Search

We followed the abundance and compared the diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the groundwater of two superimposed pristine limestone aquifers located in the Hainich region (Thuringia, Germany) over 22 months. Groundwater obtained from the upper aquifer (12 m depth) was characterized by low oxygen saturation (0-20%) and low nitrate concentrations (0-20 μM), contrasting with 50-80% oxygen saturation and 40-200 μM nitrate in the lower aquifer (48 m and 88 m depth). Quantitative PCR targeting bacterial and archaeal amoA and 16S rRNA genes suggested a much higher ammonia oxidizer fraction in the lower aquifer (0.4-7.8%) compared with the upper aquifer (0.01-0.29%). In both aquifers, AOB communities were dominated by one phylotype related to Nitrosomonas ureae, while AOA communities were more diverse. Multivariate analysis of amoA DGGE profiles revealed a stronger temporal variation of AOA and AOB community composition in the upper aquifer, pointing to a stronger influence of surface environments. Parallel fluctuations of AOA, AOB, and total microbial abundance suggested that hydrological factors (heavy rain falls, snow melt) rather than specific physicochemical parameters were responsible for the observed community dynamics. [ABSTRACT FROM AUTHOR]

Background: Yeast-like fungi inhabit soils throughout all climatic zones in a great abundance. While recent estimations predicted a plethora of prokaryotic taxa in one gram of soil, similar data are lacking for fungi, especially yeasts. Methodology/Principal Findings: We assessed the diversity of soil yeasts in different forests of central Germany using cultivation-based techniques with subsequent identification based on rDNA sequence data. Based on experiments using various pre-cultivation sample treatment and different cultivation media we obtained the highest number of yeasts by analysing mixed soil samples with a single nutrient-rich medium. Additionally, several species richness estimators were applied to incidence-based data of 165 samples. All of them predicted a similar range of yeast diversity, namely 14 to 16 species. Randomized species richness curves reached saturation in all applied estimators, thus indicating that the majority of species is detected after approximately 30 to 50 samples analysed. Conclusions/Significance: In this study we demonstrate that robust species identification as well as mathematical approaches are essential to reliably estimate the sampling effort needed to describe soil yeast communities. This approach has great potential for optimisation of cultivation techniques and allows high throughput analysis in the future. [ABSTRACT FROM AUTHOR]

16S ribosomal RNA gene clone libraries were generated to assess the prokaryotic diversity within a laminated tufa stromatolite core, obtained from the hardwater rivulet Westerhofer Bach, Lower Saxony, Germany. Libraries were obtained from the biofilm and six tufa layers, each about 4 to 8 mm thick and 2,351 partial sequences were analyzed. Cyanobacteria and other aerobic organisms dominated the 500 μ m thick biofilm and the first layer, represented by 112 and 154 phylotypes, respectively. DGGE and UniFrac analyses revealed that these two layers were clearly separated from the deeper layers which showed a higher diversity than the tufa surface with less than 350 phylotypes. The species richness of deeper layers was dominated by a broad range of phyla, predominantly of acidobacterial, bacteroidetes and alpha-, beta- and gammaproteobacterial phylotypes. In total, sequences belonging to 26 phyla were detected. Sequences related to anaerobes, including photosynthetic Proteobacteria, are present in low numbers in the deeper layers but their metabolic activities in the dark and water-aerated core remain unclear. [ABSTRACT FROM AUTHOR]

Abstract: Ferric iron reduction was studied in a pilot-scale enclosure experiment for passive biological remediation of an acidic mine pit lake in Lusatia, Germany. The metabolic properties of prokaryotes involved in Fe(III) reduction may be important for the outcome of biological remediation, as chemolithotrophic Fe(III) reduction can counteract the desired pH increase, but heterotrophic Fe(III) reduction will provide the necessary Fe(II) for precipitation of sulfide minerals following sulfate reduction. Therefore, vertical profiles of sediment parameters related to iron and sulfur cycling were determined in conjunction with viable counts of different ferric iron-reducing micro-organisms using selective media. Findings were compared to an untreated reference site. The addition of organic matter stimulated ferric iron reduction and sulfate reduction in the enclosure and led to elevated pH and accumulations of ferrous iron and reduced sulfur compounds. Numbers of neutrophilic heterotrophic Fe(III) reducers increased during treatment, those of acidophilic heterotrophic Fe(III) reducers remained similar, and those of acidophilic chemolithotrophic Fe(III) reducers decreased. Zones of ferric iron-reducing activity corresponded well with microbial depth profiles; however, viable counts of neutrophilic or acid-tolerant Fe(III) reducers must have been underestimated based on the corresponding observed activity levels. Ferric iron reduction by chemolithotrophic acidophiles seemed to be of minor importance, so a lowering of pH values due to Fe(III) reducing activity is unlikely. [Copyright &y& Elsevier]

