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Site- and horizon-specific patterns of microbial community structure and enzyme activities in permafrost-affected soils of Greenland.

Gittel A, Bárta J, Kohoutová I, Schnecker J, Wild B, Capek P, Kaiser C, Torsvik VL, Richter A, Schleper C, Urich T - Front Microbiol (2014)

Bottom Line: Sampling site and thus abiotic factors had a significant impact on microbial community structure, diversity and activity, the wet fen site exhibiting higher potential enzyme activities and presumably being a hot spot for anaerobic degradation processes such as fermentation and methanogenesis.Lowest fungal to bacterial ratios were found in topsoils that had been relocated by cryoturbation ("buried topsoils"), resulting from a decrease in fungal abundance compared to recent ("unburied") topsoils.Our study sheds light on the highly diverse, but poorly-studied communities in permafrost-affected soils in Greenland and their role in OC degradation.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Centre for Geobiology, University of Bergen Bergen, Norway ; Department of Bioscience, Center for Geomicrobiology, Aarhus University Aarhus, Denmark.

ABSTRACT
Permafrost-affected soils in the Northern latitudes store huge amounts of organic carbon (OC) that is prone to microbial degradation and subsequent release of greenhouse gasses to the atmosphere. In Greenland, the consequences of permafrost thaw have only recently been addressed, and predictions on its impact on the carbon budget are thus still highly uncertain. However, the fate of OC is not only determined by abiotic factors, but closely tied to microbial activity. We investigated eight soil profiles in northeast Greenland comprising two sites with typical tundra vegetation and one wet fen site. We assessed microbial community structure and diversity (SSU rRNA gene tag sequencing, quantification of bacteria, archaea and fungi), and measured hydrolytic and oxidative enzyme activities. Sampling site and thus abiotic factors had a significant impact on microbial community structure, diversity and activity, the wet fen site exhibiting higher potential enzyme activities and presumably being a hot spot for anaerobic degradation processes such as fermentation and methanogenesis. Lowest fungal to bacterial ratios were found in topsoils that had been relocated by cryoturbation ("buried topsoils"), resulting from a decrease in fungal abundance compared to recent ("unburied") topsoils. Actinobacteria (in particular Intrasporangiaceae) accounted for a major fraction of the microbial community in buried topsoils, but were only of minor abundance in all other soil horizons. It was indicated that the distribution pattern of Actinobacteria and a variety of other bacterial classes was related to the activity of phenol oxidases and peroxidases supporting the hypothesis that bacteria might resume the role of fungi in oxidative enzyme production and degradation of phenolic and other complex substrates in these soils. Our study sheds light on the highly diverse, but poorly-studied communities in permafrost-affected soils in Greenland and their role in OC degradation.

No MeSH data available.


Related in: MedlinePlus

Community structure as revealed from Illumina tag sequencing of the prokaryotic V4 region of the SSU rRNA gene. Left panels: Percentage of OTUs affiliated to bacterial phyla, candidate divisions and proteobacterial classes (only shown if they represented at least 1% of all sequences in any of the samples). Right panels: Percentage of archaeal phyla, candidate divisions and classes. Cand. div., candidate division; MBGA, marine benthic group A; MBGB, marine benthic group B; MCG, miscellaneous crenarchaeotal group; DSEG, deep sea euryarchaeotal group; O, organic topsoil; A, mineral topsoil; B, mineral subsoil; J, buried topsoil; PF, permafrost layer. Note the difference in scaling of archaeal reads for site 2. (More detailed information the relative abundance of bacterial and archaeal classes in Table S3).
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Figure 2: Community structure as revealed from Illumina tag sequencing of the prokaryotic V4 region of the SSU rRNA gene. Left panels: Percentage of OTUs affiliated to bacterial phyla, candidate divisions and proteobacterial classes (only shown if they represented at least 1% of all sequences in any of the samples). Right panels: Percentage of archaeal phyla, candidate divisions and classes. Cand. div., candidate division; MBGA, marine benthic group A; MBGB, marine benthic group B; MCG, miscellaneous crenarchaeotal group; DSEG, deep sea euryarchaeotal group; O, organic topsoil; A, mineral topsoil; B, mineral subsoil; J, buried topsoil; PF, permafrost layer. Note the difference in scaling of archaeal reads for site 2. (More detailed information the relative abundance of bacterial and archaeal classes in Table S3).

