Abstract
Biochar and mineral-enriched biochar (MEB) have been used as soil amendments to improve soil fertility, sequester carbon and mitigate greenhouse gas emissions. Such beneficial outcomes could be partially mediated by soil bacteria, however little is known about how they directly interact with biochar or MEB. We therefore analyzed the diversity and functions of bacterial communities on the surfaces of one biochar and two different MEBs after a 140-day incubation in soil. The results show that the biochar and the MEBs harbor distinct bacterial communities to the bulk soil. Communities on biochar and MEBs were dominated by a novel Gammaproteobacterium. Genome reconstruction combined with electron microscopy and high-resolution elemental analysis revealed that the bacterium generates energy from the oxidation of iron that is present on the surface. Two other bacteria belonging to the genus Thiobacillus and a novel group within the Oxalbacteraceae were enriched only on the MEBs and they had the genetic capacity for thiosulfate oxidation. All three surface-enriched bacteria also had the capacity to fix carbon dioxide, either in a potentially strictly autotrophic or mixotrophic manner. Our results show the dominance of chemolithotrophic processes on the surface of biochar and MEB that can contribute to carbon sequestration in soil.
Similar content being viewed by others
Log in or create a free account to read this content
Gain free access to this article, as well as selected content from this journal and more on nature.com
or
References
Abujabhah IS, Bound SA, Doyle R, Bowman JP . (2016). Effects of biochar and compost amendments on soil physico-chemical properties and the total community within a temperate agricultural soil. Appl Soil Ecol 98: 243–253.
Almeida TP, Kasama T, Muxworthy AR, Williams W, Nagy L, Hansen TW et al. (2014). Visualized effect of oxidation on magnetic recording fidelity in pseudo-single-domain magnetite particles. Nat Commun 5: 5154.
Anderson CR, Condron LM, Clough TJ, Fiers M, Stewart A, Hill RA et al. (2011). Biochar induced soil microbial community change: implications for biogeochemical cycling of carbon, nitrogen and phosphorus. Pedobiologia 54: 309–320.
Anderson MJ, Gorley RN, Clarke KR . (2008) PERMANOVA+for PRIMER: Guide to Software and Statistical Methods 1st edn, PRIMER-E Ltd: Plymouth, UK.
Aulenta F, Rossetti S, Amalfitano S, Majone M, Tandoi V . (2013). Conductive magnetite nanoparticles accelerate the microbial reductive dechlorination of trichloroethene by promoting interspecies electron transfer processes. ChemSusChem 6: 433–436.
Badger MR, Bek EJ . (2008). Multiple Rubisco forms in proteobacteria: their functional significance in relation to CO2 acquisition by the CBB cycle. J Exp Bot 59: 1525–1541.
Bardgett RD, van der Putten WH . (2014). Belowground biodiversity and ecosystem functioning. Nature 515: 505–511.
Bird LJ, Bonnefoy V, Newman DK . (2011). Bioenergetic challenges of microbial iron metabolisms. Trends Microbiol 19: 330–340.
Bruun EW, Hauggaard-Nielsen H, Ibrahim N, Egsgaard H, Ambus P, Jensen PA et al. (2011). Influence of fast pyrolysis temperature on biochar labile fraction and short-term carbon loss in a loamy soil. Biomass Bioenergy 35: 1182–1189.
Buschmann S, Warkentin E, Xie H, Langer JD, Ermler U, Michel H . (2010). The structure of cbb3 cytochrome oxidase provides insights into proton pumping. Science 329: 327–330.
Cabiscol E, Tamarit J, Ros J . (2010). Oxidative stress in bacteria and protein damage by reactive oxygen species. Int Microbiol 3: 3–8.
Cao X, Ma L, Liang Y, Gao B, Harris W . (2011). Simultaneous immobilization of lead and atrazine in contaminated soils using dairy-manure biochar. Environ Sci Technol 45: 4884–4889.
Carrondo MA . (2003). Ferritins, iron uptake and storage from the bacterioferritin viewpoint. EMBO J 22: 1959–1968.
Chen S-Y, Gloter A, Zobelli A, Wang L, Chen C-H, Colliex C . (2009). Electron energy loss spectroscopy and ab initio investigation of iron oxide nanomaterials grown by a hydrothermal process. Phys Rev B 79: 104103.
