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Fine-Scale Community Structure Analysis of ANME in Nyegga Sediments with High and Low Methane Flux.

Roalkvam I, Dahle H, Chen Y, Jørgensen SL, Haflidason H, Steen IH - Front Microbiol (2012)

Bottom Line: These data were compared with previously obtained data from the more active G11 pockmark, characterized by higher methane flux.The stratification was over a wider spatial region and at greater depth in the core with lower methane flux, and the total 16S rRNA copy numbers were two orders of magnitude lower than in the sediments at G11 pockmark.Given that the ANME-2a/b population could be sustained in less active seepage areas, this subgroup could be potential seed populations in newly developed methane-enriched environments.

View Article: PubMed Central - PubMed

Affiliation: Center for Geobiology, Department of Biology, University of Bergen Bergen, Norway.

ABSTRACT
To obtain knowledge on how regional variations in methane seepage rates influence the stratification, abundance, and diversity of anaerobic methanotrophs (ANME), we analyzed the vertical microbial stratification in a gravity core from a methane micro-seeping area at Nyegga by using 454-pyrosequencing of 16S rRNA gene tagged amplicons and quantitative PCR. These data were compared with previously obtained data from the more active G11 pockmark, characterized by higher methane flux. A down core stratification and high relative abundance of ANME were observed in both cores, with transition from an ANME-2a/b dominated community in low-sulfide and low methane horizons to ANME-1 dominance in horizons near the sulfate-methane transition zone. The stratification was over a wider spatial region and at greater depth in the core with lower methane flux, and the total 16S rRNA copy numbers were two orders of magnitude lower than in the sediments at G11 pockmark. A fine-scale view into the ANME communities at each location was achieved through operational taxonomical units (OTU) clustering of ANME-affiliated sequences. The majority of ANME-1 sequences from both sampling sites clustered within one OTU, while ANME-2a/b sequences were represented in unique OTUs. We suggest that free-living ANME-1 is the most abundant taxon in Nyegga cold seeps, and also the main consumer of methane. The observation of specific ANME-2a/b OTUs at each location could reflect that organisms within this clade are adapted to different geochemical settings, perhaps due to differences in methane affinity. Given that the ANME-2a/b population could be sustained in less active seepage areas, this subgroup could be potential seed populations in newly developed methane-enriched environments.

No MeSH data available.


Microbial community structures at different depths in 15GC, based on 454-pyrosequencing of 16S rRNA gene tagged amplicons. The distribution of selected taxa is shown at phylum/class level (A) and within the class Methanomicrobia (B).
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Figure 3: Microbial community structures at different depths in 15GC, based on 454-pyrosequencing of 16S rRNA gene tagged amplicons. The distribution of selected taxa is shown at phylum/class level (A) and within the class Methanomicrobia (B).

