Front Cover Image,Volume 116, Number 11, November 2019

CRISPR/Cas9-guided cytidine deaminase enables C:G to T:A base editing in bacterial genome without introduction of lethal double-stranded DNA break, supplement of foreign DNA template, or dependence on inefficient homologous recombination. However, limited by genome-targeting scope, editing window, and base transition capability, the application of base editing in metabolic engineering has not been explored. Herein, four Cas9 variants accepting different protospacer adjacent motif (PAM) sequences were used to increase the genome-targeting scope of bacterial base editing. After a comprehensive evaluation, we demonstrated that PAM requirement of bacterial base editing can be relaxed from NGG to NG using the Cas9 variants, providing 3.9-fold more target loci for gene inactivation in Corynebacterium glutamicum. Truncated or extended guide RNAs were employed to expand the canonical 5-bp editing window to 7-bp. Bacterial adenine base editing was also achieved with Cas9 fused to adenosine deaminase. With these updates, base editing can serve as an enabling tool for fast metabolic engineering. To demonstrate its potential, base editing was used to deregulate feedback inhibition of aspartokinase via amino acid substitution for lysine overproduction. Finally, a user-friendly online tool named gBIG was provided for designing guide RNAs for base editing-mediated inactivation of given genes in any given sequenced genome ( www.ibiodesign.net/gBIG ).     

Specific Treatment Technologies for Removing Arsenic from Water

Arsenic (As) is a highly toxic metalloid found in ground and surface water. Arsenic contamination in drinking water leads to harmful effects on human health. To eliminate arsenic from drinking water, several technologies such as coagulation, adsorption, ion exchange, filtration, membrane processes, etc., have been used. In this study, three technologies were evaluated for arsenic removal. Results from batch kinetic experiments showed that iron coated sand (IOCS‐2) can remove more than 90 % of As from synthetic water. Experiments were conducted with three different pH values (6, 7, and 8) and an initial As concentration of 260 μg/L. A new material, developed in this study, namely iron coated sponge (IOCSp), was found to have a high capacity in removing both As (V) and As (III). Each gram of IOCSp adsorbed about 160 μg of As within a 9‐hour contact period of IOCSp with As solution. Low pressure nanofiltration removed more than 94 % of As from an influent containing 440 μg/L As. The applied pressure was varied from 85 to 500 kPa.     

Metal Removal from Water Discharges by a Constructed Treatment Wetland

A full‐scale constructed wetland treatment system consisting of four pairs of wetland cells (3.2 ha total area) with water flowing through a pair of cells in series prior to discharge was investigated. A retention basin provided stable water flow to the system. Water retention time in the wetland system was approximately 48 hours, and the wetland cells operated at circumneutral pH. Vegetation development within the cells has been excellent. Copper removal efficiency was greater than 75 % from the start‐up of the system, while mercury efficiency improved with maturation of the treatment cells. Sampling of the water course through the wetlands conducted during the fourth year of operation validated continued performance, and assessed the fate of a larger suite of metals present in the water. Copper and mercury removal efficiencies were still very high, both in excess of 80 % removal from the water after passage through the wetland system. Mercury removal continued along the entire water course through the system, while copper was removed almost immediately upon entering the wetland cells. Lead removal from the water by the system was 83 %, zinc removal was 60 %, and nickel was generally unaffected. Organic carbon in the water was also increased by the system and reduced the bioavailability of some metals. Operation and maintenance of the system continued to be minimal, and mainly consisted of checking for growth of the vegetation and free flow of the water through the system. The system was entirely passive, relying on gravity as the power source of water flow. No reportable permit exceedances have been experienced since the wetland began treating an outfall discharge.     

