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Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation.

Guazzaroni ME, Herbst FA, Lores I, Tamames J, Peláez AI, López-Cortés N, Alcaide M, Del Pozo MV, Vieites JM, von Bergen M, Gallego JL, Bargiela R, López-López A, Pieper DH, Rosselló-Móra R, Sánchez J, Seifert J, Ferrer M - ISME J (2012)

Bottom Line: Using a metagenomic approach, a total of 52, 53, 14 and 12 distinct species (according to operational phylogenetic units (OPU) in our work equivalent to taxonomic species) were identified in the N, Nbs, CN1 and CN2 communities, respectively.Results indicated distinct biodegradation capabilities for the utilisation of potential growth-supporting aromatics, which results in bio-stimulated communities being extremely fit to naphthalene utilisation and non-stimulated communities exhibiting a greater metabolic window than previously predicted.The utilisation of curated databases is discussed and used for first time to reconstruct 'presumptive' degradation networks for complex microbial communities.

View Article: PubMed Central - PubMed

Affiliation: Department of Biocatalysis, Institute of Catalysis, CSIC, Madrid, Spain.

ABSTRACT
Microbial metabolism in aromatic-contaminated environments has important ecological implications, and obtaining a complete understanding of this process remains a relevant goal. To understand the roles of biodiversity and aromatic-mediated genetic and metabolic rearrangements, we conducted 'OMIC' investigations in an anthropogenically influenced and polyaromatic hydrocarbon (PAH)-contaminated soil with (Nbs) or without (N) bio-stimulation with calcium ammonia nitrate, NH(4)NO(3) and KH(2)PO(4) and the commercial surfactant Iveysol, plus two naphthalene-enriched communities derived from both soils (CN2 and CN1, respectively). Using a metagenomic approach, a total of 52, 53, 14 and 12 distinct species (according to operational phylogenetic units (OPU) in our work equivalent to taxonomic species) were identified in the N, Nbs, CN1 and CN2 communities, respectively. Approximately 10 out of 95 distinct species and 238 out of 3293 clusters of orthologous groups (COGs) protein families identified were clearly stimulated under the assayed conditions, whereas only two species and 1465 COGs conformed to the common set in all of the mesocosms. Results indicated distinct biodegradation capabilities for the utilisation of potential growth-supporting aromatics, which results in bio-stimulated communities being extremely fit to naphthalene utilisation and non-stimulated communities exhibiting a greater metabolic window than previously predicted. On the basis of comparing protein expression profiles and metagenome data sets, inter-alia interactions among members were hypothesised. The utilisation of curated databases is discussed and used for first time to reconstruct 'presumptive' degradation networks for complex microbial communities.

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Related in: MedlinePlus

A subset of the tree shown in Figure 1, where the genealogical composition of the members of the family Pseudomonadaceae is shown. Layout, reconstruction and colour codes used are the same as in Figure 1.
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fig2: A subset of the tree shown in Figure 1, where the genealogical composition of the members of the family Pseudomonadaceae is shown. Layout, reconstruction and colour codes used are the same as in Figure 1.

Mentions: DNA isolated from each investigated microbial community was employed for a PCR-based 16S recombinant DNA (rDNA) gene diversity survey of the community structures in the samples. For this purpose, clone libraries were constructed as described in the Supplementary Materials and methods, and the clones were fully sequenced to obtain the almost complete cloned 16S rDNA gene sequence. Additionally, and because of the low yields in the clone libraries of Nbs, we used the 16S rDNA gene partial sequences obtained in the metagenome survey. For this purpose, we used only those sequences that had a length >600 nucleotides. All shorter sequences were discarded. A total of 670 sequences (that is, N: 212; Nbs: 261 (86 clones+175 454 partial sequences); CN1: 90; CN2: 107) were obtained, and analysed. The overall phylogenetic composition in the libraries is shown in Figures 1, 2, 3, in which all operational phylogenetic units (OPUs) affiliated with twelve phyla of the domain Bacteria, namely, Proteobacteria followed to much lower extend by Bacteroidetes, Verrucomicrobia, Firmicutes, Actinobacteria, Chloroflexi, Cyanobacteria, Planctomycetes, Spirochaetes and the candidatus phyla OP8, TM7 and WCHB1 (Figure 4).


Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation.

