Eco-evolutionary dynamics of gut phageome in wild gibbons (Hoolock tianxing) with seasonal diet variations

It has been extensively studied that the gut microbiome provides animals flexibility to adapt to food variability. Yet, how gut phageome responds to diet variation of wild animals remains unexplored. Here, we analyze the eco-evolutionary dynamics of gut phageome in six wild gibbons (Hoolock tianxing) by collecting individually-resolved fresh fecal samples and parallel feeding behavior data for 15 consecutive months. Application of complementary viral and microbial metagenomics recovers 39,198 virulent and temperate phage genomes from the feces. Hierarchical cluster analyses show remarkable seasonal diet variations in gibbons. From high-fruit to high-leaf feeding period, the abundances of phage populations are seasonally fluctuated, especially driven by the increased abundance of virulent phages that kill the Lachnospiraceae hosts, and a decreased abundance of temperate phages that piggyback the Bacteroidaceae hosts. Functional profiling reveals an enrichment through horizontal gene transfers of toxin-antitoxin genes on temperate phage genomes in high-leaf season, potentially conferring benefits to their prokaryotic hosts. The phage-host ecological dynamics are driven by the coevolutionary processes which select for tail fiber and DNA primase genes on virulent and temperate phage genomes, respectively. Our results highlight complex phageome-microbiome interactions as a key feature of the gibbon gut microbial ecosystem responding to the seasonal diet.

Temperature, pH, and oxygen availability contributed to the functional differentiation of ancient Nitrososphaeria

Ammonia-oxidizing Nitrososphaeria are among the most abundant archaea on Earth and have profound impacts on the biogeochemical cycles of carbon and nitrogen. In contrast to these well-studied ammonia-oxidizing archaea (AOA), deep-branching non-AOA within this class remain poorly characterized because of a low number of genome representatives. Here, we reconstructed 128 Nitrososphaeria metagenome-assembled genomes from acid mine drainage and hot spring sediment metagenomes. Comparative genomics revealed that extant non-AOA are functionally diverse, with capacity for carbon fixation, carbon monoxide oxidation, methanogenesis, and respiratory pathways including oxygen, nitrate, sulfur, or sulfate, as potential terminal electron acceptors. Despite their diverse anaerobic pathways, evolutionary history inference suggested that the common ancestor of Nitrososphaeria was likely an aerobic thermophile. We further surmise that the functional differentiation of Nitrososphaeria was primarily shaped by oxygen, pH, and temperature, with the acquisition of pathways for carbon, nitrogen, and sulfur metabolism. Our study provides a more holistic and less biased understanding of the diversity, ecology, and deep evolution of the globally abundant Nitrososphaeria.

Gut microbiome responds compositionally and functionally to the seasonal diet variations in wild gibbons

Wild animals may encounter multiple challenges especially food shortage and altered diet composition in their suboptimal ranges. Yet, how the gut microbiome responds to dietary changes remains poorly understood. Prior studies on wild animal microbiomes have typically leaned upon relatively coarse dietary records and individually unresolved fecal samples. Here, we conducted a longitudinal study integrating 514 time-series individually recognized fecal samples with parallel fine-grained dietary data from two Skywalker hoolock gibbon (Hoolock tianxing) groups populating high-altitude mountainous forests in western Yunnan Province, China. 16S rRNA gene amplicon sequencing showed a remarkable seasonal fluctuation in the gibbons' gut microbial community structure both across individuals and between the social groups, especially driven by the relative abundances of Lanchnospiraceae and Oscillospiraceae associated with fluctuating consumption of leaf. Metagenomic functional profiling revealed that diverse metabolisms associated with cellulose degradation and short-chain fatty acids (SCFAs) production were enriched in the high-leaf periods possibly to compensate for energy intake. Genome-resolved metagenomics further enabled the resolving metabolic capacities associated with carbohydrate breakdown among community members which exhibited a high degree of functional redundancy. Our results highlight a taxonomically and functionally sensitive gut microbiome actively responding to the seasonally shifting diet, facilitating the survival and reproduction of the endangered gibbon species in their suboptimal habitats.

Genome-resolved metagenomics reveals depth-related patterns of microbial community structure and functions in a highly stratified, AMD overlaying mine tailings

Acid mine drainage (AMD) is a worldwide environmental problem, yet bioremediation is hampered by a limited knowledge of the reductive microbial processes in the AMD ecosystem. Here, we generate extensive metagenome and geochemical datasets to investigate how microbial populations and metabolic capacities driving major element cycles are structured in a highly stratified, AMD overlaying tailings environment. The results demonstrated an explicit depth-dependent differentiation of microbial community composition and function profiles between the surface and deeper tailings layers, paralleling the dramatic shifts in major physical and geochemical properties. Specifically, key genes involved in sulfur and iron oxidation were significantly enriched in the surface tailings, whereas those associated with reductive nitrogen, sulfur, and iron processes were enriched in the deeper layers. Genome-resolved metagenomics retrieved 406 intermediate or high-quality genomes spanning 26 phyla, including major new groups (e.g., Patescibacteria and DPANN). Metabolic models involving nitrogen, sulfur, iron, and carbon cycles were proposed based on the functional potentials of the abundant microbial genomes, emphasizing syntrophy and the importance of lesser-known taxa in the degradation of complex carbon compounds. These results have implications for in situ AMD bioremediation.

Increased Leaf Bacterial Network Complexity along the Native Plant Diversity Gradient Facilitates Plant Invasion?

Understanding the mechanisms of biological invasion is critical to biodiversity protection. Previous studies have produced inconsistent relationships between native species richness and invasibility, referred to as the invasion paradox. Although facilitative interactions among species have been proposed to explain the non-negative diversity-invasibility relationship, little is known about the facilitation of plant-associated microbes in invasions. We established a two-year field biodiversity experiment with a native plant species richness gradient (1, 2, 4, or 8 species) and analyzed the effects of community structure and network complexity of leaf bacteria on invasion success. Our results indicated a positive relationship between invasibility and network complexity of leaf bacteria of the invader. Consistent with previous studies, we also found that native plant species richness increased the leaf bacterial diversity and network complexity. Moreover, the results of the leaf bacteria community assembly of the invader suggested that the complex bacteria community resulted from higher native diversity rather than higher invader biomass. We concluded that increased leaf bacterial network complexity along the native plant diversity gradient likely facilitated plant invasion. Our findings provided evidence of a potential mechanism by which microbes may affect the plant community invasibility, hopefully helping to explain the non-negative relationship between native diversity and invasibility.

