Metabolites Associated with Adaptation of Microorganisms to an Acidophilic, Metal-Rich Environment Identified by Stable-Isotope-Enabled Metabolomics

@article{Mosier2013MetabolitesAW,
  title={Metabolites Associated with Adaptation of Microorganisms to an Acidophilic, Metal-Rich Environment Identified by Stable-Isotope-Enabled Metabolomics},
  author={Annika C. Mosier and Nicholas Justice and Benjamin P. Bowen and Richard Baran and Brian C. Thomas and Trent R. Northen and Jillian F. Banfield},
  journal={mBio},
  year={2013},
  volume={4}
}
ABSTRACT Microorganisms grow under a remarkable range of extreme conditions. Environmental transcriptomic and proteomic studies have highlighted metabolic pathways active in extremophilic communities. However, metabolites directly linked to their physiology are less well defined because metabolomics methods lag behind other omics technologies due to a wide range of experimental complexities often associated with the environmental matrix. We identified key metabolites associated with acidophilic… 
Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms
TLDR
Quantitative metabolomics analysis confirmed the diel cycling of photorespiration and fermentation in thermal chlorophototrophic microbial mat cores collected over a diel cycle in Mushroom Spring, Yellowstone National Park and formulated the following new hypotheses: the morning hours are a time of biosynthesis of amino acids, DNA, and RNA.
Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage
TLDR
Mechanisms of fungal adaptation are defined and a functional shift related to different roles in carbon and nitrogen turnover for the same species of fungi growing in closely located but distinct biofilm niches is identified.
Elevated temperature alters proteomic responses of individual organisms within a biofilm community
TLDR
This study accurately, precisely and reproducibly quantified thousands of proteins in biofilms growing at 40, 43 and 46 °C and found elevated temperature led to upregulation of proteins involved in amino-acid metabolism at the level of individual organisms and the entire community.
The Biofilm Lifestyle of Acidophilic Metal/Sulfur-Oxidizing Microorganisms
TLDR
The molecular mechanisms controlling biofilm formation in acidophilic leaching bacteria are starting to be elucidated while these operating in archaea are far less explored, and this chapter provides an overview about the biofilm lifestyle of AMOM.
Acid Mine Drainage as Habitats for Distinct Microbiomes: Current Knowledge in the Era of Molecular and Omic Technologies
TLDR
A critical synopsis of the current applications of advanced molecular techniques in probing microbial and functional diversity in AMD environments is presented.
Stable Isotope-Assisted Metabolic Profiling Reveals Growth Mode Dependent Differential Metabolism and Multiple Catabolic Pathways of l-Phenylalanine in Rubrivivax benzoatilyticus JA2.
TLDR
The study uncovered the l-phenylalanine catabolic diversity in strain JA2 and demonstrated the potential of stable isotope-assisted metabolomics in unraveling the hidden metabolic repertoire.
The microbial genomics of arsenic.
TLDR
The increasing number of genomes available and the development of descriptive and comparative approaches have made it possible not only to identify several genetic determinants of the arsenic metabolism, but also to elucidate their phylogenetic distribution and their modes of regulation.
An improved method for extraction of polar and charged metabolites from cyanobacteria
TLDR
The extraction methods were evaluated for a targeted set of metabolites that are important in 13C-MFA studies of photosynthetic organisms and a new improved method for extraction using a methanol-chloroform-NH4OH system is presented.
Transcriptomic analysis of chloride tolerance in Leptospirillum ferriphilum DSM 14647 adapted to NaCl
TLDR
Differentially expressed transcripts and experimental validations suggest that adaptation to chloride in acidophilic microorganisms involves a multifactorial response that is different from the response in other bacteria studied.
Antimicrobial activity and carbohydrate metabolism in the bacterial metagenome of the soil-living invertebrate Folsomia candida
TLDR
It is suggested that the carbohydrate- and antimicrobial-related functions encoded by Folsomia’s metagenome play a role in the digestion of recalcitrant soil-born polysaccharides and the defense against pathogens, thereby significantly contributing to the adaptation of these animals to life in the soil.
...
...

References

SHOWING 1-10 OF 71 REFERENCES
Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions
TLDR
The results confirm the importance of pH and related geochemical factors in fine-tuning acidophilic microbial community structure and function at the species and strain level, and demonstrate the broad utility of proteomics in laboratory community studies.
Cultivation and quantitative proteomic analyses of acidophilic microbial communities
TLDR
The research presented here represents the first description of the application of a metabolic labeling-based quantitative proteomic analysis at the community level and resulted in a model microbial community system ideal for testing physiological and ecological hypotheses.
In situ proteo-metabolomics reveals metabolite secretion by the acid mine drainage bio-indicator, Euglena mutabilis
TLDR
In situ proteo-metabolomic approaches revealed that the secreted metabolites are represented by a large number of amino acids, polyamine compounds, urea and some sugars but no fatty acids, suggesting a selective organic matter contribution in this ecosystem.
Deuterium-exchange metabolomics identifies N-methyl lyso phosphatidylethanolamines as abundant lipids in acidophilic mixed microbial communities
TLDR
Correlations of lyso phospholipid and proteome abundance patterns suggest a link between the lysoospholipids and the UBA-type substrain of Leptospirillum group II.
Correlating the transcriptome, proteome, and metabolome in the environmental adaptation of a hyperthermophile.
TLDR
A comprehensive characterization of global molecular changes for a model organism Pyrococcus furiosus using transcriptomic, proteomic, and metabolomic analysis as it undergoes a cold adaptation response from its optimal 95 to 72 degrees C.
Conservation of the metabolomic response to starvation across two divergent microbes
TLDR
Following 68 cellular metabolites after carbon or nitrogen starvation of Escherichia coli and Saccharomyces cerevisiae, using a filter-culture methodology that allows exponential growth, nondisruptive nutrient removal, and fast quenching of metabolism, captured a remarkable 72% of the metabolite concentration changes.
Metabolome-Proteome Differentiation Coupled to Microbial Divergence
TLDR
Tandem high-throughput proteomics and metabolomics were employed to functionally characterize natural microbial biofilm communities and demonstrated that correlations between protein and metabolite abundances allow the deconvolution of complex molecular data sets into shared and organism-specific contingents.
Untargeted metabolic footprinting reveals a surprising breadth of metabolite uptake and release by Synechococcus sp. PCC 7002.
TLDR
Surprisingly, Synechococcus was found to uptake a great diversity of metabolites dominant in and specific to its own metabolite extract including histidine betaine (hercynine), γ-glutamyl phenylalanine and a hexosamine-based trisaccharide.
Metabolite identification in Synechococcus sp. PCC 7002 using untargeted stable isotope assisted metabolite profiling.
TLDR
An integrated workflow for metabolite identification using uniform stable isotope labeling is presented and a number of metabolites absent not only from the reconstructed draft metabolic network of Synechococcus sp.
Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea
TLDR
The isolation of Candidatus “Nitrosopumilus maritimus” strain SCM1 is reported, revealing highly copper-dependent systems for ammonia oxidation and electron transport that are distinctly different from known ammonia-oxidizing bacteria.
...
...