Abstract
Despite the major influence of soils on climate change, carbon sequestration, pollution remediation, and food security, soil remains a largely unexplored media with an extreme complexity of microbes, minerals, and dead organic matter, most of them being actually poorly known. In particular, soil biofilms have recently attracted attention because they strongly influence biogeochemical reactions and processes. Here we review biofilms with focus on their behavior, proliferation, distribution, characterization methods, and applications. Characterization methods include optical, electron, scanning probe, and X-ray microscopy; metagenomics, metatranscriptomics, metaproteomics, metabolomics; and tracking approaches. Applications comprise pollution remediation by metal immobilization or organics degradation; and methane oxidation, carbon dioxide reduction, and carbon sequestration. Advanced methods such as DNA-stable isotope probing and meta-omics have uncovered the multiple functions of soil biofilms and their underlying molecular mechanisms. Investigations have improved our understanding of inter- and intra-kingdom interactions, and of gene transfer. Extracellular materials such as polysaccharides enhance the transport of substances and electrons flow among microorganisms.
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Abbas SZ, Rafatullah M (2021) Recent advances in soil microbial fuel cells for soil contaminants remediation. Chemosphere 272:129691. https://doi.org/10.1016/j.chemosphere.2021.129691
Abiraami TV, Singh S, Nain L (2020) Soil metaproteomics as a tool for monitoring functional microbial communities: promises and challenges. Rev Environ Sci Biotechnol 19:73–102. https://doi.org/10.1007/s11157-019-09519-8
Aguilar NC, Faria MCS, Pedron T et al (2020) Isolation and characterization of bacteria from a Brazilian gold mining area with a capacity of arsenic bioaccumulation. Chemosphere 240:124871. https://doi.org/10.1016/j.chemosphere.2019.124871
Al-Amshawee S, Yunus MYBM, Vo D-VN, Tran NH (2020) Biocarriers for biofilm immobilization in wastewater treatments: a review. Environ Chem Lett 18:1925–1945. https://doi.org/10.1007/s10311-020-01049-y
Albert S, Wietrzynski W, Lee C-W et al (2020) Direct visualization of degradation microcompartments at the ER membrane. Proc Natl Acad Sci 117:1069–1080. https://doi.org/10.1073/pnas.1905641117
Aloo BN, Tripathi V, Makumba BA, Mbega ER (2022) Plant growth-promoting rhizobacterial biofertilizers for crop production: the past, present, and future. Front Plant Sci. https://doi.org/10.3389/fpls.2022.1002448
Alsiyabi A, Immethun CM, Saha R (2019) Modeling the interplay between photosynthesis CO2 fixation and the quinone pool in a purple non-sulfur bacterium. Abstr Sci Rep 9(1). https://doi.org/10.1038/s41598-019-49079-z
Amundson R, Berhe AA, Hopmans JW, Olson C, Sztein AE, Sparks DL (2015) Soil and human security in the 21st century Global soil resources under stress. Science 348(6235). https://doi.org/10.1126/science.1261071
Angst G, Mueller KE, Nierop KGJ, Simpson MJ (2021) Plant- or microbial-derived? A review on the molecular composition of stabilized soil organic matter. Soil Biol Biochem 156:108189. https://doi.org/10.1016/j.soilbio.2021.108189
Arnaouteli S, Bamford NC, Stanley-Wall NR, Kovács ÁT (2021) Bacillus subtilis biofilm formation and social interactions. Nat Rev Microbiol 19:600–614. https://doi.org/10.1038/s41579-021-00540-9
Awala SI, Gwak J-H, Kim Y-M et al (2021) Verrucomicrobial methanotrophs grow on diverse C3 compounds and use a homolog of particulate methane monooxygenase to oxidize acetone. ISME J 15:3636–3647. https://doi.org/10.1038/s41396-021-01037-2
Bai X, Huang D, Chen Y et al (2023) Exploration of Fe speciation preference for aerobic methane oxidation by using isotopic Fe-modified zeolites. Chem Eng J 455:140844. https://doi.org/10.1016/j.cej.2022.140844
Banerjee S, van der Heijden MGA (2023) Soil microbiomes and one health. Nat Rev Microbiol 21:6–20. https://doi.org/10.1038/s41579-022-00779-w
Bastida F, Jehmlich N, Starke R et al (2021) Structure and function of bacterial metaproteomes across biomes. Soil Biol Biochem 160:108331. https://doi.org/10.1016/j.soilbio.2021.108331
Bay SK, Dong X, Bradley JA et al (2021a) Trace gas oxidizers are widespread and active members of soil microbial communities. Nat Microbiol 6:246–256. https://doi.org/10.1038/s41564-020-00811-w
Bay SK, Waite DW, Dong X et al (2021b) Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient. ISME J 15:3339–3356. https://doi.org/10.1038/s41396-021-01001-0
Berne C, Ellison CK, Ducret A, Brun YV (2018) Bacterial adhesion at the single-cell level. Nat Rev Microbiol 16:616–627. https://doi.org/10.1038/s41579-018-0057-5
Bhattacharyya SS, Ros GH, Furtak K et al (2022) Soil carbon sequestration—an interplay between soil microbial community and soil organic matter dynamics. Sci Total Environ 815:152928. https://doi.org/10.1016/j.scitotenv.2022.152928
Bian K, Gerber C, Heinrich AJ et al (2021) Scanning probe microscopy. Nat Rev Methods Primer 1:1–29. https://doi.org/10.1038/s43586-021-00033-2
Bickel S, Or D (2020) Soil bacterial diversity mediated by microscale aqueous-phase processes across biomes. Nat Commun 11:116. https://doi.org/10.1038/s41467-019-13966-w
Boiteau RM, Fansler SJ, Farris Y et al (2019) Siderophore profiling of co-habitating soil bacteria by ultra-high resolution mass spectrometry†. Metallomics 11:166–175. https://doi.org/10.1039/c8mt00252e
