Ponomarova O, Patil KR. Metabolic interactions in microbial communities: untangling the Gordian knot. Curr Opin Microbiol. 2015;27:37–44.
D’Souza G, Shitut S, Preussger D, Yousif G, Waschina S, Kost C. Ecology and evolution of metabolic cross-feeding interactions in bacteria. Nat Prod Rep. 2018;35:455–88.
Schink B. Energetics of syntrophic cooperation in methanogenic degradation. Microbiol Mol Biol Rev. 1997;61:262–80.
Pernthaler A, Dekas AE, Brown CT, Goffredi SK, Embaye T, Orphan VJ. Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics. Proc Natl Acad Sci USA. 2008;105:7052–7.
Men Y, Feil H, Verberkmoes NC, Shah MB, Johnson DR, Lee PKH, et al. Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: global transcriptomic and proteomic analyses. ISME J. 2012;6:410–21.
Zelezniak A, Andrejev S, Ponomarova O, Mende DR, Bork P, Patil KR. Metabolic dependencies drive species co-occurrence in diverse microbial communities. Proc Natl Acad Sci USA. 2015;112:6449–54.
Marchal M, Goldschmidt F, Derksen-Müller SN, Panke S, Ackermann M, Johnson DR. A passive mutualistic interaction promotes the evolution of spatial structure within microbial populations. BMC Evol Biol. 2017;17:106.
Thompson AW, Foster RA, Krupke A, Carter BJ, Musat N, Vaulot D, et al. Unicellular cyanobacterium symbiotic with a single-celled eukaryotic alga. Science. 2012;337:1546–50.
Zengler K, Palsson BO. A road map for the development of community systems (CoSy) biology. Nat Rev Microbiol. 2012;10:366–72.
Sachs JL, Hollowell AC. The origins of cooperative bacterial communities. MBio. 2012;3:1–3.
Johnson DR, Goldschmidt F, Lilja EE, Ackermann M. Metabolic specialization and the assembly of microbial communities. ISME J. 2012;6:1985–91.
Bull JJ, Rice WR. Distinguishing mechanisms for the evolution of co-operation. J Theor Biol. 1991;149:63–74.
Foster KR, Wenseleers T. A general model for the evolution of mutualisms. J Evol Biol. 2006;19:1283–93.
Weber KA, Achenbach LA, Coates JD. Microorganisms pumping iron: anaerobic microbial iron oxidation and reduction. Nat Rev Microbiol. 2006;4:752–64.
Lüdecke C, Reiche M, Eusterhues K, Nietzsche S, Küsel K. Acid-tolerant microaerophilic Fe(II)-oxidizing bacteria promote Fe(III)-accumulation in a fen. Environ Microbiol. 2010;12:2814–25.
Emerson D, Fleming EJ, McBeth JM. Iron-oxidizing bacteria: an environmental and genomic perspective. Annu Rev Microbiol. 2010;64:561–83.
Emerson D, Field EK, Chertkov O, Davenport KW, Goodwin L, Munk C, et al. Comparative genomics of freshwater Fe-oxidizing bacteria: implications for physiology, ecology, and systematics. Front Microbiol. 2013;4:254.
Fabisch M, Beulig F, Akob DM, Küsel K. Surprising abundance of Gallionella-related iron oxidizers in creek sediments at pH 4.4 or at high heavy metal concentrations. Front Microbiol. 2013;4:390.
Fleming EJ, Cetinić I, Chan CS, Whitney King D, Emerson D. Ecological succession among iron-oxidizing bacteria. ISME J. 2014;8:804–15.
Byrne JM, van der Laan G, Figueroa AI, Qafoku O, Wang C, Pearce CI, et al. Size dependent microbial oxidation and reduction of magnetite nano- and micro-particles. Sci Rep. 2016;6:1–13.
