Distinct symbiont lineages in three thyasirid species (Bivalvia: Thyasiridae) from the eastern Atlantic and Mediterranean Sea

Thyasiridae are one of the less studied groups of chemosymbiotic bivalves. Here, we investigated symbioses in three different thyasirid species collected at three cold seeps from the Atlantic and Mediterranean. Phylogenetic analysis of bacterial 16S ribosomal RNA gene sequences demonstrated that each thyasirid species harbours a single phylotype of symbiont that belongs to a distinct lineage of putative sulphur-oxidizing Gammaproteobacteria. This result is confirmed by other marker genes (encoding 23S rRNA and APS reductase) and fluorescence in situ hybridization. This work highlights the diversity of bacteria involved in symbiosis with thyasirids and underlines the relevance of this group as a target for future symbiosis studies.     

Direct evidence for maternal inheritance of bacterial symbionts in small deep-sea clams (Bivalvia: Vesicomyidae)

Bacterial symbiont transmission is a key step in the renewal of the symbiotic interaction at each host generation, and different modes of transmission can be distinguished. Vesicomyidae are chemosynthetic bivalves from reducing habitats that rely on symbiosis with sulfur-oxidizing bacteria, in which two studies suggesting vertical transmission of symbionts have been published, both limited by the imaging techniques used. Using fluorescence in situ hybridization and transmission electron microscopy, we demonstrate that bacterial symbionts of Isorropodon bigoti, a gonochoristic Vesicomyidae from the Guiness cold seep site, occur intracellularly within female gametes at all stages of gametogenesis from germ cells to mature oocytes and in early postlarval stage. Symbionts are completely absent from the male gonad and gametes. This study confirms the transovarial transmission of symbionts in Vesicomyidae and extends it to the smaller species for which no data were previously available.     

稻田土壤反硝化厌氧甲烷氧化菌的时空分布与群落结构分析

由"Candidatus Methylomirabilis oxyfera"主导发生的以甲烷和亚硝酸盐为底物的反硝化厌氧甲烷氧化反应(nitrite-dependent anaerobic methane-oxidizing,n-damo)的发现,将生物地球化学碳循环和氮循环以新的方式结合起来.本研究以夏季和冬季江阴稻田土壤柱状样品为研究对象,对稻田土壤M.oxyfera-like菌的时空分布和群落结构进行了考察.M.oxyfera-like菌16S rRNA基因的定量PCR结果显示M.oxyfera-like菌的丰度随着土壤深度的增加而增加,且无明显季节性差异,60~200 cm深度的稻田土壤是M.oxyfera-like菌的高丰度区域.M.oxyfera-like菌pmo A基因的系统发育分析和生物多样性分析显示M.oxyfera-like菌的群落结构具有一定的时空异质性,且生物多样性随着土壤深度的增加而增加.这些结果都说明江阴稻田深层土壤(60~200 cm)是适宜M.oxyfera-like菌生存的生态环境.     

我国东北典型河流冰封期细菌多样性的研究——以松花江为例

在我国东北松花江冰封期时采集了该河流域5个监测断面的河水样本,并分别构建16S rDNA克隆文库,通过16S rDNA序列的系统发育分析,对水样中细菌群落结构和种群多样性进行了研究.试验结果表明,5个采样点的水样pH都呈弱酸性,并且都有不同程度的多环芳烃(PAHs)污染,其中,B(九站)采样点污染最为严重.5个样品中检测到的共同细菌种类有5个:β-变形菌纲(Betaproteobacteria)、γ-变形菌纲(Gammaproteobacteria)、放线菌门(Actinobacteria)、蓝细菌门(Cyanobacteria)和拟杆菌门(Bacteroidetes).5个河水样品中的细菌与许多已知降解菌的亲缘关系较近,并以能降解多环芳烃类有机污染物的微生物种类居多,且在5个样品中均发现了指示河流富营养化的菌种,表明该河流存在普遍的富营养化趋势,特别是D、E段(佳木斯上和佳木斯下)比较严重.     

Rotavirus Occurrence in Shellfish with Low Levels of E. coli

The purpose of this study was to evaluate “in field” the accumulation of virus in shellfish and compare it with the concentration of bacterial indicators. Individuals of Mytilus galloprovincialis were placed in two sampling station located in a contaminated coastal bay and in one control station located one kilometer offshore. The presence of Rotavirus and E. coli was assessed weekly both in seawater and in shellfish samples. The Rotavirus genome was detected in water, preliminarily concentrated by tangential flow ultrafiltration method, and in hepatopancreas of mussels by Real-Time PCR. E. coli was enumerated in water matrices by a filtering method and in mussels by the MPN method. Rotaviruses were not recorded in seawater, while in mussels they were detected since third week after placement. E. coli in mussels were always below the limits set in the Regulation (EC) 854/2004. This study suggests the need for a viral indicator to insure the safety for consumption of shellfish.     

