# Bacterial isolate collection from switchgrass rhizosphere

Keara L Grady, Ashley Shade

► To cite this version:

Keara L Grady, Ashley Shade. Bacterial isolate collection from switchgrass rhizosphere. Microbiology Resource Announcements, In press, 10.1128/mra.01133-23. hal-04610811

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Submitted on 13 Jun 2024

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# Bacterial isolate collection from switchgrass rhizosphere

Keara L Grady, Ashley Shade

► To cite this version:

Keara L Grady, Ashley Shade. Bacterial isolate collection from switchgrass rhizosphere. Microbiology Resource Announcements, In press, 13 (7), 10.1128/mra.01133-23. hal-04610811

HAL Id: hal-04610811

https://hal.science/hal-04610811v1

Submitted on 13 Jun 2024

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
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<figure><img src="image_1.png" /></figure>
1

2 **Article title**

3 Bacterial isolate collection from switchgrass rhizosphere

4 **Authors**

5 Keara L. Gradyª and Ashley Shadeᵇ#

6 **Affiliations**

7 a. Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA.

8 b. Universite Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, Laboratoire d'Ecologie Microbienne

9 LEM, CNRS UMR5557, INRAE UMR1418, Villeurbanne, F-69100 France

10 **Running title**

11 Bacteria isolated from switchgrass rhizosphere.

12 **Corresponding author's email address**

13 #Address correspondence to Ashley Shade, ashley.shade@cnrs.fr

14 **Abstract**

15 We provide a collection of 78 bacterial isolates from the rhizosphere of switchgrass (Panicum virgatum
16 L.) at the Lux Arbor Reserve in Delton, MI, a site of the Great Lakes Bioenergy Research Center (GLBRC),
17 Michigan State University, MI, USA. We include information on isolation conditions and full-length 16S
18 rRNA sequences.

19 **Announcement**

20 Switchgrass (Panicum virgatum L.) is a perennial grass and biofuel feedstock that offers
21 economic and environmental benefits, including carbon sequestration in deep-rooting systems
22 and growth on marginal lands with need for minimal fertilization. Switchgrass harbors a
23 relatively stable root-associated microbial community structure, especially compared to its
1

2 **Article title**

3 Bacterial isolate collection from switchgrass rhizosphere

4 **Authors**

5 Keara L. Gradyª and Ashley Shadeᵇ#

6 **Affiliations**

7 a. Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA.

8 b. Universite Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, Laboratoire d'Ecologie Microbienne

9 LEM, CNRS UMR5557, INRAE UMR1418, Villeurbanne, F-69100 France

10 **Running title**

11 Bacteria isolated from switchgrass rhizosphere.

12 **Corresponding author's email address**

13 #Address correspondence to Ashley Shade, ashley.shade@cnrs.fr

14 **Abstract**

15 We provide a collection of 78 bacterial isolates from the rhizosphere of switchgrass (Panicum virgatum
16 L.) at the Lux Arbor Reserve in Delton, MI, a site of the Great Lakes Bioenergy Research Center (GLBRC),
17 Michigan State University, MI, USA. We include information on isolation conditions and full-length 16S
18 rRNA sequences.

19 **Announcement**

20 Switchgrass (Panicum virgatum L.) is a perennial grass and biofuel feedstock that offers
21 economic and environmental benefits, including carbon sequestration in deep-rooting systems
22 and growth on marginal lands with need for minimal fertilization. Switchgrass harbors a
23 relatively stable root-associated microbial community structure, especially compared to its
24 more dynamic phyllosphere community¹⁻³. Thus, perennial crop microbiomes may offer insights
25 into durable plant-microbe relationships.

26 Bacterial strains were isolated from the switchgrass rhizosphere (cultivar Cave-in-rock) at
27 the Lux Arbor Reserve in Delton, MI, USA (42.4764, -85.4519). Roots were collected on August
28 30th, 2018 from mature, pre-senescent plants using a 2.5 cm diameter, 20 cm depth soil corer
29 to collect soils and roots at the base. In a biosafety cabinet, bulk soil was removed from ~2 g of
30 root tissue per plant, then roots were sonicated in 10 ml of sterile phosphate-buffered saline +
31 0.01% Tween-20 (PBS-T) for 2 minutes and incubated at 4°C for 1 h to settle large soil particles.
32 Cells were pelleted from the supernatant at 6,000 x g for 10 minutes at 4°C. The pellet was
33 resuspended in 1 ml PBS + 25% glycerol, flash-frozen in liquid nitrogen, and stored at -80°C.

34 Slurries were thawed on ice, mixed thoroughly, and serially diluted into sterile PBS-T.
35 Aliquots of diluted slurry were spread onto either rhizosphere isolation medium (RIM)⁴ or
36 Reasoner's 2A (R2A) agar + 0.5% succinate, containing 0.2 g/ml cycloheximide (cyc) to prevent
37 fungal growth. Plates were incubated at 27°C in aerobic conditions for 24-72 h. Individual
38 colonies were picked onto new RIM-cyc or R2A-cyc plates and purified by streaking for isolation,
39 then stored in R2A + 25% glycerol at -80°C. Table 1 includes growth conditions for each strain.

40 Genomic DNA (gDNA) was extracted using a Quick DNA fungal-bacterial miniprep kit
41 (Zymo Research #D6005). For some isolates, gDNA was extracted using an acetone freeze-thaw
42 cycle and enzymatic lysis followed by a liquid extraction⁵,⁶. Full-length 16S rRNA sequences were
43 amplified using the 27F-1492R primer set (5'-AGAGTTTGATCCTGGCTCAG-3' and 5'-
44 GGTTACCTTGTTACGACTT-3')⁷ and Phusion High-fidelity polymerase (New England Biolabs)
45 under the following conditions: denaturation at 98°C for 1 min, then 25 cycles of denaturation
24 more dynamic phyllosphere community¹⁻³. Thus, perennial crop microbiomes may offer insights
25 into durable plant-microbe relationships.

