Culture-Independent Characterization of Archaeal Biodiversity in Swine Confinement Building Bioaerosols

It was previously demonstrated that microbial communities of pig manure were composed of both bacteria and archaea. Recent studies have shown that bacteria are aerosolized from pig manure, but none have ever focused on the airborne archaeal burden. We sought here to develop and apply molecular ecology approaches to thoroughly characterize airborne archaea from swine confinement buildings (SCBs). Eight swine operations were visited, twice in winter and once during summer. Institute of Occupational Medicine cassettes loaded with 25-mm gelatin filters were used to capture the inhalable microbial biomass. The total genomic DNA was extracted and used as a template for PCR amplification of the archaeal 16S rRNA gene. High concentrations of archaea were found in SCB bioaerosols, being as high as 10⁸ 16S rRNA gene copies per cubic meter of air. Construction and sequencing of 16S rRNA gene libraries revealed that all sequences were closely related to methanogenic archaea, such as Methanosphaera stadtmanae (94.7% of the archaeal biodiversity). Archaeal community profiles were compared by 16S rRNA gene denaturing gradient gel electrophoresis. This analysis showed similar fingerprints in each SCB and confirmed the predominance of methanogenic archaea in the bioaerosols. This study sheds new light on the nature of bioaerosols in SCBs and suggests that archaea are also aerosolized from pig manure.Over the last 30 years, swine production in Canada evolved from small family farms to industrial facilities. Pig producers have increased animal density, building mechanization, and confinement in order to decrease working and feeding time and to optimize space, leading to an increased contamination of air by bioaerosols.Even though the swine confinement building (SCB) environment has been studied for several years, little is known about the real concentration and nature of airborne microorganisms. Moreover, increasing confinement level in modern barns has raised bioaerosol levels, modifying the health risk of exposed workers. Thus far, using culture-dependent methods was the only strategy developed and used to describe SCB bioaerosol content and levels (6, 7). However, it is well known that culture-independent approaches are more likely to reveal the presence of microorganisms never suspected in most environments (2). In aerobiology, there are only a few reports using culture-independent methods (4, 15). Nehme et al. (20) applied molecular approaches to quantify and describe the bacterial aerosols in SCB and reported as much as 10⁸ bacteria per cubic meter of air, with significantly higher concentrations during winter, when the confinement is maximal. The data obtained were also compared to recent biodiversity studies of swine manures (13, 22, 25). Anaerobic gram-positive bacteria, being the greater part of the microbiological aerosols, appeared to originate from the swine manure. Those manure biodiversity studies revealed the presence of methanogenic archaea in hog wastes (22, 25). Since bacteria observed in the aerosols seem to originate from the manure, it is plausible that archaea from pig slurries are also aerosolized.We report here the characterization of the archaeal community of SCB bioaerosols by using cultivation-independent approaches. The phylogeny of airborne archaea was assessed using 16S rRNA gene sequences. Archaeal biodiversity profiles were determined with PCR-denaturing gradient gel electrophoresis (DGGE), and the concentration of aerosolized archaea was evaluated by real-time PCR by quantifying archaeal 16S rRNA gene copies in the air samples.     

The impact of zinc and lead concentrations and seasonal variation on bacterial and actinobacterial community structure in a metallophytic grassland soil

The diversity and structure of bacterial and actinobacteral diversity and communities were determined in a metallophytic grassland soil from an upland site in northern England. The community profiles were subjected to multivariate analyses using correspondence and cluster analyses. The total bacterial community diversities and structures were not significantly affected by Pb and Zn concentration in the soil. However, the community structure did show changes between winter and summer samples. Raup and Crick analysis indicated that deterministic selection lead to winter profiles exhibiting significant similarity. The actinobacterial community was also unaffected by Pb and Zn concentration. However, seasonal changes were apparent as diversity were significantly lower in winter compared to summer profiles. Moreover, the community structure showed evidence of changes of structure based on the seasonal samples with winter samples showing significant similarity to each other.     

