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熱線:021-66110819,13564362870
Email:info@vizai.cn
我們檢查了 Fe(III) 羥基氧化物表面上次生 Fe 礦物的表面結殼的存在,這可能會限制微生物 Fe (III) 還原的程度。 淡水沉積物的特征是水鐵礦占主導地位的表層含有生物莖和鞘。 1 和 2 厘米深度的 16S rRNA 基因分析結果檢測到 Fe(II) 氧化細菌 Gallionellaceae。 在 2-4 厘米的沉積物深度處,孔隙水 Fe2+ 濃度顯著增加。 在 1、2 和 4 厘米的沉積物深度檢測到異化 Fe(III) 還原菌。 根據 EXAFS 結果,建議菱鐵礦和針鐵礦在 3 cm 以下的深度沉淀。 然而,僅在 3 至 4 cm 深度之間觀察到 Fe 礦物組成的變化,并且大部分水鐵礦保持在 4 cm 以下的深度。 6 cm 以下深度濃度增加。 孔隙水中生物質的穩定同位素分析表明,7 cm以下深度存在乙酰碎屑生物質,這種生物質的產生通常受到異化Fe(III)還原的抑制。 16S rRNA 基因分析的結果表明,在 10 厘米深度處存在產甲烷古菌 Methanosarcinales。 這些結果表明,在 4 cm 以下深度水鐵礦的不完全還原不是由于缺乏有機碳。 TEM 觀察表明,莖和鞘表面的 Fe 礦物從 1 cm 深度的水鐵礦轉變為 3 cm 以下深度的菱鐵礦和針鐵礦。 此外,通過 CEYEXAFS 分析在 10 厘米深度處定量鐵礦物形態表明針鐵礦主要存在于顆粒表面。 這些結果不同于大量 EXAFS 分析結果,即水鐵礦是主要的鐵礦物種類。 根據這些結果,水鐵礦表面可能被針鐵礦包裹,這可能限制了水鐵礦在 4 cm 深度以下的還原程度。
我們感謝 M. Miyazaki 博士和 K. Yanagawa 博士在構建系統發育樹方面提出的善意建議。 本研究由 JSPS 青年科學家研究獎學金資助。 這項工作也得到了 SPring-8 (2012A1589, 2013A1613, 2014A1416) 和 KEK (2013G052, 2013G562) 的支持。
Anderson CR, James RE, Fru EC, Kennedy CB, Pedersen K (2006) In situ ecological development of a bacteriogenic iron oxide-producing microbial community from a subsurface granitic rock environment. Geobiology 4, 29–42.
Banfield JF, Welch SA, Zhang H, Ebert TT, Penn RL (2000) Aggregation-based crystal growth and microstructure development in natural iron oxyhydroxide biomineralization products. Science 289, 751–754.
Benner SG, Hansel CM, Wielinga BW, Barber TM, Fendorf S (2002) Reductive dissolution and biomineralization of iron hydroxide under dynamic flow conditions. Environmental Science & Technology 36, 1705–1711.
Bl€othe M, Roden E (2009) Microbial iron redox cycling in a circumneutral-pH groundwater seep. Applied and Environmental Microbiology 75, 468–473.
Chan CS, Fakra SC, Edwards DC, Emerson D, Banfield JF (2009) Iron oxyhydroxide mineralization on microbial extracellular polysaccharides. Geochimica et Cosmochimica Acta 73, 3807– 3818.
Chapelle FH, Lovley D (1992) Competitive exclusion of sulfate reduction by Fe(lll)-reducing bacteria: a mechanism for producing discrete zones of high-iron. Ground Water 30, 29–36.
Coates JD, Phillips EJ, Lonergan DJ, Jenter H, Lovley DR (1996) Isolation of Geobacter species from diverse sedimentary environments. Applied and Environmental Microbiology 62, 1531–1536.
Druschel GK, Emerson D, Sutka R, Suchecki P, Luther GW (2008) Low-oxygen and chemical kinetic constraints on the geochemical niche of neutrophilic iron(II) oxidizing microorganisms. Geochimica et Cosmochimica Acta 72, 3358– 3370.
Edwards KJ, Glazer BT, Rouxel OJ, Bach W, Emerson D, Davis RE, Toner BM, Chan CS, Tebo BM, Staudigel H, Moyer CL (2011) Ultra-diffuse hydrothermal venting supports Feoxidizing bacteria and massive umber deposition at 5000 m off Hawaii. The ISME Journal 5, 1748–1758.
Emerson D (2009) Potential for iron-reduction and iron-cycling in iron oxyhydroxide-rich microbial mats at Loihi Seamount. Geomicrobiology Journal 26, 639–647.
