Metabolic diversity and ecological niches of Achromatium populations revealed with single-cell genomic sequencing.

Muammar Mansor,Matthew S Fantle,Trinity L Hamilton,Jennifer L Macalady

doi:10.3389/fmicb.2015.00822

Muammar Mansor, Matthew S Fantle + Show 2 more

Open Access

https://doi.org/10.3389/fmicb.2015.00822

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Abstract

Large, sulfur-cycling, calcite-precipitating bacteria in the genus Achromatium represent a significant proportion of bacterial communities near sediment-water interfaces at sites throughout the world. Our understanding of their potentially crucial roles in calcium, carbon, sulfur, nitrogen, and iron cycling is limited because they have not been cultured or sequenced using environmental genomics approaches to date. We utilized single-cell genomic sequencing to obtain one incomplete and two nearly complete draft genomes for Achromatium collected at Warm Mineral Springs (WMS), FL. Based on 16S rRNA gene sequences, the three cells represent distinct and relatively distant Achromatium populations (91–92% identity). The draft genomes encode key genes involved in sulfur and hydrogen oxidation; oxygen, nitrogen and polysulfide respiration; carbon and nitrogen fixation; organic carbon assimilation and storage; chemotaxis; twitching motility; antibiotic resistance; and membrane transport. Known genes for iron and manganese energy metabolism were not detected. The presence of pyrophosphatase and vacuolar (V)-type ATPases, which are generally rare in bacterial genomes, suggests a role for these enzymes in calcium transport, proton pumping, and/or energy generation in the membranes of calcite-containing inclusions.

Highlights

The genus Achromatium contains morphologically striking and unusually large bacteria distinguished by their abundant calcium carbonate inclusions
Phylogeny Achromatium phylotypes have been grouped into two clusters based on phylogenetic analysis of the 16S rRNA gene and the presence/absence of a deletion affecting helix 38 in the V6 region (Glöckner et al, 1999; Gray et al, 1999a; Salman et al, 2015)
The Warm Mineral Springs (WMS) phylotypes are deeply branching sister groups to preexisting clades and do not fall neatly within existing taxonomic clusters based on phylogenetic analyses of full-length 16S rRNA genes carried out using multiple tree-building methods (Figure 3)

Summary

Introduction

The genus Achromatium contains morphologically striking and unusually large bacteria distinguished by their abundant calcium carbonate inclusions. Given the large size of Achromatium cells, at this cell density they can comprise over 90% of the bacterial biovolume within a few centimeters of the sediment-water interface (Head et al, 1995, 1996). Despite their large biomass and mysterious carbonate precipitation behavior, the Achromatium single cell genomes role of Achromatium populations in biogeochemical cycling is not well understood. A differential sedimentation technique can be used to enrich for calcite-filled Achromatium cells based on their density (de Boer et al, 1971), but has yet to yield a pure culture

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