Hatzenpichler R, Krukenberg V, Spietz RL, Jay ZJ. Next-generation physiology approaches to study microbial community function at the single-cell level. Nat Rev Microbiol. 2020;18:241–56.
Google Scholar
Ando T, Bhamidimarri SP, Brending N, Colin-York H, Collinson L, De Jonge N, et al. The 2018 correlative microscopy techniques roadmap. J Phys D: Appl Phys. 2018;51:443001.
Google Scholar
Endesfelder U. Advances in correlative single-molecule localization microscopy and electron microscopy. NanoBioImaging. 2015;1:29–37.
Google Scholar
Osborn M, Webster RE, Weber K. Individual microtubules viewed by immunofluorescence and electron microscopy in the same PtK2 cell. J Cell Biol. 1978;77:27–38.
Google Scholar
Webster RE, Osborn M, Weber K. Visualization of the same PtK2 cytoskeletons by both immunofluorescence and low power electron microscopy. Exp Cell Res. 1978;117:47–61.
Google Scholar
Perkovic M, Kunz M, Endesfelder U, Bunse S, Wigge C, Yu Z, et al. Correlative Light- and Electron Microscopy with chemical tags. J Struct Biol. 2014;186:205–13.
Google Scholar
Lange F, Agui-Gonzalez P, Riedel D, Phan NTN, Jakobs S, Rizzoli SO. Correlative fluorescence microscopy, transmission electron microscopy and secondary ion mass spectrometry (CLEM-SIMS) for cellular imaging. Plos One. 2021;16:e0240768.
Google Scholar
Pirozzi NM, Hoogenboom JP, Giepmans BNG. ColorEM: analytical electron microscopy for element-guided identification and imaging of the building blocks of life. Histochem Cell Biol. 2018;150:509–20.
Google Scholar
Loussert-Fonta C, Toullec G, Paraecattil AA, Jeangros Q, Krueger T, Escrig S, et al. Correlation of fluorescence microscopy, electron microscopy, and NanoSIMS stable isotope imaging on a single tissue section. Commun Biol. 2020;3:362.
Google Scholar
Joosten B, Willemse M, Fransen J, Cambi A, van den Dries K. Super-resolution correlative light and electron microscopy (SR-CLEM) reveals novel ultrastructural insights into dendritic cell podosomes. Front Immunol. 2018;9:1–14.
Google Scholar
Woehl TJ, Kashyap S, Firlar E, Perez-Gonzalez T, Faivre D, Trubitsyn D, et al. Correlative electron and fluorescence microscopy of magnetotactic bacteria in liquid: toward in vivo imaging. Sci Rep. 2014;4:6854.
Google Scholar
Li J, Zhang H, Menguy N, Benzerara K, Wang F, Lin X, et al. Single-cell resolution of uncultured magnetotactic bacteria via fluorescence-coupled electron microscopy. Appl Environ Microbiol. 2017;83:e00409–17.
Google Scholar
Qian XX, Santini CL, Kosta A, Menguy N, Le Guenno H, Zhang W, et al. Juxtaposed membranes underpin cellular adhesion and display unilateral cell division of multicellular magnetotactic prokaryotes. Environ Microbiol. 2020;22:1481–94.
Google Scholar
McGlynn SE, Chadwick GL, O’Neill A, Mackey M, Thor A, Deerinck TJ, et al. Subgroup characteristics of marine methane-oxidizing ANME-2 archaea and their syntrophic partners revealed by integrated multimodal analytical microscopy. Appl Environ Microbiol. 2018;84:e00399–18.
Google Scholar
Hao L, McIlroy SJ, Kirkegaard RH, Karst SM, Fernando WEY, Aslan H, et al. Novel prosthecate bacteria from the candidate phylum Acetothermia. ISME J. 2018;126:2225–37.
Google Scholar
Hapca S, Baveye PC, Wilson C, Lark RM, Otten W. Three-dimensional mapping of soil chemical characteristics at micrometric scale by combining 2D SEM-EDX data and 3D X-Ray CT images. PLoS One. 2015;10:e0137205.
