Albin Alfreider

Albin Alfreider
University of Innsbruck | UIBK · Department of Ecology

PhD

About

41
Publications
4,333
Reads
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2,281
Citations
Introduction
Additional affiliations
September 2004 - present
University of Innsbruck
Position
  • Research Assistant
December 1999 - February 2003
Helmholtz-Zentrum für Umweltforschung
Position
  • Research Associate
Description
  • Groundwater microbiology and remediation research in regionally contaminated aquifers
March 1999 - November 1999
University of Innsbruck
Position
  • PostDoc Position
Description
  • Molecular analysis of microbial-community successions during composting of organic waste

Publications

Publications (41)
Article
Full-text available
To date, little is known about the ecological significance of Comammox (COMplete AMMonia OXidizers) Nitrospira in the water column of freshwater lakes. Water samples collected along depth profiles were used to investigate the distribution of Comammox in 13 lakes characterized by a wide range of physicochemical properties. Several published primers,...
Article
Full-text available
The Calvin-Benson-Bassham (CBB) cycle and the 3-hydroxypropionate/4-hydroxybutyrate (HP/HB) cycle are two inorganic carbon assimilation pathways widely used by prokaryotic autotrophs in lakes. We investigated the effect of mixing periods and stable water stratification patterns on the trajectories of both CO2 fixation strategies in a dimictic lake...
Article
Full-text available
Niche specialisation of nitrifying prokaryotes is usually studied with tools targeting molecules involved in the oxidation of ammonia and nitrite. The ecological significance of diverse CO2 fixation strategies used by nitrifiers is, however, mostly unexplored. By analysing autotrophy-related genes in combination with amoA marker genes based on drop...
Article
Full-text available
Zooplankton from clear alpine lakes is exposed to stressful levels of solar UV radiation (UVR). As these pelagic organisms experience high UVR and large changes in solar radiation conditions between ice-free and ice-cover periods, they have evolved various strategies to minimize UVR exposure and damage. Here, we studied the relation between photopr...
Article
Full-text available
The analysis of RubisCO genes is a highly useful instrument to explore the diversity of chemoautotrophic bacteria using the Calvin–Benson–Bassham cycle for CO2 fixation. However, because of the wide taxonomic distribution of phylogenetically related RubisCO forms, environmental studies targeting chemoautotrophs are hampered in habitats dominated by...
Article
Full-text available
While mechanisms of different carbon dioxide (CO2 ) assimilation pathways in chemolithoautotrohic prokaryotes are well understood for many isolates under laboratory conditions, the ecological significance of diverse CO2 fixation strategies in the environment is mostly unexplored. Six stratified freshwater lakes were chosen to study the distribution...
Article
Full-text available
The bacterial and archaeal diversity of deep groundwater systems was investigated based on 16S rRNA-SSCP (single strand conformation polymorphism) fingerprints. The study site included five boreholes along the projected Brenner Base Tunnel in the central Alps of Tyrol, Austria. To obtain representative samples, packer-sealed fractures were sampled...
Article
Full-text available
A culture independent survey of the microbial community dynamics during the composting of organic waste in an industrial composting process was conducted by sequence analysis of (1) universal clone coding for small-subunit rRNA-genes libraries and, in parallel, with electrophoresis and sequencing of PCR-amplified 16S rDNA fragments based on DNA sin...
Article
Full-text available
Geologically and chemically distinct aquifers were screened for the presence of two genes coding for key enzymes of the reverse tricarboxylic acid (rTCA) cycle in autotrophic bacteria, 2-oxoglutarate : ferredoxin oxidoreductase (oorA) and the beta subunit of ATP citrate lyase enzymes (aclB). From 42 samples investigated, aclB genes were detected in...
Article
Full-text available
Groundwater polluted with methyl-tert-butyl ether (MTBE) and ammonium was investigated for chemolithoautotrophic CO(2) fixation capabilities based on detailed analyses of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) large subunit genes. Samples retrieved from a groundwater conditioning unit, characterized by different redox conditions,...
Article
A comparison of ribosomal RNA sequence analysis methods based on clone libraries and single-strand conformational polymorphism technique (SSCP) was performed with groundwater samples obtained between 523-555 meters below surface. The coverage of analyzed clones by phylotype-richness estimates was between 88-100%, confirming that the clone libraries...
Article
A molecular approach, based on the detection of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) large subunit genes, was applied to investigate the distribution and diversity of autotrophic bacteria in groundwater systems. DNA extracts from 48 sampling stations, including a variety of pristine and polluted, shallow and deep-subsurface gro...
Article
Full-text available
Aquatic microbial ecology aims at nothing less than explaining the world from "ecological scratch". It develops theories, concepts and models about the small and invisible living world that is at the bottom of every macroscopic aquatic system. In this paper we propose to look at the development of Aquatic Microbial Ecology as a reiteration of class...
Article
Full-text available
In order to gain insight into the community structure and the biodegradative potential of bacteria residing in a BTEX-contaminated field site, with benzene as main pollutant, an investigation strategy with a variety of cultivation-independent and -dependent approaches was undertaken. Based on 16S ribosomal DNA sequence analysis, sampling stations i...
Article
Full-text available
Studies conducted in Europe as well as in North and South America have tried to link Helicobacter pylori colonization with the drinking water supply, especially since H. pylori is known to survive quite well in water. In 2000, a cohort of 1884 grade-two children from two rural counties surrounding the city of Leipzig, Germany (77.4% of the 1991/199...
Article
