Cyanophage Diversity, Inferred from g20 Gene Analyses, in the Largest Natural Lake in France, Lake Bourget

The genetic diversity of the natural freshwater community of cyanophages and its variations over time have been investigated for the first time in the surface waters of the largest natural lake in France. This was done by random screening of clone libraries for the g20 gene and by denaturing gradient gel electrophoresis (DGGE). Nucleotide sequence analysis revealed 35 distinct cyanomyovirus g20 genotypes among the 47 sequences analyzed. Phylogenetic analyses showed that these sequences fell into seven genetically distinct operational taxonomic units (OTUs). The distances between these OTUs were comparable to those reported between marine clusters. Moreover, some of these freshwater cyanophage sequences were genetically more closely related to marine cyanophage sequences than to other freshwater sequences. Both approaches for the g20 gene (sequencing and DGGE analysis) showed that there was a clear seasonal pattern of variation in the composition of the cyanophage community that could reflect changes in its biological, chemical, and/or physical environment.     

Microbial Community Structure and Dynamics of Dark Fire-Cured Tobacco Fermentation

The Italian Toscano cigar production includes a fermentation step that starts when dark fire-cured tobacco leaves are moistened and mixed with ca. 20% prefermented tobacco to form a 500-kg bulk. The dynamics of the process, lasting ca. 18 days, has never been investigated in detail, and limited information is available on microbiota involved. Here we show that Toscano fermentation is invariably associated with the following: (i) an increase in temperature, pH, and total microbial population; (ii) a decrease in reducing sugars, citric and malic acids, and nitrate content; and (iii) an increase in oxalic acid, nitrite, and tobacco-specific nitrosamine content. The microbial community structure and dynamics were investigated by culture-based and culture-independent approaches, including denaturing gradient gel electrophoresis and single-strand conformational polymorphism. Results demonstrate that fermentation is assisted by a complex microbial community, changing in structure and composition during the process. During the early phase, the moderately acidic and mesophilic environment supports the rapid growth of a yeast population predominated by Debaryomyces hansenii. At this stage, Staphylococcaceae (Jeotgalicoccus and Staphylococcus) and Lactobacillales (Aerococcus, Lactobacillus, and Weissella) are the most commonly detected bacteria. When temperature and pH increase, endospore-forming low-G+C content gram-positive bacilli (Bacillus spp.) become evident. This leads to a further pH increase and promotes growth of moderately halotolerant and alkaliphilic Actinomycetales (Corynebacterium and Yania) during the late phase. To postulate a functional role for individual microbial species assisting the fermentation process, a preliminary physiological and biochemical characterization of representative isolates was performed.     

Biodiversity and Activity of the Microbial Community in the Kotelnikovsky Hot Springs (Lake Baikal)

Complex microbiological and chemical analyses of water and bacterial mats were performed in the Kotelnikovsky Hot Springs (Lake Baikal). Transmission electron microscopy demonstrated that short rods about 1.2–2 μm in diameter predominated in the natural microbial community. Scanning electron microscopy coupled with chemical analysis revealed a characteristic P peak in the bacteria-like mineral particles, which suggests their biogenic origin. Most strains of the thermophilic microorganisms were gram-positive spore-forming rods and can be assigned to the genus Bacillus. Assays for potential enzyme activity demonstrated that most of the strains tested were active at high temperature. The data obtained suggest high activity of the bacterial community in situ and its particular role in the functioning of the hydrothermal ecosystem. __________ Translated from Izvestiya Akademii Nauk, Seriya Biologicheskaya, No. 6, 2005, pp. 664–671. Original Russian Text Copyright ? 2005 by Bel'kova, Parfenova, Suslova, Ahn, Tazaki.     