Emerson D, Revsbech NP (1994) Investigation of an ironoxidizing microbial mat community located near Aarhus, Denmark: field studies. Applied and Environmental Microbiology 60, 4022–4031.
Emerson D, Fleming EJ, McBeth JM (2010) Iron-oxidizing bacteria: an environmental and genomic perspective. Annual Review of Microbiology 64, 561–583.
Fadrus H, Maly J (1975) Suppression of iron(III) interference in the determination of iron(II) in water by the 1, 10- phenanthroline method. Analyst 100, 549–554.
Finneran KT, Johnsen CV, Lovley D (2003) Rhodoferax ferrireducens sp. nov., a psychrotolerant, facultatively anaerobic bacterium that oxidizes acetate with the reduction of Fe (III). International Journal of Systematic and Evolutionary Microbiology 53, 669–673.
Fredrickson JK, Zachara JM, Kennedy DW, Dong H, Onstott TC, Hinman NW, Li SM (1998) Biogenic iron mineralization accompanying the dissimilatory reduction of hydrous ferric oxide by a groundwater bacterium. Geochimica et Cosmochimica Acta 62, 3239–3257.
Froelich PN, Klinkhammer GP, Bender ML (1979) Early oxidation of organic matter in pelagic sediments of the eastern equatorial Atlantic: suboxic diagenesis. Geochimica et Cosmochimica Acta 43, 1075–1090.
Gault AG, Ibrahim A, Langley S, Renaud R, Takahashi Y, Boothman C, Lloyd JR, Clark ID, Ferris FG, Fortin D (2011) Microbial and geochemical features suggest iron redox cycling within bacteriogenic iron oxide-rich sediments. Chemical Geology 281, 41–51.
Gieseke A, de Beer D (2004) Use of microelectrodes to measure in situ microbial activities in biofilms, sediments, and microbial mats. In Molecular Microbial Ecology Manual Second edition. Vol.2. (ed. Kowalchuk GA, de Bruijn FJ, Head IM, Akkermans ADL, van Elsas D) Kluwer Academic Publishers, Dordrecht, The Netherlands. pp. 1581–1612.
Graf DL (1961) Crystallographic tables for the rhombohedral carbonates. American Mineralogist 46, 1283–1316.
Hansel CM, Benner SG, Neiss J, Dohnalkova A, Kukkadapu RK, Fendorf S (2003) Secondary mineralization pathways induced by dissimilatory iron reduction of ferrihydrite under advective flow. Geochimica et Cosmochimica Acta 67, 2977–2992.
Hansel CM, Benner SG, Nico P, Fendorf S (2004) Structural constraints of ferric (hydr)oxides on dissimilatory iron reduction and the fate of Fe(II). Geochimica et Cosmochimica Acta 68, 3217–3229.
Hansel CM, Benner SG, Fendorf S (2005) Competing Fe (II)- induced mineralization pathways of ferrihydrite. Environmental Science & Technology 39, 7147–7153.
Ijiri A, Harada N, Hirota A, Hirota A, Tsunogai U, Ogawa NO, Itaki T, Khim BK, Uchida M (2012) Biogeochemical processes involving acetate in sub-seafloor sediments from the Bering Sea shelf break. Organic Geochemistry 48, 47–55.
Itai T, Takahashi Y, Uruga T, Tanida H, Iida A (2008) Selective detection of Fe and Mn species at mineral surfaces in weathered granite by conversion electron yield X-ray absorption fine structure. Applied Geochemistry 23, 2667–2675.
Kato S, Kikuchi S, Kashiwabara T, Takahashi Y, Suzuki K, Itoh T, Ohkuma M, Yamagishi A (2012) Prokaryotic abundance and community composition in a freshwater iron-rich microbial mat at circumneutral pH. Geomicrobiology Journal 29, 896– 905.
Kennedy CB, Martinez RE, Scott SD, Ferris G (2003) Surface chemistry and reactivity of bacteriogenic iron oxides from Axial Volcano, Juan de Fuca Ridge, north-east Pacific Ocean. Geobiology 1, 59–69.
Langley S, Gault A, Ibrahim A, Renaud R, Fortin D, Clark ID, Ferris FG (2009) A comparison of the rates of Fe(III) reduction in synthetic and bacteriogenic iron oxides by Shewanella putrefaciens CN32. Geomicrobiology Journal 26, 57–70.
Liu Y, Whitman WB (2008) Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Annals of the New York Academy of Sciences 1125, 171–189.
Liu C, Kota S, Zachara JM, Fredrickson JK, Brinkman CK (2001) Kinetic analysis of the bacterial reduction of goethite. Environmental Science & Technology 35, 2482–2490.
