*Author/Owner of KBase Narratives
This Narrative is part of a collection used in publications focused on the microbial ecology of fjord sediment in the high Arctic, Svalbard. This paper took a genome-centric approach to uncover novel metabolic capabilities of the Acidobacteriota clade. Metagenomic data was coupled with amplicon sequencing of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes, and transcripts (available under NCBI-Genbank Bioproject PRJNA623111), and gene expression analyses of tetrathionate-amended microcosms.
This Narrative contains the metagenomic assemblies that were constructed within KBase for reproducibility. These include:
These metagenome assemblies served as the launching point for an additional publication focused on a different clade of bacteria (Buongiorno et al., 2020). Link to that Narrative landing page here.
Please cite: Flieder, Mathias, Joy Buongiorno, Craig W. Herbold, Bela Hausmann, Thomas Rattei, Karen G. Lloyd, Alexander Loy, and Kenneth Wasmund. "Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling." The ISME Journal (2021): 1-22.
|Metagenomic sample origin*||General biogeochemical type||Sample site coordinates||Illumina read pairs||Read coverage normalised#||Lab|
|Smeerenburgfjorden; Station J, 0-4 cmbsf||Ferruginous/sulfidic||79° 42.83N, 11° 05.10E||45,996,553||Vienna|
|Smeerenburgfjorden; Station J, 10-15 cmbsf||Sulfidic||79° 42.83N, 11° 05.10E||73,362,243||Vienna|
|Smeerenburgfjorden; Station J, 17-20 cmbsf||Sulfidic||79° 42.83N, 11° 05.10E||49,176,577||Vienna|
|Smeerenburgfjorden; Station J, 59 cmbsf||Sulfidic||79° 42.83N, 11° 05.10E||56,792,638||Vienna|
|Smeerenburgfjorden; Station J, 5-10 cmbsf, microcosm with tetrathionate + molybdate||Sulfidic||79° 42.83N, 11° 05.10E||99,662,741||Vienna|
|Smeerenburgfjorden; Station J, 5-10 cmbsf, microcosm with thiosulfate + molybdate||Sulfidic||79° 42.83N, 11° 05.10E||53,175,346||Vienna|
|Smeerenburgfjorden; Station J, 5-10 cmbsf, microcosm with tetrathionate||Sulfidic||79° 42.83N, 11° 05.10E||197828199||to 100x||Vienna|
|Van Kuelenfjorden; Station AC, 18 cmbsf||Ferruginous/manganous||77°32.260’ N, 15°39.434’ E||167411750||to 100x||Vienna|
|Van Kuelenfjorden; Station AB, 0-5 cmbsf||Ferruginous/manganous||77°35.249’ N, 15°05.121’E||98,211,882||to 100x||Knoxville|
|Kongsfjorden; Station F, 0-5cmbsf||Ferruginous/manganous||78°55.075’ N, 12°15.929’ E||75,827,490||to 100x||Knoxville|
Sulfate reduction is a major process in marine sediments, the activities, distributions, and diversity of SRMs have been relatively well studied1-3. Surveys of functional marker genes for sulfite/sulfate reducers in marine sediments, i.e., of dsrAB, have repeatedly shown that dsrAB from the phylum Desulfobacterota are typically the dominant dsrAB-harboring group in marine sediments, but importantly, that several other lineages of uncultivated dsrAB-harboring organisms are also abundant and prevalent4. In this study, we aimed to gain insights into the metabolic potential of uncultured Acidobacteriota lineages in marine sediments, as well as their diversity and distributions. We therefore recovered metagenome-assembled genomes (MAGs) from abundant Acidobacteriota populations present in marine fjord sediments of Svalbard, and predicted their metabolic features. Focus was placed on MAGs from the class Thermoanaerobaculia of the Acidobacteriota, which represent a newly described lineage of dsrAB-harboring organisms that may be important sulfur cycling bacteria in marine sediments. These analyses were complemented with comparative genomics, incubation experiments, transcript analyses, and analyses of Acidobacteriota distributions in Svalbard sediments and publicly available datasets, together revealing they may play various roles in sedimentary biogeochemical cycles, and that they are a prominent group of sulfur-dissimilating organisms.
Jørgensen BB, Findlay AJ, Pellerin A. The biogeochemical sulfur cycle of marine sediments. Front Microbiol. 2019;10:849.
Revsbech NP, Barker Jorgensen B, Blackburn TH. Oxygen in the Sea Bottom Measured with a microelectrode. Science. 1980;207:1355.
Wasmund K, Mußmann M, Loy A. The life sulfuric: microbial ecology of sulfur cycling in marine sediments. Environ Microbiol Rep. 2017;9:323–44.
Müller AL, Kjeldsen KU, Rattei T, Pester M, Loy A. Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases. ISME J. 2015;9:1152–65.
Buongiorno J, Sipes K, Wasmund K, Loy A, Lloyd KG. Woeseiales transcriptional response to shallow burial in Arctic fjord surface sediment. PLOS ONE. 2020;15:e0234839.
Angel R, Claus P, Conrad R. Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions. ISME J. 2012;6:847–62.
Peng Y, Leung HCM, Yiu SM, Chin FYL. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics. 2012;28:1420–8.
Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017;27:824–34.
Li D, Liu C-M, Luo R, Sadakane K, Lam T-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015;31:1674–6.
Wu Y-W, Simmons BA, Singer SW. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics. 2016;32:605–7.
This research was supported by the Austrian Science Fund (FWF grants P29426 to KW and P25111-B22 to AL) and the MetaBac Research Platform of the University of Vienna. We thank Captain Stig Henningsen of MS Farm during Svalbard expeditions. We particularly thank Bo Barker Jørgensen, Alexander Michaud, and Susann Henkel for organizing the 2016 and 2017 Svalbard expeditions, and all members of Svalbard expeditions for help with sample collection, especially Claus Pelikan. We thank the Alfred Wegener Institute—Institute Paul Emile Victor (AWIPEV) station and staff for housing and excellent logistics support. We thank the Biomedical Sequencing Facility (BSF) Vienna for sequencing of metagenome samples, the Joint Microbiome Facility (JMF) of the Medical University of Vienna and the University of Vienna, and Microsynth for sequencing amplicons. We specifically thank Jasmin Schwarz, Gudrun Kohl, and Petra Pjevac from the JMF for assisting with amplicon sequencing. We thank Marc Mussman and Stefan Dyksma for providing the hydrogenase database. We are grateful to Bernhard Schink for help with Latin naming of taxa.