Abstract
Sea ice habitats harbour seasonally abundant microalgal communities, which can be highly productive in the spring when the availability of light increases. An active, bloom-associated prokaryotic community relies on these microalgae for their organic carbon requirements, however an analysis of the encoded metabolic pathways within them is lacking. Hence, our understanding of biogeochemical cycling within sea ice remains incomplete. Here, we generated metagenomic assembled genomes from the bottom of first-year sea ice in northwestern Hudson Bay, during a spring diatom bloom. We show that the prokaryotic community had the metabolic potential to degrade algal derived dimethylsulphoniopropionate and oxidise sulfur. Facultative anaerobic metabolisms, specifically, dissimilatory nitrate reduction and denitrification were also prevalent here, suggesting some sea ice prokaryotes are metabolically capable of adapting to fluctuating oxygen levels during algal bloom conditions. Such denitrification could be an important loss of fixed-N2 in the changing Arctic marine system.
Introduction
Sea ice creates a dynamic habitat for microorganisms, controlled by fluctuations in light, salinity and temperature caused by seasonal extremes, combined with localised variability in atmosphere-ice-ocean gas and nutrient exchange. An area of particularly high seasonal productivity is the bottom centimetres of the ice, where an abundant microalgal community develops in spring, dominated by diatoms [1]. This microalgal growth accelerates when light conditions are optimal and is supported by nutrients predominantly coming from the water column [2]. Diatom blooms release extracellular polymeric substances (EPS) into their surroundings to increase sea ice habitability [3] and the sulfur metabolite dimethylsulfoniopropionate (DMSP) [4, 5], which acts as an osmoregulator and cryoprotectant [6]. There is evidence that DMSP production varies with the composition of cold-adapted algal blooms, with species like Nitzschia spp. having driven its release in previous studies of sea ice [4]. Both EPS and DMSP can be readily metabolised by the local prokaryotic community [3, 4, 7], with DMSP representing a major source of reduced sulfur to marine prokaryotes [8, 9], although the individual species involved and metabolic pathways remain unclear for sea ice habitats. This active heterotrophic community has the potential to create localised oxygen limited environments [10, 11]. Indeed, sulphate reducing bacteria, such as Desulforhopalus (Deltaproteobacteria), have been found in Antarctic sea ice [12], and anaerobic denitrification processes have been detected in Arctic sea ice [11, 13].
In this study, we analyzed the prokaryotic communities associated with a diatom bloom in sea ice (n = 4) from northwestern Hudson Bay, to reveal a proportion of the prokaryotic community encoded for facultatively anaerobic processes. We also identified DMSP degradation and sulfur oxidation genes in dominant taxa, suggesting that algal derived DMSP is an important energy source for sea ice prokaryotes.
Results and discussion
Sea ice algal composition
Significant algal growth was documented in the bottom-ice at all sites along a transect to the ice flow edge (16,000–60,000 cells ml−1). The community was dominated by pennate diatoms (Fig. 1A, D), specifically Nitzschia spp. (Site A and C) and Entomoneis kjellmanii (Site F), which had a relative abundance of 63–82% of the community [4].
Prokaryotic diversity
Associated with the bloom was a diverse prokaryotic community, dominated by the orders Oceanospirillales (NCBI) / Pseudomonadales (GTDB), Alteromonadales (NCBI) / Enterobacterales (GTDB), Flavobacteriales and Rhodobacterales (Fig. 1B, C), which together accounted for 56–83% of prokaryotic diversity by analysis of unassembled reads (Supplementary Methods). Previous 16S rRNA studies have detected dominant Alteromonadaceae and Flavobacteriaceae in sea ice [14, 15]. In terms of metabolic functions, 14 out of 104 MAGs (1–12% of the MAGs by relative abundance) (Fig. 1E; Supplementary Table 1) encoded genes for DMSP degradation, either through lysis to dimethylsulfide (DMS) (dddL or dddP genes), or though a demethylation pathway (dmdA or dmdD) to methanethiol [7, 16], with seven MAGs further encoding the ability to oxidise methanethiol to hydrogen sulfide. Nearly all DMSP degraders (13 of 14 MAGs), and an additional 10 MAGs (1–18% of all MAGs by relative abundance) encoded sulfur oxidation genes (Fig. 2), suggesting that sulfur from DMSP degradation is utilised for energy, either through DMSP demethylation and methanethiol oxidation, or another undetermined pathway. These genes were particularly prevalent in members of the Rhodobacteraceae family, some of which are well known to metabolise DMSP [17]. In previous research on Arctic frost flowers, DMSP catabolism genes were attributed to members of the Rhizobiales [18].
