Articles | Volume 19, issue 20
© Author(s) 2022. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
© Author(s) 2022. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Composition and niche-specific characteristics of microbial consortia colonizing Marsberg copper mine in the Rhenish Massif
Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August-Universität, 37077 Göttingen, Germany
Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August-Universität, 37077 Göttingen, Germany
Geoscience Centre, Department of Geobiology, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
Geoscience Centre, Department of Geobiology, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August-Universität, 37077 Göttingen, Germany
No articles found.
Dario Fussmann, Avril Jean Elisabeth von Hoyningen-Huene, Andreas Reimer, Dominik Schneider, Hana Babková, Robert Peticzka, Andreas Maier, Gernot Arp, Rolf Daniel, and Patrick Meister
Biogeosciences, 17, 2085–2106,Short summary
Dolomite (CaMg(CO3)2) is supersaturated in many aquatic settings (e.g., seawater) on modern Earth but does not precipitate directly from the fluid, a fact known as the dolomite problem. The widely acknowledged concept of dolomite precipitation involves microbial extracellular polymeric substances (EPSs) and anoxic conditions as important drivers. In contrast, results from Lake Neusiedl support an alternative concept of Ca–Mg carbonate precipitation under aerobic and alkaline conditions.
Maximilian Rieder, Wencke Wegner, Monika Horschinegg, Stefanie Klackl, Nereo Preto, Anna Breda, Susanne Gier, Urs Klötzli, Stefano M. Bernasconi, Gernot Arp, and Patrick Meister
Solid Earth, 10, 1243–1267,Short summary
The formation of dolomite (CaMg(CO3)2), an abundant mineral in Earth's geological record, is still incompletely understood. We studied dolomites embedded in a 100 m thick succession of coastal alluvial clays of Triassic age in the southern Alps. Observation by light microscopy and Sr isotopes suggests that dolomites may spontaneously from concentrated evaporating seawater, in coastal ephemeral lakes or tidal flats along the western margin of the Triassic Tethys sea.
Blanca Rincón-Tomás, Jan-Peter Duda, Luis Somoza, Francisco Javier González, Dominik Schneider, Teresa Medialdea, Esther Santofimia, Enrique López-Pamo, Pedro Madureira, Michael Hoppert, and Joachim Reitner
Biogeosciences, 16, 1607–1627,Short summary
Cold-water corals were found at active sites in Pompeia Province (Gulf of Cádiz). Since seeped fluids are harmful for the corals, we approached the environmental conditions that allow corals to colonize carbonates while seepage occurs. As a result, we propose that chemosynthetic microorganisms (i.e. sulfide-oxidizing bacteria and AOM-related microorganisms) play an important role in the colonization of the corals at these sites by feeding on the seeped fluids and avoiding coral damage.
Related subject area
Biogeochemistry: Environmental MicrobiologyA multi-phase biogeochemical model for mitigating earthquake-induced liquefaction via microbially induced desaturation and calcium carbonate precipitationDifferentiation of cognate bacterial communities in thermokarst landscapes: implications for ecological consequences of permafrost degradationPhosphorus regulates ectomycorrhizal fungi biomass production in a Norway spruce forestReallocation of elemental content and macromolecules in the coccolithophore Emiliania huxleyi to acclimate to climate changeAbrasion of sedimentary rocks as a source of hydrogen peroxide and nutrients to subglacial ecosystemsNitrous oxide (N2O) synthesis by the freshwater cyanobacterium Microcystis aeruginosaInterdisciplinary strategy to assess the impact of meteorological variables on the biochemical composition of the rain and the dynamics of a small eutrophic lake under rain forcingDepth-related patterns in microbial community responses to complex organic matter in the western North Atlantic OceanAssessing the influence of ocean alkalinity enhancement on a coastal phytoplankton communityEddy-enhanced primary production sustains heterotrophic microbial activities in the Eastern Tropical North AtlanticDiversity and assembly processes of microbial eukaryotic communities in Fildes Peninsula Lakes (West Antarctica)Nitrophobic ectomycorrhizal fungi are associated with enhanced hydrophobicity of soil organic matter in a Norway spruce forestPhysiological control on carbon isotope fractionation in marine phytoplanktonImplementation of mycorrhizal mechanisms into soil carbon model improves the prediction of long-term processes of plant litter decompositionImpact of dust addition on the microbial food web under present and future conditions of pH and temperatureFractionation of stable carbon isotopes during acetate consumption by methanogenic and sulfidogenic microbial communities in rice paddy soils and lake sedimentsHydrothermal trace metal release and microbial metabolism in the northeastern Lau Basin of the South Pacific OceanSedimentation rate and organic matter dynamics shape microbiomes across a continental marginDisturbance triggers non-linear microbe–environment feedbacksHydrographic fronts shape productivity, nitrogen fixation, and microbial community composition in the southern Indian Ocean and the Southern OceanMicrobial and geo-archaeological records reveal the growth rate, origin and composition of desert rock surface communitiesMetagenomic insights into the metabolism of microbial communities that mediate iron and methane cycling in Lake Kinneret iron-rich methanic sedimentsSpatiotemporal patterns of N2 fixation in coastal waters derived from rate measurements and remote sensingBiotic and abiotic transformation of amino acids in cloud water: experimental studies and atmospheric implicationsPotential bioavailability of organic matter from atmospheric particles to marine heterotrophic bacteriaMicrobial functional signature in the atmospheric boundary layerNew insight to niche partitioning and ecological function of ammonia oxidizing archaea in subtropical estuarine ecosystemImpact of reactive surfaces on the abiotic reaction between nitrite and ferrous iron and associated nitrogen and oxygen isotope dynamicsReviews and syntheses: Bacterial bioluminescence – ecology and impact in the biological carbon pumpSalinity-dependent algae uptake and subsequent carbon and nitrogen metabolisms of two intertidal foraminifera (Ammonia tepida and Haynesina germanica)On giant shoulders: how a seamount affects the microbial community composition of seawater and spongesSpatial variations in sedimentary N-transformation rates in the North Sea (German Bight)Patterns of (trace) metals and microorganisms in the Rainbow hydrothermal vent plume at the Mid-Atlantic RidgeCo-occurrence of Fe and P stress in natural populations of the marine diazotroph TrichodesmiumSenescence as the main driver of iodide release from a diverse range of marine phytoplanktonReviews and syntheses: Biological weathering and its consequences at different spatial levels – from nanoscale to global scaleDeep-sea sponge grounds as nutrient sinks: denitrification is common in boreo-Arctic spongesInducing the attachment of cable bacteria on oxidizing electrodesBacterial degradation activity in the eastern tropical South Pacific oxygen minimum zoneMacromolecular fungal ice nuclei in Fusarium: effects of physical and chemical processingEffects of sea animal colonization on the coupling between dynamics and activity of soil ammonia-oxidizing bacteria and archaea in maritime AntarcticaComprehensive characterization of an aspen (Populus tremuloides) leaf litter sample that maintained ice nucleation activity for 48 yearsThe origin and role of biological rock crusts in rocky desert weatheringPyrite oxidization accelerates bacterial carbon sequestration in copper mine tailingsBiogeochemical evidence of anaerobic methane oxidation on active submarine mud volcanoes on the continental slope of the Canadian Beaufort SeaFiltration artefacts in bacterial community composition can affect the outcome of dissolved organic matter biolability assaysPredominance of methanogens over methanotrophs in rewetted fens characterized by high methane emissionsTrichodesmium physiological ecology and phosphate reduction in the western tropical South PacificPotential for phenol biodegradation in cloud watersColony formation in Phaeocystis antarctica: connecting molecular mechanisms with iron biogeochemistry
Caitlyn A. Hall, Andre van Turnhout, Edward Kavazanjian Jr., Leon A. van Paassen, and Bruce Rittmann
Biogeosciences, 20, 2903–2917,Short summary
Earthquake-induced soil liquefaction poses a significant global threat. Microbially induced desaturation and precipitation (MIDP) via denitrification is a potentially sustainable, non-disruptive bacteria-driven ground improvement technique under existing structures. We developed a next-generation biogeochemical model to understand and predict the behavior of MIDP in the natural environment to design field-based hazard mitigation treatments.
Ze Ren, Shudan Ye, Hongxuan Li, Xilei Huang, and Luyao Chen
Revised manuscript accepted for BGShort summary
Permafrost thaw initiates thermokarst landscape formation, resulting in distinct new habitats, including degraded permafrost soil, thermokarst lake sediments, and lake water. These distinct habitats harbored differentiated bacterial communities that originated from the same source, differing in diversity, assembly mechanisms, and environmental influences. The results implied ecological consequences of permafrost degradation in the face of further climate change.
Juan Pablo Almeida, Lorenzo Menichetti, Alf Ekblad, Nicholas P. Rosenstock, and Håkan Wallander
Biogeosciences, 20, 1443–1458,Short summary
In forests, trees allocate a significant amount of carbon belowground to support mycorrhizal symbiosis. In northern forests nitrogen normally regulates this allocation and consequently mycorrhizal fungi growth. In this study we demonstrate that in a conifer forest from Sweden, fungal growth is regulated by phosphorus instead of nitrogen. This is probably due to an increase in nitrogen deposition to soils caused by decades of human pollution that has altered the ecosystem nutrient regime.