26 Bacterial strains were isolated from the switchgrass rhizosphere (cultivar Cave-in-rock) at
27 the Lux Arbor Reserve in Delton, MI, USA (42.4764, -85.4519). Roots were collected on August
28 30th, 2018 from mature, pre-senescent plants using a 2.5 cm diameter, 20 cm depth soil corer
29 to collect soils and roots at the base. In a biosafety cabinet, bulk soil was removed from ~2 g of
30 root tissue per plant, then roots were sonicated in 10 ml of sterile phosphate-buffered saline +
31 0.01% Tween-20 (PBS-T) for 2 minutes and incubated at 4°C for 1 h to settle large soil particles.
32 Cells were pelleted from the supernatant at 6,000 x g for 10 minutes at 4°C. The pellet was
33 resuspended in 1 ml PBS + 25% glycerol, flash-frozen in liquid nitrogen, and stored at -80°C.

34 Slurries were thawed on ice, mixed thoroughly, and serially diluted into sterile PBS-T.
35 Aliquots of diluted slurry were spread onto either rhizosphere isolation medium (RIM)⁴ or
36 Reasoner's 2A (R2A) agar + 0.5% succinate, containing 0.2 g/ml cycloheximide (cyc) to prevent
37 fungal growth. Plates were incubated at 27°C in aerobic conditions for 24-72 h. Individual
38 colonies were picked onto new RIM-cyc or R2A-cyc plates and purified by streaking for isolation,
39 then stored in R2A + 25% glycerol at -80°C. Table 1 includes growth conditions for each strain.

40 Genomic DNA (gDNA) was extracted using a Quick DNA fungal-bacterial miniprep kit
41 (Zymo Research #D6005). For some isolates, gDNA was extracted using an acetone freeze-thaw
42 cycle and enzymatic lysis followed by a liquid extraction⁵,⁶. Full-length 16S rRNA sequences were
43 amplified using the 27F-1492R primer set (5'-AGAGTTTGATCCTGGCTCAG-3' and 5'-
44 GGTTACCTTGTTACGACTT-3')⁷ and Phusion High-fidelity polymerase (New England Biolabs)
45 under the following conditions: denaturation at 98°C for 1 min, then 25 cycles of denaturation
46 (98°C for 10 sec), annealing (58°C for 20 sec), and extension (72°C for 45 sec). Amplicons were

47 cleaned using a Wizard-SV gel/PCR Clean-up kit (Promega) and Sanger-sequenced on the ABI

48 3730xl at the MSU Research Technology Support Facility (rtsf.natsci.msu.edu). Amplicons were

49 sequenced from both directions using the above primers, and were analyzed using Geneious

50 Prime software v 2021.2.2 (Dotmatics, Table 1, Figure 1).

51 **Data and strain availability statement**

52 Full-length 16S consensus sequences are available at NCBI, accession OR754732-OR754809 and

53 raw reads are available at the NCBI SRA under Bioproject PRJNA1056287, accession numbers

54 SRR27348763-SRR27348840. The bacterial collection and individual isolates are available by

55 email request to The Great Lakes Bioenergy Research Center at Michigan State University, USA

56 (glbrc@msu.edu).

57 **Acknowledgments**

58 This work was supported by the Great Lakes Bioenergy Research Center, U.S. Department of

59 Energy, Office of Science, Office of Biological and Environmental Research under Award Number

60 DE-SC0018409. Support for field research was provided by the Great Lakes Bioenergy Research

61 Center, U.S. Department of Energy, Office of Science, Office of Biological and Environmental

62 Research (Awards DE-SC0018409 and DE-FC02-07ER64494), by the National Science Foundation

63 Long-term Ecological Research Program (DEB 1637653) at the Kellogg Biological Station, and by

64 Michigan State University AgBioResearch.

65 The authors declare no conflict of interest.

66 **References**
46 (98°C for 10 sec), annealing (58°C for 20 sec), and extension (72°C for 45 sec). Amplicons were

47 cleaned using a Wizard-SV gel/PCR Clean-up kit (Promega) and Sanger-sequenced on the ABI

48 3730xl at the MSU Research Technology Support Facility (rtsf.natsci.msu.edu). Amplicons were

49 sequenced from both directions using the above primers, and were analyzed using Geneious

50 Prime software v 2021.2.2 (Dotmatics, Table 1, Figure 1).

51 **Data and strain availability statement**

52 Full-length 16S consensus sequences are available at NCBI, accession OR754732-OR754809 and

53 raw reads are available at the NCBI SRA under Bioproject PRJNA1056287, accession numbers

54 SRR27348763-SRR27348840. The bacterial collection and individual isolates are available by

55 email request to The Great Lakes Bioenergy Research Center at Michigan State University, USA

56 (glbrc@msu.edu).

57 **Acknowledgments**

58 This work was supported by the Great Lakes Bioenergy Research Center, U.S. Department of

59 Energy, Office of Science, Office of Biological and Environmental Research under Award Number

60 DE-SC0018409. Support for field research was provided by the Great Lakes Bioenergy Research

61 Center, U.S. Department of Energy, Office of Science, Office of Biological and Environmental

62 Research (Awards DE-SC0018409 and DE-FC02-07ER64494), by the National Science Foundation

63 Long-term Ecological Research Program (DEB 1637653) at the Kellogg Biological Station, and by

64 Michigan State University AgBioResearch.

65 The authors declare no conflict of interest.

66 **References**
67 1. Bowsher, A. W., Benucci, G. M. N., Bonito, G. & Shade, A. Seasonal Dynamics of Core
68 Fungi in the Switchgrass Phyllosphere, and Co-Occurrence with Leaf Bacteria.
69 *Phytobiomes J.* PBIOMES-07-20-0 (2020) doi:10.1094/pbiomes-07-20-0051-r.

70 2. Grady, K. L., Sorensen, J. W., Stopnisek, N., Guittar, J. & Shade, A. Assembly and
71 seasonality of core phyllosphere microbiota on perennial biofuel crops. *Nat. Commun.*
72 **10**, (2019).

73 3. Howe, A. et al. Frontiers and Opportunities in Bioenergy Crop Microbiome Research
74 Networks. *Phytobiomes J.* **6**, 118–126 (2022).