Facultatively anaerobic Dissimilatory Nitrate Reduction (DNR) to ammonia and denitrification genes were prevalent in many abundant members of the prokaryotic community. Eight MAGs (Fig. 2) encoded the ability to anaerobically respire inorganic nitrate (napAB or narGHI genes), these represented 1–22% of all MAGs by relative abundance (Fig. 1E). Six of these also encoded nitrite reductase (nirBD) genes, suggesting nitrite may be further reduced to ammonia. Two Saccharospirillaceae MAGs (MAGs 595 and 939; Fig. 2), representing up to 20% of MAGs by relative abundance in site F, additionally encoded denitrification pathways from nitrate to nitrous oxide or dinitrogen, with another nine MAGs (Alteromonadaceae, Nitrincolaceae, Saccharospirillaceae, Flavobacteriaceae and Rhodobacteraceae) encoding one or more genes from the denitrification pathway (nirS/K, norBC or nosZ), showing the potential for denitrification in 5–23% of the community by MAG relative abundance (Fig. 2). The ability to anaerobically respire oxidised forms of nitrogen may be particularly advantageous to sea ice prokaryotes, which are subjected to low or fluctuating oxygen conditions [10, 11].
The respiratory reduction for nitrate may also be coupled to the oxidation of reduced sulfur to support chemolithotrophic growth, evidence for this was found in three Rhodobacteraceae MAGs (Fig. 2), one of which (MAG 328) encoded three nitrate reductase subunits (narGHI) along with a complete set of sox genes (soxXYZABCD). Concurrently, five members of the Nitrincolaceae family were represented (0–12% by relative abundance), which are known to be dominant gammaproteobacteria associated with the termination phase of diatom blooms [19] and often involved in denitrification [20]. One of these MAGs encoded a complete pathway for the dissimilatory reduction of nitrate to ammonia (napAB and nirBD) along with the soeABC enzyme complex, but without detectable CO2 fixation genes (RuBisCO), suggesting a chemoheterotrophic lifestyle. All Nitrincolaceae MAGs contained complete or partial pathways for sulfur oxidation, either via the soeABC enzyme complex, reverse-acting dissimilatory sulfate reduction (sat/aprAB) or the sox system, indicating that these organisms were all involved in sulfur cycling. Interestingly, members of the Thiomicrospirales were well represented by two partial MAGs (Thioglobus spp., MAGs 233 and 430; 0.1–21% of MAG relative abundance). Thiomicrospirales are typical oxygen minimum zone taxa [21], with Thioglobus spp. belonging to the SUP05 clade of chemoautotrophs, known to couple sulfite oxidation to nitrite reduction [22]. From our KEGG analysis, one Thioglobus sp. contained reverse-acting dissimilatory sulfate reduction genes (aprAB), whilst the other encoded a Sulfide:Quinone Oxidoreductase. Both encoded RuBisCO, which suggests a chemolithoautotrophic lifestyle, however, no dissimilatory nitrate reduction genes were identified, which may have been because of the incomplete nature of these MAGs (73–75% estimated by CheckM).
Conclusions
This study highlights a heterogeneous sea ice prokaryotic community which is metabolically capable of sea ice algal DMSP degradation and associated sulfur oxidation, whilst also encoding for facultatively anaerobic metabolisms. These findings, combined with previous observations for anoxic conditions and denitrification, show that sea ice prokaryotic communities have the potential to maintain metabolic activity under fluctuating oxygen levels and influence nutrient cycles. Whilst we show genomic potential, we cannot comment on the activity of such processes. Further investigations are now needed to characterise the activity of these metabolic pathways in concert with the extent and variability of oxygen concentrations in sea ice. An understanding of sea ice denitrification is critical for our understanding of microbial production and nutrient limitation during algal blooms in this rapidly changing habitat.
