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The methanogenic degradation of hydrocarbons plays an important role in hydrocarbon-contaminated environments in the absence of an external electron acceptor. Members of Syntrophaceae sublineages were previously reported to be responsible for syntrophic alkane degradation. However, limited information is currently available on their physiological capabilities in nature because it is very challenging to cultivate these as-yet uncultured microbes. We herein performed metagenomic sequencing of the methanogenic hexadecane-degrading culture M82 and recovered a nearly complete genome (2.75 Mb, estimated completeness ≥97%) belonging to Syntrophaceae sublineage II. The assembly genome was tentatively named "Candidatus Smithella cisternae strain M82_1". Genes encoding alkylsuccinate synthase for alkane activation were identified, suggesting that this organism is capable of oxidizing alkanes through fumarate addition. This capability was further supported by the detection of methyl pentadecyl succinic acid and methyl tetradecyl succinic acid in cultures amended with hexadecane and pentadecane, respectively. Genes encoding enzymes for the β-oxidation of long-chain fatty acids and butyrate were also identified. The electron transfer flavoprotein/DUF224 complex is presumed to link electron flow from acyl-CoA dehydrogenase to a membrane hydrogenase or formate dehydrogenase. Although no indications of Rnf complexes were detected, genes encoding electron-confurcating hydrogenase and formate dehydrogenase were proposed to couple the thermodynamically favorable oxidation of ferredoxin to generate H 2 and formate from NADH. Strain M82_1 synthesized ATP from acetyl-CoA by substrate-level phosphorylation or F 1 F 0 -ATP synthases. These results provide an insight into the potential metabolic traits and ecophysiological roles of the syntrophic alkane degrader Syntrophaceae.

Background: Over three-fifths of the world's known crude oil cannot be recovered using state-of-the-art techniques, but microbial conversion of petroleum hydrocarbons trapped in oil reservoirs to methane is one promising path to increase the recovery of fossil fuels. The process requires cooperation between syntrophic bacteria and methanogenic archaea, which can be affected by sulfate-reducing prokaryotes (SRPs). However, the effects of sulfate on hydrocarbon degradation and methane production remain elusive, and the microbial communities involved are not well understood., Results: In this study, a methanogenic hexadecane-degrading enrichment culture was treated with six different concentrations of sulfate ranging from 0.5 to 25 mM. Methane production and maximum specific methane production rate gradually decreased to 44 and 56% with sulfate concentrations up to 25 mM, respectively. There was a significant positive linear correlation between the sulfate reduction/methane production ratio and initial sulfate concentration, which remained constant during the methane production phase. The apparent methanogenesis fractionation factor ( α app ) gradually increased during the methane production phase in each treatment, the α app for the treatments with lower sulfate (0.5-4 mM) eventually plateaued at ~1.047, but that for the treatment with 10-25 mM sulfate only reached ~1.029. The relative abundance levels of Smithella and Methanoculleus increased almost in parallel with the increasing sulfate concentrations. Furthermore, the predominant sulfate reducer communities shifted from Desulfobacteraceae in the low-sulfate cultures to Desulfomonile in the high-sulfate cultures., Conclusion: The distribution of hexadecane carbon between methane-producing and sulfate-reducing populations is dependent on the initial sulfate added, and not affected during the methane production period. There was a relative increase in hydrogenotrophic methanogenesis activity over time for all sulfate treatments, whereas the total activity was inhibited by sulfate addition. Both Smithella and Methanoculleus , the key alkane degraders and methane producers, can adapt to sulfate stress. Specifically, different SRP populations were stimulated at various sulfate concentrations. These results could help to evaluate interactions between sulfate-reducing and methanogenic populations during anaerobic hydrocarbon degradation in oil reservoirs.

