Cryptic cycles of microbial hydrocarbon production and degradation along freshwater-saltwater ecosystem gradients

doi:10.21203/rs.3.rs-2246545/v1

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Cryptic cycles of microbial hydrocarbon production and degradation along freshwater-saltwater ecosystem gradients

https://doi.org/10.21203/rs.3.rs-2246545/v1

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Cyanobacteria produce vast quantities of long-chain alkanes in the ocean, yet these do not accumulate in the water column, suggesting rapid co-localized biodegradation. The identities of microbes in this cryptic hydrocarbon cycle are mostly unknown, and are unexplored across marine-freshwater gradients. Analyzing genes and metagenome assembled genomes from a remote, pristine, petroleum-free and meromictic lake in the High Arctic, we detected microbial hydrocarbon production and degradation pathways at all depths, from surface freshwaters to dark, saline, anoxic waters. In addition to Cyanobacteria, members of the phyla Flavobacteria, Nitrospina, Deltaproteobacteria, Planctomycetes and Verrucomicrobia had pathways for hydrocarbon production, providing additional sources of biogenic hydrocarbons. Classic oil-degrading microorganisms were poorly represented in the system, while long-chain hydrocarbon degradation genes were identified in various freshwater and marine lineages such as Actinobacteria, Schleiferiaceae and Marinimicrobia. This suggests that biogenic hydrocarbons could sustain a large fraction of freshwater and oceanic microbiomes, with global biogeochemical implications.

Earth and environmental sciences/Ecology/Microbial ecology

Earth and environmental sciences/Biogeochemistry/Carbon cycle

Earth and environmental sciences/Limnology

Earth and environmental sciences/Ecology/Molecular ecology

alkanes

hydrocarbons

short hydrocarbon cycle

biogeochemical cycles

lakes

sea

Hydrocarbons are widespread in the ocean, with natural oil seeps and human activities releasing between 0.47 and 8.3 million tonnes of petroleum annually ¹. These thermogenic compounds, produced over centuries, strongly affect the ecology of marine ecosystems and trigger activity by numerous aerobic and anaerobic oil-degrading microorganisms ². Microbial degradation of hydrocarbons in marine environments has been extensively studied in deep-sea sediment seepages ^3–7, and following oil spills ^8–10. Detailed investigations following the Deepwater Horizon oil spill in the Gulf of Mexico revealed multiple naturally occurring microbial lineages able to degrade hydrocarbons, and this list is expanding rapidly with metagenomic sequencing and data analysis. For example, mining of the Genome Taxonomy Database (GTDB; gtdb.ecogenomic.org) for hydrocarbon degradation genes revealed that 19% of the 31900 genomes of this database harbored the potential for hydrocarbon degradation, spanning 24 bacterial phyla ¹¹. Oxygen conditions and more broadly the redox potential of the environment influence the diversity and metabolic pathways of hydrocarbon degraders ². In addition, hydrocarbon composition has also been identified as a major structuring factor of the hydrocarbon-degrading community and metabolism, highlighting the importance of substrate preferences and specialization within the hydrocarbon degrader guild ⁷.

