A functional assessment of the response of grassland vegetation to reduced grazing and abandonment

Question: Predicting the impact of land‐use change on vegetation is vital to understanding how biodiversity and ecosystem function may respond. Is it correct to assume that abandonment is an extreme form of grazing reduction? Location: Borders and central Scotland. Methods: The analysis used data sets from two identical experiments where the impacts of two unfertilized, extensively grazed treatments and one unfertilized abandoned treatment were compared against the species dynamics of a pasture subject to normal, productive grazing management over a 16‐year period. Initial multivariate analysis using Principal Response Curves was used to assess if particular traits were associated with either extensive or abandoned treatments, and was checked using univariate tests of individual traits. RLQ analysis followed by clustering into response groups was used to assess if species behaved in a similar manner between sites. Results: For many traits/attributes the shift in value or proportion was approximately linear across the extensification treatments as grazing was removed. However, certain traits showed step changes and quadratic responses. Leaf dry matter content, an important effect trait, was in the latter group. Most traits/attributes and species behaved similarly at the two sites. However, traits such as regenerative strategy, seed length, longevity and mass and seed bank type behaved differently, indicating that they are not predictable response traits. Conclusion: The results indicate that responses to grazing removal during extensification are largely straightforward and largely independent of species pool. However, there are discrepancies that suggest that simple analyses of the impacts of land‐use changes such as grazing reduction may hide more complex responses.     

A new practical tool for deriving a functional signature for herbaceous vegetation

Hypothesis: For any one time and place a ‘functional signature’ can be derived for a sample of herbaceous vegetation in a way that concisely represents the balance between the different clusters of functional attributes that are present among component species. Methods: We developed a spreadsheet‐based tool for calculating functional signatures within the context of the C‐S‐R system of plant functional types. We used the tool to calculate and compare signatures for specimen British vegetation samples which differed in management regime and location in time. Conclusion: The integrative power of the ‘C‐S‐R signature’ is useful in comparative studies involving widely differing samples. Movements in the signature can be used to indicate degree of resistance, resilience, eutrophication and dereliction. Systems of plant functional types other than C‐S‐R might also be approached in this way. Availability: The tool can be downloaded free of charge from the first author's web pages or from the journal's electronic archive.     

Functional diversity in nematode communities across terrestrial ecosystems

Functional diversity can be defined as the distribution of trait values within a community. Hence, functional diversity can be an indicator of habitat filtering and a reliable environmental predictor of ecosystem functioning. However, there is a serious lack of studies that test how functional diversity indices change depending on the environmental conditions. The aim of this study is to provide such evidence by analyzing the distribution and variation of continuous body-mass values (i.e. functional diversity) and related shifts in body length and width in a nematode community.We used a large online dataset on nematode traits to analyze: (i) the distribution of body mass using three functional diversity indices, i.e. functional richness, functional divergence and functional evenness; (ii) the shifts in body-size traits (length and width); and (iii) the body-mass distributions of five trophic groups and of the entire nematode community.Managed grasslands exhibited the widest range of body-mass values while body-mass distribution in arable fields covered the greatest area in comparison to the other ecosystem types. The shift in body size revealed environmental filters that could not have been identified by the study of functional diversity indices per se. We found low values of functional evenness to be associated with high values of functional richness. We provide novel empirical evidence that body-mass distribution within a trophic group mirrors the effects of habitat filtering more than the distribution in the community as a whole. Hence, our trait-based approach, more than functional diversity itself, disclosed soil food-web structure and identified community responses.     

Functional diversity analysis helps to identify filters affecting community assembly after fen restoration by top-soil removal and hay transfer

Top-soil removal followed by species introduction through hay transfer has appeared as a method to restore drained fens. This method addresses abiotic constraints by restoring hydrology and nutrient status, and biotic constraints by removing an unwanted seed bank and counteracting dispersal-limitation. Restoration works by altering environmental filters. Knowledge about the restoration actions effect on functional traits is necessary to understand which types of species may establish. In this study we analyse which factors in top-soil removal followed by hay transfer influence selection and composition of functional traits. Top-soil removal followed by hay transfer from reference sites was conducted at two sites in the Całowanie fen, 33 km SE of Warsaw, Poland. Species and abundance data were recorded for three consecutive years. These data, combined with data on functional traits were used to analyse the effect of the restoration actions on four functional diversity-indices and the community weighted mean of functional traits. Our results reveal a strong habitat filter in the restoration site that follows an elevation gradient. At low elevation this filter selects low values of autochory and specific leaf area and high values of clonal lateral spread, Ellenberg moisture values, and dispersal through hydrochory. The transferred hay differs in trait characteristics compared to the reference site vegetation by having species of higher specific leaf area, lower Ellenberg moisture value and lower dispersal by autochory and hydrochory. The result presented here has three important implications for fen restoration. First, the difference in trait-characteristics between the transferred hay and the reference site it was harvested from limits the restoration potential. Second, since for several fen species important functional traits are filtered along an elevation-gradient, careful planning regarding depth of top-soil removal is needed. Finally the results illustrate how a functional analysis can be used to detect environmental filters acting during ecological restoration.     