Data availability
Raw reads are available in GenBank under BioProject PRJNA1011243, MAGs are found under BioSamples SAMN37641281-SAMN37641385. All assembled data are available from JGI (https://gold.jgi.doe.gov/projects) under GOLD Project IDs: Gp0507596 Gp0507597, Gp0507598, Gp0507599.
References
van Leeuwe M, Tedesco L, Arrigo KR, Assmy P, Campbell K, Meiners KM, et al. Microalgal community structure and primary production in Arctic and Antarctic sea ice: A synthesis. Elem Sci Anth. 2018;6:4.
Leu E, Mundy CJ, Assmy P, Campbell K, Gabrielsen TM, Gosselin M, et al. Arctic spring awakening – Steering principles behind the phenology of vernal ice algal blooms. Overarching Perspect Contemp Future Ecosyst Arct Ocean. 2015;139:151–70.
Ewert M, Deming JW. Sea ice microorganisms: environmental constraints and extracellular responses. Biology. 2013;2:603–28.
Galindo V, Levasseur M, Mundy CJ, Gosselin M, Tremblay JÉ, Scarratt M, et al. Biological and physical processes influencing sea ice, under-ice algae, and dimethylsulfoniopropionate during spring in the Canadian Arctic Archipelago. J Geophys Res Oceans. 2014;119:3746–66.
Levasseur M, Gosselin M, Michaud S. A new source of dimethylsulfide (DMS) for the arctic atmosphere: ice diatoms. Mar Biol. 1994;121:381–7.
Kirst GO, Thiel C, Wolff H, Nothnagel J, Wanzek M, Ulmke R. Dimethylsulfoniopropionate (DMSP) in ice algae and its possible biological role. Mar Chem. 1991;35:381–8.
Kiene RP, Linn LJ. The fate of dissolved dimethylsulfoniopropionate (DMSP) in seawater: Tracer studies using 35S-DMSP. Geochim Cosmochim Acta. 2000;64:2797–810.
Kiene RP, Linn LJ, Bruton JA. New and important roles for DMSP in marine microbial communities. J Sea Res. 2000;43:209–24.
Kiene RP, Linn LJ, González J, Moran MA, Bruton JA. Dimethylsulfoniopropionate and methanethiol are important precursors of methionine and protein-sulfur in marine bacterioplankton. Appl Environ Microbiol. 1999;65:4549–58.
Campbell K, Mundy CJ, Gosselin M, Landy JC, Delaforge A, Rysgaard S. Net community production in the bottom of first-year sea ice over the Arctic spring bloom: spring transition of sea ice NCP. Geophys Res Lett. 2017;44:8971–8.
Rysgaard S, Glud RN. Anaerobic N2 production in Arctic sea ice. Limnol Oceanogr. 2004;49:86–94.
Eronen-Rasimus E, Luhtanen AM, Rintala JM, Delille B, Dieckmann G, Karkman A, et al. An active bacterial community linked to high chl- a concentrations in Antarctic winter-pack ice and evidence for the development of an anaerobic sea-ice bacterial community. ISME J. 2017;11:2345–55.
Rysgaard S, Glud RN, Sejr MK, Blicher ME, Stahl HJ. Denitrification activity and oxygen dynamics in Arctic sea ice. Polar Biol. 2008;31:527–37.
Yergeau E, Michel C, Tremblay J, Niemi A, King TL, Wyglinski J, et al. Metagenomic survey of the taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic. Sci Rep. 2017;7:1–10.
Rapp JZ, Sullivan MB, Deming JW Divergent Genomic Adaptations in the Microbiomes of Arctic Subzero Sea-Ice and Cryopeg Brines. Front Microbiol [Internet]. 2021;12. Available from: https://www.frontiersin.org/articles/10.3389/fmicb.2021.701186.
