Flemming HC, Wuertz S. Bacteria and archaea on Earth and their abundance in biofilms. Nat Rev Microbiol. 2019;17:247–60.
Google Scholar
Wrighton KC, Thomas BC, Sharon I, Miller CS, Castelle CJ, VerBerkmoes NC, et al. Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science. 2012;337:1661–5.
Google Scholar
Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol. 2013;31:533–8.
Google Scholar
Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, et al. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Commun. 2016;7:1–11.
Parks DH, Rinke C, Chuvochina M, Chaumeil PA, Woodcroft BJ, Evans PN, et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat Microbiol. 2017;2:1533–42.
Google Scholar
Gleeson T, Befus KM, Jasechko S, Luijendijk E, Cardenas MB. The global volume and distribution of modern groundwater. Nat Geosci. 2016;9:161–7.
Google Scholar
Akob DM, Küsel K. Where microorganisms meet rocks in the Earth’s Critical Zone. Biogeosciences. 2011;8:3531–43.
Google Scholar
Griebler C, Lueders T. Microbial biodiversity in groundwater ecosystems. Freshw Biol. 2009;54:649–77.
Bell E, Lamminmäki T, Alneberg J, Andersson AF, Qian C, Xiong WL, et al. Active sulfur cycling in the terrestrial deep subsurface. ISME J. 2020;14:1260–72.
Google Scholar
Einsiedl F, Mayer B. Hydrodynamic and microbial processes controlling nitrate in a fissured-porous karst aquifer of the Franconian Alb, Southern Germany. Environ Sci Technol. 2006;40:6697–702.
Google Scholar
Schlesinger WH. On the fate of anthropogenic nitrogen. Proc Natl Acad Sci USA. 2009;106:203–8.
Google Scholar
McCollom TM, Seewald JS. Serpentinites, hydrogen, and life. Elements. 2013;9:129–34.
Google Scholar
Emerson JB, Thomas BC, Alvarez W, Banfield JF. Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla. Environ Microbiol. 2016;18:1686–703.
Google Scholar
Probst AJ, Ladd B, Jarett JK, Geller-McGrath DE, Sieber CMK, Emerson JB, et al. Differential depth distribution of microbial function and putative symbionts through sediment- hosted aquifers in the deep terrestrial subsurface. Nat Microbiol. 2018;3:328–36.
Google Scholar
Anantharaman K, Hausmann B, Jungbluth SP, Kantor RS, Lavy A, Warren LA, et al. Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle. ISME J. 2018;12:1715–28.
Google Scholar
Wegner CE, Gaspar M, Geesink P, Herrmann M, Marz M, Küsel K. Biogeochemical regimes in shallow aquifers reflect the metabolic coupling of the elements nitrogen, sulfur, and carbon. Appl Environ Microbiol. 2019;85:1–18.
Herrmann M, Rusznyak A, Akob DM, Schulze I, Opitz S, Totsche KU, et al. Large fractions of CO2-fixing microorganisms in pristine limestone aquifers appear to be involved in the oxidation of reduced sulfur and nitrogen compounds. Appl Environ Microbiol. 2015;81:2384–94.
Google Scholar
Probst AJ, Castelle CJ, Singh A, Brown CT, Anantharaman K, Sharon I, et al. Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations. Environ Microbiol. 2017;19:459–74.
Google Scholar
Jewell TNM, Karaoz U, Brodie EL, Williams KH, Beller HR. Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer. ISME J. 2016;10:2106–17.
Google Scholar
Handley KM, Bartels D, O’Loughlin EJ, Williams KH, Trimble WL, Skinner K, et al. The complete genome sequence for putative H2– and S-oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome. Environ Microbiol. 2014;16:3443–62.
Google Scholar
Neufeld JD, Vohra J, Dumont MG, Lueders T, Manefield M, Friedrich MW, et al. DNA stable-isotope probing. Nat Protoc. 2007;2:860–6.
Google Scholar
von Bergen M, Jehmlich N, Taubert M, Vogt C, Bastida F, Herbst FA, et al. Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology. ISME J. 2013;7:1877–85.
Taubert M, Vogt C, Wubet T, Kleinsteuber S, Tarkka MT, Harms H, et al. Protein-SIP enables time-resolved analysis of the carbon flux in a sulfate-reducing, benzene-degrading microbial consortium. ISME J. 2012;6:2291–301.
Google Scholar
Taubert M, Baumann S, von Bergen M, Seifert J. Exploring the limits of robust detection of incorporation of 13C by mass spectrometry in protein-based stable isotope probing (protein-SIP). Anal Bioanal Chem. 2011;401:1975–82.
Google Scholar
Rimstidt JD, Vaughan DJ. Pyrite oxidation: a state-of-the-art assessment of the reaction mechanism. Geochim Cosmochim Acta. 2003;67:873–80.
Google Scholar
Schippers A, Jozsa PG, Sand W. Sulfur chemistry in bacterial leaching of pyrite. Appl Environ Microbiol. 1996;62:3424–31.