武夷山常绿阔叶林土壤微生物多样性的季节动态

为了解武夷山自然保护区常绿阔叶林土壤微生物群落特征和季节变化,采用Illumina Miseq高通量测序技术分析了土壤微生物多样性的季节响应。结果表明,武夷山常绿阔叶林土壤为典型的南方酸性土壤,有效钾、土壤温度四季内存在显著差异,其他理化指标均无显著差异。土壤中的微生物多样性比较丰富,已鉴定出23门206属细菌和2门17属的古菌。夏季反映细菌总数的Chao指数最高,但反映细菌多样性的Shannon指数比春季低0.21,夏季古菌的Chao指数和Shannon指数分别比冬季高21.7%和0.27%。4个季节共有的细菌和古菌分别占总数的83.1%和70.0%,说明武夷山常绿阔叶林土壤不同季节的核心微生物组成具有很好的稳定性。在门和属水平的聚类树分析表明,春季和冬季的细菌和古菌群落组成最为接近,而夏季与其他3个季节的差异最大。冗余分析和热图分析结果表明,土壤p H是决定和影响细菌和古菌多样性的主要环境因子,有效钾、有效碳和总氮对微生物群落组成均有很大的影响。因此,随季节变化武夷山常绿阔叶林土壤微生物多样性呈现出规律性变化。     

Annual dynamics of bacterioplankton assemblages in the Gulf of Trieste (Northern Adriatic Sea)

Bacterioplankton community diversity was investigated monthly in coastal waters of the Gulf of Trieste (NE Adriatic Sea) throughout 2003. Superficial bacterial assemblages of two differently freshwater influenced stations were studied using PCR-DGGE fingerprinting techniques. Bacterial genetic diversity of the sampled area, as estimates of the number of DGGE bands was high (36-64) compared to that reported in other studies employing this fingerprint technique. The similarity index (Sorensen Index) between assemblages showed a defined operational taxonomic units (OTUs) succession pattern in the more typically marine station with stable winter communities and quickly changing summer ones. On the contrary in the station affected by riverine inputs no clear pattern was detected. In both sites, according to cluster analyses performed on the DGGE banding pattern, three seasonal assemblages were identified: winter-spring, summer and fall. Sequence analysis of fifty-six among the brightest gel bands led to the observation of bacteria affiliated to Gram positive, Cyanobacteria, Cytophaga-Flavobacteria-Bacteroides (CFB) lineages and the alpha-, gamma- and delta- subdivisions of the Proteobacteria. Gamma-Proteobacteria constituted the main fraction (60%) of sequences in the more typically marine station, whereas the river-influenced station was characterised by more heterogeneous assemblages (39% alpha-Proteobacteria, 32% Flavobacteria).     

Seasonal changes in an alpine soil bacterial community in the colorado rocky mountains

The period when the snowpack melts in late spring is a dynamic time for alpine ecosystems. The large winter microbial community begins to turn over rapidly, releasing nutrients to plants. Past studies have shown that the soil microbial community in alpine dry meadows of the Colorado Rocky Mountains changes in biomass, function, broad-level structure, and fungal diversity between winter and early summer. However, little specific information exists on the diversity of the alpine bacterial community or how it changes during this ecologically important period. We constructed clone libraries of 16S ribosomal DNA from alpine soil collected in winter, spring, and summer. We also cultivated bacteria from the alpine soil and measured the seasonal abundance of selected cultured isolates in hybridization experiments. The uncultured bacterial communities changed between seasons in diversity and abundance within taxa. The Acidobacterium division was most abundant in the spring. The winter community had the highest proportion of Actinobacteria and members of the Cytophaga/Flexibacter/Bacteroides (CFB) division. The summer community had the highest proportion of the Verrucomicrobium division and of beta-PROTEOBACTERIA: As a whole, alpha-Proteobacteria were equally abundant in all seasons, although seasonal changes may have occurred within this group. A number of sequences from currently uncultivated divisions were found, including two novel candidate divisions. The cultured isolates belonged to the alpha-, beta-, and gamma-Proteobacteria, the Actinobacteria, and the CFB groups. The only uncultured sequences that were closely related to the isolates were from winter and spring libraries. Hybridization experiments showed that actinobacterial and beta-proteobacterial isolates were most abundant during winter, while the alpha- and gamma-proteobacterial isolates tested did not vary significantly. While the cultures and clone libraries produced generally distinct groups of organisms, the two approaches gave consistent accounts of seasonal changes in microbial diversity.     

