Identification of the WRKY Gene Family and Characterization of Stress-Responsive Genes in Taraxacum kok-saghyz Rodin.

WRKY transcription factors present unusual research value because of their critical roles in plant physiological processes and stress responses. Taraxacum kok-saghyz Rodin (TKS) is a perennial herb of dandelion in the Asteraceae family. However, the research on TKS WRKY TFs is limited. In this study, 72 TKS WRKY TFs were identified and named. Further comparison of the core motifs and the structure of the WRKY motif was analyzed. These TFs were divided into three groups through phylogenetic analysis. Genes in the same group of TkWRKY usually exhibit a similar exon-intron structure and motif composition. In addition, virtually all the TKS WRKY genes contained several cis-elements related to stress response. Expression profiling of the TkWRKY genes was assessed using transcriptome data sets and Real-Time RT-PCR data in tissues during physiological development, under abiotic stress and hormonal treatments. For instance, the TkWRKY18, TkWRKY23, and TkWRKY38 genes were significantly upregulated during cold stress, whereas the TkWRKY21 gene was upregulated under heat-stress conditions. These results could provide a basis for further studies on the function of the TKS WRKY gene family and genetic amelioration of TKS germplasm.

Analysis of Bacterial Communities in Partial Nitritation and Conventional Nitrification Systems for Nitrogen Removal.

This work studied the microbial community in partial nitritation and complete nitrification processes, which were applied to treat the low Carbon Nitrogen ratio wastewater. The phospholipid fatty acid and quantitative PCR analysis showed that the sludge circulating ratio of 75% resulted in a good microbial growth and a higher abundance of ammonia oxidizing bacteria relative to the nitrite oxidizing bacteria. The Betaproteobacteria were observed to compose the most abundant sludge bacterial groups in the two processes, based on phylogenetic analysis. The phylogenetic analysis of both 16S rRNA and amoA gene indicated that the Nitrosomonas sp. were the dominant ammonia oxidizing bacteria in the partial nitritation process. The relative abundance of nitrite oxidizing bacteria, such as Nitrobacter sp. and Nitrospira sp., were significantly lower in the partial nitritation system over the complete nitrification system. The abundance of Planctomycetes was higher in the partial nitritation process, indicating the anammox reaction occurred in the partial nitritation system. These results suggested the nitrite accumulation rate of circulating ratios 75% was the highest, with an average of 92%,and a possibility to treat the low Carbon Nitrogen ratio wastewater using the partial nitritation/anammox process.

Investigating the bacterial community and amoebae population in rural domestic wastewater reclamation for irrigation.

Reclamation of domestic wastewater for agricultural irrigation is viewed as a sustainable option to create an alternative water source and address water scarcity. Free-living amoebae (FLA), which are amphizoic protozoa, are widely distributed in various environmental sources. The FLA could cause considerable environmental and health risks. However, little information is available on the risk of these protozoa. In this study, we evaluated the feasibility using rural domestic wastewater for agricultural irrigation, and analyzed dynamic changes of the microbial community structure and FLA populations in raw and treated wastewater, as well as the phyllosphere and rhizosphere of lettuce production sites that were irrigated with different water sources. The bacterial community dynamics were analyzed by terminal restriction fragment length polymorphism (T-RFLP). The bacterial community structures in the influent were similar to that in the effluent, while in some cases relative abundances varied significantly. The populations of Acanthamoeba spp. and Hartmannella vermiformis in the anaerobically treated wastewater were significantly higher than in the raw wastewater. The vegetables could harbor diverse amoebae, and the abundances of Acanthamoeba spp. and H. vermiformis in the rhizosphere were significantly higher than in the phyllosphere. Accordingly, our studies show insight into the distribution and dissemination of amoebae in wastewater treatment and irrigation practices.

Fate and behavior of dissolved organic matter in a submerged anoxic-aerobic membrane bioreactor (MBR).

