Genomics of soil depth niche partitioning in the Thaumarchaeota family Gagatemarchaeaceae.

Knowledge of deeply-rooted non-ammonia oxidising Thaumarchaeota lineages from terrestrial environments is scarce, despite their abundance in acidic soils. Here, 15 new deeply-rooted thaumarchaeotal genomes were assembled from acidic topsoils (0-15 cm) and subsoils (30-60 cm), corresponding to two genera of terrestrially prevalent Gagatemarchaeaceae (previously known as thaumarchaeotal Group I.1c) and to a novel genus of heterotrophic terrestrial Thaumarchaeota. Unlike previous predictions, metabolic annotations suggest Gagatemarchaeaceae perform aerobic respiration and use various organic carbon sources. Evolutionary divergence between topsoil and subsoil lineages happened early in Gagatemarchaeaceae history, with significant metabolic and genomic trait differences. Reconstruction of the evolutionary mechanisms showed that the genome expansion in topsoil Gagatemarchaeaceae resulted from extensive early lateral gene acquisition, followed by progressive gene duplication throughout evolutionary history. Ancestral trait reconstruction using the expanded genomic diversity also did not support the previous hypothesis of a thermophilic last common ancestor of the ammonia-oxidising archaea. Ultimately, this study provides a good model for studying mechanisms driving niche partitioning between spatially related ecosystems.

Survival after induction chemotherapy in locoregional advanced nasopharyngeal carcinoma: An updated systematic review and meta-analysis.

Background: Induction chemotherapy (ICT) augmentation is a common strategy for standard concurrent chemoradiotherapy (CCRT) of locoregionally advanced nasopharyngeal carcinoma (NPC). The survival condition is a crucial issue for patients with locoregionally advanced NPC. The survival of ICT patients with CCRT treatment versus standard CCRT alone should be elucidated via a systemic review and meta-analysis of randomized clinical trials. Methods: We compared ICT with CCRT and CCRT alone treatment to determine if ICT with CCRT can be associated with a significant benefit of survival conditions versus CCRT. Different survival indicators were analyzed for the ICT with CCRT. Twelve studies with a total of 3711 patients with locoregionally advanced NPC were enrolled. The focused outcome was the overall survival, progression-free survival, distant metastasis-free survival, and locoregional recurrence-free survival. Results: Our results showed that ICT with CCRT is associated with a significant benefit for the overall survival status versus CCRT treatment. Similar significant benefits in the survival condition were seen in progression-free survival, distant metastasis-free survival, and locoregional recurrence-free survival. Conclusions: The updated meta-analysis results suggest that the ICT with CCRT might be associated with significant benefits of survival in overall, progression-free, distant metastasis-free, as well as locoregional recurrence-free dimensions versus CCRT treatment. However, the bias of different kinds, doses, and regimens of chemotherapy agents and radiotherapy should not be ignored.

Cost-Benefit Analysis of Vaccination Strategies to Prevent Mother-to-Child Transmission of the Hepatitis B Virus Using a Markov Model Decision Tree.

Objectives: Currently, in China, several strategies exist to prevent mother-to-child transmission (MTCT) of the hepatitis B virus (HBV). These include providing Hepatitis B vaccination and hepatitis B immunoglobulin (HBIG) injection with different types of administration and dosages. The aim of this study is threefold: first, to evaluate the economic viability of current hepatitis B vaccination strategies for preventing MTCT from a public health policy perspective; second, to optimize the current immunization strategy for preventing perinatal transmission of the HBV; and third, to offer policy options to the National Health Commission in China. Methods: To simulate the disease outcome for the entire life of newborns infected with HBV, a Markov model with eight possible health states was built by using TreeAge Pro 2011 software. In the present study, the model parameters were probability and cost, which were extracted from literature and calculated using Microsoft Excel 2013. The optimal immunization strategies were identified through cost-benefit analyses. A benefit-cost ratio (BCR) > 1 indicated that the strategy had positive benefits and vice versa. A one-way sensitivity analysis was used to investigate the stability of the results. Results: From a public health care system perspective, we evaluated the economic viability of 11 strategies in China. For all 11 strategies, the BCR was > 1, which indicated that the benefits of all the strategies were greater than the costs. We recommended strategy number 9 as being optimal. In strategy number 9, babies born to hepatitis B surface antigen (HBsAg)-positive mothers were given an HBIG (200 IU) within 24 h of birth and three injections of hepatitis -B vaccine (20-µg each) at 0, 1, and 6 months, and the strategy had a BCR of 4.61. The one-way sensitivity analysis revealed that the full vaccination coverage and effective rates of protection were two factors that greatly influenced the BCR of the different prevention strategies; other factors had little effect. Conclusion: The benefits of all strategies were greater than the costs. For decision-making and application, the strategy should be based on local socio-economic conditions so that an appropriate immunization strategy can be selected.

Recovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota.