75 4. Buyer, J. S. A soil and rhizosphere microorganism isolation and enumeration medium
76 that inhibits Bacillus mycoides. *Appl. Environ. Microbiol.* **61**, 1839–1842 (1995).

77 5. Feil, W. S., Feil, H. & Copeland, A. Bacterial genomic DNA isolation using CTAB. *DOE Joint
78 Genome Institute* 9 https://jgi.doe.gov/wp-content/uploads/2014/02/JGI-Bacterial-DNA-
79 isolation-CTAB-Protocol-2012.pdf (2004).

80 6. Kutchma, A. J., Roberts, M. A., Knaebel, D. B. & Crawford, D. L. Small-scale isolation of
81 genomic DNA from *Streptomyces* mycelia or spores. *Biotechniques* **24**, 452–457 (1998).

82 7. Weisburg, W. G., Barns, S. M., Pelletier, D. A. & Lane, D. J. 16S Ribosomal DNA
83 Amplification for Phylogenetic Study. *J. Bacteriol.* **173**, 697–703 (1991).

84
67 1. Bowsher, A. W., Benucci, G. M. N., Bonito, G. & Shade, A. Seasonal Dynamics of Core
68 Fungi in the Switchgrass Phyllosphere, and Co-Occurrence with Leaf Bacteria.
69 *Phytobiomes J.* PBIOMES-07-20-0 (2020) doi:10.1094/pbiomes-07-20-0051-r.

70 2. Grady, K. L., Sorensen, J. W., Stopnisek, N., Guittar, J. & Shade, A. Assembly and
71 seasonality of core phyllosphere microbiota on perennial biofuel crops. *Nat. Commun.*
72 **10**, (2019).

73 3. Howe, A. et al. Frontiers and Opportunities in Bioenergy Crop Microbiome Research
74 Networks. *Phytobiomes J.* **6**, 118–126 (2022).

75 4. Buyer, J. S. A soil and rhizosphere microorganism isolation and enumeration medium
76 that inhibits Bacillus mycoides. *Appl. Environ. Microbiol.* **61**, 1839–1842 (1995).

77 5. Feil, W. S., Feil, H. & Copeland, A. Bacterial genomic DNA isolation using CTAB. *DOE Joint
78 Genome Institute* 9 https://jgi.doe.gov/wp-content/uploads/2014/02/JGI-Bacterial-DNA-
79 isolation-CTAB-Protocol-2012.pdf (2004).

80 6. Kutchma, A. J., Roberts, M. A., Knaebel, D. B. & Crawford, D. L. Small-scale isolation of
81 genomic DNA from *Streptomyces* mycelia or spores. *Biotechniques* **24**, 452–457 (1998).

82 7. Weisburg, W. G., Barns, S. M., Pelletier, D. A. & Lane, D. J. 16S Ribosomal DNA
83 Amplification for Phylogenetic Study. *J. Bacteriol.* **173**, 697–703 (1991).