Yong Zhang, Yong Zhang, Shuai Ma, Hanbing Chen, Jiabing Li, Zhengke Li, Kui Xu, Ruiping Huang, Hong Zhang, Yonghe Han, and Jun Sun
Biogeosciences, 20, 1299–1312,Short summary
We found that increasing light intensity compensates for the negative effects of low phosphorus (P) availability on cellular protein and nitrogen contents. Reduced P availability, increasing light intensity, and ocean acidification act synergistically to increase cellular contents of carbohydrate and POC and the allocation of POC to carbohydrate. These regulation mechanisms in Emiliania huxleyi could provide vital information for evaluating carbon cycle in marine ecosystems under global change.
Beatriz Gill-Olivas, Jon Telling, Mark Skidmore, and Martyn Tranter
Biogeosciences, 20, 929–943,Short summary
Microbial ecosystems have been found in all subglacial environments sampled to date. Yet, little is known of the sources of energy and nutrients that sustain these microbial populations. This study shows that crushing of sedimentary rocks, which contain organic carbon, carbonate and sulfide minerals, along with previously weathered silicate minerals, produces a range of compounds and nutrients which can be utilised by the diverse suite of microbes that inhabit glacier beds.
Federico Fabisik, Benoit Guieysse, Jonathan Procter, and Maxence Plouviez
Biogeosciences, 20, 687–693,Short summary
We show, for the first time, that pure cultures of the cyanobacterium Microcystis aeruginosa can synthesize the potent greenhouse gas N2O using nitrite as substrate. Our findings have broad environmental implications because M. aeruginosa is globally found in freshwater ecosystems and is often the dominant species found in algae blooms. Further research is now needed to determine the occurrence and significance of N2O emissions from ecosystems rich with M. aeruginosa.
Fanny Noirmain, Jean-Luc Baray, Frédéric Tridon, Philippe Cacault, Hermine Billard, Guillaume Voyard, Joël Van Baelen, and Delphine Latour
Biogeosciences, 19, 5729–5749,Short summary
We present a study linking rain, meteorology, and mountain lake phytoplankton dynamics on the basis of a case study at Aydat (France) in September 2020. The air mass origin mainly influences the rain chemical composition, which depends on the type of rain, convective or stratiform. Our results also highlighted a non-negligible presence of photosynthetic cells in rainwater. The impact of the atmospheric forcing on the lake could play a key role in phytoplankton dynamics in the temperate zone.
Sarah A. Brown, John Paul Balmonte, Adrienne Hoarfrost, Sherif Ghobrial, and Carol Arnosti
Biogeosciences, 19, 5617–5631,Short summary
Bacteria use extracellular enzymes to cut large organic matter to sizes small enough for uptake. We compared the enzymatic response of surface, mid-water, and deep-ocean bacteria to complex natural substrates. Bacteria in surface and mid-depth waters produced a much wider range of enzymes than those in the deep ocean and may therefore consume a broader range of organic matter. The extent to which organic matter is recycled by bacteria depends in part on its residence time at different depths.
Aaron Ferderer, Zanna Chase, Fraser Kennedy, Kai G. Schulz, and Lennart T. Bach
Biogeosciences, 19, 5375–5399,Short summary
Ocean alkalinity enhancement has the capacity to remove vast quantities of carbon from the atmosphere, but its effect on marine ecosystems is largely unknown. We assessed the effect of increased alkalinity on a coastal phytoplankton community when seawater was equilibrated and not equilibrated with atmospheric CO2. We found that the phytoplankton community was moderately affected by increased alkalinity and equilibration with atmospheric CO2 had little influence on this effect.
Quentin Devresse, Kevin W. Becker, Arne Bendinger, Johannes Hahn, and Anja Engel
Biogeosciences, 19, 5199–5219,Short summary
Eddies are ubiquitous in the ocean and alter physical, chemical, and biological processes. However, how they affect organic carbon production and consumption is largely unknown. Here we show how an eddy triggers a cascade effect on biomass production and metabolic activities of phyto- and bacterioplankton. Our results may contribute to the improvement of biogeochemical models used to estimate carbon fluxes in the ocean.
Chunmei Zhang, Huirong Li, Yinxin Zeng, Haitao Ding, Bin Wang, Yangjie Li, Zhongqiang Ji, Yonghong Bi, and Wei Luo
Biogeosciences, 19, 4639–4654,Short summary
The unique microbial eukaryotic community structure and lower diversity have been demonstrated in five freshwater lakes of the Fildes Peninsula, Antarctica. Stochastic processes and biotic co-occurrence patterns were shown to be important in shaping microbial eukaryotic communities in the area. Our study provides a better understanding of the dynamic patterns and ecological assembly processes of microbial eukaryotic communities in Antarctic oligotrophic lakes (Fildes Peninsula).
Juan Pablo Almeida, Nicholas P. Rosenstock, Susanne K. Woche, Georg Guggenberger, and Håkan Wallander
Biogeosciences, 19, 3713–3726,Short summary
Fungi living in symbiosis with tree roots can accumulate belowground, forming special tissues than can repel water. We measured the water repellency of organic material incubated belowground and correlated it with fungal growth. We found a positive association between water repellency and root symbiotic fungi. These results are important because an increase in soil water repellency can reduce the release of CO2 from soils into the atmosphere and mitigate the effects of greenhouse gasses.
Karen M. Brandenburg, Björn Rost, Dedmer B. Van de Waal, Mirja Hoins, and Appy Sluijs
Biogeosciences, 19, 3305–3315,Short summary
Reconstructions of past CO2 concentrations rely on proxy estimates, with one line of proxies relying on the CO2-dependence of stable carbon isotope fractionation in marine phytoplankton. Culturing experiments provide insights into which processes may impact this. We found, however, that the methods with which these culturing experiments are performed also influence 13C fractionation. Caution should therefore be taken when extrapolating results from these experiments to proxy applications.
Weilin Huang, Peter M. van Bodegom, Toni Viskari, Jari Liski, and Nadejda A. Soudzilovskaia
Biogeosciences, 19, 1469–1490,Short summary
This work focuses on one of the essential pathways of mycorrhizal impact on C cycles: the mediation of plant litter decomposition. We present a model based on litter chemical quality which precludes a conclusive examination of mycorrhizal impacts on soil C. It improves long-term decomposition predictions and advances our understanding of litter decomposition dynamics. It creates a benchmark in quantitatively examining the impacts of plant–microbe interactions on soil C dynamics.
Julie Dinasquet, Estelle Bigeard, Frédéric Gazeau, Farooq Azam, Cécile Guieu, Emilio Marañón, Céline Ridame, France Van Wambeke, Ingrid Obernosterer, and Anne-Claire Baudoux
Biogeosciences, 19, 1303–1319,Short summary
Saharan dust deposition of nutrients and trace metals is crucial to microbes in the Mediterranean Sea. Here, we tested the response of microbial and viral communities to simulated dust deposition under present and future conditions of temperature and pH. Overall, the effect of the deposition was dependent on the initial microbial assemblage, and future conditions will intensify microbial responses. We observed effects on trophic interactions, cascading all the way down to viral processes.
Ralf Conrad, Pengfei Liu, and Peter Claus
Biogeosciences, 18, 6533–6546,Short summary
Acetate is an important intermediate during the anaerobic degradation of organic matter. It is consumed by methanogenic and sulfidogenic microorganisms accompanied by stable carbon isotope fractionation. We determined isotope fractionation under different conditions in two paddy soils and two lake sediments and also determined the composition of the microbial communities. Despite a relatively wide range of experimental conditions, the range of fractionation factors was quite moderate.
Natalie R. Cohen, Abigail E. Noble, Dawn M. Moran, Matthew R. McIlvin, Tyler J. Goepfert, Nicholas J. Hawco, Christopher R. German, Tristan J. Horner, Carl H. Lamborg, John P. McCrow, Andrew E. Allen, and Mak A. Saito
Biogeosciences, 18, 5397–5422,Short summary
A previous study documented an intense hydrothermal plume in the South Pacific Ocean; however, the iron release associated with this plume and the impact on microbiology were unclear. We describe metal concentrations associated with multiple hydrothermal plumes in this region and protein signatures of plume-influenced microbes. Our findings demonstrate that resources released from these systems can be transported away from their source and may alter the physiology of surrounding microbes.
Sabyasachi Bhattacharya, Tarunendu Mapder, Svetlana Fernandes, Chayan Roy, Jagannath Sarkar, Moidu Jameela Rameez, Subhrangshu Mandal, Abhijit Sar, Amit Kumar Chakraborty, Nibendu Mondal, Sumit Chatterjee, Bomba Dam, Aditya Peketi, Ranadhir Chakraborty, Aninda Mazumdar, and Wriddhiman Ghosh
Biogeosciences, 18, 5203–5222,Short summary
Physicochemical determinants of microbiome architecture across continental shelves–slopes are unknown, so we explored the geomicrobiology along 3 m sediment horizons of seasonal (shallow coastal) and perennial (deep sea) hypoxic zones of the Arabian Sea. Nature, concentration, and fate of the organic matter delivered to the sea floor were found to shape the microbiome across the western Indian margin, under direct–indirect influence of sedimentation rate and water column O2 level.