The Terrestrial Miscellaneous Euryarchaeota Group has been identified in various environments, and the single genome investigated thus far suggests that these archaea are anaerobic sulfite reducers. We assemble 35 new genomes from this group that, based on genome analysis, appear to possess aerobic and facultative anaerobic lifestyles and may oxidise rather than reduce sulfite. We propose naming this order (representing 16 genera) "Lutacidiplasmatales" due to their occurrence in various acidic environments and placement within the phylum Thermoplasmatota. Phylum-level analysis reveals that Thermoplasmatota evolution had been punctuated by several periods of high levels of novel gene family acquisition. Several essential metabolisms, such as aerobic respiration and acid tolerance, were likely acquired independently by divergent lineages through convergent evolution rather than inherited from a common ancestor. Ultimately, this study describes the terrestrially prevalent Lutacidiciplasmatales and highlights convergent evolution as an important driving force in the evolution of archaeal lineages.

Differential Ecosystem Function Stability of Ammonia-Oxidizing Archaea and Bacteria following Short-Term Environmental Perturbation.

Rapidly expanding conversion of tropical forests to oil palm plantations in Southeast Asia leads to soil acidification following intensive nitrogen fertilization. Changes in soil pH are predicted to have an impact on archaeal ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and complete (comammox) ammonia oxidizers and, consequently, on nitrification. It is therefore critical to determine whether the predicted effects of pH on ammonia oxidizers and nitrification activity apply in tropical soils subjected to various degrees of anthropogenic activity. This was investigated by experimental manipulation of pH in soil microcosms from a land-use gradient (forest, riparian, and oil palm soils). The nitrification rate was greater in forest soils with native neutral pH than in converted acidic oil palm soils. Ammonia oxidizer activity decreased following acidification of the forest soils but increased after liming of the oil palm soils, leading to a trend of a reversed net nitrification rate after pH modification. AOA and AOB nitrification activity was dependent on pH, but AOB were more sensitive to pH modification than AOA, which demonstrates a greater stability of AOA than AOB under conditions of short-term perturbation. In addition, these results predict AOB to be a good bioindicator of nitrification response following pH perturbation during land-use conversion. AOB and/or comammox species were active in all soils along the land-use gradient, even, unexpectedly, under acidic conditions, suggesting their adaptation to native acidic or acidified soils. The present study therefore provided evidence for limited stability of soil ammonia oxidizer activity following intensive anthropogenic activities, which likely aggravates the vulnerability of nitrogen cycle processes to environmental disturbance.IMPORTANCE Physiological and ecological studies have provided evidence for pH-driven niche specialization of ammonia oxidizers in terrestrial ecosystems. However, the functional stability of ammonia oxidizers following pH change has not been investigated, despite its importance in understanding the maintenance of ecosystem processes following environmental perturbation. This is particularly true after anthropogenic perturbation, such as the conversion of tropical forest to oil palm plantations. This study demonstrated a great impact of land-use conversion on nitrification, which is linked to changes in soil pH due to common agricultural practices (intensive fertilization). In addition, the different communities of ammonia oxidizers were differently affected by short-term pH perturbations, with implications for future land-use conversions but also for increased knowledge of associated global nitrous oxide emissions and current climate change concerns.

Effects of high light and temperature on Microcystis aeruginosa cell growth and ß-cyclocitral emission.

Cyanobacteria always massively grow and even occur blooms in summer, with releasing amount of ß-cyclocitral. To uncover the effects of summer high irradiance and temperature on cyanobacterial growth and ß-cyclocitral emission, the cell growth, reactive oxygen species (ROS) levels, photosynthetic pigment content, chlorophyll fluorescence and ß-cyclocitral emission were investigated in Microcystis aeruginosa under high light and temperature. Compared to the control under 50 µmol m-2·s-1, the cell growth was promoted under 100 µmol m-2·s-1, but inhibited under 500 and 1000 µmol m-2·s-1. The inhibition was also detected under high temperature at 30 and 35 °C in contrast to the control at 25 °C. Under high light and high temperature, M. aeruginosa increased ROS levels and reduced photosynthetic pigment content and photosystem II (PSII) efficiency, which resulted in the inhibition on cell growth. With increasing the light intensity and temperature, 1O2 levels gradually increased, while ß-carotene content gradually decreased by quenching 1O2, with increasing ß-cyclocitral emission. In summer, high irradiance and temperature not benefited the growth of cyanobacteria, but the emission of ß-cyclocitral derived from ß-carotene quenching 1O2 may offset the disadvantages by poisoning other algae.

Linalool- and α-terpineol-induced programmed cell death in Chlamydomonas reinhardtii.

