Application of denaturing gradient gel electrophoresis (DGGE) to study the diversity of marine picoeukaryotic assemblages and comparison of DGGE with other molecular techniques

Sequestration and in vivo effect of lead on DE2009 microalga, using high-resolution microscopic techniques

Algae are primary producers in a wide variety of natural ecosystems, and these microorganisms have been used in bioremediation studies. Nevertheless, very little is known about the in vivo effect of heavy metals on individual living cells. In this paper, we have applied a method based on confocal laser scanning microscopy and lambda scan function (CLSM-λscan) to determine the effect of lead (Pb), at different concentrations, on the DE2009 microalga. At the same time, we have optimized a method based on CLSM and image-analysis software (CLSM-IA) to determine in vivo biomass of this microorganism. The results obtained by lambda scan function indicated that the pigment peak decreases while the concentration of metal increases at pH 7. On the other hand at pH 4 there is no good correlation between the concentration of metal and the intensity of the emission of fluorescence of the pigment. Also, in some cases a displacement of the Chl a peak towards 680 nm is produced. Total and individual biomass determined by CLSM-IA shows statistically significant differences between unpolluted and 10 mM polluted cultures. Complementary studies using electron microscopy techniques coupled to energy dispersive X-ray microanalysis (EDX) demonstrate that the microalga can sequestrate Pb extra- and intracellularly.

Genetic diversity of cry gene sequences of Bacillus thuringiensis strains analyzed by denaturing gradient gel electrophoresis

PCR has been widely used to identify cry-type genes, to determine their distribution, to detect new such genes and to predict insecticidal activities. We describe here a molecular approach to analyze the genetic diversity of B. thuringiensis cry-like genes based on denaturing gradient gel electrophoresis (DGGE). This analysis demonstrated that different B. thuringiensis isolates can be distinguished according to its PCR-DGGE profile of cry-like genes. Identification of the resolvable DNA fragments was easy to accomplish by DNA sequencing, which was confirmed in this work. Importantly, the strategy allowed the identification of unknown B. thuringiensis cry-like sequences present in a single strain that remained cryptic after PCR analysis using degenerate primers. The method developed in this work contributes to the availability of molecular techniques for both B. thuringiensis strains and cry-like genes identification and discovery.

A mesocosm study of the changes in marine flagellate and ciliate communities in a crude oil bioremediation trial

Protozoan grazers play an important role in controlling the density of crude-oil degrading marine communities as has been evidenced in a number of microcosm experiments. However, small bioreactors contain a low initial titre of protozoa and the growth of hydrocarbon-depleting bacteria is accompanied by the fast depletion of mineral nutrients and oxygen, which makes microcosms rather unsuitable for simulating the sequence of events after the oil spill in natural seawater environment. In the present study, the population dynamics of marine protozoan community have been analysed in a 500 l mesocosm experiment involving bioaugmented oil booms that contained oil sorbents and slow-release fertilisers. A significant increase in numbers of marine flagellates and ciliates on biofilms of oil-degrading microbes was microscopically observed as early as 8 days after the start of the experiment, when protozoa exhibited a population density peak making up to 3,000 cells ml(-1). Further, the protozoan density varied throughout the experiment, but never dropped below 80 cells ml(-1). An 18S rRNA gene-based fingerprinting analysis revealed several changes within the eukaryotic community over the whole course of the experiment. Initial growth of flagellates and small ciliates was followed by a predominance of larger protozoa. According to microscopic observations and SSU rRNA molecular analyses, most predominant were the ciliates belonging to Euplotidae and Scuticociliatia. This is the first study to characterise the eukaryotic communities specifically in a large-scale oil bioremediation trial using both microscopy-based and several molecular techniques.

Sampling strategy, occurrence and diversity of free-living protozoa in domestic refrigerators

AIMS

Evaluation of a sampling method to recover free-living protozoa (FLP) from plastic surfaces. Application of the method on different areas inside domestic refrigerators.

METHODS AND RESULTS

Plastic coupons seeded with representatives of FLP were swabbed with cotton wools. The recovery efficiency was the highest for Chilomonas paramecium, followed by Tetrahymena pyriformis and the lowest for Acanthamoeba polyphaga. From 43 refrigerators, 19 and 26 were considered FLP positive when sample cultures were incubated at 7°C and 20°C, respectively. The number of FLP-positive cultures was the highest in samples taken from vegetable trays followed by discharge gutters, whereas interior walls were rarely FLP positive. Higher numbers of taxa were observed in enrichment cultures incubated at 20°C instead of 7°C. The combination of microscopy and denaturing gradient gel electrophoresis revealed that discharge gutters occasionally were contaminated with a persistent protozoan population of flagellates (Cercozoa) and amoebae (Tubulinea). The FLP-positive status of refrigerator surfaces was correlated with a high aerobic plate count.

CONCLUSIONS

The cotton wool sampling method is useful to sample FLP from plastic surfaces. FLP are part of the microbial communities in domestic refrigerators.

SIGNIFICANCE AND IMPACT OF THE STUDY

Knowledge on the occurrence of FLP in food-related indoor environments is scarce. For the first time, a high protozoan diversity in domestic refrigerators is described.

