About

Jeffrey L. Blanchard is an Associate Professor in the Department of Biology at the University of Massachusetts Amherst. His research focuses on microbiome science, utilizing genomic and computational methods to understand the ecology and evolution of gut and forest soil microbiomes. His laboratory is equipped for standard molecular biology and microbial physiology research, with specialized equipment for isolating and culturing anaerobic bacteria. A major component of his research involves studying soil community changes resulting from long-term soil warming experiments at the Harvard Forest. His work has led to the discovery of new bacterial species and metabolic processes, contributing to fields such as probiotics and climate change understanding. Blanchard's academic background includes a B.S. in Biology from Worcester Polytechnic Institute and a Ph.D. in Botany from the University of Georgia.

Research topics

• Computational biology
• Biology
• Genetics
• Evolutionary biology
• Computer Science
• Astronomy
• Ecology
• Physics
• Library science

Selected publications

• Project Assessment for Biological and Environmental Research: Report from the BER Advisory Committee

  2024-05-01

  reportOpen access

  The construction, operation, and stewardship of large-scale scientific user facilities and cutting edge capabilities have been integral to the mission of the U.S. Department of Energy (DOE) Office of Science from its earliest days. To help identify and prioritize new or upgraded facilities critical to scientific innovation over the next 10 years, the Office of Science director issued a charge to the federal advisory committees of six of its program offices in December 2023, including the Biological and Environmental Research (BER) program. The charge letter (see p. ii) asked the advisory committees to: 1. Consider what new or upgraded facilities will be necessary to position the Office of Science at the forefront of scientific discovery. 2. Deliver a short letter report describing each facility in terms of two criteria: (a) the potential to contribute to world-leading science in the next decade and (b) the readiness for construction.

  PublisherOA PDFDOI

• From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology

  Environmental Microbiome · 2024-08-02 · 33 citations

  letterOpen accessSenior authorCorresponding

  Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.

  PublisherOA PDFDOI

• A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts

  Nature Microbiology · 2024-06-20 · 85 citations

  articleOpen access

  Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities and interactions with the soil microbiome remains limited. Here we present the Global Soil Virus Atlas, a comprehensive dataset compiled from 2,953 previously sequenced soil metagenomes and composed of 616,935 uncultivated viral genomes and 38,508 unique viral operational taxonomic units. Rarefaction curves from the Global Soil Virus Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared viral operational taxonomic units across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents an extensive characterization of soil viral diversity and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry.

  PublisherOA PDFDOI

• Solar-powered hydroponic radish garden - A senior student project

  Energies and quality journal. · 2024-07-01

  articleOpen access

  The global population has increased by 25.8% in the last 20 years and currently stands at over 8 billion. New and innovative techniques will be required to continue feeding the world and avoid malnutrition. Hydroponic and vertical farming are promising tools for achieving this goal. These tools allow for food production in a controlled environment without using soil. Although currently more expensive than conventional farming, they offer food production in a well-controlled environment. The plants are continuously monitored and adjustments in temperature, relative humidity, pH and nutrient composition are made as needed. Other benefits include relative immunity to weather conditions, pests and water contamination. Additionally, water consumption is minimized. This article reports the results of a senior-student project, the objectives of which were to design, build and test a small hydroponic system utilizing renewable energy to grow French dressing radishes. The constraints included a minimum yield of 1 kg per m2 of footprint (in 3 months), fully automatic irrigation pump/fertilization and fully solar/battery powered system. The total cost was limited to USD 250. Key words. Hydroponic Farming, Hydroponic Radishes, Solar Powered Pump

  PublisherOA PDFDOI

• Carboxysomes, Structure and Function

  Encyclopedia of Astrobiology · 2023-01-01

  book-chapter1st authorCorresponding
  PublisherDOI

• Amazing structural diversity of giant virus-like particles in forest soil

  bioRxiv (Cold Spring Harbor Laboratory) · 2023-06-30 · 19 citations

  preprintOpen accessSenior author

  Abstract Large DNA viruses of the phylum Nucleocytoviricota infect diverse eukaryotic hosts from protists to humans, with profound consequences for aquatic and terrestrial ecosystems. While nucleocytoviruses are known to be highly diverse in metagenomes, knowledge of their capsid structures is restricted to a few characterized representatives. Here, we visualize giant virus-like particles (VLPs, diameter >0.2 µm) directly from the environment using transmission electron microscopy. We found that Harvard Forest soils contain a higher diversity of giant VLP morphotypes than all hitherto isolated giant viruses combined. These included VLPs with icosahedral capsid symmetry, ovoid shapes similar to pandoraviruses, and bacilliform shapes that may represent novel viruses. We discovered giant icosahedral capsids with structural modifications that had not been described before including tubular appendages, modified vertices, tails, and capsids consisting of multiple layers or internal channels. Many giant VLPs were covered with fibers of varying lengths, thicknesses, densities, and terminal structures. These findings imply that giant viruses employ a much wider array of capsid structures and mechanisms to interact with their host cells than is currently known. We also found diverse tailed bacteriophages and filamentous VLPs, as well as ultra-small cells. Our study offers a first glimpse of the vast diversity of unexplored viral structures in soil and reinforces the potential of transmission electron microscopy for fundamental discoveries in environmental microbiology.