Chia C, Munroe P, Joseph S, Lin Y, Lehmann J, Muller D et al. (2012). Analytical electron microscopy of black carbon and microaggregated mineral matter in Amazonian dark Earth. J Microsc 245: 129–139.
Chia CH, Singh BP, Joseph S, Graber ER, Munroe P . (2014). Characterization of an enriched biochar. J Anal Appl Pyrol 108: 26–34.
Chia CH, Downie A, Munroe P . (2015) Characteristics of biochar: physical and structural properties. In: Lehmann J, Joseph S (eds). Biochar for Environmental Management: Science and Technology 2nd edn, Earthscan Books Ltd: London, pp 89–109.
Clarke TA, Edwards MJ, Gates AJ, Hall A, White GF, Bradley J et al. (2011). Structure of a bacterial cell surface decaheme electron conduit. Proc Natl Acad Sci USA 108: 9384–9389.
Cotter PA, Chepuri V, Gennis R, Gunsalus R . (1990). Cytochrome o (cyoABCDE) and d (cydAB) oxidase gene expression in Escherichia coli is regulated by oxygen, pH, and the fnr gene product. J Bacteriol 172: 6333–6338.
Darling AE, Jospin G, Lowe E, Matsen FA IV, Bik HM, Eisen JA . (2014). PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2: e243.
Ding G-C, Pronk GJ, Babin D, Heuer H, Heister K, Kögel-Knabner I et al. (2013). Mineral composition and charcoal determine the bacterial community structure in artificial soils. FEMS Microbiol Ecol 86: 15–25.
Ehrhardt C, Haymon R, Sievert SM, Holden P . (2009). An improved method for nanogold in situ hybridization visualized with environmental scanning electron microscopy. J Microsc 236: 5–10.
Feng Y, Xu Y, Yu Y, Xie Z, Lin X . (2012). Mechanisms of biochar decreasing methane emission from Chinese paddy soils. Soil Biol Biochem 46: 80–88.
Fierer N, Jackson RB . (2006). The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 103: 626–631.
Friedrich CG, Quentmeier A, Bardischewsky F, Rother D, Kraft R, Kostka S et al. (2000). Novel genes coding for lithotrophic sulfur oxidation of Paracoccus pantotrophus GB17. J Bacteriol 182: 4677–4687.
Friedrich CG, Bardischewsky F, Rother D, Quentmeier A, Fischer J . (2005). Prokaryotic sulfur oxidation. Curr Opin Microbiol 8: 253–259.
Gomila M, Gasco J, Gil J, Bernabeu R, Inigo V, Lalucat J . (2006). A molecular microbial ecology approach to studying hemodialysis water and fluid. Kidney Int 70: 1567–1576.
Hallberg KB, Hedrich S, Johnson DB . (2011). Acidiferrobacter thiooxydans, gen. nov. sp. nov.; an acidophilic, thermo-tolerant, facultatively anaerobic iron-and sulfur-oxidizer of the family Ectothiorhodospiraceae. Extremophiles 15: 271–279.
Haltia T, Puustinen A, Finel M . (1988). The Paracoccus denitrificans cytochrome aa3 has a third subunit. Eur J Biochem 172: 543–546.
Harter J, Krause H-M, Schuettler S, Ruser R, Fromme M, Scholten T et al. (2014). Linking N2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community. ISME J 8: 660–674.
Hemkemeyer M, Christensen BT, Martens R, Tebbe CC . (2015). Soil particle size fractions harbour distinct microbial communities and differ in potential for microbial mineralisation of organic pollutants. Soil Biol Biochem 90: 255–265.
Hwang C, Wu W-M, Gentry T, Carley J, Carroll S, Schadt C et al. (2006). Changes in bacterial community structure correlate with initial operating conditions of a field-scale denitrifying fluidized bed reactor. Appl Microbiol Biotechnol 71: 748–760.
Jeffery S, Verheijen F, Van Der Velde M, Bastos A . (2011). A quantitative review of the effects of biochar application to soils on crop productivity using meta-analysis. Agric Ecosyst Environ 144: 175–187.
Joseph S, Husson O, Graber ER, Van Zwieten L, Taherymoosavi S, Thomas T et al. (2015). The electrochemical properties of biochars and how they affect soil redox properties and processes. Agronomy 5: 322–340.
