Nematode diversity,food web condition,and chemical and physical properties in different soil habitats of an organic farm

The aim of this paper was to assess biodiversity among different habitats of an organic farm and the relationships between some soil properties, nematode taxonomic diversity, and soil food web condition. Eight habitats were studied in the farm: ponds, ditches, a riparian corridor, hedgerows, and four agricultural fields (mustard, oats, fallow, and legumes). The undisturbed riparian corridor had higher soil and concentrations, and potentially mineralizable N and higher abundances of bacterivore nematodes and longer food webs. Canonical correlation analysis showed associations between habitats and nematode trophic groups: predatory and bacterial-feeding nematodes in the riparian corridor and hedgerows, omnivore nematodes in the ponds and ditches, and fungal-feeding nematodes in the legume field. Soil chemical and physical properties mirrored the aboveground farm patterns and were more similar among habitats that were or had been cultivated, compared to the riparian corridor. Soil food web indices, based on functional analysis of nematode faunal composition, reflected the aboveground landscape heterogeneity. Discriminant analysis indicated that soil food web indices separated the two most disturbed habitats (ponds and tailwater ditches) from the two least disturbed habitats (the riparian corridor and hedgerows). The indices correlated with soil functioning as inferred by soil properties. Abundance of nematode taxa was not associated with aboveground landscape patterns. The complexity of the soil food web may have been influenced by (1) environmental factors that differed between years, (2) different time periods since disturbance in the various habitats, and (3) movement of nutrients and organisms by water flow between habitats in the farmscale.     

Effects of nitrogen fertilizer application rates on nitrate nitrogen distribution in saline soil in the Hai River Basin,China

Background and Objectives  

Soil nitrate nitrogen (NO₃ ⁻-N) accumulation is related closely to NO₃ ⁻ leaching, which is an important issue in groundwater pollution, especially in intensive agricultural areas with saline soils where volumes of water are used in irrigation to avoid salt accumulation in the root zone. However, in the saline environment in Hai River Basin, China, the importance of detailed research into NO₃ ⁻-N distribution in the root zone has not been adequately recognized. Considering the impacts of eco-environmental system N and crop production, the present study aimed at contributing to an understanding of the effects of N application rate on soil NO₃ ⁻-N distribution, NO₃ ⁻-N residue, N loss, and maize (Zea mays L.) yield in this region.     

Polymorphisms of the <Emphasis Type="Italic">FT</Emphasis> gene as a tool to identify underground rhizome types of bamboos

The Flowering Locus T (FT)-like genes of angiosperms are highly conserved. The FT-encoded proteins include a phosphatidylethanolamine-binding domain that is involved in the control of the shoot apical meristem identity and flowering time. In the present study, FT genes were investigated in 20 bamboo species that are grouped into sympodial, mixed and scattered bamboos based on their morphology. All examined orthologous FT genes consisted of four exons and three introns. Their encoded protein sequences contained the critical amino acid residues Tyr85, Glu109, Leu128, Tyr134, Trp138, Arg139, Gln140 and Asn152, of which each possesses a biological function. The DNA sequences were rich in single nucleotide polymorphism (SNP) sites. The SNP frequency was 1 SNP/16.8 bp, and the nucleotide diversity (π) equaled 0.265. Some SNPs altered restriction enzyme sites or resulted in changes in amino acid contents. The correlation analysis showed that several SNPs were informative in relation to the underground rhizome types of bamboos. Therefore, FT polymorphisms could be used as a tool to identify the underground rhizome types of bamboos. The phylogenetic tree constructed based on the FT gene sequences showed that the obtained clustering was consistent with the underground rhizome types. The SNP markers developed in the present study will provide information on the genetic diversity of bamboos and they can aid taxonomic study as well.     

Promoter anchored amplified polymorphism based on random amplified polymorphic DNA (PAAP-RAPD) in cotton

Non-coding sequences account for a majority of the higher plant genome, some of which have important effects in gene regulation and plant development. In an effort to develop molecular marker systems to search for polymorphisms associated with high fiber yield and quality in cotton, we have developed a methodology that could specifically target the regulatory regions of the cotton genome. In this study we designed 10-nucleotide degenerate promoter primers based on conserved core promoter sequences and tested their applicability in PCR amplifications in combination with 10-mer random amplified polymorphic DNA (RAPD) primers. The amplified markers are called promoter anchored amplified polymorphism based on RAPD (PAAP-RAPD). Forty cotton genotypes with diverse genetic and geographical backgrounds were used to test the PAAP-RAPD system using polyacrylamide gel electrophoresis. Based on PAAP-RAPD markers amplified from 12 primer combinations, the 40 genotypes were classified into five distinctive groups: two Upland cotton (Gossypium hirsutum) groups from China, another two Upland cotton groups from the USA, and one group from American Pima cotton (G. barbadense). The groupings are in general consistent with their genetic and geographical origins. Thirty-six PAAP-RAPD and RAPD fragments were cloned and four of them were further subjected to sequence analysis. Signal scanning using software PLACE confirmed that they contained an array of cis-regulatory sequences in addition to the core promoter sequences. The results demonstrate the potential application of PAAP-RAPD as a new marker system specifically targeting regulatory regions of the plant genome.     

