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Improving Biofuel Feedstock Production of Switchgrass (Panicum Virgatum L.) by Inoculation with Endophytic Rhizobacteria

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Improving Biofuel Feedstock Production of Switchgrass (Panicum Virgatum L.) by Inoculation with Endophytic Rhizobacteria A greener grass: Improving biofuel feedstock production of switchgrass (Panicum virgatum L.) by inoculation with endophytic rhizobacteria Keomany Ker Faculty of Agriculture and Environmental Sciences Department of Natural Resource Sciences Macdonald Campus of McGill University, 21111 Lakeshore Road, Ste-Anne-de-Bellevue, QC H9X 3V9 April 2012 A thesis submitted to McGill University in partial fulfillment of the requirements of the degree of DOCTOR OF PHILOSOPHY c Keomany Ker, Canada, 2012 Dedication This thesis is dedicated, with love, to my parents: my mother, Chanthalan Ker, and to my father, Tin Ker, who passed away before its completion. Without your love, courage, and hopes for a better future, this thesis would never have been possible. i Contents Dedication ................................... i Abstract .................................... vii R´esum´e ..................................... x Contributions of the authors . xii Acknowledgements .............................. xiv List of Tables ................................. xvi List of Figures . xvii List of Abbreviations ............................ xx 1 Introduction 1 2 Literature Review 4 2.1 Switchgrass (Panicum virgatum L.) . 4 2.1.1 `Model' bioenergy crop: A brief history of its selection . 4 2.1.2 The biology of switchgrass . 6 2.1.3 Switchgrass: A better biofuel? . 7 2.1.4 Improving the sustainable production of switchgrass for bioenergy 9 2.2 Sustainable biofuel production from sugarcane: The Brazilian story . 11 2.2.1 The catalysts for bioethanol research: Energy crisis and energy independence . 12 2.2.2 Sugarcane and the Brazilian National Alcohol Program . 13 2.3 Biological nitrogen fixation (BNF) . 14 ii 2.3.1 The N cycle: Mechanism of BNF . 14 2.3.2 Fertilizer use: Impacts on agriculture and environment . 15 2.3.3 N2-fixing bacteria: Contribution to crop productivity and soil fertility . 17 2.3.4 N2-fixing bacteria: Rhizobia and diazotrophs . 18 2.3.5 Other mechanisms of plant growth promotion . 21 2.4 Beneficial microbes as part of a sustainable biofuels production system 23 2.4.1 Plant-microbe interactions with sugarcane: The `model' system 23 2.4.2 Sugarcane-microbe `model' system for temperate grown biofuels? 24 2.4.3 Are there beneficial switchgrass-microbe associations? . 26 3 Research Questions and Objectives 28 Preface to Chapter 4 30 4 Isolation and identification of rhizosphere endophytes that promote the growth of switchgrass (Panicum virgatum L.) 31 4.1 Abstract . 31 4.2 Introduction . 32 4.3 Materials and Methods . 34 4.3.1 Rhizome sampling: location and site history . 34 4.3.2 Isolation of bacteria from P. virgatum rhizome tissue . 35 4.3.3 Bacterial screening bioassay . 36 4.3.4 Statistical analyses . 38 4.3.5 Phosphate solubilization . 39 4.3.6 Auxin production . 39 4.3.7 Extraction of total genomic DNA . 40 4.3.8 Molecular biology techniques . 40 4.3.9 DNA sequencing and analyses . 42 iii 4.3.10 Nucleotide sequence accession numbers . 42 4.4 Results . 43 4.4.1 Bacterial screening bioassay . 43 4.4.2 Nitrogen concentration and content . 45 4.4.3 Phosphate solubilization . 46 4.4.4 Production of IAA-like substances . 47 4.4.5 Isolate identification . 47 4.5 Discussion . 48 4.6 Conclusions . 54 4.7 Tables and Figures . 55 Preface to Chapter 5 67 5 Inoculation of switchgrass (Panicum virgatum L.) by rhizosphere endophytes improves establishment year crop productivity 68 5.1 Abstract . 68 5.2 Introduction . 69 5.3 Materials and Methods . 73 5.3.1 Field design . 73 5.3.2 Seed inoculation . 74 5.3.3 Harvest, data collection, and analyses . 75 5.3.4 Statistical analyses . 76 5.4 Results and Discussion . 76 5.4.1 Yield and yield components . 76 5.4.2 Fiber analyses: lignin, cellulose, and hemicellulose . 79 5.5 Conclusions . 79 5.6 Tables and Figures . 81 Preface to Chapter 6 88 iv 6 N dynamics of switchgrass: Effects of inoculation by endophytic plant growth promoting rhizobacteria on establishment year N use efficiency 89 6.1 Abstract . 89 6.2 Introduction . 90 6.3 Materials and Methods . 94 6.3.1 Field design . 94 6.3.2 Seed inoculation . 95 6.3.3 Harvest, data collection, and analyses . 95 6.3.4 Statistical analyses . 97 6.4 Results and Discussion . 97 6.4.1 Nitrogen concentration, translocation, and cycling . 97 6.4.2 Nitrogen removal at harvest and fertilizer recovery . 100 6.4.3 Nitrogen balance of switchgrass-microbe systems: Improved access to non-fertilizer N . 103 6.4.4 Other nutrients . 106 6.5 Conclusions . 107 6.6 Tables and Figures . 110 Preface to Chapters 7 and 8 116 7 Summary, Conclusion and Future Research 117 7.1 Summary of results . 119 7.2 Conclusion . 123 7.3 Recommendations for future research . 