Individual bacterial populations are known to respond differently toward substrate availability. To test how the availability of either pure phenol or natural humic matter (HM) selects for specific pelagic bacteria phylotypes from a humic lake (Lake Grosse Fuchskuhle, northeastern Germany), we used culture-dependent and -independent approaches. Using a batch approach, the bacterial community composition (BCC) differed depending on both the quantity and the quality of added substrates. Using a dilution-to-extinction approach, distinct BCC were detected by eliminating less abundant species. Most bacteria that were common in the lake were favored by phenol, and yet different subsets of the native BCC were enriched by HM. Specific bacterial groups with different growth requirements were consistently present, negatively influenced, or positively enriched following substrate additions. This study comprises the first explicit demonstration that bacteria such as Methylobacterium, Methylophilus, and Methylosinus spp. can be enriched on phenol or HM. Our isolation approaches led to the successful cultivation of a variety of native bacteria from the lake, such as Novosphingobium ( Alphaproteobacteria) and Flexibacter ( Bacteroidetes), or phenol-utilizing bacteria such as members of Actinobacteria or Burkholderia ( Betaproteobacteria). Enrichment and cultivation on phenol and HM as substrates revealed highly specialized bacterial communities that resemble those found in many HM-rich lakes. [ABSTRACT FROM AUTHOR]

Abstract: Late Devonian (Frasnian) pillow basalts from the Frankenwald and Thüringer Wald within the Saxothuringian zone in Germany were found to contain abundant putative biogenic filaments, indicating that the volcanic rocks once harbored microbial life. The mineralized filaments are found in calcite-filled amygdules (former vesicles), where they started to form on internal surfaces of vesicles after seawater ingress. The filaments postdate an early fibrous carbonate cement but predate later equant calcite spar, revealing syngenetic formation. A biogenic origin of filaments is indicated by their size and morphology resembling modern microorganisms, their independence of crystal faces and cleavage plans, complex branching patterns, and internal segmentation. The filamentous microorganisms represent cryptoendoliths that lived in structural cavities of the basalt. They became preserved upon microbial clay authigenesis similar to the encrustation of modern prokaryotes in iron-rich environments. Filaments consist of clay minerals with the endmember composition berthierine–chamosite and illite–glauconite. Based on the discovery of fossilized filamentous microorganisms in Late Devonian pillow basalts of the Saxothurigian zone that are similar to filaments previously found in Middle Devonian pillow basalts of the Rhenohercynian zone, it is apparent that cryptoendolithic life was more widespread than previously recognized. Structural cavities within seafloor basalt may thus represent a common, perhaps universal niche for life in the oceanic crust. [Copyright &y& Elsevier]

Bacterial incorporation of glucose, leucine, acetate and 4-hydroxybenzoic acid (HBA) was investigated in an artificially divided humic lake (Grosse Fuchskuhle, Germany). Two basins with contrasting influx of allochthonous organic carbon were sampled during late summer stratification (oxic and anoxic layers) and after autumn mixing. High total and cell-specific incorporation rates were observed for glucose and HBA in stratified and mixed waters respectively, but only a small fraction of bacteria visibly incorporated HBA. The oxic layer of the more humic-rich basin featured a significantly lower fraction of glucose incorporating cells and substantially higher proportions of acetate assimilating bacteria. Niche differentiation was observed in two betaproteobacterial populations: cells affiliated with the Polynucleobacter C subcluster efficiently incorporated acetate but little glucose, whereas the opposite was found for members of the R-BT065 clade. By contrast, leucine incorporation was variable in both taxa. Considering the high concentrations and rapid photochemical generation of organic acids in humic waters our results may help to explain the success of the Polynucleobacter C lineage in such habitats. Specific substrate or habitat preferences were also present in three subgroups of the actinobacterial acI lineage: The numerically dominant clade in oxic waters (acI-840-1) was absent in the anoxic zone and did not incorporate acetate. A second group (acI-840-2) was found both in the epi- and hypolimnion, whereas the third one (acI-840-3) only occurred in anoxic waters. Altogether our results suggest a constitutive preference for some substrates versus an adaptive utilization of others in the studied microbial groups. [ABSTRACT FROM AUTHOR]

