NifH and NifD phylogenies: an evolutionary basis for understanding nitrogen fixation capabilities of methanotrophic bacteria

Abstract

The ability to utilize dinitrogen as a nitrogen source is an important phenotypic trait in most currently known methanotrophic bacteria (MB). This trait is especially important for acidophilic MB, which inhabit acidic oligotrophic environments, highly depleted in available nitrogen compounds. Phylogenetically, acidophilic MB are most closely related to heterotrophic dinitrogen-fixing bacteria of the genus Beijerinckia. To further explore the phylogenetic linkage between these metabolically different organisms, the sequences of nifH and nifD gene fragments from acidophilic MB of the genera Methylocella and Methylocapsa, and from representatives of Beijerinckia, were determined. For reference, nifH and nifD sequences were also obtained from some type II MB of the alphaproteobacterial Methylosinus/Methylocystis group and from gammaproteobacterial type I MB. The trees constructed for the inferred amino acid sequences of nifH and nifD were highly congruent. The phylogenetic relationships among MB in the NifH and NifD trees also agreed well with the corresponding 16S rRNA-based phylogeny, except for two distinctive features. First, different methods used for phylogenetic analysis grouped the NifH and NifD sequences of strains of the gammaproteobacterial MB Methylococcus capsulatus within a clade mainly characterized by Alphaproteobacteria, including acidophilic MB and type II MB of the Methylosinus/Methylocystis group. From this and other genomic data from Methylococcus capsulatus Bath, it is proposed that an ancient event of lateral gene transfer was responsible for this aberrant branching. Second, the identity values of NifH and NifD sequences between Methylocapsa acidiphila B2 and representatives of Beijerinckia were clearly higher (98?5 and 96?6 %, respectively) than would be expected from their 16S rRNA-based relationships. Possibly, these two bacteria originated from a common acidophilic dinitrogen-fixing ancestor, and were subject to similar evolutionary pressure with regard to nitrogen acquisition. This interpretation is corroborated by the observation that, in contrast to most other diazotrophs, M. acidiphila B2 and Beijerinckia spp. are capable of active growth on nitrogen-free media under fully aerobic conditions.

A new cell morphotype among methane oxidizers: a spiral-shaped obligately microaerophilic methanotroph from northern low-oxygen environments

“…The latter is of special importance for dinitrogen-fixing type I and X methanotrophs since N 2 fixation in these bacteria is more sensitive to O 2 than in type II methanotrophs (Murrell and Dalton, 1983;Dedysh et al, 2004). In nitrogen-sufficient media, however, most described methanotrophs display best growth under fully oxic conditions.…”

Methylovirgula ligni gen. nov., sp. nov., an obligately acidophilic, facultatively methylotrophic bacterium with a highly divergent mxaF gene

“…PCR-mediated amplification of the 16S rRNA gene was performed using primers 9f and 1492r and reaction conditions described by Weisburg et al (1991). Partial fragments of the mxaF gene (encoding the large subunit of methanol dehydrogenase), the nifH gene (encoding dinitrogenase reductase) and the cbbL gene [encoding the large subunit of form I ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO)] were amplified using primers and reaction conditions described, respectively, by McDonald & Murrell (1997), Dedysh et al (2004b) and Spiridonova et al (2004). The PCR-amplified gene fragments were purified using the Wizard PCR Preps DNA Purification System (Promega) and sequenced on an ABI Prism 377 DNA sequencer (PE Applied Biosystems).…”

Bioinformatics Analysis of Hsp20 Sequences in Proteobacteria

“…All Proteobacteria are Gram negative and posses a membrane composed of lipopolysaccharides. Betaproteobacteria play a pivotal role in plant nitrogen fixation and are commonly found in environmental samples (Dedysh et al, 2004). Epsilonproteobacteria are known to inhabit the digestive tracts of animals and humans (Miroschnichenko et al, 2004).…”