Empowering marine science through genomics

Marine scientists in Europe summarize their successes with genome technologies in the marine sciences and make a plea for a concerted international effort to raise greater public education for support.     

Biodegradation of Trichloroethylene and Its Anaerobic Daughter Products in Freshwater Wetland Sediments

The wide range of redox conditions and diversity of microbial populations in organic-rich wetland sediments could enhance biodegradation of chlorinated solvents. To evaluate potential biodegradation rates of trichloroethylene (TCE) and its anaerobic daughter products (cis-1,2-dichloroethylene; trans-1,2-dichloroethylene; and vinyl chloride), laboratory microcosms were prepared under methanogenic, sulfate-reducing, and aerobic conditions using sediment and groundwater from a freshwater wetland that is a discharge area for a TCE contaminant plume. Under methanogenic conditions, biodegradation rates of TCE were extremely rapid at 0.30 to 0.37 d^-1 (half-life of about 2 days). Although the TCE biodegradation rate was slower under sulfate-reducing conditions (0.032 d^-1) than under methanogenic conditions, the rate was still two orders of magnitude higher than those reported in the literature for microcosms constructed with sandy aquifer sediments. In the aerobic microcosm experiments, biodegradation occurred only if methane consumption occurred, indicating that methanotrophs were involved. Comparison of laboratory-measured rates indicates that production of the 1,2-dichloroethylene isomers and vinyl chloride by anaerobic TCE biodegradation could be balanced by their consumption through aerobic degradation where methanotrophs are active in wetland sediment. TCE degradation rates estimated using field data (0.009 to 0.016 d^-1) agree with the laboratory-measured rates within a factor of 3 to 22, supporting the feasibility of natural attenuation as a remediation method for contaminated groundwater discharging in this wetland and other similar environments.     

Taxonomic revision of the genus <Emphasis Type="Italic">Catalpa</Emphasis> (Bignoniaceae)

A taxonomic revision of Catalpa (Bignoiaceae), a genus of perennial trees frequently used in horticulture as garden and street trees, is provided. Eight natural species and two hybrid species are recognized, four in sect. Catalpa, four in sect. Macrocatalpa, and two hybrid species in sect. Catalpa. Although C. punctata has been used for one of the tropical species, C. macrocarpa is the correct scientific name. Catalpa tibetica is synonymous with C. bignonioides, C. fargesii with C. bungei, and C. obovata with C. macrocarpa. Lectotypes are designated for: Bignonia cassinoides, Bignonia longisiliqua, Bignonia longissima, Catalpa Walter, Catalpa subsect. Corymbosae, Catalpa bignonioides var. kaempferi, Catalpa bungei, Catalpa bungei var. heterophylla, Catalpa bungei var. intermedia, Catalpa domingensis, Catalpa fargesii, Catalpa henryi, Catalpa ×hybrida, Catalpa ovata var. flavescens, Catalpa punctata var. lepidota, Catalpa purpurea, Catalpa syringifolia var. pulverulenta, Catalpa sutchuensis, Catalpa ×teasii, and Cumbulu. Second-step lectotypes are designated for: Catalpa duclouxii, Catalpa ekmaniana, Catalpa oblongata, Catalpa obovata, and Catalpa ovata. Neotypes are designated for: Bignonia triloba, Catalpa aureovittata, Catalpa bignonioides var. variegata, Catalpa ×erubescens, Catalpa ×erubescens f. purpurea, Catalpa ×galleana, Catalpa ×hybrida var. atropurpurea, Catalpa japonica, Catalpa syringifolia var. aurea, Catalpa syringifolia var. koehnei, Catalpa syringifolia var. nana, Catalpa ×teasiana, and Catalpa umbraculifera.     

First observations of temperature tolerances of adult male snow crab (Chionoecetes opilio) from the Barents Sea population and the effects on the fisheries strategy

This study investigates the effects of temperature on the survival, food intake, oxygen consumption and growth during long-term live holding of captive male snow crab (Chionoecetes opilio) (average?=?0.7?kg). The crabs were held at three different temperatures, 3, 6 and 9°C. The trials were done using groups of snow crabs held in nine land-based holding tanks (three replicates per temperature treatment). The results showed that temperature had a significant effect on survival. The survival rate at 3°C (61%) was significantly higher than at 6°C (33%) and at 9°C (28%). Specific oxygen consumption rates of unfed crab at 6°C were significantly higher than at 9°C and 3°C. In summary, the current study shows that the Barents Sea snow crab have a narrow temperature range in which they thrive compared with the Barents Sea red king crab (Paralithodes camtschaticus). Barents Sea snow crab has similar metabolic and physiological attributes to other major snow crab populations. In conditions when ambient temperatures are approximately 6°C, it may prove beneficial for animal welfare and also be financially advantageous to reduce ambient water temperatures in live snow crab holding facilities on boat or on land.     

All roads lead to weediness: Patterns of genomic divergence reveal extensive recurrent weedy rice origins from South Asian Oryza

Weedy rice (Oryza spp.), a weedy relative of cultivated rice (O. sativa), infests and persists in cultivated rice fields worldwide. Many weedy rice populations have evolved similar adaptive traits, considered part of the ‘agricultural weed syndrome’, making this an ideal model to study the genetic basis of parallel evolution. Understanding parallel evolution hinges on accurate knowledge of the genetic background and origins of existing weedy rice groups. Using population structure analyses of South Asian and US weedy rice, we show that weeds in South Asia have highly heterogeneous genetic backgrounds, with ancestry contributions both from cultivated varieties (aus and indica) and wild rice. Moreover, the two main groups of weedy rice in the USA, which are also related to aus and indica cultivars, constitute a separate origin from that of Asian weeds. Weedy rice populations in South Asia largely converge on presence of red pericarps and awns and on ease of shattering. Genomewide divergence scans between weed groups from the USA and South Asia, and their crop relatives are enriched for loci involved in metabolic processes. Some candidate genes related to iconic weedy traits and competitiveness are highly divergent between some weed‐crop pairs, but are not shared among all weed‐crop comparisons. Our results show that weedy rice is an extreme example of recurrent evolution, and suggest that most populations are evolving their weedy traits through different genetic mechanisms.     

Proteome analysis of peroxisomes from dark-treated senescent Arabidopsis leaves

Peroxisomes compartmentalize a dynamic suite of biochemical reactions and play a central role in plant metabolism, such as the degradation of hydrogen peroxide,metabolism of fatty acids, photorespiration, and the biosynthesis of plant hormones. Plant peroxisomes have been traditionally classified into three major subtypes, and in-depth mass spectrometry(MS)-based proteomics has been performed to explore the proteome of the two major subtypes present in green leaves and etiolated seedlings. Here, we carried out a comprehensive proteome analysis of peroxisomes from Arabidopsis leaves given a 48-h dark treatment.Our goal was to determine the proteome of the third major subtype of plant peroxisomes from senescent leaves, and further catalog the plant peroxisomal proteome. We identifieda total of 111 peroxisomal proteins and verified the peroxisomal localization for six new proteins with potential roles in fatty acid metabolism and stress response by in vivo targeting analysis. Metabolic pathways compartmentalized in the three major subtypes of peroxisomes were also compared, which revealed a higher number of proteins involved in the detoxification of reactive oxygen species in peroxisomes from senescent leaves. Our study takes an important step towards mapping the ful function of plant peroxisomes.