Boschker HTS, Middelburg JJ (2002) Stable isotopes and biomarkers in microbial ecology. FEMS Microbiol Ecol 40:85–95. https://doi.org/10.1111/j.1574-6941.2002.tb00940.x
Cai Y, Zheng Y, Bodelier PLE et al (2016) Conventional methanotrophs are responsible for atmospheric methane oxidation in paddy soils. Nat Commun 7:1–10. https://doi.org/10.1038/ncomms11728
Cai C, Leu AO, Xie G-J et al (2018) A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction. ISME J 12:1929–1939. https://doi.org/10.1038/s41396-018-0109-x
Cai P, Sun X, Wu Y et al (2019) Soil biofilms: microbial interactions, challenges, and advanced techniques for ex-situ characterization. Soil Ecol Lett 1:85–93. https://doi.org/10.1007/s42832-019-0017-7
Chang Y-W, Fragkopoulos AA, Marquez SM et al (2015) Biofilm formation in geometries with different surface curvature and oxygen availability. New J Phys 17:033017. https://doi.org/10.1088/1367-2630/17/3/033017
Chen S-C, Budhraja R, Adrian L et al (2021) Novel clades of soil biphenyl degraders revealed by integrating isotope probing, multi-omics, and single-cell analyses. ISME J 15:3508–3521. https://doi.org/10.1038/s41396-021-01022-9
Chi Z-L, Yu G-H, Teng HH et al (2022) Molecular trade-offs between lattice oxygen and oxygen vacancy drive organic pollutant degradation in fungal biomineralized exoskeletons. Environ Sci Technol 56:8132–8141. https://doi.org/10.1021/acs.est.2c01388
Ciofu O, Moser C, Jensen PØ, Høiby N (2022) Tolerance and resistance of microbial biofilms. Nat Rev Microbiol 20:621–635. https://doi.org/10.1038/s41579-022-00682-4
Connell JL, Kim J, Shear JB et al (2014) Real-time monitoring of quorum sensing in 3D-printed bacterial aggregates using scanning electrochemical microscopy. Proc Natl Acad Sci 111:18255–18260. https://doi.org/10.1073/pnas.1421211111
Cooper RE, Wegner C-E, Kügler S et al (2020) Iron is not everything: unexpected complex metabolic responses between iron-cycling microorganisms. ISME J 14:2675–2690. https://doi.org/10.1038/s41396-020-0718-z
Cotrufo MF, Soong JL, Horton AJ et al (2015) Formation of soil organic matter via biochemical and physical pathways of litter mass loss. Nat Geosci 8:776–779. https://doi.org/10.1038/ngeo2520
Crits-Christoph A, Diamond S, Butterfield CN et al (2018) Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis. Nature 558:440–444. https://doi.org/10.1038/s41586-018-0207-y
Crowther TW, van den Hoogen J, Wan J et al (2019) The global soil community and its influence on biogeochemistry. Science 365:eaav0550. https://doi.org/10.1126/science.aav0550
Dahlberg PD, Moerner WE (2021) Cryogenic super-resolution fluorescence and electron microscopy correlated at the nanoscale. Annu Rev Phys Chem 72:253–278. https://doi.org/10.1146/annurev-physchem-090319-051546
Daims H, Lebedeva EV, Pjevac P et al (2015) Complete nitrification by nitrospira bacteria. Nature 528:504–509. https://doi.org/10.1038/nature16461
Dong J, Quan Q, Zhao D et al (2021) A combined method for the source apportionment of sediment organic carbon in rivers. Sci Total Environ 752:141840. https://doi.org/10.1016/j.scitotenv.2020.141840
Dragoš A, Kiesewalter H, Martin M et al (2018) Division of labor during biofilm matrix production. Curr Biol 28:1903-1913.e5. https://doi.org/10.1016/j.cub.2018.04.046
Du Z-Y, Zienkiewicz K, Vande Pol N et al (2019) Algal-fungal symbiosis leads to photosynthetic mycelium. Life 8:e47815. https://doi.org/10.7554/eLife.47815
Dumont MG, Murrell JC (2005) Stable isotope probing—linking microbial identity to function. Nat Rev Microbiol 3:499–504. https://doi.org/10.1038/nrmicro1162
Ehiosun KI, Godin S, Urios L et al (2022) Degradation of long-chain alkanes through biofilm formation by bacteria isolated from oil-polluted soil. Int Biodeterior Biodegrad 175:105508. https://doi.org/10.1016/j.ibiod.2022.105508
Engelhardt IC, Patko D, Liu Y et al (2022b) Novel form of collective movement by soil bacteria. ISME J 16:2337–2347. https://doi.org/10.1038/s41396-022-01277-w
Engelhardt I, Patko D, Liu Y, et al (2022a) Collective movement by soil bacteria during the colonisation of the rhizosphere. Copernicus Meetings
Erktan A, Or D, Scheu S (2020) The physical structure of soil: determinant and consequence of trophic interactions. Soil Biol Biochem 148:107876. https://doi.org/10.1016/j.soilbio.2020.107876
Ernst L, Steinfeld B, Barayeu U et al (2022) Methane formation driven by reactive oxygen species across all living organisms. Nature 603:482–487. https://doi.org/10.1038/s41586-022-04511-9
Fan L, Schneider D, Dippold MA et al (2021) Active metabolic pathways of anaerobic methane oxidation in paddy soils. Soil Biol Biochem 156:108215. https://doi.org/10.1016/j.soilbio.2021.108215
Fang Y, Tavakkoli E, Weng Z et al (2022) Disentangling carbon stabilization in a Calcisol subsoil amended with iron oxyhydroxides: a dual-13C isotope approach. Soil Biol Biochem 170:108711. https://doi.org/10.1016/j.soilbio.2022.108711
Fang Q, Lu A, Hong H et al (2023) Mineral weathering is linked to microbial priming in the critical zone. Nat Commun 14:345. https://doi.org/10.1038/s41467-022-35671-x
Flemming H-C (1993) Biofilms and environmental protection. Water Sci Technol 27:1–10. https://doi.org/10.2166/wst.1993.0528
Flemming H-C, Wingender J (2010) The biofilm matrix. Nat Rev Microbiol 8:623–633. https://doi.org/10.1038/nrmicro2415
Flemming H-C, Wuertz S (2019) Bacteria and archaea on earth and their abundance in biofilms. Nat Rev Microbiol 17:247–260. https://doi.org/10.1038/s41579-019-0158-9