The Ascorbate-deficient vtc-1 Arabidopsis Mutant Shows Altered ABA Accumulation in Leaves and Chloroplasts

Abscisic acid (ABA) accumulation has been analyzed in irrigated and water-stressed wild-type and the vtc-1 mutant of Arabidopsis thaliana, which shows an ascorbate deficiency in leaves of approximately 60%. The amounts of ABA increased progressively up to 2.3-fold in water-stressed wild-type plants, whereas levels were kept at low levels in the irrigated plants. In contrast, initial increases followed by a sharp decrease of abscisic acid levels were observed in water-stressed vtc-1 mutants. Furthermore, the levels of this phytohormone increased up to fivefold in irrigated mutants. This differential accumulation of ABA in the mutant strongly correlated with the ascorbate redox state, but not with ascorbate levels. Changes in ABA levels in leaves paralleled those of chloroplasts. Immunolocalization studies showed a differential ABA accumulation in chloroplasts of vtc-1 mutants, which displayed the highest ABA labeling in irrigated plants. Our results indicate an altered pattern of ABA accumulation in the vtc-1 mutant compared to the wild type, under both irrigated conditions and water-stress conditions, which is strongly dependent on the ascorbate redox state.     

Effects of forest conversion into grassland on soil aggregate structure and carbon storage in Panama: evidence from soil carbon fractionation and stable isotopes

Land-use and land-cover strongly influence soil properties such as the amount of soil organic carbon (SOC), aggregate structure and SOC turnover processes. We studied the effects of a vegetation shift from forest to grassland 90 years ago in soils derived from andesite material on Barro Colorado Island (BCI), Panama. We quantified the amount of carbon (C) and nitrogen (N) and determined the turnover of C in bulk soil, water stable aggregates (WSA) of different size classes (<53 μm, 53–250 μm, 250–2000 μm and 2000–8000 μm) and density fractions (free light fraction, intra-aggregate particulate organic matter and mineral associated soil organic C). Total SOC stocks (0–50 cm) under forest (84 Mg C ha⁻¹) and grassland (64 Mg C ha⁻¹) did not differ significantly. Our results revealed that vegetation type did not have an effect on aggregate structure and stability. The investigated soils at BCI did not show higher C and N concentrations in larger aggregates, indicating that organic material is not the major binding agent in these soils to form aggregates. Based on δ¹³C values and treating bulk soil as a single, homogenous C pool we estimated a mean residence time (MRT) of 69 years for the surface layer (0–5 cm). The MRT varied among the different SOC fractions and among depth. In 0–5 cm, MRT of intra-aggregate particulate organic matter (iPOM) was 29 years; whereas mineral associated soil organic C (mSOC) had a MRT of 124 years. These soils have substantial resilience to C and N losses because the >90% of C and N is associated with mSOC, which has a comparatively long MRT.     

How do climate warming and plant species richness affect water use in experimental grasslands?

Climate warming and plant species richness loss have been the subject of numerous experiments, but studies on their combined impact are lacking. Here we studied how both warming and species richness loss affect water use in grasslands, while identifying interactions between these global changes. Experimental ecosystems containing one, three or nine grassland species from three functional groups were grown in 12 sunlit, climate-controlled chambers (2.25 m² ground area) in Wilrijk, Belgium. Half of these chambers were exposed to ambient air temperatures (unheated), while the other half were warmed by 3°C (heated). Equal amounts of water were added to heated and unheated communities, so that warming would imply drier soils if evapotranspiration (ET) was higher. After an initial ET increase in response to warming, stomatal regulation and lower above-ground productivity resulted in ET values comparable with those recorded in the unheated communities. As a result of the decreased biomass production, water use efficiency (WUE) was reduced by warming. Higher complementarity and the improved competitive success of water-efficient species in mixtures led to an increased WUE in multi-species communities as compared to monocultures, regardless of the induced warming. However, since the WUE of individual species was affected in different ways by higher temperatures, compositional changes in mixtures seem likely under climatic change due to shifts in competitiveness. In conclusion, while increased complementarity and selection of water-efficient species ensured more efficient water use in mixtures than monocultures, global warming will likely decrease this WUE, and this may be most pronounced in species-rich communities.     

