Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska

Understanding the response of permafrost microbial communities to climate warming is crucial for evaluating ecosystem feedbacks to global change. This study investigated soil bacterial and archaeal communities by Illumina MiSeq sequencing of 16S rRNA gene amplicons across a permafrost thaw gradient at different depths in Alaska with thaw progression for over three decades. Over 4.6 million passing 16S rRNA gene sequences were obtained from a total of 97 samples, corresponding to 61 known classes and 470 genera. Soil depth and the associated soil physical–chemical properties had predominant impacts on the diversity and composition of the microbial communities. Both richness and evenness of the microbial communities decreased with soil depth. Acidobacteria, Verrucomicrobia, Alpha‐ and Gamma‐Proteobacteria dominated the microbial communities in the upper horizon, whereas abundances of Bacteroidetes, Delta‐Proteobacteria and Firmicutes increased towards deeper soils. Effects of thaw progression were absent in microbial communities in the near‐surface organic soil, probably due to greater temperature variation. Thaw progression decreased the abundances of the majority of the associated taxa in the lower organic soil, but increased the abundances of those in the mineral soil, including groups potentially involved in recalcitrant C degradation (Actinomycetales, Chitinophaga, etc.). The changes in microbial communities may be related to altered soil C sources by thaw progression. Collectively, this study revealed different impacts of thaw in the organic and mineral horizons and suggests the importance of studying both the upper and deeper soils while evaluating microbial responses to permafrost thaw.     

Recovery of Aboveground Plant Biomass and Productivity After Fire in Mesic and Dry Black Spruce Forests of Interior Alaska

Plant biomass accumulation and productivity are important determinants of ecosystem carbon (C) balance during post-fire succession. In boreal black spruce (Picea mariana) forests near Delta Junction, Alaska, we quantified aboveground plant biomass and net primary productivity (ANPP) for 4 years after a 1999 wildfire in a well-drained (dry) site, and also across a dry and a moderately well-drained (mesic) chronosequence of sites that varied in time since fire (2 to ∼116 years). Four years after fire, total biomass at the 1999 burn site had increased exponentially to 160 ± 21 g m⁻² (mean ± 1SE) and vascular ANPP had recovered to 138 ± 32 g m⁻² y⁻¹, which was not different than that of a nearby unburned stand (160 ± 48 g m⁻² y⁻¹) that had similar pre-fire stand structure and understory composition. Production in the young site was dominated by re-sprouting graminoids, whereas production in the unburned site was dominated by black spruce. On the dry and mesic chronosequences, total biomass pools, including overstory and understory vascular and non-vascular plants, and lichens, increased logarithmically (dry) or linearly (mesic) with increasing site age, reaching a maximum of 2469 ± 180 (dry) and 4008 ± 233 g m⁻² (mesic) in mature stands. Biomass differences were primarily due to higher tree density in the mesic sites because mass per tree was similar between sites. ANPP of vascular and non-vascular plants increased linearly over time in the mesic chronosequence to 335 ± 68 g m⁻² y⁻¹ in the mature site, but in the dry chronosequence it peaked at 410 ± 43 g m⁻² y⁻¹ in a 15-year-old stand dominated by deciduous trees and shrubs. Key factors regulating biomass accumulation and production in these ecosystems appear to be the abundance and composition of re-sprouting species early in succession, the abundance of deciduous trees and shrubs in intermediate aged stands, and the density of black spruce across all stand ages. A better understanding of the controls over these factors will help predict how changes in climate and fire regime will affect the carbon balance of Interior Alaska. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Retinoid status and responsiveness to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in mice lacking retinoid binding protein or retinoid receptor forms

We have investigated the role of Vitamin A (retinoid) proteins in hepatic retinoid processing under normal conditions and during chemical stress induced by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), a chemical known to interfere with retinoid turnover and metabolism. Three separate studies were performed in wildtype control mice and transgenic mice that lack one or more isoforms of retinoic acid receptors (RAR), retinoid X receptors (RXR), or intracellular retinoid-binding proteins (CRABP I, CRABP II, CRBP I). Body and organ weight development was monitored from 2 weeks of age to adult, and hepatic levels of retinyl esters, retinol, and retinoic acid were investigated. In addition, hepatic concentrations of 9-cis-4-oxo-13,14-dihydro-retinoic acid, a recently discovered retinoid metabolite that has proven sensitive to both TCDD exposure and Vitamin A status, were also determined. Mice absent in the three proteins CRBP I, CRABP I, and CRABP II (CI/CAI/CAII-/-) displayed significantly lower hepatic retinyl ester, retinol, and all-trans-retinoic acid levels compared to wildtype mice, whereas the liver concentrations of 9-cis-4-oxo-13,14-dihydro-retinoic acid was considerably higher. After treatment with TCDD, hepatic total retinoids were almost entirely depleted in the CI/CAI/CAII-/- mice, whereas wildtype mice and mice lacking CRABP I, and CRABP II (CAI/CAII-/-) retained approximately 60-70% of their Vitamin A content compared to controls at 28 days. RAR and RXR knockout mice responded similarly to wildtype mice with respect to TCDD-induced retinoid disruption, with the exception of RXRbeta-/- mice which showed no decrease in hepatic Vitamin A concentration, suggesting that the role of RXRbeta in TCDD-induced retinoid disruption should be further investigated. Overall, the abnormal retinoid profile in the triple knockout mice (CI/CAI/CAII-/-), but not double knockout (CAI/CAII-/-) mice, suggests that a loss of CRBP I may account for the difference in retinoid profile in CI/CAI/CAII-/- mice, and is likely to result in an increased susceptibility to hepatic retinoid depletion following dioxin exposure.     