Flemming H-C, Wingender J, Szewzyk U et al (2016) Biofilms: an emergent form of bacterial life. Nat Rev Microbiol 14:563–575. https://doi.org/10.1038/nrmicro.2016.94
Flemming H-C, Baveye P, Neu TR et al (2021) Who put the film in biofilm? The migration of a term from wastewater engineering to medicine and beyond. NPJ Biofilms Microbiomes 7:1–5. https://doi.org/10.1038/s41522-020-00183-3
French KE, Zhou Z, Terry N (2020) Horizontal ‘gene drives’ harness indigenous bacteria for bioremediation. Sci Rep 10:15091. https://doi.org/10.1038/s41598-020-72138-9
Frolov EN, Kublanov IV, Toshchakov SV et al (2019) Form III RubisCO-mediated transaldolase variant of the Calvin cycle in a chemolithoautotrophic bacterium. Proc Natl Acad Sci 116:18638–18646. https://doi.org/10.1073/pnas.1904225116
Fu L, Feng A, Xiao J et al (2021) Remediation of soil contaminated with high levels of hexavalent chromium by combined chemical-microbial reduction and stabilization. J Hazard Mater 403:123847. https://doi.org/10.1016/j.jhazmat.2020.123847
Fu J, Gao B, Xu H et al (2023) Effects of biofilms on the retention and transport of PFOA in saturated porous media. J Hazard Mater 443:130392. https://doi.org/10.1016/j.jhazmat.2022.130392
Furuno S, Foss S, Wild E et al (2012) Mycelia promote active transport and spatial dispersion of polycyclic aromatic hydrocarbons. Environ Sci Technol 46:5463–5470. https://doi.org/10.1021/es300810b
Georgiou K, Jackson RB, Vindušková O et al (2022) Global stocks and capacity of mineral-associated soil organic carbon. Nat Commun 13:3797. https://doi.org/10.1038/s41467-022-31540-9
Gilbert A, Sherwood Lollar B, Musat F et al (2019) Intramolecular isotopic evidence for bacterial oxidation of propane in subsurface natural gas reservoirs. Proc Natl Acad Sci 116:6653–6658. https://doi.org/10.1073/pnas.1817784116
Glasauer S, Fakra SC, Schooling S et al (2022) The transformation of U(VI) and V(V) in carnotite group minerals during dissimilatory respiration by a metal reducing bacterium. Chem Geol 591:120726. https://doi.org/10.1016/j.chemgeo.2022.120726
Goff JL, Chen Y, Thorgersen MP et al (2023) Mixed heavy metal stress induces global iron starvation response. ISME J 17:382–392. https://doi.org/10.1038/s41396-022-01351-3
Golding CG, Lamboo LL, Beniac DR, Booth TF (2016) The scanning electron microscope in microbiology and diagnosis of infectious disease. Sci Rep 6:26516. https://doi.org/10.1038/srep26516
Gong Y, Gu T, Ling L et al (2022) Visualizing hazardous solids with cryogenic electron microscopy (Cryo-EM). J Hazard Mater 436:129192. https://doi.org/10.1016/j.jhazmat.2022.129192
Guibaud G, Comte S, Bordas F et al (2005) Comparison of the complexation potential of extracellular polymeric substances (EPS), extracted from activated sludges and produced by pure bacteria strains, for cadmium, lead and nickel. Chemosphere 59:629–638. https://doi.org/10.1016/j.chemosphere.2004.10.028
Gunina A, Kuzyakov Y (2022) From energy to (soil organic) matter. Glob Change Biol 28:2169–2182. https://doi.org/10.1111/gcb.16071
Guo Z, Hua X, Lan X et al (2012) Evidence for a mutual effect of biofilms, suspended particles and sediments on DDT sorption. Environ Chem Lett 10:407–411. https://doi.org/10.1007/s10311-012-0369-z
Guzman MS, Rengasamy K, Binkley MM et al (2019) Phototrophic extracellular electron uptake is linked to carbon dioxide fixation in the bacterium Rhodopseudomonas palustris. Nat Commun 10:1–13. https://doi.org/10.1038/s41467-019-09377-6
Gwak J-H, Awala SI, Nguyen N-L et al (2022) Sulfur and methane oxidation by a single microorganism. Proc Natl Acad Sci 119:e2114799119. https://doi.org/10.1073/pnas.2114799119
Hamdan HZ, Salam DA (2023) Sediment microbial fuel cells for bioremediation of pollutants and power generation: a review. Environ Chem Lett 21:2761–2787. https://doi.org/10.1007/s10311-023-01625-y
He Z, Cai C, Wang J et al (2016) A novel denitrifying methanotroph of the NC10 phylum and its microcolony. Sci Rep 6:32241. https://doi.org/10.1038/srep32241
Heaton TJ, Bard E, Bronk Ramsey C et al (2021) Radiocarbon: a key tracer for studying Earth’s dynamo, climate system, carbon cycle, and Sun. Science 374:eabd7096. https://doi.org/10.1126/science.abd7096
Heintzmann R, Huser T (2017) Super-resolution structured illumination microscopy. Chem Rev 117:13890–13908. https://doi.org/10.1021/acs.chemrev.7b00218
Hengge R (2020) Linking bacterial growth, survival, and multicellularity—small signaling molecules as triggers and drivers. Curr Opin Microbiol 55:57–66. https://doi.org/10.1016/j.mib.2020.02.007
Hou L, Xi J, Chen X et al (2019) Biodegradability and ecological impacts of polyethylene-based mulching film at agricultural environment. J Hazard Mater 378:120774. https://doi.org/10.1016/j.jhazmat.2019.120774
Huang H, Chen H-P, Kopittke PM et al (2021a) The voltaic effect as a novel mechanism controlling the remobilization of cadmium in paddy soils during drainage. Environ Sci Technol 55:1750–1758. https://doi.org/10.1021/acs.est.0c06561
Huang L, Yu Q, Liu W et al (2021b) Molecular determination of organic adsorption sites on smectite during Fe redox processes using ToF-SIMS analysis. Environ Sci Technol 55:7123–7134. https://doi.org/10.1021/acs.est.0c08407
Huang L, Liu X, Zhang Z et al (2022) Light-driven carbon dioxide reduction to methane by Methanosarcina barkeri in an electric syntrophic coculture. ISME J 16:370–377. https://doi.org/10.1038/s41396-021-01078-7
