@article{NwosuBrauerKaiseretal.2021, author = {Nwosu, Ebuka Canisius and Brauer, Achim and Kaiser, J{\´e}r{\^o}me and Horn, Fabian and Wagner, Dirk and Liebner, Susanne}, title = {Evaluating sedimentary DNA for tracing changes in cyanobacteria dynamics from sediments spanning the last 350 years of Lake Tiefer See, NE Germany}, series = {Journal of paleolimnology}, volume = {66}, journal = {Journal of paleolimnology}, number = {3}, publisher = {Springer}, address = {Dordrecht}, issn = {0921-2728}, doi = {10.1007/s10933-021-00206-9}, pages = {279 -- 296}, year = {2021}, abstract = {Since the beginning of the Anthropocene, lacustrine biodiversity has been influenced by climate change and human activities. These factors advance the spread of harmful cyanobacteria in lakes around the world, which affects water quality and impairs the aquatic food chain. In this study, we assessed changes in cyanobacterial community dynamics via sedimentary DNA (sedaDNA) from well-dated lake sediments of Lake Tiefer See, which is part of the Klocksin Lake Chain spanning the last 350 years. Our diversity and community analysis revealed that cyanobacterial communities form clusters according to the presence or absence of varves. Based on distance-based redundancy and variation partitioning analyses (dbRDA and VPA) we identified that intensified lake circulation inferred from vegetation openness reconstructions, delta C-13 data (a proxy for varve preservation) and total nitrogen content were abiotic factors that significantly explained the variation in the reconstructed cyanobacterial community from Lake Tiefer See sediments. Operational taxonomic units (OTUs) assigned to Microcystis sp. and Aphanizomenon sp. were identified as potential eutrophication-driven taxa of growing importance since circa common era (ca. CE) 1920 till present. This result is corroborated by a cyanobacteria lipid biomarker analysis. Furthermore, we suggest that stronger lake circulation as indicated by non-varved sediments favoured the deposition of the non-photosynthetic cyanobacteria sister clade Sericytochromatia, whereas lake bottom anoxia as indicated by subrecent- and recent varves favoured the Melainabacteria in sediments. Our findings highlight the potential of high-resolution amplicon sequencing in investigating the dynamics of past cyanobacterial communities in lake sediments and show that lake circulation, anoxic conditions, and human-induced eutrophication are main factors explaining variations in the cyanobacteria community in Lake Tiefer See during the last 350 years.}, 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{LiuAdlerLipusetal.2020, author = {Liu, Qi and Adler, Karsten and Lipus, Daniel and K{\"a}mpf, Horst and Bussert, Robert and Plessen, Birgit and Schulz, Hans-Martin and Krauze, Patryk and Horn, Fabian and Wagner, Dirk and Mangelsdorf, Kai and Alawi, Mashal}, title = {Microbial signatures in deep CO2-saturated miocene sediments of the active Hartousov mofette system (NW Czech Republic)}, series = {Frontiers in microbiology}, volume = {11}, journal = {Frontiers in microbiology}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {1664-302X}, doi = {10.3389/fmicb.2020.543260}, pages = {21}, year = {2020}, abstract = {The Hartousov mofette system is a natural CO2 degassing site in the central Cheb Basin (Eger Rift, Central Europe). In early 2016 a 108 m deep core was obtained from this system to investigate the impact of ascending mantle-derived CO2 on indigenous deep microbial communities and their surrounding life habitat. During drilling, a CO2 blow out occurred at a depth of 78.5 meter below surface (mbs) suggesting a CO2 reservoir associated with a deep low-permeable CO2-saturated saline aquifer at the transition from Early Miocene terrestrial to lacustrine sediments. Past microbial communities were investigated by hopanoids and glycerol dialkyl glycerol tetraethers (GDGTs) reflecting the environmental conditions during the time of deposition rather than showing a signal of the current deep biosphere. The composition and distribution of the deep microbial community potentially stimulated by the upward migration of CO2 starting during Mid Pleistocene time was investigated by intact polar lipids (IPLs), quantitative polymerase chain reaction (qPCR), and deoxyribonucleic acid (DNA) analysis. The deep biosphere is characterized by microorganisms that are linked to the distribution and migration of the ascending CO2-saturated groundwater and the availability of organic matter instead of being linked to single lithological units of the investigated rock profile. Our findings revealed high relative abundances of common soil and water bacteria, in particular the facultative, anaerobic and potential iron-oxidizing Acidovorax and other members of the family Comamonadaceae across the whole recovered core. The results also highlighted the frequent detection of the putative sulfate-oxidizing and CO2-fixating genus Sulfuricurvum at certain depths. A set of new IPLs are suggested to be indicative for microorganisms associated to CO2 accumulation in the mofette system.