Effect of the concentration of suspended solids on the enzymatic activities and biodiversity of a submerged membrane bioreactor for aerobic treatment of domestic wastewater

A pilot-scale submerged membrane bioreactor was used for the treatment of domestic wastewater in order to study the influence of the variations in the concentration of volatile suspended solids (VSS) on the enzymatic activities (acid and alkaline phosphatases, glucosidase, protease, esterase, and dehydrogenase) and biodiversity of the bacterial community in the sludge. The influence of VSS concentration was evaluated in two separated experiments, which were carried out in two different seasons of the year (experiment 1 through spring–summer and experiment 2 through autumn–winter). Cluster analysis of the temperature gradient gel electrophoresis (TGGE) profiles demonstrated that the community composition was significantly different in both experiments. Within the same experiment, the bacterial community experienced sequential shifts as the biomass accumulated, as shown by the evolution of the population profiles through time as VSS concentration increased. All enzymatic activities studied were significantly lower during experiment 2, except for glucosidase. Concentrations of VSS over 8 g/l induced a strong descent of all enzymatic activities, which overlapped with a significant modification of the community composition. Sequences of the major TGGE bands were identified as representatives of the Alpha-proteobacteria, filamentous bacteria (Thiotrix), and nitrite oxidizers (Nitrospira). Some sequences which were poorly related to any validated bacterial taxon were obtained.     

Investigation of methanogen population structure in biogas reactor by molecular characterization of methyl-coenzyme M reductase A (mcrA) genes

The methanogen community in biogas reactor running on cattle dung was investigated in two different seasons; summer (April, 36 °C) and winter (December, 24 °C), in the year 2004 by a culture-independent approach. Community structure was determined by phylogenetic analyses of 343 and 278 mcrA clones belonging to summer and winter month libraries, respectively. In summer month’s library, 41.7% clones were affiliated to Methanomicrobiales, 30% to Methanosarcinales, 19% to Methanobacteriales, 5% to Methanococcales and a total of 4.3% clones belonged to unclassified euryarchaeotal lineages. In winter month’s library, Methanomicrobiales encompassed 98.6% clones, and Methanobacteriales included 1.4% of total clone diversity. Biogas plant performance data collected during the winter month indicated significant reduction in daily biogas produced as compared to summer month because of lowering in ambient temperature and associated shift in microbial community. Results from this molecular study showed the existence of highly diverse and complex methanogens communities present in biogas plant.     

基于高通量测序的缢蛏及其养殖池塘菌群结构的季节变化

为探究缢蛏养殖过程中养殖环境和缢蛏体内的细菌群落结构季节变化特征及其与环境因子的相关性,采用高通量测序技术对缢蛏养殖池塘的水体、沉积物及缢蛏内脏团细菌菌群进行了研究.结果表明: 水体中冬季的细菌菌群结构与其他3季差异显著,沉积物和缢蛏内脏团4季的细菌菌群结构均无显著差异.水体各季节细菌群落的Shannon多样性指数无明显差异,沉积物及缢蛏内脏团细菌群落Shannon多样性指数夏季最低,冬季最高.门水平上,蓝细菌门、变形菌门和拟杆菌门为水体的优势菌群;变形菌门、绿弯菌门和拟杆菌门为沉积物的优势菌群;柔膜菌门和变形菌门为缢蛏内脏团的优势菌群.属水平上,水体冬季的优势菌属为NS3a_marine_group,而其余3季为聚球藻属;沉积物优势菌属为厌氧绳菌科下的一类菌属norank_f_Anaerolineacea和硝化螺旋菌属;内脏团优势菌属为支原体属和弓形菌属.环境因子与菌群的相关性分析表明: 水体的优势菌属聚球藻属与水温、化学需氧量(COD)、PO₄^--P、NH₄⁺-N、pH和透明度呈正相关;沉积物的优势菌属厌氧绳菌科菌属norank_f_Anaerolineacea与COD、水温、总磷呈正相关;缢蛏内脏团的优势菌属支原体属与水温、pH、NH₄⁺-N、PO₄^--P和透明度呈正相关.这表明不同季节的缢蛏养殖池塘及缢蛏体内细菌群落结构及多样性差异较大,水体细菌菌群受养殖环境的影响明显,尤其是水温及氮磷含量.     

