Interaction between Hydrophilic Ionic Liquid and Phospholipid/Cholesterol Mixed Film.

Surface pressure (π)-area (A) isotherms were studied to analyze the interactions between a hydrophilic ionic liquid (IL) (ethyl(2-hydroxyethyl)dimethylammonium methanesulfonate) and a pure dipalmitoylphosphatidylcholine (DPPC) film or a DPPC-cholesterol mixed film. When the hydrophilic IL was added to an underlayer solution, the isotherm shifted toward higher areas. Intriguingly, when the hydrophilic IL was added, the packing of the film materials became loose and the elastic modulus decreased, resulting in increased flexibility. This phenomenon was most evident under a cholesterol mole fraction of 0.2. This composition resembles that of cell membranes, which typically comprise phospholipids and cholesterol, suggesting that this hydrophilic IL may be able to interact significantly with biological membranes.

Priorities for research in soil ecology.

The ecological interactions that occur in and with soil are of consequence in many ecosystems on the planet. These interactions provide numerous essential ecosystem services, and the sustainable management of soils has attracted increasing scientific and public attention. Although soil ecology emerged as an independent field of research many decades ago, and we have gained important insights into the functioning of soils, there still are fundamental aspects that need to be better understood to ensure that the ecosystem services that soils provide are not lost and that soils can be used in a sustainable way. In this perspectives paper, we highlight some of the major knowledge gaps that should be prioritized in soil ecological research. These research priorities were compiled based on an online survey of 32 editors of Pedobiologia - Journal of Soil Ecology. These editors work at universities and research centers in Europe, North America, Asia, and Australia.The questions were categorized into four themes: (1) soil biodiversity and biogeography, (2) interactions and the functioning of ecosystems, (3) global change and soil management, and (4) new directions. The respondents identified priorities that may be achievable in the near future, as well as several that are currently achievable but remain open. While some of the identified barriers to progress were technological in nature, many respondents cited a need for substantial leadership and goodwill among members of the soil ecology research community, including the need for multi-institutional partnerships, and had substantial concerns regarding the loss of taxonomic expertise.

A quantitative protocol for DNA metabarcoding of springtails (Collembola).

We developed a novel protocol with superior quantitative analysis results for DNA metabarcoding of Collembola, a major soil microarthropod order. Degenerate PCR primers were designed for conserved regions in the mitochondrial cytochrome c oxidase subunit I (mtCOI) and 16S ribosomal RNA (mt16S) genes based on published collembolan mitogenomes. The best primer pair was selected based on its ability to amplify each gene, irrespective of the species. DNA was extracted from 10 natural communities sampled in a temperate forest (with typically 25-30 collembolan species per 10 soil samples) and 10 mock communities (with seven cultured collembolan species). The two gene regions were then amplified using the selected primers, ligated with adapters for 454 technology, and sequenced. Examination of the natural community samples showed that 32 and 36 operational taxonomic units (defined at a 90% sequence similarity threshold) were recovered from the mtCOI and mt16S data, respectively, which were comparable to the results of the microscopic identification of 25 morphospecies. Further, sequence abundances for each collembolan species from the mtCOI and mt16S data of the mock communities, after normalization by using a species as the internal control, showed good correlation with the number of individuals in the samples (R = 0.91-0.99), although relative species abundances within a mock community sample estimated from sequences were skewed from community composition in terms of the number of individuals or biomass of the species. Thus, this protocol enables the comparison of collembolan communities in a quantitative manner by metabarcoding.

Radiocesium immobilization to leaf litter by fungi during first-year decomposition in a deciduous forest in Fukushima.

Vast forest areas in eastern Japan have been contaminated with radio-isotopes by the Fukushima Daiichi Nuclear Power Plant (FDNPP) accident. Radiocesium (radioCs) is known to remain bioavailable in forest ecosystems for a long time, and it is necessary to terminate the cycling process to decontaminate the forest ecosystem. We observed radiocesium concentrations of leaf litter during decomposition on a forest floor where radiocesium ((137)Cs) contamination was ∼155 kBq/m(2). Litter bag experiments were conducted with newly fallen mixed deciduous leaf litter in a deciduous forest (alt. 610 m) about 50 km from the FDNPP. Litter bags were retrieved in April, June, August, October, and December 2012. Fresh litter (137)Cs concentration was ∼3000 Bq/kg in December 2011. During the decomposition process on the forest floor, litter (137)Cs concentration increased rapidly and exceeded 25,000 Bq/kg after 6 months, whereas potassium (K) concentration in the litter was rather stable, indicating that radiocesium and K showed contrasting dynamics during the early decomposition phase. Nitrogen, phosphorus, and (137)Cs contents were positively correlated to fungal biomass, evaluated by phospholipid fatty acids in the litter during decomposition. The increase of radiocesium concentration mainly occurred during from April to October, when fungal growth peaked. Therefore, this suggests fungal translocation of nutrients from outside the litter substrate (immobilization) is the mechanism to increase radiocesium in the decomposing litter. The amount of (137)Cs contained in the 1-year-old decomposed leaf litter was estimated to be 4% per area of the soil-contaminated (137)Cs.