Trypsin digest coupled with two-dimensional shotgun proteomics reveals the involvement of multiple signaling pathways in functional remodeling of late-gestation uteri in rats

Pregnant uteri become quiescent after functional remodeling but details are not fully known. Here we revealed uterine proteins of late-gestation rats by 2-D shotgun proteomic analysis and correlated protein expression with uterine functions. After duplication, 239 proteins were identified. About 190 proteins commonly found in duplicate analyses were subjected to functional annotation. The proteins associated with signal transduction fell into three known pathways. Western blotting and functional data indicated that: (i) a reduction of Na(+)/K(+)-ATPase-related proteins was associated with the decrease of contraction rate, (ii) a reduction of tyrosine hydroxylase and cyclic AMP-dependent protein kinase type II-alpha regulatory chain (PKARII alpha) was associated with an increase in the relaxation response to 8-bromo-cAMP, and (iii) in the presence of Ras, an increased expression of nucleolin was associated with the elevation of Bcl-xL, an antiapoptotic protein. In conclusion, 2-D shotgun proteomic analysis provides a global database of uterine proteins for hypothesis-driven studies. Our data suggest that in late-gestation uteri down-regulation of PKARII alpha and Na(+)/K(+)-ATPase may cause functional remodeling and lead to uterine quiescent. Up-regulation of antiapoptotic proteins (nucleolin and Bcl-xL) in the Ras-mediated pathway may maintain cell survival and counteract cell loss during remodeling.     

Novel eye-specific calmodulin methylation characterized by protein mapping in Drosophila melanogaster

Post-translational methylation of the epsilon-amino group of lysine residues regulates a number of protein functions. Calmodulin, a key modulator of intracellular calcium signaling, is methylated on lysine 115 in many species. Although the amino acid sequence of calmodulin is highly conserved in eukaryotes, it has been shown that lysine 115 is not methylated in Drosophila calmodulin and no other methylation site has been reported. In this study, we characterized in vivo modification states of Drosophila calmodulin using proteomic methodology involving the protein mapping of microdissected Drosophila tissues on 2-D gels. We found that Drosophila calmodulin was highly expressed in methylated forms in the compound eye, whereas its methylation was hardly detected in other tissues. We identified that lysine 94 located in an EF-hand III is the methylation site in Drosophila calmodulin. The predominance of methylated calmodulin in the compound eye may imply the involvement of calmodulin in photoreceptor-specific functions through methylation.     

Functional regularity: a neglected aspect of functional diversity

Functional diversity has been identified as a key to understanding ecosystem and community functioning. However, due to the lack of a sound definition its nature and measurement are still poorly understood. In the same way that species diversity can be split into species richness and species evenness, so functional diversity can be split into functional richness (i.e. the amount of functional trait/character/attribute space filled) and functional evenness (i.e. the evenness of abundance distribution in functional trait space). We propose a functional regularity index (FRO) as a measure of functional evenness for situations where species are represented only by a single functional trait value (e.g. mean, median or mode), and species abundances are known. This new index is based on the Bulla O index of species evenness. When dealing with functional types or categorical functional traits, the Bulla O or any other accepted species evenness index may be used directly to measure functional evenness. The advantage of FRO is that it supplies a measure of functional evenness for continuous trait data. The FRO index presented in this paper fulfils all the a priori criteria required. We demonstrate with two example datasets that a range of FRO values may be obtained for both plant and animal communities. Moreover, FRO was strongly related to ecosystem function as seen in photosynthetic biomass in plant communities, and was able to differentiate sampling stations in a lagoon based on the functional traits of fish. Thus, the FRO index is potentially a highly useful tool for measuring functional diversity in a variety of ecological situations.     

Adsorption of 6-mercaptopurine and 6-mercaptopurine-ribosideon silver colloid: a pH-dependent surface-enhanced Raman spectroscopy and density functional theory study. II. 6-mercaptopurine-riboside

