Monitoring results of plague vector fleas in Yulong ，Yunnan Province from 2019 to 2021 / 上海预防医学

ObjectiveTo analyze the community structure and dynamics of parasitic fleas on the body surface of host animals and nested fleas in different seasons in the natural foci of wild rat plague in Yulong County，Yunnan Province， to explore the relationship between seasonal fluctuation of fleas and the prevalence of plague among animals， so as to provide evidence for plague prevention and control in the natural foci. MethodsNanxi Village， Huangshan Town， the core area of plague epidemic in Yulong County， was selected as the monitoring sample area in December 2019 （winter）， August 2020（summer）， October 2020（autumn） and March 2021（spring）. Host animals were captured by rattrap at night and rat nests were excavated for collecting parasitic fleas on host animals and rat nest fleas in different seasons. Excel 2010 and SPSS 26.0 software were used to analyze the data， and Chi square test was used to compare the rate. Community ecological indicators were used to analyze the community structure and species diversity of the host animals and their parasitic fleas. ResultsA total of 355 vector fleas were captured， belonging to 7 species of 5 genera in 2 families. 441 small animals were captured and 138 rat body fleas were detected with the flea infection rate of 14.51% and the flea index 0.31. 96 effective rat holes were excavated and 217 fleas were detected with the flea infection rate of 35.42% and the flea index 2.26. Among the four seasons， the flea infection rates of rat body and rat nests were higher in summer and winter， showing a significant difference in general （χ2=15.851， P<0.01； χ2=16.398， P<0.01）. The dominant species of flea community were Ctenophthalmus quadratus， Stenischia humilis， Neopsylla specialis and Frontopsylla spadix， with a dominance index of 0.434， 0.254， 0.180 and 0.110， respectively. The diversity and evenness of rat body fleas showed a distribution characteristic of decreasing， increasing and then decreasing again with season changes， and both were the highest in spring， while the ecological dominance showed an opposite trend. The diversity and evenness of rat nest fleas showed a distribution characteristic of increasing first and then decreasing in summer， autumn and winter， with the highest in autumn， while the ecological dominance was diametrically opposite. ConclusionThe fleas community structure is relatively stable in Yulong County， but the number of species in the community is unevenly distributed by seasons， and the status of dominant species is prominent. Local authorities should carry out timely preventive deratization and depulization measures according to the results of daily monitoring， so as to effectively avoid the prevalence and spread of plague among animals in plague foci.

Metagenomic characterization of the culturable bacterial community structure of Tapuy, a Philippine indigenous rice wine, reveals significant presence of potential probiotic bacteria

Background@#Tapuy is an indigenous fermented rice wine produced in the Northern areas of the Philippines. Fermented foods and drinks have gained interest due to their associated health benefits, attributable to probiotic bacteria in the food items. However, pathogenic bacteria may also be present in fermented food and pose health risks, signifying a need for standardization. Currently, there is limited knowledge on the bacterial content of tapuy. @*Objectives@#This study aimed to characterize the bacterial diversity and community structure of culturable bacteria in traditionally fermented tapuy samples, to perform standardization of tapuy fermentation, and to compare the bacterial diversity and community structure of culturable bacteria in laboratory fermented tapuy with that of the traditional samples. @*Methods@#Tapuy samples were obtained from four municipalities in Benguet, Philippines. Laboratory fermentation of tapuy was performed simultaneously with the fermentation in the sampling site using a standardized protocol. Samples were plated on de Man, Rogosa, and Sharpe (MRS) agar and NA, and the colonies were harvested for DNA extraction. DNA samples were sent for 16S rDNA metagenomic sequencing. Results. Metagenomic analysis revealed the presence of many bacterial species that were previously unreported in tapuy. Traditional tapuy samples were composed primarily of members of the genera Bacillus and Lactobacillus in varying proportions. Potential probiotic bacteria were abundant in Kapangan (97.42%) and Sablan (99.89%) field samples. B. wiedmannii was present in all samples and was identified as a harmful species. Laboratory fermentation increased the abundance of potential probiotic bacteria in Itogon and La Trinidad samples (differences of 75.36% and 78.36%, respectively). It decreased the quantity of B. wiedmannii in La Trinidad (a difference of 97.1%). Laboratory fermented samples generally exhibited higher bacterial diversity and species richness compared to field samples. @*Conclusions@#Traditionally fermented tapuy samples contained a significant proportion of potential probiotic bacteria belonging to the genera Bacillus and Lactobacillus. Laboratory fermented samples were found to have higher bacterial diversity and richness compared to field samples. The significant presence of potential probiotic bacteria suggests that tapuy is a good candidate for development into functional food and a good source of likely probiotic species that could be explored for health applications. The presence of harmful bacteria suggests the need for possible standardization of fermentation practices.