Plant allelochemicals effectively inhibit and/ or control algal growth, and have potential to use as algaecide. To uncover the lethal mechanism of 2 anti-algal compounds linalool and α-terpineol identified from Cinnamomum camphora extracts, and promote their development as algaecide, the H2O2 production, photosynthetic abilities, caspase-like activities, nuclear changes and DNA degradation were investigated in Chlamydomonas reinhardtii treated with the 2 compounds. H2O2 content burst in linalool treatment at 0.5 h and in α-terpineol treatment at 1 h, with increases of 2.7 folds and 1.3 folds, respectively, compared to that at 0 h. The photosynthetic pigments gradually degraded, and Fv/Fm gradually declined to zero, indicating that the cell death was not a necrosis due to the gradual disappearance of physiological process. In C. reinhardtii cells, the caspase-9-like and caspase-3-like were activated in the treatments with the 2 compounds for 1 h. With prolonging the treatment time, the fluorescent intensity of the cell nucleuses stained by DAPI gradually enhanced and then faded, and the genomic DNA isolated from the cells gradually degraded. These hallmarks indicated that the death of C. reinhardtii cells in linalool and α-terpineol treatments was a programmed cell death (PCD) triggered by the increased reactive oxygen species (ROS). Compared to α-terpineol treatment, linalool treatment showed stronger promoting effects on PCD at the same time point, which may be caused by the higher ROS content inducing higher caspase-9-like and caspase-3-like activities in a short time.

Algicidal properties of extracts from Cinnamomum camphora fresh leaves and their main compounds.

Plant allelochemicals are considered as the source of effective, economic and friendly-environmental algaecides. To uncover the anti-algal activities of Cinnamomum camphora fresh leaves and their main algicidal agents, we investigated the inhibitory effects of water and methanol extracts from C. camphora fresh leaves on Microcystis aeruginosa and Chlamydomonas reinhardtii cell growth, analyzed the composition of the water and methanol extracts, and determined the main compounds in extracts on the growth of the two algae and their anti-algal mechanism from photosynthetic abilities. Water and methanol extracts from C. camphora fresh leaves can inhibit M. aeruginosa and C. reinhardtii cell growth, and methanol extracts showed stronger inhibitory effects, due to their more compounds and higher molar concentration. There were 23 compounds in the water extracts, mainly including terpenoids, esters, alcohols, and ketones. Compared to the water extracts, 9 new compounds were detected in the methanol extracts, and the molar concentration of total compounds in methanol extracts increased by 1.3 folds. Camphor, α-terpineol and linalool were 3 main compounds in the water and methanol extracts. Their mixture (1: 3: 6) and individual compound showed remarkable inhibition on M. aeruginosa and C. reinhardtii cell growth. The degradation of photosynthetic pigments and the reduction of maximum quantum yield of photosystem II (PSII) photochemistry, coefficient of photochemical quenching as well as apparent electron transport rate in C. reinhardtii cells aggravated gradually with increasing the concentration of the mixture and individual compound, while the non-photochemical dissipation of absorbed light energy increased gradually, which led to the decline of photosynthetic abilities. This indicated that camphor, α-terpineol and linalool were 3 main algicidal agents in C. camphora fresh leaf extracts, and they inhibited algal growth by inducing photosynthetic pigment degradation and declining PSII efficiency. Therefore, C. camphora fresh leaf extracts and their main components have potential utilization values as algaecides.

Archaeal community diversity and abundance changes along a natural salinity gradient in estuarine sediments.

Archaea are widespread in marine sediments, but their occurrence and relationship with natural salinity gradients in estuarine sediments is not well understood. This study investigated the abundance and diversity of Archaea in sediments at three sites [Brightlingsea (BR), Alresford (AR) and Hythe (HY)] along the Colne Estuary, using quantitative real-time PCR (qPCR) of 16S rRNA genes, DNA hybridization, Archaea 16S rRNA and mcrA gene phylogenetic analyses. Total archaeal 16S rRNA abundance in sediments were higher in the low-salinity brackish sediments from HY (2-8 × 10(7) 16S rRNA gene copies cm(-3)) than the high-salinity marine sites from BR and AR (2 × 10(4)-2 × 10(7) and 4 × 10(6)-2 × 10(7) 16S rRNA gene copies cm(-3), respectively), although as a proportion of the total prokaryotes Archaea were higher at BR than at AR or HY. Phylogenetic analysis showed that members of the 'Bathyarchaeota' (MCG), Thaumarchaeota and methanogenic Euryarchaeota were the dominant groups of Archaea. The composition of Thaumarchaeota varied with salinity, as only 'marine' group I.1a was present in marine sediments (BR). Methanogen 16S rRNA genes from low-salinity sediments at HY were dominated by acetotrophic Methanosaeta and putatively hydrogentrophic Methanomicrobiales, whereas the marine site (BR) was dominated by mcrA genes belonging to methylotrophic Methanococcoides, versatile Methanosarcina and methanotrophic ANME-2a. Overall, the results indicate that salinity and associated factors play a role in controlling diversity and distribution of Archaea in estuarine sediments.