All nifH sequences also were initially processed using the pyrosequencing pipeline tools on RDP's Web site. For Michigan, this modest difference was accounted for by increases of both bacteria and fungi under the perennial grasses, with a slightly higher proportion of AMF in mixed grasses and prairie (Fig. Prokaryote sequences accounted for 86.3% of the recovered sequences and eukaryote sequences accounted for 9.2% (Fig. When anova was significant, treatment contrasts were made with the TukeyHSD function of the r package stats. Bacterial and SF biomasses were similar among treatments for intensive sites in both states. Figure S8. IndVal results based on 28S rRNA sequences for genera distinguishing extensive sites by crop. Prairie Sky. All agricultural activity affects biodiversity, soil fertility, and water resources (Groom et al., 2008), and these factors should be assessed when evaluating the sustainability of biofuel cropping systems. The one exception to this generalization was that the lipid data did reveal a crop effect on microbial community structure for the intensive Wisconsin sites. Genera contributing the most to the ordination were Geobacter, most abundant in the Michigan switchgrass samples, and Hyphomicrobium, characteristic of prairie sites in both states. Twenty microliter PCRs were performed in duplicate and pooled to minimize PCR bias using 0.4 μl Advantage GC 2 Polymerase Mix (Advantage‐2 GC PCR Kit, Clonetech, Mountain View, CA, USA), 4 μl 5× GC PCR buffer, 2 μl 5 m GC Melt Solution, 0.4 μl 10 mm dNTP mix (MBI Fermentas, Amherst, MA, USA), 1.0 μl of each 25 nm primer, and 10 ng sample DNA. Matches to the Deltaproteobacteria were most abundant in the Michigan extensive switchgrass sites, dominating all three replicates. One design consisted of side‐by‐side plots where plant communities were in their second year since establishment (i.e., intensive sites), and the other consisted of regionally distributed fields where plant communities had been in place for at least 10 years (i.e., extensive sites). Biomass and biofuel crop effects on biodiversity and ecosystem services in the North Central US. Bars represent ±1 standard error. Soil microbial community structure and enzymatic activity responses to nitrogen management and landscape positions in switchgrass (Panicum virgatum L.). Previous researchers found Paraglomerales are difficult to detect in roots and soils and that commonly used primers for AMF fail to amplify Paraglomerales sequences (Lumini et al., 2010; Gosling et al., 2014). Microbial Diversity and Soil Health in Tropical Agroecosystems. Total carbon concentrations were compared by analysis of variance (anova) using the lm function of the r package stats and a cutoff value of α = 0.05. Chicken Noodle soup has been there through the many days where I needed to feel comfort, warmth and taste something that is familiar. Figure S7. All three approaches revealed similar differences among cropping systems in community structure. Associative nitrogen fixation (ANF) in switchgrass (Panicum virgatum) across a nitrogen input gradient. PCA for extensive site NifH data aggregated by genera. Thanks to Doug Landis and Ben Werling for help with sampling and providing information on the extensive sites in Michigan; Tim Meehan for help with sampling on the extensive sites in Wisconsin; Susanna Tringe, Stephanie Malfatti, Tijana Galvina del Rio at the Joint Genome Institute for SSU rRNA pyrotag sequencing; James Cole from the Ribosomal Database Project for support and comments with sequence data analysis; Harry Read for lipid analysis; and David Duncan for soil physicochemical analysis. The strong upright growth produces a lovely cloud of airy seed heads in the fall. The grass persists into winter. Bars represent ±1 standard error. 