Byrne JM, Klueglein N, Pearce C, Rosso KM, Appel E, Kappler A. Redox cycling of Fe(II) and Fe(III) in magnetite by Fe-metabolizing bacteria. Science. 2015;347:1473–6.
Braunschweig J, Bosch J, Meckenstock RU. Iron oxide nanoparticles in geomicrobiology: from biogeochemistry to bioremediation. N. Biotechnol. 2013;30:793–802.
Bosch J, Heister K, Hofmann T, Meckenstock RU. Nanosized iron oxide colloids strongly enhance microbial iron reduction. Appl Environ Microbiol. 2010;76:184–9.
Küsel K, Blöthe M, Schulz D, Reiche M, Drake HL. Microbial reduction of iron and porewater biogeochemistry in acidic peatlands. Biogeosci Discuss. 2008;5:2165–96.
Marsili E, Baron DB, Shikhare ID, Coursolle D, Gralnick JA, Bond DR. Shewanella secretes flavins that mediate extracellular electron transfer. Proc Natl Acad Sci USA. 2008;105:3968–73.
Royer RA, Burgos WD, Fisher AS, Unz RF, Dempsey BA. Enhancement of biological reduction of hematite by electron shuttling and Fe(II) complexation. Environ Sci Technol. 2002;36:1939–46.
Beckwith CR, Edwards MJ, Lawes M, Shi L, Butt JN, Richardson DJ, et al. Characterization of MtoD from Sideroxydans lithotrophicus: a cytochrome c electron shuttle used in lithoautotrophic growth. Front Microbiol. 2015;6:332.
Hartshorne RS, Reardon CL, Ross D, Nuester J, Clarke TA, Gates AJ, et al. Characterization of an electron conduit between bacteria and the extracellular environment. Proc Natl Acad Sci USA. 2009;106:22169–74.
White GF, Shi Z, Shi L, Wang Z, Dohnalkova AC, Marshall MJ, et al. Rapid electron exchange between surface-exposed bacterial cytochromes and Fe(III) minerals. Proc Natl Acad Sci USA. 2013;110:6346–51.
Venkateswaran K, Moser DP, Dollhopf ME, Lies DP, Saffarini DA, MacGregor BJ, et al. Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov. Int J Syst Bacteriol. 1999;49:705–24.
Myers CR, Nealson KH. Bacterial manganese reduction and growth with manganese oxide as the sole electron acceptor. Science. 1988;240:1319–21.
Myers CR, Nealson KH. Respiration-linked proton translocation coupled to anaerobic reduction of manganese(IV) and iron(III) in Shewanella putrefaciensMR-1. J Bacteriol. 1990;172:6232–8.
McBeth JM, Little BJ, Ray RI, Farrar KM, Emerson D. Neutrophilic iron-oxidizing ‘Zetaproteobacteria’ and mild steel corrosion in nearshore marine environments. Appl Environ Microbiol. 2011;77:1405–12.
Mori JF, Ueberschaar N, Lu S, Cooper RE, Pohnert G, Küsel K. Sticking together: inter-species aggregation of bacteria isolated from iron snow is controlled by chemical signaling. ISME J. 2017;11:1075–86.
Tamura H, Goto K, Yotsuyanagi T, Nagayama M. Spectrophotometric determination of iron(II) with 1,10-phenanthroline in the presence of large amounts of iron(III). Talanta. 1974;21:314–8.
Cooper RE, Wegner C-E, McAllister SM, Shevchenko O, Chan CS, Küsel K. Draft genome sequence of Sideroxydanssp. Strain CL21, an Fe(II)-oxidizing bacterium. Microbiol Resour Announc. 2020;9:1–2.
Wegner C-E, 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;8:1–19.
Andrews S. FastQC: a quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc..40.
Bushnell B. BBMap short read aligner. https://www.sourceforge.net/projects/bbmap/..41.
Kopylova E, Noé L, Touzet H, Noe L, Touzet H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics. 2012;28:3211–7.
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–6.
Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, et al. Rfam 11.0: 10 years of RNA families. Nucleic Acids Res. 2013;41:D226–32.
Heidelberg JF, Paulsen IT, Nelson KE, Gaidos EJ, Nelson WC, Read TD, et al. Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat Biotechnol. 2002;20:1118–23.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAM tools. Bioinformatics. 2009;25:2078–9.
Liao Y, Smyth GK, Shi W. The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Res. 2013;41:e108.
Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30:923–30.
R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. 2018.
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–40.
Tautenhahn R, Patti GJ, Rinehart D, Siuzdak G. XCMS Online: a web-based platform to process untargeted metabolomic data. Anal Chem. 2012;84:5035–9.
Stettin D, Poulin RX, Pohnert G. Metabolomics benefits fom orbitrap GC-MS—Comparison of low- and high-resolution GC-MS. Metabolites. 2020;10:1–16.
Chong J, Yamamoto M, Xia J. MetaboAnalystR 2.0: from raw spectra to biological insights. Metabolites. 2019;9:1–10.
Hummel J, Strehmel N, Bölling C, Schmidt S, Walther D, Kopka J. Mass Spectral search and analysis using the golm metabolome database. In: Weckwerth W, Kahl G (eds). The handbook of plant metabolomics. 2013. Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany, p. 321–43.
Lueder U, Druschel G, Emerson D, Kappler A, Schmidt C. Quantitative analysis of O2 and Fe2+ profiles in gradient tubes for cultivation of microaerophilic Iron(II)-oxidizing bacteria. FEMS Microbiol Ecol. 2018;94:1–15.
Lefevre E, Bossa N, Wiesner MR, Gunsch CK. A review of the environmental implications of in situ remediation by nanoscale zero valent iron (nZVI): behavior, transport and impacts on microbial communities. Sci Total Environ. 2016;565:889–901.
Kirschling TL, Gregory KB, Minkley EG Jr, Lowry GV, Tilton RD. Impact of nanoscale zero valent iron on geochemistry and microbial populations in trichloroethylene contaminated aquifer materials. Environ Sci Technol. 2010;44:3474–80.
Wu S, Cajthaml T, Semerád J, Filipová A, Klementová M, Skála R, et al. Nano zero-valent iron aging interacts with the soil microbial community: a microcosm study. Environ Sci: Nano. 2019;6:1189–206.
Auffan M, Rose J, Wiesner MR, Bottero J-Y. Chemical stability of metallic nanoparticles: a parameter controlling their potential cellular toxicity in vitro. Environ Pollut. 2009;157:1127–33.
Anza M, Salazar O, Epelde L, Alkorta I, Garbisu C. The application of nanoscale zero-valent iron promotes soil remediation while negatively affecting soil microbial biomass and activity. Front Environ Sci. 2019;7:1–6.
Friedrich B, Magasanik B. Enzymes of agmatine degradation and the control of their synthesis in Klebsiella aerogenes. J Bacteriol. 1979;137:1127–33.
Kurihara S, Oda S, Kato K, Kim HG, Koyanagi T, Kumagai H, et al. A novel putrescine utilization pathway involves gamma-glutamylated intermediates of Escherichia coli K-12. J Biol Chem. 2005;280:4602–8.
Hädrich A, Taillefert M, Akob DM, Cooper RE, Litzba U, Wagner FE, et al. Microbial Fe(II) oxidation by Sideroxydans lithotrophicus ES-1 in the presence of Schlöppnerbrunnen fen-derived humic acids. FEMS Microbiol Ecol. 2019;95:1–19.
Cooper RE, Eusterhues K, Wegner C-E, Totsche KU, Küsel K. Ferrihydrite-associated organic matter (OM) stimulates reduction by Shewanella oneidensis MR-1 and a complex microbial consortia. Biogeosciences. 2017;14:5171–88.