Bacterial diversity in dry modern freshwater stromatolites from Ruidera Pools Natural Park, Spain

Ruidera Pools Natural Park, Spain, constitutes one of the most representative systems of carbonate precipitation in Europe. The prokaryotic community of a dry modern stromatolite recovered from the park has been analyzed by molecular techniques that included denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone library analysis, together with microscopic observations from the sample and cultures. Ribosomal RNA was directly extracted to study the putatively active part of the microbial community present in the sample. A total of 295 16S rRNA gene sequences were analyzed. Libraries were dominated by sequences related to Cyanobacteria, most frequently to the genus Leptolyngbya. A diverse and abundant assemblage of non-cyanobacterial sequences was also found, including members of Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Acidobacteria,Planctomycetes and Chloroflexi groups. No amplification was obtained when using archaeal primers. The results showed that at the time of sampling, when the pool was dry, the bacterial community of the stromatolites was dominated by groups of highly related Cyanobacteria, including new groups that had not been previously reported, although a high diversity outside this phylogenetic group was also found. The results indicated that part of the Cyanobacteria assemblage was metabolically active and could thus play a role in the mineralization processes inside the stromatolites.

Dormancy contributes to the maintenance of microbial diversity

Dormancy is a bet-hedging strategy used by a variety of organisms to overcome unfavorable environmental conditions. By entering a reversible state of low metabolic activity, dormant individuals become members of a seed bank, which can determine community dynamics in future generations. Although microbiologists have documented dormancy in both clinical and natural settings, the importance of seed banks for the diversity and functioning of microbial communities remains untested. Here, we develop a theoretical model demonstrating that microbial communities are structured by environmental cues that trigger dormancy. A molecular survey of lake ecosystems revealed that dormancy plays a more important role in shaping bacterial communities than eukaryotic microbial communities. The proportion of dormant bacteria was relatively low in productive ecosystems but accounted for up to 40% of taxon richness in nutrient-poor systems. Our simulations and empirical data suggest that regional environmental cues and dormancy synchronize the composition of active communities across the landscape while decoupling active microbes from the total community at local scales. Furthermore, we observed that rare bacterial taxa were disproportionately active relative to common bacterial taxa, suggesting that microbial rank-abundance curves are more dynamic than previously considered. We propose that repeated transitions to and from the seed bank may help maintain the high levels of microbial biodiversity that are observed in nearly all ecosystems.

Application of the denaturing gradient gel electrophoresis (DGGE) technique as an efficient diagnostic tool for ciliate communities in soil

Ciliates (or Ciliophora) are ubiquitous organisms which can be widely used as bioindicators in ecosystems exposed to anthropogenic and industrial influences. The evaluation of the environmental impact on soil ciliate communities with methods relying on morphology-based identification may be hampered by the large number of samples usually required for a statistically supported, reliable conclusion. Cultivation-independent molecular-biological diagnostic tools are a promising alternative to greatly simplify and accelerate such studies. In this present work a ciliate-specific fingerprint method based on the amplification of a phylogenetic marker gene (i.e. the 18S ribosomal RNA gene) with subsequent analysis by denaturing gradient gel electrophoresis (DGGE) was developed and used to monitor community shifts in a polycyclic aromatic hydrocarbon (PAH) polluted soil. The semi-nested approach generated ciliate-specific amplification products from all soil samples and allowed to distinguish community profiles from a PAH-polluted and a non-polluted control soil. Subsequent sequence analysis of excised bands provided evidence that polluted soil samples are dominated by organisms belonging to the class Colpodea. The general DGGE approach presented in this study might thus in principle serve as a fast and reproducible diagnostic tool, complementing and facilitating future ecological and ecotoxicological monitoring of ciliates in polluted habitats.

Spatio-temporal variations in protistan communities along an O/HS gradient in the anoxic Framvaren Fjord (Norway)

Despite its relevance for ecology and biodiversity, the stability of spatial microeukaryote diversity patterns in time has received only little attention using gene-based strategies, and there is little knowledge about the relation of spatial vs. temporal variation. We addressed this subject by investigating seasonal fluctuations in protistan communities in three ecologically distinct marine habitats. We analyzed 3360 eukaryote small subunit rRNA gene sequences collected along an O(2)/H(2)S gradient in a Norwegian fjord in order to reveal shifts in protistan community composition and structure in three different seasons. In all nine clone libraries, ciliates and stramenopiles accounted for the largest proportion. Yet, as expected, at the phylotype level, the protistan communities from distinct habitats differed significantly, with the number of shared phylotypes between two habitats being as low as 18%. This confirmed previous notions that environmental factors along the stratification gradient shape biodiversity patterns. Surprisingly, the intrahabitat community composition and structure varied at a comparable order of magnitude over time, with only 18-28% phylotypes shared within the same habitat. Our study demonstrates that the consideration of local fluctuations in microeukaryote diversity over time offers additional information for diversity surveys and can significantly contribute to the revelation of spatial protistan community patterns.

Abundance and community of snow bacteria from three glaciers in the Tibetan Plateau

Bacterial abundance and diversity in snow of East Rongbuk, Laohugou and Hailuogou glaciers on the Tibetan Plateau were investigated through epifluorescence microscope and denaturing gradient gel electrophoresis. Cell abundance ranged from 4.0 x 10(3) to 290.2 x 10(3) cells/mL. The phylogenetic trees placed the 16S rRNA sequences in four major groups: Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Brevundimonas, Flavobacterium, Hymenobacter, Bacillus, Polaromonas, Rhodoferax and Streptomyces were widely distributed bacteria in glaciers from different cold regions. The remaining five genera of Hylemonella, Delftia, Zoogloea, Blastococcus and Rhodococcus were endemism, only recovered from our investigated glaciers. It is proposed that the three glaciers on the Tibetan Plateau provide a specific ecological niche for prolonging survival of diverse microbial lineages.

