| 1. |
- Kattge, Jens, et al.
(författare)
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TRY plant trait database - enhanced coverage and open access
- 2020
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Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Tidskriftsartikel (refereegranskat)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 2. |
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| 3. |
- Heid, Iris M, et al.
(författare)
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Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution
- 2010
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 42:11, s. 949-960
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Tidskriftsartikel (refereegranskat)abstract
- Waist-hip ratio (WHR) is a measure of body fat distribution and a predictor of metabolic consequences independent of overall adiposity. WHR is heritable, but few genetic variants influencing this trait have been identified. We conducted a meta-analysis of 32 genome-wide association studies for WHR adjusted for body mass index (comprising up to 77,167 participants), following up 16 loci in an additional 29 studies (comprising up to 113,636 subjects). We identified 13 new loci in or near RSPO3, VEGFA, TBX15-WARS2, NFE2L3, GRB14, DNM3-PIGC, ITPR2-SSPN, LY86, HOXC13, ADAMTS9, ZNRF3-KREMEN1, NISCH-STAB1 and CPEB4 (P = 1.9 × 10⁻⁹ to P = 1.8 × 10⁻⁴⁰) and the known signal at LYPLAL1. Seven of these loci exhibited marked sexual dimorphism, all with a stronger effect on WHR in women than men (P for sex difference = 1.9 × 10⁻³ to P = 1.2 × 10⁻¹³). These findings provide evidence for multiple loci that modulate body fat distribution independent of overall adiposity and reveal strong gene-by-sex interactions.
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| 4. |
- Locke, Adam E, et al.
(författare)
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Genetic studies of body mass index yield new insights for obesity biology.
- 2015
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 518:7538, s. 197-401
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Tidskriftsartikel (refereegranskat)abstract
- Obesity is heritable and predisposes to many diseases. To understand the genetic basis of obesity better, here we conduct a genome-wide association study and Metabochip meta-analysis of body mass index (BMI), a measure commonly used to define obesity and assess adiposity, in up to 339,224 individuals. This analysis identifies 97 BMI-associated loci (P < 5 × 10(-8)), 56 of which are novel. Five loci demonstrate clear evidence of several independent association signals, and many loci have significant effects on other metabolic phenotypes. The 97 loci account for ∼2.7% of BMI variation, and genome-wide estimates suggest that common variation accounts for >20% of BMI variation. Pathway analyses provide strong support for a role of the central nervous system in obesity susceptibility and implicate new genes and pathways, including those related to synaptic function, glutamate signalling, insulin secretion/action, energy metabolism, lipid biology and adipogenesis.
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| 5. |
- Palmer, Nicholette D, et al.
(författare)
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A genome-wide association search for type 2 diabetes genes in African Americans.
- 2012
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Ingår i: PloS one. - San Francisco : Public Library of Science (PLoS). - 1932-6203. ; 7:1, s. e29202-
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Tidskriftsartikel (refereegranskat)abstract
- African Americans are disproportionately affected by type 2 diabetes (T2DM) yet few studies have examined T2DM using genome-wide association approaches in this ethnicity. The aim of this study was to identify genes associated with T2DM in the African American population. We performed a Genome Wide Association Study (GWAS) using the Affymetrix 6.0 array in 965 African-American cases with T2DM and end-stage renal disease (T2DM-ESRD) and 1029 population-based controls. The most significant SNPs (n = 550 independent loci) were genotyped in a replication cohort and 122 SNPs (n = 98 independent loci) were further tested through genotyping three additional validation cohorts followed by meta-analysis in all five cohorts totaling 3,132 cases and 3,317 controls. Twelve SNPs had evidence of association in the GWAS (P<0.0071), were directionally consistent in the Replication cohort and were associated with T2DM in subjects without nephropathy (P<0.05). Meta-analysis in all cases and controls revealed a single SNP reaching genome-wide significance (P<2.5×10(-8)). SNP rs7560163 (P = 7.0×10(-9), OR (95% CI) = 0.75 (0.67-0.84)) is located intergenically between RND3 and RBM43. Four additional loci (rs7542900, rs4659485, rs2722769 and rs7107217) were associated with T2DM (P<0.05) and reached more nominal levels of significance (P<2.5×10(-5)) in the overall analysis and may represent novel loci that contribute to T2DM. We have identified novel T2DM-susceptibility variants in the African-American population. Notably, T2DM risk was associated with the major allele and implies an interesting genetic architecture in this population. These results suggest that multiple loci underlie T2DM susceptibility in the African-American population and that these loci are distinct from those identified in other ethnic populations.
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| 6. |
- Speliotes, Elizabeth K., et al.
