Response of the metabolic activity and taxonomic composition of bacterial communities to mosaically varying soil salinity and alkalinity

Soil salinity and sodicity is a worldwide problem that affects the composition and activity of bacterial communities and results from elevated salt and sodium contents. Depending on the degree of environmental pressure and the combined effect of other factors, haloalkalitolerant and haloalkaliphilic bacterial communities will be selected. These bacteria play a potential role in the maintenance and restoration of salt-affected soils; however, until recently, only a limited number of studies have simultaneously studied the bacterial diversity and activity of saline-sodic soils. Soil samples were collected to analyse and compare the taxonomic composition and metabolic activity of bacteria from four distinct natural plant communities at three soil depths corresponding to a salinity‒sodicity gradient. Bacterial diversity was detected using 16S rRNA gene Illumina MiSeq amplicon sequencing. Community-level physiological profiles (CLPPs) were analysed using the MicroResp™ method. The genus-level bacterial composition and CLPPs differed significantly in soils with different alkaline vegetation. The surface soil samples also significantly differed from the intermediate and deep soil samples. The results showed that the pH, salt content, and Na+ content of the soils were the main edaphic factors influencing both bacterial diversity and activity. With salinity and pH, the proportion of the phylum Gemmatimonadota increased, while the proportions of Actinobacteriota and Acidobacteriota decreased.

Calcium carbonate precipitating extremophilic bacteria in an Alpine ice cave

Extensive research has provided a wealth of data on prokaryotes in caves and their role in biogeochemical cycles. Ice caves in carbonate rocks, however, remain enigmatic environments with limited knowledge of their microbial taxonomic composition. In this study, bacterial and archaeal communities of the Obstans Ice Cave (Carnic Alps, Southern Austria) were analyzed by next-generation amplicon sequencing and by cultivation of bacterial strains at 10 °C and studying their metabolism. The most abundant bacterial taxa were uncultured Burkholderiaceae and Brevundimonas spp. in the drip water, Flavobacterium, Alkanindiges and Polaromonas spp. in the ice, Pseudonocardia, Blastocatella spp., uncultured Pyrinomonadaceae and Sphingomonadaceae in carbonate precipitates, and uncultured Gemmatimonadaceae and Longimicrobiaceae in clastic cave sediments. These taxa are psychrotolerant/psychrophilic and chemoorganotrophic bacteria. On a medium with Mg2+/Ca2+ = 1 at 21 °C and 10 °C, 65% and 35% of the cultivated strains precipitated carbonates, respectively. The first ~ 200 µm-size crystals appeared 2 and 6 weeks after the start of the cultivation experiments at 21 °C and 10 °C, respectively. The crystal structure of these microbially induced carbonate precipitates and their Mg-content are strongly influenced by the Mg2+/Ca2+ ratio of the culture medium. These results suggest that the high diversity of prokaryotic communities detected in cryogenic subsurface environments actively contributes to carbonate precipitation, despite living at the physical limit of the presence of liquid water.

Habitat-related variability in the morphological and taxonomic diversity of microbial communities in two Hungarian epigenic karst caves

The physical and chemical characteristics of the bedrock, along with the geological and hydrological conditions of karst caves may influence the taxonomic and functional diversity of prokaryotes. Most studies so far have focused on microbial communities of caves including only a few samples and have ignored the chemical heterogeneity of different habitat types such as sampling sites, dripping water, carbonate precipitates, cave walls, cave sediment and surface soils connected to the caves. The aim of the present study was to compare the morphology, the composition and physiology of the microbiota in caves with similar environmental parameters (temperature, host rock, elemental and mineral composition of speleothems) but located in different epigenic karst systems. Csodabogyós Cave and Baradla Cave (Hungary) were selected for the analysis of bacterial and archaeal communities using electron microscopy, amplicon sequencing, X-ray diffraction, and mass spectroscopic techniques. The microbial communities belonged to the phyla Pseudomonadota, Acidobacteriota, Nitrospirota and Nitrososphaerota, and they showed site-specific variation in composition and diversity. The results indicate that morphological and physiological adaptations provide survival for microorganisms according to the environment. In epigenic karst caves, prokaryotes are prone to increase their adsorption surface, cooperate in biofilms, and implement chemolithoautotrophic growth with different electron-donors and acceptors available in the microhabitats.

Planktonic and epilithic prokaryota community compositions in a large temperate river reflect climate change related seasonal shifts

In freshwaters, microbial communities are of outstanding importance both from ecological and public health perspectives, however, they are threatened by the impact of global warming. To reveal how different prokaryotic communities in a large temperate river respond to environment conditions related to climate change, the present study provides the first detailed insight into the composition and spatial and year-round temporal variations of planktonic and epilithic prokaryotic community. Microbial diversity was studied using high-throughput next generation amplicon sequencing. Sampling was carried out monthly in the midstream and the littoral zone of the Danube, upstream and downstream from a large urban area. Result demonstrated that river habitats predominantly determine the taxonomic composition of the microbiota; diverse and well-differentiated microbial communities developed in water and epilithon, with higher variance in the latter. The composition of bacterioplankton clearly followed the prolongation of the summer resulting from climate change, while the epilithon community was less responsive. Rising water temperatures was associated with increased abundances of many taxa (such as phylum Actinobacteria, class Gammaproteobacteria and orders Synechococcales, Alteromonadales, Chitinophagales, Pseudomonadales, Rhizobiales and Xanthomonadales), and the composition of the microbiota also reflected changes of several further environmental factors (such as turbidity, TOC, electric conductivity, pH and the concentration of phosphate, sulphate, nitrate, total nitrogen and the dissolved oxygen). The results indicate that shift in microbial community responding to changing environment may be of crucial importance in the decomposition of organic compounds (including pollutants and xenobiotics), the transformation and accumulation of heavy metals and the occurrence of pathogens or antimicrobial resistant organisms.

Variation in Sodic Soil Bacterial Communities Associated with Different Alkali Vegetation Types

In this study, we examined the effect of salinity and alkalinity on the metabolic potential and taxonomic composition of microbiota inhabiting the sodic soils in different plant communities. The soil samples were collected in the Pannonian steppe (Hungary, Central Europe) under extreme dry and wet weather conditions. The metabolic profiles of microorganisms were analyzed using the MicroResp method, the bacterial diversity was assessed by cultivation and next-generation amplicon sequencing based on the 16S rRNA gene. Catabolic profiles of microbial communities varied primarily according to the alkali vegetation types. Most members of the strain collection were identified as plant associated and halophilic/alkaliphilic species of Micrococcus, Nesterenkonia, Nocardiopsis, Streptomyces (Actinobacteria) and Bacillus, Paenibacillus (Firmicutes) genera. Based on the pyrosequencing data, the relative abundance of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes and Bacteroidetes also changed mainly with the sample types, indicating distinctions within the compositions of bacterial communities according to the sodic soil alkalinity-salinity gradient. The effect of weather extremes was the most pronounced in the relative abundance of the phyla Actinobacteria and Acidobacteria. The type of alkali vegetation caused greater shifts in both the diversity and activity of sodic soil microbial communities than the extreme aridity and moisture.