Jünemann S . (1997). Cytochrome bd terminal oxidase. Biochim Biophys Acta 1321: 107–127.
Kang DD, Froula J, Egan R, Wang Z . (2015). MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 3: e1165.
Klüpfel L, Keiluweit M, Kleber M, Sander M . (2014a). Redox properties of plant biomass-derived black carbon (biochar). Environ Sci Technol 48: 5601–5611.
Klüpfel L, Piepenbrock A, Kappler A, Sander M . (2014b). Humic substances as fully regenerable electron acceptors in recurrently anoxic environments. Nat Geosci 7: 195–200.
Kolton M, Harel YM, Pasternak Z, Graber ER, Elad Y, Cytryn E . (2011). Impact of biochar application to soil on the root-associated bacterial community structure of fully developed greenhouse pepper plants. Appl Environ Microbiol 77: 4924–4930.
Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD . (2013). Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol 79: 5112–5120.
Krzywinski M, Altman N . (2014). Points of significance: comparing samples-part II. Nat Methods 11: 355–356.
Kumar S, Nei M, Dudley J, Tamura K . (2008). MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 9: 299–306.
Lagier J-C, Gimenez G, Robert C, Raoult D, Fournier P-E . (2012). Non-contiguous finished genome sequence and description of Herbaspirillum massiliense sp. nov. Stand Genomic Sci 7: 200–209.
Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA et al. (2013). Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31: 814–821.
Langmead B, Salzberg SL . (2012). Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357–359.
Larkin MA, Blackshields G, Brown N, Chenna R, McGettigan PA, McWilliam H et al. (2007). Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947–2948.
Lehmann J, Gaunt J, Rondon M . (2006). Bio-char sequestration in terrestrial ecosystems–a review. Mitig Adapt Strategies Glob Chang 11: 395–419.
Lehmann J, Rillig MC, Thies J, Masiello CA, Hockaday WC, Crowley D . (2011). Biochar effects on soil biota–a review. Soil Biol Biochem 43: 1812–1836.
Lehmann J, Joseph S . (2015) Biochar for Environmental Management: Science, Technology and Implementation 2nd edn. Routledge: London and New York.
Liao X, Chen C, Chang C-H, Wang Z, Zhang X, Xie S . (2012). Heterogeneity of microbial community structures inside the up-flow biological activated carbon (BAC) filters for the treatment of drinking water. Biotechnol Bioprocess Eng 17: 881–886.
Liao X, Chen C, Wang Z, Wan R, Chang C-H, Zhang X et al. (2013). Changes of biomass and bacterial communities in biological activated carbon filters for drinking water treatment. Process Biochem 48: 312–316.
Lin Y, Munroe P, Joseph S, Kimber S, Van Zwieten L . (2012). Nanoscale organo-mineral reactions of biochars in ferrosol: an investigation using microscopy. Plant Soil 357: 369–380.
Liu X, Zheng J, Zhang D, Cheng K, Zhou H, Zhang A et al. (2016). Biochar has no effect on soil respiration across Chinese agricultural soils. Sci Total Environ 554: 259–265.
Liu Y, Wang Z, Liu J, Levar C, Edwards MJ, Babauta JT et al. (2014). A trans‐outer membrane porin‐cytochrome protein complex for extracellular electron transfer by Geobacter sulfurreducens PCA. Environ Microbiol Rep 6: 776–785.
Lovley DR, Holmes DE, Nevin KP . (2004). Dissimilatory fe (iii) and mn (iv) reduction. Adv Microb Physiol 49: 219–286.
Markowitz VM, Chen I-MA, Palaniappan K, Chu K, Szeto E, Grechkin Y et al. (2012). IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res 40: D115–D122.
Mills AL . (2003). Keeping in touch: microbial life on soil particle surfaces. Adv Agron 78: 1–43.
Morgulis A, Coulouris G, Raytselis Y, Madden TL, Agarwala R, Schäffer AA . (2008). Database indexing for production MegaBLAST searches. Bioinformatics 24: 1757–1764.
Nielsen S, Minchin T, Kimber S, van Zwieten L, Gilbert J, Munroe P et al. (2014). Comparative analysis of the microbial communities in agricultural soil amended with enhanced biochars or traditional fertilisers. Agric Ecosyst Environ 191: 73–82.
