Bacterial Community Structure in Patagonian Andean Lakes Above and Below Timberline: From Community Composition to Community Function

Lakes located above the timberline are remote systems with a number of extreme environmental conditions, becoming physically harsh ecosystems, and sensors of global change. We analyze bacterial community composition and community-level physiological profiles in mountain lakes located in an altitude gradient in North Patagonian Andes below and above the timberline, together with dissolved organic carbon (DOC) characterization and consumption. Our results indicated a decrease in 71 % of DOC and 65 % in total dissolved phosphorus (TDP) concentration as well as in bacteria abundances along the altitude range (1,380 to 1,950 m a.s.l.). Dissolved organic matter (DOM) fluorescence analysis revealed a low global variability composed by two humic-like components (allochthonous substances) and a single protein-like component (autochthonous substances). Lakes below the timberline showed the presence of all the three components, while lakes above the timberline the protein-like compound constituted the main DOC component. Furthermore, bacterial community composition similarity and ordination analysis showed that altitude and resource concentration (DOC and TDP) were the main variables determining the ordination of groups. Community-level physiological profiles showed a mismatch with bacteria community composition (BCC), indicating the absence of a relationship between genetic and functional diversity in the altitude gradient. However, carbon utilization efficiencies varied according to the presence of different compounds in DOM bulk. The obtained results suggest that the different bacterial communities in these mountain lakes seem to have similar metabolic pathways in order to be able to exploit the available DOC molecules.     

Vertical distribution of bacterial community structure in the sediments of two eutrophic lakes revealed by denaturing gradient gel electrophoresis (DGGE) and multivariate analysis techniques

Vertical distribution of bacterial community structure was investigated in the sediments of two eutrophic lakes of China, Lake Taihu and Lake Xuanwu. Profiles of bacterial communities were generated using a molecular fingerprinting technique, denaturing gradient gel electrophoresis (DGGE) followed by DNA sequence analysis, and the results were interpreted with multivariate statistical analysis. To assess changes in the genetic diversity of bacterial communities with changing depth, DGGE banding patterns were analysed by cluster analysis. Distinct clusters were recognized in different sampling stations of Lake Taihu. Canonical correspondence analysis (CCA) was carried out to infer the relationship between environmental variables and bacterial community structure. DGGE samples collected at the same sampling site clustered together in both lakes. Total phosphorus, organic matter and pH were considered to be the key factors driving the changes in bacterial community composition.     

The Modulating Role of Dissolved Organic Matter on Spatial Patterns of Microbial Metabolism in Lake Erie Sediments

To evaluate the role of dissolved organic matter (DOM) on microbial community metabolism, we established extracellular enzyme activity (EEA) and substrate-induced respiration (SIR) profiles of sediment samples collected from littoral and profundal regions of the western, central, and eastern basins of Lake Erie. Lake Erie is spatially structured such that the central and western basins receive relatively major inputs of allochthonous DOM in comparison to the eastern basin. Overall, spatial patterns of EEA and SIR profiles suggest both greater metabolic diversity and activity in the littoral regions of the central and western basins. In contrast, the eastern basin demonstrated much less structuring between littoral and profundal areas. To evaluate whether the observed spatial patterns are the result of microbial community adaptations to local DOM availability, we performed three experimental treatments by inoculating sediment samples with polyvinylpyrrolidone, which sequesters large polyphenols, or with either vanillin or catechol, two small phenolic compounds. Our results revealed that esterase and glycosidase EEA from the eastern basin were induced by small phenolics and inhibited by large polyphenols. In contrast, the addition of small phenolics decreased esterase and glycosidase activities from the central basin, while polyphenols had a negligible effect. These results suggest that the source and composition of DOM play a significant role in the local adaptation of microbial communities, determining large-scale spatial patterns of microbial functional diversity in Lake Erie sediments.     

