Izquierdo Javier A, Nüsslein Klaus
Department of Microbiology, University of Massachusetts, Amherst, MA, USA.
Microb Ecol. 2006 May;51(4):441-52. doi: 10.1007/s00248-006-9044-x. Epub 2006 Apr 28.
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 microm to the clay fraction at < 75 microm 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.
固氮细菌在水生环境中的多样性已有充分描述；然而，陆地分析大多仍偏向于根瘤菌与植物的微生物关联。我们通过使用从一系列土壤微环境中提取的核苷酸序列信息，将本研究的分辨率提升到了最高水平，这些微环境的范围从直径2000微米的大团聚体到直径小于75微米的黏粒部分。此外，我们尝试通过将不依赖培养的技术与一系列来源独特不同的天然土壤环境相结合，来概述陆地固氮菌在这些微环境中的分布情况。基于全球范围内三种不同土壤的微环境，对来自12个中型克隆文库的600条陆地nifH序列进行了系统发育分析，以研究土壤中固氮微生物的多样性。对nifH基因克隆文库进行统计分析，以估计覆盖率、确定序列重叠程度并比较聚类分布。这些分析揭示了热带土壤（19个系统型）和北极土壤（17个系统型）中存在广泛的多样性，而温带土壤中的多样性适中（11个系统型）。在每种土壤中，对不同团聚体大小级分的比较描绘了种群内nifH基因簇的变化以及序列重叠程度，其范围从显著不同（北极、热带）到显著相似（温带）。我们认为这是由于不同大小类别的团聚体之间存在种群分离，这是由团聚体作为微生物群落生态位的时间稳定性差异导致的。本研究不仅提供了土壤微观尺度上固氮群落排列的新知识，还为公共数据库中土壤nifH序列知识的不足做出了贡献。