Fate of aerobic bacterial granules with fungal contamination under different organic loading conditions

Aerobic sludge granulation is an attractive new technology for biological wastewater treatment. However, the instability of aerobic granules caused by fungal growth is still one of the main problems encountered in granular bioreactors. In this study, laboratory experiments were conducted to investigate the fate and transformation of aerobic granules under different organic loading conditions. Bacterial granules (2-3mm) in a poor condition with fungi-like black filamentous growth were seeded into two 1L batch reactors. After more than 100d of cultivation, the small seed granules in the two reactors had grown into two different types of large granules (>20mm) with different and unique morphological features. In reactor R1 with a high organic loading rate of 2.0g COD L(-1)d(-1), the black filaments mostly disappeared from the granules, and the dominance of rod-shaped bacteria was recovered. In contrast, at a low loading of 0.5g COD L(-1)d(-1) in reactor R2, the filaments eventually became dominant in the black fungal granules. The bacteria in R1 granules had a unique web-like structure with large pores of a few hundred microm in size, which would allow for effective substrate and oxygen transport into the interior of the granules. DNA-based molecular analysis indicated the evolution of the bacterial population in R1 and that of the eukaryal community in R2. The experimental results suggest that a high loading rate can be an effective means of helping to control fungal bloom, recover bacterial domination and restore the stability of aerobic granules that suffer from fungal contamination.

Effect of environmental variables on eukaryotic microbial community structure of land-fast Arctic sea ice

Sea ice microbial community structure affects carbon and nutrient cycling in polar seas, but its susceptibility to changing environmental conditions is not well understood. We studied the eukaryotic microbial community in sea ice cores recovered near Point Barrow, AK in May 2006 by documenting the composition of the community in relation to vertical depth within the cores, as well as light availability (mainly as variable snow cover) and nutrient concentrations. We applied a combination of epifluorescence microscopy, denaturing gradient gel electrophoresis and clone libraries of a section of the 18S rRNA gene in order to compare the community structure of the major eukaryotic microbial phylotypes in the ice. We find that the community composition of the sea ice is more affected by the depth horizon in the ice than by light availability, although there are significant differences in the abundance of some groups between light regimes. Epifluorescence microscopy shows a shift from predominantly heterotrophic life styles in the upper ice to autotrophy prevailing in the bottom ice. This is supported by the statistical analysis of the similarity between the samples based on the denaturing gradient gel electrophoresis banding patterns, which shows a clear difference between upper and lower ice sections with respect to phylotypes and their proportional abundance. Clone libraries constructed using diatom-specific primers confirm the high diversity of diatoms in the sea ice, and support the microscopic counts. Evidence of protistan grazing upon diatoms was also found in lower sections of the core, with implications for carbon and nutrient recycling in the ice.

Morphological, bacterial, and secondary metabolite changes of Aplysina aerophoba upon long-term maintenance under artificial conditions

The aim of this study was to analyze successional changes in the bacterial community over a period of 6 months of cultivation of Aplysina aerophoba sponges under different artificial cultivation conditions by use of denaturing gradient gel electrophoresis (DGGE). The cultivation conditions varied concerning the water temperature (20 +/- 2 degrees C and 25 +/- 2 degrees C) of the aquaria, additional illumination of one aquarium, and feeding of the sponges. Amplicons from DGGE separation of dominant colonizing or variably appearing bacteria were sequenced and aligned for taxonomical identification. In addition, secondary metabolites typically found in A. aerophoba were analyzed to investigate changes in the natural product profile during cultivation. The cultivation of sponges under any given condition did not lead to a depletion of their bacterial community in the course of the experiment. On the contrary, the distinctive set of associated bacteria was maintained in spite of a dramatic loss of biomass and morphological degradation during the cultivation period. Generally, all sequences obtained from the DGGE gels were related to bacteria of five phyla: Actinobacteria, Cyanobacteria, alpha-Proteobacteria, gamma-Proteobacteria, and Chloroflexi. Despite the overall stability of the bacterial community in A. aerophoba, an unambiguous variability was detected for the Cyanobacteria "A. aerophoba clone TK09". This variability was ascribed to the predominant light conditions. The analysis of the metabolic pattern revealed that the concentration of a class of characteristic-brominated compounds typically found in A. aerophoba, like aeroplysinin-1, aerophobin-1, aerophobin-2, and isofistularin-3, increased over the 6 months of cultivation.

Evidence that chytrids dominate fungal communities in high-elevation soils

Periglacial soils are one of the least studied ecosystems on Earth, yet they are widespread and are increasing in area due to retreat of glaciers worldwide. Soils in these environments are cold and during the brief summer are exposed to high levels of UV radiation and dramatic fluctuations in moisture and temperature. Recent research suggests that these environments harbor immense microbial diversity. Here we use sequencing of environmental DNA, culturing of isolates, and analysis of environmental variables to show that members of the Chytridiomycota (chytrids) dominate fungal biodiversity and perhaps decomposition processes in plant-free, high-elevation soils from the highest mountain ranges on Earth. The zoosporic reproduction of chytrids requires free water, yet we found that chytrids constituted over 70% of the ribosomal gene sequences of clone libraries from barren soils of the Himalayas and Rockies; by contrast, they are rare in other soil environments. Very few chytrids have been cultured, although we were successful at culturing chytrids from high-elevation sites throughout the world. In a more focused study of our sites in Colorado, we show that carbon sources that support chytrid growth (eolian deposited pollen and microbial phototrophs) are abundant and that soils are saturated with water for several months under the snow, thus creating ideal conditions for the development of a chytrid-dominated ecosystem. Our work broadens the known biodiversity of the Chytridomycota, and describes previously unsuspected links between aquatic and terrestrial ecosystems in alpine regions.

