@article{BartholomaeusLipusMitzscherlingetal.2022, author = {Bartholom{\"a}us, Alexander and Lipus, Daniel and Mitzscherling, Julia and MacLean, Joana and Wagner, Dirk}, title = {Draft Genome Sequence of Nocardioides alcanivorans NGK65(T), a Hexadecane-Degrading Bacterium}, series = {Microbiology Resource Announcements}, volume = {11}, journal = {Microbiology Resource Announcements}, number = {8}, publisher = {American Society for Microbiology}, address = {Washington}, issn = {2576-098X}, doi = {10.1128/mra.01213-21}, pages = {2}, year = {2022}, abstract = {The Gram-positive bacterium Nocardioides alcanivorans NGK65(T) was isolated from plastic-polluted soil and cultivated on medium with polyethylene as the single carbon source. Nanopore sequencing revealed the presence of candidate enzymes for the biodegradation of polyethylene. Here, we report the draft genome of this newly described member of the terrestrial plastisphere.}, language = {en} } @article{BernhardMoskwaSchmidtetal.2018, author = {Bernhard, Nadine and Moskwa, Lisa-Marie and Schmidt, Karsten and Oeser, Ralf Andreas and Aburto, Felipe and Bader, Maaike Y. and Baumann, Karen and von Blanckenburg, Friedhelm and Boy, Jens and van den Brink, Liesbeth and Brucker, Emanuel and Buedel, Burkhard and Canessa, Rafaella and Dippold, Michaela A. and Ehlers, Todd and Fuentes, Juan P. and Godoy, Roberto and Jung, Patrick and Karsten, Ulf and Koester, Moritz and Kuzyakov, Yakov and Leinweber, Peter and Neidhardt, Harald and Matus, Francisco and Mueller, Carsten W. and Oelmann, Yvonne and Oses, Romulo and Osses, Pablo and Paulino, Leandro and Samolov, Elena and Schaller, Mirjam and Schmid, Manuel and Spielvogel, Sandra and Spohn, Marie and Stock, Svenja and Stroncik, Nicole and Tielboerger, Katja and Uebernickel, Kirstin and Scholten, Thomas and Seguel, Oscar and Wagner, Dirk and K{\"u}hn, Peter}, title = {Pedogenic and microbial interrelations to regional climate and local topography}, series = {Catena : an interdisciplinary journal of soil science, hydrology, geomorphology focusing on geoecology and landscape evolution}, volume = {170}, journal = {Catena : an interdisciplinary journal of soil science, hydrology, geomorphology focusing on geoecology and landscape evolution}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0341-8162}, doi = {10.1016/j.catena.2018.06.018}, pages = {335 -- 355}, year = {2018}, abstract = {The effects of climate and topography on soil physico-chemical and microbial parameters were studied along an extensive latitudinal climate gradient in the Coastal Cordillera of Chile (26 degrees-38 degrees S). The study sites encompass arid (Pan de Azucar), semiarid (Santa Gracia), mediterranean (La Campana) and humid (Nahuelbuta) climates and vegetation, ranging from arid desert, dominated by biological soil crusts (biocrusts), semiarid shrubland and mediterranean sclerophyllous forest, where biocrusts are present but do have a seasonal pattern to temperate-mixed forest, where biocrusts only occur as an early pioneering development stage after disturbance. All soils originate from granitic parent materials and show very strong differences in pedogenesis intensity and soil depth. Most of the investigated physical, chemical and microbiological soil properties showed distinct trends along the climate gradient. Further, abrupt changes between the arid northernmost study site and the other semi-arid to humid sites can be shown, which indicate non-linearity and thresholds along the climate gradient. Clay and total organic carbon contents (TOC) as well as Ah horizons and solum depths increased from arid to humid climates, whereas bulk density (BD), pH values and base saturation (BS) decreased. These properties demonstrate the accumulation of organic matter, clay formation and element leaching as key-pedogenic processes with increasing humidity. However, the soils in the northern arid climate do not follow this overall latitudinal trend, because texture and BD are largely controlled by aeolian input of dust and sea salts spray followed by the formation of secondary evaporate minerals. Total soil DNA concentrations and TOC increased from arid to humid sites, while areal coverage by biocrusts exhibited an opposite trend. Relative bacterial