Landscape genetics of the foundational salt marsh plant species black needlerush (<Emphasis Type="Italic">Juncus roemerianus</Emphasis> Scheele) across the northeastern Gulf of Mexico

Context

Common species important for ecosystem restoration stand to lose as much genetic diversity from anthropogenic habitat fragmentation and climate change as rare species, but are rarely studied. Salt marshes, valuable ecosystems in widespread decline due to human development, are dominated by the foundational plant species black needlerush (Juncus roemerianus Scheele) in the northeastern Gulf of Mexico.

Objectives

We assessed genetic patterns in J. roemerianus by measuring genetic and genotypic diversity, and characterizing population structure. We examined population connectivity by delineating possible dispersal corridors, and identified landscape factors influencing population connectivity.

Methods

A panel of 19 microsatellite markers was used to genotype 576 samples from ten sites across the northeastern Gulf of Mexico from the Grand Bay National Estuarine Research Reserve (NERR) to the Apalachicola NERR. Genetic distances (F_ST and D_ch) were used in a least cost transect analysis (LCTA) within a hierarchical model selection framework.

Results

Genetic and genotypic diversity results were higher than expected based on life history literature, and samples structured into two large, admixed genetic clusters across the study area, indicating sexual reproduction may not be as rare as predicted in this clonal macrophyte. Digitized coastal transects buffered by 500 m may represent possible dispersal corridors, and developed land may significantly impede population connectivity in J. roemerianus.

Conclusions

Results have important implications for coastal restoration and management that seek to preserve adaptive potential by sustaining natural levels of genetic diversity and conserving population connectivity. Our methodology could be applied to other common, widespread and understudied species.

     

Genotypic variation for cellular thermotolerance in <Emphasis Type="Italic">Aegilops tauschii</Emphasis> Coss., the D genome progenitor of wheat

Corn leaf aphids (Rhopalosiphum maidis Fitch) are found throughout the year on maize in Hawaii and occasionally cause yield loss. Sweet corn inbred Hi38-71 was observed to have high field resistance to aphids and was chosen for this genetic study. An artificial infestation technique was developed using hair-pin clip cages (2.2 cm diameter) which we devised and built. The cages were applied to field-grown plants into which three wingless viviparous adults were placed. Aphid populations were classified on a 1–10 rating scale after about 2 weeks based on digital images of the cages. Mean aphid coverage ratings were 2.97 for the resistant parent and 7.28 for the susceptible parent (representing >200 insects per cage). The F₁ hybrids showed similar susceptibility (6.72), showing resistance to be recessive in nature. Six generations of the cross between Hi38-71 and susceptible inbred Hi27 were artificially infested to provide a generation mean analysis of 360 treated plants over two growing seasons. A joint scaling test showed that the fit to a 3-parameter additive-dominance model satisfactorily explained the observed variability with no assumed linkage or epistasis. We conclude that resistance to corn leaf aphid in Hi38-71 is conferred by a single recessive gene labeled aph. These results concur with a previous study under uncontrolled natural infestation in a single environment. The hair-pin clip cage method was most effective in distinguishing resistant and susceptible genotypes under diverse natural growing conditions in Hawaii.     

Estimation of the spawning grounds of chub mackerel <Emphasis Type="Italic">Scomber japonicus</Emphasis> and spotted mackerel <Emphasis Type="Italic">Scomber australasicus</Emphasis> in the East China Sea based on catch statistics and biometric data

The spawning grounds of the chub mackerel (Scomber japonicus) and spotted mackerel (Scomber australasicus) in the East China Sea were estimated based on catch statistics of the Japanese large- and medium-type purse seine fishery from 1992 to 2006. Biometric data were obtained from specimens caught by purse seiners in the East China Sea from 1998 to 2006. Gonadosomatic index (GSI) at 50% sexual maturity of chub mackerel and spotted mackerel females was 2.5 and 2.6, respectively. Using this criterion for GSI, chub mackerel larger than 275 mm and spotted mackerel larger than 310 mm in fork length were considered to be mature. Mature chub mackerel was observed in the area of 15–22°C sea surface temperature (SST), and mature spotted mackerel was observed in the area of 17–25°C SST. The spawning period of chub mackerel ranged from February to June, and that of spotted mackerel ranged from February to May in the East China Sea. The spawning grounds were estimated from the distributions of catch per unit effort (CPUE) of spawners and SST. As a result, the spawning ground of chub mackerel was estimated to be in the central and southern part of the East China Sea and the area west of Kyushu in February, March, and April, and in the central part of the East China Sea, the area west of Kyushu and Tsushima Straight in May, and in Tsushima Straight and western part of the Sea of Japan in June. The spawning ground of spotted mackerel was estimated to be in the central and southern part of the East China Sea and southern coastal area of Kyushu in February, March, and April, and the central and southern part of the East China Sea and the area west of Kyushu in May.     

