Influence of irrigated agriculture on soil microbial diversity James A. Entry a, *, DeEtta Mills b , Kalai Mathee b , Krish Jayachandran c , R.E. Sojka a , Giri Narasimhan d a USDA Agricultural Research Service, Northwest Irrigation and Soils Research Laboratory, 3793 North, 3600 East, Kimberly, ID 83341, United States b Department of Biological Sciences, Florida International University, University Park, Miami, FL, United States c Department of Environmental Studies, Florida International University, University Park, Miami, FL, United States d School of Computing & Information Science, Florida International University, University Park, Miami 1. Introduction Land use changes can impact the amount of organic carbon (C) stored in the soil by altering C inputs and losses. In forest, grassland and wetland ecosystems, conversion of native vegetation to agricultural cropping has resulted in substantial C transfer to the atmosphere as a result of loss of climax vegetation to the lower equilibrium C concentration in soil (Baker et al., 2007; VandenBygaart et al., 2003; Wang et al., 1999). Farm management practices, including conservation tillage and erosion control, have reduced the amount of CO 2 emitted to the atmosphere in both Canada and the United States (VandenBygaart et al., 2003; West and Marland, 2002; Paustian et al., 1997). Irrigation also increases C input to soils via increased litter and root production. In arid and semi-arid environments, plant survival and growth is limited by available water and irrigation is required to increase plant production to the point where crops become economically viable. Intensively managed crop or pastureland has potential for C gain through the use of improved grazing regimes, fertilization practices and irrigation management (Entry et al., 2002; Follett, 2001; Bruce et al., 1999). applied soil ecology 40 (2008) 146–154 article info Article history: Received 15 June 2006 Received in revised form 21 March 2008 Accepted 28 March 2008 Keywords: Carbon Irrigation Amplicon length heterogeneity Bacterial biomass Fungal biomass abstract Organic carbon (C), bacterial biomass and structural community diversity were measured in Southern Idaho soils with long term cropping histories. The soils tested were native sagebrush vegetation (NSB), irrigated moldboard plowed crops (IMP), irrigated conservation – chisel – tilled crops (ICT) and irrigated pasture systems (IP). Organic C concentration in soils decreased in the order NSB 0–5 cm > IP 0–30 cm = ICT 0–15 cm > IMP 0–30 cm > NSB 5–15 cm = NSB 15– 30 cm. Active bacterial, fungal and microbial biomass correlated with soil C as measured by the Walkely Black method in positive curvilinear relationships (r 2 = 0.93, 0.80 and 0.76, respec- tively). Amplicon length heterogeneity (LH-PCR) DNA profiling was used to access the eubac- terial diversity in all soils and at all depths. The Shannon–Weaver diversity index was used to measure the differences using the combined data from three hypervariable domains of the eubacterial 16S rRNA genes. Diversity was greatest in NSB 15–30 cm soil and lowest in the IMP soil. With the exception of IMP with the lowest diversity index, the samples highest in C (NSB 0– 5 cm, IP 0–30 cm, ICT 0–15 cm) reflected lower diversity indices. However, these indices were not significantly different from each other. ICT and IP increase soil C and to some extent increase diversity relative to IMP. Since soil bacteria respond quickly to environmental changes, monitoring microbial communities may be one way to assess the impact of agri- cultural practices such as irrigation and tillage regimes. Published by Elsevier B.V. * Corresponding author. Tel.: +1 208 423 6553; fax: +1 208 423 6555. E-mail addresses: jentry@nwisrl.ars.usda.gov, James_Entry@nps.gov (J.A. Entry). available at www.sciencedirect.com journal homepage: www.elsevier.com/locate/apsoil 0929-1393/$ – see front matter . Published by Elsevier B.V. doi:10.1016/j.apsoil.2008.03.012 1268