Limits...
Factors influencing the diversity of iron uptake systems in aquatic microorganisms.

Desai DK, Desai FD, Laroche J - Front Microbiol (2012)

Bottom Line: A multivariate statistical approach demonstrated that in phototrophic organisms, there is a clear influence of the ecological niche on the diversity of Fe uptake systems.Extending the analyses to the metagenome database from the Global Ocean Sampling expedition, we demonstrated that the Fe uptake and homeostasis mechanisms differed significantly across marine niches defined by temperatures and dFe concentrations, and that this difference was linked to the distribution of microbial taxa in these niches.Using the dN/dS ratios (which signify the rate of non-synonymous mutations) of the nucleotide sequences, we identified that genes encoding for TonB, Ferritin, Ferric reductase, IdiA, ZupT, and Fe(2+) transport proteins FeoA and FeoB were evolving at a faster rate (positive selection pressure) while genes encoding ferrisiderophore, heme and Vitamin B12 uptake systems, siderophore biosynthesis, and IsiA and IsiB were under purifying selection pressure (evolving slowly).

View Article: PubMed Central - PubMed

Affiliation: Biological Oceanography Division, Helmholtz-Zentrum für Ozeanforschung Kiel (GEOMAR) Kiel, Germany.

ABSTRACT
Iron (Fe) is an essential micronutrient for many processes in all living cells. Dissolved Fe (dFe) concentrations in the ocean are of the order of a few nM, and Fe is often a factor limiting primary production. Bioavailability of Fe in aquatic environments is believed to be primarily controlled through chelation by Fe-binding ligands. Marine microbes have evolved different mechanisms to cope with the scarcity of bioavailable dFe. Gradients in dFe concentrations and diversity of the Fe-ligand pool from coastal to open ocean waters have presumably imposed selection pressures that should be reflected in the genomes of microbial communities inhabiting the pelagic realm. We applied a hidden Markov model (HMM)-based search for proteins related to cellular iron metabolism, and in particular those involved in Fe uptake mechanisms in 164 microbial genomes belonging to diverse taxa and occupying different aquatic niches. A multivariate statistical approach demonstrated that in phototrophic organisms, there is a clear influence of the ecological niche on the diversity of Fe uptake systems. Extending the analyses to the metagenome database from the Global Ocean Sampling expedition, we demonstrated that the Fe uptake and homeostasis mechanisms differed significantly across marine niches defined by temperatures and dFe concentrations, and that this difference was linked to the distribution of microbial taxa in these niches. Using the dN/dS ratios (which signify the rate of non-synonymous mutations) of the nucleotide sequences, we identified that genes encoding for TonB, Ferritin, Ferric reductase, IdiA, ZupT, and Fe(2+) transport proteins FeoA and FeoB were evolving at a faster rate (positive selection pressure) while genes encoding ferrisiderophore, heme and Vitamin B12 uptake systems, siderophore biosynthesis, and IsiA and IsiB were under purifying selection pressure (evolving slowly).

No MeSH data available.


Principal Components Analysis of GOS samples using similarities of the environmental parameter profiles. The samples are labeled according to the ocean basins (Atlantic or Pacific) combined with niche groups (Open Ocean or Coastal).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3475125&req=5

Figure 5: Principal Components Analysis of GOS samples using similarities of the environmental parameter profiles. The samples are labeled according to the ocean basins (Atlantic or Pacific) combined with niche groups (Open Ocean or Coastal).

Mentions: The environmental matrix for the 30 GOS samples belonging to the Open Ocean and Coastal niche groups was subjected to a PCA (Figure 5). The Atlantic and Pacific samples were separated along the first PC, where the environmental parameters accounting for the separation were Longitude, Latitude, and Temperature. Within each ocean basin group (Atlantic or Pacific), along the second PC, the water column depth gradient separated the samples into Open Ocean and Coastal groups. The dFe gradient separated the Atlantic Open Ocean samples from the Pacific Open Ocean and Coastal samples (Figure 5). The first PC, which included the temperature gradient in addition to the dFe, also separated the samples into Temperate and Tropical groups (Figure 5).


