Microbial iron metabolism as revealed by gene expression profiles in contrasted Southern Ocean regimes

Type Article
Date 2019-07
Language English
Author(s) Debeljak Pavla1, 2, Toulza Eve3, Beier Sara4, Blain Stephane1, Obernosterer Ingrid1
Affiliation(s) 1 : Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne, LOMIC F‐66650 Banyuls/mer ,France
2 : Department of Limnology and Bio‐OceanographyUniversity of Vienna A‐1090 Vienna ,Austria
3 : Université Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier F‐66860 Perpignan ,France
4 : Leibniz Institute for Baltic Sea Research Warnemünde, Germany
Source Environmental Microbiology (1462-2912) (Wiley), 2019-07 , Vol. 21 , N. 7 , P. 2360-2374
DOI 10.1111/1462-2920.14621
WOS© Times Cited 21
Abstract

Iron (Fe) is a limiting nutrient in large regions of the ocean, but the strategies of prokaryotes to cope with this micronutrient are poorly known. Using a gene‐specific approach from metatranscriptomics data, we investigated 7 Fe‐related metabolic pathways in microbial communities from High Nutrient Low Chlorophyll and naturally Fe‐fertilized waters in the Southern Ocean. We observed major differences in the contribution of prokaryotic groups at different taxonomic levels to transcripts encoding Fe uptake‐mechanisms, intracellular Fe storage and replacement, and Fe‐related pathways in the tricarboxylic acid (TCA) cycle. The composition of the prokaryotic communities contributing to the transcripts of a given Fe‐related pathway was overall independent of the in situ Fe supply, indicating that microbial taxa utilize distinct Fe‐related metabolic processes. Only a few prokaryotic groups contributed to the transcripts of more than one Fe‐uptake mechanism, suggesting limited metabolic versatility. Taxa‐specific expression of individual genes varied among prokaryotic groups and was substantially higher for all inspected genes in Fe‐limited as compared to naturally fertilized waters, indicating the link between transcriptional state and Fe regime. Different metabolic strategies regarding low Fe concentrations in the Southern Ocean are discussed for two abundant prokaryotic groups, Pelagibacteraceae and Flavobacteriaceae.
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Supplementary Figure 1. Blast results of subsets for assigned to non‐assigned reads 1 KB Open access
Supplementary Figure 2. Relative contribution of prokaryotic groups to pathway specific transcripts. Prokaryotic group is defined until taxonomic family level. Number 1 and 2 refer to the ... 13 KB Open access
Supplementary Figure 3. A‐C Detailed view of relative contribution of Alpha‐ and Gammaproteobacteria and FCB cluster to pathway specific transcripts. Note the different y‐axis for ... 16 KB Open access
Supplementary Figure 4. Percentage of ribosomal protein transcripts to all prokaryotic transcripts. 21 KB Open access
Supplementary Figure 5. A‐G. Relative contribution of prokaryotic groups to pathway specific transcripts and relative abundance of 16S rRNA gene sequences. Prokaryotic group is defined until... 437 KB Open access
Supplementary Figure 6. Simple illustration of the glyoxylate shunt (inside of the circle) in which isocitrate lyase cleaves isocitrate into glyoxylate and succinate. 41 KB Open access
Supplementary Figure 7. Detailed plots for duplicates on the phylum, class and order level for each pathway. 883 KB Open access
Supplementary Table 1. General information on sequencing results and reads. 1 86 KB Open access
Supplementary Table 2. Relative contribution of prokaryotic groups to pathway specific transcripts. For each group, mean value ± standard deviation of 2 replicates are shown. Error estimates are ... 8 164 KB Open access
Supplementary Table 3. Taxa‐specific transcript abundance (per 105 cells) of a given pathway at Station F‐L and R‐2. For each group, mean value ± standard deviation of 2 replicates are shown. Error .. 5 82 KB Open access
Supplementary Table 4. Information of databases constructed or modified from Toulza et al. (2012) and retrieved by NCBI 1 86 KB Open access
Supplementary Table 5. Pathways and corresponding KEGG‐Id numbers that were chosen for further analysis 1 83 KB Open access
Supplementary Table 6. Cells per L for prokaryotic groups in Figure 6 for station R‐2 and F‐L, calculated as described in experimental procedures. 1 147 KB Open access
Publisher's official version 15 1 MB Open access
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