Interactions between transcription factors and DNA lie at the centre of many biological processes including DNA recombination, replication, repair and transcription. Most bacteria encode diverse proteins that act as transcription factors to regulate various traits. Several technologies for identifying protein–DNA interactions at the genomic level have been developed. Bind-n-seq is a high-throughput in vitro method first deployed to analyse DNA interactions associated with eukaryotic zinc-finger proteins. The method has three steps (i) binding protein to a randomised oligonucleotide DNA target library, (ii) deep sequencing of bound oligonucleotides, and (iii) a computational algorithm to define motifs among the sequences. The classical Bind-n-seq strategy suffers from several limitations including a lengthy wet laboratory protocol and a computational algorithm that is difficult to use. We introduce here an improved, rapid, and simplified Bind-n-seq protocol coupled with a user-friendly downstream data analysis and handling algorithm, which has been optimized for bacterial target proteins. We validate this new protocol by showing the successful characterisation of the DNA-binding specificities of YipR (YajQ interacting protein regulator), a well-known transcriptional regulator of virulence genes in the bacterial phytopathogen Xanthomonas campestris pv. campestris (Xcc).

Root exudates are crucial for plants returning organic matter to soils, which is assumed to be a major source of carbon for the soil microbial community. This study investigated the influence of root exudates on the fate of arsenic (As) with a lab simulation experiment. Our findings suggested that root exudates had a dose effect on the soil physicochemical properties, As speciation transformation and the microbial community structure at different concentrations. The addition of root exudates increased the soil pH while decreased the soil redox potential (Eh). These changes in the soil pH and Eh increased As and ferrous (Fe(II)) concentrations in soil porewater. Results showed that 40 mg/L exudates addition significantly increased arsenite (As(III)) and arsenate (As(V)) by 541 and 10 times respectively within 30 days in soil porewater. The relative abundance of Fe(III)-reducing bacteria Geobacter and Anaeromyxobacter increased with the addition of root exudates, which enhanced microbial Fe reduction. Together these results suggest that investigating how root exudates affect the mobility and transformation of As in paddy soils is helpful to systematically understand the biogeochemical cycle of As in soil-rice system, which is of great significance for reducing the health risk of soil As contamination.Copyright © 2022. Published by Elsevier B.V.

为减少化肥的过量施用，提高湖南宜章植烟土壤肥力和烟叶生产效益，以烤烟品种‘K326’为材料，采用田间试验研究了不同比例生物有机肥与化肥减量配施对土壤养分及烟叶产量与品质的影响。结果表明：增施适当比例生物有机肥配合化肥减量能不同程度地改善土壤肥力质量，促进烟株的生长。随着生物有机肥比例的增加与化肥用量的减少，烤烟的各项生长农艺性状、感官评吸质量、产量、产值以及上等烟比例呈先升后降的趋势。其中，以减量20%化学追肥的T₂处理对烟株的生长和烟叶的品质表现最好。与常规施肥的对照(CK)相比，烟草株高、有效叶片数和最大叶面积分别增加8.24%~17.00%、13.81%~23.22%和12.63%~16.86%，C3F烟叶中总糖和钾含量分别达到26.51%~30.01%和2.16%~2.86%，C3F和B2F烟叶的感官评吸质量分别提高1.67%~2.98%和3.12%~4.10%，烟叶产量、上等烟比例和产值分别提高3.76%~6.58%、3.38%~3.79%和8.24%~9.58%。研究结果为湘南植烟区应用生物有机肥与化肥减量配施提供了科学参考依据。

Declining soil fertility and climatic extremes are among major problems for agricultural production in most dryland agro-ecologies of sub-Saharan Africa. In response, the agroforestry technology intercropping of Gliricidia (Gliricidia sepium (Jacq.)) and Maize (Zea mays L.) was developed to complement conventional soil fertility management technologies. However, diversified information on the profitability of Gliricidia-Maize intercropping system in dryland areas is scanty. Using data from the Gliricidia and maize models of the Next Generation version of the Agriculture Production Systems sIMulator (APSIM), this study estimates the profitability of the Gliricidia-Maize system relative to an unfertilized sole maize system. Results show significant heterogeneity in profitability indicators both in absolute and relative economic terms. Aggregated over a 20-year cycle, Gliricidia-Maize intercropping exhibited a higher Net Present Value (NPV = Tsh 19,238,798.43) and Benefit Cost Ratio (BCR = 4.27) than the unfertilized sole maize system. The NPV and BCR of the latter were Tsh 10,934,669.90 and 3.59, respectively. Moreover, the returns to labour per person day in the Gliricidia-Maize system was 1.5 times those of the unfertilized sole maize system. Sensitivity analysis revealed that the profitability of the Gliricidia-Maize system is more negatively affected by the decrease in output prices than the increase in input prices. A 30% decrease in the former leads to a decrease in NPV and BCR by 38% and 30%, respectively. Despite the higher initial costs of the agroforestry establishment, the 30% increase in input prices affects more disproportionally unfertilized sole maize than the Gliricidia-Maize system in absolute economic terms, i.e., 11.1% versus 8.8% decrease in NPV. In relative economic terms, an equal magnitude of change in input prices exerts the same effect on the unfertilized sole maize and the Gliricidia-maize systems. This result implies that the monetary benefits accrued after the first year of agroforestry establishment offset the initial investment costs. The Gliricidia-Maize intercropping technology therefore is profitable with time, and it can contribute to increased household income and food security. Helping farmers to overcome initial investment costs and manage agroforestry technologies well to generate additional benefits is critical for the successful scaling of the Gliricidia-Maize intercropping technology in dryland areas of Dodoma, Tanzania.

为减少化肥的过量施用，提高湖南宜章植烟土壤肥力和烟叶生产效益，以烤烟品种‘K326’为材料，采用田间试验研究了不同比例生物有机肥与化肥减量配施对土壤养分及烟叶产量与品质的影响。结果表明：增施适当比例生物有机肥配合化肥减量能不同程度地改善土壤肥力质量，促进烟株的生长。随着生物有机肥比例的增加与化肥用量的减少，烤烟的各项生长农艺性状、感官评吸质量、产量、产值以及上等烟比例呈先升后降的趋势。其中，以减量20%化学追肥的T₂处理对烟株的生长和烟叶的品质表现最好。与常规施肥的对照(CK)相比，烟草株高、有效叶片数和最大叶面积分别增加8.24%~17.00%、13.81%~23.22%和12.63%~16.86%，C3F烟叶中总糖和钾含量分别达到26.51%~30.01%和2.16%~2.86%，C3F和B2F烟叶的感官评吸质量分别提高1.67%~2.98%和3.12%~4.10%，烟叶产量、上等烟比例和产值分别提高3.76%~6.58%、3.38%~3.79%和8.24%~9.58%。研究结果为湘南植烟区应用生物有机肥与化肥减量配施提供了科学参考依据。