Effects of a municipal effluent on the freshwater mussel Elliptio complanata following challenge with Vibrio anguillarum

The purpose of this study was to examine the cumulative effects of exposure to a pathogenic bacteria and municipal effluent in the freshwater mussel Elliptio complanata. Mussels were exposed to increasing concentrations of an ozone-treated effluent at 15°C for 7 days. A sub-group of mussels was inoculated with Vibrio anguillarum and exposed to the same conditions as above.After the exposure period, mussels were collected to assess hemocyte count and viability,immunocompetence(phagocytosis and nitrite production), oxidative stress/inflammation(cyclooxygenase and lipid peroxidation) and oxygen radical/xenobiotic scavenging activity(metallothioniens, glutathione S-transferase). The results showed that mussels exposed to municipal effluent had increased hemocyte counts, phagocytosis, nitrites, lipid peroxidation and metallothioneins. In the inoculated mussels, the same responses were observed, in addition to cyclooxygenase and glutathione S-transferase activities. Multivariate analyses revealed that(1)the response pattern changed with effluent concentration, where increased responses observed at low effluent concentrations(10%, V/V) were attenuated at higher effluent concentrations,(2)the effluent produced more pronounced changes in lipid peroxidation, metallothionein and hemocyte viability, and(3) the simultaneous presence of V. anguillarum led to more important changes in hemocyte count and viability and nitrite levels. In conclusion, the presence of V.anguillarum could alter the response of mussels to municipal effluent, which could lead to increased inflammation in mussels.     

寒区水体中溶藻铜绿假单胞菌的分离和性质研究

我国北方,尤其是东北地区的一些水体由于富营养化导致的水华现象呈增加趋势,成为急需解决的水环境问题.溶藻菌可从生态调控的角度来控制水华的爆发,因此,在富营养化水体治理方面逐渐得到重视.本文从寒区水华爆发水体中分离获得了一株溶藻细菌JM1,系统发育分析表明,菌株JM1与铜绿假单胞菌的同源性最高.VITEK系统鉴定表明,菌株JM1与铜绿假单胞菌的相似度为98%.菌株JM1在不同的碳源和氮源培养基中可产生不同颜色和p H值的代谢产物,而以葡萄糖和蛋白胨分别为碳源和氮源时发酵液的溶藻效果明显好于其它培养基.菌株JM1的溶藻效果随藻细胞初始密度的降低而增强,随发酵液添加量的增加而增加;当菌体细胞的密度达到1011CFU·m L-1时,可单一抑制藻细胞的生长;当菌体细胞的密度大于105CFU·m L-1时,菌体细胞可促进发酵液的溶藻作用.发酵液作用于藻细胞6 h时可明显影响其恢复能力,当暴露时间达18 h时,藻细胞彻底丧失了恢复能力.菌株JM1发酵液在中性和偏碱性的藻液中的溶藻效果最强,并且经过酸化、碱化和高温处理后,仍然保持较高的溶藻活性.本研究可为基于微生物作用过程的水华控制提供优势的土著菌种及其应用上的技术支持.     

Extended mutualism between termites and gut microbes: nutritional symbionts contribute to nest hygiene

All higher eukaryotes have established symbiotic relationships with diverse microorganisms. One of the most well-characterized symbiotic systems is that of termites and their intestinal microorganisms, which digest cellulose. Recently, diverse types of symbioses between gut microbes and host organisms including humans have received growing attention for various features of their complex interactions beyond nutrition. In termites, researchers are beginning to explore such function of gut symbionts, but only the contribution to internal immunity against entomopathogen is known in a few species. Here, we report that gut symbionts of the dampwood termite Zootermopsis nevadensis protect nests from the spread of the commensal bacterium Serratia marcescens, which has pathogenic potential. Defaunated termites dispersed S. marcescens in the surrounding environment by feeding on the bacteria, which then survived passage through their alimentary tracts, while non-defaunated termites did not. Loss of gut symbionts caused a significant reduction in intestinal acetate, which is an important carbon source for termites. Culture experiments showed that acetate had significant inhibitory effects on S. marcescens at a concentration as low as 12 mM, which indicated that the intestinal acetate of non-defaunated termites (40–130 mM) was capable of suppressing this bacterium. These results suggest that digestive derivatives produced by intestinal symbionts play an essential role in nest hygiene in addition to their nutritional function for termites. Our study provides a better understanding of the multifunctionality of symbiotic relationships in diverse organisms beyond nutrition.     

