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Researchers Investigate How Changes in Small-Scale Environmental Conditions Impact Microbial Structure and Function3 min read

by Julie Bobyock on April 25, 2022

Climate and Ecosystem Sciences Division

 

A) Visualized pangenome of the 41 Arthrobacter isolates with fully circularized genomes including core (present in all genomes), soft-core (present in 95–99% of genomes) shell (present in 5–95% of genomes), and cloud (present in 1–5% of genomes) gene clusters. B) Number of carbohydrate-active enzyme protein-coding genes present in the core, soft-core, shell, and cloud genomes. C) Gene clusters were categorized by KEGG Brite category and the fraction of gene clusters from each category contributing to each KEGG Brite module was plotted as a bar graph by core (green), soft-core (black stripe), shell (gold), and cloud (pink pattern). Gene clusters not mapping to a KEGG Brite module were not included in fraction calculation.

Just one teaspoon of soil or sediment can contain up to one billion microbes. These microorganisms in Earth’s subsurface, although invisible, largely influence the global carbon cycle through their ability to break down organic material, which releases carbon dioxide in the process. However, environmental conditions within Earth’s subsurface such as moisture, nutrient availability, and pH can significantly vary on incredibly small scales. Even at very small resolutions, these different environmental niches can largely impact the structure, function, and genomic potential of  microorganisms – which can affect the important role microbes play in carbon and nutrient cycling.  

A recent paper in ISME Communications led by Berkeley Lab Ecology Department Head Romy Charkaborty’s group aimed to study how these environmental niches shaped the genomic potential of  bacteria in the genus Arthrobacter, which are commonly found in the soil and subsurface, and are known for their ability to break down larger and harder to degrade carbon molecules. To better understand and model the carbon cycle, scientists must study how changes in small-scale environmental conditions affect carbon metabolism and other cellular functions in closely related microbes (connect ecotypes to phenotypes and genotypes).

“It’s important to investigate how niche micro-environments influence microbes because microbes evolve and adapt to these environments, and will transform carbon differently,” explained lead author Sara Gushgari-Doyle, who performed this research while serving as an EESA postdoc fellow in Chakraborty’s lab and is now a scientist at ZymoChem. “Understanding these differences could even help us design strategies to predict and even manipulate the carbon cycle.”

Close-up of Arthrobacter bacteria.

 

The team, which included members from Adam Arkin’s group in the Environmental Genomics and Systems Biology division at Berkeley Lab and Michael Adams’ group at the University of Georgia, isolated and cultivated seven distinct strains belonging to the genus Arthrobacter from varying depths of a single sediment core and associated groundwater from an adjacent well. These Arthrobacter isolates demonstrated functional and genomic capacities specific to the biogeochemical conditions of where they were sampled. They found that microbial strains, despite close spatial origin and phylogenetic relationships, break down carbon differently and had different sets of genes for carbon degradation. Further study of their genomes, along with 40 other Arthrobacter strains, revealed that the genus can indefinitely increase its set of genes and shows adaptability to available complex carbon substrates. 

Understanding how very closely related bacteria transform carbon differently at small scales can advance global carbon cycle models and predictions of how microbes may affect the carbon cycle in a changing climate. 

News & Events

Chun Chang Places Second in Annual Berkeley Lab Pitch Competition3 min read

January 18, 2023

Commercializing Berkeley Lab inventions is an important part of the Lab’s mission, and one that requires strong communication skills. For example, Lab inventors need to be able to pitch their ideas to external partners and potential funders.  The annual Berkeley Lab Pitch Competition occurred on October 27, 2022 and is a part of an entrepreneurship…

EESA Scientists Collaborate With Universities to bring Environmental Science Research Opportunities and Training to Students Underrepresented in STEM3 min read

January 13, 2023

  EESA researchers are collaborators in three of the 41 projects awarded in December by DOE through its Reaching a New Energy Sciences Workforce (RENEW) initiative.  RENEW aims to build foundations for research at institutions that have been historically underrepresented in the Office of Science (SC) research portfolio. The initiative provides opportunities for undergraduate and…

New Report Explores Revolutionary Environmental Artificial Intelligence Infrastructure5 min read

January 10, 2023

In a collaborative effort between the U.S. Department of Energy’s (DOE) Office of Biological and Environmental Research (BER) and DOE’s Advanced Scientific Computing Research (ASCR) program, as well as with community experts, the Artificial Intelligence for Earth System Predictability (AI4ESP) workshop was held from October through December 2021. BER developed the process as the Model-Experiment paradigm, or ModEx, and a report released this fall outlines the key takeaways of last year’s event.

A Q&A With Postdoc Kunxiaoja Yuan3 min read

January 4, 2023

  Kunxiaojia Yuan received her Bachelor’s of Engineering in remote sensing and Ph.D. in geographic information engineering from Wuhan University. She is a postdoctoral researcher in EESA, with a research focus on global carbon, energy, and water cycle analysis and model evaluation using machine learning and causal inference. What motivated you to pursue a postdoc…

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