In situ modelling of biofilm formation in a hydrothermal spring cave

Attachment of microorganisms to natural or artificial surfaces and the development of biofilms are complex processes which can be influenced by several factors. Nevertheless, our knowledge on biofilm formation in karstic environment is quite incomplete. The present study aimed to examine biofilm development for a year under controlled conditions in quasi-stagnant water of a hydrothermal spring cave located in the Buda Thermal Karst System (Hungary). Using a model system, we investigated how the structure of the biofilm is formed from the water and also how the growth rate of biofilm development takes place in this environment. Besides scanning electron microscopy, next-generation DNA sequencing was used to reveal the characteristic taxa and major shifts in the composition of the bacterial communities. Dynamic temporal changes were observed in the structure of bacterial communities. Bacterial richness and diversity increased during the biofilm formation, and 9-12 weeks were needed for the maturation. Increasing EPS production was also observed from the 9-12 weeks. The biofilm was different from the water that filled the cave pool, in terms of the taxonomic composition and metabolic potential of microorganisms. In these karstic environments, the formation of mature biofilm appears to take place relatively quickly, in a few months.

Bacterial Diversity of a High-Altitude Permafrost Thaw Pond Located on Ojos del Salado (Dry Andes, Altiplano-Atacama Region)

Microbial ecology of permafrost, due to its ecological and astrobiological importance, has been in the focus of studies in past decades. Although permafrost is an ancient and stable environment, it is also subjected to current climate changes. Permafrost degradation often results in generation of thaw ponds, a phenomenon not only reported mainly from polar regions but also present in high-altitude permafrost environments. Our knowledge about microbial communities of thaw ponds in these unique, remote mountain habitats is sparse. This study presents the first culture collection and results of the next-generation DNA sequencing (NGS) analysis of bacterial communities inhabiting a high-altitude permafrost thaw pond. In February 2016, a permafrost thaw pond on the Ojos del Salado at 5900 m a.s.l. (meters above sea level) was sampled as part of the Hungarian Dry Andes Research Programme. A culture collection of 125 isolates was established, containing altogether 11 genera belonging to phyla Bacteroidetes, Actinobacteria, and Proteobacteria. Simplified bacterial communities with a high proportion of candidate and hitherto uncultured bacteria were revealed by Illumina MiSeq NGS. Water of the thaw pond was dominated by Bacteroidetes and Proteobacteria, while in the sediment of the lake and permafrost, members of Acidobacteria, Actinobacteria, Bacteroidetes, Patescibacteria, Proteobacteria, and Verrucomicrobia were abundant. This permafrost habitat can be interesting as a potential Mars analog.

Effects of Active Volcanism on Bacterial Communities in the Highest-Altitude Crater Lake of Ojos del Salado (Dry Andes, Altiplano-Atacama Region)

Periglacial and volcanic environments are considered terrestrial analogs of Mars with regard to astrobiological characteristics due to their specific set of extreme features. Ojos del Salado, the highest volcano on Earth (6893 m a.s.l.), is surrounded by several craters, one of which harbors the highest known altitude lake (6480 m a.s.l.), which is influenced by a rare combination of extreme environmental factors, that is, low mean temperature, permafrost, fumarolic activity, acidity, and extreme low organic matter content. To assess the genetic diversity and ecological tolerance of bacteria, samples were taken in February 2016 from the sediments covered with acidic cold (pH 4.88, 3.8°C) and warm (pH 2.08, 40.8°C) water. As a control, a nonvolcanic high-altitude lake (at 5900 m a.s.l.) was also studied by both cultivation-based and next-generation DNA sequencing methods. Isolates from the crater lake showed tolerance toward acidic pH values, unlike isolates from the nonvolcanic lake. Illumina MiSeq sequencing of the 16S rRNA gene exposed simplified, although characteristically different, bacterial communities in the warm and cold water-saturated sediments. In the fumarolic creek sediments, acidophilic iron oxidizers (Ferrithrix, Gallionella) and iron reducers (Acidiphilium) were abundant, and bacteria involved in the sulfur oxidation (Hydrogenobaculum, Thiomonas) and reduction (Desulfosporosinus) were also detected. Therefore, we propose an integrated model that addresses the potential role of bacteria in the sulfur and iron geomicrobiological cycles.

Cave bacteria-induced amorphous calcium carbonate formation

Amorphous calcium carbonate (ACC) is a precursor of crystalline calcium carbonates that plays a key role in biomineralization and polymorph evolution. Here, we show that several bacterial strains isolated from a Hungarian cave produce ACC and their extracellular polymeric substance (EPS) shields ACC from crystallization. The findings demonstrate that bacteria-produced ACC forms in water-rich environment at room temperature and is stable for at least half year, which is in contrast to laboratory-produced ACC that needs to be stored in a desiccator and kept below 10 °C for avoiding crystallization. The ACC-shielding EPS consists of lipids, proteins, carbohydrates and nucleic acids. In particular, we identified large amount of long-chain fatty acid components. We suggest that ACC could be enclosed in a micella-like formula within the EPS that inhibits water infiltration. As the bacterial cells lyse, the covering protective layer disintegrates, water penetrates and the unprotected ACC grains crystallize to calcite. Our study indicates that bacteria are capable of producing ACC, and we estimate its quantity in comparison to calcite presumably varies up to 20% depending on the age of the colony. Since diverse bacterial communities colonize the surface of cave sediments in temperate zone, we presume that ACC is common in these caves and its occurrence is directly linked to bacterial activity and influences the geochemical signals recorded in speleothems.

Radioactive environment adapted bacterial communities constituting the biofilms of hydrothermal spring caves (Budapest, Hungary)

The thermal waters of Gellért Hill discharge area of the Buda Thermal Karst System (Hungary) are characterized by high (up to 1000 Bq/L) ²²²Rn-activity due to the radium-accumulating biogeochemical layers. Samples were taken from these ferruginous and calcareous layers developed on spring cave walls and water surface. Accumulation of potentially toxic metals (e.g. As, Hg, Pb, Sn, Sr, Zn) in the dense extracellular polymeric substance containing bacterial cells and remains was detected by inductively coupled plasma mass spectrometry. The comparison of bacterial phylogenetic diversity of the biofilm samples was performed by high throughput next generation sequencing (NGS). The analysis showed similar sets of mainly unidentified taxa of phyla Chloroflexi, Nitrospirae, Proteobacteria, Planctomycetes; however, large differences were found in their abundance. Cultivation-based method complemented with irradiation assay was performed using 5, 10 and 15 kGy doses of gamma-rays from a ⁶⁰Co-source to reveal the extreme radiation-resistant bacteria. The phyla Actinobacteria, Firmicutes, Proteobacteria (classes Alpha- Beta- and Gammaproteobacteria), Bacteriodetes and Deinococcus-Thermus were represented among the 452 bacterial strains. The applied irradiation treatments promoted the isolation of 100 different species, involving candidate novel species, as well. The vast majority of the isolates belonged to bacterial taxa previously unknown as radiation-resistant microorganisms. Members of the genera Paracoccus, Marmoricola, Dermacoccus and Kytococcus were identified from the 15 kGy dose irradiated samples. The close relatives of several known radiation-tolerant bacteria were also detected from the biofilm samples, alongside with bacteria capable of detoxification by metal accumulation, adsorption and precipitation in the form of calcium-carbonate which possibly maintain the viability of the habitat. The results suggest the establishment of a unique, extremophilic microbiota in the studied hydrothermal spring caves.

Dual bloom of green algae and purple bacteria in an extremely shallow soda pan

In April 2014, dual bloom of green algae and purple bacteria occurred in a shallow, alkaline soda pan (Kiskunság National Park, Hungary). The water was only 5 cm deep, in which an upper green layer was clearly separated from a near-sediment purple one. Based on microscopy and DNA-based identification, the upper was inhabited by a dense population of the planktonic green alga, Oocystis submarina Lagerheim, while the deeper layer was formed by purple, bacteriochlorophyll-containing bacteria, predominated by Thiorhodospira and Rhodobaca. Additional bacterial taxa with a presumed capability of anoxygenic phototrophic growth belonged to the genera Loktanella and Porphyrobacter. Comparing the bacterial community of the purple layer with a former blooming event in a nearby soda pan, similar functional but different taxonomic composition was revealed. Members from many dominant bacterial groups were successfully cultivated including potentially new species, which could be the result of the application of newly designed media.

