Jed A Fuhrman

Jed A Fuhrman
University of Southern California | USC · Department of Biological Sciences

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277
Publications
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Publications

Publications (277)
Article
Marine protists form complex communities that are shaped by environmental and biological ecosystem properties, as well as ecological interactions between organisms. While all of these factors play a role in shaping protistan communities, the specific ways in which these properties and interactions influence protistan communities remain poorly under...
Article
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Marine microbial ecologists seek measurements of organismal abundance and diversity at high taxonomic resolution to understand ecosystem state and function. Conventional flow cytometry accurately estimates microbial cell abundance but only discerns broad groups with distinct optical properties. While amplicon sequencing resolves more comprehensive...
Preprint
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Nucleocytoplasmic Large DNA Viruses (NCLDVs, also called giant viruses) are widespread in marine systems and infect a broad range of microbial eukaryotes (protists). Recent biogeographic work has provided global snapshots of NCLDV diversity and community composition across the world's oceans, yet little information exists about the guiding 'rules'...
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Microbial ecological functions are an emergent property of community composition. For some ecological functions this link is strong enough that community composition can be used to estimate the quantity of an ecological function. Here, we apply random forest regression models to compare the predictive performance of community composition and enviro...
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Understanding the patterns of marine microbial diversity (Bacteria + Archaea) is essential, as variations in their alpha‐ and beta‐diversities can affect ecological processes. Investigations of microbial diversity from global oceanographic expeditions and basin‐wide transects show positive correlations between microbial diversity and either tempera...
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Sequence classification facilitates a fundamental understanding of the structure of microbial communities. Binary metagenomic sequence classifiers are insufficient because environmental metagenomes are typically derived from multiple sequence sources. Here we introduce a deep-learning based sequence classifier, DeepMicroClass, that classifies metag...
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Linking sequence-derived microbial taxa abundances to host (patho-)physiology or habitat characteristics in a reproducible and interpretable manner has remained a formidable challenge for the analysis of microbiome survey data. Here, we introduce a flexible probabilistic modeling framework, VI-MIDAS (Variational Inference for MIcrobiome survey DAta...
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Microbial heterotrophs (‘picoheterotrophs’) drive global carbon cycling, but how to quantitatively organize their functional complexity remains unclear. Here, we generate a global-scale, mechanistic understanding of marine picoheterotrophic functional biogeography with a novel model-data synthesis. We build picoheterotrophic diversity into a trait-...
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Biological nitrogen fixation, the conversion of N 2 gas into a bioavailable form, is vital to sustaining marine primary production. Studies have shifted beyond traditionally studied tropical diazotrophs. Candidatus Atelocyanobacterium thalassa (or UCYN-A) has emerged as a focal point due to its streamlined metabolism, intimate partnership with a ha...
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Cyanophages exert important top-down controls on their cyanobacteria hosts; however, concurrent analysis of both phage and host populations is needed to better assess phage–host interaction models. We analyzed picocyanobacteria Prochlorococcus and Synechococcus and T4-like cyanophage communities in Pacific Ocean surface waters using five years of m...
Preprint
Biological nitrogen fixation, the conversion of N2 gas into a more bioavailable form, is vital to sustaining marine primary production. Studies have shifted beyond traditionally studied tropical diazotrophs. Candidatus Atelocyanobacterium thalassa (or UCYN-A) has emerged as a research focal point due to its streamlined metabolism, intimate partners...
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Full-text available
Trait inference from mixed-species assemblages is a central problem in microbial ecology. Frequently, sequencing information from an environment is available, but phenotypic measurements from individual community members are not. With the increasing availability of molecular data for microbial communities, bioinformatic approaches that map metageno...
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Motivation: Phage-host associations play important roles in microbial communities. But in natural communities, as opposed to culture-based lab studies where phages are discovered and characterized metagenomically, their hosts are generally not known. Several programs have been developed for predicting which phage infects which host based on variou...
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Bacteria are single-celled organisms that live out their lives at a microscopic scale. We can find bacteria everywhere we look for them, including inside of our own bodies. Bacteria are incredibly diverse and come in many shapes and sizes. They also vary widely in how they live and grow. Some bacteria grow very quickly and others grow slowly. We wa...
