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Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea.

Yelton AP, Comolli LR, Justice NB, Castelle C, Denef VJ, Thomas BC, Banfield JF - BMC Genomics (2013)

Bottom Line: These results greatly expand genomic information available for this archaeal order.These results indicate that subtle, but important genomic differences, coupled with unknown differences in gene expression, distinguish these organisms enough to allow for co-existence.Overall this study reveals shared features of organisms from the Thermoplasmatales lineage and provides new insights into the functioning of AMD communities.

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Affiliation: Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA.

ABSTRACT

Background: Metal sulfide mineral dissolution during bioleaching and acid mine drainage (AMD) formation creates an environment that is inhospitable to most life. Despite dominance by a small number of bacteria, AMD microbial biofilm communities contain a notable variety of coexisting and closely related Euryarchaea, most of which have defied cultivation efforts. For this reason, we used metagenomics to analyze variation in gene content that may contribute to niche differentiation among co-occurring AMD archaea. Our analyses targeted members of the Thermoplasmatales and related archaea. These results greatly expand genomic information available for this archaeal order.

Results: We reconstructed near-complete genomes for uncultivated, relatively low abundance organisms A-, E-, and Gplasma, members of Thermoplasmatales order, and for a novel organism, Iplasma. Genomic analyses of these organisms, as well as Ferroplasma type I and II, reveal that all are facultative aerobic heterotrophs with the ability to use many of the same carbon substrates, including methanol. Most of the genomes share genes for toxic metal resistance and surface-layer production. Only Aplasma and Eplasma have a full suite of flagellar genes whereas all but the Ferroplasma spp. have genes for pili production. Cryogenic-electron microscopy (cryo-EM) and tomography (cryo-ET) strengthen these metagenomics-based ultrastructural predictions. Notably, only Aplasma, Gplasma and the Ferroplasma spp. have predicted iron oxidation genes and Eplasma and Iplasma lack most genes for cobalamin, valine, (iso)leucine and histidine synthesis.

Conclusion: The Thermoplasmatales AMD archaea share a large number of metabolic capabilities. All of the uncultivated organisms studied here (A-, E-, G-, and Iplasma) are metabolically very similar to characterized Ferroplasma spp., differentiating themselves mainly in their genetic capabilities for biosynthesis, motility, and possibly iron oxidation. These results indicate that subtle, but important genomic differences, coupled with unknown differences in gene expression, distinguish these organisms enough to allow for co-existence. Overall this study reveals shared features of organisms from the Thermoplasmatales lineage and provides new insights into the functioning of AMD communities.

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Cryo-EM of surface-layer on an AMD plasma cell from the Richmond Mine. Insets show a higher magnification. Arrows point to putative surface-layer proteins. Panel A and panel B show evidence of proteinaceous surface layers in two different cells collected from the Richmond Mine AMD.
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Figure 3: Cryo-EM of surface-layer on an AMD plasma cell from the Richmond Mine. Insets show a higher magnification. Arrows point to putative surface-layer proteins. Panel A and panel B show evidence of proteinaceous surface layers in two different cells collected from the Richmond Mine AMD.

Mentions: Thermoplasmatales cells are generally bounded by a single membrane, except for two Picrophilus species that have a single membrane surrounded by a surface-layer (S-layer) [13]. We characterized archaeal-rich biofilm communities via cryo-electron microscopy and identified surface layers on many single membrane bound cells (Figure 3, Additional file 11). Thus, we looked for the genes needed for surface layer structural proteins and their post-translational modifications (i.e., N-glycosylation). We found putative S-layer genes in all of the AMD plasma genomes (except Fer1) that are homologous with the predicted P. torridus S-layer genes (Additional file 12) [28], but found no homology to the predicted S-layer genes in their next closest relative, Acidiloprofundum boonei[29]. We also found genes potentially involved in archaeal S-layer protein N-glycosylation. Of particular interest were homologs to the AglD and AglB genes of Haloferax volcanii, which have been shown to be essential to S-layer protein N-glycosylation in that organism [30]. Many of the Iplasma S-layer-related genes occur in a cluster, and several have conserved gene order in distant relatives, including several enzymes that attach sugars to a dolichol that might serve as a membrane anchor for the formation of an oligosaccharide during N-glycosylation. The Iplasma genome contains a gene cluster syntenous with distant relatives that encodes all of the proteins in the ADP-L-glycero-β-D-manno-heptose (AGMH) biosynthesis pathway (Additional file 12). AGMH is attached to S-layer proteins in gram-positive bacteria [31-33], suggesting that this may be involved in S-layer glycosylation in Iplasma as well. Finally, in the same genomic region genes are found for the biosynthesis of GDP-L-fucose, a glycoprotein component, and dTDP-L-rhamnose, a lipopolysaccharide component, indicating that these may make up part of the AMD plasma S-layer polysaccharides.


Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea.

