microbes
microbes

Update: December 19, 2012 Andrew identified University of Colorado Alpine Microbial Observatory that can do sequencing with support from Craig. Ready to do first test with controls on the making the sterile cotton candy sponge mechanism for collecting DNA out of the air, and need to do so before mid-February. We learned that if we scale up in the future, we can make our own sterile sucrose. Update: November 10, 2012 During EcoHack3, a large group of people including Andrew Hill, Mariko Kosaka, Valerie Farber, JD Godchaux, Alyssa Wright, Craig Mills, David Danziger, Erin ???, Liz Barry, and more worked together to sketch out and early prototype this project. See the Research Note of our blackboard brainstorming. DESCRIPTION OF PROJECT EcoHack III - Living Sky This November, as part of the EcoHack conference, we will work with a portion of the participants to build a kit to sample microbes in the environment in a way never done before, through citizen science and balloon-based sampling. Over the course of Saturday, teams will hack on numerous projects, among those we intend to support a group that will design and test hardware that will enable microbial sampling from helium balloons. The hardware will include apparatus for microbe sampling as well as the collection of environmental data. On a day following Ecohack (to target overcast skies), teams will spread throughout the New York City metro area with balloon sampling kits. Teams will deploy helium filled balloons carrying environmental sensors and microbial sampling kits. Sampling will be done at or around 500 feet. Samples will be retrieved and prepared for transport back to storage and preparation facilities. All samples will be given a unique identifier that will allow them to be linked back to sampling and environmental data collected. Over the course of the following weeks, samples will be sequenced and published online. IMPACTS Airborn microbial populations may have profound impact on the world around us. Some known areas of interest include, climate and weather, human health, agricultural health, and global environmental change. It has been found previously that clouds offer a unique environment for fairly abundant microbial populations (see Amato 2012) and that there are enough microbes in the clouds to affect physicochemical processes. SEQUENCING WORKFLOW coming... Collection Filtering DNA Extraction and Amplification being done by Krista McGuire and lab techs. Extraction is important because when you take an air sample, you collect much more than just DNA. Amplification takes those extracted DNA strands and replicates them. This step tests for presence of particular organisms, not for abundance or concentration. Once amplified, we'll send a small part of that sample off to get sequenced, and freeze the rest. Sequencing and Assembly MICROBE COLLECTION The challenge is designing a balloon mounted device that can collect microbes from the air column. Commonly, air sampling of microbes relies on industrial vacuums with filters. These devices are too large and too expensive for our study (for now). Some other options exist. - Impaction of suspended water droplets on a surface. Drawback is that we would have to perform under cloudy/foggy condition and our collection would not be limited to microbes only. See Mohen, 1989 - Novel filters. The industrial vacuum is needed because traditional filters are very hard to pass air through. Perhaps we can conceive a filter that is 'sticky' enough to collect microbes without being so fine as to be difficult to pass air through. - Air transport. Collect air instead to be filtered later instead of filtering on the balloon. Drawback is that this method will be very labor intensive, no solution exists, and the equipment would still be difficult to transport. SAMPLE DESIGN Replicating the study enough times (both globally and in the same location) to build a substantial metagenomic (see Wooley et al. for an overview) dataset of cloud biodiversity over space and time. ENVIRONMENTAL DATA coming.. Importance of metadata Combing sampling with the environmental sampling technologies developed in EcoHackII to record the environment of our sample. SAMPLING SCHEMA location and replications per location (e.g. 10 samples in NYC), coming... FUTURE DIRECTIONS We intend to seek funding for continued sampling events and to cover the cost of continued sequencing. Funding will be used to ship the sampling kit to groups across the globe interested in replicating the study (classrooms, science events, and others). Ideally, this funding will be gathered through a combination of agency support (i.e. UNEP) and a microfunding campaign through a site such as Kickstarter or Petridish. Funding a travelling microbial sampling kit has valuable implications for scientific research, education, public health, and human safety. Knowing which microbes dominate the biodiversity in clouds over Manhattan, versus those in the skies over a city such as Dubai will help us better understand the links between microbes and air quality, climate, and disease. While the primary goal of the travelling kit will be new scientific knowledge, we will not be directly pursuing a publication from the data. Instead, data will be made available immediately following collection to anyone interested, likely including some of our partners. In this way, the citizens collecting the data can help advance a broad diversity of scientific missions. The project will represent many firsts in microbiology, aeromicrobiology, citizen science, and global biology research. PREVIOUS SAMPLING METHODS Bauer et al., Cultivable airborne microorganisms were collected directly from the ambient air under out-of-cloud conditions onto sterile cellulose nitrate filters (Sartorius, 47 mm ∅, bacteria: pore width: 0.45 μm; fungi: pore width: 0.8 μm), which were mounted in open face polycarbonate filter holders, which have been disinfected with 70% ethanol and isopropanol prior to sampling. The sampling time was 5 min at a flow rate of 24 l min−1. Loaded filters were placed onto agar plates within 10 min. SCIENTIFIC PUBLICATIONS Amato P. 2012. Clouds Provide Atmospheric Oases for Microbes. Microbe Bauer, H., A. Kasper-Giebl, M. Löflund, H. Giebl, R. Hitzenberger, F. Zibuschka, and H. Puxbaum. 2002. The contribution of bacteria and fungal spores to the organic carbon content of cloud water, precipitation and aerosols. Atmos. Res. 64:109-119. Wooley JC, Godzik A, Friedberg I (2010) A Primer on Metagenomics. PLoS Comput Biol 6(2): e1000667. doi:10.1371/journal.pcbi.1000667...