(författare)
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Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index
- 2010
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 42:11, s. 937-948
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Tidskriftsartikel (refereegranskat)abstract
- Obesity is globally prevalent and highly heritable, but its underlying genetic factors remain largely elusive. To identify genetic loci for obesity susceptibility, we examined associations between body mass index and ~2.8 million SNPs in up to 123,865 individuals with targeted follow up of 42 SNPs in up to 125,931 additional individuals. We confirmed 14 known obesity susceptibility loci and identified 18 new loci associated with body mass index (P < 5 × 10−8), one of which includes a copy number variant near GPRC5B. Some loci (at MC4R, POMC, SH2B1 and BDNF) map near key hypothalamic regulators of energy balance, and one of these loci is near GIPR, an incretin receptor. Furthermore, genes in other newly associated loci may provide new insights into human body weight regulation.
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| 7. |
- Saxena, Richa, et al.
(författare)
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Genetic variation in GIPR influences the glucose and insulin responses to an oral glucose challenge
- 2010
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 42:2, s. 142-148
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Tidskriftsartikel (refereegranskat)abstract
- Glucose levels 2 h after an oral glucose challenge are a clinical measure of glucose tolerance used in the diagnosis of type 2 diabetes. We report a meta-analysis of nine genome-wide association studies (n = 15,234 nondiabetic individuals) and a follow-up of 29 independent loci (n = 6,958–30,620). We identify variants at the GIPR locus associated with 2-h glucose level (rs10423928, β (s.e.m.) = 0.09 (0.01) mmol/l per A allele, P = 2.0 × 10−15). The GIPR A-allele carriers also showed decreased insulin secretion (n = 22,492; insulinogenic index, P = 1.0 × 10−17; ratio of insulin to glucose area under the curve, P = 1.3 × 10−16) and diminished incretin effect (n = 804; P = 4.3 × 10−4). We also identified variants at ADCY5 (rs2877716, P = 4.2 × 10−16), VPS13C (rs17271305, P = 4.1 × 10−8), GCKR (rs1260326, P = 7.1 × 10−11) and TCF7L2 (rs7903146, P = 4.2 × 10−10) associated with 2-h glucose. Of the three newly implicated loci (GIPR, ADCY5 and VPS13C), only ADCY5 was found to be associated with type 2 diabetes in collaborating studies (n = 35,869 cases, 89,798 controls, OR = 1.12, 95% CI 1.09–1.15, P = 4.8 × 10−18).
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| 8. |
- Perry, John R. B., et al.
(författare)
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Stratifying Type 2 Diabetes Cases by BMI Identifies Genetic Risk Variants in LAMA1 and Enrichment for Risk Variants in Lean Compared to Obese Cases
- 2012
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Ingår i: PLoS Genetics. - : Public Library of Science (PLoS). - 1553-7404. ; 8:5
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Tidskriftsartikel (refereegranskat)abstract
- Common diseases such as type 2 diabetes are phenotypically heterogeneous. Obesity is a major risk factor for type 2 diabetes, but patients vary appreciably in body mass index. We hypothesized that the genetic predisposition to the disease may be different in lean (BMI<25 Kg/m(2)) compared to obese cases (BMI >= 30 Kg/m(2)). We performed two case-control genome-wide studies using two accepted cut-offs for defining individuals as overweight or obese. We used 2,112 lean type 2 diabetes cases (BMI<25 kg/m(2)) or 4,123 obese cases (BMI >= 30 kg/m(2)), and 54,412 un-stratified controls. Replication was performed in 2,881 lean cases or 8,702 obese cases, and 18,957 un-stratified controls. To assess the effects of known signals, we tested the individual and combined effects of SNPs representing 36 type 2 diabetes loci. After combining data from discovery and replication datasets, we identified two signals not previously reported in Europeans. A variant (rs8090011) in the LAMA1 gene was associated with type 2 diabetes in lean cases (P = 8.4610 29, OR = 1.13 [95% CI 1.09-1.18]), and this association was stronger than that in obese cases (P = 0.04, OR = 1.03 [95% CI 1.00-1.06]). A variant in HMG20A-previously identified in South Asians but not Europeans-was associated with type 2 diabetes in obese cases (P = 1.3 x 10(-8), OR= 1.11 [95% CI 1.07-1.15]), although this association was not significantly stronger than that in lean cases (P = 0.02, OR = 1.09 [95% CI 1.02-1.17]). For 36 known type 2 diabetes loci, 29 had a larger odds ratio in the lean compared to obese (binomial P = 0.0002). In the lean analysis, we observed a weighted per-risk allele OR = 1.13 [95% CI 1.10-1.17], P = 3.2 x 10(-14). This was larger than the same model fitted in the obese analysis where the OR = 1.06 [95% CI 1.05-1.08], P = 2.2 x 10(-16). This study provides evidence that stratification of type 2 diabetes cases by BMI may help identify additional risk variants and that lean cases may have a stronger genetic predisposition to type 2 diabetes.
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| 9. |
- Voight, Benjamin F., et al.