Mentions: Most of the detected bacterial taxa were found in the shallower horizons, including phyla such as Proteobacteria, Planctomycetes, Deinococcus-Thermus, and the Candidate division OP8, all decreasing in abundance to less than 1% below horizons at 80–120 cmbsf (Figure 3A). Similarly, the abundance of the phylum Chloroflexi decreased rapidly in horizons below 80 cmbsf, although comprising up to 2% in some of these horizons. The Bacteria was dominated by the Candidate division JS-1, which was present throughout the sediments with the highest abundance at 10 and 30 cmbsf accounting for 13.2 and 28% of the total number of reads, respectively. In each sediment horizon, uncultivated lineages of Archaea dominated, congruent with the quantitative PCR-data (Figure 2). Low-abundance archaeal taxa, such as MCG (1.1–1.8%) and Group C3 (group 1.2; 1.2–2.6%) within Crenarchaeota and Thermoplasmata (0.3–4.2%) and Archaeoglobi (1.2%) within Euryarchaeota were mainly present in horizons between 10 and 80 cmbsf. Different depth profiles of the most abundant taxa MG-1, DSAG, and Methanomicrobia were observed (Figure 3A). The shallower horizons (10–120 cmbsf) above the SMTZ had high abundance of MG-1, ranging between 15.2 and 61.4%, which rapidly decreased toward the SMTZ (5.2% at 180 cmbsf and further to <1% in deeper parts of the core). The DSAG did not reach as high relative abundance as the MG-1, but represented a high share of the microbial community above and within the SMTZ, comprising between 16.2 and 29.2% in horizons at 10–240 cmbsf, except at 270 cmbsf where the abundance was reduced to 3.9% (Figure 3A). In the deeper horizons (180–270 cmbsf), where methane concentrations up to 3.6 mmol/L has been detected in the pore-water (Vaular, 2011), ANME clades affiliated with Methanomicrobia were increasingly dominant. A similar stratification of dominating ANME clades with increasing depth as in 29ROV was observed with a transition from an ANME-2a/b dominated community to an ANME-1 dominated community. However, the stratification was over wider sediment depths in 15GC ranging from 120 to 270 cmbsf in comparison to 4–22 cmbsf in 29ROV. The highest abundance of the ANME-2a/b clade was found at 120 and 180 cmbsf, with 16.9 and 33.3% of the total reads respectively (Figure 3B), and hence comprising a similar share of the community as in 29ROV (Roalkvam et al., 2011). The abundance of ANME-2a/b decreased gradually to <1% with increasing depth, while ANME-1 increased from 11.1 to 47.9% between 180 and 240 cmbsf. A further increase to 82.2% at 270 cmbsf was observed, which was the highest abundance of ANME-1 in 15GC (Figure 3B). The highest relative abundance of ANME-1 in 15GC (47.9–82.2%) corresponded to the abundance of ANME-1 in 29ROV (64–89%; Roalkvam et al., 2011). However, the abundance of ANME-2c increased to a maximum of 60% at 20–22 cmbsf in 29ROV (Roalkvam et al., 2011), which is considerable higher than the maximum value of 5.7% at 270 cmbsf in 15GC.


Fine-Scale Community Structure Analysis of ANME in Nyegga Sediments with High and Low Methane Flux.

Roalkvam I, Dahle H, Chen Y, Jørgensen SL, Haflidason H, Steen IH - Front Microbiol (2012)

Microbial community structures at different depths in 15GC, based on 454-pyrosequencing of 16S rRNA gene tagged amplicons. The distribution of selected taxa is shown at phylum/class level (A) and within the class Methanomicrobia (B).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3375579&req=5

