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Unearthing Cornerstones in Root Microbiomes

Defining core members of a microbial community for normal plant growth Like the tip of an iceberg, a plant sprouting from the soil barely hints at what lies beneath. At the nexus where roots and soil intersect are thriving microbial communities that play important roles in plant health and growth. Understanding how plant yields can… [Read More]

The MiSIng Piece Revealed: Classifying microbial species in the genomics era

The rapid explosion in the throughput of DNA sequencing due to new technology platforms is fueling an increase in the number of sequenced microbial genomes and driving much greater availability of these data to the research community. Traditionally, identifying the microorganisms selected for sequencing is often decided on the basis of a single universal marker… [Read More]

Confirming Microbial Lineages Through Cultivation-Independent Means

Collaborative work culminates in evidence of a single candidate bacterial phylum. The number of microbes found on Earth has been compared to the number of stars in the Milky Way. Yet the proportion of those microbes that can actually be grown under laboratory conditions is so small it would be akin to those stars that… [Read More]

Automating Microbial Genome Sequence Decontamination

Single cell genomics and metagenomics are pioneering techniques that have helped researchers assess environmental microbial community structure and function. As projects applying these techniques scale up, however, researchers are hindered by the lack of a high-throughput process to review assembled genome sequences. Currently, sequence decontamination of the microbial genomes being uploaded to public databases is… [Read More]

Longer DNA Fragments Reveal Rare Species Diversity

New sequence assembly technologies help reconstruct environmental microbial communities. Many microbes cannot be cultivated in a laboratory setting, hindering attempts to understand Earth’s microbial diversity. Since microbes are heavily involved in, and critically important to environmental processes from nutrient recycling, to carbon processing, to the fertility of topsoils, to the health and growth of plants… [Read More]

Characterizing Permafrost Microbes in a Changing Climate

In the effort to curb climate change by reducing global greenhouse gas (GHG) emissions, thawing permafrost poses a critical challenge. These reservoirs of frozen organic matter embedded in Arctic soils are one of the major (~1.5 billion tons) stores of carbon on Earth. One of the abiding concerns regarding permafrost is that as global temperatures… [Read More]

Retracing the Roots of Fungal Symbioses

Understanding how plants and fungi developed symbiotic relationships. With apologies to the poet John Donne, and based on recent work from the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science user facility, it can be said that no plant is an island, entire of itself. Unseen by the human… [Read More]

Termite of the Sea’s Wood Destruction Strategy Revealed

Directed production of wood-degrading enzymes begins away from the gut The sight of termites anywhere near one’s house is enough to raise a homeowner’s concerns about the potential damage these insects might inflict. Shipbuilders and engineers have similar feelings about shipworms, worm-like wood-eating marine clams that have also been called the “termites of the sea.”… [Read More]

Discovering the Undiscovered

Advancing New Tools to Fill in the Microbial Tree of Life To paraphrase a famous passage from Coleridge’s “The Rime of the Ancient Mariner”: microbes, microbes everywhere, though most we do not know. This is changing, though. In a perspective piece published November 6 in the journal Science, Eddy Rubin, Director of the U.S. Department… [Read More]

2015 DOE JGI’s Science Portfolio Delves Deeper into the Earth’s Data Mine

The U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science user facility, has announced that 32 new projects have been selected for the 2015 Community Science Program (CSP). From sampling Antarctic lakes to Caribbean waters, and from plant root micro-ecosystems, to the subsurface underneath the water table in forested watersheds,… [Read More]