Biology subjects

Greer, C. W.

Publications and source records attributed to Greer, C. W..

8 recordsLinked to original sources

bioRxiv2026

Long-term patterns of ultra-low sulfur fuel oil bioremediation in Arctic shorelines using in situ mesocosms

New maritime regulations restricting high-sulfur fuels have led to the transition to new low sulfur fuel oils (LFSOs). We do not know how LSFOs will behave in marine environments and how they will respond to available remediation strategies, presenting an environmental risk. The risk will be even higher in the remote high Arctic, especially along the Northwest Passage (NWP), for which an increase in shipping traffic is expected by the end of the century. In this study, we evaluated the long-term (one year) biodegradation potential of the native microbial community of NWP beach sediment using in situ mesocosm experiments with two different types of LSFOs: a marine gas oil (Marine diesel) and an ultra-low sulfur fuel oil (ULSFO). We observed that the lighter Marine diesel was biodegraded better (72.0%) than the heavier ULSFO (32.5%). We described composition of the microbial community of the mesocosms using 16S rRNA gene amplicon sequencing and observed a decrease in microbial diversity for the fuel-treated samples compared to the untreated controls. Despite the decrease in overall diversity, we observed significantly higher abundances of known hydrocarbon degrading microbes (e.g., Oleispira, Altererythrobacter, Gilvibacter, Pseudohongiella) in the fuel mesocosms. Our study showed the potential to implement biodegradation as a remediation strategy under the cold and oligotrophic environmental conditions present throughout the NWP. However, we also observed that microbes on their own cannot degrade the entirety of the removed fuel and other types of remediation will need to be considered to complement the natural biodegradation observed here.

microbiology↗

bioRxiv2025

From Northwest Passage shores to molecular pathways: Comparative transcriptomic responses of a novel Arctic marine fuel-degrading Flavobacterium species

Accelerated sea-ice decline is opening the Arctic to increased shipping, elevating the risk of marine fuel spills in fragile ecosystems where extreme cold and remoteness limit cleanup options. While microbial biodegradation is the primary removal mechanism, the metabolic strategies of abundant polar taxa remain poorly understood, particularly those lacking canonical degradation genes. We characterized the hydrocarbon degradation mechanisms of Flavobacterium sp. strain R2B_3I, a psychrotolerant isolate from high Arctic beach sediments in Resolute Bay, Nunavut, Canada. During three-month incubations with ultra-low sulfur fuel oil at 4 {degrees}C, R2B_3I mounted a systems-level response involving the upregulation of diverse non-canonical oxidoreductases, membrane remodeling systems, cold-shock, and oxidative stress defenses. Crucially, this strain achieved efficient degradation in the complete absence of alkB alkane hydroxylases, challenging the reliance on alkB as a universal biomarker for hydrocarbon biodegradation. Transcriptomic analysis revealed distinct temporal shifts, linking specific gene clusters to the degradation of complex petroleum mixtures under environmentally relevant conditions. These results demonstrate that Flavobacterium, a dominant genus in polar oceans, utilize a "cryptic" metabolic network to process hydrocarbons, effectively bypassing the pathways typically monitored in environmental surveys. By uncovering alternative mechanisms, our study revises current models of microbial oil degradation, highlighting the overlooked potential of non-canonical degraders in determining the fate of marine fuel spills in a warming Arctic.

microbiology↗

bioRxiv2025

Transcriptomic analyses unveil hydrocarbon degradation mechanisms in a novel polar Rhodococcus sp. strain R1B_2T from a high Arctic intertidal zone exposed to ultra-low sulfur fuel oil.