Erratum to Bacterial diversity in toxic<Emphasis Type="Italic"> Alexandrium tamarense</Emphasis> blooms off the Orkney Isles and the Firth of Forth

The genetic diversity of the bacterial community associated with Alexandrium tamarense blooms was studied in blooms of the toxic dinoflagellates in the waters around the Orkney Isles and the Firth of Forth (Scotland). For toxin and molecular analysis of the bacterial communities associated with the toxic bloom, water samples were taken in 1998 and 1999 from A. tamarense blooms. The bacterial community structure, as determined by DGGE (denaturing gradient gel electrophoresis) showed clear differences between all three investigated size fractions (dinoflagellate-associated bacteria, attached bacteria and free-living bacteria), with high diversity within each sample. DNA sequence analysis of the dominant and most frequent DGGE bands revealed the dominance of α Proteobacteria, mainly of the Roseobacter clade, with similarities of 91–99%. Moreover, DGGE bands occurring at the same position in the gel throughout in most samples corroborate the presence of several specific α Proteobacteria of the Roseobacter clade. Overall, 500 bacteria were isolated from the bloom and partly phylogenetically analysed. They were members of two prokaryotic phyla, the Proteobacteria and the Bacteroidetes, related to Proteobacteria of the α and γ subdivisions (Alteromonas, Pseudoalteromonas and Colwellia). All bacteria were tested for the production of sodium channel blocking (SCB) toxins using mouse neuroblastoma assay. No production of SCB toxins was found and high performance liquid chromatography (HPLC) analysis confirmed these results. The content of total paralytic shellfish poisoning (PSP) toxin in the water samples, as measured within the toxic dinoflagellate blooms using HPLC, ranged from 53 to 2191 ng PSP l^?1 in 1998 and from 0 to 478 ng PSP l^?1 in 1999. Changes in PSP toxin content were not accompanied by changes of DGGE band patterns. We therefore presume that the bacterial groups identified in this study were not exclusively associated with toxic A. tamarense, but were generally associated with the phytoplankton.     

Seasonality in bacterial diversity in north-west Mediterranean coastal waters: assessment through clone libraries, fingerprinting and FISH

We combined denaturing gradient gel electrophoresis (DGGE), catalysed reporter deposition-FISH (CARD-FISH) and clone libraries to investigate the seasonality of the bacterial assemblage composition in north-west Mediterranean coastal waters. DGGE analysis indicated that bacterial diversity changed gradually throughout the year, although with a clear distinction of the summer period. Alphaproteobacteria were the dominant group on an annual basis [29% of the DAPI (4',6-diamidino-2-phenylindole) counts by CARD-FISH, and 70% of the bacterial clones]. The SAR11 clade was most abundant during spring and summer (>20% of DAPI counts), while the Roseobacter clade was abundant primarily in winter and spring (up to 7% of DAPI counts). The phylum Bacteroidetes constituted the second most important group and was quantitatively uniform throughout the year (average 11% of the DAPI counts). Gammaproteobacteria showed a peak during summer (8% of DAPI counts), when most of them belonged to the NOR5 cluster. Clone libraries and CARD-FISH showed reasonable agreement in the quantitative proportions of Bacteroidetes and Gammaproteobacteria, but Alphaproteobacteria were overrepresented in clone libraries. Sequencing of the most predominant DGGE bands failed to detect the SAR11 group despite their high abundance. The combination of the three molecular approaches allowed a comprehensive assessment of seasonal changes in bacterial diversity.     

