Metagenomic Insights into the Composition and Function of Microbes Associated with the Rootzone of Datura inoxia
Abstract
:1. Introduction
2. Materials and Methods
3. Results
3.1. Soil Samples WGS and MG-RAST Taxonomic and Functional Assignments
3.2. Functional Analysis in STAMP
3.3. Purple Line Analysis and Comparison
3.4. Differential Abundance Analysis in DESeq2
3.5. Microbial Barcoding and Essential Oil Trial
4. Discussion
Genetic Engineering and the Flavonoid Biosynthesis Pathway
- Structural derivatives of phenyl-substituted propylbenzenes with a C15 backbone,
- Phenyl-substituted propylbenzene derivatives with a C16 skeleton, or
- Phenyl-substituted propylbenzenes condensed with C6-C3 lignan precursors to form flavonolignans.
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Map Unit Name | pH | CEC | % Sand | % Silt | % Clay | % OM |
---|---|---|---|---|---|---|
Cropley-Urban Land Complex, 0 to 2% | 7.9 | 37.5 | 22.1 | 27.9 | 50 | 1.5 |
Sample No. | Field | Colony Color | Morphology | Antibiotic Used | Media | Absorbed CR |
---|---|---|---|---|---|---|
1 | Marquis C | Transl yellow | Unkown | NA | Nutrient agar | NA |
2 | Marquis D | White/tan | Unkown | Penicillin | Nutrient agar | NA |
3 | Field 28 | White/tan | Unkown | Penicillin | Nutrient agar | NA |
4 | Marquis A | Yellow | Unkown | Streptomycin | Nutrient agar | NA |
5 | Marquis A | Yellow | Raised | NA | Nutrient agar | NA |
6 | Arboretum | White | Spreading | NA | TYES-CR | absorbed cr |
7 | Marquis A | Transl yellow | Raised | NA | Nutrient agar | NA |
8 | Marquis A | White | Gliding | NA | Nutrient agar | NA |
9 | Marquis A | Transl yellow | Gliding | NA | Nutrient agar | NA |
10 | Marquis A | Yellow | Flat | NA | Nutrient agar | NA |
11 | Marquis A | Transl Yellow | Highly motile at 4 °C | NA | Nutrient agar | NA |
12 | Arboretum | Clear/tan | Mucoid | NA | TYES | Intense pink |
13 | Arboretum | White | Flat | NA | TYES | Dark red |
14 | Marquis A | Yellow | Raised | NA | Nutrient agar | NA |
15 | Arboretum | Clear/tan | Small mucoid | NA | TYES | Light pink |
16 | Marquis A | Clear/tan | Mucoid | NA | TYES | NA |
17 | Marquis A | Transl yellow | Mucoid | NA | TYES | NA |
18 | Arboretum | Clear/tan | Gliding | NA | TYES | Abs cr |
19 | Arboretum | White | Spreading | NA | TYES | Abs cr ring |
20 | Marquis A | Transl yellow | Raised, wrinkled | NA | 1/2 NA + AC | NA |
21 | Marquis A | Transl yellow | Small colony | NA | 1/2 NA +AC | NA |
22 | Marquis A | Transl yellow | Small colony | Griseofulvin | ISP-6 | NA |
23 | Marquis A | Yellow/orange | raised | Griseofulvin | ISP-6 | NA |
24 | Marquis A | White/grey | Large colony | Griseofulvin | ISP-6 | NA |
25 | Marquis A | Transl yellow | Wrinkled | Griseofulvin | ISP-6 | NA |
OTUID | Genus | log2FoldChange | p-adj. |
---|---|---|---|
OTU149 | Cavemovirus | −8.74069944 | 1.46 × 10−11 |
OTU494 | Pantoea | −3.382739635 | 5.9 × 10−18 |
OTU168 | Chryseobacterium | −2.894493584 | 0.000172 |
OTU332 | Janthinobacterium | −2.396801275 | 5.53 × 10−6 |
OTU307 | Herbaspirillum | −2.385130454 | 2.86 × 10−8 |
OTU505 | Pedobacter | −2.384332893 | 6 × 10−5 |
OTU247 | Erwinia | −2.324319999 | 3.84 × 10−35 |
OTU738 | unclassified (derived from Flavobacteriaceae) | −2.299754251 | 0.00078 |
OTU273 | Gemmata | −2.299386567 | 3.76 × 10−19 |
OTU308 | Herminiimonas | −2.1461305 | 2.3 × 10−5 |
OTU693 | Variovorax | −2.033564378 | 1.25 × 10−7 |
OTU759 | unclassified (derived from Verrucomicrobia subdivision 3) | −1.966909323 | 5.46 × 10−18 |
OTU169 | Chthoniobacter | −1.924054848 | 5.19 × 10−11 |
OTU440 | Mucilaginibacter | −1.920113231 | 6.47 × 10−5 |
OTU263 | Fluoribacter | −1.819462381 | 0.006919 |
OTU569 | Riemerella | −1.783874932 | 0.008796 |
OTU488 | Oxalobacter | −1.775720869 | 1.2 × 10−6 |
OTU339 | Klebsiella | −1.680008901 | 0.00538 |
OTU277 | Geodermatophilus | −1.67277933 | 0.000157 |
OTU463 | Nitrospira | −1.638446217 | 0.000467 |
OTU262 | Flavobacterium | −1.633855026 | 0.007125 |
OTU156 | Chitinophaga | −1.588995265 | 0.000676 |
OTU696 | Verrucomicrobium | −1.523905486 | 3.61 × 10−5 |
OTU234 | Dyadobacter | −1.505907596 | 0.005228 |
OTU480 | Opitutus | −1.500266429 | 5.62 × 10−5 |
OTU598 | Serratia | −1.489698167 | 2.49 × 10−10 |
OTU421 | Methylobacterium | −1.448043272 | 2.59 × 10-12 |
OTU136 | Candidatus Solibacter | −1.428079685 | 1.1 × 10−15 |
OTU624 | Stigmatella | −1.392596868 | 6.52 × 10−7 |
OTU751 | unclassified (derived from Proteobacteria) | −1.373840383 | 0.003172 |
OTU180 | Conexibacter | −1.373047754 | 0.000188 |
OTU651 | Terriglobus | −1.362530369 | 6.27 × 10−16 |
OTU532 | Polaromonas | −1.340071098 | 9.35 × 10−6 |
OTU727 | unclassified (derived from Candidatus Poribacteria) | −1.330571533 | 0.00172 |
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Senn, S.; Pangell, K.; Bowerman, A.L. Metagenomic Insights into the Composition and Function of Microbes Associated with the Rootzone of Datura inoxia. BioTech 2022, 11, 1. https://doi.org/10.3390/biotech11010001
Senn S, Pangell K, Bowerman AL. Metagenomic Insights into the Composition and Function of Microbes Associated with the Rootzone of Datura inoxia. BioTech. 2022; 11(1):1. https://doi.org/10.3390/biotech11010001
Chicago/Turabian StyleSenn, Savanah, Kelly Pangell, and Adrianna L. Bowerman. 2022. "Metagenomic Insights into the Composition and Function of Microbes Associated with the Rootzone of Datura inoxia" BioTech 11, no. 1: 1. https://doi.org/10.3390/biotech11010001