Lovley DR (1991) Dissimilatory Fe(III) and Mn(IV) reduction. Microbiological Reviews 55, 259–287.
Lovley D (1994) Microbial Fe(III) reduction in subsurface environments. FEMS Microbiology Reviews 20, 305–313.
Lovley D, Klug MJ (1986) Model for the distribution of sulfate reduction and methanogenesis in freshwater sediments. Geochimica et Cosmochimica Acta 50, 11–18.
Lovley DR, Phillips EJP (1986a) Organic matter mineralization with reduction of ferric iron in anaerobic sediments. Applied and Environmental Microbiology 51, 683–689.
Lovley DR, Phillips EJ (1986b) Availability of ferric iron for microbial reduction in bottom sediments of the freshwater tidal Potomac River. Applied and Environmental Microbiology 52, 751–757.
Lovley DR, Phillips EJ (1987a) Competitive mechanisms for inhibition of sulfate reduction and methane production in the zone of ferric iron reduction in sediments. Applied and Environmental Microbiology 53, 2636–2641.
Lovley DR, Phillips E (1988) Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron or manganese. Applied Environmental Microbiology 54, 1472–1480.
Lovley D, Stolz JF, Nord GL, Phillips E (1987b) Anaerobic production of magnetite by a dissimilatory iron-reducing microorganism. Nature 330, 252–254.
Lovley DR, Giovannoni SJ, White DC, Champine JE, Phillips EJP, Gorby YA, Goodwin S (1993) Geobacter metallireducens gen. nov. sp. nov., a microorganisms capable of iron and other metals. Archives of Microbiology 159, 336–344.
Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar Buchner A, Lai T, Steppi S, Jobb G, Fo¨ster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, Ko¨ning A, Liss T, Lu¨mann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer KH (2004) ARB: a software environment for sequence data. Nucleic Acids Research 32, 1363–1371.
Mitsunobu S, Shiraishi F, Makita H, Orcutt BN, Kikuchi S, Jorgensen BB, Takahashi Y (2012) Bacteriogenic Fe(III) (oxyhydr)oxides characterized by synchrotron microprobe coupled with spatially resolved phylogenetic analysis. Environmental Science & Technology 46, 3304–3311.
Nealson KH, Saffarini D (1994) Iron and manganese in anaerobic respiration –environmental significance, physiology, and regulation. Annual Review of Microbiololgy 48, 311–343.
Nunoura T, Takai Y, Kazama H, Hirai M, Ashi J, Imachi H, Takai K (2012) Microbial diversity in deep-sea methane seep sediments presented by SSU rRNA gene tag sequencing. Microbes and Environments 27, 382–390.
Pallud C, Kausch M, Fendorf S, Meile C (2010a) Spatial patterns and modeling of reductive ferrihydrite transformation observed in artificial soil aggregates. Environmental Science & Technology 44, 74–79.
Pallud C, Masue-slowey Y, Fendorf S (2010b) Aggregate-scale spatial heterogeneity in reductive transformation of ferrihydrite resulting from coupled biogeochemical and physical processes. Geochimica et Cosmochimica Acta 74, 2811–2825.
Phillips EJ, Lovley DR, Roden E (1993) Composition of nonmicrobially reducible Fe(III) in aquatic sediments. Applied and Environmental Microbiology 59, 2727–2729.
Poulton SW, Canfield DE (2005) Development of a sequential extraction procedure for iron: implications for iron partitioning in continentally derived particulates. Chemical Geology 214, 209–221.
Ravel B, Newville M (2005) ATHENA, ARTEMIS, HEPHAESTUS: data analysis for X-ray absorption spectroscopy using IFEFFIT. Journal of Synchrotron Radiation 12, 537–541.
Roden EE (2003) Diversion of electron flow from methanogenesis to crystalline Fe(III) oxide reduction in carbon-limited cultures of wetland sediment microorganisms. Applied and Environmental Microbiology 69, 5702–5706.
Roden E, Urrutia MM (1999) Ferrous iron removal promotes microbial reduction of crystalline iron(III) oxides. Environmental Science & Technology 33, 1847–1853.
Roden E, Urrutia MM (2002) Influence of biogenic Fe (II) on bacterial crystalline Fe (III) oxide reduction. Geomicrobiology Journal 19, 209–251.
Roden E, Wetzel RG (1996) Organic carbon oxidation and suppression of methane production by microbial Fe(III) oxide reduction in vegetated and unvegetated freshwater wetland sediments. Limnology and Oceanography 41, 1733–1748.
Roden EE, Wetzel RG (2003) Competition between Fe(III)- reducing and methanogenic bacteria for acetate in iron-rich freshwater sediments. Microbial Ecology 45, 252–258.