Unraveling microbe-mediated degradation of lignin and lignin-derived aromatic fragments in the Pearl River Estuary sediments

Estuaries are one of the most crucial areas for the transformation and burial of terrestrial organic carbon (TerrOC), playing an important role in the global carbon cycle. While the transformation and degradation of TerrOC are mainly driven by microorganisms, the specific taxa and degradation processes involved remain largely unknown in estuaries. We collected surface sediments from 14 stations along the longitudinal section of the Pearl River Estuary (PRE), P. R. China. By combining analytical chemistry, metagenomics, and bioinformatics methods, we analyzed composition, source and degradation pathways of lignin/lignin-derived aromatic fragments and their potential decomposers in these samples. A diversity of bacterial and archaeal taxa, mostly those from Proteobacteria (Deltaproteobacteria, Gammaproteobacteria etc.), including some lineages (e.g., Nitrospria, Polyangia, Tectomicrobia_uc) not previously implicated in lignin degradation, were identified as potential polymeric lignin or its aromatic fragments degraders. The abundance of lignin degradation pathways genes exhibited distinct spatial distribution patterns with the area adjacent to the outlet of Modaomen as a potential degradation hot zone and the Syringyl lignin fragments, 3,4-PDOG, and 4,5-PDOG pathways as the primary potential lignin aromatic fragments degradation processes. Notably, the abundance of ferulic acid metabolic pathway genes exhibited significant correlations with degree of lignin oxidation and demethylation/demethoxylization and vegetation source. Additionally, the abundance of 2,3-PDOG degradation pathways genes also showed a positive significant correlation with degree of lignin oxidation. Our study provides a meaningful insight into the microbial ecology of TerrOC degradation in the estuary.

Microbial diversity in extreme environments

A wide array of microorganisms, including many novel, phylogenetically deeply rooted taxa, survive and thrive in extreme environments. These unique and reduced-complexity ecosystems offer a tremendous opportunity for studying the structure, function and evolution of natural microbial communities. Marker gene surveys have resolved patterns and ecological drivers of these extremophile assemblages, revealing a vast uncultured microbial diversity and the often predominance of archaea in the most extreme conditions. New omics studies have uncovered linkages between community function and environmental variables, and have enabled discovery and genomic characterization of major new lineages that substantially expand microbial diversity and change the structure of the tree of life. These efforts have significantly advanced our understanding of the diversity, ecology and evolution of microorganisms populating Earth's extreme environments, and have facilitated the exploration of microbiota and processes in more complex ecosystems.

Diversity and Genomic Characterization of a Novel Parvarchaeota Family in Acid Mine Drainage Sediments

Recent genome-resolved metagenomic analyses of microbial communities from diverse environments have led to the discovery of many novel lineages that significantly expand the phylogenetic breadth of Archaea. Here, we report the genomic characterization of a new archaeal family based on five metagenome-assembled genomes retrieved from acid mine drainage sediments. Phylogenomic analyses placed these uncultivated archaea at the root of the candidate phylum Parvarchaeota, which expand this lesser-known phylum into two family levels. Genes involved in environmental adaptation and carbohydrate and protein utilization were identified in the ultra-small genomes (estimated size 0.53–0.76 Mb), indicating a survival strategy in this harsh environment (low pH and high heavy metal content). The detection of genes with homology to sulfocyanin suggested a potential involvement in iron cycling. Nevertheless, the absence of the ability to synthesize amino acids and nucleotides implies that these archaea may acquire these biomolecules from the environment or other community members. Applying evolutionary history analysis to Parvarchaeota suggested that members of the two families could broaden their niches by acquiring the potentials of utilizing different substrates. This study expands our knowledge of the diversity, metabolic capacity, and evolutionary history of the Parvarchaeota.

Metal-Resistance in Bacteria: Why Care?

Heavy metal resistance is more than the tolerance one has towards a particular music genera [...].

Revegetation approach and plant identity unequally affect structure, ecological network and function of soil microbial community in a highly acidified mine tailings pond

Owing to its sustainability and low cost, direct revegetation (DR) has been considered a promising alternative to capped revegetation (CR) for dealing with the serious environmental problem derived from various types of mine wastelands that are widespread in the world. However, a direct comparison of the performance of these two revegetation approaches for reclamation of extremely acidic mine wastelands and the underlying mechanisms is still lacking. To bridge this critical knowledge gap, we established 5000 m² of vegetation on a highly acidified (pH < 3) Pb/Zn mine tailings pond employing both CR and DR schemes (2500 m² for each scheme). We then profiled the structure, ecological network and function of soil microbial communities associated with two dominant plant species of the vegetations via high-throughput sequencing. Our results showed that CR and DR achieved a vegetation coverage of 59.7% and 90.5% within two years, respectively. This pattern was accompanied by higher concentrations of plant nutrients and lower acidification potentials in topsoils of the rhizospheres of the vegetation established by DR compared to those of CR. Revegetation approach, rather than plant identity, mostly affected the structure, ecological network and function of soil microbial community in the mine tailings pond. Rhizosphere soils of the vegetation established by DR generally had higher microbial diversity, higher relative abundances of dominant microbial phyla (e.g. Nitrospirae) that can aid plant uptake of nutrients, more complicated microbial interactive networks and more microbial genes responsible for nutrient cycling than those by CR. As the first report on a direct comparison of CR and DR schemes for reclamation of an extremely acidic mine wasteland, our study has important implications for not only the understanding of microbial ecology in revegetated mine wastelands but also the further development of sustainable revegetation schemes.

Depth-related variability in viral communities in highly stratified sulfidic mine tailings

BACKGROUND

Recent studies have significantly expanded our knowledge of viral diversity and functions in the environment. Exploring the ecological relationships between viruses, hosts, and the environment is a crucial first step towards a deeper understanding of the complex and dynamic interplays among them.

RESULTS

Here, we obtained extensive 16S rRNA gene amplicon, metagenomics sequencing, and geochemical datasets from different depths of two highly stratified sulfidic mine tailings cores with steep geochemical gradients especially pH, and explored how variations in viral community composition and functions were coupled to the co-existing prokaryotic assemblages and the varying environmental conditions. Our data showed that many viruses in the mine tailings represented novel genera, based on gene-sharing networks. Siphoviridae, Podoviridae, and Myoviridae dominated the classified viruses in the surface tailings and deeper layers. Both viral richness and normalized coverage increased with depth in the tailings cores and were significantly correlated with geochemical properties, for example, pH. Viral richness was also coupled to prokaryotic richness (Pearson's r = 0.65, P = 0.032). The enrichment of prophages in the surface mine tailings suggested a preference of lysogenic viral lifestyle in more acidic conditions. Community-wide comparative analyses clearly showed that viruses in the surface tailings encoded genes mostly with unknown functions while viruses in the deeper layers contained genes mainly annotated as conventional functions related to metabolism and structure. Notably, significantly abundant assimilatory sulfate reduction genes were identified from the deeper tailings layers and they were widespread in viruses predicted to infect diverse bacterial phyla.

CONCLUSIONS

Overall, our results revealed a depth-related distribution of viral populations in the extreme and heterogeneous tailings system. The viruses may interact with diverse hosts and dynamic environmental conditions and likely play a role in the functioning of microbial community and modulate sulfur cycles in situ. Video Abstract.