Mechanism of trehalose-enhanced metabolism of heterotrophic nitrification-aerobic denitrification community under high-salt stress / 生物工程学报

Heterotrophic nitrification-aerobic denitrification (HN-AD) bacteria are aerobic microorganisms that can remove nitrogen under high-salt conditions, but their performance in practical applications are not satisfactory. As a compatible solute, trehalose helps microorganisms to cope with high salt stress by participating in the regulation of cellular osmotic pressure, and plays an important role in promoting the nitrogen removal efficiency of microbial populations in the high-salt environment. We investigated the mechanism of exogenous-trehalose-enhanced metabolism of HN-AD community under high-salt stress by starting up a membrane aerobic biofilm reactor (MABR) to enrich HN-AD bacteria, and designed a C150 experimental group with 150 μmol/L trehalose addition and a C0 control group without trehalose. The reactor performance and the community structure showed that NH4+-N, total nitrogen (TN) and chemical oxygen demand (COD) removal efficiency were increased by 29.7%, 28.0% and 29.1%, respectively. The total relative abundance of salt-tolerant HN-AD bacteria (with Acinetobacter and Pseudofulvimonas as the dominant genus) in the C150 group reached 66.8%, an 18.2% increase compared with that of the C0 group. This demonstrated that trehalose addition promoted the enrichment of salt-tolerant HN-AD bacteria in the high-salt environment to enhance the nitrogen removal performance of the system. In-depth metabolomics analysis showed that the exogenous trehalose was utilized by microorganisms to improve proline synthesis to increase resistance to high-salt stress. By regulating the activity of cell proliferation signaling pathways (cGMP-PKG, PI3K-Akt), phospholipid metabolism pathway and aminoacyl-tRNA synthesis pathway, the abundances of phosphoethanolamine, which was one of the glycerophospholipid metabolites, and purine and pyrimidine were up-regulated to stimulate bacterial aggregation and cell proliferation to promote the growth of HN-AD bacteria in the high-salt environment. Meanwhile, the addition of trehalose accelerated the tricarboxylic acid (TCA) cycle, which might provide more electron donors and energy to the carbon and nitrogen metabolisms of HN-AD bacteria and promote the nitrogen removal performance of the system. These results may facilitate using HN-AD bacteria in the treatment of high-salt and high-nitrogen wastewater.

Effect of Potassium Solubilizing Bacteria on Rhizosphere Soil Microenvironment of Paris polyphylla var. yunnanensis / 中国实验方剂学杂志

ObjectiveTo investigate the effects of the inoculation of potassium-solubilizing bacteria on the rhizosphere soil microenvironment of Paris polyphylla var. yunnanensis. MethodThe effects of different potassium-solubilizing bacteria on the physical and chemical properties， microbial community structure， and soil enzyme activity in the rhizosphere soil of P. polyphylla var. yunnanensis were investigated by pot planting at room temperature. The correlation of various indexes was analyzed. ResultThe inoculation with different potassium-solubilizing bacteria could significantly affect the physical and chemical properties of rhizosphere soil of P. polyphylla var. yunnanensis. The mass fractions of available nitrogen， available phosphorus， and available potassium were 24.5-90.5 mg·kg-1， 2.53-25.9 mg·kg-1， and 132-312 mg·kg-1， respectively， and the soil pH was 7.08-7.75， which were in line with the optimal ranges of P. polyphylla var. yunnanensis planting. The inoculation of different potassium-solubilizing bacteria could affect the number of bacteria， actinomycetes， and fungi in rhizosphere soil to varying degrees. The transformation of soil from "fungal type" to "bacterial type" marks the improvement of soil fertility. It also affected the enzyme activity of rhizosphere soil， and the activities of neutral phosphatase， protease， and polyphenol oxidase showed an increasing trend. The correlation analysis showed that the number of bacteria was negatively correlated with the number of fungi （r=-0.856， P<0.01）， positively correlated with the number of actinomycetes， the content of available nitrogen and available potassium， and negatively correlated with soil pH. ConclusionThe inoculation of potassium-solubilizing bacteria can effectively improve the content of available potassium， available nitrogen， available phosphorus， and other nutrients in the rhizosphere soil of P. polyphylla var. yunnanensis， improve soil fertility， alleviate the continuous cropping obstacles of P. polyphylla var. yunnanensis， and lay a theoretical foundation for the green and sustainable development of P. polyphylla var. yunnanensis.

How silicon fertilizer improves nitrogen and phosphorus nutrient availability in paddy soil? / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

In order to reveal the mechanism of silicon (Si) fertilizer in improving nitrogen (N) and phosphorus (P) nutrient availability in paddy soil, we designed a series of soil culture experiments by combining application of varying Si fertilizer concentrations with fixed N and P fertilizer concentrations. Following the recommendations of fertilizer manufacturers and local farmers, we applied Si in concentrations of 0, 5.2, 10.4, 15.6, and 20.8 μg/kg. At each concentration of added Si, the availability of soil N and P nutrients, soil microbial activity, numbers of ammonia-oxidizing bacteria and P-decomposing bacteria which means that the organic P is decomposed into inorganic nutrients which can be absorbed and utilized by plants, and urease and phosphatase activity first increased, and then decreased, as Si was added to the soil. These indicators reached their highest levels with a Si application rate of 15.6 μg/kg, showing values respectively 19.78%, 105.09%, 8.34%, 73.12%, 130.36%, 28.12%, and 20.15% higher than those of the controls. Appropriate Si application (10.4 to 15.6 µg/kg) could significantly increase the richness of the soil microbial community involved in cycling of N and P nutrients in the soil. When the Si application rate was 15.6 μg/kg, parameters for characterizing microbial abundance such as sequence numbers, operational taxonomic unit (OTU) number, and correlation indices of microbial community richness such as Chao1 index, the adaptive coherence estimator (ACE) index, Shannon index, and Simpson index all reached maximum values, with amounts increased by 14.46%, 10.01%, 23.80%, 30.54%, 0.18%, and 2.64%, respectively, compared with the control group. There is also a good correlation between N and P mineralization and addition of Si fertilizer. The correlation coefficients between the ratio of available P/total P (AP/TP) and the number of ammonia-oxidizing bacteria, AP/TP and acid phosphatase activity (AcPA), AP/TP and the Shannon index, the ratio of available N/total amount of N (AN/TN) and the number of ammoniated bacteria, and AN/TN and AcPA were 0.9290, 0.9508, 0.9202, 0.9140, and 0.9366, respectively. In summary, these results revealed that enhancement of soil microbial community structure diversity and soil microbial activity by appropriate application of Si is the key ecological mechanism by which application of Si fertilizer improves N and P nutrient availability.