A synthetic strategy for novel nonsymmetrical bola amphiphiles based on carbohydrates

A number of novel nonionic bolaform amphiphiles with nonidentical aldityl head groups, 1-(1-deoxy-D-galactitol-1-ylamino)-6-(1-deoxy-D-glucitol-1-ylamino)hexane, 1-(1-deoxy-D-mannitol-1-ylamino)-6-(1-deoxy-D-glucitol-1-ylamino)hexane, and 1-(1-deoxy-D-galactitol-1-ylamino)-6-(1-deoxy-D-mannitol-1-ylamino)hexane were synthesized by two successive reductive aminations involving 1,6-diaminohexane (1) and the appropriate D-aldohexoses (D-glucose, D-mannose, and D-galactose) using 5% Pd on carbon as the catalyst. Typical reaction conditions were 40 degrees C, 4MPa hydrogen and a reaction time of 4.5 h. The compounds were isolated as white solids in yields ranging from 39% to 72%. The intermediate aminoalditols, 1-(1-deoxy-D-glucitol-1-ylamino)-6-aminohexane and 1-(1-deoxy-D-galactitol-1-ylamino)-6-aminohexane were obtained as off-white solids in 80-85% yield. The bolaform amphiphiles containing 1-deoxy-D-glucitol head group(s) showed markedly lower melting points than the compounds with the 1-deoxy-D-mannitol and 1-deoxy-D-galactitol head groups, due to the presence of 1,3-syn interactions within the carbohydrate moiety. The novel bolaform compounds are potential starting materials for the synthesis of a broad range of gemini surfactants with nonidentical, carbohydrate-based head groups.     

Human prion diseases in the Netherlands (1998-2009): clinical, genetic and molecular aspects

Prion diseases are rare and fatal neurodegenerative disorders that can be sporadic, inherited or acquired by infection. Based on a national surveillance program in the Netherlands we describe here the clinical, neuropathological, genetic and molecular characteristics of 162 patients with neuropathologically confirmed prion disease over a 12-year period (1998-2009). Since 1998, there has been a relatively stable mortality of Creutzfeldt-Jakob disease (CJD) in the Netherlands, ranging from 0.63 to 1.53 per million inhabitants per annum. Genetic analysis of the codon 129 methionine/valine (M/V) polymorphism in all patients with sporadic CJD (sCJD) showed a trend for under-representation of VV cases (7.0%), compared with sCJD cohorts in other Western countries, whereas the MV genotype was relatively over-represented (22,4%). Combined PrP(Sc) and histopathological typing identified all sCJD subtypes known to date, except for the VV1 subtype. In particular, a "pure" phenotype was demonstrated in 60.1% of patients, whereas a mixed phenotype was detected in 39.9% of all sCJD cases. The relative excess of MV cases was largely accounted for by a relatively high incidence of the MV 2K subtype. Genetic analysis of the prion protein gene (PRNP) was performed in 161 patients and showed a mutation in 9 of them (5.6%), including one FFI and four GSS cases. Iatrogenic CJD was a rare phenomenon (3.1%), mainly associated with dura mater grafts. Three patients were diagnosed with new variant CJD (1.9%) and one with variably protease-sensitive prionopathy (VPSPr). Post-mortem examination revealed an alternative diagnosis in 156 patients, most commonly Alzheimer's disease (21.2%) or vascular causes of dementia (19.9%). The mortality rates of sCJD in the Netherlands are similar to those in other European countries, whereas iatrogenic and genetic cases are relatively rare. The unusual incidence of the VV2 sCJD subtype compared to that reported to date in other Western countries deserves further investigation.     