5), and there were no significant differences in dispersion (α = 0.05). PCR amplicons were purified using SPRI Beads and quantified using a Qubit fluorometer (Thermo Fisher Scientific Inc., Waltham, MA, USA). Field‐grown transgenic switchgrass (Panicum virgatum L.) with altered lignin does not affect soil chemistry, microbiology, and carbon storage potential. We assume, however, that soil type is the key factor because of the sharp difference in soil texture and fertility between our intensive sites in the two states (Fig. A trade‐off exists between finding primers and conditions that give the best coverage for groups important in the habitat and reliable amplification. Indeed, there is evidence that perennial grasses with potential for biofuel production, such as Miscanthus, may be associated with N2‐fixing bacteria (Tjepkema & Burris, 1976; Davis et al., 2010; Mao et al., 2013; Keymer & Kent, 2014), which points to N2‐fixing microorganisms as an important target group. HABITAT & HARDINESS: The parent species, Panicum virgatum, ranges through most of the southern Canadian provinces and the United States. Two years ago, we used sheep to plant a diverse mixture of cover crops and perennial pasture plants. Detailed amplification and purification protocols are given in Penton et al. Scaling 2 depicts higher correlations between variables as smaller angles between vectors. Microbes for Climate Resilient Agriculture. The higher number of OTUs observed under prairie may be a consequence of its higher plant diversity, because a greater diversity of plant hosts creates a greater diversity of niches for AMF. blond little girl standing in front of pampas grass - switchgrass stock pictures, royalty-free photos & images. Nestled on 48 acres, the Prairie at Post is a community for neighbors who love the modern farmhouse architecture and good friendships. FrameBot, included in the Fungene Pipeline (Fish et al., 2013), was used to match representative sequences from each cluster to 187 of 782 unique NifH reference sequences. Annual crops such as corn continue to be the most readily abundant and available crops for biofuel production in the United States (US‐DOE, 2011), while canola and soybeans have been used to produce biodiesel (IEA, 2007). [Wilkommen] [Die Pflanze] [Sorten] [Anbau] [Verwertung] [Forschung] [Neuigkeiten] [Kontakt]. Easily grown in a variety of conditions, it tolerates both clay and sandy soils. (2010). The Michigan soils we studied are sandier and have lower fertility than the Wisconsin soils, which are loess‐derived. By continuing to browse this site, you agree to its use of cookies as described in our, I have read and accept the Wiley Online Library Terms and Conditions of Use. After frame shift correction and translation into amino acids, they were clustered at a distance of 0.05 yielding 2799 OTUs. Binomial name. 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. Significance codes: ***0.001; **0.01; *0.05; NS, non significant. The lipid data separated corn from switchgrass and prairie (Fig. These samples were aligned and clustered into 10 092 clusters (OTUs) at a distance of 3%; 6628 of these clusters were global singletons with Good's estimated sample coverage of 52 to 92% and averaging 85%. In another experiment, Jangid et al. Considering the impacts on microbial soil communities is an important component of this assessment because most soil‐based ecosystems services such as organic matter degradation, nitrogen fixation, nitrification, denitrification, soil aggregation, and water retention are driven by microbial activity (Swift et al., 2004). S7). In more productive soils, it may be more important to have a particular plant community, for example, one that includes the most productive taxa, to minimize inputs, while improving stability and resilience (Adler et al., 2009). Tender young foliage is browsed by deer and livestock and dense upright growth provides winter cover for wildlife. Wisconsin extensive sites exhibited higher microbial biomass per treatment than corresponding intensive sites, especially for the corn and prairie sites. Additionally, recently reported results showed that mycorrhizae increased the amount of total N in shoots of switchgrass (Schroeder‐Moreno et al., 2012), indicating that mycorrhizae can also contribute to the increased utilization of this nutrient. Andere Beispiele hierfür sind Hanf, Miscanthus oder Sudangras (Sorghum sudanese) welche, sofern Wirtschaftlichkeit und Vermarktungsmöglichkeit gegeben sind, mittlerweile (wieder) vermehrt angebaut werden. We decided the Poly primers were the current best choice because amplification with the broader coverage Zehr & McReynolds (1989) primers was troublesome, probably because of their high degeneracy. Watch Store Tour. Hauptgründe für diese Entwicklung sind Preisschwankungen auf den Agrarmärkten und relativ sichere Rahmenbedingungen für die Bioenergieproduktion. Theoretically, more diverse plant communities will improve