浅谈肠道菌落群调节免疫反应增强肿瘤治疗效果

肠道菌落是否正常与人体健康有密切的联系,正常健康的菌落有利于人体消化系统、免疫系统等的平衡,一旦肠道菌落出现异常,就可能导致糖尿病、心脑血管疾病、肿瘤等多种疾病的发生。最新一项研究表明,在抗肿瘤的药物治疗中,肠道菌落也起到了非常重要的作用,肠道菌落群能够通过调节免疫反应,达到增强肿瘤治疗效果的目的。

阜新煤气厂含酚污水处理过程中优势菌落群的筛选

阜新市煤气厂自1989年投产以来,改变了民用燃料的构成,缓解了燃煤对空气的污染,改善了市容环境,给人们生活带来了极大的方便。但煤气厂大量含酚废水的排放对环境的污染是严重的。煤气厂在煤气洗涤等生产过程中,每天要排放污水约80t。酚浓度为800～1000mg/

缩节胺和硝普钠对棉花幼苗根际土壤酶活性及细菌群落的影响

【目的】研究棉花幼苗施用缩节胺(1,1-dimethyl piperidinium chloride,DPC)和一氧化氮供体硝普钠(sodium nitroprusside,SNP)后根际土壤酶活性及细菌群落的变化,探讨与棉花幼苗生长相关的根际生物学指标。【方法】采用陆地棉品系A201进行穴盘育苗试验。于棉花1叶1心期分别在叶片均匀涂抹50 mg·L^(-1)DPC、500μmol·L^(-1)SNP,以涂抹去离子水为对照。于3叶1心期取根际土壤分析蔗糖酶、脲酶、过氧化氢酶、碱性磷酸酶活性,采用16S rRNA测序技术分析根际细菌多样性。【结果】DPC和SNP处理显著促进棉花根系生长,显著提高茎粗和植株干物质质量。DPC处理显著提高土壤脲酶和蔗糖酶的活性,SNP处理显著提高土壤蔗糖酶活性但显著降低脲酶的活性,但是DPC和SNP处理均未显著影响过氧化氢酶和碱性磷酸酶活性。DPC处理显著提高髌骨菌门(Patescibacteria)的相对丰度和土壤细菌群落的辛普森多样性指数(Simpson's diversity index),显著降低了绿弯菌门(Chloroflexi)和酸杆菌门(Acidobacteria)的相对丰度以及土壤细菌群落的香农-维纳多样性指数(Shannon Wiener’s diversity index)。冗余分析显示,DPC处理组的酵母菌科(Saccharimonadaceae)、TM7a属细菌的相对丰度比SNP处理组和对照组高;SNP处理组的纤维弧菌属(Cellvibrionaceae)细菌相对丰度高于DPC处理组和对照组;DPC和SNP处理组的根瘤菌科(Rhizobiaceae)细菌的相对丰度高于对照组,硝化螺旋菌科(Nitrospiraceae)和硝化螺旋菌属(Nitrospira)细菌的相对丰度低于对照组。脲酶活性与酵母菌科、TM7a属细菌的相对丰度呈显著正相关关系。【结论】DPC和SNP能够促进棉花幼苗根系及植株生长,并影响棉苗根际的土壤酶活性及细菌群落结构。

Variations of phyllosphere microorganisms in asymptomatic and tobacco brown spot leaves before and after spraying 12% difenoconazole + fluxapyroxad SC