}, language = {en} } @article{MitzscherlingHornWinterfeldetal.2019, author = {Mitzscherling, Julia and Horn, Fabian and Winterfeld, Maria and Mahler, Linda and Kallmeyer, Jens and Overduin, Pier Paul and Schirrmeister, Lutz and Winkel, Matthias and Grigoriev, Mikhail N. and Wagner, Dirk and Liebner, Susanne}, title = {Microbial community composition and abundance after millennia of submarine permafrost warming}, series = {Biogeosciences}, volume = {16}, journal = {Biogeosciences}, number = {19}, publisher = {Copernicus}, address = {G{\"o}ttingen}, issn = {1726-4170}, doi = {10.5194/bg-16-3941-2019}, pages = {3941 -- 3958}, year = {2019}, abstract = {Warming of the Arctic led to an increase in permafrost temperatures by about 0.3 degrees C during the last decade. Permafrost warming is associated with increasing sediment water content, permeability, and diffusivity and could in the long term alter microbial community composition and abundance even before permafrost thaws. We studied the long-term effect (up to 2500 years) of submarine permafrost warming on microbial communities along an onshore-offshore transect on the Siberian Arctic Shelf displaying a natural temperature gradient of more than 10 degrees C. We analysed the in situ development of bacterial abundance and community composition through total cell counts (TCCs), quantitative PCR of bacterial gene abundance, and amplicon sequencing and correlated the microbial community data with temperature, pore water chemistry, and sediment physicochemical parameters. On timescales of centuries, permafrost warming coincided with an overall decreasing microbial abundance, whereas millennia after warming microbial abundance was similar to cold onshore permafrost. In addition, the dissolved organic carbon content of all cores was lowest in submarine permafrost after millennial-scale warming. Based on correlation analysis, TCC, unlike bacterial gene abundance, showed a significant rank-based negative correlation with increasing temperature, while bacterial gene copy numbers showed a strong negative correlation with salinity. Bacterial community composition correlated only weakly with temperature but strongly with the pore water stable isotopes delta O-18 and delta D, as well as with depth. The bacterial community showed substantial spatial variation and an overall dominance of Actinobacteria, Chloroflexi, Firmicutes, Gemmatimonadetes, and Proteobacteria, which are amongst the microbial taxa that were also found to be active in other frozen permafrost environments. We suggest that, millennia after permafrost warming by over 10 degrees C, microbial community composition and abundance show some indications for proliferation but mainly reflect the sedimentation history and paleoenvironment and not a direct effect through warming.}, language = {en} } @article{MeierKrauzePrateretal.2019, author = {Meier, Lars A. and Krauze, Patryk and Prater, Isabel and Horn, Fabian and Schaefer, Carlos Ernesto Reynaud and Scholten, Thomas and Wagner, Dirk and M{\"u}ller, Carsten Werner and K{\"u}hn, Peter}, title = {Pedogenic and microbial interrelation in initial soils under semiarid climate on James Ross Island, Antarctic Peninsula region}, series = {Biogeosciences}, volume = {16}, journal = {Biogeosciences}, number = {12}, publisher = {Copernicus}, address = {G{\"o}ttingen}, issn = {1726-4170}, doi = {10.5194/bg-16-2481-2019}, pages = {2481 -- 2499}, year = {2019}, abstract = {James Ross Island (JRI) offers the exceptional opportunity to study microbial-driven pedogenesis without the influence of vascular plants or faunal activities (e.g., penguin rookeries). In this study, two soil profiles from JRI (one at Santa Martha Cove - SMC, and another at Brandy Bay BB) were investigated, in order to gain information about the initial state of soil formation and its interplay with prokaryotic activity, by combining pedological, geochemical and microbiological methods. The soil profiles are similar with respect to topographic position and parent material but are spatially separated by