April marks both the 50th celebration of Earth Day on April 22, and DNA Day on April 25. As both Earth and DNA are close to our JGI hearts, we’re highlighting genomic science research that feels especially relevant to living on a changing planet.
Mo Kaze is a University of California (UC), Merced graduate student working with Susannah Tringe, JGI’s User Programs deputy and head of the Microbial Systems group through the DOE Office of Science Graduate Student Research (SCGSR) program. Her research project, “Microbial Community Structure and Methane Production in California’s Canal System,” focuses on anthropogenic impacts on wetland microbiome composition and metabolism, work on which she is expanding with her study of microbes in California’s manmade water transport canals.
Inspired by Randall Munroe’s xkcd comic “Up Goer Five” and his subsequent book Thing Explainer, Kaze took on the challenge of explaining her research using the ten hundred most commonly used words in the English language. (Try it yourself here.) She translated her abstract from a 2019 conference. Both versions appear side-by-side below:
|2019 ASM Microbe poster abstract:||Ten Hundred Words Translation:|
| Wetland restoration confers important ecosystem services: from economic, aesthetic, and environmental success to carbon accretion and sequestration. Microbial biogeochemical processes influence carbon flux, and sequestration is mitigatory of global warming effects. Analysis of California Bay Area restored wetlands, where 70% of the wetlands were converted to industrial and agricultural uses, indicate unexpected carbon emissions. Many factors effect microbial community structure and it is important to investigate and understand potential impacts. |
In this study we used bioinformatic analyses of a large metagenomic data set of Bay Area historic and restored wetland sediments to determine factors influencing community structures. Sequences were assembled, normalized, and aligned with MetaPhlan and R. Heavy metal concentrations were compiled from USGS, EPA, JGI, and CA Water Board data and mapped using ggmaps in R. Clusters of orthologous genes (COG) were quantified using JGI’s IGM/M tools and R.
Restored wetlands had a greater diversity of phyla when compared to the historic wetlands. Methanogenic genera included: Methanobacterium Methanosaeta, and Methanosarcina; Methanobacterium and Methanosarcina were present in larger amounts at restored sites. Methanotrophs Methylocystis, Methylomonas, and Methylosinus, were also identified. Heavy metal resistance COGs contained genes for resistance to arsenic, cadmium, cobalt and lead, chromate efflux pumps, and a mercury resistance gene family. Statistical analysis indicated depth as a significant determinant of microbial community structure.
Differences in quantity of methanogens and methanotrophs may explain some of the variation in carbon flux observed between historic and restored sites. While heavy metal resistance COGs were present and related to the contaminants present in the Bay, there was no clear pattern between historic and restored. Mayberry had smaller number of heavy metal resistance COGs and a larger amount of methanogens, which could explain why this restored wetland has been emitting methane in higher than expected amounts. Methanotrophic metabolism occurring in restored Westpond may be mitigating carbon loss.
Differences in oxygen requirements of community members likely explains why depth appears as a significant, influential factor. Further investigation into how these, and yet to be identified, factors interact will provide deeper understanding of these important environments.
|Is man made stuff stopping our tiniest friends (who live in wet lands) from holding on to bad stuff for us? |
Warming is a big, immediate, important problem with lots of parts that need explaining. We need to look at our home and study it to make sure we keep it safe and happy. One part of our home is made of places called wet lands where water meets land. They are beautiful, grow many green things like food, house cute animals, and are enjoyed by lots of us. They are also home to all kinds of our oldest, tiniest friends.
Our tiniest friends who live in wet lands have lots to say about our world and we should listen to them. They can tell us about what they are giving away and putting out in the wet lands and into the air. Fixing wet lands that were once used for businesses might make our tiniest friends hold onto bad green house stuff for us by keeping it to themselves. Which is great and really nice of them; we love it when they hold onto bad stuff for us and keep it out of the air!
But… fixing up wet lands might make our tiniest friends eat and work a lot and they might let go of bad stuff that makes green house air even worse. We should definitely find out exactly who our tiny friends really are! Then we can match up the ones living in older wet lands to newer, fixed wet lands and find out if they are doing different things. I think they are doing different things in different places. There are lots of man made things, like lead and other stuff that goes into paint and making cars, left in wet lands that have made some of them really not clean. I think this man made stuff might be stopping our tiniest friends from holding on tight to bad stuff and is stopping them from helping us out.
I used computers to figure out that there are different groups and families of tiny friends hanging out in different places in the wet lands. Computers also told me that man made stuff might not be as big a deal as I thought, but how far down in the ground our tiniest friends live might explain a few things. We will have to come up with some new, cool, ideas and look at even more things with the computer. Which I will definitely do, because our very loved wet lands are really important!
Kaze was part of the 2018 cohort of the JGI-UC Merced Genomics Internship Program, and is part of Mark Sistrom’s lab at the UC Merced School of Natural Sciences. The JGI-UC Merced Internship Program was developed between the two institutions to help train the next generation workforce.