Hünninghaus M, Dibbern D, Kramer S et al (2019) Disentangling carbon flow across microbial kingdoms in the rhizosphere of maize. Soil Biol Biochem 134:122–130. https://doi.org/10.1016/j.soilbio.2019.03.007
Hyder S, Rizvi ZF, los Santos-Villalobos SD et al (2023) Applications of plant growth-promoting rhizobacteria for increasing crop production and resilience. J Plant Nutr. https://doi.org/10.1080/01904167.2022.2160742
Jansson JK, Hofmockel KS (2018) The soil microbiome—from metagenomics to metaphenomics. Curr Opin Microbiol 43:162–168. https://doi.org/10.1016/j.mib.2018.01.013
Jansson JK, Hofmockel KS (2020) Soil microbiomes and climate change. Nat Rev Microbiol 18:35–46. https://doi.org/10.1038/s41579-019-0265-7
Jassey VEJ, Walcker R, Kardol P et al (2022) Contribution of soil algae to the global carbon cycle. New Phytol 234:64–76. https://doi.org/10.1111/nph.17950
Joshi VS, Kreth J, Koley D (2017a) Pt-decorated MWCNTs–ionic liquid composite-based hydrogen peroxide sensor to study microbial metabolism using scanning electrochemical microscopy. Anal Chem 89:7709–7718. https://doi.org/10.1021/acs.analchem.7b01677
Joshi VS, Sheet PS, Cullin N et al (2017b) Real-time metabolic interactions between two bacterial species using a carbon-based pH microsensor as a scanning electrochemical microscopy probe. Anal Chem 89:11044–11052. https://doi.org/10.1021/acs.analchem.7b03050
Kallenbach CM, Frey SD, Grandy AS (2016) Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls. Nat Commun 7:1–10. https://doi.org/10.1038/ncomms13630
Kearns DB (2010) A field guide to bacterial swarming motility. Nat Rev Microbiol 8:634–644. https://doi.org/10.1038/nrmicro2405
Khan N, Muge E, Mulaa FJ et al (2023) Mycelial nutrient transfer promotes bacterial co-metabolic organochlorine pesticide degradation in nutrient-deprived environments. ISME J. https://doi.org/10.1038/s41396-023-01371-7
Klassen A, Faccio AT, Canuto GAB et al (2017) Metabolomics: definitions and significance in systems biology. Springer, Cham
Kleber M, Bourg IC, Coward EK et al (2021) Dynamic interactions at the mineral–organic matter interface. Nat Rev Earth Environ 2:402–421. https://doi.org/10.1038/s43017-021-00162-y
Klementiev AD, Jin Z, Whiteley M (2020) Micron scale spatial measurement of the O2 gradient surrounding a bacterial biofilm in real time. Mbio 11:e02536-20. https://doi.org/10.1128/mBio.02536-20
Knight R, Vrbanac A, Taylor BC et al (2018) Best practices for analysing microbiomes. Nat Rev Microbiol 16:410–422. https://doi.org/10.1038/s41579-018-0029-9
Kreutzberger MAB, Sobe RC, Sauder AB et al (2022) Flagellin outer domain dimerization modulates motility in pathogenic and soil bacteria from viscous environments. Nat Commun 13:1422. https://doi.org/10.1038/s41467-022-29069-y
Leu AO, Cai C, McIlroy SJ et al (2020a) Anaerobic methane oxidation coupled to manganese reduction by members of the methanoperedenaceae. ISME J 14:1030–1041. https://doi.org/10.1038/s41396-020-0590-x
Leu AO, McIlroy SJ, Ye J et al (2020b) Lateral gene transfer drives metabolic flexibility in the anaerobic methane-oxidizing archaeal family methanoperedenaceae. Mbio 11:e01325-e1420. https://doi.org/10.1128/mBio.01325-20
Li R, Jiang Y, Xi B et al (2018) Raw hematite based Fe(III) bio-reduction process for humified landfill leachate treatment. J Hazard Mater 355:10–16. https://doi.org/10.1016/j.jhazmat.2018.05.002
Li H, Su J-Q, Yang X-R et al (2019) RNA stable isotope probing of potential feammox population in paddy soil. Environ Sci Technol 53:4841–4849. https://doi.org/10.1021/acs.est.8b05016
Li Z-Y, Li X, Tan B et al (2020) NC10 bacteria promoted methane oxidation coupled to chlorate reduction. Biodegradation 31:319–329. https://doi.org/10.1007/s10532-020-09912-z
Li C, Hurley A, Hu W et al (2021) Social motility of biofilm-like microcolonies in a gliding bacterium. Nat Commun 12:5700. https://doi.org/10.1038/s41467-021-25408-7
Li R, Wang J, Li T, Zhou Q (2022a) Recent advances in improving the remediation performance of microbial electrochemical systems for contaminated soil and sediments. Crit Rev Environ Sci Technol. https://doi.org/10.1080/10643389.2022.2040327
Li W, Siddique MS, Graham N, Yu W (2022b) Influence of temperature on biofilm formation mechanisms using a gravity-driven membrane (GDM) system: insights from microbial community structures and metabolomics. Environ Sci Technol 56:8908–8919. https://doi.org/10.1021/acs.est.2c01243
Liang C, Schimel JP, Jastrow JD (2017) The importance of anabolism in microbial control over soil carbon storage. Nat Microbiol 2:1–6. https://doi.org/10.1038/nmicrobiol.2017.105
Liang C, Amelung W, Lehmann J, Kästner M (2019) Quantitative assessment of microbial necromass contribution to soil organic matter. Glob Change Biol 25:3578–3590. https://doi.org/10.1111/gcb.14781
Liao H, Hao X, Qin F et al (2023) Microbial autotrophy explains large-scale soil CO2 fixation. Glob Change Biol 29:231–242. https://doi.org/10.1111/gcb.16452
Lin Z-Q, Shao W, Xu J, Sheng G-P (2019) Accurately quantifying the reductive capacity of microbial extracellular polymeric substance by mediated electrochemical oxidation method. Sci Total Environ 673:541–545. https://doi.org/10.1016/j.scitotenv.2019.04.130
Liu X, Ramsey MM, Chen X et al (2011) Real-time mapping of a hydrogen peroxide concentration profile across a polymicrobial bacterial biofilm using scanning electrochemical microscopy. Proc Natl Acad Sci 108:2668–2673. https://doi.org/10.1073/pnas.1018391108
