This study explored the persistence and spatial distribution of a diverse Archaeal assemblage inhabiting a temperate mixed forest ecosystem. Persistence under native conditions was measured from 2001 to 2010, 2011, and 2012 by comparison of 16S rRNA gene clone libraries. The Archaeal assemblages at each of these time points were found to be significantly different (AMOVA, ), and the nature of this difference was dependent on taxonomic rank. For example, the cosmopolitan genus g_Ca. Nitrososphaera (I.1b) was detected at all time points, but within this taxon the abundance of s_SCA1145, s_SCA1170, and s_Ca. N. gargensis fluctuated over time. In addition, spatial heterogeneity (patchiness) was measured at these time points using 1D TRFLP-SSCP fingerprinting to screen soil samples covering multiple spatial scales. This included soil collected from small volumes of 3 cubic centimeters to larger scales—over a surface area of 50？m2, plots located 1.3？km apart, and a separate locality 23？km away. The spatial distribution of Archaea in these samples changed over time, and while g_Ca. Nitrososphaera (I.1b) was dominant over larger scales, patches were found at smaller scales that were dominated by other taxa. This study measured the degree of change for Archaeal taxon composition and patchiness over time in temperate mixed forest soil. 1. Introduction Our understanding of Archaea inhabiting soils has expanded exponentially in the last few decades through the use of culture-independent molecular tools. This has led to the discovery of novel Archaeal lineages in terrestrial environments [1] including the recently recognized phylum, Thaumarchaeota [2, 3], members of which have subsequently been shown to play a vital role in the global nitrogen cycle by performing the rate-limiting step for nitrification in most soils [4]. Within the last decade Archaeal phylogeny has been greatly improved by the successful cultivation of Thaumarchaeota in isolation and as dominant members of enrichments from a number of environments. These environments vary, for example, marine, Nitrosopumilus maritimus [5]; hot springs in North America and Siberia, Nitrosocaldus yellowstonii and Nitrososphaera gargensis [6, 7]; and recently from a number of different mesophilic soil sites, Ca. Nitrosoarchaeum koreensis, Ca. Nitrosotalea devanaterra, and Ca. Nitrososphaera viennensis strain EN76 and JG1 [8–11]. In terms of cultivated species representing the most abundant soil taxa, g_Ca. Nitrososphaera , s_Ca. N. gargensis has three cultured representatives [7, 8, 11], s_SCA1145 was enriched but at
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