an orographic barrier and therefore represent windward and leeward locations towards the mainly southwesterly winds. These different positions result in differences in electric conductivity of the soils caused by additional input of bases by sea spray at the windward site and opposing trends in the depth functions of soil pH and electric conductivity. Both soils are classified as Cryosols, dominated by bacterial taxa such as Actinobacteria, Proteobacteria, Acidobacteria, Gemmatimonadetes and Chloroflexi. A shift in the dominant taxa was observed below 20 cm in both soils as well as an increased abundance of multiple operational taxonomic units (OTUs) related to potential chemolithoautotrophic Acidiferrobacteraceae. This shift is coupled by a change in microstructure. While single/pellicular grain microstructure (SMC) and platy microstructure (BB) are dominant above 20 cm, lenticular microstructure is dominant below 20 cm in both soils. The change in microstructure is caused by frequent freeze-thaw cycles and a relative high water content, and it goes along with a development of the pore spacing and is accompanied by a change in nutrient content. Multivariate statistics revealed the influence of soil parameters such as chloride, sulfate, calcium and organic carbon contents, grain size distribution and pedogenic oxide ratios on the overall microbial community structure and explained 49.9\% of its variation. The correlation of the pedogenic oxide ratios with the compositional distribution of microorganisms as well as the relative abundance certain microorganisms such as potentially chemolithotrophic Acidiferrobacteraceae-related OTUs could hint at an interplay between soil-forming processes and microorganisms.}, language = {en} } @article{WenUngerJurasinskietal.2018, author = {Wen, Xi and Unger, Viktoria and Jurasinski, Gerald and Koebsch, Franziska and Horn, Fabian and Rehder, Gregor and Sachs, Torsten and Zak, Dominik and Lischeid, Gunnar and Knorr, Klaus-Holger and Boettcher, Michael E. and Winkel, Matthias and Bodelier, Paul L. E. and Liebner, Susanne}, title = {Predominance of methanogens over methanotrophs in rewetted fens characterized by high methane emissions}, series = {Biogeosciences}, volume = {15}, journal = {Biogeosciences}, number = {21}, publisher = {Copernicus}, address = {G{\"o}ttingen}, issn = {1726-4170}, doi = {10.5194/bg-15-6519-2018}, pages = {6519 -- 6536}, year = {2018}, abstract = {The rewetting of drained peatlands alters peat geochemistry and often leads to sustained elevated methane emission. Although this methane is produced entirely by microbial activity, the distribution and abundance of methane-cycling microbes in rewetted peatlands, especially in fens, is rarely described. In this study, we compare the community composition and abundance of methane-cycling microbes in relation to peat porewater geochemistry in two rewetted fens in northeastern Germany, a coastal brackish fen and a freshwater riparian fen, with known high methane fluxes. We utilized 16S rRNA high-throughput sequencing and quantitative polymerase chain reaction (qPCR) on 16S rRNA, mcrA, and pmoA genes to determine microbial community composition and the abundance of total bacteria, methanogens, and methanotrophs. Electrical conductivity (EC) was more than 3 times higher in the coastal fen than in the riparian fen, averaging 5.3 and 1.5 mS cm(-1), respectively. Porewater concentrations of terminal electron acceptors (TEAs) varied within and among the fens. This was also reflected in similarly high intra- and inter-site variations of microbial community composition. Despite these differences in environmental conditions and electron acceptor availability, we found a low abundance of methanotrophs and a high abundance of methanogens, represented in particular by Methanosaetaceae, in both fens. This suggests that rapid (re) establishment of methanogens and slow (re) establishment of methanotrophs contributes to prolonged increased methane emissions following rewetting.