Plasmid pSmeSM11a, residing in the indigenous Sinorhizobium meliloti strain SM11 originating from a field in Strassmoos (Bavaria, Germany), was analysed previously at the genomic level. Thirty-seven indigenous S. meliloti strains, originating from two different locations in Germany, were screened for genes identified previously on pSmeSM11a. Seven of these strains harbour accessory plasmids that are very similar to pSmeSM11a. The identified pSmeSM11a-like plasmids are c. 130–150 kb in size and possess nearly identical restriction profiles. Up to 30 genes identified previously on pSmeSM11a could be detected on these plasmids by hybridisation experiments, e.g., the nodulation genes nodP and nodQ, the ethylene level modulation gene acdS and the taurine metabolism gene tauD. A few pSmeSM11a genes were also detected on other plasmids. The reference plasmid pSmeSM11a contains a region that is similar to a segment of S. meliloti strain Rm1021 pSymA. Regions with similarity to pSymA were also detected on the aforementioned seven pSmeSM11a-like plasmids. The specifications of these regions are nearly identical to the one on pSmeSM11a and differ from Rm1021 pSymA as determined by nucleotide sequence analysis. Two further plasmids similar to pSmeSM11a completely lack the pSymA-region. Those strains carrying accessory plasmids that contain the acdS gene encoding 1-aminocyclopropane-1-carboxylate deaminase are able to grow on 1-aminocyclopropane-1-carboxylate as the sole source of nitrogen, demonstrating functionality of the acdS gene product. About 36% of the analysed plasmids, including three pSmeSM11a-like plasmids, could be transferred to another S. meliloti recipient strain, allowing for their dissemination in S. meliloti populations. [ABSTRACT FROM AUTHOR]

Prokaryotic life along the salt gradient of the potash marsh resulting from mining waste at Schreyahn, Northern Germany, was screened for the distribution of total prokaryote (assessed by the 16S rRNA gene) and of N2-fixing (nifH gene), denitrifying (nosZ) and nitrifying (amoA) microorganisms. Information on prokaryotes was retrieved from the different soil sites (a) by culturing in conventional media, (b) by isolating the DNA, amplifying the target genes by PCR followed by sequencing, (c) by employing the recently developed computer program (TReFID [Rösch, C. , Bothe, H. , 2005. Improved assessment of denitrifying, N2-fixing, and total-community bacteria by terminal restriction fragment length polymorphism analysis using multiple restriction enzymes. Applied and Environmental Microbiology 71, 2026–2035]) based on tRFLP data. New sequences were obtained as well as ones that were almost identical to those found at far distant locations. Whereas the distribution of plants strictly follows the salt gradient, this is apparently not the case with prokaryotes. Bacteria of hypersaline areas coexist with salt-non-tolerant species. The recently developed TReFID program is successfully applied to characterize a prokaryote community structure. [Copyright &y& Elsevier]

The understanding of agro-ecosystems is the key to estimating the influence of long-term agricultural production methods on the environment. The present study aimed to improve the knowledge of functional and structural soil microbial diversity influenced by differentiated fertilization at four German long-term field experiments. Soil microbial biomass, β-glucosidase, protease, alkaline phosphatase, DMSO-reduction and TTC-dehydrogenase were evaluated in soils from three different fertilizer treatments (control, farmyard manure, mineral fertilizer) at four sites (Lauterbach, Bad Lauchstädt, Halle, Thyrow). Profiles of 29 identified phospholipid fatty acids were used for the evaluation of structural diversity. The results obtained showed that fertilization applied over several decades or even more than a century has led to distinct alterations of the soil ecosystem. There was a clear separation of the sites by microbial biomass and metabolic activities into dependence of soil properties and fertilization treatments. In contrast to the control, microbial biomass and enzyme activities of the FYM soils increased more strongly than in the NPK plots. The results of PLFA analyses indicate that the community of the autochthonous microflora has differently changed among sites and fertilizer application. Principle component analyses revealed that bacteria especially Gram-positive bacteria and eukaryotes were responsible for these differences. [ABSTRACT FROM AUTHOR]

