Changes in bacterial CO2 fixation with depth in agricultural soils
详细信息 查看全文
- 作者：Xiaohong Wu (1) (2)
Tida Ge (1) (2) (5)
Hongzhao Yuan (1)
Baozhen Li (1) (2)
Hanhua Zhu (1)
Ping Zhou (1) (2)
Fanggong Sui (3)
Anthony G. O’Donnell (2) (4)
Jinshui Wu (1) (2) (5) - 关键词：Autotrophic bacteria ; Atmospheric CO2 fixation ; RubisCO ; cbbL genes ; 14C continuous labeling ; Soil organic carbon (SOC) ; Soil depth
- 刊名：Applied Microbiology and Biotechnology
- 出版年：2014
- 出版时间：March 2014
- 年：2014
- 卷：98
- 期：5
- 页码：2309-2319
- 全文大小：445 KB
- 参考文献：1. Alfreider A, Schirmer M, Vogt C (2011) Diversity and expression of different forms of RubisCO genes in polluted groundwater under different redox conditions. FEMS Microbiol Ecol 79:649-60 CrossRef
2. Andersson I, Backlund A (2008) Structure and function of Rubisco. Plant Physiol Biochem 46:275-91 CrossRef
3. Ashida H, Danchin A, Yokota A (2005) Was photosynthetic RubisCO recruited by acquisitive evolution from RuBisCO–like proteins involved in sulfur metabolism? Res Microbiol 156:611-18 CrossRef
4. Butler JL, Williams MA, Bottomley PJ, Myrold DD (2003) Microbial community dynamics associated with rhizosphere carbon flow. Appl Environ Microbiol 69:6793-800 CrossRef
5. Cannon GC, Bradburne CE, Aldrich HC, Baker SH, Heinhorst S, Shively JM (2001) Microcompartments in prokaryotes: carboxysomes and related polyhedra. Appl Environ Microbiol 67:5351-361 CrossRef
6. Dannenberg S, Conrad R (1999) Effect of rice plants on methane production and rhizospheric metabolism in paddy soil. Biogeochemistry 45:53-1
7. Ezaki S, Maeda N, Kishimoto T, Atomi H, Imanaka T (1999) Presence of a structurally novel type ribulose–bisphosphate carboxylase/oxygenase in the hyperthermophilic archaeon, / Pyrococcus kodakaraensis KOD1. J Biol Chem 274:5078-082 CrossRef
8. Fang CM, Moncrieff JB (2005) The variation of soil microbial respiration with depth in relation to soil carbon composition. Plant Soil 268:243-53 CrossRef
9. Freeman KR, Pescador MY, Reed SC, Costello EK, Robeson M, Schmidt SK (2009) Soil CO2 flux and photoautotrophic community composition in high-elevation, 'barren' soil. Environ Microbiol 11:674-86 CrossRef
10. Friedrich B, Hogrefe C, Schlegel HG (1981) Naturally occurring genetic transfer of hydrogen-oxidizing ability between strains of / Alcaligenes eutrophus. J Bacteriol 147:198-05
11. Ge TD, Yuan HZ, Zhu HH, Wu XH, Nie SA, Liu C, Tong CL, Wu J, Brookes P (2012) Biological carbon assimilation and dynamics in a flooded rice–soil system. Soil Biol Biochem 48:39-6 CrossRef
12. Ge TD, Wu XH, Chen XJ, Yuan HZ, Zou ZY, Li BZ, Zhou P, Liu SL, Tong CL, Brookes P, Wu JS (2013) Microbial phototrophic fixation of atmospheric CO2 in China subtropical upland and paddy soils. Geochim Cosmochim Acta 113:70-8 CrossRef
13. Guo LP, Lin ED (2001) Carbon sink in cropland soils and the emission of greenhouse gases from paddy soils: a review of work in China. Chemosphere 3:413-18
14. Hanson TE, Tabita FR (2001) A ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO)–like protein from / Chlorobium tepidum that is involved with sulfur metabolism and the response to oxidative stress. PNAS 98:4397-402 CrossRef
15. Hart KM, Oppenheimer SF, Moran BW, Allen CCR, Kouloumbos V, Simpson AJ, Kulakov LA, Barron L, Kelleher BP (2013) CO2 uptake by a soil microcosm. Soil Biol Biochem 57:615-24 CrossRef
16. Jenkins SN, Rushton SP, Lanyon CV, Whiteley AS, Waite IS, Brookes PC, Kemmitt S, Evershed RP, O'Donnell AG (2010) Taxon-specific responses of soil bacteria to the addition of low level C inputs. Soil Biol Biochem 42:1624-631 CrossRef