Wine yeast molecular typing using a simplified method for simultaneously extracting mtDNA, nuclear DNA and virus dsRNA

Quick and accurate methods are required for the identification of industrial, environmental, and clinical yeast strains. We propose a rapid method for the simultaneous extraction of yeast mtDNA, nuclear DNA, and virus dsRNA. It is simpler, cheaper, and faster than the previously reported methods. It allows one to choose among a broad range of molecular analysis approaches for yeast typing, avoiding the need to use of several different methods for the separate extraction of each nucleic acid type. The application of this method followed by the combined analysis of mtDNA and dsRNA (ScV-M and W) is a highly attractive option for fast and efficient wine yeast typing.

Genetic diversity of eukaryotic plankton assemblages in Eastern Tibetan Lakes differing by their salinity and altitude

Eukaryotic plankton assemblages in 11 high-mountain lakes located at altitudes of 2,817 to 5,134 m and over a total area of ca. one million square kilometers on the Eastern Tibet Plateau, spanning a salinity gradient from 0.2 (freshwater) to 187.1 g l(-1) (hypersaline), were investigated by cultivation independent methods. Two 18S rRNA gene-based fingerprint approaches, i.e., the terminal restriction fragment length polymorphism and denaturing gradient gel electrophoresis (DGGE) with subsequent band sequencing were applied. Samples of the same lake type (e.g., freshwater) generally shared more of the same bands or T-RFs than samples of different types (e.g., freshwater versus saline). However, a certain number of bands or T-RFs among the samples within each lake were distinct, indicating the potential presence of significant genetic diversity within each lake. PCA indicated that the most significant environmental gradient among the investigated lakes was salinity. The observed molecular profiles could be further explained (17-24%) by ion percentage of chloride, carbonate and bicarbonate, and sulfate, which were also covaried with change of altitude and latitude. Sequence analysis of selected major DGGE bands revealed many sequences (largely protist) that are not related to any known cultures but to uncultured eukaryotic picoplankton and unidentified eukaryotes. One fourth of the retrieved sequences showed < or =97% similarity to the closest sequences in the GenBank. Sequences related to well-known heterotrophic nanoflagellates were not retrieved from the DGGE gels. Several groups of eukaryotic plankton, which were found worldwide and detected in low land lakes, were also detected in habitats located above 4,400 m, suggesting a cosmopolitan distribution of these phylotypes. Collectively, our study suggests that there was a high beta-diversity of eukaryotic plankton assemblages in the investigated Tibetan lakes shaped by multiple geographic and environmental factors.

Molecular diversity of myxomycetes associated with decaying wood and forest floor leaf litter

Denaturing gradient gel electrophoresis (DGGE) fingerprinting was used to assess the molecular diversity of myxomycetes from environmental samples (decaying wood and forest floor litter) collected at the Mushroom Research Centre in northern Thailand. Total genomic DNA was extracted directly from environmental samples on which myxomycetes were not apparent. Part of the small subunit ribosomal RNA gene (SSU rDNA) was amplified and DNA sequences analyzed. DGGE gels revealed up to 17 operational taxonomic units (OTU) from decaying wood and 10 OTU from forest floor litter samples, but only seven (wood) and six (litter) OTU could be re-amplified and/or sequenced. Based on results obtained with the BLAST analysis program, the species involved appeared to correspond most closely to Diderma saundersii, Didymium iridis, Stemonitis flavogenita and Hyperamoeba sp. strain W2i on decaying wood and to Diderma saundersii and Physarum didermoides on forest floor litter. Our results suggest that then PCR-DGGE can be used to obtain data on the presence of myxomycetes in their primary microhabitats without the need to observe the sporocarps of these organisms. As such the technique would seem to have considerable potential for contributing to a more complete understanding of myxomycete diversity and ecology in terrestrial ecosystems.

Subsurface ecosystem resilience: long-term attenuation of subsurface contaminants supports a dynamic microbial community

The propensity for groundwater ecosystems to recover from contamination by organic chemicals (in this case, coal-tar waste) is of vital concern for scientists and engineers who manage polluted sites. The microbially mediated cleanup processes are also of interest to ecologists because they are an important mechanism for the resilience of ecosystems. In this study we establish the long-term dynamic nature of a coal-tar waste-contaminated site and its microbial community. We present 16 years of chemical monitoring data, tracking responses of a groundwater ecosystem to organic contamination (naphthalene, xylenes, toluene, 2-methyl naphthalene and acenaphthylene) associated with coal-tar waste. In addition, we analyzed small-subunit (SSU) ribosomal RNA (rRNA) genes from two contaminated wells at multiple time points over a 2-year period. Principle component analysis of community rRNA fingerprints (terminal-restriction fragment length polymorphism (T-RFLP)) showed that the composition of native microbial communities varied temporally, yet remained distinctive from well to well. After screening and analysis of 1178 cloned SSU rRNA genes from Bacteria, Archaea and Eukarya, we discovered that the site supports a robust variety of eukaryotes (for example, alveolates (especially anaerobic and predatory ciliates), stramenopiles, fungi, even the small metazoan flatworm, Suomina) that are absent from an uncontaminated control well. This study links the dynamic microbial composition of a contaminated site with the long-term attenuation of its subsurface contaminants.