Innate humoural immunity is related to eggshell bacterial load of European birds: a comparative analysis

Fitness benefits associated with the development of a costly immune system would include not only self-protection against pathogenic microorganisms but also protection of host offspring if it reduces the probability and the rate of vertical transmission of microorganisms. This possibility predicts a negative relationship between probabilities of vertical transmission of symbionts and level of immune response that we here explore inter-specifically. We estimated eggshell bacterial loads by culturing heterotrophic bacteria, Enterococcus, Staphylococcus and Enterobacteriaceae on the eggshells of 29 species of birds as a proxy of vertical transmission of bacteria from mother to offspring. For this pool of species, we also estimated innate immune response (natural antibody and complement (lysis)) of adults, which constitute the main defence against bacterial infection. Multivariate general linear models revealed the predicted negative association between natural antibodies and density of bacteria on the eggshell of 19 species of birds for which we sampled the eggs in more than one nest. Univariate analyses revealed significant associations for heterotrophic bacteria and for Enterobacteriaceae, a group of bacteria that includes important pathogens of avian embryos. Therefore, these results suggest a possible trans-generational benefit of developing a strong immune system by reducing vertical transmission of pathogens.     

Distribution and dietary regulation of an associated facultative Rhizobiales-related bacterium in the omnivorous giant tropical ant,Paraponera clavata

We document a facultative Bartonella-like Rhizobiales bacterium in the giant tropical ant, Paraponera clavata. In a lowland tropical rainforest in Costa Rica, 59 colonies were assayed for the prevalence of the Bartonella-like bacterium (BLB), 14 of which were positive. We addressed three questions: First, how does the prevalence of BLB within colonies vary with environmental conditions? Second, how does diet affect the prevalence of BLB in P. clavata? Third, how does the distribution of BLB among colonies reflect ambient differences in food resources and foraging habits? A variety of environmental variables that may be predictive of the presence of BLB were measured, and diet manipulations were conducted to test whether the prevalence of BLB responded to supplemental carbohydrate or prey. The ambient frequency of BLB is much higher in young secondary forests, but is nearly absent from older secondary forests. The prevalence of BLB inside field colonies increased over the duration of a 2-week carbohydrate supplementation; however, water and prey supplementation did not alter the prevalence of BLB. The diets of the colonies located in young secondary forest, compared to other habitats, have a diet richer in carbohydrates and lower in prey. The abundance of carbohydrate, or the relative lack of N, in a colony’s diet influences the occurrence of the BLB microbe in P. clavata. As experimental diet manipulations can affect the facultative presence of an N-cycling microbe, a consistent diet shift in diet may facilitate the emergence of tighter symbioses.     

Characteristics of the microbial communities in the integrated vertical-flow constructed wetlands

Microorganisms play an important role in removing pollutants from constructed wetlands. We investigated the microbial characteristics in a novel integrated vertical-flow constructed wetland (IVCW), which has been in operation in Wuhan, China since 1998. We used phospholipid fatty acid (PLFA) and amoA gene to analyze the structure and diversity of the microbial community within the IVCW. PLFA results suggested that the amount of bacterial PLFA was significantly higher than that of fungal PLFA, but the total microbial biomass represented by PLFA index was low in the system. Microbial spatial distribution showed significantly higher bacterial (both G⁺ and G⁻) and fungal biomass in the surface than in the subsurface layers. The ratios of monounsaturated to branched PLFA demonstrated that an anaerobic layer sandwiched by two aerobic layers existed in the IVCW, consistent with the redox potential results. Analysis of the amoA revealed the presence of Nitrosomonas-like sequences in the surface substrate of the downflow chamber and apparent diversities of ammonia-oxidizing bacteria in the system. These results suggest that microorganisms, despite their relatively low biomass, have inhabited the IVCW, and the results will offer some valuable information on microbe to system designers and managers.     

Spatial and seasonal variations in bacterial communities of the Yellow Sea by T-RFLP analysis

Four typical coastal sites (rocky shore, sandy shore, mud flat shore, and artificial harbor) at the Yellow Sea were chosen to investigate the spatial and seasonal variations in bacterial communities. This was accomplished by using terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR amplified 16S rDNA fragments. Two kinds of tetrameric restriction enzymes, HhaI and MspI, were used in the experiment to depict the bacterial community diversity in different marine environments. It was found that the community compositions digested by the two enzymes separately were different. However, the results of bacterial community diversity derived from them were similar. The MDA analysis results of T-RFLP profiles coming from HhaI and MspI both exhibited a significant seasonal community shift for bacteria and a relatively low spatial variation among the four locations. With HhaI as the sample, the pair wise T-tests also revealed that variations were minor between each pair of marine environments, with R ranging from 0.198 to 0.349. However, the bacterial community structure in the mud flat site depicted a larger difference than each of the other three sites (R ranging from 0.282 to 0.349).     

