Identification of Nitrogen Fixation Genes in Lactococcus Isolated from Maize Using Population Genomics and Machine Learning
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Isolation, DNA Extraction and Whole Genome Sequencing
2.2. Whole Genome Assembly, Comparison and Taxonomic Analysis
2.3. Pangenome Analysis
2.4. Identification of BNF Associated Genes by Pan-GWAS Analysis
2.5. Identification of Important Genes Using Random Forests
2.6. Functional Annotation of Identified Protein Coding Sequences
2.7. Materials Availability
3. Results
3.1. Comparison of WGS Assemblies Revealed Genomic Distance between Mucilage and Dairy Isolates
3.2. The Lactococcal Pangenome Revealed a Unique Genotype in Mucilage Isolates
3.3. Statistical and Machine Learning Analysis Identified L. lactis Genes Associated with BNF
3.4. Domain Annotations Elucidated Predicted Functions of Genes Associated with the BNF Trait
4. Discussion
4.1. L. lactis Isolates from Mucilage Have Genomes Distinguished from Dairy Isolates
4.2. Mucilage Lactococci Exhibit Genomic Potential to Create a Suitable Environment for BNF
4.2.1. Mucilage Lactococci Exhibit the Potential to Utilize Mucilage Carbohydrates as Energy for BNF
4.2.2. Diazotrophic L. lactis Genomes Are Enriched with Iron Accumulation Genes
4.2.3. L. lactis Is Capable of Molecular O2 Depletion
4.2.4. Diazotrophic Lactococci Possess Genes with Domains Analogous to Nitrogenase Proteins
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Gene ID | Interproscan Annotation | N Mucilage | N Dairy |
---|---|---|---|
araA | L-arabinose isomerase | 15 | 2 |
btuD_9 | ABC Transporter Type 1 | 17 | 0 |
ddrA | Rad52/22 family double-strand break repair protein | 0 | 64 |
feuA | Iron–siderophore periplasmic ABC transporter | 16 | 0 |
group_1791 | No match | 17 | 0 |
group_1793 | Putative Lactococcus lactis phage r1t holin | 12 | 0 |
group_1931 | Intrinsically disordered protein | 0 | 60 |
group_2085 | Glyoxalase/Bleomycin resistance/Dihydroxybiphenyl dioxygenase | 23 | 3 |
group_2262 | Intrinsically disordered protein | 11 | 0 |
group_2959 | MepB-like Protein of Unknown Function | 14 | 0 |
group_2960 | No match | 11 | 0 |
group_3301 | WxL domain surface cell wall-binding | 6 | 68 |
group_3932 | Putative DNA-binding domain superfamily | 11 | 0 |
group_5428 | Winged helix/Mga helix-turn-helix DNA binding | 17 | 1 |
group_5436 | Membrane-bound galactosyl-transferase/GT1 | 13 | 1 |
group_5483 | No match | 12 | 0 |
group_5487 | Protein of unknown function DUF3892 | 12 | 0 |
group_5497 | No match | 12 | 0 |
group_5503 | No match | 11 | 0 |
group_5623 | Type I DNA methyltransferase | 11 | 0 |
group_5626 | No match | 11 | 0 |
group_6294 | ROK (Repressor, ORF, Kinase) DNA-Binding Transcription Factor | 18 | 3 |
group_696 | No match | 13 | 1 |
group_7770 | Prokaryotic membrane lipoprotein lipid attachment | 15 | 1 |
group_7798 | Extracellular arabinose binding protein | 13 | 1 |
group_7961 | ABC Transporter Type 1 | 13 | 1 |
group_8186 | FEMO cofactor biosynthesis protein NIFB | 13 | 1 |
group_8190 | RGG_Cterm: transcriptional activator, Rgg/GadR/MutR family | 17 | 0 |
group_8270 | No match | 11 | 0 |
pspA | Histidine Phosphatase | 23 | 3 |
scrB | Sucrose-6-phosphate hydrolase/glycosyl hydrolase family 32 | 17 | 5 |
xylT_1 | SP: MFS transporter, sugar porter (SP) family | 15 | 2 |
xylT_2 | SP: MFS transporter, sugar porter (SP) family | 20 | 3 |
ybiR | Citrate transporter | 23 | 3 |
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Higdon, S.M.; Huang, B.C.; Bennett, A.B.; Weimer, B.C. Identification of Nitrogen Fixation Genes in Lactococcus Isolated from Maize Using Population Genomics and Machine Learning. Microorganisms 2020, 8, 2043. https://doi.org/10.3390/microorganisms8122043
Higdon SM, Huang BC, Bennett AB, Weimer BC. Identification of Nitrogen Fixation Genes in Lactococcus Isolated from Maize Using Population Genomics and Machine Learning. Microorganisms. 2020; 8(12):2043. https://doi.org/10.3390/microorganisms8122043
Chicago/Turabian StyleHigdon, Shawn M., Bihua C. Huang, Alan B. Bennett, and Bart C. Weimer. 2020. "Identification of Nitrogen Fixation Genes in Lactococcus Isolated from Maize Using Population Genomics and Machine Learning" Microorganisms 8, no. 12: 2043. https://doi.org/10.3390/microorganisms8122043