Variation in physicochemical properties and bacterial community structure in rhizosphere soil of Coptis chinensis tow cropping modes / 中国中药杂志

The natural forest and artificial shed are the main cropping modes of Coptis chinensis. This study is aimed to reveal the rhizosphere soil bacterial community structure difference between under tow C. chinensis cropping modes-natural forest and artificial shed, and to assist us to completely understand soil quality condition,and provide theoretical guidance for soil improvement and C. chinensis planting. The rhizosphere soil samples of 1-5-year-old C. chinensis under tow cropping modes-natural forest and artificial shed were collected. Illumina high-throughput sequencing technology was used to analyze the alpha diversity, community composition, community structure of soil bacteria under the tow cropping modes,and the effects of soil nutriment indices on soil bacterial community structure. Through the analysis of species number, Shannon, Chao1 index and ACE index of bacterial community, it was found that the bacterial diversity of 1-year-old C. chinensis soil under natural forest cropping mode was significantly lower than that under artificial shed cropping mode, and the diversity of bacterial communities in soil of 2-5-years old C. chinensis were not significant different between two cropping modes. A total of 53 phyla,60 classes,140 orders and 266 families were detected in the rhizosphere soil of C. chinensis under the cropping modes of natural forest, respectively. The rhizosphere soil of C. chinensis under the cropping modes of artificial shed included 54 phyla,65 classes,140 orders and 264 families, respectively. Under the two cropping modes, the top 10 dominant species of bacterial community abundance are the same, they are Proteobacteria, Acidobacteria, Actinobacteria,Bacteroidetes, Planctomycetes, Chloroflexi, Verrucomicrobia, Gemmatimonadetes, Firmicutes and Cyanobacteria, but there are differences in the abundance sequence. The top 10 dominant species of bacterial community abundance accounted for 74.36% to 74.30% of the total bacteria, and 3.15% to 3.92% of the bacteria are unclassified. The results of Metastat analysis showed that the abundance of Gemmatimonadetes in the rhizosphere soil of C. chinensis under the cropping modes the artificial shed was significantly higher than that under the natural forest cropping mode(P<0.05). MRPP analysis of community structure differences showed that under tow cropping modes, there were significant differences in the bacterial community structure of 1-4-year-old soil bacteria, among which the difference between 1-year-old soil samples was the largest. With the increase of cropping years, the difference gradually decreases, and there is no significant difference in the bacterial community structure between 5-year-old soil samples. RDA analysis and correlation analysis of bacterial community structure and soil physical and chemical properties showed that the order of environmental factors on the rhizosphere soil bacteria of Coptis chinensis was: pH>available P> total P> total K>bulk density>total N>available N>organic matter. The results are helpful to understand the soil health of C. chinensis and provide scientific basis and theoretical guidance for soil improvement and C. chinensis planting.

Community ecology of the metazoan parasites of the Atlantic thread herring, Opisthonema oglinum (Lesueur, 1818) (Actinopterygii: Clupeidae) from the Sepetiba Bay, Rio de Janeiro, Brazil / Ecologia da comunidade dos metazoários parasitos da sardinha bandeira Opisthonema oglinum (Lesueur, 1818) (Actinopterygii: Clupeidae) da Baía de Sepetiba, Rio de Janeiro, Brasil

This study aimed to evaluate the parasitic fauna of Opisthonema oglinum (Lesueur, 1818) from Southeastern Brazil. Between September 2017 and March 2018, a total of 100 specimens of O. oglinum from the Sepetiba Bay, Rio de Janeiro, Brazil (22°54'S, 43°34'W) were examined. Ninety one specimens of O. oglinum were parasitized by at least one species of metazoan with a mean of 5.84 ± 7.98 parasites/fish. Seven species were collected: 2 digeneans, 2 monogeneans, 2 copepods and 1 nematode. The digenean Parahemiurus merus (Linton) was the most abundant and dominant species, representing 43% of metazoan parasites collected. The parasite species richness was positively correlated with the total length of the hosts. Only Neobomolochus elongatus Cressey showed a positive correlation between host's total length and parasite prevalence. The mean parasite species diversity was not correlated with host's total length, but significant differences among the mean parasite diversity between males and females was observed. Opisthonema oglinum represents a new host record for Caligus mutabilis Wilson, Hysterothylacium sp. and Cribomazocraes travassosi Santos and Kohn. The copepod N. elongatus is recorded for the first time on the Brazilian coast.

Este estudo teve como objetivo avaliar a fauna parasitária de Opisthonema oglinum (Lesueur, 1818) do Sudeste do Brasil. No período entre setembro de 2017 e março de 2018, um total de 100 espécimes de O. oglinum provenientes da Baía de Sepetiba, Rio de Janeiro, Brasil (22°54'S; 43°34'O), foram examinados. Noventa espécimes de O. oglinum estavam parasitados por pelo menos uma espécie de metazoário com média de 5,84 ± 7,98 parasitos/peixe. Sete espécies foram coletadas: 2 digenéticos, 2 monogenéticos, 2 copépodes e 1 nematoide. O digenético Parahemiurus merus (Linton) foi à espécie mais abundante e dominante, representando 43% dos metazoários parasitos coletados. A riqueza parasitária foi correlacionada com o comprimento total do hospedeiro. Apenas Neobomolochus elongatus Cressey apresentou correlação positiva entre o comprimento total do hospedeiro e a prevalência parasitária. A diversidade média de espécies de parasitos não apresentou correlação com o comprimento total do hospedeiro, mas foram observadas diferenças significativas entre a diversidade média de parasitos entre machos e fêmeas. Opisthonema oglinum representa um novo registro de hospedeiro para Caligus mutabilis Wilson, Hysterothylacium sp. e Cribomazocraes travassosi Santos and Kohn. O copépode N. elongatus é registrado pela primeira vez na costa Brasileira.

