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Using pyrosequencing to shed light on deep mine microbial ecology.

Edwards RA, Rodriguez-Brito B, Wegley L, Haynes M, Breitbart M, Peterson DM, Saar MO, Alexander S, Alexander EC, Rohwer F - BMC Genomics (2006)

Bottom Line: In addition, the communities were also completely different from other microbial communities sequenced to date.We anticipate that pyrosequencing will be widely used to sequence environmental samples because of the speed, cost, and technical advantages.Furthermore, subsystem comparisons rapidly identify the important metabolisms employed by the microbes in different environments.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, San Diego State University, San Diego, USA. redwards@salmonella.org

ABSTRACT

Background: Contrasting biological, chemical and hydrogeological analyses highlights the fundamental processes that shape different environments. Generating and interpreting the biological sequence data was a costly and time-consuming process in defining an environment. Here we have used pyrosequencing, a rapid and relatively inexpensive sequencing technology, to generate environmental genome sequences from two sites in the Soudan Mine, Minnesota, USA. These sites were adjacent to each other, but differed significantly in chemistry and hydrogeology.

Results: Comparisons of the microbes and the subsystems identified in the two samples highlighted important differences in metabolic potential in each environment. The microbes were performing distinct biochemistry on the available substrates, and subsystems such as carbon utilization, iron acquisition mechanisms, nitrogen assimilation, and respiratory pathways separated the two communities. Although the correlation between much of the microbial metabolism occurring and the geochemical conditions from which the samples were isolated could be explained, the reason for the presence of many pathways in these environments remains to be determined. Despite being physically close, these two communities were markedly different from each other. In addition, the communities were also completely different from other microbial communities sequenced to date.

Conclusion: We anticipate that pyrosequencing will be widely used to sequence environmental samples because of the speed, cost, and technical advantages. Furthermore, subsystem comparisons rapidly identify the important metabolisms employed by the microbes in different environments.

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Related in: MedlinePlus

Cations and Anions found in the Soudan Mine. The pie chart shows the abundance of cations and anions found in the mine. The numbers in parentheses are the concentrations (in ppm) of each ion in the "Black" and "Red" samples respectively. The minor ions are shown expanded in the rightmost pie.
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Figure 5: Cations and Anions found in the Soudan Mine. The pie chart shows the abundance of cations and anions found in the mine. The numbers in parentheses are the concentrations (in ppm) of each ion in the "Black" and "Red" samples respectively. The minor ions are shown expanded in the rightmost pie.

Mentions: Several subsystems involved in iron uptake and utilization such as siderophores and ABC transporters for ferrichrome and heme are more common in the Black sample. The overall concentration of iron at the two sites was similar (Table 3; Figure 5). However, the iron in the Black sample is present as either Fe2+ dissolved in the water or as ferroan [(Mg,Fe)6(Si,Al)4O10(OH)8]. In either case, the ferrous iron can not be assimilated biologically, and the microbes are forced to scavenge for the limited ferric iron (Fe3+) available. In contrast, in the Red sample, goethite [FeO(OH)] is present and ferric iron is more readily available for biological utilization. The Black sample is enriched for amino acid degradation pathways and microbes may be assimilating nitrogen or carbon through these pathways. It is not currently apparent from where free amino acids would be supplied.


Using pyrosequencing to shed light on deep mine microbial ecology.

Edwards RA, Rodriguez-Brito B, Wegley L, Haynes M, Breitbart M, Peterson DM, Saar MO, Alexander S, Alexander EC, Rohwer F - BMC Genomics (2006)

Cations and Anions found in the Soudan Mine. The pie chart shows the abundance of cations and anions found in the mine. The numbers in parentheses are the concentrations (in ppm) of each ion in the "Black" and "Red" samples respectively. The minor ions are shown expanded in the rightmost pie.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1483832&req=5

Figure 5: Cations and Anions found in the Soudan Mine. The pie chart shows the abundance of cations and anions found in the mine. The numbers in parentheses are the concentrations (in ppm) of each ion in the "Black" and "Red" samples respectively. The minor ions are shown expanded in the rightmost pie.
Mentions: Several subsystems involved in iron uptake and utilization such as siderophores and ABC transporters for ferrichrome and heme are more common in the Black sample. The overall concentration of iron at the two sites was similar (Table 3; Figure 5). However, the iron in the Black sample is present as either Fe2+ dissolved in the water or as ferroan [(Mg,Fe)6(Si,Al)4O10(OH)8]. In either case, the ferrous iron can not be assimilated biologically, and the microbes are forced to scavenge for the limited ferric iron (Fe3+) available. In contrast, in the Red sample, goethite [FeO(OH)] is present and ferric iron is more readily available for biological utilization. The Black sample is enriched for amino acid degradation pathways and microbes may be assimilating nitrogen or carbon through these pathways. It is not currently apparent from where free amino acids would be supplied.

Bottom Line: In addition, the communities were also completely different from other microbial communities sequenced to date.We anticipate that pyrosequencing will be widely used to sequence environmental samples because of the speed, cost, and technical advantages.Furthermore, subsystem comparisons rapidly identify the important metabolisms employed by the microbes in different environments.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, San Diego State University, San Diego, USA. redwards@salmonella.org

ABSTRACT

Background: Contrasting biological, chemical and hydrogeological analyses highlights the fundamental processes that shape different environments. Generating and interpreting the biological sequence data was a costly and time-consuming process in defining an environment. Here we have used pyrosequencing, a rapid and relatively inexpensive sequencing technology, to generate environmental genome sequences from two sites in the Soudan Mine, Minnesota, USA. These sites were adjacent to each other, but differed significantly in chemistry and hydrogeology.

Results: Comparisons of the microbes and the subsystems identified in the two samples highlighted important differences in metabolic potential in each environment. The microbes were performing distinct biochemistry on the available substrates, and subsystems such as carbon utilization, iron acquisition mechanisms, nitrogen assimilation, and respiratory pathways separated the two communities. Although the correlation between much of the microbial metabolism occurring and the geochemical conditions from which the samples were isolated could be explained, the reason for the presence of many pathways in these environments remains to be determined. Despite being physically close, these two communities were markedly different from each other. In addition, the communities were also completely different from other microbial communities sequenced to date.

Conclusion: We anticipate that pyrosequencing will be widely used to sequence environmental samples because of the speed, cost, and technical advantages. Furthermore, subsystem comparisons rapidly identify the important metabolisms employed by the microbes in different environments.

Show MeSH
Related in: MedlinePlus