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Basin-scale biogeographic observations of marine pelagic pro- and eukaryotic communities are necessary to understand forces driving community composition and for providing a baseline to monitor global change. Deep sequencing of rRNA genes provides community composition at high resolution; yet, it is unclear how the choice of primers affects biogeog...
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Community dynamics are central in microbial ecology, yet we lack studies comparing diversity patterns among marine protists and prokaryotes over depth and multiple years. Here, we characterized microbes at the San-Pedro Ocean Time series (2005–2018), using SSU rRNA gene sequencing from two size fractions (0.2–1 and 1–80 μm), with a universal primer...
Preprint
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Sequence classification is valuable for reducing the complexity of metagenomes and providing a fundamental understanding of the composition of metagenomic samples. Binary metagenomic classifiers offer an insufficient solution because metagenomes of most natural environments are typically derived from multiple sequence sources including prokaryotes,...
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Small subunit rRNA (SSU rRNA) amplicon sequencing can quantitatively and comprehensively profile natural microbiomes, representing a critically important tool for studying diverse global ecosystems. However, results will only be accurate if PCR primers perfectly match the rRNA of all organisms present. To evaluate how well marine microorganisms acr...
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Universal primers for SSU rRNA genes allow profiling of natural communities by simultaneously amplifying templates from Bacteria, Archaea, and Eukaryota in a single PCR reaction. Despite the potential to show relative abundance for all rRNA genes, universal primers are rarely used, due to various concerns including amplicon length variation and its...
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All known phototrophic metabolisms on Earth are based on one of three energy-converting pigments: chlorophyll- a , bacteriochlorophyll- a , and retinal, which is the chromophore in rhodopsins [1]. While the contribution of chlorophylls to global energy flows and marine carbon cycling has been studied for decades, the role of retinal-based phototrop...
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The ITS protocol detailed here is designed to amplify fungal microbial eukaryotic lineages using paired-end community sequencing on the Illumina platform with primersITS1f-ITS2 (EMP.ITSkabir).
Preprint
Short time-scale observations are valuable for understanding microbial ecological processes. We assessed dynamics in relative abundance and potential activities by sequencing the small sub-unit ribosomal RNA gene (rDNA) and rRNA molecules (rRNA), of Bacteria, Archaea and Eukaryotes once to twice-daily between March and May in the surface ocean off...
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The 16S protocol detailed here is designed to amplify prokaryotes (bacteria and archaea) using paired-end 16S community sequencing on the Illumina platform. Primers515F-806R target the V4 region of the 16S SSU rRNA. For running these libraries on the MiSeq and HiSeq, please make sure you read the supplementary methods of Caporaso et al. (2012). You...
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Aquatic environments contain diverse microbial communities whose complex interactions mediate the cycling of major and trace nutrients such as vitamins. B-vitamins are essential coenzymes that many organisms cannot synthesize. Thus their exchange among de-novo synthesizers and auxotrophs is expected to play an important role in the microbial consor...
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Alignment-free genome and metagenome comparisons are increasingly important with the development of next generation sequencing (NGS) technologies. Recently developed state-of-the-art k-mer based alignment-free dissimilarity measures including CVTree, $d_2^*$ and $d_2^S$ are more computationally expensive than measures based solely on the k-mer freq...
Article
Numerous ecological processes, such as bacteriophage infection and phytoplankton–bacterial interactions, often occur via strain-specific mechanisms. Therefore, studying the causes of microbial dynamics should benefit from highly resolving taxonomic characterizations. We sampled daily to weekly over 5 months following a phytoplankton bloom off South...
Article
Marine Thaumarchaeota are abundant ammonia-oxidizers but have few representative laboratory-cultured strains. We report the cultivation of Candidatus Nitrosomarinus catalina SPOT01, a novel strain that is less warm-temperature tolerant than other cultivated Thaumarchaeota. Using metagenomic recruitment, strain SPOT01 comprises a major portion of Th...