Community structure and dynamics of small eukaryotes targeted by new oligonucleotide probes: new insight into the lacustrine microbial food web

The seasonal dynamics of the small eukaryotic fraction (cell diameter, 0.2 to 5 microm) was investigated in a mesotrophic lake by tyramide signal amplification-fluorescence in situ hybridization targeting seven different phylogenetic groups: Chlorophyceae, Chrysophyceae, Cryptophyceae, Cercozoa, LKM11, Perkinsozoa (two clades), and Fungi. The abundance of small eukaryotes ranged from 1,692 to 10,782 cells ml(-1). The dominant groups were the Chrysophyceae and the Chlorophyceae, which represented 19.6% and 17.9% of small eukaryotes, respectively. The results also confirmed the quantitative importance of putative parasites, Fungi and Perkinsozoa, in the small heterotrophic eukaryotic assemblage. The relative abundances recorded for the Perkinsozoa group reached as much as 31.6% of total targeted eukaryotes during the summer. The dynamics of Perkinsozoa clade 1 coincided with abundance variations in Peridinium and Ceratium spp. (Dinoflagellates), while the dynamics of Perkinsozoa clade 2 was linked to the presence of Dinobryon spp. (Chrysophyceae). Fungi, represented by chytrids, reached maximal abundance in December (569 cells ml(-1)) and were mainly correlated with the dynamics of diatoms, especially Melosira varians. A further new finding of this study is the recurrent presence of Cercozoa (6.2%) and LKM11 (4.5%) cells. This quantitative approach based on newly designed probes offers a promising means of in-depth analysis of microbial food webs in lakes, especially by revealing the phylogenetic composition of the small heterotrophic flagellate assemblage, for which an important fraction of cells are generally unidentified by classical microscopy (on average, 96.8% of the small heterotrophic flagellates were identified by the specific probes we used in this study).

Vertical distribution of metabolically active eukaryotes in the water column and sediments of the Black Sea

Recent DNA-based phylogenetic studies have reported high eukaryotal diversities in a wide range of settings including samples obtained from anoxic environments. However, parallel RNA-based surveys are required in order to verify whether the species detected are in fact metabolically active in such extreme environments. The Black Sea is the World's largest anoxic basin but remains undersampled with respect to molecular eukaryotic diversity studies. Here, we report the distribution of active eukaryotes (18S rRNA-based survey) along a vertical nutrient and redox gradient in the water column and surface sediments of the Black Sea. A wide variety of eukaryotes were active in suboxic deep waters. Notably, certain species were active but escaped detection during a parallel 18S rDNA survey. The 18S rDNA survey from surface sediments yielded taxa of pelagic origin but none of these were identified from the water column at the time of sampling. Our data also indicate that gene transcripts do not always provide unequivocal proof that active microorganisms are indigenous to a specific position in an environmental gradient, because certain zoo- and phytoplankton species were still viable with detectable 18S rRNA in up to 300-year-old sulfidic sediments that underlie approximately 830 m of sulfidic waters.

Phylogenetic diversity and antimicrobial activities of fungi associated with Haliclona simulans isolated from Irish coastal waters

The diversity and antimicrobial activities of 80 fungi isolated from Haliclona simulans were assessed using different fungal media containing either agar or gellum gum. In total, 19 different genotypes were detected. These fungal isolates could be classified as members of the Agaricomycotina, Mucoromycotina, Saccharomycotina, and Pezizomycotina, although the majority of the isolates were associated with the latter class. Some of these fungal isolates showed antimicrobial inhibition of Escherichia coli, Bacillus sp., Staphylococcus aureus, and Candida glabrata. Fungal 18S rRNA gene sequences belonging to Eurotiales, Calosphaeriales, and Chaetothyriales were amplified from DNA and RNA extracted from this marine sponge. This study indicates that in contrast to the low diversity of fungi detected by polymerase chain reaction (PCR) and reverse transcription (RT)-PCR amplification from extracts of this marine sponge, a much higher diversity of fungi could be cultured. The data suggests that some fungi live in symbiosis with H. simulans, whereas other fungi may have been ingested from the surrounding seawater.

Relative diversity and community structure of ciliates in stream biofilms according to molecular and microscopy methods

Ciliates are an important component of aquatic ecosystems, acting as predators of bacteria and protozoa and providing nutrition for organisms at higher trophic levels. Understanding of the diversity and ecological role of ciliates in stream biofilms is limited, however. Ciliate diversity in biofilm samples from four streams subject to different impacts by human activity was assessed using microscopy and terminal restriction fragment length polymorphism (T-RFLP) analysis of 18S rRNA sequences. Analysis of 3' and 5' terminal fragments yielded very similar estimates of ciliate diversity. The diversity detected using microscopy was consistently lower than that suggested by T-RFLP analysis, indicating the existence of genetic diversity not apparent by morphological examination. Microscopy and T-RFLP analyses revealed similar relative trends in diversity between different streams, with the lowest level of biofilm-associated ciliate diversity found in samples from the least-impacted stream and the highest diversity in samples from moderately to highly impacted streams. Multivariate analysis provided evidence of significantly different ciliate communities in biofilm samples from different streams and seasons, particularly between a highly degraded urban stream and less impacted streams. Microscopy and T-RFLP data both suggested the existence of widely distributed, resilient biofilm-associated ciliates as well as ciliate taxa restricted to sites with particular environmental conditions, with cosmopolitan taxa being more abundant than those with restricted distributions. Differences between ciliate assemblages were associated with water quality characteristics typical of urban stream degradation and may be related to factors such as nutrient availability and macroinvertebrate communities. Microscopic and molecular techniques were considered to be useful complementary approaches for investigation of biofilm ciliate communities.