Linkage analysis for plasma amyloid beta levels in persons with hypertension implicates Aβ-40 levels to presenilin 2

Plasma concentrations of Aβ40 and Aβ42 rise with age and are increased in people with mutations that cause early-onset Alzheimer’s disease (AD). Amyloid beta (Aβ) plasma levels were successfully used as an (endo)phenotype for gene discovery using a linkage approach in families with dominant forms of disease. Here, we searched for loci involved in Aβ plasma levels in a series of non-demented patients with hypertension in the Erasmus Rucphen Family study. Aβ40 and Aβ42 levels were determined in 125 subjects with severe hypertension. All patients were genotyped with a 6,000 single nucleotide polymorphisms (SNPs) illumina array designed for linkage analysis. We conducted linkage analysis of plasma Aβ levels. None of the linkage analyses yielded genome-wide significant logarithm of odds (LOD) score over 3.3, but there was suggestive evidence for linkage (LOD?>?1.9) for two regions: 1q41 (LOD?=?2.07) and 11q14.3 (LOD?=?2.97), both for Aβ40. These regions were followed up with association analysis in the study subjects and in 320 subjects from a population-based cohort. For the Aβ40 region on chromosome 1, association of several SNPs was observed at the presenilin 2 gene (PSEN2) (p?=?2.58?×?10^?4 for rs6703170). On chromosome 11q14-21, we found some association (p?=?3.1?×?10^?3 for rs2514299). This linkage study of plasma concentrations of Aβ40 and Aβ42 yielded two suggestive regions, of which one points toward a known locus for familial AD.     

Stable nitrogen isotope patterns of trees and soils altered by long-term nitrogen and phosphorus addition to a lowland tropical rainforest

Foliar nitrogen (N) isotope ratios (δ¹⁵N) are used as a proxy for N-cycling processes, including the “openness” of the N cycle and the use of distinct N sources, but there is little experimental support for such proxies in lowland tropical forest. To address this, we examined the δ¹⁵N values of soluble soil N and canopy foliage of four tree species after 13 years of factorial N and P addition to a mature lowland rainforest. We hypothesized that N addition would lead to ¹⁵N-enriched soil N forms due to fractionating losses, whereas P addition would reduce N losses as the plants and microbes adjusted their stoichiometric demands. Chronic N addition increased the concentration and δ¹⁵N value of soil nitrate and δ¹⁵N in live and senesced leaves in two of four tree species, but did not affect ammonium or dissolved organic N. Phosphorus addition significantly increased foliar δ¹⁵N in one tree species and elicited significant N × P interactions in two others due to a reduction in foliar δ¹⁵N enrichment under N and P co-addition. Isotope mixing models indicated that three of four tree species increased their use of nitrate relative to ammonium following N addition, supporting the expectation that tropical trees use the most available form of mineral N. Previous observations that anthropogenic N deposition in this tropical region have led to increasing foliar δ¹⁵N values over decadal time-scales is now mechanistically linked to greater usage of ¹⁵N-enriched nitrate.     

Soil Microbial Community Responses to a Decade of Warming as Revealed by Comparative Metagenomics

Soil microbial communities are extremely complex, being composed of thousands of low-abundance species (<0.1% of total). How such complex communities respond to natural or human-induced fluctuations, including major perturbations such as global climate change, remains poorly understood, severely limiting our predictive ability for soil ecosystem functioning and resilience. In this study, we compared 12 whole-community shotgun metagenomic data sets from a grassland soil in the Midwestern United States, half representing soil that had undergone infrared warming by 2°C for 10 years, which simulated the effects of climate change, and the other half representing the adjacent soil that received no warming and thus, served as controls. Our analyses revealed that the heated communities showed significant shifts in composition and predicted metabolism, and these shifts were community wide as opposed to being attributable to a few taxa. Key metabolic pathways related to carbon turnover, such as cellulose degradation (∼13%) and CO₂ production (∼10%), and to nitrogen cycling, including denitrification (∼12%), were enriched under warming, which was consistent with independent physicochemical measurements. These community shifts were interlinked, in part, with higher primary productivity of the aboveground plant communities stimulated by warming, revealing that most of the additional, plant-derived soil carbon was likely respired by microbial activity. Warming also enriched for a higher abundance of sporulation genes and genomes with higher G+C content. Collectively, our results indicate that microbial communities of temperate grassland soils play important roles in mediating feedback responses to climate change and advance the understanding of the molecular mechanisms of community adaptation to environmental perturbations.     

A First Exploration of Health Impact Assessment of Chemical Exposure: Assigning Weights to Subclinical Effects Based on Animal Studies

Health impact assessments (HIA) have become an important tool for applying evidence-based policy. Recently, the concept of HIA has been introduced in the field of chemical substances. Two main issues are encountered, i.e., the focus of risk assessment is deriving safe levels and on first signs of adverse effects. These adverse effects, often at a subclinical level, fall outside the scope of a HIA. However, the number of subjects with subclinical effects can be extensive, thus relevant to consider in HIA and subsequent risk management policies and socioeconomic analyses (e.g., under REACH). The approach to include subclinical effects in a HIA relies on the dose–response relationship for toxicological endpoints, which are indicative for subclinical and clinical effects. Assessment of (sub)clinical effect sizes requires expertise from toxicologists, pathologists, and risk assessors. The clinical effect is appraised by a disability weight in the disability adjusted life year (DALY) concept. Subsequently, a derivative thereof, the severity weight, is assigned to parameter value changes in the range of subclinical effect sizes to appraise subclinical effects. Ultimately, if the approach is repeated for many substances, severity weights may be assigned based on changes in endpoints alone, making it a valuable tool for health impact assessors of chemical substances.