Toward broader applications of iron ore waste in pollution control: Adsorption of norfloxacin.

Norfloxacin, a kind of antibiotic frequently detected in environments, represents a group of non-persistent organic pollutants with latent risks to the ecosystem. Iron ore waste, generated and accumulated in large quantities from the iron/steel industry, was evaluated as a potential sorbent for norfloxacin removal. Kinetics analysis showed that the adsorption process reached equilibrium at 72 h, and the adsorption process could be best defined by the pseudo-second-order kinetics with the primary mechanism of norfloxacin adsorption suggested to be cation exchange. Further, adsorption of norfloxacin to iron ore waste was shown to be facilitated by the pH range of 2-10, low cation concentration, and low temperature, which are characteristic of natural surface waters, suggesting the potential of practical applications in aquatic environments. These findings provide new insight into the potentials of beneficial reuse for iron ore waste in the adsorptive removal of environmental pollutants.

Comparative genome analysis and mining of secondary metabolites of Paenibacillus polymyxa.

Paenibacillus polymyxa is a well-known Gram-positive biocontrol bacterium. It has been reported that many P. polymyxa strains can inhibit bacteria, fungi and other plant pathogens. Paenibacillus polymyxa employs a variety of mechanisms to promote plant growth, so it is necessary to understand the biocontrol ability of bacteria at the genome level. In the present study, thanks to the widespread availability of Paenibacillus genome data and the development of bioinformatics tools, we were able to analyze and mine the genomes of 43 P. polymyxa strains. The strain NCTC4744 was determined not to be P. polymyxa according to digital DNA-DNA hybridization and average nucleotide identity. By analysis of the pan-genome and the core genome, we found that the pan-genome of P. polymyxa was open and that there were 3,192 core genes. In a gene cluster analysis of secondary metabolites, 797 secondary metabolite gene clusters were found, of which 343 are not similar to known clusters and are expected to reveal a large number of new secondary metabolites. We also analyzed the plant growth-promoting genes that were mined and found, surpisingly, that these genes are highly conserved. The results of the present study not only reveal a large number of unknown potential secondary metabolite gene clusters in P. polymyxa, but also suggest that plant growth promotion characteristics are evolutionary adaptations of P. polymyxa to plant-related habitats.

Genomics and LC-MS Reveal Diverse Active Secondary Metabolites in Bacillus amyloliquefaciens WS-8.

Bacillus amyloliquefaciens is an important plant disease-preventing and growth-promoting microorganism. B. amyloliquefaciens WS-8 can stimulate plant growth and has strong antifungal properties. In this study, we sequenced the complete genome of B. amyloliquefaciens WS-8 by Pacific Biosciences RSII (PacBio) Single Molecule Real-Time (SMRT) sequencing. The genome consists of one chromosome (3,929,787 bp) and no additional plasmids. The main bacteriostatic substances were determined by genome, transcriptome, and mass spectrometry data. We thereby laid a theoretical foundation for the utilization of the strain. By genomic analysis, we identified 19 putative biosynthetic gene clusters for secondary metabolites, most of which are potentially involved in the biosynthesis of numerous bioactive metabolites, including difficidin, fengycin, and surfactin. Furthermore, a potential class II lanthipeptide biosynthetic gene cluster and genes that are involved in auxin biosynthesis were found. Through the analysis of transcriptome data, we found that the key bacteriostatic genes, as predicted in the genome, exhibited different levels of mRNA expression. Through metabolite isolation, purification, and exposure experiments, we found that a variety of metabolites of WS-8 exert an inhibitory effect on the necrotrophic fungus Botrytis cinerea, which causes gray mold; by mass spectrometry, we found that the main substances are mainly iturins and fengycins. Therefore, this strain has the potential to be utilized as an antifungal agent in agriculture.

The archaeal RNA chaperone TRAM0076 shapes the transcriptome and optimizes the growth of Methanococcus maripaludis.

TRAM is a conserved domain among RNA modification proteins that are widely distributed in various organisms. In Archaea, TRAM occurs frequently as a standalone protein with in vitro RNA chaperone activity; however, its biological significance and functional mechanism remain unknown. This work demonstrated that TRAM0076 is an abundant standalone TRAM protein in the genetically tractable methanoarcheaon Methanococcus maripaludis. Deletion of MMP0076, the gene encoding TRAM0076, markedly reduced the growth and altered transcription of 55% of the genome. Substitution mutations of Phe39, Phe42, Phe63, Phe65 and Arg35 in the recombinant TRAM0076 decreased the in vitro duplex RNA unfolding activity. These mutations also prevented complementation of the growth defect of the MMP0076 deletion mutant, indicating that the duplex RNA unfolding activity was essential for its physiological function. A genome-wide mapping of transcription start sites identified many 5' untranslated regions (5'UTRs) of 20-60 nt which could be potential targets of a RNA chaperone. TRAM0076 unfolded three representative 5'UTR structures in vitro and facilitated the in vivo expression of a mCherry reporter system fused to the 5'UTRs, thus behaving like a transcription anti-terminator. Flag-tagged-TRAM0076 co-immunoprecipitated a large number of cellular RNAs, suggesting that TRAM0076 plays multiple roles in addition to unfolding incorrect RNA structures. This work demonstrates that the conserved archaeal RNA chaperone TRAM globally affects gene expression and may represent a transcriptional element in ancient life of the RNA world.

