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Journal ArticleDOI

Organic carbon transformations in high-Arctic peat soils: key functions and microorganisms

01 Feb 2013-The ISME Journal (Nature Publishing Group)-Vol. 7, Iss: 2, pp 299-311
TL;DR: It is concluded that these Arctic peat soils will turn into CO2 sources owing to increased active layer depth and prolonged growing season, however, the extent of future CH4 emissions will critically depend on the response of the methanotrophic bacteria.
Abstract: A substantial part of the Earths’ soil organic carbon (SOC) is stored in Arctic permafrost peatlands, which represent large potential sources for increased emissions of the greenhouse gases CH4 and CO2 in a warming climate. The microbial communities and their genetic repertoire involved in the breakdown and mineralisation of SOC in these soils are, however, poorly understood. In this study, we applied a combined metagenomic and metatranscriptomic approach on two Arctic peat soils to investigate the identity and the gene pool of the microbiota driving the SOC degradation in the seasonally thawed active layers. A large and diverse set of genes encoding plant polymer-degrading enzymes was found, comparable to microbiotas from temperate and subtropical soils. This indicates that the metabolic potential for SOC degradation in Arctic peat is not different from that of other climatic zones. The majority of these genes were assigned to three bacterial phyla, Actinobacteria, Verrucomicrobia and Bacteroidetes. Anaerobic metabolic pathways and the fraction of methanogenic archaea increased with peat depth, evident for a gradual transition from aerobic to anaerobic lifestyles. A population of CH4-oxidising bacteria closely related to Methylobacter tundripaludum was the dominating active group of methanotrophs. Based on the in-depth characterisation of the microbes and their genes, we conclude that these Arctic peat soils will turn into CO2 sources owing to increased active layer depth and prolonged growing season. However, the extent of future CH4 emissions will critically depend on the response of the methanotrophic bacteria. The ISME Journal (2013) 7, 299–311; doi:10.1038/ismej.2012.99; published online 6 September 2012 Subject Category: integrated genomics and post-genomics approaches in microbial ecology

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Citations
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Journal ArticleDOI
TL;DR: It is argued that although making direct linkage of genomes to global phenomena is a significant challenge, many connections at intermediate scales are viable with integrated application of new systems biology approaches and powerful analytical and modelling techniques.

348 citations

Journal ArticleDOI
TL;DR: The activity of the abundant ectomycorrhizal fungi was reduced in winter, which indicates that plant photosynthetic production was likely one of the major drivers of changes in the functioning of microbial communities in this coniferous forest.
Abstract: Understanding the ecology of coniferous forests is very important because these environments represent globally largest carbon sinks. Metatranscriptomics, microbial community and enzyme analyses were combined to describe the detailed role of microbial taxa in the functioning of the Picea abies-dominated coniferous forest soil in two contrasting seasons. These seasons were the summer, representing the peak of plant photosynthetic activity, and late winter, after an extended period with no photosynthate input. The results show that microbial communities were characterized by a high activity of fungi especially in litter where their contribution to microbial transcription was over 50%. Differences in abundance between summer and winter were recorded for 26-33% of bacterial genera and < 15% of fungal genera, but the transcript profiles of fungi, archaea and most bacterial phyla were significantly different among seasons. Further, the seasonal differences were larger in soil than in litter. Most importantly, fungal contribution to total microbial transcription in soil decreased from 33% in summer to 16% in winter. In particular, the activity of the abundant ectomycorrhizal fungi was reduced in winter, which indicates that plant photosynthetic production was likely one of the major drivers of changes in the functioning of microbial communities in this coniferous forest.

290 citations


Cites background from "Organic carbon transformations in h..."

  • ...…transcription among soils from various 323 depths has also been previously observed in Svalbard peat soils, but this environment is quite 324 different and is also characterized by low fungal biomass and oxygen limitation (Tveit et al., 2013; 325 Tveit et al., 2014), which our soils did not have....

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  • ...Currently, however, there exist only a few published 80 metatranscriptomic studies from soils (Nacke et al., 2014; Tveit et al., 2013; Tveit et al., 2014), and 81 the understanding of soil functioning based on these studies is still fragmentary....

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  • ...Differences in microbial transcription among soils from various 323 depths has also been previously observed in Svalbard peat soils, but this environment is quite 324 different and is also characterized by low fungal biomass and oxygen limitation (Tveit et al., 2013; 325 Tveit et al., 2014), which our soils did not have....

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Journal ArticleDOI
TL;DR: In this paper, the authors review the current knowledge of key physical and hydraulic properties related to the structure of globally available peat soils and briefly discuss their implications for water storage, flow and the migration of solutes.

