Samples were diluted to 10 ng μl−1 and mixed in equal concentrations. The intensive plots were located at the Kellogg Biological Station (KBS) in Michigan and at the Arlington Agricultural Research Station (AARS) in Wisconsin. Crops are corn (CO), mixed grasses (MP), prairie (PR) and switchgrass (SW). NifH nucleotide sequences were deposited in the European Nucleotide Archive (http://www.ebi.ac.uk/ena) as part of study PRJEB6704 under accession numbers ERR571353 through ERR571395. Lipid analysis provided general taxonomic information coupled to biomass estimates that gave insight into ecosystem function (Kirk et al., 2004). Corn is presently the major crop used for ethanol production in the United States, and soil microbial communities under corn and prairie have often been contrasted, showing differences in microbial community composition and improved carbon storage and soil aggregation under prairie (Bailey et al., 2002; Allison et al., 2005; Bach et al., 2010; Fierer et al., 2013; Murphy & Foster, 2014). Soil samples were collected from sites in southern Michigan and southern Wisconsin under two different designs that have been used for other studies by the Great Lakes Bioenergy Research Center (GLBRC) (Fig. Actinomycetes and protozoa markers were more abundant in Wisconsin; however, there were no apparent differences in these two groups among treatments for either state (Fig. As arbuscular mycorrhizal fungi (AMF) were identified by lipids analysis as an abundant group, we sought to identify fungal sequences belonging to this group in the 28S rRNA gene pyrosequencing data. For this reason, we used a more holistic approach for our study. 2b), which plots farthest from corn in Fig. All sites had been under their respective vegetation for at least 10 years. However, none of these soil variables separated sites by crop. S3). Azospirillum, Dechloromonas, and Leptothrix‐like sequences did not distinguish samples by state, being more related to the pH gradient. A native seed mix designed for wetter soils like the Detention Basin Seed Mix would disrupt the function of the ditch - and that would be a good thing! In most cases, small sample size and high variance precluded detection of statistically significant among treatment differences in lipids characterizing various microbial groups. While we could specifically link SSU rRNA gene sequences to crops and soils, and given that these sequences provide better taxonomical resolution, the detection of large numbers of uncultured organisms and taxa with no clearly defined roles limited physiological and functional interpretation. Wisconsin extensive sites exhibited higher microbial biomass per treatment than corresponding intensive sites, especially for the corn and prairie sites. HABITAT & HARDINESS: The parent species Panicum virgatum ranges through most of the southern Canadian provinces and the contiguous United States. Our results agree with those of Mao et al. The growing interest in using switchgrass and other grasses for cellulosic biomass production has sparked similar investigations contrasting soil microbial communities under these grasses with those under corn (Jesus et al., 2010; Mao et al., 2011, 2013; Liang et al., 2012). Switchgrass utilization is an emerging market currently in the research and demonstration-project arena. Bars represent ±1 standard error. Sequences were binned by genus if identified with confidence of 0.5 or greater, or otherwise to the lowest rank category for which confidence was at least 0.5, resulting in 639 categories. One of my subscribers suggested that i keep mowing it down an it will die. Its slick, free-flowing seed can be planted with most seed drills or with a broadcast spreader. Figure S8. (2013). Previous experiments by Murphy & Foster (2014) and Buckley & Schmidt (2003) demonstrated that despite changes in plant cover and management, soil microbial communities remained similar even after 6 and 7 years, respectively. A Manual and Software for Common Statistical Methods for Ecological and Biodiversity Studies, Methods of studying soil microbial diversity, Filamentous fungi: the indeterminate lifestyle and microbial ecology, PyroTagger: a fast, accurate pipeline for analysis of rRNA amplicon pyrosequence data, Ecologically meaningful transformations for ordination of species data, Soil microbial communities under model biofuel cropping systems in southern Wisconsin, USA: impact of crop species and soil properties, Accurate, rapid taxonomic classification of fungal large‐subunit rRNA genes, Disclosing arbuscular mycorrhizal fungal biodiversity in soil through a land‐use gradient using a pyrosequencing approach, Influence of phylogeny on fungal community assembly and ecosystem functioning, Changes in N‐transforming Archaea and Bacteria in soil during the establishment of bioenergy crops, Impact of different bioenergy crops on N‐cycling bacterial and archaeal communities in soil, Soil properties and spatial processes influence bacterial metacommunities within a grassland restoration experiment, Nitrous oxide emissions during establishment of eight alternative cellulosic bioenergy crops in the North Central United States, Fungal diversity in permafrost and tallgrass prairie soils under experimental warming conditions, Improvement in the RFLP procedure for studying the diversity of, R: A language and environment for statistical computing, labdsv: Ordination and Multivariate Analysis for Ecology, Pyrosequencing enumerates and contrasts soil microbial diversity, Mechanical soil disturbance as a determinant of arbuscular mycorrhizal fungal communities in semi‐natural grassland, Mycorrhizal‐mediated nitrogen acquisition in switchgrass under elevated temperatures and N enrichment. 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