Investigación traslacional en microbioma (InTraMic): un área de interés común y creciente en el IMTIB, Hospital Italiano e Instituto Universitario / Translational research in microbiome (InTraMic): an area of common and growing interest at IMTIB, Hospital Italiano and Instituto Universitario

Se estima que aproximadamente 100 trillones de microorganismos (incluidos bacterias, virus y hongos) residen en el intestino humano adulto y que el total del material genético del microbioma es 100 veces superior al del genoma humano. Esta comunidad, conocida como microbioma se adquiere al momento del nacimiento a través de la flora comensal de la piel, vagina y heces de la madre y se mantiene relativamente estable a partir de los dos años desempeñando un papel crítico tanto en el estado de salud como en la enfermedad. El desarrollo de nuevas tecnologías, como los secuenciadores de próxima generación (NGS), permiten actualmente realizar un estudio mucho más preciso de ella que en décadas pasadas cuando se limitaba a su cultivo. Si bien esto ha llevado a un crecimiento exponencial en las publicaciones, los datos sobre las poblaciones Latinoamérica son casi inexistentes. La investigación traslacional en microbioma (InTraMic) es una de las líneas que se desarrollan en el Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB). Esta se inició en 2018 con la línea de cáncer colorrectal (CCR) en una colaboración con el Colorectal Cancer Research Group del Leeds Institute of Medical Research en el proyecto Large bowel microbiome disease network: Creation of a proof of principle exemplar in colorectal cancer across three continents. A fines de 2019 se cumplió el objetivo de comprobar la factibilidad de la recolección, envío y análisis de muestras de MBF en 5 continentes, incluyendo muestras provenientes de la Argentina, Chile, India y Vietnam. Luego de haber participado de capacitaciones en Inglaterra, se ha cumplido con el objetivo de la etapa piloto, logrando efectivizar la recolección, envío y análisis metagenómico a partir de la secuenciación de la región V4 del ARNr 16S. En 2019, la línea de enfermedad de hígado graso no alcohólico se sumó a la InTraMic iniciando una caracterización piloto en el marco de una colaboración con el laboratorio Novartis. Los resultados de ese estudio, así como el de cáncer colorrectal, están siendo enviados a publicación. En 2020, con la incorporación de la línea de trasplante alogénico de células progenitoras hematopoyéticas, fue presentado un proyecto para un subsidio del CONICET que ha superado la primera etapa de evaluación. En el presente artículo se brinda una actualización sobre la caracterización taxonómica de microbioma y se describen las líneas de investigación en curso. (AU)

It is estimated that approximately 100 trillion microorganisms (including bacteria, viruses, and fungi) reside in the adult human intestine, and that the total genetic material of the microbiome is 100 times greater than that of the human genome. This community, known as the microbiome, is acquired at birth through the commensal flora of the mother's skin, vagina, and feces and remains relatively stable after two years, playing a critical role in both the state of health and in disease. The development of new technologies, such as next-generation sequencers (NGS), currently allow for a much more precise study of it than in past decades when it was limited to cultivation. Although this has led to exponential growth in publications, data on Latin American populations is almost non-existent. Translational research in microbiome (InTraMic) is one of the lines developed at the Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB). This started in 2018 with the Colorectal Cancer Line (CRC) in a collaboration with the Colorectal Cancer Research Group of the Leeds Institute of Medical Research in the project "Large bowel microbiome disease network: Creation of a proof of principle exemplar in colorectal cancer across three continents". At the end of 2019, the objective of verifying the feasibility of collecting, sending and analyzing MBF samples on 5 continents, including samples from Argentina, Chile, India and Vietnam, was met. After having participated in training in England, the objective of the pilot stage has been met, achieving the collection, delivery and metagenomic analysis from the sequencing of the V4 region of the 16S rRNA. In 2019, the non-alcoholic fatty liver disease line joined InTraMic, initiating a pilot characterization in the framework of a collaboration with the Novartis laboratory. The results of that study, as well as that of colorectal cancer, are being published. In 2020, with the incorporation of the allogeneic hematopoietic stem cell transplantation line, a project was presented for a grant from the CONICET that has passed the first stage of evaluation. This article provides an update on the taxonomic characterization of the microbiome and describes the lines of ongoing research. (AU)

Diversity and community structure of endophytic fungi in Corydalis yanhusuo tuber and their correlations with tetrahydropalmatine content / 中草药

