Gene-guided identifications of a structure-chimeric cyclotide viphi I from Viola philippica: Potential functions against cadmium and nematodes.

The cyclic peptides, cyclotides, are identified mostly with 29-31-aa (amino acid residues) but rarely with ≥ 34-aa in plants. Viola philippica is a well-known medicinal plant but a rare metallophyte with cyclotides. A hypothesis was hence raised that the potential novel 34-aa cyclotide of Viola philippica would clearly broaden the structural and functional diversities of plant cyclotides. After homology-cloning the cyclotide precursor gene of VpCP5, a 34-aa cyclotide (viphi I) was identified to be larger than 22 other known cyclotides in V. philippica. It had a chimeric primary structure, due to its unusual loop structures (8 residues in loop 2 and 6 residues in loop 5) and aa composition (3 E and 5 R), by using phylogenetic analyses and an in-house cyclotide analysis tool, CyExcel_V1. A plasmid pCYC-viphi_I and a lab-used recombinant process were specially constructed for preparing viphi I. Typically, 0.12 or 0.25 mg ml-1 co-exposed viphi I could significantly remain cell activities with elevating Cd2+-exposed doses from 10-8 to 10-6 mol l-1 in MCF7 cells. In the model nematode Caenorhabditis elegans, IC50 values of viphi I to inhibit adult ratios and to induce death ratios, were 184.7 and 585.9 µg ml-1, respectively; the median lifespan of adult worms decreased from 14 to 2 d at viphi I doses ranging from 0.05 to 2 mg ml-1. Taken together, the newly identified viphi I exhibits functional potentials against cadmium and nematodes, providing new insights into structural and functional diversity of chimeric cyclotides in plants.

CyanoStrainChip: A Novel DNA Microarray Tool for High-Throughput Detection of Environmental Cyanobacteria at the Strain Level.

Detecting cyanobacteria in environments is an important concern due to their crucial roles in ecosystems, and they can form blooms with the potential to harm humans and nonhuman entities. However, the most widely used methods for high-throughput detection of environmental cyanobacteria, such as 16S rRNA sequencing, typically provide above-species-level resolution, thereby disregarding intraspecific variation. To address this, we developed a novel DNA microarray tool, termed the CyanoStrainChip, that enables strain-level comprehensive profiling of environmental cyanobacteria. The CyanoStrainChip was designed to target 1277 strains; nearly all major groups of cyanobacteria are included by implementing 43,666 genome-wide, strain-specific probes. It demonstrated strong specificity by in vitro mock community experiments. The high correlation (Pearson's R > 0.97) between probe fluorescence intensities and the corresponding DNA amounts (ranging from 1-100 ng) indicated excellent quantitative capability. Consistent cyanobacterial profiles of field samples were observed by both the CyanoStrainChip and next-generation sequencing methods. Furthermore, CyanoStrainChip analysis of surface water samples in Lake Chaohu uncovered a high intraspecific variation of abundance change within the genus Microcystis between different severity levels of cyanobacterial blooms, highlighting two toxic Microcystis strains that are of critical concern for Lake Chaohu harmful blooms suppression. Overall, these results suggest a potential for CyanoStrainChip as a valuable tool for cyanobacterial ecological research and harmful bloom monitoring to supplement existing techniques.

Comparative Transcriptomic Studies on a Cadmium Hyperaccumulator Viola baoshanensis and Its Non-Tolerant Counterpart V. inconspicua.

Many Viola plants growing in mining areas exhibit high levels of cadmium (Cd) tolerance and accumulation, and thus are ideal organisms for comparative studies on molecular mechanisms of Cd hyperaccumulation. However, transcriptomic studies of hyperaccumulative plants in Violaceae are rare. Viola baoshanensis is an amazing Cd hyperaccumulator in metalliferous areas of China, whereas its relative V. inconspicua is a non-tolerant accumulator that resides at non-metalliferous sites. Here, comparative studies by transcriptome sequencing were performed to investigate the key pathways that are potentially responsible for the differential levels of Cd tolerance between these two Viola species. A cascade of genes involved in the ubiquitin proteosome system (UPS) pathway were observed to have constitutively higher transcription levels and more activation in response to Cd exposure in V. baoshanensis, implying that the enhanced degradation of misfolded proteins may lead to high resistance against Cd in this hyperaccumulator. Many genes related to sucrose metabolism, especially those involved in callose and trehalose biosynthesis, are among the most differentially expressed genes between the two Viola species, suggesting a crucial role of sucrose metabolism not only in cell wall modification through carbon supply but also in the antioxidant system as signaling molecules or antioxidants. A comparison among transcriptional patterns of some known transporters revealed that several tonoplast transporters are up-regulated in V. baoshanensis under Cd stress, suggesting more efficient compartmentalization of Cd in the vacuoles. Taken together, our findings provide valuable insight into Cd hypertolerance in V. baoshanensis, and the corresponding molecular mechanisms will be useful for future genetic engineering in phytoremediation.