Sediment Enzyme Activities and Microbial Community Diversity in an Oligotrophic Drinking Water Reservoir,Eastern China

Drinking water reservoir plays a vital role in the security of urban water supply, yet little is known about microbial community diversity harbored in the sediment of this oligotrophic freshwater environmental ecosystem. In the present study, integrating community level physiological profiles (CLPPs), nested polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) and clone sequence technologies, we examined the sediment urease and protease activities, bacterial community functional diversity, genetic diversity of bacterial and fungal communities in sediments from six sampling sites of Zhou cun drinking water reservoir, eastern China. The results showed that sediment urease activity was markedly distinct along the sites, ranged from 2.48 to 11.81 mg NH₃-N/(g·24h). The highest average well color development (AWCD) was found in site C, indicating the highest metabolic activity of heterotrophic bacterial community. Principal component analysis (PCA) revealed tremendous differences in the functional (metabolic) diversity patterns of the sediment bacterial communities from different sites. Meanwhile, DGGE fingerprints also indicated spatial changes of genetic diversity of sediment bacterial and fungal communities. The sequence BLAST analysis of all the sediment samples found that Comamonas sp. was the dominant bacterial species harbored in site A. Alternaria alternate, Allomyces macrogynus and Rhizophydium sp. were most commonly detected fungal species in sediments of the Zhou cun drinking water reservoir. The results from this work provide new insights about the heterogeneity of sediment microbial community metabolic activity and genetic diversity in the oligotrophic drinking water reservoir.     

Bacterial diversity and their metabolic profiles in the sedimentary environments of Ny-Ålesund,Arctic

Sedimentary environments in the Arctic are known to harbor diverse microbial communities playing a crucial role in the remineralization of organic matter and associated biogeochemical cycles. In this study, we used a combination of culture-dependent and culture-independent approaches to understanding the bacterial community composition associated with the sediments of a terrestrial versus fjord system in the Svalbard Arctic. Community-level metabolic profiling and growth response of retrieved bacterial isolates towards different carbon substrates at varying temperatures were also studied to assess the metabolic response of communities and isolates in the system. Bacterial species belonging to Cryobacterium and Psychrobacter dominated the terrestrial and fjord sediment retrievable fraction. Amplicon sequencing analysis revealed higher bacterial diversity in the terrestrial sediments (Shannon index; 8.135 and 7.935) as compared to the fjord sediments (4.5–5.37). Phylum Proteobacteria and Bacteroidetes dominated both terrestrial and fjord sediments. Phylum Verrucomicrobia and Cyanobacteria were abundant in terrestrial sediments while Epsilonbacteraeota and Fusobacteriia dominated the fjord sediments. Significant differences were observed in the carbon substrate utilization profiles between the terrestrial and fjord sediments at both 4 °C and 20 °C incubations (p?<?0.005). Utilization of N-acetyl-D-glucosamine, D-mannitol and Tween-80 by the sediment communities and bacterial isolates from both systems, irrespective of their temperature incubations implies the affinity of bacteria for such substrates as energy sources and for their survival in cold environments. Our results suggest the ability of sediment bacterial communities to adjust their substrate utilization profiles according to condition changes in the ecosystems and are found to be less influenced by their phylogenetic relatedness.

     

A Comparison of the Benthic Bacterial Communities Within and Surrounding <Emphasis Type="Italic">Dreissena</Emphasis> Clusters in Lakes

The impact of Dreissena (Dreissena polymorpha and D. bugensis) on the benthic bacterial community in lakes is largely unknown. Therefore, we quantified differences in the structure and activity of bacterial communities living in sediments (1) associated with Dreissena clusters, and (2) unassociated with established clusters (lake bottom sediments). Dreissena clusters and sediments were collected from locations in Lake Erie, Lake Ontario, and several inland lakes. Denaturing gradient gel electrophoresis (DGGE) analysis of the benthic bacterial community showed that the bacterial populations selected for by Dreissena represent a subset of the bottom communities and are geographically distinct. Community-level physiological profiling (CLPP) showed that overall bacterial activity and metabolic diversity were enhanced by the presence of clusters in all samples, with the exception of those harvested from the two Lake Erie sites. Therefore, Dreissena appears to affect both structure and metabolic function of the benthic bacterial community and may have yet unexplored ecosystem and food web consequences.     