O’Neill B, Grossman J, Tsai M, Gomes J, Lehmann J, Peterson J et al. (2009). Bacterial community composition in Brazilian anthrosols and adjacent soils characterized using culturing and molecular identification. Microb Ecol 58: 23–35.
Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O'Hara RB et al. (2015). vegan: Community Ecology package. R package version 2: 2–1.
Parks DH, Tyson GW, Hugenholtz P, Beiko RG . (2014). STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics 30: 3123–3124.
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW . (2015). CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25: 1043–1055.
Peng X, Yu H, Ai L, Li N, Wang X . (2013). Time behavior and capacitance analysis of nano-Fe3O4 added microbial fuel cells. Bioresour Technol 144: 689–692.
Peng Y, Leung HC, Yiu S-M, Chin FY . (2012). IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28: 1420–1428.
Pietikäinen J, Kiikkilä O, Fritze H . (2000). Charcoal as a habitat for microbes and its effect on the microbial community of the underlying humus. Oikos 89: 231–242.
Price MN, Dehal PS, Arkin AP . (2010). FastTree 2–approximately maximum-likelihood trees for large alignments. PloS One 5: e9490.
Pruesse E, Peplies J, Glockner FO . (2012). SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28: 1823–1829.
Quilliam RS, Glanville HC, Wade SC, Jones DL . (2013). Life in the ‘charosphere’–Does biochar in agricultural soil provide a significant habitat for microorganisms? Soil Biol Biochem 65: 287–293.
Rawal A, Joseph SD, Hook JM, Chia CH, Munroe PR, Donne SW et al. (2016). Mineral-biochar composites: molecular structure and porosity. Environ Sci Technol 50: 7706–7714.
Richardson DJ, Butt JN, Fredrickson JK, Zachara JM, Shi L, Edwards MJ et al. (2012). The ‘porin–cytochrome’model for microbe‐to‐mineral electron transfer. Mol Microbiol 85: 201–212.
Rondon MR, Goodman RM, Handelsman J . (1999). The Earth’s bounty: assessing and accessing soil microbial diversity. Trends Biotechnol 17: 403–409.
Schmieder R, Edwards R . (2011). Quality control and preprocessing of metagenomic datasets. Bioinformatics 27: 863–864.
Sessitsch A, Weilharter A, Gerzabek MH, Kirchmann H, Kandeler E . (2001). Microbial population structures in soil particle size fractions of a long-term fertilizer field experiment. Appl Environ Microbiol 67: 4215–4224.
Singer E, Emerson D, Webb EA, Barco RA, Kuenen JG, Nelson WC et al. (2011a). Mariprofundus ferrooxydans PV-1 the first genome of a marine Fe (II) oxidizing Zetaproteobacterium. PloS One 6: e25386.
Singer E, Webb EA, Nelson WC, Heidelberg JF, Ivanova N, Pati A et al. (2011b). Genomic potential of Marinobacter aquaeolei, a biogeochemical 'opportunitroph'. Appl Environ Microbiol 77: 2763–2771.
Singer E, Heidelberg JF, Dhillon A, Edwards KJ . (2013). Metagenomic insights into the dominant Fe (II) oxidizing Zetaproteobacteria from an iron mat at Lo'ihi, Hawai'i. Front Microbiol 4: 52.
Sun D, Meng J, Xu EG, Chen W . (2016). Microbial community structure and predicted bacterial metabolic functions in biochar pellets aged in soil after 34 months. Appl Soil Ecol 100: 135–143.
Sun Y, Wei J, Liang P, Huang X . (2012). Microbial community analysis in biocathode microbial fuel cells packed with different materials. AMB Express 2: 21.
Tabita FR, Satagopan S, Hanson TE, Kreel NE, Scott SS . (2008). Distinct form I, II, III, and IV Rubisco proteins from the three kingdoms of life provide clues about Rubisco evolution and structure/function relationships. J Exp Bot 59: 1515–1524.
Trüper HG . (1994). Reverse siroheme sulfite reductase from Thiobacillus denitrificans. Methods Enzymol 243: 422–426.
Waite JL . (2012) Characterization of Cytochrome c Peroxidase of Marinobacter Aquaeolei. Los Angeles, California: University of Southern California.
