Minimum reporting standards for plant biology context information in metabolomic studies

Plant metabolomics has matured over the past 8 years. Plant biologists routinely use comprehensive analyses of plant metabolites to discover new responses to genetic or environmental perturbation, or to validate initial hypotheses on the function and in vivo action of gene products. The wealth of scientific findings has increasingly provoked interest to share and review raw or processed data from plant metabolomics reports. We here suggest a minimum of parameters to be reported in order to define details of experimental study designs in plant metabolomics studies.     

Trait–performance relationships of grassland plant species differ between common garden and field conditions

The way functional traits affect growth of plant species may be highly context‐specific. We asked which combinations of trait values are advantageous under field conditions in managed grasslands as compared to conditions without competition and land‐use. In a two‐year field experiment, we recorded the performance of 93 species transplanted into German grassland communities differing in land‐use intensity and into a common garden, where species grew unaffected by land‐use under favorable conditions regarding soil, water, and space. The plants’ performance was characterized by two independent dimensions (relative growth rates (RGR) of height and leaf length vs. aboveground biomass and survival) that were differently related to the eight focal key traits in our study (leaf dry matter content (LDMC), specific leaf area (SLA), height, leaf anatomy, leaf persistence, leaf distribution, vegetative reproduction, and physical defense). We applied multivariate procrustes analyses to test for the correspondence of the optimal trait–performance relationships between field and common garden conditions. RGRs were species‐specific and species ranks of RGRs in the field, and the common garden were significantly correlated. Different traits explained the performance in the field and the common garden; for example, leaf anatomy traits explained species performance only in the field, whereas plant height was found to be only important in the common garden. The ability to reproduce vegetatively, having leaves that are summer‐persistent and with high leaf dry matter content (LDMC) were traits of major importance under both settings, albeit the magnitude of their influence differed slightly between the field and the common garden experiment. All optimal models included interactions between traits, pointing out the necessity to analyze traits in combination. The differences between field and common garden clearly demonstrate context dependency of trait‐based growth models, which results in limited transferability of favorable trait combinations between different environmental settings.     

A new species of Schoutedenichia Jadin & Vercammen-Grandjean, 1954 from Madagascar and a re-description of S. dutoiti (Radford, 1948) from South Africa (Acariformes: Trombiculidae)

A new chigger mite species, Schoutedenichia microcebi n. sp. is described from the grey mouse lemur Microcebus murinus (J.F. Miller) from Madagascar. The new species is closely related to S. dutoiti (Radford, 1948), a species described from a single specimen collected on a rodent in South Africa. Examination of the holotype and new material on S. dutoiti from South Africa enabled us to re-describe this species and provide new data on its hosts and geographical distribution.

     

Nitrogen dynamics and soil nitrate retention in a <Emphasis Type="Italic">Coffea arabica</Emphasis>—<Emphasis Type="Italic">Eucalyptus deglupta</Emphasis> agroforestry system in Southern Costa Rica

Nitrogen fertilization is a key factor for coffee production but creates a risk of water contamination through nitrate (NO₃⁻) leaching in heavily fertilized plantations under high rainfall. The inclusion of fast growing timber trees in these coffee plantations may increase total biomass and reduce nutrient leaching. Potential controls of N loss were measured in an unshaded coffee (Coffea arabica L.) plot and in an adjacent coffee plot shaded with the timber species Eucalyptus deglupta Blume (110 trees ha⁻¹), established on an Acrisol that received 180 kg N ha⁻¹ as ammonium-nitrate and 2,700 mm yr⁻¹ rainfall. Results of the one year study showed that these trees had little effect on the N budget although some N fluxes were modified. Soil N mineralization and nitrification rates in the 0–20 cm soil layer were similar in both systems (≈280 kg N ha⁻¹ yr⁻¹). N export in coffee harvest (2002) was 34 and 25 kg N ha⁻¹ yr⁻¹ in unshaded and shaded coffee, and N accumulation in permanent biomass and litter was 25 and 45 kg N ha⁻¹ yr⁻¹, respectively. The losses in surface runoff (≈0.8 kg mineral N ha⁻¹ yr⁻¹) and N₂O emissions (1.9 kg N ha⁻¹ yr⁻¹) were low in both cases. Lysimeters located at 60, 120, and 200 cm depths in shaded coffee, detected average concentrations of 12.9, 6.1 and 1.2 mg NO₃⁻-N l⁻¹, respectively. Drainage was slightly reduced in the coffee-timber plantation. NO₃⁻ leaching at 200 cm depth was about 27 ± 10 and 16 ± 7 kg N ha⁻¹ yr⁻¹ in unshaded and shaded coffee, respectively. In both plots, very low NO₃⁻ concentrations in soil solution at 200 cm depth (and in groundwater) were apparently due to NO₃⁻ adsorption in the subsoil but the duration of this process is not presently known. In these conventional coffee plantations, fertilization and agroforestry practices must be refined to match plant needs and limit potential NO₃⁻ contamination of subsoil and shallow soil water.     

Nuclear insertions of organellar DNA can create novel patches of functional exon sequences

Recent nuclear transfer of organellar DNA is thought to result mainly in nonfunctional nuclear sequences or in genetic dysfunction. Here we show that nuclear exons encoding novel protein sequences can be generated by insertions of organellar DNA. Most of the protein sequences do not correspond to preexisting organellar coding sequences or they represent markedly reshaped protein domains, reflecting the recruitment and adaptation of encoded proteins to new functions. Organelle-derived DNA insertions might be responsible for many more ancient functional exon acquisitions that are not directly detectable.