In addition to this long-term cycle of petroleum production and degradation, a cryptic and short-term hydrocarbon cycle has been proposed to widely occur in the ocean ¹². In this short cycle, hydrocarbons in the form of long-chain alkanes such as n-pentadecane and n-heptadecane are produced by Prochlorococcus and Synechococcus species, which are the most abundant cyanobacteria in the ocean ¹³. Extrapolated to the volume of the ocean and the distribution of these lineages, oceanic hydrocarbon production could be up to 500 fold larger than abiotic hydrocarbon releases, which is estimated as 0.47 to 8.3 million tonnes of petroleum annually, with cyanobacteria producing up to 300 and 800 million tonnes of alkanes per year ¹². The ecological function or potential benefit of hydrocarbon production for the small pico-sized cyanobacteria remains unclear. Alkanes might increase their membrane fluidity to counter cold or salinity stresses, or enhance the efficiency of the light-harvesting thylakoids ¹⁴. As these cyanobacterial hydrocarbons are not found to accumulate in the ocean, alkane loss rates would be equivalent to the production rates, leading to the hypothesis that alkane-producers and degrading microorganisms occupy the same habitat, with potentially rapid cycling of hydrocarbon production and degradation. However, the diversity and metabolic pathways involved in this putative recycling of biogenic long-chain alkanes remain cryptic. Some cultivated oil degrading aerobic microorganisms such as Alcanivorax have been found to degrade pentadecane ¹⁵ and to bloom following cyanobacterial pentadecane amendments in seawater incubations ¹². However, there is a gap in knowledge of in situ diversity of bacterial hydrocarbon degraders in the absence of petroleum (thermogenic) hydrocarbons that confound interpretations. Similarly, the contribution of non-phototrophic microorganisms to hydrocarbon production in marine waters has been little explored, yet the aphotic zone represents 90% of the ocean volume and non-cyanobacterial alkane production pathways have been identified ^16,17. In addition, the distribution of this cryptic hydrocarbon cycle along oxygen, salinity and light gradients of aquatic ecosystems has not been addressed to date, notably under freshwater conditions where Cyanobacteria also flourish.

The polar regions host numerous marine-derived lakes that formed following the isostatic rebound of the continents triggered by the melting of the ice sheets. Physically isolated from the ocean, freshwater from melting snow and ice accumulates over the trapped marine water. Due to the strong density and temperature differences between these waters, these lakes are highly stratified, with a mixolimnion consisting of the oxic surface freshwater layer immediately beneath the ice, and an anoxic (oxygen below detection; < 1 µM) marine monimolimnion at the bottom. The chemocline at the interface between these layers is the zone of highest chemical reactivity, associated with elevated microbial activities ^18,19. Lake A is one such lake at the extreme north of the Canadian High Arctic, and is a remote pristine ecosystem and natural laboratory to investigate microbial community assemblages and metabolism. The microbiome of the Lake A has been previously investigated ^20–22, revealing a marked stratification of stable and active microorganisms and associated metabolic potentials following the salinity, light and redox gradients of the water column (Fig. 1).

Lake A has physical, chemical and microbiological similarities with freshwater-, marine-, hadal- and deep-sea-like environments, and therefore offered an outstanding opportunity to investigate the hydrocarbon short cycle over a broad range of environmental conditions that are relevant to marine and freshwater ecosystems, and without interference from anthropogenic contaminants and natural seepage. Specifically, we analysed metagenomes from throughout the water column to address the questions: i) are biogenic hydrocarbon genes present and how are they distributed across the pronounced vertical gradients of the Lake A environment; ii) what is the associated microbial diversity; iii) how would these hydrocarbons be degraded in the system; and iv) are these hydrocarbon cycles linked to other biogeochemical cycles ?

Biogenic hydrocarbon producing genes.

Lake A metagenomes from eight depths (2 to 65 m) were sequenced and then analyzed for genes coding for fatty aldehyde decarbonylase (FAD), aldehyde deformylating oxygenase (ADO) and olefin beta-lactone synthetase (OleC), which confer the capability to produce long-chain alkanes and olefinic hydrocarbons (alkenes) respectively ¹⁶. Overall, up to 3200 genes of hydrocarbon-producing proteins were identified in the dataset. FAD genes, phylogenetically related to Flavobacteriaceae were identified at 2m (Fig. 2). Numerous ADO genes, affiliated to the phylum Cyanobacteria were detected in the freshwater aerobic layer and the chemocline, with up to 1463 genes at 14m depth, corresponding to the bottom of the euphotic zone (Fig. 2). By contrast, OleC genes were more abundant in the saline anoxic (< 1 µM oxygen) water with a maximum of 263 genes at 40m. Phylogenetic analysis of OleC genes indicated that most of the detected sequences were related to Deltaproteobacteria (Desulfobacteraceae, Desulfuromonadales and Myxoccocales) and the PVC superphylum (Planctomycetes, Verrucomicrobia, Lentispheraceae and Gemmataceae). Below 40m depth, the number of hydrocarbon-producing genes declined with depth, down to 23 ADO and FAD genes and 81 OleC genes at 65m (Fig. 2).