Google Scholar
Schluter S, Eickhorst T, Mueller CW. Correlative imaging reveals holistic view of soil microenvironments. Environ Sci Technol. 2019;53:829–37.
Google Scholar
Marlow J, Spietz R, Kim KY, Ellisman M, Girguis P, Hatzenpichler R. Spatially resolved correlative microscopy and microbial identification reveal dynamic depth- and mineral-dependent anabolic activity in salt marsh sediment. Environ Microbiol. 2021;23:4756–77.
Google Scholar
Musat N, Musat F, Weber PK, Pett-Ridge J. Tracking microbial interactions with NanoSIMS. Curr Opin Biotechnol. 2016;41:114–21.
Google Scholar
Berry D, Mader E, Lee TK, Woebken D, Wang Y, Zhu D, et al. Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells. Proc Natl Acad Sci USA. 2015;112:E194–203.
Google Scholar
Huang WE, Stoecker K, Griffiths R, Newbold L, Daims H, Whiteley AS, et al. Raman-FISH: combining stable-isotope Raman spectroscopy and fluorescence in situ hybridization for the single cell analysis of identity and function. Environ Microbiol. 2007;9:1878–89.
Google Scholar
Waite DW, Chuvochina M, Pelikan C, Parks DH, Yilmaz P, Wagner M, et al. Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities. Int J Syst Evol Microbiol. 2020;70:5972–6016.
Google Scholar
Keim CN, Martins JL, de Barros HL, Lins U, MF Structure, behavior, ecology and diversity of multicellular magnetotactic prokaryotes. Magnetoreception and magnetosomes in bacteria. (Springer, Berlin, Heidelberg, 2006):103–32.
Abreu F, Silva KT, Martins JL, Lins U. Cell viability in magnetotactic multicellular prokaryotes. Int Microbiol. 2006;9:267–72.
Google Scholar
Abreu F, Martins JL, Silveira TS, Keim CN, de Barros HG, Filho FJ, et al. ‘Candidatus Magnetoglobus multicellularis’, a multicellular, magnetotactic prokaryote from a hypersaline environment. Int J Syst Evol Microbiol. 2007;57:1318–22.
Google Scholar
Abreu F, Silva KT, Leao P, Guedes IA, Keim CN, Farina M, et al. Cell adhesion, multicellular morphology, and magnetosome distribution in the multicellular magnetotactic prokaryote Candidatus Magnetoglobus multicellularis. Microsc Microanal. 2013;19:535–43.
Google Scholar
Faivre D, Schuler D. Magnetotactic bacteria and magnetosomes. Chem Rev. 2008;108:4875–98.
Google Scholar
Greening C, Lithgow T. Formation and function of bacterial organelles. Nat Rev Microbiol. 2020;18:677–89.
Google Scholar
Uebe R, Schuler D. Magnetosome biogenesis in magnetotactic bacteria. Nat Rev Microbiol. 2016;14:621–37.
Google Scholar
Shapiro OH, Hatzenpichler R, Buckley DH, Zinder SH, Orphan VJ. Multicellular photo-magnetotactic bacteria. Env Microbiol Rep. 2011;3:233–8.
Google Scholar
Simmons SL, Edwards KJ. Unexpected diversity in populations of the many-celled magnetotactic prokaryote. Environ Microbiol. 2007;9:206–15.
Google Scholar
Wilbanks EG, Jaekel U, Salman V, Humphrey PT, Eisen JA, Facciotti MT, et al. Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh. Environ Microbiol. 2014;16:3398–415.
Google Scholar
Wilbanks EG, Salman-Carvalho V, Jaekel U, Humphrey PT, Eisen JA, Buckley DH, et al. The Green Berry Consortia of the Sippewissett Salt Marsh: millimeter-sized aggregates of diazotrophic unicellular cyanobacteria. Front Microbiol. 2017;8:1–12.
Google Scholar
Larsen S, Nielsen LP, Schramm A. Cable bacteria associated with long-distance electron transport in New England salt marsh sediment. Env Microbiol Rep. 2015;7:175–9.
Google Scholar
Salman V, Yang TT, Berben T, Klein F, Angert E, Teske A. Calcite-accumulating large sulfur bacteria of the genus Achromatium in Sippewissett Salt Marsh. ISME J. 2015;9:2503–14.