sustainability by requiring fewer inputs than monocultures, although support for this hypothesis in agricultural production settings is scant (but see Tilman et al., 2006; Webster et al., 2010). This work was funded by the DOE Great Lakes Bioenergy Research Center (DOE BER Office of Science DE‐FC02‐07ER64494). This grass along with Andropogon gerardii, Schizachyrium scoparium and Sorghastrum nutans are sometimes called "The Four Horsemen of the Prairie". One possible explanation is that the biomass (hyphae) measured by lipid may not be filled with protoplasm or with nuclei. Figure S6. The only significant difference in dispersion (α = 0.05) was for the NifH data by location (Fig. IndVal results indicated Geobacter was significantly associated with Michigan sites and Bradyrhizobium and Rubrivivax were significantly associated with Wisconsin sites. . (2014) also reported total biomass, and especially AMF biomass, was higher under restored prairie than corn two years after establishment at Wisconsin intensive sites. Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes. Principal components analysis of soil microbial communities from Michigan and Wisconsin intensive sites as evaluated by sequencing of SSU rRNA genes (a), lipid analysis, (b) and NifH sequences (c). One of my subscribers suggested that i keep mowing it down an it will die. Bradyrhizobium and Rubrivivax‐related sequences were more characteristic of Wisconsin: Rubrivivax‐like sequences accounted for more than 17% of the sequences from soils under corn, prairie, and switchgrass in that state. Bridging biofuel sustainability indicators and ecosystem services through stakeholder engagement. 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. But for the most part, these studies have been performed in local settings and the need to carry out studies at larger geographic scales, including sites with different management types, different times since crop establishment, and for a range of soil conditions is necessary to better examine shifts in microbial communities. Switchgrass (Panicum virgatum L.) is a native grass of the United States and is widely adapted to prairie soils, open woods, brackish marshes, and pinewoods openings [23]. Primer sequences were modified by the addition of 454 A or B adapter sequences (lower case). Microbial biomass per treatment was higher for the extensive sites in Wisconsin than for those in Michigan, but markedly so only for the prairie sites. In Deutschland ist Switchgrass bisher hauptsächlich als Zierpflanze (Rutenhirse) bekannt. These primers target a 625 bp fragment of the large subunit (LSU) rRNA gene in fungi. S2). Center for Microbial Ecology and DOE Great Lakes Bioenergy Research Center, Michigan State University, 540 Plant and Soil Sciences Building, East Lansing, MI, 48824‐1325 USA. The three most abundant identifiable phyla were Ascomycota (67% of total sequences), Basidiomycota (15%), and Chytridiomycota (4%) (Fig. Chemical attributes of soils from Michigan (MI) and Wisconsin (WI) intensive and extensive sites. Scaling 1 depicts distances between sites. Our source-identified ecotypes come from our ever-expanding production fields and from a network of more than 70 seed producers located throughout the Midwest. NifH gene libraries were sequenced by the Research Technology Support Facility (RTSF) at Michigan State University (East Lansing). Damit verbunden werden auch “neue” Kulturpflanzen wie Switchgrass für den Anbau immer interessanter. Our initial hypothesis was that the cultivation of switchgrass and mixed grasses would lead to microbial communities more similar to those under prairie species, implying a more sustainable system. Bacterial Communities of the Canola Rhizosphere: Network Analysis Reveals a Core Bacterium Shaping Microbial Interactions. The AARS symbol masks the symbol for one corn extensive site (WIE.Co.1) and one switchgrass extensive site (WIE.Sw.1). No significant differences among locations or treatments were evident at the phylum level. Additionally, the lipid and NifH data separated the samples by location (Table 2 and Fig. Bacterial and fungal biomasses, especially biomass of arbuscular mycorrhizal fungi, were higher under perennial grasses and restored prairie, suggesting a more active carbon pool and greater microbial processing potential, which should be beneficial for plant acquisition and ecosystem retention of carbon, water, and nutrients. The importance of site selection. 