Soil properties differently influence estimates of soil CO2 efflux from three chamber-based measurement systems

Soil CO₂ efflux is a major component of net ecosystem productivity (NEP) of forest systems. Combining data from multiple researchers for larger-scale modeling and assessment will only be valid if their methodologies provide directly comparable results. We conducted a series of laboratory and field tests to assess the presence and magnitude of soil CO₂ efflux measurement system × environment interactions. Laboratory comparisons were made with a dynamic, steady-state CO₂ flux generation apparatus, wherein gas diffusion drove flux without creating pressure differentials through three artificial soil media of varying air-filled porosity. Under these conditions, two closed systems (Li-6400-09 and SRC-1) exhibited errors that were dependent on physical properties of the artificial media. The open system (ACES) underestimated CO₂ flux. However, unlike the two other systems, the ACES results could be corrected with a single calibration equation that was unaffected by physical differences in artificial media. Both scale and rank changes occurred among the measurement systems across four sites. Our work clearly shows that soil CO₂ efflux measurement system × environment interactions do occur and can substantially impact estimates of soil CO₂ efflux. Until reliable calibration techniques are developed and applied, such interactions make direct comparison of published rates, and C budgets estimated using such rates, difficult.     

Effect of frost nights and day and night temperature during dormancy induction on frost hardiness, tolerance to cold storage and bud burst in seedlings of Norway spruce

For trees, the ability to obtain and maintain sufficient levels of frost hardiness in late autumn, winter and spring is crucial. We report that temperatures during dormancy induction influence bud set, frost hardiness, tolerance to cold storage, timing of bud burst and spring frost hardiness in seedlings of Norway spruce (Picea abies (L.) Karst.). Bud set occurred later in 12°C than in 21°C, and later in cool nights (7°C) than in constant temperature. One weekly frost night (−2.5°C) improved frost hardiness. Cool nights reduced frost hardiness early, but improved hardiness later during cold acclimation. Buds and stems were slightly hardier in 21°C than in 12°C, while needles were clearly hardier in 12°C. Cold daytime temperature, cool nights and one weekly frost night improved cold storability (0.7°C). Seedlings receiving high daytime temperatures burst buds later, and were less injured by light frost some days after bud burst.     

High-resolution array comparative genomic hybridization analysis reveals unanticipated complexity of genetic deficiencies on chromosome V in <Emphasis Type="Italic">Caenorhabditis elegans</Emphasis>

Genomic rearrangements are widely used in Caenorhabditis elegans research but many remain incompletely characterized at the physical level. We have used oligo-array comparative genomic analysis to assess the physical structure of 20 deficiencies and a single duplication of chromosome V. We find that while deletions internal to the chromosome appear simple in structure, terminal deletions are complex, containing duplications in addition to the deletion. Additionally, we confirm that transposon-induced deficiencies contain breakpoints that initiate at Tc1 elements. Finally, 13 of these deficiencies are known to suppress recombination far beyond the extent of the deletion. These deficiencies fall into two classes: strong and weak suppressors of adjacent recombination. Analysis of the deleted regions in these deficiencies reveals no common physical sites to explain the observed differences in recombination suppression. However, we find a strong correlation between the size of the rearranged chromosome and the severity of recombination suppression. Rearranged chromosomes that have a minor effect on recombination fall within 2% of normal chromosome size. Our observations highlight the use of array-based approaches for the analysis of rearranged genomes, revealing previously unidentified deficiency characteristics and addressing biologically relevant questions.     

Molecular and phenotypic divergence in the bluethroat (Luscinia svecica) subspecies complex

Subspecies complexes may provide valuable insights into the early stages of the speciation process. The bluethroat (Luscinia svecica) consists of many morphologically distinct subspecies that differ most strikingly in the ornamental colour pattern of the male throat. We investigated the genetic and phenotypic differentiation in this subspecies complex, using (i) microsatellite genotyping (11 loci) of a sample of 364 individuals from bluethroat populations in Europe and Asia, and (ii) spectrometric and morphological measurements of a sample of 131 museum skin specimens. Population genetic analyses, based on microsatellite allele frequency variation, revealed a slight but significant overall population differentiation (F(ST) = 0.042). There was a well-differentiated southern group of subspecies with white or no throat spots and a less-differentiated northern group of chestnut-spotted populations. Phylogenetic analyses indicated that the southern all-blue and white-spotted forms are ancestral to the chestnut-spotted subspecies. In addition to the qualitative variation in throat plumage pattern already described in the literature, we found significant quantitative variation among subspecies in hue, chroma and brightness of the ultraviolet (UV)/blue throat coloration, and this variation seemed to be unrelated to the phylogenetic distance between subspecies.     