12%difenoconazole+fluxapyroxad SC(commercial name:Jiangong)was first released by BASF in China in 2016.It has been registered to control many diseases,including pear scab,apple Alternaria leaf spot,tomato early blight,cucumber powdery mildew,etc.This study evaluated the bioactivity of Jiangong against Alternaria alternata and explored variations of phyllosphere microorganisms in both asymptomatic and tobacco brown spot leaves at different persistence periods(0,5,10,and 15 days post-fungicide application)using high-throughput sequencing technology.The results indicated that Jiangong effectively inhibited mycelial growth(average EC_(50) value of 0.51μg/mL),conidia germination(average EC_(50) value of 3.47μg/mL),and the carbon metabolism of A.alternata.Both asymptomatic and symptomatic leaves presented complex microbial communities.Higher fungal diversity was noted in asymptomatic leaves,while higher bacterial diversity was found in symptomatic leaves.After application,the diversity and abundance of microbial community structures in both types of leaves changed over time.Fungal microbiome communities showed greater sensitivity than bacterial groups,with the microbiome communities of asymptomatic leaves being more affected than those of symptomatic leaves.Fungal community diversity decreased for both symptomatic and asymptomatic leaves after 5 days of application,while the diversity of fungal community in symptomatic leaves showed an upward trend after 10 days of application.Meanwhile,bacterial community diversity increased in both symptomatic and asymptomatic leaves after 5 days of application but then declined in asymptomatic leaves after 15 days.The abundance of the dominant function group of phyllosphere bacteria(metabolism,genetic information processing,environmental information processing)was not affected by the application of Jiangong.However,the abundance of the dominant function group of phyllosphere fungi(animal pathogen-endophyte-wood saprotroph,endophyte-plant pathogen,plant pathogen-undefined saprotroph)was significantly affected by the application of Jiangong,and high variation was found in symptomatic leaves than that of asymptomatic leaves.The application of Jiangong-induced alterations in the community structure of the tobacco phyllosphere microbiome provides a basis for future tobacco brown spot control strategies based on phyllospheric microecology.

High efficient mixed culture screening and selected microbial community shift for bioleaching process

To screen the high efficient mixed culture and understand the bioleaching behaviors of mixed culture for low-grade copper sulfide ore bioleaching,ten mixed cultures were collected and screened from different acid mine drainages obtained from sulfide mines of China.The leaching rate was set as criterion to screen the mixed culture and the metagenomic approach.Community genome array（CGA） was used for analyzing the mixed culture microbial community shift during the bioleaching process.The results indicate that the mixed culture obtained from Yinshan（YS） lead-zinc mine in Dexing of Jiangxi province in China reaches the maximum copper extraction（68.89%） during the one bioleaching period of 24 d.CGA results show that YS culture contains nine kinds of bacteria which are belong to six divisions,and the microbial community structure is changing during the bioleaching process.This provides a good way to accelerate the bioleaching process and reveals the microbial community shift during the bioleaching process.

Analysis on Bacterial Community Structure in Mushroom(Agaricus bisporus) Compost Using PCR-DGGE

This study aimed to investigate the bacterial communities in mushroom compost piles composed of rice straw, corn stover, and cow dung. Bacterial com- munities of samples at the beginning of composting, at the end of fermentation phase I and II were collected and analyzed using Polymerase Chain Reaction-De- naturing Gradient Gel Electrophoresis （PCR-DGGE） based on 16S rDNA universal primers from Escherichia coli. A total of 56 different clone sequences were obtained （GenBank accession number： KF630598-KF630653）. They were classified into seven phyla and 42 genera. Dominant microflora during composting belonged to phylum Proteobacteria, Firmicutes, and Actinobacteria, with the dominant genera of Bacillus, Paenibacillus, Thermomonospora, Thermasporomyces, Pseudomonas, and Cellvibrio. Bacterial diversity （Shannon index） analysis showed that bacterial species in com- post pile composed mainly of rice straw continuously increased during composting, while those in compost pile composed mainly of corn stover firstly increased and then reduced. Principal component analysis showed that corn stover compost sam- ples at the end of fermentation phase I and phase II were clustered into one group, suggesting that corn stover composted faster than anticipated. In general, rice straw compost has higher bacterial diversity but longer composting time period, while corn stover compost has lower bacterial diversity but shorter composting time period.

Changes of Bacterial Community Structure in Copper Mine Tailings After Colonization of Reed (Phragmites communis)

Soil samples were collected from both bare and vegetated mine railings to study the changes in bacterial communities and soil chemical properties of copper mine tailings due to reed （Phragmites communis） colonization. The structures of bacterial communities were investigated using culture-independent 16S rRNA gene sequencing method. The bacterial diversity in the bare mine tailing was lower than that of the vegetated mine tailing. The former was dominated by sulfur metabolizing bacteria, whereas the latter was by nitrogen fixing bacteria. The bare mine tailing was acidic （pH = 3.78）, whereas the vegetated mine tailing was near neutral （pH ： 7.28）. The contents of organic matter, total nitrogen, and ammonium acetate-extractable potassium in vegetated mine tailings were significantly higher than those in the bare mine railings （P 〈 0.01）, whereas available phosphorus and electrical conductivity were significantly lower than those in the bare mine tailings （P 〈 0.01）. The results demonstrated that 16S rRNA gene sequencing could be successfully used to study the bacterial diversity in mine tailings. The colonization of the mine tailings by reed significantly changed the bacterial community and the chemical properties of tailings. The complex interactions between bacteria and plants deserve further investigation.