Sediment Microbial Community Structure and Mercury Methylation in Mercury-Polluted Clear Lake, California

Spatial and temporal variations in sediment microbial community structure in a eutrophic lake polluted with inorganic mercury were identified using polar lipid fatty acid (PLFA) analysis. Microbial community structure was strongly related to mercury methylation potential, sediment organic carbon content, and lake location. Pore water sulfate, total mercury concentrations, and organic matter C/N ratios showed no relationships with microbial community structure. Seasonal changes and changes potentially attributable to temperature regulation of bacterial membranes were detectable but were less important influences on sediment PLFA composition than were differences due to lake sampling location. Analysis of biomarker PLFAs characteristic of Desulfobacter and Desulfovibrio groups of sulfate-reducing bacteria suggests that Desulfobacter-like organisms are important mercury methylators in the sediments, especially in the Lower Arm of Clear Lake.     

Survey of (Meta)genomic Approaches for Understanding Microbial Community Dynamics

Advancement in the next generation sequencing technologies has led to evolution of the field of genomics and metagenomics in a slim duration with nominal cost at precipitous higher rate. While metagenomics and genomics can be separately used to reveal the culture-independent and culture-based microbial evolution, respectively, (meta)genomics together can be used to demonstrate results at population level revealing in-depth complex community interactions for specific ecotypes. The field of metagenomics which started with answering “who is out there?” based on 16S rRNA gene has evolved immensely with the precise organismal reconstruction at species/strain level from the deeply covered metagenome data outweighing the need to isolate bacteria of which 99% are de facto non-cultivable. In this review we have underlined the appeal of metagenomic-derived genomes in providing insights into the evolutionary patterns, growth dynamics, genome/gene-specific sweeps, and durability of environmental pressures. We have demonstrated the use of culture-based genomics and environmental shotgun metagenome data together to elucidate environment specific genome modulations via metagenomic recruitments in terms of gene loss/gain, accessory and core-genome extent. We further illustrated the benefit of (meta)genomics in the understanding of infectious diseases by deducing the relationship between human microbiota and clinical microbiology. This review summarizes the technological advances in the (meta)genomic strategies using the genome and metagenome datasets together to increase the resolution of microbial population studies.     

Estimates of protozoan- and viral-mediated mortality of bacterioplankton in Lake Bourget (France)

1. We performed three, 1‐week in situ experiments in March‐April (expt 1), May (expt 2) and August (expt 3) 2003 in order to assess protozoan and virus‐induced mortality of heterotrophic bacteria in a French lake. Viral and bacterial abundances were obtained using flow cytometry (FCM) while protozoa were counted using epifluorescence microscopy (EFM). 2. A dilution approach, applied to pretreated grazer‐free samples, allowed us to estimate that viral lysis could be responsible for 60% (expt 1), 35% (expt 2) and 52% (expt 3) of daily heterotrophic bacterial mortality. Flagellate (both mixotrophic and heterotrophic) grazing in untreated samples, was responsible for 56% (expt 1), 63% (expt 2) and 18% (expt 3) of daily heterotrophic bacteria removal. 3. These results therefore suggest that both viral lysis and flagellate grazing had a strong impact on bacterial mortality, and this impact varied seasonally. 4. From parallel transmission electron microscopy (TEM) analysis, we found that the burst size (i.e. the number of viruses potentially released per lysed cell) ranged from nine to 25 (expt 1), 10 to 35 (expt 2) and eight to 25 (expt 3). The percentage of infected heterotrophic bacteria was 5.7% (expt 1), 3.4% (expt 2) and 5.7% (expt 3) so that the calculated percentage of bacterial mortality induced by viruses was 6.3% (expt 1), 3.7% (expt 2) and 6.3% (expt 3). 5. It is clear that the dilution‐FCM and TEM methods yielded different estimates of viral impact, although both methods revealed an increased impact of viruses during summer.     

单链构象多态性技术在微生物群落动态监测中的应用

详述了单链构象多态性技术实现的基本过程和关键步骤．以及在微生物群落结构和动态分析中的应用。还针对SSCP技术存在的问题,根据实践经验提出了一些改进建议,认为在进行复杂微生物群落分析时,应采用低pH值(pH77)的TBE电泳缓冲液,并以λ核酸外切酶将PER产物中的反意义链去掉,从而减少大量非特异的异源双链带的出现,提高技术的分辨率。采用淡技术能够很好地监测到群落中优势种群的动态变化,从而为工艺运行提供了可靠的依据。     