The fungal colonisation of rock-art caves: experimental evidence

The conservation of rock-art paintings in European caves is a matter of increasing interest. This derives from the bacterial colonisation of Altamira Cave, Spain and the recent fungal outbreak of Lascaux Cave, France-both included in the UNESCO World Heritage List. Here, we show direct evidence of a fungal colonisation of rock tablets in a testing system exposed in Altamira Cave. After 2 months, the tablets, previously sterilised, were heavily colonised by fungi and bacteria. Most fungi isolated were labelled as entomopathogens, while the bacteria were those regularly identified in the cave. Rock colonisation was probably promoted by the dissolved organic carbon supplied with the dripping and condensation waters and favoured by the displacement of aerosols towards the interior of the cave, which contributed to the dissemination of microorganisms. The role of arthropods in the dispersal of spores may also help in understanding fungal colonisation. This study evidences the fragility of rock-art caves and demonstrates that microorganisms can easily colonise bare rocks and materials introduced into the cavity.

Comparative study of three analysis methods (TTGE, flow cytometry and HPLC) for xenobiotic impact assessment on phytoplankton communities

The impacts of the fungicide Opus (epoxiconazole) on marine phytoplankton communities were assessed in a 12-day field experiment using in situ microcosms maintained underwater at 6 m depth. Three community analysis methods were compared for their sensitivity threshold in fungicide impact detection. When phytoplankton communities were exposed to 1 microg l(-1) of epoxiconazole, no effects could be demonstrated using TTGE (Temporal Temperature Gradient gel Electrophoresis), flow cytometry or HPLC. When exposed to 10 microg l(-1), TTGE fingerprints from PCR amplified 18S rDNA of communities exhibited significant differences compared with controls (ANOSIM, P = 0.028). Neither flow cytometry counts, nor HPLC pigment profiles allowed to show significant differences in microcosms exposed to 10 microg l(-1) of epoxiconazole. When exposed to 100 microg l(-1), all three methods allowed to detect significant differences in treated microcosms, as compared to controls. The TTGE analysis appears in this study as the most sensitive method for fungicide impact assessment on eukaryote microbial communities.

Influence of nutrient status and grazing pressure on the fate of Francisella tularensis in lake water

The natural reservoir of Francisella tularensis, the causative agent of tularaemia, is yet to be identified. We investigated the possibility that Francisella persists in natural aquatic ecosystems between outbreaks. It was hypothesized that nutrient-rich environments, with strong protozoan predation, favour the occurrence of the tularaemia bacterium. To investigate the differences in adaptation to aquatic environments of the species and subspecies of Francisella, we screened 23 strains for their ability to survive grazing by the ciliate Tetrahymena pyriformis. All the Francisella strains tested were consumed at a low rate, although significant differences between subspecies were found. The survival and virulence of gfp-labelled F. tularensis ssp. holarctica were then studied in a microcosm experiment using natural lake water, with varying food web complexities and nutrient availabilities. High nutrient conditions in combination with high abundances of nanoflagellates were found to favour F. tularensis ssp. holarctica. The bacterium was observed both free-living and within the cells of a nanoflagellate. Francisella tularensis entered a viable but nonculturable state during the microcosm experiment. When studied over a longer period of time, F. tularensis ssp. holarctica survived in the lake water, but loss of virulence was not prevented by either high nutrient availability or the presence of predators.

Effect of soil sample preservation, compared to the effect of other environmental variables, on bacterial and eukaryotic diversity

Archived soil samples are a valuable source for retrospective ecological studies, and their recent analysis using molecular ecological approaches has drawn significant attention within the scientific community. However, the possibility of addressing ecological questions regarding detectable microbiota in dried and extensively stored soils has not yet been fully evaluated. To achieve this, soil samples collected from two long-term grassland experiments in the United Kingdom and The Netherlands were subjected to air-drying at 40-42 degrees C and stored at room temperature. Total bacterial, Bacillus benzoevorans-related and eukaryotic communities associated with these samples were analyzed by DGGE-fingerprinting of PCR-amplified ribosomal RNA gene fragments. Changes in microbial community structure due to drying and storage were evaluated by multivariate analysis in relation to changes caused by other environmental conditions, such as soil pH, type of fertilizer and vegetation. Soil drying and storage affected the detectable community structure, but did not materially impair our capacity to identify the effect of soil parameters studied in long-term grassland experiments. Although, in some cases, the amplitude of the influence of a given parameter changed due to sample preservation, analyses revealed that pH, fertilization and soil type significantly influenced microbial community structure in the analyzed samples.

Spatial distribution of bacterial communities in sediment of a eutrophic lake revealed by denaturing gradient gel electrophoresis and multivariate analysis

Bacterial community structure and the effects of several environmental factors on the microbial community distribution were investigated in the sediment of the eutrophic Lake Xuanwu. Profiles of bacterial communities were generated using denaturing gradient gel electrophoresis (DGGE), and the results were interpreted with multivariate statistical analysis. Five major variables in sediment were examined in a principal component analysis, which indicates notable differences of physicochemical parameters among different sites of the lake. To assess changes in the genetic diversity of bacterial communities of different sampling sites, DGGE band patterns were analyzed by multidimensional scaling analysis, which indicated that sampling sites having similar environmental characteristics also have the similar microbial communities. Canonical correspondence analysis demonstrated that pH and redox potential had significant effects on the bacterial community composition in the sediments. Analysis of DNA sequences revealed that the dominant bacterial groups in Lake Xuanwu belonged to Proteobacteria , Actinobacteria , Verrucomicrobia , and Nitrospirae , which are commonly isolated from freshwater ecosystems.