Diversity of Fungi on Decomposing Leaf Litter in a Sugarcane Plantation and Their Response to Tillage Practice and Bagasse Mulching: Implications for Management Effects on Litter Decomposition.

To minimize the degradation of soil organic matter (SOM) content in conventional sugarcane cropping, it is important to understand how the fungal community contributes to SOM dynamics during the decomposition of sugarcane leaf litter. However, our knowledge of fungal diversity in tropical agroecosystems is currently limited. Thus, we determined the fungal community structure on decomposing sugarcane leaf litter and their response to different soil management systems using the internal transcribed spacer region 1 (ITS1) amplicon sequencing method afforded by Ion Torrent Personal Genome Machine (PGM). The results indicate that no-tillage had positive effects on the relative abundance of Zygomycota and of some taxa that may prefer a moist environment over conventional tillage, whereas bagasse mulching decreased the richness of operational taxonomic units (OTUs) and had positive effect on the relative abundance of slow-growing taxa, which may prefer poor nutrient substrates. Furthermore, a combination of no-tillage and bagasse mulching increased the abundance of unique OTUs. We suggest that the alteration of fungal communities through the changes in soil management practices produces an effect on litter decomposition.

Concordance and discordance between taxonomic and functional homogenization: responses of soil mite assemblages to forest conversion.

The compositional characteristics of ecological assemblages are often simplified; this process is termed "biotic homogenization." This process of biological reorganization occurs not only taxonomically but also functionally. Testing both aspects of homogenization is essential if ecosystem functioning supported by a diverse mosaic of functional traits in the landscape is concerned. Here, we aimed to infer the underlying processes of taxonomic/functional homogenization at the local scale, which is a scale that is meaningful for this research question. We recorded species of litter-dwelling oribatid mites along a gradient of forest conversion from a natural forest to a monoculture larch plantation in Japan (in total 11 stands), and collected data on the functional traits of the recorded species to quantify functional diversity. We calculated the taxonomic and functional ß-diversity, an index of biotic homogenization. We found that both the taxonomic and functional ß-diversity decreased with larch dominance (stand homogenization). After further deconstructing ß-diversity into the components of turnover and nestedness, which reflect different processes of community organization, a significant decrease in the response to larch dominance was observed only for the functional turnover. As a result, there was a steeper decline in the functional ß-diversity than the taxonomic ß-diversity. This discordance between the taxonomic and functional response suggests that species replacement occurs between species that are functionally redundant under environmental homogenization, ultimately leading to the stronger homogenization of functional diversity. The insights gained from community organization of oribatid mites suggest that the functional characteristics of local assemblages, which support the functionality of ecosystems, are of more concern in human-dominated forest landscapes.

Biotic homogenization and differentiation of soil faunal communities in the production forest landscape: taxonomic and functional perspectives.

Biotic homogenization has been reported worldwide. Although simplification of communities across space is often significant at larger scales, it could also occur at the local scale by changing biotic interactions. This study aimed to elucidate local community processes driving biotic homogenization of soil faunal communities, and the possibility of biotic re-differentiation. We recorded species of oribatid mites in litter and soil layers along a gradient of forest conversion from monoculture larch plantation to primary forests in central Japan. We collected data for functional traits of the recorded species to quantify functional diversity. Then we quantified their taxonomic/functional turnover. Litter diversity was reduced in the larch-dominated stands, leading to habitat homogenization. Consequently, litter communities were biologically homogenized and differentiated in the plantations and in the natural forest, respectively. Turnover of functional traits for litter communities was lower and higher than expected by chance in the plantations and in the natural stand, respectively. This result suggests that the dominant assembly process shifts from limiting similarity to habitat filtering along the forest restoration gradient. However, support for such niche-based explanations was not observed for communities in the soil layer. In the monocultures, functional diversity expected from a given regional species pool significantly decreased for litter communities but not for those in the soil layer. Such discrepancy between communities in different layers suggests that communities more exposed to anthropogenic stresses are more vulnerable to the loss of their functional roles. Our study explains possible community processes behind the observed patterns of biological organization, which can be potentially useful in guiding approaches for restoring biodiversity.