Figure 3: Microbial community structures at different depths in 15GC, based on 454-pyrosequencing of 16S rRNA gene tagged amplicons. The distribution of selected taxa is shown at phylum/class level (A) and within the class Methanomicrobia (B).
Mentions: Most of the detected bacterial taxa were found in the shallower horizons, including phyla such as Proteobacteria, Planctomycetes, Deinococcus-Thermus, and the Candidate division OP8, all decreasing in abundance to less than 1% below horizons at 80–120 cmbsf (Figure 3A). Similarly, the abundance of the phylum Chloroflexi decreased rapidly in horizons below 80 cmbsf, although comprising up to 2% in some of these horizons. The Bacteria was dominated by the Candidate division JS-1, which was present throughout the sediments with the highest abundance at 10 and 30 cmbsf accounting for 13.2 and 28% of the total number of reads, respectively. In each sediment horizon, uncultivated lineages of Archaea dominated, congruent with the quantitative PCR-data (Figure 2). Low-abundance archaeal taxa, such as MCG (1.1–1.8%) and Group C3 (group 1.2; 1.2–2.6%) within Crenarchaeota and Thermoplasmata (0.3–4.2%) and Archaeoglobi (1.2%) within Euryarchaeota were mainly present in horizons between 10 and 80 cmbsf. Different depth profiles of the most abundant taxa MG-1, DSAG, and Methanomicrobia were observed (Figure 3A). The shallower horizons (10–120 cmbsf) above the SMTZ had high abundance of MG-1, ranging between 15.2 and 61.4%, which rapidly decreased toward the SMTZ (5.2% at 180 cmbsf and further to <1% in deeper parts of the core). The DSAG did not reach as high relative abundance as the MG-1, but represented a high share of the microbial community above and within the SMTZ, comprising between 16.2 and 29.2% in horizons at 10–240 cmbsf, except at 270 cmbsf where the abundance was reduced to 3.9% (Figure 3A). In the deeper horizons (180–270 cmbsf), where methane concentrations up to 3.6 mmol/L has been detected in the pore-water (Vaular, 2011), ANME clades affiliated with Methanomicrobia were increasingly dominant. A similar stratification of dominating ANME clades with increasing depth as in 29ROV was observed with a transition from an ANME-2a/b dominated community to an ANME-1 dominated community. However, the stratification was over wider sediment depths in 15GC ranging from 120 to 270 cmbsf in comparison to 4–22 cmbsf in 29ROV. The highest abundance of the ANME-2a/b clade was found at 120 and 180 cmbsf, with 16.9 and 33.3% of the total reads respectively (Figure 3B), and hence comprising a similar share of the community as in 29ROV (Roalkvam et al., 2011). The abundance of ANME-2a/b decreased gradually to <1% with increasing depth, while ANME-1 increased from 11.1 to 47.9% between 180 and 240 cmbsf. A further increase to 82.2% at 270 cmbsf was observed, which was the highest abundance of ANME-1 in 15GC (Figure 3B). The highest relative abundance of ANME-1 in 15GC (47.9–82.2%) corresponded to the abundance of ANME-1 in 29ROV (64–89%; Roalkvam et al., 2011). However, the abundance of ANME-2c increased to a maximum of 60% at 20–22 cmbsf in 29ROV (Roalkvam et al., 2011), which is considerable higher than the maximum value of 5.7% at 270 cmbsf in 15GC.

Bottom Line: These data were compared with previously obtained data from the more active G11 pockmark, characterized by higher methane flux.The stratification was over a wider spatial region and at greater depth in the core with lower methane flux, and the total 16S rRNA copy numbers were two orders of magnitude lower than in the sediments at G11 pockmark.Given that the ANME-2a/b population could be sustained in less active seepage areas, this subgroup could be potential seed populations in newly developed methane-enriched environments.

View Article: PubMed Central - PubMed

Affiliation: Center for Geobiology, Department of Biology, University of Bergen Bergen, Norway.

ABSTRACT
To obtain knowledge on how regional variations in methane seepage rates influence the stratification, abundance, and diversity of anaerobic methanotrophs (ANME), we analyzed the vertical microbial stratification in a gravity core from a methane micro-seeping area at Nyegga by using 454-pyrosequencing of 16S rRNA gene tagged amplicons and quantitative PCR. These data were compared with previously obtained data from the more active G11 pockmark, characterized by higher methane flux. A down core stratification and high relative abundance of ANME were observed in both cores, with transition from an ANME-2a/b dominated community in low-sulfide and low methane horizons to ANME-1 dominance in horizons near the sulfate-methane transition zone. The stratification was over a wider spatial region and at greater depth in the core with lower methane flux, and the total 16S rRNA copy numbers were two orders of magnitude lower than in the sediments at G11 pockmark. A fine-scale view into the ANME communities at each location was achieved through operational taxonomical units (OTU) clustering of ANME-affiliated sequences. The majority of ANME-1 sequences from both sampling sites clustered within one OTU, while ANME-2a/b sequences were represented in unique OTUs. We suggest that free-living ANME-1 is the most abundant taxon in Nyegga cold seeps, and also the main consumer of methane. The observation of specific ANME-2a/b OTUs at each location could reflect that organisms within this clade are adapted to different geochemical settings, perhaps due to differences in methane affinity. Given that the ANME-2a/b population could be sustained in less active seepage areas, this subgroup could be potential seed populations in newly developed methane-enriched environments.

No MeSH data available.