As Arctic shipping increases due to climate change, characterized by rising temperature and decreasing sea-ice coverage, the risk of oil spills through the Northwest Passage in this fragile ecosystem grows, necessitating effective bioremediation strategies. Research on bioremediation using Arctic coastal sediment bacteria has gained attention, particularly Rhodococcus species that play key roles in hydrocarbon degradation (HD) under extreme conditions. This study investigates the HD capabilities of a novel cryophilic Arctic Rhodococcus sp. strain R1B_2T isolated from Canadian high Arctic beach sediment in Resolute Bay, exposed to ultra-low sulfur fuel oil for three months at 5 {degrees}C. Comparative transcriptomics analyses revealed dynamic responses and metabolic plasticity, with upregulation of genes for aliphatic, aromatic, and polycyclic aromatic hydrocarbons, biosurfactant production (rhamnolipid), cold adaptation, and stress responses. The strain possesses several key alkane degradation genes (alkB, almA, CYP153, ladA), with co-expression network analysis highlighting synergistic mechanisms between alkB and CYP153 that target different chain-length alkanes (alkB: [~]C5-C20; CYP153: [~]C5-C12 and >C30) demonstrating complementary degradation strategies. The findings reveal adaptive mechanisms and degradation kinetics of native Arctic bacteria, highlighting the potential of Arctic cryophilic and halotolerant Rhodococcus species for oil spill remediation in polar marine environments. HIGHLIGHTS- Novel cryophilic Arctic Rhodococcus strain R1B_2T demonstrates robust hydrocarbon degradation capabilities at 4{degrees}C - Transcriptomic analysis reveals upregulation of key genes for aliphatic, aromatic, and PAH degradation pathways - Synergistic expression between alkB, almA and CYP153 genes enables efficient degradation of varied hydrocarbon chain lengths - Concurrent upregulation of biosurfactant production linked to hydrocarbon biodegradation, cold adaptation, and stress response mechanisms GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=146 SRC="FIGDIR/small/664532v1_ufig1.gif" ALT="Figure 1"> View larger version (65K): org.highwire.dtl.DTLVardef@16fa663org.highwire.dtl.DTLVardef@114e2a2org.highwire.dtl.DTLVardef@2b244borg.highwire.dtl.DTLVardef@5bb803_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

Characterization of skin- and intestine microbial communities in migrating high Arctic lake whitefish and cisco

At high latitudes, lake whitefish (Coregonus clupeaformis) and others in the closely related Coregonus species complex (CSC), including cisco (C. autumnalis and C. sardinella), can be diadromous, seasonally transitioning between freshwater lakes and the Arctic Ocean. CSC skin- and intestine microbiomes were collected, facilitated by Inuit fishers at sites on and around King William Island, Nunavut, at the northern range limits of lake whitefish. Community composition was explored using 16S rRNA gene sequencing, with significant differences in microbiota dispersions depending on fishing site salinity for lake whitefish intestine and skin, as well as cisco skin. Overall, lake whitefish intestine communities appeared more variable than cisco and had higher Shannon diversity, suggesting that lake whitefish and their microbiomes could be more susceptible to environmental stress possibly leading to dysbiosis. Although cisco condition was similar among distinct seasonal habitats, the higher average lake whitefish condition in freshwater rivers suggests that fishing these diadromous whitefish in estuaries may be optimal from a sustainable fishery perspective. Taken together, the impact of changing habitats on fish condition and different microbial composition may inform new approaches to CSC health in fisheries and aquaculture, in addition to being relevant for northern Indigenous peoples with subsistence and economic interests in these resources.

microbiology↗

bioRxiv2022

High resolution shotgun metagenomics: the more data, the better?