Factors influencing the diversity of iron uptake systems in aquatic microorganisms.

Desai DK, Desai FD, Laroche J - Front Microbiol (2012)

Principal Components Analysis of GOS samples using similarities of the environmental parameter profiles. The samples are labeled according to the ocean basins (Atlantic or Pacific) combined with niche groups (Open Ocean or Coastal).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3475125&req=5

Figure 5: Principal Components Analysis of GOS samples using similarities of the environmental parameter profiles. The samples are labeled according to the ocean basins (Atlantic or Pacific) combined with niche groups (Open Ocean or Coastal).
Mentions: The environmental matrix for the 30 GOS samples belonging to the Open Ocean and Coastal niche groups was subjected to a PCA (Figure 5). The Atlantic and Pacific samples were separated along the first PC, where the environmental parameters accounting for the separation were Longitude, Latitude, and Temperature. Within each ocean basin group (Atlantic or Pacific), along the second PC, the water column depth gradient separated the samples into Open Ocean and Coastal groups. The dFe gradient separated the Atlantic Open Ocean samples from the Pacific Open Ocean and Coastal samples (Figure 5). The first PC, which included the temperature gradient in addition to the dFe, also separated the samples into Temperate and Tropical groups (Figure 5).

Bottom Line: A multivariate statistical approach demonstrated that in phototrophic organisms, there is a clear influence of the ecological niche on the diversity of Fe uptake systems.Extending the analyses to the metagenome database from the Global Ocean Sampling expedition, we demonstrated that the Fe uptake and homeostasis mechanisms differed significantly across marine niches defined by temperatures and dFe concentrations, and that this difference was linked to the distribution of microbial taxa in these niches.Using the dN/dS ratios (which signify the rate of non-synonymous mutations) of the nucleotide sequences, we identified that genes encoding for TonB, Ferritin, Ferric reductase, IdiA, ZupT, and Fe(2+) transport proteins FeoA and FeoB were evolving at a faster rate (positive selection pressure) while genes encoding ferrisiderophore, heme and Vitamin B12 uptake systems, siderophore biosynthesis, and IsiA and IsiB were under purifying selection pressure (evolving slowly).

View Article: PubMed Central - PubMed

Affiliation: Biological Oceanography Division, Helmholtz-Zentrum für Ozeanforschung Kiel (GEOMAR) Kiel, Germany.

ABSTRACT
Iron (Fe) is an essential micronutrient for many processes in all living cells. Dissolved Fe (dFe) concentrations in the ocean are of the order of a few nM, and Fe is often a factor limiting primary production. Bioavailability of Fe in aquatic environments is believed to be primarily controlled through chelation by Fe-binding ligands. Marine microbes have evolved different mechanisms to cope with the scarcity of bioavailable dFe. Gradients in dFe concentrations and diversity of the Fe-ligand pool from coastal to open ocean waters have presumably imposed selection pressures that should be reflected in the genomes of microbial communities inhabiting the pelagic realm. We applied a hidden Markov model (HMM)-based search for proteins related to cellular iron metabolism, and in particular those involved in Fe uptake mechanisms in 164 microbial genomes belonging to diverse taxa and occupying different aquatic niches. A multivariate statistical approach demonstrated that in phototrophic organisms, there is a clear influence of the ecological niche on the diversity of Fe uptake systems. Extending the analyses to the metagenome database from the Global Ocean Sampling expedition, we demonstrated that the Fe uptake and homeostasis mechanisms differed significantly across marine niches defined by temperatures and dFe concentrations, and that this difference was linked to the distribution of microbial taxa in these niches. Using the dN/dS ratios (which signify the rate of non-synonymous mutations) of the nucleotide sequences, we identified that genes encoding for TonB, Ferritin, Ferric reductase, IdiA, ZupT, and Fe(2+) transport proteins FeoA and FeoB were evolving at a faster rate (positive selection pressure) while genes encoding ferrisiderophore, heme and Vitamin B12 uptake systems, siderophore biosynthesis, and IsiA and IsiB were under purifying selection pressure (evolving slowly).

No MeSH data available.