Characterizing the Gut Microbial Communities of Native and Invasive Freshwater Bivalves after Long-Term Sample Preservation
Abstract
:1. Introduction
2. Materials and Methods
2.1. DNA Extraction, Amplification, and Sequencing
2.2. Statistical Analysis
3. Results
3.1. Characterization of the Gut Microbiomes of Ethanol-Preserved and Frozen C. fluminea
3.2. Characterization of the Gut Microbiomes of Long-Term-Stored Museum Mussels
3.3. Amplicon Sequence Variants
3.4. Comparison of the C. fluminea and Native Mussel Gut Microbiomes
4. Discussion
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Mussel Tribe | Mussel Species | Preservation Year | River of Origin | Sample ID |
---|---|---|---|---|
Alasmidontini | Alasmidonta triangulata | 2019 | Flint (AL) | At19F1 |
Alasmidonta triangulata | 2019 | Flint (AL) | At19F2 | |
Cambarunio nebulosus | 2019 | Shoal Creek (AL) | Cn19SH1 | |
Cambarunio nebulosus | 2019 | Shoal Creek (AL) | Cn19SH2 | |
Venustaconcha trabalis | 2015 | Hiwassee (TN) | Vt15H1 | |
Venustaconcha trabalis | 2015 | Hiwassee (TN) | Vt15H2 | |
Venustaconcha trabalis | 2015 | Hiwassee (TN) | Vt15H3 | |
Lampsilini | Hamiota altilis | 2019 | Cahaba (AL) | Ha19C1 |
Hamiota altilis | 2019 | Cahaba (AL) | Ha19C2 1 | |
Hamiota altilis | 2019 | Shoal Creek (AL) | Ha19SH1 | |
Hamiota altilis | 2019 | Shoal Creek (AL) | Ha19SH2 | |
Hamiota altilis | 2019 | Shoal Creek (AL) | Ha19SH3 | |
Lampsilis virescens | 2015 | Paint Rock (AL) | Lv15P1 | |
Lampsilis virescens | 2015 | Paint Rock (AL) | Lv15P2 | |
Lampsilis virescens | 2015 | Paint Rock (AL) | Lv15P3 | |
Lampsilis virescens | 2016 | Paint Rock (AL) | Lv16P1 | |
Lampsilis virescens | 2016 | Paint Rock (AL) | Lv16P2 | |
Lampsilis virescens | 2016 | Paint Rock (AL) | Lv16P3 | |
Pseudodontoideus connasaugaensis | 2012 | Shoal Creek (AL) | Pc12SH1 | |
Pseudodontoideus connasaugaensis | 2012 | Shoal Creek (AL) | Pc12SH2 | |
Pseudodontoideus connasaugaensis | 2016 | Shoal Creek (AL) | Pc16SH1 | |
Ptychobranchus foremanianus | 2019 | Cahaba (AL) | Pf19C1 | |
Ptychobranchus foremanianus | 2019 | Cahaba (AL) | Pf19C2 | |
Margaritifera marrianae | 2017 | Sandy Creek (AL) | Mm17SA1 | |
Margaritiferini | Margaritifera marrianae | 2017 | Sandy Creek (AL) | Mm17SA2 |
Margaritifera marrianae | 2017 | Sandy Creek (AL) | Mm17SA3 | |
Pleurobemini | Theliderma cylindrica | 2012 | Paint Rock (AL) | Tc12P1 |
Theliderma cylindrica | 2012 | Paint Rock (AL) | Tc12P2 1 | |
Theliderma cylindrica | 2012 | Paint Rock (AL) | Tc12P3 1 |
Specimen | ASV | Identification | Frequency a |
---|---|---|---|
Ethanol C. fluminea | ASV 8 | Romboutsia sedimentorum (Firmicutes) | 10/11 |
ASV 15 | Peptostreptococcaceae (Firmicutes) | 9/11 | |
ASV 2 | Paeniclostridium (Firmicutes) | 9/11 | |
ASV 26 | Lacipirellula (Planctomycetes) | 8/11 | |
ASV 23 | Romboutsia (Firmicutes) | 8/11 | |
ASV 19 | Clostridiales (Firmicutes) | 8/11 | |
ASV 31 | Peptostreptococcaceae (Firmicutes) | 7/11 | |
ASV 28 | Romboutsia (Firmicutes) | 7/11 | |
ASV 22 | Methylocystis (Alphaproteobacteria) | 7/11 | |
ASV 7 | Clostridium chauvoei (Firmicutes) | 7/11 | |
Frozen C. fluminea | ASV 8 | Romboutsia sedimentorum (Firmicutes) | 10/10 |
ASV 15 | Peptostreptococcaceae (Firmicutes) | 9/10 | |
ASV 2 | Paeniclostridium (Firmicutes) | 9/10 | |
