Biodiversity of soil biota and plants in abandoned arable fields and grasslands under restoration management

The currently widespread abandoning of agricultural land use in Western Europe offers new opportunities for ecological restoration and nature conservation. This is illustrated for abandoned arable fields and for permanent grasslands cut for hay after the cessation of fertilizer application. Although initiated by a sudden reduction of nutrient input to the system, the changing nutrient supply from the soil is considered to be the main driving force of succession. The soil nutrient supply is affected by soil organisms, both directly (root symbionts and herbivores) and indirectly (nutrient mineralization from dead organic matter). It is argued that because of the close association of changes in species diversity with changes in the functioning of ecosystems, biodiversity has to be studied in an ecosystem ecology context.     

Photophysiology and phytochrome content of long-hypocotyl mutant and wild-type cucumber seedlings

Photomorphogenetic responses have been studied in a cucumber (Cucumis sativus L.) mutant (lh), which has long hypocotyls in white light (WL). While etiolated seedlings of this mutant have a similar phytochrome content and control of hypocotyl elongation as wild type, deetiolation is retarded and WL-grown seedlings show reduced phytochrome control. Spectrophotometric measurements exhibit that WL-grown tissues of the lh mutant (flower petals and Norflurazon-bleached leaves) contain 35 to 50% of the phytochrome level in the wild type. We propose that this is a consequence of a lack of light-stable phytochrome, in agreement with our hypothesis proposed on the basis of physiological experiments. The lh mutant lacks an end-of-day far-red light response of hypocotyl elongation. This enables the end-of-day far-red light response, clearly shown by the wild type, to be ascribed to the phytochrome, deficient in the lh mutant. Growth experiments in continuous blue light (BL) and continuous BL + red light (RL) show that when RL is added to BL, hypocotyl growth remains inhibited in the wild type, whereas the lh mutant exhibits significant growth promotion compared to BL alone. It is proposed that the hypocotyls fail to grow long in low fluence rate BL because photosynthesis is insufficient to sustain growth.     

Plasmid-borne Tn5 insertion mutation resulting in accumulation of gentisate from salicylate.

Plasmid-borne Tn5 insertion mutants of a Pseudomonas species which accumulated 2,5-dihydroxybenzoate (gentisate) following growth on 2-hydroxybenzoate (salicylate) were obtained from a pool of mutants that were unable to grow on naphthalene. One such mutant was characterized further. The ability of this mutant to oxidize gentisate was 100-fold less than the ability of a Nah+ Sal+ strain harboring the unmutagenized plasmid, although both strains oxidized and grew on salicylate. These bacteria were presumably able to metabolize salicylate via catechol, since they possessed an inducible, plasmid-encoded catechol 2,3-dioxygenase. Our results suggest that there is an alternate, plasmid-encoded route of salicylate degradation via gentisate and that some plasmid-associated relationship between this pathway and naphthalene oxidation exists.     

Ancient paralogy in the cpDNA trnL-F region in Annonaceae: implications for plant molecular systematics

The plastid trnL-F region has proved useful in molecular phylogenetic studies addressing diverse evolutionary questions from biogeographic history to character evolution in a broad range of plant groups. An important assumption for phylogenetic reconstruction is that data used in combined analyses contain the same phylogenetic signal. The trnL-F region is often used in combined analyses of multiple chloroplast markers. These markers are assumed to contain congruent phylogenetic signal due to lack of recombination. Here we show that trnL-F sequences display a phylogenetic signal conflicting with that of other chloroplast markers in Annonaceae, and we demonstrate that this conflict results from ancient paralogy. TrnL-F copy 2 diverged from trnL-F copy 1 (as used in family-wide phylogenetic analyses) in a direct ancestor of the Annonaceae. Although this divergence dates back 88 million years or more, the exons of both copies appear to be intact. In this case, assuming that (putative) chloroplast markers contain the same phylogenetic signal results in an incorrect topology and an incorrect estimate of ages. Our study demonstrates that researchers should be cautious when interpreting gene phylogenies, irrespective of the genome from which they are presumed to have been sampled.     

Sex differences in oxytocin receptor binding in forebrain regions: Correlations with social interest in brain region- and sex- specific ways

