Biology subjects

Coelho, J. T.

Publications and source records attributed to Coelho, J. T..

6 recordsLinked to original sources

bioRxiv2026

Enrichment of polyphenol metabolism within the ubiquitous SAR116 Puniceispirillales bacterioplankton

Marine dissolved organic matter (DOM) is a complex pool of substrates, and a central challenge in marine biogeochemistry is to determine which DOM compounds are produced, consumed, or exchanged by microorganisms. Aromatic compounds, including polyphenols, comprise an important chemical class of marine DOM generated both in situ and also supplied via atmospheric deposition, terrestrial runoff, or natural seeps. Here we demonstrate, through pangenomics and metabolic reconstruction, the enrichment of genes for degradation of a wide variety of polyphenols in the cosmopolitan SAR116 bacterioplankton (Puniceispirillales). Gene and pathway conservation, the evolutionary history of key ring-cleaving dioxygenases, and expression patterns from global ocean surveys support the conclusion that these transformations represent core elements of SAR116 ecophysiology. The degradation pathway for protocatechuate, an end member for many polyphenol transformations, occurred in all subclades, and we found evidence of different evolutionary histories for genes in this pathway, including gene loss, analogous substitution, and retention of horizontally transferred genes from the Gammaproteobacteria. Furthermore, variation in these and other pathway-specific gene losses suggest that some SAR116 polyphenol metabolism may occur through a division of labor in concert with other community members and/or require novel or promiscuous enzymes. The enrichment and expression of polyphenol degradation pathways define a previously underappreciated metabolic niche for SAR116 and provides new evidence emphasizing the importance of polyphenol metabolism in the marine carbon cycle.

microbiology↗

bioRxiv2025

Detergent-based separation of microbes from marine particles

Marine particles, typically composed of organic detritus and cellular debris, harbor microbial communities that are distinct from the planktonic, or free-living, communities in the pelagic ocean. However, without being first separated from the particle and microbial consortia, these microbes are inaccessible to further investigation via single-cell microbiology methods like flow cytometry, cell-sorting, and dilution-based isolation. To confront this obstacle, we compared the dissociative effects of two commonly used detergents, Tween20 and Tween80, on particle-associated marine microbial communities. The ability of Tween treatments to liberate cells from particles, and to maintain cell integrity, was quantified by flow cytometry from multiple communities across seasons and locations. Both Tween20 and Tween80, at 185 RPM shaking, gently dissociated microbes from their particles, causing very little cell mortality. Additionally, Tween80 liberated a greater number of particle-associated cells into the free-living fraction. We also analyzed the effects of Tween treatments on the microbial community composition for one of these collections via 16S rRNA gene amplicon sequencing of the particle-associated and free-living fractions relative to unamended controls. Tween20 and Tween80 were both effective for microbial dissolution from particles, however Tween80 treatments displayed greater uniformity in the dissociated communities and significantly enriched for the most abundant particle-associated members. Together these data indicate that Tween80 was most effective at gently dissociating particle-associated cells. ImportanceMicrobes that reside on marine particulate organic matter are vital facets of marine biogeochemistry. As they degrade the particle on which they reside, the resulting concentrated region of activity influences surrounding biogeochemistry and redox gradients, making particle-associated microbes significant to overall marine ecology. To understand single-cell activities amidst the microbial assemblage on the particle, cells must first be removed from the substrate for downstream analyses. Methods for microbial dissociation from solid surfaces or sediment communities have been described, however, analogous methods for more ephemeral particles, that also maintain cell viability and preserve DNA for next-generation sequencing, are understudied. Here we optimized a method that leveraged detergents to dissociate microbes from marine particles. We evaluated effectiveness through filter size-fractionation, flow cytometry, and community composition analyses, and provide recommendations to gently and effectively remove microbes from marine particles.

microbiology↗

bioRxiv2025

Culture-supported ecophysiology of the SAR116 clade demonstrates metabolic and spatial niche partitioning

Marine SAR116 bacterioplankton are ubiquitous in surface waters across global oceans and form their own order, Puniceispirillales, within the Alphaproteobacteria. To date no comparative physiology among diverse SAR116 isolates has been performed to capture the functional diversity within the clade, and further, diversity through the lens of metabolic potential and environmental preferences via clade-wide pangenomics remains poorly constrained. Using high-throughput dilution-to-extinction cultivation, we isolated and genome sequenced five new and diverse SAR116 isolates from the northern Gulf of Mexico. Here we present a comparative physiological analysis of these SAR116 isolates, along with a pangenomic investigation of the SAR116 clade using a combination of metagenome-assembled genomes (MAGs, n=258), single-amplified genomes (SAGs, n=84), previously existing (n=2), and new isolate genomes (n=5), totaling 349 SAR116 genomes. Phylogenomic investigation supported the division of SAR116 into three distinct subclades, each with additional structure totalling 15 monophyletic groups. Our SAR116 isolates belonged to three groups within subclade I representing distinct genera with different morphologies and varied phenotypic responses to salinity and temperature. Overall, SAR116 genomes encoded differences in vitamin and amino acid synthesis, trace metal transport, and osmolyte synthesis and transport. They also had genetic potential for diverse sulfur oxidation metabolisms, placing SAR116 at the confluence of the organic and inorganic sulfur pools. SAR116 subclades showed distinct patterns in habitat preferences across open ocean, coastal, and estuarine environments, and three of our isolates represented the most abundant coastal and estuarine subclade. This investigation provides the most comprehensive exploration of SAR116 to date anchored by new culture genomes and physiology.

