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

Frontiers in Microbiology
Muammar MansorJennifer L Macalady

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,...Continue Reading

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Datasets Mentioned

BETA
SRR1771809
JXSN00000000
JXSO00000000
KP694216
KP694218

Methods Mentioned

BETA
flow cytometry
PCR
Light microscopy
Phase contrast microscopy

Software Mentioned

Trimmomatic
Velvet
CodonCode Aligner
MrBayes
MEGA
XRNA
IDBA
SINA Webaligner
ARB
A5

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