高矿浆浓度下黄铜矿浸出过程中微生物群落结构变化规律

目的：为阐明微生物群落演替及功能与浸出效率之间关系奠定基础,以及如何提高黄铜矿生物浸出效率和铜回收率提供理 论依据。方法：通过连续传代培养进行驯化,使得复合菌群的矿浆浓度耐受能力达到25 %（w/v）。采用该复合菌群在25 %矿浆浓 度下浸出黄铜矿,同时利用变性梯度凝胶电泳和克隆文库技术分析浸出过程中的微生物多样性。最后,采用实时荧光定量PCR 对 浸出过程中微生物群落结构进行定量解析。结果：28天内黄铜矿浸出率能够达到95.1 %,而驯化前的浸出率只有51.5%。该复合 菌群主要由Acidithiobacillus caldus, Sulfobacillus acidophilus,和Fereoplasma theroplasma thermophilum组成,其中Acidithbacillus caldus是浸出前期和后期的优势种群,而Sulfobacillus acidophilus在浸出中期均有竞争优势, Ferroplasma thermophilum在整个浸出过程中占 据整个群落的比例均较低。结论：本研究获得的复合菌群具有较强的浸出黄铜矿能力, Acidithiobacillus caldus和Sulfobacillus acidophilus在浸出过程中起着重要的作用,pH 值和铜浸出率与群落结构相关性较高。     

Seasonal Dynamics of Shallow-Hyporheic-Zone Microbial Community Structure along a Heavy-Metal Contamination Gradient

Heavy metals contaminate numerous freshwater streams and rivers worldwide. Previous work by this group demonstrated a relationship between the structure of hyporheic microbial communities and the fluvial deposition of heavy metals along a contamination gradient during the fall season. Seasonal variation has been documented in microbial communities in numerous terrestrial and aquatic environments, including the hyporheic zone. The current study was designed to assess whether relationships between hyporheic microbial community structure and heavy-metal contamination vary seasonally by monitoring community structure along a heavy-metal contamination gradient for more than a year. No relationship between total bacterial abundance and heavy metals was observed (R² = 0.02, P = 0.83). However, denaturing gradient gel electrophoresis pattern analysis indicated a strong and consistent linear relationship between the difference in microbial community composition (populations present) and the difference in the heavy metal content of hyporheic sediments throughout the year (R² = 0.58, P < 0.001). Correlations between heavy-metal contamination and the abundance of four specific phylogenetic groups (most closely related to the α, β, and γ-proteobacteria and cyanobacteria) were apparent only during the fall and early winter, when the majority of organic matter is deposited into regional streams. These seasonal data suggest that the abundance of susceptible populations responds to heavy metals primarily during seasons when the potential for growth is highest.     

海绵中可培养与原位微生物组成的DGGE指纹分析

采用不依赖于分离培养的PCR-DGGE基因指纹技术对我国南海4种海绵体内的原位微生物种群组成以及混合培养的海绵微生物组成进行分析,通过比较不同指纹图间的差异与相似性,揭示可培养微生物与海绵原位存在的微生物的关系。由实验可以看出,来自同一海域的不同海绵体内的微生物存在宿主特异性,不同的培养条件是影响微生物可培养的重要因素,目前所能培养的海绵微生物还仅占自然环境下海绵微生物总量的很少一部分。     

The Structure of Microbial Community and Degradation of Diatoms in the Deep Near-Bottom Layer of Lake Baikal

Insight into the role of bacteria in degradation of diatoms is important for understanding the factors and components of silica turnover in aquatic ecosystems. Using microscopic methods, it has been shown that the degree of diatom preservation and the numbers of diatom-associated bacteria in the surface layer of bottom sediments decrease with depth; in the near-bottom water layer, the majority of bacteria are associated with diatom cells, being located either on the cell surface or within the cell. The structure of microbial community in the near-bottom water layer has been characterized by pyrosequencing of the 16S rRNA gene, which has revealed 149 208 unique sequences. According to the results of metagenomic analysis, the community is dominated by representatives of Proteobacteria (41.9%), Actinobacteria (16%); then follow Acidobacteria (6.9%), Cyanobacteria (5%), Bacteroidetes (4.7%), Firmicutes (2.8%), Nitrospira (1.6%), and Verrucomicrobia (1%); other phylotypes account for less than 1% each. For 18.7% of the sequences, taxonomic identification has been possible only to the Bacteria domain level. Many bacteria identified to the genus level have close relatives occurring in other aquatic ecosystems and soils. The metagenome of the bacterial community from the near-bottom water layer also contains 16S rRNA gene sequences found in previously isolated bacterial strains possessing hydrolytic enzyme activity. These data show that potential degraders of diatoms occur among the vast variety of microorganisms in the near-bottom water of Lake Baikal.     