(författare)
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Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis
- 2010
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 42:7, s. 579-589
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Tidskriftsartikel (refereegranskat)abstract
- By combining genome-wide association data from 8,130 individuals with type 2 diabetes (T2D) and 38,987 controls of European descent and following up previously unidentified meta-analysis signals in a further 34,412 cases and 59,925 controls, we identified 12 new T2D association signals with combined P < 5 x 10(-8). These include a second independent signal at the KCNQ1 locus; the first report, to our knowledge, of an X-chromosomal association (near DUSP9); and a further instance of overlap between loci implicated in monogenic and multifactorial forms of diabetes (at HNF1A). The identified loci affect both beta-cell function and insulin action, and, overall, T2D association signals show evidence of enrichment for genes involved in cell cycle regulation. We also show that a high proportion of T2D susceptibility loci harbor independent association signals influencing apparently unrelated complex traits.
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| 10. |
- Craddock, Nick, et al.
(författare)
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Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls
- 2010
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7289, s. 713-720
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Tidskriftsartikel (refereegranskat)abstract
- Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed,19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated similar to 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with disease-IRGM for Crohn's disease, HLA for Crohn's disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetes-although in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases.
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| 11. |
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| 12. |
- Blume-Werry, Gesche, 1985-, et al.
(författare)
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Arctic rooting depth distribution influences modelled carbon emissions but cannot be inferred from aboveground vegetation type
- 2023
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Ingår i: New Phytologist. - : John Wiley & Sons. - 0028-646X .- 1469-8137. ; 240:2, s. 502-514
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Tidskriftsartikel (refereegranskat)abstract
- The distribution of roots throughout the soil drives depth-dependent plant–soil interactions and ecosystem processes, particularly in arctic tundra where plant biomass, is predominantly belowground. Vegetation is usually classified from aboveground, but it is unclear whether such classifications are suitable to estimate belowground attributes and their consequences, such as rooting depth distribution and its influence on carbon cycling. We performed a meta-analysis of 55 published arctic rooting depth profiles, testing for differences both between distributions based on aboveground vegetation types (Graminoid, Wetland, Erect-shrub, and Prostrate-shrub tundra) and between ‘Root Profile Types’ for which we defined three representative and contrasting clusters. We further analyzed potential impacts of these different rooting depth distributions on rhizosphere priming-induced carbon losses from tundra soils. Rooting depth distribution hardly differed between aboveground vegetation types but varied between Root Profile Types. Accordingly, modelled priming-induced carbon emissions were similar between aboveground vegetation types when they were applied to the entire tundra, but ranged from 7.2 to 17.6 Pg C cumulative emissions until 2100 between individual Root Profile Types. Variations in rooting depth distribution are important for the circumpolar tundra carbon-climate feedback but can currently not be inferred adequately from aboveground vegetation type classifications.
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| 13. |
- Hicks, Lettice C., et al.
(författare)
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Toward a function-first framework to make soil microbial ecology predictive
- 2022
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Ingår i: Ecology. - : Wiley. - 0012-9658 .- 1939-9170. ; 103:e03594
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Tidskriftsartikel (refereegranskat)abstract
- Soil microbial communities perform vital ecosystem functions, such as the decomposition of organic matter to provide plant nutrition. However, despite the functional importance of soil microorganisms, attribution of ecosystem function to particular constituents of the microbial community has been impeded by a lack of information linking microbial function to community composition and structure. Here, we propose a function-first framework to predict how microbial communities influence ecosystem functions. We first view the microbial community associated with a specific function as a whole and describe the dependence of microbial functions on environmental factors (e.g., the intrinsic temperature dependence of bacterial growth rates). This step defines the aggregate functional response curve of the community. Second, the contribution of the whole community to ecosystem function can be predicted, by combining the functional response curve with current environmental conditions. Functional response curves can then be linked with taxonomic data in order to identify sets of “biomarker” taxa that signal how microbial communities regulate ecosystem functions. Ultimately, such indicator taxa may be used as a diagnostic tool, enabling predictions of ecosystem function from community composition. In this paper, we provide three examples to illustrate the proposed framework, whereby the dependence of bacterial growth on environmental factors, including temperature, pH, and salinity, is defined as the functional response curve used to interlink soil bacterial community structure and function. Applying this framework will make it possible to predict ecosystem functions directly from microbial community composition.
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| 14. |
- Keuper, Frida, et al.
(författare)
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A frozen feast : thawing permafrost increases plant-available nitrogen in subarctic peatlands
- 2012
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Ingår i: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 18:6, s. 1998-2007
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Tidskriftsartikel (refereegranskat)abstract
- Many of the world's northern peatlands are underlain by rapidly thawing permafrost. Because plant production in these peatlands is often nitrogen (N)-limited, a release of N stored in permafrost may stimulate net primary production or change species composition if it is plant-available. In this study, we aimed to quantify plant-available N in thawing permafrost soils of subarctic peatlands. We compared plant-available N-pools and -fluxes in near-surface permafrost (010cm below the thawfront) to those taken from a current rooting zone layer (515cm depth) across five representative peatlands in subarctic Sweden. A range of complementary methods was used: extractions of inorganic and organic N, inorganic and organic N-release measurements at 0.5 and 11 degrees C (over 120days, relevant to different thaw-development scenarios) and a bioassay with Poa alpina test plants. All extraction methods, across all peatlands, consistently showed up to seven times more plant-available N in near-surface permafrost soil compared to the current rooting zone layer. These results were supported by the bioassay experiment, with an eightfold larger plant N-uptake from permafrost soil than from other N-sources such as current rooting zone soil or fresh litter substrates. Moreover, net mineralization rates were much higher in permafrost soils compared to soils from the current rooting zone layer (273mgNm-2 and 1348mgNm-2 per growing season for near-surface permafrost at 0.5 degrees C and 11 degrees C respectively, compared to -30mgNm-2 for current rooting zone soil at 11 degrees C). Hence, our results demonstrate that near-surface permafrost soil of subarctic peatlands can release a biologically relevant amount of plant available nitrogen, both directly upon thawing as well as over the course of a growing season through continued microbial mineralization of organically bound N. Given the nitrogen-limited nature of northern peatlands, this release may have impacts on both plant productivity and species composition.