and archaeal abundances were lower in the arid site, but for the other sites the local variability exceeds the variability along the climate gradient. Differences in soil properties between topographic positions were most pronounced at the study sites with the mediterranean and humid climate, whereas microbial abundances were independent on topography across all study sites. In general, the regional climate is the strongest controlling factor for pedogenesis and microbial parameters in soils developed from the same parent material. Topographic position along individual slopes of limited length augmented this effect only under humid conditions, where water erosion likely relocated particles and elements downward. The change from alkaline to neutral soil pH between the arid and the semi-arid site coincided with qualitative differences in soil formation as well as microbial habitats. This also reflects non-linear relationships of pedogenic and microbial processes in soils depending on climate with a sharp threshold between arid and semi-arid conditions. Therefore, the soils on the transition between arid and semi-arid conditions are especially sensitive and may be well used as indicators of long and medium-term climate changes. Concluding, the unique latitudinal precipitation gradient in the Coastal Cordillera of Chile is predestined to investigate the effects of the main soil forming factor - climate - on pedogenic processes.}, language = {en} } @misc{deVeraAlawiBackhausetal.2019, author = {de Vera, Jean-Pierre Paul and Alawi, Mashal and Backhaus, Theresa and Baque, Mickael and Billi, Daniela and Boettger, Ute and Berger, Thomas and Bohmeier, Maria and Cockell, Charles and Demets, Rene and de la Torre Noetzel, Rosa and Edwards, Howell and Elsaesser, Andreas and Fagliarone, Claudia and Fiedler, Annelie and Foing, Bernard and Foucher, Frederic and Fritz, J{\"o}rg and Hanke, Franziska and Herzog, Thomas and Horneck, Gerda and H{\"u}bers, Heinz-Wilhelm and Huwe, Bj{\"o}rn and Joshi, Jasmin Radha and Kozyrovska, Natalia and Kruchten, Martha and Lasch, Peter and Lee, Natuschka and Leuko, Stefan and Leya, Thomas and Lorek, Andreas and Martinez-Frias, Jesus and Meessen, Joachim and Moritz, Sophie and Moeller, Ralf and Olsson-Francis, Karen and Onofri, Silvano and Ott, Sieglinde and Pacelli, Claudia and Podolich, Olga and Rabbow, Elke and Reitz, G{\"u}nther and Rettberg, Petra and Reva, Oleg and Rothschild, Lynn and Garcia Sancho, Leo and Schulze-Makuch, Dirk and Selbmann, Laura and Serrano, Paloma and Szewzyk, Ulrich and Verseux, Cyprien and Wadsworth, Jennifer and Wagner, Dirk and Westall, Frances and Wolter, David and Zucconi, Laura}, title = {Limits of life and the habitability of Mars}, series = {Astrobiology}, volume = {19}, journal = {Astrobiology}, number = {2}, publisher = {Liebert}, address = {New Rochelle}, issn = {1531-1074}, doi = {10.1089/ast.2018.1897}, pages = {145 -- 157}, year = {2019}, abstract = {BIOMEX (BIOlogy and Mars EXperiment) is an ESA/Roscosmos space exposure experiment housed within the exposure facility EXPOSE-R2 outside the Zvezda module on the International Space Station (ISS). The design of the multiuser facility supports-among others-the BIOMEX investigations into the stability and level of degradation of space-exposed biosignatures such as pigments, secondary metabolites, and cell surfaces in contact with a terrestrial and Mars analog mineral environment. In parallel, analysis on the viability of the investigated organisms has provided relevant data for evaluation of the habitability of Mars, for the limits of life, and for the likelihood of an interplanetary transfer of life (theory of lithopanspermia). In this project, lichens, archaea, bacteria, cyanobacteria, snow/permafrost algae, meristematic black fungi, and bryophytes from alpine and polar habitats were embedded, grown, and cultured on a mixture of martian and lunar regolith analogs or other terrestrial minerals. The organisms and regolith analogs and terrestrial mineral mixtures were then exposed to space and to simulated Mars-like conditions by way of the EXPOSE-R2 facility. In this special issue, we present the first set of data obtained in reference to our investigation into the habitability of Mars and limits of life. This project was initiated and implemented by the BIOMEX group, an international and interdisciplinary consortium of 30 institutes in 12 countries on 3 continents. Preflight tests for sample selection, results from ground-based simulation experiments, and the space experiments themselves are presented and include a complete overview of the scientific processes required for this space experiment and postflight analysis. The presented BIOMEX concept could be scaled up to future exposure experiments on the Moon and will serve as a pretest in low Earth orbit.