Genomic insights into cryptic cycles of microbial hydrocarbon production and degradation in contiguous freshwater and marine microbiomes

Shotgun metagenomics reveals the flexibility and diversity of Arctic marine microbiomes

Polar oceanographic regions are exposed to rapid changes in temperature, salinity, and light fields that determine microbial species distributions, but resilience to an increasingly unstable climate is unknown. To unravel microbial genomic potential of the Northern Baffin Bay's polynya, we constructed eight metagenomes from the same latitude but targeting two sides of Pikialasorsuaq (The North Water) that differ by current systems, stratification, and temperature regimes. Samples from the surface and subsurface chlorophyll maximum (SCM) of both sides were collected 13 months apart. Details of metabolic pathways were determined for 18 bacteria and 10 microbial eukaryote metagenome-assembled genomes (MAGs). The microbial eukaryotic MAGs were associated with the dominant green algae in the Mamiellales and diatoms in the Mediophyceae, which tended to respectively dominate the eastern and western sides of Pikialasorsuaq. We show that microbial community taxonomic and functional signatures were ca. 80% similar at the latitude sampled with only 20% of genes associated with local conditions. From the metagenomes we found genes involved in osmotic regulation, antifreeze proteins, and photosystem protection, with hydrocarbon biodegradation and methane oxidation potential detected. The shared genomic compliment was consistent with adaptation to the Arctic's extreme fluctuating conditions, with implications for their evolutionary history and the long-term survival of a pan-arctic microbiome. In particular, previously unrecognized genetic capabilities for methane bio-attenuation and hydrocarbon metabolism in eukaryotic phytoplankton suggest adaptation to dark conditions that will remain, despite climate warming, in the high latitude offshore waters of a future Arctic.

Maintaining ocean ecosystem health with hydrocarbonoclastic microbes

Accidental spills and persisting hydrocarbon pollution caused by petroleum exploitation have deeply disrupted marine ecosystems, including those in the deep oceans and the Arctic Ocean. While physicochemical methods are available for emergency cleanup, microorganisms are ultimately responsible for mineralizing the hydrocarbons. The understanding of environmental effects on the composition and efficiency of hydrocarbon-degrading microbial communities has greatly improved current microorganism-based remediation strategies. This review summarizes recent findings on the physiology, metabolism, and ecology of marine obligate hydrocarbonoclastic microorganisms. Strategies for improved biotechnological solutions based on the use of hydrocarbon-degrading microbes are discussed for hydrocarbon remediation in marine water columns, sediments, beaches, and the Arctic.

Arctic's hidden hydrocarbon degradation microbes: investigating the effects of hydrocarbon contamination, biostimulation, and a surface washing agent on microbial communities and hydrocarbon biodegradation pathways in high-Arctic beaches

BACKGROUND

Canadian Arctic summer sea ice has dramatically declined due to global warming, resulting in the rapid opening of the Northwest Passage (NWP), slated to be a major shipping route connecting the Atlantic and Pacific Oceans by 2040. This development elevates the risk of oil spills in Arctic regions, prompting growing concerns over the remediation and minimizing the impact on affected shorelines.

RESULTS

This research aims to assess the viability of nutrient and a surface washing agent addition as potential bioremediation methods for Arctic beaches. To achieve this goal, we conducted two semi-automated mesocosm experiments simulating hydrocarbon contamination in high-Arctic beach tidal sediments: a 32-day experiment at 8 °C and a 92-day experiment at 4 °C. We analyzed the effects of hydrocarbon contamination, biostimulation, and a surface washing agent on the microbial community and its functional capacity using 16S rRNA gene sequencing and metagenomics. Hydrocarbon removal rates were determined through total petroleum hydrocarbon analysis. Biostimulation is commonly considered the most effective strategy for enhancing the bioremediation process in response to oil contamination. However, our findings suggest that nutrient addition has limited effectiveness in facilitating the biodegradation process in Arctic beaches, despite its initial promotion of aliphatic hydrocarbons within a constrained timeframe. Alternatively, our study highlights the promise of a surface washing agent as a potential bioremediation approach. By implementing advanced -omics approaches, we unveiled highly proficient, unconventional hydrocarbon-degrading microorganisms such as Halioglobus and Acidimicrobiales genera.

CONCLUSIONS

Given the receding Arctic sea ice and the rising traffic in the NWP, heightened awareness and preparedness for potential oil spills are imperative. While continuously exploring optimal remediation strategies through the integration of microbial and chemical studies, a paramount consideration involves limiting traffic in the NWP and Arctic regions to prevent beach oil contamination, as cleanup in these remote areas proves exceedingly challenging and costly.