石油降解菌的分离鉴定及4株芽胞杆菌种间效应

通过富集培养和分离纯化的方法,从天津大港油田石油污染土壤和渤海海上钻井平台洗油污水中分离出6株石油降解细菌,生理生化试验及16S r DNA序列分析鉴定表明,它们分别属于Bacillus芽胞杆菌属(S1、S2、S3、S4)、Pseudomonas假单胞菌属(W1)和Ochrobactrum苍白杆菌属(W2),其中,S3具有最高的烷烃(41.3%)和芳烃(30.9%)降解率,从石油污染场地中筛选出的内源微生物对本油田石油的降解效果优于外源物种.对4株芽胞杆菌属菌株构建微生物组进行石油降解实验,结果表明,由S1和S4构成的微生物组F3具有最高的烷烃(50.5%)和芳烃(54.0%)降解率,比单菌降解率分别提高了69.9%和156.1%,同时比最优降解单菌S3的降解率分别高出22.1%和74.6%,而由S2和S3构成的微生物组F4对烷烃和芳烃的降解率最低,分别为18.5%和18.9%,比单菌降解率降低了55.3%和39.0%,实验表明同菌属微生物种间对石油的降解同时存在协同促进和拮抗抑制作用,芽胞杆菌属内亲缘性近的菌株之间对石油降解主要表现为促进作用.     

西湖底泥中厌氧氨氧化菌的分子生物学检测

厌氧氨氧化（anaerobic ammonium oxidation,anammox）在海洋氮素循环中起了重要作用,而有关天然淡水生态系统中anammox的研究报道并不多.本研究采用16SrRNA基因克隆文库技术首次考察了西湖淡水底泥中anammox菌的分布与种群多样性水平.16SrRNA系统发育分析表明,西湖底泥中的...     

高效水解酸化UASB活性污泥的菌群结构分析

采用454高通量测序技术对低能耗、低污泥产量且具有脱氮效能的印染废水处理工艺中UASB污泥的微生物菌群结构进行了分析.结果表明,UASB内污泥的微生物菌种呈多样性分布且优势菌群突出,通过菌群鉴定发现,脱硫橄榄样菌属(Desulfobacula)、Levilinea、长绳菌属(Longilinea)、Candidatus Tammella、Paludibacter、索氏菌属(Thauera)、Tepidimicrobium、杆状脱硫菌属(Desulforhabdus)、类芽孢杆菌属(Paenibacillus)、梭菌属(Clostridium)是主要的优势菌属.其中,梭菌属是起到产酸和污泥减量作用的主要菌种.另外,具有脱氮效能的原因可能是由于发生了硫酸盐型厌氧氨氧化作用.通过Shannon、Chao、Simpson、Shannon指数的计算,发现该UASB中微生物较其他废水处理系统,群落结构拥有较高的多样性和丰度,有利于稳定产酸.     

丹江口库区库滨带植被土壤细菌群落多样性及PICRUSt功能预测分析

微生物是土壤元素生物地球化学循环的主要驱动力,目前库滨带植物截留和消减污染物质过程中细菌群落及其功能研究尚未清楚.本研究选取适宜丹江口库区库滨带生长的4种典型植物(草本植物香根草、芦苇、乔木植物杜梨和灌木植物假奓包叶),采用16S r DNA Miseq高通量测序技术研究根际细菌群落组成,发现其主要由变形菌门、拟杆菌门、放线菌门等31个门、343个属的细菌组成,表现出群落组成的丰富性.细菌群落分析表明香根草和芦苇细菌群落结构较为相似,但和杜梨细菌群落结构差异最大.PICRUSt功能预测分析表明,库滨带植物根际细菌主要涉及次生产物代谢的生物合成、转录、多糖生物合成和代谢、细胞生长和死亡等38个子功能,表现出功能上的丰富性.库滨带植物根际细菌代谢能力整体趋势为假奓包叶芦苇香根草杜梨.本研究初步探讨了丹江口库区库滨带不同植物根际细菌群落和功能,为丹江口水库库滨带植被构建及其水环境保护提供了参考依据.     