Objective: To analyze the diversity and community structure of endophytic fungi in Corydali yanhusuo tuber and their correlations with tetrahydropalmatine content. Methods The endophytic fungi in C. yanhusuo tuber from eight localities (Pan’an of Zhejiang Province, Dongyang of Zhejiang Province, Jinyun of Zhejiang Province, Sanhe of Shanxi Province, Dongjiaying of Shanxi Province, Kaixian of Chongqing, Xuancheng of Anhui Province and Xinyang of Henan Province) were isolated and identified according to the morphology and ITS sequences, so as to analyze the community structure of endophytic fungi; HPLC was used to determine tetrahydropalmatine content, and Excel and SPSS were used to analyze their correlations and establish multiple linear regression equations at different levels of dominant genera and species. Results: A total of 1 742 endophytic fungi were isolated and divided into 19 taxa (14 were identified to species level and five to genera level), belonging to 3 phyla, 5 classes, 10 orders, 14 families and 15 genera; The tetrahydropalmatine content in C. yanhusuo tuber from eight localities was higher than the standard of Chinese Pharmacopoeia (2015 edition); The richness (S) and diversity index (H’) of endophytic fungi in C. yanhusuo tuber and tetrahydropalmatine content in Zhejiang Province were extremely significant or significantly higher than those in the other localities. The diversity index (H’) was significantly positive correlated with the tetrahydropalmatine content; There was the largest positive correlation between the tetrahydropalmatine content and T83 (Trichoderma sp.) (correlation coefficient: 0.793). Conclusion: There are abundant endophytic fungi resources in C. yanhusuo; T83 as a dominant endophytic fungus probably related to the accumulation of tetrahydropalmatine.

Effects of biocontrol strain BZJN1 and streptoprofen on physicochemical properties and bacteria structure of rhizosphere soil of Atractylodes macrocephala / 中国中药杂志

Soil microorganisms are one of the important biological indictors of soil quality and can reflct the comprehensive ecological environment characteristics of the soil. The research of soil microbial diversity is the key to know the ecological functions and balance with soil. In this paper, high-throughput sequencing on PCR-amplified 16 S rRNA gene V3-V4 fragments was used to determine the bacterial diversity in rhizosphere soil of A. macrocephala under the treatment with BZJN1 or streptoprofen. The results showed that there were no significant differences of the bacteria in A. macrocephala rhizosphere soil of the streptoprofen treatment group and the biocontrol BZJN1 treatment group. All the soil bacteria was classified into 25 categories,67 classes, 108 orders, 167 families and 271 generas, except some unidentified bacteria. Proteobacteria(30.7%-34.8%) was the dominant phylum, of which Alphaproteobacteria(16.8%-18.5%) was the dominant subgroup. Compared with the control group, the relative abundance of multiple phylums bacteria in the rhizosphere soil of A. macrocephala was significantly changed in the streptoprofen treatment group and the biocontrol BZJN1 treatment group. In addition, RDA analysis showed that there was connection with different environmental factors and microbial communities. The abundance of the three genera in the rhizosphere soil of A. macrocephala was significantly positively correlated with Invertase, Urease and AP. PICRUSt function prediction results showed that BZNJ1 could enhance some bacterial functions and promote the plant growth. Biocontrol is a new type of green and safety control pest method. BZNJ1 significantly enhances some bacterial functions on the basis of effectively preventing root rot of A. macrocephala and promoting plant growth, and has no significant effect on the soil bacterial community structure. All the results can provide theoretical support for popularization of BZNJ1.

Analysis of bacteria distribution characteristics in different layers of agarwood based on Hiseq sequencing / 中国中药杂志

To explore the diversity of bacterial community structure between different layers of agarwood, Hiseq(high-throughput sequencing) was used to analyze the bacterial community structure of samples from different layers of agarwood. Our results showed that 1 150 096 optimized sequences and 9 690 OTUs were obtained from 15 samples of 5 layers of agarwood, which belonged to 28 bacterial phyla, 61 classes, 110 orders, 212 families and 384 genera. Further analysis revealed that the normal layer(NL) had the lowest bacterial species richness and the smallest number of OTUs. And the total number of OTUs of the agarwood layer(AL) and NL was zero, which was quite different.At the same time, there were significant differences in bacterial community structure and species diversity between NL and the other four layers. While there were some common dominant bacterial genera in both transition layer(TL) and NL. The similarity of bacterial distribution in 4 non-NL layers was relatively high, which had four common genera, such as Acidibacter, Bradyrhizobium, Acidothemus and Sphingomonas. While Acidibacter, Bradyrhizobium and Acidothemus were the dominant bacterial genus of DA and AL, and all of these layers contained volatile oil. In addition, the Bradyrhizobium was the most abundant in agarwood layer. Our results showed that bacterial community diversity and abundance were decreasing from DL to AL, and different layers showed significant differences in bacterial enrichment. It provided the clues to investigate how bacteria participate in the formation of agarwood.

Changes in Cold and Hot Syndrome and Gastrointestinal Bacterial Community Structure in Mice by Intervention with Food of Different Nature / 中国结合医学杂志

OBJECTIVE@#To reveal the effect of foods with different natures on cold or hot syndrome and gastrointestinal bacterial community structure in mice.@*METHODS@#Forty-five 6-week-old male ICR Kunming mice of clean grade were divided into 5 groups, 9 per group, including the control (CK), hot nature herbs (HM), Hong Qu glutinous rice wine (RW), tea rice wine (TW), and cold nature herbs (CM) groups. Distilled water or corresponding herbs were administered to mice (0.01 mL/g body weight) in the 5 groups by gastric infusion respectively, once daily for 28 d. Appearance, behavior, and serum biochemical indicators, including 5-hydroxytryptamine (5-HT), thyroid stimulating hormone (TSH), noradrenaline (NE), cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP), the hot nature index, as well as the gastrointestinal bacterial community structure were analyzed in all groups after treatment.@*RESULTS@#After supplementation for 28 d, CM and TW mice showed different degrees of cold syndrome, and HM and RW mice showed different degrees of hot syndrome. Compared with the HM and RW mice, the TSH, NE, cAMP levels and hot nature indices in the CM and TW mice were significantly decreased and 5-HT and cGMP levels were significantly increased (P<0.05). There was no obvious change in appearance or behavior in CK mice. Results of clustering analysis showed that the gastrointestinal bacterial community structures were highly similar in TW and CM mice as well as in RW and HM mice, and that they were from the same branch, respectively, when the distance was 0.02. The key microbes associated with cold syndrome were Lachnospiraceae uncultured, Lactococcus, etc., and the key microbes associated with hot syndrome were S24-7 norank, Ruminococcaceae uncultured, etc. CONCLUSION: The interventions with different nature foods could change cold or hot syndrome in mice, leading to changes in gastrointestinal bacterial community structure.