Hydrocarbon Degrading Genes

Overall, around 4670 genes coding for proteins involved in hydrocarbon degradation pathways were detected (Fig. 3). The total number of known genes for hydrocarbon degrading proteins identified in the metagenomes exceeded those of hydrocarbon production at each analysed depth, except at 14m where the number of genes of both degrading and producing pathways were maximal and similar (1595 vs 1592). Consistent with the oxygen profile of the water column, aerobic alkane degradation genes (alkB, CYP153, ladA, prmA) were abundant from the surface to 22m, with a maximum of 1451 genes at 14m (Fig. 3). By contrast, anaerobic alkane degradation genes (assA, bssA) predominated in the anoxic saline waters with up to 380 genes at 34m before slowly declining with depth, supporting the absence of deep natural seepages at the bottom of Lake A. The number of aromatic hydrocarbon degradation genes increased with depth until 14m for aerobic pathways (tmoABE, cymA, and MAHαβ), and throughout the water column for anaerobic pathways (ebdA, nmsA), reaching 109 genes at 65m (Fig. 3).

Hydrocarbon Cycling Microbial Populations

A total of 250 MAGs with > 50% completeness and < 5% contamination levels were recovered from the combined metagenomic dataset. Among them, 89 MAGs (35.6%) harbored genes for hydrocarbon cycling (Fig. 4 and Supplementary Fig. 1). ADO genes were identified in only one MAG affiliated with marine Cyanobacteria recovered from the lower chemocline zone. Nonetheless, ADO genes with high coverage were also identified at 6 and 14m samples in unbinned contigs taxonomically affiliated to the cyanobacterial taxon Synechoccocus. In addition, one contig from the 2m metagenomic dataset and related to Flavobacteraceae (Bacteroidia) included a long-chain fatty aldehyde decarbonylase gene (Fig. 4). Olefinic hydrocarbon production genes were identified in 26 MAGs, of which 14 were assigned to PVC lineages (Planctomycetota, Pirellula, Lentisphaerae, Gemmataceae and Opitutaceae) and 8 were related to Deltaproteobacteria (Fig. 4 and Supplementary Fig. 1). Olefinic hydrocarbon producers in the oxic freshwater were related to PVC and Nitrospinaceae, whereas highly abundant Deltaproteobacteria MAGs were predominant in anoxic saline waters. Six low abundance PVC MAGs with OleC were also detected at the deepest depth (Supplementary Fig. 1).

Hydrocarbon degradation pathways were identified in 63 taxonomically diverse MAGs (Fig. 4 and Supplementary Fig. 1). Aerobic alkane degradation genes (alkB, CYP153) were detected in Actinobacteria (Nanopelagicales), Bacteroidetes (Sediminibacterium, Schleiferiaceae) and Alpha-(Rhodobacteraceae), Beta (Polaromonas)- and Gamma-proteobacteria (SAR86, Porticoccaceae, Woeseiaceae, Pseudohongiellaceae). Long chain alkane monooxygenase genes (ladA) were also identified in Actinobacteria (Microbacteriaceae, Alpinimonas) recovered at 2m. Aerobic aromatic hydrocarbon degradation pathways were detected in Alphaproteobacteria (Rhodospirillales) and in Rhodothermales MAGs. Based on the average coverage of the MAGs, Nanopelagicales and Schleiferiaceae were the most abundant aerobic hydrocarbon degrading lineages of the system (Fig. 4 and Supplementary Fig. 1). In addition, anaerobic alkane degradation pathways (assA and bssA) genes were identified in Marinimicrobia, Deltaproteobacteria (Desulfobacteraceae, Desulfatiglans, Syntrophales), Bacteroidetes, Chloroflexi as well as in poorly characterized lineages (candidate divisionKSB1, Aminicenantes) and Abyssubacteria that also possessed aromatic hydrocarbon degradation genes. Coverage of the MAGs indicated that populations of Marinimicrobia were the most abundant anaerobic hydrocarbon degraders in low oxygen waters (Fig. 4 and Supplementary Fig. 1).

