The effects of short-term, long-term, and reapplication of biochar on the remediation of heavy metal-contaminated soil.

Biochar, a cost-effective amendment, has been reported to play pivotal roles in improving soil fertility and immobilizing soil pollutants due to its well-developed porous structure and tunable functionality. However, the properties of biochar and soils can vary inconsistently after field application. This may affect the remediation of biochar on heavy metal (HM)-contaminated soil being altered. Therefore, we selected lettuce as a model crop to determine the effects of short-term, long-term, and reapplication of biochar on soil physicochemical properties, microbial community, HM bioavailability, and plant toxicity. Our investigation revealed that the long-term application of biochar remarkably improved soil fertility, increased the relative abundance of the phylum Proteobacteria which was highly resistant to HMs, and reduced the abundance of phylum Acidobacteria. These changes in soil properties decreased the accumulation of Cd and Pb in lettuce tissues. The short- and long-term applications of biochar had no substantial effects on biomass, quality, and photosynthesis of lettuce. Moreover, the short-term and reapplication of biochar had no significant effects on soil bacterial communities but decreased the accumulation of Cd and Pb in lettuce tissues. It showed that the changes in the physical, chemical, and biological properties of soil after long-term application of biochar promoted the remediation of HM-contaminated soil. Furthermore, microbial community compositions varied with metal stress and biochar application, while the relative abundance of the phylum Actinobacteria in HM-contaminated soil with long-term biochar application was markedly higher than in HM-contaminated soil without biochar application.

Study on the physicochemical properties changes of field aging biochar and its effects on the immobilization mechanism for Cd2+ and Pb2.

It has been widely reported that biochar can be used as a cost-effective amendment to immobilize of heavy metal contaminants in soil. While less research has been conducted on effect of biochar long-term field aging on its properties and the adsorption capability. In this study, the characteristics of aged biochar were investigated by comprehensive characterization to elucidate its mechanism transformation for heavy metal immobilization. Our results showed that, compared to fresh biochar, the relative content of C of aged biochar was reduced by 34.12%, while O was increased by 8.79%. Additionally, the specific surface area, pore volume, pore size and oxygen-containing functional groups of aged biochar were significantly increased compared to the fresh biochar. Batch adsorption experiment indicated that the maximum adsorption for Cd2+ (Qm = 32.157 mg/g) and Pb2+ (Qm = 39.216 mg/g) on aged biochar surface was much larger than that of Cd2+ (Qm = 7.573 mg/g) and Pb2+ (Qm = 8.134 mg/g) on fresh biochar. The underlying adsorption mechanisms for Cd2+ and Pb2+ on fresh biochar were dominated by coprecipitation, cation exchange and cation-π interaction, whereas surface complexation and cation exchange appeared to be more vital for aged biochar, as more active adsorption sites and Oxygen-containing functional groups were formed on its surface during aging, which was well explained by BET, XPS, FTIR and Elemental Analysis. Our study found that the physicochemical properties of biochar changed significantly during field aging. Although these changes increased the adsorption of heavy metals by biochar, the reduced stability of biochar to passivated heavy metal ions.

A novel negative-stranded RNA virus of the order Bunyavirales identified in Brassica campestris L. ssp. chinensis.

Here, we report the full-length genome sequence of a novel cogu-like virus identified in Brassica campestris L. ssp. Chinensis (B. campestris), an economically important vegetable in China. This virus, tentatively named "Brassica campestris chinensis coguvirus 1" (BCCoV1), has a bipartite genome that consists of two RNA molecules (RNA1 and RNA2). The negative-stranded (ns) RNA1 is 6757 nt in length, encoding the putative RNA-dependent RNA polymerase (RdRp), and the ambisense RNA2 is 3061 nt long, encoding the putative movement protein (MP) and nucleocapsid protein (NP). A homology search of the RdRp, MP, and NP showed that they are closely related to five other recently discovered negative-stranded RNA (nsRNA) viruses infecting plants, belonging to the new genus Coguvirus. Phylogenetic analysis of the 252-kDa RdRp confirmed the classification of this virus, showing that BCCoV1 possibly belongs to the genus Coguvirus, family Phenuiviridae, order Bunyavirales. The present study improves our understanding of the viral diversity in B. campestris and the evolution of nsRNA viruses.

