The team aims to study organic sulfur biogeochemistry in a coastal ocean ecosystem. In fall 2014, the Monterey Bay Aquarium Research Institute (MBARI) Environmental Sample Processor (ESP) was deployed in Monterey Bay, CA to collect a high-resolution microbial community time-series for analysis of bacterially-mediated organic sulfur transformations. Concurrent data on chlorophyll concentrations, bacterial and phytoplankton cell…

The genus Suillus is one the more iconic and easily recognized genera of mushrooms. As symbiotic ectomycorrhizal fungi (EMF), Suillus spp. play critical roles in the function of forest ecosystems by providing their plant hosts with mineral resources in exchange for photosynthetically fixed carbon. Our project seeks to generate a comprehensive understanding of the co-evolutionary…

How do microbes respond to such a wide range of pressures? To study this question, the team will use strains of the genus Carnobacterium, which are psychrotolerant, facultatively anaerobic Gram-positive bacteria that grow at both low and high P extremes. Their working hypothesis is that bacteria adapt to the P environment by altering both their methylomes…

To understand how patterns of oxygen (O2) availability alter microbial community structure, activity and biogeochemical fluxes, the team conducted a redox oscillation study with Luquillo Experimental Forest (LEF), Puerto Rico soils, and preserved samples for molecular analysis and geochemical data (Fe speciation and spectroscopy, P availability, pH, trace gases, and organic matter turnover and fate). In…

Descriptions of soil emissions of reactive nitrogen (NOy) in climate models are underdeveloped or nonexistent, due to the fact that details of the mechanisms leading to nitrous acid (HONO) and nitrogen dioxide (NO2) formation in soil are lacking. This represents a major gap in our understanding of a significant land-atmosphere interaction that prevents us from…

The team aims to understand system-level temporal dynamics of microbial interactions in a synthetic bacterial community. The overarching goal is to understand how the interactions among members of microbial communities determine the emergent properties of the system. Do multi-member microbial communities perform differently, given different membership compositions, then expected by the summation of individual member performances? If…

This proposal aims to explore the genetic diversity of Melampsora americana willow rust in the Northeast United States by performing full de novo Illumina and PacBio sequencing of a representative isolate to act as a reference genome for future analyses. Melampsora spp. rusts remain the most threatening pathogens of Salicaceae bioenergy crops in the Northern…

The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched approximately 10 years ago to systematically fill sequence space in the bacterial and archaeal phylogenetic tree of life. The results from this study had tremendous impact in terms of the reconstruction of phylogenetic histories, the discovery of new protein families, and the prediction of…

The aim is to determine the pangenomes of 100-200 species of soil or plant-associated prokaryotes. While the genome sequence of the type strain captures much of the genotype of a species, the sequence of any single strain also neglects a large part of the genetic diversity. A more complete description of the species is given by…

The team plans de novo sequencing of the (nuclear and organellar) genomes of two species of Zygnematales: Mesotaenium kramstae and Zygnema circumcarinatum. They also aim to conduct transcriptome sequencing (RNA-seq), to facilitate genome annotation, and small RNA sequencing, to study the potential regulatory roles of miRNAs in green algae and to assess whether miRNAs have conserved…