Google Scholar
Kohlhepp B, Lehmann R, Seeber P, Küsel K, Trumbore SE, Totsche KU. Aquifer configuration and geostructural links control the groundwater quality in thin-bedded carbonate-siliciclastic alternations of the Hainich CZE, central Germany. Hydrol Earth Syst Sci. 2017;21:6091–116.
Google Scholar
Grimm F, Franz B, Dahl C. Thiosulfate and sulfur oxidation in purple sulfur bacteria. In: Dahl C, Friedrich CG, editors. Microbial Sulfur Metabolism. Berlin, Heidelberg: Springer; 2008. p. 101–16.
Ghosh W, Dam B. Biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse Bacteria and Archaea. FEMS Microbiol Rev. 2009;33:999–1043.
Google Scholar
Kumar S, Herrmann M, Blohm A, Hilke I, Frosch T, Trumbore SE, et al. Thiosulfate- and hydrogen-driven autotrophic denitrification by a microbial consortium enriched from groundwater of an oligotrophic limestone aquifer. FEMS Microbiol Ecol. 2018;94:fiy141.
Google Scholar
R Core Team. R: a language and environment for statistical computing. Vienna, Austria: R Core Team; 2019 [cited 2021]; Available from: https://www.R-project.org/.
Ryabchykov O, Bocklitz T, Ramoji A, Neugebauer U, Foerster M, Kroegel C, et al. Automatization of spike correction in Raman spectra of biological samples. Chemom Intell Lab. 2016;155:1–6.
Google Scholar
Dörfer T, Bocklitz T, Tarcea N, Schmitt M, Popp J. Checking and improving calibration of Raman spectra using chemometric approaches. Z Phys Chem. 2011;225:753–64.
Bocklitz TW, Dörfer T, Heinke R, Schmitt M, Popp J. Spectrometer calibration protocol for Raman spectra recorded with different excitation wavelengths. Spectrochim Acta A. 2015;149:544–9.
Google Scholar
Guo SX, Heinke R, Stöckel S, Rösch P, Bocklitz T, Popp J. Towards an improvement of model transferability for Raman spectroscopy in biological applications. Vib Spectrosc. 2017;91:111–8.
Google Scholar
Liland KH, Almoy T, Mevik BH. Optimal choice of baseline correction for multivariate calibration of spectra. Appl Spectrosc. 2010;64:1007–16.
Google Scholar
Taubert M, Stöckel S, Geesink P, Girnus S, Jehmlich N, von Bergen M, et al. Tracking active groundwater microbes with D2O labelling to understand their ecosystem function. Environ Microbiol. 2018;20:369–84.
Google Scholar
Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.
Google Scholar
Seifert J, Taubert M, Jehmlich N, Schmidt F, Völker U, Vogt C, et al. Protein-based stable isotope probing (protein-SIP) in functional metaproteomics. Mass Spectrom Rev. 2012;31:683–97.
Google Scholar
Taubert M. SIsCA. 2020 [updated 23.10.2020; cited 2021]; Available from: https://github.com/m-taubert/SIsCA.
MacCoss MJ, Wu CC, Matthews DE, Yates JR. Measurement of the isotope enrichment of stable isotope-labeled proteins using high-resolution mass spectra of peptides. Anal Chem. 2005;77:7646–53.
Google Scholar
Dixon P. VEGAN, a package of R functions for community ecology. J Veg Sci. 2003;14:927–30.
Friedrich CG, Rother D, Bardischewsky F, Quentmeier A, Fischer J. Oxidation of reduced inorganic sulfur compounds by bacteria: Emergence of a common mechanism? Appl Environ Microbiol. 2001;67:2873–82.
Google Scholar
Kelly DP, Shergill JK, Lu WP, Wood AP. Oxidative metabolism of inorganic sulfur compounds by bacteria. Antonie Van Leeuwenhoek. 1997;71:95–107.
Google Scholar
Beller HR, Letain TE, Chakicherla A, Kane SR, Legler TC, Coleman MA. Whole-genome transcriptional analysis of chemolithoautotrophic thiosulfate oxidation by Thiobacillus denitrificans under aerobic versus denitrifying conditions. J Bacteriol. 2006;188:7005–15.
Google Scholar
Beller HR, Chain PSG, Letain TE, Chakicherla A, Larimer FW, Richardson PM, et al. The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitfificans. J Bacteriol. 2006;188:1473–88.
Google Scholar
McKinlay JB, Harwood CS. Carbon dioxide fixation as a central redox cofactor recycling mechanism in bacteria. Proc Natl Acad Sci USA. 2010;107:11669–75.
Google Scholar
Tabita FR. Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: a different perspective. Photosyn Res. 1999;60:1–28.
Google Scholar
Berg IA. Ecological aspects of the distribution of different autotrophic CO2 fixation pathways. Appl Environ Microbiol. 2011;77:1925–36.
Google Scholar
Overholt WA, Trumbore S, Xu X, Bornemann TL, Probst AJ, Krüger M, et al. Rates of primary production in groundwater rival those in oligotrophic marine systems. bioRxiv 2021 [Preprint]. 2021. Available from: https://doi.org/10.1101/2021.10.13.464073.