Complete nucleotide sequence of a novel partitivirus from Brassica campestris L. ssp. chinensis.

In the present work, we report the discovery and complete genome sequence of a novel partitivirus identified from Brassica campestris L. ssp. chinensis, which we have named "Brassica campestris chinensis cryptic virus 1" (BCCV1). Next-generation sequencing (NGS) combined with adapter-ligation-mediated amplification allowed assembly of the full-length genome sequence of BCCV1. The genome of BCCV1 contains two dsRNA segments, dsRNA1 (1595 bp) and dsRNA2 (1591 bp), which encode a conserved RNA-dependent RNA polymerase (RdRp) and a putative capsid protein (CP), respectively. Homology searches and phylogenetic analysis of the 479-aa RdRp and 438-aa CP showed that BCCV1 is a new member of the genus Deltapartitivirus, family Partitiviridae. This is the first report of the identification of a member of the family Partitiviridae in Brassica campestris L. ssp. chinensis.

Comparative transcript profiling and cytological observation of the newly bred recessive genic male sterility non-heading Chinese cabbage (Brassica rapa ssp. chinensis) line WS24-3A.

BACKGROUND: WS24-3A is a newly bred non-heading Chinese cabbage genic male-sterile line, in which sterility is controlled by a recessive gene, designated as Bra2ms. WS24-3A has been used for hybrid breeding. OBJECTIVE: To reveal the underlying molecular mechanisms responsible for the sterility of WS24-3A. METHODS: Cytological observation of the process of sterile/fertile anther development was performed to determine the tissue and stage in which sterility occurs. Phenotyping and transcriptomic analyses were performed to identify differentially expressed genes (DEGs) between sterile and fertile flower buds at different stages. RESULTS: Cytological analysis revealed no tetrads at stage 7 or at later stages of anther development, and the degradation of callose was delayed. Abnormal meiocytes were surrounded by sustaining callose that degenerated gradually in WS24-3A. Comparative transcript profiling identified 3282 DEGs during three anther developmental stages, namely, pre-meiotic anther, meiotic anther, and anthers with single-celled pollen stage. The difference in DEG percentage between up-regulated and down-regulated at meiotic anther stage was obviously larger than at the other two stages; further, most DEGs are important for male meiosis, callose synthesis and dissolution, and tapetum development. Ten DEGs were found to be involved in anther and pollen development, which were analyzed by quantitative PCR. CONCLUSION: Bra2ms affected gene expression in meiocytes and associated with callose synthesis, degradation and tapetum development. Our results provide clues to elucidate the molecular mechanism of genic male sterility in non-heading Chinese cabbage.

Genome-wide analysis of long non-coding RNAs unveils the regulatory roles in the heat tolerance of Chinese cabbage (Brassica rapa ssp.chinensis).

Long non-coding RNAs (lncRNAs) mediate important epigenetic regulation in various biological processes related to the stress response in plants. However, the systematic analysis of the lncRNAs expressed in Brassica rapa under heat stress has been elusive. In this study, we performed a genome-wide analysis of the lncRNA expression profiles in non-heading Chinese cabbage leaves using strand-specific RNA-sequencing. A total of 4594 putative lncRNAs were identified with a comprehensive landscape of dynamic lncRNA expression networks under heat stress. Co-expression networks of the interactions among the differentially expressed lncRNAs, mRNAs and microRNAs revealed that several phytohormones were associated with heat tolerance, including salicylic acid (SA) and brassinosteroid (BR) pathways. Of particular importance is the discovery of 25 lncRNAs that were highly co-expressed with 10 heat responsive genes. Thirty-nine lncRNAs were predicted as endogenous target mimics (eTMs) for 35 miRNAs, and five of them were validated to be involved in the heat tolerance of Chinese cabbage. Heat responsive lncRNA (TCONS_00048391) is an eTM for bra-miR164a, that could be a sponge for miRNA binding and may be a competing endogenous RNA (ceRNA) for the target gene NAC1 (Bra030820), affecting the expression of bra-miR164a in Chinese cabbage. Thus, these findings provide new insights into the functions of lncRNAs in heat tolerance and highlight a set of candidate lncRNAs for further studies in non-heading Chinese cabbage.