Mentions: Twenty-seven samples covering the four different soil horizons (O and A, B, J, and PF) were subjected to Illumina tag sequencing of the V4 SSU rRNA gene region (sequence and metadata available from http://www.microbio.me/emp/, study no. 1034). Sequencing was successful for 20 of these samples (Table 3, Table S3) and yielded a total of 1,975,888 bacterial and archaeal SSU rRNA gene sequences after extensive read-quality filtering (see Materials and Methods for details) with 86% being taxonomically classified using closed-reference OTU picking. Bacterial and archaeal sequences clustered in 10,309 OTUs, representing 157 classes (147 bacterial and 10 archaeal) within 55 phyla (including 30 candidate phyla). The dominant phyla were Proteobacteria (α, β, δ, and γ), Acidobacteria, Actinobacteria, Verrucomicrobia, Bacteroidetes, and Firmicutes accounting for ~84% of all sequences (Figure 2). In addition, Chloroflexi, Gemmatimonadetes, Planctomycetes, Cyanobacteria, and Nitrospirae were present in all soil horizons, but at lower abundances (~12% of all sequences), and 38 other rare phyla (<0.5% each) were identified. Rare phyla included archaeal taxa that represented 0.3% of all sequence reads. The majority of archaeal reads was assigned to the classes Methanomicrobia and Methanobacteria within the Euryarchaeota comprising 39.8% of all archaeal reads. For site 2, sequence reads assigned to archaeal taxa comprised 0.9% of all reads obtained from site 2 samples, whereas they only accounted for 0.05 and 0.01% at sites 1 and 3, respectively (Figure 2). This finding was in line with lower archaeal SSU rRNA gene abundances at sites 1 and 3 than at site 2 (as determined by qPCR). Furthermore, the majority of sequences retrieved from site 2 was affiliated with methanogenic taxa of the families Methanosarcinaceae, Methanobacteriaceae, and Methanosaetaceae in the phylum Euryarchaoeta, whereas members of the Thaumarchaeota and several other non-methanogenic archaea dominated at sites 1 and 3 (Figure 2).


Site- and horizon-specific patterns of microbial community structure and enzyme activities in permafrost-affected soils of Greenland.

Gittel A, Bárta J, Kohoutová I, Schnecker J, Wild B, Capek P, Kaiser C, Torsvik VL, Richter A, Schleper C, Urich T - Front Microbiol (2014)

Community structure as revealed from Illumina tag sequencing of the prokaryotic V4 region of the SSU rRNA gene. Left panels: Percentage of OTUs affiliated to bacterial phyla, candidate divisions and proteobacterial classes (only shown if they represented at least 1% of all sequences in any of the samples). Right panels: Percentage of archaeal phyla, candidate divisions and classes. Cand. div., candidate division; MBGA, marine benthic group A; MBGB, marine benthic group B; MCG, miscellaneous crenarchaeotal group; DSEG, deep sea euryarchaeotal group; O, organic topsoil; A, mineral topsoil; B, mineral subsoil; J, buried topsoil; PF, permafrost layer. Note the difference in scaling of archaeal reads for site 2. (More detailed information the relative abundance of bacterial and archaeal classes in Table S3).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4199454&req=5

