Micro to Macro Water Pollution

Background Information

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

Aims

To answer: Does the presence of macropollutants on the shores of Lac Leman correlate with micropollutants (biological, chemical, particulate, etc.) in the lake water?

Brainstorm Results

brainstorm board

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

Collaboration Defined

The collaboration between Hammerdirt and BIO-DESIGN for the REAL WORLD as of 2016
1st stage:

• water collection protocols appropriate for each read-out
• coliform bacteria counting

• easygel
• DIY version

• community bioreporter kit field version for Switzerland

• robust hardware
• easy to manipulate wetware (remove possibility of error in the protocol - including standard curve generation, etc.)

• a water multimeter

• pH, conductivity, dissolved O2, temperature

Action Plans

• Hammerdirt collects baseline and routine water samples for testing
• Research what other relevant datasets are out there and document it

Documentation and Collaboration Tools

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Agree on documentation and collaboration tools

• Internal communication - hackuarium slack
• Calendar? - we have a biodesign google calendar
• Protocols - [1]?
• Electronic Lab Notebook - [2]? - 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

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Coliform Bacteria Counting

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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.

Easy Gel

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.

Other Media

• 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.

Other Methods

• Good "travaux pratique" protocol for bacterial counting and salts concentration from Bioutils, UNIGE
  
• Other protocol proposing several direct and indirect methods
  

Biodesign has tried:

• Hack-a-Taq
• This early post has a pdf at the end summarizing techniques, including portable sensor, paper strip, etc.

Scaling

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

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• 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.

Otherwise, the system for working with the bioreporters has been approved with the Swiss authorities.

Water Multi-meter

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• (Art)ScienceBLR
• Student Project 2016

References

Previous documents

• Clean Beach Project 2015 Draft

Literature

2014 Report on Leman biomass
2014 Physico-chemical Leman report

Relevant Links

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