降解纤维素产甲烷的四菌复合系

自然环境中通常是微生物群落协同完成纤维素的降解,构建可降解纤维素的混菌体系是认识微生物相互作用的关键.利用富集培养法,结合变性梯度凝胶电泳(DGGE)指纹检测技术以及厌氧滚管技术,建立了一种筛选简单降解纤维素产甲烷复合菌系的方法.利用此方法从青藏高原若尔盖高寒湿地分离到一个由4株菌构成的降解纤维素产甲烷的稳定菌系.结果表明,该复合菌系由纤维素水解菌Clostridium glycolicum、非纤维素水解菌Trichococcus flocculiformis和Parabacteroides merdae、产甲烷古菌Methanobacterium subterraneum等具有不同功能的4种菌株组成,且在这4株菌的共同作用下可将纤维素直接转化为CH4.该简单复合系的获得为今后纤维素转化甲烷复合菌系的代谢控制和遗传改造提供了一个平台.     

New molecular method to detect denitrifying anaerobic methane oxidation bacteria from different environmental niches

The denitrifying anaerobic methane oxidation is an ecologically important process for reducing the potential methane emission into the atmosphere. The responsible bacterium for this process was Candidatus Methylomirabilis oxyfera belonging to the bacterial phylum of NC10. In this study, a new pair of primers targeting all the five groups of NC10 bacteria was designed to amplify NC10 bacteria from different environmental niches. The results showed that the group A was the dominant NC10 phylum bacteria from the sludges and food waste digestate while in paddy soil samples, group A and group B had nearly the same proportion. Our results also indicated that NC10 bacteria could exist in a high pH environment (pH 9.24) from the food waste treatment facility. The Pearson relationship analysis showed that the pH had a significant positive relationship with the NC10 bacterial diversity (p < 0.05). The redundancy analysis further revealed that the pH, volatile solid and nitrite nitrogen were the most important factors in shaping the NC10 bacterial structure (p = 0.01) based on the variation inflation factors selection and Monte Carlo test (999 times). Results of this study extended the existing molecular tools for studying the NC10 bacterial community structures and provided new information on the ecological distributions of NC10 bacteria.     

Achieving partial nitrification by inhibiting the activity of Nitrospira-like bacteria under high-DO conditions in an intermittent aeration reactor

It is generally accepted that a low dissolved oxygen(DO) concentration is more beneficial for achieving partial nitrification than high-DO. In this study, partial nitrification was not established under low-DO conditions in an intermittent aeration reactor for treating domestic wastewater. During the operational period of low-DO conditions(DO: 0.3 ±0.14 mg/L), stable complete nitrification was observed. The abundance of Nitrospira-like bacteria, which were the major nitrite-oxidizing bacteria, increased from 1.03 × 10~6to2.64 × 10~6cells/m L. At the end of the low-DO period, the batch tests showed that high-DO concentration(1.5, 2.0 mg/L) could inhibit nitrite oxidation, and enhance ammonia oxidation. After switching to the high-DO period(1.8 ± 0.32 mg/L), partial nitrification was gradually achieved. Nitrospira decreased from 2.64 × 10~6 to 8.85 × 10~5cells/m L. It was found that suddenly switching to a high-DO condition could inhibit the activity and abundance of Nitrospira-like bacteria, resulting in partial nitrification.     

北京市居家空气微生物污染特征

在北京市选取31户有1岁至10岁儿童的家庭进行空气微生物取样,系统研究了室内家庭空气微生物污染特征.结果表明,北京市居家环境空气微生物总浓度变化范围为269～13066 CFU·m-3,均值为2658 CFU· m-3,空气细菌浓度变化范围为47 ～ 12341 CFU·m-3,均值为1821 CFU·m-3,空气真菌浓度变化范围为62～3498 CFU·m-3,均值为837 CFU·m-3.空气细菌和真菌浓度百分比分别为61.0％和39.0％,细菌浓度明显高于真菌浓度.居家环境优势细菌属依次为微球菌属(Micrococcus)、芽孢杆菌属(Bacillus)、葡萄球菌属(Staphylococcus)和库克菌属(Kocuria),4属细菌百分比约占63.1％ ～70.9％,优势真菌属为青霉属(Penicillium)、枝孢属(Cladosporium)、曲霉属(Aspergillus)、链格孢属(Alternaria)和茎点霉属(Phoma),分别约占总数的36.0％、17.8％、9.3％、5.3％和3.6％.文中最后针对北京市居家环境空气微生物污染的现状及其来源,从宠物饲养、空调清理、室内外优良环境的保持及垃圾处理、室内花卉种植等方面提出了治理建议.