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Appl. Environ. Microbiol. doi:10.1128/AEM.02611-06
Copyright (c) 2007, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Biogeography of Actinomycete Communities and Type II Polyketide Synthase Genes in Soils Collected in New Jersey and Central Asia

Biotechnology Center for Agriculture and the Environment, Department of Biochemistry and Microbiology, Department of Environmental Sciences, and Institute of Marine and Coastal Sciences; at Rutgers University, Cook College, New Brunswick, New Jersey 08901-8521 USA; Uzbekistan Academy of Sciences Institute of Microbiology, Tashkent, Uzbekistan 700128

^* To whom correspondence should be addressed. Email: kerkhof{at}marine.rutgers.edu.

	Abstract

Soil microbial communities are believed to be comprised of thousands of different bacterial species. One prevailing idea is that ‘everything is everywhere, and the environment selects’, implying that all types of bacteria will be found in all environments where their growth requirements are met. We tested this hypothesis with respect to actinomycete communities and type II polyketide synthase (PKS) genes found in soils collected from New Jersey and Uzbekistan (n=91). Terminal restriction fragment length polymorphism (TRFLP) analysis using actinomycete 16S rRNA and type II PKS genes was employed to determine community profiles. Terminal fragment frequencies in soil samples followed a log normal distribution indicating that the majority of actinomycete phylotypes and PKS pathways are infrequently observed in the environment. Less than 1% of peaks were detected in more than 50% of samples, and as many as 18% of fragments were unique and only detected in one sample. Actinomycete 16S fingerprints clustered by country of origin indicating the presence of unique populations in North America and Central Asia. Sequence analysis of type II PKS gene fragments cloned from Uzbek soil revealed 35 novel sequence clades whose identities to genes from GenBank ranged between 68% and 92%. The data indicate that actinomycetes are patchily distributed but that distinct populations can be found in North American and Central Asia. These results have implications for microbial bioprospecting and indicate the number of cosmopolitan actinomycete species and PKS pathways may only be a small proportion of the total diversity found in soil.