Ciprofloxacin degradation in anaerobic sulfate-reducing bacteria (SRB) sludge system: Mechanism and pathways.

Ciprofloxacin (CIP), a fluoroquinolone antibiotic, removal was examined for the first time, in an anaerobic sulfate-reducing bacteria (SRB) sludge system. About 28.0% of CIP was biodegraded by SRB sludge when the influent CIP concentration was 5000 µg/L. Some SRB genera with high tolerance to CIP (i.e. Desulfobacter), were enriched at CIP concentration of 5000 µg/L. The changes in antibiotic resistance genes (ARGs) of SRB sludge coupled with CIP biodegradation intermediates were used to understand the mechanism of CIP biodegradation for the first time. The percentage of efflux pump genes associated with ARGs increased, while the percentage of fluoroquinolone resistance genes that inhibit the DNA copy of bacteria decreased during prolonged exposure to CIP. It implies that some intracellular CIP was extruded into extracellular environment of microbial cells via efflux pump genes to reduce fluoroquinolone resistance genes accumulation caused by exposure to CIP. Additionally, the degradation products and the possible pathways of CIP biodegradation were also examined using the new method developed in this study. The results suggest that CIP was biodegraded intracellularly via desethylation reaction in piperazinyl ring and hydroxylation reaction catalyzed by cytochrome P450 enzymes. This study provides an insight into the mechanism and pathways of CIP biodegradation by SRB sludge, and opens-up a new opportunity for the treatment of CIP-containing wastewater using sulfur-mediated biological process.

Microbial community structure and function in sediments from e-waste contaminated rivers at Guiyu area of China.

The release of toxic organic pollutants and heavy metals by primitive electronic waste (e-waste) processing to waterways has raised significant concerns, but little is known about their potential ecological effects on aquatic biota especially microorganisms. We characterized the microbial community composition and diversity in sediments sampled along two rivers consistently polluted by e-waste, and explored how community functions may respond to the complex combined pollution. High-throughput 16S rRNA gene sequencing showed that Proteobacteria (particularly Deltaproteobacteria) dominated the sediment microbial assemblages followed by Bacteroidetes, Acidobacteria, Chloroflexi and Firmicutes. PICRUSt metagenome inference provided an initial insight into the metabolic potentials of these e-waste affected communities, speculating that organic pollutants degradation in the sediment might be mainly performed by some of the dominant genera (such as Sulfuricurvum, Thiobacillus and Burkholderia) detected in situ. Statistical analyses revealed that toxic organic compounds contributed more to the observed variations in sediment microbial community structure and predicted functions (24.68% and 8.89%, respectively) than heavy metals (12.18% and 4.68%), and Benzo(a)pyrene, bioavailable lead and electrical conductivity were the key contributors. These results have shed light on the microbial assemblages in e-waste contaminated river sediments, indicating a potential influence of e-waste pollution on the microbial community structure and function in aquatic ecosystems.

Field comparison of the effectiveness of agricultural and nonagricultural organic wastes for aided phytostabilization of a Pb-Zn mine tailings pond in Hunan Province, China.

