Impact of artificial mixing and oxygenation on bacteria in a water transfer reservoir: Community succession and the role in water quality improvement

Artificial mixing and oxygenation induced by water-lifting aerations (WLAs) have the potential to improve water quality in reservoirs. However, there is a limited understanding of the bacterial community composition, assembly, and mechanisms behind water quality improvement under the influence of WLAs, especially in a water transfer reservoir. Here, the dynamics and relationship between water quality, bacterial diversity, and composition during the pre-operation, in-operation, and post-operation stages of WLAs were analyzed using high-throughput sequencing technology to explore the effects of artificially regulated bacteria on water quality improvement. WLAs operation led to the elimination of water stratification, significant bottom oxygenation, and reduction in nutrient concentrations. In addition, the operation of WLAs significantly changed the bacterial community composition, with an increase in richness, negligible difference in diversity, and a significant increase in the abundance of species with pollutant degradation functions, resulting in a shift from stochastic to deterministic processes of the bacterial community assembly. As a result, enhancement of the dominant bacteria responsible for organic matter degradation and denitrification and suppression of the emergence of algae-related bacteria were observed during the WLAs operation, and the ecosystem stability improved. Multiple analyses indicated a direct correlation between artificial mixing and oxygenation; changes in the bacterial community; and the reduction of nitrogen, phosphorus, and permanganate index in the water column. This study provides novel insights into in situ water quality enhancement and a valuable reference for understanding bacterial change patterns under artificially intervened conditions in water transfer reservoirs.

The residue of tetracycline antibiotics in soil and Brassica juncea var. gemmifera, and the diversity of soil bacterial community under different livestock manure treatments

Tetracycline antibiotics (TCs) are a broad-spectrum antibiotic, widely used in livestock and poultry breeding. Residue of tetracycline antibiotics in animal manure may cause changes in vegetable TCs content and soil microbial community. On the basis of the investigation and analysis of TCs pollution in the soil of main vegetable bases and the livestock manure of major large-scale farms in Chongqing, China, field experiment was conducted to study the residues of tetracycline antibiotics in Brassica juncea var. gemmifera and soil under different kinds and different dosages of livestock manures. Effects of tetracycline antibiotics on the structure and diversity of soil microbial community were also investigated by high-throughput sequencing. TCs content in soil was increased by applying livestock manure. The contents of tetracycline, oxytetracycline (OTC) and chlortetracycline (CTC) in the soil under pig manure treatment were 171.07-660.20 μg kg^-1, 25.38-345.78 μg kg^-1 and 170.77-707.47 μg kg^-1, respectively. The contents of TC, OTC and CTC in the soil under the treatment of chicken manure were 166.62-353.61 μg kg^-1, 122.25-251.23 μg kg^-1 and 15.12-80.91 μg kg^-1, respectively. TCs in edible parts of Brassica juncea var. gemmifera was increased after livestock manure treatment Proteobacteria, Acidobacteria, Actinobacteria, Chioroflexi and Bacteroidetes under livestock manure treatment were the dominant phyla, accounting for 85.2-92.4% of the total abundance of soil bacteria. The soil OTUs under the treatment of pig manure was higher than that under the treatment of chicken manure. Biogas residue (Livestock manure after fermentation treatment) can effectively reduce the environmental and ecological risks caused by antibiotic residues.

Effects of ultrasound-assisted chitosan grafted caffeic acid coating on the quality and microbial composition of pompano during ice storage

The effects of ultrasound-assisted chitosan grafted caffeic acid coating on the quality and microbial composition of fresh pompano (Trachinotus ovatus) fillets during ice storage for 24 days were evaluated. Samples were treated by distilled water (CK), ultrasound (US), chitosan grafted caffeic acid coating (G), and chitosan grafted caffeic acid coating with ultrasound-assisted (USG). Results showed that samples treated with USG could inhibit the formation of corrupt substances such as TVB-N, TBA, biogenic amines (BAs), hypoxanthine (Hx), and hypoxanthine riboside (HxR) when compared to the CK group.The results of high-throughput sequencing technology observed that the major bacteria genus of fresh samples was Acinetobacter.The diversity of bacterial communities at the initial stage was more diverse than that at the end of stage. With the extension of storage time, the USG treatment could maintain the microbial diversity. The dominant microbiota was Shewanella and Brochothrix in the CK group after 24 days of storage. In addition, Brochothrix in treated groups was effectively decreased. The microbial communities of samples in all treatments were changed during storage. At the end of storage, there was a significant difference in bacterial composition between the CK and treated samples, indicating that the treatment can effectively inhibit the growth of microorganisms, especially spoilage microorganisms, and reduce the quality deterioration caused by bacteria.

