Variation of sperm morphology in Pacific oyster precludes its use as a species marker but enables intraspecific geo-authentification and aquatic monitoring

According to recent reports, shell morphology is unreliable for the identification of oysters because of the high phenotypic plasticity of these bivalves. Using COI DNA barcoding and sperm morphology, we reinvestigated the species validity of wild Pacific oyster Crassostrea gigas habituating the Peter the Great Bay (Sea of Japan). DNA barcoding confirmed the species validity of samples collected. Application of the single sperm pattern was not possible for species identification due to pronounced sperm plasticity being found. Six sperm morphs were discovered in the testes of each oyster collected. The amount of abundant sperm morphs and the type of the most dominant sperm pattern are particular to geographical localities that are individual depending on the environmental factors. Ecological monitoring of marine areas and commercially assigned intraspecific geo-authentification of the Pacific oyster seems possible based on the analysis of this species’ heterogenic sperm. Further work will be needed to test if sperm heterogeneity exists in other Ostreidae species and if heterogenic sperms could be used for interspecific analysis.     

IPD3 controls the formation of nitrogen-fixing symbiosomes in pea and Medicago Spp

A successful nitrogen-fixing symbiosis requires the accommodation of rhizobial bacteria as new organelle-like structures, called symbiosomes, inside the cells of their legume hosts. Two legume mutants that are most strongly impaired in their ability to form symbiosomes are sym1/TE7 in Medicago truncatula and sym33 in Pisum sativum. We have cloned both MtSYM1 and PsSYM33 and show that both encode the recently identified interacting protein of DMI3 (IPD3), an ortholog of Lotus japonicus (Lotus) CYCLOPS. IPD3 and CYCLOPS were shown to interact with DMI3/CCaMK, which encodes a calcium- and calmodulin-dependent kinase that is an essential component of the common symbiotic signaling pathway for both rhizobial and mycorrhizal symbioses. Our data reveal a novel, key role for IPD3 in symbiosome formation and development. We show that MtIPD3 participates in but is not essential for infection thread formation and that MtIPD3 also affects DMI3-induced spontaneous nodule formation upstream of cytokinin signaling. Further, MtIPD3 appears to be required for the expression of a nodule-specific remorin, which controls proper infection thread growth and is essential for symbiosome formation.     

Conformational Studies of a Melittin—Inhibitor Complex

The conformation of a melittin—inhibitor complex was studied by solution NMR, solid-state NMR, and circular dichroism. In solution, binding was studied by titrating inhibitor against melittin in dimethyl sulfoxide, methanol, aqueous buffer, and dodecylphosphocholine micelles. The change in chemical shift of Trp19 resonances and the formation of a precipitate at 1:1 molar ratio indicated that the inhibitor was bound to melittin. Solid-state NMR also showed a change in chemical shift of two labeled carbons of melittin near Pro14 and a change in ¹H T ₁ relaxation times when complexed with inhibitor. Rotational resonance experiments of melittin labeled in the proline region indicated a change in conformation for melittin complexed with inhibitor. This observation was also supported by circular dichroism measurements, indicating a reduction in α-helical structure for increasing ratios of inhibitor bound to melittin.     

Carbon sequestration and turnover in soil under the energy crop Miscanthus: repeated 13C natural abundance approach and literature synthesis

