Dynamics of Leptospira colony formation on solid nutrient media]

The formation of Leptospira colonies on solid culture media varying in composition were studied. In all species of Leptospira 3 main periods of colony development were revealed, each of them having its characteristic morphological changes connected with the growth of the colony deeply into agar.     

Effect of biostimulation on the microbial community in PCB-contaminated sediments through periodic amendment of sediment with iron

Reductive dehalogenation of polychlorinated biphenyls (PCBs) by indigenous dehalorespiring microorganisms in contaminated sediments may be enhanced via biostimulation by supplying hydrogen generated through the anaerobic corrosion of elemental iron added to the sediment. In this study, the effect of periodic amendment of sediment with various dosages of iron on the microbial community present in sediment was investigated using phospholipid fatty acid analysis (PLFA) over a period of 18 months. Three PCB-contaminated sediments (two freshwater lake sediments and one marine sediment) were used. Signature biomarker analysis of the microbial community present in all three sediments revealed the enrichment of Dehalococcoides species, the population of which was sustained for a longer period of time when the sediment microcosms were amended with the lower dosage of iron (0.01 g iron per g dry sediment) every 6 months as compared to the blank system (without iron). Lower microbial stress levels were reported for the system periodically amended with 0.01 g of iron per g dry sediment every 6 months, thus reducing the competition from other hydrogen-utilizing microorganisms like methanogens, iron reducers, and sulfate reducers. The concentration of hydrogen in the system was found to be an important factor influencing the shift in microbial communities in all sediments with time. Periodic amendment of sediment with larger dosages of iron every 3 months resulted in the early prevalence of Geobacteraceae and sulfate-reducing bacteria followed by methanogens. An average pH of 8.4 (range of 8.2–8.6) and an average hydrogen concentration of 0.75% (range of 0.3–1.2%) observed between 6 and 15 months of the study were found to be conducive to sustaining the population of Dehalococcoides species in the three sediments amended with 0.01 g iron per g dry sediment. Biostimulation of indigenous PCB dechlorinators by the periodic amendment of contaminated sediments with low dosages of iron metal may therefore be an effective technology for remediation of PCB-contaminated sediments.     

不同生草处理对苹果园土壤微生物群落的影响

以自然生草为对照,采用高通量测序技术分析种植黑麦草、白三叶、鼠茅草和长柔毛野豌豆对山东省阳谷县苹果园土壤微生物群落的影响,并揭示其与土壤养分含量及理化性质的相关性.结果表明: 种植黑麦草可提高土壤中链格孢菌和曲霉的相对丰度,白三叶处理可提高土壤赤霉的相对丰度,鼠茅草处理可增加土壤短梗菌属和毛壳属真菌的相对丰度,长柔毛野豌豆处理可增加土壤亚硝化螺菌和绿僵菌等有益菌的相对丰度,而自然生草则会使土壤青枯菌等病原细菌数量增加.Spearman相关性分析发现,土壤芽孢杆菌与有机质呈极显著正相关;曲霉与速效磷、速效钾和阳离子交换量(CEC)、有机质呈显著负相关;绿僵菌与pH、CEC呈显著正相关.研究表明,苹果园行间种植长柔毛野豌豆,有助于在一定程度上提高土壤有机质及养分含量,改善土壤微生态环境.     

Eutrophication as a driver of microbial community structure in lake sediments

Lake sediments are globally important carbon sinks. Although the fate of organic carbon in lake sediments depends significantly on microorganisms, only few studies have investigated controls on lake sedimentary microbial communities. Here we investigate the impact of anthropogenic eutrophication, which affects redox chemistry and organic matter (OM) sources in sediments, on microbial communities across five lakes in central Switzerland. Lipid biomarkers and distributions of microbial respiration reactions indicate strong increases in aquatic OM contributions and microbial activity with increasing trophic state. Across all lakes, 16S rRNA genes analyses indicate similar depth-dependent zonations at the phylum- and class-level that follow vertical distributions of OM sources and respiration reactions. Yet, there are notable differences, such as higher abundances of nitrifying Bacteria and Archaea in an oligotrophic lake. Furthermore, analyses at the order-level and below suggest that changes in OM sources due to eutrophication cause permanent changes in bacterial community structure. By contrast, archaeal communities are differentiated according to trophic state in recently deposited layers, but converge in older sediments deposited under different trophic regimes. Our study indicates an important role for trophic state in driving lacustrine sediment microbial communities and reveals fundamental differences in the temporal responses of sediment Bacteria and Archaea to eutrophication.     