Bacterial Community of the Largest Oligosaline Lake,Namco on the Tibetan Plateau

Bacterial abundances and diversity in the surface water of Lake Namco, the largest oligosaline lake on the Tibetan Plateau, were examined using flow cytometry approach and constructing 16S rRNA gene clone libraries. Bacterial abundances were from 0.08 × 10⁶ to 1.6 × 10⁶ cells mL^?1, and were in the reported range of other lakes of the Tibetan Plateau and high mountain regions. Bacterial abundances were significantly correlated with the concentrations of chlorophyll a (chl a), but showed no significant relationship with the dissolved organic carbon (DOC), which suggested that the amount of DOC released by algae was the key factor determining the bacterial abundance rather than the total DOC. The total trace elements concentrations also obviously connected with bacterial abundances, and 9 of 20 elements showed significant relationship. Bacterial 16S rRNA gene clone sequences were affiliated to the α-, β-, γ-, δ-, and ?-Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, Acidobacteria, Planctomycetes, Verrucomicrobia, Candidate division OD1, or unclassified, and among these the β-Proteobacteria dominated. Bacteria in Lake Namco were most closely related to those retrieved from freshwater habitats. Relatively few sequences were closely related to those recovered from saline habitats. Eleven of 34 typical freshwater bacterial clusters were detected in the oligosaline Lake Namco. Bacterial diversity within the lake varied and was connected with the concentrations of DOC and chl a.     

Effects of Larval Mosquitoes (Aedes triseriatus) and Stemflow on Microbial Community Dynamics in Container Habitats

The dynamics of the microbial food sources for Aedes triseriatus larvae in microcosms were found to be strongly influenced by larval presence. The total abundance of bacteria in water samples generally increased in response to larvae, including populations of cultivable, facultatively anaerobic bacteria. Additionally, a portion of the community shifted from Pseudomonaceae to Enterobacteriaceae. Bacterial abundance on leaf material was significantly reduced in the presence of actively feeding larvae. Principle-component analysis of whole community fatty acid methyl ester (FAME) profiles showed that larvae changed the microbial community structure in both the water column and the leaf material. Cyclopropyl FAMEs, typically associated with bacteria, were reduced in microcosms containing larvae; however, other bacterial fatty acids showed no consistent response. Long-chain polyunsaturated fatty acids characteristic of microeukaryotes (protozoans and meiofauna) declined in abundance when larvae were present, indicating that larval feeding reduced the densities of these microorganisms. However, presumed fungal lipid markers either increased or were unchanged in response to larvae. Larval presence also affected microbial nitrogen metabolism through modification of the physiochemical conditions or by grazing on populations of bacteria involved in nitrification-denitrification. Stemflow primarily influenced inorganic ion and organic compound concentrations in the microcosms and had less-pronounced effects on microbial community parameters than did larval presence. Stemflow treatments diluted concentrations of all inorganic ions (chloride, sulfate, and ammonium) and organic compounds (total dissolved organic carbon, soluble carbohydrates, and total protein) measured, with the exceptions of nitrite and nitrate. Stemflow addition did not measurably affect larval biomass in the microcosms but did enhance development rates and early emergence patterns of adults.     