Google Scholar
Mackey KRM, Hunter-Cevera K, Britten GL, Murphy LG, Sogin ML, Huber JA. Seasonal succession and spatial patterns of synechococcus microdiversity in a salt marsh estuary revealed through 16S rRNA gene oligotyping. Front Microbiol. 2017;8.
Bowen JL, Morrison HG, Hobbie JE, Sogin ML. Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates. ISME J. 2012;6:2014–23.
Google Scholar
Lewis AT, Gaifulina R, Isabelle M, Dorney J, Woods ML, Lloyd GR, et al. Mirrored stainless steel substrate provides improved signal for Raman spectroscopy of tissue and cells. J Raman Spectrosc. 2017;48:119–25.
Google Scholar
Eder SH, Gigler AM, Hanzlik M, Winklhofer M. Sub-micrometer-scale mapping of magnetite crystals and sulfur globules in magnetotactic bacteria using confocal Raman micro-spectrometry. PLoS One. 2014;9:e107356.
Google Scholar
Stoecker K, Dorninger C, Daims H, Wagner M. Double labeling of oligonucleotide probes for fluorescence in situ hybridization (DOPE-FISH) improves signal intensity and increases rRNA accessibility. Appl Environ Microbiol. 2010;76:922–6.
Google Scholar
Daims H, Stoecker K, Wagner M. Fluorescence in situ hybridization for the detection of prokaryotes. Taylor & Francis, 2004; Mol Microbial Ecol:208–28.
Daims H, Brühl A, Amann R, Schleifer K-H, Wagner M. The domain-specific probe EUB338 is insufficient for the detection of all bacteria: development and evaluation of a more comprehensive probe set. Syst Appl Microbiol. 1999;22:434–44.
Google Scholar
Stahl DA, Amann RI. Development and application of nucleic acid probes. Stackebrandt E and Goodfellow M, editors. Nucleic acid techniques in bacterial systematics. John Wiley & Sons; 1991. p. 205–48.
Behrens S, Ruhland C, Inacio J, Huber H, Fonseca A, Spencer-Martins I, et al. In situ accessibility of small-subunit rRNA of members of the domains Bacteria, Archaea, and Eucarya to Cy3-labeled oligonucleotide probes. Appl Environ Microbiol. 2003;69:1748–58.
Google Scholar
Wallner G, Amann R, Beisker W. Optimizing fluorescent insitu hybridization with ribosomal-Rna-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry. 1993;14:136–43.
Google Scholar
Zimmermann M, Escrig S, Hubschmann T, Kirf MK, Brand A, Inglis RF, et al. Phenotypic heterogeneity in metabolic traits among single cells of a rare bacterial species in its natural environment quantified with a combination of flow cell sorting and NanoSIMS. Front Microbiol. 2015;6:243.
Google Scholar
Grieb A, Bowers RM, Oggerin M, Goudeau D, Lee J, Malmstrom RR, et al. A pipeline for targeted metagenomics of environmental bacteria. Microbiome. 2020;8:21.
Google Scholar
Meyer NR, Fortney JL, Dekas AE. NanoSIMS sample preparation decreases isotope enrichment: magnitude, variability and implications for single-cell rates of microbial activity. Environ Microbiol. 2021;23:81–98.
Google Scholar
Musat N, Stryhanyuk H, Bombach P, Adrian L, Audinot JN, Richnow HH. The effect of FISH and CARD-FISH on the isotopic composition of (13)C- and (15)N-labeled Pseudomonas putida cells measured by nanoSIMS. Syst Appl Microbiol. 2014;37:267–76.
Google Scholar
Amann R, Fuchs BM. Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques. Nat Rev Microbiol. 2008;6:339–48.
Google Scholar
Lee KS, Landry Z, Pereira FC, Wagner M, Berry D, Huang WE, et al. Raman microspectroscopy for microbiology. Nat Rev Methods Primers. 2021;1:1–25.
Google Scholar
Wang Y, Huang WE, Cui L, Wagner M. Single-cell stable isotope probing in microbiology using Raman microspectroscopy. Curr Opin Biotechnol. 2016;41:34–42.
