Limits...
Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage.

Chen LX, Hu M, Huang LN, Hua ZS, Kuang JL, Li SJ, Shu WS - ISME J (2014)

Bottom Line: Taxonomic analysis uncovered unexpectedly high microbial biodiversity of these extremely acidophilic communities, and the abundant taxa of Acidithiobacillus, Leptospirillum and Acidiphilium exhibited high transcriptional activities.Community-wide comparative analyses clearly showed that the AMD microorganisms adapted to the different environmental conditions via regulating the expression of genes involved in multiple in situ functional activities, including low-pH adaptation, carbon, nitrogen and phosphate assimilation, energy generation, environmental stress resistance, and other functions.Overall, these findings demonstrate that the gene transcriptional profiles of AMD microorganisms are closely related to the site physiochemical characteristics, providing clues into the microbial response and adaptation mechanisms in the oligotrophic, extremely acidic environments.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, People's Republic of China.

ABSTRACT
The microbial communities in acid mine drainage have been extensively studied to reveal their roles in acid generation and adaption to this environment. Lacking, however, are integrated community- and organism-wide comparative gene transcriptional analyses that could reveal the response and adaptation mechanisms of these extraordinary microorganisms to different environmental conditions. In this study, comparative metagenomics and metatranscriptomics were performed on microbial assemblages collected from four geochemically distinct acid mine drainage (AMD) sites. Taxonomic analysis uncovered unexpectedly high microbial biodiversity of these extremely acidophilic communities, and the abundant taxa of Acidithiobacillus, Leptospirillum and Acidiphilium exhibited high transcriptional activities. Community-wide comparative analyses clearly showed that the AMD microorganisms adapted to the different environmental conditions via regulating the expression of genes involved in multiple in situ functional activities, including low-pH adaptation, carbon, nitrogen and phosphate assimilation, energy generation, environmental stress resistance, and other functions. Organism-wide comparative analyses of the active taxa revealed environment-dependent gene transcriptional profiles, especially the distinct strategies used by Acidithiobacillus ferrivorans and Leptospirillum ferrodiazotrophum in nutrients assimilation and energy generation for survival under different conditions. Overall, these findings demonstrate that the gene transcriptional profiles of AMD microorganisms are closely related to the site physiochemical characteristics, providing clues into the microbial response and adaptation mechanisms in the oligotrophic, extremely acidic environments.

No MeSH data available.


Related in: MedlinePlus

Relative abundances (%) of transcripts associated with the in situ functional activities of the four AMD communities, including ribosomal proteins (RP), low pH adaptation, carbon assimilation, nitrogen assimilation, phosphate assimilation, energy generation and environment stress resistance (molecular chaperons, heavy metal stress and oxidative stress). The bar showing the number of relative abundance was log scaled.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4478699&req=5

fig3: Relative abundances (%) of transcripts associated with the in situ functional activities of the four AMD communities, including ribosomal proteins (RP), low pH adaptation, carbon assimilation, nitrogen assimilation, phosphate assimilation, energy generation and environment stress resistance (molecular chaperons, heavy metal stress and oxidative stress). The bar showing the number of relative abundance was log scaled.

Mentions: The expression levels of housekeeping function associated genes, including those for DNA-directed RNA polymerase, ribosomal proteins, elongation factors, cytochromes and ATP synthase, varied across the four communities (Supplementary Table 3). The lowest abundance of ribosomal protein transcripts (3.65% Figure 3) indicated that the microorganisms in FK community were likely with the lowest average growth rates. This speculation was supported by the fact that most of the archaeal taxa in this community showed very low activities (Figure 1b and c).


Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage.

Chen LX, Hu M, Huang LN, Hua ZS, Kuang JL, Li SJ, Shu WS - ISME J (2014)

Relative abundances (%) of transcripts associated with the in situ functional activities of the four AMD communities, including ribosomal proteins (RP), low pH adaptation, carbon assimilation, nitrogen assimilation, phosphate assimilation, energy generation and environment stress resistance (molecular chaperons, heavy metal stress and oxidative stress). The bar showing the number of relative abundance was log scaled.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4478699&req=5

fig3: Relative abundances (%) of transcripts associated with the in situ functional activities of the four AMD communities, including ribosomal proteins (RP), low pH adaptation, carbon assimilation, nitrogen assimilation, phosphate assimilation, energy generation and environment stress resistance (molecular chaperons, heavy metal stress and oxidative stress). The bar showing the number of relative abundance was log scaled.
Mentions: The expression levels of housekeeping function associated genes, including those for DNA-directed RNA polymerase, ribosomal proteins, elongation factors, cytochromes and ATP synthase, varied across the four communities (Supplementary Table 3). The lowest abundance of ribosomal protein transcripts (3.65% Figure 3) indicated that the microorganisms in FK community were likely with the lowest average growth rates. This speculation was supported by the fact that most of the archaeal taxa in this community showed very low activities (Figure 1b and c).

Bottom Line: Taxonomic analysis uncovered unexpectedly high microbial biodiversity of these extremely acidophilic communities, and the abundant taxa of Acidithiobacillus, Leptospirillum and Acidiphilium exhibited high transcriptional activities.Community-wide comparative analyses clearly showed that the AMD microorganisms adapted to the different environmental conditions via regulating the expression of genes involved in multiple in situ functional activities, including low-pH adaptation, carbon, nitrogen and phosphate assimilation, energy generation, environmental stress resistance, and other functions.Overall, these findings demonstrate that the gene transcriptional profiles of AMD microorganisms are closely related to the site physiochemical characteristics, providing clues into the microbial response and adaptation mechanisms in the oligotrophic, extremely acidic environments.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, People's Republic of China.

ABSTRACT
The microbial communities in acid mine drainage have been extensively studied to reveal their roles in acid generation and adaption to this environment. Lacking, however, are integrated community- and organism-wide comparative gene transcriptional analyses that could reveal the response and adaptation mechanisms of these extraordinary microorganisms to different environmental conditions. In this study, comparative metagenomics and metatranscriptomics were performed on microbial assemblages collected from four geochemically distinct acid mine drainage (AMD) sites. Taxonomic analysis uncovered unexpectedly high microbial biodiversity of these extremely acidophilic communities, and the abundant taxa of Acidithiobacillus, Leptospirillum and Acidiphilium exhibited high transcriptional activities. Community-wide comparative analyses clearly showed that the AMD microorganisms adapted to the different environmental conditions via regulating the expression of genes involved in multiple in situ functional activities, including low-pH adaptation, carbon, nitrogen and phosphate assimilation, energy generation, environmental stress resistance, and other functions. Organism-wide comparative analyses of the active taxa revealed environment-dependent gene transcriptional profiles, especially the distinct strategies used by Acidithiobacillus ferrivorans and Leptospirillum ferrodiazotrophum in nutrients assimilation and energy generation for survival under different conditions. Overall, these findings demonstrate that the gene transcriptional profiles of AMD microorganisms are closely related to the site physiochemical characteristics, providing clues into the microbial response and adaptation mechanisms in the oligotrophic, extremely acidic environments.

No MeSH data available.


Related in: MedlinePlus