Distinct microbiota dysbiosis in patients with laryngopharynx reflux disease compared to healthy controls

OBJECTIVE

To compare the differences in the laryngopharynx microbiome between patients with laryngopharyngeal reflux disease (LPRD) and healthy people and further explore the influence of related risk factors pharyngeal microbiome.

METHODS

This was a case-control study. Patients with a reflux symptom index (RSI) score > 13 or reflux finding score (RFS) score > 7 were diagnosed with suspected LPRD at the Department of Otolaryngology-Head and Neck Surgery of The 900th Hospital of Joint Logistic Support Force. Patients were assessed using a related risk factors questionnaire survey and examined by electronic naso-laryngoscopy. Simultaneously, laryngopharynx secretions were collected from the patients. The patients received at least eight weeks of proton pump inhibitor therapy, and those who responded were enrolled in the final experimental group. In parallel, laryngopharynx secretions were collected from healthy volunteers as the control group, and the laryngopharynx microbiota were analyzed using second-generation high-throughput sequencing.

RESULTS

A total of 23 cases each in the experimental and control group were included in this study. The experimental group microbiota were composed of Streptococcus, Prevotella, Haemophilus, Neisseria, Actinobacillus, Fusobacterium, and Porphyromonas. There was no significant difference in microbial alpha and beta-diversity analysis between the two groups. However, some advantageous bacterium groups were significantly different. The abundance of Prevotella in the experimental group was significantly higher than that of the control group (U = 117, P < 0.05), while the abundance of Fusobacterium (U = 140, P = 0.006) and Porphyromonas (U = 120, P = 0.002) was significantly lower than the control group. Smoking was positively correlated with Pectin (r = 0.46, P = 0.037), Lactobacillus (r = 0.48, P = 0.027), and Clostridium (r = 0.46, P = 0.037), while alcohol was negatively correlated with Streptococcus (r = - 0.5539, P = 0.0092).

CONCLUSION

The dominant microflora in the laryngopharynx of LPRD patients was significantly different from that of healthy people, suggesting that the change of laryngopharynx microflora may play an important role in the pathogenesis of LPRD. Smoking, drinking, eating habits, and age correlated with different genus levels of the laryngopharynx microbiota.

Archaeal and bacterial community structures of rural household biogas digesters with different raw materials in Qinghai Plateau

The present study aims to investigate microbial community structures household biogas digesters with different raw materials in Qinghai Plateau rural. High-throughput 16S rRNA gene sequencing analysis revealed that Firmicutes, Bacteroidetes, and Proteobacteria are the most abundant bacterial phyla (64.08%). Prevotella group 7 was the most abundant genus in digester YL9 and YL10 (69.72% and 26.96%, respectively) using vegetable waste raw materials. Trichococcus exhibited the highest abundance (14.55%) in YL1 digester using sheep and pig manure. Clostridium sensu stricto 1 (13.89%) and Synergistaceae_uncultured (15.52%) comprised the highest abundances in digester YL5 with mixed raw materials (i.e., dairy manure, sheep manure, and human feces). In addition, Proteiniphilum and Pseudomonas exhibited the highest abundances among bacterial genera in YL4 digester using pig manure. Methanomicrobiales was the most dominant archaeal communities, ranging from 13.35% to 81.34% in abundance. Methanocorpusculum exhibited dominant abundances in all digesters using various raw materials. Methanogenium was the most abundant archaeal genera in YL4 and YL6 digesters, which consume pig manure as primary raw material. In addition, Methanosarcina and Methanosaeta exhibited the highest abundances in digester YL1 (55.03%) and YL9 (51.40%), respectively. Moreover, fermentation temperatures and pH both contributed to the archaeal and bacterial community structures in all the investigated digesters. Specially, fermentation temperature showed positive correlation with the abundances of Synergistaceae_uncultured, Methanogenium, and Methanosaeta, and pH was positively correlated with the abundances of Prevotella group 7 and Methanosarcina abundances.