Google Scholar
Eichorst SA, Strasser F, Woyke T, Schintlmeister A, Wagner M, Woebken D. Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils. FEMS Microbiol Ecol. 2015;91:1–16.
Google Scholar
Li J, Liu P, Tamaxia A, Zhang H, Liu Y, Wang J, et al. Diverse intracellular inclusion types within magnetotactic bacteria: implications for biogeochemical cycling in aquatic environments. J Geophys Res Biogeosci. 2021;126:e2021JG006310.
Google Scholar
Matanfack GA, Taubert M, Guo S, Houhou R, Bocklitz T, Kusel K, et al. Influence of carbon sources on quantification of deuterium incorporation in heterotrophic bacteria: a Raman-stable isotope labeling approach. Anal Chem. 2020;92:11429–37.
Google Scholar
Amor M, Tharaud M, Gelabert A, Komeili A. Single-cell determination of iron content in magnetotactic bacteria: implications for the iron biogeochemical cycle. Environ Microbiol. 2020;22:823–31.
Google Scholar
Farina M, Esquivel DMS, Debarros HGPL. Magnetic iron-sulfur crystals from a magnetotactic microorganism. Nature. 1990;343:256–8.
Google Scholar
Wenter R, Wanner G, Schuler D, Overmann J. Ultrastructure, tactic behaviour and potential for sulfate reduction of a novel multicellular magnetotactic prokaryote from North Sea sediments. Environ Microbiol. 2009;11:1493–505.
Google Scholar
Zhang R, Chen YR, Du HJ, Zhang WY, Pan HM, Xiao T, et al. Characterization and phylogenetic identification of a species of spherical multicellular magnetotactic prokaryotes that produces both magnetite and greigite crystals. Res Microbiol. 2014;165:481–9.
Google Scholar
Teng Z, Zhang Y, Zhang W, Pan H, Xu J, Huang H, et al. Diversity and characterization of multicellular magnetotactic prokaryotes from coral reef habitats of the Paracel Islands, South China Sea. Front Microbiol. 2018;9:2135.
Google Scholar
Bourdoiseau J-A, Jeannin M, Rémazeilles C, Sabot R, Refait P. The transformation of mackinawite into greigite studied by Raman spectroscopy. J Raman Spectrosc. 2011;42:496–504.
Google Scholar
Mann S, Sparks NH, Board RG. Magnetotactic bacteria: microbiology, biomineralization, palaeomagnetism and biotechnology. Adv Microb Physiol. 1990;31:125–81.
Google Scholar
Posfai M, Buseck PR, Bazylinski DA, Frankel RB. Iron sulfides from magnetotactic bacteria: structure, composition, and phase transitions. Am Mineral. 1998;83:1469–81.
Google Scholar
Betzig E, Patterson GH, Sougrat R, Lindwasser OW, Olenych S, Bonifacino JS, et al. Imaging intracellular fluorescent proteins at nanometer resolution. Science. 2006;313:1642–5.
Google Scholar
Rust MJ, Bates M, Zhuang X. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat Methods. 2006;3:793–5.
Google Scholar
Hatzenpichler R, Scheller S, Tavormina PL, Babin BM, Tirrell DA, Orphan VJ. In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry. Environ Microbiol. 2014;16:2568–90.
Google Scholar
Smriga S, Samo TJ, Malfatti F, Villareal J, Azam F. Individual cell DNA synthesis within natural marine bacterial assemblages as detected by ‘click’ chemistry. Aquat Microb Ecol. 2014;72:269–80.
Google Scholar
Siegrist MS, Whiteside S, Jewett JC, Aditham A, Cava F, Bertozzi CR. (D)-Amino acid chemical reporters reveal peptidoglycan dynamics of an intracellular pathogen. ACS Chem Biol. 2013;8:500–5.
Google Scholar
Keim CN, Abreu F, Lins U, Lins de Barros H, Farina M. Cell organization and ultrastructure of a magnetotactic multicellular organism. J Struct Biol. 2004;145:254–62.
Google Scholar
Source: Ecology - nature.com
