Biology subjects

LaRoche, J.

Publications and source records attributed to LaRoche, J..

7 recordsLinked to original sources

bioRxiv2026

Lateral gene transfer shapes the distribution of nitrogen fixation within a cosmopolitan clade of marine Thalassolituus

Biological nitrogen fixation converts dinitrogen gas into ammonia, supplying new bioavailable nitrogen to marine ecosystems, but the evolutionary processes shaping its distribution among heterotrophic bacteria remain unresolved. Thalassolituus, a genus within the family Oceanospirillaceae (order Oceanospirillales), is best known for hydrocarbon degradation, yet nitrogen fixation has been confirmed in only one cultured isolate. We analyzed 74 quality-filtered genomes assigned to Thalassolituus within a broader dataset of 421 Oceanospirillaceae genomes to reconstruct the distribution and evolutionary history of the minimal nifHDKENB gene set. Twenty-five genomes encoded complete or near-complete nif loci and occurred in four well-supported clades interspersed with genomes lacking the pathway. Statistical topology tests rejected the species-tree topology for concatenated NifHDK and NifHDKENB protein alignments, and eleven recombination events across nif loci were supported by at least four detection methods. The core nifHDK gene order remained broadly conserved, but accessory neighborhoods differed among clades, and structural nifHDK genes showed stronger codon adaptation than biosynthesis nifENB genes. Clade 2 combined species-gene tree congruence, conserved gene neighborhoods, and comparatively high nifH codon adaptation, whereas Clades 1 and 4 showed greater phylogenetic discordance, more recombination, and weaker codon adaptation. These results support a reticulate history in Thalassolituus, in which lateral acquisition introduced nitrogen fixation into distinct lineages, vertical inheritance preserved it within some clades, and homologous recombination continued to reshape nif loci. These processes help explain why nitrogen fixation is unevenly distributed among closely related marine heterotrophic bacteria.

microbiology↗

bioRxiv2026

Particle lability drives degradation dynamics and bacterial community assembly during a Phaeocystis bloom decline

Microbial degradation of suspended and sinking organic carbon regulates long-term oceanic carbon storage by controlling the efficiency of the biological pump. Yet microbial controls on carbon export and remineralization remain poorly constrained, limiting predictions of how ocean carbon cycling will respond to climate change. Here, we combined in situ sampling with ship-based incubations to quantify prokaryote-driven removal rates of suspended and sinking total organic carbon (TOC). Samples were collected below the mixed layer during three stages of a spring Phaeocystis pouchetii bloom in the Labrador Sea. Phaeocystis blooms can dominate regional phytoplankton biomass and are expected to increase under future climate. Removal rates were used as a proxy for carbon lability and combined with 16S rRNA metabarcoding and carbon composition analyses to link microbial community structure with substrate characteristics. Removal rates of sinking particles (0.02-0.06 d-1) were an order of magnitude higher than those of suspended TOC (0.002 d-1) during bloom-decline and non-bloom. In contrast, during late-bloom, suspended carbon exhibited rates of 0.01 d-1, comparable to sinking particles, and was enriched in exopolymer-rich colonies. Prokaryotic community composition varied primarily among bloom stages rather than carbon fractions, indicating that bloom stage-- and thus particle origin and composition--was the dominant control on bacterial degradation and assembly. Bacterial diversity peaked where carbon was refractory and originated from mixed phytoplankton. Together, these results demonstrate that suspended Phaeocystis-derived carbon can be rapidly remineralized when blooms produce exopolymer-rich colonies and highlight bloom stage as key regulator of microbial carbon processing and biological pump efficiency.

microbiology↗

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↗

bioRxiv2024

Seasonal patterns in b-vitamins and cobalamin co-limitation in the Northwest Atlantic

B-vitamins are important co-enzymes that have long been hypothesized to play key roles in marine ecosystems. However, environmental measurements remain scarce, which limits our understanding of their potential impact. Here, we present mass spectrometry-based measurements of b-vitamins (B1, B2, B3, B5, B6, B12) and related vitamers along a transect in the Northwest Atlantic Ocean, in both particulate phase and dissolved in seawater, seasonally over 5 years, and couple this with targeted investigations of the impact of B12 (cobalamin) on phytoplankton growth. We show that these metabolites are present at femto to pico-molar concentrations and demonstrate that season explains most variance in particulate phase b-vitamins but not dissolved, offering further evidence that metabolite inventories in these two phases are often decoupled. We find correlations between particulate organic carbon with particulate B1 and B3, and between chlorophyll a and particulate B2 and DMB in fall but not spring, indicating unique seasonal drivers of vitamin inventories. Of all measured vitamins, only cobalamin was enriched in the particulate over dissolved phase, predominantly in spring. We documented nitrogen and cobalamin co-limitation of phytoplankton growth during spring bloom decline, when dissolved cobalamin is seemingly drawn down, but not during fall, when dissolved cobalamin concentrations remain elevated. These seasonal differences may be underpinned by the increased importance of cobalamin remodeling and recycling during the fall. This study provides insights into the absolute concentrations, stoichiometry, and variability of b-vitamins in the ocean and offers evidence that cobalamin exerts seasonally-varying controls on Northwest Atlantic marine ecosystems.

microbiology↗

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↗

bioRxiv2024

Pseudocobalamin production and use in Synechococcus cultures and communities

Cobalamin influences marine microbial communities because an exogenous source is required by most eukaryotic phytoplankton, and demand can exceed supply. Pseudocobalamin is a cobalamin analog that is produced and used by most cyanobacteria but is not directly available to eukaryotic phytoplankton. Some microbes can remodel pseudocobalamin into cobalamin, but a scarcity of pseudocobalamin measurements impedes our ability to evaluate its importance for marine cobalamin production. Here, we perform simultaneous measurements of pseudocobalamin and methionine synthase (MetH), the key protein that uses it as a co-factor, in Synechococcus cultures and communities. In Synechococcus sp. WH8102, pseudocobalamin quota decreases in low temperature (17 {degrees}C) and low N:P, while MetH did not. Pseudocobalamin and MetH quotas were influenced by culture methods and growth phase. Despite the variability present in cultures, we found a comparably consistent quota of 300 {+/-} 100 pseudocobalamin molecules per cyanobacterial cell in the Northwest Atlantic Ocean, suggesting that cyanobacterial cell counts may be sufficient to estimate pseudocobalamin inventories in this region. This work offers insights into cellular pseudocobalamin metabolism, and the environmental and physiological conditions that may influence it, and provides environmental measurements to further our understanding of when and how pseudocobalamin can influence marine microbial communities.

microbiology↗