Deinococcus fonticola sp. nov., isolated from a radioactive thermal spring in Hungary

A Gram-stain-negative, aerobic, non-motile and coccus-shaped bacterium, designated strain FeSDHB5-19^T, was isolated from a biofilm sample collected from a radioactive thermal spring (Budapest, Hungary), after exposure to 5 kGy gamma radiation. A polyphasic approach was used to study the taxonomic properties of strain FeSDHB5-19^T, which had highest 16S rRNA gene sequence similarity to Deinococcus antarcticus G3-6-20^T (96.5 %). The 16S rRNA gene sequence similarity to type strains of other Deinococcus species were 93.0 % or lower. The DNA G+C content of the draft genome sequence, consisting of 3.9 Mb, was 63.9 mol%. Strain FeSHDB5-19^T was found to grow at temperatures of 10-32 °C (optimum, 28 °C) and pH 5-10 (pH 6.5-7.5) and tolerated up to 1.5 % NaCl (w/v) with optimum growth at 0-0.5 % NaCl. The predominant fatty acids (>10 %) were C16 : 0 and C16 : 1ω7c. The cell-wall peptidoglycan type was A3β l-Orn-Gly1-2. The whole-cell sugars were glucose and low amounts of galactose. Strain FeSDHB5-19^T possessed MK-8 as the predominant respiratory quinone, typical of the genus Deinococcus. The polar lipid profile contained unidentified phosphoglycolipids and unidentified glycolipids. The isolate was found to be highly resistant to gamma (D10<8 kGy) and UV (D10~800 J m^-2) radiation. According to its genotypic, phenotypic and chemotaxonomic characteristics, strain FeSDHB5-19^T represents a novel species in the genus Deinococcus, for which the name Deinococcusfonticola sp. nov. is proposed. The type strain is FeSDHB5-19^T (=NCAIM B.02639^T=DSM 106917^T).

Bacterial diversity in soils of different Hungarian karst areas

Karst areas have great environmental importance as sources of subsurface water and often maintain very sensitive ecosystems. In recent years, increasing number of microbiological studies focused on the bacterial communities of karst soils. In this study, diversity examinations on two distinct Hungarian karst areas, Aggtelek and Tapolca, were performed using parallel cultivation and molecular cloning methods. The phylogenetic affiliation of bacterial strains and molecular clones was determined based on their 16S rRNA gene sequences. Bacterial isolates were identified as members of the phyla Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. Besides the taxa identified by cultivation, members of the phyla Chloroflexi, Cyanobacteria, Acidobacteria, Verrucomicrobia, and Gemmatimonadetes were detected by the cloning. The difference in the composition of soil bacterial communities was related to geographic locations and soil types. Both the highest and the lowest bacterial diversities were detected in samples from Aggtelek National Park, characterized by Leptic Luvisol and Rendzic Leptosol soil types. The difference in the composition of bacterial communities between Rendzic Leptosol and Leptic Phaeozem soil types at Tapolca could be the result of human impacts.

Unexpected consequences of bombing. Community level response of epiphytic diatoms to environmental stress in a saline bomb crater pond area

The spatial response of epiphytic diatom communities to environmental stress was studied in a moderately saline wetland area located in the plain of Danube-Tisza Interfluve, Hungary. The area is characterised by World War II bomb crater ponds and can be regarded as an excellent ecological model system where the dispersion of species is slightly limited by distance. To study the effect of environmental variables on the communities, canonical correspondence analysis was applied. Salinity, pH, total suspended solids, total phosphorous and depth proved to be significant environmental drivers in this analysis. The ecological status of the ponds was assessed with Ziemann’s halobity index, as the trophity-depending metric cannot be applied to these habitats (due to the naturally high phosphorus content). Ponds in “good” ecological status significantly differed from those appertaining to water quality category of “not-good” ecological status considering characteristic of natural astatic soda pans (e.g. salinity, pH, ammonium, total phosphorous concentration, nitrogen:phosphorous ratio and turbidity). The differences between epiphytic diatom communities inhabiting the ponds were detected using non-parametric multidimensional scaling. The samples formed three groups according to the types of ponds (“transparent”, “transitional” and “turbid”) based on the width of the macrophyte belt around them. Indicator species related to the ecological status of the ponds and diatom communities contributing to the separation of groups of ponds were identified. One of the indicator species differed from species already described. Light and scanning electron microscopy features and phylogenetic analyses based on three genes (18S and 28S rRNA genes, rbcL) proved that it was a new species of Nitzschia genus, closely related to Nitzschia frustulum and Nitzschia inconspicua. Therefore, description of a new species, Nitzschia reskoi Ács, Duleba, C.E.Wetzel & Ector is proposed. We concluded that the increasing abundance of Nitzschia reskoi was a signal of the degradation of the intermittent saline wetlands.

Biofilm forming bacteria and archaea in thermal karst springs of Gellért Hill discharge area (Hungary)

The Buda Thermal Karst System (BTKS) is an extensive active hypogenic cave system located beneath the residential area of the Hungarian capital. At the river Danube, several thermal springs discharge forming spring caves. To reveal and compare the morphological structure and prokaryotic diversity of reddish-brown biofilms developed on the carbonate rock surfaces of the springs, scanning electron microscopy (SEM), and molecular cloning were applied. Microbial networks formed by filamentous bacteria and other cells with mineral crystals embedded in extracellular polymeric substances were observed in the SEM images. Biofilms were dominated by prokaryotes belonging to phyla Proteobacteria, Chloroflexi and Nitrospirae (Bacteria) and Thaumarchaeota (Archaea) but their abundance showed differences according to the type of the host rock, geographic distance, and different water exchange. In addition, representatives of phyla Acidobacteria, Actinobacteria, Caldithrix, Cyanobacteria, Firmicutes Gemmatimonadetes, and several candidate divisions of Bacteria as well as Crenarchaeota and Euryarchaeota were detected in sample-dependent higher abundance. The results indicate that thermophilic, anaerobic sulfur-, sulfate-, nitrate-, and iron(III)-reducing chemoorganotrophic as well as sulfur-, ammonia-, and nitrite-oxidizing chemolithotrophic prokaryotes can interact in the studied biofilms adapted to the unique and extreme circumstances (e.g., aphotic and nearly anoxic conditions, oligotrophy, and radionuclide accumulation) in the thermal karst springs.

Efficiency of temporary storage of geothermal waters in a lake system: Monitoring the changes of water quality and bacterial community structures

Disposal of used geothermal waters in Hungary often means temporary storage in reservoir lakes to reduce temperature and improve water quality. In this study, the physical and chemical properties and changes in the bacterial community structure of a reservoir lake system in southeast region of Hungary were monitored and compared through 2 years, respectively. The values of biological oxygen demand, concentrations of ammonium ion, total inorganic nitrogen, total phosphorous, and total phenol decreased, whereas oxygen saturation, total organic nitrogen, pH, and conductivity increased during the storage period. Bacterial community structure of water and sediment samples was compared by denaturing gradient gel electrophoresis (DGGE) following the amplification of the 16S rRNA gene. According to the DGGE patterns, greater seasonal than spatial differences of bacterial communities were revealed in both water and sediment of the lakes. Representatives of the genera Arthrospira and Anabaenopsis (cyanobacteria) were identified as permanent and dominant members of the bacterial communities.