Ethoxylated rapeseed oil derivatives as novel adjuvants for herbicides

Ethoxylates of rapeseed oil and of methylated rapeseed oil were synthesized and tested as adjuvants for 2,4-D and phenmedipham. Provided they had less than 6 units of ethylene oxide (EO), 1.0 to 10 g litre(-1) ethoxylates in water induced droplet spreading on barley leaves. In an acetone-based medium all derivatives strongly promoted the foliar uptake of 2,4-D, with no clear influence of the ethoxylation degree. In the same medium there was a negative influence of ethoxylate chain length on the foliar uptake of phenmedipham. In a water-based medium, phenmedipham applied with rapeseed oil emulsified with ethoxylated (20 EO) rapeseed oil displayed uptake rates close to a commercial preparation. The same was true for phenmedipham applied with ethoxylated (2 EO) methylated rapeseed oil. In bioassays, phenmedipham prepared with methylated rapeseed oil emulsified with ethoxylated (20 EO) rapeseed oil was as efficacious on barley as a commercial formulation. The same was true for phenmedipham prepared with ethoxylated (2 EO) methylated rapeseed oil. However, neither rapeseed oil nor methylated rapeseed oil emulsified with ethoxylated (2 EO) methylated rapeseed oil conferred good efficacy to phenmedipham. Hence, ethoxylated rapeseed oil derivatives are promising adjuvants or formulants for herbicides.     

Variability of the quality and quantity of organic matter in soil affected by multiple wildfires

Purpose

Fire in mountainous areas can lead to increased variability of their soil organic matter (SOM) due to spatial inhomogeneity and pre-fire fuel distribution. Here, we elucidated if this was the case in our study area and how this affected the reliability of solid-state ¹³C NMR spectroscopy applied for the study of the medium-term impact of fire on SOM

Materials and methods

The study occurred in the Sierra de Aznalcóllar, Southern Spain, which experienced their last intense fire 7 years before sampling. In a first approach (method 1), the corners and the center of a randomly chosen square with a side length of 15 m were sampled and analyzed separately. For comparison, composite samples (method 2) were obtained from three soils. We characterized material from unburnt, burnt, and double burnt regions. Data describing the physical and chemical properties of the soils together with the NMR spectroscopic characterization were analyzed using ANOVA.

Results and discussion

Both sampling methods yielded comparable results with comparable standard errors. No major differences between the fire-affected and unburnt soils were observed with respect to physical and chemical properties and C and N contents, but solid-state ¹³C NMR spectroscopy indicated a small but significant elevation of aromaticity in the soils with fire history.

Conclusions

The analysis showed that sampling with reduced replicates (method 1) can still lead to representative NMR data. The more complex sampling of comparing three composite samples (method 2) did not decrease the standard error. Our results also indicate that in the study area typical properties of the soil and its SOM induced by former burnings will not persist beyond a few decades.

     

Salinity stress response in estuarine fishes from the Murray Estuary and Coorong,South Australia

Estuaries are unstable ecosystems and can be changed by the environmental and anthropogenic impact. The Murray Estuary and Coorong were degraded by drought and low freshwater input in the last decade and therefore transformed into the largest hyper-saline lagoon in Australia. This study evaluates the physiological stress of two estuarine fish species (small-mouthed hardyhead Atherinosoma microstoma and Tamar goby Afurcagobius tamarensis) to the induced salinity change in captivity. The test fishes were collected from the Coorong and transported to the laboratory in the water from the Coorong. Each fish species was exposed to different levels of salinity, and a number of enzymes were assessed to measure the stress response of fish to salinity change. The activity of reactive oxygen species was significantly increased with the salinity change in both fish species compared with the fish in the control. Significant salinity effect on superoxide dismutase activity was observed on Tamar goby but not on small-mouthed hardyhead. Conversely, the impact of salinity on catalase activity was detected on small-mouthed hardyhead but not on Tamar goby. The study reveals that the induction of physical stress by salinity changes occurred in both Tamar goby and small-mouthed hardyhead despite the varying response of antioxidant enzymes between fish species. The study provides an insight into the understanding of physiological adaptation in estuarine fish to salinity change. The results could improve our knowledge on stress response and resilience of estuarine fish to hypo- and hyper-salinity stress.