We report the draft genome sequences of five native nitrogen-fixing bacteria associated with roots of switchgrass isolated from the tallgrass prairies of Oklahoma. Nitrogen-fixing genes, including the nif cluster, are conserved across the Klebsiella and Kosakonia strains.


Switchgrass (Panicum virgatum L.) is an intensely studied, warm-season perennial species that is being developed as a bioenergy crop for liquid fuels and other bioproducts (1). It generally requires application of synthetic fertilizer for maximal, sustained biomass yields. However, an alternative source of nitrogen is biological nitrogen fixation (BNF), in which associated, diazotrophic bacteria convert atmospheric nitrogen to ammonia for the plant. In order to study and potentially enhance plant-diazotroph interactions, five BNF bacteria were isolated from switchgrass roots in the tallgrass prairies of northern Oklahoma, in the United States (36.7689, −96.3904), during the summer growing season of 2010 and were grown on nitrogen-deficient medium as described previously (2, 3). Here, we present the draft genomes of these five switchgrass rhizoplane diazotrophs, including their nitrogen fixation (nif) genes and other genes.
Bacterial isolates were grown in 869 medium from a single colony (4). DNA was extracted using the DNeasy plant minikit (Qiagen, Inc., Germantown, MD). Two hundred nanograms of DNA was sheared to 300 bp using the LE220 focused ultrasonicator (Covaris, Inc., Woburn, MA) and size selected by double solid-phase reversible immobilization (SPRI) (Beckman Coulter, Brea, CA). The Illumina library creation kit (Kapa Biosystems, Wilmington, MA) was used for end repair, A tailing, ligation of Illumina adapters (IDT, Inc., San Jose, CA), and multiplexing following the manufacturer’s instructions. Libraries were quantified by quantitative PCR using the KAPA library quantification kit for Illumina. The pooled paired-ended library was prepared and sequenced at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) (USA) on an Illumina HiSeq 2500 sequencer using TruSeq sequencing-by-synthesis (SBS) kits, version 4, with a 2 × 150-bp indexed run recipe.
The resulting sequencing reads were quality control filtered and assembled into scaffolds with AllPaths-LG, version r46652 (5) and annotated with the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (6). Taxonomic classification was performed using the 16S rRNA sequences for BLASTn searches (7).
Two Kosakonia radicincitans (formerly Enterobacter) species (strains NFIX03 and NFIX09) and three Klebsiella quasipneumoniae species (strains NFIX19, NFIX42, and NFIX56) were identified. The genomic characteristics are listed in Table 1. The conserved nif cluster (nifHDKBCENQSUVL) required for nitrogenase biosynthesis and BNF activity is present in all five isolates. The nif transcriptional activator (nifA) is present in all Klebsiella strains but absent in the Kosakonia strains, suggesting different regulation of nif expression. The amtB and glnAB genes required for ammonia transport and utilization, respectively, are present in all five genomes. The Kosakonia strains have more plant colonization genes, including those involved in chemotaxis (cheABRVWYZ, mcpBC, and motB), mobility (chpACDE and pilGHIJK), and biofilm formation (flgE, fliCF, and motA), than the Klebsiella strains, which have no biofilm genes, only the cheY chemotaxis gene, and the chpCDE and pilIJK mobility genes, indicating that Kosakonia strains may be better colonizers of switchgrass.
TABLE 1 Genomic information and accession numbers for five nitrogen-fixing bacterial strains isolated from switchgrass rootsa
Bacterial isolatebGenome size (bp)No. of scaffoldsScaffold N50 (bp)No. of sequencing readsTotal bp sequencedTotal no. of genesG+C content (%)GenBank accession no.SRA accession no.
Kosakonia radicincitans NFIX035,597,19634288,5336,831,9961,024,799,4005,35753.99FPJU00000000SRX2122634
Kosakonia radicincitans NFIX095,483,348143,027,5406,152,934922,940,1005,28054.03FOHP01000000SRX2122594
Klebsiella quasipneumoniae NFIX195,217,29821373,4216,826,7161,024,007,4004,91058.21FOAU00000000SRX2122607
Klebsiella quasipneumoniae NFIX425,292,30921531,6236,097,090914,563,5005,03458.08FMVG00000000SRX2122649
Klebsiella quasipneumoniae NFIX565,439,06433286,2126,642,240996,336,0005,15757.93FPJQ00000000SRX2122658
Default parameters were used for all software unless otherwise specified.
Strains were classified on the basis of ≥99% similarity with 16S rRNA genomic sequences.
The draft genome sequences of the five switchgrass isolates will serve as references to modify and improve the ability of the isolates to supply fixed nitrogen and improve plant growth for sustainable bioenergy production.

