Metagenomic De Novo Assembly of an Aquatic Representative of the Verrucomicrobial Class Spartobacteria

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Metagenomic De Novo Assembly of an Aquatic Representative of the Verrucomicrobial Class Spartobacteria

Herlemann, Daniel P. R. (author): Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Germany

Lundin, Daniel (author): KTH,Genteknologi,Science for Life Laboratory, SciLifeLab,KTH Royal Institute of Technology,Jarone Pinhassi

Labrenz, Matthias (author): Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Germany

Jürgens, Klaus (author): Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Germany

Zheng, Zongli (author): Karolinska Institutet

Aspeborg, Henrik (author): KTH,Glykovetenskap,KTH Royal Institute of Technology

Andersson, Anders F. (author): KTH,Genteknologi,Science for Life Laboratory, SciLifeLab,KTH Royal Institute of Technology

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(creator_code:org_t)

2013
2013
English.
In: mBio. - 2161-2129 .- 2150-7511. ; 4:3, s. e00569-12-

Related links:: https://doi.org/10.1...; show more...; https://urn.kb.se/re...; https://doi.org/10.1...; http://kipublication...; https://urn.kb.se/re...; show less...

Journal article (peer-reviewed)

Abstract Subject headings

The verrucomicrobial subdivision 2 class Spartobacteria is one of the most abundant bacterial lineages in soil and has recently also been found to be ubiquitous in aquatic environments. A 16S rRNA gene study from samples spanning the entire salinity range of the Baltic Sea indicated that, in the pelagic brackish water, a phylotype of the Spartobacteria is one of the dominating bacteria during summer. Phylogenetic analyses of related 16S rRNA genes indicate that a purely aquatic lineage within the Spartobacteria exists. Since no aquatic representative from the Spartobacteria has been cultured or sequenced, the metabolic capacity and ecological role of this lineage are yet unknown. In this study, we reconstructed the genome and metabolic potential of the abundant Baltic Sea Spartobacteria phylotype by metagenomics. Binning of genome fragments by nucleotide composition and a self-organizing map recovered the near-complete genome of the organism, the gene content of which suggests an aerobic heterotrophic metabolism. Notably, we found 23 glycoside hydrolases that likely allow the use of a variety of carbohydrates, like cellulose, mannan, xylan, chitin, and starch, as carbon sources. In addition, a complete pathway for sulfate utilization was found, indicating catabolic processing of sulfated polysaccharides, commonly found in aquatic phytoplankton. The high frequency of glycoside hydrolase genes implies an important role of this organism in the aquatic carbon cycle. Spatiotemporal data of the phylotype's distribution within the Baltic Sea indicate a connection to Cyanobacteria that may be the main source of the polysaccharide substrates. IMPORTANCE The ecosystem roles of many phylogenetic lineages are not yet well understood. One such lineage is the class Spartobacteria within the Verrucomicrobia that, despite being abundant in soil and aquatic systems, is relatively poorly studied. Here we circumvented the difficulties of growing aquatic Verrucomicrobia by applying shotgun metagenomic sequencing on a water sample from the Baltic Sea. By using a method based on sequence signatures, we were able to in silico isolate genome fragments belonging to a phylotype of the Spartobacteria. The genome, which represents the first aquatic representative of this clade, encodes a diversity of glycoside hydrolases that likely allow degradation of various complex carbohydrates. Since the phylotype cooccurs with Cyanobacteria, these may be the primary producers of the carbohydrate substrates. The phylotype, which is highly abundant in the Baltic Sea during summer, may thus play an important role in the carbon cycle of this ecosystem.

Subject headings

NATURVETENSKAP -- Biologi -- Mikrobiologi (hsv//swe)
NATURAL SCIENCES -- Biological Sciences -- Microbiology (hsv//eng)
MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Mikrobiologi inom det medicinska området (hsv//swe)
MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Microbiology in the medical area (hsv//eng)
NATURVETENSKAP -- Biologi -- Ekologi (hsv//swe)
NATURAL SCIENCES -- Biological Sciences -- Ecology (hsv//eng)

Keyword

Multiple sequence alignment
central baltic sea
genome sequence
gen. Nov.
bacterioplankton communities
phylum verrucomicrobia
phylogenetic diversity
substrate-specificity
bacterial communities
microbial communities
Ecology

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ref (subject category)
art (subject category)

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NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Microbiology

MEDICAL AND HEALTH SCIENCES: MEDICAL AND HEAL ...; and Basic Medicine; and Microbiology in ...

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Ecology

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