In shotgun metagenomics (SM), the state of the art bioinformatic workflows are referred to as high resolution shotgun metagenomics (HRSM) and require intensive computing and disk storage resources. While the increase in data output of the latest iteration of high throughput DNA sequencing systems can allow for unprecedented sequencing depth at a minimal cost, adjustments in HRSM workflows will be needed to properly process these ever-increasing sequence datasets. One potential adaptation is to generate so-called shallow SM datasets that contain fewer sequencing data per sample as compared to the more classic high coverage sequencing. While shallow sequencing is a promising avenue for SM data analysis, detailed benchmarks using real data are lacking. In this case study, we took four public SM datasets, one massive and the others moderate in size and subsampled each dataset at various levels to mimic shallow sequencing datasets of various sequencing depths. Our results suggest that shallow SM sequencing is a viable avenue to obtain sound results regarding microbial community structures and that high depth sequencing does not bring additional elements for ecological interpretation. More specifically, results obtained by subsampling as little as 0.5M sequencing clusters per sample were similar to the results obtained with the largest subsampled dataset for the human gut and agricultural soil datasets. For the Antarctic dataset, which contained only a few samples, 4M sequencing clusters per sample was found to generate comparable results to the full dataset. One area where ultra-deep sequencing and maximizing the usage of all data was undeniably beneficial was in the generation of metagenome-assembled genomes (MAGs). Key points- Three public multi-sample shotgun metagenomic NovaSeq datasets totalling 12,389,583 and 202 Gb, respectively were analyzed at various sequencing depths to evaluate the accuracy of shallow shotgun metagenomic sequencing using a high resolution shotgun metagenomic bioinformatic workflow. A synthetic mock community of 20 bacterial genomes was also analyzed for validation purposes. - Datasets subsampled to low sequencing depths gave nearly identical ecological patterns (taxonomic and functional composition and beta-alpha-diversity) compared to high depth subsampled datasets. - Rare taxa and functions could be uncovered with high sequencing depth vs. low sequencing depth datasets, but did not affect global ecological patterns. - High sequencing depth was positively correlated with both quantity and quality of recovered metagenome-assembled genomes.

bioinformatics↗

bioRxiv2019

Coherence of Microcystis species revealed through population genomics

Microcystis is a genus of freshwater cyanobacteria which causes harmful blooms in ecosystems worldwide. Some Microcystis strains produce harmful toxins such as microcystin, impacting drinking water quality. Microcystis colony morphology, rather than genetic similarity, is often used to classify Microcystis into morphospecies. However, colony morphology is a plastic trait which can change depending on environmental and laboratory culture conditions, and is thus an inadequate criterion for species delineation. Furthermore, Microcystis populations are thought to disperse globally and constitute a homogeneous gene pool. However, this assertion is based on relatively incomplete characterization of Microcystis genomic diversity. To better understand these issues, we performed a population genomic analysis of 33 newly sequenced genomes (of which 19 were resequenced to check for mutation in culture) mainly from Canada and Brazil. We identified eight Microcystis clusters of genomic similarity, only four of which correspond to named morphospecies and monophyletic groups. Notably, M. aeruginosa is paraphyletic, distributed across four genomic clusters, suggesting it is not a coherent species. Most monophyletic groups are specific to a unique geographic location, suggesting biogeographic structure over relatively short evolutionary time scales. Higher homologous recombination rates within than between clusters further suggest that monophyletic groups might adhere to a Biological Species-like concept, in which barriers to gene flow maintain species distinctness. However, certain genes - including some involved in microcystin and micropeptin biosynthesis - are recombined between monophyletic groups in the same geographic location, suggesting local adaptation. Together, our results show the importance of using genomic criteria for Microcystis species delimitation and suggest the existence of locally adapted lineages and genes. ImportanceThe genus Microcystis is responsible for harmful and often toxic cyanobacterial blooms across the world, yet it is unclear how and if the genus should be divided into ecologically and genomically distinct species. To resolve the controversy and uncertainty surrounding Microcystis species, we performed a population genomic analysis of Microcystis genome from public databases, along with new isolates from Canada and Brazil. We inferred that significant genetic substructure exists within Microcystis, with several species being maintained by barriers to gene flow. Thus, Microcystis appears to be among a growing number of bacteria that adhere to a Biological Species-like Concept (BSC). Barriers to gene flow are permeable, however, and we find evidence for relatively frequent cross-species horizontal gene transfer (HGT) of genes that may be involved in local adaptation. Distinct clades of Microcystis (putative species) tend to have distinct profiles of toxin biosynthesis genes, and yet toxin genes are also subject to cross-species HGT and local adaptation. Our results thus pave the way for more informed classification, monitoring and understanding of harmful Microcystis blooms.