Nesterenkonia pannonica sp. nov., a novel alkaliphilic and moderately halophilic actinobacterium

An alkaliphilic and moderately halophilic bacterial strain characterized by optimal growth at pH 9.0-10.0 and with 5-7 % (w/v) NaCl, designated BV-35^T, was isolated from water of a soda pan located in Kiskunság National Park, Hungary. Cells of the orange-pigmented colony were Gram-stain-positive, non-motile and non-endospore-forming coccoid rods. The isolate was strictly aerobic, catalase-positive and oxidase-negative. Strain BV-35^T displayed a peptidoglycan similar to type A4α, l-Lys-l-Glu (A11.54 according to www.peptidoglycan-types.info) but containing additionally 4-aminobutyric acid. Menaquinone-7 (MK-7) was the predominant isoprenoid quinone, and anteiso-C15 : 0 and anteiso-C17 : 0 were its major cellular fatty acids. The DNA G+C content of strain BV-35^T was 65.4 mol%. Based on 16S rRNA gene sequence similarities, the novel isolate showed the closest relationship to Nesterenkonia populi GP 10-3^T (97.9 %). The DNA-DNA relatedness between BV-35^T and N. populi was 46.7 %. The distinguishing phenotypic and genetic results of this polyphasic study revealed that strain BV-35^T represents a novel member of the genus Nesterenkonia, for which the name Nesterenkonia pannonica sp. nov. is proposed. The type strain is BV-35^T (=DSM 29786^T=NCAIM B 02606^T).

Gut content microbiota of introduced bigheaded carps (Hypophthalmichthys spp.) inhabiting the largest shallow lake in Central Europe

Studying the microbiota in the alimentary tract of bigheaded carps (Hypophthalmichthys spp.) gained special interest recently, as these types of investigations on non-native fish species may lead to a better understanding of their ecological role and feeding habits in an invaded habitat. For microbiological examinations, bigheaded carp gut contents and water column samples from Lake Balaton (Hungary) were collected from spring to autumn in 2013. Denaturing Gradient Gel Electrophoresis (DGGE) and pyrosequencing of the 16S rRNA gene were performed to reveal the composition. According to the DGGE patterns, bacterial communities of water samples separated clearly from that of the intestines. Moreover, the bacterial communities in the foreguts and hindguts were also strikingly dissimilar. Based on pyrosequencing, both foregut and hindgut samples were predominated by the fermentative genus Cetobacterium (Fusobacteria). The presence of some phytoplankton taxa and the high relative abundance of cellulose-degrading bacteria in the guts suggest that intestinal microbes may have an important role in digesting algae and making them utilizable for bigheaded carps that lack cellulase enzyme. In turn, the complete absence of typical heterotrophic freshwater bacteria in all studied sections of the intestines indicated that bacterioplankton probably has a negligible role in the nutrition of bigheaded carps.

Deinococcus budaensis sp. nov., a mesophilic species isolated from a biofilm sample of a hydrothermal spring cave

Following the exposure of a biofilm sample from a hydrothermal spring cave (Gellért Hill, Budapest, Hungary) to gamma radiation, a strain designated FeSTC15-38T was isolated and studied by polyphasic taxonomic methods. The spherical-shaped cells stained Gram-negative, and were aerobic and non-motile. The pH range for growth was pH 6.0-9.0, with an optimum at pH 7.0. The temperature range for growth was 20-37 °C, with an optimum at 28 °C. Phylogenetic analysis based on the 16S rRNA gene sequence of the isolate indicated that the organism belongs to the genus Deinococcus. The highest sequence similarities appeared with Deinococcus hopiensis KR-140T (94.1 %), Deinococcus aquaticus PB314T (93.3 %) and Deinococcus aerophilus 5516T-11T (92.7 %). The DNA G+C content of the novel strain was 68.2 mol%. The predominant fatty acids (>10 %) were iso-C16 : 0 and C16 : 1ω7c, and the cell-wall peptidoglycan type was A3β l-Orn-Gly2-3, corroborating the assignment of the strain to the genus Deinococcus. Strain FeSTC15-38T contained MK-8 as the major menaquinone and several unidentified phospholipids, glycolipids and phosphoglycolipids. Resistance to gamma radiation (D10) of strain FeSTC15-38T was <3.0 kGy. According to phenotypic and genotypic data, strain FeSTC15-38T represents a novel species for which the name Deinococcus budaensis sp. nov. is proposed. The type strain is FeSTC15-38T (=NCAIM B.02630T=DSM 101791T).

Changes in the water quality and bacterial community composition of an alkaline and saline oxbow lake used for temporary reservoir of geothermal waters

Geothermal waters exploited in the southeastern region of Hungary are alkali-hydrogen-carbonate type, and beside the high amount of dissolved salt, they contain a variety of aromatic, heteroaromatic, and polyaromatic hydrocarbons. The majority of these geothermal waters used for heating are directed into surface waters following a temporary storage in reservoir lakes. The aim of this study was to gain information about the temporal and spatial changes of the water quality as well as the bacterial community composition of an alkaline and saline oxbow lake operated as reservoir of used geothermal water. On the basis of the water physical and chemical measurements as well as the denaturing gradient gel electrophoresis (DGGE) patterns of the bacterial communities, temporal changes were more pronounced than spatial differences. During the storage periods, the inflow, reservoir water, and sediment samples were characterized with different bacterial community structures in both studied years. The 16S ribosomal RNA (rRNA) gene sequences of the bacterial strains and molecular clones confirmed the differences among the studied habitats. Thermophilic bacteria were most abundant in the geothermal inflow, whereas the water of the reservoir was dominated by cyanobacteria and various anoxygenic phototrophic prokaryotes. In addition, members of several facultative anaerobic denitrifying, obligate anaerobic sulfate-reducing and syntrophic bacterial species capable of decomposition of different organic compounds including phenols were revealed from the water and sediment of the reservoir. Most of these alkaliphilic and/or halophilic species may participate in the local nitrogen and sulfur cycles and contribute to the bloom of phototrophs manifesting in a characteristic pink-reddish discoloration of the water of the reservoir.

Diversity of extremophilic bacteria in the sediment of high-altitude lakes located in the mountain desert of Ojos del Salado volcano, Dry-Andes

Ojos del Salado, the highest volcano on Earth is surrounded by a special mountain desert with extreme aridity, great daily temperature range, intense solar radiation, and permafrost from 5000 meters above sea level. Several saline lakes and permafrost derived high-altitude lakes can be found in this area, often surrounded by fumaroles and hot springs. The aim of this study was to gain information about the bacterial communities inhabiting the sediment of high-altitude lakes of the Ojos del Salado region located between 3770 and 6500 m. Altogether 11 sediment samples from 4 different altitudes were examined with 16S rRNA gene based denaturing gradient gel electrophoresis and clone libraries. Members of 17 phyla or candidate divisions were detected with the dominance of Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes. The bacterial community composition was determined mainly by the altitude of the sampling sites; nevertheless, the extreme aridity and the active volcanism had a strong influence on it. Most of the sequences showed the highest relation to bacterial species or uncultured clones from similar extreme environments.