Biomass estimation of the terrestrial ecotoxicological species Folsomia candida (Collembola) using a real-time polymerase chain reaction.

The abundance and growth of the Folsomia candida soil arthropod have been widely used to assess the environmental impact of a range of soil pollutants, and increasing concerns about environmental pollution require advanced and rapid methods to estimate ecological toxicity. Here, we developed a quantitative polymerase chain reaction (qPCR)-based assay for determining the biomass of F. candida. Prior to DNA extraction, an appropriate amount of an artificial sequence was spiked into the test samples, allowing us to assess the extraction efficiency used for normalisation. We designed primers based on the sequencing information of the nuclear RNA polymerase II (Pol II) and mitochondrial cytochrome c oxidase subunit I (mtCOI) genes of F. candida. Assays were performed on samples containing a different number of individuals at the same body length (individually same biomass; same age) and samples containing the same number of individuals at a different body length (individually different biomass; different age). Biomass was estimated from the body lengths of collembolan samples. For both genes, DNA quantity showed a significant linear relationship between increased collembolan numbers and the estimated biomass; DNA quantity in different ages of collembolans showed a significant correlation with body length and a linear relationship with the estimated biomass. We believe that this rapid and accurate technique could be used to detect and quantify soil animals and thus would improve ecotoxicological testing.

Biomarker responses reveal that food quality affects cadmium exposure in the soil collembolan Folsomia candida.

Food quality affects the food consumption rate, flux through the gut, and exposure to contaminants in animals. This study evaluated the effects of food quality on cadmium exposure in the soil collembolan Folsomia candida. Animals were exposed to constant concentrations of cadmium for 38 h via artificial food consisting of an agar medium with various concentrations of sugar (glucose), total nutrients (baker's yeast), or fungal odour (1-octen-3-ol). The expression of the gene encoding a deduced metallothionein-like motif containing protein was used as a biomarker of cadmium exposure. Glucose concentrations of 2% or higher reduced the expression levels of the biomarker. Within the range of 0.1-8% yeast, medium concentrations led to higher biomarker levels. At high concentrations of 1-octen-3-ol (2000 mg/l), feeding and the biomarker response were reduced. These results suggest that even at equivalent cadmium concentrations, food quality affects cadmium exposure by altering food consumption rates.

Solvation effects with a photoresponsive two-component 12-hydroxystearic acid-azobenzene additive organogel.

A "light-triggerable" azobenzene amine derivative (additive 1) was synthesized and then introduced into organogels of 12-hydroxystearic acid (HSA) in the molar ratio of 1:3. The organogels (HSA/1) consisting of additive 1 and HSA were analyzed by (1)H nuclear magnetic resonance (NMR), Fourier transform-infrared (FT-IR), and X-ray diffraction (XRD). The homogeneity of the gel networks was observed using field emission scanning electron microscopy (FE-SEM). Additive 1 formed a complex with HSA in HSA organogels due to salification between the terminal amine group of additive 1 and the carboxylic acid group of HSA. Additive 1 in the gels of HSA/1 showed the potential for photo-isomerization, and we achieved a reversible control of HSA/1 sol-gel transition in toluene by the alternating irradiation with UV and visible light. Interestingly, the opposite phenomenon was observed in CHCl(3) system, namely, the orange solution of HSA/1 in CHCl(3) was turned to a red-transparent gel by exposure to UV light.

Molecular characterization of fungal communities in non-tilled, cover-cropped upland rice field soils.

This study aimed to characterize soil fungal communities in upland rice fields managed with tillage/non-tillage and winter cover-cropping (hairy vetch and cereal rye) practices, using PCR-based molecular methods. The study plots were maintained as upland fields for 5 years and the soils sampled in the second and fifth years were analyzed using T-RFLP (terminal restriction fragment length polymorphism) profiling and clone libraries with the internal transcribed spacer (ITS) region and domain 1 (D1) of the fungal large-subunit (fLSU) rRNA (D1(fLSU)) as the target DNA sequence. From the 2nd-year-sample, 372 cloned sequences of fungal ITS-D1(fLSU) were obtained and clustered into 80 nonredundant fungal OTUs (operational taxonomic units) in 4 fungal phyla. The T-RFLP profiling was performed with the 2nd- and 5th-year-samples and the major T-RFs (terminal restriction fragments) were identified using a theoretical fragment analysis of the ITS-D1(fLSU) clones. These molecular analyses showed that the fungal community was influenced more strongly by the cover-cropping than tillage practices. Moreover, the non-tilled, cover-cropped soil was characterized by a predominance of Cryptococcus sp. in the phylum Basidiomycota. We provided a genetic database of the fungal ITS-D1(fLSU)s in the differently managed soils of upland rice fields.