84
<table><caption>TABLE 1. NCBI BLAST Taxonomy, isolation media, and DNA conditions of 78 bacterial isolates from switchgrass rhizosphere, as described in this study.</caption><thead><tr><th>Isolate_ID</th><th>Assembly_BLAST_Genus</th><th>Assembly_BLAST_T{species}</th><th>BLAST_Grade<sup>a</sup></th><th>BLAST_Hit_Accession</th><th>Isolation_Media<sup>b</sup></th><th>DNA_Method</th><th>NCBI_Accession_number</th><th>SRA_Accession_number</th></tr></thead><tbody><tr><td>PvR001</td><td>Rhodococcus</td><td>fascians</td><td>99.7</td><td>NR_119126</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754732</td><td>SRR27348840</td></tr><tr><td>PvR006</td><td>Streptomyces</td><td>zaomyceticus</td><td>100</td><td>NR_112376</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td><td>OR754733</td><td>SRR27348839</td></tr><tr><td>PvR008</td><td>Paenibacillus</td><td>terrae</td><td>99.1</td><td>NR_025170</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td><td>OR754734</td><td>SRR27348828</td></tr><tr><td>PvR012</td><td>Burkholderia</td><td>diffusa</td><td>99.8</td><td>NR_042633</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754735</td><td>SRR27348817</td></tr><tr><td>PvR013</td><td>Chryseobacterium</td><td>lactis</td><td>99.7</td><td>NR_126256</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754736</td><td>SRR27348806</td></tr><tr><td>PvR015</td><td>Chryseobacterium</td><td>lactis</td><td>99.1</td><td>NR_126256</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754737</td><td>SRR27348785</td></tr><tr><td>PvR016</td><td>Rhizobium</td><td>phaseoli</td><td>99.3</td><td>NR_113671</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754738</td><td>SRR27348774</td></tr><tr><td>PvR017</td><td>Burkholderia</td><td>ambifaria</td><td>99.8</td><td>NR_074687</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754739</td><td>SRR27348763</td></tr><tr><td>PvR018</td><td>Paenibacillus</td><td>sp.</td><td>99.8</td><td>NR_112906</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754740</td><td>SRR27348796</td></tr><tr><td>PvR019</td><td>Mycolicibacterium</td><td>mucogenicum</td><td>99.6</td><td>NR_042919</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td><td>OR754741</td><td>SRR27348795</td></tr><tr><td>PvR021</td><td>Pantoea</td><td>agglomerans</td><td>99.9</td><td>NR_111998</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754742</td><td>SRR27348838</td></tr><tr><td>PvR022</td><td>Burkholderia</td><td>contaminans</td><td>99.9</td><td>NR_104978</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754743</td><td>SRR27348837</td></tr><tr><td>PvR023</td><td>Burkholderia</td><td>ambifaria</td><td>99.7</td><td>NR_074687</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754744</td><td>SRR27348836</td></tr><tr><td>PvR024</td><td>Cupriavidus</td><td>necator</td><td>99.9</td><td>NR_102851</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754745</td><td>SRR27348835</td></tr><tr><td>PvR025</td><td>Agrobacterium</td><td>rhizogenes<br>lindaniclasticu</td><td>99.9</td><td>NR_113607</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754746</td><td>SRR27348834</td></tr><tr><td>PvR029</td><td>Novosphingobium</td><td>m</td><td>99.5</td><td>NR_118312</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754747</td><td>SRR27348833</td></tr><tr><td>PvR033</td><td>Burkholderia</td><td>contaminans<br>spiroverticillatu</td><td>99.6</td><td>NR_104978</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754748</td><td>SRR27348832</td></tr><tr><td>PvR034</td><td>Streptomyces</td><td>s</td><td>99.6</td><td>NR_112582</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754749</td><td>SRR27348831</td></tr><tr><td>PvR038</td><td>Burkholderia</td><td>stabilis</td><td>99.9</td><td>NR_114522</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754750</td><td>SRR27348830</td></tr><tr><td>PvR040</td><td>Rhodococcus</td><td>qingshengii</td><td>99.8</td><td>NR_115708</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754751</td><td>SRR27348829</td></tr><tr><td>PvR041</td><td>Enterobacter</td><td>ludwigii</td><td>100</td><td>NR_042349</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754752</td><td>SRR27348827</td></tr><tr><td>PvR042</td><td>Pseudomonas</td><td>protegens</td><td>99.9</td><td>NR_114749</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754753</td><td>SRR27348826</td></tr><tr><td>PvR043</td><td>Novosphingobium</td><td>capsulatum</td><td>99.7</td><td>NR_113591</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754754</td><td>SRR27348825</td></tr><tr><td>PvR044</td><td>Rhodococcus</td><td>oryzae<br>lindaniclasticu</td><td>99.8</td><td>NR_170410</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td><td>OR754755</td><td>SRR27348824</td></tr><tr><td>PvR045</td><td>Novosphingobium</td><td>m</td><td>99.3</td><td>NR_118312</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754756</td><td>SRR27348823</td></tr><tr><td>PvR048</td><td>Burkholderia</td><td>stabilis</td><td>99.8</td><td>NR_114522</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754757</td><td>SRR27348822</td></tr></tbody></table>
<table><caption>TABLE 1. NCBI BLAST Taxonomy, isolation media, and DNA conditions of 78 bacterial isolates from switchgrass rhizosphere, as described in this study.</caption><thead><tr><th>Isolate_ID</th><th>Assembly_BLAST_Genus</th><th>Assembly_BLAST_T species</th><th>BLAST_Grade<sup>a</sup></th><th>BLAST_Hit_Accession</th><th>Isolation_Media<sup>b</sup></th><th>DNA_Method</th><th>NCBI_Accession_number</th><th>SRA_Accession_number</th></tr></thead><tbody><tr><td>PvR001</td><td>Rhodococcus</td><td>fascians</td><td>99.7</td><td>NR_119126</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754732</td><td>SRR27348840</td></tr><tr><td>PvR006</td><td>Streptomyces</td><td>zaomyceticus</td><td>100</td><td>NR_112376</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td><td>OR754733</td><td>SRR27348839</td></tr><tr><td>PvR008</td><td>Paenibacillus</td><td>terrae</td><td>99.1</td><td>NR_025170</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td><td>OR754734</td><td>SRR27348828</td></tr><tr><td>PvR012</td><td>Burkholderia</td><td>diffusa</td><td>99.8</td><td>NR_042633</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754735</td><td>SRR27348817</td></tr><tr><td>PvR013</td><td>Chryseobacterium</td><td>lactis</td><td>99.7</td><td>NR_126256</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754736</td><td>SRR27348806</td></tr><tr><td>PvR015</td><td>Chryseobacterium</td><td>lactis</td><td>99.1</td><td>NR_126256</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754737</td><td>SRR27348785</td></tr><tr><td>PvR016</td><td>Rhizobium</td><td>phaseoli</td><td>99.3</td><td>NR_113671</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754738</td><td>SRR27348774</td></tr><tr><td>PvR017</td><td>Burkholderia</td><td>ambifaria</td><td>99.8</td><td>NR_074687</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754739</td><td>SRR27348763</td></tr><tr><td>PvR018</td><td>Paenibacillus</td><td>sp.