Viral abundance, production, decay rates and life strategies (lysogeny versus lysis) in Lake Bourget (France)

We have investigated the ecology of viruses in Lake Bourget (France) from January to August 2008. Data were analysed for viral and bacterial abundance and production, viral decay, frequency of lysogenic cells, the contribution of bacteriophages to prokaryotic mortality and their potential influence on nutrient dynamics. Analyses and experiments were conducted on samples from the epilimnion (2 m) and the hypolimnion (50 m), taken at the reference site of the lake. The abundance of virus‐like particles (VLP) varied from 3.4 × 10⁷ to 8.2 × 10⁷ VLP ml^?1; with the highest numbers and virus‐to‐bacterium ratio (VBR = 69) recorded in winter. Viral production varied from 3.2 × 10⁴ VLP ml^?1 h^?1 (July) to 2 × 10⁶ VLP ml^?1 h^?1 (February and April), and production was lower in the hypolimnion. Viral decay rate reached 0.12–0.15 day^?1, and this parameter varied greatly with sampling date and methodology (i.e. KCN versus filtration). Using transmission electron microscopy (TEM) analysis, viral lysis was responsible for 0% (January) to 71% (February) of bacterial mortality, while viral lysis varied between 0% (April) and 53% (January) per day when using a modified dilution approach. Calculated from viral production and burst size, the virus‐induced bacterial mortality varied between 0% (January) and 68% (August). A weak relationship was found between the two first methods (TEM versus dilution approach). Interestingly, flow cytometry analysis performed on the dilution experiment samples revealed that the viral impact was mostly on high DNA content bacterial cells whereas grazing, varying between 8.3% (June) and 75.4% (April), was reflected in both HDNA and LDNA cells equally. The lysogenic fraction varied between 0% (spring/summer) and 62% (winter) of total bacterial abundance, and increased slightly with increasing amounts of mitomycin C added. High percentages of lysogenic cells were recorded when bacterial abundance and activity were the lowest. The calculated release of carbon and phosphorus from viral lysis reached up to 56.5 µgC l^?1 day^?1 (assuming 20 fgC cell^?1) and 1.4 µgP l^?1 day^?1 (assuming 0.5 fgP cell^?1), respectively, which may represent a significant fraction of bacterioplankton nutrient demand. This study provides new evidence of the quantitative and functional importance of the virioplankton in the functioning of microbial food webs in peri‐alpine lakes. It also highlights methodologically dependent results.     

Cyanobacterial bloom termination: the disappearance of Planktothrix rubescens from Lake Bourget (France) after restoration

相似文献   

Meromixis and Seasonal Dynamics of Vertical Structure of Lake Uchum (South Siberia)

The seasonal dynamics of the vertical structure of small saline Lake Uchum, located in the steppe arid zone of the south of Siberia (Krasnoyarsk krai), has been studied in detail for the first time. This lake is a meromictic water body. We have revealed a heterogeneous vertical distribution of plankton organisms and a dense population of purple sulfuric bacteria in the redox zone. The taxonomic composition and seasonal dynamics of phyto- and zooplankton are described. Presumably, the meromixis of Lake Uchum is due to the inflow of fresh water to the surface of the saline water body during the rise of its level in the early 20th century, similarly to lakes Shira and Shunet located nearby. The processes of salt displacement into the solution during the formation of ice, as well as the precipitation of salts in the winter, also contribute to the maintenance of permanent stratification. The information on the current state of the lake can be useful for reconstructing the climate by bottom sediments, as well as for creating a model of water quality and investigating the therapeutic properties of lake mud.     

Abundance and Community Structure of Picoplankton and Protists in the Microbial Food Web of Barguzin Bay,Lake Baikal