NEW STREPTOPHYTE GREEN ALGAE FROM TERRESTRIAL HABITATS AND AN ASSESSMENT OF THE GENUS INTERFILUM (KLEBSORMIDIOPHYCEAE, STREPTOPHYTA)(1)

Sarcinoid aeroterrestrial green algae were isolated from three arid locations in Ukraine and the Czech Republic. Although gross morphology suggested an affinity with Desmococcus (for taxonomic authorities, see Table S1 in the supplementary material), the cellular morphological characteristics were reminiscent of those of Geminella terricola. However, the presence of a complex of ultrastructural features indicated that these isolates were members of the streptophyte lineage in the green plants. 18S rDNA sequence phylogenies provided evidence of a close relationship with Klebsormidium in the Streptophyta, while the position of Desmococcus was within the Trebouxiophyceae. In the internal transcribed spacer (ITS) rDNA phylogeny, the sarcinoid isolates were closely related with strains of G. terricola and Interfilum paradoxum. Strains of that clade were morphologically united by a specific type of cell division that involves the association of persistent, cap-shaped remains of the mother cell wall with daughter cells. Consequently, these strains were assigned to a redefined genus Interfilum, and a new species, I. massjukiae, was described to accommodate one of the sarcinoid isolates. As the position of the genus Geminella was in the Trebouxiophyceae, the streptophyte G. terricola was transferred to Interfilum, as I. terricola comb. nov., but the ITS rDNA analyses proved inconclusive to resolve its affinities with other species of Interfilum due to intragenomic polymorphisms. The species of Interfilum had a closer relationship with K. flaccidum than with other species of Klebsormidium. The latter genus may not be monophyletic in its present circumscription.

A window of environmental dependence is evident in multiple phylogenetically distinct subgroups in the faecal community of piglets

Microbial colonization in neonates has a profound impact on host development. In pigs, we have observed that a window of environmental dependence occurs during neonatal development. This was evident by the sudden onset of faecal community similarity in cohoused neonatal piglets at 3 weeks of age. This effect is postulated to represent a general change in gut community structure. Here, three phylogenetic groups (Clostridium leptum subgroup, Bacteroides and enterobacteria) that were predicted to have distinct ecological roles were monitored using nested denaturing gradient gel electrophoresis to determine the extent to which this window of environmental dependence was exerted throughout the gut community. Colonization trends were found to be similar for all subgroups despite predicted differences in the functional role and niche, and increased similarity between cohabiting piglets occurred in multiple phylogenetic subgroups. This supports the hypothesis that a distinct phase in neonatal development commences after 2 weeks whereby multiple subcommunities of the gut are strongly influenced by the environment.

High beta diversity of bacteria in the shallow terrestrial subsurface

While there have been a vast number of studies on bacterial alpha diversity in the shallow terrestrial subsurface, beta diversity - how the bacterial community composition changes with spatial distance - has received surprisingly limited attention. Here, bacterial beta diversity and its controlling factors are investigated by denaturing gradient gel electrophoresis and cloning of samples from a 700-cm-long sediment core, the lower half of which consisted of marine-originated sediments. According to canonical correspondence analysis with variation partitioning, contemporary environmental variables explain beta diversity in a greater proportion than depth. However, we also found that community similarity decayed significantly with spatial distance and the slopes of the distance-decay relationships are relatively high. The high beta diversity indicates that the bacterial distribution patterns are not only controlled by contemporary environments, but also related to historical events, that is, dispersal or depositional history. This is highlighted by the different beta diversity patterns among studied sediment layers. We thus conclude that the high beta diversity in the shallow terrestrial subsurface is a trade-off between historical events and environmental heterogeneity. Furthermore, we suggest that the high beta diversity of bacteria is likely to be recapitulated in other terrestrial sites because of the great frequency of high geochemical and/or historical variations along depth.

Reproducing stone monument photosynthetic-based colonization under laboratory conditions

In order to understand the biodeterioration process occurring on stone monuments, we analyzed the microbial communities involved in these processes and studied their ability to colonize stones under controlled laboratory experiments. In this study, a natural green biofilm from a limestone monument was cultivated, inoculated on stone probes of the same lithotype and incubated in a laboratory chamber. This incubation system, which exposes stone samples to intermittently sprinkling water, allowed the development of photosynthetic biofilms similar to those occurring on stone monuments. Denaturing gradient gel electrophoresis (DGGE) analysis was used to evaluate the major microbial components of the laboratory biofilms. Cyanobacteria, green microalgae, bacteria and fungi were identified by DNA-based molecular analysis targeting the 16S and 18S ribosomal RNA genes. The natural green biofilm was mainly composed by the Chlorophyta Chlorella, Stichococcus, and Trebouxia, and by Cyanobacteria belonging to the genera Leptolyngbya and Pleurocapsa. A number of bacteria belonging to Alphaproteobacteria, Bacteroidetes and Verrucomicrobia were identified, as well as fungi from the Ascomycota. The laboratory colonization experiment on stone probes showed a colonization pattern similar to that occurring on stone monuments. The methodology described in this paper allowed to reproduce a colonization equivalent to the natural biodeteriorating process.

