Phenanthrene regulates metabolic pathways for hydrogen accumulation in sludge alkaline dark fermentation.

The influence of phenanthrene (PHE), a general polycyclic aromatic hydrocarbon in waste activated sludge, on sludge alkaline dark fermentation for hydrogen accumulation was investigated prospectively. The yield of hydrogen was 16.2 mL/g TSS with 50 mg/kg TSS PHE, which was 1.3-fold greater than that of the control. Mechanism research demonstrated that hydrogen production and the abundance of functional microorganisms were facilitated, whereas those of homoacetogenesis were reduced. The activity of pyruvate ferredoxin oxidoreductase in the conversion of pyruvate to reduced ferredoxin for hydrogen production was promoted by 57.2%, and that of carbon monoxide dehydrogenase and formyltetrahydrofolate synthetase, closely associated with hydrogen consumption, was suppressed by 60.5% and 55.9%, respectively. Moreover, the encoding genes involved in pyruvate metabolism were significantly up-regulated, while genes related to consuming hydrogen to reduce carbon dioxide and produce 5-methyltetrahydrofolate were down-regulated. This study notably illustrates the effect of PHE on hydrogen accumulation from metabolic pathways.

Polycyclic aromatic hydrocarbons stimulate acidogenesis, acetogenesis and methanogenesis during anaerobic co-digestion of waste activated sludge and food waste.

Polycyclic aromatic hydrocarbons (PAHs) have been reported to influence acetic acid production during anaerobic treatment. However, investigations of the impacts of PAHs on the anaerobic co-digestion of waste activated sludge and food waste are limited. Therefore, the effects of PAHs on anaerobic co-digestion were explored in this study. Four kinds of PAHs all exhibited positive contributions to methane production, especially phenanthrene. Mechanism exploration revealed that acidogenesis, acetogenesis, and methanogenesis were improved in the presence of phenanthrene, and acetotrophic methanogenesis had the greatest improvement with 69.4%. Dominant bacteria and archaea related to acetic acid and methane accumulation were changed by phenanthrene. Moreover, extracellular polymeric substances, coenzyme F420, and McrA gene copy number were promoted by phenanthrene, which was beneficial for the generation of acetic acid and methane. Overall, this study provides new insights into the role of organic pollutants in the anaerobic co-digestion of solid wastes.

Amino Acid Configuration Affects Volatile Fatty Acid Production during Proteinaceous Waste Valorization: Chemotaxis, Quorum Sensing, and Metabolism.

During proteinaceous waste valorization to produce volatile fatty acids (VFAs), protein needs to be hydrolyzed to amino acids (AAs), but the effects of the configuration of AAs on their biotransformation and VFA production have not been investigated. In this study, more residual d-AAs than their corresponding l-AAs were observed after VFAs were produced from kitchen waste in a pilot-scale bioreactor. For all AAs investigated, the VFA production from d-AAs was lower than that from corresponding l-AAs. The metagenomics and metaproteomics analyses revealed that the l-AA fermentation system exhibited greater bacterial chemotaxis and quorum sensing (QS) than d-AAs, which benefited the establishment of functional microorganisms (such as Clostridium, Sedimentibacter, and Peptoclostridium) and expression of functional proteins (e.g., substrate transportation cofactors, l-AA dehydrogenase, and acidogenic proteins). In addition, d-AAs need to be racemized to l-AAs before being metabolized, and the difference of VFA production between d-AAs and l-AAs decreased with the increase of racemization activity. The findings of the AA configuration affecting bacterial chemotaxis and QS, which altered microorganism communities and functional protein expression, provided a new insight into the reasons for higher l-AA metabolism than d-AAs and more d-AAs left during VFA production from proteinaceous wastes.

Volatile fatty acids production from waste activated sludge during anaerobic fermentation: The effect of superfine sand.

Superfine sand in waste activated sludge (WAS) increased the uncertainty of anaerobic fermentation. Experiments showed that VFAs production from WAS was positively affected by superfine sand, with an increase from 2513 mg COD/L in the control (without superfine sand) to 3002 mg COD/L with superfine sand. A mechanism study demonstrated that the main factor responsible for the improved VFAs accumulation in response to superfine sand was acetic acid, which increased by nearly 30%. Further investigation exhibited that the process of solubilization and acidification were facilitated by superfine sand and the abundance of anaerobic functional microorganisms was greatly increased. Moreover, the activities of acetate kinase (AK) as well as the quantity of AK encoding gene were greatly promoted by superfine sand. The heat release during WAS anaerobic fermentation with superfine sand was higher than that without superfine sand (25.8 × 10-3 versus 24.7 × 10-3 W·min at about 70 min).