Arabidopsis cryptochrome 2 (CRY2) is a blue-light receptor mediating blue-light inhibition of hypocotyl elongation and photoperiodic promotion of floral initiation. CRY2 is a constitutive nuclear protein that undergoes blue-light-dependent phosphorylation, ubiquitination, photobody formation, and degradation in the nucleus, but the relationship between these blue-light-dependent events remains unclear. It has been proposed that CRY2 phosphorylation triggers a conformational change responsible for the subsequent ubiquitination and photobody formation, leading to CRY2 function and/or degradation. We tested this hypothesis by a structure-function study, using mutant CRY2-GFP fusion proteins expressed in transgenic Arabidopsis. We show that changes of lysine residues of the NLS (Nuclear Localization Signal) sequence of CRY2 to arginine residues partially impair the nuclear importation of the CRY2K541R and CRY2K554/5R mutant proteins, resulting in reduced phosphorylation, physiological activities, and degradation in response to blue light. In contrast to the wild-type CRY2 protein that forms photobodies exclusively in the nucleus, the CRY2K541R and CRY2K554/5R mutant proteins form protein bodies in both the nucleus and cytosol in response to blue light. These results suggest that photoexcited CRY2 molecules can aggregate to form photobody-like structure without the nucleus-dependent protein modifications or the association with the nuclear CRY2-interacting proteins. Taken together, the observation that CRY2 forms photobodies markedly faster than CRY2 phosphorylation in response to blue light, we hypothesize that the photoexcited cryptochromes form oligomers, preceding other biochemical changes of CRY2, to facilitate photobody formation, signal amplification, and propagation, as well as desensitization by degradation.

Based on statistical analysis of field N2O measurements in rice paddies in China, the models on direct N2O emissions under different water regimes were established. After successes in model validation and input data verification, the models were used to quantify changes in direct N2O emissions from paddy fields during the rice growing season in mainland China between the 1950s and the 1990s. Due to increases in rice planting area and nitrogen input and changes in water regime, the models predicted that seasonal N2O-N emissions from rice paddies have increased from 9.55 Gg each year in the 1950s to 32.26 Gg N2O-N in the 1990s, which was accompanied by the increase in rice yield over the period 1950s-1990s. During the period 1950s-1990s, seasonal N2O-N emissions from rice paddies have increased, on average, at a rate of 6.74 Gg per decade. Seasonal N2O fluxes in rice paddies were estimated to be 0.32 kg x hm(-2) in the 1950s and 1.00 kg x hm(-2) in the 1990s, which accounted for 0.37% and 0.46% of the seasonal total N inputs, respectively. The uncertainties in N2O estimate were estimated to be 59.8% in the 1950s and 37.5% in the 1990s. Seasonal N2O emissions from rice paddies in the region of middle and lower Yangtze River contributed 51% -56% to its national total. In the 1990s, N2O emissions during the rice growing season accounted for 8%-11% of the reported annual total of N2O emissions from croplands in China, suggesting that paddy rice development could have contributed to mitigating agricultural N2O emissions in the past decades. However, seasonal N2O emissions would be increased given that saving-water irrigation and nitrogen inputs are increasingly adopted in rice paddies in China.

The models on direct N2O emissions from rice paddies under different water regimes developed by the authors were validated against field measurements in China reported in 2005-2007 and in other regions. In flooding rice paddies (F), N2O emission predicted by the model was consistent with previous reports in other regions. Under the water regime of flooding-midseason drainage-reflooding (F-D-F), the model developed in this study was comparable to that established by using worldwide database. The models also well fitted N2O emissions from rice paddies under the water regime of flooding-midseason drainage-reflooding-moisture but without waterlogging (F-D-F-M) in China. Consistency of rice production data derived from the database of this study with those reported in previous studies suggests that the model input data of rice production had high reliability. The input data showed that water management and nitrogen input regimes have greatly changed in rice paddies since the 1950s. During the 1950s-1970s, about 20%-25% of the rice paddy was continuous water logging, and 75%-80% under the water regime of F-D-F. Since the 1980s, about 12%-16%, 77% and 7%-12% of paddy fields were under the water regimes of F, F-D-F and F-D-F-M, respectively. Total N input during the rice growing season averaged 87.49 kg x hm(-2) in the 1950s and 224.64 kg x hm(-2) in the 1990s. Chemical N input during the rice growing season has increased from 37.4 kg x hm(-2) in the 1950s to 198.8 kg x hm(-2) in the 1990s, accounting for 43% and 88% of the seasonal total N inputs, respectively. Manure N input was applied at stable rate, ranging from 45.2 kg x hm(-2) to 48.2 kg x hm(-2) during the 1950s-1970s, but thereafter it decreased over time. The contribution of manure N to total N inputs has decreased from 52% in the 1950s to 9% in the 1990s. Crop residue N retained during the rice growing season has increased from 4.9 kg x hm(-2) in the 1950s to 6.3 kg x hm(-2) in the 1980s. A high spatial variation of nitrogen inputs during the rice growing season was found in the 1950s-1970s, while it was not pronounced in the 1980s-1990s. Overall, the results of this study suggest that the models could be used to quantify direct N2O emissions from rice paddies under various water regimes in China.