}, language = {en} } @article{deVeraBoettgerdelaTorreNoetzeletal.2012, author = {de Vera, Jean-Pierre Paul and B{\"o}ttger, Ute and de la Torre N{\"o}tzel, Rosa and Sanchez, Francisco J. and Grunow, Dana and Schmitz, Nicole and Lange, Caroline and H{\"u}bers, Heinz-Wilhelm and Billi, Daniela and Baque, Mickael and Rettberg, Petra and Rabbow, Elke and Reitz, G{\"u}nther and Berger, Thomas and M{\"o}ller, Ralf and Bohmeier, Maria and Horneck, Gerda and Westall, Frances and J{\"a}nchen, Jochen and Fritz, J{\"o}rg and Meyer, Cornelia and Onofri, Silvano and Selbmann, Laura and Zucconi, Laura and Kozyrovska, Natalia and Leya, Thomas and Foing, Bernard and Demets, Rene and Cockell, Charles S. and Bryce, Casey and Wagner, Dirk and Serrano, Paloma and Edwards, Howell G. M. and Joshi, Jasmin Radha and Huwe, Bj{\"o}rn and Ehrenfreund, Pascale and Elsaesser, Andreas and Ott, Sieglinde and Meessen, Joachim and Feyh, Nina and Szewzyk, Ulrich and Jaumann, Ralf and Spohn, Tilman}, title = {Supporting Mars exploration BIOMEX in Low Earth Orbit and further astrobiological studies on the Moon using Raman and PanCam technology}, series = {Planetary and space science}, volume = {74}, journal = {Planetary and space science}, number = {1}, publisher = {Elsevier}, address = {Oxford}, issn = {0032-0633}, doi = {10.1016/j.pss.2012.06.010}, pages = {103 -- 110}, year = {2012}, abstract = {The Low Earth Orbit (LEO) experiment Biology and Mars Experiment (BIOMEX) is an interdisciplinary and international space research project selected by ESA. The experiment will be accommodated on the space exposure facility EXPOSE-R2 on the International Space Station (ISS) and is foreseen to be launched in 2013. The prime objective of BIOMEX is to measure to what extent biomolecules, such as pigments and cellular components, are resistant to and able to maintain their stability under space and Mars-like conditions. The results of BIOMEX will be relevant for space proven biosignature definition and for building a biosignature data base (e.g. the proposed creation of an international Raman library). The library will be highly relevant for future space missions such as the search for life on Mars. The secondary scientific objective is to analyze to what extent terrestrial extremophiles are able to survive in space and to determine which interactions between biological samples and selected minerals (including terrestrial, Moon- and Mars analogs) can be observed under space and Mars-like conditions. In this context, the Moon will be an additional platform for performing similar experiments with negligible magnetic shielding and higher solar and galactic irradiation compared to LEO. Using the Moon as an additional astrobiological exposure platform to complement ongoing astrobiological LEO investigations could thus enhance the chances of detecting organic traces of life on Mars. We present a lunar lander mission with two related objectives: a lunar lander equipped with Raman and PanCam instruments which can analyze the lunar surface and survey an astrobiological exposure platform. This dual use of testing mission technology together with geo- and astrobiological analyses will significantly increase the science return, and support the human preparation objectives. It will provide knowledge about the Moon's surface itself and, in addition, monitor the stability of life-markers, such as cells, cell components and pigments, in an extraterrestrial environment with much closer radiation properties to the surface of Mars. The combination of a Raman data base of these data together with data from LEO and space simulation experiments, will lead to further progress on the analysis and interpretation of data that we will obtain from future Moon and Mars exploration missions.