Synergetic effect of combined ensiling of freshly harvested and excessively wilted maize stover for efficient biogas production.

This study investigated the synergetic effects of ensiling freshly harvested maize stover (FHM) and excessively wilted maize stover (EWM) on biogas production. FHM and EWM were mixed in various proportions to obtain dry matter (DM) contents of 30%, 35% and 40%. For reference, FHM alone was ensiled and stored in open-air. Successful storage performance was obtained by the ensiling treatments, and the organic matter loss of 1.1-2.2% was far lower than in open-air storage (63.1%). An initial water-soluble carbohydrate (WSC) of 5% DM is adequate for the combined ensiling of maize stover with the highest WSC degradation rate of 81.2%. Combined ensiling enhanced the activity of Weissella, a genus of heterofermentative lactic acid bacteria, under relatively high pH conditions. Therefore, the combined ensiling can preserve FHM and enhance the digestibility of EWM (theoretical specific methane yield increased 16.5%), which would be a promising storage strategy for efficient biogas production.

Unexpected competitiveness of Methanosaeta populations at elevated acetate concentrations in methanogenic treatment of animal wastewater.

Acetoclastic methanogenesis is a key metabolic process in anaerobic digestion, a technology with broad applications in biogas production and waste treatment. Acetoclastic methanogenesis is known to be performed by two archaeal genera, Methanosaeta and Methanosarcina. The conventional model posits that Methanosaeta populations are more competitive at low acetate levels (<1 mM) than Methanosarcina and vice versa at higher acetate concentrations. While this model is supported by an extensive body of studies, reports of inconsistency have grown that Methanosaeta were observed to outnumber Methanosarcina at elevated acetate levels. In this study, monitoring of anaerobic digesters treating animal wastewater unexpectedly identified Methanosaeta as the dominant acetoclastic methanogen population at both low and high acetate levels during organic overloading. The surprising competitiveness of Methanosaeta at elevated acetate was further supported by the enrichment of Methanosaeta with high concentrations of acetate (20 mM). The dominance of Methanosaeta in the methanogen community could be reproduced in anaerobic digesters with the direct addition of acetate to above 20 mM, again supporting the competitiveness of Methanosaeta over Methanosarcina at elevated acetate levels. This study for the first time systematically demonstrated that the dominance of Methanosaeta populations in anaerobic digestion could be linked to the competitiveness of Methanosaeta at elevated acetate concentrations. Given the importance of acetoclastic methanogenesis in biological methane production, findings from this study could have major implications for developing strategies for more effective control of methanogenic treatment processes.

Complete genome sequence of Bacillus subtilis BSD-2, a microbial germicide isolated from cultivated cotton.

Bacillus subtilis BSD-2, isolated from cotton (Gossypium spp.), had strong antagonistic activity to Verticillium dahlia Kleb and Botrytis cinerea. We sequenced and annotated the BSD-2 complete genome to help us the better use of this strain, which has surfactin, bacilysin, bacillibactin, subtilosin A, Tas A and a potential class IV lanthipeptide biosynthetic pathways.

Linkages of Firmicutes and Bacteroidetes populations to methanogenic process performance.

To identify potential linkages between specific bacterial populations and process performance in anaerobic digestion, the dynamics of bacterial community structure was monitored with high-throughput sequencing in triplicate anaerobic digesters treating animal waste. Firmicutes and Bacteroidetes were found as the two most abundant populations, however, with contrasting population dynamics in response to organic overloading. Firmicutes dominated the bacterial community during stable process performance at low organic loading rate, representing over 50 % of the bacterial abundance. In contrast, the onset of organic overloading raised the relative abundance of Bacteroidetes from 20 ± 2.6 to 44 ± 3.1 %. In addition to the significant negative correlation between the relative abundance of Firmicutes and Bacteroidetes, populations of Firmicutes and Bacteroidetes were found to be linked to process parameters including organic loading rate, volatile fatty acids concentration, and methane production. Therefore, the population abundance ratio of Firmicutes to Bacteroidetes (F/B ratio) was suggested as a potential indicator for process performance. The interactions between Firmicutes and Bacteroidetes populations could be exploited to develop strategies for the prevention of performance perturbation in anaerobic digestion processes.

[Transfer RNAs inhibit the growth of L929 cells in vitro].

AIM: To explore the effects of tRNA on the growth of mammalian cells. METHODS: L929, NIH3T3, MCF-7 and PC12 cells were seeded in 96 well culture plate individually, and incubated at 37 degrees C in 5% CO2 for 4 h, the tRNAs from different species were added to the culture media individually. After certain time of incubation, the viability of the cells was evaluated by the MTT methods. Sub-confluent L929 cells were incubated with 200 microg/ml ytRNA for different times, then the cells were pooled and analyzed with flow cytometry assay. RESULTS: tRNA specifically inhibited the growth of L929 cells in a dose-dependent manner. The sizes of tRNA-treated cells showed larger sizes and longer processes than those of untreated cells. Flow cytometric analysis further showed that most of tRNA-treated cells were arrested in S phase of the cell cycle. CONCLUSION: The cell growth inhibitory effects of tRNAs were caused mainly by their degraded fragments. The results suggested that tRNA or its degraded fragments might play important roles in regulation of cell proliferation.