Guazzaroni ME, Herbst FA, Lores I, Tamames J, Peláez AI, López-Cortés N, Alcaide M, Del Pozo MV, Vieites JM, von Bergen M, Gallego JL, Bargiela R, López-López A, Pieper DH, Rosselló-Móra R, Sánchez J, Seifert J, Ferrer M - ISME J (2012)

A subset of the tree shown in Figure 1, where the genealogical composition of the members of the family Pseudomonadaceae is shown. Layout, reconstruction and colour codes used are the same as in Figure 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3526184&req=5

fig2: A subset of the tree shown in Figure 1, where the genealogical composition of the members of the family Pseudomonadaceae is shown. Layout, reconstruction and colour codes used are the same as in Figure 1.
Mentions: DNA isolated from each investigated microbial community was employed for a PCR-based 16S recombinant DNA (rDNA) gene diversity survey of the community structures in the samples. For this purpose, clone libraries were constructed as described in the Supplementary Materials and methods, and the clones were fully sequenced to obtain the almost complete cloned 16S rDNA gene sequence. Additionally, and because of the low yields in the clone libraries of Nbs, we used the 16S rDNA gene partial sequences obtained in the metagenome survey. For this purpose, we used only those sequences that had a length >600 nucleotides. All shorter sequences were discarded. A total of 670 sequences (that is, N: 212; Nbs: 261 (86 clones+175 454 partial sequences); CN1: 90; CN2: 107) were obtained, and analysed. The overall phylogenetic composition in the libraries is shown in Figures 1, 2, 3, in which all operational phylogenetic units (OPUs) affiliated with twelve phyla of the domain Bacteria, namely, Proteobacteria followed to much lower extend by Bacteroidetes, Verrucomicrobia, Firmicutes, Actinobacteria, Chloroflexi, Cyanobacteria, Planctomycetes, Spirochaetes and the candidatus phyla OP8, TM7 and WCHB1 (Figure 4).

Bottom Line: Using a metagenomic approach, a total of 52, 53, 14 and 12 distinct species (according to operational phylogenetic units (OPU) in our work equivalent to taxonomic species) were identified in the N, Nbs, CN1 and CN2 communities, respectively.Results indicated distinct biodegradation capabilities for the utilisation of potential growth-supporting aromatics, which results in bio-stimulated communities being extremely fit to naphthalene utilisation and non-stimulated communities exhibiting a greater metabolic window than previously predicted.The utilisation of curated databases is discussed and used for first time to reconstruct 'presumptive' degradation networks for complex microbial communities.

View Article: PubMed Central - PubMed

Affiliation: Department of Biocatalysis, Institute of Catalysis, CSIC, Madrid, Spain.

ABSTRACT
Microbial metabolism in aromatic-contaminated environments has important ecological implications, and obtaining a complete understanding of this process remains a relevant goal. To understand the roles of biodiversity and aromatic-mediated genetic and metabolic rearrangements, we conducted 'OMIC' investigations in an anthropogenically influenced and polyaromatic hydrocarbon (PAH)-contaminated soil with (Nbs) or without (N) bio-stimulation with calcium ammonia nitrate, NH(4)NO(3) and KH(2)PO(4) and the commercial surfactant Iveysol, plus two naphthalene-enriched communities derived from both soils (CN2 and CN1, respectively). Using a metagenomic approach, a total of 52, 53, 14 and 12 distinct species (according to operational phylogenetic units (OPU) in our work equivalent to taxonomic species) were identified in the N, Nbs, CN1 and CN2 communities, respectively. Approximately 10 out of 95 distinct species and 238 out of 3293 clusters of orthologous groups (COGs) protein families identified were clearly stimulated under the assayed conditions, whereas only two species and 1465 COGs conformed to the common set in all of the mesocosms. Results indicated distinct biodegradation capabilities for the utilisation of potential growth-supporting aromatics, which results in bio-stimulated communities being extremely fit to naphthalene utilisation and non-stimulated communities exhibiting a greater metabolic window than previously predicted. On the basis of comparing protein expression profiles and metagenome data sets, inter-alia interactions among members were hypothesised. The utilisation of curated databases is discussed and used for first time to reconstruct 'presumptive' degradation networks for complex microbial communities.

Show MeSH
Related in: MedlinePlus