Effects of DNA extraction and universal primers on 16S rRNA gene-based DGGE analysis of a bacterial community from fish farming water

Among many reports investigating microbial diversity from environmental samples with denaturing gradient gel electrophoresis (DGGE), limited attention has been given to the effects of universal primers and DNA extraction on the outcome of DGGE analysis. In this study, these effects were tested with 16S rRNA gene-based DGGE on a bacterial community from farming water samples. The results indicate that the number of discernable bands in the DGGE fingerprint differed with the primer pairs used; the bands produced by 63f/518r, 341f/926r and 933f/1387r primer pairs were obviously fewer than those by 968f/1401r. Also, we found that each DNA extraction method resulted in different community profiles, reflected by the number and intensity of bands in the DGGE fingerprint. Furthermore, the main bands (theoretically representing dominant bacteria) differed with the extraction methods applied. It is therefore believed that the effects of universal primers and DNA extraction should be given more attention and carefully chosen before performing an investigation into a new environment with DGGE.

Design of Vibrio 16S rRNA Gene Specific Primers and Their Application in the Analysis of Seawater Vibrio Community

The pathogenic species of genus Vibrio cause vibriosis, one of the most prevalent diseases of maricultured animals and seafood consumers. Monitoring their kinetics in the chain of seafood production, processing and consumption is of great importance for food and mariculture safety. In order to enrich Vibrio-representing 16S ribosomal RNA gene （rDNA） fragments and identify these bacteria further real-timely and synchronously among bacterial flora in the chain, a pair of primers that selectively amplify Vibrio 16S rDNA fragments were designed with their specificities and coverage testified in the analysis of seawater Vibrio community. The specificities and coverage of two primers, VF169 and VR744, were determined theoretically among bacterial 16S rDNAs available in GenBank by using BLAST program and practically by amplifying Vibrio 16S rDNA fragments from seawater DNA. More than 88.3% of sequences in GenBank, which showed identical matches with VR744, belong to Vibrio genus. A total of 33 clones were randomly selected and sequenced. All of the sequences showed their highest similarities to and clustered around those of diverse known Vibrio species. The primers designed are capable of retrieving a wide range of Vibrio 16S rDNA fragments specifically among bacterial flora in seawater, the most important natural environment of seafood cultivation.

Bacterial Community Structure in a Mollisol Under Long-Term Natural Restoration, Cropping, and Bare Fallow History Estimated by PCR-DGGE

Soil microbial biomass and community structures are commonly used as indicators for soil quality and fertility. A investigation was performed to study the effects of long-term natural restoration, cropping, and bare fallow managements on the soil microbial biomass and bacterial community structures in depths of 0-10, 20 30, and 40-50 cm in a black soil （Mollisol）. Microbial biomass was estimated from chloroform fumigation-extraction, and bacterial community structures were determined by analysis of 16S rDNA using polymerase chain reaction-denaturing gradient gel electrophoresis （PCR- DGGE）. Experimental results showed that microbial biomass significantly declined with soil depth in the managements of restoration and cropping, but not in the bare fallow. DGGE profiles indicated that the band number in top 0-10 cm soils was less than that in depth of 20-30 or 40-50 cm. These suggested that the microbial population was high but the bacterial community structure was simple in the topsoil. Cluster and principle component analysis based on DGGE banding patterns showed that the bacterial community structure was affected by soil depth more primarily than by managements, and the succession of bacterial community as increase of soil depth has a similar tendency in the three managements. Fourteen predominating DGGE bands were excised and sequenced, in which 6 bands were identified as the taxa of Verrueomicrobia, 2 bands as Actinobacteria, 2 bands as α-Proteobacteria, and the other 4 bands as 8-Proteobacteria, Aeidobacteria, Nitrospira, and unclassified bacteria. In addition, the sequences of 11 DGGE bands were closely related to uncultured bacteria. Thus, the bacterial community structure in black soil was stable, and the predominating bacterial groups were uncultured.

