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Original articles

Distribution and potential roles of microbial protoporphyrin IX in marine sediments

, , , &
Pages 491-506 | Received 22 Aug 2023, Accepted 03 Nov 2023, Published online: 03 Dec 2023

References

  • Bender DA. 2012. Amino acid metabolism. Chichester: Wiley.
  • Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nature Methods. 7:335–6. doi:10.1038/nmeth.f.303.
  • Cheng H, Mai Z, Wang Y, Liu D, Sun Y. 2022. Role of extracellular polymeric substances in metal sequestration during mangrove restoration. Chemosphere. 306:135550. doi:10.1016/j.chemosphere.2022.135550.
  • Coates JD, Ellis DJ, Gaw CV, Lovley DR. 1999. Geothrix fermentans gen. nov., sp. nov., a novel Fe(III)-reducing bacterium from a hydrocarbon-contaminated aquifer. International Journal of Systematic and Evolutionary Microbiology. 49:1615–1622. doi:10.1099/00207713-49-4-1615.
  • Crowther TW, van den Hoogen J, Wan J, Mayes MA, Keiser AD, Mo L, Averill C, Maynard DS. 2019. The global soil community and its influence on biogeochemistry. Science. 365:eaav0550. doi:10.1126/science.aav0550.
  • Dailey HA, Meissner PN. 2013. Erythroid heme biosynthesis and its disorders. Cold Spring Harbor Perspectives in Medicine. 3:a011676. doi:10.1101/cshperspect.a011676.
  • Danton M, Lim CK. 2006. Porphyrin profiles in blood, urine and faeces by HPLC/electrospray ionization tandem mass spectrometry. Biomedical Chromatography. 20:612–21. doi:10.1002/bmc.656.
  • de Chaves MG, Silva GGZ, Rossetto R, Edwards RA, Tsai SM, Navarrete AA. 2019. Acidobacteria subgroups and their metabolic potential for carbon degradation in sugarcane soil amended with vinasse and nitrogen fertilizers. Frontiers in Microbiology. 10:1680. doi:10.3389/fmicb.2019.01680.
  • Duhamel S, Jacquet S. 2006. Flow cytometric analysis of bacteria- and virus-like particles in lake sediments. Journal of Microbiological Methods. 64:316–32. doi:10.1016/j.mimet.2005.05.008.
  • Dyksma S, Bischof K, Fuchs BM, Hoffmann K, Meier D, Meyerdierks A, Pjevac P, Probandt D, Richter M, Stepanauskas R, Mußmann M. 2016. Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments. The ISME Journal. 10:1939–1953. doi:10.1038/ismej.2015.257.
  • Edgar RC. 2013. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods. 10:996–8. doi:10.1038/nmeth.2604.
  • Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics (Oxford, England). 27:2194–2200.
  • Espinas NA, Kobayashi K, Takahashi S, Mochizuki N, Masuda T. 2012. Evaluation of unbound free heme in plant cells by differential acetone extraction. Plant and Cell Physiology. 53:1344–54. doi:10.1093/pcp/pcs067.
  • Fagervold SK, Bourgeois S, Pruski AM, Charles F, Kerhervé P, Vétion G, Galand PE. 2014. River organic matter shapes microbial communities in the sediment of the Rhône prodelta. The ISME Journal. 8:2327–2338. doi:10.1038/ismej.2014.86.
  • Falkowski P. 2012. Ocean science: the power of plankton. Nature. 483:S17–S20. doi:10.1038/483S17a.
  • Flieder M, Buongiorno J, Herbold CW, Hausmann B, Rattei T, Lloyd KG, Loy A, Wasmund K. 2021. Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling. The ISME Journal. 15:3159–3180. doi:10.1038/s41396-021-00992-0.
  • Fyrestam J, Bjurshammar N, Paulsson E, Johannsen A, Ostman C. 2015. Determination of porphyrins in oral bacteria by liquid chromatography electrospray ionization tandem mass spectrometry. Analytical and Bioanalytical Chemistry. 407:7013–23. doi:10.1007/s00216-015-8864-2.
  • Fyrestam J, Östman C. 2017. Determination of heme in microorganisms using HPLC-MS/MS and cobalt(III) protoporphyrin IX inhibition of heme acquisition in Escherichia coli. Analytical and Bioanalytical Chemistry. 409:6999–7010. doi:10.1007/s00216-017-0610-5.