Social interest reflects the motivation to approach a conspecific for the assessment of social cues and is measured in rats by the amount of time spent investigating conspecifics. Virgin female rats show lower social interest towards unfamiliar juvenile conspecifics than virgin male rats. We hypothesized that the neuropeptide oxytocin (OT) may modulate sex differences in social interest because of the involvement of OT in pro-social behaviors. We determined whether there are sex differences in OT system parameters in the brain and whether these parameters would correlate with social interest. We also determined whether estrus phase or maternal experience would alter low social interest and whether this would correlate with changes in OT system parameters. Our results show that regardless of estrus phase, females have significantly lower OT receptor (OTR) binding densities than males in the majority of forebrain regions analyzed, including the nucleus accumbens, caudate putamen, lateral septum, bed nucleus of the stria terminalis, medial amygdala, and ventromedial hypothalamus. Interestingly, male social interest correlated positively with OTR binding densities in the medial amygdala, while female social interest correlated negatively with OTR binding densities in the central amygdala. Proestrus/estrus females showed similar social interest to non-estrus females despite increased OTR binding densities in several forebrain areas. Maternal experience had no immediate or long-lasting effects on social interest or OT brain parameters except for higher OTR binding in the medial amygdala in primiparous females. Together, these findings demonstrate that there are robust sex differences in OTR binding densities in multiple forebrain regions of rats and that OTR binding densities correlate with social interest in brain region- and sex-specific ways.     

Exopolysaccharides produced by Lactococcus lactis: from genetic engineering to improved rheological properties?

Over the last years, important advances have been made in the study of the production of exopolysaccharides (EPS) by several lactic acid bacteria, including Lactococcus lactis. From different EPS-producing lactococcal strains the specific eps gene clusters have been characterised. They contain eps genes, which are involved in EPS repeating unit synthesis, export, polymerisation, and chain length determination. The function of the glycosyltransferase genes has been established and the availability of these genes opened the way to EPS engineering. In addition to the eps genes, biosynthesis of EPS requires a number of housekeeping genes that are involved in the metabolic pathways leading to the EPS-building blocks, the nucleotide sugars. The identification and characterisation of several of these housekeeping genes (galE, galU, rfbABCD) allows the design of metabolic engineering strategies that should lead to increased EPS production levels by L. lactis. Finally, model developme nt has been initiated in order to predict the physicochemical consequences of the addition of a EPS to a product.     

Impact of herbivores on nitrogen cycling: contrasting effects of small and large species

Herbivores are reported to slow down as well as enhance nutrient cycling in grasslands. These conflicting results may be explained by differences in herbivore type. In this study we focus on herbivore body size as a factor that causes differences in herbivore effects on N cycling. We used an exclosure set-up in a floodplain grassland grazed by cattle, rabbits and common voles, where we subsequently excluded cattle and rabbits. Exclusion of cattle lead to an increase in vole numbers and a 1.5-fold increase in net annual N mineralization at similar herbivore densities (corrected to metabolic weight). Timing and height of the mineralization peak in spring was the same in all treatments, but mineralization in the vole-grazed treatment showed a peak in autumn, when mineralization had already declined under cattle grazing. This mineralization peak in autumn coincides with a peak in vole density and high levels of N input through vole faeces at a fine-scale distribution, whereas under cattle grazing only a few patches receive all N and most experience net nutrient removal. The other parameters that we measured, which include potential N mineralization rates measured under standardized laboratory conditions and soil parameters, plant biomass and plant nutrient content measured in the field, were the same for all three grazing treatments and could therefore not cause the observed difference. When cows were excluded, more litter accumulated in the vegetation. The formation of this litter layer may have added to the higher mineralization rates under vole grazing, through enhanced nutrient return through litter or through modification of microclimate. We conclude that different-sized herbivores have different effects on N cycling within the same habitat. Exclusion of large herbivores resulted in increased N annual mineralization under small herbivore grazing.     

Germination and early establishment of lower salt-marsh species in grazed and mown salt marsh

Abstract. Lower salt-marsh species occur more in the grazed than in the mown sites of a salt marsh in Schiermonnikoog in the Netherlands. This was demonstrated by a sowing experiment which determined which characteristic of the stand structure, height of the canopy or percentage of bare soil, is responsible for this difference. The total number of seedlings which emerged was negatively related to the height of the canopy and positively to the percentage of bare soil. The survival of seedlings of Suaeda maritima and Plantago maritima could be explained by the height of the canopy and for the latter species also by the percentage of bare soil. The survival of Aster tripolium and Plantago maritima was higher in grazed than in mown sites. Since the amount of bare soil was higher than seemed necessary for germination and survival, it was concluded that the taller canopy was responsible for the absence of lower salt-marsh species in the mown sites.     

Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis

The multispecies coalescent provides an elegant theoretical framework for estimating species trees and species demographics from genetic markers. However, practical applications of the multispecies coalescent model are limited by the need to integrate or sample over all gene trees possible for each genetic marker. Here we describe a polynomial-time algorithm that computes the likelihood of a species tree directly from the markers under a finite-sites model of mutation effectively integrating over all possible gene trees. The method applies to independent (unlinked) biallelic markers such as well-spaced single nucleotide polymorphisms, and we have implemented it in SNAPP, a Markov chain Monte Carlo sampler for inferring species trees, divergence dates, and population sizes. We report results from simulation experiments and from an analysis of 1997 amplified fragment length polymorphism loci in 69 individuals sampled from six species of Ourisia (New Zealand native foxglove).