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| 15. |
- Krab, Eveline J., et al.
(författare)
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Microbial and soil fauna diversity responses to winter climate change and greening in cryoturbated arctic tundra
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- At high latitudes, winter warming facilitates vegetation expansion into barren frost-affected soils. The interplay of changes in winter climate and plant presence may alter soil carbon dynamics via effects on decomposers. Responses of decomposer soil fauna and microorganisms to such changes likely differ from each other, since their life histories, dispersal mechanisms and microhabitats vary greatly. We investigated the relative impacts of short-term winter warming and long-term increases in plant cover on bacteria and collembola community composition in cryoturbated, non-sorted circle (NSC) tundra. By covering NSCs with insulating gardening fiber cloth (fleeces) or using stone walls accumulating snow, we imposed two climate-change scenarios: snow accumulation increased autumn-to-late winter soil temperatures by 1.4°C, while fleeces warmed soils during that period by 1°C and increased spring temperatures by 1.1°C. Summer bacteria and collembola communities were sampled from within-circle locations differing in vegetation abundance and soil properties, representing stages in long-term NSC overgrowth. Two years of winter warming had no effects on both decomposer communities. Instead, their community compositions were strongly determined by sampling location: communities in barren circle centers were distinct from those in vegetated outer rims, while communities in sparsely vegetated patches of circle centers were intermediate. Diversity patterns indicate that collembola communities are tightly linked to plant presence while bacteria communities correlated with soil properties. Our results thus suggest that short-term effects of winter warming are likely to be minimal, but longer-term vegetation overgrowth of NSCs affects decomposer community composition substantially. At decadal timescales, collembola community changes may follow rapidly after plant establishment into barren areas, whereas bacteria communities may take longer to respond. If shifts in decomposer community composition are indicative for changes in their decomposition activity, vegetation overgrowth will likely have much stronger effects on carbon losses from frost-affected tundra than short-term winter warming.
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| 16. |
- Krab, Eveline J, et al.
(författare)
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Plant expansion drives bacteria and collembola communities under winter climate change in frost-affected tundra
- 2019
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Ingår i: Soil Biology and Biochemistry. - : Elsevier. - 0038-0717 .- 1879-3428. ; 138
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Tidskriftsartikel (refereegranskat)abstract
- At high latitudes, winter warming facilitates vegetation expansion into barren frost-affected soils. The interplay of changes in winter climate and plant presence may alter soil functioning via effects on decomposers. Responses of decomposer soil fauna and microorganisms to such changes likely differ from each other, since their life histories, dispersal mechanisms and microhabitats vary greatly.We investigated the relative impacts of short-term winter warming and increases in plant cover on bacteria and collembola community composition in cryoturbated, non-sorted circle tundra. By covering non-sorted circles with insulating gardening fibre cloth (fleeces) or using stone walls accumulating snow, we imposed two climate-change scenarios: snow accumulation increased autumn-to-late winter soil temperatures (−1 cm) by 1.4 °C, while fleeces warmed soils during that period by 1 °C and increased spring temperatures by 1.1 °C. Summer bacteria and collembola communities were sampled from within-circle locations differing in vegetation abundance and soil properties.Two years of winter warming had no effects on either decomposer community. Instead, their community compositions were strongly determined by sampling location: communities in barren circle centres were distinct from those in vegetated outer rims, while communities in sparsely vegetated patches of circle centres were intermediate. Diversity patterns indicate that collembola communities are tightly linked to plant presence while bacteria communities correlated with soil properties.Our results thus suggest that direct effects of short-term winter warming are likely to be minimal, but that vegetation encroachment on barren cryoturbated ground will affect decomposer community composition substantially. At decadal timescales, collembola community changes may follow relatively fast after warming-driven plant establishment into barren areas, whereas bacteria communities may take longer to respond. If shifts in decomposer community composition are indicative for changes in their activity, vegetation overgrowth will likely have much stronger effects on soil functioning in frost-affected tundra than short-term winter warming.
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| 17. |
- Lango Allen, Hana, et al.
(författare)
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Hundreds of variants clustered in genomic loci and biological pathways affect human height.
