SOIL MICROBIOLOGY Diversity and Distribution of Actinobacterial Aromatic Ring Oxygenase Genes Across Contrasting Soil Properties Christopher A. Weidow & Hee-Sung Bae & Ashvini Chauhan & Andrew Ogram Received: 12 June 2014 /Accepted: 16 September 2014 # Springer Science+Business Media New York 2014 Abstract The diversity of a gene family encoding Actinobacterial aromatic ring oxygenases (AAROs) was de- tected by the PCR-cloning approach using a newly designed PCR primer set. The distribution of AAROs was investigated in 11 soils representing different land management and vege- tation zones and was correlated with several geochemical parameters including pH, organic matter (OM), total Kjeldahl nitrogen (TKN), and nitrogen oxides (NO x –N: most- ly NO 3 - –N). The distribution of individual clades encoding enzymes with potentially different substrates were correlated with different environmental factors, suggesting differential environmental controls on the distribution of specific enzymes as well as sequence diversity. For example, individual clades associated with phthalate dioxygenases were either strongly negatively correlated with pH, or not correlated with pH but showed strong positive correlation with organic carbon content. A large number of clones clustering in a clade related to PAH oxygenases were positively correlated with pH and nitrogen, but not with organic matter. This analysis may yield insight into the ecological forces driving the distribution of these catabolic genes. Introduction Actinobacteria are among the major Bacterial phyla in soils [1] and a growing body of work has shown that representa- tives of the Actinobacteria are capable of metabolizing a range of mono- and polyaromatic hydrocarbons [2–4]; however, little attention has been paid to the diversity and distribution of Actinobacterial aromatic hydrocarbon degraders in soils. Far more work has been conducted to describe the ecology, genetics, and biochemistry of aromatic hydrocarbon metabo- lism by Pseudomonas species [5–7], which may respond differently to environmental forces than the Actinobacteria [8]. In addition, most previous work on the distribution of these genes in soils has focused on their relations to anthro- pogenic contamination [9–13], rather than on carbon cycling in soils not directly contaminated with pollutants. Soil organic matter is a complex mixture of molecules of varying sizes and chemical properties, and little is known of the relationships between specific groups of soil bacteria and the roles they play in metabolism of naturally occuring organic molecules in soils. As with the pseudomonads, aromatic hydrocarbon metab- olism by the Actinobacteria involves Rieske protein- containing dioxygenases and monooxygenases [14–18]. Differences exist between the biochemical pathways for aro- matic hydrocarbon metabolism between pseudomonads and at least some Actinobacteria. For example, salicylate formation is a common funnel point in polyaromatic hydrocarbon (PAH) metabolism for most pseudomonads [19], while o-phthalic acid is an intermediate of at least some Actinobacterial PAH pathways [3, 17, 18, 20]. o-phthalic acid has also been shown to be among root exudates [20] and may be an intermediate product in the metabolism of some alleopathic root exudates [21]. A greater understanding of the diversity of genes encoding Actinobacterial aromatic oxygenases (AARO), and of the Electronic supplementary material The online version of this article (doi:10.1007/s00248-014-0501-7) contains supplementary material, which is available to authorized users. C. A. Weidow : H.<S. Bae : A. Ogram (*) Soil and Water Science Department, University of Florida, PO Box 110290, Gainesville, FL 32611-0290, USA e-mail: aogram@ufl.edu A. Chauhan School of the Environment, Florida A&M University, Tallahassee, FL 32307, USA Microb Ecol DOI 10.1007/s00248-014-0501-7