Influence of TNT transformation on microbial community structure in four different lake microcosms

After World War II, large amounts of obsolete ammunition were dumped in various lakes in Sweden. Trinitrotoluene, TNT, was one of the main components of the dumped explosives. In this study, four different lake microcosms originating from lakes where relatively large amounts of ammunition were dumped were used to mimic the effect of TNT release on the natural microbial community. Increased microbial growth was found in lake microcosms amended with TNT. However, negligible mineralization of TNT was detected, suggesting that TNT was not utilized as a carbon source, but as a nitrogen source. Random amplified polymorphic DNA (RAPD) analysis indicated that the TNT induced no significant differences in microbial community composition and therefore, no major changes in natural selection, despite the increased microbial growth in the presence of the compound. More than 95% of the added TNT bound irreversibly to the sediments, possibly as a result of microbial transformation to reactive metabolites that subsequently bound covalently to components of the sediment. The results, taken together, suggest that no permanent change in the microbial ecology occurred as a result of the TNT amendment. This was probably due partly to the transient exposure of the microbial communities to the TNT before it became irreversibly bound to the sediment, and partly to the fact that TNT was not a primary growth substrate that strongly affects natural selection.     

Effect of gelling agent on growth and development ofCeratozamia hildae somatic embryos

Individual somatic proembryos ofCeratozamia hildae were exposed to media that differed only in gelling agent utilized. Five different gelling agents were compared in the first experiment: Bacto agar, Agargel, Gel-Gro, Phytagar, and TC agar. In addition, the effect of agar was examined at two levels. Growth, proliferation, and development were assessed. The lower level of agar did not support good somatic proembryo growth. Agargel and the high agar concentration produced cultures with good proliferation. Proembryos exposed to Phytagar, Gel-Gro, and TC agar had the highest proliferation rates. Overall, Gel-Gro was considered the best gelling agent tested. The three concentrations of Gel-Gro used in the second experiment were 2, 4, and 6 g·1⁻, with the lowest concentration representing the control, the recommended concentration. As gelling agent concentration increased, so did mortality; however, the highest Gel-Gro concentration also produced the highest numbers of good-quality, mature somatic embryos. Proliferation rate was greatest at the lowest concentration. These results suggest thatCeratozamia cultures should be exposed to different gelling agents or concentrations of gelling agents at different developmental stages in order to produce the greatest number and highest quality of somatic embryos.     

Anodic microbial community analysis of microbial fuel cells based on enriched inoculum from freshwater sediment

Bioprocess and Biosystems Engineering - The characterization of anodic microbial communities is of great importance in the study of microbial fuel cells (MFCs). These kinds of devices mainly...     

北京市妫水河底泥微生物群落结构特征

微生物对外界环境变化较为敏感,常被作为指示生物用于监测和反映水质情况。为满足延庆世园会和冬奥会举办对妫水河水质的调控要求,探讨妫水河底泥微生物群落结构特征及环境因子对其分布的影响。基于妫水河12个不同断面的水样和底泥样品,进行了水质、底泥理化性质分析,并对底泥的微生物群落结构特征进行了研究。结果表明,妫水河中、下游水体水质COD、NH~+_4-N、TN超标,其中上覆水TN含量与底泥TN含量呈极显著正相关(P=0.914);MiSeq高通量测序发现,妫水河底泥微生物共检出70门228纲1168属,变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)、酸杆菌门(Acidobacteria)、放线菌门(Actinobacteria)、绿弯菌门(Chloroflexi)、厚壁菌门(Firmicutes)、蓝细菌门(Cyanobacteria)、绿菌门(Chlorobi)、疣微菌门(Verrucomicrobia)和硝化螺旋菌门(Nitrospirae)是妫水河底泥微生物群落结构中的主要菌门,在各个样品中相对丰度之和均占84%以上,其中变形菌门为第一优势门,占比达到45.3%—69.1%,而不同断面样品的优势菌属有所不同。妫水河底泥微生物群落丰度总体较高,多样性也相对较高,其中世园段D7点Ace丰富度指数和Shannon多样性指数均较其他点位低,分别为2673和6.56。RDA(redundancy analysis)分析表明,底泥氨氮和温度是影响其微生物群落结构的主要因子(F=2.92,P=0.038;F=2.81,P=0.014),妫水河底泥的优势反硝化菌属为脱氮单孢菌属和硫杆状菌属,其丰度与NH~+_4-N、水温呈正相关,同时与DO呈负相关。研究结果对妫水河水生态环境保护和水质管理提供数据支撑及理论指导意义。     

