Distribution of archaea in a black smoker chimney structure

Abstract

Archaeal community structures in microhabitats in a deep-sea hydrothermal vent chimney structure were evaluated through the combined use of culture-independent molecular analyses and enrichment culture methods. A black smoker chimney was obtained from the PACMANUS site in the Manus Basin near Papua New Guinea, and subsamples were obtained from vertical and horizontal sections. The elemental composition of the chimney was analyzed in different subsamples by scanning electron microscopy and energy-dispersive X-ray spectroscopy, indicating that zinc and sulfur were major components while an increased amount of elemental oxygen in exterior materials represented the presence of oxidized materials on the outer surface of the chimney. Terminal restriction fragment length polymorphism analysis revealed that a shift in archaeal ribotype structure occurred in the chimney structure. Through sequencing of ribosomal DNA (rDNA) clones from archaeal rDNA clone libraries, it was demonstrated that the archaeal communities in the chimney structure consisted for the most part of hyperthermophilic members and extreme halophiles and that the distribution of such extremophiles in different microhabitats of the chimney varied. The results of the culture-dependent analysis supported in part the view that changes in archaeal community structures in these microhabitats are associated with the geochemical and physical dynamics in the black smoker chimney.

FIG. 1

Schematic drawings of the morphological and structural features of a black smoker chimney and the subsampling method used. (A) Appearance of the surface. (B) Vertical section of the whole chimney structure. (C) Horizontal section of the root part of the chimney. The part where each of the subsamples was taken and the preliminary morphological and structural features of the subsamples are indicated.

FIG. 2

Typical electropherograms of archaeal T-RFLP generated from rDNA with a labeled reverse primer and HhaI digest obtained from subsamples. The numbers on the peaks indicate major ribotypes commonly observed in various subsamples. Shown are a typical archaeal pattern from the top part of the chimney (subsample I) (A), the surface layer grazed from subsample I (subsample II) (B), the surface layer grazed from the middle part of the chimney (subsample III) (C), the vent surface (subsample IV) (D), the inner soft and porous structure in the root part of the chimney (subsample V) (E), and the outer black and solid structure in the root part of the chimney (subsample VI) (F).

FIG. 3

Phylogenetic trees based on SSU rDNA sequences including various rDNA clones obtained from the black smoker chimney at the PACMANUS site in the Manus Basin. Each of the trees was inferred by neighbor-joining analysis of approximately 600 homologous positions of the rDNA sequence. (A) A tree indicating the phylogenetic relationship among the domains of Bacteria and Eucarya, the deep branches of uncultivated archaea, and the crenarchaeotic and euryarchaeotic kingdoms. (B) A tree indicating the phylogenetic organization among the hyperthermophilic crenarchaeota, Thermoproteales, Igniococcales, and Sulfolobales. (C) A tree indicating the phylogenetic relationship within the hyperthermophilic and thermophilic euryarchaeota and the possible thermophilic euryarchaeotic phylotypes. (D) A tree indicating the phylogenetic organization within the genus Haloarcula. The numbers on the branches represent the bootstrap confidence values. The scale bars indicate the expected changes per sequence position. Abbreviations indicate rDNA clones corresponding to uncultivated organisms derived from the following environments: pMC1A, pMC2A, pISA, and pIVWA from deep-sea hydrothermal vent environments (51); pOWA and pUWA from shallow marine hydrothermal vent water and terrestrial acidic hot spring water, respectively (55); pJP and pSL from sediments in Yellowstone National Park hot springs (3, 4); CRA and APA from deep-sea sediments (59); pHGPA from deep subsurface geothermal water (50); VC2.1 Arc from an in situ growth chamber (Vent Cap) deployed at a deep-sea hydrothermal vent (44); and pPACMA from a black smoker chimney at the PACMANUS site in the Manus Basin.