Kiene RP. Production of methanethiol from dimethylsulfoniopropionate in marine surface waters. Mar Chem. 1996;54:69–83.
Bullock HA, Luo H, Whitman WB. Evolution of dimethylsulfoniopropionate metabolism in marine phytoplankton and bacteria. Front Microbiol. 2017;8:1–17.
Bowman JS, Berthiaume CT, Armbrust EV, Deming JW. The genetic potential for key biogeochemical processes in Arctic frost flowers and young sea ice revealed by metagenomic analysis. FEMS Microbiol Ecol. 2014;89:376–87.
Liu Y, Blain S, Crispi O, Rembauville M, Obernosterer I. Seasonal dynamics of prokaryotes and their associations with diatoms in the Southern Ocean as revealed by an autonomous sampler. Environ Microbiol. 2020;22:3968–84.
Mori JF, Chen LX, Jessen GL, Rudderham SB, McBeth JM, Lindsay MBJ, et al. Putative mixotrophic nitrifying-denitrifying gammaproteobacteria implicated in nitrogen cycling within the ammonia/oxygen transition zone of an oil sands pit lake. Front Microbiol. 2019;10:1–15.
Pajares S, Varona-Cordero F, Hernández-Becerril DU. Spatial distribution patterns of bacterioplankton in the oxygen minimum zone of the tropical mexican pacific. Microb Ecol. 2020;80:519–36.
Spietz RL, Lundeen RA, Zhao X, Nicastro D, Ingalls AE, Morris RM. Heterotrophic carbon metabolism and energy acquisition in Candidatus Thioglobus singularis strain PS1, a member of the SUP05 clade of marine Gammaproteobacteria. Environ Microbiol. 2019;21:2391–401.
Acknowledgements
The authors wish to acknowledge the support of C.J. Mundy, Zou Zou Kuzyk and Jens Ehn (University of Manitoba), the Korean Polar Research Institute (KOPRI) and the community of Coral Harbour, Nunavut, in the collection of data for this work.
Funding
Field work and logistics were supported via collaborative contributions from the Marine Environmental Observation, Prediction and Response Network of Centres of Excellence (MEOPAR-NCE) for the Southampton Island Marine Ecosystem Project (SIMEP), an NSERC-matched grant for the 2017-2018 Belmont Forum and BiodivERsA joint call for research proposals under the BiodivScen ERA-Net CO-FUND programme to the project ACCES: De-icing of Arctic Coasts (Critical or new opportunities for marine biodiversity and Ecosystem Services). Support was also provided from an ArcticNet National Centres of Excellence grant, as well as NSERC Discovery Grants and Northern Research Supplement to CJ Mundy, Jens Ehn and Zou Zou Kuzyk. This work is a contribution to the Diatom ARCTIC project (NE/R012849/1; 03F0810A), part of the Changing Arctic Ocean program, jointly funded by the UKRI Natural Environment Research Council and the German Federal Ministry of Education (BMBF). It is also a contribution to the Research Council of Norway BREATHE (Bottom sea ice Respiration and nutrient Exchanges Assessed for THE Arctic) project (325405). Support was also provided to K. Campbell through the MICRO NutriENT project funded by the UK Arctic Office’s UK-Canada Arctic Partnership: Bursary Programme. C. Bellas was also supported by the Austrian Science Fund (FWF P-34620). P. Sanchez- Baracaldo was supported by a Royal Society University Research Fellowship.
Author information
Authors and Affiliations
Contributions
CMB, PS-B, KC, MT: conceived the ideas and wrote the manuscript. KC: collected all samples. CMB: performed all data analysis.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing interests.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary information
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
About this article
Cite this article
Bellas, C.M., Campbell, K., Tranter, M. et al. Nitrogen and sulfur metabolisms encoded in prokaryotic communities associated with sea ice algae. ISME COMMUN. 3, 131 (2023). https://doi.org/10.1038/s43705-023-00337-2
Received:
Revised:
Accepted:
Published:
DOI: https://doi.org/10.1038/s43705-023-00337-2