Surface-enhanced Raman spectroscopy (SERS) has been applied to characterize the interaction of 6-mercaptopurine-ribose (6MPR), an active drug used in chemotherapy of acute lymphoblastic leukemia, with a model biological substrate at therapeutic concentrations and as function of the pH value. Therefore, a detailed vibrational analysis of crystalline and solvated (6MPR) based on Density Functional Theory (DFT) calculations of the thion and thiol tautomers has been performed. 6MPR adopts the thion tautomeric form in the polycrystalline state. The SERS spectra of 6MPR and 6-mercaptopurine (6MP) recorded on silver colloid provided evidence that the ribose derivative shows different adsorption behavior compared with the free base. Under acidic conditions, the adsorption of 6MPR on the metal surface via the N7 and possibly S atoms was proposed to have a perpendicular orientation, while 6MP is probably adsorbed through the N9 and N3 atoms. Under basic conditions both molecules are adsorbed through the N1 and possibly S atoms, but 6MP has a more tilted orientation on the silver colloidal surface while 6MPR adopts a perpendicular orientation. The reorientation of the 6MPR molecule on the surface starts at pH 8 while in the case of 6MP the reorientation starts around pH 6. Under basic conditions, the presence of the anionic molecular species for both molecules is suggested. The deprotonation of 6MP is completed at pH 8 while the deprotonation of the riboside is finished at pH 10. For low drug concentrations under neutral conditions and for pH values 8 and 9, 6MPR interacts with the substrate through both N7 and N1 atoms, possibly forming two differently adsorbed species, while for 6MP only one species adsorbed via N1 was evidenced.     

Plant diversity,species turnover and shifts in functional traits in coastal dune vegetation: Results from permanent plots over a 52‐year period

Question: What is the relationship between plant diversity and species turnover in coastal dune vegetation plots? How is the long‐term change in species composition of vegetation plots related to shifts in functional traits, and what does it tell us about the dominant processes? Location: Coastal dunes, the Netherlands. Methods: Our data set comprised 52 years of vegetation data from 35 permanent plots in grassland/scrub/woodland vegetation. Vegetation dynamics were described in terms of changes in species composition and abundance, and shifts in 13 functional traits related to resources capture and forage quality, regeneration and dispersal. Results: Species turnover in the plots was high, because of local extinction and colonization. Species‐rich plots were more stable in terms of species abundance and composition compared with species‐poor plots. Over time, the plots converged with respect to their abiotic conditions, as reflected by Ellenberg indicator values – indicating that the prevailing process was succession. The high species turnover reflected high invasibility: accordingly, the relative importance of annuals increased. Most newcomer annuals, however, were competitive generalists of little conservation value. The functional trait analysis allowed us to unravel the complexity of effects of disturbances and succession, and yielded information on the processes driving the observed vegetation dynamics. Conclusions: In this study, small‐scale species turnover was negatively related to species diversity, indicating more stability in species‐rich communities. Regarding shifts in trait diversity, unifying filters appeared to be more dominant than diversifying filters. Counteracting this homogenization process poses a challenge for nature management.     

Effects of different components of diversity on productivity in artificial plant communities

In an experiment on artificial plant communities, the effects of three components of plant diversity—plant species diversity, plant functional group diversity and plant functional diversity—on community productivity and soil water content were compared. We found that simple regression analysis showed a positive diversity effect on ecosystem processes (productivity and soil water content). However, when three components of diversity were included in the multiple regression analyses, the results showed that functional group diversity and functional diversity had more important effects on productivity and resource use efficiency. These results suggested that, compared with species number, functional differences among species and the range of functional traits carried by plants are the basis of biodiversity effects on ecosystem functioning. These diversity effects of increasing functional group diversity or functional diversity were likely because species differing greatly in size, life form, phenology and capacity to capture and use resources efficiently in diverse communities realize complementary resource use in temporal, spatial, and biological ways.     

A sequential expression system for high-throughput functional genomic analysis

A method employing sequential rounds of cell-free protein synthesis (CFPS) was developed to identify gene products influencing the complex metabolic systems that result in protein accumulation and folding in vitro. The first round of CFPS creates an array of cell extracts individually enriched with a single gene product expressed in-parallel from linear DNA expression templates (ETs). The cell extract is engineered to enhance template stability and to provide reaction conditions conducive for general protein activation. Following first-round expression, linear templates are selectively degraded and a plasmid template for a reporter enzyme is added to initiate a subsequent round of protein expression. Reporter concentration and activity identify first-round gene products that affect amino acid and nucleic acid stability, energy supply, protein expression, stability, and activation. This sequential CFPS system provides a unique format for the functional genomic identification of broadly diverse metabolic activities.     

Back to the future—The value of single protein species investigations

In proteomics, in the past years, there was a focus on high throughput and reaching of large numbers of identified proteins with the basic discourse of protein expression. To avoid the impression of producing pure lists attempts are usually made to correlate proteins changed in amount between two biological situations to different pathways or protein interactions. This discourse is based on two simplifications, which limit the applicability of proteomics drastically: (i) it is sufficient to quantify a protein from several enzymatic digestion products; (ii) a biological situation is sufficiently described, if a peptide with its PTM is identified, resulting in long lists of modified peptides with data amounts, which are not anymore made accessible for the reader of a publication. The elucidation of N‐terminal methylation of proteasome subunit Rpt1 in yeast by Kimura et al. (Proteomics 2013, 13, 3167–3174) , which represents the focus on one protein, shows the value of solid chemical analysis with a complete data documentation and paves the way to proteomics based on the protein speciation discourse.