124 8 Contributions to Knowledge 128 References 131 v Abstract Switchgrass (SG, Panicum virgatum L.), a temperate perennial grass, was chosen by the US Department of Energy's Herbaceous Energy Crops Program as the `model' bioenergy crop for further research in North America. Current research on SG for bioenergy feedstock production focuses on improving breeding selection, agronomy and crop physiology, energy potential, and its contribution to mitigating greenhouse gas emissions. However, there is a lack of knowledge regarding plant-microbe inter- actions with SG, how these associations play a role in its growth and productivity, and their function and potential role in agro-ecosystems. Moreover, as SG has been reported to produce high biomass yields with minimal to no synthetic nitrogen (N) fertilizer, this suggested to us that SG could be obtaining at least some of the N to meet its requirements from plant growth promoting rhizobacteria (PGPR) capable of biological N2-fixation (BNF). The objectives of this research were to determine if: (1) SG associates with PGPR, (2) PGPR we isolated from SG can be used as inoculants capable of promoting SG growth under a controlled environment, and (3) inoculation with PGPR can increase the growth and productivity of SG for biofuel production under a low-N input system. Switchgrass rhizomes were collected in Qu´ebec, Canada, from a discontinued biomass trial of 11 varieties that had not received N fertilizer or any other management input since 2000. Isolates were chosen on N-free solidified me- dia and screened for their ability to promote plant growth using plant assays conducted in growth chambers. Switchgrass seedlings were inoculated, or not, with batches of mixed isolates and fertilized with N-free Hoagland's solution. Molecular analyses of vi 16S rRNA gene sequences identified the mixed bacterial inoculum as Paenibacillus polymyxa, a N2-fixing bacterium, and several other PGPR (Pseudomonas, Serratia and Rahnella spp.) capable of producing auxin and/or solubilizing phosphate. Field trials of inoculated SG seeds were conducted in 2010 on three sites comprising differ- ent soil types. The factors tested were the bacterial treatment, either uninoculated control or seed inoculated, and a fertilizer treatment, either 0 or 100 kg N ha−1. Establishment year results showed that inoculation of SG plants with a mixed PGPR culture produced higher tiller density and larger tillers than uninoculated plants, which was the probable cause of the 40% yield increase. This 40% yield in- crease persisted under N fertilization, at least at the 100 kg N ha−1 rate. Inoculated SG plants also had better N cycling than uninoculated plants, as they contained more N within tillers during anthesis but not after senescence, suggesting a greater amount of N was translocated to below-ground roots and rhizomes of inoculated than uninoc- ulated plants. Greater N storage in roots and rhizomes could mean better early-season regrowth and provide an advantage over weeds. PGPR inoculation also affected the N balance of the harvested biomass by contributing additional non-fertilizer N (ANFN) to SG plants. Interestingly, this bacterial effect was not inhibited in the presence of N fertilizer. The combination of PGPR and N fertilizer provided a substantial N contribution to SG, although the exact amount will require additional research. This investigation showed that SG does associate with PGPR and that PGPR can be ef- fectively utilized as inoculants to enhance SG yields in low-N input systems. This research will help in the development of an environmentally beneficial switchgrass- microbe system, reduces N requirements and has the potential to become a best N management practice. vii R´esum´e Le panic raide (PR, Panicum virgatum L.) est un gramin´eesvivace qui pousse dans les climats temp´eres.Le PR a ´et´echoisi dans le cadre du programme de recherche sur les agrocarburants, The Herbaceous Energy Crops Program , du d´epartement de l'´energieam´ericain comme ´etant le mod`ele de culture agro´energ´etiquepour l'avancement de la recherche en Am´eriquedu Nord. La recherche actuelle sur l'emploi du PR dans la production de biocarburant est principalement ax´eesur la s´election de cultivars plus productifs, l'agronomie et la physiologie de la plante, son potentiel ´energ´etiqueainsi que sa contribution `ala r´eductiondes gaz `aeffet de serre. Pourtant, il y a un manque de connaissance par rapport aux interactions plante-microbe chez le PR et le r^oleque jouent ces associations sur la productivit´ede la culture ainsi que leur fonction et leur r^oledans l'agro´ecosyst`eme. De plus, il a ´et´ed´emontr´eque PR donne de hauts rendements sans apport ou avec un apport minime d'azote (N) fertilisant synth´etique.Ceci nous porte `acroire que les besoins en N pourraient ^etrecombl´espar l'interaction avec des rhizobact´eriesqui favorisent la croissance des plantes, connues sous le terme RFCP capable de fixation biologique de l'azote. L'objectif de l'´etude ici pr´esent´eeest de d´eterminersi : (1) le PR s'associe avec les RFCP, (2) les RFCP que nous avons isol´esdes rhizomes du PR sont capable de promouvoir la croissance de la plante dans un environnement contr^ol´e,et finalement (3) inoculation de RFCP peut augmenter la croissance et la productivit´edu PR pour de la production de biocarburant sous un apport minime de fertilisant N.
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