[The clinical characteristics of severe influenza virus pneumonia complicated with invasive pulmonary aspergillosis: a retrospective study of 15 cases]

Objective: To explore the clinical characteristics, risk factors and possible inflammatory response mechanisms in critically ill patients with influenza and invasive pulmonary aspergillosis co-infection. Methods: Sixty-four patients with severe influenza virus pneumonia were included in the RICU of the China-Japanese Friendship Hospital from November 1(st), 2017 to March 31(th), 2018. There were 33 males and 31 females, with an average age of (55±14) years. T-tests or χ(2) test were applied for comparisons between the two groups. Fifteen patients were complicated with IPA and were classified as the IPA group, while the other 49 served as the control group. The clinical characteristics, laboratory examinations, and endoscopic manifestations were compared between the two groups and the risk factors for severe influenza virus pneumonia with IPA were analyzed by multivariate logistic regression. The possible mechanisms of inflammatory response were explored by comparing the differences of plasma inflammatory factors between the two groups. Results: Seven patients (7/15, 47.7%) in the IPA group died. The percentage of wheezing in the IPA group (n=13) was significantly higher than that in the control group (n=25) (P<0.05). The values of WBC [(11.0±2.7)×10(9)/L], and the levels of blood GM [(2.46±0.80) μg/L] and BALF GM [(5.30±0.98) μg/L] in the IPA group were significantly higher than those in the control group, while PCT was lower than that in the control group[(6.1±3.3)×10(9)/L, (0.33±0.07) μg/L and (0.73±0.17) μg/L, respectively] (P<0.01). Compared with the control group, the chest CT of the IPA group showed more nodules along the bronchial bundle (n=11), massive consolidation shadow (n=9), halo sign (n=3) and cavity/air crescent sign (n=5) (control group: 8, 11, 0 and 4, respectively) (P<0.05). Airway mucosal pseudomembrane formation (n=12) and airway stenosis (n=10) were significantly higher in the IPA group than in the control group (2 and 17) (P<0.05). Multivariate logistic regression analysis suggested that the history of glucocorticoid use after ICU admission, normal PCT, multiple nodules, halo signs and pseudomembrane formation under endoscopy were risk factors for severe influenza virus pneumonia with IPA. The plasma pro-inflammatory factors IFN-γ [IPA group: 34.9 (20.6-64.0) μg/L] and IL-2 [16.2 (8.9-20.7) μg/L] were significantly lower than in patients without IPA [control group: 65.2 (43.8-124.5) μg/L and 20.4 (14.6-28.8) μg/L, respectively] (P<0.05); while the inflammatory inhibitors IL-4 [51.6 (32.7-69.7) μg/L) and IL-10 [15.7 (11.8-92.5) μg/L] were higher in IPA group [control group 8.9 (6.1-15.0) μg/L and 7.8 (3.6-21.8) μg/L] (P<0.05). SOFA scores showed a negative correlation with IFN-γ (r=-0.658, P=0.02) and IL-6 (r=-0.602, P=0.038), but a positive correlation with IL-10 (r=0.641, P=0.025) by Spearman correlation analysis. Conclusions: Some relatively specific clinical characteristics could be found in severe influenza pneumonia complicated with IPA. IPA should be highly suspected when a patient had a history of glucocorticoid use after ICU admission, high WBCs in the course of treatment without significant increase of PCT,multiple nodules along the airway distribution and the characteristic pseudomembrane formation under bronchoscopy. Influenza virus caused imbalance of immune responses, leading to a weakened pro-inflammatory response and a strengthened inflammatory suppression, which might be a possible mechanism for IPA development.

[A functional magnetic resonance imaging study of exercise addiction]

Objective: To investigate the brain activities of exercise addiction (EA) group people with the task-functional magnetic resonance image (task-fMRI). Methods: A total of 29 exercise addicts (addiction group, average age 46±4 years) and 26 non-exercise addicts (control group, average age 46±6 years) matched by sex, age, average education level and sports dependence degree were selected by using exercise addiction index (EAI) through questionnaires to members of Jiangsu Local Fitness and Long-distance Running Association between January 2018 and June 2018. The participants were scanned with fMRI while watching sports pictures or non-sports pictures. The brain responses of the two groups under two stimulation tasks were analyzed and compared. Results: Compared with the control group, while watching sports pictures, the right fusiform gyrus (MNI:x=30, y=-87, z=0), left posterior central gyrus (MNI:x=-51, y=-21, z=54), left medial superior frontal gyrus (MNI:x=-9, y=54, z=30), and right middle occipital gyrus (MNI:x=42, y=-72, z=36) were significantly inhibited in the addiction group (t-test, all P<0.05). When watching non-sports pictures, the addictive group showed the left superior frontal gyrus (MNI:x=-12, y=54, z=30), left middle frontal gyrus (MNI:x=-30, y=18, z=45), right inferior frontal gyrus (MNI:x=42, y=33, z=-12), right occipital gyrus (MNI:x=42, y=-72, z=36), and they were more significantly inhibited than the control group (t-test, all P<0.05). Conclusion: Compared to the control group, the EA group shows significant brain inhibition with visual stimulation, particularly with non-sports pictures.

Insights into ecological role of a new deltaproteobacterial order Candidatus Acidulodesulfobacterales by metagenomics and metatranscriptomics

Several abundant but yet uncultivated bacterial groups exist in extreme iron- and sulfur-rich environments, and the physiology, biodiversity, and ecological roles of these bacteria remain a mystery. Here we retrieved four metagenome-assembled genomes (MAGs) from an artificial acid mine drainage (AMD) system, and propose they belong to a new deltaproteobacterial order, Candidatus Acidulodesulfobacterales. The distribution pattern of Ca. Acidulodesulfobacterales in AMDs across Southeast China correlated strongly with ferrous iron. Reconstructed metabolic pathways and gene expression profiles showed that they were likely facultatively anaerobic autotrophs capable of nitrogen fixation. In addition to dissimilatory sulfate reduction, encoded by dsrAB, dsrD, dsrL, and dsrEFH genes, these microorganisms might also oxidize sulfide, depending on oxygen concentration and/or oxidation reduction potential. Several genes with homology to those involved in iron metabolism were also identified, suggesting their potential role in iron cycling. In addition, the expression of abundant resistance genes revealed the mechanisms of adaptation and response to the extreme environmental stresses endured by these organisms in the AMD environment. These findings shed light on the distribution, diversity, and potential ecological role of the new order Ca. Acidulodesulfobacterales in nature.

Spencerozyma acididurans sp. nov., an acid-tolerant basidiomycetous yeast species isolated from acid mine drainage

Strain SYSU-17, representing a novel acid-tolerant yeast species which can grow at pH 2.0 weakly, was isolated from acid mine drainage collected in a tailing impoundment of the Fankou Lead/Zinc Mine, Guangdong Province, PR China. Phylogenetic analysis of strain SYSU-17 based on the internal transcribed spacer (ITS) region and the D1/D2 domains of the large subunit ribosomal RNA (LSU rRNA) gene suggested that strain SYSU-17 was a novel species belonging to the genus Spencerozyma (class Microbotryomycetes, subphylum Pucciniomycotina). It differed from the type strain of the closest related species, Spencerozyma crocea CBS 2029^T, by 0.7 % sequence divergence (three gaps and one nucleotide substitution out of 594 bp) in the D1/D2 domains of the LSU rRNA gene and 7.6 % sequence divergence (32 gaps and 22 nucleotide substitutions out of 714 bp) in the ITS region. In contrast to the physiological properties of S. crocea, the novel yeast species was unable to assimilate galactose, d-ribose, xylitol, succinate, d-xylose, ethanol, nitrate and nitrite. The name Spencerozyma acididurans sp. nov. is proposed and SYSU-17 is designated as the holotype.

