Bacterial inoculation while transplanting coupled with a later harvesting time point yields a reproducible microbial community The Science m-CAFEs researchers used model plant Brachypodium distachyon, shown here in a quartz sand-filled fabricated ecosystem (EcoFAB) inside a Magenta box, to study soil-plant-microbe interactions. . Increasing pressure on agricultural systems and environmental degradation has created a need to examine new methods for developing sustainable agricultural … [Read more...]
CasPEDIA Database: a Functional Classification System for Class 2 CRISPR-Cas Enzymes
m-CAFEs researchers present new database for the collection, classification and utilization of CRISPR-Cas enzymes. The Science m-CAFEs researchers developed CasPEDIA, the Cas Protein Effector Database of Information and Assessment, a new database which provides summary information about the capabilities and limitations of Class 2 Cas technologies to facilitate tool selection and highlight opportunities for future biotechnological development. They also introduce CasID, a Cas enzyme … [Read more...]
Genome-wide fitness profiling reveals molecular mechanisms that bacteria use to interact with Trichoderma atroviride exometabolites
The Science The rhizosphere that surrounds plant roots is a hotspot for bacteria, fungi, and other microorganisms. While how roots interact with bacteria is relatively understood, the dynamics between bacteria and fungi in the rhizosphere are less clear. In this work, m-CAFEs researchers at UC Berkeley focused on Trichoderma atroviride, a fungus in the root zone that produces complex substances influencing plant-microbe interactions. Observing lab-altered bacteria revealed that exposure to … [Read more...]
Researchers Close Rhizosphere Microbiome Knowledge Gaps
The Science m-CAFEs researchers studied microbial communities at different zones of the roots in three different types of growth containers: conventional pots, tubes, and standardized fabricated ecosystems (EcoFABs), designed to mimic conditions of a natural environment. The goal was to characterize microbial communities on the tips of the roots, the soil at the base of the roots and regular bulk soil that was not in the rhizosphere environment. The EcoFAB 2.0 is a standardized device for … [Read more...]
A new tool visualizing vitamin interdependencies
Combining network analyses with metagenomics uncovers microbial interactions and a vitamin super-producer m-CAFEs researchers at University of California, Berkeley demonstrated a new method for identifying bacteria that are interacting and determining the nature of the interaction. They predicted and confirmed experimentally that a Variovorax bacterium in a bioreactor community was producing significant amounts of vitamin B1 for other community members, yielding new insight into the … [Read more...]
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