Aditi Sengupta, Sarah J. Fansler, Rosalie K. Chu, Robert E. Danczak, Vanessa A. Garayburu-Caruso, Lupita Renteria, Hyun-Seob Song, Jason Toyoda, Jacqueline Hager, and James C. Stegen
Biogeosciences, 18, 4773–4789,Short summary
Conceptual models link microbes with the environment but are untested. We test a recent model using riverbed sediments. We exposed sediments to disturbances, going dry and becoming wet again. As the length of dry conditions got longer, there was a sudden shift in the ecology of microbes, chemistry of organic matter, and rates of microbial metabolism. We propose a new model based on feedbacks initiated by disturbance that cascade across biological, chemical, and functional aspects of the system.
Cora Hörstmann, Eric J. Raes, Pier Luigi Buttigieg, Claire Lo Monaco, Uwe John, and Anya M. Waite
Biogeosciences, 18, 3733–3749,Short summary
Microbes are the main drivers of productivity and nutrient cycling in the ocean. We present a combined approach assessing C and N uptake and microbial community diversity across ecological provinces in the Southern Ocean and southern Indian Ocean. Provinces showed distinct genetic fingerprints, but microbial activity varied gradually across regions, correlating with nutrient concentrations. Our study advances the biogeographic understanding of microbial diversity across C and N uptake regimes.
Nimrod Wieler, Tali Erickson Gini, Osnat Gillor, and Roey Angel
Biogeosciences, 18, 3331–3342,Short summary
Biological rock crusts (BRCs) are common microbial-based assemblages covering rocks in drylands. BRCs play a crucial role in arid environments because of the limited activity of plants and soil. Nevertheless, BRC development rates have never been dated. Here we integrated archaeological, microbiological and geological methods to provide a first estimation of the growth rate of BRCs under natural conditions. This can serve as an affordable dating tool in archaeological sites in arid regions.
Michal Elul, Maxim Rubin-Blum, Zeev Ronen, Itay Bar-Or, Werner Eckert, and Orit Sivan
Biogeosciences, 18, 2091–2106,
Mindaugas Zilius, Irma Vybernaite-Lubiene, Diana Vaiciute, Donata Overlingė, Evelina Grinienė, Anastasija Zaiko, Stefano Bonaglia, Iris Liskow, Maren Voss, Agneta Andersson, Sonia Brugel, Tobia Politi, and Paul A. Bukaveckas
Biogeosciences, 18, 1857–1871,Short summary
In fresh and brackish waters, algal blooms are often dominated by cyanobacteria, which have the ability to utilize atmospheric nitrogen. Cyanobacteria are also unusual in that they float to the surface and are dispersed by wind-driven currents. Their patchy and dynamic distribution makes it difficult to track their abundance and quantify their effects on nutrient cycling. We used remote sensing to map the distribution of cyanobacteria in a large Baltic lagoon and quantify their contributions.
Saly Jaber, Muriel Joly, Maxence Brissy, Martin Leremboure, Amina Khaled, Barbara Ervens, and Anne-Marie Delort
Biogeosciences, 18, 1067–1080,Short summary
Our study is of interest to atmospheric scientists and environmental microbiologists, as we show that clouds can be considered a medium where bacteria efficiently degrade and transform amino acids, in competition with chemical processes. As current atmospheric multiphase models are restricted to chemical degradation of organic compounds, our conclusions motivate further model development.
Kahina Djaoudi, France Van Wambeke, Aude Barani, Nagib Bhairy, Servanne Chevaillier, Karine Desboeufs, Sandra Nunige, Mohamed Labiadh, Thierry Henry des Tureaux, Dominique Lefèvre, Amel Nouara, Christos Panagiotopoulos, Marc Tedetti, and Elvira Pulido-Villena
Biogeosciences, 17, 6271–6285,
Romie Tignat-Perrier, Aurélien Dommergue, Alban Thollot, Olivier Magand, Timothy M. Vogel, and Catherine Larose
Biogeosciences, 17, 6081–6095,Short summary
The adverse atmospheric environmental conditions do not appear suited for microbial life. We conducted the first global comparative metagenomic analysis to find out if airborne microbial communities might be selected by their ability to resist these adverse conditions. The relatively higher concentration of fungi led to the observation of higher proportions of stress-related functions in air. Fungi might likely resist and survive atmospheric physical stress better than bacteria.
Yanhong Lu, Shunyan Cheung, Ling Chen, Shuh-Ji Kao, Xiaomin Xia, Jianping Gan, Minhan Dai, and Hongbin Liu
Biogeosciences, 17, 6017–6032,Short summary
Through a comprehensive investigation, we observed differential niche partitioning among diverse ammonia-oxidizing archaea (AOA) sublineages in a typical subtropical estuary. Distinct AOA communities observed at DNA and RNA levels suggested that a strong divergence in ammonia-oxidizing activity among different AOA groups occurs. Our result highlights the importance of identifying major ammonia oxidizers at RNA level in future studies.
Anna-Neva Visser, Scott D. Wankel, Pascal A. Niklaus, James M. Byrne, Andreas A. Kappler, and Moritz F. Lehmann
Biogeosciences, 17, 4355–4374,Short summary
This study focuses on the chemical reaction between Fe(II) and nitrite, which has been reported to produce high levels of the greenhouse gas N2O. We investigated the extent to which dead biomass and Fe(II) minerals might enhance this reaction. Here, nitrite reduction was highest when both additives were present but less pronounced if only Fe(II) minerals were added. Both reaction systems show distinct differences, rather low N2O levels, and indicated the abiotic production of N2.
Lisa Tanet, Séverine Martini, Laurie Casalot, and Christian Tamburini
Biogeosciences, 17, 3757–3778,Short summary
Bioluminescent bacteria, the most abundant light-emitting organisms in the ocean, can be free-living, be symbiotic or colonize organic particles. This review suggests that they act as a visual target and may indirectly influence the sequestration of biogenic carbon in oceans by increasing the attraction rate for consumers. We summarize the instrumentation available to quantify this impact in future studies and propose synthetic figures integrating these ecological and biogeochemical concepts.
Michael Lintner, Bianca Biedrawa, Julia Wukovits, Wolfgang Wanek, and Petra Heinz
Biogeosciences, 17, 3723–3732,Short summary
Foraminifera are unicellular marine organisms that play an important role in the marine element cycle. Changes of environmental parameters such as salinity or temperature have a significant impact on the faunal assemblages. Our experiments show that changing salinity in the German Wadden Sea immediately influences the foraminiferal community. It seems that A. tepida is better adapted to salinity fluctuations than H. germanica.
Kathrin Busch, Ulrike Hanz, Furu Mienis, Benjamin Mueller, Andre Franke, Emyr Martyn Roberts, Hans Tore Rapp, and Ute Hentschel
Biogeosciences, 17, 3471–3486,Short summary
Seamounts are globally abundant submarine structures that offer great potential to study the impacts and interactions of environmental gradients at a single geographic location. In an exemplary way, we describe potential mechanisms by which a seamount can affect the structure of pelagic and benthic (sponge-)associated microbial communities. We conclude that the geology, physical oceanography, biogeochemistry, and microbiology of seamounts are even more closely linked than currently appreciated.
Alexander Bratek, Justus E. E. van Beusekom, Andreas Neumann, Tina Sanders, Jana Friedrich, Kay-Christian Emeis, and Kirstin Dähnke
Biogeosciences, 17, 2839–2851,Short summary
The following paper highlights the importance of benthic N-transformation rates in different sediment types in the southern North Sea as a source of fixed nitrogen for primary producers and also as a sink of fixed nitrogen. Sedimentary fluxes of dissolved inorganic nitrogen support ∼7 to 59 % of the average annual primary production. Semi-permeable and permeable sediments contribute ∼68 % of the total benthic N2 production rates, counteracting eutrophication in the southern North Sea.
Sabine Haalboom, David M. Price, Furu Mienis, Judith D. L. van Bleijswijk, Henko C. de Stigter, Harry J. Witte, Gert-Jan Reichart, and Gerard C. A. Duineveld
Biogeosciences, 17, 2499–2519,Short summary
Mineral mining in deep-sea hydrothermal settings will lead to the formation of plumes of fine-grained, chemically reactive, suspended matter. Understanding how natural hydrothermal plumes evolve as they disperse from their source, and how they affect their surrounding environment, may help in characterising the behaviour of the diluted part of mining plumes. The natural plume provided a heterogeneous, geochemically enriched habitat conducive to the development of a distinct microbial ecology.
Noelle A. Held, Eric A. Webb, Matthew M. McIlvin, David A. Hutchins, Natalie R. Cohen, Dawn M. Moran, Korinna Kunde, Maeve C. Lohan, Claire Mahaffey, E. Malcolm S. Woodward, and Mak A. Saito
Biogeosciences, 17, 2537–2551,Short summary
Trichodesmium is a globally important marine nitrogen fixer that stimulates primary production in the surface ocean. We surveyed metaproteomes of Trichodesmium populations across the North Atlantic and other oceans, and we found that they experience simultaneous phosphate and iron stress because of the biophysical limits of nutrient uptake. Importantly, nitrogenase was most abundant during co-stress, indicating the potential importance of this phenotype to global nitrogen and carbon cycling.
