Microbial Ecology

, Volume 51, Issue 4, pp 441–452 | Cite as

Distribution of Extensive nifH Gene Diversity Across Physical Soil Microenvironments

  • Javier A. Izquierdo
  • Klaus NüssleinEmail author


The diversity of nitrogen-fixing bacteria is well described for aquatic environments; however, terrestrial analyses remain mostly biased to rhizobial plant–microbe associations. We maximized the level of resolution for this study through the use of nucleotide sequence information extracted from a series of soil microenvironments, ranging from macroaggregates at 2000 μm to the clay fraction at <75 μm in diameter. In addition, we attempted to create an overview of the distribution of terrestrial nitrogen fixers across such microenvironments by combining culture-independent techniques with a suite of natural soil environments from uniquely different origins. Soil diazotroph diversity was analyzed phylogenetically for 600 terrestrial nifH sequences from 12 midsized clone libraries based on microenvironments of three separate soils across a global scale. Statistical analyses of nifH gene clone libraries were used to estimate coverage, establish degrees of sequence overlap, and compare cluster distributions. These analyses revealed an extensive diversity in a tropical (19 phylotypes) and an arctic soil (17 phylotypes), and moderate diversity in a temperate soil (11 phylotypes). Within each soil, comparisons across aggregate size fractions delineated nifH gene cluster shifts within populations and degrees of sequence overlap that ranged from significantly different (arctic, tropical) to significantly similar (temperate). We suggest that this is due to population separation across aggregates of different size classes, which results from differences in the temporal stability of aggregates as niches for microbial communities. This study not only provides new knowledge of the arrangement of diazotrophic communities at the soil microscale, but it also contributes to the underrepresented knowledge of soil nifH sequences in the public databases.


Clone Library nifH Gene Arctic Tundra Arctic Soil nifH Sequence 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



The authors thank Dr. William Mohn, University of British Columbia, for providing us access to the arctic tundra soil sample. The authors also acknowledge Abraham Sandel's contribution to the preliminary DGGE and RFLP analyses that led to this study. This research has been partially funded by USDA Hatch grants HA824 and HA896 and McIntire-Stennis grant MS87.


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Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  1. 1.Department of MicrobiologyUniversity of MassachusettsAmherstUSA

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