microbiology↗

bioRxiv2018

Nitrogen- and phosphorus-starved Triticum aestivum show distinct belowground microbiome profiles

Many plants have natural partnerships with microbes that can boost their nitrogen (N) and/or phosphorus (P) acquisition. To assess whether wheat may have undiscovered associations of these types, we tested if N/P-starved Triticum aestivum show microbiome profiles that are simultaneously different from those of N/P-amended plants and those of their own bulk soils. The bacterial and fungal communities of root, rhizosphere, and bulk soil samples from the Historical Dryland Plots (Lethbridge, Canada), which hold T. aestivum that is grown both under N/P fertilization and in conditions of extreme N/P-starvation, were taxonomically described and compared (bacterial 16S rRNA genes and fungal Internal Transcribed Spacers - ITS). As the list may include novel N- and/or P-providing wheat partners, we then identified all the operational taxonomic units (OTUs) that were proportionally enriched in one or more of the nutrient starvation- and plant-specific communities. These analyses revealed: a) distinct N-starvation root and rhizosphere bacterial communities that were proportionally enriched, among others, in OTUs belonging to families Enterobacteriaceae, Chitinophagaceae, Comamonadaceae, Caulobacteraceae, Cytophagaceae, Streptomycetaceae, b) distinct N-starvation root fungal communities that were proportionally enriched in OTUs belonging to taxa Lulworthia, Sordariomycetes, Apodus, Conocybe, Ascomycota, Crocicreas, c) a distinct P-starvation rhizosphere bacterial community that was proportionally enriched in an OTU belonging to genus Agrobacterium, and d) a distinct P-starvation root fungal community that was proportionally enriched in OTUs belonging to genera Parastagonospora and Phaeosphaeriopsis. Our study might have exposed wheat-microbe connections that can form the basis of novel complementary yield-boosting tools.

microbiology↗

bioRxiv2017

Niche separation increases with genetic distance among bloom-forming cyanobacteria

Bacterial communities are composed of distinct groups of potentially interacting lineages, each thought to occupy a distinct ecological niche. It remains unclear, however, how quickly niche preference evolves and whether more closely related lineages are more likely to share ecological niches. We addressed these questions by following the dynamics of two bloom-forming cyanobacterial genera over an 8-year time-course in Lake Champlain, Canada, using 16S amplicon sequencing and measurements of several environmental parameters. The two genera, Microcystis (M) and Dolichospermum (D), are frequently observed simultaneously during bloom events and thus have partially overlapping niches. However, the extent of their niche overlap is debated, and it is also unclear to what extent niche partitioning occurs among strains within each genus. To identify strains within each genus, we applied minimum entropy decomposition (MED) to 16S rRNA gene sequences. We confirmed that at a genus level, M and D have different preferences for nitrogen and phosphorus concentrations. Within each genus, we also identified strains differentially associated with temperature, precipitation, and concentrations of nutrients and toxins. In general, niche similarity between strains (as measured by co-occurrence over time) declined with genetic distance. This pattern is consistent with habitat filtering - in which closely-related taxa are ecologically similar, and therefore tend to co-occur under similar environmental conditions. In contrast with this general pattern, similarity in certain niche dimensions (notably particulate nitrogen and phosphorus) did not decline linearly with genetic distance, and instead showed a complex polynomial relationship. This observation suggests the importance of processes other than habitat filtering - such as competition between closely-related taxa, or convergent trait evolution in distantly-related taxa - in shaping particular traits in microbial communities.

ecology↗