环境因素对东平湖沉积物细菌群落结构的影响

【目的】探讨环境因素对东平湖沉积物细菌群落结构的影响。【方法】应用T-RFLP(Terminal RestrictionFragment Length Polymorphism)技术分析和比较了6个不同位置的东平湖沉积物在丰水期和枯水期的细菌多样性,并结合不同样品环境因子的差异,采用主成分分析(PCA)和典型对应分析(CCA),探讨了环境因子对细菌多样性的影响。【结果】不同沉积物样品的T-RFLP图谱具有较高的相似性。除2号样品外,所有枯水期样品的细菌群落具有较高的丰富度、多样性、均匀度和较低的优势度。CCA结果表明,558bp T-RF的丰度与总磷、总氮、总有机碳、铵态氮和硝态氮含量呈负相关而与碳氮比和水深呈正相关;64.5、164、509和543bp T-RFs的丰度与总氮、总有机碳、铵态氮、硝态氮、碳氮比和水深呈正相关;而其它14种主要的T-RFs在不同样品间分布较为稳定受环境因子影响不大。90、136.5、138和488bp等T-RFs可能代表了东平湖沉积物中占优势地位的土著菌群。通过Phylogenetic Assignment Tool在线分析结果推测,东平湖沉积物中的优势菌群可能属于Firmicutes和Proteobacteria门。【结论】环境因素对东平湖沉积物的细菌多样性产生显著影响,但对其土著菌群的影响不大。     

Functional Diversity of Bacterioplankton in Three North Florida Freshwater Lakes over an Annual Cycle

The phylogenetic diversity of freshwater bacterioplankton is widely known; however, there is minimal information on the functional diversity of the bacterial communities in these systems. Understanding the functional diversity of freshwater bacterial communities is important because heterotrophic bacteria can be impacted by anthropogenic perturbation, which in turn can alter biogeochemical cycling. The objective of this study was to use Biolog EcoPlates to acquire spatial and temporal community-level physiological profiles (CLPPs) for three freshwater lakes of different trophic levels and to assess the phylogenetic affiliation of the bacteria responsible for utilizing the various carbon guilds within them by denaturing gradient gel electrophoresis (DGGE). CLPP results showed that bacterial communities utilized the carbon guilds similarly between sites within the three lakes. However, when the metabolic profile of each lake was compared, Lake Bradford and Moore Lake were more similar to one another than to Lake Munson, the eutrophic lake. Additionally, although the bacteria that utilized the five carbon guilds included representatives from the classes α-, β-, γ-Proteobacteria, Flavobacteria and Sphingobacteria, Lake Munson had the largest number of Flavobacteria and γ-Proteobacteria in comparison to Moore Lake and Lake Bradford. Overall, Biolog analysis was useful in identifying differences in the functional diversity of bacterial communities between lakes of different trophic statuses and can be used as a tool to assess ecosystem health.     

Effect of humic material on the bacterioplankton community composition in boreal lakes and mesocosms

The bacterioplankton community composition in two Finnish forest lakes with different content of humic substances was studied by denaturing gradient gel electrophoresis (DGGE) and sequencing of the major bands. The same dominant bacterial phylotypes were detected in the bacterioplankton communities of clear-water Lake Ahvenlammi and humic Lake Sammalisto. For 4 years, in every water layer, Actinobacteria was the dominant and Verrucomicrobia the second most common phylum. In the hypolimnion, other dominant phyla were also found. We set up a mesocosm experiment to assess the effect of a sudden load of allochthonous humus extract to the bacterioplankton community composition. Changes in the bacterial communities were followed in four control and four humus extract-added mesocosms for 50 days. In the humic mesocosms the phylotypes of allochthonous Proteobacteria arriving with the humus extract were initially prevalent but disappeared during the first weeks. After this the Actinobacteria-dominated communities resembled the bacterioplankton communities of the control mesocosms and Lake Ahvenlammi. Towards the end of the experiment the community patterns in all the mesocosms started to change slightly because of erratic occurrence of new proteobacterial phylotypes. Thus the effects of a sudden load of allochthonous humic material and bacteria to the bacterioplankton community composition were transient.     

Links between plant and rhizoplane bacterial communities in grassland soils, characterized using molecular techniques

Molecular analysis of grassland rhizosphere soil has demonstrated complex and diverse bacterial communities, with resultant difficulties in detecting links between plant and bacterial communities. These studies have, however, analyzed "bulk" rhizosphere soil, rather than rhizoplane communities, which interact most closely with plants through utilization of root exudates. The aim of this study was to test the hypothesis that plant species was a major driver for bacterial rhizoplane community composition on individual plant roots. DNA extracted from individual roots was used to determine plant identity, by analysis of the plastid tRNA leucine (trnL) UAA gene intron, and plant-related bacterial communities. Bacterial communities were characterized by analysis of PCR-amplified 16S rRNA genes using two fingerprinting methods: terminal restriction fragment length polymorphisms (T-RFLP) and denaturing gradient gel electrophoresis (DGGE). Links between plant and bacterial rhizoplane communities could not be detected by visual examination of T-RFLP patterns or DGGE banding profiles. Statistical analysis of fingerprint patterns did not reveal a relationship between bacterial community composition and plant species but did demonstrate an influence of plant community composition. The data also indicated that topography and other, uncharacterized, environmental factors are important in driving bacterial community composition in grassland soils. T-RFLP had greater potential resolving power than DGGE, but findings from the two methods were not significantly different.     