Helmke Hepach, Claire Hughes, Karen Hogg, Susannah Collings, and Rosie Chance
Biogeosciences, 17, 2453–2471,Short summary
Tropospheric iodine takes part in numerous atmospheric chemical cycles, including tropospheric ozone destruction and aerosol formation. Due to its significance for atmospheric processes, it is crucial to constrain its sources and sinks. This paper aims at investigating and understanding features of biogenic iodate-to-iodide reduction in microalgal monocultures. We find that phytoplankton senescence may play a crucial role in the release of iodide to the marine environment.
Roger D. Finlay, Shahid Mahmood, Nicholas Rosenstock, Emile B. Bolou-Bi, Stephan J. Köhler, Zaenab Fahad, Anna Rosling, Håkan Wallander, Salim Belyazid, Kevin Bishop, and Bin Lian
Biogeosciences, 17, 1507–1533,Short summary
Effects of biological activity on mineral weathering operate at scales ranging from short-term, microscopic interactions to global, evolutionary timescale processes. Microorganisms have had well-documented effects at large spatio-temporal scales, but to establish the quantitative significance of microscopic measurements for field-scale processes, higher-resolution studies of liquid chemistry at local weathering sites and improved upscaling to soil-scale dissolution rates are still required.
Christine Rooks, James Kar-Hei Fang, Pål Tore Mørkved, Rui Zhao, Hans Tore Rapp, Joana R. Xavier, and Friederike Hoffmann
Biogeosciences, 17, 1231–1245,Short summary
Sponge grounds are known as nutrient sources, providing nitrate and ammonium to the ocean. We found that they also can do the opposite: in six species from Arctic and North Atlantic sponge grounds, we measured high rates of denitrification, which remove these nutrients from the sea. Rates were highest when the sponge tissue got low in oxygen, which happens when sponges stop pumping because of stress. Sponge grounds may become nutrient sinks when exposed to stress.
Cheng Li, Clare E. Reimers, and Yvan Alleau
Biogeosciences, 17, 597–607,Short summary
Novel filamentous cable bacteria that grow in the top layer of intertidal mudflat sediment were attracted to electrodes poised at a positive electrical potential. Several diverse morphologies of Desulfobulbaceae filaments, cells, and colonies were observed on the electrode surface. These observations provide information to suggest conditions that will induce cable bacteria to perform electron donation to an electrode, informing future experiments that culture cable bacteria outside of sediment.
Marie Maßmig, Jan Lüdke, Gerd Krahmann, and Anja Engel
Biogeosciences, 17, 215–230,Short summary
Little is known about the rates of bacterial element cycling in oxygen minimum zones (OMZs). We measured bacterial production and rates of extracellular hydrolytic enzymes at various in situ oxygen concentrations in the OMZ off Peru. Our field data show unhampered bacterial activity at low oxygen concentrations. Meanwhile bacterial degradation of organic matter substantially contributed to the formation of the OMZ.
Anna T. Kunert, Mira L. Pöhlker, Kai Tang, Carola S. Krevert, Carsten Wieder, Kai R. Speth, Linda E. Hanson, Cindy E. Morris, David G. Schmale III, Ulrich Pöschl, and Janine Fröhlich-Nowoisky
Biogeosciences, 16, 4647–4659,Short summary
A screening of more than 100 strains from 65 different species revealed that the ice nucleation activity within the fungal genus Fusarium is more widespread than previously assumed. Filtration experiments suggest that the single cell-free Fusarium IN is smaller than 100 kDa (~ 6 nm) and that aggregates can be formed in solution. Exposure experiments, freeze–thaw cycles, and long-term storage tests demonstrate a high stability of Fusarium IN under atmospherically relevant conditions.
Qing Wang, Renbin Zhu, Yanling Zheng, Tao Bao, and Lijun Hou
Biogeosciences, 16, 4113–4128,Short summary
We investigated abundance, potential activity, and diversity of soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) in five Antarctic tundra patches, including penguin colony, seal colony, and tundra marsh. We have found (1) sea animal colonization increased AOB population size.; (2) AOB contributed to ammonia oxidation rates more than AOA in sea animal colonies; (3) community structures of AOB and AOA were closely related to soil biogeochemical processes associated with animal activities.
Yalda Vasebi, Marco E. Mechan Llontop, Regina Hanlon, David G. Schmale III, Russell Schnell, and Boris A. Vinatzer
Biogeosciences, 16, 1675–1683,Short summary
Ice nucleation particles (INPs) help ice form at temperatures as high as −4 °C and contribute to the formation of precipitation. Leaf litter contains a high concentration of INPs, but the organisms that produce them are unknown. Here, we cultured two bacteria and one fungus from leaf litter that produce INPs similar to those found in leaf litter. This suggests that leaf litter may be an important habitat of these organisms and supports a role of these organisms as producers of atmospheric INPs.
Nimrod Wieler, Hanan Ginat, Osnat Gillor, and Roey Angel
Biogeosciences, 16, 1133–1145,Short summary
In stony deserts, when rocks are exposed to atmospheric conditions, they undergo weathering. The cavernous (honeycomb) weathering pattern is one of the most common, but it is still unclear exactly how it is formed. We show that microorganisms, which differ from the surrounding soil and dust, form biological crusts on exposed rock surfaces. These microbes secrete polymeric substances that mitigate weathering by reducing evaporation rates and, consequently, salt transport rates through the rock.
Yang Li, Zhaojun Wu, Xingchen Dong, Zifu Xu, Qixin Zhang, Haiyan Su, Zhongjun Jia, and Qingye Sun
Biogeosciences, 16, 573–583,Short summary
This paper contributes to the study of bacterial carbon sequestration in mine tailings. Previous studies focused on carbonate mineral precipitation, while the role of autotrophs in carbon sequestration has been neglected. Carbon sequestration in two mine tailings treated with FeS2 was analyzed using 13C isotope labeling, pyrosequencing, and DNA SIP to identify carbon fixers. This paper is the first to investigate carbon sequestration by autotrophic groups in mine tailings.
Dong-Hun Lee, Jung-Hyun Kim, Yung Mi Lee, Alina Stadnitskaia, Young Keun Jin, Helge Niemann, Young-Gyun Kim, and Kyung-Hoon Shin
Biogeosciences, 15, 7419–7433,Short summary
In this study, we provide first evidence of lipid biomarker patterns and phylogenetic identities of key microbes mediating anaerobic oxidation of methane (AOM) communities in active mud volcanoes (MVs) on the continental slope of the Canadian Beaufort Sea. Our lipid and 16S rRNA results indicate that archaea of the ANME-2c and ANME-3 clades are involved in AOM in the MVs investigated.
Joshua F. Dean, Jurgen R. van Hal, A. Johannes Dolman, Rien Aerts, and James T. Weedon
Biogeosciences, 15, 7141–7154,Short summary
Lakes, rivers, ponds and streams are significant contributors of the greenhouse gas carbon dioxide to the atmosphere. This is partly due to the decomposition of plant and soil organic matter transported through these aquatic systems by microbial communities. In determining how vulnerable this organic material is to decomposition during aquatic transport, we show that standardized treatments in experiments can affect the way microbial communities behave and potentially the experimental outcome.
Xi Wen, Viktoria Unger, Gerald Jurasinski, Franziska Koebsch, Fabian Horn, Gregor Rehder, Torsten Sachs, Dominik Zak, Gunnar Lischeid, Klaus-Holger Knorr, Michael E. Böttcher, Matthias Winkel, Paul L. E. Bodelier, and Susanne Liebner
Biogeosciences, 15, 6519–6536,Short summary
Rewetting drained peatlands may lead to prolonged emission of the greenhouse gas methane, but the underlying factors are not well described. In this study, we found two rewetted fens with known high methane fluxes had a high ratio of microbial methane producers to methane consumers and a low abundance of methane consumers compared to pristine wetlands. We therefore suggest abundances of methane-cycling microbes as potential indicators for prolonged high methane emissions in rewetted peatlands.
Kyle R. Frischkorn, Andreas Krupke, Cécile Guieu, Justine Louis, Mónica Rouco, Andrés E. Salazar Estrada, Benjamin A. S. Van Mooy, and Sonya T. Dyhrman
Biogeosciences, 15, 5761–5778,Short summary
Trichodesmium is a keystone genus of marine cyanobacteria that is estimated to supply nearly half of the ocean’s fixed nitrogen, fuelling primary productivity and the cycling of carbon and nitrogen in the ocean. In our study we characterize Trichodesmium ecology across the western tropical South Pacific using gene and genome sequencing and geochemistry. We detected genes for phosphorus reduction, providing a mechanism for the noted importance of this organism in the ocean's phosphorus cycle.
Audrey Lallement, Ludovic Besaury, Elise Tixier, Martine Sancelme, Pierre Amato, Virginie Vinatier, Isabelle Canet, Olga V. Polyakova, Viatcheslay B. Artaev, Albert T. Lebedev, Laurent Deguillaume, Gilles Mailhot, and Anne-Marie Delort
Biogeosciences, 15, 5733–5744,Short summary
The main objective of this work was to evaluate the potential degradation of phenol, a highly toxic pollutant, by cloud microorganisms. Phenol concentrations measured on five cloud samples collected at the PUY station in France were from 0.15 to 0.74 µg L−1. Metatranscriptomic analysis suggested that phenol could be biodegraded directly in clouds, likely by Gammaproteobacteria. A large screening showed that 93 % of 145 bacterial strains isolated from clouds were able to degrade phenol.