Analysis and comparison of the bacterial community in fermented grains during the fermentation for two different styles of Chinese liquor

Bacterial populations in fermented grains during fermentation may play important roles in Chinese liquor flavor. PCR-based denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene library analysis were performed to analyze the bacterial community structure of two styles of liquor. The results of DGGE profiles showed that bacterial diversity decreased with the fermentation process and Lactobacillus acetotolerans became the predominant species at the end of the fermentation. But the obvious differences of bacterial community appeared in the middle stage of two styles of liquor fermentation, in which the different upstream production techniques were used. Moreover, 16S rRNA gene libraries of two styles were constructed. A total of 125 and 107 clones, chosen from two libraries, were grouped into 46 and 49 operational taxonomic units (OTUs) by amplified ribosomal DNA restriction analysis. According to sequencing results of clones, the predominant bacteria in strong aroma style fermented grains were those from the class Bacilli, Bacteroidetes, and Clostridia, whereas the predominant bacteria in fermented grains of roasted sesame aroma style belonged to Bacilli, Flavobacteria, and Gammaproteobacteria. Molecular analysis of the bacterial diversity of the liquor fermentation will benefit the analysis of important microorganisms playing key roles in the formation of liquor flavor components.     

腾格里沙漠东南缘不同生物土壤结皮细菌多样性及其季节动态特征

微生物多样性对于生物土壤结皮在沙漠生态系统中改善局部环境以及提升生态功能具有重要作用。本研究对腾格里沙漠东南缘沙坡头地区藻结皮、藓结皮及其下层的四季样品进行了16S rDNA高通量测序, 以期阐明细菌多样性及其在生物土壤结皮演替过程中的季节变化规律。结果表明4种类型样品的细菌丰富度在夏季显著低于其他3个季节。4种类型样品中主要的细菌类群为变形菌门、放线菌门、绿弯菌门、酸杆菌门、蓝细菌门等, 其中变形菌门和放线菌门为优势类群, 夏季时变形菌门的相对多度显著高于春季、秋季、冬季, 且在结皮层中相对多度显著高于结皮下层。放线菌门的相对多度在春季、夏季显著高于秋季、冬季, 且结皮下层相对多度高于结皮层。生物土壤结皮演替过程中细菌多样性及其相对多度季节动态变化表明其对沙漠土壤局部环境的变化作出了响应, 这为深入理解生物土壤结皮在沙漠生态系统中的生态功能提供了微生物多样性数据。     

Seasonal Changes in an Alpine Soil Bacterial Community in the Colorado Rocky Mountains

The period when the snowpack melts in late spring is a dynamic time for alpine ecosystems. The large winter microbial community begins to turn over rapidly, releasing nutrients to plants. Past studies have shown that the soil microbial community in alpine dry meadows of the Colorado Rocky Mountains changes in biomass, function, broad-level structure, and fungal diversity between winter and early summer. However, little specific information exists on the diversity of the alpine bacterial community or how it changes during this ecologically important period. We constructed clone libraries of 16S ribosomal DNA from alpine soil collected in winter, spring, and summer. We also cultivated bacteria from the alpine soil and measured the seasonal abundance of selected cultured isolates in hybridization experiments. The uncultured bacterial communities changed between seasons in diversity and abundance within taxa. The Acidobacterium division was most abundant in the spring. The winter community had the highest proportion of Actinobacteria and members of the Cytophaga/Flexibacter/Bacteroides (CFB) division. The summer community had the highest proportion of the Verrucomicrobium division and of β-Proteobacteria. As a whole, α-Proteobacteria were equally abundant in all seasons, although seasonal changes may have occurred within this group. A number of sequences from currently uncultivated divisions were found, including two novel candidate divisions. The cultured isolates belonged to the α-, β-, and γ-Proteobacteria, the Actinobacteria, and the CFB groups. The only uncultured sequences that were closely related to the isolates were from winter and spring libraries. Hybridization experiments showed that actinobacterial and β-proteobacterial isolates were most abundant during winter, while the α- and γ-proteobacterial isolates tested did not vary significantly. While the cultures and clone libraries produced generally distinct groups of organisms, the two approaches gave consistent accounts of seasonal changes in microbial diversity.     

