The transcriptional response of prokaryotes to phytoplankton-derived dissolved organic matter in seawater
Summary To better understand the functional responses in prokaryotes to dissolved organic matter (DOM), we compared the transcriptional pattern of natural prokaryotic communities grown in continuous cultures on seawater amended with phytoplankton‐derived DOM. Metatranscriptomic reads were classified...
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| Published in | Environmental microbiology Vol. 17; no. 10; pp. 3466 - 3480 |
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| Main Authors | , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Blackwell Publishing Ltd
01.10.2015
Wiley Subscription Services, Inc |
| Subjects | |
| Online Access | Get full text |
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| Summary: | Summary
To better understand the functional responses in prokaryotes to dissolved organic matter (DOM), we compared the transcriptional pattern of natural prokaryotic communities grown in continuous cultures on seawater amended with phytoplankton‐derived DOM. Metatranscriptomic reads were classified taxonomically (by genomic binning) and functionally (using Kyoto Encyclopedia of Genes and Genomes), and the relative gene expression of individual taxa (genome bins) was compared with the total community response. In the first experiment comparing seawater and seawater amended with diatom‐derived DOM, metatranscriptomes revealed pronounced differences in pathways involved in carbohydrate and lipid metabolism. In the second experiment comparing seawater amended with cyanobacteria‐ and diatom‐derived DOM, metatranscriptomes had similar functional profiles, likely reflecting more similar DOM regimes in this experimental setup. Among the five most abundant taxa investigated in more detail, two featured pronounced differences in transcript abundance between treatments suggesting that they were specialized in the use of only one of the two DOM regimes. However, these two taxa were less involved in carbohydrate metabolism than others and had few genes that were significantly regulated in response to the DOM source. Our results indicate that both substrate composition and the competitive interplay of community members were decisive for the functional response of a microbial system. |
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| Bibliography: | Gordon and Betty Moore Foundation istex:8C4BF153A815D0DB3CF5AC20059CD496D90CB6D6 ArticleID:EMI12434 Fig. S1. Chemical characteristics of the input media and the two DOM sources published previously by (Landa et al., 2013b). Composition (mol%) of total hydrolysable neutral sugars (A) and amino acids (B) in the diatom DOM medium and the cyanobacterial DOM medium. van Krevelen diagram based on analysis by FT-ICR MS showing ratios of H/C and O/C for compounds specific of diatom DOM and cyanobacterial DOM in the PPL-extracted fraction (C). For the two phytoplankton DOM sources, the PPL recovery efficiency was 8% of total DOC. Areas tentatively assigned as carboxylic-rich alicyclic molecules (CRAM), proteins, lipids, condensed hydrocarbons and amino sugars are also shown.Fig. S2. Dendrograms (Bray-Curtis dissimilarity, Ward's linkage) based on a normalized count data set after taxonomic (A) and functional (B) binning of the sequence data. Filled circles indicate technical replicates from Exp_SwDi and open circles indicate technical replicates from Exp_CyDi.Fig. S3. In order to display differences in expression patterns between the outliers cyano2b/diatom1a (Exp_CyDi, Supporting Information Fig. S1) and the remaining technical replicates, this heatmap highlights genes that were significantly differently expressed between outliers and the remaining technical replicates. The heatmap illustrates that differences between the outliers, and the remaining samples were mostly due to genes that were highly enriched in the outlier samples, but low in abundance or undetected in the remaining samples. This pattern might be caused by contamination with genomic DNA. DNA contamination would also explain why samples cyano2b/diatom1a (Exp_CyDi) clustered as outliers in the functional but not in the taxonomic cluster analysis (Supporting Information Fig. S1). Significance was tested following the differential expression analysis in the DESeq package (Anders and Huber, 2010) and a significance level of P < 0.1 with the P-value adjusted for multiple testing using the Benjamini-Hochberg procedure. The displayed subset of genes was not scaled for the heatmap but originates from the total data set, which was normalized by sample according to the DESeq package. SwDi or CyDi before the technical replicate designates its origin from Exp_SwDi and Exp_CyDi.Table S1. Concentrations of dissolved organic carbon (DOC), nitrate + nitrite (NO3-+NO2-) and phosphate (PO43-) in the input media and the biological replicates during the experimental period. In Exp_CyDi, nitrogen was also added in the form of NH4+ to the input medium (20 μM final concentration). Mean values ± SD are given. For each time point, the average value of the two replicate + DOM cultures was used. n = number of time points for which chemical analyses were carried out.Table S2. List of all genes with KEGG number (ko) that were analysed for differential expression in pathways in the metabolism class, and in transporter protein categories [ABC transporters (path:ko02010), phosphotransferase system (PTS) (path:ko02060)]. Kegg_colour gives the colour codes used in the colour-mapping tool provided by KEGG (http://www.genome.jp/kegg/tool/map_pathway2.html) in order to map significantly (intense colour) or non-significantly (light colour) enriched (green) and decreased (red) genes (with respect to the diatom treatment in both experiments). Genes with pko = 1 are indicated with a blue border, with the pko value representing the probability of a gene contributing to a certain pathway. The colour coding was used for grouping of genes after visual inspection in order to use these groups of genes as units for PI calculation. The units of genes used for PI calculation are designated in the column pathway/module. The fold change indicates an enrichment or decrease of a gene in the diatom treatment of both experiments, if values are > 0 or < 0 respectively. The terms class, category, pathway and description indicate the KEGG BRITE nomenclature. P-values adjusted with the Benjamini-Hochberg procedure were obtained for each gene from differential expression analysis for all genes or transcriptomes of the key taxa. Genes are highlighted in red if significantly decreased and green if significantly increased in the diatom treatment in Exp_SwDi and Exp_CyDi (significance level: padj < 0.1). Indicator genes (IV > 50, more than 10 reads) are displayed in yellow (gammaproteobacterium IMCC1989), blue (N. caesariensis), violet (Alcanivorax sp.), pink (C. psychrerythraea) or turquois (Glaciecola sp. HTCC2999). ark:/67375/WNG-QRMMPM06-J Agence Nationale de la Recherche - No. ANR-08-BLAN-0 309 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
| ISSN: | 1462-2912 1462-2920 |
| DOI: | 10.1111/1462-2920.12434 |