Seasonal and Spatial Changes of Planktonic Bacterial Communities Inhabiting the Natural Thermal Lake Hévíz, Hungary

Lake Hévíz is a unique thermal spa located in Hungary. Owing to the thermal springs nourishing the lake, it has a relatively rapid water turnover. In spring 2011 a comprehensive embankment reconstruction was performed to preserve the water supply of the surrounding wetland habitats. The physical and chemical parameters as well as the planktonic microbial communities were studied with special respect to the effect of the disturbance of the water of Lake Hévíz. According to the abiotic components, both temporal and spatial differences were revealed with the exception of autumn samples. The reconstruction resulted in a short term but dramatic alteration of the total planktonic bacterial and cyanobacterial community structures as revealed by denaturing gradient gel electrophoresis. In addition, greater seasonal than spatial differences of bacterial communities were also observed. Planktonic bacterial community composition of Lake Hévíz included mainly typical freshwater species within phylum Actinobacteria, Chloroflexi, Cyanobacteria and class Alpha-, Beta- and Gamma-proteobacteria. Most of them were aerobic or facultative anaerobic heterotrophic but chemolitotrophic (e.g. Thiobacillus) or photolithotrophic (e.g. Cyanobacteria and Chloroflexi) autotrophic microbes were also identified.

Diversity and ecological tolerance of bacteria isolated from the rhizosphere of halophyton plants living nearby Kiskunság soda ponds, Hungary

Many halophytes and halophilic microorganisms are capable to adapt to the extremities of saline habitats. This study reveals the taxonomic diversity and ecological tolerance of bacteria isolated from the rhizosphere of three different halophytes (Bolboschoenus maritimus, Puccinellia limosa and Aster tripolium) living in the vicinity of Kiskunság soda ponds. Following a sampling in September 2013, altogether 76 bacterial strains were isolated using two different media. The strains were identified on the basis of 16S rRNA gene sequencing following ARDRA grouping. Salt and pH tolerance of the strains were examined by measuring their growth in broths containing 0-15% NaCl (w/V) and characterized with pH 7-12 values. Among the strains genera of Anaerobacillus, Bacillus and Exiguobacterium (Firmicutes), Agromyces, Isoptericola, Microbacterium, Micrococcus, Nocardiopsis, Nesterenkonia and Streptomyces (Actinobacteria), Halomonas and Idiomarina (Proteobacteria) and Anditalea (Bacteroidetes) were identified. The Bolboschoenus and Puccinellia samples characterized with the highest pH and electric conductivity values were dominated by Bacillus, Halomonas and Nesterenkonia, respectively. The salt tolerance of the bacterial strains was strongly dependent on the sampling location and plant species. In contrast, growth of bacterial strains in broths with alkaline pH values was more balanced. The strains from the Puccinellia sample showed the widest salt and pH tolerance.

Thermophilic prokaryotic communities inhabiting the biofilm and well water of a thermal karst system located in Budapest (Hungary)

In this study, scanning electron microscopy (SEM) and 16S rRNA gene-based phylogenetic approach were applied to reveal the morphological structure and genetic diversity of thermophilic prokaryotic communities of a thermal karst well located in Budapest (Hungary). Bacterial and archaeal diversity of the well water (73.7 °C) and the biofilm developed on the inner surface of an outflow pipeline of the well were studied by molecular cloning method. According to the SEM images calcium carbonate minerals serve as a surface for colonization of bacterial aggregates. The vast majority of the bacterial and archaeal clones showed the highest sequence similarities to chemolithoautotrophic species. The bacterial clone libraries were dominated by sulfur oxidizer Thiobacillus (Betaproteobacteria) in the water and Sulfurihydrogenibium (Aquificae) in the biofilm. A relatively high proportion of molecular clones represented genera Thermus and Bellilinea in the biofilm library. The most abundant phylotypes both in water and biofilm archaeal clone libraries were closely related to thermophilic ammonia oxidizer Nitrosocaldus and Nitrososphaera but phylotypes belonging to methanogens were also detected. The results show that in addition to the bacterial sulfur and hydrogen oxidation, mainly archaeal ammonia oxidation may play a decisive role in the studied thermal karst system.

Phreatobacter oligotrophus gen. nov., sp. nov., an alphaproteobacterium isolated from ultrapure water of the water purification system of a power plant

Strains of a novel alphaproteobacterium were isolated from ultrapure water of a Hungarian power plant on a newly developed medium. Phylogenetic analysis of the 16S rRNA gene sequences of the novel strains showed that these bacteria belong to a distinct lineage far from any known taxa. Based on the 16S rRNA gene sequences, strains PI_31, PI_25 and PI_21(T) exhibited the highest sequence similarity to Bosea minatitlanensis AMX51(T) (93.43 %) and Bosea thiooxidans DSM 9653(T) (93.36 %); similarity to all other taxa was less than 93.23 %. Fatty acid profiles, matrix-assisted laser-desorption/ionization time-of-flight mass spectra of cell extracts as well as physiological and biochemical characteristics indicated that our strains represent a novel genus and species within the class Alphaproteobacteria. The major isoprenoid quinone of the strains was Q-10, the major cellular fatty acids were C18 : 1ω7c and 11-methyl C18 : 1ω7c and the polar lipid profiles of the strains contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and several unknown phospholipids and other lipids. The characteristic diamino acid in their cell wall was meso-diaminopimelic acid. The G+C content of DNA of the proposed type strain PI_21(T) was 68.9 mol%. A new genus and species, Phreatobacter oligotrophus gen. nov., sp. nov., is proposed to accommodate the strains. Strain PI_21(T) ( = DSM 25521(T) = NCAIM B 02510(T)) is the type strain of Phreatobacter oligotrophus.

Spatial and temporal changes of bacterial communities inhabiting the well waters of Harkány Spa

In this study, changes in the bacterial community composition of the well waters of Harkány Spa were examined. Physical and chemical properties of mixing subsurface cold and thermal karst waters were correlated to shifts in bacterial community structures analyzed by denaturing gradient gel electrophoresis (DGGE) and principal component analysis (PCA). In addition, mineral components of the pellets were investigated by scanning electron microscopy. Samples from the effluent waters of Büdöstapolca I and II, Matty and Thermal VI wells were taken seasonally in 2007 and 2008. The comparison of the results of DGGE and PCA analyses showed that bacterial communities from the Büdöstapolca wells were distinct from those of Matty and Thermal VI, but seasonal changes were not detected. According to the phylogenetic analysis of the excised DGGE bands, presence of chemolithotrophic Proteobacteria (Thiobacillus, Thiothrix, and distant relatives of Sulfurospirillum) were typical in the Büdöstapolca wells, while members of Actinobacteria (Plantibacter, Actinobacterium, Microbacterium) and Firmicutes (Planococcus) were characteristic to the Matty and Thermal VI wells. In the pellets pyrite framboid crystals were observed by electron microscopy, which are minerals known to be biologically induced by dissimilatory iron- and sulfur (sulfate)-reducing bacteria.

Phylogenetic diversity of bacterial communities inhabiting the sediment of Lake Hévíz - a comparison of cultivation and cloning

Lake Hévíz is the largest natural warm water lake of Europe. The curative mud of the lake comprises volcanic and marsh components although their species composition is hardly known yet. The aim of the present study was to gain information about the distribution and species diversity of bacterial communities inhabiting the sediment of Lake Hévíz using cultivation-based and molecular cloning methods. Samples from two depths and locations were taken in 2004 and 2007. Representatives of the altogether 255 bacterial isolates were affiliated with the phyla Firmicutes, Actinobacteria, Proteobacteria and Bacteroidetes. The most abundant groups belonged to the genus Bacillus (Firmicutes). Many of Lake Hévíz isolates showed the highest sequence similarity to bacteria known to be plant associated or members of normal human microbiota as well as participating in decomposition of highly resistant organic materials. In the three clone libraries, phylotypes belonging to altogether different phyla (Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Cyanobacteria, Chlorobi, Chloroflexi, Deferribacteres, Nitrospirae, Spirochaetes and Verrucomicrobia) were revealed from which members of Gammaproteobacteria and Cyanobacteria proved to be the most abundant. Regardless of the sampling times and methodology used, high spatial heterogeneities of bacterial community structures were characteristic of the sediment of Lake Hévíz.

