Molecular and Pigment Analyses Provide Comparative Results When Reconstructing Historic Cyanobacterial Abundances from Lake Sediment Cores
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Sites and Sediment Core Sampling
2.2. Cyanobacteria Primers Modification
2.3. Water Content Determination
2.4. DNA Extraction and Droplet Digital PCR
2.5. Pigment Extraction and High-Performance Liquid Chromatography
2.6. Data Analysis
3. Results
3.1. Cyanobacterial 16S rRNA Gene Primer Comparison
3.2. Cyanobacterial 16S rRNA Genes in Sediment Cores
3.3. Cyanobacterial Pigments
3.4. Proxy Relationships within Each Lake
4. Discussion
4.1. Cyanobacterial-Specific Primer Design and Testing
4.2. Correlation between Cyanobacterial 16S Ribosomal RNA Gene Copies and Cyanopigments
4.3. The Sum of All Cyanopigments—A Better Proxy for Total Cyanobacterial Biomass?
4.4. Reasons for Discrepancies between the Two Methods
4.5. Comparing the Pros and Cons of ddPCR and HPLC to Track Historic Cyanobacteria Abundances
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Primer | Sequence | Source |
---|---|---|
CYAN108F | 5′-ACGGGTGAGTAACRCGTRA-3′ | [41] |
CYAN107F | 5′-GACGGGTGAGTAACRCGTRRG-3’ | This paper |
CYAN377R | 5′-CCATGGCGGAAAATTCCCC-3′ | [41] |
CYAN377R_mod | 5’-CCATTGCGGAAAATTCCCC-3’ | This paper |
Pigment | RT | Wavelength | Equivalence Factor |
---|---|---|---|
Lutein | 9.6 | 435–455 | - |
Zeaxanthin | 10.3 | 435–455 | 1.56 |
Myxoxanthophyll | 12.7 | 460–480 | 1.26 |
Canthaxanthin | 16.1 | 460–480 | 1.06 |
Echinenone | 32.9 | 435–455 | 0.63 |
Method | Pros | Cons |
---|---|---|
HPLC |
|
|
ddPCR |
|
|
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Picard, M.; Wood, S.A.; Pochon, X.; Vandergoes, M.J.; Reyes, L.; Howarth, J.D.; Hawes, I.; Puddick, J. Molecular and Pigment Analyses Provide Comparative Results When Reconstructing Historic Cyanobacterial Abundances from Lake Sediment Cores. Microorganisms 2022, 10, 279. https://doi.org/10.3390/microorganisms10020279
Picard M, Wood SA, Pochon X, Vandergoes MJ, Reyes L, Howarth JD, Hawes I, Puddick J. Molecular and Pigment Analyses Provide Comparative Results When Reconstructing Historic Cyanobacterial Abundances from Lake Sediment Cores. Microorganisms. 2022; 10(2):279. https://doi.org/10.3390/microorganisms10020279
Chicago/Turabian StylePicard, Maïlys, Susanna A. Wood, Xavier Pochon, Marcus J. Vandergoes, Lizette Reyes, Jamie D. Howarth, Ian Hawes, and Jonathan Puddick. 2022. "Molecular and Pigment Analyses Provide Comparative Results When Reconstructing Historic Cyanobacterial Abundances from Lake Sediment Cores" Microorganisms 10, no. 2: 279. https://doi.org/10.3390/microorganisms10020279