Five bacterial strains (Acidovorax facilis B517, Cellulomonas turbata B529, Pseudomonas veronii B547, Pseudomonas veronii B549, and Paenibacillus polymyxa B550) isolated on chlorobenzene as the sole source of carbon and energy were screened for the accumulation of the putative metabolic intermediate 3-chlorocatechol during growth on chlorobenzene u...
Article
New in situ reactive barrier technologies were tested nearby a local aquifer in Bitterfeld, Saxonia-Anhalt, Germany, which is polluted mainly by chlorobenzene (CB), in concentrations up to 450 microM. A reactor filled with original aquifer sediment was designed for the microbiological remediation of the ground water by indigenous bacterial communit...
Article
Full-text available
To test our hypothesis that microbial autotrophic CO2 fixation plays an important role in subsurface systems of two large groundwater remediation projects, several anaerobic/microaerobic aquifer and groundwater samples were taken and used to investigate the distribution and phylogenetic diversity of ribulose-1,5-bisphosphate carboxylase/oxygenase (...
Article
Full-text available
In order to evaluate the in situ degradative capabilities of microorganisms in an underground reactor facility housing two flowthrough columns filled with aquifer soil, we examined the distribution and phylogeny of gene transcripts encoding enzymes capable of catalyzing the cleavage of the chlorinated aromatic ring during transformation of the main...
Article
A molecular approach based on the construction of 16S ribosomal DNA clone libraries was used to investigate the microbial diversity of an underground in situ reactor system filled with the original aquifer sediments. After chemical steady state was reached in the monochlorobenzene concentration between the original inflowing groundwater and the rea...
Article
In two reactors of the SAFIRA pilot plant, the microbial degradation of chlorobenzene (CB) by indigenous bacteria in native aquifer sediment were tested under oxic and anoxic conditions. Under anoxic conditions, no definite degradation was observed. Adding hydrogen peroxide (2.94 mM) and nitrate (2 mM) in one of the two reactors caused the degradat...
Article
The SAFIRA in situ pilot plant in Bitterfeld, Saxonia-Anhalt, Germany, currently serves as the test site for eight different in situ approaches to remediate anoxic chlorobenzene (CB)-contaminated ground water. Two reactors, both filled with originallignite-containing aquifer material, are designed for themicrobiological in situ remediation of the g...
Article
Bacterial abundances and activity, estimated by 4′,6-diamidino-2-phenylindole staining (DAPI) and the reduction of 2-(p-iodophenyl)-3-(p-nitrophenyl)-5-phenyl tetrazolium chloride (INT), were investigated in two oligotrophic artificial groundwater lakes and the surrounding aquifers. To evaluate the effect of lake water on groundwater downstream, sa...
Article
Full-text available
We studied the influence of methodology on the variability of bacterial direct counts and biomass estimates. Two frequently used fluorochromes, 4,6-diamidino-2-phenylindole (DAPI) and 3, 6-bis(dimethylamino)acridine (acridine orange (AO)), were applied to determine bacterial abun- dances and sizes along a vertical profile in a oligo-mesotrophic fre...
Article
Full-text available
Coastal plumes of low salinity water that extend hundreds of kilometers offshore into oligotrophic waters are often found in the Gulf of Mexico. To characterize one such feature, a series of photoautotrophic activity and biomass parameters were measured at 2 stations in the eastern Gulf of Mexico, including pigments by high performance liquid chrom...
Article
Full-text available
Ribulose-1,5-diphosphate carboxylase/oxygenase (RuBisCO) large subunit genes (rbcL) were obtained by amplification and cloning of 554 or 614 bp sequences of indigenous phytoplankton populations at 2 stations in the southeastern Gulf of Mexico. One station (Stn 4) was located in a low salinity, high chlorophyll plume (the 'Green River') which has pr...
Article
Full-text available
The seasonal variations in community structure and cell morphology of pelagic procaryotes from a high mountain lake (Gossenkollesee, Austria) were studied by in situ hybridization with rRNA-targeted fluorescently labeled oligonucleotide probes (FISH) and image-analyzed microscopy. Compositional changes and biomass fluctuations within the assemblage...
Article
The seasonal variations in community structure and cell morphology of pelagic procaryotes from a high mountain lake (Gossenköllesee, Austria) were studied by in situ hybridization with rRNA-targeted fluorescently labeled oligonucleotide probes (FISH) and image-analyzed microscopy. Compositional changes and biomass fluctuations within the assemblage...
Article
Full-text available
We describe a procedure to measure the cell sizes of pelagic bacteria after determinative hybridization with rRNA-targeted fluorescently labeled oligonucleotide probes. Our approach is based on established image analysis techniques modified for objects simultaneously stained with two fluorescent dyes. It allows the estimation of biomass and cell si...
Article
Total cell numbers, abundance of respiring bacteria and [3H]thymidine and [14C]leucine incorporation rates were investigated in four groundwater wells of low nutrient content. Total cell numbers in the pumped groundwater were low (14 × 103 to 279 × 103 cells mL−1), and [3Hthymidine and [14C]leucine incorporation rates were, with one exception, belo...
Article
Full-text available
We present an improvement of the INT [2-(p-iodophenyl)-3-(p-nitrophenyl)-5-phenyltetrazolium chloride)] reduction method using Cyto-Clear slides, the fluorochrome DAPI (4(prm1),6(prm1)-diamidino-2 phenylindole), and an image analysis system. With this method we were able to simultaneously measure cell dimensions and formazan crystals as indicators...
Article
The fraction of planktonic bacteria in oligo- and mesotrophic lakes that can be classified by in situ hybridization has been significantly increased with an optimized protocol. By the use of white polycarbonate filters, CY3-monolabeled oligonucleotide probes, and high quality fluorescence filter sets between 29 and 64% of the cells visualized by 4'...
Article
Full-text available
The bacterial community structure in the winter cover and pelagic zone of a high mountain lake was analyzed by in situ hybridization with fluorescently labeled rRNA-targeted oligonucleotide probes. Cells fixed on membrane filters were hybridized with a probe specific for the domain Bacteria as well as with probes for the alpha, beta, and gamma subc...