Variation in fungal community structures in rhizosphere soil of Coptis chinensis with cropping mode under natural forest and artificial shed / 中国中药杂志

This study is aimed to reveal the rhizosphere soil fungal community structure difference of Coptis chinensis cropping between natural forest and artificial shed modes, and provide theoretical guidance for soil improvement and C. chinensis planting. The rhizosphere soil samples of 1-5-year-old C. chinensis under natural forest and artificial shed modes were collected. Illumina high-throughput sequencing technology was used to analyze the community structure and diversity of soil fungi under the tow cropping modes,and the effects of soil nutriment indices on soil fungal community structure. The results suggested that the abundance and diversity of fungal communities in soil of 2-5-year-old C. chinensis were not significant different in both two cropping modes, but it was significantly higher than that in the 1-year-old C. chinensis. Comparing soil samples from the same year-old C. chinensis under the two cropping modes, it was found that there was no significant difference in the abundance and diversity of fungal communities. The fungal community of the rhizosphere soil was different in composition and abundance between tow cropping modes, and between different planting years. The 17 phyla,59 classes and 155 orders,and 17 phyla,59 classes and 157 orders were detected in the rhizosphere soil of C. chinensis under the cropping modes of natural forest and the artificial shed, respectively. Ascomycota, Basidiomycota and Mortierellomycota were dominant phyla in rhizosphere soil, and the average abundance of the 3 phyla accounted for 74.36% and 74.30% of the total fungi. The results of analysis of similarities showed that there were significant differences in the fungal community structure of 1-year-old and 2-year-old C. chinensis soil fungi, and there was no significant difference in the community structure of 3-5-year-old samples. Under the natural forest cropping mode, there were significant differences among the samples of different years. Under the artificial shed cropping, there were significant differences in fungal community structure between 1-year-old and 3-5-year-old C. chinensis soil, and between 2-year-old and 3-5-year-old C. chinensis soil. The results of canonical correlation analysis showed that soil pH and soil organic matter content were the main factors affecting the soil fungal community structure. Soil organic matter content was positively correlated with Basidiomycota and Cryptomycota, pH was negatively correlated with Basidiomycota and C. ryptomycota. The planting of C. chinensis has promoted the diversity and abundance of rhizosphere fungal community significantly. For the same year-old C. chinensis soil, abundance of fungal community was no significant difference between two cropping modes. There are significant differences in the rhizosphere soil fungal community structure between tow cropping modes in the first two years of planting. Through the interaction between the rhizosphere and the soil and the continuous selection of the rhizosphere to the fungal community, the fungal community structure tended to be the same between the two cropping modes in rhizosphere soil of 3-5-year old C. chinensis. The soil pH and orga-nic matter content were the main factors affecting the change of fungal community structure.

Effect of Polygonum multiflorum-Andrographis paniculata intercropping system on rhizosphere soil actinomycetes community structure and diversity of P. multiflorum / 中国中药杂志

To investigate the effect of Polygonum multiflorum-Andrographis paniculata intercropping system on rhizosphere soil actinomycetes of P. multiflorum, the community structure and diversity of soil actinomycetes were studied by using the original soil as the control group and the rhizosphere soil actinomycetes communities of P. multiflorum under monoculture and intercropping systems as the experimental group. In this study 655 221 effective sequences were obtained with an average length of 408 bp. OTU coverage and rarefaction curve showed that the sequencing could represent the real situation of soil actinomycetes. According to the results of alpha diversity analysis, the diversity soil actinomycetes varied as follows: original soil>intercropping soil>monoculture soil. The soil actinomycetes community structure and the relative abundance of dominant genera were significantly changed by both monoculture and intercropping, especially monoculture. OTU clustering and PCA analysis of soil samples showed that all the soil samples were divided into three distinct groups and the original soil was more similar to intercropping soil. In addition, intercropping increased the relative abundance of some beneficial actinomyces, such as Kitasatospora and Mycobacterium, which was beneficial to maintain soil health and reduce the occurrence of soil-borne diseases. The results show that, P. multiflorum-A. paniculata intercropping reduced the change of community structure and the decrease of diversity of soil actinomycetes caused by P. multiflorum monoculture, and made the actinomycete community in rhizosphere soil of P. multiflorum close to the original soil.