The effect of earthworms on copper fractionation of freshly and long-term polluted soils.

We investigated the effects of earthworm activity on the bioavailability of Cu in soil. The bioavailable fraction was estimated using sequential extraction, and the results of diethylenetriaminepentaacetic acid (DTPA) extraction were analyzed for comparison. Changes in the Cu fraction were compared in Cu-spiked soil (high bioavailability) and long-term polluted field soil (low bioavailability) with approximately equivalent total Cu concentrations. Earthworm activity decreased the bioavailable fraction in the Cu-spiked soil, where earthworm body Cu concentrations did not affect the bioavailable fraction. Soil pH was not a factor in the bioavailability differences between soils with and without earthworms in this study. The bioavailable fraction appears to be more heavily affected by biological and physical mechanisms than by soil pH. The two extraction methods showed different trends; the bioavailable fraction method was better than DTPA extraction, because the former gives clear insight into the aging process of Cu in soil.

Effects of acute gamma irradiation on Folsomia candida (Collembola) in a standard test.

An understanding of the effects of ionizing radiation on non-human biota is required by the International Commission on Radiological Protection for the radiological protection of the environment. We examined dose-effect relationships for gamma radiation on survival, growth, and reproduction in the soil invertebrate Folsomia candida (Collembola) in a standard laboratory test. F. candida were acutely irradiated at increasing doses of gamma radiation, and subsequent survival, growth in body length, and number of neonates produced by irradiated specimens were examined. The 50% lethal dose was at 1356 Gy, and the 10% and 50% effective doses (ED10 and ED50) for growth were at 32 and 144 Gy, respectively. The ED10 and ED50 values for reproduction were at 7.1 and 21.9 Gy, respectively. These data establish important baselines for the radiological protection of terrestrial ecosystems based on scientific principles.

Archaeal Diversity of Upland Rice Field Soils Assessed by the Terminal Restriction Fragment Length Polymorphism Method Combined with Real Time Quantitative-PCR and a Clone Library Analysis.

The PCR amplification-based analysis of microbial diversity is subject to potential problems. In this study, to minimize the bias toward a 1:1 ratio in multitemplate PCR, a real-time PCR assay was carried out using a quenching fluorescence dye primer and amplification efficiency was monitored. Then terminal-restriction fragment length polymorphism (T-RFLP) profiling was performed using the PCR product with minimized PCR bias. This method was applied to an analysis of the diversity of the archaeal community in an upland rice field under different tillage systems and winter cover cropping. Terminal restriction fragments (T-RFs) of PCR-amplified archaeal 16S rRNA genes were assigned to the gene sequences recovered from the same soil by using an archaeal 16S rRNA gene clone library. Our results indicated that soil archaeal members were not influenced but the relative abundance of archaeal species particularly those belonging to Crenarchaeota which changed between the tillage and non-tillage treatments.

Species-specific heavy metal accumulation patterns of earthworms on a floodplain in Japan.

We identified all earthworm species found on a floodplain contaminated by heavy metals (Cu, Zn, Cd, and Pb) from an old mine in central Japan and compared their abundance, biomass, and heavy metal concentrations in tissue. There were six species belonging to three families: Megascolecidae, Moniligastridae, and Lumbricidae. Earthworm community structure seemed to be influenced mostly by soil properties, especially pH and clay fraction. Despite the same endogeic characteristics, species-specific patterns of heavy metal accumulation were observed: species in Megascolecidae and Lumbricidae had relatively lower concentrations compared to those in Moniligastridae. Within Moniligastridae, Drawida sp. accumulated Cu and Pb markedly higher than Drawida japonica. Based on heavy metal concentrations in extracts of CaCl(2) and diethylenetriaminepentaacetic acid, the aging caused remarkably low concentrations in pore water, indicating low availability by dermal uptake. Therefore the different patterns of heavy metal accumulation among species would partly result from species-specific gut process.