Microbial community composition and functional potential in Bothnian Sea sediments is linked to Fe and S dynamics and the quality of organic matter

Olivia Rasigraf*, Niels A.G.M. van Helmond, Jeroen Frank, Wytze K. Lenstra, Matthias Egger, Caroline P. Slomp, Mike S.M. Jetten

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

The Bothnian Sea is an oligotrophic brackish basin characterized by low salinity and high concentrations of reactive iron, methane, and ammonium in its sediments, enabling the activity and interactions of many microbial guilds. Here, we studied the microbial network in these sediments by analyzing geochemical and microbial community depth profiles at one offshore and two near coastal sites. Analysis of 16S rRNA gene amplicons revealed a distinct depth stratification of both archaeal and bacterial taxa. The microbial communities at the two near coastal sites were more similar to each other than the offshore site, which is likely due to differences in the quality and rate of organic matter degradation. The abundance of methanotrophic archaea of the ANME-2a clade was shown to be related to the presence of methane and varied with sediment iron content. Metagenomic sequencing of sediment-derived DNA from below the sulfate–methane transition zone revealed a broad potential for respiratory sulfur metabolism via partially reduced sulfur species. The potential for nitrogen cycling was dominated by reductive processes via a truncated denitrification pathway encoded exclusively by bacterial lineages. Gene-centric fermentative metabolism analysis indicated a potential importance for acetate, formate, alcohol, and hydrogen metabolism. Methanogenic/-trophic pathways were dominated by Methanosaetaceae, Methanosarcinaceae, Methanomassiliicoccaceae, Methanoregulaceae, and ANME-2 archaea. Our results indicated flexible metabolic capabilities of core microbial community taxa, which could adapt to changing redox conditions, and with a spatial and depth distribution that is likely governed by the quality and input of available organic substrates and, for ANME-2, of iron oxides.

Original languageEnglish
Pages (from-to)5113-5133
Number of pages21
JournalLimnology and Oceanography
Volume65
Issue numberS1
DOIs
Publication statusPublished - Jan 2020

Funding

We would like to thank Theo van Alen and Geert Cremers for sequencing the metagenomes. The captain, crew, and scientific participants aboard R/V Lotty are thanked for their assistance during sampling in August 2015. This work was carried out on the Dutch national e‐infrastructure with the support of SURF Cooperative. LABGeM (Genoscope, Institute of Genomics, CEA Sciences) and the National infrastructure “France Génomique” are acknowledged for support within the MicroScope annotation platform. O.R., M.S.M.J., and C.P.S. were supported by NESSC (Netherlands Organization for Scientific Research, grant number 024.002.001), J.F. and M.S.M.J were supported by the SIAM Gravitation Grant on Anaerobic Microbiology (Netherlands Organization for Scientific Research, grant number 024.002.002) and European Research Council (ERC AG, grant number 339880), C.P.S., W.L., and N.A.G.M.v.H. were supported by NWO (grant number 865.13.005) and the European Union and FORMAS through BONUS COCOA (grant number 2112932‐1).

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