Complete Genome Sequence of “Candidatus Viadribacter manganicus” Isolated from a German Floodplain Area

Iron- and manganese-depositing bacteria occur in many soils and all water systems, and their biogenic depositions of ochre in technical systems may cause severe clogging problems and monetary losses. “Candidatus Viadribacter manganicus” is a small coccoid, iron- and manganese-depositing bacterium isolated from the Lower Oder Valley National Park, Germany.BMBF, 02WU0715, Verbundprojekt: Entwicklung eines Indikatorsystems für Verockerungsprozesse - Teilprojekt 1: Untersuchung der Biofilme der Oder-Auen: Diversität und umweltbiotechnologisches Potenzial; Teilprojekt 3: Klärung des Abbaus persistenter organischer Schadstoffe bei mikrobiellen Prozesse

Draft Genome Sequence of the Gram-Positive Neutrophilic Iron-Precipitating Kineosporia sp. Strain A_224

We report here the draft genome sequence of the neutrophilic iron-precipitating Kineosporia sp. strain A_224. Analysis of the predicted genes may improve our knowledge of its role in ochrous formations in natural and technical water systems. This is the first public genome sequence of a Kineosporia aurantiaca strain.BMBF, 02WU0715, Verbundprojekt: Entwicklung eines Indikatorsystems für Verockerungsprozesse - Teilprojekt 1: Untersuchung der Biofilme der Oder-Auen: Diversität und umweltbiotechnologisches Potenzial; Teilprojekt 3: Klärung des Abbaus persistenter organischer Schadstoffe bei mikrobiellen Prozesse

Draft genome sequence of strain B 225, an iron-depositing isolate of the genus Novosphingobium

Here, we report the draft genome sequence of Novosphingobium sp. strain B 225, an iron-depositing bacterium isolated from a phenazone-amended naturally grown biofilm. This biofilm was grown in the Unteres Odertal National Park, Germany. Illumina NextSeq sequencing was used to determine the genome of the strain.DFG, 325093850, Open Access Publizieren 2017 - 2018 / Technische Universität Berli

Draft Genome Sequence of Ideonella sp. Strain A 288, Isolated from an Iron-Precipitating Biofilm

Here, we report the draft genome sequence of the betaproteobacterium Ideonella sp. strain A_228. This isolate, obtained from a bog iron ore-containing floodplain area in Germany, provides valuable information about the genetic diversity of neutrophilic iron-depositing bacteria. The Illumina NextSeq technique was used to sequence the draft genome sequence of the strain.BMBF, 02WU0715, Verbundprojekt: Entwicklung eines Indikatorsystems für Verockerungsprozesse - Teilprojekt 1: Untersuchung der Biofilme der Oder-Auen: Diversität und umweltbiotechnologisches Potenzial; Teilprojekt 3: Klärung des Abbaus persistenter organischer Schadstoffe bei mikrobiellen Prozesse

Evaluating the Impact of Wastewater Effluent on Microbial Communities in the Panke, an Urban River

Pharmaceuticals are consumed in high amounts and can enter as emerging organic compounds in surface waters as they are only partially retained in wastewater treatment plants (WWTPs). Receiving pharmaceuticals may burden the aquatic environment, as they are designed to be bioactive even at low concentrations. Sediment biofilm populations were analyzed in river sediments due to the exposure of an inflow of WWTP effluents. Illumina MiSeq 16S rRNA gene amplicon sequencing was performed of 108 sediment samples, which were taken from multiple cores within three sampling locations in the Panke River, with one sampling site located downstream of the inflow. Sequencing data were processed to infer microbial community structure in samples concerning the environmental variables, such as micropollutants and physicochemical parameters measured for each core. More than 25 different micropollutants were measured in pore water samples, in which bezafibrate, clofibric acid, carbamazepine, and diclofenac were detected at high concentrations. Bacterial 16S rRNA gene amplicons revealed Nitrospirae, Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, Bacteroidetes, and Ignavibacteriae as the most abundant groups in the samples. Differences in microbial community composition were observed with respect to micropollutants. However, our findings revealed that the composition of the microbial community was not only governed by the effluent. The significant changes in the alpha- and beta-diversity were explained by phenobarbital and SO42−, which did not originate from the WWTP indicating that more unobserved factors are also likely to play a role in affecting the biofilm community’s composition.DFG, 414044773, Open Access Publizieren 2019 - 2020 / Technische Universität BerlinDFG, 248198858, GRK 2032: Grenzzonen in urbanen Wassersysteme