- 2010
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 467:7317, s. 832-8
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Tidskriftsartikel (refereegranskat)abstract
- Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (P<0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.
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| 18. |
- Monteux, Sylvain, 1989-
(författare)
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A song of ice and mud : Interactions of microbes with roots, fauna and carbon in warming permafrost-affected soils
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Permafrost-affected soils store a large quantity of soil organic matter (SOM) – ca. half of worldwide soil carbon – and currently undergo rapid and severe warming due to climate change. Increased SOM decomposition by microorganisms and soil fauna due to climate change, poses the risk of a positive climate feedback through the release of greenhouse gases. Direct effects of climate change on SOM decomposition, through such mechanisms as deepening of the seasonally-thawing active layer and increasing soil temperatures, have gathered considerable scientific attention in the last two decades. Yet, indirect effects mediated by changes in plant, microbial, and fauna communities, remain poorly understood. Microbial communities, which may be affected by climate change-induced changes in vegetation composition or rooting patterns, and may in turn affect SOM decomposition, are the primary focus of the work described in this thesis.We used (I) a field-scale permafrost thaw experiment in a palsa peatland, (II) a laboratory incubation of Yedoma permafrost with inoculation by exotic microorganisms, (III) a microcosm experiment with five plant species grown either in Sphagnum peat or in newly-thawed permafrost peat, and (IV) a field-scale cold season warming experiment in cryoturbated tundra to address the indirect effects of climate change on microbial drivers of SOM decomposition. Community composition data for bacteria and fungi were obtained by amplicon sequencing and phospholipid fatty acid extraction, and for collembola by Tullgren extraction, alongside measurements of soil chemistry, CO2 emissions and root density.We showed that in situ thawing of a palsa peatland caused colonization of permafrost soil by overlying soil microbes. Further, we observed that functional limitations of permafrost microbial communities can hamper microbial metabolism in vitro. Relieving these functional limitations in vitro increased cumulative CO2 emissions by 32% over 161 days and introduced nitrification. In addition, we found that different plant species did not harbour different rhizosphere bacterial communities in Sphagnum peat topsoil, but did when grown in newly-thawed permafrost peat. Plant species may thus differ in how they affect functional limitations in thawing permafrost soil. Therefore, climate change-induced changes in vegetation composition might alter functioning in the newly-thawed, subsoil permafrost layer of northern peatlands, but less likely so in the topsoil. Finally, we observed that vegetation encroachment in barren cryoturbated soil, due to reduced cryogenic activity with higher temperatures, change both bacterial and collembola community composition, which may in turn affect soil functioning.This thesis shows that microbial community dynamics and plant-decomposer interactions play an important role in the functioning of warming permafrost-affected soils. More specifically, it demonstrates that the effects of climate change on plants can trickle down on microbial communities, in turn affecting SOM decomposition in thawing permafrost.
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| 19. |
- Monteux, Sylvain, et al.
(författare)
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Carbon and nitrogen cycling in Yedoma permafrost controlled by microbial functional limitations
- 2020
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Ingår i: Nature Geoscience. - : Nature Publishing Group. - 1752-0894 .- 1752-0908. ; 13:12, s. 794-
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Tidskriftsartikel (refereegranskat)abstract
- Warming-induced microbial decomposition of organic matter in permafrost soils constitutes a climate-change feedback of uncertain magnitude. While physicochemical constraints on soil functioning are relatively well understood, the constraints attributable to microbial community composition remain unclear. Here we show that biogeochemical processes in permafrost can be impaired by missing functions in the microbial community-functional limitations-probably due to environmental filtering of the microbial community over millennia-long freezing. We inoculated Yedoma permafrost with a functionally diverse exogenous microbial community to test this mechanism by introducing potentially missing microbial functions. This initiated nitrification activity and increased CO2 production by 38% over 161 days. The changes in soil functioning were strongly associated with an altered microbial community composition, rather than with changes in soil chemistry or microbial biomass. The present permafrost microbial community composition thus constrains carbon and nitrogen biogeochemical processes, but microbial colonization, likely to occur upon permafrost thaw in situ, can alleviate such functional limitations. Accounting for functional limitations and their alleviation could strongly increase our estimate of the vulnerability of permafrost soil organic matter to decomposition and the resulting global climate feedback. Carbon dioxide emissions from permafrost thaw are substantially enhanced by relieving microbial functional limitations, according to incubation experiments on Yedoma permafrost.
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| 20. |
- Monteux, Sylvain, et al.