microbiology↗

bioRxiv2024

New isolates refine the ecophysiology of the Roseobacter CHAB-I-5 lineage

The CHAB-I-5 cluster is a pelagic lineage that can comprise a significant proportion of all roseobacters in surface oceans and have predicted roles in biogeochemical cycling via heterotrophy, aerobic anoxygenic photosynthesis (AAnP), CO oxidation, DMSP degradation, and other metabolisms. Though cultures of CHAB-I-5 have been reported, none have been explored and the best known representative, strain SB2, was lost from culture after obtaining the genome sequence. We have isolated two new CHAB-I-5 representatives, strains US3C007 and FZCC0083, and assembled complete, circularized genomes with 98.7% and 92.5% average nucleotide identities with the SB2 genome. Comparison of these three with 49 other unique CHAB-I-5 metagenome-assembled and single-cell genomes indicated that the cluster represents a genus with two species, and we identified subtle differences in genomic content between the two species subclusters. Metagenomic recruitment from over fourteen hundred samples expanded their known global distribution and highlighted both isolated strains as representative members of the clade. FZCC0083 grew over twice as fast as US3C007 and over a wider range of temperatures. The axenic culture of US3C007 occurs as pleomorphic cells with most exhibiting a coccobacillus/vibrioid shape. We propose the name Thalassovivens spotae, gen nov., sp. nov. for the type strain US3C007T.

microbiology↗

bioRxiv2020

Dual thermal ecotypes detected within a nearly genetically-identical population of the unicellular marine cyanobacterium Synechococcus

The extent and ecological significance of intraspecific diversity within marine microbial populations is still poorly understood, and it remains unclear if such strain-level microdiversity will affect fitness and persistence in a rapidly changing ocean environment. In this study, we cultured 11 sympatric strains of the ubiquitous marine picocyanobacterium Synechococcus isolated from a Narragansett Bay (Rhode Island, USA) phytoplankton community thermal selection experiment. Despite all 11 isolates being highly similar (with average nucleotide identities of >99.9%, with 98.6-100% of the genome aligning), thermal performance curves revealed selection at warm and cool temperatures had subdivided the initial population into thermotypes with pronounced differences in maximum growth temperatures. Within the fine-scale genetic diversity that did exist within this population, the two divergent thermal ecotypes differed at a locus containing genes for the phycobilisome antenna complex. Our study demonstrates that present-day marine microbial populations can contain microdiversity in the form of cryptic but environmentally-relevant thermotypes that may increase their resilience to future rising temperatures. SignificanceNumerous studies exist comparing the responses of distinct taxonomic groups of marine microbes to a warming ocean (interspecific thermal diversity). For example, Synechococcus, a nearly globally distributed unicellular marine picocyanobacterium that makes significant contributions to oceanic primary productivity, contains numerous taxonomically distinct lineages with well documented temperature relationships. Little is known though about the diversity of functional responses to temperature within a given population where genetic similarity is high (intraspecific thermal diversity). This study suggests that understanding the extent of this functional intraspecific microdiversity is an essential prerequisite to predicting the resilience of biogeochemically essential microbial groups such as marine Synechococcus to a changing climate.

microbiology↗

bioRxiv2020

A CURE for physiological characterization of bacterioplankton in liquid culture

Bacterial characterization is an important aspect of microbiology that includes experimentally determining growth rates, environmental conditions conducive to growth, and the types of energy sources microorganisms can use. Researchers use this information to help understand and predict an organisms ecological distribution and environmental functions. Microbiology students generally conduct bacterial characterization experiments in their coursework; however they are frequently restricted to model organisms without ecological relevance and for which the results have been known for decades. We present a course-based undergraduate research experience (CURE) curriculum to involve students in characterization of previously untested, ecologically relevant bacterioplankton cultures to identify the carbon substrates used for growth, as well as the temperature and salinity ranges conducive to growth. Students use these results to connect their organisms physiology to the isolation environment. This curriculum also exposes students to advanced microbiology methods such as flow cytometry for measuring cell concentrations, teaches them to use the programming language R for data plotting, and emphasizes scientific communication through writing, speaking, poster creation/presentation, and social media. This CURE is an attractive introduction to scientific research and was successfully tested with 147 students during the fall semester of 2018.

scientific communication and education↗