Distinct and diverse anaerobic bacterial communities in boreal lakes dominated by candidate division OD1

Lakes have a central role in the carbon cycle of the boreal landscape. These systems typically stratify in summer and their hypolimnetic microbial communities influence burial of biogenic organic matter in sediments. The composition of bacterial communities in these suboxic habitats was studied by pyrosequencing of 16S rRNA amplicons from five lakes with variable dissolved organic carbon (DOC) concentrations. Bacterioplankton communities in the hypolimnetic waters were clearly different from the surface layer with candidate division OD1, Chlorobi and Bacteroidetes as dominant community members. Several operational taxonomic units (OTUs) affiliated with candidate division OD1 were abundant and consistently present in the suboxic hypolimnion in these boreal lakes. The overall representation of this group was positively correlated with DOC and methane concentrations. Network analysis of time-series data revealed contrasting temporal patterns but suggested similar ecological roles among the abundant OTUs affiliated with candidate division OD1. Together, stable isotope data and taxonomic classification point to methane oxidation and autotrophic denitrification as important processes in the suboxic zone of boreal lakes. Our data revealed that while hypolimnetic bacterial communities are less dynamic, they appear to be more diverse than communities from the oxic surface layer. An appreciable proportion of the hypolimnetic bacteria belong to poorly described phyla.     

Diversity analysis of bacterial community compositions in sediments of urban lakes by terminal restriction fragment length polymorphism (T-RFLP)

Bacteria are crucial components in lake sediments and play important role in various environmental processes. Urban lakes in the densely populated cities are often small, shallow, highly artificial and hypereutrophic compared to rural and natural lakes and have been overlooked for a long time. In the present study, bacterial community compositions in surface sediments of three urban lakes (Lake Mochou, Lake Qianhu and Lake Zixia) in Nanjing City, China, were investigated using the terminal restriction fragment length polymorphism (T-RFLP) of PCR-amplified 16S rRNA gene and clone libraries. Remarkable differences in the T-RFLP patterns were observed in different lakes or different sampling stations of the same lake. Canonical correspondence analysis indicated that total nitrogen (TN) had significant effects on bacterial community structure in the lake sediments. Chloroflexi were the most dominant bacterial group in the clone library from Lake Mochou (21.7?% of the total clones) which was partly associated with its higher TN and organic matters concentrations. However, Bacteroidetes appeared to be dominated colonizers in the sediments of Lake Zixia (20.4?% of the total clones). Our study gives a comprehensive insight into the structure of bacterial community of urban lake sediments, indicating that the environmental factors played a key role in influencing the bacterial community composition in the freshwater ecosystems.     

Climate Change and Physical Disturbance Manipulations Result in Distinct Biological Soil Crust Communities

Biological soil crusts (biocrusts) colonize plant interspaces in many drylands and are critical to soil nutrient cycling. Multiple climate change and land use factors have been shown to detrimentally impact biocrusts on a macroscopic (i.e., visual) scale. However, the impact of these perturbations on the bacterial components of the biocrusts remains poorly understood. We employed multiple long-term field experiments to assess the impacts of chronic physical (foot trampling) and climatic changes (2°C soil warming, altered summer precipitation [wetting], and combined warming and wetting) on biocrust bacterial biomass, composition, and metabolic profile. The biocrust bacterial communities adopted distinct states based on the mechanism of disturbance. Chronic trampling decreased biomass and caused small community compositional changes. Soil warming had little effect on biocrust biomass or composition, while wetting resulted in an increase in the cyanobacterial biomass and altered bacterial composition. Warming combined with wetting dramatically altered bacterial composition and decreased Cyanobacteria abundance. Shotgun metagenomic sequencing identified four functional gene categories that differed in relative abundance among the manipulations, suggesting that climate and land use changes affected soil bacterial functional potential. This study illustrates that different types of biocrust disturbance damage biocrusts in macroscopically similar ways, but they differentially impact the resident soil bacterial communities, and the communities'' functional profiles can differ depending on the disturbance type. Therefore, the nature of the perturbation and the microbial response are important considerations for management and restoration of drylands.     

