitrogen Fixation, as Assessed by NifD . J Mol Evol 58, 390–399 (2004). https://doi.org/10.1007/s00239-003-2560-0

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