Author Comment Last activity Moderation
mamamia0819 "Nice project! Our company(https://www.creative-biogene.com) is also engaged in microbe species. Your task is quite useful. " | Read more » about 1 year ago
humanetechnologies "Hi @warren, I am sorry for the delayed response. Thanks much for your understanding. I have just modified the page to avoid any such confusion. Tha..." | Read more » almost 4 years ago
warren "Thanks for the clarification! Would you mind changing it on this page as well? I appreciate your sharing of the plans, even if you aren't able to f..." | Read more » about 4 years ago
humanetechnologies "Hi @warren, thank you for the question and providing us the open-source hardware definition. After going through it, we agree that our MicrobeMeter..." | Read more » about 4 years ago
warren "Hi, thank you for posting! This looks like a really interesting project; thanks for sharing. I wanted to ask for a clarification -- you mention th..." | Read more » about 4 years ago
Ag8n "Thanks! Give me a couple of days and I'll email you a more detailed description. The help is appreciated! " | Read more » over 4 years ago
stevie "Woah interesting question! can you give me some context or background for it? I'll volunteer to do some hunting for someone who can help answer :) " | Read more » over 4 years ago
Ag8n "A partial answer. Each block of analyzers is heated to 37.0 C . They do not use a spectrometer. Instead, each cell in the analyzers has a led (a..." | Read more » over 4 years ago
warren "@matej check this out! " | Read more » over 5 years ago
liz "I think the original idea about what kind of thing to haul up into the sky was that it would be a like a sponge, allowing the air to pass through a..." | Read more » over 6 years ago
nshapiro "Thanks @liz ! the sterile sugar matrix sounds amazing. @kosamari is cost the reason for the sugar matrix over petri dishes? Keeping the media steri..." | Read more » over 6 years ago
mathew "Hi Nick, I think you could collect particles at altitude, since the wind hitting a free-flight balloon should be within the range that the Passive ..." | Read more » over 6 years ago
liz "This question has come up before, at EcoHack 2012, when @kosamari DIY manufactured cotton candy using a sodacan, power drill, a box of sugar, and a..." | Read more » over 6 years ago
warren "Again, super write-up. Some thoughts that might be helpful: for cfl calibrations without moving the device -- what about putting a small mirror o..." | Read more » almost 10 years ago
Jayesh "Hi Martin, Thanks for the description and tips. I will try to implement it and will tell you results :) " | Read more » almost 10 years ago
mkoistinen "@Jayesh, Hi! Re: Tips on the spectrometer. Well, I basically just made it up as I went along, guided by the fine work by the fine folks at Public..." | Read more » almost 10 years ago
Jayesh "Hi Martin, This is fantastic and encouraging. I am looking to build up the spectrometer like you made. Need some tips for the same. I want to get ..." | Read more » almost 10 years ago
donblair "Martin -- this is truly fantastic! Truly a huge leap for DIY Spectroscopy. How often do you think you'll be able to take spectra of the same batc..." | Read more » almost 10 years ago
gonzoearth "This looks like fun " | Read more » about 10 years ago