Redox fluctuation structures microbial communities in a wet tropical soil

Frequent high-amplitude redox fluctuation may be a strong selective force on the phylogenetic and physiological composition of soil bacterial communities and may promote metabolic plasticity or redox tolerance mechanisms. To determine effects of fluctuating oxygen regimens, we incubated tropical soils under four treatments: aerobic, anaerobic, 12-h oxic/anoxic fluctuation, and 4-day oxic/anoxic fluctuation. Changes in soil bacterial community structure and diversity were monitored with terminal restriction fragment length polymorphism (T-RFLP) fingerprints. These profiles were correlated with gross N cycling rates, and a Web-based phylogenetic assignment tool was used to infer putative community composition from multiple fragment patterns. T-RFLP ordinations indicated that bacterial communities from 4-day oxic/anoxic incubations were most similar to field communities, whereas those incubated under consistently aerobic or anaerobic regimens developed distinctly different molecular profiles. Terminal fragments found in field soils persisted either in 4-day fluctuation/aerobic conditions or in anaerobic/12-h treatments but rarely in both. Only 3 of 179 total fragments were ubiquitous in all soils. Soil bacterial communities inferred from in silico phylogenetic assignment appeared to be dominated by Actinobacteria (especially Micrococcus and Streptomycetes), "Bacilli," "Clostridia," and Burkholderia and lost significant diversity under consistently or frequently anoxic incubations. Community patterns correlated well with redox-sensitive processes such as nitrification, dissimilatory nitrate reduction to ammonium (DNRA), and denitrification but did not predict patterns of more general functions such as N mineralization and consumption. The results suggest that this soil's indigenous bacteria are highly adapted to fluctuating redox regimens and generally possess physiological tolerance mechanisms which allow them to withstand unfavorable redox periods.     

Microbial diversity in lake sediments detected by PCR-DGGE

In this study,PCR-denaturing gradient gel electrophoresis (DGGE) was applied to analyze the microbial communities in lake sediments from Lake Xuanwu,Lake Mochou in Nanjing and Lake Taihu in Wuxi.Sediment samples from seven locations in three lakes were collected and their genomic DNAs were extracted.The DNA yields of the sediments of Lake Xuanwu and Lake Mochou were high (10 μg/g),while that of sediments in Lake Taihu was relatively low.After DNA purification,the 16S rDNA genes (V3 to V5 region) were amplified and the amplified DNA fragments were separated by parallel DGGE.The DGGE profiles showed that there were five common bands in all the lake sediment samples indicating that there were similarities among the populations of microorganisms in all the lake sediments.The DGGE profiles of Lake Xuanwu and Lake Mochou were similar and about 20 types of micro-organisms were identified in the sediment samples of both lakes.These results suggest that the sediment samples of these two city lakes (Xuanwu,Mochou) have similar microbial communities.However,the DGGE profiles of sediment samples in Lake Taihu were significantly differ-ent from these two lakes.Furthermore,the DGGE pro-files of sediment samples in different locations in Lake Taihu were also different,suggesting that the microbial communities in Lake Taihu are more diversified than those in Lake Xuanwu and Lake Mochou.The differences in microbial diversity may be caused by the different environmental conditions,such as redox potential,pH,and the concentrations of organic matters.Seven major bands of 16S rDNA genes fragments from the DGGE profiles of sediment samples were further re-amplified and sequenced.The results of sequencing analysis indicate that five sequences shared 99%-100% homology with known sequences (Bacillus and Brevibacillus,uncultured bacteria),while the other two sequences shared 93%-96% homology with known sequences (Acinetobacter,and Bacillus).The study shows that the PCR-DGGE tech-nique combined with sequence analysis is a feasible and efficient method for the determination of microbial com-munities in sediment samples.     