Liu L, Li W, Song W, Guo M (2018) Remediation techniques for heavy metal-contaminated soils: principles and applicability. Sci Total Environ 633:206–219. https://doi.org/10.1016/j.scitotenv.2018.03.161
Liu X, Huang L, Rensing C et al (2021) Syntrophic interspecies electron transfer drives carbon fixation and growth by Rhodopseudomonas palustris under dark, anoxic conditions. Sci Adv 7:eabh1852. https://doi.org/10.1126/sciadv.abh1852
López HM, Gachelin J, Douarche C et al (2015) Turning bacteria suspensions into superfluids. Phys Rev Lett 115:028301. https://doi.org/10.1103/PhysRevLett.115.028301
Lv X, Jin K, Sun G et al (2022) Microscopy imaging of living cells in metabolic engineering. Trends Biotechnol 40:752–765. https://doi.org/10.1016/j.tibtech.2021.10.010
Ma W, Peng D, Walker SL et al (2017) Bacillus subtilis biofilm development in the presence of soil clay minerals and iron oxides. NPJ Biofilms Microbiomes 3:1–9. https://doi.org/10.1038/s41522-017-0013-6
MacLeod M, Arp HPH, Tekman MB, Jahnke A (2021) The global threat from plastic pollution. Science 373:61–65. https://doi.org/10.1126/science.abg5433
Maier S, Tamm A, Wu D et al (2018) Photoautotrophic organisms control microbial abundance, diversity, and physiology in different types of biological soil crusts. ISME J 12:1032–1046. https://doi.org/10.1038/s41396-018-0062-8
Marks RG, Jochmann MA, Brand WA, Schmidt TC (2022) How to couple LC-IRMS with HRMS─ a proof-of-concept study. Anal Chem 94:2981–2987. https://doi.org/10.1021/acs.analchem.1c05226
McGivern BB, Tfaily MM, Borton MA et al (2021) Decrypting bacterial polyphenol metabolism in an anoxic wetland soil. Nat Commun 12:2466. https://doi.org/10.1038/s41467-021-22765-1
McIlroy SJ, Leu AO, Zhang X et al (2023) Anaerobic methanotroph ‘candidatus methanoperedens nitroreducens’ has a pleomorphic life cycle. Nat Microbiol 8:321–331. https://doi.org/10.1038/s41564-022-01292-9
Mestre M, Höfer J (2021) The microbial conveyor belt: connecting the globe through dispersion and dormancy. Trends Microbiol 29:482–492. https://doi.org/10.1016/j.tim.2020.10.007
Mo F, Song C, Zhou Q et al (2023) The optimized Fenton-like activity of Fe single-atom sites by Fe atomic clusters–mediated electronic configuration modulation. Proc Natl Acad Sci 120:e2300281120. https://doi.org/10.1073/pnas.2300281120
Moinet GYK, Hijbeek R, van Vuuren DP, Giller KE (2023) Carbon for soils, not soils for carbon. Glob Change Biol. https://doi.org/10.1111/gcb.16570
Monachon M, Albelda-Berenguer M, Joseph E (2019) Chapter one—biological oxidation of iron sulfides. In: Gadd GM, Sariaslani S (eds) Advances in applied microbiology. Academic Press, New York, pp 1–27
Moore-Ott JA, Chiu S, Amchin DB et al (2022) A biophysical threshold for biofilm formation. Elife 11:e76380. https://doi.org/10.7554/eLife.76380
Muñoz-Dorado J, Marcos-Torres FJ, García-Bravo E et al (2016) Myxobacteria: moving, killing, feeding, and surviving together. Front Microbiol. https://doi.org/10.3389/fmicb.2016.00781
Murguia-Flores F, Ganesan AL, Arndt S, Hornibrook ERC (2021) Global uptake of atmospheric methane by soil from 1900 to 2100. Glob Biogeochem Cycles 35:e2020GB006774. https://doi.org/10.1029/2020GB006774
Němcová L, Bystrianský L, Hujslová M et al (2022) Detection of biofilm and planktonic microbial communities in litter/soil mixtures. Appl Soil Ecol 179:104589. https://doi.org/10.1016/j.apsoil.2022.104589
Neu J, Shipps CC, Guberman-Pfeffer MJ et al (2022) Microbial biofilms as living photoconductors due to ultrafast electron transfer in cytochrome OmcS nanowires. Nat Commun 13:5150. https://doi.org/10.1038/s41467-022-32659-5
Nunan N (2017) The microbial habitat in soil: Scale, heterogeneity and functional consequences. J Plant Nutr Soil Sci 180:425–429. https://doi.org/10.1002/jpln.201700184
Op De Beeck M, Persson P, Tunlid A (2021) Fungal extracellular polymeric substance matrices—highly specialized microenvironments that allow fungi to control soil organic matter decomposition reactions. Soil Biol Biochem 159:108304. https://doi.org/10.1016/j.soilbio.2021.108304
Or D, Smets BF, Wraith JM et al (2007) Physical constraints affecting bacterial habitats and activity in unsaturated porous media—a review. Adv Water Resour 30:1505–1527. https://doi.org/10.1016/j.advwatres.2006.05.025
Papenfort K, Bassler BL (2016) Quorum sensing signal–response systems in Gram-negative bacteria. Nat Rev Microbiol 14:576–588. https://doi.org/10.1038/nrmicro.2016.89
Peng M-W, Qi J, Yan P et al (2022) Insight into the structure and metabolic function of iron-rich nanoparticles in anammox bacteria. Sci Total Environ 806:150879. https://doi.org/10.1016/j.scitotenv.2021.150879
Pereira J, de Nooy S, Sleutels T, ter Heijne A (2022) Opportunities for visual techniques to determine characteristics and limitations of electro-active biofilms. Biotechnol Adv 60:108011. https://doi.org/10.1016/j.biotechadv.2022.108011
Posada LF, Álvarez JC, Romero-Tabarez M et al (2018) Enhanced molecular visualization of root colonization and growth promotion by Bacillus subtilis EA-CB0575 in different growth systems. Microbiol Res 217:69–80. https://doi.org/10.1016/j.micres.2018.08.017
Pucetaite M, Hitchcock A, Obst M et al (2022) Nanoscale chemical mapping of exometabolites at fungal–mineral interfaces. Geobiology 20:650–666. https://doi.org/10.1111/gbi.12504
