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Personal Background and First Video Interview

Hi everyone,


Welcome to the new website! For the first post here, I thought I would introduce myself a bit more. I realized, I've only talked about my background in live presentations and there are a lot of readers who have found this blog by other means.


I cover most of my background in this recent Youtube interview I did with Leighton Morrison (below). Be warned it is 2 hours long but the first 10 minutes or so are me introducing myself.... then we talk about compost and microbiology for the rest. Feel free to listen for as long as you would like.




Background

I was born and raised in the suburbs of the Bay Area, what is now considered a part of Silicon Valley. I am now 38, married with 2 kids, live in Fort Collins Colorado, and have started an agricultural microbiome company.


I'll do my best to summarize this journey below. I believe it's important to understand the motivations behind who you get information from and what inherent biases they have from past experiences. I hope that sharing my journey so far will help you understand my motivations behind this blog and Aggrego Data.


Early Life

As a kid I always loved yard work and gardening. My parents helped me create a small garden in the front of our suburban house. Every year we would make a trip to our municipal maintenance area where our city would provide fresh, steaming compost by the truck load. This compost was actually made from the residential yard trimmings collected throughout the year by the city. I always thought this is how it worked everywhere. As a young kid, my career goal was to become a gardener and mow people's lawns.


Left: In the yard waste can with my sister Right: Me showing off my harvest


At some point in elementary school my interest in science, especially biology, began to grow. In high school, the human genome project was completed (2003). The idea of tiny, programable, replicating life to breakdown plastics seemed like a real possibility. This potential of using microorganisms to remediate pollutions was a big motivator to pursue the field of microbiology in college.


College

After graduating high school (2004), I attended the University of California San Diego majoring in Microbiology. At the time, the field of microbiology was mostly identifying

organisms by growing them on different medias and identifying them under a microscope by morphology. Sequencing a single gene from an isolated colony to identify an organism was a pretty big deal. Sequencing a gene from multiple organisms in a community by cloning them into E coli (called a clone library) was considered extremely cutting edge in microbiome research. Topic wise, the field microbiology mostly focused on food safety, water treatment, and pathogens. How to properly kill microorganisms was all the rage, and there was almost zero education on environmental microbiology and beneficial microorganisms.


I graduated in 2008 (yes, the housing crisis year) and managed to find a job at a molecular diagnostic company in San Diego. We made chemical and biological reagents for clinical tests to detect STD's and other blood born diseases. During that time, I started an aquarium and learned about the microbial nitrogen cycle that treated the water in my small 10 gallon tank. This hobby, combined with what was a less than exciting job, inspired me to apply for graduate school to pursue environmental microbiology.


PhD Research

I moved out of San Diego to the small brewery and college town of Golden, home of Coors Brewery and the Colorado School of Mines. I started in the Department of Environmental Science and Engineering in the fall of 2010 under a recently hired professor Dr. Josh Sharp.



I quickly fell in love with Colorado and the town of Golden. I completed a non-thesis Masters (just classes) in a year. Fortunately, this coincided with the beginning of a multi-institution decade long grant to Reinvent the Nations Urban Water Infrastructure (ReNUIt) which would fund the next 6 years of my PhD. This research center was a collaboration with Stanford, Berkeley, and New Mexico State to understand and break the barriers of innovation in the water field. Interestingly, we discovered barrier is rarely technology - it's almost always policy and education related which is one reason why I am passionate about sharing knowledge.


In this time, the field of microbiology goes exponential and forever changes the understanding of microbial life with the advent of high throughput sequencing. In undergrad we would sequence a single gene from 1 organism - 3 years later we were sequencing 10 million genes from thousands of organisms. In 1998 Norman Pace published the seminal paper that we had only cultured and studied 1%- 0.1% of the total species of bacteria on Earth. Ninety-nine percent of life was still poorly understood, and the technology to explore this new frontier was now widely available.


Most of my time in grad school was spent learning a lot of molecular biology, culturing bacteria, different microscopy techniques, and analytical chemistry. My primary system of study was an engineered wetland system for treating nutrient and organic chemical pollution from urban wastewater. The two wetland treatment systems I studied were a small pilot scale wetland (left) whose design later scaled up to treat water from the Santa Anna River in Orange County, CA (right, 3 long uniform cells).



The primary topics I investigated were microbial pharmaceutical degradation (publications here and here), microbial carbon degradation, nitrogen cycling and removal from water (publication I'm proudest of), and a microbial ecology paper demonstrating that the two wetland systems independently developed similar microbial communities. I also had a lot of exposure to PFAS contamination, heavy metal bioremediation, and frack water treatment. My full publication list can be found here.