In this study, the production, composition, and characteristics of dissolved organic matter (DOM) in an anoxic-aerobic submerged membrane bioreactor (MBR) were investigated. The average concentrations of proteins and carbohydrates in the MBR aerobic stage were 3.96 ± 0.28 and 8.36 ± 0.89 mg/L, respectively. After membrane filtration, these values decreased to 2.9 ± 0.2 and 2.8 ± 0.2 mg/L, respectively. High performance size exclusion chromatograph (HP-SEC) analysis indicated a bimodal molecular weight (MW) distribution of DOMs, and that the intensities of all the peaks were reduced in the MBR effluent compared to the influent. Three-dimensional fluorescence excitation emission matrix (FEEM) indicated that fulvic and humic acid-like substances were the predominant DOMs in biological treatment processes. Precise identification and characterization of low-MW DOMs was carried out using gas chromatography-mass spectrometry (GC-MS). The GC-MS analysis indicated that the highest peak numbers (170) were found in the anoxic stage, and 54 (32%) compounds were identified with a similarity greater than 80%. Alkanes (28), esters (11), and aromatics (7) were the main compounds detected. DOMs exhibited both biodegradable and recalcitrant characteristics. There were noticeable differences in the low-MW DOMs present down the treatment process train in terms of numbers, concentrations, molecular weight, biodegradability, and recalcitrance.

Diversity of culturable aerobic denitrifying bacteria in the sediment, water and biofilms in Liangshui River of Beijing, China.

Aerobic denitrification is a process reducing the nitrate into gaseous nitrogen forms in the presence of oxygen gas, which makes the nitrification and denitrification performed simultaneously. However, little was known on the diversity of the culturable aerobic denitrifying bacteria in the surface water system. In this study, 116 strains of aerobic denitrifying bacteria were isolated from the sediment, water and biofilm samples in Liangshui River of Beijing. These bacteria were classified into 14 genera based on the 16 S rDNA, such as Pseudomonas, Rheinheimera, and Gemmobacter. The Pseudomonas sp., represented by the Pseudomonas stutzeri, Pseudomonas mendocina and Pseudomonas putida, composed the major culturable aerobic denitrifiers of the river, followed by Ochrobactrum sp. and Rheinheimera sp. The PCA plot showed the unclassified Pseudomonas sp. and Rheinheimera pacifica preferred to inhabit in biofilm phase while one unclassified Ochrobactrum sp. and Pseudomonas resinovorans had higher abundance in the sediment. In the overlying water, the Pseudomonas stutzeri and Ochrobactrum rhizosphaerae were found to have higher abundance, indicating these aerobic denitrifiers had different habitat-preferable characteristics among the 3 phases of river system. The findings may help select the niche to isolate the aerobic denitrifiers and facilitate the bioaugmentation-based purification of the nitrate polluted surface water.

Succession of biofilm communities responsible for biofouling of membrane bio-reactors (MBRs).

Biofilm formation is one of the main factors associated with membrane biofouling in membrane bioreactors (MBRs). As such, it is important to identify the responsible organisms to develop targeted strategies to control biofouling. This study investigated the composition and changes in the microbial communities fouling MBR membranes over time and correlated those changes with an increase in transmembrane pressure (TMP). Based on qPCR data, bacteria were the dominant taxa of the biofilm (92.9-98.4%) relative to fungi (1.5-6.9%) and archaea (0.03-0.07%). NMDS analysis indicated that during the initial stages of operation, the biofilm communities were indistinguishable from those found in the sludge. However, the biofilm community significantly diverged from the sludge over time and ultimately showed a unique biofilm profile. This suggested that there was strong selection for a group of organisms that were biofilm specialists. This pattern of succession and selection was correlated with the rapid increase in TMP, where bacteria including Rhodospirillales, Sphingomonadales and Rhizobiales dominated the biofilm at this time. While most of the identified fungal OTUs matched Candida sp., the majority of fungal communities were unclassified by 18S rRNA gene sequencing. Collectively, the data suggests that bacteria, primarily, along with fungi may play an important role in the rapid TMP increase and loss of system performance.

N-acylhomoserine lactone-regulation of genes mediating motility and pathogenicity in Pseudomonas syringae pathovar tabaci 11528.

Pseudomonas syringae pathovar tabaci 11528 (P. syringae 11528) is a phytopathogen that causes wild-fire disease in soybean and tobacco plants. It utilizes a cell density-dependent regulation system known as quorum sensing (QS). In its QS system, the psyI is responsible for the biosynthesis of N-acylhomoserine lactones (AHLs). By comparing the transcripts from P. syringae 11528 wild-type strain with those of the ΔpsyI mutant using RNA sequencing (RNA-seq) technology, 1118 AHL-regulated genes were identified in the transition from exponential to stationary growth phase. Numerous AHL-regulated genes involved in pathogenicity were negatively controlled, including genes linked to flagella, chemotaxis, pilus, extracellular polysaccharides, secretion systems, and two-component system. Moreover, gene ontology and pathway enrichment analysis revealed that the most pronounced regulation was associated with bacterial motility. Finally, phenotypic assays showed that QS-regulated traits were involved in epiphytic growth of pathogens and disease development in plants. These findings imply that the AHL-mediated QS system in P. syringae 11528 plays significant roles in distinct stages of interactions between plants and pathogens, including early plant colonization and late plant infection.