Delimiting sub-areas in water bodies using multivariate data analysis on the example of Lake Balaton (W Hungary)

The main aim of the European Water Framework Directive (WFD, 2000) is to commit European Union Member states to the achievement of good qualitative and quantitative status for all water bodies by 2015. To achieve this, a reference state has to be determined and appropriate monitoring has to be carried out. Based on the fact that the WFD classifies Lake Balaton, the largest shallow freshwater lake in Central Europe, as one water body, and due to the lack of funds, the number of sampling locations on the lake was decreased. The aim of this study was to determine how many sub-areas with different WFD-related attributes (in this case, parameters) can be delimited in the so-called one water body of Lake Balaton, so that a number of representative sampling locations might be retained. To determine Lake Balaton's different water quality areas (i.e. sub-areas of water body) 23 parameters (inorganic compounds) were examined from 10 sampling locations for the time interval 1985-2004 using cluster- and discriminant analysis, and Wilks' lambda distribution. With cluster analysis we were able to determine two time intervals (1985-1997 and 1998-2004) with three patterns of sub-areas, two from the first and one from the latter interval. These patterns pointed to the fact that for the whole investigated time interval (1985-2004) a total of five sub-areas were present, changing in number and alignment. Then the results were verified using discriminant analysis, and the parameters which influenced the sub-areas the most were determined using Wilks' lambda distribution. The conclusion was that to be able to follow the changes in alignment of the sub-areas and to get a comprehensive picture of Lake Balaton, a minimum of five sampling locations should be retained, one in each sub-area. Based on this study the Water Authorities chose to keep five out of ten sampling locations so that the sub-areas could be described. We consider this a great success and the methodology as an example for setting up sub-areas in a water body.

Phylogenetic diversity of bacterial and archaeal communities inhabiting the saline Lake Red located in Sovata, Romania

Lake Red is one of the saline lakes which were formed as a consequence of salt massif dissolution at the foot of the Gurghiu Mountains (Central Romania) at the end of the nineteenth century. The lake water had approximately 15 % w/v salt content. Phylogenetic diversity of prokaryotes inhabiting the water and sediment of the lake was studied using cultivation and cultivation-independent methods following a sampling in spring 2009. According to the results of 16S rRNA gene-based denaturing gradient gel electrophoresis (DGGE), the richness of Bacteria was higher than Archaea on the basis of the number and position of dominant bands in the gel. Sequences from DGGE bands were affiliated with Gammaproteobacteria (Halomonas and Alkalilimnicola) and Bacteroidetes (Psychroflexus) as well as Euryarchaeota. Cultivation from five different saline media resulted in 101 bacterial strains of which Gammaproteobacteria (Halomonas, Marinobacter and Salinivibrio) were the most abundant. Firmicutes (Bacillus) and Alphaproteobacteria (Aurantimonas and Roseovarius) were also identified among the isolated strains. The 16S rRNA genes from 82 bacterial and 95 archaeal clones were also phylogenetically analyzed. Bacterial clones were related to various genera of Gammaproteobacteria (Alkalilimnicola, Alkalispirillum, Arhodomonas, Halomonas, Saccharospirillum), Bacteroidetes (Gracilimonas, Psychroflexus) and Alphaproteobacteria (Oceanicola, Roseinatronobacter, Roseovarius). All of the archaeal clones sequenced corresponded to a homologous cluster affiliated with Halopelagius.

Bacillus alkalisediminis sp. nov., an alkaliphilic and moderately halophilic bacterium isolated from sediment of extremely shallow soda ponds

Alkaliphilic strains characterized by optimal growth at pH 9.0 and 5 % (w/v) NaCl designated K1-25T and H3-93 were isolated from extremely shallow soda ponds located in Hungary. Cells of both strains were Gram-stain-positive, non-motile, straight rods and formed central, ellipsoidal endospores with swollen sporangia. The isolates were aerobic, catalase-positive, oxidase-negative and contained a peptidoglycan of type A1γ based on meso-diaminopimelic acid. In both strains, menaquinone-7 (MK-7) was the predominant isoprenoid quinone and the major cellular fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The DNA G+C contents of strains K1-25T and H3-93 were 39.0 and 36.3 mol%, respectively. 16S rRNA gene sequence-based phylogenetic analysis revealed 99.2 % similarity between strains K1-25T and H3-93 and the novel isolates had the highest similarities to Bacillus akibai 1139T (97.8 and 98.3 %, respectively), Bacillus wakoensis N-1T (97.0 and 97.4 %), Bacillus okhensis Kh10-101T (97.1 and 97.4 %) and Bacillus krulwichiae AM31DT (96.9 and 97.1 %). DNA–DNA hybridization between our strains and the type strains of closely related Bacillus species was lower than 70 %. Although DNA–DNA hybridization between strains K1-25T and H3-93 was 27 %, the phenotypic and chemotaxonomic data did not support the differentiation of these two strains into separate species. Therefore, they represent genomovars of a novel species, for which the name Bacillus alkalisediminis sp. nov. is proposed. The type strain is K1-25T ( = DSM 21670T  = NCAIM B02301T).

Cellulomonas phragmiteti sp. nov., a cellulolytic bacterium isolated from reed (Phragmites australis) periphyton in a shallow soda pond

An alkalitolerant and moderately halophilic strain, designated KB23T, characterized by optimal growth at pH 8.0–9.0 and in the presence of 5–7 % (w/v) NaCl, was isolated from a reed (Phragmites australis) periphyton sample originating from an extremely shallow, alkaline soda pond located in Hungary. Cells of strain KB23T were Gram-stain-positive, motile straight rods. Strain KB23T was facultatively anaerobic, catalase-positive, oxidase-negative and contained peptidoglycan type A4β (l-Orn–d-Asp). MK-9(H4) was the predominant isoprenoid quinone and anteiso-C15 : 0, C16 : 0 and anteiso-C15 : 1 were the major cellular fatty acids. The DNA G+C content of strain KB23T was 74.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that this strain belongs to the genus Cellulomonas and that it is related most closely to Cellulomonas flavigena DSM 20109T (97.35 % similarity), Cellulomonas terrae DB5T (96.81 %), Cellulomonas iranensis OT (96.75), Cellulomonas chitinilytica X.bu-bT (96.60 %), Cellulomonas persica IT (96.53 %), Cellulomonas composti TR7-06T (96.45 %), Cellulomonas biazotea DSM 20112T (96.34 %) and Cellulomonas fimi DSM 20113T (96.20 %). According to these results, together with DNA–DNA hybridization and physiological data, strain KB23T is considered to represent a novel species of the genus Cellulomonas, for which the name Cellulomonas phragmiteti sp. nov. is proposed. The type strain is KB23T ( = DSM 22512T  = NCAIM B002303T).

