John Heidelberg

About

Dr. John Heidelberg is a Professor of Biological Sciences and Environmental Studies at USC Dornsife. His research focuses on microbial genomics, specifically studying the metabolic potential of common and abundant marine bacteria through DNA sequencing. He employs advanced DNA sequencing technologies to analyze the genomes of uncultured bacteria, which cannot be studied using traditional microbiological techniques due to the inability to bring most bacteria into pure culture. His work contributes to understanding microbial communities in marine environments, including their energy acquisition mechanisms and ecological roles in oceanic systems.

Research topics

• Biology
• Genetics
• Ecology
• Oceanography
• Geology
• History
• Evolutionary biology
• Zoology
• Microbiology
• Biochemistry

Selected publications

• The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans

  Scientific Data · 2018-01-16 · 576 citations

  articleOpen accessSenior author

  Microorganisms play a crucial role in mediating global biogeochemical cycles in the marine environment. By reconstructing the genomes of environmental organisms through metagenomics, researchers are able to study the metabolic potential of Bacteria and Archaea that are resistant to isolation in the laboratory. Utilizing the large metagenomic dataset generated from 234 samples collected during the Tara Oceans circumnavigation expedition, we were able to assemble 102 billion paired-end reads into…

  PublisherOA PDFDOI

• Potential for primary productivity in a globally-distributed bacterial phototroph

  The ISME Journal · 2018-03-05 · 310 citations

  articleOpen access

  Aerobic anoxygenic phototrophs (AAnPs) are common in marine environments and are associated with photoheterotrophic activity. To date, AAnPs that possess the potential for carbon fixation have not been identified in the surface ocean. Using the Tara Oceans metagenomic dataset, we have identified draft genomes of nine bacteria that possess the genomic potential for anoxygenic phototrophy, carbon fixation via the Calvin-Benson-Bassham cycle, and the oxidation of sulfite and thiosulfate. Forming a…

  PublisherOA PDFDOI

• BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation

  PeerJ · 2017-03-08 · 206 citations

  articleOpen access

  Metagenomics has become an integral part of defining microbial diversity in various environments. Many ecosystems have characteristically low biomass and few cultured representatives. Linking potential metabolisms to phylogeny in environmental microorganisms is important for interpreting microbial community functions and the impacts these communities have on geochemical cycles. However, with metagenomic studies there is the computational hurdle of 'binning' contigs into phylogenetically related…

  PublisherDOI

• 290 metagenome-assembled genomes from the Mediterranean Sea: a resource for marine microbiology

  PeerJ · 2017-07-10 · 99 citations

  articleOpen accessSenior author

  Expedition has provided large, publicly-accessible microbial metagenomic datasets from a circumnavigation of the globe. Utilizing several size fractions from the samples originating in the Mediterranean Sea, we have used current assembly and binning techniques to reconstruct 290 putative draft metagenome-assembled bacterial and archaeal genomes, with an estimated completion of ≥50%, and an additional 2,786 bins, with estimated completion of 0-50%. We have submitted our results, including initial…

  PublisherDOI

• Effects of depth-cycling on nutrient uptake and biomass production in the giant kelp Macrocystis pyrifera

  Renewable and Sustainable Energy Reviews · 2021 · 51 citations

  Seasonal or chronic nutrient limitations in the photic zone limit large-scale cultivation of seaweed (macroalgae) in much of the world's oceans, hindering the development of macroalgae as a biofuel feedstock. One possible solution is to supply nutrients using a diel depth-cycling approach, physically moving the macroalgae between deep nutrient-rich water at night and shallow depths within the photic zone during the day. This study tested the effects of depth-cycling on the growth, morphology, an…

  PublisherDOI

Recent grants

• Collaborative Proposal: Are abundant bacteria more active than rare bacteria in the Sargasso Sea?

  NSF · $337k · 2008–2013

• NIH Grant U01AI049034

  NIH · $608k · 2002

Frequent coauthors

• William Nelson

  Pacific Northwest National Laboratory

  166 shared

• Jonathan A. Eisen

  106 shared

• Claire M. Fraser

  University of Maryland, Baltimore

  93 shared

• Robert J. Dodson

  83 shared

• Robert T. DeBoy

  University of Maryland, Baltimore

  80 shared

• Ian T. Paulsen

  Macquarie University

  72 shared

• Ramana Madupu

  J. Craig Venter Institute

  66 shared

• R. Seshadri

  65 shared

Education

• PhD, Marine-Estuarine-Environmental Sciences

  University of Maryland

  1997

• BA, Biology

  Maryville College

  1987

Similar researchers at University of Southern California

• David J. Bottjerh-83
• Joe Arvaih-42
• Karla Heidelbergh-34