Bacterial, archaeal, and eukaryal diversity in the intestines of Korean people

The bacterial, archaeal, and eukaryal diversity in fecal samples from ten Koreans were analyzed and compared by using the PCR-fingerprinting method, denaturing gradient gel electrophoresis (DGGE). The bacteria all belonged to the Firmicutes and Bacteroidetes phyla, which were known to be the dominant bacterial species in the human intestine. Most of the archaeal sequences belonged to the methane-producing archaea but several halophilic archarea-related sequences were also detected unexpectedly. While a small number of eukaryal sequences were also detected upon DGGE analysis, these sequences were related to fungi and stramenopiles (Blastocystis hominis). With regard to the bacterial and archaeal DGGE analysis, all ten samples had one and two prominent bands, respectively, but many individual-specific bands were also observed. However, only five of the ten samples had small eukaryal DGGE bands and none of these bands was observed in all five samples. Unweighted pair group method and arithmetic averages clustering algorithm (UPGMA) clustering analysis revealed that the archaeal and bacterial communities in the ten samples had relatively higher relatedness (the average Dice coefficient values were 68.9 and 59.2% for archaea and bacteria, respectively) but the eukaryal community showed low relatedness (39.6%).

Genetic diversity of eukaryotic microorganisms in Lake Taihu, a large shallow subtropical lake in china

We investigated the genetic diversity of eukaryotic microorganisms (0.8-20 microm) by sequencing cloned 18S rRNA genes in six genetic libraries constructed from six locations in Lake Taihu, a large shallow subtropical lake in China. Genetic libraries of eukaryotic ribosomal RNA were screened by restriction fragment length polymorphism (RFLP) analysis, and one clone representative of each RFLP pattern was partially sequenced. A total of 528 clones were clustered into 165 RFLP patterns and finally into 131 operational taxonomic unit (OTUs). Phylogenetic analysis revealed that each library included many unique OTUs, as well as members of distantly related phylogenetic groups. A majority of the clones were from alveolates, stramenopiles, cercozoa, cryptophytes, chlorophytes, and fungi, with members of choanoflagellida, euglenida, centroheliozoa, ancyromonadidae, ichthyosporea, and kathablepharid representing a minor fraction of the library. Six OTUs (15 clones) were not related to any known eukaryotic group. Canonical correspondence analysis suggested that the differences in eukaryotic microorganism community composition of in the six regions were partially related to trophic status, sediment resuspension, and top-down regulation by metazooplankton.

Diversity and dynamics of Antarctic marine microbial eukaryotes under manipulated environmental UV radiation

In the light of the predicted global climate change, it is essential that the status and diversity of polar microbial communities is described and understood. In the present study, molecular tools were used to investigate the marine eukaryotic communities of Prydz Bay, Eastern Antarctica, from November 2002 to January 2003. Additionally, we conducted four series of minicosm experiments, where natural Prydz Bay communities were incubated under six different irradiation regimes, in order to investigate the effects of natural UV radiation on marine microbial eukaryotes. Denaturing gradient gel electrophoresis (DGGE) and 18S rRNA gene sequencing revealed a eukaryotic Shannon diversity index averaging 2.26 and 2.12, respectively. Phylogenetic analysis of 472 sequenced clones revealed 47 phylotypes, belonging to the Dinophyceae, Stramenopiles, Choanoflagellidae, Ciliophora, Cercozoa and Metazoa. Throughout the studied period, three communities were distinguished: a postwinter/early spring community comprising dinoflagellates, ciliates, cercozoans, stramenopiles, viridiplantae, haptophytes and metazoans; a dinoflagellate-dominated community; and a diatom-dominated community that developed after sea ice breakup. DGGE analysis showed that size fraction and time had a strong shaping effect on the community composition; however, a significant contribution of natural UV irradiance towards microeukaryotic community composition could not be detected. Overall, dinoflagellates dominated our samples and their diversity suggests that they fulfill an important role in Antarctic coastal marine ecosystems preceding ice breakup as well as between phytoplankton bloom events.

13C-isotope analyses reveal that chemolithoautotrophic Gamma- and Epsilonproteobacteria feed a microbial food web in a pelagic redoxcline of the central Baltic Sea

Marine pelagic redoxclines are zones of high dark CO(2) fixation rates, which can correspond up to 30% of the surface primary production. However, despite this significant contribution to the pelagic carbon cycle, the identity of most chemolithoautotrophic organisms is still unknown. Therefore, the aim of this study was to directly link the dark CO(2) fixation capacity of a pelagic redoxcline in the central Baltic Sea (Landsort Deep) with the identity of the main chemolithoautotrophs involved. Our approach was based on the analysis of natural carbon isotope signatures in fatty acid methyl esters (FAMEs) and on measurements of CO(2) incorporation in (13)C-bicarbonate pulse experiments. The incorporation of (13)C into chemolithoautotrophic cells was investigated by rRNA-based stable isotope probing (RNA-SIP) and FAME analysis after incubation for 24 and 72 h under in situ conditions. Our results demonstrated that fatty acids indicative of Proteobacteria were significantly enriched in (13)C slightly below the chemocline. RNA-SIP analyses revealed that two different Gammaproteobacteria and three closely related Epsilonproteobacteria of the Sulfurimonas cluster were active dark CO(2)-fixing microorganisms, with a time-dependent community shift between these groups. Labelling of Archaea was not detectable, but after 72 h of incubation the (13)C-label had been transferred to a potentially bacterivorous ciliate related to Euplotes sp. Thus, RNA-SIP provided direct evidence for the contribution of chemolithoautotrophic production to the microbial food web in this marine pelagic redoxcline, emphasizing the importance of dark CO(2)-fixing Proteobacteria within this habitat.