Difference between revisions of "Micro to Macro Water Pollution"
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=== Documentation and Collaboration Tools ===
=== Documentation and Collaboration Tools ===
Revision as of 09:27, 14 May 2016
- 1 Background Information
- 2 Aims
- 3 Brainstorm Results
- 4 Collaboration Defined
- 5 Water Quality and Analysis
- 5.1 Spring and Summer 2016
- 5.2 Documentation and Collaboration Tools
- 5.3 Water Collection Protocols
- 5.4 Coliform Bacteria Counting
- 5.5 Community Bioreporter Kit for Switzerland
- 5.6 Water Multi-meter
- 6 References
Hammerdirt came to the BIO-DESIGN for the REAL WORLD's Winter School with data on the macropollutants washing up on the local beaches in and around Montreux (CH). The data format conforms to international norms, and over two years, some patterns can be observed in the level of litter on the shores. The collaboration will be an exchange and complement to what is already on-going at Hammerdirt.
The presentation can be found here:How we can work together
To answer: Does the presence of macropollutants on the shores of Lac Leman correlate with micropollutants (biological, chemical, particulate, etc.) in the lake water?
At Open Hackuarium #88, we came up with some initial ideas.
- Data Analysis
- Image analysis and machine learning to readily tabulate the macro-pollutants collected on the beach
- synching the above data with a phone application in the internationally accepted format
- Add lake existing data (lake current, meterology, etc.)
- Water collection and Analysis
- Standardizing Collection Methods
- Water chemistry testing - turbidity, pO2, pH, conductivity, temperature
- DIY free NH2
- Microparticle counting - DIY
- Heavy metal analysis DIY equipment of BIODESIGN to be more robust - or
- Make a fluorescent plate reader for higher throughput (CAUTION: still need P1 to use bioreporters here)
- antibiotic resistant bacteria (CAUTION: we cannot amplify/concentrate possible pathogens)
- Fish diseases - ask Maison de la Rivière?
- Awareness Raising - Recycling
- Recycle plastics using the extruder and use it to 3D print objects
- Biodegradation with mycelium
|ACTION FOR GENOMIC INTEGRITY THROUGH RESEARCH!||Technical oversight for the microbial assays, training of hammerdirt staff, quality control of laboratory operations and of sample processing and analyses.|
|HACKUARIUM||Laboratory infrastructure and security, testing equipment and supplies for biologicals|
|HAMMERDIRT||Collection and processing of samples, data storage and administration. Communication of analyses and results.|
|BIODESIGN.CC||Analysis of samples for mercury, Cadmium Zinc, Alkanes and arsenic using the bio-reporters|
Water Quality and Analysis
Spring and Summer 2016
One of the benefits of a “Community Based Environmental Monitoring” (CBEM) project is to expand the monitoring capacity of government agencies and engage the public in environmental stewardship. (1) (2) In response to questions from the public and our own professional curiosity we have decided to initiate a limited CBEM project.
As part of the Montreux Clean Beach Project II(MCBPII), a water quality testing (WQT) program is being initiated at selected sites of the MCBPII. Symptoms reported by members and frequent bathers in the lake during previous summer seasons have sometimes been attributed to low bathing water quality, influenced by increased anthropogenic pressure of lakefront activities during certain times of the year. This year's WQT aims to gather microbiological data over a six week period in order to test this hypothesis.
Meetings at “La Maison de la Rivière” and the “Institut National de Recherche Agronomique” support the idea that the WQT information proposed is not regularly collected at the Haut-Lac locations covered by the MCBPII.
CBEM programs are designed to educate the public, involve local citizens in environmental stewardship and provide reliable data for government and other interested organizations. In this regard the MCBPII CBEM program is no different than that of any other existing project. (3) (2) (4)
Specifically, the goals for this project are to:
1. Collect reliable water quality data as defined by the World Water Monitoring Challenge (5)
2. Collect and enumerate the quantity of key bacteriological indicators, in particular those related to fecal contamination (6)
3. Increase the skills of hammerdirt staff in regards to collecting and processing water samples.
4. Make the obtained data free and open to use for all concerned
5. Inform the public about affordable and simple water monitoring techniques
6. Inform the public of community based resources designed to advance scientific literacy
This project is a joint effort between hammerdirt association, biodesign.cc, AGiR!, and the Hackuarium.
Documentation and Collaboration Tools
Agree on documentation and collaboration tools
- Internal communication - hackuarium slack
- Calendar? - we have a biodesign google calendar
- Protocols - ?
- Electronic Lab Notebook - ? - a template system where people can write down what they do would be nice, should it be the same as the Data entry format where you comment on unusual procedures or events?
- Data entry and sharing - Hammerdirt github, compliance with the international standards
- Hardware design - biodesign github
Water Collection Protocols
Coliform Bacteria Counting
Coliform bacteria is an indirect indication of fecal contamination of the waters. There are several methods to distinguish coliform bacteria vs other microorganisms that may grow on an agar plate.
Micrology Labs Coliscan Easygel
- Rachel asked for an offer including shipping and the 15% discount for the a coliform bacteria testing medium.
- reminder request sent again 18 April to Jonathan Roth (CEO of Micrology Labs) and Doug Wengerd (who eventually answers notes to their 'info' address)
Protocol from the Micrology Labs
To note: the Micrology Lab ECA Easygel plates are more expensive, but can assay up to 5ml of sampled water per plate for ready scoring and disposal. Another currently proposed plate media would not only be less discriminating, but require more equipment for the sterile setup and final cleanup, and probably only allow 0.5ml to be assayed/plate.
- Endo agar where gram negatives are favored to grow. Fermentation of lactose in the medium by coliform bacteria gives metallic green sheen to those colonies.
- MacConkey agar - also contains lactose and neutral red as a pH indicator, bile salts to inhibit gram-positive bacteria growth
- MacConkey agar with sorbitol is used to isolate E. coli O157, a pathogenic enteric bacteria
- Eosin Methylene Blue agar - Lactose fermenting bacteria turn a dark color, gram positive bacteria also inhibited
Automatic Colony Counter and Plate Counting
This is not a DIY gel, but ENDO agar was used for the workshops Lifepatch conducted in Indonesia: Quantification of e. coli contamination in water
From Lifepatch, we have set this up DIY automatic colony counter.
- Good "travaux pratique" protocol for bacterial counting and salts concentration from Bioutils, UNIGE
- Other protocol proposing several direct and indirect methods
Biodesign has tried:
- This early post has a pdf at the end summarizing techniques, including portable sensor, paper strip, etc.
Basic calculation for cost for one time analysis:
- number of plates = number of sites x number of dilutions x number of replicates + positive control + negative control
Use glass petri-dishes for recycling - we can as Lifepatch how they set it up.
Community Bioreporter Kit for Switzerland
- Our current prototype needs to be field-ready - the final design parameters need to be discussed.
- The protocol for the bioreporter assay needs to be simplified.
- Student Project 2016
Discard Studies publishes interesting articles on Water Pollution
- Pharmaceuticals Out of Bounds - conference coming up in 2016
- DIY Plastics Collector "Babylegs"
- Redefining pollution and action - article
Electronic Lab Notebooks
- A universal open-source Electronic Laboratory Notebook Bioinformatics 2013 29(13):1710-2. doi: 10.1093/bioinformatics/btt253