Difference between revisions of "Freshwater Aquarium Microbiome"
| Line 5: | Line 5: | ||
===Water Sampling=== | ===Water Sampling=== | ||
Sterivex Filters | Sterivex Filters | ||
| + | :1 L of water from the surface of the freshwater fish tank and saltwater fish tank were filtered through separate 0.22 um sterivex filter units via a peristaltic pump. Air was pushed through following filtration to initiate the removal of residual water contained in the filter units. | ||
Nanopure Filtration | Nanopure Filtration | ||
| − | + | : Due to the low concentration of DNA extracted from filtering 1 L of water through the sterivex filter unit, 2 L of water from the freshwater and saltwater fish tanks were filtered through the free 0.22 um filter membranes via a reusable filter funnel and with a vacuum source. | |
[https://waterra.com/product/spectra-field-pro-peristaltic-pump/ Spectra Field-Pro Peristaltic Pump (~$2600)] | [https://waterra.com/product/spectra-field-pro-peristaltic-pump/ Spectra Field-Pro Peristaltic Pump (~$2600)] | ||
:- [https://youtu.be/XBaSQcmXc0s eDNA Sampler Usage] | :- [https://youtu.be/XBaSQcmXc0s eDNA Sampler Usage] | ||
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===DNA Extraction=== | ===DNA Extraction=== | ||
[[:File:PowerWater_Sterivex.pdf]] | [[:File:PowerWater_Sterivex.pdf]] | ||
| + | |||
| + | ===Primer Construction=== | ||
===PCR Amplification=== | ===PCR Amplification=== | ||
===Sequencing=== | ===Sequencing=== | ||
| + | |||
| + | ===Bioinformatics=== | ||
==Results== | ==Results== | ||
Revision as of 04:19, 19 May 2021
Introduction
Microbiomes, the communities of microorganisms living together in particular habitats, are vital for maintaining ecological balance. The habitat hosting the microbial communities can be anything from the gastrointestinal tract of a cow to the soils of the land. Of recent particular interest are those of aquatic ecosystems, which contain diverse arrays of bacterial communities. The fish themselves oftentimes possess more microbial cells than fish cells in their bodies (2) Up until 2012, there have not been very many studies pertaining to the characterization of the microbiome pertaining to the water associated with freshwater ornamental fishes (3)...This experiment aims to obtain a report on the bacterial community composition of the freshwater fish tank housing four generations of convict cichlids. To accomplish this, a protocol modeled after Smith et al will be established. 600 mL of aquarium water will be filtered through a 0.22 um filter unit. The concentrated microbial biomass trapped on the filter will be treated with a Puregene Qiagen kit with some modifications from the protocol. Afterwards amplification of the bacterial 16S rRNA gene will be carried out and sequencing at the University of Illinois will ensue.
Materials and Methods
Water Sampling
Sterivex Filters
- 1 L of water from the surface of the freshwater fish tank and saltwater fish tank were filtered through separate 0.22 um sterivex filter units via a peristaltic pump. Air was pushed through following filtration to initiate the removal of residual water contained in the filter units.
Nanopure Filtration
- Due to the low concentration of DNA extracted from filtering 1 L of water through the sterivex filter unit, 2 L of water from the freshwater and saltwater fish tanks were filtered through the free 0.22 um filter membranes via a reusable filter funnel and with a vacuum source.
Spectra Field-Pro Peristaltic Pump (~$2600)
DNA Extraction
Primer Construction
PCR Amplification
Sequencing
Bioinformatics
Results
Discussion
References
2. Savage, D. C. Microbial ecology of the gastrointestinal tract. Ann Rev Microbiol. 1977. 31. 107-133.
3. Smith, K. F.; Schmidt, V.; Rosen, G. E.; Amaral-Zettler, L. Microbial Diversity and Potential Pathogens in Ornamental Fish Aquarium Water. Public Library of Science One. 2012. 7.
Page History
This page was created by Sara L Simonson in the spring of 2021