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

Mansor M, Hamilton TL, Fantle MS, Macalady JL - Front Microbiol (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Geosciences Department, Pennsylvania State University University Park, PA, USA.

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.

No MeSH data available.


(A) Sampling sites at Warm Mineral Springs. (B) Water column depth profile of H2S (gray) and dissolved oxygen (black) within the basin. Solid and dashed lines indicate profiles for June 2012 and 28 October 2013 respectively.
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Figure 1: (A) Sampling sites at Warm Mineral Springs. (B) Water column depth profile of H2S (gray) and dissolved oxygen (black) within the basin. Solid and dashed lines indicate profiles for June 2012 and 28 October 2013 respectively.

Mentions: Warm Mineral Springs (WMS) is a water-filled sinkhole located in the city of North Port, Florida, United States (27.06°N, 82.26°W). The spring consists of a central basin and a single outflow with tidal fluctuations up to 20 cm (Figure 1A). The spring basin is approximately 70 m deep and is fed by multiple warm springs that enter near the bottom. It has been popular as a spa since the 1960s due to its warm temperature of 30°C, a near-neutral pH of 7, and brackish composition equivalent to approximately 50% of seawater salinity. Human and animal remains and cultural artifacts are well preserved in the spring basin due to perennially low dissolved oxygen in the water column, making it an important archeological site (Clausen et al., 1975). A constant supply of dissolved sulfide in the water column, high sediment organic carbon content and nitrate levels of about 0.8 μM likely contribute to the diversity of sulfur-oxidizing bacteria found in the basin and spring outflow stream, including Beggiatoa, Thiothrix, Thiovulum, and Achromatium species described in reports since the early 1960s (Lackey and Lackey, 1961; Brigmon et al., 1994; Larkin et al., 1994). Bicarbonate concentration in the spring water is approximately 2 mM and elemental sulfur (S(0)) is present in the sandy sediments (Lackey and Lackey, 1961). Discharge from the basin is high (3.4 × 106 L/day, Lackey and Lackey, 1961; Clausen et al., 1975) and flows into a narrow channel that runs approximately 1.3 km downstream before joining the Myakka River.


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

Mansor M, Hamilton TL, Fantle MS, Macalady JL - Front Microbiol (2015)

(A) Sampling sites at Warm Mineral Springs. (B) Water column depth profile of H2S (gray) and dissolved oxygen (black) within the basin. Solid and dashed lines indicate profiles for June 2012 and 28 October 2013 respectively.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4530308&req=5

Figure 1: (A) Sampling sites at Warm Mineral Springs. (B) Water column depth profile of H2S (gray) and dissolved oxygen (black) within the basin. Solid and dashed lines indicate profiles for June 2012 and 28 October 2013 respectively.
Mentions: Warm Mineral Springs (WMS) is a water-filled sinkhole located in the city of North Port, Florida, United States (27.06°N, 82.26°W). The spring consists of a central basin and a single outflow with tidal fluctuations up to 20 cm (Figure 1A). The spring basin is approximately 70 m deep and is fed by multiple warm springs that enter near the bottom. It has been popular as a spa since the 1960s due to its warm temperature of 30°C, a near-neutral pH of 7, and brackish composition equivalent to approximately 50% of seawater salinity. Human and animal remains and cultural artifacts are well preserved in the spring basin due to perennially low dissolved oxygen in the water column, making it an important archeological site (Clausen et al., 1975). A constant supply of dissolved sulfide in the water column, high sediment organic carbon content and nitrate levels of about 0.8 μM likely contribute to the diversity of sulfur-oxidizing bacteria found in the basin and spring outflow stream, including Beggiatoa, Thiothrix, Thiovulum, and Achromatium species described in reports since the early 1960s (Lackey and Lackey, 1961; Brigmon et al., 1994; Larkin et al., 1994). Bicarbonate concentration in the spring water is approximately 2 mM and elemental sulfur (S(0)) is present in the sandy sediments (Lackey and Lackey, 1961). Discharge from the basin is high (3.4 × 106 L/day, Lackey and Lackey, 1961; Clausen et al., 1975) and flows into a narrow channel that runs approximately 1.3 km downstream before joining the Myakka River.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Geosciences Department, Pennsylvania State University University Park, PA, USA.

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.

No MeSH data available.