Author

J. A. Fuhrman

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

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Microbiology· 7 Ecology· 3

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Assay:metagenomics· 7 Approach:statistical model· 6 Approach:experimental assay· 5 Research Focus:ecology & biodiversity· 3 Organism:bacteria (other)· 2 Research Focus:benchmarking· 2 Research Focus:host-pathogen & immune response· 2 Assay:bulk RNA-seq· 1

Frequent Co-Authors

D. M. Needham· 3 shared J. L. Weissman· 3 shared S. Hou· 3 shared E. B. Fichot· 2 shared J. C. McNichol· 2 shared J. Weissman· 2 shared S. Laperriere· 2 shared Y.-C. Yeh· 2 shared

Activity by Year

2018-2024 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 20 mutual co-author links

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3 shared papersMicrobiology

D. M. Needham

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Author profile →

10 papers

Recent·Most cited

Functional biogeography of marine microbial heterotrophs

E. J. Zakem, J. McNichol, J. L. Weissman, Y. Raut, L. Xu, E. R. Halewood, C. A. Carlson, S. Dutkiewicz, J. A. Fuhrman, N. M. Levine

The paper synthesizes genetic data with a marine ecosystem model to analyze functional biogeography of marine heteroprokaryotes, identifying key ecological factors shaping their distribution.

bioRxiv · Feb 14, 2024Ecology

Estimating global variation in the maximum growth rates of eukaryotic microbes from cultures and metagenomes via codon usage patterns

J. Weissman, E.-R. O. Dimbo, A. I. Krinos, C. Neely, Y. Yagues, D. Nolin, S. Hou, S. Laperriere, D. A. Caron, B. L. Tully, H. Alexander, J. A. Fuhrman

The paper estimates maximum growth rates of eukaryotic microbes using codon usage patterns from genomes and metagenomes, revealing differences in growth potential between prokaryotic and eukaryotic communities in marine environments.

bioRxiv · Oct 15, 2021 · PreprintMicrobiology

Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns

J. L. Weissman, S. Hou, J. A. Fuhrman

This paper develops a method to estimate microbial maximal growth rates using codon usage patterns and applies it to over 200,000 genomes, revealing biases in culture collections towards fast-growing organisms.

Proceedings of the National Academy of Sciences · Mar 15, 2021Peer-reviewedMicrobiology

Evaluating and Improving SSU rRNA PCR Primer Coverage for Bacteria, Archaea, and Eukaryotes Using Metagenomes from Global Ocean Surveys

J. C. McNichol, P. M. Berube, S. J. Biller, J. A. Fuhrman

This paper evaluates marine PCR primers for SSU rRNA and 18S rRNA across bacteria, archaea, and eukaryotes using global ocean metagenomes, finding that 515Y/926R performs best overall and proposing improvements for universal primer sets.

bioRxiv · Nov 9, 2020Ecology

Ribosome-linked mRNA-rRNA chimeras reveal active novel virus-host associations.

J. C. Ignacio-Espinoza, S. Laperriere, Y.-C. Yeh, J. Weissman, S. Hou, A. Long, J. A. Fuhrman

The paper links marine viral gene expression to specific hosts using mRNA-rRNA chimeras, identifying novel virus-host associations and validating the method's accuracy.

bioRxiv · Oct 30, 2020 · PreprintMicrobiology

Immune Lag Is a Major Cost of Prokaryotic Adaptive Immunity During Viral Outbreaks

J. L. Weissman, E. O. Alseth, S. Meaden, E. R. Westra, J. A. Fuhrman

The paper shows that immune lag during viral outbreaks is costly for prokaryotes, even for completely immune hosts, by analyzing host-virus dynamics.

bioRxiv · Sep 30, 2020Microbiology

Comprehensive single-PCR 16S and 18S rRNA community analysis validated with mock communities and denoising algorithms

Y.-C. Yeh, J. C. McNichol, D. M. Needham, E. B. Fichot, J. A. Fuhrman

The paper validates universal 16S and 18S rRNA primers for comprehensive microbial community profiling using mock communities and shows their effectiveness over eukaryote-specific primers.

bioRxiv · Dec 6, 2019 · PreprintMicrobiology

Metagenomics and stable isotope probing offer insights into metabolism of polycyclic aromatic hydrocarbons degraders in chronically polluted seawater

E. T. Sieradzki, M. Morando, J. A. Fuhrman

The paper investigates PAH-degrading communities in chronically polluted seawater using metagenomics and stable isotope probing, revealing a shift from generalist to specialized degraders and highlighting gaps in PAH degradation pathways.

bioRxiv · Sep 23, 2019 · PreprintMicrobiology

Influence of light on particulate organic matter utilization by attached and free-living marine bacteria

L. Gomez-Consarnau, D. M. Needham, P. K. Weber, J. A. Fuhrman, X. Mayali

This study shows light affects particle degradation and C/N incorporation by marine bacteria, altering microbial community structure and metabolism.

bioRxiv · Jan 31, 2019Ecology

Dynamics and interactions of highly resolved marine plankton via automated high frequency sampling

D. M. Needham, E. B. Fichot, E. Wang, L. Berdjeb, J. A. Cram, C. G. Fichot, J. A. Fuhrman

The paper uses high-frequency rRNA gene and rRNA sequencing to study marine plankton dynamics and interactions, revealing rapid responses and ecological correlations.

bioRxiv · Mar 23, 2018Microbiology