Bacterial rhodopsin: evidence for a new type of phototrophy in the sea

Extremely halophilic archaea contain retinal-binding integral membrane proteins called bacteriorhodopsins that function as light-driven proton pumps. So far, bacteriorhodopsins capable of generating a chemiosmotic membrane potential in response to light have been demonstrated only in halophilic archaea. We describe here a type of rhodopsin derived from bacteria that was discovered through genomic analyses of naturally occuring marine bacterioplankton. The bacterial rhodopsin was encoded in the genome of an uncultivated gamma-proteobacterium and shared highest amino acid sequence similarity with archaeal rhodopsins. The protein was functionally expressed in Escherichia coli and bound retinal to form an active, light-driven proton pump. The new rhodopsin exhibited a photochemical reaction cycle with intermediates and kinetics characteristic of archaeal proton-pumping rhodopsins. Our results demonstrate that archaeal-like rhodopsins are broadly distributed among different taxa, including members of the domain Bacteria. Our data also indicate that a previously unsuspected mode of bacterially mediated light-driven energy generation may commonly occur in oceanic surface waters worldwide.     

Spin-dependent WIMP limits from a bubble chamber

Bubble chambers were the dominant technology used for particle detection in accelerator experiments for several decades, eventually falling into disuse with the advent of other techniques. We report here on a new application for these devices. We operated an ultraclean, room-temperature bubble chamber containing 1.5 kilograms of superheated CF3I, a target maximally sensitive to spin-dependent and -independent weakly interacting massive particle (WIMP) couplings. An extreme intrinsic insensitivity to the backgrounds that commonly limit direct searches for dark matter was measured in this device under operating conditions leading to the detection of low-energy nuclear recoils like those expected from WIMPs. Improved limits on the spin-dependent WIMP-proton scattering cross section were extracted during our experiments, excluding this type of coupling as a possible explanation for a recent claim of particle dark-matter detection.     

Effects of permanent magnetic fields on the proliferation of Phalaenopsis protocorm-like bodies using liquid medium

Magnetic fields (MFs) have been applied for the first time in orchid micropropagation. Protocorm-like bodies (PLBs) – approximately 3 mm in diameter – first derived from leaf segment culture of Phalaenopsis Gallant Beau ‘George Vazquez’, were subcultured every 2 months, and served as initial explants. The proliferation of Phalaenopsis PLBs in liquid medium in the Miracle Pack^® culture system was affected by the action of different intensities and polarities of MFs: 0.1, 0.15 and 0.2 Tesla (T) at North (N) and South (S) poles. The MF of 0.1 T – S resulted in the greatest fresh weight of regenerated PLBs. The average number of neo-PLBs formed per clusters in the PLB treated by MF: 0.1–0.2 T was decreased compared to the control exposed to natural MF (5 × 10⁻⁶ T). The proliferation of PLBs under 0.15 T – MF at both N and S poles for 2 and 7 weeks demonstrated that a longer duration of exposure to an MF of 0.15 T, regardless of the polarity, resulted in greater biomass of newly formed PLBs and smaller average number of newly formed PLBs. The S pole of MF had stronger effects on Phalaenopsis PLBs proliferation than the N pole did in all treatments.     

How do earthworms influence organic matter quantity and quality in tropical soils?