284 citations

Journal ArticleDOI
16 Jul 2018-Nature
TL;DR: Analysis of more than 1,500 microbial genomes sheds light on the processing of carbon released as permafrost thaws, and links changing biogeochemistry to specific microbial lineages involved in carbon processing, and provides key information for predicting the effects of climate change onpermafrost systems.
Abstract: As global temperatures rise, large amounts of carbon sequestered in permafrost are becoming available for microbial degradation. Accurate prediction of carbon gas emissions from thawing permafrost is limited by our understanding of these microbial communities. Here we use metagenomic sequencing of 214 samples from a permafrost thaw gradient to recover 1,529 metagenome-assembled genomes, including many from phyla with poor genomic representation. These genomes reflect the diversity of this complex ecosystem, with genus-level representatives for more than sixty per cent of the community. Meta-omic analysis revealed key populations involved in the degradation of organic matter, including bacteria whose genomes encode a previously undescribed fungal pathway for xylose degradation. Microbial and geochemical data highlight lineages that correlate with the production of greenhouse gases and indicate novel syntrophic relationships. Our findings link changing biogeochemistry to specific microbial lineages involved in carbon processing, and provide key information for predicting the effects of climate change on permafrost systems.

262 citations

Journal ArticleDOI
TL;DR: This metatranscriptomic study provides the most comprehensive picture of active protist communities in soils to date, which is essential to target the ecological roles of protists in the complex soil system.
Abstract: The high numbers and diversity of protists in soil systems have long been presumed, but their true diversity and community composition have remained largely concealed. Traditional cultivation-based methods miss a majority of taxa, whereas molecular barcoding approaches employing PCR introduce significant biases in reported community composition of soil protists. Here, we applied a metatranscriptomic approach to assess the protist community in 12 mineral and organic soil samples from different vegetation types and climatic zones using small subunit ribosomal RNA transcripts as marker. We detected a broad diversity of soil protists spanning across all known eukaryotic supergroups and revealed a strikingly different community composition than shown before. Protist communities differed strongly between sites, with Rhizaria and Amoebozoa dominating in forest and grassland soils, while Alveolata were most abundant in peat soils. The Amoebozoa were comprised of Tubulinea, followed with decreasing abundance by Discosea, Variosea and Mycetozoa. Transcripts of Oomycetes, Apicomplexa and Ichthyosporea suggest soil as reservoir of parasitic protist taxa. Further, Foraminifera and Choanoflagellida were ubiquitously detected, showing that these typically marine and freshwater protists are autochthonous members of the soil microbiota. To the best of our knowledge, this metatranscriptomic study provides the most comprehensive picture of active protist communities in soils to date, which is essential to target the ecological roles of protists in the complex soil system.

231 citations


Cites methods or result from "Organic carbon transformations in h..."

  • ...cDNA synthesis was performed as described before (Radax et al., 2012; Tveit et al., 2013)....

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  • ...…acid extraction, cDNA synthesis and sequencing Nucleic acids were extracted from 5 g of mineral soil and 1.2 g of litter and peat and processed as The ISME Journal previously described (Urich et al., 2008). cDNA synthesis was performed as described before (Radax et al., 2012; Tveit et al., 2013)....

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  • ...Arctic peat soils were sampled as described in the study by Tveit et al. (2013)....

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  • ...Raw reads were processed as described in the study by Tveit et al. (2013)....

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  • ...Although the fraction of SSU rRNA originating from protists is comparably small in metatranscriptomes, recent studies showed that the sequencing depth even with 454 pyrosequencing yielded sizable datasets of protist SSU rRNAs (Urich et al., 2008; Turner et al., 2013; Tveit et al., 2013)....

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References
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TL;DR: Copyright (©) 1999–2012 R Foundation for Statistical Computing; permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and permission notice are preserved on all copies.
Abstract: Copyright (©) 1999–2012 R Foundation for Statistical Computing. Permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and this permission notice are preserved on all copies. Permission is granted to copy and distribute modified versions of this manual under the conditions for verbatim copying, provided that the entire resulting derived work is distributed under the terms of a permission notice identical to this one. Permission is granted to copy and distribute translations of this manual into another language, under the above conditions for modified versions, except that this permission notice may be stated in a translation approved by the R Core Team.

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TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Abstract: The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.

70,111 citations

01 Jan 2007
TL;DR: The first volume of the IPCC's Fourth Assessment Report as mentioned in this paper was published in 2007 and covers several topics including the extensive range of observations now available for the atmosphere and surface, changes in sea level, assesses the paleoclimatic perspective, climate change causes both natural and anthropogenic, and climate models for projections of global climate.
Abstract: This report is the first volume of the IPCC's Fourth Assessment Report. It covers several topics including the extensive range of observations now available for the atmosphere and surface, changes in sea level, assesses the paleoclimatic perspective, climate change causes both natural and anthropogenic, and climate models for projections of global climate.