Qian Y, Chen K, Liu Y, Li J (2019) Assessment of hexachlorcyclohexane biodegradation in contaminated soil by compound-specific stable isotope analysis. Environ Pollut 254:113008. https://doi.org/10.1016/j.envpol.2019.113008
Qian L, Ye X, Xiao J et al (2022) Nitrogen concentration acting as an environmental signal regulates cyanobacterial EPS excretion. Chemosphere 291:132878. https://doi.org/10.1016/j.chemosphere.2021.132878
Qin S, Yu L, Yang Z et al (2019) Electrodes donate electrons for nitrate reduction in a soil matrix via DNRA and denitrification. Environ Sci Technol 53:2002–2012. https://doi.org/10.1021/acs.est.8b03606
Qu C, Qian S, Chen L et al (2019) Size-dependent bacterial toxicity of hematite particles. Environ Sci Technol 53:8147–8156. https://doi.org/10.1021/acs.est.9b00856
Rathod J, Jean J-S, Jiang W-T et al (2019) Micro-colonization of arsenic-resistant Staphylococcus sp. As-3 on arsenopyrite (FeAsS) drives arsenic mobilization under anoxic sub-surface mimicking conditions. Sci Total Environ 669:527–539. https://doi.org/10.1016/j.scitotenv.2019.03.084
Rumbaugh KP, Sauer K (2020) Biofilm dispersion. Nat Rev Microbiol 18:571–586. https://doi.org/10.1038/s41579-020-0385-0
Sankaran J, Karampatzakis A, Rice SA, Wohland T (2018) Quantitative imaging and spectroscopic technologies for microbiology. FEMS Microbiol Lett 365:fny075. https://doi.org/10.1093/femsle/fny075
Schaible GA, Kohtz AJ, Cliff J, Hatzenpichler R (2022) Correlative SIP-FISH-Raman-SEM-NanoSIMS links identity, morphology, biochemistry, and physiology of environmental microbes. ISME Commun 2:1–10. https://doi.org/10.1038/s43705-022-00134-3
Shrestha HK, Appidi MR, Villalobos Solis MI et al (2021) Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance. BMC Microbiol 21:1–17. https://doi.org/10.1186/s12866-021-02370-4
Singh R, Paul D, Jain RK (2006) Biofilms: implications in bioremediation. Trends Microbiol 14:389–397. https://doi.org/10.1016/j.tim.2006.07.001
Sokol NW, Bradford MA (2019) Microbial formation of stable soil carbon is more efficient from belowground than aboveground input. Nat Geosci 12:46–53. https://doi.org/10.1038/s41561-018-0258-6
Srisawat P, Higuchi-Takeuchi M, Numata K (2022) Microbial autotrophic biorefineries: perspectives for biopolymer production. Polym J 54:1139–1151. https://doi.org/10.1038/s41428-022-00675-3
Tang FHM, Lenzen M, McBratney A, Maggi F (2021) Risk of pesticide pollution at the global scale. Nat Geosci 14:206–210. https://doi.org/10.1038/s41561-021-00712-5
Tang S, Ma Q, Zhou J et al (2023) Use of untargeted metabolomics to analyse changes in extractable soil organic matter in response to long-term fertilisation. Biol Fertil Soils 59:301–316. https://doi.org/10.1007/s00374-023-01706-8
Tao F, Huang Y, Hungate BA et al (2023) Microbial carbon use efficiency promotes global soil carbon storage. Nature. https://doi.org/10.1038/s41586-023-06042-3
Täumer J, Marhan S, Groß V et al (2022) Linking transcriptional dynamics of CH4-cycling grassland soil microbiomes to seasonal gas fluxes. ISME J 16:1788–1797. https://doi.org/10.1038/s41396-022-01229-4
Tecon R, Or D (2017) Biophysical processes supporting the diversity of microbial life in soil. FEMS Microbiol Rev 41:599–623. https://doi.org/10.1093/femsre/fux039
Teng Z, Shao W, Zhang K et al (2019) Pb biosorption by Leclercia adecarboxylata: protective and immobilized mechanisms of extracellular polymeric substances. Chem Eng J 375:122113. https://doi.org/10.1016/j.cej.2019.122113
Tian Z, Vila J, Yu M et al (2018) Tracing the biotransformation of polycyclic aromatic hydrocarbons in contaminated soil using stable isotope-assisted metabolomics. Environ Sci Technol Lett. https://doi.org/10.1021/acs.estlett.7b00554
Tian T, Sun B, Shi H et al (2021) Sucrose triggers a novel signaling cascade promoting Bacillus subtilis rhizosphere colonization. ISME J 15:2723–2737. https://doi.org/10.1038/s41396-021-00966-2
Torrentó C, Ponsin V, Lihl C et al (2021) Triple-element compound-specific stable isotope analysis (3D-CSIA): added value of Cl isotope ratios to assess herbicide degradation. Environ Sci Technol 55:13891–13901. https://doi.org/10.1021/acs.est.1c03981
Turkowyd B, Virant D, Endesfelder U (2016) From single molecules to life: microscopy at the nanoscale. Anal Bioanal Chem 408:6885–6911. https://doi.org/10.1007/s00216-016-9781-8
Tveit AT, Hestnes AG, Robinson SL et al (2019) Widespread soil bacterium that oxidizes atmospheric methane. Proc Natl Acad Sci 116:8515–8524. https://doi.org/10.1073/pnas.1817812116
Ummadi JG, Downs CJ, Joshi VS et al (2016) Carbon-based solid-state calcium ion-selective microelectrode and scanning electrochemical microscopy: a quantitative study of pH-dependent release of calcium ions from bioactive glass. Anal Chem 88:3218–3226. https://doi.org/10.1021/acs.analchem.5b04614
Védère C, Vieublé Gonod L, Nunan N, Chenu C (2022) Opportunities and limits in imaging microorganisms and their activities in soil microhabitats. Soil Biol Biochem 174:108807. https://doi.org/10.1016/j.soilbio.2022.108807
Vert M, Doi Y, Hellwich K-H et al (2012) Terminology for biorelated polymers and applications (IUPAC Recommendations 2012). Pure Appl Chem 84:377–410. https://doi.org/10.1351/PAC-REC-10-12-04
Viacava K, Qiao J, Janowczyk A et al (2022) Meta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacterium. ISME J 16:1740–1749. https://doi.org/10.1038/s41396-022-01220-z
Vondrák J, Svoboda S, Zíbarová L et al (2023) Alcobiosis, an algal-fungal association on the threshold of lichenisation. Sci Rep 13:2957. https://doi.org/10.1038/s41598-023-29384-4