Abstract: Three single-filament isolates of Aphanizomenon flos-aquae from two German lakes were found to produce remarkable amounts of the cyanobacterial hepatotoxin cylindrospermopsin (CYN). CYN-synthesis of the strains were evidenced both by LC-MS/MS analysis and detection of PCR products of gene fragments which are implicated in the biosynthesis of the toxin. The strains contain CYN in the range of 2.3–6.6mgg−1 of cellular dry weight. To our knowledge this is the first report of CYN in A. flos-aquae. [Copyright &y& Elsevier]

Vertical profiles of soluble and particulate nutrients were analyzed at the end of summer stratification in two dimictic lakes located in northeast Germany. In addition, irradiance and plankton biomass were deter- mined. The concentrations of particulate organic carbon and phytoplankton biomass in the epilimnion were higher in Lake Tiefer than in Lake Dudinghausen, even though the apparent trophic status of Lake Tiefer was higher than Lake Dudinghausen. In Lake Dudinghausen, phototrophic sulfur bacteria accumulated in the hypolimnion between 8 and 10 m, whereas in Lake Tiefer low light penetration prevented the development of phototrophic bacteria in those horizons in which sulfide might be present. Because both lakes have anoxic hypolimnia, we assumed that in both cases phosphorus was released from the sediment into the hypolimnion. In Lake Tiefer, redox conditions and the presence of nitrate and nitrite limited the water depth range in which P-release occurred. In I Lake Dudinghausen, part of the released soluble reactive phosphorus was in-corporated into the phototrophic sulfur bacteria biomass and thus transformed to particulate phosphorus. As much as 70 % of the particulate phosphorus in the hypolimnion was found in the phototrophic sulfur bacterial layer, with 15-20% of this particulate phosphorus consisting of polyphosphate storage compounds. The low ratio of soluble reactive phosphorus to particulate phosphorus in the hypolimnion was, therefore, attributed to phototrophic sulfur bacteria. The phototrophic sulfur bacteria appear to act as an internal nutrient filter and convert soluble reactive phosphorus into particulate phosphorus. [ABSTRACT FROM AUTHOR]

Details the topics discussed in the Proteolysis in Prokaryotes: Protein Quality Control and Regulatory Principles conference held in Schwetszingen, Germany on October 25-27, 2002. Mechanisms of proteolytic systems; Protease structures and molecular recognition; Unfolding, translocation and processing of substrates; Physiology and biodiversity of proteolysis.

Prokaryotic diversity in Alpine salt sediments was investigated by polymerase chain reaction (PCR) amplification of 16S rRNA genes, sequencing of cloned products, and comparisons with culturable strains. DNA was extracted from the residue following filtration of dissolved Permo-Triassic rock salt. Fifty-four haloarchaeal sequences were obtained, which could be grouped into at least five distinct clusters. Similarity values of three clusters to known 16S rRNA genes were less than 90%–95%, suggesting the presence of uncultured novel taxa; two clusters were 98% and 99% similar to isolates from Permo-Triassic or Miocene salt from England and Poland, and to Halobacterium salinarum, respectively. Some rock salt samples, including drilling cores, yielded no amplifiable DNA and no cells or only a few culturable cells. This result suggested a variable distribution of haloarchaea within different strata, probably consistent with the known geologic heterogeneity of Alpine salt deposits. We recently reported identical culturable Halococcus salifodinae strains in Permo-Triassic salt sediments from England, Germany, and Austria; together with the data presented here, those results suggest one plausible scenario to be an ancient continuous hypersaline ocean (Zechstein sea) populated by haloarchaea, whose descendants are found today in the salt sediments. The novelty of the sequences also suggested avoidance of haloarchaeal contaminants during our isolation of strains, preparation of DNA, and PCR reactions. [ABSTRACT FROM AUTHOR]