The antifungal, anti-bacterical, anti-brine shrimp activities of SD22 isolated from Paenibacillus daejeonensis Bacteria SS02 were studied. The separation steps included ultracentrifugation, ultrafiltration and (NH4)2SO4 fractional precipitation, further purification was performed by SephadexG-75 and DEAE-32 chromatography. Its molecular weight determined by SDS-PAGE was 56.0 kD and its isoelectfic point was 6.4. SD22 was thermostable to some extent and stable to ultraviolet, but sensitive to some of the enzyme. SD22 could kill most pathogens from propagation, such as Rhizoctonia cerealis, Sclerotinia sclerotiorum Physalospora piricala, Trichodema viride, Gliocladium viride, Curvularia leaf spot, Fusarium sp, Fusarium head blight, Beauveria Bassiana, Escherichia coli, Staphylococcus aureus, Bacillus subtilis , Candidal vaginitis, Fusarium oxysporum Schl. emend. Sayder & Hansem et al. The results will be helpful to find out a novel antifungal protein.

The transgenic wheat of improved resistance to the storage pest was production. We have introduced the cowpea trypsin inhibitor gene (CpTI) into cultured embryonic callus cells of immature embryos of wheat elite line by Agrobacterium-mediated method. Independent plantlets were obtained from the kanamycin-resistant calli after screening. PCR and real time PCR analysis, PCR-Southern and Southern blot hybridization indicated that there were 3 transgenic plants viz. transformed- I, II and III (T- I, T-II and T-III). The transformation frequencies were obviously affected by Agrobacterium concentration, the infection duration and transformation treatment. The segregations of CpTI in the transgenic wheat progenies were not easily to be elucidated, and some transgenic wheat lines (T- I and T-III) showed Mendelian segregations. The determinations of insect resistance to the stored grain insect of wheat viz. the grain moth (Sitotroga cerealella Olivier) indicated that the 3 transgenic wheat progeny seeds moth-resistance was improved significantly. The seed moth-eaten ratio of T- I, T-II, T-III and nontransformed control was 19.8%, 21.9%, 32.9% and 58.3% respectively. 3 transgenic wheat T1 PCR-positive plants revealed that the 3 transgenic lines had excellent agronomic traits. They supplied good germplasm resource of insect-resistance for wheat genetic improvement.

Two endophytic strains SS01 and SS02 with the potential for producing steroidal saponins were isolated from the underground stems of Paris polyphylla var. chinensis Franch. The TLC comparison indicated that there are 3 sports with similar R(f) between the metabolites of SS01 and the saponins of Paris polyphylla var. chinensis Franch. And there are 2 sports with similar R(f) between the metabolites of SS02 and the saponins of Paris polyphylla var. chinensis The and that biochemical SS01 Franch. characteristics of morphology, physiological belonged showed to Enterobacteriaceae and SS02 belonged to Bacillus sp.. The 16S rDNA of SS01 and SS02 were PCR and sequenced. The accessions of GenBank are AY842143 and AY842144, respectively. The two 16S rDNA phylogenetic trees were constructed by comparing with the published 16S rDNA sequences of the relative bacteria species. In the first phylogenetic tree SS01 and Cedecea davisae DSM 4568 was the closest relative with 98.9% sequence similarity, and in the second phylogenetic tree SS02 and Paenibacillus daejeonensis was the closest relative with 97.7% sequence similarity. According to the phylogenetic analysis they were identified as Cedecea davisae SS01 and Paenibacillus daejeonensis SS02, respectively.