The stability and turnover of soil organic matter (SOM) are a very important but poorly understood part of carbon (C) cycling. Conversion of C₃ grassland to the C₄ energy crop Miscanthus provides an ideal opportunity to quantify medium‐term SOM dynamics without disturbance (e.g., plowing), due to the natural shift in the δ¹³C signature of soil C. For the first time, we used a repeated ¹³C natural abundance approach to measure C turnover in a loamy Gleyic Cambisol after 9 and 21 years of Miscanthus cultivation. This is the longest C₃–C₄ vegetation change study on C turnover in soil under energy crops. SOM stocks under Miscanthus and reference grassland were similar down to 1 m depth. However, both increased between 9 and 21 years from 105 to 140 mg C ha^?1 (P < 0.05), indicating nonsteady state of SOM. This calls for caution when estimating SOM turnover based on a single sampling. The mean residence time (MRT) of old C (>9 years) increased with depth from 19 years (0–10 cm) to 30–152 years (10–50 cm), and remained stable below 50 cm. From 41 literature observations, the average SOM increase after conversion from cropland or grassland to Miscanthus was 6.4 and 0.4 mg C ha^?1, respectively. The MRT of total C in topsoil under Miscanthus remained stable at ~60 years, independent of plantation age, corroborating the idea that C dynamics are dominated by recycling processes rather than by C stabilization. In conclusion, growing Miscanthus on C‐poor arable soils caused immediate C sequestration because of higher C input and decreased SOM decomposition. However, after replacing grasslands with Miscanthus, SOM stocks remained stable and the MRT of old C₃‐C increased strongly with depth.     

Stimulation of r- vs. K-selected microorganisms by elevated atmospheric CO2 depends on soil aggregate size

Increased root exudation under elevated atmospheric CO₂ and the contrasting environments in soil macro- and microaggregates could affect microbial growth strategies. We investigated the effect of elevated CO₂ on the contribution of fast- ( r -strategists) and slow-growing ( K -strategists) microorganisms in soil macro- and microaggregates. We fractionated the bulk soil from the ambient and elevated (for 5 years) CO₂ treatments of FACE-Hohenheim (Stuttgart) into large macro- (>2 mm), small macro- (0.25–2.00 mm), and microaggregates (<0.25 mm) using 'optimal moist' sieving. Microbial biomass (C_mic), the maximum specific growth rate (μ), growing microbial biomass (GMB) and lag-period ( t _lag) were estimated by the kinetics of CO₂ emission from bulk soil and aggregates amended with glucose and nutrients. Although C_org and C_mic were unaffected by elevated CO₂, μ values were significantly higher under elevated than ambient CO₂ for bulk soil, small macroaggregates, and microaggregates. Substrate-induced respiratory response increased with decreasing aggregate size under both CO₂ treatments. Based on changes in μ, GMB and lag period, we conclude that elevated atmospheric CO₂ stimulated the r- selected microorganisms, especially in soil microaggregates. Such an increase in r -selected microorganisms indicates acceleration of available C mineralization in soil, which may counterbalance the additional C input by roots in soils in a future elevated atmospheric CO₂ environment.     

Thermodynamic examination of 1- to 5-nt purine bulge loops in RNA and DNA constructs

Bulge loops are common features of RNA structures that are involved in the formation of RNA tertiary structures and are often sites for interactions with proteins and ions. Minimal thermodynamic data currently exist on the bulge size and sequence effects. Using thermal denaturation methods, thermodynamic properties of 1- to 5-nt adenine and guanine bulge loop constructs were examined in 10 mM MgCl₂ or 1 M KCl. The ΔG37∘ loop parameters for 1- to 5-nt purine bulge loops in RNA constructs were between 3.07 and 5.31 kcal/mol in 1 M KCl buffer. In 10 mM magnesium ions, the ΔΔG° values relative to 1 M KCl were 0.47–2.06 kcal/mol more favorable for the RNA bulge loops. The ΔG37∘ loop parameters for 1- to 5-nt purine bulge loops in DNA constructs were between 4.54 and 5.89 kcal/mol. Only 4- and 5-nt guanine constructs showed significant change in stability for the DNA constructs in magnesium ions. A linear correlation is seen between the size of the bulge loop and its stability. New prediction models are proposed for 1- to 5-nt purine bulge loops in RNA and DNA in 1 M KCl. We show that a significant stabilization is seen for small bulge loops in RNA in the presence of magnesium ions. A prediction model is also proposed for 1- to 5-nt purine bulge loop RNA constructs in 10 mM magnesium chloride.