Adrm1, a putative cell adhesion regulating protein, is a novel proteasome-associated factor

We have identified Adrm1 as a novel component of the regulatory ATPase complex of the 26 S proteasome: Adrm1 was precipitated with an antibody to proteasomes and vice versa. Adrm1 co-migrated with proteasomes on gel-filtration chromatography and non-denaturing polyacrylamide gel electrophoresis. Adrm1 has been described as an interferon-gamma-inducible, heavily glycosylated membrane protein of 110 kDa. However, we found Adrm1 in mouse tissues only as a 42 kDa peptide, corresponding to the mass of the non-glycosylated peptide chain, and it could not be induced in HeLa cells with interferon. Adrm1 was present almost exclusively in soluble 26 S proteasomes, albeit a small fraction was membrane-associated, like proteasomes. Adrm1 was found in cells in amounts equimolar with S6a, a 26 S proteasome subunit. HeLa cells contain no pool of free Adrm1 but recombinant Adrm1 could bind to pre-existing 26 S proteasomes in cell extracts. Adrm1 may be distantly related to the yeast proteasome subunit Rpn13, mutants of which are reported to display no obvious phenotype. Accordingly, knock-down of Adrm1 in HeLa cells had no effect on the amount of proteasomes, or on degradation of bulk cell protein, or accumulation of polyubiquitinylated proteins. This indicates that Adrm1 has a specialised role in proteasome function.     

Excess of de novo deleterious mutations in genes associated with glutamatergic systems in nonsyndromic intellectual disability

Little is known about the genetics of nonsyndromic intellectual disability (NSID). We hypothesized that de novo mutations (DNMs) in synaptic genes explain an important fraction of sporadic NSID cases. In order to investigate this possibility, we sequenced 197 genes encoding glutamate receptors and a large subset of their known interacting proteins in 95 sporadic cases of NSID. We found 11 DNMs, including ten potentially deleterious mutations (three nonsense, two splicing, one frameshift, four missense) and one neutral mutation (silent) in eight different genes. Calculation of point-substitution DNM rates per functional and neutral site showed significant excess of functional DNMs compared to neutral ones. De novo truncating and/or splicing mutations in SYNGAP1, STXBP1, and SHANK3 were found in six patients and are likely to be pathogenic. De novo missense mutations were found in KIF1A, GRIN1, CACNG2, and EPB41L1. Functional studies showed that all these missense mutations affect protein function in cell culture systems, suggesting that they may be pathogenic. Sequencing these four genes in 50 additional sporadic cases of NSID identified a second DNM in GRIN1 (c.1679_1681dup/p.Ser560dup). This mutation also affects protein function, consistent with structural predictions. None of these mutations or any other DNMs were identified in these genes in 285 healthy controls. This study highlights the importance of the glutamate receptor complexes in NSID and further supports the role of DNMs in this disorder.     

Sustained effects of atmospheric [CO2] and nitrogen availability on forest soil CO2 efflux

Soil CO₂ efflux (F_soil) is the largest source of carbon from forests and reflects primary productivity as well as how carbon is allocated within forest ecosystems. Through early stages of stand development, both elevated [CO₂] and availability of soil nitrogen (N; sum of mineralization, deposition, and fixation) have been shown to increase gross primary productivity, but the long‐term effects of these factors on F_soil are less clear. Expanding on previous studies at the Duke Free‐Air CO₂ Enrichment (FACE) site, we quantified the effects of elevated [CO₂] and N fertilization on F_soil using daily measurements from automated chambers over 10 years. Consistent with previous results, compared to ambient unfertilized plots, annual F_soil increased under elevated [CO₂] (ca. 17%) and decreased with N (ca. 21%). N fertilization under elevated [CO₂] reduced F_soil to values similar to untreated plots. Over the study period, base respiration rates increased with leaf productivity, but declined after productivity saturated. Despite treatment‐induced differences in aboveground biomass, soil temperature and water content were similar among treatments. Interannually, low soil water content decreased annual F_soil from potential values – estimated based on temperature alone assuming nonlimiting soil water content – by ca. 0.7% per 1.0% reduction in relative extractable water. This effect was only slightly ameliorated by elevated [CO₂]. Variability in soil N availability among plots accounted for the spatial variability in F_soil, showing a decrease of ca. 114 g C m^?2 yr^?1 per 1 g m^?2 increase in soil N availability, with consistently higher F_soil in elevated [CO₂] plots ca. 127 g C per 100 ppm [CO₂] over the +200 ppm enrichment. Altogether, reflecting increased belowground carbon partitioning in response to greater plant nutritional needs, the effects of elevated [CO₂] and N fertilization on F_soil in this stand are sustained beyond the early stages of stand development and through stabilization of annual foliage production.     

Species‐specific communication bars interspecific mating between syntopic species of Zwicknia stoneflies (Plecoptera: Capniidae)

Most Northern Hemisphere stoneflies have species‐specific mating signals that are generally thought to constitute a barrier against interspecific mating. We tested this hypothesis in two species of the genus Zwicknia that have only very recently been recognised as distinct species, and that were found to occur together in a stream in Lower Saxony, Germany. Analyses of molecular markers COI and 28S in combination with wing length (distinguishing males of both species) and mating signals revealed no instance of hybridisation among 23 studied specimens. In addition, eleven further males identified on the basis of morphology alone all produced the expected species‐specific signal. Females and males of both species were presented with played back conspecific and heterospecific signals and duetting sequences, and responded only to conspecific stimuli. This lends support to the hypothesis that the intersexual communication system functions as an important pre‐mating barrier against gene flow, although post‐mating isolation cannot be excluded. Interspecific mating did occur when a mixed pair was confined together in a small container. Males of both species were found to call in response to played back duetting sequences with stereotypic latencies that are clearly longer than the latencies in male‐female duets. We interpret this as an indication of eavesdropping behaviour coupled with attempts to take over the perceived duet. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 969–980.