KBase community member Clifton Bueno de Mesquita shares how KBase is used for understanding how sea level rise may affect microbial communities in coastal wetlands.
May 29, 2024

Community Highlight: Clifton Bueno de Mesquita

Microbial Ecologist, Clifton (Cliff) Bueno de Mesquita’s (CBM) primary interests are to understand both ecosystem responses to climate change and the microbial drivers of greenhouse gas emissions. This led him to study the structure and function of microbial communities across many environments – air, snow, soils, sediments, roots, leaves, seeds, and guts. Clifton completed his PhD at the University of Colorado and was a postdoctoral researcher at the Joint Genome Institute (JGI) for three and a half years before his current position as a postdoc at the University of Colorado – Boulder.

One of his postdoc projects was a recent publication (Narrative) that investigates how sulfate and seawater ions affect microbial communities in coastal wetlands, which is relevant for understanding how these important ecosystems will respond to rising sea levels. 

How has using KBase supported this project at the JGI?

(CBM) For this project, we generated metagenomes from freshwater wetland soils that received a treatment of either artificial seawater (with and without sulfate), sulfate alone, or deionized water (as a control) in a laboratory environment. While most of the metagenomic analysis was done outside of KBase, KBase was very useful for generating and analyzing metagenome assembled genomes (MAGs). KBase enabled me to quickly generate MAGs, assess their quality, annotate their function, and build a phylogenetic tree.

Picture of a lake, surrounded by green trees and liked with cattails and floating plants, like waterlilies.

Photo of Timberlake circa 2013, courtesy of Marcelo Ardón.

How have you benefited from collaborating with KBase?

(CBM) I have benefitted from collaborating with KBase on a number of projects involving genomic and metabolomic datasets. In a separate project, we collaborated closely with KBase to improve metabolic modeling capabilities for organisms that produce methane.

What is your favorite aspect of the KBase Narrative (or platform)? 

(CBM) My favorite aspect of KBase is the graphical user interface, and the ease and speed with which you can run programs which would otherwise be a pain to install and/or use a lot of computational resources.

What role do you see KBase having in open science principles (related to your work)? 

(CBM) The ability to share KBase Narratives is a great feature and great for open science.

Bonus Q: What is one “behind the scenes” thing you want to share about your project?

(CBM) This experiment was done by our collaborator Marcelo Ardón way back in 2010. Before I arrived at the JGI, a previous JGI postdoc, Wyatt Hartman, coordinated with Marcelo to perform DNA sequencing from frozen soils from the experiment. After Wyatt left and I arrived, I took over the project and am happy to have it published, 14 years after the original experiment was conducted! The results of the experiment are quite interesting as we show increases in methane emissions following seawater addition whereas most other studies show decreases.

LINKS

Publication: C.P. Bueno de Mesquita, W.H. Hartman, M. Ardón, S.G. Tringe. “Disentangling the effects of sulfate and other seawater ions on microbial communities and greenhouse gas emissions in a coastal forested wetland.” ISME Communications, 4:1, (2024) https://doi.org/10.1093/ismeco/ycae040.

FAIR Narrative: https://doi.org/10.25982/138721.208/2336591

Ellen Dow
Ellen Dow
Lawrence Berkeley National Laboratory

Ellen G. Dow, Ph.D. is a member of the outreach, communications, and user development team. Inspired by involvement in science outreach throughout graduate school, she left the bench to gain experience in informal education and cultivate community engagement from the general public to science sectors. A molecular biologist by training, Ellen applies her research experience to support scientists and develop resources for the KBase community.