Growing Interest In Vermicomposting and Agriculture

You may have noticed that I haven't mentioned much about compost or agriculture yet. My interest in agriculture returned in graduate school when I joined a community garden. Around the same time, I met my now wife who was also an avid community gardener. Additionally, I learned about Cuban vermicomposting in response to being internationally isolated. I also started a worm composter in 2014 and met Victor, a Denver urban worm farmer, who provided me with my starter red wigglers.


Cuban concrete vermicomposting bins (https://www.sustainablemarketfarming.com/)


I sequenced some of Victor's vermicompost, bokashi, and compost teas blog post coming soon, likely making me the first person to look at the vermicompost microbiome with this technology. Unlike bokashi, I was blown away by the sheer diversity of bacteria in his vermicompost. Victor was really happy to better understand his product and this was really the first time I saw the potential of DNA based microbiome analysis having a direct application to an industry.


My interest in large scale agriculture came from my graduate studies around water. Near the end of my graduate career I realized that urban water usage only accounted for about 10% of total water usage nationally. Agriculture was the other 90% of water usage and also accounted for the vast majority of nutrient and chemical pollution in US aquifers, waterways, and dead zones in the oceans.


Instead of endlessly treating water pollution, I wanted to find a water solution. This solution would have to greatly reduce or eliminate the need for synthetic fertilizers, pesticides and herbicides. The idea of replacing chemicals with compost, beneficial microorganisms, and organic fertilizers, ultimately led me to start the Vermi-Microbiome Project.


Post Graduation

I graduated from the Colorado School of Mines in 2017 with my PhD in Environmental Engineering and Science and was recruited to a post doctorate research position in Sydney, Australia. Long story short, it wasn't a great experience and ended any thoughts I had about continuing in academia. However, even in Australia my now wife and I continued vermicomposting and I met a professor doing agricultural research which continued to peak my interest in agriculture.


After 6 months in Australia, we quickly returned to the States and started looking for jobs. The water industry seemed largely uninterested in my skillset and I decided I wanted to pick up on the vermicomposting research I started in graduate school. I wrote a grant proposal for a Western Sustainable Agriculture Research and Education (WSARE) Grant to use DNA sequencing technology to study the microbial ecology of vermicompost and teas. I needed collaborators (vermicompost producers) for this grant, and I made my case at the 2019 NC State Vermicomposting Conference thanks to Rhonda Sherman. I recruited over 25 vermicompost producers to join the grant which was submitted at the end of 2019.


Vermi-Microbiome Project

The Vermi-Microbiome Project was awarded funding March 2020 which coincided with my first kid being born and of course the start of COVID-19. What was supposed to be a quick and fun year long project turned into a 2 year marathon. I lost all lab access for the project and being the caretaker of a newborn was a bit more work than anticipated. We didn't get sequencing data back until near the end of the 2 years and did not have nearly enough time to fully digest the data behind close to 300 samples. On top of this we had less than ideal sample preparation due to losing lab space causing use to not get enough sequences for many samples.


Despite these challenges we were still able to show that there appeared to be a conserved group of beneficial organisms found in all vermicomposts. We also generated preliminary data for vermitea which showed a dramatically different community than found in vermicompost. As hypothesized, we showed that vermicomposting process increased microbial diversity from manure -->pre-compost--> vermicompost. The full project report can be found here. I presented the data and conclusions at the 2022 NC State Vermicomposting Conference.


Overall, I still felt like I didn't fully understand what made vermicompost special. The final goal of understanding how to manipulate composting inputs and conditions to optimize the microbial community was not reached and still something I hope to better understand. To continue to try and answer these questions, Aggrego Data was created.


Aggrego Data to Present

As I mentioned at the start of the post, I am living in Fort Collins, CO with my wife Vaida and two kids Vera (4 y/o) and Osten (1 y/o). We are still avid gardeners and slowly turning our suburban backyard into a market style garden. We grow a little of everything but tomatoes and cucumbers for sauces and pickles are top priority in our house. We operate 4 Urban Worm Bags continuous flow vermicomposters and a coupe of tower worm farms to manage our household organic waste.




I started Aggrego Data after the compeletion of the Vermi-microbiome Project, with the goal of continuing research and education through community science and providing cutting edge microbiome analysis to agricultural producers. The company currently consists of just myself and a former graduate school friend/colleague Dr. Chris Trivedi. Chris does all of the bioinformatic analysis to generate the reports after the sequencing is done. Aggrego Data is currently consulting on two grants related to large scale vermicompost application to various crop types and a vermitea brewing grant (more info to come for both!) We will officially launch a Bacteria Microbiome and Beneficial Organisms Analysis for vermicompost and teas in the coming months that we are very excited about.


Please keep following along as we have some exiting projects coming up. If there are any topics or research questions in the field of agricultural microbiology you would like to know more about please let me know and I would be happy to add it to the list of upcoming posts!

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