}, language = {en} } @article{FrankFahleYergeauGreeretal.2014, author = {Frank-Fahle, Beatrice A. and Yergeau, Etienne and Greer, Charles W. and Lantuit, Hugues and Wagner, Dirk}, title = {Microbial functional potential and community composition in permafrost-affected soils of the NW canadian arctic}, series = {PLoS one}, volume = {9}, journal = {PLoS one}, number = {1}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0084761}, pages = {12}, year = {2014}, abstract = {Permafrost-affected soils are among the most obvious ecosystems in which current microbial controls on organic matter decomposition are changing as a result of global warming. Warmer conditions in polygonal tundra will lead to a deepening of the seasonal active layer, provoking changes in microbial processes and possibly resulting in exacerbated carbon degradation under increasing anoxic conditions. To identify current microbial assemblages in carbon rich, water saturated permafrost environments, four polygonal tundra sites were investigated on Herschel Island and the Yukon Coast, Western Canadian Arctic. Ion Torrent sequencing of bacterial and archaeal 16S rRNA amplicons revealed the presence of all major microbial soil groups and indicated a local, vertical heterogeneity of the polygonal tundra soil community with increasing depth. Microbial diversity was found to be highest in the surface layers, decreasing towards the permafrost table. Quantitative PCR analysis of functional genes involved in carbon and nitrogen-cycling revealed a high functional potential in the surface layers, decreasing with increasing active layer depth. We observed that soil properties driving microbial diversity and functional potential varied in each study site. These results highlight the small-scale heterogeneity of geomorphologically comparable sites, greatly restricting generalizations about the fate of permafrost-affected environments in a warming Arctic.}, language = {en} } @article{GefenTrevesKedemWeissetal.2019, author = {Gefen-Treves, Shany and Kedem, Isaac and Weiss, Gad and Wagner, Dirk and Tchernov, Dan and Kaplan, Aaron}, title = {Acclimation of a rocky shore algal reef builder Neogoniolithon sp. to changing illuminations}, series = {Limnology and oceanography e-lectures / Association for the Sciences of Limnology and Oceanography}, volume = {65}, journal = {Limnology and oceanography e-lectures / Association for the Sciences of Limnology and Oceanography}, number = {1}, publisher = {Wiley}, address = {Hoboken}, issn = {0024-3590}, doi = {10.1002/lno.11245}, pages = {27 -- 36}, year = {2019}, abstract = {Vermetid reefs and rocky shores are hot spots of biodiversity, often referred to as the subtropical equivalent of coral reefs. The development of the ecosystem depends on the activity of several reef builders, including red crustose coralline algae (CCA) such as Neogoniolithon brassica-florida. Despite its importance, little is known about Neogoniolithon sp. acclimation to rapid changes in light intensity and corresponding photosynthetic activity. To overcome the large spatial variability in the light field (due to location and the porous nature of the rocks) we grew Neogoniolithon sp. on glass slides and characterized its photosynthetic performance in response to various light intensities by following O-2 exchange and fluorescence parameters. This was also performed on rock-inhabiting thalli collected from the east Mediterranean basin. Generally, maximal photosynthetic rate was reached when Neogoniolithon sp. thalli grown under low illumination (such as in protected niches where the light intensity can be as low as 1\% of surface illumination) were examined. When exposed to light intensities higher than those experienced during growth, Neogoniolithon sp. activates adaptive/protective mechanisms such as state transition and nonphotochemical fluorescence quenching and increases the dark respiration thereafter. We find that the Fv/Fm parameter (variable/maximal fluorescence) is not suitable to assess photosynthetic performance in Neogoniolithon sp. and propose using instead an alternative parameter recently developed. Our findings help to clarify why Neogoniolithon sp. is usually observed in shaded niches along the reef surfaces.