Effect of microbial community structure of activated sludge in an Anaerobic-anoxic-oxic process with Actinic reaction enzyme system start-up / 生物工程学报

In order to explore the microbial communities and functions of activated sludge in an Anaerobic-anoxic-oxic (A²/O) process under the start-up of Actinic reaction enzyme system (ARES) system and to understand the impact of the ARES system in domestic sewage treatment process, the activated sludge microbial community structure in the A²/O process system before and after ARES system start-up was analyzed by Illumina-HiSeq 2000 high-throughput sequencing platform. By combining with the main parameters related to the effect of sewage treatment, we analyzed the environmental functions of the microbial communities. The microbial community structure of activated sludge was significantly different before and after the ARES system start-up. There were 9 main bacterial phyla in the system (average relative abundance ≥1%), accounting for 96%-98% of the total bacteria sequenced. After the ARES system was started, the relative abundance of Betaproteobacteria and Chlorobi increased by 3.45%-3.85% and 0.45%-2.61%, respectively. In the anaerobic unit, the relative abundance of Bacteroidetes increased by 12.97%, while the Actinobacteria and Firmicutes decreased by 9.60% and 1.45%, respectively. At the genus level of bacteria, the relative abundance of Denitratisoma increased by 0.80%-3.27%, while the Haliangium and Arcobacter decreased by 3.36%-4.52% and 1.48%-3.45%, respectively. The relative abundance of bacteria was significantly different before and after the ARES system start-up. There were 7 abundant fungi phyla (average relative abundance ≥1%) in the system. After the ARES system was started, the relative abundance of Rozellomycota decreased by 42.71%-46.77%. In the anaerobic unit, the relative abundance of Ascomycota decreased by 13.39%, while the relative abundance of Glomeromycota increased by 13.86%. At the genus level of fungi. The relative abundance of Entomophthoraceae sp. and Glomcromycota sp. increased by 31.35%-36.50% and 6.27%-13.84%, respectively, while the Rozellomycota sp. and Xylochrysis lucida decreased by 42.71%-46.77% and 3.67%-5.54%, respectively. Our results showed that the application of ARES system caused the response of the microbial community to environmental changes, especially for the fungi communities, in the meanwhile, improved the effluent quality, especially the removal rate of total nitrogen.

Effects of Comamonas testosteroni on PAHs degradation and bacterial community structure in Leymus chinensis rhizosphere soil / 生物工程学报

To investigate the degradation of polycyclic aromatic hydrocarbons (PAHs) and the changes of rhizosphere microorganisms in the rhizosphere soil of Leymus chinensis during the remediation of PAHs contaminated soil by Comamonas testosteroni (C.t)-assisted Leymus chinensis, we evaluated the removal of PAHs in the rhizosphere of Leymus chinensis using gas chromatography-mass spectrometry (GC-MS), analyzed the bacterial community and the diversity in Leymus chinensis rhizosphere soil by high-throughput sequencing technology, characterized the correlation among PAHs degradation and bacterial community components performing redundancy analysis (RDA) and network analysis, and predicted PAHs degradation potential via PICRUSt software in this paper. The degradation of PAHs in the rhizosphere of Leymus chinensis was promoted, the abundance and diversity of bacteria and the correlation among bacteria and PAHs were changed, and the degradation potential of PAHs in Leymus chinensis rhizosphere soil was enhanced in the later stage of phytoremediation (60-120 d) due to the incorporation of C.t. The accelerated degradation of three PAHs (Nap, Phe, BaP) was accompanied by the differ abundance and correlation of Proteobacteria (Sphingomonas, MND1, Nordella), Actinomycetes (Rubrobacter, Gaiella), Acidobacteria (RB41) and Bacteroides (Flavobacterium) affected by C.t. The results provide new insight into the microorganism choices for microbial assisted plant remediation of soil PAHs and the mechanisms of enhanced PAHs degradation via the combination of Comamonas testosteroni engineering bacteria and plants.

Anurans of a remnant of Mixed Rainforest in southern Brazil / Anuros de um remanescente de Floresta Ombrófila Mista no sul do Brasil

Abstract: The Brazilian Atlantic Forest is one of the world's most biodiverse biomes, with large numbers of endemic and threatened species. However, this biome has suffered extensive deforestation and habitat fragmentation, with a drastic reduction of its original vegetation cover. The compilation of data on the occurrence patterns of anurans and their natural history is important for the development of effective conservation strategies. Here, we present the results of a survey of the anuran fauna of Parque Estadual do Papagaio Charão (PEPC) in Rio Grande do Sul state, southern Brazil, providing information on species endemism, conservation status, and reproductive modes. We collected data on the local anurans between March 2018 and February 2019 using active searches and pitfall traps. We recorded 26 anuran species distributed in seven families, with eight different reproductive modes. The largest number of species (20) was found at the forest edge, followed by the interior of the forest and open area, each with 16 species. The most abundant species were Leptodactylus plaumanni (41.7% of records), Physalaemus cuvieri (27.1%), and P. carrizorum (16.5%). Greater species richness and abundance were recorded during the rainier months, while temperature influenced only the abundance of the anurans. Rhinella henseli, Rhinella icterica, Vitreorana uranoscopa, Aplastodiscus perviridis, Boana curupi, Boana leptolineata and Proceratophrys brauni are all endemic to the Atlantic Forest. Melanophryniscus devincenzii is classified as Endangered by the IUCN, and Proceratophrys bigibbosa as Near Threatened. Boana curupi is considered to be Endangered in Rio Grande do Sul state, and Vulnerable in Brazil, while V. uranoscopa is Near Threatened in Rio Grande do Sul. Our findings emphasize the importance of protected areas, such as the PEPC, for the maintenance of anuran populations and communities in the Mixed Rainforest formations of southern Brazil.

