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Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms.

Kim YM, Nowack S, Olsen MT, Becraft ED, Wood JM, Thiel V, Klapper I, Kühl M, Fredrickson JK, Bryant DA, Ward DM, Metz TO - Front Microbiol (2015)

Bottom Line: A limited number of predominant taxa inhabit this community and their functional potentials have been previously identified through metagenomic and metatranscriptomic analyses and in situ metabolisms, and metabolic interactions among these taxa have been hypothesized.Our metabolomics results confirmed the diel cycling of photorespiration (e.g., glycolate) and fermentation (e.g., acetate, propionate, and lactate) products, the carbon storage polymers polyhydroxyalkanoates, and dissolved gasses (e.g., H2 and CO2) in the waters overlying the mat, which were hypothesized to occur in major mat chlorophototrophic community members.In addition, we have formulated the following new hypotheses: (1) the morning hours are a time of biosynthesis of amino acids, DNA, and RNA; (2) photo-inhibited cells may also produce lactate via fermentation as an alternate metabolism; (3) glycolate and lactate are exchanged among Synechococcus and Roseiflexus spp.; and (4) fluctuations in many metabolite pools (e.g., wax esters) at different times of day result from species found at different depths within the mat responding to temporal differences in their niches.

View Article: PubMed Central - PubMed

Affiliation: Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA.

ABSTRACT
Dynamic environmental factors such as light, nutrients, salt, and temperature continuously affect chlorophototrophic microbial mats, requiring adaptive and acclimative responses to stabilize composition and function. Quantitative metabolomics analysis can provide insights into metabolite dynamics for understanding community response to such changing environmental conditions. In this study, we quantified volatile organic acids, polar metabolites (amino acids, glycolytic and citric acid cycle intermediates, nucleobases, nucleosides, and sugars), wax esters, and polyhydroxyalkanoates, resulting in the identification of 104 metabolites and related molecules in thermal chlorophototrophic microbial mat cores collected over a diel cycle in Mushroom Spring, Yellowstone National Park. A limited number of predominant taxa inhabit this community and their functional potentials have been previously identified through metagenomic and metatranscriptomic analyses and in situ metabolisms, and metabolic interactions among these taxa have been hypothesized. Our metabolomics results confirmed the diel cycling of photorespiration (e.g., glycolate) and fermentation (e.g., acetate, propionate, and lactate) products, the carbon storage polymers polyhydroxyalkanoates, and dissolved gasses (e.g., H2 and CO2) in the waters overlying the mat, which were hypothesized to occur in major mat chlorophototrophic community members. In addition, we have formulated the following new hypotheses: (1) the morning hours are a time of biosynthesis of amino acids, DNA, and RNA; (2) photo-inhibited cells may also produce lactate via fermentation as an alternate metabolism; (3) glycolate and lactate are exchanged among Synechococcus and Roseiflexus spp.; and (4) fluctuations in many metabolite pools (e.g., wax esters) at different times of day result from species found at different depths within the mat responding to temporal differences in their niches.

No MeSH data available.


Related in: MedlinePlus

Heat map view of z-scored polar metabolite abundances over a diel cycle. A total of 58 metabolites were reproducibly detected (n = 3) and confidently identified in the mat samples. The scale bar indicates the z-score transformed average intensity values of metabolites. K-means clustering was performed to categorize the metabolites based on their diel abundance patterns. Cluster A—increase in early morning; Cluster B—increase in late morning; Cluster C—increase in afternoon; Cluster D—increase in late afternoon/early evening; Cluster E—increase at night.
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Figure 2: Heat map view of z-scored polar metabolite abundances over a diel cycle. A total of 58 metabolites were reproducibly detected (n = 3) and confidently identified in the mat samples. The scale bar indicates the z-score transformed average intensity values of metabolites. K-means clustering was performed to categorize the metabolites based on their diel abundance patterns. Cluster A—increase in early morning; Cluster B—increase in late morning; Cluster C—increase in afternoon; Cluster D—increase in late afternoon/early evening; Cluster E—increase at night.

Mentions: Untargeted metabolomics analyses were performed to identify fluctuations in polar metabolites. This analysis resulted in identification of 58 metabolites that were reproducibly detected in the 42 samples over the diel cycle. The time-course abundance patterns of these 58 metabolites are shown individually in Supplemental Figure S1. K-means clustering was used to categorize these patterns of temporal changes in relative abundances, resulting in five clusters of metabolites (Table 2) that each contained metabolites sharing similar patterns of abundance fluctuation over the diel cycle (Figure 2).


Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms.

Kim YM, Nowack S, Olsen MT, Becraft ED, Wood JM, Thiel V, Klapper I, Kühl M, Fredrickson JK, Bryant DA, Ward DM, Metz TO - Front Microbiol (2015)

Heat map view of z-scored polar metabolite abundances over a diel cycle. A total of 58 metabolites were reproducibly detected (n = 3) and confidently identified in the mat samples. The scale bar indicates the z-score transformed average intensity values of metabolites. K-means clustering was performed to categorize the metabolites based on their diel abundance patterns. Cluster A—increase in early morning; Cluster B—increase in late morning; Cluster C—increase in afternoon; Cluster D—increase in late afternoon/early evening; Cluster E—increase at night.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4400912&req=5

Figure 2: Heat map view of z-scored polar metabolite abundances over a diel cycle. A total of 58 metabolites were reproducibly detected (n = 3) and confidently identified in the mat samples. The scale bar indicates the z-score transformed average intensity values of metabolites. K-means clustering was performed to categorize the metabolites based on their diel abundance patterns. Cluster A—increase in early morning; Cluster B—increase in late morning; Cluster C—increase in afternoon; Cluster D—increase in late afternoon/early evening; Cluster E—increase at night.
Mentions: Untargeted metabolomics analyses were performed to identify fluctuations in polar metabolites. This analysis resulted in identification of 58 metabolites that were reproducibly detected in the 42 samples over the diel cycle. The time-course abundance patterns of these 58 metabolites are shown individually in Supplemental Figure S1. K-means clustering was used to categorize these patterns of temporal changes in relative abundances, resulting in five clusters of metabolites (Table 2) that each contained metabolites sharing similar patterns of abundance fluctuation over the diel cycle (Figure 2).

Bottom Line: A limited number of predominant taxa inhabit this community and their functional potentials have been previously identified through metagenomic and metatranscriptomic analyses and in situ metabolisms, and metabolic interactions among these taxa have been hypothesized.Our metabolomics results confirmed the diel cycling of photorespiration (e.g., glycolate) and fermentation (e.g., acetate, propionate, and lactate) products, the carbon storage polymers polyhydroxyalkanoates, and dissolved gasses (e.g., H2 and CO2) in the waters overlying the mat, which were hypothesized to occur in major mat chlorophototrophic community members.In addition, we have formulated the following new hypotheses: (1) the morning hours are a time of biosynthesis of amino acids, DNA, and RNA; (2) photo-inhibited cells may also produce lactate via fermentation as an alternate metabolism; (3) glycolate and lactate are exchanged among Synechococcus and Roseiflexus spp.; and (4) fluctuations in many metabolite pools (e.g., wax esters) at different times of day result from species found at different depths within the mat responding to temporal differences in their niches.

View Article: PubMed Central - PubMed

Affiliation: Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA.

ABSTRACT
Dynamic environmental factors such as light, nutrients, salt, and temperature continuously affect chlorophototrophic microbial mats, requiring adaptive and acclimative responses to stabilize composition and function. Quantitative metabolomics analysis can provide insights into metabolite dynamics for understanding community response to such changing environmental conditions. In this study, we quantified volatile organic acids, polar metabolites (amino acids, glycolytic and citric acid cycle intermediates, nucleobases, nucleosides, and sugars), wax esters, and polyhydroxyalkanoates, resulting in the identification of 104 metabolites and related molecules in thermal chlorophototrophic microbial mat cores collected over a diel cycle in Mushroom Spring, Yellowstone National Park. A limited number of predominant taxa inhabit this community and their functional potentials have been previously identified through metagenomic and metatranscriptomic analyses and in situ metabolisms, and metabolic interactions among these taxa have been hypothesized. Our metabolomics results confirmed the diel cycling of photorespiration (e.g., glycolate) and fermentation (e.g., acetate, propionate, and lactate) products, the carbon storage polymers polyhydroxyalkanoates, and dissolved gasses (e.g., H2 and CO2) in the waters overlying the mat, which were hypothesized to occur in major mat chlorophototrophic community members. In addition, we have formulated the following new hypotheses: (1) the morning hours are a time of biosynthesis of amino acids, DNA, and RNA; (2) photo-inhibited cells may also produce lactate via fermentation as an alternate metabolism; (3) glycolate and lactate are exchanged among Synechococcus and Roseiflexus spp.; and (4) fluctuations in many metabolite pools (e.g., wax esters) at different times of day result from species found at different depths within the mat responding to temporal differences in their niches.

No MeSH data available.


Related in: MedlinePlus