M. B. Sullivan

Ubiquity of inverted 'gelatinous' ecosystem pyramids in the global ocean

The paper quantifies plankton community structure globally, revealing inverted biomass pyramids dominated by gelatinous organisms and predicting future shifts in oceanic carbon cycles.

A functional microbiome catalog crowdsourced from North American rivers

The paper creates GROWdb, a microbiome database from North American rivers, revealing microbial community structures and functional traits across watersheds.

Population ecology and potential biogeochemical impacts of ssDNA and dsDNA soil viruses along a permafrost thaw gradient

The paper analyzes ssDNA and dsDNA soil viruses along a permafrost thaw gradient to assess their ecological roles and biogeochemical impacts on carbon processing.

Abundant deep ocean heterotrophic bacteria are culturable

The paper shows that a significant portion of deep ocean heterotrophic bacteria can be cultured, with isolates matching abundant 16S ASVs in bathypelagic samples.

From genome wide SNPs to genomic islands of differentiation: the quest for species diagnostic markers in two scleractinian corals, Pocillopora and Porites

The paper develops a genotyping method called 'Divergent Fragment' to accurately assign coral samples to species within two genera, using sequencing of a diagnostic genomic fragment from metagenomic data.

Global observation of plankton communities from space

The paper uses satellite data and machine learning to predict global plankton community distributions with 67% accuracy, outperforming temperature and chlorophyll a alone.

Long-read powered viral metagenomics in the oligotrophic Sargasso Sea

This study uses long-read sequencing to analyze viral communities in the Sargasso Sea, identifying new phage populations and highlighting the importance of long reads for viral genome diversity and function.

Quantitative stable-isotope probing (qSIP) with metagenomics links microbial physiology and activity to soil moisture in Mediterranean-climate grassland ecosystems

This study uses qSIP with metagenomics to link microbial activity and physiology to soil moisture in Mediterranean grasslands, finding that precipitation levels influence microbial growth and phage dynamics.

Uncharted biosynthetic potential of the ocean microbiome

This study identifies over 40,000 putative biosynthetic gene clusters in ocean microbes, revealing novel biosynthetic potential and a new candidate genus with diverse metabolic capabilities.

Ocean-wide comparisons of mesopelagic planktonic community structures

This study compares mesopelagic planktonic community structures across different oxygen conditions and identifies environmental drivers and community modules.

Novel integrative elements and genomic plasticity in ocean ecosystems

The paper identifies tycheposons, mobile genetic elements in Prochlorococcus, that drive genomic plasticity through gene exchange and contribute to microbial adaptation in ocean ecosystems.

Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

The paper analyzes plankton genomic distribution across oceans to show how large-scale currents shape biogeography, revealing size-dependent patterns and basin-scale transport effects.

In vitro analysis of colistin and ciprofloxacin antagonism of Pseudomonas aeruginosa phage PEV2 infection activities

This study evaluates how colistin and ciprofloxacin affect the infection activities of Pseudomonas aeruginosa phage PEV2, finding that colistin significantly interferes while ciprofloxacin has minimal impact.

Genome-resolved viral ecology in a marine oxygen minimum zone (OMZ)

This study analyzes viral metagenomes from an OMZ to reveal ecological patterns and diversity, finding low viral diversity and high endemism in anoxic waters.

Environmental vulnerability of the global ocean plankton community interactome

The paper assesses the vulnerability of the global ocean plankton community interactome to environmental change using niche modeling and Tara Oceans data.

VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature

VirION2 improves viral metagenomics by integrating short- and long-read sequencing, enhancing genome recovery and microdiversity detection in low-biomass samples.

Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean

This study links viral community composition to carbon export efficiency in the global ocean, finding that viral marker genes explain 67% of variation in CEE.

Cenote-Taker 2 Democratizes Virus Discovery and Sequence Annotation

Cenote-Taker 2 identifies and annotates viral sequences from contigs, improving virome discovery and database curation.

Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages

The paper identifies 227 auxiliary metabolic genes in 191 phages from twelve environments, showing their role in sulfur and thiosulfate oxidation and ecological impact on biogeochemistry.

Capturing in situ Virus-Host Range and Interaction Dynamics through Gene Fusion with epicPCR

The paper uses epicPCR to study virus-host interactions in the Chesapeake Bay, revealing ecological differences between generalist and specialist viruses.

DRAM for distilling microbial metabolism to automate the curation of microbiome function

DRAM automates microbiome function curation by translating genomic data into microbial traits, accurately assigning metabolic roles in soil and gut communities.

Glacier ice archives fifteen-thousand-year-old viruses

This paper develops clean sampling methods to study microbes and viruses in glacier ice, revealing 33 viral populations including potential novel genera and their associations with bacteria.

Discovery of several thousand highly diverse circular DNA viruses

The paper identifies and characterizes thousands of new circular DNA viruses from animal samples using a bioinformatics pipeline and artificial neural networks.

Metabolic Architecture of the Deep Ocean Microbiome

The paper analyzes deep ocean microbial metagenomes to reveal functional diversity and metabolic strategies in the dark ocean.

Soil viruses are underexplored players in ecosystem carbon processing

This study identifies 53 viral populations in permafrost thawing soils, revealing their ecological diversity and potential role in carbon cycling through host infection and auxiliary metabolic genes.

Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Bacteriophages

The paper evaluates taxonomy methods for bacteriophages using Spounavirinae as a case study, finding they should be divided into at least five subfamilies.

Experimental and Computational Investigation of the Structure of Peptide Monolayers on Gold Nanoparticles

The paper develops a computational model of peptide-capped gold nanoparticles, validated by experiments, revealing new structural features of monolayers.