Sara J. Bender, Dawn M. Moran, Matthew R. McIlvin, Hong Zheng, John P. McCrow, Jonathan Badger, Giacomo R. DiTullio, Andrew E. Allen, and Mak A. Saito
Biogeosciences, 15, 4923–4942,Short summary
Phaeocystis antarctica is an important phytoplankter of the Antarctic coastal environment where it dominates the early season bloom after sea ice retreat. Iron nutrition was found to be an important factor that results in Phaeocystis colony formation and a large restructuring of the proteome, including changes associated with the flagellate to colonial transition and adaptive responses to iron scarcity. Analysis of Phaeocystis proteins from the Ross Sea revealed the presence of both cell types.
Amin, N., Schneider, D., and Hoppert, M.: Bioleaching potential of bacterial communities in historic mine waste areas, Environ. Earth Sci., 77, 542, https://doi.org/10.1007/s12665-018-7714-x, 2018.
Andrei, A., Öztürk, Y., Khalfaoui-Hassani, B., Rauch, J., Marckmann, D., Trasnea, P.-I., Daldal, F., and Koch, H.-G.: Cu homeostasis in bacteria: the ins and outs, Membranes, 10, 242, https://doi.org/10.3390/membranes10090242, 2020.
Anton, A., Große, C., Reißmann, J., Pribyl, T., and Nies, D. H.: CzcD is a heavy metal ion transporter involved in regulation of heavy metal resistance in Ralstonia sp. strain CH34, J. Bacteriol., 181, 6876–6881, https://doi.org/10.1128/JB.181.22.6876-6881.1999, 1999.
Argüllo, J. M., Raimunda, D., and Padilla-Benavides, T.: Mechanisms of copper homeostasis in bacteria, Frontiers in cellular and infection microbiology, Front. Cell. Infect. Mi., 3, 73, https://doi.org/10.3389/fcimb.2013.00073, 2013.
Arif, S.: Organic-rich shales as archive and resource for microbial extremophiles, Georg-August-Universität Göttingen, http://hdl.handle.net/21.11130/00-1735-0000-0008-5906-E, last access: 10 October 2021a.
Arif, S.: Composition and Niche-Specific Characteristics of Microbial Consortia Colonizing Marsberg Copper Mine in the Rhenish Massif, GRO.data [data set], V1, https://doi.org/10.25625/DFFZ9R, 2021b.
Arif, S.: Pathway maps for Metagenome-assembled genome sequences from Marsberg Kilianstollen, GRO.data [data set], https://doi.org/10.25625/W9PWCX, 2021c.
Arif, S., Nacke, H., and Hoppert, M.: Metagenome-assembled genome sequences of a biofilm derived from Marsberg copper mine, Microbiol. Resour. Announ., 10, e01253-20, https://doi.org/10.1128/MRA.01253-20, 2021a.
Arif, S., Schliekmann, E., and Hoppert, M.: 16S rRNA Amplicon sequencing of microbial biofilms from Marsberg copper mine, Germany, Microbiol. Resour. Announ., 10, e01315-20, https://doi.org/10.1128/MRA.01315-20, 2021b.
Arif, S., Willenberg, C., Dreyer, A., Nacke, H., and Hoppert, M.: Sasso Pisano Geothermal Field environment harbours diverse Ktedonobacteria representatives and illustrates habitat-specific adaptations, Microorganisms, 9, 1402, https://doi.org/10.3390/microorganisms9071402, 2021c.
Arndt, D., Xia, J., Liu, Y., Zhou, Y., Guo, A. C., Cruz, J. A., Sinelnikov, I., Budwill, K., Nesbø, C. L., and Wishart, D. S.: METAGENassist: a comprehensive web server for comparative metagenomics, Nucl. Acid. Res., 40, 88–95, https://doi.org/10.1093/nar/gks497, 2012.
Azzouzi, A., Steunou, A. S., Durand, A., Khalfaoui-Hassani, B., Bourbon, M. l., Astier, C., Bollivar, D. W., and Ouchane, S.: Coproporphyrin III excretion identifies the anaerobic coproporphyrinogen III oxidase HemN as a copper target in the Cu+-ATPase mutant copA- of Rubrivivax gelatinosus, Mol. Microbiol., 88, 339–351, https://doi.org/10.1111/mmi.12188, 2013.
Barton, H. A., Giarrizzo, J. G., Suarez, P., Robertson, C. E., Broering, M. J., Banks, E. D., Vaishampayan, P. A., and Venkateswaran, K.: Microbial diversity in a Venezuelan orthoquartzite cave is dominated by the Chloroflexi (Class Ktedonobacterales) and Thaumarchaeota Group I, Front. Microbiol., 5, 615, https://doi.org/10.3389/fmicb.2014.00615, 2014.
Borgonie, G., Magnabosco, C., García-Moyano, A., Linage-Alvarez, B., Ojo, A. O., Freese, L. B., Van Jaarsveld, C., Van Rooyen, C., Kuloyo, O., Cason, E. D., Vermeulen, J., Pienaar, C., Van Heerden, E., Sherwood Lollar, B., Onstott, T. C., and Mundle, S. O. C.: New ecosystems in the deep subsurface follow the flow of water driven by geological activity, Sci. Rep., 9, 3310, https://doi.org/10.1038/s41598-019-39699-w, 2019.
Broxton, C. N. and Culotta, V. C.: SOD Enzymes and microbial pathogens: surviving the oxidative storm of infection, PLoS Pathog., 12, e1005295, https://doi.org/10.1371/journal.ppat.1005295, 2016.
Busenlehner, L. S., Pennella, M. A., and Giedroc, D. P.: The SmtB/ArsR family of metalloregulatory transcriptional repressors: structural insights into prokaryotic metal resistance, FEMS Microbiol. Rev., 27, 131–143, https://doi.org/10.1016/S0168-6445(03)00054-8, 2003.
Caspi, R., Billington, R., Keseler, I. M., Kothari, A., Krummenacker, M., Midford, P. E., Ong, W. K., Paley, S., Subhraveti, P., and Karp, P. D.: The MetaCyc database of metabolic pathways and enzymes – a 2019 update, Nucl. Acid. Res., 48, D445–D453, https://doi.org/10.1093/nar/gkz862, 2019.
Cavaletti, L., Monciardini, P., Bamonte, R., Schumann, P., Rohde, M., Sosio, M., and Donadio, S.: New lineage of filamentous, spore-forming, gram-positive bacteria from soil, Appl. Environ. Microbiol., 72, 4360–4369, https://doi.org/10.1128/AEM.00132-06, 2006.
Cha, J.-S. and Cooksey, D. A.: Copper hypersensitivity and uptake in Pseudomonas syringae containing cloned components of the copper resistance operon, Appl. Environ. Microbiol., 59, 1671–1674, https://doi.org/10.1128/aem.59.5.1671-1674.1993, 1993.
Chang, Y.-J., Land, M., Hauser, L., Chertkov, O., Del Rio, T. G., Nolan, M., Copeland, A., Tice, H., Cheng, J.-F., and Lucas, S.: Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21 T), Stand. Genomic Sci., 5, 97–111, https://doi.org/10.4056/sigs.2114901, 2011.
Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P., and Parks, D. H.: GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database, Bioinformatics, 36, 1925–1927, https://doi.org/10.1093/bioinformatics/btz848, 2020.
Chen, S., Zhou, Y., Chen, Y., and Gu, J.: fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, 34, i884–i890, https://doi.org/10.1093/bioinformatics/bty560, 2018.
Chillappagari, S., Seubert, A., Trip, H., Kuipers, O. P., Marahiel, M. A., and Miethke, M.: Copper stress affects iron homeostasis by destabilizing iron-sulfur cluster formation in Bacillus subtilis, J. Bacteriol., 192, 2512–2524, https://doi.org/10.1128/JB.00058-10, 2010.
Donaire, A., Jiménez, B., Fernández, C. O., Pierattelli, R., Niizeki, T., Moratal, J.-M., Hall, J. F., Kohzuma, T., Hasnain, S. S., and Vila, A. J.: Metal–ligand interplay in blue copper proteins studied by 1H NMR Spectroscopy: Cu (II)-pseudoazurin and Cu (II)-rusticyanin, J. Am. Chem. Soc., 124, 13698–13708, https://doi.org/10.1021/ja0267019, 2002.
Dong, X., Kleiner, M., Sharp, C. E., Thorson, E., Li, C., Liu, D., and Strous, M.: Fast and simple analysis of MiSeq amplicon sequencing data with MetaAmp, Front. Microbiol., 8, 1461, https://doi.org/10.1101/131631, 2017.
Dube, J. P., Valverde, A., Steyn, J. M., Cowan, D. A., and Van der Waals, J. E.: Differences in bacterial diversity, composition and function due to long-term agriculture in soils in the eastern free State of South Africa, Diversity, 11, 61, https://doi.org/10.3390/d11040061, 2019.
