Stable isotope probing with 15N2 reveals novel noncultivated diazotrophs in soil.
Biological nitrogen fixation is a fundamental component of the nitrogen cycle and is the dominant natural process through which fixed nitrogen is made available to the biosphere. While the process of nitrogen fixation has been studied extensively with a limited set of cultivated isolates, examinations of nifH gene diversity in natural systems reveal the existence of a wide range of noncultivated diazotrophs. These noncultivated diazotrophs remain uncharacterized, as do their contributions to nitrogen fixation in natural systems. We have employed a novel 15N2-DNA stable isotope probing (5N2-DNA-SIP) method to identify free-living diazotrophs in soil that are responsible for nitrogen fixation in situ. Analyses of 16S rRNA genes from 15N-labeled DNA provide evidence for nitrogen fixation by three microbial groups, one of which belongs to the Rhizobiales while the other two represent deeply divergent lineages of noncultivated bacteria within the Betaproteobacteria and Actinobacteria, respectively. Analysis of nifH genes from 15N-labeled DNA also revealed three microbial groups, one of which was associated with Alphaproteobacteria while the others were associated with two noncultivated groups that are deeply divergent within nifH cluster I. These results reveal that noncultivated free-living diazotrophs can mediate nitrogen fixation in soils and that 15N2-DNA-SIP can be used to gain access to DNA from these organisms. In addition, this research provides the first evidence for nitrogen fixation by Actinobacteria outside of the order Actinomycetales.
Buckley
Daniel H
DH
Department of Crop and Soil Sciences, 705 Bradfield Hall, Cornell University, Ithaca, NY 14853, USA. dhb28@cornell.edu
Huangyutitham
Varisa
V
Hsu
Shi-Fang
SF
Nelson
Tyrrell A
TA
D039903:Actinobacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D020561:Alphaproteobacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D001483:Base Sequence; D020562:Betaproteobacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D004269:DNA, Bacterial / Q000032:analysis* / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D007553:Isotope Labeling; D008969:Molecular Sequence Data; D009586:Nitrogen Fixation; D009587:Nitrogen Isotopes; D010088:Oxidoreductases / Q000235:genetics; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D012988:Soil Microbiology
D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D009587:Nitrogen Isotopes; D010088:Oxidoreductases; C029130:nitrogenase reductase