Nitrogen-doped porous carbon derived from digested sludge for electrochemical reduction of carbon dioxide to formate.

Carbon-based materials have been applied as cost-effective electrocatalysts to reduce carbon dioxide (CO2) into valuable chemicals. Here, an environment-friendly method is proposed to obtain nitrogen-doped porous carbons (NPCs) from digested sludge, which is an abundant waste product from sewage treatment plants. The materials were used as a metal-free electrocatalyst for electrochemical reduction of CO2 to formate. The synthesized material (NPC-600) had a mesoporous and microporous structure with a specific surface area of 246.21 m2 g-1 and pore volume of 0.494 cm3 g-1. Active sites based on nitrogen atoms accounted for 2.98 atom% of the content and included pyrrolic-, pyridinic-, and graphitic-N, which is useful for CO2 adsorption and electron transfer in electrochemical reduction. The Faradaic efficiency for formate production from CO2 in the presence of NPC-600 was 68% at the potential of -1.5 V vs. SCE. Tafel analysis indicated that the pathway of CO2 conversion involved the reduction of CO2 to CO2*- intermediate, which was then converted to HCOO*- and finally formate.

Boron-, sulfur-, and phosphorus-doped graphene for environmental applications.

The control of environmental pollutants is a global concern. Recently, heteroatom-doped graphene has drawn increasing attention due to their widespread applications in removing and detecting environmental pollutants. Owing to the introduction of heteroatoms into pristine graphene, the properties of heteroatom-doped graphene have been significantly enhanced in physic, chemistry, and biology. This review focuses on the approaches for synthesis and characterization of boron-, sulfur-, and phosphorus-doped graphene and their applications in the fields of adsorption, catalysis, and detection for environmental pollutants. The mechanisms of environmental applications, including π-π interactions, complexation, hydrophobic interactions, electronic conductivity, and active sites and reactive radicals, are elaborated. Furthermore, the challenges associated with the use of heteroatom-doped graphene materials and their prospective applications are also proposed.

Significance of manganese resistant bacillus cereus strain WSE01 as a bioinoculant for promotion of plant growth and manganese accumulation in Myriophyllum verticillatum.

Endophytic bacteria are generally helpful for plant growth and protection. Strain WSE01, which was identified as bacillus cereus, was isolated from the stem of Myriophyllum verticillatum and it displayed a high tolerance to Mn (1500 mg/L). The strain was found to be able to produce indole-3-acetic acid (IAA) and siderophores, fix the atmospheric nitrogen and dissolve potassium from insoluble K-bearing minerals. In hydroponic culture experiments, the inoculation of strain WSE01 significantly promoted the growth and increased the leaf enzyme activity in the inoculated plant M. verticillatum. Furthermore, the manganese content was increased by 36.4% in stems and by 54.7% in leaves of the inoculated plant under Mn stress at 400 mg/L, compared to the non-inoculated group. This study suggests that the strain WSE01 has the potential to be used as biocontrol and/or biofertilizing agents for application in macrophyte M. verticillatum and conduces to achieving more effective phytoremediation of metal-contaminated waters.

A novel manganese oxidizing bacterium-Aeromonas hydrophila strain DS02: Mn(II) oxidization and biogenic Mn oxides generation.

The extensive applications of biogenic manganese oxides (BioMnOx) generated by manganese oxidizing bacteria (MOB) have attracted considerable attentions. In this study, we report on a novel MOB that has been isolated from sediments and identified as Aeromonas hydrophila strain DS02. The Mn(II) oxidation activity of strain DS02 under Mn(II) stress and the application of the associated BioMnOx products were investigated. Nearly 90.0% (495 mg L-1) of the soluble Mn(II) were removed and 45.6% (240 mg L-1) was converted to Mn(III/IV). Fitting the XPS data showed that Mn(IV)-oxide is the major component (82.0%) of the flake-shaped BioMnOx, corresponding to an average Mn oxidation number of 3.71. When the BioMnOx were coupled with the PMS activation, a 99.5% catalytic degradation of 2,4-dimethylaniline was observed after 80 min, revealing a high degradation efficiency.