Sulfur And Nitrogen Cycle Genes In Hydrocarbon Short Cycle Populations

Genome analysis of the hydrocarbon short cycle populations indicated that 86.5% of the MAGs harbored nitrogen cycling (70% of the MAGs) or sulfur cycling (71% of the MAGs) genes, and 54% included genes from both cycles (Supplementary Fig. 1). Nitrite and nitrate reduction pathways were the most represented pathways in hydrocarbon producers, notably in Planctomycetes, Nitrospina and Deltaproteobacteria (Myxococcota, Desulfatibia and Desulfobia). The Cyanobacteria MAG also included the potential for nitrate and urea assimilation. By contrast, genes coding for enzymes involved in the oxidation of sulfide (SQR) and thiosulfate (doxD, tsdA) and sulfate reduction (aprAB, dsrAB) were the most detected in hydrocarbon degraders. Potential sulfide oxidizers included members of the Marinimicrobia, Bacteroidales and Alphaproteobacteria lineages, whereas thiosulfate oxidizers were related to other Bacteroidetes lineages (Flavobacteriales including Scheiferiaceae, Cytophagales and Cryomorphaceae). Sulfate reduction pathway genes were identified in Desulfatiglandales, Syntrophales, Desulfobacteraceae Chloroflexi and Abyssubacteria. In addition, dissimilatory nitrate reductase and sulfur oxidation genes were also identified in the highly dominant Nanopelagicales MAG with hydrocarbon degradation genes, whereas in the highly dominant Marinimicrobia MAGs sulfur oxidation genes were identified along nitrous-oxide reductase genes (Supplementary Fig. 1).

Freshwater hydrocarbon short cycle

The upper water layer (0–12 m) of meromictic Lake A is derived from the snow and ice melt, leading to a freshwater stable environment (salinity < 0.7 ppt) ²³. This was consistent with, the microbial community composition being dominated by freshwater taxa, including Flavobacteriales (Bacteroidia), Burkholderiales (Betaproteobacteria), Nanopelagicales (ex Actinobacteria acl) and Cyanobacteria (Fig. 1), which are frequent major lineages in cold lakes and rivers ^24,25. These lineages were previously detected using 16S rRNA sequencing, supporting an active metabolism at these depths ²⁰. Cyanobacteria have been also detected in the anoxic dark waters, as in other polar meromictic lakes ²⁶ and are a major constituent of the phototrophic plankton of Lake A ²⁷. Multiple genes of long-chain fatty aldehyde decarbonylase (FAD) and aldehyde deformylating oxygenase (ADO), both producing C₁₆-C₁₈ alkanes ¹¹, were identified in the 2m and 6m metagenomes, suggesting a strong potential for bacterial long-chain alkane production in the upper freshwater layer of the lake. Based on the taxonomic affiliation of the contigs and MAGs with those genes, lacustrine Flavobacteriaceae and Cyanobacteria populations were likely the main hydrocarbon producers in this freshwater habitat. This indicates a new ecological role for Flavobacteriaceae members in these ecosystems, and suggests that the potential for hydrocarbon production in Cyanobacteria is not limited to marine species, providing field confirmation of results based on Cyanobacteria culture studies ²⁸.