Draft Genome Sequence of Rheinheimera sp. Strain SA_1 Isolated from Iron Backwash Sludge in Germany

Rheinheimera sp. strain SA_1 is an iron-depositing bacterium for which we report a draft genome sequence. Strain SA_1 was isolated from iron backwash sludge of a waterworks in Germany. The Illumina MiSeq technique was used to sequence the genome of the strain.BMBF, 02WT1184, Verbundprojekt Mikrobielle Verockerung, Teilprojekt 1: Mikrobiologie, Wasserreinhaltung & Fluidsystemdynami

Draft genome sequence of actinobacterial strain Kineosporia sp. R_H_3, a neutrophilic iron-depositing bacterium

The draft genome sequence of a neutrophilic iron-depositing actinobacterial strain, Kineosporia sp. R_H_3, is reported here. Detailed analysis of the genome can elucidate the role of specific cytochromes for Fe oxidation and how this organism might receive energy from Fe oxidation. To date, this is the second publicly available genome sequence of a Kineosporia strain.DFG, 325093850, Open Access Publizieren 2017 - 2018 / Technische Universität Berli

Glacial refugia and postglacial expansion of the alpine-prealpine plant species Polygala chamaebuxus

The shrubby milkwort (Polygala chamaebuxus L.) is widely distributed in the Alps, but occurs also in the lower mountain ranges of Central Europe such as the Franconian Jura or the Bohemian uplands. Populations in these regions may either originate from glacial survival or from postglacial recolonization. In this study, we analyzed 30 populations of P.chamaebuxus from the whole distribution range using AFLP (Amplified Fragment Length Polymorphism) analysis to identify glacial refugia and to illuminate the origin of P.chamaebuxus in the lower mountain ranges of Central Europe. Genetic variation and the number of rare fragments within populations were highest in populations from the central part of the distribution range, especially in the Southern Alps (from the Tessin Alps and the Prealps of Lugano to the Triglav Massiv) and in the middle part of the northern Alps. These regions may have served, in accordance with previous studies, as long-term refugia for the glacial survival of the species. The geographic pattern of genetic variation, as revealed by analysis of molecular variance, Bayesian cluster analysis and a PopGraph genetic network was, however, only weak. Instead of postglacial recolonization from only few long-term refugia, which would have resulted in deeper genetic splits within the data set, broad waves of postglacial expansion from several short-term isolated populations in the center to the actual periphery of the distribution range seem to be the scenario explaining the observed pattern of genetic variation most likely. The populations from the lower mountain ranges in Central Europe were more closely related to the populations from the southwestern and northern than from the nearby eastern Alps. Although glacial survival in the Bohemian uplands cannot fully be excluded, P.chamaebuxus seems to have immigrated postglacially from the southwestern or central-northern parts of the Alps into these regions during the expansion of the pine forests in the early Holocene

Molekulare und mikrobiologische Untersuchungen der bakteriellen Gemeinschaft eines urbanen Bodens

