Biology subjects

Tolman, J.

Publications and source records attributed to Tolman, J..

4 recordsLinked to original sources

bioRxiv2026

Thalassolituus haligoni sp. nov., BB40, a model species for non-cyanobacterial diazotrophs within Oceanospirillales isolated from a Fjord-like Inlet in Kjipuktuk

Marine non-cyanobacterial diazotrophs (NCDs) are recognized as globally distributed, however, few representatives have been isolated in pure cultures. As a result, understanding the physiology, growth rate, substrate preference and dinitrogen (N2) fixation capabilities proves difficult. Thalassolituus haligoni. sp. nov., BB40 was isolated from a fjord-like inlet within Kjipuktuk (Halifax), Nova Scotia. The fully sequenced genome displayed all necessary genes required for N2 fixation, and various carbon uptake pathways. The gram-negative flagellated rod shape bacterium displayed significantly higher growth rates in medium amended with nitrate (NO3-) or ammonia (NH3), compared to dissolved N2, as the sole nitrogen source. Biological N2 fixation rates were detectable across all conditions, measuring a range from 9.34 x 10-6 to 1.4 x 10-1 fmol N cell-1 day-1. Growth of the isolate was successful between 4 {degrees}C up to 35 {degrees}C, with a Topt of 20 {degrees}C for N2, and between 27 - 30 {degrees}C for fixed nitrogen (NO3- and NH3). The closest relatives to T. haligoni, were found to be the uncultured Arc-gamma-03 (99% average nucleotide identity (ANI)) and Oceanobacter antarcticus (81% ANI). T. haligoni also displays versatile capabilities for growth on various carbon, and nitrogen sources, and antibiotics. Collectively this study provides an in-depth physiological assessment of an Oceanospirillales diazotrophic species which we presently have limited knowledge of.

ecology↗

bioRxiv2025

Automated eDNA and eRNA Profiling for Biodiversity Monitoring in Marine and Freshwater Ecosystems

Automated sampling enables the collection and analysis of eDNA from regions that are limited by site access, sampling times, and operator safety. eDNA sampling devices must be rigorously tested against existing technologies to demonstrate fitness across different operational settings and sample quality. The Dartmouth Ocean Technologies, Inc. (DOT) automated eDNA sampler preserves samples and can be deployed at a range of temperatures and depths. The DOT sampler has previously been tested in marine environments for up to three months, with validation against manual protocols. In this study we tested the DOT sampler in four water bodies in Nova Scotia, Canada, with an expanded set of genetic analyses. We successfully profiled prokaryotes, eukaryotes, and fish using the 16S, 18S, and 12S ribosomal RNA genes respectively, in a brackish pond, a freshwater lake, and two marine harbours. eDNA samples collected by the DOT sampler were statistically concordant with manual Niskin-bottle samples in a range of aqueous habitats. We detected taxonomic groups consistent with the salinity level of each sampled habitat, including invasive species such as smallmouth bass and chain pickerel in the freshwater lake. One marine harbour was sampled at pre-defined time intervals in the days following a significant rainfall event during which site access was limited. We detected ten times as many probable fecal-associated bacteria by proportion at this site relative to the other marine harbour. Onboard preservation of samples in RNAlater allowed the identification of groups with different levels of metabolic activity, and shotgun metagenomic analysis identified key metabolic pathways and a small number of sequences with homology to known antimicrobial-resistance genes.

ecology↗

bioRxiv2025

Comparison of spatio-temporal dynamics and composition in size-fractionated and unfractionated Northwestern Atlantic microbial communities

Size fractionation is a widely applied approach to target specific microbial size ranges, differentiating between larger particle-associated, and smaller free-living microorganisms. To characterize its impact on microbial diversity and its comparability to unfractionated samples, we analyzed 16 weekly ocean samples across five depths during a spring bloom. A universal marker was used to characterize prokaryotes, eukaryotes and chloroplasts comparing single (0.2 {micro}m) or sequential (3 {micro}m and 0.2 {micro}m) filtration. We analyzed unfractionated, fractionated (small and large fractions) and de-fractionated samples. The particle-associated fraction defines the most different community from the other fractions, and combining size fractions (de-fractionating) before or after sequencing produces a community that is most similar to unfractionated samples in terms of composition, and richness dynamics with the exception of very rare taxa. Between 75% and 97% of features are shared, but some discrepancies in relative abundances were unresolved, including for some lineages of free-living Proteobacteria like OM43. The richness trends were consistent, and ANCOM detected at most one significantly different feature between fractionated, and de-fractionated samples, highlighting the similarity in community composition and temporal dynamics between the sets.

molecular biology↗

bioRxiv2024

Targeted metagenomics reveals pangenomic diversity of the nitroplast (UCYN-A) and its algal host plastid

UCYN-A (Cand. Atelocyanobacterium thalassa) has recently been recognized as a globally-distributed, early stage, nitrogen-fixing organelle (the nitroplast) of cyanobacterial origin present in select species of haptophyte algae (e.g., Braarudosphaera bigelowii). Although the nitroplast was recognized as the UCYN-A2 sublineage, it is yet to be confirmed in other sublineages of the algal/UCYN-A complex. We used water samples collected from Halifax Harbour (Bedford Basin, Nova Scotia, Canada) and the offshore Scotian Shelf to further our understanding of B. bigelowii and UCYN-A in the coastal Northwest Atlantic. Sequencing data revealed UCYN-A-associated haptophyte signatures and yielded near-complete metagenome-assembled genomes (MAGs) for UCYN-A1, UCYN-A4, and the plastid of the A4-associated haptophyte. Comparative genomics provided new insights into the pangenome of UCYN-A. The UCYN-A4 MAG is the first genome sequenced from this sublineage and shares [~]85% identity with the UCYN-A2 nitroplast. Genes missing in the reduced genome of the nitroplast were also missing in the A4 MAG supporting its likely classification as a nitroplast as well. The UCYN-A1 MAG was found to be nearly 100% identical to the reference genome despite coming from different ocean basins. Time-series data paired with the recurrence of specific microbes in enrichment cultures gave insight into the microbes that frequently co-occur with the algal/UCYN-A complex (e.g., Pelagibacter ubique). Overall, our study expands knowledge of UCYN-A and its host across major ocean basins and investigates their co-occurring microbes in the coastal Northwest Atlantic (NWA), thereby facilitating future studies on the underpinnings of haptophyte-associated diazotrophy in the sea.

microbiology↗