New Nitrite-Oxidizing Isolate Reveals Unexpected Nitrogen-Cycling Potential - Researchers have isolated Nitrobacter vulgaris strain MLSD-S22 from subsurface groundwater at the Oak Ridge Reservation, where contamination has created challenging conditions for nitrogen-cycling microbes. The new strain shows strong growth and nitrite oxidation across a wide range of environmental conditions, with high affinities for nitrite and oxygen that… News Article →
GenomeDepot: Data Management System for Microbial Comparative Genomics - GenomeDepot Enables Web-Based Annotation and Comparative Analysis of Microbial Genomes GenomeDepot is an open-source, web-based platform for microbial genome annotation, management, and comparative analysis. Built to help researchers quickly organize genome collections and explore genomic features, including ortholog families, protein domains, operons, regulatory interactions, and strain and sample… News Article →
Interactive tools for functional annotation of bacterial genomes - ###How to predict a protein’s function or a bacterium’s capabilities Predicting what a bacterium can do from its genome is a complex task that involves understanding the functions of its encoded proteins. While automated software for predicting protein function is widely used, it is prone to errors, with… News Article →
New Tool Enables Overexpression Libraries for High-throughput Protein Characterization - The development of a high-throughput method by for determining the function of predicted proteins of unknown function marks a significant advancement in the field of microbial biology. By utilizing DNA barcode sequencing and auxotrophic strains of E. coli, ENIGMA Researchers at Lawrence Berkeley National Laboratory can now assign… News Article →
Microbial Remains Shape Community Composition and Growth of Soil Microorganisms - The Science Microbes, which include organisms like bacteria, are tiny living things that inhabit virtually every environment on Earth. Soil microbes play a crucial role in breaking down organic matter and are crucial drivers of global nutrient cycles that support all terrestrial ecosystems. ENIGMA scientists studied what happens… News Article →
Functional Resilience in Microbes found in Groundwater - ENIGMA researchers studied microbes living in groundwater at a site contaminated with metal, acid, and other waste. They compared wells with high, medium, low, and no levels of contamination. They found that even when microbial species count decreased under stress, groups of microbes compensated to sustain essential functions. News Article →
Goff Uses KBase to Analyze Genetic Factors Impacting Microbial Fitness in Contaminated Environments - A recent KBase community highlight summarized research accomplishments from Jennifer Goff, who was a postdoctoral researcher with the ENIGMA Science Focus Area in Mike Adams' lab at the University of Georgia (UGA) and is now a professor at SUNY College of Environmental Science and Forestry (ESF). Several of… News Article →
Adding Nutrients to Groundwater Yields Reproducible Response in Nearby Microbial Communities - Emulsified vegetable oil injections into groundwater promoted reproducible geochemical and microbial changes across an eight-year time gap. News Article →
Machine Learning Reveals Patterns of REC Protein Domain Evolution - Bacteria can evolve by exchanging genetic material through a process called recombination. This study used machine learning models combined with functional laboratory experiments to show that after recombination, a bacterial signaling system changed and expanded its protein family, despite considerable selective pressures in place that constrained new modifications. News Article →
How Bacteria Adapt to Stress - Berkeley Lab researchers uncovered a distinctive adaptation that some bacteria use to quickly form protective communities called biofilms, which help them survive in adverse environments. The work could lead to better stewardship of areas with high levels of heavy metals, nutrients, or other forms of hazardous waste. News Article →
From Field-to-Lab and Lab-to-Field: How Microbes Evolve, Form Partnerships and Work Together - Researchers in the Institute for Systems Biology’s Baliga Lab examined model organisms from two classes of microbes whose interaction converts over a gigaton of carbon to methane each year and found that gene mutations selected for over a relatively short timeframe in the two microbes –Desulfovibrio vulgaris (Dv)… News Article →
Huang Explores How Bacteria Store Carbon at 2024 BioEPIC Research SLAM - Congratulations to Joshua Jiaqi Huang, a UC Berkeley graduate student researcher in Biosciences senior faculty scientist Adam Arkin’s group, who represented ENIGMA and Biosciences at the 2024 BioEPIC Research SLAM. News Article →