Resumo: A Mata Atlântica abriga a maior biodiversidade do planeta, com elevados números de endemismos e espécies ameaçadas de extinção. Entretanto, esse bioma tem sofrido extensa perda e fragmentação do habitat, com redução drástica da sua cobertura vegetacional original. Suprir lacunas sobre a história natural e os padrões de ocorrências de anuros auxiliam no desenvolvimento de estratégias de conservação para esse grupo. Neste estudo apresentamos a anurofauna do Parque Estadual do Papagaio Charão (PEPC), no estado do Rio Grande do Sul, sul do Brasil, com informações sobre endemismos, status de conservação e modos reprodutivos das espécies. Nossas amostragens em campo ocorreram entre março de 2018 e fevereiro de 2019 e utilizamos procura ativa e pitfalls traps para a coleta dos anuros. Registramos 26 espécies de anuros distribuídas em sete famílias e oito modos reprodutivos. Um número maior de espécies foi encontrado na borda (20 espécies), seguida da floresta e área aberta (16 espécies cada). As espécies mais abundantes foram Leptodactylus plaumanni (41,7%), Physalaemus cuvieri (27,1%) e P. carrizorum (16,5%). Maior riqueza e abundância foram registradas no período com maior pluviosidade e a temperatura influenciou somente a abundância dos anuros. Rhinella henseli, R. icterica, Vitreorana uranoscopa, Aplastodiscus perviridis, Boana curupi, B. leptolineata e Proceratophrys brauni são endêmicas da Mata Atlântica. Melanophryniscus devincenzii está classificada como "Em perigo" e Proceratophrys bigibbosa como "Quase ameaçada" pela IUCN. Boana curupi é considerada "Em perigo" no estado do Rio Grande do Sul e "Vulnerável" no Brasil. Vitreorana uranoscopa consta como "Quase ameaçada" no Rio Grande do Sul. Nossos resultados mostram a importância de áreas protegidas, como o PEPC, para a manutenção das populações e comunidades de anuros da Floresta Ombrófila Mista.

The effects of two abundant ant species on soil nutrients and seedling recruitment in Brazilian Atlantic Forest

ABSTRACT Ants can influence soil fertility and the spatial distribution of seeds, with possible effects on seedling recruitment. The ant species Pachycondyla striata Fr. Smith, 1858 and Odontomachus chelifer (Latreille, 1802) co-occur in many forest areas in the Neotropics. We assessed soil fertility and seed bank structure in soil samples close and distant (control) from ant nests in forest fragments. We also assessed the richness and abundance of seedlings on nests and control sites. In soil samples from ant nests, the concentration of phosphorus and potassium were respectively 55.6% and 36% higher than in control sites. Aluminium was 11-15% lower in soil samples from ant nests. In the greenhouse, soils from ant nests had higher plant abundance and species richness, but the same species composition in comparison with control sites. Although more plants emerged from soil samples of O. chelifer nests, in the field, the density and richness of seedlings were similar for the two ant species studied. Seedlings in the nest sites were, on average, 1.8 times more abundant and 1.6 times richer in species than in control sites. Our results showed that ant species can play a key role in seedling recruitment in forest fragments, where other animals with equivalent and positive effects, such as mammals, are missing.

Microbiome and imputed metagenome study of crude and refined petroleum-oil-contaminated soils: Potential for hydrocarbon degradation and plant-growth promotion

Microbial community structure of crude petroleum oil (CP)- and refined petroleum oil (RP)-contaminated soil wasinvestigated. The taxonomical and functional diversity of such soils can be a great source of information about microbialcommunity and genes involved in petroleum hydrocarbon (PHC) degradation. In this study, microbial diversity of soilscontaminated by RP from urban biome of Pune, India, and CP from agricultural biome of Gujarat, India, were assessed by16S rRNA amplicon sequencing on Illumina MiSeq platform. Association between the soil microbial community and thephysicochemical parameters were investigated for their potential role. In RP- and CP-contaminated soils, the microbiomeanalysis showed Proteobacteria as most dominant phylum followed by Actinobacteria. Interestingly, Firmicutes were mostprevailing in a CP-contaminated sample while they were least prevailing in RP-contaminated soils. Soil moisture content,total organic carbon and organic nitrogen content influenced the taxa diversity in these soils. Species richness was more inRP as compared to CP soils. Further prediction of metagenome using PICRUSt revealed that the RP and CP soils containmicrobial communities with excellent metabolic potential for PHC degradation. Microbial community contributing to genesessential for soil health improvement and plant growth promotion was also gauged. Our analysis showed promising resultsfor future bioaugmentation assisted phytoremediation (BAP) strategies for treating such soils.

Effects of the introduction of an omnivorous fish on the biodiversity and functioning of an upland Amazonian lake

The introduction of nonnative species is one of the main threats to freshwater ecosystems. Although omnivory and intraguild predation are common in those systems, little is known about the effects of introduced omnivorous fish on pelagic and littoral communities. This study tested predictions of food-web theory regarding the effects of omnivorous fish introduction on previously fishless lakes in the Amazonian uplands of Serra dos Carajás, Pará, Brazil. The trophic structure of two similar lakes, one with and the other without the introduced omnivorous fish Astyanax bimaculatus, was compared using a data series of biotic variables collected from both lakes twice a year from 2010 to 2013. Zooplankton was more abundant in the lake with fish, and the zooplankton composition differed between lakes. Phytoplankton richness and chlorophyll-a were higher in the lake with the introduced fish than in the fishless lake regardless of phosphorus limitation. For the benthic macroinvertebrate communities, species richness and biomass were higher in the fishless lake. Our results also indicate that A. bimaculatus has the potential to link pelagic and littoral habitats through nutrient cycling. The differences observed between the studied lakes are consistent with predictions from food-web theory regarding the effects of multichain omnivorous fish on trophic dynamics. Despite limitations regarding replication at the ecosystem level, it is possible to infer from our findings that the introduction of an omnivorous fish might have changed lake overall functioning. (AU)