</td><td>99.8</td><td>NR_112906</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754740</td><td>SRR27348796</td></tr><tr><td>PvR019</td><td>Mycolicibacterium</td><td>mucogenicum</td><td>99.6</td><td>NR_042919</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td><td>OR754741</td><td>SRR27348795</td></tr><tr><td>PvR021</td><td>Pantoea</td><td>agglomerans</td><td>99.9</td><td>NR_111998</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754742</td><td>SRR27348838</td></tr><tr><td>PvR022</td><td>Burkholderia</td><td>contaminans</td><td>99.9</td><td>NR_104978</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754743</td><td>SRR27348837</td></tr><tr><td>PvR023</td><td>Burkholderia</td><td>ambifaria</td><td>99.7</td><td>NR_074687</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754744</td><td>SRR27348836</td></tr><tr><td>PvR024</td><td>Cupriavidus</td><td>necator</td><td>99.9</td><td>NR_102851</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754745</td><td>SRR27348835</td></tr><tr><td>PvR025</td><td>Agrobacterium</td><td>rhizogenes<br>lindaniclasticu</td><td>99.9</td><td>NR_113607</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754746</td><td>SRR27348834</td></tr><tr><td>PvR029</td><td>Novosphingobium</td><td>m</td><td>99.5</td><td>NR_118312</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754747</td><td>SRR27348833</td></tr><tr><td>PvR033</td><td>Burkholderia</td><td>contaminans<br>spiroverticillatu</td><td>99.6</td><td>NR_104978</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754748</td><td>SRR27348832</td></tr><tr><td>PvR034</td><td>Streptomyces</td><td>s</td><td>99.6</td><td>NR_112582</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754749</td><td>SRR27348831</td></tr><tr><td>PvR038</td><td>Burkholderia</td><td>stabilis</td><td>99.9</td><td>NR_114522</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754750</td><td>SRR27348830</td></tr><tr><td>PvR040</td><td>Rhodococcus</td><td>qingshengii</td><td>99.8</td><td>NR_115708</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754751</td><td>SRR27348829</td></tr><tr><td>PvR041</td><td>Enterobacter</td><td>ludwigii</td><td>100</td><td>NR_042349</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754752</td><td>SRR27348827</td></tr><tr><td>PvR042</td><td>Pseudomonas</td><td>protegens</td><td>99.9</td><td>NR_114749</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754753</td><td>SRR27348826</td></tr><tr><td>PvR043</td><td>Novosphingobium</td><td>capsulatum</td><td>99.7</td><td>NR_113591</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754754</td><td>SRR27348825</td></tr><tr><td>PvR044</td><td>Rhodococcus</td><td>oryzae<br>lindaniclasticu</td><td>99.8</td><td>NR_170410</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754755</td><td>SRR27348824</td></tr><tr><td>PvR045</td><td>Novosphingobium</td><td>m</td><td>99.3</td><td>NR_118312</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754756</td><td>SRR27348823</td></tr><tr><td>PvR048</td><td>Burkholderia</td><td>stabilis</td><td>99.8</td><td>NR_114522</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754757</td><td>SRR27348822</td></tr></tbody></table>
<table><tr><td>PvR052</td><td>Paenibacillus sp.</td><td>99.8</td><td>NR_112906</td><td>RIM</td></tr><tr><td>PvR053</td><td>Paenibacillus sp.</td><td>99.9</td><td>NR_112906</td><td>RIM</td></tr><tr><td>PvR055</td><td>Chryseobacterium lactis</td><td>99</td><td>NR_126256</td><td>RIM</td></tr><tr><td>PvR056</td><td>Dyella japonica</td><td>100</td><td>NR_114075</td><td>RIM</td></tr><tr><td>PvR057</td><td>Agromyces allii</td><td>99.7</td><td>NR_043931</td><td>RIM</td></tr><tr><td>PvR058</td><td>Nocardioides endophyticus</td><td>99.7</td><td>NR_135731</td><td>RIM</td></tr><tr><td>PvR059</td><td>Nocardioides endophyticus</td><td>99.7</td><td>NR_135731</td><td>RIM</td></tr><tr><td>PvR060</td><td>Novosphingobium hassiacum</td><td>98.7</td><td>NR_028962</td><td>RIM</td></tr><tr><td>PvR061</td><td>Enterobacter ludwigii</td><td>100</td><td>NR_042349</td><td>RIM</td></tr><tr><td>PvR062</td><td>Mycobacterium hackensackense</td><td>99.4</td><td>NR_115184</td><td>RIM</td></tr><tr><td>PvR063</td><td>Burkholderia stabilis chlorophenolicum</td><td>99.7</td><td>NR_114522</td><td>RIM</td></tr><tr><td>PvR064</td><td>Sphingobium m</td><td>99.5</td><td>NR_113840</td><td>RIM</td></tr><tr><td>PvR065</td><td>Mesorhizobium jarvisii</td><td>99.9</td><td>NR_135858</td><td>RIM</td></tr><tr><td>PvR066</td><td>Amycolatopsis vastitatis</td><td>99.5</td><td>NR_164904</td><td>RIM</td></tr><tr><td>PvR072</td><td>Rhizobium alamii</td><td>99.9</td><td>NR_042687</td><td>RIM</td></tr><tr><td>PvR077</td><td>Burkholderia contaminans</td><td>99.8</td><td>NR_104978</td><td>RIM</td></tr><tr><td>PvR079</td><td>Dyella koreensis frederiksbergen</td><td>99.6</td><td>NR_113947</td><td>RIM</td></tr><tr><td>PvR083</td><td>Pseudomonas sis</td><td>99.8</td><td>NR_117177</td><td>RIM</td></tr><tr><td>PvR085</td><td>Novosphingobium capsulatum</td><td>99.7</td><td>NR_113591</td><td>RIM</td></tr><tr><td>PvR087</td><td>Dyella koreensis</td><td>99.1</td><td>NR_113947</td><td>RIM</td></tr><tr><td>PvR089</td><td>Dyella koreensis</td><td>99.2</td><td>NR_113947</td><td>RIM</td></tr><tr><td>PvR090</td><td>Novosphingobium capsulatum</td><td>99.8</td><td>NR_113591</td><td>RIM</td></tr><tr><td>PvR092</td><td>Lysobacter soli</td><td>99.3</td><td>NR_116074</td><td>RIM</td></tr><tr><td>PvR093</td><td>Mesorhizobium amorphae</td><td>99.9</td><td>NR_114122</td><td>RIM</td></tr><tr><td>PvR094</td><td>Mycolicibacterium septicum</td><td>99.9</td><td>NR_114492</td><td>RIM</td></tr><tr><td>PvR095</td><td>Novosphingobium capsulatum</td><td>99.7</td><td>NR_113591</td><td>RIM</td></tr><tr><td>PvR096</td><td>Mycolicibacterium mucogenicum</td><td>99.4</td><td>NR_114656</td><td>RIM</td></tr><tr><td>PvR097</td><td>Microbacterium flavescens</td><td>99.5</td><td>NR_029350</td><td>RIM</td></tr><tr><td>PvR098</td><td>Paenibacillus sp.</td><td>99.6</td><td>NR_112906</td><td>RIM</td></tr><tr><td>PvR100</td><td>Nocardioides cavernae</td><td>99.7</td><td>NR_156135</td><td>RIM</td></tr></table>