SEASTAR: systematic evaluation of alternative transcription start sites in RNA.

Alternative first exons diversify the transcriptomes of eukaryotes by producing variants of the 5' Untranslated Regions (5'UTRs) and N-terminal coding sequences. Accurate transcriptome-wide detection of alternative first exons typically requires specialized experimental approaches that are designed to identify the 5' ends of transcripts. We developed a computational pipeline SEASTAR that identifies first exons from RNA-seq data alone then quantifies and compares alternative first exon usage across multiple biological conditions. The exons inferred by SEASTAR coincide with transcription start sites identified directly by CAGE experiments and bear epigenetic hallmarks of active promoters. To determine if differential usage of alternative first exons can yield insights into the mechanism controlling gene expression, we applied SEASTAR to an RNA-seq dataset that tracked the reprogramming of mouse fibroblasts into induced pluripotent stem cells. We observed dynamic temporal changes in the usage of alternative first exons, along with correlated changes in transcription factor expression. Using a combined sequence motif and gene set enrichment analysis we identified N-Myc as a regulator of alternative first exon usage in the pluripotent state. Our results demonstrate that SEASTAR can leverage the available RNA-seq data to gain insights into the control of gene expression and alternative transcript variation in eukaryotic transcriptomes.

The identification of switch-like alternative splicing exons among multiple samples with RNA-Seq data.

Alternative splicing is an ubiquitous phenomenon in most human genes and has important functions. The switch-like exon is the type of exon that has a high level of usage in some tissues, but has a low level of usage in the other tissues. They usually undergo strong tissue-specific regulations. There is still a lack a systematic method to identify switch-like exons from multiple RNA-seq samples. We proposed a novel method called iterative Tertile Absolute Deviation around the mode (iTAD) to profile the distribution of exon relative usages among multiple samples and to identify switch-like exons and other types of exons using a robust statistic estimator. We validated the method with simulation data, and applied it on RNA-seq data of 16 human body tissues and detected 3,100 switch-like exons. We found that switch-like exons tend to be more associated with Alu elements in their flanking intron regions than other types of exons.

Opportunities and methods for studying alternative splicing in cancer with RNA-Seq.

The biogenesis, development and metastases of cancer are associated with many variations in the transcriptome. Alternative splicing of genes is a major post-transcriptional regulation mechanism that is involved in many types of cancer. The next-generation sequencing applied on RNAs (RNA-Seq) provides a new technology for studying transcriptomes. It provides an unprecedented opportunity for quantitatively studying alternative splicing in a systematic way. This mini-review summarizes the current RNA-Seq studies on cancer transcriptomes especially studies on cancer-related alternative splicing, and discusses the strategy for quantitative study of alternative splicing in cancers with RNA-Seq, the bioinformatics methods available and existing questions.

Identifying differentially spliced genes from two groups of RNA-seq samples.

Recent study revealed that most human genes have alternative splicing and can produce multiple isoforms of transcripts. Differences in the relative abundance of the isoforms of a gene can have significant biological consequences. Identifying genes that are differentially spliced between two groups of RNA-sequencing samples is an important basic task in the study of transcriptomes with next-generation sequencing technology. We use the negative binomial (NB) distribution to model sequencing reads on exons, and propose a NB-statistic to detect differentially spliced genes between two groups of samples by comparing read counts on all exons. The method opens a new exon-based approach instead of isoform-based approach for the task. It does not require information about isoform composition, nor need the estimation of isoform expression. Experiments on simulated data and real RNA-seq data of human kidney and liver samples illustrated the method's good performance and applicability. It can also detect previously unknown alternative splicing events, and highlight exons that are most likely differentially spliced between the compared samples. We developed an NB-statistic method that can detect differentially spliced genes between two groups of samples without using a prior knowledge on the annotation of alternative splicing. It does not need to infer isoform structure or to estimate isoform expression. It is a useful method designed for comparing two groups of RNA-seq samples. Besides identifying differentially spliced genes, the method can highlight on the exons that contribute the most to the differential splicing. We developed a software tool called DSGseq for the presented method available at http://bioinfo.au.tsinghua.edu.cn/software/DSGseq.