Wadhwa N, Berg HC (2022) Bacterial motility: machinery and mechanisms. Nat Rev Microbiol 20:161–173. https://doi.org/10.1038/s41579-021-00626-4
Walker WS, Gorelik SR, Cook-Patton SC et al (2022) The global potential for increased storage of carbon on land. Proc Natl Acad Sci 119:e2111312119. https://doi.org/10.1073/pnas.2111312119
Wang J, Li J-H (2022) Scanning transmission X-ray microscopy at the Canadian light source: progress and selected applications in geosciences. At Spectrosc 43:84–98
Wang F, Gu Y, O’Brien JP et al (2019) Structure of microbial nanowires reveals stacked hemes that transport electrons over micrometers. Cell 177:361-369.e10. https://doi.org/10.1016/j.cell.2019.03.029
Wang B, An S, Liang C et al (2021a) Microbial necromass as the source of soil organic carbon in global ecosystems. Soil Biol Biochem 162:108422. https://doi.org/10.1016/j.soilbio.2021.108422
Wang Y, Liu Y, Zheng K et al (2021b) The role of extracellular polymeric substances (EPS) in the reduction of Cr(VI) by Pannonibacter phragmitetus BB. J Environ Chem Eng 9:106163. https://doi.org/10.1016/j.jece.2021.106163
Wang H, Yang M, Liu K et al (2022a) Insights into the synergy between functional microbes and dissolved oxygen partition in the single-stage partial nitritation-anammox granules system. Biores Technol 347:126364. https://doi.org/10.1016/j.biortech.2021.126364
Wang Q, Kalathil S, Pornrungroj C et al (2022b) Bacteria–photocatalyst sheet for sustainable carbon dioxide utilization. Nat Catal 5:633–641. https://doi.org/10.1038/s41929-022-00817-z
Wang Y, Fu M, Wu B et al (2022c) Insight into biofilm-forming patterns: biofilm-forming conditions and dynamic changes in extracellular polymer substances. Environ Sci Pollut Res. https://doi.org/10.1007/s11356-022-21645-5
Wang H, Yang D, Chen Y, Dai X (2023a) Improving the anammox performance in municipal wastewater treatment based on the powder functional carriers: a critical review. Chem Eng J 470:144167. https://doi.org/10.1016/j.cej.2023.144167
Wang G, Yu G, Chi T et al (2023b) Insights into the enhanced effect of biochar on cadmium removal in vertical flow constructed wetlands. J Hazard Mater 443:130148. https://doi.org/10.1016/j.jhazmat.2022.130148
Waschulin V, Borsetto C, James R et al (2022) Biosynthetic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing. ISME J 16:101–111. https://doi.org/10.1038/s41396-021-01052-3
Whalen ED, Grandy AS, Sokol NW et al (2022) Clarifying the evidence for microbial- and plant-derived soil organic matter, and the path toward a more quantitative understanding. Glob Change Biol 28:7167–7185. https://doi.org/10.1111/gcb.16413
Wiederhold JG (2015) Metal stable isotope signatures as tracers in environmental geochemistry. Environ Sci Technol 49:2606–2624. https://doi.org/10.1021/es504683e
Wilpiszeski RL, Aufrecht JA, Retterer ST et al (2019) Soil aggregate microbial communities: towards understanding microbiome interactions at biologically relevant scales. Appl Environ Microbiol 85:e00324-e419. https://doi.org/10.1128/AEM.00324-19
Wisnoski NI, Lennon JT (2022) Scaling up and down: movement ecology for microorganisms. Trends Microbiol. https://doi.org/10.1016/j.tim.2022.09.016
Woodcroft BJ, Singleton CM, Boyd JA et al (2018) Genome-centric view of carbon processing in thawing permafrost. Nature 560:49–54. https://doi.org/10.1038/s41586-018-0338-1
Wu Y, Cai P, Jing X et al (2019) Soil biofilm formation enhances microbial community diversity and metabolic activity. Environ Int 132:105116. https://doi.org/10.1016/j.envint.2019.105116
Wu C, Ma Y, Wang D et al (2022) Integrated microbiology and metabolomics analysis reveal plastic mulch film residue affects soil microorganisms and their metabolic functions. J Hazard Mater 423:127258. https://doi.org/10.1016/j.jhazmat.2021.127258
Xiao J, Dufrêne YF (2016) Optical and force nanoscopy in microbiology. Nat Microbiol 1:1–13. https://doi.org/10.1038/nmicrobiol.2016.186
Xiao Y, Zhang E, Zhang J et al (2017) Extracellular polymeric substances are transient media for microbial extracellular electron transfer. Sci Adv 3:e1700623. https://doi.org/10.1126/sciadv.1700623
Xiao K-Q, Ge T-D, Wu X-H et al (2021) Metagenomic and 14C tracing evidence for autotrophic microbial CO2 fixation in paddy soils. Environ Microbiol 23:924–933. https://doi.org/10.1111/1462-2920.15204
Xiao K-Q, Zhao Y, Liang C et al (2023) Introducing the soil mineral carbon pump. Nat Rev Earth Environ 4:135–136. https://doi.org/10.1038/s43017-023-00396-y
Xu X, Thornton PE, Post WM (2013) A global analysis of soil microbial biomass carbon, nitrogen and phosphorus in terrestrial ecosystems. Glob Ecol Biogeogr 22:737–749. https://doi.org/10.1111/geb.12029
Xu L, Dong Z, Chiniquy D et al (2021) Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics. Nat Commun 12:3209. https://doi.org/10.1038/s41467-021-23553-7
Yagüe P, Willemse J, Koning RI et al (2016) Subcompartmentalization by cross-membranes during early growth of Streptomyces hyphae. Nat Commun 7:1–11. https://doi.org/10.1038/ncomms12467
Yalcin SE, O’Brien JP, Gu Y et al (2020) Electric field stimulates production of highly conductive microbial OmcZ nanowires. Nat Chem Biol 16:1136–1142. https://doi.org/10.1038/s41589-020-0623-9
Yan H, Liu C, Yu W et al (2023) The aggregate distribution of Pseudomonas aeruginosa on biochar facilitate quorum sensing and biofilm formation. Sci Total Environ 856:159034. https://doi.org/10.1016/j.scitotenv.2022.159034