Alfreider A, Vogt C, Geiger-Kaiser M, Psenner R. Distribution and diversity of autotrophic bacteria in groundwater systems based on the analysis of RubisCO genotypes. Syst Appl Microbiol. 2009;32:140–50.
Google Scholar
Herrmann M, Geesink P, Yan L, Lehmann R, Totsche KU, Küsel K. Complex food webs coincide with high genetic potential for chemolithoautotrophy in fractured bedrock groundwater. Water Res. 2020;170:115306.
Google Scholar
Yan LJ, Herrmann M, Kampe B, Lehmann R, Totsche KU, Küsel K. Environmental selection shapes the formation of near-surface groundwater microbiomes. Water Res. 2020;170:115341.
Google Scholar
Mattes TE, Alexander AK, Richardson PM, Munk AC, Han CS, Stothard P, et al. The genome of Polaromonas sp. strain JS666: Insights into the evolution of a hydrocarbon- and xenobiotic-degrading bacterium, and features of relevance to biotechnology. Appl Environ Microbiol. 2008;74:6405–16.
Google Scholar
Salinero KK, Keller K, Feil WS, Feil H, Trong S, Di Bartolo G, et al. Metabolic analysis of the soil microbe Dechloromonas aromatica str. RCB: indications of a surprisingly complex life-style and cryptic anaerobic pathways for aromatic degradation. BMC Genomics. 2009;10:1–23.
Kämpfer P, Schulze R, Jäckel U, Malik KA, Amann R, Spring S. Hydrogenophaga defluvii sp. nov. and Hydrogenophaga atypica sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol. 2005;55:341–4.
Google Scholar
Jin CZ, Zhuo Y, Wu XW, Ko SR, Li TH, Jin FJ, et al. Genomic and metabolic insights into denitrification, sulfur oxidation, and multidrug efflux pump mechanisms in the bacterium Rhodoferax sediminis sp. nov. Microorganisms. 2020;8:262.
Google Scholar
Geisel N. Constitutive versus responsive gene expression strategies for growth in changing environments. PLoS ONE. 2011;6:e27033.
Google Scholar
Boden R, Hutt LP, Rae AW. Reclassification of Thiobacillus aquaesulis (Wood & Kelly, 1995) as Annwoodia aquaesulis gen. nov., comb. nov., transfer of Thiobacillus (Beijerinck, 1904) from the Hydrogenophilales to the Nitrosomonadales, proposal of Hydrogenophilalia class. nov within the ‘Proteobacteria’, and four new families within the orders Nitrosomonadales and Rhodocyclales. Int J Syst Evol Microbiol. 2017;67:1191–205.
Google Scholar
Katayama-Fujimura Y, Tsuzaki N, Hirata A, Kuraishi H. Polyhedral inclusion-bodies (Carboxysomes) in Thiobacillus species with reference to the taxonomy of the genus Thiobacillus. J Gen Appl Microbiol. 1984;30:211–22.
Google Scholar
Küsel K, Totsche KU, Trumbore SE, Lehmann R, Steinhäuser C, Herrmann M. How deep can surface signals be traced in the Critical Zone? Merging biodiversity with biogeochemistry research in a Central German Muschelkalk landscape. Front Earth Sci. 2016;4:32.
Roth VN, Lange M, Simon C, Hertkorn N, Bucher S, Goodall T, et al. Persistence of dissolved organic matter explained by molecular changes during its passage through soil. Nat Geosci. 2019;12:755–61.
Google Scholar
Herrmann M, Wegner CE, Taubert M, Geesink P, Lehmann K, Yan LJ, et al. Predominance of Cand. Patescibacteria in groundwater is caused by their preferential mobilization from soils and flourishing under oligotrophic conditions. Front Microbiol. 2019;10:1407.
Google Scholar
Gray CM, Monson RK, Fierer N. Emissions of volatile organic compounds during the decomposition of plant litter. J Geophys Res Biogeosci. 2010;115:G03015.
Benk SA, Yan LJ, Lehmann R, Roth VN, Schwab VF, Totsche KU, et al. Fueling diversity in the subsurface: composition and age of dissolved organic matter in the Critical Zone. Front Earth Sci. 2019;7:296.
Schwab VF, Nowak ME, Elder CD, Trumbore SE, Xu XM, Gleixner G, et al. 14C-free carbon is a major contributor to cellular biomass in geochemically distinct groundwater of shallow sedimentary bedrock aquifers. Water Resour Res. 2019;55:2104–21.
Google Scholar
Eiler A. Evidence for the ubiquity of mixotrophic bacteria in the upper ocean: Implications and consequences. Appl Environ Microbiol. 2006;72:7431–7.
Google Scholar
Hansson TH, Grossart HP, del Giorgio PA, St-Gelais NF, Beisner BE. Environmental drivers of mixotrophs in boreal lakes. Limnol Oceanogr. 2019;64:1688–705.
Google Scholar
Perez-Riverol Y, Csordas A, Bai JW, Bernal-Llinares M, Hewapathirana S, Kundu DJ, et al. The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Res. 2019;47:D442–D50.
Google Scholar
Source: Ecology - nature.com