Liu J, Wang Z, Belchik SM, Edwards MJ, Liu C, Kennedy DW, et al. Identification and characterization of MtoA: a decaheme c-type cytochrome of the neutrophilic Fe(II)-oxidizing bacterium Sideroxydans lithotrophicus ES-1. Front Microbiol. 2012;3:37.
DiChristina TJ, Moore CM, Haller CA. Dissimilatory Fe(III) and Mn(IV) reduction by Shewanella putrefaciens requires ferE, a homolog of the pulE (gspE) type II protein secretion gene. J Bacteriol. 2002;184:142–51.
Meshulam-Simon G, Behrens S, Choo AD, Spormann AM. Hydrogen metabolism in Shewanella oneidensis MR-1. Appl Environ Microbiol. 2007;73:1153–65.
Shi L, Belchik SM, Plymale AE, Heald S, Dohnalkova AC, Sybirna K, et al. Purification and characterization of the [NiFe]-hydrogenase of Shewanella oneidensis MR-1. Appl Environ Microbiol. 2011;77:5584–90.
Vignais PM, Billoud B, Meyer J. Classification and phylogeny of hydrogenases. FEMS Microbiol Rev. 2001;25:455–501.
Reiche M, Torburg G, Küsel K. Competition of Fe(III) reduction and methanogenesis in an acidic fen. FEMS Microbiol Ecol. 2008;65:88–101.
Reiche M, Haedrich A, Lischeid G, Kuesel K, Hädrich A, Lischeid G, et al. Impact of manipulated drought and heavy rainfall events on peat mineralization processes and source-sink functions of an acidic fen. J Geophys Res-Biogeosci. 2009;114:1–13.
Hädrich A, Heuer VB, Herrmann M, Hinrichs K-U, Küsel K. Origin and fate of acetate in an acidic fen. FEMS Microbiol Ecol. 2012;81:339–54.
Hamberger A, Horn MA, Dumont MG, Murrell JC, Drake HL. Anaerobic consumers of monosaccharides in a moderately acidic fen. Appl Environ Microbiol. 2008;74:3112–20.
Wüst PK, Horn MA, Drake HL. Trophic links between fermenters and methanogens in a moderately acidic fen soil. Environ Microbiol. 2009;11:1395–409.
Tabor CW, Tabor H. Polyamines. Annu Rev Biochem. 1984;53:749–90.
Karatan E, Watnick P. Signals, regulatory networks, and materials that build and break bacterial biofilms. Microbiol Mol Biol Rev. 2009;73:310–47.
Bachrach U, Heimer YM. The physiology of polyamines. 1989. CRC Press Taylor and Francis Group, Boca Raton, FL, USA.
Karatan E, Duncan TR, Watnick PI. NspS, a predicted polyamine sensor, mediates activation of Vibrio cholerae biofilm formation by norspermidine. J Bacteriol. 2005;187:7434–43.
Cockerell SR, Rutkovsky AC, Zayner JP, Cooper RE, Porter LR, Pendergraft SS, et al. Vibrio cholerae NspS, a homologue of ABC-type periplasmic solute binding proteins, facilitates transduction of polyamine signals independent of their transport. Microbiology. 2014;160:832–43.
Matthysse AG, Yarnall HA, Young N. Requirement for genes with homology to ABC transport systems for attachment and virulence of Agrobacterium tumefaciens. J Bacteriol. 1996;178:5302–8.
Sauer K, Camper AK. Characterization of phenotypic changes in Pseudomonas putida in response to surface-associated growth. J Bacteriol. 2001;183:6579–89.
Patel CN, Wortham BW, Lines JL, Fetherston JD, Perry RD, Oliveira MA. Polyamines are essential for the formation of plague biofilm. J Bacteriol. 2006;188:2355–63.
Capdevila DA, Wang J, Giedroc DP. Bacterial strategies to maintain zinc metallostasis at the host–pathogen interface. J Biol Chem. 2016;291:20858–68.