Dupont, C. L., Grass, G., and Rensing, C.: Copper toxicity and the origin of bacterial resistance – new insights and applications, Metallomics, 3, 1109–1118, 2011.
Dziewit, L., Pyzik, A., Szuplewska, M., Matlakowska, R., Mielnicki, S., Wibberg, D., Schlüter, A., Pühler, A., and Bartosik, D.: Diversity and role of plasmids in adaptation of bacteria inhabiting the Lubin copper mine in Poland, an environment rich in heavy metals, Front. Microbiol., 6, 152, https://doi.org/10.1039/c1mt00107h, 2015.
Edgar, R. C.: Search and clustering orders of magnitude faster than BLAST, Bioinformatics, 26, 2460–2461, https://doi.org/10.1093/bioinformatics/btq461, 2010.
Edgar, R. C.: UPARSE: highly accurate OTU sequences from microbial amplicon reads, Nat. Methods, 10, 996–998, https://doi.org/10.1038/nmeth.2604, 2013.
Emmerich, H. P. H., A: Sekundärmineralbildung aus Grubenwässern im Kupferbergwerk Niedermarsberg [Secondary mineral formation from mine water in the Niedermarsberg copper mine], Der Aufschluss, 38, 149–156, 1987.
Epelde, L., Lanzen, A., Blanco, F., Urich, T., and Garbisu, C.: Adaptation of soil microbial community structure and function to chronic metal contamination at an abandoned Pb-Zn mine, FEMS Microbiol. Ecol., 91, 1–11, https://doi.org/10.1093/femsec/fiu007, 2015.
Farrenschon, J., Oesterreich, B., Blumenstein, S., Holzinger, M., and Wrede, V.: Geologische Karte von Nordrhein-Westfalen 1:25 000, Erläuterungen zu Blatt 4519 Marsberg, Geological Map of North Rhine-Westphalia, Explanatory notes to sheet 4519 Marsberg, https://www.gd.nrw.de/pr_kd_geologische-karte-25000.php (last access: 2 February 2021), 2008.
Festa, R. A. and Thiele, D. J.: Copper: an essential metal in biology, Curr. Biol., 21, R877–R883, https://doi.org/10.1016/j.cub.2011.09.040, 2011.
Fong, S. T., Camakaris, J., and Lee, B. T. O.: Molecular genetics of a chromosomal locus involved in copper tolerance in Escherichia coli K-12, Mol. Microbiol., 15, 1127–1137, https://doi.org/10.1111/j.1365-2958.1995.tb02286.x, 1995.
Fu, Y., Chang, F.-M. J., and Giedroc, D. P.: Copper transport and trafficking at the host-bacterial pathogen interface, Accounts Chem. Res., 47, 3605–3613, https://doi.org/10.1021/ar500300n, 2014.
Fuchs, G., Boll, M., and Heider, J.: Microbial degradation of aromatic compounds – from one strategy to four, Nat. Rev. Microbiol., 9, 803–816, https://doi.org/10.1038/nrmicro2652, 2011.
Ghezzi, D., Sauro, F., Columbu, A., Carbone, C., Hong, P. Y., Vergara, F., De Waele, J., and Cappelletti, M.: Transition from unclassified Ktedonobacterales to Actinobacteria during amorphous silica precipitation in a quartzite cave environment, Sci. Rep., 11, 1–18, https://doi.org/10.1038/s41598-021-83416-5, 2021.
Ghosal, D., Ghosh, S., Dutta, T. K., and Ahn, Y.: Current State of Knowledge in Microbial Degradation of Polycyclic Aromatic Hydrocarbons (PAHs): A Review, Front. Microbiol., 7, 1369, https://doi.org/10.3389/fmicb.2016.01369, 2016.
Gibson, M. M., Bagga, D. A., Miller, C. G., and Maguire, M. E.: Magnesium transport in Salmonella typhimurium: the influence of new mutations conferring CO resistance on the CorA Mg transport system, Mol. Microbiol., 5, 2753–2762, https://doi.org/10.1111/j.1365-2958.1991.tb01984.x, 1991.
Glöckner, F. O.: The SILVA Database Project: An ELIXIR core data resource for high-quality ribosomal RNA sequences, Biodiv. Inf. Sci. Stand., 3, e36125, https://doi.org/10.3897/biss.3.36125, 2019.
González-Guerrero, M. and Argüello, J. M.: Mechanism of Cu+-transporting ATPases: soluble Cu+ chaperones directly transfer Cu+ to transmembrane transport sites, P. Natl. Acad. Sci. USA, 105, 5992–5997, https://doi.org/10.1073/pnas.0711446105, 2008.
Gordon, A. S., Howell, L. D., and Harwood, V.: Responses of diverse heterotrophic bacteria to elevated copper concentrations, Can. J. Microbiol., 40, 408–411, https://doi.org/10.1139/m94-067, 1994.
Gupta, A., Dutta, A., Sarkar, J., Panigrahi, M. K., and Sar, P.: Low-abundance members of the Firmicutes facilitate bioremediation of soil impacted by highly acidic mine drainage from the Malanjkhand copper project, India, Front. Microbiol., 9, 2882, https://doi.org/10.3389/fmicb.2018.02882, 2018.
Hernández-Montes, G., Argüello, J. M., and Valderrama, B.: Evolution and diversity of periplasmic proteins involved in copper homeostasis in gamma proteobacteria, BMC Microbiol., 12, 249, https://doi.org/10.1186/1471-2180-12-249, 2012.
Hobman, J. L., Yamamoto, K., and Oshima, T.: Transcriptomic responses of bacterial cells to sublethal metal ion stress, in: Molecular microbiology of heavy metals, Springer, 73–115, https://doi.org/10.1007/7171_2006_074, 2007.
Huang, K., Xu, Y., Packianathan, C., Gao, F., Chen, C., Zhang, J., Shen, Q., Rosen, B. P., and Zhao, F.-J.: Arsenic methylation by a novel ArsM As(III) S-adenosylmethionine methyltransferase that requires only two conserved cysteine residues, Mol. Microbiol., 107, 265–276, https://doi.org/10.1111/mmi.13882, 2018.
Îskar, G. and William, P.: Erläuterungen zur geologischen Karte von Preußen und benachbarten deutschen Ländern, Blatt 4519 Marberg, Geological map of Prussia and neighboring German countries, 4519 Marsberg, https://katalog.slub-dresden.de/id/0-1390418065 (last access: 2 February 2021), 1936.
Jiang, Z., Li, P., Jiang, D., Dai, X., Zhang, R., Wang, Y., and Wang, Y.: Microbial community structure and arsenic biogeochemistry in an acid vapor-formed spring in Tengchong Geothermal Area, China, PloS One, 11, e0146331, https://doi.org/10.1007/7171_2006_074, 2016.
Jones, D. S., Lapakko, K. A., Wenz, Z. J., Olson, M. C., Roepke, E. W., Sadowsky, M. J., Novak, P. J., and Bailey, J. V.: Novel microbial assemblages dominate weathered sulfide-bearing rock from copper-nickel deposits in the Duluth complex, Minnesota, USA, Appl. Environ. Microbiol., 83, e00909-17, https://doi.org/10.1128/AEM.00909-17, 2017.
Karp, P. D., Latendresse, M., and Caspi, R.: The pathway tools pathway prediction algorithm, Stand. Genomic Sci., 5, 424–429, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3368424/ (last access: 27 September 2022), 2011.
Karp, P. D., Latendresse, M., Paley, S. M., Krummenacker, M., Ong, Q. D., Billington, R., Kothari, A., Weaver, D., Lee, T., Subhraveti, P., Spaulding, A., Fulcher, C., Keseler, I. M., and Caspi, R.: Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology, Brief. Bioinform., 17, 877–890, https://doi.org/10.1093/bib/bbv079, 2015.
Kersey, C. M., Agyemang, P. A., and Dumenyo, C. K.: CorA, the magnesium/nickel/cobalt transporter, affects virulence and extracellular enzyme production in the soft rot pathogen Pectobacterium carotovorum, Mol. Plant Pathol., 13, 58–71, https://doi.org/10.1111/j.1364-3703.2011.00726.x, 2012.
Kertesz, M. A.: Bacterial transporters for sulfate and organosulfur compounds, Res. Microbiol., 152, 279–290, https://doi.org/10.1016/s0923-2508(01)01199-8, 2001.
Kim, B.-E., Nevitt, T., and Thiele, D. J.: Mechanisms for copper acquisition, distribution and regulation, Nat. Chem. Biol., 4, 176–185, https://doi.org/10.1038/nchembio.72, 2008.
Klindworth, A., Pruesse, E., Schweer, T., Peplies, J., Quast, C., Horn, M., and Glöckner, F. O.: Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies, Nucl. Acid. Res., 41, e1, https://doi.org/10.1093/nar/gks808, 2012.
Koch, D., Nies, D. H., and Grass, G.: The RcnRA (YohLM) system of Escherichia coli: a connection between nickel, cobalt and iron homeostasis, Biometals, 20, 759–771, https://doi.org/10.1007/s10534-006-9039-6, 2007.