Characterization of microbial communities in wetland mesocosms receiving caffeine-enriched wastewater.

A 454 high-throughput pyrosequencing approach was used to characterize the structures of microbial communities in wetland mesocosms receiving caffeine-enriched wastewater at a concentration of 250 µg L(-1). The removal efficiencies of caffeine in the planted beds (93.0 %) were significantly (p < 0.05) higher than those in the unplanted beds (81.4 %). Bacterial diversity was decreased by 25 and 22.4 %, respectively, in both planted and unplanted mesocosms after 210-day operation. The results of taxonomic analyses suggested that chronic exposure of wetland ecosystems to caffeine could lead to moderate shifts in microbial community composition. In total, 2156 operational taxonomic units (OTUs) were generated and 20 phyla comprising 260 genera were identified. The major phylogenetic groups at phylum level included Firmicutes (39 %), Actinobacteria (25.1 %), Proteobacteria (17.1 %), Synergistetes (5.6 %), and Chloroflexi (5.5 %). Bacilli and Synergistia increased in abundance in the planted mesocosms, while for the unplanted mesocosms, Actinobacterial, Clostridia and Betaproteobacteria exhibited increased proportion under the exposure of caffeine. At genus level, Propionibacterium, Staphylococcus, Bacillus, and Streptococcus were found to be increased in abundance after caffeine treatment. As for the response of fungal community to caffeine enrichment, genus like Cladosporium, Emericellopsis, Aspergillus, and Phoma were found to be resistant to caffeine disturbance. When compared to the microbial community between planted and unplanted mesocosms, a distinct community profile for both bacteria and fungi community was observed. The presence of plants had a remarkable effect on the structure of microbial community, helping buffer against the stress associated with caffeine exposure.

Ibuprofen removal in horizontal subsurface flow constructed wetlands: treatment performance and fungal community dynamics.

The treatment performance of ibuprofen (IBP)-enriched wastewater by horizontal subsurface flow constructed wetlands planted with cattail (Typha angustifolia) and unplanted control mesocosms was investigated. Removal efficiencies of IBP were significantly (p < .05) enhanced in the planted mesocosms (78.5%) compared to those in the unplanted beds (57.9%). An 18S rRNA gene high-throughput pyrosequencing approach was used to investigate the effects of IBP on the structure of the fungal community in these wetland systems. The overall diversity of the fungal community was reduced under the IBP exposure. Taxonomic analysis revealed that 62.2% of the fungal sequences were affiliated with Basidiomycota, followed by Ascomycota (37.4%) at the phylum level. Uncultured fungus (48.2%), Chaetomium sp. (14.2%), Aspergillus sp. (12.4%), Trichoderma sp. (5.7%), Cladosporium sp. (5.4%), and Emericellopsis sp. (5.2%) were identified as dominant genera. At the genus level, a distinct profile of the fungal community in the IBP-enriched mesocosms was observed as compared to the control beds, and as well specific fungal genera were enhanced in the planted beds, regardless of IBP enrichment. However, despite these differences, the composition of the fungal community (as measured by Bray-Curtis similarity) was mostly unaffected by the significant IBP enrichment. On the other hand, a consistent similarity pattern of fungal community structure in the planted mesocosms suggests that the presence of higher macrophytes in the wetland systems may well help shape the fungal community structure.

Bioremediation of petroleum hydrocarbon contaminated soil by Rhodobacter sphaeroides biofertilizer and plants.