Consistent with the bacterial production of long chain alkanes, genes coding for C₁₅-C₃₆ alkane monooxygenase (LadA), conferring the ability to degrade long-chain alkanes were also detected at 2m and 6m. The identification of these genes in two MAGs affiliated to Actinomycetales and Alpinimonas (Microbacteriaceae) that were recovered at 2m, suggests that long chain alkanes produced by the Flavobacteriaceae and Cyanobacteria could be readily degraded by members of the Actinobacteria phylum (Fig. 5). Likewise, numerous genes coding for alkane monooxygenase (alkB), and in lesser proportion cytochrome P450 alkane hydroxylase (CYP153), were also detected in the freshwater layer. Identified in MAGs affiliated to Burkholderiales, Sediminibacterium, Alphaproteobacteria and Nanopelagicales, these genes code for enzymes that confer the ability to degrade a large variety of (C₅-C₁₆) alkanes and alkenes that fall within the range of fatty aldehyde decarbonylase and aldehyde deformylating oxygenase products. By contrast, genes encoding for shorter hydrocarbon (methane, butane, propane) oxidation and aromatic hydrocarbon degradation were either not or little detected, suggesting that the hydrocarbon catabolism is centered on bacterial long-chain alkanes. Together these results indicate that long-chain hydrocarbon cycling, suspected to occur in oceans, also occurs in the upper low-conductivity layer of Lake A, extending the potential niche for this cycle to freshwaters. Fuelled by predominant and widespread freshwater lineages of Cyanobacteria and Flavobacteriales, then recycled by Nanopelagicales and Burkholderiales that also represent major components of the freshwater microbiome ^25,29, this freshwater hydrocarbon short cycle is likely to occur in other cold lakes and rivers. Our results suggest the need to extend the range of ecological functions carried out by the dominant lineages of freshwater bacteria, with a new potential role in the previously unconsidered hydrocarbon short cycle that could represent a major carbon source, notably in oligotrophic waters.

Hydrocarbon Biosynthesis Under Aphotic And Low Oxygen Conditions

The depth distribution of ADO genes, as well as the high coverage of ADO gene-bearing contigs and MAGs related to Synechococcus, suggested that Cyanobacteria are the major hydrocarbon producers in the euphotic, upper saline waters of Lake A. This result is consistent with previous studies of cultivated isolates from the ocean that estimated a production of up to 649 Tg of pentadecane per year by Cyanobacteria ¹². In addition, we also detected the olefinic/alkene hydrocarbon synthesis pathway in the euphotic and oxic marine water in a Nitrospina MAG with nitrite oxidation pathways (nirADK, nxrAB). Nitrospina species are widespread nitrifying bacteria in ocean and play a major role in the marine nitrogen cycle by oxidizing nitrite ³⁰. This observation suggests that non-photosynthetic but ecologically important microorganisms could also contribute to the biogenic long-chain alkene pool in the ocean (Fig. 5). Finally, our detection of numerous OleC genes in the deep anoxic marine waters of Lake A suggests that hydrocarbon bacterial production is not limited to the euphotic zone but could also occur under aphotic and low oxygen conditions. Phylogenetic analysis of OleC genes (Fig. 2) and mining of the Lake A MAGs (Fig. 4) revealed that various Deltaproteobacteria and Planctomycetes populations might contribute to olefinic hydrocarbons production in this environment. Members of Candidatus Desulfaltia and Desulfatibia, that were identified as the most abundant populations with olefinic hydrocarbon production genes in the ecosystem, have been previously detected in significant proportions in low oxygen marine waters (< 1 µM) ³¹, suggesting that olefinic hydrocarbon production could represent an important source of hydrocarbons in oceanic oxygen minimum zones. These hypoxic/anoxic zones represent 10 million km³ or approximately 1% of the ocean volume and are expanding in oceans ³². Our results indicate that olefinic hydrocarbon production from non-phototrophic microorganisms in oceans could increase in the future. Together our findings suggest that the current estimation of bacterial hydrocarbon production could be substantially underestimated by neglecting non-cyanobacterial production and by not taking low oxygen zones into account.