Yang Y, Wang Z, Gan C et al (2021) Long-distance electron transfer in a filamentous Gram-positive bacterium. Nat Commun 12:1709. https://doi.org/10.1038/s41467-021-21709-z
Yang G, Ryo M, Roy J et al (2022) Multiple anthropogenic pressures eliminate the effects of soil microbial diversity on ecosystem functions in experimental microcosms. Nat Commun 13:4260. https://doi.org/10.1038/s41467-022-31936-7
Yang W, Shen L, Bai Y (2023) Role and regulation of anaerobic methane oxidation catalyzed by NC10 bacteria and ANME-2d archaea in various ecosystems. Environ Res 219:115174. https://doi.org/10.1016/j.envres.2022.115174
Ye D, Li X, Shen J, Xia X (2022) Microbial metabolomics: From novel technologies to diversified applications. TrAC Trends Anal Chem 148:116540. https://doi.org/10.1016/j.trac.2022.116540
Yi Q, Wu S, Southam G et al (2021) Acidophilic iron- and sulfur-oxidizing bacteria, Acidithiobacillus ferrooxidans, drives alkaline pH neutralization and mineral weathering in Fe ore tailings. Environ Sci Technol 55:8020–8034. https://doi.org/10.1021/acs.est.1c00848
Yu Z, Fischer R (2019) Light sensing and responses in fungi. Nat Rev Microbiol 17:25–36. https://doi.org/10.1038/s41579-018-0109-x
Yu H, Leadbetter JR (2020) Bacterial chemolithoautotrophy via manganese oxidation. Nature 583:453–458. https://doi.org/10.1038/s41586-020-2468-5
Yu GL, Wang GL, Li JB et al (2020) Enhanced Cd2+ and Zn2+ removal from heavy metal wastewater in constructed wetlands with resistant microorganisms. Bioresour Technol 316:123898. https://doi.org/10.1016/j.biortech.2020.123898
Yu GL, Wang GL, Chi TY et al (2022) Enhanced removal of heavy metals and metalloids by constructed wetlands: a review of approaches and mechanisms. Sci Total Environ 821:153516. https://doi.org/10.1016/j.scitotenv.2022.153516
Yuan S, Yu Z, Pan S et al (2020) Deciphering the succession dynamics of dominant and rare genera in biofilm development process. Sci Total Environ 739:139961. https://doi.org/10.1016/j.scitotenv.2020.139961
Zhang H, Zhou Z (2018) Recalcitrant carbon controls the magnitude of soil organic matter mineralization in temperate forests of northern China. For Ecosyst 5:17. https://doi.org/10.1186/s40663-018-0137-z
Zhang X, Huang W, Wang X et al (2011) Biofilm-electrode process with high efficiency for degradation of 2,4-dichlorophenol. Environ Chem Lett 9:383–388. https://doi.org/10.1007/s10311-010-0290-2
Zhang P, Misra S, Guo Z et al (2019) Stable isotope labeling of metal/metal oxide nanomaterials for environmental and biological tracing. Nat Protoc 14:2878–2899. https://doi.org/10.1038/s41596-019-0205-z
Zhang T, Shi X-C, Ding R et al (2020) The hidden chemolithoautotrophic metabolism of Geobacter sulfurreducens uncovered by adaptation to formate. ISME J 14:2078–2089. https://doi.org/10.1038/s41396-020-0673-8
Zhang J-W, Dong H-P, Hou L-J et al (2021a) Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway. ISME J 15:1826–1843. https://doi.org/10.1038/s41396-020-00890-x
Zhang W, Gregory AS, Whalley WR et al (2021b) Characteristics of soil organic matter within an erosional landscape under agriculture in Northeast China: stock, source, and thermal stability. Soil Tillage Res 209:104927. https://doi.org/10.1016/j.still.2020.104927
Zhang X, Li R, Song J et al (2021c) Combined phyto-microbial-electrochemical system enhanced the removal of petroleum hydrocarbons from soil: a profundity remediation strategy. J Hazard Mater 420:126592. https://doi.org/10.1016/j.jhazmat.2021.126592
Zhang K, Schumacher L, Maltais-Landry G et al (2022a) Integrating perennial bahiagrass into the conventional rotation of cotton and peanut enhances interactions between microbial and nematode communities. Appl Soil Ecol 170:104254. https://doi.org/10.1016/j.apsoil.2021.104254
Zhang X, Li R, Wang J et al (2022b) Construction of conductive network using magnetite to enhance microflora interaction and petroleum hydrocarbons removal in plant-rhizosphere microbial electrochemical system. Chem Eng J 433:133600. https://doi.org/10.1016/j.cej.2021.133600
Zhou Q, Li D, Wang T, Hu X (2021) Leaching of graphene oxide nanosheets in simulated soil and their influences on microbial communities. J Hazard Mater 404:124046. https://doi.org/10.1016/j.jhazmat.2020.124046
Zhou Q, Song C, Wang P et al (2023) Generating dual-active species by triple-atom sites through peroxymonosulfate activation for treating micropollutants in complex water. Proc Natl Acad Sci 120:e2300085120. https://doi.org/10.1073/pnas.2300085120
Zhu G, Liu W, Wen Y et al (2021) Potential of arsenate-reducing bacterial inoculants to enhance field-scale remediation of arsenic contaminated soils by Pteris vittata L. Ecol Eng 169:106312. https://doi.org/10.1016/j.ecoleng.2021.106312
Acknowledgements
We wish to acknowledge the support of the National Natural Science Foundation of China as a young scholar project (52100189), the National Key R&D Program of China (grant No. 2023YFC3709001), and the National Natural Science Foundation of China as a Shandong joint project (grant No. U1906222).
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Wang, G., Li, T., Zhou, Q. et al. Characterization and environmental applications of soil biofilms: a review. Environ Chem Lett (2024). https://doi.org/10.1007/s10311-024-01735-1
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DOI: https://doi.org/10.1007/s10311-024-01735-1