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Background The study of virus-host infectious association is important for understanding the functions and dynamics of microbial communities. Both cellular and fractionated viral metagenomic data generate a large number of viral contigs with missing host information. Although relative simple methods based on the similarity between the word frequenc...
Article
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Viruses and their host genomes often share similar oligonucleotide frequency (ONF) patterns, which can be used to predict the host of a given virus by finding the host with the greatest ONF similarity. We comprehensively compared 11 ONF metrics using several k-mer lengths for predicting host tax-onomy from among ∼32 000 prokaryotic genomes for 1427...
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With high-throughput sequencing (HTS), we are able to explore the hidden world of microscopic organisms to an unpre-cedented level. The fast development of molecular technology and statistical methods means that microbial ecologists must keep their toolkits updated. Here, we review and evaluate some of the more widely adopted and emerging technique...
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Motivation: The advent of next-generation sequencing (NGS) technologies enables researchers to sequence complex microbial communities directly from environment. Since assembly typically produces only genome fragments, also known as contigs, instead of entire genome, it is crucial to group them into operational taxonomic units (OTUs) for further ta...
Preprint
Full-text available
The advent of next-generation sequencing (NGS) technologies enables researchers to sequence complex microbial communities directly from environment. Since assembly typically produces only genome fragments, also known as contigs, instead of entire genome, it is crucial to group them into operational taxonomic units (OTUs) for further taxonomic profi...
Article
Marine phytoplankton perform approximately half of global carbon fixation, with their blooms contributing disproportionately to carbon sequestration1, and most phytoplankton production is ultimately consumed by heterotrophic prokaryotes2. Therefore, phytoplankton and heterotrophic community dynamics are important in modelling carbon cycling and the...
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Disruption of healthy microbial communities has been linked to numerous diseases, yet microbial interactions are little understood. This is due in part to the large number of bacteria, and the much larger number of interactions (easily in the millions), making experimental investigation very difficult at best and necessitating the nascent field of...
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Marine viruses are critical drivers of ocean biogeochemistry, and their abundances vary spatiotemporally in the global oceans, with upper estimates exceeding 108 per ml. Over many years, a consensus has emerged that virus abundances are typically tenfold higher than microbial cell abundances. However, the true explanatory power of a linear relation...
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We continue to uncover a wealth of information connecting microbes in important ways to human and environmental ecology. As our scientific knowledge and technical abilities improve, the tools used for microbiome surveys can be modified to improve the accuracy of our techniques, ensuring that we can continue to identify groundbreaking connections be...
Article
Proteorhodopsins (PR) are light-driven proton pumps widely distributed in bacterioplankton. Although they have been thoroughly studied for more than a decade, it is still unclear how the proton motive force (pmf) generated by PR is used in most organisms. Notably, very few PR-containing bacteria show growth enhancement in the light. It has been sug...
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Background: Local trend (i.e. shape) analysis of time series data reveals co-changing patterns in dynamics of biological systems. However, slow permutation procedures to evaluate the statistical significance of local trend scores have limited its applications to high-throughput time series data analysis, e.g., data from the next generation sequenc...
Article
Microbial community analysis via high-throughput sequencing of amplified 16S rRNA genes is an essential microbiology tool. We found the popular primer pair 515F (515F-C) and 806R greatly underestimated (e.g. SAR11) or overestimated (e.g. Gammaproteobacteria) common marine taxa. We evaluated marine samples and mock communities (containing 11 or 27 m...
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The diversity of diazotrophs was studied in the sediment of mangrove forests (Twin Cays, Belize) subjected to a long-term fertilization with nitrogen and phosphorus. Terminal Restriction Fragment Length Polymorphism (TRFLP) and cloning of PCR-amplified nifH genes were combined via in silico analysis to assign clones to TRFLP-nifH phylotypes, as wel...
Article
Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a singl...
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Interactions among microbes and stratification across depths are both believed to be important drivers of microbial communities, though little is known about how microbial associations differ between and across depths. We have monitored the free-living microbial community at the San Pedro Ocean Time-series station, monthly, for a decade, at five di...