不同季节使用微生态制剂后养殖海水细菌群落特征

细菌是维持养殖水体稳定的重要类群,可以反映出水质情况,微生态制剂作为一种可以去除有害物质的生物方法,目前被广泛应用。了解微生态制剂在投入养殖海水后细菌群落结构和多样性变化,探讨不同季节的水质环境因子对细菌群落的影响。通过高通量测序技术对细菌16S rRNA V3、V4区进行扩增,分析冬、春、夏3个季节下使用完商品型菌剂后,养殖海水中细菌群落分布规律及其多样性,采用冗余分析(Redundancy analysis,RDA)探讨不同季节的水质指标与细菌群落之间的关系。养殖海水中细菌多样性丰富,3个季节主要的优势菌门为变形菌门和拟杆菌门,其中Tenacibaculum(38.28%),卓贝尔氏菌属(Zobellella,30.78%)、盐单胞菌属(Halomonas,13.55%)为冬季优势属;Glycocaulis(34.00%)、盐单胞菌属(11.36%)、Planktosalinus(9.67%)为春季优势属;Pseudofulvimonas(28.94%)、Zobellella(17.51%)、Planktosalinus(15.86%)、海杆菌属(Marinobacter,12.30%)为夏季优势属,不同时期细菌属水平发生显著变化。RDA分析表明,不同时期水质环境因子对细菌群落影响不同,温度、盐度、pH、溶解氧与3个季节中10个优势属的丰度有显著相关性,冬季和春季优势属主要与盐度和溶解氧呈正相关,夏季优势属主要与温度和p H呈显著正相关。微生态制剂在净化养殖水体方面有很大优势,其在不同季节中应用虽细菌群落结构和多样性产生一定变化,但整体都发挥出各自的调控能力,该研究为以后养殖海水治理和微生态制剂应用提供新的思路。     

Denaturing gradient gel electrophoresis analysis of bacterial populations in 5-stage biological nutrient removal process with step feed system for wastewater treatment

Changes in the bacterial populations of a 5-stage biological nutrient removal (BNR) process, with a step feed system for wastewater treatment, were monitored by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S ribosomal DNA fragments. DGGE analysis indicated seasonal community changes were observed, however, community profiles of the total bacteria of each reactor showed only minor differences in the samples obtained from the same season. The number of major bands was higher in the summer samples, and decreased during the winter period, indicating that the microbial community structure became simpler at low temperatures. Since the nitrogen and phosphate removal efficiencies were highly maintained throughout the winter operation period, the bacteria which still remaining in the winter sample can be considered important, playing a key role in the present 5-stage BNR sludge. The prominent DGGE bands were excised, and sequenced to gain insight into the identities of the predominant bacterial populations present, and most were found to not be closely related to previously characterized bacteria. These data suggest the importance of culture-independent methods for the quality control of wastewater treatment.     

Influence of meteorological factors on the level and characteristics of culturable bacteria in the air in Gliwice,Upper Silesia (Poland)

Numerous studies have focused on occupational and indoor environments because people spend more than 90% of their time in them. Nevertheless, air is the main source of bacteria in indoors, and outdoor exposure is also crucial. Worldwide studies have indicated that bacterial concentrations vary among different types of outdoor environments, with considerable seasonal variations as well. Conducting comprehensive monitoring of atmospheric aerosol concentrations is very important not only for environmental management but also for the assessment of the health impacts of air pollution. To our knowledge, this is the first study to present outdoor and seasonal changes of bioaerosol data regarding an urban area of Poland. This study aimed to characterize culturable bacteria populations present in outdoor air in Gliwice, Upper Silesia Region, Poland, over the course of four seasons (spring, summer, autumn and winter) through quantification and identification procedures. In this study, the samples of bioaerosol were collected using a six-stage Andersen cascade impactor (with aerodynamic cut-off diameters of 7.0, 4.7, 3.3, 2.1, 1.1 and 0.65 μm). Results showed that the concentration of airborne bacteria ranged from 4 CFU m^?3, measured on one winter day, to a maximum equal to 669 CFU m^?3 on a spring day. The average size of culturable bacterial aerosol over the study period was 199 CFU m^?3. The maximal seasonally averaged concentration was found in the spring season and reached 306 CFU m^?3, and the minimal seasonally averaged concentration was found in the winter 49 CFU m^?3. The most prevalent bacteria found outdoors were gram-positive rods that form endospores. Statistically, the most important meteorological factors related to the viability of airborne bacteria were temperature and UV radiation. These results may contribute to the promotion and implementation of preventative public health programmes and the formulation of recommendations aimed at providing healthier outdoor environments.     