Bio-augmentation is a promising technique for remediation of polluted soils. This study aimed to evaluate the bio-augmentation effect of Rhodobacter sphaeroides biofertilizer (RBF) on the bioremediation of total petroleum hydrocarbons (TPH) contaminated soil. A greenhouse pot experiment was conducted over a period of 120 days, three methods for enhancing bio-augmentation were tested on TPH contaminated soils, including single addition RBF, planting, and combining of RBF and three crop species, such as wheat (W), cabbage (C) and spinach (S), respectively. The results demonstrated that the best removal of TPH from contaminated soil in the RBF bio-augmentation rhizosphere soils was found to be 46.2%, 65.4%, 67.5% for W+RBF, C+RBF, S+RBF rhizosphere soils respectively. RBF supply impacted on the microbial community diversity (phospholipid fatty acids, PLFA) and the activity of soil enzymes, such as dehydrogenase (DH), alkaline phosphatase (AP) and urease (UR). There were significant difference among the soil only containing crude oil (CK), W, C and S rhizosphere soils and RBF bio-augmentation soils. Moreover, the changes were significantly distinct depended on crops species. It was concluded that the RBF is a valuable material for improving effect of remediation of TPH polluted soils.

The application of nitric oxide to control biofouling of membrane bioreactors.

A novel strategy to control membrane bioreactor (MBR) biofouling using the nitric oxide (NO) donor compound PROLI NONOate was examined. When the biofilm was pre-established on membranes at transmembrane pressure (TMP) of 88-90 kPa, backwashing of the membrane module with 80 µM PROLI NONOate for 45 min once daily for 37 days reduced the fouling resistance (Rf ) by 56%. Similarly, a daily, 1 h exposure of the membrane to 80 µM PROLI NONOate from the commencement of MBR operation for 85 days resulted in reduction of the TMP and Rf by 32.3% and 28.2%. The microbial community in the control MBR was observed to change from days 71 to 85, which correlates with the rapid TMP increase. Interestingly, NO-treated biofilms at 85 days had a higher similarity with the control biofilms at 71 days relative to the control biofilms at 85 days, indicating that the NO treatment delayed the development of biofilm bacterial community. Despite this difference, sequence analysis indicated that NO treatment did not result in a significant shift in the dominant fouling species. Confocal microscopy revealed that the biomass of biopolymers and microorganisms in biofilms were all reduced on the PROLI NONOate-treated membranes, where there were reductions of 37.7% for proteins and 66.7% for microbial cells, which correlates with the reduction in TMP. These results suggest that NO treatment could be a promising strategy to control biofouling in MBRs.

Characterization of the archaeal community fouling a membrane bioreactor.

Biofilm formation, one of the primary causes of biofouling, results in reduced membrane flux or increased transmembrane pressure and thus represents a major impediment to the wider implementation of membrane bioreactor (MBR) technologies for water purification. Most studies have focused on the role of bacteria in membrane fouling as they are the most dominant and best studied organisms present in the MBR. In contrast, there is limited information on the role of the archaeal community in biofilm formation in MBRs. This study investigated the composition of the archaeal community during the process of biofouling in an MBR. The archaeal community was observed to have lower richness and diversity in the biofilm than the sludge during the establishment of biofilms at low transmembrane pressure (TMP). Clustering of the communities based on the Bray-Curtis similarity matrix indicated that a subset of the sludge archaeal community formed the initial biofilms. The archaeal community in the biofilm was mainly composed of Thermoprotei, Thermoplasmata, Thermococci, Methanopyri, Methanomicrobia and Halobacteria. Among them, the Thermoprotei and Thermoplasmata were present at higher relative proportions in the biofilms than they were in the sludge. Additionally, the Thermoprotei, Thermoplasmata and Thermococci were the dominant organisms detected in the initial biofilms at low TMP, while as the TMP increased, the Methanopyri, Methanomicrobia, Aciduliprofundum and Halobacteria were present at higher abundances in the biofilms at high TMP.

The correlation between biofilm biopolymer composition and membrane fouling in submerged membrane bioreactors.

Biofouling, the combined effect of microorganism and biopolymer accumulation, significantly reduces the process efficiency of membrane bioreactors (MBRs). Here, four biofilm components, alpha-polysaccharides, beta-polysaccharides, proteins and microorganisms, were quantified in MBRs. The biomass of each component was positively correlated with the transmembrane pressure increase in MBRs. Proteins were the most abundant biopolymer in biofilms and showed the fastest rate of increase. The spatial distribution and co-localization analysis of the biofouling components indicated at least 60% of the extracellular polysaccharide (EPS) components were associated with the microbial cells when the transmembrane pressure (TMP) entered the jump phase, suggesting that the EPS components were either secreted by the biofilm cells or that the deposition of these components facilitated biofilm formation. It is suggested that biofilm formation and the accumulation of EPS are intrinsically coupled, resulting in biofouling and loss of system performance. Therefore, strategies that control biofilm formation on membranes may result in a significant improvement of MBR performance.