Response of the microbial community to salt stress and its stratified effect in constructed wetlands

Nitrogen removal in constructed wetlands (CWs) may be inhibited by salinity. The clarification of the response of microbial community to salt stress is a premise for developing strategies to improve nitrogen removal efficiency in CWs under saline conditions. Results showed that the ammonia nitrogen (NH₄⁺-N), nitrate nitrogen (NO₃^--N), and total nitrogen (TN) removal percentages significantly (p < 0.05) decreased in CWs with increasing salinity. The structure and abundance of the microbial community varied with different salinity levels and sampling depths in CWs. Compared with a non-saline condition, the abundances of some bacteria with a denitrification function (e.g., Arthrobacter) significantly (p < 0.05) decreased in CWs under saline conditions (i.e., EC of 15 and 30 mS/cm). Aerobic bacteria (e.g., Sphingomonas) exhibited more abundance in soil and upper gravel samples in CWs than those in bottom gravel samples, while the abundance of some denitrifying bacteria (e.g., Thauera and Azoarcus) was significantly (p < 0.05) higher in bottom gravel samples compared with soil and upper gravel samples, respectively. This study provides both microbiological evidence for explaining the impact of salt stress on nitrogen removal in CWs and scientific reference for developing enhanced strategies to improve the nitrogen removal capacity of CWs.

The different toxic effects of metalaxyl and metalaxyl-M on Tubifex tubifex

Metalaxyl and Metalaxyl-M are the fungicides that widely used in many countries. In this study, the environmental behaviors between metalaxyl and metalaxyl-M in Tubifex tubifex (T. tubifex) were quantitative analyzed by using a high performance liquid chromatography with photo-diode-array-detector (HPLC-DAD). Results demonstrated that there was no significant difference (p > 0.05) in the concentration of metalaxyl and metalaxyl-M in T. tubifex during the exposure process. However, the dissipation behaviors of metalaxyl and metalaxyl-M in T. tubifex were different (p < 0.05) during the non-exposure culture process. Meanwhile, the toxic effects were also evaluated by comparing the different influences of these two compounds on related physiological indicators, and functional enzyme activities. The survival rates of T. tubifex were 63.33 ± 15.28% (20 mg L^-1), 63.33 ± 5.77% (200 mg L^-1) treated with metalaxyl and were 50.00 ± 10.00% (20 mg L^-1), 46.67 ± 11.55 (200 mg L^-1) treated with metalaxyl-M at the non-exposure culture process. The autotomy rates were increased significantly compared with the initial in all treatments. Besides, the activities of CAT, SOD, and GST in T. tubifex were also inhibited by metalaxyl and metalaxyl-M treatments. Finally, the high-throughput transcriptome sequencing technology was applied to investigate the metabolic pathways of target analytes in T. tubifex, and results proved that the metabolic pathways associated with human diseases (such as viral myocarditis) were up-regulated expression for metalaxyl and metalaxyl-M treatments, and metalaxyl-M up-regulated more significantly. All the results demonstrated that metalaxyl-M had a higher toxicity than metalaxyl on T. tubifex.

