Rapid succession of uncultured marine bacterial and archaeal populations in a denitrifying continuous culture
Marine denitrification constitutes an important part of the global nitrogen cycle and the diversity, abundance and process rates of denitrifying microorganisms have been the focus of many studies. Still, there is little insight in the ecophysiology of marine denitrifying communities. In this study,...
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| Published in | Environmental microbiology Vol. 16; no. 10; pp. 3275 - 3286 |
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| Main Authors | , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Oxford
Blackwell Science
01.10.2014
Blackwell Publishing Ltd Blackwell Wiley Subscription Services, Inc |
| Subjects | |
| Online Access | Get full text |
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| Summary: | Marine denitrification constitutes an important part of the global nitrogen cycle and the diversity, abundance and process rates of denitrifying microorganisms have been the focus of many studies. Still, there is little insight in the ecophysiology of marine denitrifying communities. In this study, a heterotrophic denitrifying community from sediments of a marine intertidal flat active in nitrogen cycling was selected in a chemostat and monitored over a period of 50 days. The chemostat enabled the maintenance of constant and well‐defined experimental conditions over the time‐course of the experiment. Analysis of the microbial community composition by automated ribosomal intergenic spacer analysis (ARISA), Illumina sequencing and catalyzed reporter deposition fluorescence in situ hybridization (CARD‐FISH) revealed strong dynamics in community composition over time, while overall denitrification by the enrichment culture was stable. Members of the genera Arcobacter, Pseudomonas, Pseudovibrio, Rhodobacterales and of the phylum Bacteroidetes were identified as the dominant denitrifiers. Among the fermenting organisms co‐enriched with the denitrifiers was a novel archaeon affiliated with the recently proposed DPANN‐superphylum. The pan‐genome of populations affiliated to Pseudovibrio encoded a NirK as well as a NirS nitrite reductase, indicating the rare co‐occurrence of both evolutionary unrelated nitrite reductases within coexisting subpopulations. |
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| Bibliography: | http://dx.doi.org/10.1111/1462-2920.12552 Note S1. Supplementary methods. Fig. S1. Separation of contigs belonging to the most abundant populations in the samples of four different time points by combined tetranucleotide and interpolated Markov Model binning. Left panel: The distribution of the contigs on a sequencing coverage versus GC plot shows clouds each corresponding to a different bin and population. The contigs of the different populations were clearly separated from each other except for bin G and H, two Vibrionales subpopulations, and bin I, as well as bin D and K. They only show a small difference in GC content. The two separate clouds differing in coverage for bin E at day 46 may result from different subpopulations. The squares indicate the contigs, that encode the nitrite reductases of bin E (blue: nirS; red: nirK). Right panel: The pie charts show the taxonomic distribution of blast hits of fragmented contigs to reference genomes. The distance of each slice from the centre of the pie is a measure for the median e-value of the associated hits (larger e-value correspond to larger distances from the centre).The low number, relatively high e-values and scattering of blast hits obtained for bin A (Archaeon) is caused by the distant relationship of the bin to any available reference. Fig. S2. Phylogenetic tree of bacterial 16S rRNA sequences. Phylogenetic affiliations were determined by maximum likelihood (RAxML). Bootstrap values were generated from 100 replicates. Bootstrap values higher than 50% are given. Sequences from this study are written in bold. Fig. S3. Phylogenetic analysis of archaeal 16S rRNA sequences. Phylogenetic affiliations were determined by maximum likelihood (RAxML). Bootstrap values were generated from 100 replicates. Bootstrap values higher than 50% are given. The sequence from this study is written in bold. Fig. S4. Phylogenetic analysis of nirS sequences (aa). Phylogenetic affiliations were determined by maximum likelihood (RAxML). Bootstrap values were generated from 100 replicates. NirN was used as outgroup. Bootstrap values higher than 50% are given. Sequences from this study are written in bold. Fig. S5. Phylogenetic analysis of nirK sequences (aa). Phylogenetic affiliations were determined by maximum likelihood (RAxML). Bootstrap values were generated from 100 replicates. Bootstrap values higher than 50% are given. The sequence from this study is written in bold. Table S1. Assembly results of the four sequenced metagenomes. Table S2. Closest relatives (based on blast) to reconstructed 16S rRNA gene sequences. Table S3. Squared Pearson product-moment correlation coefficients between bin coverages and 16S rRNA gene coverages over four samples. Rows: Bin coverages; Columns: 16S rRNA coverages. Table S4. List of oligonucleotide probes and primers used. ArticleID:EMI12552 ERC ark:/67375/WNG-BDM576SJ-V istex:FAB1A552E19D412211140213AFF842F2C34FC42F German Federal State North Rhine Westfalia Max Planck Society ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
| ISSN: | 1462-2912 1462-2920 |
| DOI: | 10.1111/1462-2920.12552 |