  • Gao P, Chen Z, Zhao-Karger Z, Mueller JE, Jung C, Klyatskaya S, Diemant T, Fuhr O, Jacob T, Behm RJ, et al. 2017. A porphyrin complex as a self-conditioned electrode material for high-performance energy storage. Angewandte Chemie International Edition. 56:10341–10346. doi:10.1002/anie.201702805.
  • Gu L, Yue X, Zhong H, Mei K, Wang D. 2022. A new technique of quantifying protoporphyrin IX in microbial cells in seawater. Frontiers in Marine Science. 9:991126. doi:10.3389/fmars.2022.991126.
  • Guo K, Feng X, Sun W, Han S, Wu S, Gao H. 2022. Napb restores cytochrome c biosynthesis in bacterial dsbD-deficient mutants. Communications Biology. 5:87. doi:10.1038/s42003-022-03034-3.
  • Hamilton TL, Bryant DA, Macalady JL. 2016. The role of biology in planetary evolution: cyanobacterial primary production in low-oxygen Proterozoic oceans. Environmental Microbiology. 18:325–40. doi:10.1111/1462-2920.13118.
  • Harada Y, Murayama Y, Takamatsu T, Otsuji E, Tanaka H. 2022. 5-Aminolevulinic Acid-Induced Protoporphyrin IX fluorescence imaging for tumor detection: recent advances and challenges. International Journal of Molecular Sciences. 23:6478. doi:10.3390/ijms23126478.
  • Hausmann B, Pelikan C, Herbold CW, Köstlbacher S, Albertsen M, Eichorst SA, Glavina Del Rio T, Huemer M, Nielsen PH, Rattei T, et al. 2018. Peatland Acidobacteria with a dissimilatory sulfur metabolism. The ISME Journal. 12:1729–1742. doi:10.1038/s41396-018-0077-1.
  • Havens KE. 2008. Cyanobacteria blooms: effects on aquatic ecosystems. Advances in Experimental Medicine and Biology. 619:733–47. doi:10.1007/978-0-387-75865-7_33.
  • Herlemann DP, Labrenz M, Jürgens K, Bertilsson S, Waniek JJ, Andersson AF. 2011. Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. The ISME Journal. 5:1571–9. doi:10.1038/ismej.2011.41.
  • Hirota R, Kuroda A, Kato J, Ohtake H. 2010. Bacterial phosphate metabolism and its application to phosphorus recovery and industrial bioprocesses. Journal of Bioscience and Bioengineering. 109:423–432. doi:10.1016/j.jbiosc.2009.10.018.
  • Hugerth LW, Wefer HA, Lundin S, Jakobsson HE, Lindberg M, Rodin S, Engstrand L, Andersson AF. 2014. Degeprime, a program for degenerate primer design for broad-taxonomic-range PCR in microbial ecology studies. Applied and Environmental Microbiology. 80:5116–23. doi:10.1128/AEM.01403-14.
  • Hur Y, Han SB, Kang SW, Lee Y. 2014. Quantitative analysis of porphyrins in dried blood spots using liquid chromatography-tandem mass spectrometry with pre-column derivatization. Bulletin of the Korean Chemical Society. 35:3103–3106. doi:10.5012/bkcs.2014.35.10.3103.
  • Jinchang Liang JL, Wang X, Lin H, Liu J, Zhou S, Sun H, Zhang X-H. 2019. Spatiotemporal dynamics of free-living and particle-associated vibrio communities in the Northern Chinese marginal seas. Applied and Environmental Microbiology. 85:e00217–19.
  • Kim S, Kang I, Lee JW, Jeon CO, Giovannoni SJ, Cho JC. 2021. Heme auxotrophy in abundant aquatic microbial lineages. Proceedings of the National Academy of Sciences. 118:e2102750118. doi:10.1073/pnas.2102750118.
  • Kuypers MMM, Marchant HK, Kartal B. 2018. The microbial nitrogen-cycling network. Nature Reviews Microbiology. 16:263–276. doi:10.1038/nrmicro.2018.9.