ASV 23 | Romboutsia (Firmicutes) | 8/10 | |
ASV 19 | Clostridiales (Firmicutes) | 8/10 | |
ASV 31 | Peptostreptococcaceae (Firmicutes) | 7/10 | |
ASV 26 | Lacipirellula (Planctomycetes) | 7/10 | |
ASV 22 | Methylocystis (Alphaproteobacteria) | 7/10 | |
ASV 7 | Clostridium chauvoei (Firmicutes) | 6/10 | |
ASV 39 | Methylocystis (Alphaproteobacteria) | 6/10 |
Mussel Tribe | Mussel Species | ASV | Identification | Frequency a |
---|---|---|---|---|
Alasmidonta triangulata | ASV 41 | Isosphaeraceae (Planctomycetes) | 2/2 | |
Alasmidontini | ASV 16 | Pirellulales (Planctomycetes) | 2/2 | |
ASV 12 | Pirellulales (Planctomycetes) | 2/2 | ||
Cambarunio nebulosus | ASV 25 | Clostridiaceae_1 (Firmicutes) | 2/2 | |
ASV 24 | Turicibacter (Firmicutes) | 2/2 | ||
ASV 21 | Clostridiaceae_1 (Firmicutes) | 2/2 | ||
Venustaconcha trabalis | ASV 24 | Turicibacter (Firmicutes) | 3/3 | |
ASV 18 | Methylocystis (Alphaproteobacteria) | 3/3 | ||
ASV 8 | Romboutsia sedimentorum (Firmicutes) | 3/3 | ||
Lampsilini | Hamiota altilis | ASV 8 | Romboutsia sedimentorum (Firmicutes) | 3/4 |
ASV 24 | Turicibacter (Firmicutes) | 2/4 | ||
ASV 720 | Planctomicrobium (Planctomycetes) | 1/4 | ||
Lampsilis virescens | ASV 22 | Methylocystis (Alphaproteobacteria) | 6/6 | |
ASV 18 | Methylocystis (Alphaproteobacteria) | 6/6 | ||
ASV 8 | Romboutsia sedimentorum (Firmicutes) | 6/6 | ||
Pseudodontoideus connasaugaensis | ASV 16 | Pirellulales (Planctomycetes) | 3/3 | |
ASV 12 | Pirellulales (Planctomycetes) | 3/3 | ||
ASV 8 | Romboutsia sedimentorum (Firmicutes) | 3/3 | ||
Ptychobranchus foremanianus | ASV 14 | Bacteroides luti (Bacteroidetes) | 2/2 | |
ASV 10 | Aeromonas (Gammaproteobacteria) | 2/2 | ||
ASV 965 | Peptostreptococcaceae (Firmicutes) | 1/2 | ||
Margaritifera marrianae | ASV 4 | Gemmataceae (Planctomycetes) | 3/3 | |
Margaritiferini | ASV 131 | Chryseobacterium (Bacteroidetes) | 2/3 | |
ASV 52 | Pseudomonas (Gammaproteobacteria) | 2/3 | ||
Theliderma cylindrica | ASV 471 | Selenomonadaceae (Firmicutes) | 1/1 | |
Pleurobemini | ASV 14 | Bacteroides luti (Bacteroidetes) | 1/1 | |
ASV 9 | Anaerobacter (Firmicutes) | 1/1 |
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Vaughn, S.N.; Atkinson, C.L.; Johnson, P.D.; Jackson, C.R. Characterizing the Gut Microbial Communities of Native and Invasive Freshwater Bivalves after Long-Term Sample Preservation. Microorganisms 2023, 11, 2489. https://doi.org/10.3390/microorganisms11102489
Vaughn SN, Atkinson CL, Johnson PD, Jackson CR. Characterizing the Gut Microbial Communities of Native and Invasive Freshwater Bivalves after Long-Term Sample Preservation. Microorganisms. 2023; 11(10):2489. https://doi.org/10.3390/microorganisms11102489
Chicago/Turabian StyleVaughn, Stephanie N., Carla L. Atkinson, Paul D. Johnson, and Colin R. Jackson. 2023. "Characterizing the Gut Microbial Communities of Native and Invasive Freshwater Bivalves after Long-Term Sample Preservation" Microorganisms 11, no. 10: 2489. https://doi.org/10.3390/microorganisms11102489
APA StyleVaughn, S. N., Atkinson, C. L., Johnson, P. D., & Jackson, C. R. (2023). Characterizing the Gut Microbial Communities of Native and Invasive Freshwater Bivalves after Long-Term Sample Preservation. Microorganisms, 11(10), 2489. https://doi.org/10.3390/microorganisms11102489