Effects of disturbance intensity and frequency on bacterial community composition and function

Disturbances influence community structure and ecosystem functioning. Bacteria are key players in ecosystems and it is therefore crucial to understand the effect of disturbances on bacterial communities and how they respond to them, both compositionally and functionally. The main aim of this study was to test the effect of differences in disturbance strength on bacterial communities. For this, we implemented two independent short-term experiments with dialysis bags containing natural bacterial communities, which were transplanted between ambient and 'disturbed' incubation tanks, manipulating either the intensity or the frequency of a salinity disturbance. We followed changes in community composition by terminal restriction fragment analysis (T-RFLP) and measured various community functions (bacterial production, carbon substrate utilization profiles and rates) directly after and after a short period of recovery under ambient conditions. Increases in disturbance strength resulted in gradually stronger changes in bacterial community composition and functions. In the disturbance intensity experiment, the sensitivity to the disturbance and the ability of recovery differed between different functions. In the disturbance frequency experiment, effects on the different functions were more consistent and recovery was not observed. Moreover, in case of the intensity experiment, there was also a time lag in the responses of community composition and functions, with functional responses being faster than compositional ones. To summarize, our study shows that disturbance strength has the potential to change the functional performance and composition of bacterial communities. It further highlights that the overall effects, rates of recovery and the degree of congruence in the response patterns of community composition and functioning along disturbance gradients depend on the type of function and the character of the disturbance.     

Links between Plant and Rhizoplane Bacterial Communities in Grassland Soils, Characterized Using Molecular Techniques

Molecular analysis of grassland rhizosphere soil has demonstrated complex and diverse bacterial communities, with resultant difficulties in detecting links between plant and bacterial communities. These studies have, however, analyzed “bulk” rhizosphere soil, rather than rhizoplane communities, which interact most closely with plants through utilization of root exudates. The aim of this study was to test the hypothesis that plant species was a major driver for bacterial rhizoplane community composition on individual plant roots. DNA extracted from individual roots was used to determine plant identity, by analysis of the plastid tRNA leucine (trnL) UAA gene intron, and plant-related bacterial communities. Bacterial communities were characterized by analysis of PCR-amplified 16S rRNA genes using two fingerprinting methods: terminal restriction fragment length polymorphisms (T-RFLP) and denaturing gradient gel electrophoresis (DGGE). Links between plant and bacterial rhizoplane communities could not be detected by visual examination of T-RFLP patterns or DGGE banding profiles. Statistical analysis of fingerprint patterns did not reveal a relationship between bacterial community composition and plant species but did demonstrate an influence of plant community composition. The data also indicated that topography and other, uncharacterized, environmental factors are important in driving bacterial community composition in grassland soils. T-RFLP had greater potential resolving power than DGGE, but findings from the two methods were not significantly different.     

Microbial diversity in lake sediments detected by PCR-DGGE

In this study, PCR-denaturing gradient gel electrophoresis (DGGE) was applied to analyze the microbial communities in lake sediments from Lake Xuanwu, Lake Mochou in Nanjing and Lake Taihu in Wuxi. Sediment samples from seven locations in three lakes were collected and their genomic DNAs were extracted. The DNA yields of the sediments of Lake Xuanwu and Lake Mochou were high (10 μg/g), while that of sediments in Lake Taihu was relatively low. After DNA purification, the 16S rDNA genes (V3 to V5 region) were amplified and the amplified DNA fragments were separated by parallel DGGE. The DGGE profiles showed that there were five common bands in all the lake sediment samples indicating that there were similarities among the populations of microorganisms in all the lake sediments. The DGGE profiles of Lake Xuanwu and Lake Mochou were similar and about 20 types of microorganisms were identified in the sediment samples of both lakes. These results suggest that the sediment samples of these two city lakes (Xuanwu, Mochou) have similar microbial communities. However, the DGGE profiles of sediment samples in Lake Taihu were significantly different from these two lakes. Furthermore, the DGGE profiles of sediment samples in different locations in Lake Taihu were also different, suggesting that the microbial communities in Lake Taihu are more diversified than those in Lake Xuanwu and Lake Mochou. The differences in microbial diversity may be caused by the different environmental conditions, such as redox potential, pH, and the concentrations of organic matters. Seven major bands of 16S rDNA genes fragments from the DGGE profiles of sediment samples were further re-amplified and sequenced. The results of sequencing analysis indicate that five sequences shared 99%–100% homology with known sequences (Bacillus and Brevibacillus, uncultured bacteria), while the other two sequences shared 93%–96% homology with known sequences (Acinetobacter, and Bacillus). The study shows that the PCR-DGGE technique combined with sequence analysis is a feasible and efficient method for the determination of microbial communities in sediment samples. __________ Translated from Acta Ecologica Sinica, 2006, 26(11): 3610–3616 [译自: 生态学报]     