}, language = {en} } @article{GenderjahnAlawiMangelsdorfetal.2018, author = {Genderjahn, Steffi and Alawi, Mashal and Mangelsdorf, Kai and Horn, Fabian and Wagner, Dirk}, title = {Desiccation- and saline-solerant bacteria and archaea in kalahari an sediments}, series = {Frontiers in microbiology}, volume = {9}, journal = {Frontiers in microbiology}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-302X}, doi = {10.3389/fmicb.2018.02082}, pages = {15}, year = {2018}, abstract = {More than 41\% of the Earth's land area is covered by permanent or seasonally arid dryland ecosystems. Global development and human activity have led to an increase in aridity, resulting in ecosystem degradation and desertification around the world. The objective of the present work was to investigate and compare the microbial community structure and geochemical characteristics of two geographically distinct saline pan sediments in the Kalahari Desert of southern Africa. Our data suggest that these microbial communities have been shaped by geochemical drivers, including water content, salinity, and the supply of organic matter. Using Illumina 16S rRNA gene sequencing, this study provides new insights into the diversity of bacteria and archaea in semi-arid, saline, and low-carbon environments. Many of the observed taxa are halophilic and adapted to water-limiting conditions. The analysis reveals a high relative abundance of halophilic archaea (primarily Halobacteria), and the bacterial diversity is marked by an abundance of Gemmatimonadetes and spore-forming Firmicutes. In the deeper, anoxic layers, candidate division MSBL1, and acetogenic bacteria (Acetothermia) are abundant. Together, the taxonomic information and geochemical data suggest that acetogenesis could be a prevalent form of metabolism in the deep layers of a saline pan.}, language = {en} } @article{GenderjahnAlawiWagneretal.2018, author = {Genderjahn, Steffi and Alawi, Mashal and Wagner, Dirk and Schueller, I. and Wanke, A. and Mangelsdorf, Kai}, title = {Microbial community responses to modern environmental and Past Climatic Conditions in Omongwa Pan, Western Kalahari}, series = {Journal of geophysical research : Biogeosciences}, volume = {123}, journal = {Journal of geophysical research : Biogeosciences}, number = {4}, publisher = {American Geophysical Union}, address = {Washington}, issn = {2169-8953}, doi = {10.1002/2017JG004098}, pages = {1333 -- 1351}, year = {2018}, abstract = {Due to a lack of well-preserved terrestrial climate archives, paleoclimate studies are sparse in southwestern Africa. Because there are no perennial lacustrine systems in this region, this study relies on a saline pan as an archive for climate information in the western Kalahari (Namibia). Molecular biological and biogeochemical analyses were combined to examine the response of indigenous microbial communities to modern and past climate-induced environmental conditions. The 16S rRNA gene high-throughput sequencing was applied to sediment samples from Omongwa pan to characterize the modern microbial diversity. Highest diversity of microorganisms, dominated by the extreme halophilic archaeon Halobacteria and by the bacterial phylum Gemmatimonadetes, was detected in the near-surface sediments of Omongwa pan. In deeper sections abundance and diversity significantly decreases and Bacillus, known to form spores, become dominant. Lipid biomarkers for living and past microbial life were analyzed to track the influence of climate variation on the abundance of microbial communities from the Last Glacial Maximum to Holocene time. Since water is an inevitable requirement for microbial life, in this dry region the abundance of past microbial biomarkers was evaluated to conclude on periods of increased paleoprecipitation in the past. The data point to a period of increased humidity in the western Kalahari during the Last Glacial to Holocene transition indicating a southward shift of the Intertropical Convergence Zone during this period. Comparison with results from a southwestern Kalahari pan suggests complex displacements of the regional atmospheric systems since the Last Glacial Maximum.