FIG. 3

Phylogenetic trees based on SSU rDNA sequences including various rDNA clones obtained from the black smoker chimney at the PACMANUS site in the Manus Basin. Each of the trees was inferred by neighbor-joining analysis of approximately 600 homologous positions of the rDNA sequence. (A) A tree indicating the phylogenetic relationship among the domains of Bacteria and Eucarya, the deep branches of uncultivated archaea, and the crenarchaeotic and euryarchaeotic kingdoms. (B) A tree indicating the phylogenetic organization among the hyperthermophilic crenarchaeota, Thermoproteales, Igniococcales, and Sulfolobales. (C) A tree indicating the phylogenetic relationship within the hyperthermophilic and thermophilic euryarchaeota and the possible thermophilic euryarchaeotic phylotypes. (D) A tree indicating the phylogenetic organization within the genus Haloarcula. The numbers on the branches represent the bootstrap confidence values. The scale bars indicate the expected changes per sequence position. Abbreviations indicate rDNA clones corresponding to uncultivated organisms derived from the following environments: pMC1A, pMC2A, pISA, and pIVWA from deep-sea hydrothermal vent environments (51); pOWA and pUWA from shallow marine hydrothermal vent water and terrestrial acidic hot spring water, respectively (55); pJP and pSL from sediments in Yellowstone National Park hot springs (3, 4); CRA and APA from deep-sea sediments (59); pHGPA from deep subsurface geothermal water (50); VC2.1 Arc from an in situ growth chamber (Vent Cap) deployed at a deep-sea hydrothermal vent (44); and pPACMA from a black smoker chimney at the PACMANUS site in the Manus Basin.

FIG. 3

Phylogenetic trees based on SSU rDNA sequences including various rDNA clones obtained from the black smoker chimney at the PACMANUS site in the Manus Basin. Each of the trees was inferred by neighbor-joining analysis of approximately 600 homologous positions of the rDNA sequence. (A) A tree indicating the phylogenetic relationship among the domains of Bacteria and Eucarya, the deep branches of uncultivated archaea, and the crenarchaeotic and euryarchaeotic kingdoms. (B) A tree indicating the phylogenetic organization among the hyperthermophilic crenarchaeota, Thermoproteales, Igniococcales, and Sulfolobales. (C) A tree indicating the phylogenetic relationship within the hyperthermophilic and thermophilic euryarchaeota and the possible thermophilic euryarchaeotic phylotypes. (D) A tree indicating the phylogenetic organization within the genus Haloarcula. The numbers on the branches represent the bootstrap confidence values. The scale bars indicate the expected changes per sequence position. Abbreviations indicate rDNA clones corresponding to uncultivated organisms derived from the following environments: pMC1A, pMC2A, pISA, and pIVWA from deep-sea hydrothermal vent environments (51); pOWA and pUWA from shallow marine hydrothermal vent water and terrestrial acidic hot spring water, respectively (55); pJP and pSL from sediments in Yellowstone National Park hot springs (3, 4); CRA and APA from deep-sea sediments (59); pHGPA from deep subsurface geothermal water (50); VC2.1 Arc from an in situ growth chamber (Vent Cap) deployed at a deep-sea hydrothermal vent (44); and pPACMA from a black smoker chimney at the PACMANUS site in the Manus Basin.

FIG. 3

Phylogenetic trees based on SSU rDNA sequences including various rDNA clones obtained from the black smoker chimney at the PACMANUS site in the Manus Basin. Each of the trees was inferred by neighbor-joining analysis of approximately 600 homologous positions of the rDNA sequence. (A) A tree indicating the phylogenetic relationship among the domains of Bacteria and Eucarya, the deep branches of uncultivated archaea, and the crenarchaeotic and euryarchaeotic kingdoms. (B) A tree indicating the phylogenetic organization among the hyperthermophilic crenarchaeota, Thermoproteales, Igniococcales, and Sulfolobales. (C) A tree indicating the phylogenetic relationship within the hyperthermophilic and thermophilic euryarchaeota and the possible thermophilic euryarchaeotic phylotypes. (D) A tree indicating the phylogenetic organization within the genus Haloarcula. The numbers on the branches represent the bootstrap confidence values. The scale bars indicate the expected changes per sequence position. Abbreviations indicate rDNA clones corresponding to uncultivated organisms derived from the following environments: pMC1A, pMC2A, pISA, and pIVWA from deep-sea hydrothermal vent environments (51); pOWA and pUWA from shallow marine hydrothermal vent water and terrestrial acidic hot spring water, respectively (55); pJP and pSL from sediments in Yellowstone National Park hot springs (3, 4); CRA and APA from deep-sea sediments (59); pHGPA from deep subsurface geothermal water (50); VC2.1 Arc from an in situ growth chamber (Vent Cap) deployed at a deep-sea hydrothermal vent (44); and pPACMA from a black smoker chimney at the PACMANUS site in the Manus Basin.