Comparison of intestinal bacterial communities in grass carp,Ctenopharyngodon idellus,from two different habitats

The intestinal bacteria of vertebrates form a close relationship with their host.External and internal conditions of the host,including its habitat,affect the intestinal bacterial community.Similarly,the intestinal bacterial community can,in turn,influence the host,particularly with respect to disease resistance.We compared the intestinal bacterial communities of grass carp that were collected from farm-ponds or a lake.We conducted denaturing gradient gel electrophoresis of amplified 16S rRNA genes,from which 66 different operational taxonomic units were identified.Using both the unweighted pair-group method with arithmetic means clustering and principal component analysis ordination,we found that the intestinal bacterial communities from the two groups of pond fish were clustered together and inset into the clusters of wild fish,except for DF-7,and there was no significant correlation between genetic diversity of grass carp and their intestinal bacterial communities(Mantel one-tailed test,R=0.157,P=0.175).Cetobacterium appeared more frequently in the intestine of grass carp collected from pond.A more thorough understanding of the role played by intestinal microbiota on fish health would be of considerable benefit to the aquaculture industry.

Response of soil fungal community to long-term chromium contamination

To further study the fungal community in heavy metal contaminated ecosystems,soil samples were collected from an abandoned chromium(Cr)factory,and fungal community was analyzed by Illumina sequencing of Internal Transcribed Spacer(ITS)amplicons.The results showed that Cr contamination changed the composition and structure of soil fungal community,but didn’t change the diversity.Fungus showed various responses to Cr contamination.LEfSe analysis revealed that the biomarker changed a lot in the Cr-contaminated samples in comparison with that in the control samples.The changes in fungal community may be caused by the direct toxic effects on fungi by high concentration of Cr and the significant change in soil properties resulting from Cr contamination.Among all the Cr fractions,organic matter-bound Cr and exchangeable Cr showed significant effects on the fungal community and organic matter also showed a significant effect on soil fungal community.

A Review of Methods for Studying Microbial Diversity in Soils

Soil microorganisms play a central role in decomposing organic matter, in determining the release of mineral nutrients, and in nutrient cycling. Recently, extensive studies have focused on soil microbial diversity. However, understanding the diversity of this complex microbial community in the soil environment is a challenging task. Thus, it is important to master and comprehend appropriate methods for studying soil microbial diversity. Concepts of soil microbial diversity and major methods of study are briefly introduced in this paper. Then, the application of biochemical-based and molecular-based techniques in this area, and their advantages and disadvantages are evaluated. Based on recent related research, perspectives for studying microbial diversity in soils are presented.

Co-invasion of daisy fleabane and Canada goldenrod pose synergistic impacts on soil bacterial richness

Understanding the impacts of co-invasion of multiple invaders on soil bacterial communities is significant in understanding the mechanisms driving successful invasion.This study aimed to determine the response of soil bacterial communities to co-invasion of two invaders daisy fleabane(Erigeron annuus)and Canada goldenrod(Solidago canadensis).Daisy fleabane and/or Canada goldenrod invasion significantly enhanced the operational taxonomic unit richness,Shannon index,and Chao1 index of soil bacterial communities.Canada goldenrod under light degree of invasion and co-invasion of daisy fleabane and Canada goldenrod regardless of invasion degree signally improved the ACE index of soil bacterial communities.Thus,the two invaders can enhance soil bacterial diversity and richness to facilitating subsequent invasion due to the fact that higher soil bacterial diversity and richness can enhance the levels of soil function and nutrients acquisition of plant species.ACE index of soil bacterial communities subjected to co-invasion of daisy fleabane and Canada goldenrod regardless of invasion degree was greater than that under the independent invasion of either daisy fleabane or Canada goldenrod.Hence,co-invasion of the two invaders can impose synergistic impacts on soil bacterial richness,which may build a preferable soil micro-environment via the intensified soil bacterial communities,which is contributive to their following invasion.