Schoepp-Cothenet B, van Lis R, Philippot P, Magalon A, Russell MJ, Nitschke W. The ineluctable requirement for the trans-iron elements molybdenum and/or tungsten in the origin of life. Sci Rep. 2012;2:263.
Reda T, Plugge CM, Abram NJ, Hirst J. Reversible interconversion of carbon dioxide and formate by an electroactive enzyme. Proc Natl Acad Sci USA. 2008;105:10654–8.
Hartmann T, Schwanhold N, Leimkühler S. Assembly and catalysis of molybdenum or tungsten-containing formate dehydrogenases from bacteria. Biochim Biophys Acta. 2015;1854:1090–1100.
Ilbert M, Bonnefoy V. Insight into the evolution of the iron oxidation pathways. Biochim Biophys Acta. 2013;1827:161–75.
Lovley DR, Holmes DE, Nevin KP. Dissimilatory Fe(III) and Mn(IV) reduction. Adv Micro Physiol. 2004;49:219–86.
Melton ED, Swanner ED, Behrens S, Schmidt C, Kappler A. The interplay of microbially mediated and abiotic reactions in the biogeochemical Fe cycle. Nat Rev Microbiol. 2014;12:797–808.
Maisch M, Lueder U, Laufer K, Scholze C, Kappler A, Schmidt C. Contribution of microaerophilic Iron(II)-oxidizers to Iron(III) mineral formation. Environ Sci Technol. 2019;53:8197–204.
Hong Y, Wu J, Wilson S, Song B. Vertical stratification of sediment microbial communities along geochemical gradients of a subterranean estuary located at the Gloucester Beach of Virginia, United States. Front Microbiol. 2018;9:3343.
Liptzin D, Silver WL. Spatial patterns in oxygen and redox sensitive biogeochemistry in tropical forest soils. Ecosphere. 2015;6:art211.
Borer B, Tecon R, Or D. Spatial organization of bacterial populations in response to oxygen and carbon counter-gradients in pore networks. Nat Commun. 2018;9:769.
Widder S, Allen RJ, Pfeiffer T, Curtis TP, Wiuf C, Sloan WT, et al. Challenges in microbial ecology: building predictive understanding of community function and dynamics. ISME J. 2016;10:2557–68.
Frey PA, Reed GH. The ubiquity of iron. ACS Chem Biol. 2012;7:1477–81.
Edwards KJ, Bach W, McCollom TM, Rogers DR. Neutrophilic iron-oxidizing bacteria in the ocean: their habitats, diversity, and roles in mineral deposition, rock alteration, and biomass production in the deep-sea. Geomicrobiol J. 2004;21:393–404.
Bondici VF, Khan NH, Swerhone GDW, Dynes JJ, Lawrence JR, Yergeau E, et al. Biogeochemical activity of microbial biofilms in the water column overlying uranium mine tailings. J Appl Microbiol. 2014;117:1079–94.
Lee AK, Newman DK. Microbial iron respiration: impacts on corrosion processes. Appl Microbiol Biotechnol. 2003;62:134–9.
Glasser NR, Saunders SH, Newman DK. The colorful world of extracellular electron shuttles. Annu Rev Microbiol. 2017;71:731–51.
Philips J, Verbeeck K, Rabaey K, Arends JBA. Electron transfer mechanisms in biofilms. In: Scott K, Yu EH (eds). Microbial electrochemical and fuel cells. 2016. Woodhead Publishing, Sawston, Cambridge, United Kingdom, p. 67–113.
Gao L, Lu X, Liu H, Li J, Li W, Song R, et al. Mediation of extracellular polymeric substances in microbial reduction of hematite by Shewanella oneidensis MR-1. Front Microbiol. 2019;10:575.
Roden EE, McBeth JM, Blöthe M, Percak-Dennett EM, Fleming EJ, Holyoke RR, et al. The microbial ferrous wheel in a neutral pH groundwater seep. Front Microbiol. 2012;3:172.
Source: Ecology - nature.com
