Methanotroph pmoA Gene Sequences — Main Cropping System Experiment (MCSE)
Data in the KBS LTER core database may not be published without written permission of the lead investigator or project director Full terms of use
Methanotroph pmoA gene sequences extracted from soils of the Main Cropping System Experiment. The number of pmoA (particulate methane monooxygenase subunit A) Operational Taxonomic Units (OTUs) is used to measure the diversity of methanotrophs in a given site. The number of pmoA OTUs was determined by creating clone libraries for pmoA, clustering the sequences at 94% similarity for an OTU and counting the number of OTUs for each site. The number of pmoA OTUs indicates the diversity of methanotrophs at a given site. Sequencing was done through MSU GTSF (Genomics Technology Support facility).
This datatable is part of the Soil Microbial Gene Sequences dataset.
This dataset contains gene sequences extracted from soils of LTER Experiments.
Note
| Experiment: | Main Cropping System Experiment (MCSE) |
| Data available from: | December 2004 to September 2009 |
| Dataset: | KBS082 |
| Datatable ID: | KBS082-003.24 |
| Core Areas | Populations,Disturbance |
| Repository link: | http://doi.org/10.6073/pasta/584815caee76519da84f47c34185236f |
| Related Tables: | |
| Personnel: |
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| Last Updated | 2023-10-24 |
| Variate | Description | Units |
|---|---|---|
| sample date | date the sample was collected | |
| treatment | treatment that was sampled | |
| replicate | replicate plot that was sampled | |
| primer set | primer set used | |
| sequencing method | sequencing method used | |
| gene | gene studied | |
| pubmed id | accession number to the pubmed database | |
| accession | accession id to the genebank database | |
| name | lab name of the sequence | |
| note | comments or notes | |
| sequence | gene sequence |
| Protocols |
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Data Excerpt
| sample_date | treatment | replicate | primer_set | sequencing_method | gene | pubmed_id | accession | name | notes | sequence |
|---|---|---|---|---|---|---|---|---|---|---|
| 2008-12-01 | T1 | 1 | A189-A682 | Sanger | pmoA | K1AB0002 | ATCGATTGGAAGGATCGGCAATTTTGGGTAACGGTCACACCGATCGTAGAGGTGATGTATCCCGGTGCGATCATGTACTATTTTTGGACGTTTTACCGGCAACCGTTTGGTGCAACATTAAGTATCACAGGGCTACTCGTCGGAAAGTGGATTACCATTATATTCGCCTGGTACTGGTGGGCTAATTTCCCCGCAAACTTTGTGATGCCTGCCACTATGGTATCCAGTGCATTGATCCTCGATGCCACCCTGCTCTTGACAAGGAGCTGGATGCTCACCGCGATCTTCGGAGTATGGGCATTTGCGATGATGTTTAACCCGACACAATACGCACTATTCGGATACAGTCATCAGCCAGTCGTAGTGGACGGGCAGCTGATGTCACTGGCCGACTACATGGGATTCACCTTTGTCCGTACAGGAACGCCAGAGTATATCCGGATCATCGAGGTGGGTTCGCTCCGTACATTCGGTGGACACACCGTCTGGATCTCA | |||