(författare)
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Long-term in situ permafrost thaw effects on bacterial communities and potential aerobic respiration
- 2018
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Ingår i: The ISME Journal. - : Springer Nature. - 1751-7362 .- 1751-7370. ; 12:9, s. 2129-2141
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Tidskriftsartikel (refereegranskat)abstract
- The decomposition of large stocks of soil organic carbon in thawing permafrost might depend on more than climate change-induced temperature increases: indirect effects of thawing via altered bacterial community structure (BCS) or rooting patterns are largely unexplored. We used a 10-year in situ permafrost thaw experiment and aerobic incubations to investigate alterations in BCS and potential respiration at different depths, and the extent to which they are related with each other and with root density. Active layer and permafrost BCS strongly differed, and the BCS in formerly frozen soils (below the natural thawfront) converged under induced deep thaw to strongly resemble the active layer BCS, possibly as a result of colonization by overlying microorganisms. Overall, respiration rates decreased with depth and soils showed lower potential respiration when subjected to deeper thaw, which we attributed to gradual labile carbon pool depletion. Despite deeper rooting under induced deep thaw, root density measurements did not improve soil chemistry-based models of potential respiration. However, BCS explained an additional unique portion of variation in respiration, particularly when accounting for differences in organic matter content. Our results suggest that by measuring bacterial community composition, we can improve both our understanding and the modeling of the permafrost carbon feedback.
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| 21. |
- Monteux, Sylvain, et al.
(författare)
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Permafrost peatland plant rhizobiome : limited effects of plant presence in Sphagnum peat contrast with strong, species-specific effects in newly-thawed permafrost
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Sphagnum peatlands in the permafrost region store large amounts of carbon. Changes in plant communities or increasing CO2 concentrations may alter rhizodeposition and in turn soil carbon cycling, yet the response of rhizosphere processes to climate change is insufficiently understood. Microbial communities in the rhizosphere – the rhizobiome – may be important in determining the rates of such processes, and often depend on both soil types and plant species. Sphagnum peat is very acidic and contains numerous secondary metabolites, which may override rhizodeposits effects on the rhizobiome, while newly-thawed, but more decomposed permafrost peat layers may be more favourable to the formation of a distinct rhizobiome. These two soil types may thus have different sensitivities to plant community-driven shifts in microbial communities. However, plant species effects on the bacterial rhizobiome have never been investigated in Sphagnum peat and in newly-thawed permafrost.We grew five vascular peatland plant species, abundant across the circum-arctic and encompassing different plant functional and mycorrhizal types, in Sphagnum peat or in newly-thawed permafrost peat, and compared their bacterial rhizobiome to communities in non-planted controls. The rhizobiome of three plant species out of five was not distinct from non-planted Sphagnum peat, while only the rhizobiome of Andromeda polifolia and, to a lesser extent, Rubus chamaemorus were distinct. In contrast, in newly-thawed permafrost soil, all five plant species had a rhizobiome distinct from non-planted controls, and also exhibited plant species-specific differences. While the differences between rhizosphere and non-planted newly-thawed permafrost soil were overall similar between plant species at the phylum-level, many of the OTUs that differed were specific to a single plant species, particularly so for B. nana and E. vaginatum. The small or absence of differences between the rhizobiomes and Sphagnum peat for most plant species is likely due to acidity and Sphagnum secondary metabolites. Changes in aboveground vegetation may therefore not affect soil processes in Sphagnum peat through altered bacterial communities. In contrast, the strong and plant species-specific effects on the rhizobiome in newly-thawed permafrost soil is due to either less constraining conditions or because permafrost bacterial communities are more vulnerable to rhizosphere effects. Deep-rooting plants can colonize newly-thawed permafrost, and even shallow-rooting species can do so after soil mixing events that bring thawed permafrost to the surface. Therefore, different bacterial communities can be expected depending on permafrost thaw scenario and existing plant community. Plant roots of different species may thus differ in their effects on carbon and nutrient cycling in newly-thawed permafrost not only through differing rhizodeposits but also through species-specific rhizobiomes.
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| 22. |
- Poppeliers, Sanne W. M., et al.
(författare)
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Functional microbial ecology in arctic soils : the need for a year-round perspective
- 2022
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press. - 0168-6496 .- 1574-6941. ; 98:12
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Forskningsöversikt (refereegranskat)abstract
- The microbial ecology of arctic and sub-arctic soils is an important aspect of the global carbon cycle, due to the sensitivity of the large soil carbon stocks to ongoing climate warming. These regions are characterized by strong climatic seasonality, but the emphasis of most studies on the short vegetation growing season could potentially limit our ability to predict year-round ecosystem functions. We compiled a database of studies from arctic, subarctic, and boreal environments that include sampling of microbial community and functions outside the growing season. We found that for studies comparing across seasons, in most environments, microbial biomass and community composition vary intra-annually, with the spring thaw period often identified by researchers as the most dynamic time of year. This seasonality of microbial communities will have consequences for predictions of ecosystem function under climate change if it results in: seasonality in process kinetics of microbe-mediated functions; intra-annual variation in the importance of different (a)biotic drivers; and/or potential temporal asynchrony between climate change-related perturbations and their corresponding effects. Future research should focus on (i) sampling throughout the entire year; (ii) linking these multi-season measures of microbial community composition with corresponding functional or physiological measurements to elucidate the temporal dynamics of the links between them; and (iii) identifying dominant biotic and abiotic drivers of intra-annual variation in different ecological contexts.
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| 23. |
- Rijkers, Ruud, et al.