青藏高原淡水湖普莫雍错和盐水湖阿翁错湖底沉积物中细菌群落的垂直分布

【目的】湖泊沉积物中存储着大量独特的微生物,这些微生物在湖泊生态系统生物地球化学循环中扮演着非常重要的角色。然而,很少有研究报道微生物群落在湖泊沉积物中的垂直分布。本文比较研究青藏高原淡水湖普莫雍错和盐水湖阿翁错沉积物在不同深度下细菌的丰度和群落结构。【方法】利用定量PCR(q PCR)和变性梯度凝胶电泳(DGGE)技术分别测定细菌群落的丰度与群落结构。【结果】定量PCR结果显示,湖泊沉积物中细菌丰度均随深度增加而降低,盐水湖阿翁错和淡水湖普莫雍错的细菌丰度分别从1011数量级降到108数量级,从1012数量级降到1010数量级。在相对应的沉积物层,淡水湖沉积物的细菌丰度比盐水湖高1-2个数量级。变性梯度凝胶电泳(DGGE)指纹图谱的分析表明,淡水湖沉积物细菌群落的DGGE条带数(丰富度)显著高于盐水湖(P=0.014);淡水与盐水湖泊沉积物细菌群落结构明显不同,同时在同一湖泊沉积物中上层(0-6 cm)和下层(7-20 cm)细菌群落结构也呈明显分异。系统发育分析表明,盐水湖阿翁错沉积物特有菌门为Gamma-变形菌、拟杆菌门、蓝细菌和栖热菌门,而淡水湖普莫雍错沉积物中特有菌门为Delta-和Beta-变形菌、酸杆菌和绿弯菌门。【结论】青藏高原淡水与盐水湖泊沉积物细菌丰度与群落结构具有明显的差异;同时,细菌群落结构在沉积物的不同深度也表现出差异。这些结果可为进一步阐明青藏高原湖泊生态系统中微生物对气候环境变化的响应提供科学依据。     

Cultivable bacterial composition and BIOLOG catabolic diversity of biofilm communities developed on Phragmites australis

Biofilm samples formed on submerged young and old stems of reed, Phragmites australis (Cav.) Trin ex Steudel were taken during summer at different sites of Lake Velencei, Hungary. BIOLOG GN microplates were used to analyze the patterns of sole carbon source utilizations by microbial communities. From the carbon sources, carbohydrates and amino acids were preferred by all microbial communities. In the case of the old reed stem samples, higher number of carbohydrates, carboxylic acids and polymers were used than in young samples. Biofilm bacterial communities from the old reed samples of the nature conservation area of the lake used the highest number of (≥50% of the available) substrates. In principal component analysis (PCA), the metabolic potential of the microbial communities from the middle open water region of the lake showed the smallest variability. The variability within metabolic potential of the reed stem microbial communities from a given sampling site was the largest in the case of samples originating from the western, reed-covered nature conservation area. A total of 251 bacterial isolates obtained after serial dilutions and plating onto different media were characterized by traditional phenotypic tests. The strains showed high activities mainly in the hydrolysis of certain biopolymers (gelatine and casein). PCA was used to evaluate the phenotypic variability of strain groups of different sampling sites. The two open water regions were similar to each other, and separated from the western reed covered part of the lake. Similarly to the BIOLOG community-level physiological profiles, strain groups of the young and old reed stem samples originating from the nature conservation area had the largest metabolic potential. On the basis of 16S rDNA sequence analysis, 23 representative strains with different ARDRA patterns were identified. The cultivation-based investigations of bacterial diversity showed characteristic differences in the number of identified taxa in connection with the sampling sites. No characteristic differences could be observed according to medium or sample type (young, first year and more than 1-year old stems) among the identified species. 16S rDNA sequence comparisons resulted in the identification of the genera Aureobacterium, Arthrobacter, Kocuria, Microbacterium, Micrococcus, Rhodococcus, Bacillus, Marinibacillus, Rhodobacter, Defluvibacter, Pseudomonas, Klebsiella, Serratia and Aeromonas. The results of the cultivation-based and BIOLOG investigations revealed characteristic differences in the bacterial community composition and activities of the open water region and the reed covered nature conservation part of the lake.