[The expression and significance of CD(276) and CD(133) in colorectal cancer and precancerous lesions]

In order to study the significance of CD(276) and CD(133) in the development and progression of colorectal cancer (CRC), the expression of CD(276) and CD(133) was detected by immunohistochemistry in CRC and precancerous lesions. The results showed that the intensity of CD(276) and CD(133) in CRC samples was higher than that in adenoma group and non-adenoma group. CD(276) and CD(133) single and double positive expression were significantly correlated with CRC lymph node metastasis, distant metastasis and survival. CD(276) and CD(133) are significantly correlated to the development and progression of CRC and associated with poor prognosis.

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.

Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota

Small acidophilic archaea belonging to Micrarchaeota and Parvarchaeota phyla are known to physically interact with some Thermoplasmatales members in nature. However, due to a lack of cultivation and limited genomes on hand, their biodiversity, metabolisms, and physiologies remain largely unresolved. Here, we obtained 39 genomes from acid mine drainage (AMD) and hot spring environments around the world. 16S rRNA gene based analyses revealed that Parvarchaeota were only detected in AMD and hot spring habitats, while Micrarchaeota were also detected in others including soil, peat, hypersaline mat, and freshwater, suggesting a considerable higher diversity and broader than expected habitat distribution for this phylum. Despite their small genomes (0.64-1.08 Mb), these archaea may contribute to carbon and nitrogen cycling by degrading multiple saccharides and proteins, and produce ATP via aerobic respiration and fermentation. Additionally, we identified several syntenic genes with homology to those involved in iron oxidation in six Parvarchaeota genomes, suggesting their potential role in iron cycling. However, both phyla lack biosynthetic pathways for amino acids and nucleotides, suggesting that they likely scavenge these biomolecules from the environment and/or other community members. Moreover, low-oxygen enrichments in laboratory confirmed our speculation that both phyla are microaerobic/anaerobic, based on several specific genes identified in them. Furthermore, phylogenetic analyses provide insights into the close evolutionary history of energy related functionalities between both phyla with Thermoplasmatales. These results expand our understanding of these elusive archaea by revealing their involvement in carbon, nitrogen, and iron cycling, and suggest their potential interactions with Thermoplasmatales on genomic scale.

[Forensic Psychiatric Assessment for Organic Personality Disorders after Craniocerebral Trauma]

OBJECTIVES

To explore the occurrence and the differences of clinical manifestations of organic personality disorder with varying degrees of craniocerebral trauma.

METHODS

According to the International Classification of Diseases-10, 396 subjects with craniocerebral trauma caused by traffic accidents were diagnosed, and the degrees of craniocerebral trauma were graded. The personality characteristics of all patients were evaluated using the simplified Neuroticism Extraversion Openness Five-Factor Inventory （NEO-FFI）.

RESULTS

The occurrence rate of organic personality disorder was 34.6% while it was 34.9% and 49.5% in the patients with moderate and severe craniocerebral trauma, respectively, which significantly higher than that in the patients （18.7%） of mild craniocerebral trauma （P<0.05）. Compared with the patients without personality disorder, the neuroticism, extraversion and agreeableness scores all showed significantly differences （P<0.05） in the patients of mild craniocerebral trauma with personality disorder; the neuroticism, extraversion, agreeableness and conscientiousness scores showed significantly differences （ P>0.05） in the patients of moderate and severe craniocerebral trauma with personality disorder. The agreeableness and conscientiousness scores in the patients of moderate and severe craniocerebral trauma with personality disorder were significantly lower than that of mild craniocerebral trauma, and the patients of severe craniocerebral trauma had a lower score in extraversion than in the patients of mild craniocerebral trauma.

CONCLUSIONS

The severity of craniocerebral trauma is closely related to the incidence of organic personality disorder, and it also affects the clinical features of the latter, which provides a certain significance and help for forensic psychiatric assessment.

Microbial Ecology and Evolution in the Acid Mine Drainage Model System

Acid mine drainage (AMD) is a unique ecological niche for acid- and toxic-metals-adapted microorganisms. These low-complexity systems offer a special opportunity for the ecological and evolutionary analyses of natural microbial assemblages. The last decade has witnessed an unprecedented interest in the study of AMD communities using 16S rRNA high-throughput sequencing and community genomic and postgenomic methodologies, significantly advancing our understanding of microbial diversity, community function, and evolution in acidic environments. This review describes new data on AMD microbial ecology and evolution, especially dynamics of microbial diversity, community functions, and population genomes, and further identifies gaps in our current knowledge that future research, with integrated applications of meta-omics technologies, will fill.

Yeast one-hybrid screening the potential regulator of CYP6B6 overexpression of Helicoverpa armigera under 2-tridecanone stress

In insect, the cytochrome P450 plays a pivotal role in detoxification to toxic allelochemicals. Helicoverpa armigera can tolerate and survive in 2-tridecanone treatment owing to the CYP6B6 responsive expression, which is controlled by some regulatory DNA sequences and transcription regulators. Therefore, the 2-tridecanone responsive region and transcription regulators of the CYP6B6 are responsible for detoxification of cotton bollworm. In this study, we used yeast one-hybrid to screen two potential transcription regulators of the CYP6B6 from H. armigera that respond to the plant secondary toxicant 2-tridecanone, which were named Prey1 and Prey2, respectively. According to the NCBI database blast, Prey1 is the homology with FK506 binding protein (FKBP) of Manduca sexta and Bombyx mori that belongs to the FKBP-C superfamily, while Prey2 may be a homology of an unknown protein of Papilio or the fcaL24 protein homology of B. mori. The electrophoretic mobility shift assays revealed that the FKBP of prokaryotic expression could specifically bind to the active region of the CYP6B6 promoter. After the 6th instar larvae of H. armigera reared on 2-tridecanone artificial diet, we found there were similar patterns of CYP6B6 and FKBP expression of the cotton bollworm treated with 10 mg g-1 2-tridecanone for 48 h, which correlation coefficient was the highest (0.923). Thus, the FKBP is identified as a strong candidate for regulation of the CYP6B6 expression, when the cotton bollworm is treated with 2-tridecanone. This may lead us to a better understanding of transcriptional mechanism of CYP6B6 and provide very useful information for the pest control.

Ecological effects of combined pollution associated with e-waste recycling on the composition and diversity of soil microbial communities

The crude processing of electronic waste (e-waste) has led to serious contamination in soils. While microorganisms may play a key role in remediation of the contaminated soils, the ecological effects of combined pollution (heavy metals, polychlorinated biphenyls, and polybrominated diphenyl ethers) on the composition and diversity of microbial communities remain unknown. In this study, a suite of e-waste contaminated soils were collected from Guiyu, China, and the indigenous microbial assemblages were profiled by 16S rRNA high-throughput sequencing and clone library analysis. Our data revealed significant differences in microbial taxonomic composition between the contaminated and the reference soils, with Proteobacteria, Acidobacteria, Bacteroidetes, and Firmicutes dominating the e-waste-affected communities. Genera previously identified as organic pollutants-degrading bacteria, such as Acinetobacter, Pseudomonas, and Alcanivorax, were frequently detected. Canonical correspondence analysis revealed that approximately 70% of the observed variation in microbial assemblages in the contaminated soils was explained by eight environmental variables (including soil physiochemical parameters and organic pollutants) together, among which moisture content, decabromodiphenyl ether (BDE-209), and copper were the major factors. These results provide the first detailed phylogenetic look at the microbial communities in e-waste contaminated soils, demonstrating that the complex combined pollution resulting from improper e-waste recycling may significantly alter soil microbiota.

Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics

High-throughput sequencing is expanding our knowledge of microbial diversity in the environment. Still, understanding the metabolic potentials and ecological roles of rare and uncultured microbes in natural communities remains a major challenge. To this end, we applied a 'divide and conquer' strategy that partitioned a massive metagenomic data set (>100 Gbp) into subsets based on K-mer frequency in sequence assembly to a low-diversity acid mine drainage (AMD) microbial community and, by integrating with an additional metatranscriptomic assembly, successfully obtained 11 draft genomes most of which represent yet uncultured and/or rare taxa (relative abundance <1%). We report the first genome of a naturally occurring Ferrovum population (relative abundance >90%) and its metabolic potentials and gene expression profile, providing initial molecular insights into the ecological role of these lesser known, but potentially important, microorganisms in the AMD environment. Gene transcriptional analysis of the active taxa revealed major metabolic capabilities executed in situ, including carbon- and nitrogen-related metabolisms associated with syntrophic interactions, iron and sulfur oxidation, which are key in energy conservation and AMD generation, and the mechanisms of adaptation and response to the environmental stresses (heavy metals, low pH and oxidative stress). Remarkably, nitrogen fixation and sulfur oxidation were performed by the rare taxa, indicating their critical roles in the overall functioning and assembly of the AMD community. Our study demonstrates the potential of the 'divide and conquer' strategy in high-throughput sequencing data assembly for genome reconstruction and functional partitioning analysis of both dominant and rare species in natural microbial assemblages.

Microbial communities evolve faster in extreme environments

Evolutionary analysis of microbes at the community level represents a new research avenue linking ecological patterns to evolutionary processes, but remains insufficiently studied. Here we report a relative evolutionary rates (rERs) analysis of microbial communities from six diverse natural environments based on 40 metagenomic samples. We show that the rERs of microbial communities are mainly shaped by environmental conditions, and the microbes inhabiting extreme habitats (acid mine drainage, saline lake and hot spring) evolve faster than those populating benign environments (surface ocean, fresh water and soil). These findings were supported by the observation of more relaxed purifying selection and potentially frequent horizontal gene transfers in communities from extreme habitats. The mechanism of high rERs was proposed as high mutation rates imposed by stressful conditions during the evolutionary processes. This study brings us one stage closer to an understanding of the evolutionary mechanisms underlying the adaptation of microbes to extreme environments.

Different magnitude of resistance to non-depolarizing muscle relaxants in dexamethasone-treated rat diaphragm associated with altered acetylcholine receptor expression

The aim of this study was to investigate the influence of chronic dexamethasone (Dex) administration on rat diaphragm sensitivity to non-depolarizing muscle relaxants (NDMRs) and muscular nicotinic acetylcholine receptor (nAChR) expression, which may help direct future administration of NDMRs. Adult male Sprague-Dawley rats were randomized to receive a daily intraperitoneal injection of Dex (600 μg/kg body mass) or an equivalent volume of saline (N = 20 in each group) for 14 days. We evaluated isometric twitch tensions of nerve-hemidiaphragm preparations elicited by indirect supramaximal stimulation at 0.1 Hz. Real-time quantitative PCR was performed to determine the mRNA expression of two nAChR subunits (ε-subunit and γ-subunit) in the diaphragm. Dex administration markedly (P < 0.01) increased the 50% twitch depression (IC50) of the three NDMRs. The IC50 ratio, which standardized the magnitudes of the resistance, was the largest for atracurium, with the second largest for vecuronium and the smallest for rocuronium (P < 0.01). The ε- and γ-subunit mRNAs were both upregulated with an increased γ/ε ratio in rats exposed to Dex. The results indicated that chronic Dex administration induces hyposensitivity to NDMRs, the degree of which depends on the kind of neuromuscular blocker, and is associated with increased nAChR expression.

Improving nitrogen removal in an ANAMMOX reactor using a permeable reactive biobarrier

A novel ANAMMOX biofilm reactor that combines the advantages of conventional biofilm reactors and membrane bioreactors (MBRs) was developed in an attempt to decrease the levels of nitrogen in the reactor filtrate. In this reactor, nonwoven fabric modules served as both biofilm carriers and membrane-like separators, and the biofilm acted as a permeable reactive barrier for the removal of nitrogen species from the bulk liquid. Long-term monitoring suggests that the nitrogen removal rates (NRR) of the reactor reached ca. 1.6 kg-N/(m(3) d). Interestingly, large fractions of the ammonium (ca. 27%) and nitrite (ca. 48%) remaining in the bulk liquid were removed during their transport through the biofilm; thus, the reactive barrier process of the biofilm contributed ca. 11% to the total NRR. With an increase in the imposed flux, the contribution of the reactive barrier process to the removal of nitrogen from the reactor bulk liquid increased significantly, e.g., it contributed 26% to the NRR at 17.4 L/(m(2) h). Additionally, the nonwoven modules could retain free bacteria effectively; they maintained a non-fouling state during the entire operation period of approximately 400 days. Sequence analysis shows that Candidatus Kuenenia-like species dominated the ANAMMOX bacteria in the reactor. These results clearly demonstrate that this innovative reactor holds great promise for improving the ANAMMOX process, thus decreasing nitrogen levels in the effluent.

Correlating microbial diversity patterns with geochemistry in an extreme and heterogeneous environment of mine tailings

Recent molecular surveys have advanced our understanding of the forces shaping the large-scale ecological distribution of microbes in Earth's extreme habitats, such as hot springs and acid mine drainage. However, few investigations have attempted dense spatial analyses of specific sites to resolve the local diversity of these extraordinary organisms and how communities are shaped by the harsh environmental conditions found there. We have applied a 16S rRNA gene-targeted 454 pyrosequencing approach to explore the phylogenetic differentiation among 90 microbial communities from a massive copper tailing impoundment generating acidic drainage and coupled these variations in community composition with geochemical parameters to reveal ecological interactions in this extreme environment. Our data showed that the overall microbial diversity estimates and relative abundances of most of the dominant lineages were significantly correlated with pH, with the simplest assemblages occurring under extremely acidic conditions and more diverse assemblages associated with neutral pHs. The consistent shifts in community composition along the pH gradient indicated that different taxa were involved in the different acidification stages of the mine tailings. Moreover, the effect of pH in shaping phylogenetic structure within specific lineages was also clearly evident, although the phylogenetic differentiations within the Alphaproteobacteria, Deltaproteobacteria, and Firmicutes were attributed to variations in ferric and ferrous iron concentrations. Application of the microbial assemblage prediction model further supported pH as the major factor driving community structure and demonstrated that several of the major lineages are readily predictable. Together, these results suggest that pH is primarily responsible for structuring whole communities in the extreme and heterogeneous mine tailings, although the diverse microbial taxa may respond differently to various environmental conditions.

