Biology subjects

Paerl, R. W.

Publications and source records attributed to Paerl, R. W..

3 recordsLinked to original sources

bioRxiv2026

Quantitative metagenomics reveals fine-scale population dynamics across bacteria, archaea, and microbial eukaryotes in an estuarine-coastal continuum

Microbial communities are foundational to marine ecosystem function, yet their diversity is often obscured by broad taxonomic groupings and relative-abundance surveys that mask the dynamics of individual populations. This limitation is especially important across estuarine-coastal gradients, where microbial standing stocks, environmental conditions, and community composition vary sharply over space and time. Here, we used quantitative, genome-resolved metagenomics to examine microbial population dynamics across a one-year estuary-to-ocean transect spanning the Neuse River Estuary, Pamlico Sound, and adjacent North Atlantic shelf waters. Internal standard normalization enabled absolute abundance estimates for single-copy genes and metagenome-assembled genomes (MAGs), allowing individual populations to be tracked as genome equivalents per liter. Bacterial standing stocks were higher in estuarine waters, and communities varied primarily with salinity and season. We recovered 415 MAGs, including 386 bacterial genomes that represented, on average, 52% of bacterial genome equivalents, along with archaeal and eukaryotic representatives. Many abundant MAGs lacked close reference genomes, demonstrating that numerically important coastal populations remain poorly characterized. Genome-resolved abundances revealed pronounced niche partitioning among closely related taxa, including seasonal and spatial turnover of Synechococcus, Cyanobium, and Vulcanococcus populations associated with distinct pigment-defined cytometric groups. Rhodobacteraceae MAGs also showed population-specific correlations with picoeukaryotic MAGs, including a winter offshore Planktomarina population that reached 18% of total bacterial genome equivalents during a Micromonas-associated bloom. By providing absolute population abundances, this study transformed coastal microbiome surveys into numerical frameworks for resolving microbial population structure, ecological interactions, and biogeochemical relevance across dynamic environmental gradients. IMPORTANCEEstuarine and coastal waters contain diverse microbial communities that help regulate food webs and the cycling of carbon and nutrients, but many of the individual microbial populations responsible for these processes remain poorly understood. In this study, we examined bacteria, archaea, and small algae across the Neuse River Estuary, Pamlico Sound, and nearby coastal ocean waters over one year. By measuring the absolute abundance of individual microbial genomes, rather than only their relative proportions, we showed that closely related populations can have very different seasonal and spatial patterns. This was especially clear for cyanobacteria related to Synechococcus and heterotrophic bacteria in the family Rhodobacteraceae, which showed distinct population dynamics and associations with small algae. These results demonstrate how quantitative genome-resolved measurements can reveal hidden microbial population structure and improve our understanding of how microorganisms shape coastal ecosystem function.

genomics↗

bioRxiv2026

Novel connections between B-vitamins and microbial communities along biogeochemical gradients in a large temperate estuary

As B-vitamins are organic cofactors required by prokaryotic and eukaryotic planktonic cells, their availability impacts aquatic microbial communities and associated biogeochemistry. Contrary to inorganic nutrients, measurements of B-vitamins from brackish systems are scarce and relationships between B-vitamins and plankton composition in estuaries are unclear, limiting our understanding of estuary biology in general as well as how B-vitamins are distributed and dispersed in marine systems. Here, we quantify multiple B-vitamins and their vitamers in particulate and dissolved phases, and characterize microbial community composition, across fresh to polyhaline zones of the Neuse River Estuary (NRE), North Carolina, USA. We uncover elevated concentrations of B-vitamins within the mid-estuary, Chlorophyll a maximum along with a unique suite of dissolved B-vitamin associated with sporadic surges in pico- and microplankton populations. The dynamics of both dissolved and particulate B-vitamin concentrations in space and time were striking - from subpicomolar to high picomolar levels observed and strong short-term (weeks) variability. We find notable autochtonous B-vitamin production in the estuary, but we expect the ability of the system to deliver these micronutrients to the ocean will depend on flushing as well as changes in microbial community. We identify vitamin B1, B12, psB12 (pseudocobalamin), and B3 as key explanatory variables for change in prokaryotic and eukaryotic NRE plankton, providing new evidence of B-vitamin influence upon estuarine plankton community composition. Our work reveals new complexities in B-vitamin production and consumption within zones of estuaries while underscoring these micronutrients as key drivers of microbial plankton composition.

ecology↗

bioRxiv2021

The exchange of vitamin B1 and its biosynthesis intermediates in synthetic microbial communities shapes the community composition and reveals complexities of nutrient sharing

Microbial communities occupy diverse niches in nature, and exchanges of metabolites such as carbon sources, amino acids, and vitamins occur routinely among the community members. While large-scale metagenomic and metabolomic studies shed some light on these exchanges, the contribution of individual species and the molecular details of specific interactions are difficult to track. Here, we explore the molecular picture of vitamin B1 (thiamin) metabolism occurring in synthetic communities of Escherichia coli thiamin auxotrophs which engage in the exchange of thiamin and its biosynthesis intermediates. In E. coli, the two parts of thiamin - the 4-amino-5-hydroxymethyl-2-methylpyrimidine and the 4-methyl-5-(2-hydroxyethyl)thiazole - are synthesized by separate pathways using enzymes ThiC and ThiG, respectively, and are then joined by ThiE to form thiamin. We observed that even though E. coli {Delta}thiC, {Delta}thiE, and{Delta} thiG mutants are thiamin auxotrophs, co-cultures of{Delta} thiC-{Delta}thiE and{Delta} thiC-{Delta}thiG grow in a thiamin-deficient minimal medium, whereas the{Delta} thiE-{Delta}thiG co-culture does not. Analysis of the exchange of thiamin and its intermediates in Vibrio anguillarum co-cultures, and in mixed co-cultures of V. anguillarum and E. coli revealed that the general pattern of thiamin metabolism and exchange among microbes is conserved across species. Specifically, the microorganisms exchange HMP and thiamin easily among themselves but not THZ. Furthermore, we observe that the availability of exogenous thiamin in the media affects whether these strains interact with each other or grow independently. This underscores the importance of the exchange of essential metabolites as a defining factor in building and modulating synthetic or natural microbial communities.

microbiology↗