Wang Z, Leary DH, Malanoski AP, Li RW, Hervey WJ, Eddie BJ et al. (2015). A previously uncharacterized, nonphotosynthetic member of the Chromatiaceae is the primary CO2-fixing constituent in a self-regenerating biocathode. Appl Environ Microbiol 81: 699–712.
Wang J, Xiong Z, Kuzyakov Y . (2016). Biochar stability in soil: meta-analysis of decomposition and priming effects. GCB Bioenergy 8: 512–523.
Westram R, Bader K, Prüsse E, Kumar Y, Meier H, Glöckner FO et al. (2011). ARB: a software environment for sequence data. In: de Bruijn FJ (ed.) Handbook of Molecular Microbial Ecology I. Hoboken, NJ: John Wiley & Sons, Inc., 399–406.
Woolf D, Amonette JE, Street-Perrott FA, Lehmann J, Joseph S . (2010). Sustainable biochar to mitigate global climate change. Nat Commun 1: 56.
Xia X, Sun Y, Liang P, Huang X . (2012). Long-term effect of set potential on biocathodes in microbial fuel cells: electrochemical and phylogenetic characterization. Bioresour Technol 120: 26–33.
Yariv S, Cross H . (2001) Organo-Clay Complexes and Interactions. Taylor & Francis: New York.
Ye J, Nielsen S, Joseph S, Thomas T . (2015). High-resolution and specific detection of bacteria on complex surfaces using nanoparticle probes and electron microscopy. PloS One 10: e0126404.
Ye J, Zhang R, Nielsen S, Joseph SD, Huang D, Thomas T . (2016). A combination of biochar-mineral complexes and compost improves soil bacterial processes, soil quality and plant properties. Front Microbiol 7: 372.
Yeates TO, Kerfeld CA, Heinhorst S, Cannon GC, Shively JM . (2008). Protein-based organelles in bacteria: carboxysomes and related microcompartments. Nat Rev Microbiol 6: 681–691.
Yin Y, Huang G, Tong Y, Liu Y, Zhang L . (2013). Electricity production and electrochemical impedance modeling of microbial fuel cells under static magnetic field. J Power Sources 237: 58–63.
Yu L, Yuan Y, Tang J, Wang Y, Zhou S . (2015). Biochar as an electron shuttle for reductive dechlorination of pentachlorophenol by Geobacter sulfurreducens. Sci Rep 5: 16221.
Acknowledgements
We acknowledge Dr Simon Hager from the Electron Microscopy Unit and Dr Bill Bin Gong from the Solid State and Elemental Analysis Unit at UNSW for technical support. We thank Professor Gene Tyson (Australian Centre for Ecogenomics) for advise on the metagenomic sequencing. We also thank Professor Xiaohua Zhang (Ocean University of China) for kindly providing strain Catenovulum agarivorans YM01. JY would like to thank the support of China Scholarship Council (File ID: 201206230085). This research was supported by the Australian Research Council (LP120200418) and Renewed Carbon Pty Ltd.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors declare no conflict of interest.
Additional information
Supplementary Information accompanies this paper on The ISME Journal website
Rights and permissions
About this article
Cite this article
Ye, J., Joseph, S., Ji, M. et al. Chemolithotrophic processes in the bacterial communities on the surface of mineral-enriched biochars. ISME J 11, 1087–1101 (2017). https://doi.org/10.1038/ismej.2016.187
Received:
Revised:
Accepted:
Published:
Issue date:
DOI: https://doi.org/10.1038/ismej.2016.187
This article is cited by
-
Exploring prokaryotic diversity in permafrost-affected soils of Ladakh’s Changthang region and its geochemical drivers
Scientific Reports (2025)
-
Effects of biochar and compost on the bioavailability of heavy metals in soil aggregates with varying particle sizes
Journal of Soils and Sediments (2025)
-
Integrated Biochar, Manure, and Inorganic Fertilizers Sustain Microbial-Mediated Nitrogen Supply and Plant Nutrition in a Degraded Subtropical Soil
Journal of Soil Science and Plant Nutrition (2025)
-
Comparison of microbial communities in unleached and leached ionic rare earth mines
Environmental Science and Pollution Research (2024)
-
Functionalized organo-mineral composites of biochar for the effectual immobilization of arsenic in contaminated soil
Journal of Soils and Sediments (2024)
