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Roles of DNA methylation in prokaryotes

Single-molecule sequencing technology assists microbial DNA methylation study. The Science Researchers sequenced 230 diverse archaeal and bacterial genomes to learn more about the roles DNA methylation plays in prokaryotes. The Impact The epigenome of a cell is the collected set of changes made to specific bases in its genomic DNA that affect how the genome… [Read More]

A window into fungal endophytism

Comparative genomics highlight genes that may determine fungal lifestyles. The Science Researchers sequenced a fungal endophyte of rubber trees and compared its genome to 36 other fungi, focusing on genes that are crucial to host-fungus interactions. The Impact Endophytes reside within living plant cells and can play roles not just in plant health but also… [Read More]

Multiple methods for microbial diversity in one lake

Nine-year study tracks how distinct microbial communities evolve in freshwater lakes. The Science Researchers sequenced, assembled and analyzed bacterial genomes from a nine-year study tracking the evolution of microbial communities in a Wisconsin freshwater lake. The Impact Competing models have been put forward to answer the fundamental question of how microbes evolve, but it remains… [Read More]

Strategy to Uncover More Microbial Lineages

Biases in current sequencing technologies hide true breadth of microbial diversity. The Science DOE JGI researchers employed datasets from the Integrated Microbial Genomes (IMG) system to determine how many microbial lineages might be missed from available sequences in existing datasets due to mismatches with currently used Polymerase Chain Reaction (PCR) primers. PCR is a technology… [Read More]

Tracking Microbial Mat Formation in Yellowstone

Assessing real-time contributions of microbial communities toward mat formation. The Science Researchers determined the contributions of different microbes toward the establishment of microbial mat communities in the hot and acidic environments of the Yellowstone Hot Springs. The Impact Microbial mats serve as model systems for studying microbial interactions and their influence over biogeochemical processes. Understanding… [Read More]

Better Microbial Genome Binning with MetaBAT

DOE JGI researchers develop an automated software tool that can scale to handle complex metagenome datasets. The Science: DOE JGI researchers have developed an automated tool called MetaBAT that automatically groups large genomic fragments assembled from metagenome sequences to reconstruct single microbial genomes. The Impact: The ability to accurately and efficiently reconstruct individual microbial genomes… [Read More]

A History of Phage-Host Interactions With Help From CRISPRs

A tool to help microbial ecologists link phages to hosts in ecological studies. The Science: Using metagenomic datasets produced from the Iron Mountain site in Northern California and customized tools, researchers used bacterial spacer sequences commonly called CRISPRs to link phage and hosts in ecological studies. The Impact: Interactions between uncultivated microbes and their phage… [Read More]

A Single-Cell Pipeline for Soil Samples

Scientists evaluate a process that uses NanoSIMS and Raman microspectroscopy for in situ microbial studies. The Science: To investigate in situ function of uncultivated microbes, scientists evaluated a process for preparing soil samples for single-cell analysis methods. The Impact: The process allows researchers to efficiently analyze microbial activities at the single-cell level in soil systems,… [Read More]

Expanding Barley Genetics Resources

Genomic regions containing two-thirds of all annotated barley genes have been sequenced. The Science: Researchers generated nearly 16,000 sequences of gene-containing regions for barley, mapping approximately two-thirds of all annotated barley genes. The Impact: While researchers continue to work on a complete reference sequence for the barley genome, the determination of improved sequence assemblies for… [Read More]

Seeking “Gold Standard” Wastewater Treatments

Metagenomic analyses lend insights into how microbes break down wastewater contaminants. The Science: Researchers conducted analyses of microbial communities in laboratory-scale bioreactors breaking down contaminated wastewater from gold ore processing. The Impact: In this “first application of genome-resolved metagenomics” to characterize bioreactors involved in gold ore processing, the data reveal how the bioreactors utilize available… [Read More]