Microscale decoupling of sediment oxygen consumption and microbial biomass in an oligotrophic lake

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Effect of dilution rate on the microbial structure of a mesophilic butyrate-degrading methanogenic community during continuous cultivation

We constructed two mesophilic anaerobic chemostats that were continuously fed with synthetic wastewater containing butyrate as the sole source of carbon and energy. Steady-state conditions were achieved at dilution rates between 0.025 and 0.7 day⁻¹. Butyrate, fed into the chemostat, was almost completely mineralized to CH₄ and CO₂ at dilution rates below 0.5 day⁻¹. The butyrate-degrading methanogenic communities in the chemostats at dilution rates between 0.025 and 0.7 day⁻¹ were monitored based on the 16S rRNA gene, using molecular biological techniques including clone library analysis, denaturing gradient gel electrophoresis, and quantitative real-time polymerase chain reaction. The aceticlastic methanogen Methanosaeta and the hydrogenotrophic methanogen Methanoculleus dominated in methanogens at low dilution rates, whereas the aceticlastic methanogen Methanosaeta, Methanosarcina, the hydrogenotrophic methanogen Methanoculleus, and Methanospirillum dominated at high dilution rates. Bacteria affiliated with the family Syntrophaceae in the phylum Proteobacteria predominated at the low dilution rate of 0.025 day⁻¹, whereas bacteria affiliated with the phylum Firmicutes and Candidate division OP3 predominated at high dilution rates. A significant quantity of bacteria closely related to the genus Syntrophomonas was detected at high dilution rates. Dilution rate showed an apparent effect on archaeal and bacterial communities in the butyrate-fed chemostats.     

Implications of temperature and sediment characteristics on methane formation and oxidation in lake sediments

Methane emissions from aquatic environments depend on methane formation (MF) and methane oxidation (MO) rates. One important question is to what extent increased temperatures will affect the balance between MF and MO. We measured potential MF and MO rates simultaneously at 4, 10, 20 and 30°C in sediment from eight different lakes representing typical boreal and northern temperate lake types. Potential MF rates ranged between 0.002 and 3.99 μmol CH₄ g_d.w. ^?1 day^?1, potential MO rates ranged from 0.01 to 0.39 CH₄ g_d.w. ^?1 day^?1. The potential MF rates were sensitive to temperature and increased 10 to 100 fold over the temperature interval studied. MF also differed between lakes and was correlated to sediment water content, percent of organic material and C:N ratio. Potential MO did not depend on temperature or sediment characteristics but was instead well explained by MF rates at the in situ temperature. It implies that elevated temperatures will enhance MF rates which may cause increased methane release from sediments until MO increases as well, as a response to higher methane levels.     

Short-term stability of the microbial community structure in a maritime Antarctic lake

. Spatial and temporal changes in the microbial community structure in a maritime Antarctic freshwater lake were investigated over a single day/night cycle in December 1999. The community structure of key microbial planktonic groups varied with depth and this was related to both physical and chemical stratification. However, in most cases, the community structure observed at specific depths did not change over the time period studied. These results suggested short-term stability in community structure, with only some minor effects of the diel changes in irradiance on the vertical distribution of planktonic organisms. This is in marked contrast to medium- and long-term studies, which show significant changes in microbial community structure with both time and depth.     