Sediment bacterial communities are more complex in coastal shallow straits than in oceanic deep straits

Straits are ideal models to investigate the bacterial community assembly in complex hydrological environments. However, few studies have focused on bacterial communities in them. Here, comparable bacterial communities in costal shallow Bohai Strait(BS) and oceanic deep Fram Strait(FS) were studied. The Shannon and Chao1 indices were both higher in BS than in FS. The relative abundances of the classes Deltaproteobacteria and Bacilli and the family Halieaceae were higher in BS than in FS, in contrast to the families OM1_clade and JTB255_marine_benthic_group, revealing typical characteristics of bacterial communities in coastal and oceanic regions. Cluster analysis based on the Bray-Curtis index showed that samples were clustered by depth layer in FS and BS, indicating that structures of bacterial communities would diff er with increasing water depth in straits. Additionally, the cluster relationships among samples in abundant and rare communities were both similar to those in entire communities. However, the dissimilarities among samples showed a descending order as rare communities, entire communities and abundant communities. Network analysis indicated that the BS network was obviously more complex than the FS network. Filamentous bacteria Desulfobulbaceae exhibited high degree values in BS but not in FS, indicating key roles of Desulfobulbaceae in the BS. Our study provides different and common evidences for understanding microbial ecology in coastal shallow and oceanic deep straits.

Characterization and in-vivo evaluation of potential probiotics of the bacterial flora within the water column of a healthy shrimp larviculture system

A thorough understanding of the normal bacterial flora associated with shrimp larviculture systems contributes to probiotic screening and disease control. The bacterial community of the water column over a commercial Litopenaeus vannamei larval rearing run was characterized with both culture-dependent and culture-independent methods. A total of 27 phylotypes at the species level were isolated and identified based on 16S rDNA sequence analysis. Denaturing gradient gel electrophoresis （DGGE） analysis of the V3-V5 region of 16S rRNA genes showed a dynamic bacterial community with major changes occurred from stages zoea to mysis during the rearing run. The sequences retrieved were affiliated to four phyla, Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes, with the family Rhodobacteraceae being the most frequently recovered one. Subsequently, 13 representative strains conferred higher larval survival than the control when evaluated in the in-vivo experiments; in particular, three candidates, assigned to Phaeobacter sp., Arthrobacter sp., and Microbacteriurn sp., significantly improved larval survival （P〈0.05）. Therefore, the healthy shrimp larviculture system harbored a diverse and favorable bacterial flora, which contribute to larval development and are of great importance in exploiting novel probiotics.

Characterization of Bacterial Communities Associating with Larval Development of Yesso Scallop(Patinopecten yessoensisis Jay, 1857) by High-Throughput Sequencing

Bacterial community presumably plays an essential role in inhibiting pathogen colonization and maintaining the health of scallop larvae, but limiting data are available for Yesso scallop （Patinopecten yessoensisis Jay, 1857） larval development stages. The aim of this study was to characterize and compare the bacterial communities associating with Yesso scallop larval development at fertilized egg S l, trochophora S2, D-shaped larvae S3, umbo larvae S4, and juvenile scallop S5 stages by Illumina high-throughput sequencing. Genomic DNA was extracted from the larvae and their associating baetera, and a gene segment covering V3-V4 region of 16S rRNA gene was amplified and sequenced using an Illumina Miseq sequencer. Overall, 106760 qualified sequences with an average length of 449 bp were obtained. Sequences were compared with those retrieved from 16S rRNA gene databases, and 4 phyla, 7 classes, 15 orders, 21 families, 31 genera were identified. Proteobacteria was predominant phylum, accounting for more than 99%, at all 5 larval development stages. At genus level, Pseudomonas was dominant at stages S1 （80.60%）, S2 （87.77%） and S5 （68.71%）, followed by Photobacterium （17.06%） and Aeromonas （1.64%） at stage S1, Serratia （6.94%）, Stenotrophomonas （3.08%） and Acinetobacter （1.2%） at stage S2, Shewanella （25.95%） and Pseudoalteromonas （4.57%） at stage S5. Moreover, genus Pseudoal- teromonas became dominant at stages S3 （44.85%） and S4 （56.02%）, followed by Photobacterium （29.82%）, Pseudomonas （11.86%）, Aliivibrio （8.60%） and Shewanella （3.39%） at stage S3, Pseudomonas （18.16%）, Aliivibrio （14.29%）, Shewanella （4.11%）, Psychro- monas （4.04%） and Psychrobacter （1.81%） at stage S4. From the results, we concluded that the bacterial community changed sig- nificantly at different development stages of Yesso Scallop larvae.

