BackgroundSoil contaminated with the heavy metal Cadmium (Cd) is a widespread problem in many parts of the world. Based on metagenomic analysis, we investigated the functional potential and structural diversity of the microbial community in Cd-contaminated and non-contaminated soil samples and we explored the associated metabolic pathway network in cluster of orthologous groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG).ResultsThe results showed that microorganisms in these soils were quite abundant, and many of them possessed numerous physiological functions. However, Cd-contamination has the potential to reduce the microbial diversity and further alter the community structure in the soil. Notably, function analysis of the crucial microorganisms (e. g. Proteobacteria, Sulfuricella and Thiobacillus) indicated that these bacteria and their corresponding physiological functions were important for the community to cope with Cd pollution. The COG annotation demonstrated that the predominant category was the microbial metabolism cluster in both soil samples, while the relative abundance of metabolic genes was increased in the Cd-contaminated soil. The KEGG annotation results exhibited that the non-contaminated soil had more genes, pathways, modules, orthologies and enzymes involved in metabolic pathways of microbial communities than the Cd-contaminated soil. The relative abundance of some dominant KEGG pathways increased in the Cd contaminated soil, and they were mostly enriched to the metabolism, biosynthesis and degradation of amino acids, fatty acids and nucleotides, which was related to Cd tolerance of the microorganisms.ConclusionsCd-contamination can decrease the taxonomic species of microbes in soil and change the soil microbial composition. The functional pathways involved in the soil change with microbial structure variation, many of which are related to the heavy metal tolerance of soil microbes. The Cd-contaminated soil microbes is a potential resource for exploring cadmium resistant or tolerant bacteria.Electronic supplementary materialThe online version of this article (10.1186/s12866-018-1152-5) contains supplementary material, which is available to authorized users.

Reporter systems are routinely used in plant genetic engineering and functional genomics research. Most such plant reporter systems cause accumulation of foreign proteins. Here, we demonstrate a protein-independent reporter system, 3WJ-4 × Bro, based on a fluorescent RNA aptamer. Via transient expression assays in both Escherichia coli and Nicotiana benthamiana, we show that 3WJ-4 × Bro is suitable for transgene identification and as an mRNA reporter for expression pattern analysis. Following stable transformation in Arabidopsis thaliana, 3WJ-4 × Bro co-segregates and co-expresses with target transcripts and is stably inherited through multiple generations. Further, 3WJ-4 × Bro can be used to visualize virusmediated RNA delivery in plants. This study demonstrates a protein-independent reporter system that can be used for transgene identification and in vivo dynamic analysis of mRNA.

Summary Bidirectional green tissue‐specific promoters have important application prospects in genetic engineering and crop genetic improvement. However, there is no report on the application of them, mainly due to undiscovered natural bidirectional green tissue‐specific promoters and the lack of a comprehensive approach for the synthesis of these promoters. In order to compensate for this vacancy, the present study reports a novel strategy for the expression regulatory sequence selection and the bidirectional green tissue‐specific synthetic promoter construction. Based on this strategy, seven promoters were synthesized and introduced into rice by agrobacterium‐mediated transformation. The functional identification of these synthetic promoters was performed by the expression pattern of GFP and GUS reporter genes in two reverse directions in transgenic rice. The results indicated that all the synthetic promoters possessed bidirectional expression activities in transgenic rice, and four synthetic promoters (BiGSSP2, BiGSSP3, BiGSSP6, BiGSSP7) showed highly bidirectional expression efficiencies specifically in green tissues (leaf, sheath, panicle, stem), which could be widely applied to agricultural biotechnology. Our study provided a feasible strategy for the construction of synthetic promoters, and we successfully created four bidirectional green tissue‐specific synthetic promoters. It is the first report on bidirectional green tissue‐specific promoters that could be efficiently applied in genetic engineering.

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Cadmium (Cd) pollution in soil is becoming increasingly serious due to anthropogenic activities, which not only poses a threat to the ecological environment, but also causes serious damage to human health via the biological chain. Consequently, special concerns should be paid to develop and combine multiple remediation strategies. In this study, different subspecies of oilseed rape, Brassica campestris, Brassica napus and Brassica juncea were applied, combined with three organic acids, acetic acid, oxalic acid and citric acid, in a simulated Cd-contaminated soil. Various physiological and biochemical indexes were monitored in both plant seedling, growth period and mature stage. The results showed that organic acids significantly promoted the growth of Brassica campestris and Brassica juncea under Cd stress. The photosynthesis and antioxidant enzyme activities in Brassica campestris and Brassica juncea were induced at seedling stage, while that in Brassica napus were suppressed and disturbed. The enrichment of Cd in oilseed rape was also obviously increased. Brassica juncea contained relatively high resistance and Cd content in plant but little Cd in seed. Among the three acids, oxalic acids exhibited the most efficient promoting effect on the accumulation of Cd by oilseed rape. Here, a comprehensive study on the combined effects of oilseed rape and organic acids on Cd contaminated soil showed that Brassica juncea and oxalic acid possessed the best effect on phytoremediation of Cd contaminated soil. Our study provides an optimal way of co-utilizing oilseed rape and organic acid in phytoremediation of Cd contaminated soil.