Biohydrocarbon Degradation In Petroleum Free Marine Ecosystems

Due to its remote location and permanent ice cover, pristine Lake A and its trapped seawater are free of natural seepage and chemical pollution, providing a unique opportunity to elucidate the identity of microorganisms involved in the marine hydrocarbon short cycle without interference from specialist petroleum and oil-degrading microorganisms. Based on the detection of alkane monooxygenase gene (alkB) in MAGs and the average coverage of the contigs, our results indicate that marine populations of Schleiferiaceae and Actinomycetales were the predominant hydrocarbon degraders in saline oxygenated waters, followed by a population of marine Planctomycetota and various alpha (Rhodobacteraceae, Parasphingorhabdus, SHVP01) and Gamma-proteobacterial populations (Woeseiaceae, ex JTB255 and SAR86), frequently and ubiquitously identified in marine environments ^33–35. Although these genomic results need to be confirmed by activity-based approaches, multiple marine Actinobacteria strains and cultivated marine species of the family Schleiferiaceae degrade hydrocarbons under aerobic conditions ^36,37. However, our results strongly contrast with previous experiments that proposed bloom-forming, oil-degrading microorganisms Alcanivorax and Thalassolitus as potential biogenic hydrocarbon degraders ¹². Previous studies that identified hydrocarbon degraders using enrichment of Gulf of Mexico or North Atlantic subtropical gyre waters with pentadecane might have been biased by petroleum hydrocarbon contaminations or the priming effect of these contaminations, and similar experiments with Lake A inoculate would provide a better background survey of naturally occurring pentadecane degraders.

Our analysis of the trapped anoxic marine waters of Lake A revealed that populations of Marinimicrobia (previously SAR406) were the most abundant anaerobic hydrocarbon degraders under these conditions, extending the known metabolic capability of the members of this phylum. Members of this metabolically versatile phylum are widespread in the ocean, flourishing in low oxygen waters and oxygen minimum zones ³⁸. In the context of global warming and extension of hypoxic zones in oceans, these results suggest a major role of Marinimicrobia in the oceanic hydrocarbon short cycle. By contrast, known anaerobic hydrocarbon degraders related to Desulfatiglandales ³⁹ represented a minor proportion of the community, suggesting that oil-degrading species are less adapted to the degradation of biogenic long-chain alkanes and confirming the substrate preferences and specialization within the hydrocarbon degrader guild ⁷. Together our data indicate that under both oxic and anoxic conditions, biogenic hydrocarbon degradation is likely separate and decoupled from petroleum hydrocarbon degradation, and involves a previously unrecognized diversity of microorganisms.

Hydrocarbon Short Cycles Connect To Sulfur And Nitrogen Cycles

Genome analysis of hydrocarbon short cycle populations revealed a strong interconnection with nitrogen and sulfur cycles (Fig. 5, Supplementary Fig. 1). The most abundant hydrocarbon-degrading lineages Nanopelagicales and Marinimicrobia were potentially involved in sulfide oxidation coupled to nitrate or nitrous-oxide reduction respectively. Genes coding for the transformation of sulfur cycle intermediates (sulfide, thiosulfate) were also frequently detected in hydrocarbon producer and degraders, including in potentially major hydrocarbon degraders related to Marinimicrobia and Schleiferiaceae lineages. The results suggest that these substrates fuel a large part of the hydrocarbon short cycle, further underscoring their ecological importance in aquatic ecosystem functioning ²⁰. Neither nitrate nor nitrite were found to accumulate in Lake A ²³. However, genomic data indicated that nitrite might also play a major role in the hydrocarbon cycle, fuelling the energetic metabolism of various major hydrocarbon producers (Planctomycetes, Myxococcota and Nitrospina) and degraders (Sedimentisphaerales, Vicinamibacterales, Betaproteobacteria). These results suggest a rapid depletion by microbial communities and add another line of evidence for the central role of nitrite in ocean geochemistry ^40,41. They also indicate that biogeochemical intermediates in oxidative and reductive processes may occupy a major place in the hydrocarbon short cycle. Although energetically less efficient than end-products, utilisation of sulfur and nitrogen cycle intermediates might allow the development of microorganisms over a broader spectrum of environmental gradients, supporting a wide distribution of the hydrocarbon short cycle in aquatic environments, as observed in this study.