Earthworms are important regulators of soil structure and soil organic matter (SOM) dynamics; however, quantifying their influence on SOM cycling in tropical ecosystems remains little studied. Simulated rainfall was used to disrupt casts produced by Amynthas khami and their surrounding soil (control) into a range of small sized aggregates (50-250, 250-500, 500-2000 and 2000-5000 μm). To gain insight into how earthworms influence SOM biogeochemical composition in the aggregates, we carried out elemental and stable isotope analysis, and analytical pyrolysis (Py GC/MS). We also characterized their lignin component after oxidation with cupric oxide (CuO).The C content of smaller size fractions (<500 μm) in the control soil was higher than in the larger fractions. Our study therefore suggests that the aggregate hierarchy concept, which is used to understand soil aggregates and SOM dynamics in temperate soils, may not be applicable to the tropical Acrisol studied here. Earthworms modified SOM organization in soil aggregates. Although the isotope analyses were useful for highlighting SOM enrichment in the earthworm casts, aggregate fractions could not be classified according to particle size. Molecular analyses were necessary to indicate that SOM in all size fractions of casts consisted of relatively undecomposed material. Protection of the most labile SOM structures occurred in the smallest aggregate size fraction (50-250 μm). Py GC/MS showed that earthworm casts and control aggregates <2000 μm could be clearly distinguished according to the molecular properties of their SOM. Aggregates larger than 2000 μm, however, were most probably composed of all fractions and were not different. As a consequence, our results indicate that studies to determine the impact of earthworms on SOM turnover in soil are spatially dependant on the scale of observation.     

Implications of global and regional patterns of highly pathogenic avian influenza virus H5N1 clades for risk management

This paper analyses the publicly available data on the distribution and evolution of highly pathogenic avian influenza virus (HPAIV) H5N1 clades, whilst acknowledging the biases resulting from the non-random selection of isolates for gene sequencing. The data indicate molecular heterogeneity in the global distribution of HPAIV H5N1, in particular in different parts of East and Southeast Asia. Analysis of the temporal pattern of haemagglutinin clade data shows a progression from clade 0 (the ‘dominant’ clade between 1996 and 2002) to clade 1 (2003–2005) and then to clade 2.3.4 (2005 onwards). This process continuously produces variants, depending on the frequency of virus multiplication in the host population, which is influenced by geographical variation in poultry density, poultry production systems and also HPAI risk management measures such as vaccination. Increased multilateral collaboration needs to focus on developing enhanced disease surveillance and control targeted at evolutionary ‘hotspots’.     

Effect of drying and rewetting on phosphorus transformations in red brown soils with different soil organic matter content

In this study, the effect of drying and rewetting on native P transformations in two red brown soils with different management history was investigated. Three treatments, T1 (constantly moist), T2 (dried for 4 days and then kept dry), T3 (rewetted after 4 days drying) were used. Drying and rewetting caused a rapid increase in microbial P (Pm) and labile organic P (labile Po) within 1 day and a gradual increase in available inorganic P (Colwell). These increases were only temporarily, as Pm and labile Po decreased with time and were at the same level as in the constantly moist soil by the end of the incubation period of 21 days. The effect of drying and rewetting on P transformations strongly depended on soil organic matter content, being more pronounced in the soil with high organic matter content, compared to the soil with low soil organic matter content.     

Additions of maize root mucilage to soil changed the structure of the bacterial community

The organic compounds released from roots (rhizodeposits) stimulate the growth of the rhizosphere microbial community. They may be responsible for the differences in the structure of the microbial communities commonly observed between the rhizosphere and the bulk soil. Rhizodeposits consists of a broad range of compounds including root mucilage. The aim of this study was to investigate if additions of maize root mucilage, at a rate of 70 μg C g⁻¹ day⁻¹ for 15 days, to an agricultural soil could affect the structure of the bacterial community. Mucilage additions moderately increased microbial C (+23% increase relative to control), which suggests that the turnover rate of microorganisms consuming this substrate was high. Consistent with this, the number of cultivable bacteria was enhanced by +450%. Catabolic (Biolog^® GN2) and 16S-23S intergenic spacer fingerprints exhibited significant differences between control and mucilage treatments. These data indicate that mucilage can affect both the metabolic and genetic structure of the bacterial community as shown by a greater catabolic potential for carbohydrates. We concluded that mucilage is likely to significantly contribute to differences in the structure of the bacterial communities present in the rhizosphere compared to the bulk soil.     