Roden E, Zachara JM (1996) Microbial reduction of crystalline iron(III) oxides: influence of oxide surface area and potential for cell growth. Environmental Science & Technology 30, 1618–1628.
Roden EE, Urrutia MM, Mann CJ (2000) Bacterial reductive dissolution of crystalline Fe(III) oxide in continuous-flow column reactors. Applied and Environmental Microbiology 66, 1062–1065.
Roden EE, McBeth JM, Bl€othe M, Percak-Dennett EM, Fleming EJ, Holyoke RR, Luther GW III, Emerson D, Schieber J (2012) The microbial ferrous wheel in a neutral pH groundwater seep. Frontiers in Microbiology 3, article 172.
Shiraishi F, Okumura T, Takahashi Y, Kano A (2010) Influence of microbial photosynthesis on tufa stromatolite formation and ambient water chemistry, SW Japan. Geochimica et Cosmochimica Acta 74, 5289–5304.
Slobodkin A, Reysenbach AL, Strutz N, Dreier M, Wiegel J (1997) Thermoterrabacterium ferrireducens gen. nov., sp. nov., a thermophilic anaerobic dissimilatory Fe(III)-reducing bacterium from a continental hot spring. International Journal of Systematic Bacteriology 47, 541–547.
Snoeyenbos-West OL, Nevin KP, Anderson RT, Lovley DR (2000) Enrichment of Geobacter species in response to stimulation of Fe(III) reduction in sandy aquifer sediments. Microbial Ecology 39, 153–167.
Straub KL, Hanzlik M, Buchholz-Cleven B (1998) The use of biologically produced ferrihydrite for the isolation of novel iron-reducing bacteria. Systematic and Applied Microbiology 21, 442–449.
Suzuki T, Hashimoto H, Matsumoto N, Furutani M, Kunoh H, Takada J (2011) Nanometer-scale visualization and structural analysis of the inorganic/organic hybrid structure of Gallionella ferruginea twisted stalks. Applied and Environmental Microbiology 77, 2877–2881.
Suzuki T, Hashimoto H, Itadani A, Matsumoto N, Kunoh H, Takada J (2012) Silicon and phosphorus linkage with iron via oxygen in the amorphous matrix of Gallionella ferruginea stalks. Applied and Environmental Microbiology 78, 236–241.
Takahashi Y, Hirata T, Shimizu H, Ozaki T, Fortin D (2007) A rare earth element signature of bacteria in natural waters? Chemical Geology 244, 569–583.
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28, 2731– 2739.
Teh YA, Dubinsky EA, Silver WL, Carlson CM (2008) Suppression of methanogenesis by dissimilatory Fe(III)-reducing bacteria in tropical rain forest soils: implications for ecosystem methane flux. Global Change Biology 14, 413–422.
Toner BM, Santelli CM, Marcus MA, Wirth R, Chan CS, McCollom T, Bach W, Edwards KJ (2009) Biogenic iron oxyhydroxide formation at mid-ocean ridge hydrothermal vents: Juan de Fuca Ridge. Geochimica et Cosmochimica Acta 73, 388–403.
Toner BM, Bequo TS, Michel FM, Sorensen JV, Templeton AS, Edwards KJ (2012) Mineralogy of iron microbial mats from Loihi Seamount. Frontiers in Microbiology 3, article 118. Urrutia MM, Roden EE, Fredrickson JK, Zachara JM (1998) Microbial and surface chemistry controls on reduction of synthetic Fe(III) oxide minerals by the dissimilatory ironreducing bacterium Shewanella alga. Geomicrobiology Journal. 15, 269–291.
Whiticar MJ (1999) Carbon and hydrogen isotope systematics of bacterial formation and oxidation of methane. Chemical Geology 161, 291–314.
Yu R, Gan P, MacKay AA, Zhang S, Smets BF (2010) Presence, distribution, and diversity of iron-oxidizing bacteria at a landfill leachate-impacted groundwater surface water interface. FEMS Microbiology Ecology 71, 260–271.
Zachara JM, Fredrickson JK, Li SM (1998) Bacterial reduction of crystalline Fe3+ oxides in single phase suspensions and subsurface materials. American Mineralogist 83, 1426–1443.
Zachara JM, Kukkadapu RK, Fredrickson JK, Gorby YA, Smith SC (2002) Biomineralization of poorly crystalline Fe(III) oxides by dissimilatory metal reducing bacteria (DMRB). Geomicrobiology Journal 19, 179–207.
Additional Supporting Information may be found in the online version of this article:
Fig. S1. Representative SEM images of sediment at 1 cm (A), 3 cm (B), 5 cm (C), 7 cm (D), and 9 cm (E).
Fig. S2. The XRD patterns of sediment up to 10 cm depths.