Kämpfer, P.: Actinobacteria, in: Handbook of Hydrocarbon and Lipid Microbiology, edited by: Timmis, K. N., Springer Berlin Heidelberg, Berlin, Heidelberg, 1819–1838, https://doi.org/10.1007/978-3-540-77587-4_133, 2010.
Kujala, K., Mikkonen, A., Saravesi, K., Ronkanen, A.-K., and Tiirola, M.: Microbial diversity along a gradient in peatlands treating mining-affected waters, FEMS Microbiol. Ecol., 94, fiy145, https://doi.org/10.1093/femsec/fiy145, 2018.
Lozupone, C., Lladser, M. E., Knights, D., Stombaugh, J., and Knight, R.: UniFrac: an effective distance metric for microbial community comparison, ISME J., 5, 169–172, https://doi.org/10.1038/ismej.2010.133, 2011.
Macomber, L. and Imlay, J. A.: The iron-sulfur clusters of dehydratases are primary intracellular targets of copper toxicity, P. Natl. Acad. Sci. USA, 106, 8344–8349, https://doi.org/10.1073/pnas.0812808106, 2009.
Makui, H., Roig, E., Cole, S. T., Helmann, J. D., Gros, P., and Cellier, M. F. M.: Identification of the Escherichia coli K-12 Nramp orthologue (MntH) as a selective divalent metal ion transporter, Mol. Microbiol., 35, 1065–1078, https://doi.org/10.1046/j.1365-2958.2000.01774.x, 2000.
Martin, P., DeMel, S., Shi, J., Gladysheva, T., Gatti, D. L., Rosen, B. P., and Edwards, B. F. P.: Insights into the structure, solvation, and mechanism of ArsC arsenate reductase, a novel arsenic detoxification enzyme, Structure, 9, 1071–1081, https://doi.org/10.1016/s0969-2126(01)00672-4, 2001.
Maupin-Furlow, J. A., Rosentel, J. K., Lee, J. H., Deppenmeier, U., Gunsalus, R., and Shanmugam, K.: Genetic analysis of the modABCD (molybdate transport) operon of Escherichia coli, J. Bacteriol., 177, 4851–4856, https://doi.org/10.1128/jb.177.17.4851-4856.1995, 1995.
Mengoni, A. and Bazzicalupo, M.: The statistical treatment of data and the Analysis of MOlecular VAriance (AMOVA) in molecular microbial ecology, Ann. Microbiol., 52, 95–102, 2002.
Newton, G. L., Av-Gay, Y., and Fahey, R. C.: A novel mycothiol-dependent detoxification pathway in Mycobacteria involving mycothiol S-Conjugate amidase, Biochemistry, 39, 10739–10746, https://doi.org/10.1021/bi000356n, 2000.
Newton, G. L., Buchmeier, N., and Fahey, R. C.: Biosynthesis and Functions of Mycothiol, the Unique Protective Thiol of Actinobacteria, Microbiol. Mol. Biol. Rev., 72, 471–494, https://doi.org/10.1128/MMBR.00008-08, 2008.
Nies, D. H.: Efflux-mediated heavy metal resistance in prokaryotes, FEMS Microbiol. Rev., 27, 313–339, https://doi.org/10.1016/S0168-6445(03)00048-2, 2003.
Novoa-Aponte, L., Ramírez, D., and Argüello, J. M.: The interplay of the metallosensor CueR with two distinct CopZ chaperones defines copper homeostasis in Pseudomonas aeruginosa, J. Biol. Chem., 294, 4934–4945, https://doi.org/10.1074/jbc.RA118.006316, 2019.
Nurk, S., Meleshko, D., Korobeynikov, A., and Pevzner, P. A.: metaSPAdes: a new versatile metagenomic assembler, Genome Res., 27, 824–834, https://doi.org/10.1101/gr.213959.116, 2017.
Osman, D., Waldron, K. J., Denton, H., Taylor, C. M., Grant, A. J., Mastroeni, P., Robinson, N. J., and Cavet, J. S.: Copper homeostasis in Salmonella is atypical and copper-CueP is a major periplasmic metal complex, J. Biol. Chem., 285, 25259–25268, https://doi.org/10.1074/jbc.m110.145953, 2010.
Outten, F. W., Huffman, D. L., Hale, J. A., and O'Halloran, T. V.: The independent cue and cus systems confer copper tolerance during aerobic and anaerobic growth in Escherichia coli, J. Biol. Chem., 276, 30670–30677, https://doi.org/10.1074/jbc.m104122200, 2001.
Papp-Wallace, K. M. and Maguire, M. E.: Manganese transport and the role of manganese in virulence, Annu. Rev. Microbiol., 60, 187–209, https://doi.org/10.1146/annurev.micro.60.080805.142149, 2006.
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., and Tyson, G. W.: CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes, Genome Res., 25, 1043–1055, https://doi.org/10.1101/gr.186072.114, 2015.
Parks, D. H., Chuvochina, M., Chaumeil, P.-A., Rinke, C., Mussig, A. J., and Hugenholtz, P.: Selection of representative genomes for 24,706 bacterial and archaeal species clusters provide a complete genome-based taxonomy, BioRxiv [preprint], https://doi.org/10.1101/771964, 2019.
Paul Chowdhury, S., Babin, D., Sandmann, M., Jacquiod, S., Sommermann, L., Sørensen, S. J., Fliessbach, A., Mäder, P., Geistlinger, J., and Smalla, K.: Effect of long-term organic and mineral fertilization strategies on rhizosphere microbiota assemblage and performance of lettuce, Environ. Microbiol., 21, 2426–2439, https://doi.org/10.1111/1462-2920.14631, 2019.
Rademacher, C. and Masepohl, B.: Copper-responsive gene regulation in bacteria, Microbiology, 158, 2451, https://doi.org/10.1099/mic.0.058487-0, 2012.
Rae, T. D., Schmidt, P. J., Pufahl, R. A., Culotta, V. C., and O'Halloran, T. V.: Undetectable intracellular free copper: the requirement of a copper chaperone for superoxide dismutase, Science, 284, 805–808, https://doi.org/10.1126/science.284.5415.805, 1999.
Redinbo, M. R., Yeates, T. O., and Merchant, S.: Plastocyanin: structural and functional analysis, J. Bioenerg. Biomembr., 26, 49–66, https://doi.org/10.1007/BF00763219, 1994.
Rensing, C. and Mitra, B.: Zinc, cadmium, and lead resistance and homeostasis, in: Molecular microbiology of heavy metals, Springer, 321–341, https://doi.org/10.1007/7171_2006_083, 2007.
Richard, H. and Foster, J. W.: Escherichia coli glutamate- and arginine-dependent acid resistance systems increase internal pH and reverse transmembrane potential, J. Bacteriol., 186, 6032–6041, https://doi.org/10.1128/JB.186.18.6032-6041.2004, 2004.
Ridge, J. P., Lin, M., Larsen, E. I., Fegan, M., McEwan, A. G., and Sly, L. I.: A multicopper oxidase is essential for manganese oxidation and laccase-like activity in Pedomicrobium sp. ACM 3067, Environ. Microbiol., 9, 944–953, https://doi.org/10.1111/j.1462-2920.2006.01216.x, 2007.
Rosen, B. P.: Biochemistry of arsenic detoxification, FEBS Lett., 529, 86–92, https://doi.org/10.1016/S0014-5793(02)03186-1, 2002.
Rowland, J. L. and Niederweis, M.: A multicopper oxidase is required for copper resistance in Mycobacterium tuberculosis, J. Bacteriol., 195, 3724–3733, https://doi.org/10.1128/jb.00546-13, 2013.
Sambrook, J. and Russell, D. W.: Molecular cloning: A laboratory manual, 3rd Edn., Cold spring harbor laboratory press, Cold Spring Harbor, New York, ISBN 978-0-87969-577-4, 2001.
Schippers, A. and Sand, W.: Bacterial leaching of metal sulfides proceeds by two indirect mechanisms via thiosulfate or via polysulfides and sulfur, Appl. Environ. Microbiol., 65, 319–321, https://doi.org/10.1128/AEM.65.1.319-321.1999, 1999.
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., Sahl, J. W., Stres, B., Thallinger, G. G., Van Horn, D. J., and Weber, C. F.: Introducing mothur: Open-Source, platform-independent, community-supported software for describing and comparing microbial communities, Appl. Environ. Microbiol., 75, 7537, https://doi.org/10.1128/AEM.01541-09, 2009.
Schmidt, A., Haferburg, G., Sineriz, M., Merten, D., Büchel, G., and Kothe, E.: Heavy metal resistance mechanisms in actinobacteria for survival in AMD contaminated soils, Geochemistry, 65, 131–144, https://doi.org/10.1016/j.chemer.2005.06.006, 2005.
Seemann, T.: Prokka: rapid prokaryotic genome annotation, Bioinformatics, 30, 2068–2069, https://doi.org/10.1093/bioinformatics/btu153, 2014.
Self, W. T., Grunden, A. M., Hasona, A., and Shanmugam, K. T.: Molybdate transport, Res. Microbiol., 152, 311–321, https://doi.org/10.1007/s002030050508, 2001.