Contrasting bacterioplankton community composition and seasonal dynamics in two neighbouring hypertrophic freshwater lakes

We characterized the bacterioplankton community and its seasonal dynamics in two neighbouring hypertrophic lakes by denaturing gradient gel electrophoresis (DGGE) analysis of short (193 bp) 16S ribosomal DNA polymerase chain reaction (PCR) products obtained with primers specific for the domain Bacteria. Lake Blankaart is turbid and has a high phytoplankton biomass and episodic cyanobacterial blooms, whereas biomanipulated Lake Visvijver is characterized by clearwater conditions and the establishment of a dense charophyte vegetation. Both lakes were dominated by bacterial groups commonly found in freshwater habitats (e.g. ACK4 cluster of Actinomycetes; ACK stands for clones isolated from the Adirondack mountain lakes) . Yet, cluster analysis and principal components analysis (PCA) revealed that taxon composition of the bacterioplankton community of the two lakes differs substantially and consistently throughout the season. During the study year (1998), the bacterioplankton community of both lakes showed a distinct seasonal pattern. Lake Blankaart showed a clear differentiation between winter, spring, summer and autumn. In Lake Visvijver, summer samples differed greatly from spring, autumn and winter samples. We hypothesize that the contrasting bacterioplankton in the two neighbouring shallow lakes is determined largely by the presence or absence of macrophytes.     

Changes in bacterial communities from swine feces during continuous culture with starch

Bacteria from swine feces were grown in continuous culture with starch as the sole carbohydrate in order to monitor changes during fermentation and to determine how similar fermenter communities were to each other. DNA extracted from fermenter samples was analyzed by denaturing gradient gel electrophoresis (DGGE). A significant decrease in diversity was observed, the Shannon–Weaver index dropped from 1.92 to 1.13 after 14 days of fermentation. Likewise, similarity of fermenter communities to those in the fecal inoculum also decreased over time. Both diversity and similarity to the inoculum decreased most rapidly in the first few days of fermentation, reflecting a period of adaptation. Sequencing of DGGE bands indicated that the same species were present in replicate fermenters. Most of these bacteria were placed in the Clostridium coccoides/Eubacterium rectale group (likely saccharolytic butyrate producers), a dominant bacterial group in the intestinal tract of pigs. DGGE proved useful to monitor swine fecal communities in vitro and indicated the selection and maintenance of native swine intestinal bacteria during continuous culture.     

新疆博州地区三民族儿童口腔优势菌群结构

目的研究新疆博州地区汉族、维吾尔族和蒙古族3～5岁儿童的口腔唾液细菌优势菌群结构多样性的差异,并探讨与低龄儿童龋发生的相关性。方法从本课题组在新疆博州地区3～5岁儿童口腔流行病学调查时建立的资料样本库中选取唾液样本120例(汉族40例,维吾尔族40例,蒙古族40例)作为研究对象,其中每个民族中高龋组(ECC)各20例,无龋组(CF)各20例,取非刺激性唾液,提取细菌DNA后进行聚合酶链反应(PCR)扩增和变性梯度凝胶电泳(DGGE)分析,采用Quantity One软件对PCR-DGGE指纹图谱进行数据分析。结果 DGGE总体图谱表明:口腔微生物菌群结构具有民族差异性和个体差异性;维吾尔族总的条带数和多样性指数(条带数:87.00±10.40,多样性指数:5.99±1.12)大于汉族(条带数:63.00±8.07,多样性指数:3.29±0.74)和蒙古族(条带数:71.60±5.79,多样性指数:4.98±0.50)(P0.05),高龋儿童组的细菌菌群结构多样性小于无龋儿童组(P0.05),无龋儿童组的细菌菌群结构多样性存在民族差异(P0.05);聚类分析发现:每个民族组内大部分样本均表现出明显的聚类群。结论博州地区儿童口腔唾液细优势菌群结构多样性在民族之间差异明显,在低龄儿童龋病进展中,细菌多样性逐渐减少。