}, language = {en} } @article{VuilleminHornFrieseetal.2018, author = {Vuillemin, Aurele and Horn, Fabian and Friese, Andre and Winkel, Matthias and Alawi, Mashal and Wagner, Dirk and Henny, Cynthia and Orsi, William D. and Crowe, Sean A. and Kallmeyer, Jens}, title = {Metabolic potential of microbial communities from ferruginous sediments}, series = {Environmental microbiology}, volume = {20}, journal = {Environmental microbiology}, number = {12}, publisher = {Wiley}, address = {Hoboken}, issn = {1462-2912}, doi = {10.1111/1462-2920.14343}, pages = {4297 -- 4313}, year = {2018}, abstract = {Ferruginous (Fe-rich, SO4-poor) conditions are generally restricted to freshwater sediments on Earth today, but were likely widespread during the Archean and Proterozoic Eons. Lake Towuti, Indonesia, is a large ferruginous lake that likely hosts geochemical processes analogous to those that operated in the ferruginous Archean ocean. The metabolic potential of microbial communities and related biogeochemical cycling under such conditions remain largely unknown. We combined geochemical measurements (pore water chemistry, sulfate reduction rates) with metagenomics to link metabolic potential with geochemical processes in the upper 50 cm of sediment. Microbial diversity and quantities of genes for dissimilatory sulfate reduction (dsrAB) and methanogenesis (mcrA) decrease with increasing depth, as do rates of potential sulfate reduction. The presence of taxa affiliated with known iron- and sulfate-reducers implies potential use of ferric iron and sulfate as electron acceptors. Pore-water concentrations of acetate imply active production through fermentation. Fermentation likely provides substrates for respiration with iron and sulfate as electron donors and for methanogens that were detected throughout the core. The presence of ANME-1 16S and mcrA genes suggests potential for anaerobic methane oxidation. Overall our data suggest that microbial community metabolism in anoxic ferruginous sediments support coupled Fe, S and C biogeochemical cycling.}, 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{LiuKaempfBussertetal.2018, author = {Liu, Qi and K{\"a}mpf, Horst and Bussert, Robert and Krauze, Patryk and Horn, Fabian and Nickschick, Tobias and Plessen, Birgit and Wagner, Dirk and Alawi, Mashal}, title = {Influence of CO2 degassing on the microbial community in a dry mofette field in Hartoušov, Czech Republic (Western Eger Rift)}, series = {Frontiers in Microbiology}, volume = {9}, journal = {Frontiers in Microbiology}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {1664-302X}, doi = {10.3389/fmicb.2018.02787}, pages = {17}, year = {2018}, abstract = {The Cheb Basin (CZ) is a shallow Neogene intracontinental basin filled with fluvial and lacustrine sediments that is located in the western part of the Eger Rift. The basin is situated in a seismically active area and is characterized by diffuse degassing of mantle-derived CO2 in mofette fields. The Hartousov mofette field shows a daily CO2 flux of 23-97 tons of CO2 released over an area of 0.35 km(2) and a soil gas concentration of up to 100\% CO2. The present study aims to explore the geo-bio interactions provoked by the influence of elevated CO2 concentrations on the geochemistry and microbial community of soils and sediments. To sample the strata, two 3-m cores were recovered. One core stems from the center of the degassing structure, whereas the other core was taken 8 m from the ENE and served as an undisturbed reference site. The sites were compared regarding their geochemical features, microbial abundances, and microbial community structures. The mofette site is characterized by a low pH and high TOC/sulfate contents. Striking differences in the microbial community highlight the substantial impact of elevated CO2 concentrations and their associated side effects on microbial processes. The abundance of microbes did not show a typical decrease with depth, indicating that the uprising CO2-rich fluid provides sufficient substrate for chemolithoautotrophic anaerobic microorganisms. Illumine MiSeq sequencing of the 16S rRNA genes and multivariate statistics reveals that the pH strongly influences microbial composition and explains around 38.7\% of the variance at the mofette site and 22.4\% of the variance between the mofette site and the undisturbed reference site. Accordingly, acidophilic microorganisms (e.g., OTUs assigned to Acidobacteriaceae and Acidithiobacillus) displayed a much higher relative abundance at the mofette site than at the reference site. The microbial community at the mofette site is characterized by a high relative abundance of methanogens and taxa involved in sulfur cycling. The present study provides intriguing insights into microbial life and geo-bio interactions in an active seismic region dominated by emanating mantle-derived CO2-rich fluids, and thereby builds the basis for further studies, e.g., focusing on the functional repertoire of the communities. However, it remains open if the observed patterns can be generalized for different time-points or sites.}, 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} }