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The mitochondrial genome of the ethanol-metabolizing, wine cellar mold Zasmidium cellare is the smallest for a filamentous ascomycete

Fungi in the class Dothideomycetes often live in extreme environments or have unusual physiology. One of these, the wine cellar mold Zasmidium cellare, produces thick curtains of mycelia in cellars with high humidity, and its ability to metabolize volatile organic compounds is thought to improve air quality. Whether these abilities have affected its mitochondrial genome… [Read More]

The Cacti Microbiome: Interplay between Habitat-Filtering and Host-Specificity

Cactaceae represents one of the most species-rich families of succulent plants native to arid and semi-arid ecosystems, yet the associations Cacti establish with microorganisms and the rules governing microbial community assembly remain poorly understood. We analyzed the composition, diversity, and factors influencing above- and below-ground bacterial, archaeal, and fungal communities associated with two native and… [Read More]

Analysis of Amino Acid Substitutions in AraC Variants that Respond to Triacetic Acid Lactone

The Escherichia coli regulatory protein AraC regulates expression of ara genes in response to L-arabinose. In efforts to develop genetically-encoded molecular reporters, we previously engineered an AraC variant that responds to the compound triacetic acid lactone (TAL). This variant (named “AraC-TAL1”) was isolated by screening a library of AraC variants in which five amino acid… [Read More]

Spatiotemporal distribution of bacterioplankton functional groups along a freshwater estuary to pelagic gradient in Lake Michigan

Freshwater bacteria play key roles in biogeochemical cycling and contribute significantly to biomass and energy fluxes. However, studies of Great Lakes ecosystem dynamics often omit bacteria. Here, we used high throughput sequencing to analyze how bacterial diversity and community composition (BCC) vary seasonally along the long-term Muskegon estuary to pelagic research transect. Diversity was higher… [Read More]

A Droplet Microfluidic Platform for Automating Genetic Engineering

We present a water-in-oil droplet microfluidic platform for transformation, culture and expression of recombinant proteins in multiple host organisms including bacteria, yeast and fungi. The platform consists of a hybrid digital microfluidic/channel-based droplet chip with integrated temperature control to allow complete automation and integration of plasmid addition, heat-shock transformation, addition of selection medium, culture, and… [Read More]

Detection of short-term cropping system-induced changes to soil bacterial communities differs among four molecular characterization methods

Perennial grass-based agroecosystems are under consideration as sustainable sources of bioenergy feedstocks. Establishing these systems on land previously used for conventional agricultural production is expected to dramatically alter the composition and functional capacity of their associated soil bacterial communities, but the rate at which these changes will occur is unclear. Methods for characterizing bacterial communities… [Read More]

Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria

Most free-living planktonic cells are streamlined and in spite of their limitations in functional flexibility, their vast populations have radiated into a wide range of aquatic habitats. Here we compared the metabolic potential of subgroups in the Alphaproteobacteria lineage SAR11 adapted to marine and freshwater habitats. Our results suggest that the successful leap from marine… [Read More]

Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs

Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum (‘Candidatus Kryptonia’) found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden… [Read More]