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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

Sampling from the Soudan Mine. The Soudan Mine is an Algoma-type Iron Formation rich in hematite. Panel A shows a cross-section of the mine looking East-North-East at 78.5°. Panel B depicts a three dimensional view of the mine, including the cross-section shown in Panel A, and with the sampling sites shown for the "Red" and "Black" samples. Panel C shows the overall flow of water in the mine at level 27, located 714 meters below the surface (Panel D). Panels E and F show a close up of the two sampling sites.
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Figure 1: Sampling from the Soudan Mine. The Soudan Mine is an Algoma-type Iron Formation rich in hematite. Panel A shows a cross-section of the mine looking East-North-East at 78.5°. Panel B depicts a three dimensional view of the mine, including the cross-section shown in Panel A, and with the sampling sites shown for the "Red" and "Black" samples. Panel C shows the overall flow of water in the mine at level 27, located 714 meters below the surface (Panel D). Panels E and F show a close up of the two sampling sites.

Mentions: The two environments sampled within the Soudan Mine are shown in Figure 1. Groundwater is not very abundant in the banded iron formations of the mine at our sampling depth of 714 m below the surface. However, small amounts of water emerge steadily from exploration boreholes that extend downward from the deepest level of the mine. The two sets of samples were collected from water trickling out of two such boreholes that are separated by about 100 meters (Figure 1). This water is a calcium, sodium, chloride solution about twice as salty as seawater. It is anoxic, with up to 150 ppm of dissolved ferrous iron and variable enrichments of several trace elements. At both locations, the water emerging from the boreholes produces cm-scale "Black" environments that appear to extend down into the borehole. The water flowing away from each borehole, on the floor of the mine tunnel, is exposed to the oxygenated mine atmosphere, and transitions to a sequence of "Red" environments within a few cm of the orifices. The oxidized environments are continuously fed by anoxic water flowing from the boreholes. The water in the borehole, which yielded the Black sample, as well as a number of similar sites found throughout the mine, has a pH of 6.70 and redox potential of -142 mV. Some of the Black areas are associated with bubbling of gas. The Black sediment contained 5.8 × 105 microbes per ml. X-ray diffraction analyses of the minerals in this area show that chlorite-serpentine [(Mg,Al)6(Si,Al)4O10(OH)8], clinochlore, ferroan [(Mg,Fe)6(Si,Al)4O10(OH)8], quartz, and silinaite [LiNaSiO5·HCl] are present in the Black sediments. Water slowly flows from the borehole into the stream running down the main mine tunnel. As the water comes in contact with oxygen in the passageway, the pH rapidly decreases to 4.37 and redox potential increases to -8 mV. The Red sample contained 1.2 × 106 microbes per ml, and these sediments include goethite [FeO(OH)], followed by szaibelyite [(Mg,Mn)BO2(OH)], and sussexite [(Mn,Mg)BO2(OH)].


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)

Sampling from the Soudan Mine. The Soudan Mine is an Algoma-type Iron Formation rich in hematite. Panel A shows a cross-section of the mine looking East-North-East at 78.5°. Panel B depicts a three dimensional view of the mine, including the cross-section shown in Panel A, and with the sampling sites shown for the "Red" and "Black" samples. Panel C shows the overall flow of water in the mine at level 27, located 714 meters below the surface (Panel D). Panels E and F show a close up of the two sampling sites.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Sampling from the Soudan Mine. The Soudan Mine is an Algoma-type Iron Formation rich in hematite. Panel A shows a cross-section of the mine looking East-North-East at 78.5°. Panel B depicts a three dimensional view of the mine, including the cross-section shown in Panel A, and with the sampling sites shown for the "Red" and "Black" samples. Panel C shows the overall flow of water in the mine at level 27, located 714 meters below the surface (Panel D). Panels E and F show a close up of the two sampling sites.
Mentions: The two environments sampled within the Soudan Mine are shown in Figure 1. Groundwater is not very abundant in the banded iron formations of the mine at our sampling depth of 714 m below the surface. However, small amounts of water emerge steadily from exploration boreholes that extend downward from the deepest level of the mine. The two sets of samples were collected from water trickling out of two such boreholes that are separated by about 100 meters (Figure 1). This water is a calcium, sodium, chloride solution about twice as salty as seawater. It is anoxic, with up to 150 ppm of dissolved ferrous iron and variable enrichments of several trace elements. At both locations, the water emerging from the boreholes produces cm-scale "Black" environments that appear to extend down into the borehole. The water flowing away from each borehole, on the floor of the mine tunnel, is exposed to the oxygenated mine atmosphere, and transitions to a sequence of "Red" environments within a few cm of the orifices. The oxidized environments are continuously fed by anoxic water flowing from the boreholes. The water in the borehole, which yielded the Black sample, as well as a number of similar sites found throughout the mine, has a pH of 6.70 and redox potential of -142 mV. Some of the Black areas are associated with bubbling of gas. The Black sediment contained 5.8 × 105 microbes per ml. X-ray diffraction analyses of the minerals in this area show that chlorite-serpentine [(Mg,Al)6(Si,Al)4O10(OH)8], clinochlore, ferroan [(Mg,Fe)6(Si,Al)4O10(OH)8], quartz, and silinaite [LiNaSiO5·HCl] are present in the Black sediments. Water slowly flows from the borehole into the stream running down the main mine tunnel. As the water comes in contact with oxygen in the passageway, the pH rapidly decreases to 4.37 and redox potential increases to -8 mV. The Red sample contained 1.2 × 106 microbes per ml, and these sediments include goethite [FeO(OH)], followed by szaibelyite [(Mg,Mn)BO2(OH)], and sussexite [(Mn,Mg)BO2(OH)].

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