Molecular biological investigations on the bacterial communities of curative well waters of Harkány Spa

Bacterial communities from the sulfide containing curative well waters of Harkány Spa (Hungary) were investigated by cultivation independent molecular cloning and Denaturing Gradient Gel Electrophoresis (DGGE) methods between 2006 and 2008. The DGGE profiles of the bacterial communities originated from the wells of lukewarm waters showed seasonal similarities and were highly different from the thermal well. From the four clone libraries 22 different eubacterial species or genera were identified by sequence analysis. The majority of the clones of the lukewarm waters belonged to unidentified Epsilon-proteobacteria, Desulfocapsa sp. and Thiothrix spp., while the dominant clones of the thermal water were affiliated with the genus Denitratisoma sp. Most of the identified species and genera were related to bacteria with obligate or facultative chemolithotrophic sulfur metabolism, so the microbes of the curative waters may participate in the sulfur-cycle of the wells.

Phylogenetic and metabolic bacterial diversity of Phragmites australis periphyton communities in two Hungarian soda ponds

Bacterial diversity of reed (Phragmites australis) periphyton communities of Kelemen-szék and Nagy-Vadas (two Hungarian soda ponds) was investigated using molecular cloning and cultivation-based techniques. The majority of the 80 Kelemen-szék and 72 Nagy-Vadas bacterial isolates proved to be moderately halophilic and alkaliphilic. A great proportion of the isolates showed phosphatase and urease activity, utilized aesculin, citrate and certain biopolymers (e.g., gelatine and tween 80). Partial 16S rDNA sequence analysis of 33 Kelemen-szék and 20 Nagy-Vadas ARDRA group representatives showed Gram-positive (Nesterenkonia, Cellulomonas, Dietzia, Bacillus and Planococcus) dominance at both sampling sites. Species of the genera Acidovorax, Hydrogenophaga (beta-Proteobacteria) and Flavobacterium, Sphingobacterium (Bacteroidetes) were represented only from Kelemen-szék. Altogether 16 isolates showed low sequence similarity with yet described bacteria and may represent novel taxa. Screening of the 16S rRNA gene libraries of 129 Kelemen-szék and 158 Nagy-Vadas clones resulted in 30 and 28 different ARDRA groups, respectively. Sequence analysis revealed a Gram-negative (Rheinheimera, Aquimonas, Cellvibrio, Flavobacterium and Sphingobacterium) dominated phylogenetic diversity. A high number of the clones were affiliated with uncultured bacterial clones described from diverse environmental samples.

Bacillus aurantiacus sp. nov., an alkaliphilic and moderately halophilic bacterium isolated from Hungarian soda lakes

Three alkaliphilic and moderately halophilic strains designated K1-5T, K1-10 and B1-1, characterized by optimal growth at pH 9.0-10.0 and at 3-7 % (w/v) NaCl, were isolated from extremely shallow, alkaline soda lakes located in Hungary. Cells of the strains are Gram-positive, straight rods and form a central to subterminal, ellipsoidal endospore. The isolates are strictly aerobic, catalase-positive, oxidase-negative and contain a peptidoglycan of type A1 gamma based on meso-diaminopimelic acid. In strain K1-5T, menaquinone-7 (MK-7) is the predominant isoprenoid quinone and anteiso-C15 : 0 is the major cellular fatty acid. The DNA G+C content of strain K1-5T is 42.9 mol%. 16S rRNA gene-based phylogenetic analysis revealed that the strains exhibit levels of sequence similarity of less than 95.8 % to known Bacillus species. According to the polyphasic characterization, the strains represent a novel species, for which the name Bacillus aurantiacus sp. nov. is proposed. The type strain is K1-5T (=DSM 18675T =CCM 7447T =NCAIM B002265T).

Diversity of sulfate-reducing bacteria inhabiting the rhizosphere of Phragmites australis in Lake Velencei (Hungary) revealed by a combined cultivation-based and molecular approach

The community structure of sulfate-reducing bacteria (SRB) associated with reed (Phragmites australis) rhizosphere in Lake Velencei (Hungary) was investigated by using cultivation-based and molecular methods. The cultivation methods were restricted to recover lactate-utilizing species with the exclusion of Desulfobacter and some Desulfobacterium species presumably not being dominant members of the examined community. The most-probable-number (MPN) estimations of lactate-utilizing SRB showed that the cell counts in reed rhizosphere were at least one order of magnitude higher than that in the bulk sediment. The number of endospores was low compared to the total SRB counts. From the highest positive dilution of MPN series, 47 strains were isolated and grouped by restriction fragment length polymorphism (RFLP) analysis of the amplified 16S ribosomal RNA (rRNA) and dsrAB (dissimilatory sulfite reductase) genes. Contrary to the physiological diversity of the isolates, the combined results of RFLP analysis revealed higher diversity at species as well as at subspecies level. Based on the partial 16S rRNA sequences, the representative strains were closely affiliated with the genera Desulfovibrio and Desulfotomaculum. The partial dsrAB sequences of the clones, recovered after isolation and PCR amplification of the community DNA, were related to hitherto uncultured species of the genera Desulfovibrio and Desulfobulbus. Nevertheless, the representative of the second largest clone group was shown to be closely affiliated with the sequenced dsrAB gene of a strain isolated from the same environment and identified as Desulfovibrio alcoholivorans. Another clone sequence was closely related to a possible novel species also isolated within the scope of this work.

Nocardioides daphniae sp. nov., isolated from Daphnia cucullata (Crustacea: Cladocera)

A Gram-positive, rod-shaped or coccoid, yellow-pigmented bacterial strain, D287(T), was isolated from the water flea Daphnia cucullata (Crustacea: Cladocera) collected from Lake Balaton in Hungary. Phylogenetic analysis on the basis of 16S rRNA gene sequence comparisons revealed that the strain represented a distinct lineage within the cluster of the genera Nocardioides and Marmoricola. The following characteristics were consistent with the affiliation of strain D287(T) to the genus Nocardioides: peptidoglycan based on LL-2,6-diaminopimelic acid, MK-8(H(4)) as the major menaquinone, iso-C(16:0) as the predominant cellular fatty acid, the presence of phosphatidylglycerol and diphosphatidylglycerol and a DNA G+C content of 69.9 mol%. Owing to characteristic differences in physiological traits and levels of 16S rRNA gene sequence similarity to its phylogenetically closest neighbours that were below 97%, strain D287(T) is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides daphniae sp. nov. is proposed. The type strain is D287(T) (=DSM 18664(T)=CCM 7403(T)).

Metabolic activity and phylogenetic diversity of reed (Phragmites australis) periphyton bacterial communities in a hungarian shallow soda lake

In the present study, the species composition and potential metabolic activities of bacterial communities of reed Phragmites australis (Cav.) (Trin. ex Steudel) periphyton from Lake Velencei were studied by cultivation-based and metabolic fingerprinting methods. Serially diluted spring biofilm samples were used to test the community-level physiological profiling (CLPP) using BIOLOG microplates, and for plating onto different media. On the basis of their morphological, biochemical, and physiological test results, 173 strains were clustered by numerical analysis. Representatives of amplified ribosomal DNA restriction analysis (ARDRA) groups were identified by their 16S rDNA sequence comparison. Based on the results of the CLPP investigations, regional differences were detected among the utilized substrate numbers and types, parallel with the increase in incubation time. The phenotypic test results of the strains showed considerable variability with respect to the sampling sites and the media used for cultivation. The most frequently isolated strains were identified as members of genera Agrobacterium, Pseudomonas (P. anguilliseptica, P. marginalis, P. alcaligenes, P. fragi) with aerobic or facultative anaerobic respiratory metabolism, and the species Aeromonas sobria and A. veronii with strong facultative fermentative metabolism. Other strains were identified as Gram-positive Arthrobacter, Bacillus, and Kocuria species. The rarely isolated strains were members of beta-Proteobacteria (Acidovorax, Delftia, Hydrogenophaga, and Rhodoferax), gamma-Proteobacteria (Psychrobacter and Shewanella), low G + C Gram-positives (Brevibacillus, Paenibacillus, and Exiguobacterium) and high G + C Gram-positives (Aureobacterium and Microbacterium).