Drought-inhibited ribulose-1,5-bisphosphate carboxylase activity is mediated through increased release of ethylene and changes in the ratio of polyamines in pakchoi.

To study the mechanisms of drought inhibiting photosynthesis and the role of PAs and ethylene, the photosynthetic rate (Pn), the maximal photochemical efficiency of PSII (Fv/Fm), the intercellular CO2 concentration (Ci), photorespiratory rate (Pr), the amount of chlorophyll (chl), antioxidant enzyme activity, ethylene levels, RuBPC (ribulose-1,5-bisphosphate carboxylase) activity and endogenous polyamine levels of pakchoi were examined, and an inhibitor of S-adenosylmethionine decarboxylase (SAMDC) and an inhibitor of ethylene synthesis and spermidine (Spd) were used to induce the change of endogenous polyamine levels. The results show that drought induced a decrease in Pn and RuBPC activity, an increase in the intercellular CO2 concentration (Ci), but no change in the actual photochemical efficiency of PSII (ΦPSII), and chlorophyll content. In addition, drought caused an increase in the free putrescine (fPut), the ethylene levels, a decrease in the Spd and spermine (Spm) levels, and the PAs/fPut ratio in the leaves. The exogenous application of Spd and amino oxiacetic acid (AOAA, an inhibitor of ethylene synthesis) markedly reversed these drought-induced effects on polyamine, ethylene, Pn, the PAs/fPut ratio and RuBPCase activity in leaves. Methylglyoxal-bis(guanylhydrazone) (MGBG), an inhibitor of SAMDC resulting in the inability of activated cells to synthesize Spd and Spm, exacerbates the negative effects induced by drought. These results suggest that the decrease in Pn is at least partially attributed to the decrease of RuBPC activity under drought stress and that drought inhibits RuBPC activity by decreasing the ratio of PAs/fPut and increasing the release of ethylene.

The sacred lotus genome provides insights into the evolution of flowering plants.

Sacred lotus (Nelumbo nucifera) is an ornamental plant that is also used for food and medicine. This basal eudicot species is especially important from an evolutionary perspective, as it occupies a critical phylogenetic position in flowering plants. Here we report the draft genome of a wild strain of sacred lotus. The assembled genome is 792 Mb, which is approximately 85-90% of genome size estimates. We annotated 392 Mb of repeat sequences and 36,385 protein-coding genes within the genome. Using these sequence data, we constructed a phylogenetic tree and confirmed the basal location of sacred lotus within eudicots. Importantly, we found evidence for a relatively recent whole-genome duplication event; any indication of the ancient paleo-hexaploid event was, however, absent. Genomic analysis revealed evidence of positive selection within 28 embryo-defective genes and one annexin gene that may be related to the long-term viability of sacred lotus seed. We also identified a significant expansion of starch synthase genes, which probably elevated starch levels within the rhizome of sacred lotus. Sequencing this strain of sacred lotus thus provided important insights into the evolution of flowering plant and revealed genetic mechanisms that influence seed dormancy and starch synthesis.

Isolation and characterization of 13 new polymorphic microsatellite markers in the Phaseolus vulgaris L. (Common Bean) genome.

In this study, 13 polymorphic microsatellite markers were isolated from the Phaseolus vulgaris L. (common bean) by using the Fast Isolation by AFLP of Sequence COntaining Repeats (FIASCO) protocol. These markers revealed two to seven alleles, with an average of 3.64 alleles per locus. The polymorphic information content (PIC) values ranged from 0.055 to 0.721 over 13 loci, with a mean value of 0.492, and 7 loci having PIC greater than 0.5. The expected heterozygosity (H(E)) and observed heterozygosity (H(O)) levels ranged from 0.057 to 0.814 and from 0.026 to 0.531, respectively. Cross-species amplification of the 13 prime pairs was performed in its related specie of Vigna unguiculata L. Seven out of all these markers showed cross-species transferability. These markers will be useful for future genetic diversity and population genetics studies for this agricultural specie and its related species.