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TL;DR: In this article, the authors present a historical overview of climate change science, including changes in atmospheric constituents and radiative forcing, as well as changes in snow, ice, and frozen ground.
Abstract: Summary for policymakers -- Technical summary -- Historical overview of climate change science -- Changes in atmospheric constituents and radiative forcing -- Observations: atmospheric surface and climate change -- Observations: changes in snow, ice, and frozen ground -- Observations: ocean climate change and sea level -- Paleoclimate -- Coupling between changes in the climate system and biogeochemistry -- Climate models and their evaluation -- Understanding and attributing climate change -- Global climate projections -- Regional climate projections -- Annex I: Glossary -- Annex II: Contributors to the IPCC WGI Fourth Assessment Report -- Annex III: Reviewers of the IPCC WGI Fourth Assessment Report -- Annex IV: Acronyms.

7,738 citations

Journal ArticleDOI
TL;DR: The third generation of the CAP sequence assembly program is described, which has a capability to clip 5' and 3' low-quality regions of reads and uses forward-reverse constraints to correct assembly errors and link contigs.
Abstract: The shotgun sequencing strategy has been used widely in genome sequencing projects. A major phase in this strategy is to assemble short reads into long sequences. A number of DNA sequence assembly programs have been developed (Staden 1980; Peltola et al. 1984; Huang 1992; Smith et al. 1993; Gleizes and Henaut 1994; Lawrence et al. 1994; Kececioglu and Myers 1995; Sutton et al. 1995; Green 1996). The FAKII program provides a library of routines for each phase of the assembly process (Larson et al. 1996). The GAP4 program has a number of useful interactive features (Bonfield et al. 1995). The PHRAP program clips 5′ and 3′ low-quality regions of reads and uses base quality values in evaluation of overlaps and generation of contig sequences (Green 1996). TIGR Assembler has been used in a number of megabase microbial genome projects (Sutton et al. 1995). Continued development and improvement of sequence assembly programs are required to meet the challenges of the human, mouse, and maize genome projects. We have developed the third generation of the CAP sequence assembly program (Huang 1992). The CAP3 program includes a number of improvements and new features. A capability to clip 5′ and 3′ low-quality regions of reads is included in the CAP3 program. Base quality values produced by PHRED (Ewing et al. 1998) are used in computation of overlaps between reads, construction of multiple sequence alignments of reads, and generation of consensus sequences. Efficient algorithms are employed to identify and compute overlaps between reads. Forward–reverse constraints are used to correct assembly errors and link contigs. Results of CAP3 on four BAC data sets are presented. The performance of CAP3 was compared with that of PHRAP on a number of BAC data sets. PHRAP often produces longer contigs than CAP3 whereas CAP3 often produces fewer errors in consensus sequences than PHRAP. It is easier to construct scaffolds with CAP3 than with PHRAP on low-pass data with forward–reverse constraints. An unusual feature of CAP3 is the use of forward–reverse constraints in the construction of contigs. A forward–reverse constraint is often produced by sequencing of both ends of a subclone. A forward–reverse constraint specifies that the two reads should be on the opposite strands of the DNA molecule within a specified range of distance. By sequencing both ends of each subclone, a large number of forward–reverse constraints are produced for a cosmid or BAC data set. A difficulty with use of forward–reverse constraints in assembly is that some of the forward–reverse constraints are incorrect because of errors in lane tracking and cloning. Our strategy for dealing with this difficulty is based on the observation that a majority of the constraints are correct and wrong constraints usually occur randomly. Thus, a few unsatisfied constraints in a contig may not be sufficient to indicate an assembly error in the contig. However, if a sufficient number of constraints are all inconsistent with a join in a contig and all support an alternative join, it is likely that the current join is an error, and the alternative join should be made.

5,074 citations


"Organic carbon transformations in h..." refers methods in this paper

  • ...SSU ribo-tags assigned to the order Methylococcales were assembled into ribo-contigs using CAP3 (Huang and Madan, 1999), using two subsequent rounds of assembly with (1) a minimum overlap of 150 bp with a minimum similarity threshold of 99% and mismatch and gap scores of 130 and 150, and (2)…...

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  • ...SSU ribo-tags assigned to the order Methylococcales were assembled into ribo-contigs using CAP3 (Huang and Madan, 1999), using two subsequent rounds of assembly with (1) a minimum overlap of 150 bp with a minimum similarity threshold of 99% and mismatch and gap scores of 130 and 150, and (2) minimum overlap of 150 bp and minimum 97% similarity threshold, respectively....

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