Heterotrophic denitrification strategy for marine recirculating aquaculture wastewater treatment using mariculture solid wastes fermentation liquid as carbon source: Optimization of COD/NO3--N ratio and hydraulic retention time

Heterotrophic denitrification using mariculture solid wastes (MSW) fermentation liquid as carbon source is an economically and environmentally sustainable strategy for NO₃^--N removal in marine recycling aquaculture systems (RAS). The optimization of COD/NO₃^--N ratio (C/N) and hydraulic retention times (HRT) with respect to MSW fermentation liquid driven denitrification for marine RAS wastewater treatment was investigated. The optimum C/N of 8 and HRT of 6 h for heterotrophic denitrification was obtained with NO₃^--N removal efficiency of 97.8% and 94.2%, respectively. Using MSW fermentation liquid as carbon source, the utilization of VFAs was more effective than that of carbohydrates and proteins, and effluent COD concentration decreased with an increment in HRT from 4 to 8 h. The results of high-throughput sequencing analysis showed microbial communities were enriched selectively in the reactors by optimizing C/N and HRT, which obviously enhanced the nitrogen removal in respect to MSW fermentation liquid driven denitrification.

Comparation of thermophilic bacteria (TB) pretreated primary and secondary waste sludge carbon sources on denitrification performance at different HRTs

In this study, thermophilic bacteria pretreated primary and secondary waste sludge hydrolysis and acidification liquid were used as denitrification carbon sources at different HRTs (hydraulic retention time). The NO₃^--N removal rate of 99.3%, 99.0%, 99.9% and 99.2% was achieved at the optimal HRT of 8, 8, 4 and 6 h, respectively. Meanwhile, the utilization of COD (Chemical oxygen demand), proteins, carbohydrates, and VFAs (Volatile fatty acids) in carbon source during denitrification was also investigated. High-throughput sequencing technology showed that the microbial community changed with the different sludge carbon sources. And the dominant genus in both reactors was Thauera, which played a key role in denitrification.

Complete chloroplast genome of the medicinal plant Amomum compactum: gene organization, comparative analysis, and phylogenetic relationships within Zingiberales

Background

Amomum compactum is one of the basic species of the traditional herbal medicine amomi fructus rotundus, with great pharmacology effect. The system position of A. compactum is not clear yet, and the introduction of this plant has been hindered by many plant diseases. However, the correlational molecular studies are relatively scarce.

Methods

The total chloroplast (cp) DNA was extracted according to previous studies, and then sequenced by 454 GS FLX Titanium platform. Sequence assembly was complished by Newbler. Genome annotation was preformed by CPGAVAS and tRNA-SCAN. Then, general characteristics of the A. compactum cp genome and genome comparsion with three Zingiberaceae species was analyzed by corresponding softwares. Additionally, phylogenetical trees were reconstructed, based on the shared protein-coding gene sequences among 15 plant taxa by maximum parsimony (MP) and maximum likelihood (ML) methods.

Results

The A. compactum cp genome with a classic quadripartite structure, consisting of a pair of reverse complement repeat regions (IRa/IRb) of 29,824 bp, a large single copy (LSC, 88,535 bp) region as well as a small single copy (SSC, 15,370 bp) region, is 163,553 bp in total size. The total GC content of this cp genome is 36.0%. The A. compactum cp genome owns 135 functional genes, that 113 genes are unique, containing eighty protein-coding genes, twenty-nine tRNA (transfer RNA) genes and four rRNA (ribosomal RNA) genes. Codon usage of the A. compactum cp genome is biased toward codons ending with A/T. Total 58 SSR loci and 24 large repeats are detected in the A. compactum cp genome. Relative to three other Zingiberaceae cp genomes, the A. compactum cp genome exhibits an obvious expansion in the IR regions. In A. compactum cp genome, the ycf1 pseudogene is 2969 bp away from the IRa/SSC border, whereas in other Zingiberaceae species, it is only 4-5 bp away from the IRa/SSC border. Comparative cp genome sequences analysis of A. compactum with other Zingiberaceae reveals that the gene order and gene content differ slightly among Zingiberaceae species. The phylogenetic analysis based on 67 protein-coding gene sequences supports the phylogenetic position of A. compactum.

Conclusions

The study has identified unique features of the A. compactum cp genome which would be helpful for us to understand the cp genome evolution and offer useful information for phylogenetics and further studies of this traditional medicinal plant.