Effects of Acetochlor and Methamidophos on Fungal Communities in Black Soils

Using plate counting and ergosterol assay, single and joint effects of acetochlor and methamidophos on the dynamicsof soil fungal population and total fungal biomass in the black soil zone of Northeast China were investigated. The resultsdemonstrated that acetochlor at high concentration levels (150 and 250 mg kg-1) had an acute and mostly chronic toxicityon both the soil fungal population and total fungal biomass, but at a low concentration (50 mg kg-1) generally had astimulating effect that was stronger with total fungal biomass than with the soil fungal population. Methamidophos ata high concentration level (250 mg kg-1) alone and almost all of its combinations with various dosages of acetochlorincreased the soil fungal population, whereas at most sampling dates with 250 mg methamidophos kg-1 soil, total fungalbiomass increased, but in combination with acetochlor it was decreased in the early period of incubation and then increased28 days after incubation. Thus, through measuring the number of colony forming unit of the soil fungal population alongwith the total fungal biomass, a better understanding on effects of agrochemicals on soil fungi could be made.

Soil Cellulase Activity and Fungal Community Responses to Wetland Degradation in the Zoige Plateau, China

Four soil types(peat, marsh, meadow, and sandy) in the Zoige Plateau of China are associated with the severity of wetland degradation. The effects of wetland degradation on the structure and abundance of fungal communities and cellulase activity were assessed in these 4 soil types at 3 depths using DGGE(Denatured Gradient Gel Electrophoresis), q PCR(Quantitative Real-time PCR),and 3,5-dinitrosalicylic acid assays. Cellulase activity and abundance of the fungal community declined in parallel to the level of wetland degradation(from least to most disturbed). DGGE analysis indicated a major shift in composition of fungal communities among the4 soil types consistent with the level of degradation.Water content(WC), organic carbon(OC), total nitrogen(TN), total phosphorus(TP), available nitrogen(AN), and available phosphorus(AP) were strongly correlated with cellulase activity and the structure and abundance of the fungal community.The results indicate that soil physicochemical properties(WC, OC, TN, TP, AN, and AP), cellulase activity, and diversity and abundance of fungal communities are sensitive indicators of the relative level of wetland degradation. WC was the major factorinvolved in Zoige wetland degradation and lower WC levels contributed to declines in the abundance and diversity of the fungal community and reduction in cellulase activity.

Efficiency,mechanism and microbial community of Cd(Ⅱ)removal by mixed bacteria enriched from heavy metals mine soil

Mixed bacteria were enriched from heavy metals mine soil for cadmium(Cd(Ⅱ))-containing wastewater treatment. Batch adsorption experiment results showed that the optimal pH, temperature, initial Cd(Ⅱ) concentration, and biomass dosage were 6.0, 30 ℃, 20 mg/L, and 1 g/L, respectively. Living biomass exhibited better Cd(Ⅱ) removal efficiency(91.97%) than autoclaved biomass(79.54%) under optimal conditions. The isotherms and kinetics of living biomass conformed to the Langmuir isotherm model and pseudo-first-order kinetic model, respectively. FTIR results implied that amine groups, hydroxyl groups and phosphoric acid play an important role in the Cd(Ⅱ) adsorption process, while XRD results showed that crystalline Cd(OH)and CdO were obtained. After Cd(Ⅱ)-containing wastewater treatment exposure, the dominant bacteria genera included Comamonas(39.94%), unclassified_f__Enterobacteriaceae(34.96%), Ochrobactrum(14.07%), Alcaligenes(4.84%), Bordetella(2.07%), Serratia(1.04%), and Bacillus(1.01%). Function prediction showed that the abundance of metabolic genes changed significantly. This study proposes the potential application of mixed bacteria for Cd(Ⅱ)-containing wastewater treatment.