Soil water depletion by Eucalyptus spp. integrated into dryland agricultural systems

Spatial patterns of soil water depletion by Eucalyptus spp. were surveyed to assess the potential of tree belts and short rotation phase farming with trees for groundwater recharge reduction and salinity control. Soils were sampled to depths of up to 10 m in transects perpendicular to 4- to 7-year-old mallee eucalypt belts (Eucalyptus horistes, E. kochii ssp. plenissima, E. loxophleba ssp. lissophloia, E. polybractea) and in a 4 year-old block of E. astringens. Results indicate that the eucalypt species can exploit soil water to depths of at least 8–10 m within 7 years of planting. The root systems of these eucalypts were able to penetrate clayey subsoils with bulk densities of up to 2.0 g cm⁻³. Leaf area indexes of tree belts were 2–10 times greater than those predicted for natural vegetation, probably as a result of exploiting a greater amount of soil water stored under the agricultural system. The lateral influence of mallee belts, as indicated by soil water contents that were depleted to wilting point, ranged from 15–42 m. The resulting dry soil zone provided an effective barrier to groundwater recharge by incident rainfall thereby lessening the risk of salinisation in the agricultural landscape. The width of this barrier to recharge was predicted to range from 7 m to 54 m based on leaf area.     

豚草叶片和果实气体交换特性与11种土壤重金属相关性

对10个样地中Cu、Pb、Zn、Mn、Cr、Co、Ni、Cd、As、Sb和Hg11种土壤重金属含量及样地内豚草叶片和果实气体交换特性进行测定.结果表明,样地内豚草叶片的净光合速率在1·88~9·41μmol·m-2·s-1,而果实的净光合速率最高可达2·81μmol·m-2·s-1.叶片的呼吸速率、气孔导度、光合速率和水分利用效率的平均值分别为1·81μmol·m-2·s-1、75·7mmol·m-2·s-1、6·05μmol·m-2·s-1和4·72μmol·mmol-1,分别是果实的5·26、0·64、1·31和1·69倍,说明非同化器官幼嫩果实具有与叶片相当,甚至更强的呼吸、光合能力和水分利用效率;研究地点重金属Ni达到轻微污染水平,其它重金属含量都接近或者显著低于重金属污染的阈值.相关分析和多元回归分析显示,大部分土壤重金属(如Cu、Pb、Zn、Cd、As、Sb和Hg)含量的高低对豚草气体交换特性没有显著影响,仅部分重金属含量与豚草的叶片、果实气体交换特性密切相关,如Ni和Cr对豚草叶片、果实的气孔导度及水分利用效率显著相关;Cr与豚草叶片饱和光合速率显著相关;而As与豚草果实的气孔导度显著相关.表明大部分土壤重金属对叶片和球果的气体交换没有直接影响,而Ni、Cr和As可以在轻微污染甚至没有达到污染水平时影响豚草的气体交换特性.     

菱角萤叶甲种群抽样技术研究

在研究菱角萤叶甲各虫态空间分布型的基础上,利用负二项公共Kc值;Iwao回归式中的α,β;Teylor幂法则中的a,b以及Morisita的I_δ求得理论抽样模型,从而导出在不同置信度t,不同的平均虫口密度(?)和不同允许误差D下的理论抽样数．同时利用Kuno(1969),Iwao(1975)和Willson(1983)提出的序贯抽样法,得到菱角萤叶甲各虫态的序贯抽样模型,并对这些模型进行比较．最后,结合Kuno和Iwao模型获得了菱角萤叶甲各虫态的Kuno-Iwao复合序贯抽样法,从而大大减少了在某种情况下的抽样数．     

生物修复的研究和应用现状及发展前景

综述了生物修复的研究和应用现状及发展前景。内容涉及生物修复的研究方法和手段、生物修复在土壤和水体中的应用、生物修复的发展前景等。