To date, very few attempts have been made to systematically compare the effectiveness of agricultural and nonagricultural organic wastes for aided phytostabilization of mine tailings under field conditions. In this study, we performed a field trial to compare the effectiveness of three agricultural organic wastes: chicken manure (CM), crop straw (CS), and spent mushroom compost (SMC), with that of three nonagricultural organic wastes, municipal sludge (MS), medicinal herb residues (MHR), and sweet sorghum vinasse (SSV) for aided phytostabilization of a Pb-Zn mine tailings pond in Hunan Province, China. Eight plant species naturally established in the vicinity of the mine were selected and seeded onto trial plots. It was found that the CM-amended plots had the highest (p < 0.05) vegetation cover (86%) and biomass production (881 g m-2), compared to other treatments. CM was also one of the best amendments in terms of improving soil nutrient status, increasing activities of soil enzymes, and immobilizing soil Pb. In addition, CM-amended plots were characterized by their higher microbial diversity and distinct microbial community structure as compared to the control plots. MS was the second best amendment in promoting vegetation cover (71%) and biomass production (461 g m-2), and it performed as well as CM for improving nutrient status, immobilizing heavy metals, and increasing the activities of enzymes in the mine tailings. Suggestions for further lines of research are made in order to develop future investigations.

Fine-scale spatial patterns in microbial community composition in an acid mine drainage.

Microbial community composition is essential for aquatic ecosystem functions and has been explored across diverse environments and various spatial scales. However, documented patterns are often based on samples from spatially/geographically separated locations or sites. Here, we define sampling volume as spatial scale and examine (by Illumina 16S rRNA sequencing) microbial community composition over a scale of 1 mL to 10 L in an acid mine drainage. ß-Diversity analysis revealed that all samples grouped very tightly according to spatial scales and variations between every two scales were significant. Notably, mean ß-diversity within each group was negatively correlated with spatial scales, indicating patchy microbial distribution. Partition of ß-diversity further revealed that it was the relative abundances of some microbial taxa that largely changed among spatial scales. Phylogenetic analysis showed that microbial lineages were not randomly distributed, but displayed a tendency of more phylogenetically clustering at smaller spatial scales. Thus, we documented fine-scale spatial patterns in microbial community composition within a continuous aquatic environment, which may have practical implications for adequate sampling of aquatic systems in future studies.

Conservation of Species- and Trait-Based Modeling Network Interactions in Extremely Acidic Microbial Community Assembly.

Understanding microbial interactions is essential to decipher the mechanisms of community assembly and their effects on ecosystem functioning, however, the conservation of species- and trait-based network interactions along environmental gradient remains largely unknown. Here, by using the network-based analyses with three paralleled data sets derived from 16S rRNA gene pyrosequencing, functional microarray, and predicted metagenome, we test our hypothesis that the network interactions of traits are more conserved than those of taxonomic measures, with significantly lower variation of network characteristics along the environmental gradient in acid mine drainage. The results showed that although the overall network characteristics remained similar, the structural variation was significantly lower at trait levels. The higher conserved individual node topological properties at trait level rather than at species level indicated that the responses of diverse traits remained relatively consistent even though different species played key roles under different environmental conditions. Additionally, the randomization tests revealed that it could not reject the null hypothesis that species-based correlations were random, while the tests suggested that correlation patterns of traits were non-random. Furthermore, relationships between trait-based network characteristics and environmental properties implied that trait-based networks might be more useful in reflecting the variation of ecosystem function. Taken together, our results suggest that deterministic trait-based community assembly results in greater conservation of network interaction, which may ensure ecosystem function across environmental regimes, emphasizing the potential importance of measuring the complexity and conservation of network interaction in evaluating the ecosystem stability and functioning.

The effects of phylogenetic relatedness on invasion success and impact: deconstructing Darwin's naturalisation conundrum.

Darwin's naturalisation conundrum describes the paradox that the relatedness of exotic species to native residents could either promote or hinder their success through opposing mechanisms: niche pre-adaptation or competitive interactions. Previous studies focusing on single snapshots of invasion patterns have provided support to both sides of the conundrum. Here, by examining invasion dynamics of 480 plots over 40 years, we show that exotic species more closely related to native species were more likely to enter, establish and dominate the resident communities, and that native residents more closely related to these successful exotics were more likely to go locally extinct. Therefore, non-random displacement of natives during invasion could weaken or even reverse the negative effects of exotic-native phylogenetic distances on invasion success. The scenario that exotics more closely related to native residents are more successful, but tend to eliminate their closely related natives, may help to reconcile the 150-year-old conundrum.