Optimisation and performance of NaClO-assisted maintenance cleaning for fouling control in membrane bioreactors

Based on conventional chemical cleaning and physical backflush methods, a novel in situ chemical backflush method, i.e., chemically assisted maintenance cleaning with NaClO as the principal reagent, was developed for membrane fouling control in membrane bioreactors (MBRs). The results demonstrated that, compared with a control MBR with water backflush, the use of low NaClO loads had few adverse effects on nutrient removal; on the contrary, the exposure to NaClO enhanced the denitrification performance of the MBR as a result of the formation of sludge granules. Measurements of transmembrane pressure (TMP) showed that an NaClO backflush at 0.2 ppm could achieve effective membrane fouling control in MBRs. Ex situ backflush tests showed that an NaClO backflush enhanced the detachment of biopolymers from the fouled membranes compared with a water backflush. Comparative 16S rRNA sequencing showed differing bacterial community composition in the fouling layers of the two MBRs. Specifically, the NaClO backflush could suppress filament-caused membrane fouling (i.e., lowered the abundance of Thiothrix eikelboomii in the fouling layers). Both the water and NaClO backflush resulted in significant increases in the pure water permeability of the membranes as a result of the enlargement of membrane pores. The results of Fourier transform infrared spectrometry indicated that the frequent NaClO backflush did not change the functional groups of the active layer of the membranes significantly. This study could provide an alternative for the implementation of membrane cleaning in MBR plants.

Contemporary environmental variation determines microbial diversity patterns in acid mine drainage

A wide array of microorganisms survive and thrive in extreme environments. However, we know little about the patterns of, and controls over, their large-scale ecological distribution. To this end, we have applied a bar-coded 16S rRNA pyrosequencing technology to explore the phylogenetic differentiation among 59 microbial communities from physically and geochemically diverse acid mine drainage (AMD) sites across Southeast China, revealing for the first time environmental variation as the major factor explaining community differences in these harsh environments. Our data showed that overall microbial diversity estimates, including phylogenetic diversity, phylotype richness and pairwise UniFrac distance, were largely correlated with pH conditions. Furthermore, multivariate regression tree analysis also identified solution pH as a strong predictor of relative lineage abundance. Betaproteobacteria, mostly affiliated with the 'Ferrovum' genus, were explicitly predominant in assemblages under moderate pH conditions, whereas Alphaproteobacteria, Euryarchaeota, Gammaproteobacteria and Nitrospira exhibited a strong adaptation to more acidic environments. Strikingly, such pH-dependent patterns could also be observed in a subsequent comprehensive analysis of the environmental distribution of acidophilic microorganisms based on 16S rRNA gene sequences previously retrieved from globally distributed AMD and associated environments, regardless of the long-distance isolation and the distinct substrate types. Collectively, our results suggest that microbial diversity patterns are better predicted by contemporary environmental variation rather than geographical distance in extreme AMD systems.

Shifts in microbial community composition and function in the acidification of a lead/zinc mine tailings

In an attempt to link the microbial community composition and function in mine tailings to the generation of acid mine drainage, we simultaneously explored the geochemistry and microbiology of six tailings collected from a lead/zinc mine, i.e. primary tailings (T1), slightly acidic tailings (T2), extremely acidic tailings (T3, T4 and T5) and orange-coloured oxidized tailings (T6). Geochemical results showed that the six tailings (from T1 to T6) likely represented sequential stages of the acidification process of the mine tailings. 16S rRNA pyrosequencing revealed a contrasting microbial composition between the six tailings: Proteobacteria-related sequences dominated T1-T3 with relative abundance ranging from 56 to 93%, whereas Ferroplasma-related sequences dominated T4-T6 with relative abundance ranging from 28 to 58%. Furthermore, metagenomic analysis of the microbial communities of T2 and T6 indicated that the genes encoding key enzymes for microbial carbon fixation, nitrogen fixation and sulfur oxidation in T2 were largely from Thiobacillus and Acidithiobacillus, Methylococcus capsulatus, and Thiobacillus denitrificans respectively; while those in T6 were mostly identified in Acidithiobacillus and Leptospirillum, Acidithiobacillus and Leptospirillum, and Acidithiobacillus respectively. The microbial communities in T2 and T6 harboured more genes suggesting diverse metabolic capacities for sulfur oxidation/heavy metal detoxification and tolerating low pH respectively.

Biodiversity, abundance, and activity of nitrogen-fixing bacteria during primary succession on a copper mine tailings

Microorganisms are important in soil development, inputs and biogeochemical cycling of nutrients and organic matter during early stages of ecosystem development, but little is known about their diversity, distribution, and function in relation to the chemical and physical changes associated with the progress of succession. In this study, we characterized the community structure and activity of nitrogen-fixing microbes during primary succession on a copper tailings. Terminal fragment length polymorphism (T-RFLP) and clone sequencing of nifH genes indicated that different N(2) -fixing communities developed under primary succession. Phylogenetic analysis revealed a diversity of nifH sequences that were mostly novel, and many of these could be assigned to the taxonomic divisions Proteobacteria, Cyanobacteria, and Firmicutes. Members of the Cyanobacteria, mostly affiliated with Nostocales or not closely related to any known organisms, were detected exclusively in the biological soil crusts and represented a substantial fraction of the respective diazotrophic communities. Quantitative PCR (and statistical analyses) revealed that, overall, copy number of nifH sequences increased with progressing succession and correlated with changes in physiochemical properties (including elementary elements such as carbon and nitrogen) and the recorded nitrogenase activities of the tailings. Our study provides an initial insight into the biodiversity and community structure evolution of N(2) -fixing microorganisms in ecological succession of mine tailings.

Biodiversity and population dynamics of microorganisms in a full-scale membrane bioreactor for municipal wastewater treatment

The total, ammonia-oxidizing, and denitrifying Bacteria in a full-scale membrane bioreactor (MBR) were evaluated monthly for over one year. Microbial communities were analyzed by denaturing gradient gel electrophoresis (DGGE) and clone library analysis of the 16S rRNA and ammonia monooxygenase (amoA) and nitrous oxide reductase (nosZ) genes. The community fingerprints obtained were compared to those from a conventional activated sludge (CAS) process running in parallel treating the same domestic wastewater. Distinct DGGE profiles for all three molecular markers were observed between the two treatment systems, indicating the selection of specific bacterial populations by the contrasting environmental and operational conditions. Comparative 16S rRNA sequencing indicated a diverse bacterial community in the MBR, with phylotypes from the α- and β-Proteobacteria and Bacteroidetes dominating the gene library. The vast majority of sequences retrieved were not closely related to classified organisms or displayed relatively low levels of similarity with any known 16S rRNA gene sequences and thus represent organisms that constitute new taxa. Similarly, the majority of the recovered nosZ sequences were novel and only moderately related to known denitrifiers from the α- and β-Proteobacteria. In contrast, analysis of the amoA gene showed a remarkably simple ammonia-oxidizing community with the detected members almost exclusively affiliated with the Nitrosomonas oligotropha lineage. Major shifts in total bacteria and denitrifying community were detected and these were associated with change in the external carbon added for denitrification enhancement. In spite of this, the MBR was able to maintain a stable process performance during that period. These results significantly expand our knowledge of the biodiversity and population dynamics of microorganisms in MBRs for wastewater treatment.