(författare)
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Optimal growth temperature of Arctic soil bacterial communities increases under experimental warming
- 2022
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Ingår i: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 28:20, s. 6050-6064
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Tidskriftsartikel (refereegranskat)abstract
- Future climate warming in the Arctic will likely increase the vulnerability of soil carbon stocks to microbial decomposition. However, it remains uncertain to what extent decomposition rates will change in a warmer Arctic, because extended soil warming could induce temperature adaptation of bacterial communities. Here we show that experimental warming induces shifts in the temperature–growth relationships of bacterial communities, which is driven by community turnover and is common across a diverse set of 8 (sub) Arctic soils. The optimal growth temperature (Topt) of the soil bacterial communities increased 0.27 ± 0.039 (SE) and 0.07 ± 0.028°C per °C of warming over a 0–30°C gradient, depending on the sampling moment. We identify a potential role for substrate depletion and time-lag effects as drivers of temperature adaption in soil bacterial communities, which possibly explain discrepancies between earlier incubation and field studies. The changes in Topt were accompanied by species-level shifts in bacterial community composition, which were mostly soil specific. Despite the clear physiological responses to warming, there was no evidence for a common set of temperature-responsive bacterial amplicon sequence variants. This implies that community composition data without accompanying physiological measurements may have limited utility for the identification of (potential) temperature adaption of soil bacterial communities in the Arctic. Since bacterial communities in Arctic soils are likely to adapt to increasing soil temperature under future climate change, this adaptation to higher temperature should be implemented in soil organic carbon modeling for accurate predictions of the dynamics of Arctic soil carbon stocks.
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| 24. |
- Schafmayer, Clemens, et al.
(författare)
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Genome-wide association analysis of diverticular disease points towards neuromuscular, connective tissue and epithelial pathomechanisms
- 2019
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Ingår i: Gut. - : BMJ. - 0017-5749 .- 1468-3288. ; 68:5, s. 854-865
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Tidskriftsartikel (refereegranskat)abstract
- Objective Diverticular disease is a common complex disorder characterised by mucosal outpouchings of the colonic wall that manifests through complications such as diverticulitis, perforation and bleeding. We report the to date largest genome-wide association study (GWAS) to identify genetic risk factors for diverticular disease. Design Discovery GWAS analysis was performed on UK Biobank imputed genotypes using 31 964 cases and 419 135 controls of European descent. Associations were replicated in a European sample of 3893 cases and 2829 diverticula-free controls and evaluated for risk contribution to diverticulitis and uncomplicated diverticulosis. Transcripts at top 20 replicating loci were analysed by real-time quatitative PCR in preparations of the mucosal, submucosal and muscular layer of colon. The localisation of expressed protein at selected loci was investigated by immunohistochemistry. Results We discovered 48 risk loci, of which 12 are novel, with genome-wide significance and consistent OR in the replication sample. Nominal replication (p< 0.05) was observed for 27 loci, and additional 8 in meta-analysis with a population-based cohort. The most significant novel risk variant rs9960286 is located near CTAGE1 with a p value of 2.3x10-10 and 0.002 (OR allelic = 1.14 (95% CI 1.05 to 1.24)) in the replication analysis. Four loci showed stronger effects for diverticulitis, PHGR1 (OR 1.32, 95% CI 1.12 to 1.56), FAM155A-2 (OR 1.21, 95% CI 1.04 to 1.42), CALCB (OR 1.17, 95% CI 1.03 to 1.33) and S100A10 (OR 1.17, 95% CI 1.03 to 1.33). Conclusion I n silico analyses point to diverticulosis primarily as a disorder of intestinal neuromuscular function and of impaired connective fibre support, while an additional diverticulitis risk might be conferred by epithelial dysfunction.
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| 25. |
- Verbrigghe, Niel, et al.
(författare)
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Soil carbon loss in warmed subarctic grasslands is rapid and restricted to topsoil
- 2022
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Ingår i: Biogeosciences. - : Copernicus. - 1726-4170 .- 1726-4189. ; 19:14, s. 3381-3393
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Tidskriftsartikel (refereegranskat)abstract
- Global warming may lead to carbon transfers from soils to the atmosphere, yet this positive feedback to the climate system remains highly uncertain, especially in subsoils . Using natural geothermal soil warming gradients of up to +6.4 °C in subarctic grasslands , we show that soil organic carbon (SOC) stocks decline strongly and linearly with warming (-2.8tha-1 °C-1). Comparison of SOC stock changes following medium-term (5 and 10 years) and long-term (>50 years) warming revealed that all SOC stock reduction occurred within the first 5 years of warming, after which continued warming no longer reduced SOC stocks. This rapid equilibration of SOC observed in Andosol suggests a critical role for ecosystem adaptations to warming and could imply short-lived soil carbon-climate feedbacks. Our data further revealed that the soil C loss occurred in all aggregate size fractions and that SOC stock reduction was only visible in topsoil (0-10cm). SOC stocks in subsoil (10-30cm), where plant roots were absent, showed apparent conservation after >50 years of warming. The observed depth-dependent warming responses indicate that explicit vertical resolution is a prerequisite for global models to accurately project future SOC stocks for this soil type and should be investigated for soils with other mineralogies.