| 2008-12-01 | T1 | 1 | A189-A682 | Sanger | pmoA | K1AB0009 | ATCGATTGGAAGGATCGGCAATTTTGGGTAACGGTCACACCGATCGTAGAGGTGATGTATCCCGGTGCGATCATGTACTATTTTTGGACGTTCTATCGGCAACCGTTTGGTGCAACATTAAGTATCACAGGGCTACTCGTCGGAAAGTGGATTACCATTATATTCGCCTGGTACTGGTGGGCTAATTTCCCCGCAAACTTTGTGATGCCTGCCACTATGGTATCCAGTGCATTGATCCTCGATGCCACCTTGCTCTTGACAAGGAGCTGGATGCTCACCGCGATCTTCGGAGTATGGGCATTTGCGATGATGTTTAACCCGACACAATACGCACTATTCGGATACAGTCATCAGCCAGTCGTAGTGGACGGGCAGCTGATGTCACTGGCCGACTACATGGGATTCACCTTTGTCCGTACAGGAACGCCAGAGTATATCCGGATCATCGAGGTGGGTTCGCTCCGTACATTCGGTGGACACACCGTCTGGATCTCA | |||
| 2008-12-01 | T1 | 2 | A189-A682 | Sanger | pmoA | K1AB0013 | ATCGATTGGAAGGATCGGCAGTTCTGGGTAACGGTCACACCAATTGTAGAAGTGATGTATCCCGGTGCGATCATGTATTACTTCTGGACATTCTACCGGCAACCGTTCGGTGCTACGTTGAGCATCACGGGACTACTTGTCGGAAAGTGGATTACAATTGTATTTGCTTGGTACTGGTGGGCCAATTTCCCAGCAAACTTCGTTATGCCAGCCACCATGGTCTCCAGTGCATTGATTCTTGACTGTACCCTTTTGCTGACTCGGAGCTGGATGCTCACGGCAATATTCGGGGTATGGGCATTTGCAATGATGTTTAACCCCACACAATACGCCCTGTTCGGATACAGCCACCAACCGGTGGTCGTGGACGGTCAGCTCCTTTCGCTGGCCGACTACATGGGCTTCACCTTTGTTAGGACCGGGACGCCTGAATATATCCGTATCATCGAGGTGGGATCGCTGCGTACGTTCGGCGGACACACCGTCTGGATCTCG | |||
| 2008-12-01 | T1 | 2 | A189-A682 | Sanger | pmoA | K1AB0016 | ATCGATTGGAAGGATCGGCAGTTCTGGGTAACGGTCACACCAATTGTAGAAGTGATGTATCCCGGTGCGATCATGTATTACTTCTGGACATTCTACCGGCAACCGTTCGGTGCTACGTTGAGCATCACGGGACTACTTGTCGGAAAGTGGATTACAATTGTATTTGCTTGGTACTGGTGGGCCAATTTCCCAGCAAACTTCGTTATGCCAGCCACCATGGTCTCCAGTGCATTGATTCTTGACTGTACCCTTTTGCTGACTCGGAGCTGGATGCTCACGGCAATATTCGGGGTATGGGCATTTGCAATGATGTTTAACCCCACACAATACGCCCTGTTCGGATACAGCCACCAACCGGTGGTCGTGGACGGTCAGCTCCTTTCGCTGGCCGACTACATGGGCTTCACCTTTGTTAGGACCGGGACGCCTGAATATATCCGTACCATCGAGGTGGGA--------------------------------------- | |||
| 2008-12-01 | T1 | 2 | A189-A682 | Sanger | pmoA | K1AB0017 | ATCGATTGGAAGGATCGGCAGTTCTGGGTAACGGTCACACCAATTGTAGAAGTGATGTATCCCGGTGCGATCATGTATTACTTCTGGACATTCTACCGGCAACCGTTCGGTGCTACGTTGAGCATCACGGGACTACTTGTCGGAAAGTGGATTACAATTGTATTTGCTTGGTACTGGTGGGCCAATTTCCCAGCAAACTTCGTTATGCCAGCCACCATGGTCTCCAGTGCATTGATTCTTGACTGTACCCTTTTGCTGACTCGGAGCTGGATGCTCACGGCAATATTCGGGGTATGGGCATTTGCAATGATGTTTAACCCCACACAATACGCCCTGTTCGGATACAGCCACCAACCGGTGGTCGTGGACGGTCAGCTCCTTTCGCTGGCCGACTACATGGGCTTCACCTTTGTTAGGACCGGGACGCCTGAATATATCCGTATCATCGAGGTGGGATCGCTGCGTACGTTCGGCGGACACACCGTCTGGATCTCG |