Yelton AP, Comolli LR, Justice NB, Castelle C, Denef VJ, Thomas BC, Banfield JF - BMC Genomics (2013)

Cryo-EM of surface-layer on an AMD plasma cell from the Richmond Mine. Insets show a higher magnification. Arrows point to putative surface-layer proteins. Panel A and panel B show evidence of proteinaceous surface layers in two different cells collected from the Richmond Mine AMD.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3750248&req=5

Figure 3: Cryo-EM of surface-layer on an AMD plasma cell from the Richmond Mine. Insets show a higher magnification. Arrows point to putative surface-layer proteins. Panel A and panel B show evidence of proteinaceous surface layers in two different cells collected from the Richmond Mine AMD.
Mentions: Thermoplasmatales cells are generally bounded by a single membrane, except for two Picrophilus species that have a single membrane surrounded by a surface-layer (S-layer) [13]. We characterized archaeal-rich biofilm communities via cryo-electron microscopy and identified surface layers on many single membrane bound cells (Figure 3, Additional file 11). Thus, we looked for the genes needed for surface layer structural proteins and their post-translational modifications (i.e., N-glycosylation). We found putative S-layer genes in all of the AMD plasma genomes (except Fer1) that are homologous with the predicted P. torridus S-layer genes (Additional file 12) [28], but found no homology to the predicted S-layer genes in their next closest relative, Acidiloprofundum boonei[29]. We also found genes potentially involved in archaeal S-layer protein N-glycosylation. Of particular interest were homologs to the AglD and AglB genes of Haloferax volcanii, which have been shown to be essential to S-layer protein N-glycosylation in that organism [30]. Many of the Iplasma S-layer-related genes occur in a cluster, and several have conserved gene order in distant relatives, including several enzymes that attach sugars to a dolichol that might serve as a membrane anchor for the formation of an oligosaccharide during N-glycosylation. The Iplasma genome contains a gene cluster syntenous with distant relatives that encodes all of the proteins in the ADP-L-glycero-β-D-manno-heptose (AGMH) biosynthesis pathway (Additional file 12). AGMH is attached to S-layer proteins in gram-positive bacteria [31-33], suggesting that this may be involved in S-layer glycosylation in Iplasma as well. Finally, in the same genomic region genes are found for the biosynthesis of GDP-L-fucose, a glycoprotein component, and dTDP-L-rhamnose, a lipopolysaccharide component, indicating that these may make up part of the AMD plasma S-layer polysaccharides.

Bottom Line: These results greatly expand genomic information available for this archaeal order.These results indicate that subtle, but important genomic differences, coupled with unknown differences in gene expression, distinguish these organisms enough to allow for co-existence.Overall this study reveals shared features of organisms from the Thermoplasmatales lineage and provides new insights into the functioning of AMD communities.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA.

ABSTRACT

Background: Metal sulfide mineral dissolution during bioleaching and acid mine drainage (AMD) formation creates an environment that is inhospitable to most life. Despite dominance by a small number of bacteria, AMD microbial biofilm communities contain a notable variety of coexisting and closely related Euryarchaea, most of which have defied cultivation efforts. For this reason, we used metagenomics to analyze variation in gene content that may contribute to niche differentiation among co-occurring AMD archaea. Our analyses targeted members of the Thermoplasmatales and related archaea. These results greatly expand genomic information available for this archaeal order.

Results: We reconstructed near-complete genomes for uncultivated, relatively low abundance organisms A-, E-, and Gplasma, members of Thermoplasmatales order, and for a novel organism, Iplasma. Genomic analyses of these organisms, as well as Ferroplasma type I and II, reveal that all are facultative aerobic heterotrophs with the ability to use many of the same carbon substrates, including methanol. Most of the genomes share genes for toxic metal resistance and surface-layer production. Only Aplasma and Eplasma have a full suite of flagellar genes whereas all but the Ferroplasma spp. have genes for pili production. Cryogenic-electron microscopy (cryo-EM) and tomography (cryo-ET) strengthen these metagenomics-based ultrastructural predictions. Notably, only Aplasma, Gplasma and the Ferroplasma spp. have predicted iron oxidation genes and Eplasma and Iplasma lack most genes for cobalamin, valine, (iso)leucine and histidine synthesis.

Conclusion: The Thermoplasmatales AMD archaea share a large number of metabolic capabilities. All of the uncultivated organisms studied here (A-, E-, G-, and Iplasma) are metabolically very similar to characterized Ferroplasma spp., differentiating themselves mainly in their genetic capabilities for biosynthesis, motility, and possibly iron oxidation. These results indicate that subtle, but important genomic differences, coupled with unknown differences in gene expression, distinguish these organisms enough to allow for co-existence. Overall this study reveals shared features of organisms from the Thermoplasmatales lineage and provides new insights into the functioning of AMD communities.

Show MeSH
Related in: MedlinePlus