Our analysis of hydrocarbon cycling genes and populations of a petroleum-free model ecosystem that is physically, chemically and microbiologically relevant to many aquatic biomes revealed that the hydrocarbon short cycle is not limited to marine waters and likely occurs under a broad range of salinity and oxygen concentrations, from oxic freshwaters to anoxic marine waters (Fig. 5). Entangled with sulfur and nitrogen cycles, the hydrocarbon short cycle involved diverse microorganisms, including lineages that are common and often predominate in freshwater and marine ecosystems. Although Cyanobacteria were found as major drivers of the hydrocarbon production in the euphotic zone, our results also pointed out that widely distributed lineages of the Flavobacteriaceae, PVC, Nitrospina and Deltaproteobacteria phyla could contribute to the hydrocarbon biogenic production (Fig. 5). Analysis of hydrocarbon degradation genes highlighted that the degradation of bacterial alkanes involved a large diversity of microbial lineages that differ from petroleum hydrocarbon degrading species. Since the efficiency and rapidity of the microbial response to oil inputs could be linked to the history of contamination ⁴², a major consequence of this decoupling is that hydrocarbons produced by bacteria might have little or no priming effect on attenuating oil spills. The ability of these microorganisms to degrade petroleum hydrocarbons should be investigated to test this hypothesis. However, particular attention must be paid to pristine environments, such as High-Arctic ecosystems that are increasingly threatened by oil exploitation and shipping, to prevent any oil contamination that might remain undegraded by the native microbial population.

Site description, sample collection and nucleic acid extraction

High-Arctic Canadian Lake A (Ellesmere Island, 82° 59.667’ N, 75° 26.602’ W) is a permanently ice-covered, highly stratified meromictic saline lake with an oxygenated freshwater layer (14.1 mg/L of oxygen; salinity < 0.7 ppt) located under the ice down to 12m depth, a chemo- and halocline located below the freshwater down to 24m and an anoxic marine-derived saline (oxygen below detection limit of the profiler; salinity > 30 ppt) and sulfate (~ 20 mM) and sulfide (~ 0.3 mM) rich waters below 24 m. Light penetrates through the ice to the water column beneath, with an oxygen-containing euphotic zone that extends to 22 m.

Water samples were collected in summer 2017 from three separate 24 cm-diameter holes drilled in the center of Lake A through the 0.6 m thick ice cover. The sampling strategy and experimental procedures used in this study were previously detailed ²⁰. Briefly, one litter of water was collected at eight different depths (2m, 6m, 14m, 22m, 34m, 40m, 55m and 65m) in the three holes, spanning the oxygen, salinity and temperature gradients of the lake water column. Triplicate water samples were filtered through separate 0.22 µm pore size Sterivex filters™ (Merck Milipore) and then stored below − 50ºC until nucleic acid extraction. Nucleic acids were extracted using the Qiagen Allprep DNA/RNA Mini Kit with modifications ⁴³.

Metagenomic library preparation, sequencing and analysis.

One metagenomic library per sampled depth was prepared using Illumina Nextera XT kit and each library were sequenced in two Illumina MiSeq (2*300 bp) runs and one Illumina NexSeq run (2*150 bp) at the Institut de Biologie Integrative et des Systèmes (IBIS) sequencing platform (Université Laval, Canada) and at the CGEB – Integrated Microbiome Resource (Dalhousie University, Canada) respectively. Datasets were quality filtered using Trimmomatic v.0.39 ⁴⁴. Reads of ribosomal small subunit were extracted from metagenomic reads using Infernal v.1.1.4 ⁴⁵, and taxonomic affiliation of the extracted 16S rRNA reads longer than 100 bp were determined using BLAST against Silva database release 138 as reference ⁴⁶. Since metagenomic 16S rRNA reads spanned various regions of the 16S rRNA gene, taxonomic assignments were limited to the genus level. For each sample, quality-filtered metagenomic reads from the different sequencing runs were pooled and assembled using SPAdes (option meta) ⁴⁷. Assembled contigs longer than 200 bp and mapping files (BAM files generated using BBmap ⁴⁸) were uploaded to the IMG/MR platform for gene calling and functional annotation using pipeline v.4.16.6 ⁴⁹. Genes involved in hydrocarbons degradation were also identified using HMM profiles of the CANT-HYD database with noise cut-off thresholds ¹¹. To account for differences in sequencing depth between samples, metagenomes were normalized to the size of the smallest dataset.