Plant-by-plant variations of bacterial communities associated with leaves of the nickel hyperaccumulator Alyssum bertolonii Desv

Bacteria associated with tissues of metal-hyperaccumulating plants are of great interest due to the multiple roles they may play with respect to plant growth and resistance to heavy metals. The variability of bacterial communities associated with plant tissues of three populations of Alyssum bertolonii, a Ni hyperaccumulator endemic of serpentine outcrops of Central Italy, was investigated. Terminal-restriction fragment length polymorphism (T-RFLP) analysis of bacterial 16S rRNA genes was applied to DNA extracted from leaf tissues of 30 individual plants from three geographically separated serpentine outcrops. Moreover, T-RFLP fingerprinting was also performed on DNA extracted from the same soils from which the plants were collected. Fifty-nine unique terminal-restriction fragments (TRFs) were identified, with more than half of the taxonomically interpreted TRFs assigned to Alpha- and Gamma-Proteobacteria and Clostridia. Data were then used to define the extent of variation of bacterial communities due to single plants or to plant populations. Results indicated a very high plant-by-plant variation of leaf-associated community (more than 93% of total variance observed). However, a core (numerically small) of plant-specific TRFs was found. This work demonstrates that plant-associated bacterial communities represent a large reservoir of biodiversity and that the high variability existing between plants, even from the same population, should be taken into account in future studies on association between bacteria and metal-hyperaccumulating plants.

Diverse and distinct bacterial communities induced biofilm fouling in membrane bioreactors operated under different conditions

We conducted a laboratory-scale experiment using real municipal wastewater with identical submerged membrane bioreactors (MBR) operated under different conditions (sludge retention time (SRT) and membrane flux) for nearly 6 months. Membrane biofilm samples were periodically retrieved, and cultivation-independent molecular approaches were used to systematically elucidate the community composition and diversity of microorganisms responsible for biofilm formation in the MBRs. Membrane fouling occurred earlier and faster in the low-SRT reactors which had more active mixed liquor biomasses and higher concentrations of dissolved organic matters. Denaturing gradient gel electrophoresis (DGGE) analysis and comparative rRNA sequencing revealed that diverse and distinct bacterial communities significantly differing from those in the planktonic biomass developed on the microfiltration membrane surfaces, with phylotypes from the Proteobacteria (particularly the alpha and beta subdivisions) and Bacteroidetes dominating the 16S rRNA gene libraries. This indicated that specific groups of bacteria were preferentially growing in the membrane habitats. Membrane flux had great impact on the predominant populations selected in the fouling biofilms. At lower fluxes, biofilm community composition was quite similar independent of sludge ages and biofilm formation seemed to be the result of a more natural process of colonization and biofilm development. In contrast, distinct biofilm communities developed on membrane surfaces at high fluxes. Despite the high convective forces, the biofilm composition was significantly different from the planktonic biomass, and selective enrichments of certain species were observed. Our study suggests that the microbial communities responsible for membrane biofouling in MBRs are far more complex and variable than expected and thus could be challenging to control.

Continued study of the psychometric properties of the McGill quality of life questionnaire

The McGill Quality of Life Questionnaire (MQOL) is a widely used tool that has been specifically developed to measure the quality of life of patients facing a life-threatening illness. Preferably, a self-report instrument has an equal number of items worded positively and negatively. However, all the psychological scales of the MQOL are worded so that a high score is negative, whereas the existential scales are worded so that a high score is positive. The goal of this study was to investigate the influence of MQOL item formatting on patient responses. In order to do so, a modified version of the questionnaire was distributed to and completed by 205 patients in two oncology clinics. The modified version had an equal amount of items worded in a positive direction and negative direction in each of the domains. Results of this study were found to be different from those of other studies: the loading of the items was partly based on scale direction. These changes support the idea that the MQOL formatting has some impact on patient responses. However, factors were also determined by content. Given that MQOL has been widely used and the original formatting provides conceptually clearer subscales, we suggest maintaining the original format, keeping in mind the effect of formatting when interpreting scores.

Culturable and molecular phylogenetic diversity of microorganisms in an open-dumped, extremely acidic Pb/Zn mine tailings

A combination of cultivation-based and molecular-based approaches was used to reveal the culturable and molecular diversity of the microbes inhabiting an open-dumped Pb/Zn mine tailings that was undergoing intensive acid generation (pH 1.9). Culturable bacteria found in the extremely acidic mine tailings were Acidithiobacillus ferrooxidans, Leptospirillum ferriphilum, Sulfobacillus thermotolerans and Acidiphilium cryptum, where the number of acidophilic heterotrophs was ten times higher than that of the iron- and sulfur-oxidizing bacteria. Cloning and phylogenetic analysis revealed that, in contrast to the adjacent AMD, the mine tailings possessed a low microbial diversity with archaeal sequence types dominating the 16S rRNA gene library. Of the 141 clones examined, 132 were represented by two sequence types phylogenetically affiliated with the iron-oxidizing archaea Ferroplasma acidiphilum and three belonged to two tentative groups within the Thermoplasma lineage so far represented by only a few environmental sequences. Six clones in the library were represented by the only bacterial sequence type and were closely related to the well-described iron-oxidizer L. ferriphilum. The significant differences in the prokaryotic community structures of the extremely acidic mine tailings and the AMD associated with it highlights the importance of studying the microbial communities that are more directly involved in the iron and sulfur cycles of mine tailings.

Anthropogenic N2O production from landfill leachate treatment

The results of a field survey and laboratory study indicated that nitrogenous landfill leachate treatment can be a significant potential source of N2O emission. Nil (raw leachate) to 58.8ngmL(-1)h(-1) (sequential batch reactor) N2O emission was detected at five treatment plants in South China. The production and emission of N2O was especially high soon after the raw leachate was aerated. The emission was positively correlated with the dissolved N2O content in leachate; detected dissolved N2O ranged from 0 to 1309ngmL(-1). All leachate treatment plants studied were effective in NH4+-N removal (>95%); however, the highest N2O emission was estimated to be 0.25g N2Ocapita(-l)year(-1), comparable with the rate of N2O emission in conventional sewage treatment process.

Cut-off net acid generation pH in predicting acid-forming potential in mine spoils

Acidification of mine wastes can lead to a series of environmental problems, such as acid drainage, heavy metal mobilization, and ecosystem degradation. Prediction of acid-forming potential is one of the key steps in management of sulfide-bearing mine wastes. In this paper, the acid-forming potential of 180 mine waste samples collected from 17 mine sites in China were studied using a net acid generation (NAG) method. The samples contained different contents of total sulfur (ranging from 0.6 to 200 g kg(-1)), pyritic sulfur (ranging from 0 to 100 g kg(-1)), and acid neutralization capacity (ANC, ranging from -41 to 274 kg H2SO4 t(-1)). Samples with high acid-forming potential are generally due to their high sulfur content or low acid neutralization capacity. After the samples were oxidized by H2O2, the amounts of acid generation and the final NAG pH were measured. Results indicated that the final NAG pH gave a well-defined demarcation between acid-forming and non-acid-forming materials. Samples with final NAG pH >or= 5 could be classified as non-acid-forming materials, while those with NAG pH <or= 2.5 could be classified as moderate to strong acid-forming materials. Materials with NAG pH > 2.5, but < 5, had low risk of being acid-forming. The confirmation of cut-off NAG pH will be used as a rapid and cost-effective operational monitoring tool for the in-pit prediction of acid-forming potential of mine wastes and classification of waste types.