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| 26. |
- Väisänen, Maria, et al.
(författare)
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Meshes in mesocosms control solute and biota exchange in soils : A step towards disentangling (a)biotic impacts on the fate of thawing permafrost
- 2020
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Ingår i: Agriculture, Ecosystems & Environment. Applied Soil Ecology. - : Elsevier. - 0929-1393 .- 1873-0272. ; 151
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Tidskriftsartikel (refereegranskat)abstract
- Environmental changes feedback to climate through their impact on soil functions such as carbon (C) and nutrient sequestration. Abiotic conditions and the interactions between above- and belowground biota drive soil responses to environmental change but these (a)biotic interactions are challenging to study. Nonetheless, better understanding of these interactions would improve predictions of future soil functioning and the soil-climate feedback and, in this context, permafrost soils are of particular interest due to their vast soil C-stores. We need new tools to isolate abiotic (microclimate, chemistry) and biotic (roots, fauna, microorganisms) components and to identify their respective roles in soil processes. We developed a new experimental setup, in which we mimic thermokarst (permafrost thaw-induced soil subsidence) by fitting thawed permafrost and vegetated active layer sods side by side into mesocosms deployed in a subarctic tundra over two growing seasons. In each mesocosm, the two sods were separated from each other by barriers with different mesh sizes to allow varying degrees of physical connection and, consequently, (a)biotic exchange between active layer and permafrost. We demonstrate that our mesh-approach succeeded in controlling 1) lateral exchange of solutes between the two soil types, 2) colonization of permafrost by microbes but not by soil fauna, and 3) ingrowth of roots into permafrost. In particular, experimental thermokarst induced a similar to 60% decline in permafrost nitrogen (N) content, a shift in soil bacteria and a rapid buildup of root biomass (+33.2 g roots m(-2) soil). This indicates that cascading plant-soil-microbe linkages are at the heart of biogeochemical cycling in thermokarst events. We propose that this novel setup can be used to explore the effects of (a)biotic ecosystem components on focal biogeochemical processes in permafrost soils and beyond.
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| 27. |
- Walker, Tom W.N., et al.
(författare)
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A systemic overreaction to years versus decades of warming in a subarctic grassland ecosystem
- 2020
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Ingår i: Nature Ecology and Evolution. - : Springer Science and Business Media LLC. - 2397-334X. ; 4:1, s. 101-108
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Tidskriftsartikel (refereegranskat)abstract
- Temperature governs most biotic processes, yet we know little about how warming affects whole ecosystems. Here we examined the responses of 128 components of a subarctic grassland to either 5–8 or >50 years of soil warming. Warming of >50 years drove the ecosystem to a new steady state possessing a distinct biotic composition and reduced species richness, biomass and soil organic matter. However, the warmed state was preceded by an overreaction to warming, which was related to organism physiology and was evident after 5–8 years. Ignoring this overreaction yielded errors of >100% for 83 variables when predicting their responses to a realistic warming scenario of 1 °C over 50 years, although some, including soil carbon content, remained stable after 5–8 years. This study challenges long-term ecosystem predictions made from short-term observations, and provides a framework for characterization of ecosystem responses to sustained climate change.
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| 28. |
- Weedon, James T., et al.
(författare)
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Community adaptation to temperature explains abrupt soil bacterial community shift along a geothermal gradient on Iceland
- 2023
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Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717. ; 177
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Tidskriftsartikel (refereegranskat)abstract
- Understanding how and why soil microbial communities respond to temperature changes is important for understanding the drivers of microbial distribution and abundance. Studying soil microbe responses to warming is often made difficult by concurrent warming effects on soil and vegetation and by a limited number of warming levels preventing the detection of non-linear effects. A unique area in Iceland, where soil temperatures have recently increased due to geothermic activity, created a stable warming gradient in both grassland (dominated by Agrostis capillaris) and forest (Picea sitchensis) vegetation. By sampling soils which had been subjected to four years of temperature elevation (ambient (MAT 5.2 °C) to +40 °C), we investigated the shape of the response of soil bacterial communities to warming, and their associated community temperature adaptation. We used 16S rRNA amplicon sequencing to profile bacterial communities, and bacterial growth-based assays (3H-Leu incorporation) to characterize community adaptation using a temperature sensitivity index (SI, log (growth at 40 °C/4 °C)). Despite highly dissimilar bacterial community composition between the grassland and forest, they adapted similarly to warming. SI was 0.6 (equivalent to a minimum temperature for growth of between −6 and −7 °C) in both control plots. Both diversity and community composition, as well as SI, showed similar threshold dynamics along the soil temperature gradient. There were no significant changes up to soil warming of 6–9 °C above ambient, beyond which all indices shifted in parallel, with SI increasing from 0.6 to 1.5. The consistency of these responses provide evidence for an important role for temperature as a direct driver of bacterial community shifts along soil temperature gradients.
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