A thiotrophic microbial community in an acidic brine lake in Northern Chile

The endorheic basins of the Northern Chilean Altiplano contain saline lakes and salt flats. Two of the salt flats, Gorbea and Ignorado, have high acidic brines. The causes of the local acidity have been attributed to the occurrence of volcanic native sulfur, the release of sulfuric acid by oxidation, and the low buffering capacity of the rocks in the area. Understanding the microbial community composition and available energy in this pristine ecosystem is relevant in determining the origin of the acidity and in supporting the rationale of conservation policies. Besides, a comparison between similar systems in Australia highlights key microbial components and specific ones associated with geological settings and environmental conditions. Sediment and water samples from the Salar de Gorbea were collected, physicochemical parameters measured and geochemical and molecular biological analyses performed. A low diversity microbial community was observed in brines and sediments dominated by Actinobacteria, Algae, Firmicutes and Proteobacteria. Most of the constituent genera have been reported to be either sulfur oxidizing microorganisms or ones having the potential for sulfur oxidation given available genomic data and information drawn from the literature on cultured relatives. In addition, a link between sulfur oxidation and carbon fixation was observed. In contrast, to acid mine drainage communities, Gorbea microbial diversity is mainly supported by chemolithoheterotrophic, facultative chemolithoautotrophic and oligotrophic sulfur oxidizing populations indicating that microbial activity should also be considered as a causative agent of local acidity.     

A high-throughput ultrasonic spraying inoculation method promotes colony cultivation of rare microbial species

Current method for obtaining microbial colonies still relies on traditional dilution and spreading plate (DSP) procedures, which is labor-intensive, skill-dependent, low-throughput and inevitably causing dilution-to-extinction of rare microorganisms. Herein, we proposed a novel ultrasonic spraying inoculation (USI) method that disperses microbial suspensions into millions of aerosols containing single cells, which lately be deposited freely on a gel plate to achieve high-throughput culturing of colonies. Compared with DSP, USI significantly increased both distributing uniformity and throughput of the colonies on agar plates, improving the minimal colony-forming abundance of rare Escherichia coli mixed in a lake sample from 1% to 0.01%. Applying this novel USI to a lake sample, 16 cellulose-degrading colonies were screened out among 4766 colonies on an enlarged 150-mm-diameter LB plate. Meanwhile, they could only be occasionally observed when using commonly used DSP procedures. 16S rRNA sequencing further showed that USI increased colony-forming species from 11 (by DSP) to 23, including seven completely undetectable microorganisms in DSP-reared communities. In addition to avoidance of dilution-to-extinction, operation-friendly USI efficiently inoculated microbial samples on the agar plate in a high-throughput and single-cell form, which eliminated masking or out-competition from other species in associated groups, thereby improving rare species cultivability.     

The use of psyllium (isubgol) as an alternative gelling agent for microbial culture media

Psyllium (Isubgol), the mucilage husk of Plantago ovata, was successfully used as an alternative gelling agent (5% w/v as ground husk for pouring medium and 4% w/v as ground husk in combination with 0.5% w/v agar for slant) for microbial culture. Most of the undesirable features of psyllium-gelled media (slant as well as pouring) were removed by adding the u.v.-treated (20min) or oven-sterilized (120^°C for 1h) psyllium as ground husk to autoclaved medium at 50–60^°C under aseptic condition just before pouring.     

Microbial community structures in anoxic freshwater lake sediment along a metal contamination gradient

Contamination, such as by heavy metals, has frequently been implicated in altering microbial community structure. However, this association has not been extensively studied for anaerobic communities, or in freshwater lake sediments. We investigated microbial community structure in the metal-contaminated anoxic sediments of a eutrophic lake that were impacted over the course of 80 years by nearby zinc-smelting activities. Microbial community structure was inferred for bacterial, archaeal and eukaryotic populations by evaluating terminal restriction fragment length polymorphism (TRFLP) patterns in near-surface sediments collected in triplicate from five areas of the lake that had differing levels of metal contamination. The majority of the fragments in the bacterial and eukaryotic profiles showed no evidence of variation in association with metal contamination levels, and diversity revealed by these profiles remained consistent even as metal concentrations varied from 3000 to 27 000 mg kg⁻¹ total Zn, 0.125 to 11.2 μ pore water Zn and 0.023 to 5.40 μ pore water As. Although most archaeal fragments also showed no evidence of variation, the prevalence of a fragment associated with mesophilic Crenarchaeota showed significant positive correlation with total Zn concentrations. This Crenarchaeota fragment dominated the archaeal TRFLP profiles, representing between 35% and 79% of the total measured peak areas. Lake DePue 16S rRNA gene sequences corresponding to this TRFLP fragment clustered with anaerobic and soil mesophilic Crenarchaeota sequences. Although Crenarchaeota have been associated with metal-contaminated groundwater and soils, this is a first report (to our knowledge) documenting potential increased prevalence of Crenarchaeota associated with elevated levels of metal contamination.