We examined the vertical abundance of bacteria, phytoplankton and protists along a transect of six stations from near-shore (Stn. 1) to off-shore (Stn. 6) in Barguzin Bay of Lake Baikal, in the summer of 2002. Chlorophyll concentrations at Stn. 1 were higher (>10μg l⁻¹) than at the other five stations (<3μg l⁻¹). Planktonic and sessile diatoms dominated at Stn. 1, while pico-phytoplankon was dominant at other stations. Densities of heterotrophic bacteria were high in both the epilimnion and the thermocline at all stations. Nanoflagellates were abundant in the epilimnion, and ciliates in the thermocline, but no horizontal trend could be found for these heterotrophs. At Stn. 1, not only filter feeding (Strombidium and Strobilidium) and raptorial (Balanion) ciliates but also predatory ciliates (Prorodon and Spathidiosus) dominated, while at other stations only the filter feeding and raptorial ciliates were dominant. In off-shore stations (Stns. 5 and 6), significant correlations were detected between concentrations of chlorophyll a and density of filter feeding or raptorial ciliates, suggesting tight food linkages between phytoplankton and these ciliates. The concentration of dissolved organic carbon (DOC) was significantly correlated with chlorophyll a concentration, although there was no significant correlation between DOC concentration and bacterial density. We suggest that there is a shift of the dominant food linkage from a herbivorous food chain in near-shore areas to a microbial food web in off-shore areas in Barguzin Bay of Lake Baikal.     

Spatial variability in the abundance and composition of the free-living bacterioplankton community in the pelagic zone of Lake Bourget (France)

Spatial variations in the abundance and diversity of the free-living bacterioplankton community of a large Alpine lake, Lake Bourget (France), were investigated in the pelagic zone by means of two two-dimensional samplings taken in 2003. Lake-water samples were collected in winter during water mixing, and in early summer during stratification. The population abundance in each sample was determined by flow cytometry. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments from organisms measuring less than 2 mum was used to assess eubacterioplankton community composition. In winter, no obvious differences were observed in either the abundance or the diversity of the bacterial community, on either the horizontal or the vertical scales. The only influence detected was that of river water input, but this was at a very minor scale relative to the surface area of the lake. In early summer, changes were found in the community composition on the vertical scale related to the thermal stratification of the water column. There were also marked differences on the horizontal scale at 15 m depth due to internal waves. The implications of these findings for sampling strategies are very important from the perspective of comparative studies of free-living bacterial community diversity and functioning in large and deep lakes.     

Contribution of mathematical modeling to lake ecosystem understanding: Lake Bourget (Savoy,France)

This paper demonstrates how mathematical modeling can contribute to improve understanding of lake behavior. Since the 60's Lake Bourget, one of the largest in France, had been suffering from eutrophication which was checked in 1980 by the diversion of the main sewers entering the lake. A research program was implemented between 1987 and 1990, including an on-site sampling campaign conducted concurrently with thermal and biogeochemical modeling of lake behavior. The model helped provide a better understanding of the ecosystem, displaying some processes hitherto misunderstood: (1) Winter overturn does not reach the bottom of the water column when the weather is mild. This leads to a incomplete reoxygenation of the hypolimnion and to redox conditions inducing the release of orthophosphate from the sediment, (2) Grazing by herbivorous zooplankton is getting more important in the control of spring algal growth as eutrophication of the lake regresses, (3) Settling of particulate phosphorus seems a complex and very important process in Lake Bourget, showing high sedimentation rates for particulate mineral phosphorus.     

Metagenomic Characterisation of the Viral Community of Lough Neagh,the Largest Freshwater Lake in Ireland

Lough Neagh is the largest and the most economically important lake in Ireland. It is also one of the most nutrient rich amongst the world’s major lakes. In this study, 16S rRNA analysis of total metagenomic DNA from the water column of Lough Neagh has revealed a high proportion of Cyanobacteria and low levels of Actinobacteria, Acidobacteria, Chloroflexi, and Firmicutes. The planktonic virome of Lough Neagh has been sequenced and 2,298,791 2×300 bp Illumina reads analysed. Comparison with previously characterised lakes demonstrates that the Lough Neagh viral community has the highest level of sequence diversity. Only about 15% of reads had homologs in the RefSeq database and tailed bacteriophages (Caudovirales) were identified as a major grouping. Within the Caudovirales, the Podoviridae and Siphoviridae were the two most dominant families (34.3% and 32.8% of the reads with sequence homology to the RefSeq database), while ssDNA bacteriophages constituted less than 1% of the virome. Putative cyanophages were found to be abundant. 66,450 viral contigs were assembled with the largest one being 58,805 bp; its existence, and that of another 34,467 bp contig, in the water column was confirmed. Analysis of the contigs confirmed the high abundance of cyanophages in the water column.