Metagenomic survey reveals hydrocarbon biodegradation potential of Canadian high Arctic beaches

BACKGROUND

Decreasing sea ice coverage across the Arctic Ocean due to climate change is expected to increase shipping activity through previously inaccessible shipping routes, including the Northwest Passage (NWP). Changing weather conditions typically encountered in the Arctic will still pose a risk for ships which could lead to an accident and the uncontrolled release of hydrocarbons onto NWP shorelines. We performed a metagenomic survey to characterize the microbial communities of various NWP shorelines and to determine whether there is a metabolic potential for hydrocarbon degradation in these microbiomes.

RESULTS

We observed taxonomic and functional gene evidence supporting the potential of NWP beach microbes to degrade various types of hydrocarbons. The metagenomic and metagenome-assembled genome (MAG) taxonomy showed that known hydrocarbon-degrading taxa are present in these beaches. Additionally, we detected the presence of biomarker genes of aerobic and anaerobic degradation pathways of alkane and aromatic hydrocarbons along with complete degradation pathways for aerobic alkane degradation. Alkane degradation genes were present in all samples and were also more abundant (33.8 ± 34.5 hits per million genes, HPM) than their aromatic hydrocarbon counterparts (11.7 ± 12.3 HPM). Due to the ubiquity of MAGs from the genus Rhodococcus (23.8% of the MAGs), we compared our MAGs with Rhodococcus genomes from NWP isolates obtained using hydrocarbons as the carbon source to corroborate our results and to develop a pangenome of Arctic Rhodococcus. Our analysis revealed that the biodegradation of alkanes is part of the core pangenome of this genus. We also detected nitrogen and sulfur pathways as additional energy sources and electron donors as well as carbon pathways providing alternative carbon sources. These pathways occur in the absence of hydrocarbons allowing microbes to survive in these nutrient-poor beaches.

CONCLUSIONS

Our metagenomic analyses detected the genetic potential for hydrocarbon biodegradation in these NWP shoreline microbiomes. Alkane metabolism was the most prevalent type of hydrocarbon degradation observed in these tidal beach ecosystems. Our results indicate that bioremediation could be used as a cleanup strategy, but the addition of adequate amounts of N and P fertilizers, should be considered to help bacteria overcome the oligotrophic nature of NWP shorelines.

Broad-spectrum hydrocarbon-degrading microbes in the global ocean metagenomes

Understanding the diversity and functions of hydrocarbon-degrading microorganisms in marine environments is crucial for both advancing knowledge of biogeochemical processes and improving bioremediation methods. In this study, we leveraged nearly 20,000 metagenome-assembled genomes (MAGs), recovered from a wide array of marine samples across the global oceans, to map the diversity of aerobic hydrocarbon-degrading microorganisms. A broad bacterial diversity was uncovered, with a notable preference for degrading aliphatic hydrocarbons over aromatic ones, primarily within Proteobacteria and Actinobacteriota. Three types of broad-spectrum hydrocarbon-degrading bacteria were identified for their ability to degrade various hydrocarbons and possession of multiple copies of hydrocarbon biodegradation genes. These bacteria demonstrate extensive metabolic versatility, aiding their survival and adaptability in diverse environmental conditions. Evidence of gene duplication and horizontal gene transfer in these microbes suggested a potential enhancement in the diversity of hydrocarbon-degrading bacteria. Positive correlations were observed between the abundances of hydrocarbon-degrading genes and environmental parameters such as temperature (-5 to 35 °C) and salinity (20 to 42 PSU). Overall, our findings offer valuable insights into marine hydrocarbon-degrading microorganisms and suggest considerations for selecting microbial strains for oil pollution remediation.

Discovery of a novel bacterial class with the capacity to drive sulfur cycling and microbiome structure in a paleo-ocean analog

Uncultivated microbial taxa represent a large fraction of global microbial diversity and likely drive numerous biogeochemical transformations in natural ecosystems. Geographically isolated, polar ecosystems are complex microbial biomes and refuges of underexplored taxonomic and functional biodiversity. Combining amplicon sequencing with genome-centric metagenomic analysis of samples from one of the world's northernmost lakes (Lake A, Ellesmere Island, Canadian High Arctic), we identified a novel bacterial taxon that dominates in the bottom layer of anoxic, sulfidic, relict sea water that was isolated from the Arctic Ocean some 3000 years ago. Based on phylogenomic comparative analyses, we propose that these bacteria represent a new Class within the poorly described Electryoneota/AABM5-125-24 candidate phylum. This novel class, for which we propose the name Tariuqbacteria, may be either a relict of ancient ocean conditions or endemic to this High Arctic system, provisionally providing a rare example of high-taxonomy level endemism. Consistent with the geochemistry of the bottom water, the genetic composition of the Candidatus Tariuqbacter genome revealed a strictly anaerobic lifestyle with the potential for sulfate and sulfur reduction, a versatile carbon metabolism and the capability to eliminate competing bacteria through methylarsenite production, suggesting an allelochemical influence on microbiome structure by this planktonic microbe.