Shi, X., Festa, R. A., Ioerger, T. R., Butler-Wu, S., Sacchettini, J. C., Darwin, K. H., and Samanovic, M. I.: The copper-responsive RicR regulon contributes to Mycobacterium tuberculosis virulence, MBio, 5, e00876-13, https://doi.org/10.1128/mBio.00876-13, 2014.
Siegmund, H., Trappe, J., and Oschmann, W.: Sequence stratigraphic and genetic aspects of the Tournaisian “Liegender Alaunschiefer” and adjacent beds, Int. J. Earth Sci., 91, 934–949, https://doi.org/10.1007/s00531-001-0252-9, 2002.
Silver, S. and Hobman, J. L.: Mercury microbiology: resistance systems, environmental aspects, methylation, and human health, in: Molecular Microbiology of Heavy Metals, edited by: Nies, D. H., and Silver, S., Springer Berlin Heidelberg, Berlin, Heidelberg, 357–370, https://doi.org/10.1007/7171_2006_085, 2007.
Silver, S. and Phung, L. T.: A bacterial view of the periodic table: genes and proteins for toxic inorganic ions, J. Ind. Microbiol. Biotechnol., 32, 587–605, https://doi.org/10.1007/s10295-005-0019-6, 2005.
Silver, S. and Walderhaug, M.: Gene regulation of plasmid-and chromosome-determined inorganic ion transport in bacteria, Microbiol. Mol. Biol. R., 56, 195–228, https://doi.org/10.1128/mr.56.1.195-228.1992, 1992.
Smaldone, G. T. and Helmann, J. D.: CsoR regulates the copper efflux operon copZA in Bacillus subtilis, Microbiology, 153, 4123, https://doi.org/10.1099/mic.0.2007/011742-0, 2007.
Stecher, G., Tamura, K., and Kumar, S.: Molecular evolutionary genetics analysis (MEGA) for macOS, Mol. Biol. Evol., 37, 1237–1239, https://doi.org/10.1093/molbev/msz312, 2020.
Stribrny, B.: Die Kupfererzlagerstätte Marsberg im Rheinischen Schiefergebirge – Rückblick und Stand der Forschung, Erzmetall, 40, 423–427, 1987.
Stribrny, B. and Urban, H.: Zur Geologie und Lagerstättenbildung des Kupfererzvorkommens von Marsberg im Rheinischen Schiefergebirge, On the geology and formation of the copper ore deposit of Marsberg in the Rhenish region Slate Mountains, 347–416, https://nwbib.de/HT013094414 (last access: 2 April 2021), 2000.
Thomas Iv, J. C., Oladeinde, A., Kieran, T. J., Finger Jr, J. W., Bayona-Vásquez, N. J., Cartee, J. C., Beasley, J. C., Seaman, J. C., McArthur, J. V., and Rhodes Jr., O. E.: Co-occurrence of antibiotic, biocide, and heavy metal resistance genes in bacteria from metal and radionuclide contaminated soils at the Savannah River Site, Microb. Biotechnol., 13, 1179–1200, https://doi.org/10.1111/1751-7915.13578, 2020.
Thompson, A. K., Gray, J., Liu, A., and Hosler, J. P.: The roles of Rhodobacter sphaeroides copper chaperones PCuAC and Sco (PrrC) in the assembly of the copper centers of the aa3-type and the cbb3-type cytochrome c oxidases, Biochim. Biophys. Acta, 1817, 955–964, https://doi.org/10.1016/j.bbabio.2012.01.003, 2012.
Tiwari, K. and Gupta, R. K.: Rare actinomycetes: a potential storehouse for novel antibiotics, Cr. Rev. Biotechn., 32, 108–132, https://doi.org/10.3109/07388551.2011.562482, 2012.
Tsai, M.-F. and Miller, C.: Substrate selectivity in arginine-dependent acid resistance in enteric bacteria, P. Natl. Acad. Sci. USA, 110, 5893, https://doi.org/10.1073/pnas.1301442110, 2013.
Urban, H., Stribrny, B., Zereini, F., and Ye, Y.: Geochemistry and metallogenesis of Lower Carboniferous black shale-hosted ore deposits, NE Rhenish Massif, FR Germany, Ore Geol. Rev., 9, 427–443, https://doi.org/10.1016/0169-1368(94)00023-H, 1995.
Villafane, A., Voskoboynik, Y., Ruhl, I., Sannino, D., Maezato, Y., Blum, P., and Bini, E.: CopR of Sulfolobus solfataricus represents a novel class of archaeal-specific copper-responsive activators of transcription, Microbiology, 157, 2808, https://doi.org/10.1099/mic.0.051862-0, 2011.
Vita, N., Landolfi, G., Baslé, A., Platsaki, S., Lee, J., Waldron, K. J., and Dennison, C.: Bacterial cytosolic proteins with a high capacity for Cu(I) that protect against copper toxicity, Sci. Rep., 6, 39065, https://doi.org/10.1038/srep39065, 2016.
Waters, L. S., Sandoval, M., and Storz, G.: The Escherichia coli MntR miniregulon includes genes encoding a small protein and an efflux pump required for manganese homeostasis, J. Bacteriol., 193, 5887–5897, https://doi.org/10.1128/jb.05872-11, 2011.
Wegner, C.-E. and Liesack, W.: Unexpected dominance of elusive Acidobacteria in early industrial soft coal slags, Front. Microbiol., 8, 1023, https://doi.org/10.3389/fmicb.2017.01023, 2017.
Wolfram, L., Friedrich, B., and Eitinger, T.: The Alcaligenes eutrophus protein HoxN mediates nickel transport in Escherichia coli, J. Bacteriol., 177, 1840–1843, https://doi.org/10.1128/jb.177.7.1840-1843.1995, 1995.
Wu, Y.-W., Simmons, B. A., and Singer, S. W.: MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets, Bioinformatics, 32, 605–607, https://doi.org/10.1093/bioinformatics/btv638, 2015.
Xia, Z., Lei, L., Zhang, H.-Y., and Wei, H.-L.: Characterization of the ModABC molybdate transport system of Pseudomonas putida in nicotine degradation, Front. Microbiol., 9, 3213, https://doi.org/10.3389/fmicb.2018.03030, 2018.
Xu, L., Dong, Z., Fang, L., Luo, Y., Wei, Z., Guo, H., Zhang, G., Gu, Y. Q., Coleman-Derr, D., and Xia, Q.: OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species, Nucl. Acid. Res., 47, W52–W58, https://doi.org/10.1093/nar/gkz333, 2019.
Yabe, S., Aiba, Y., Sakai, Y., Hazaka, M., and Yokota, A.: Thermogemmatispora onikobensis gen. nov., sp. nov. and Thermogemmatispora foliorum sp. nov., isolated from fallen leaves on geothermal soils, and description of Thermogemmatisporaceae fam. nov. and Thermogemmatisporales ord. nov. within the class Ktedonobacteria, Int. J. Syst. Evol. Micr., 61, 903–910, https://doi.org/10.1099/ijs.0.024877-0, 2011.
Yabe, S., Sakai, Y., Abe, K., and Yokota, A.: Diversity of Ktedonobacteria with Actinomycetes-like Morphology in terrestrial environments, Microb. Environ., 32, 61–70, https://doi.org/10.1264/jsme2.ME16144, 2017a.
Yabe, S., Sakai, Y., Abe, K., Yokota, A., Také, A., Matsumoto, A., Sugiharto, A., Susilowati, D., Hamada, M., and Nara, K.: Dictyobacter aurantiacus gen. nov., sp. nov., a member of the family Ktedonobacteraceae, isolated from soil, and emended description of the genus Thermosporothrix, Int. J. Syst. Evol. Micr., 67, 2615–2621, https://doi.org/10.1099/ijsem.0.001985, 2017b.
Zaballa, M.-E., Abriata, L. A., Donaire, A., and Vila, A. J.: Flexibility of the metal-binding region in apo-cupredoxins, P. Natl. Acad. Sci. USA, 109, 9254–9259, https://doi.org/10.1073/pnas.1119460109, 2012.
Zeng, X.-C., Yang, Y., Shi, W., Peng, Z., Chen, X., Zhu, X., and Wang, Y.: Microbially mediated methylation of arsenic in the arsenic-rich soils and sediments of Jianghan Plain, Front. Microbiol., 9, 1389, https://doi.org/10.3389/fmicb.2018.01389, 2018.
Zhang, Z., Zhang, Z., Chen, H., Liu, J., Liu, C., Ni, H., Zhao, C., Ali, M., Liu, F., and Li, L.: Surface Mn (II) oxidation actuated by a multicopper oxidase in a soil bacterium leads to the formation of manganese oxide minerals, Sci. Rep., 5, 10895, https://doi.org/10.1038/srep10895, 2015.
The natural enrichment of Chloroflexi (Ktedonobacteria) at the Kilianstollen Marsberg copper mine rocks being exposed to the acidic sulfate-rich leachate led to an investigation of eight metagenomically assembled genomes (MAGs) involved in copper and other transition heavy metal resistance in addition to low pH resistance and aromatic compounds degradation. The present study offers functional insights about a novel cold-adapted Ktedonobacteria MAG extremophily along with other phyla MAGs.
The natural enrichment of Chloroflexi (Ktedonobacteria) at the Kilianstollen Marsberg copper...