High-throughput sequencing technology reveals that continuous cropping of American ginseng results in changes in the microbial community in arable soil

BACKGROUND

American ginseng (Panax quinquefolius L.) is renowned worldwide for its eutherapeutic effects. The replantation of American ginseng usually fails due to problems associated with continuous cropping. An imbalance in the microbial community is thought to be responsible for this, but the overall changes in microbial communities under a continuous cropping system are unclear.

METHODS

This study used quantitative polymerase chain reaction combined with high-throughput sequencing methods to confirm changes in a microbial community under continuous cropping of American ginseng.

RESULTS

Copy numbers of bacteria and fungi significantly declined by 47.7 and 45.5%, respectively, upon American ginseng cropping over 3 years. A total of 66,391 classified sequences were obtained from high-throughput sequencing analyses of 16S and 18S rRNA in six soil samples. A decline in bacterial diversity and an increase in fungal diversity were observed in the continuous cropping soils of American ginseng compared to those of traditional crops. Compared with soils used for traditional crops, the relative abundance of bacterial and fungal groups changed in soils subjected to continuous cropping with American ginseng.

CONCLUSIONS

Our results revealed that the diversity and composition of soil bacterial and fungal communities changed in the continuous cropping of American ginseng compared to those of traditional crops. Those data provided comprehensive insight into microbial communities at the agro-ecosystem scale and contributed to the understanding of micro-ecological environments in the rhizosphere of medicinal plants.

High-throughput sequencing technology to reveal the composition and function of cecal microbiota in Dagu chicken

BACKGROUND

The chicken gut microbiota is an important and complicated ecosystem for the host. They play an important role in converting food into nutrient and energy. The coding capacity of microbiome vastly surpasses that of the host's genome, encoding biochemical pathways that the host has not developed. An optimal gut microbiota can increase agricultural productivity. This study aims to explore the composition and function of cecal microbiota in Dagu chicken under two feeding modes, free-range (outdoor, OD) and cage (indoor, ID) raising.

RESULTS

Cecal samples were collected from 24 chickens across 4 groups (12-w OD, 12-w ID, 18-w OD, and 18-w ID). We performed high-throughput sequencing of the 16S rRNA genes V4 hypervariable regions to characterize the cecal microbiota of Dagu chicken and compare the difference of cecal microbiota between free-range and cage raising chickens. It was found that 34 special operational taxonomic units (OTUs) in OD groups and 4 special OTUs in ID groups. 24 phyla were shared by the 24 samples. Bacteroidetes was the most abundant phylum with the largest proportion, followed by Firmicutes and Proteobacteria. The OD groups showed a higher proportion of Bacteroidetes (>50 %) in cecum, but a lower Firmicutes/Bacteroidetes ratio in both 12-w old (0.42, 0.62) and 18-w old groups (0.37, 0.49) compared with the ID groups. Cecal microbiota in the OD groups have higher abundance of functions involved in amino acids and glycan metabolic pathway.

CONCLUSION

The composition and function of cecal microbiota in Dagu chicken under two feeding modes, free-range and cage raising are different. The cage raising mode showed a lower proportion of Bacteroidetes in cecum, but a higher Firmicutes/Bacteroidetes ratio compared with free-range mode. Cecal microbiota in free-range mode have higher abundance of functions involved in amino acids and glycan metabolic pathway.

The High-throughput sequencing of Sillago japonica mitochondrial genome reveals the phylogenetic position within the genus Sillago

The complete mitogenome of Sillago japonica was determined through high-throughput DNA sequencing technology. The circular mtDNA molecule was 16 645 bp in size and encoded 13 protein-coding genes, 2 rRNAs, 22 tRNAs and 2 non-coding regions, with the gene arrangement and content identical to other typical vertebrate mitogenomes. The identity analysis revealed that the mitogenome sequence of S. japonica shared a relatively high sequence identity to S. asiatica (81.5%) compared with S. aeolus (77.5%), S. indica (77.1%), and S. sihama (76.3%). The neighbor-joining tree of complete mitogenome sequence showed that S. japonica firstly clustered together with S. asiatica, then grouped with S. indica and S. sihama, and finally gathered with S. aeolus. Taken together, the results absolutely supported the evolutionary position of S. japonica and provided new insights into phylogenetic relationships of Sillago.