Article
Recent advances in studying the dynamics of marine microbial communities have shown that the composition of these communities follows predictable patterns and involves complex network interactions, which shed light on the underlying processes regulating these globally important organisms. Such 'holistic' (or organism- and system-based) studies of t...
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Viral lysis of microbial hosts releases organic matter that can then be assimilated by nontargeted microorganisms. Quantitative estimates of virus-mediated recycling of carbon in marine waters, first established in the late 1990s, were originally extrapolated from marine host and virus densities, host carbon content and inferred viral lysis rates....
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Microbial activities that affect global oceanographic and atmospheric processes happen throughout the water column, yet the long-term ecological dynamics of microbes have been studied largely in the euphotic zone and adjacent seasonally mixed depths. We investigated temporal patterns in the community structure of free-living bacteria, by sampling a...
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The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of g...
Chapter
Microbial biogeography examines the distribution of microorganisms over space and time, shedding light on the relative importance of the ecological and evolutionary processes that lead to those distributions. This “map” of microbial diversity also aids in predicting the response of microbes, and the ecosystem processes they mediate, to changing env...
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Characterizing ecological relationships between viruses, bacteria and protists in the ocean are critical to understanding ecosystem function, yet these relationships are infrequently investigated together. We evaluated these relationships through microbial association network analysis of samples collected approximately monthly from March 2008 to Ja...
Article
Factors controlling the spatial distribution of bacterial diversity have been intensely studied, whereas less is known about temporal changes. To address this, we tested whether the mechanisms that underlie bacterial temporal beta-diversity vary across different scales in three marine microbial communities. While seasonal turnover was detected, at...
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Full-text available
Time-series are critical to understanding long-term natural variability in the oceans. Bacterial communities in the euphotic zone were investigated for over a decade at the San Pedro Ocean Time-series station (SPOT) off southern California. Community composition was assessed by Automated Ribosomal Intergenic Spacer Analysis (ARISA) and coupled with...
Article
An inter-laboratory study of the accuracy of microbial source tracking (MST) methods was conducted using challenge fecal and sewage samples that were spiked into artificial freshwater and provided as unknowns (blind test samples) to the laboratories. The results of the Source Identification Protocol Project (SIPP) are presented in a series of paper...
Article
To test whether within-species and among-species patterns of abundance and latitudinal range in marine bacteria resemble those found for macro-organisms, and whether these patterns differ along latitudinal clines. Global pelagic marine environments. Taxon-specific sequence abundance and location were retrieved from the open-access V6-rRNA pyrotag s...
Data
Accession numbers of rhodopsin protein sequences in Figure 2. (DOCX)
Data
Summary of genomic DNA sequencing (A) and fosmid sequencing (B). (DOCX)
Data
Overview of strains encoding rhodopsin homologues related to the second rhodopsin in PRO95. (DOCX)
Data
Genes acquired by lateral gene transfer. (XLSX)
Data
Accession numbers of sequences in Figure 3. (DOCX)
Article
Full-text available
Proteorhodopsin (PR) photoheterotrophy in the marine flavobacterium Dokdonia sp. PRO95 has previously been investigated, showing no growth stimulation in the light at intermediate carbon concentrations. Here we report the genome sequence of strain PRO95 and compare it to two other PR encoding Dokdonia genomes: that of strain 4H-3-7-5 which shows th...
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Observation of short-term temporal variation in bacterial and viral communities is important for understanding patterns of aquatic microbial diversity. We collected surface seawater once daily for 38 consecutive days with seven more samples interspersed over 40 more days at one location ∼2 km from Santa Catalina Island, California. Bacterial commun...
Article
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Motivation: Local similarity analysis of biological time series data helps elucidate the varying dynamics of biological systems. However, its applications to large scale high-throughput data are limited by slow permutation procedures for statistical significance evaluation. Results: We developed a theoretical approach to approximate the statisti...
Article
Full-text available
Microbes dominate most global biogeochemical cycles, and microbial metagenomics (studying the collective microbial genomes) provides invaluable new insights into microbial systems, independent of cultivation. Metagenomic approaches targeting specific genes, e.g. small subunit (ssu) ribosomal RNA (rRNA), can be used to investigate microbial communit...