  • Laura Gómez-Consarnau JAR, Levine NM, Cutter LS, Wang D, Seegers B, Arístegui J, Fuhrman JA, Gasol JM, Sañudo-Wilhelmy SA. 2019. Microbial rhodopsins are major contributors to the solar energy captured in the sea. Science Advances. 5:eaaw8855. doi:10.1126/sciadv.aaw8855.
  • Li J, Cai Z, Xu S, Liao C, Song X, Chen L. 2011. Analysis of urinary porphyrins by high performance liquid chromatography-electrospray ionization mass spectrometry. Journal of Liquid Chromatography & Related Technologies. 34:1578–1593. doi:10.1080/10826076.2011.575981.
  • Lipsewers YA, Bale NJ, Hopmans EC, Schouten S, Sinninghe Damste JS, Villanueva L. 2014. Seasonality and depth distribution of the abundance and activity of ammonia oxidizing microorganisms in marine coastal sediments (North Sea). Frontiers in Microbiology. 5:472–484.
  • Liu J, Zhu S, Liu X, Yao P, Ge T, Zhang X-H. 2020. Spatiotemporal dynamics of the archaeal community in coastal sediments: assembly process and co-occurrence relationship. The ISME Journal. 14:1463–1478.
  • Liu X, Shi L, Gu JD. 2018. Microbial electrocatalysis: redox mediators responsible for extracellular electron transfer. Biotechnology Advances. 36:1815–1827. doi:10.1016/j.biotechadv.2018.07.001.
  • Ma Q, Tan H, Song J, Li M, Wang Z, Parales RE, Li L, Ruan Z. 2022. Effects of long-term exposure to the herbicide nicosulfuron on the bacterial community structure in a factory field. Environmental Pollution. 307:119477. doi:10.1016/j.envpol.2022.119477.
  • Magoč T, Salzberg SL. 2011. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics (Oxford, England). 27:2957–2963. doi:10.1093/bioinformatics/btr507.
  • Mann G, Mora S, Madu G, Adegoke OAJ. 2021. Branched-chain amino acids: catabolism in skeletal muscle and implications for muscle and whole-body metabolism. Frontiers in Physiology. 12:702826. doi:10.3389/fphys.2021.702826.
  • Mo Y, Zhang W, Yang J, Lin Y, Yu Z, Lin S. 2018. Biogeographic patterns of abundant and rare bacterioplankton in three subtropical bays resulting from selective and neutral processes. The ISME Journal. 12:2198–2210. doi:10.1038/s41396-018-0153-6.
  • Monteverde DR, Sylvan JB, Suffridge C, Baronas JJ, Fichot E, Fuhrman J, Berelson W, Sanudo-Wilhelmy SA. 2018. Distribution of extracellular Flavins in a coastal marine basin and their relationship to redox gradients and microbial community members. Environmental Science & Technology. 52:12265–12274. doi:10.1021/acs.est.8b02822.
  • Pfeffer C, Larsen S, Song J, Dong M, Besenbacher F, Meyer RL, Kjeldsen KU, Schreiber L, Gorby YA, El-Naggar MY, et al. 2012. Filamentous bacteria transport electrons over centimetre distances. Nature. 491:218–221. doi:10.1038/nature11586.
  • Qian F, Huang X, Su X, Bao Y. 2022. Responses of microbial communities and metabolic profiles to the rhizosphere of Tamarix ramosissima in soils contaminated by multiple heavy metals. Journal of Hazardous Materials. 438:129469. doi:10.1016/j.jhazmat.2022.129469.
  • Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research. 41:D590–D596. doi:10.1093/nar/gks1219.
  • Sachar M, Anderson KE, Ma X. 2016. Protoporphyrin IX: the good, the bad, and the ugly. Journal of Pharmacology and Experimental Therapeutics. 356:267–275. doi:10.1124/jpet.115.228130.
  • Sander BC, Kalff J. 1993. Factors controlling bacterial production in marine and freshwater sediments. Microbial Ecology. 26:79–99. doi:10.1007/BF00177045.
  • Senge M, Ryan A, Letchford K, MacGowan S, Mielke T. 2014. Chlorophylls, symmetry, chirality, and photosynthesis. Symmetry. 6:781–843. doi:10.3390/sym6030781.