<table><tr><td>Zymo Quick-DNA Fungal/Bacterial 96 kit CTAB-phenol-chloroform with acetone freeze/thaw cycle</td><td>OR754758</td><td>SRR27348821</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td><td>OR754759</td><td>SRR27348820</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td><td>OR754760</td><td>SRR27348819</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td><td>OR754761</td><td>SRR27348818</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td><td>OR754762</td><td>SRR27348816</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td><td>OR754763</td><td>SRR27348815</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754764</td><td>SRR27348814</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td><td>OR754765</td><td>SRR27348813</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial 96 kit CTAB-phenol-chloroform with acetone freeze/thaw cycle</td><td>OR754766</td><td>SRR27348812</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754767</td><td>SRR27348811</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754768</td><td>SRR27348810</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td><td>OR754769</td><td>SRR27348809</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial 96 kit CTAB-phenol-chloroform with acetone freeze/thaw cycle</td><td>OR754770</td><td>SRR27348808</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754771</td><td>SRR27348807</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754772</td><td>SRR27348805</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754773</td><td>SRR27348794</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td><td>OR754774</td><td>SRR27348793</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754775</td><td>SRR27348792</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754776</td><td>SRR27348791</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754777</td><td>SRR27348790</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td><td>OR754778</td><td>SRR27348789</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td><td>OR754779</td><td>SRR27348788</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial 96 kit CTAB-phenol-chloroform with acetone freeze/thaw cycle</td><td>OR754780</td><td>SRR27348787</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754781</td><td>SRR27348786</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754782</td><td>SRR27348784</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754783</td><td>SRR27348783</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754784</td><td>SRR27348782</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754785</td><td>SRR27348781</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754786</td><td>SRR27348780</td></tr><tr><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td><td>OR754787</td><td>SRR27348779</td></tr></table>
<table>
  <tr>
    <td>PvR052</td>
    <td>Paenibacillus sp.</td>
    <td>99.8</td>
    <td>NR_112906</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR053</td>
    <td>Paenibacillus sp.</td>
    <td>99.9</td>
    <td>NR_112906</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR055</td>
    <td>Chryseobacterium lactis</td>
    <td>99</td>
    <td>NR_126256</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR056</td>
    <td>Dyella japonica</td>
    <td>100</td>
    <td>NR_114075</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR057</td>
    <td>Agromyces allii</td>
    <td>99.7</td>
    <td>NR_043931</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR058</td>
    <td>Nocardioides endophyticus</td>
    <td>99.7</td>
    <td>NR_135731</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR059</td>
    <td>Nocardioides endophyticus</td>
    <td>99.7</td>
    <td>NR_135731</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR060</td>
    <td>Novosphingobium hassiacum</td>
    <td>98.7</td>
    <td>NR_028962</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR061</td>
    <td>Enterobacter ludwigii</td>
    <td>100</td>
    <td>NR_042349</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR062</td>
    <td>Mycobacterium hackensackense</td>
    <td>99.4</td>
    <td>NR_115184</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR063</td>
    <td>Burkholderia stabilis chlorophenolicum</td>
    <td>99.7</td>
    <td>NR_114522</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR064</td>
    <td>Sphingobium m</td>
    <td>99.5</td>
    <td>NR_113840</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR065</td>
    <td>Mesorhizobium jarvisii</td>
    <td>99.9</td>
    <td>NR_135858</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR066</td>
    <td>Amycolatopsis vastitatis</td>
    <td>99.5</td>
    <td>NR_164904</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR072</td>
    <td>Rhizobium alamii</td>
    <td>99.9</td>
    <td>NR_042687</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR077</td>
    <td>Burkholderia contaminans</td>
    <td>99.8</td>
    <td>NR_104978</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR079</td>
    <td>Dyella koreensis frederiksbergen</td>
    <td>99.6</td>
    <td>NR_113947</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR083</td>
    <td>Pseudomonas sis</td>
    <td>99.8</td>
    <td>NR_117177</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR085</td>
    <td>Novosphingobium capsulatum</td>
    <td>99.7</td>
    <td>NR_113591</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR087</td>
    <td>Dyella koreensis</td>
    <td>99.1</td>
    <td>NR_113947</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR089</td>
    <td>Dyella koreensis</td>
    <td>99.2</td>
    <td>NR_113947</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR090</td>
    <td>Novosphingobium capsulatum</td>
    <td>99.8</td>
    <td>NR_113591</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR092</td>
    <td>Lysobacter soli</td>
    <td>99.3</td>
    <td>NR_116074</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR093</td>
    <td>Mesorhizobium amorphae</td>
    <td>99.9</td>
    <td>NR_114122</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR094</td>
    <td>Mycolicibacterium septicum</td>
    <td>99.9</td>
    <td>NR_114492</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR095</td>
    <td>Novosphingobium capsulatum</td>
    <td>99.7</td>
    <td>NR_113591</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR096</td>
    <td>Mycolicibacterium mucogenicum</td>
    <td>99.4</td>
    <td>NR_114656</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR097</td>
    <td>Microbacterium flavescens</td>
    <td>99.5</td>
    <td>NR_029350</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR098</td>
    <td>Paenibacillus sp.</td>
    <td>99.6</td>
    <td>NR_112906</td>
    <td>RIM</td>
  </tr>
  <tr>
    <td>PvR100</td>
    <td>Nocardioides cavernae</td>
    <td>99.7</td>
    <td>NR_156135</td>
    <td>RIM</td>
  </tr>
</table>