}, language = {en} } @article{GenderjahnLewinHornetal.2021, author = {Genderjahn, Steffi and Lewin, Simon and Horn, Fabian and Schleicher, Anja M. and Mangelsdorf, Kai and Wagner, Dirk}, title = {Living lithic and sublithic bacterial communities in Namibian drylands}, series = {Microorganisms : open access journal}, volume = {9}, journal = {Microorganisms : open access journal}, number = {2}, publisher = {MDPI}, address = {Basel}, issn = {2076-2607}, doi = {10.3390/microorganisms9020235}, pages = {20}, year = {2021}, abstract = {Dryland xeric conditions exert a deterministic effect on microbial communities, forcing life into refuge niches. Deposited rocks can form a lithic niche for microorganisms in desert regions. Mineral weathering is a key process in soil formation and the importance of microbial-driven mineral weathering for nutrient extraction is increasingly accepted. Advances in geobiology provide insight into the interactions between microorganisms and minerals that play an important role in weathering processes. In this study, we present the examination of the microbial diversity in dryland rocks from the Tsauchab River banks in Namibia. We paired culture-independent 16S rRNA gene amplicon sequencing with culture-dependent (isolation of bacteria) techniques to assess the community structure and diversity patterns. Bacteria isolated from dryland rocks are typical of xeric environments and are described as being involved in rock weathering processes. For the first time, we extracted extra- and intracellular DNA from rocks to enhance our understanding of potentially rock-weathering microorganisms. We compared the microbial community structure in different rock types (limestone, quartz-rich sandstone and quartz-rich shale) with adjacent soils below the rocks. Our results indicate differences in the living lithic and sublithic microbial communities.}, language = {en} } @article{KrauzeKaempfHornetal.2017, author = {Krauze, Patryk and K{\"a}mpf, Horst and Horn, Fabian and Liu, Qi and Voropaev, Andrey and Wagner, Dirk and Alawi, Mashal}, title = {Microbiological and Geochemical Survey of CO2-Dominated Mofette and Mineral Waters of the Cheb Basin, Czech Republic}, series = {Frontiers in microbiology}, volume = {8}, journal = {Frontiers in microbiology}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-302X}, doi = {10.3389/fmicb.2017.02446}, pages = {16}, year = {2017}, abstract = {The Cheb Basin (NW Bohemia, Czech Republic) is a shallow, neogene intracontinental basin. It is a non-volcanic region which features frequent earthquake swarms and large-scale diffuse degassing of mantle-derived CO2 at the surface that occurs in the form of CO2-rich mineral springs and wet and dry mofettes. So far, the influence of CO2 degassing onto the microbial communities has been studied for soil environments, but not for aquatic systems. We hypothesized, that deep-trenching CO2 conduits interconnect the subsurface with the surface. This admixture of deep thermal fluids should be reflected in geochemical parameters and in the microbial community compositions. In the present study four mineral water springs and two wet mofettes were investigated through an interdisciplinary survey. The waters were acidic and differed in terms of organic carbon and anion/cation concentrations. Element geochemical and isotope analyses of fluid components were used to verify the origin of the fluids. Prokaryotic communities were characterized through quantitative PCR and Illumina 16S rRNA gene sequencing. Putative chemolithotrophic, anaerobic and microaerophilic organisms connected to sulfur (e.g., Sulfuricurvum, Sulfurimonas) and iron (e.g., Gallionella, Sideroxydans) cycling shaped the core community. Additionally, CO2-influenced waters form an ecosystem containing many taxa that are usually found in marine or terrestrial subsurface ecosystems. Multivariate statistics highlighted the influence of environmental parameters such as pH, Fe2+ concentration and conductivity on species distribution. The hydrochemical and microbiological survey introduces a new perspective on mofettes. Our results support that mofettes are either analogs or rather windows into the deep biosphere and furthermore enable access to deeply buried paleo-sediments.}, language = {en} }