Berkeley Lab


To jumpstart the discovery process, Berkeley Lab’s Microbes-to-Biomes initiative is targeting two key systems: the soil-plant biome and the gut microbiome.

The Soil-Plant Biome

The functioning of the soil-plant biome is controlled by interactions and feedbacks among its mineral-microbe-fluid-metazoan (such as worms and insects)-and plant components. Microbes in this biome support plant health and growth, neutralize toxins, and help plants resist disease and environmental stresses (including drought), and are key to soil carbon stabilization.

The roles and responsibilities are not uniform, however. Some bacteria and fungi enhance plant growth, health and disease resistance; others act as pathogens and disease agents, reducing productivity, increasing mortality, and even limiting plant species distributions. Sorting the differences and quantifying how microbes “live and work” to regulate the plant-soil biome is challenging for a number of reasons– the diversity of relationships, the range of spatial and temporal scales over which important interactions occur, and the poor characterization of these mostly uncultivated microbes and the environment they inhabit.

Furthermore, metazoans, particularly worms and insects, affect ecosystems by serving as accelerated “bioreactors” for the gut-dwelling microbes they deliver to the soil and by physically engineering their local environments.  These characteristics and actions can profoundly alter plant health and impact everything from the decomposition of plant polymers and nitrogen fixation to the rate at which phosphorus is released to plants.

Related FY2015 LDRD projects:

Harnessing the soil microbiome for food and fuel security (Eoin Brodie (ESD)/Peter Nico (ESD) – PIs)

Increasing the availability of phosphorus to plants by engineering phosphate solubilizing plant-associated bacteria (Matthew Blow (GND/JGI)/Adam Deutschbauer (PBD) – PIs)

The Soil Metazoan Microbiome: A key functional compartment of importance to plant health and root C stabilization (Javier Ceja Navarro (ESD)/Trent Northen (PBD) – PIs)

Capturing carbon degrading microbes with fluorescent substrate bait (Tanja Woyke (GND/JGI) – PI)


The Gut Microbiome as a key Interface to the Environment

Within the human body, the microbiome has long been known as an important provider of essential nutrients and co-factors. More recently, though, imbalances in the body’s microbial communities – which compete for space and resources — have been directly associated with such diseases and disorders as obesity (metabolic), asthma (inflammatory) and autism (neurologic).

Some have suggested that the significant rise in these illnesses and a corresponding decline in infectious diseases are being influenced by such key environmental interactions as toxicant exposure, diet and patterns of early life microbial exposure. What is certain at this point is that microorganisms have the potential to regulate the development of our immune system and to mitigate or worsen the effects of toxicants or dietary components in ways that we have only begun to perceive. Indeed, the gut microbiome is increasingly viewed as a virtual organ, complete with strategies for transplantation.

This new view of microorganisms comes at a time when our Earth’s subsystems, including freshwater, forests, agro-ecosystems, oceans, urban centers and the atmosphere itself, are being radically transformed by human activities.  Understanding how our changing planet might in turn be changing our own health is a grand challenge for public science and one that could yield new technologies for prediction, manipulation and therapy.

Related FY2015 LDRD projects:

Microbiome adaptation in response to environmental challenges (Susan Celniker – PI)