<table>
  <tr>
    <td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td>
    <td>OR754758</td>
    <td>SRR27348821</td>
  </tr>
  <tr>
    <td>CTAB-phenol-chloroform with acetone freeze/thaw cycle</td>
    <td>OR754759</td>
    <td>SRR27348820</td>
  </tr>
  <tr>
    <td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td>
    <td>OR754760</td>
    <td>SRR27348819</td>
  </tr>
  <tr>
    <td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td>
    <td>OR754761</td>
    <td>SRR27348818</td>
  </tr>
  <tr>
    <td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td>
    <td>OR754762</td>
    <td>SRR27348816</td>
  </tr>
  <tr>
    <td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td>
    <td>OR754763</td>
    <td>SRR27348815</td>
  </tr>
  <tr>
    <td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td>
    <td>OR754764</td>
    <td>SRR27348814</td>
  </tr>
  <tr>
    <td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td>
    <td>OR754765</td>
    <td>SRR27348813</td>
  </tr>
  <tr>
    <td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td>
    <td>OR754766</td>
    <td>SRR27348812</td>
  </tr>
  <tr>
    <td>CTAB-phenol-chloroform with acetone freeze/thaw cycle</td>
    <td>OR754767</td>
    <td>SRR27348811</td>
  </tr>
  <tr>
    <td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td>
    <td>OR754768</td>
    <td>SRR27348810</td>
  </tr>
  <tr>
    <td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td>
    <td>OR754769</td>
    <td>SRR27348809</td>
  </tr>
  <tr>
    <td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td>
    <td>OR754770</td>
    <td>SRR27348808</td>
  </tr>
  <tr>
    <td>CTAB-phenol-chloroform with acetone freeze/thaw cycle</td>
    <td>OR754771</td>
    <td>SRR27348807</td>
  </tr>
  <tr>
    <td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td>
    <td>OR754772</td>
    <td>SRR27348805</td>
  </tr>
  <tr>
    <td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td>
    <td>OR754773</td>
    <td>SRR27348794</td>
  </tr>
  <tr>
    <td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td>
    <td>OR754774</td>
    <td>SRR27348793</td>
  </tr>
  <tr>
    <td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td>
    <td>OR754775</td>
    <td>SRR27348792</td>
  </tr>
  <tr>
    <td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td>
    <td>OR754776</td>
    <td>SRR27348791</td>
  </tr>
  <tr>
    <td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td>
    <td>OR754777</td>
    <td>SRR27348790</td>
  </tr>
  <tr>
    <td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td>
    <td>OR754778</td>
    <td>SRR27348789</td>
  </tr>
  <tr>
    <td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td>
    <td>OR754779</td>
    <td>SRR27348788</td>
  </tr>
  <tr>
    <td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td>
    <td>OR754780</td>
    <td>SRR27348787</td>
  </tr>
  <tr>
    <td>CTAB-phenol-chloroform with acetone freeze/thaw cycle</td>
    <td>OR754781</td>
    <td>SRR27348786</td>
  </tr>
  <tr>
    <td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td>
    <td>OR754782</td>
    <td>SRR27348784</td>
  </tr>
  <tr>
    <td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td>
    <td>OR754783</td>
    <td>SRR27348783</td>
  </tr>
  <tr>
    <td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td>
    <td>OR754784</td>
    <td>SRR27348782</td>
  </tr>
  <tr>
    <td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td>
    <td>OR754785</td>
    <td>SRR27348781</td>
  </tr>
  <tr>
    <td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td>
    <td>OR754786</td>
    <td>SRR27348780</td>
  </tr>
  <tr>
    <td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td>
    <td>OR754787</td>
    <td>SRR27348779</td>
  </tr>
</table>
<table><tr><td>PvR101</td><td>Sphingobium japonicum</td><td>99.3</td><td>NR_102886</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754788</td><td>SRR27348778</td></tr><tr><td>PvR102</td><td>Dyella marensis<br>eurypsychrophil</td><td>100</td><td>NR_042691</td><td>RIM</td><td></td><td>OR754789</td><td>SRR27348777</td></tr><tr><td>PvR103</td><td>Polaromonas a</td><td>99.2</td><td>NR_149767</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754790</td><td>SRR27348776</td></tr><tr><td>PvR104</td><td>Mycolicibacterium neworleansense</td><td>99.5</td><td>NR_115113</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754791</td><td>SRR27348775</td></tr><tr><td>PvR105</td><td>Mesorhizobium jarvisii</td><td>100</td><td>NR_135858</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754792</td><td>SRR27348773</td></tr><tr><td>PvR106</td><td>Rhizobium tibeticum</td><td>99.1</td><td>NR_116254</td><td>RIM</td><td></td><td>OR754793</td><td>SRR27348772</td></tr><tr><td>PvR107</td><td>Methylobacterium phyllostachyos</td><td>99.9</td><td>NR_108242</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td><td>OR754794</td><td>SRR27348771</td></tr><tr><td>PvR108</td><td>Chryseobacterium lactis</td><td>99.4</td><td>NR_126256</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754795</td><td>SRR27348770</td></tr><tr><td>PvR112</td><td>Sphingobacterium cladoniae</td><td>99.4</td><td>NR_108441</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754796</td><td>SRR27348769</td></tr><tr><td>PvR114</td><td>Burkholderia ambifaria</td><td>99.9</td><td>NR_074687</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754797</td><td>SRR27348768</td></tr><tr><td>PvR115</td><td>Agrobacterium rhizogenes</td><td>99.9</td><td>NR_113607</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754798</td><td>SRR27348767</td></tr><tr><td>PvR116</td><td>Lelliottia nimipressuralis</td><td>99.5</td><td>NR_044976</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754799</td><td>SRR27348766</td></tr><tr><td>PvR117</td><td>Rhizobium alamii</td><td>99.9</td><td>NR_042687</td><td>R2A</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754800</td><td>SRR27348765</td></tr><tr><td>PvR118</td><td>Pseudomonas protegens</td><td>99.8</td><td>NR_114749</td><td>R2A</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754801</td><td>SRR27348764</td></tr><tr><td>PvR119</td><td>Pseudomonas protegens</td><td>99.8</td><td>NR_114749</td><td>R2A</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754802</td><td>SRR27348804</td></tr><tr><td>PvR122</td><td>Roseococcus suduntuyensis</td><td>98.7</td><td>NR_044369</td><td>R2A</td><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td><td>OR754803</td><td>SRR27348803</td></tr><tr><td>PvR126</td><td>Burkholderia ambifaria</td><td>99.7</td><td>NR_074687</td><td>R2A</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754804</td><td>SRR27348802</td></tr><tr><td>PvR127</td><td>Burkholderia ambifaria</td><td>99.7</td><td>NR_074687</td><td>R2A</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754805</td><td>SRR27348801</td></tr><tr><td>PvR132</td><td>Burkholderia stabilis</td><td>99.8</td><td>NR_114522</td><td>R2A</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754806</td><td>SRR27348800</td></tr><tr><td>PvR133</td><td>Paenibacillus peoriae</td><td>99.9</td><td>NR_117743</td><td>R2A</td><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td><td>OR754807</td><td>SRR27348799</td></tr><tr><td>PvR147</td><td>Leclercia sp.</td><td>97.5</td><td>NR_114154</td><td>R2A</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754808</td><td>SRR27348798</td></tr><tr><td>PvR148</td><td>Paenibacillus sp.</td><td>99.8</td><td>NR_112906</td><td>R2A</td><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td><td>OR754809</td><td>SRR27348797</td></tr></table>