Data availability.

The draft genome sequences from this study were deposited in DDBJ/ENA/GenBank and the raw sequencing reads in the NCBI Sequence Read Archive (SRA). The corresponding GenBank and SRA accession numbers are listed in Table 1.


The work conducted by the U.S. DOE JGI, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. DOE under contract DE-AC02-05CH11231. Part of this work was also funded by the U.S. DOE Office of Biological and Environmental Research, through the Center for Bioenergy Innovation.


Bouton J. 2008. Improvement of switchgrass as a bioenergy crop, p 309–345. In Vermerris W (ed), Genetic improvement of bioenergy crops. Springer, New York, NY.
Baldani JI, Reis VM, Videira SS, Boddey LH, Baldani VLD. 2014. The art of isolating nitrogen-fixing bacteria from non-leguminous plants using N-free semi-solid media: a practical guide for microbiologists. Plant Soil 384:413–431.
Ghimire SR, Charlton ND, Bell JD, Krishnamurthy YL, Craven KD. 2011. Biodiversity of fungal endophyte communities inhabiting switchgrass (Panicum virgatum L.) growing in the native tallgrass prairie of northern Oklahoma. Fungal Divers 47:19–27.
Mergeay M, Nies D, Schlegel HG, Gerits J, Charles P, Van Gijsegem F. 1985. Alcaligenes eutrophus CH34 is a facultative chemolithotroph with plasmid-bound resistance to heavy metals. J Bacteriol 162:328–334.
Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, Berlin AM, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, Jaffe DB. 2011. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A 108:1513.
Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2016. NCBI Prokaryotic Genome Annotation Pipeline. Nucleic Acids Res 44:6614–6624.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215:403–410.

Information & Contributors


Published In

cover image Microbiology Resource Announcements
Microbiology Resource Announcements
Volume 10Number 2127 May 2021
eLocator: 10.1128/mra.00284-21
Editor: David A. Baltrus, University of Arizona


Received: 24 March 2021
Accepted: 4 May 2021
Published online: 27 May 2021



Noble Research Institute, LLC, Ardmore, Oklahoma, USA
Chi Myoung-Hwan
Noble Research Institute, LLC, Ardmore, Oklahoma, USA
Venkatacha Lakshmanan
Noble Research Institute, LLC, Ardmore, Oklahoma, USA
Present address: Venkatacha Lakshmanan, Soil Carbon Company, Saint Paul, Minnesota, USA.
Ivone Torres-Jerez
Noble Research Institute, LLC, Ardmore, Oklahoma, USA
Yuhong Tang
Noble Research Institute, LLC, Ardmore, Oklahoma, USA
Maira Sparks
Noble Research Institute, LLC, Ardmore, Oklahoma, USA
Nicole R. Shapiro
Department of Energy Joint Genome Institute, Berkeley, California, USA
Kelly D. Craven
Noble Research Institute, LLC, Ardmore, Oklahoma, USA
Noble Research Institute, LLC, Ardmore, Oklahoma, USA


David A. Baltrus
University of Arizona

Metrics & Citations


Note: There is a 3- to 4-day delay in article usage, so article usage will not appear immediately after publication.

Citation counts come from the Crossref Cited by service.


If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download.

View Options

Figures and Media






Share the article link

Share with email

Email a colleague

Share on social media

American Society for Microbiology ("ASM") is committed to maintaining your confidence and trust with respect to the information we collect from you on websites owned and operated by ASM ("ASM Web Sites") and other sources. This Privacy Policy sets forth the information we collect about you, how we use this information and the choices you have about how we use such information.
FIND OUT MORE about the privacy policy