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Project (1)
Project
Chemolithoautotrophic prokaryotes fix carbon dioxide (CO2) through energy not acquired from light but from inorganic substrates. To date, six different mechanisms are known by which chemolithoautotrophic bacteria and archaea assimilate CO2. While the biochemistry and molecular biology of CO2 fixation pathways are well understood for many isolates under laboratory conditions, the driving forces and biogeochemical processes determining the occurrence of diverse chemolithoautotophic CO2 fixation strategies in the environment are mostly unexplored. In this project, we assess which CO2 fixation pathways are used by chemolithoautotrophic prokaryotic communities, studying lakes with distinct stratification patterns. These lakes, characterized by different concentration gradients of oxygen and redox states of elements such as carbon, nitrogen, sulfur and iron, are particularly suitable for the investigation of chemoautotrophic microbial communities in a well-defined framework of habitat heterogeneity. Our research focuses on the analysis of genes coding for selected key enzymes for the assimilation of CO2 in the Calvin-Benson-Bassham cycle, the reductive tricarboxylic acid cycle, and the recently discovered 3-hydroxypropionate/4-hydroxybutyrate pathway. We are especially interested to determine which CO2 assimilation pathways are used under in situ conditions and plan to ascertain which prokaryotes are responsible for specific chemoautotrophic activities. Methods based on sequence analysis of functional genes, quantitative polymerase chain reaction (qPCR) and DNA stable-isotope probing (DNA-SIP) after 13C-bicarbonate incorporation are powerful tools by which we plan to identify active CO2 fixation pathways in association with the phylogenetic profile of the respective organisms. Ultimately, we expect to gain insight on whether the diversity of CO2 fixation pathways correspond to ecologically distinct groups and to identify which drivers and processes are most influential for the dynamic of chemolithoautotrophic prokaryotic community structures and carbon fixation strategies in aquatic environments. Funding agency: Austrian Science Fund (Project: P 25703)