  PublisherOA PDFDOI

• Data Carpentry Genomics Curriculum Example Data

  Figshare · 2023-01-01

  datasetOpen access

  p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 16.0px 'Andale Mono'; color: #29f914; background-color: #000000} span.s1 {font-variant-ligatures: no-common-ligatures} These files are intended for use with the Data Carpentry Genomics curriculum (https://datacarpentry.org/genomics-workshop/). Files will be useful for instructors teaching this curriculum in a workshop setting, as well as individuals working through these materials on their own. <br> This curriculum is normally taught using Amazon Web Services (AWS). Data Carpentry maintains an AWS image that includes all of the data files needed to use these lesson materials. For information on how to set up an AWS instance from that image, see https://datacarpentry.org/genomics-workshop/setup.html. Learners and instructors who would prefer to teach on a different remote computing system can access all required files from this FigShare dataset. <br> This curriculum uses data from a long term evolution experiment published in 2016: Tempo and mode of genome evolution in a 50,000-generation experiment (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4988878/) by Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL, Dasgupta A, Wu GC, Wielgoss S, Cruveiller S, Médigue C, Schneider D, and Lenski RE. (doi: 10.1038/nature18959). All sequencing data sets are available in the NCBI BioProject database under accession number PRJNA294072 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA294072). <br> backup.tar.gz: contains original fastq files, reference genome, and subsampled fastq files. Directions for obtaining these files from public databases are given during the lesson https://datacarpentry.org/wrangling-genomics/02-quality-control/index.html). On the AWS image, these files are stored in <code>~/.backup</code> directory. 1.3Gb in size. <br> Ecoli_metadata.xlsx: an example Excel file to be loaded during the R lesson. <br> shell_data.tar.gz: contains the files used as input to the Introduction to the Command Line for Genomics lesson (https://datacarpentry.org/shell-genomics/). <br> sub.tar.gz: contains subsampled fastq files that are used as input to the Data Wrangling and Processing for Genomics lesson (https://datacarpentry.org/wrangling-genomics/). 109Mb in size. <br> solutions: contains the output files of the Shell Genomics and Wrangling Genomics lessons, including <code>fastqc</code> output, sam, bam, bcf, and vcf files. <br> vcf_clean_script.R: converts vcf output in .solutions/wrangling_solutions/variant_calling_auto to single tidy data frame.<br> <br> combined_tidy_vcf.csv: output of vcf_clean_script.R <br>

  PublisherDOI

• Unraveling the functional dark matter through global metagenomics

  Nature · 2023 · 193 citations

  • Computational biology
  • Evolutionary biology
  • Biology

  . Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.

  PublisherOA PDFDOI

• Expansion of the global RNA virome reveals diverse clades of bacteriophages

  Cell · 2022 · 294 citations

  • Biology
  • Genetics
  • Evolutionary biology
  PublisherOA PDFDOI

• Thousands of small, novel genes predicted in global phage genomes

  Cell Reports · 2022 · 55 citations

  • Biology
  • Computational biology
  • Genetics

  Small genes (<150 nucleotides) have been systematically overlooked in phage genomes. We employ a large-scale comparative genomics approach to predict >40,000 small-gene families in ∼2.3 million phage genome contigs. We find that small genes in phage genomes are approximately 3-fold more prevalent than in host prokaryotic genomes. Our approach enriches for small genes that are translated in microbiomes, suggesting the small genes identified are coding. More than 9,000 families encode potentially secreted or transmembrane proteins, more than 5,000 families encode predicted anti-CRISPR proteins, and more than 500 families encode predicted antimicrobial proteins. By combining homology and genomic-neighborhood analyses, we reveal substantial novelty and diversity within phage biology, including small phage genes found in multiple host phyla, small genes encoding proteins that play essential roles in host infection, and small genes that share genomic neighborhoods and whose encoded proteins may share related functions.

  PublisherOA PDFDOI

Recent grants

• I-Corps: Probiotics to Prevent Metabolic Changes Associated with Starch Induced Laminitis

  NSF · $50k · 2013–2015

Frequent coauthors

• Nikos C. Kyrpides

  Joint Genome Institute

  15 shared

• Richard E. Lenski

  Michigan United

  14 shared

• Tanja Woyke

  University of California, Santa Barbara

  13 shared

• Petr Baldrián

  Czech Academy of Sciences, Institute of Microbiology

  12 shared

• Thomas Möck

  University of East Anglia

  11 shared

• Olivier Tenaillon

  Université Paris Cité

  11 shared

• Dana E. Hunt

  University of South Carolina Beaufort

  11 shared

• Natalia Ivanova

  Joint Genome Institute

  11 shared

Education

• B.S.

  Worcester Polytechnic Institute

  1987

• Other

  Vermont Technical College

  1983

• Ph.D., Botany

  University of Georgia

  1995