For metagenome assembled genome reconstruction, all quality filtered sequences were pooled and co-assembled using MEGAHIT ⁵⁰. Read coverage of the contigs was carried out using bwa-mem (http://bio-bwa.sourceforge.net), followed by contig binning using MetaBAT-2 ⁵¹ with contigs longer than 2000 bp. The completeness and contamination level of the MAGs were evaluated using CheckM ⁵². Only bins with a contamination level under 5% and completeness above 40% were analysed (Supplementary Fig. 1). Taxonomic affiliation of the MAGs was carried out using GTDB-tk ⁵³. Hydrocarbon cycling genes in the MAGs were identified using IMG/MR annotations and CANT-HYD HMM profiles as for metagenomic dataset. Relative abundance of the MAGs was estimated with the average coverage of the contigs determined using bwa-mem and averaged using the jgi_summarize_bam_contig_depths script. Genetic composition of the MAGs was determined using Kegg Orthologies (KO). List of KOs detected per MAG is available in Supplementary dataset 1.

For phylogenetic analysis of hydrocarbon producing genes, amino acid sequences of fatty aldehyde decarbonylase, aldehyde deformylating oxygenase and olefin beta-lactone synthetase were recovered from the metagenomic dataset and compared against NCBI database. Sequences with the best hit of blast were downloaded and aligned with the metagenomic sequences using Clustal Omega ⁵⁴. Maximum likelihood tree of 145 sequences with 725 amino acid sites was constructed using IQTree with 1000 bootstraps and the LG + F + I + G4 model ⁵⁵.

Data Availability

Assembled metagenome data are available in IMG/MR (https://img.jgi.doe.gov/mer/) under the following accession numbers: 3300033443, 3300033444, 3300033445, 3300033439, 3300033411, 3300033473, 3300033474, 3300033495 Co-assembly is also available on IMG/MR under accession number 3300033064. Raw amplicon sequences and bin files were deposited in the NCBI public database under Bioproject PRJNA616293 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA616293). List of KOs detected per MAG is available in Supplementary dataset 1. Environmental metadata were previously published ^20,23 and additional data are available in the Nordicana D database (http://www.cen.ulaval.ca/nordicanad).

Acknowledgements

We thank Alexander Culley (Université Laval), Denis Sarrazin (Centre d’études nordiques) and other members of the Northern Ellesmere Island in the Global Environment (NEIGE) team for collaborating in the sampling effort; Parks Canada for access to facilities; Polar Continental Shelf Program and Canadian Helicopter Ltd. for the logistic support; and Compute Canada and Calcul Quebec for computing resources and technical support. This work was supported by the program Sentinel North financed by the Canada First Research Excellence Fund (CFREF); the Natural Sciences and Engineering Research Council of Canada (NSERC); the CNR (Italy) – Universite Laval UMI-MicroMeNu program; the fond de Recherche du Quebec Nature et Technologies (FQRNT); and the Network of Centres of Excellence ArcticNet.

Author contributions: A.V. and W.F.V. designed the research, W.F.V. obtained funding, logistics and permits for the research; W.F.V. conducted the field sampling; C.L provided laboratory and computational access; A.V. generated the molecular data; A.V. and P.C. analyzed the data; A.V. wrote the paper with W.F.V., P.C. and C.L.

Competing interests: Authors declare no competing interest

Material & Correspondence: Material request should be addressed to A.V

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Dataset 1

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Cryptic cycles of microbial hydrocarbon production and degradation along freshwater-saltwater ecosystem gradients

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Abstract

Figures

Introduction

Results

Hydrocarbon Degrading Genes

Hydrocarbon Cycling Microbial Populations

Sulfur And Nitrogen Cycle Genes In Hydrocarbon Short Cycle Populations

Discussion

Freshwater hydrocarbon short cycle

Hydrocarbon Biosynthesis Under Aphotic And Low Oxygen Conditions

Biohydrocarbon Degradation In Petroleum Free Marine Ecosystems

Hydrocarbon Short Cycles Connect To Sulfur And Nitrogen Cycles

Conclusions

Material And Methods

Site description, sample collection and nucleic acid extraction

Declarations

References

Additional Declarations

Supplementary Files

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