Evaluation of fly ash,apatite and rice straw derived-biochar in varying combinations for in situ remediation of soils contaminated with multiple heavy metals

ABSTRACT

In

-situ sorbent amendment is a relatively low-cost, low-impact approach for remediation of soil contaminated with heavy metals (HMs), and thus is considered a way to be favored in developing countries. In this study, materials of non-hazardous, alkaline agronomic and industrial by-products were used as sorbents to explore their capacity of in situ immobilization of multiple HMs in mining-impacted arable soil. These sorbents included fly ash (FA), biochar (BC) and apatite (AP) and they were implemented with varying ratios of combinations. Results of soil microcosm tests showed that after incubation for 90 days, concentrations of Pb, Zn, and Cd in their exchangeable forms determined by a sequential extraction method significantly decreased in amended soils, as opposed to the unamended control. Of the five sets of amendments, the composite of FA, BC, and AP resulted in the maximum reduction (up to 80%) in the mobility of Pb, Zn, and Cd in soils. The mechanisms underlying the immobilization of HMs in amended soils might involve processes of surface precipitation, ion exchange and complexation, in which the physicochemical properties of sorbent materials played an important role. The immobilization efficacy of sorbent amendments on HMs in soil was further supported by pot experiments in which significant inhibition of HM accumulation in the belowground and aboveground tissues of maize was observed after 50-day cultivation in amended soils as compared with control soil. Together, these results suggest that the application of cost-saving and environmentally friendly materials derived from wastes as sorbents to remediate soils contaminated with multiple HMs is promising for developing countries like Vietnam.     

Regional Sediment Deficits in the Dutch Lowlands: Implications for Long-Term Land-Use Options (8 pp)

Background, Aim and Scope   Coastal and river plains are the surfaces of depositional systems, to which sediment input is a parameter of key-importance. Their habitation and economic development usually requires protection with dikes, quays, etc., which are effective in retaining floods but have the side effect of retarding sedimentation in their hinterlands. The flood-protected Dutch lowlands (so-called dike-ring areas) have been sediment-starved for up to about a millennium. In addition to this, peat decomposition and soil compaction, brought about by land drainage, have caused significant land subsidence. Sediment deficiency, defined as the combined effect of sediment-starvation and drainage-induced volume losses, has already been substantial in this area, and it is expected to become urgent in view of the forecasted effects of climate change (sea-level rise, intensified precipitation and run-off). We therefore explore this deficiency, compare it with natural (Holocene) and current human sediment inputs, and discuss it in terms of long-term land-use options. Materials and Methods: We use available 3D geological models to define natural sediment inputs to our study area. Recent progress in large-scale modelling of peat oxidation and compaction enables us to address volume loss associated with these processes. Human sediment inputs are based on published minerals statistics. All results are given as first-order approximations. Results: The current sediment deficit in the diked lowlands of the Netherlands is estimated at 136 ± 67 million m3/a. About 85% of this volume is the hypothetical amount of sediment required to keep up with sea-level rise, and 15% is the effect of land drainage (peat decomposition and compaction). The average Holocene sediment input to our study area (based on a total of 145 km3) is ~14 million m3/a, and the maximum (millennium-averaged) input ~26 million m3/a. Historical sediment deficiency has resulted in an unused sediment accommodation space of about 13.3 km3. Net human input of sediment material currently amounts to ~23 million m3/a. Discussion: As sedimentary processes in the Dutch lowlands have been retarded, the depositional system's natural resilience to sea-level rise is low, and all that is left to cope is human countermeasure. Preserving some sort of status quo with water management solutions may reach its limits in the foreseeable future. The most viable long-term solutions therefore seem a combination of allowing for more water in open country (anything from flood-buffer zones to open water) and raising lands that are to be built up (enabling their lasting protection). As to the latter, doubling or tripling the use of filling sand in a planned and sustained effort may resolve up to one half of the Dutch sediment deficiency problems in about a century. Conclusions: Conclusions, Recommendations and Perspectives. We conclude that sediment deficiency – past, present and future – challenges the sustainable habitation of the Dutch lowlands. In order to explore possible solutions, we recommend the development of long-term scenarios for the changing lowland physiography, that include the effects of Global Change, compensation measures, costs and benefits, and the implications for long-term land-use options. Recommendations and Perspectives: -