<footnote>ªThe BLAST grade, an informative alternative to percent sequence identity, is a weighted score composed of the e-value, pairwise identity, and query coverage reported for the top hit⁸. ᵇRIM is rhizosphere isolation media and R2A is Reasoner's 2A media.</footnote>
<table><tr><td>PvR101</td><td>Sphingobium japonicum</td><td>99.3</td><td>NR_102886</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754788</td><td>SRR27348778</td></tr><tr><td>PvR102</td><td>Dyella marensis<br>eurypsychrophil</td><td>100</td><td>NR_042691</td><td>RIM</td><td></td><td>OR754789</td><td>SRR27348777</td></tr><tr><td>PvR103</td><td>Polaromonas a</td><td>99.2</td><td>NR_149767</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754790</td><td>SRR27348776</td></tr><tr><td>PvR104</td><td>Mycolicibacterium neworleansense</td><td>99.5</td><td>NR_115113</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754791</td><td>SRR27348775</td></tr><tr><td>PvR105</td><td>Mesorhizobium jarvisii</td><td>100</td><td>NR_135858</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit<br>CTAB-phenol-chloroform with acetone<br>freeze/thaw cycle</td><td>OR754792</td><td>SRR27348773</td></tr><tr><td>PvR106</td><td>Rhizobium tibeticum</td><td>99.1</td><td>NR_116254</td><td>RIM</td><td></td><td>OR754793</td><td>SRR27348772</td></tr><tr><td>PvR107</td><td>Methylobacterium phyllostachyos</td><td>99.9</td><td>NR_108242</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td><td>OR754794</td><td>SRR27348771</td></tr><tr><td>PvR108</td><td>Chryseobacterium lactis</td><td>99.4</td><td>NR_126256</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754795</td><td>SRR27348770</td></tr><tr><td>PvR112</td><td>Sphingobacterium cladoniae</td><td>99.4</td><td>NR_108441</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754796</td><td>SRR27348769</td></tr><tr><td>PvR114</td><td>Burkholderia ambifaria</td><td>99.9</td><td>NR_074687</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754797</td><td>SRR27348768</td></tr><tr><td>PvR115</td><td>Agrobacterium rhizogenes</td><td>99.9</td><td>NR_113607</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754798</td><td>SRR27348767</td></tr><tr><td>PvR116</td><td>Lelliottia nimipressuralis</td><td>99.5</td><td>NR_044976</td><td>RIM</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754799</td><td>SRR27348766</td></tr><tr><td>PvR117</td><td>Rhizobium alamii</td><td>99.9</td><td>NR_042687</td><td>R2A</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754800</td><td>SRR27348765</td></tr><tr><td>PvR118</td><td>Pseudomonas protegens</td><td>99.8</td><td>NR_114749</td><td>R2A</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754801</td><td>SRR27348764</td></tr><tr><td>PvR119</td><td>Pseudomonas protegens</td><td>99.8</td><td>NR_114749</td><td>R2A</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754802</td><td>SRR27348804</td></tr><tr><td>PvR122</td><td>Roseococcus suduntuyensis</td><td>98.7</td><td>NR_044369</td><td>R2A</td><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td><td>OR754803</td><td>SRR27348803</td></tr><tr><td>PvR126</td><td>Burkholderia ambifaria</td><td>99.7</td><td>NR_074687</td><td>R2A</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754804</td><td>SRR27348802</td></tr><tr><td>PvR127</td><td>Burkholderia ambifaria</td><td>99.7</td><td>NR_074687</td><td>R2A</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754805</td><td>SRR27348801</td></tr><tr><td>PvR132</td><td>Burkholderia stabilis</td><td>99.8</td><td>NR_114522</td><td>R2A</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754806</td><td>SRR27348800</td></tr><tr><td>PvR133</td><td>Paenibacillus peoriae</td><td>99.9</td><td>NR_117743</td><td>R2A</td><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td><td>OR754807</td><td>SRR27348799</td></tr><tr><td>PvR147</td><td>Leclercia sp.</td><td>97.5</td><td>NR_114154</td><td>R2A</td><td>Zymo Quick-DNA Fungal/Bacterial 96 kit</td><td>OR754808</td><td>SRR27348798</td></tr><tr><td>PvR148</td><td>Paenibacillus sp.</td><td>99.8</td><td>NR_112906</td><td>R2A</td><td>Zymo Quick-DNA Fungal/Bacterial miniprep kit</td><td>OR754809</td><td>SRR27348797</td></tr></table>

<footnote>ªThe BLAST grade, an informative alternative to percent sequence identity, is a weighted score composed of the e-value, pairwise identity, and query coverage reported for the top hit⁸. ᵇRIM is rhizosphere isolation media and R2A is Reasoner's 2A media.</footnote>
**Figure**

<figure><img src="image_2.png" /><figcaption>Figure 1: Taxonomic summary of the bacterial collection cultivated from switchgrass rhizosphere, genera identified by full-length 16S rRNA gene sequencing (Sanger) with taxonomy assigned by match (BLAST) to the NCBI 16S rRNA database, determined using Geneious Prime Megablast function to access the NCBI 16S ribosomal RNA database using default parameters on 18 January 2023</figcaption></figure>
## Figure

<figure><img src="image_2.png" /><figcaption>Figure 1: Taxonomic summary of the bacterial collection cultivated from switchgrass rhizosphere, genera identified by full-length 16S rRNA gene sequencing (Sanger) with taxonomy assigned by match (BLAST) to the NCBI 16S rRNA database, determined using Geneious Prime Megablast function to access the NCBI 16S ribosomal RNA database using default parameters on 18 January 2023</figcaption></figure>