28S rRNA gene nucleotide sequences were deposited in the European Nucleotide Archive (http://www.ebi.ac.uk/ena) as part of study PRJEB6704 under accession numbers ERR571439 through ERR571456. Bacteria were further subdivided into Gram‐positive (Gm+) and Gram‐negative (Gm−) categories, and the fungi, into arbuscular mycorrhizal fungi (AMF) and saprophytic fungi (SF) (Liang et al., 2012). Cropping history shapes fungal, oomycete and nematode communities in arable soils and affects cavity spot in carrot. MII = Michigan intensive sites; MIE = Michigan extensive sites; WII = Wisconsin intensive sites; WIE = Wisconsin extensive sites; Co = corn; Mp = mixed grasses; Pr = prairie; Sw = switchgrass. A layout like this would encourage plants to self-seed and spread, filling up the spaces to achieve the look of a small drier or upland prairie. Contact Us . The 28S rRNA gene data separated prairie and corn sites from each other, but samples from the switchgrass sites overlapped both (Fig. Any queries (other than missing content) should be directed to the corresponding author for the article. 1a). As I hike today, I’ll listen to the breeze shush the big bluestem and switchgrass. Seeds; Plants; Seed Mixes; Tool Shed ; Eco-Grass; Gift Certificates; Price List; Blog; Customer Service . Box 61 … Thus, our data indicate that Midwestern prairies may be good places to study the diversity and ecology of this lesser known AMF genus. Of the many genera characteristic of the prairie, unclassified Helotiales, Clavaria, and Tricladium were the most abundant. Among these, there was a greater abundance and richness (number of OTUs) of AMF under prairies for both states, including groups known to have distinct functional traits, such as Paraglomerales and Diversisporales (van der Heijden & Scheublin, 2007). Switchgrass. Principal components analysis of soil microbial communities from Michigan and Wisconsin extensive sites as evaluated by 28S rRNA gene sequences (a), lipid analysis (b and c), SSU rRNA gene sequences (d), and NifH protein sequences(e and f). Nine fields were sampled in each state – three in corn, three in switchgrass, and three in restored prairie – but only the corn fields were harvested. Total lipid biomass (a) and total carbon (b) under different biofuel cropping systems at intensive and extensive sites in Wisconsin and Michigan. However, these crops are monocultures that require high‐energy inputs to maintain, lose soil and nutrients, and serve as key food crops for humans and/or livestock. (2013) who also compared microbial soil communities under biofuel crops by pyrosequencing 16S rRNA and nifH genes and found that site‐to‐site variation surpassed variation stemming from plant type. illinois prairie grass - switchgrass stock pictures, royalty-free photos & images. The differential response to crops observed between intensive and extensive experiments is likely related to the length of time the crops had been grown at the sites. (2013), however, were not able to detect differences in N2‐fixing communities between crops, while we did for the extensive sites. The full text of this article hosted at iucr.org is unavailable due to technical difficulties. Relative abundances of fungal phyla at extensive sites determined from 28S rRNA gene sequences. Their use for biofuel may increase food costs and may encourage more land to be converted to agriculture, which has negative ramifications for ecosystem carbon balance, wildlife habitat, and a host of other ecosystem services (Fargione et al., 2008). switchgrass.lucas@gmail.com 205 South Main Lucas, KS 67648 P.O. The reason for this large discrepancy is important to resolve for proper accounting of this important group of soil fungi. Michigan and Wisconsin intensive sites differed markedly in their physical and chemical soil attributes (Fig. In our case, we targeted the nifH gene, which codes for dinitrogenase reductase, a component of nitrogenase, the enzyme responsible for N2 fixation. , respectively, were excluded for yielding too few sequences associations and effects biodiversity... The pH gradient and Joe Simmons for managing the intensive sites differed in..., among sample categories a potential biofuel feedstock and is highly adapted to areas with to... 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