Figure 2: Community structure as revealed from Illumina tag sequencing of the prokaryotic V4 region of the SSU rRNA gene. Left panels: Percentage of OTUs affiliated to bacterial phyla, candidate divisions and proteobacterial classes (only shown if they represented at least 1% of all sequences in any of the samples). Right panels: Percentage of archaeal phyla, candidate divisions and classes. Cand. div., candidate division; MBGA, marine benthic group A; MBGB, marine benthic group B; MCG, miscellaneous crenarchaeotal group; DSEG, deep sea euryarchaeotal group; O, organic topsoil; A, mineral topsoil; B, mineral subsoil; J, buried topsoil; PF, permafrost layer. Note the difference in scaling of archaeal reads for site 2. (More detailed information the relative abundance of bacterial and archaeal classes in Table S3).
Mentions: Twenty-seven samples covering the four different soil horizons (O and A, B, J, and PF) were subjected to Illumina tag sequencing of the V4 SSU rRNA gene region (sequence and metadata available from http://www.microbio.me/emp/, study no. 1034). Sequencing was successful for 20 of these samples (Table 3, Table S3) and yielded a total of 1,975,888 bacterial and archaeal SSU rRNA gene sequences after extensive read-quality filtering (see Materials and Methods for details) with 86% being taxonomically classified using closed-reference OTU picking. Bacterial and archaeal sequences clustered in 10,309 OTUs, representing 157 classes (147 bacterial and 10 archaeal) within 55 phyla (including 30 candidate phyla). The dominant phyla were Proteobacteria (α, β, δ, and γ), Acidobacteria, Actinobacteria, Verrucomicrobia, Bacteroidetes, and Firmicutes accounting for ~84% of all sequences (Figure 2). In addition, Chloroflexi, Gemmatimonadetes, Planctomycetes, Cyanobacteria, and Nitrospirae were present in all soil horizons, but at lower abundances (~12% of all sequences), and 38 other rare phyla (<0.5% each) were identified. Rare phyla included archaeal taxa that represented 0.3% of all sequence reads. The majority of archaeal reads was assigned to the classes Methanomicrobia and Methanobacteria within the Euryarchaeota comprising 39.8% of all archaeal reads. For site 2, sequence reads assigned to archaeal taxa comprised 0.9% of all reads obtained from site 2 samples, whereas they only accounted for 0.05 and 0.01% at sites 1 and 3, respectively (Figure 2). This finding was in line with lower archaeal SSU rRNA gene abundances at sites 1 and 3 than at site 2 (as determined by qPCR). Furthermore, the majority of sequences retrieved from site 2 was affiliated with methanogenic taxa of the families Methanosarcinaceae, Methanobacteriaceae, and Methanosaetaceae in the phylum Euryarchaoeta, whereas members of the Thaumarchaeota and several other non-methanogenic archaea dominated at sites 1 and 3 (Figure 2).

Bottom Line: Sampling site and thus abiotic factors had a significant impact on microbial community structure, diversity and activity, the wet fen site exhibiting higher potential enzyme activities and presumably being a hot spot for anaerobic degradation processes such as fermentation and methanogenesis.Lowest fungal to bacterial ratios were found in topsoils that had been relocated by cryoturbation ("buried topsoils"), resulting from a decrease in fungal abundance compared to recent ("unburied") topsoils.Our study sheds light on the highly diverse, but poorly-studied communities in permafrost-affected soils in Greenland and their role in OC degradation.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Centre for Geobiology, University of Bergen Bergen, Norway ; Department of Bioscience, Center for Geomicrobiology, Aarhus University Aarhus, Denmark.

ABSTRACT
Permafrost-affected soils in the Northern latitudes store huge amounts of organic carbon (OC) that is prone to microbial degradation and subsequent release of greenhouse gasses to the atmosphere. In Greenland, the consequences of permafrost thaw have only recently been addressed, and predictions on its impact on the carbon budget are thus still highly uncertain. However, the fate of OC is not only determined by abiotic factors, but closely tied to microbial activity. We investigated eight soil profiles in northeast Greenland comprising two sites with typical tundra vegetation and one wet fen site. We assessed microbial community structure and diversity (SSU rRNA gene tag sequencing, quantification of bacteria, archaea and fungi), and measured hydrolytic and oxidative enzyme activities. Sampling site and thus abiotic factors had a significant impact on microbial community structure, diversity and activity, the wet fen site exhibiting higher potential enzyme activities and presumably being a hot spot for anaerobic degradation processes such as fermentation and methanogenesis. Lowest fungal to bacterial ratios were found in topsoils that had been relocated by cryoturbation ("buried topsoils"), resulting from a decrease in fungal abundance compared to recent ("unburied") topsoils. Actinobacteria (in particular Intrasporangiaceae) accounted for a major fraction of the microbial community in buried topsoils, but were only of minor abundance in all other soil horizons. It was indicated that the distribution pattern of Actinobacteria and a variety of other bacterial classes was related to the activity of phenol oxidases and peroxidases supporting the hypothesis that bacteria might resume the role of fungi in oxidative enzyme production and degradation of phenolic and other complex substrates in these soils. Our study sheds light on the highly diverse, but poorly-studied communities in permafrost-affected soils in Greenland and their role in OC degradation.

No MeSH data available.


Related in: MedlinePlus