Nicht benetzbare Böden stellen ein allgemeines und weltweites Problem dar, welches durch physische, chemische und biologische Faktoren beeinflusst wird. Die Benetzungshemmung der Bodenoberfläche hat einen Einfluss auf die Wasserinfiltration und die räumliche Verteilung der Bodenfeuchte. Änderungen in der Benetzbarkeit des Bodens können einen bedeutenden Stressfaktor für bakterielle Bodengemeinschaften darstellen und die bakterielle Zusammensetzung sowie mikrobielle Prozesse im Boden beeinflussen. Über die Auswirkungen von nicht benetzbaren Böden auf die bakterielle Bodengemeinschaft und umgekehrt ist bisher nur wenig bekannt. Ziel dieser Dissertation ist zum einen den Einfluss der Benetzungshemmung des Bodens auf die bakterielle Bodengemeinschaft zu ermitteln, sowie die Charakterisierung von Bakterien in einem Bodenprofil. Weiterhin sollte der Einfluss von Wasserstress auf die bakterielle Gemeinschaft durch Trocknung und Wiederbefeuchtung in Mikrokosmosversuchen untersucht werden. Letztlich wurde der Einfluss von hydrophilen und hydrophoben Biofilmen auf die Benetzbarkeit des Bodens ermittelt. Um Änderungen in der bakteriellen Zusammensetzung und ihres physiologischen Potentials zu bestimmen, wurden kultivierungsabhängige und –unabhängige Methoden verwendet. Mit der Anwendung von kultivierungsunabhängigen Methoden war keine Unterscheidung von benetzbaren und nicht benetzbaren Bodenproben möglich. Die Erzeugung von metabolischen Fingerabdrücken, sowie die Bestimmung der Kolonie bildenden Einheiten zeigte jedoch Unterschiede zwischen benetzbaren und nicht benetzbaren Bodenbereichen. Innerhalb des Bodenprofils konnten Variationen in der Zusammensetzung und des physiologischen Potentials, sowie der Aktivität ermittelt werden. Diese Ergebnisse weisen darauf hin, dass die Benetzungshemmung von Böden keinen signifikanten Einfluss auf die gesamte genetische Diversität hat, den physiologischen Status der Gemeinschaft jedoch beeinflusst. Die Untersuchungen von Wasserstress in Mikrokosmosexperimenten zeigten keinen Einfluss auf die bakterielle Bodengemeinschaft, da keine feuchtigkeitsabhängigen Veränderungen beobachtet werden konnten. Daher scheinen die bakteriellen Gemeinschaften dieses urbanen Bodens an die unterschiedlichen Bodenfeuchten angepasst zu sein, indem sie ihre physiologische Zellaktivität regeln. Um Einblicke zu gewinnen, wie Biofilme Oberflächeneigenschaften von Böden beeinflussen können, wurden Bodenproben mit Bakterien verschiedener Hydrophobizität der Zelloberfläche beimpft: Bacillus sphaericus (hydrophil), Variovorax paradoxus (hydrophob) und ein α- Proteobacterium (hydrophob). Die Ergebnisse zeigten, dass Biofilme einen Einfluss auf die Benetzbarkeit des Bodens haben können, da sie in der Lage sind Bodenproben zu hydrophilisieren bzw. zu hydrophobisieren.Soil water repellency is a common phenomenon which occurs throughout the world and is influenced by physical, chemical and biological factors. It prevents water from infiltrating into the soil and influences soil properties. Changes in soil wettability may represent a significant source of stress for microbial communities and affect bacterial composition and soil microbial processes. Up till now, little is known about the effects of water repellency on soil bacterial communities and vice versa. The aim of this study was to gain a more profound insight into the bacterial community structure of wettable and water repellent soils. The horizontal and vertical distribution of the bacterial population was analyzed with regard to soil water repellency. Furthermore, the molecular diversity and active bacterial population subjected to water stress was monitored in microcosm experiments. Finally, the effects of hydrophilic and hydrophobic bacterial biofilms on soil wettability were investigated. For determination of alterations in the bacterial structure and their metabolic potential cultivation- and molecular methods were combined. The application of cultivation independent methods did not allow to distinguish between water repellent and wettable soil samples. Whereas determination of CFU and metabolic fingerprints resulted in differences between wettable and water repellent soil areas. Variations in community structure as well as in community function and activity were observed within the soil profile. These data indicated that water repellency did not have a significant effect on the total genetic diversity present but affected the physiological status, so that the bacteria capable of responding to laboratory culture methods were altered in activity without changes in phylogenetic distribution. Therefore, the bacterial communities of this urban soil seemed to be adapted to different moisture conditions by regulating their physiological cell activity. Microcosm experiments revealed no effects of water stress on the bacterial community, as no moisture related changes in the bacterial population were observed. To gain insights how biofilms may affect surface properties of soil, soil samples were inoculated with bacteria of different cell surface hydrophobicity: Bacillus sphaericus (hydrophilic), Variovorax paradoxus (hydrophobic) and an α- Proteobacterium (hydrophobic). The results demonstrated the effect that bacterial biofilms can have on soil wettability, as biofilms were able to hydrophilize or hydrophobize soil samples