Key roles for freshwater Actinobacteria revealed by deep metagenomic sequencing

Freshwater ecosystems are critical but fragile environments directly affecting society and its welfare. However, our understanding of genuinely freshwater microbial communities, constrained by our capacity to manipulate its prokaryotic participants in axenic cultures, remains very rudimentary. Even...

Full description

Saved in:

Bibliographic Details
Published in:	Molecular ecology Vol. 23; no. 24; pp. 6073 - 6090
Main Authors:	Ghai, Rohit, Mizuno, Carolina Megumi, Picazo, Antonio, Camacho, Antonio, Rodriguez-Valera, Francisco
Format:	Journal Article
Language:	English
Published:	England Blackwell Publishing Ltd 01-12-2014
Subjects:	Actinobacteria Actinobacteria - classification Actinobacteria - genetics Actinomycetales Aquatic ecosystems Contig Mapping Cyanobacteria DNA, Bacterial - genetics Fresh Water - microbiology Freshwater freshwater reservoir Genome, Bacterial Genomics High-Throughput Nucleotide Sequencing lignin degradation Metagenomics Micrococcineae Molecular Sequence Data Phylogeny rhodopsins RNA, Ribosomal, 16S - genetics Sequence Analysis, DNA Spain Water Microbiology Spain freshwater reservoir Actinobacteria rhodopsins lignin degradation metagenomics Cyanobacteria
Online Access:	Get full text
Tags:	Add Tag No Tags, Be the first to tag this record!

Description
Summary:	Freshwater ecosystems are critical but fragile environments directly affecting society and its welfare. However, our understanding of genuinely freshwater microbial communities, constrained by our capacity to manipulate its prokaryotic participants in axenic cultures, remains very rudimentary. Even the most abundant components, freshwater Actinobacteria, remain largely unknown. Here, applying deep metagenomic sequencing to the microbial community of a freshwater reservoir, we were able to circumvent this traditional bottleneck and reconstruct de novo seven distinct streamlined actinobacterial genomes. These genomes represent three new groups of photoheterotrophic, planktonic Actinobacteria. We describe for the first time genomes of two novel clades, acMicro (Micrococcineae, related to Luna2,) and acAMD (Actinomycetales, related to acTH1). Besides, an aggregate of contigs belonged to a new branch of the Acidimicrobiales. All are estimated to have small genomes (approximately 1.2 Mb), and their GC content varied from 40 to 61%. One of the Micrococcineae genomes encodes a proteorhodopsin, a rhodopsin type reported for the first time in Actinobacteria. The remarkable potential capacity of some of these genomes to transform recalcitrant plant detrital material, particularly lignin‐derived compounds, suggests close linkages between the terrestrial and aquatic realms. Moreover, abundances of Actinobacteria correlate inversely to those of Cyanobacteria that are responsible for prolonged and frequently irretrievable damage to freshwater ecosystems. This suggests that they might serve as sentinels of impending ecological catastrophes.
Bibliography:	Generalitat Valenciana - No. ACOMP/2014/024; No. AORG 2014/032; No. PROMETEO II/2014/012 Spanish Ministerio de Ciencia e Innovación - No. CSD2009-00006 ArticleID:MEC12985 ark:/67375/WNG-D50Z3DL5-Z Spanish Ministerio de Economía y Competitividad - No. BFPU2013-48007-P; No. CGL2012-38909 istex:C685B65F2E845B464C504168F37F204E5BAA5CDC Table S1 Main environmental variables of the Amadorio reservoir corresponding to the sampled depth (10 m) on February 1st, 2012, during the mixing period. Table S2 Key residues in diverse rhodopsin sequences. Fig. S1 Vertical profiles of the main environmental variables in the Amadorio reservoir at the date of sampling (February 1st, 2012). Fig. S2 16S rRNA read classifications of the Amadorio freshwater reservoir and several other freshwater metagenomic datasets. Fig. S3 Genome size vs. GC content. Fig. S4 Genomic GC content vs. median intergenic spacer content. Fig. S5 16S rRNA phylogeny using maximum likelihood. Fig. S6 Microscopic FISH image of samples from Amadorio reservoir. Fig. S7 Abundance and size (maximum cell dimension) structure of the bacterioplankton community in the Amadorio reservoir as determined by flow cytometry. Fig. S8 Metabolic overview of the freshwater Actinobacteria acAcidi group. Fig. S9 Metabolic overview of the freshwater Actinobacteria acAMD-5. Fig. S10 Metabolic overview of the freshwater Actinobacteria acMicro-4. Fig. S11 (a) Gene cluster encoding genes for the protocatechuate degradation pathway in acMicro-1 genome. (b) The biochemical pathway of protocatechuate degradation.Data S1 (A) Metabolic pathway comparison. (B) Transporter comparison. (C) Carbohydrate-active enzyme comparison. (D) Actinobacterial core. European Commission FP7 - No. 311975 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0962-1083 1365-294X
DOI:	10.1111/mec.12985