  • Sitte E, Senge MO. 2020. The red color of life transformed – synthetic advances and emerging applications of Protoporphyrin IX in chemical biology. European Journal of Organic Chemistry. 2020:3171–3191. doi:10.1002/ejoc.202000074.
  • Su Z, Dai T, Tang Y, Tao Y, Huang B, Mu Q, Wen D. 2018. Sediment bacterial community structures and their predicted functions implied the impacts from natural processes and anthropogenic activities in coastal area. Marine Pollution Bulletin. 131:481–495. doi:10.1016/j.marpolbul.2018.04.052.
  • Suffridge C, Cutter L, Sañudo-Wilhelmy SA. 2017. A new analytical method for direct measurement of particulate and dissolved B-vitamins and their congeners in seawater. Frontiers in Marine Science. 4:11–22. doi:10.3389/fmars.2017.00011.
  • Suffridge CP, Gómez-Consarnau L, Monteverde DR, Cutter L, Arístegui J, Alvarez-Salgado XA, Gasol JM, Sañudo-Wilhelmy SA. 2018. B vitamins and their congeners as potential drivers of microbial community composition in an oligotrophic marine ecosystem. Journal of Geophysical Research: Biogeosciences. 123:2890–2907. doi:10.1029/2018JG004554.
  • Ta D, Lap B, Thanh L, Harada M, Hiramatsu K, Tabata T. 2021. Eutrophication status of lakes in inner Hanoi and a case study of Cu Chinh Lake. Journal of the Faculty of Agriculture, Kyushu University. 66:97–104. doi:10.5109/4363557.
  • Wang D, Gao Y, Larsson K, Lin W. 2016. Speciation of dissolved copper in human impacted freshwater and saltwater lakes. Environmental Science and Pollution Research. 23:10832–10840. doi:10.1007/s11356-016-6140-4.
  • Wang L, Yu M, Liu Y, Liu J, Wu Y, Li L, Liu J, Wang M, Zhang X-H. 2018. Comparative analyses of the bacterial community of hydrothermal deposits and seafloor sediments across Okinawa Trough. Journal of Marine Systems. 180:162–172. doi:10.1016/j.jmarsys.2016.11.012.
  • Wang Y, Ye F, Wu S, Wu J, Yan J, Xu K, Hong Y. 2020. Biogeographic pattern of bacterioplanktonic community and potential function in the Yangtze River: roles of abundant and rare taxa. Science of the Total Environment. 747:141335. doi:10.1016/j.scitotenv.2020.141335.
  • Xie Z, Guo J, Lu C, Song Y, Xing Y, Yang Q, Han Y, Li H. 2018. Biocatalysis mechanisms and characterization of a novel denitrification process with porphyrin compounds based on the electron transfer chain. Bioresource Technology. 265:548–553. doi:10.1016/j.biortech.2018.05.069.
  • Yamanaka T, Okunuki K. 1974. Chapter 14 - cytochromes. In: J. B. Neilands, editor. Berkeley, California: Microbial iron metabolism. Academic Press; p. 349–400.
  • Yang H, Zhou Y, Liu J. 2021. Porphyrin metalation catalyzed by DNAzymes and nanozymes. Inorganic Chemistry Frontiers. 8:2183–2199. doi:10.1039/D1QI00105A.
  • Yang S, Chen Q, Zheng T, Chen Y, Zhao X, He Y, Sun W, Zhong S, Li Z, Wang J. 2022. Multiple metal(loid) contamination reshaped the structure and function of soil archaeal community. Journal of Hazardous Materials. 436:129186. doi:10.1016/j.jhazmat.2022.129186.
  • Yu D, Chen N, Krom MD, Lin J, Cheng P, Yu F, Guo W, Hong H, Gao X. 2019. Understanding how estuarine hydrology controls ammonium and other inorganic nitrogen concentrations and fluxes through the subtropical Jiulong River Estuary, S.E. China under baseflow and flood-affected conditions. Biogeochemistry. 142:443–466. doi:10.1007/s10533-019-00546-9.
  • Zhou J, Lao YM, Song JT, Jin H, Zhu JM, Cai ZH. 2020. Temporal heterogeneity of microbial communities and metabolic activities during a natural algal bloom. Water Research. 183:116020. doi:10.1016/j.watres.2020.116020.

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