Leachates from municipal solid waste disposal sites harbor similar, novel nitrogen-cycling bacterial communities

High emissions of nitrous oxide (N(2)O) have recently been documented at municipal solid waste (MSW) landfills. However, the biodiversity of the bacterial populations involved remains unexplored. In this study, we investigated communities of ammonia-oxidizing bacteria (AOB) and denitrifying bacteria associated with the leachates from three MSW disposal sites by examining the diversity of the ammonia monooxygenase structural gene amoA and the nitrous oxide reductase gene nosZ, respectively. Cloning and phylogenetic analysis of the functional genes revealed novel and similar groups of prokaryotes involved in nitrogen cycling in the leachates with different chemical compositions. All amoA sequences recovered grouped within the Nitrosomonas europaea cluster in the Betaproteobacteria, with the vast majority showed only relatively moderate sequence similarities to known AOB but were exclusively most similar to environmental clones previously retrieved from wastewater treatment plants. All nosZ sequences retrieved did not cluster with any hitherto reported nosZ genes and were only remotely related to recognized denitrifiers from the Gammaproteobacteria and thus could not be affiliated. Significant overlap was found for the three denitrifying nosZ leachate communities. Our study suggests a significant selection of the novel N-cycling groups by the unique environment at these MSW disposal sites.

Cultivation-dependent and cultivation-independent characterization of the microbial community in acid mine drainage associated with acidic Pb/Zn mine tailings at Lechang, Guangdong, China

Cultivation-based and molecular approaches were used to characterize the phylogenetic composition and structure of the microbial community in an extremely acidic (pH 2.0) acid mine drainage (AMD) associated with Pb/Zn mine tailings that were undergoing vigorous acid generation. Acidophilic bacteria were isolated and enumerated on solid media, and were found to be restricted to isolates related to Acidithiobacillus ferrooxidans and Acidiphilium cryptum. By contrast, cloning and phylogenetic analysis of 16S rRNA genes revealed that, although low in total taxonomically distinct groups, the tailings AMD ecosystem harbored a wide range of phylogenetically diverse microbes. Of the 141 clones examined, 104 were phylogenetically affiliated with the recently discovered, iron-oxidizing Leptospirillum group III within the Nitrospira. It thus appears that iron serves as the major electron donor in this habitat. Thirty clones were affiliated with the Proteobacteria, half of which belonged to organisms related to Alphaproteobacteria species capable of ferric iron reduction. Other clones were grouped with Betaproteobacteria and Gammaproteobacteria (six clones each), and even with Deltaproteobacteria (three clones), a subdivision with anaerobic sulfate or metal (iron) reduction as the predominant physiological trait of its members. Finally, four clones were clustered within the Firmicutes and the Acidobacteria. Approximately half of the sequence types representing the majority of the total clones fell into lineages that are poorly represented by cultured organisms or have thus far been represented by only a few environmental sequences. Thus, the present study extends our knowledge of the biodiversity of microorganisms populating highly acidic AMD environments.

Molecular phylogenetic diversity of bacteria associated with the leachate of a closed municipal solid waste landfill

A 16S rDNA-based molecular study was performed to determine the nature of the bacterial constituents of the leachate from a closed municipal solid waste landfill. Total community DNA was extracted and bacterial 16S rRNA genes were subsequently amplified and cloned. Recombinant rDNA clones in the library were randomly selected, and they were sequenced for a single run and then grouped. A total of 76 sequence types representing 138 randomly selected nonchimeric clones were identified. Full-length sequencing and phylogenetic analysis of the sequence types revealed that more than 90% of the screened clones were affiliated with low-G+C gram-positive bacteria (38.4%), Proteobacteria (35.5%), the Cytophaga Flexibacter Bacteroides group (11.6%), and Spirochaetes (5.1%). Minor portions were affiliated with Verrucomicrobia (2.9%), candidate division OP11 (2.2%), and the green nonsulfur bacteria, Cyanobacteria and the Deinococcus Thermus group (each <1.0%). Although some rDNA sequences clustered with genera or taxa that were classically identified within anaerobic treatment systems and expected with known functions, a substantial fraction of the clone sequences showed relatively low levels of similarity with any other reported rDNA sequences and thus were derived from unknown taxa. These results suggest that bacterial communities in landfill environment are far more complex than previously expected and remain largely unexplored.

Diversity and structure of the archaeal community in the leachate of a full-scale recirculating landfill as examined by direct 16S rRNA gene sequence retrieval

The diversity and structure of the archaeal community in the effluent leachate from a full-scale recirculating landfill was characterized by direct 16S rRNA gene (16S rDNA) retrieval. Total-community DNA was extracted from the microbial assemblages in the landfill leachate, and archaeal 16S rDNAs were amplified with a universally conserved primer and an Archaea-specific primer. The amplification product was then used to construct a 16S rDNA clone library, and 70 randomly selected archaeal clones in the library were grouped by restriction fragment length polymorphism (RFLP) analysis. Sequencing and phylogenetic analysis of representatives from each unique RFLP type showed that the archaeal library was dominated by methanogen-like rDNAs. Represented in the kingdom of Euryarchaeota were phylotypes highly similar to the methanogenic genera Methanoculleus, Methanosarcina, Methanocorpusculum, Methanospirillum and Methanogenium, where the clone distribution was 48, 11, 3, 1 and 1, respectively. No sequences related to known Methanosaeta spp. were retrieved. Four rDNA clones were not affiliated with the known methanogenic Archaea, but instead, they were clustered with the uncultured archaeal sequences recently recovered from anaerobic habitats. Two chimeric sequences were identified among the clones analyzed.

Cloning and Expression of Chinese Duck Interferon-gamma Gene

The efficacy of cytokine therapy has been demonstrated in several viral diseases. Interferon-gamma is a cytokine that has potent antiviral property and immunomodulatory activity. To investigate the role of IFN-gamma in viral clearance during natural infection and to define the antiviral mechanism, DHBV-infected ducks was used as an animal model. To clone, express, and develop the method of quantifying DuIFN-gamma gene transcription and expression, DuIFN -gamma cDNA was amplified by RT-PCR from PHA stimulated duck PBMC. Recombinant plasmid expressing DuIFN-gamma was used to transfect COS-7, and the cell culture supernatant was analyzed by CPE inhibitory assay and MTT methods to determine the antiviral titer of IFN-gamma. The GST-DuIFN-gamma fusion protein was expressed in E.coli and purified using the GST sepharose 4B. Results indicated that the supernatant collected from COS-7 cells transfected with DuIFN-gamma cDNA was able to prevent duck fibroblasts from VSV induced CPE in a dose dependent manner. An anti-DuIFN-gamma antibody neutralized this antiviral activity.