Proposal to replace the illegitimate genus name Schineria Toth et al. 2001 with the genus name Ignatzschineria gen. nov. and to replace the illegitimate combination Schineria larvae Toth et al. 2001 with Ignatzschineria larvae comb. nov

The prokaryotic, generic name Schineria Tóth et al. 2001 is illegitimate owing to the prior existence of the name Schineria for a genus within the Diptera [Principle 2, Rule 51b(4) of the Bacteriological Code (1990 Revision)]. Therefore, a new genus name, Ignatzschineria gen. nov., is proposed for this taxon. As a result, a new combination is required for the type species, Ignatzschineria larvae comb. nov., to replace the illegitimate combination Schineria larvae Tóth et al. 2001.

Chemical and biological characterisation of biofilms formed on different substrata in Tisza river (Hungary)

Natural biofilms were simultaneously grown on granite, polished granite, andesite, polycarbonate and Plexi-glass substrata for six weeks in the Tisza River. Biofilm production and abundance of algae were influenced by the substratum. Magnitude of the substratum effect was andesite<polished granite<Plexi-glass<granite<polycarbonate. The benthic diatom community on polycarbonate had a high population of Achnantes helvetica. Bacterial activity was similar among substrates for 95 different carbon sources. The concentrations of essential elements and heavy metal pollutants (Zn, Ni, Pb and Cu) were highest in biofilms on polished granite or granite. On basis of algological, bacteriological and chemical investigations, as well as literature data, the Plexi-glass substratum is recommended for biomonitoring of river benthic microbiota.

Bacteria isolated from the different developmental stages and larval organs of the obligate parasitic fly, Wohlfahrtia magnifica (Diptera: Sarcophagidae)

Wohlfahrtia magnifica (Diptera: Sarcophagidae) is the major myiasis-causing fly species in the whole of Eurasia for most important domestic animals. The aim of the present work was to obtain data on the culturable bacteria isolated under aerobic conditions from this fly: bacteria were isolated from all developmental stages (larvae, pupa, and imago) of Wohlfahrtia magnifica, and the third-stage larval organs were also sampled. To determine the possible antagonistic effects between the dominant bacterial groups, an antibiosis assay was carried out. Plating and isolation of bacteria was performed by classical microbiological methods. Characterization of the isolated strains was carried out via a polyphasic approach; classical phenotypic tests, chemotaxonomical examinations, and 16S rDNA sequence analyses were also applied. In the case of maggot macerate samples, members of the family Enterobacteriaceae were characteristic. Members of a new genus (Schineria) belonging to the gamma subdivision of proteobacteria were also isolated. According to our data, the shifts in the Schineria and Proteus populations within the larvae are strongly influenced by their interactions with each other and among the members of the family Enterobacteriaceae. The pupa and imago samples contained several other Gram-negative bacteria (Stenotrophomonas, Brevundimonas, etc.). Among Gram-positive bacteria, in all maggot macerate samples, members of the genus Bacillus and the Arthrobacter-Micrococcus group of actinobacteria were dominant (neither of them was a producer or sensitive to the compounds of other microorganisms), and bacteria related to the genus Corynebacterium were also found. From the larvae Aureobacterium liquefaciens and Enterococcus faecalis were isolated, and from the pupae Dietzia maris and Enterococcus faecalis. In the samples of third-stage larval organs, the dominant groups were the same as in the third-stage larval macerate sample; however, several additional genera/species were observed (Rhodococcus fascians, Streptomyces sp., Rathayibacter sp., Bacillus thuringiensis/cereus).

Diversity of alkaliphilic and alkalitolerant bacteria cultivated from decomposing reed rhizomes in a Hungarian soda lake

Bacterial communities associated with decomposing rhizomes of Phragmites australis were investigated in Lake Ferto (Neusiedlersee, Hungary). Alkaliphilic and alkalitolerant strains were isolated on cellulose-containing alkaline medium spread with dilutions of scrapings taken from the surface of the decaying plant material. Fifty-one strains were grouped by numerical analysis based on physiological tests and BIOLOG sole carbon source utilization data. The strains identified by 16S rDNA sequence comparisons included members of low G+C Gram positives (Marinibacillus marinus, Bacillus cereus, and Exiguobacterium aurantiacum), high G+C Gram positives (Nesterenkonia halobia and Dietzia natronolimnea), alpha-proteobacteria (Pannonibacter phragmitetus), and gamma-proteobacteria (Pseudomonas pseudoalcaligenes and Halomonas venusta). Most of the strains were characterized by aerobic chemoorganotrophic respiratory metabolism and utilized several different carbon sources, although no direct cellulolytic activity was observed. Results of the pH and salt tolerance tests revealed optimuma in most cases at pH 11 and at the presence of 2.5-5% NaCl. These bacteria probably occupy niches in the aerobic, alkaline, water-influenced environments on the decomposing reed surfaces.

Pannonibacter phragmitetus gen. nov., sp. nov., a novel alkalitolerant bacterium isolated from decomposing reed rhizomes in a Hungarian soda lake

Three alkalitolerant bacterial strains were isolated from the surface of decomposing rhizomes of reed [Phragmites australia (Cav.) Trin. et Steudel] in Lake Fertö (Hungary). Cells of the novel isolates were Gram-negative, motile rods and formed star-shaped aggregates. They were facultatively anaerobic and chemo-organotrophic. Bacteriochlorophyll a was not synthesized under aerobic conditions. The strains were catalase and oxidase positive, produced acid from D-glucose under aerobic and anaerobic conditions and reduced nitrate to nitrogen. They tolerated pH values from 7.0 to 11.0 and grew in the absence of NaCl as well as in up to 5% (w/v) NaCl. The G + C content of the DNA was 64.6 mol% and the major isoprenoid quinone was Q-10. The dominant cellular fatty acid was C18 : 1omega7c. The cell membrane contained phosphatidyl glycerol, diphosphatidyl glycerol, phosphatidyl ethanolamine, phosphatidyl serine and one unknown phospholipid as polar lipids. Polyphasic taxonomic characterization revealed that strain C6/19T is most closely related to the Stappia-Roseibium cluster in the alpha-subclass of the Proteobacteria (showing 95.8-93.6% 16S rDNA sequence similarity). According to the phylogenetic and phenotypic evidence presented, a new genus and species is proposed, Pannonibacter phragmitetus gen. nov., sp. nov. The type strain is C6/19T (=DSM 14782T =NCAIM B02025T).

Comparative studies on Aeromonas strains isolated from Lakes Balaton (Hungary) and Fertó/Neusiedlersee (Hungary)

Ecological and comparative taxonomic investigations were carried out on 49 Aeromonas strains isolated from water samples of two moderately alkaline lakes of Hungary, Lake Balaton and Lake Fertó/Neusiedlersee together with 3 authentic strains of Aeromonas hydrophila. Five phena were created at greater than 92% similarity value using the UPGMA method with the Jaccard coefficient. Strains isolated from Lake Balaton were determined as A. hydrophila, while strains originated from Lake Fertó were identified as A. hydrophila and A. sobria. The Fertó isolates of A. hydrophila grew only at higher salt concentration (5% NaCl). This might be an adaptation to the higher salt contents in the water of Lake Fertó. However, no specific differences were detected in their behaviour against alkaline pH values. The wide range of their degradative enzymes indicate that aeromonads can play an important role in nutrient cycling.