17. Kellermann C, Selesi D, Lee N, Hügler M, Esperschütz J, Hartmann A, Griebler C (2012) Microbial CO2 fixation potential in a tar-oil-contaminated porous aquifer. FEMS Microbiol Ecol 81:172-87 CrossRef
18. Kellogg CE (1993) Soil survey division staff: soil survey manual. United States Department of Agriculture, Washington
19. Kimura M, Murase J, Lu YH (2004) Carbon cycling in rice field ecosystems in the context of input, decomposition and translocation of organic materials and the fates of their end products (CO2 and CH4). Soil Biol Biochem 36:1399-416 CrossRef
20. Kleiveland CR, Hult LTO, Kuczkowska K, Jacobsen M, Lea T, Pope PB (2012) Draft genome sequence of the Methane-oxidizing bacterium / Methylococcus capsulatus (Texas). J Bacteriol 194:6626 CrossRef
21. K?gel-Knabner I, Amelung W, Cai Z, Fiedler S, Frenzel P, Jahn R, Kalbitz K, K?lbl A, Schloter M (2010) Biogeochemistry of paddy soils. Geoderma 157:1-4 CrossRef
22. Kusian B, Bowien B (1997) Organization and regulation of / cbb CO2 assimilation genes in autotrophic bacteria. FEMS Microbiol Rev 21:135-55 CrossRef
23. Kuzyakov Y, Schneckenberger K (2004) Review of estimation of plant rhizodeposition and their contribution to soil organic matter formation. Arch Agron Soil Sci 50:115-32 CrossRef
24. Kuzyakov Y, Ehrensberger H, Stahr K (2001) Carbon partitioning and below-ground translocation by / Lolium perenne. Soil Biol Biochem 33:61-4 CrossRef
25. Lacis AA, Schmidt GA, Rind D, Ruedy RA (2010) Atmospheric CO2: principal control knob governing earth's temperature. Science 330:356-59 CrossRef
26. Lal R (2002) Soil carbon sequestration in China through agricultural intensification, and restoration of degraded and desertified ecosystems. Land Degrad Dev 13:469-78 CrossRef
27. Lee JC, Kim JH, Chang WS, Park D (2012) Biological conversion of CO2 to CH4 using hydrogenotrophic methanogen in a fixed bed reactor. J Chem Technol Biotechnol 87:844-47 CrossRef
28. Liang BC, Wang XL, Ma BL (2002) Maize root–induced change in soil organic carbon pools. Soil Sci Soc Am J 66:845-47 CrossRef
29. Lu YH, Watanabe A, Kimura M (2004a) Contribution of plant photosynthates to dissolved organic carbon in a flooded rice soil. Biogeochemistry 71:1-5 CrossRef
30. Lu YH, Murase J, Watanabe A, Sugimoto A, Kimura M (2004b) Linking microbial community dynamics to rhizosphere carbon flow in a wetland rice soil. FEMS Microbiol Ecol 48:179-86 CrossRef
31. Miltner A, Richnow HH, Kopinke FD, Stner MK (2004) Assimilation of CO2 by soil microorganisms and transformation into soil organic matter. Org Geochem 35:1015-024 CrossRef
32. Miltner A, Kopinke FD, Kindler R, Selesi D, Hartmann A, K?stner M (2005) Non-phototrophic CO2 fixation by soil microorganisms. Plant Soil 269:193-03 CrossRef
33. Müller T, H?per H (2004) Soil organic matter turnover as a function of the soil clay content: consequences for model applications. Soil Biol Biochem 36:877-88 CrossRef
34. Nanba K, King GM, Dunfield K (2004) Analysis of facultative lithotrophic distribution and diversity on volcanic deposits by use of the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase. Appl Environ Microbiol 70:2245-253 CrossRef
35. O’Donnell AG, Jenkins SN, Whiteley AS (2011) RNA-radioisotope probing for studying carbon metabolism in soils. In: Murrell JC, Whiteley AS (eds) Stable isotope probing and related technologies. Washington DC, ASM Press, pp 317-32
36. Pachauri RK, Reisinger A (2007) Climate change 2007: synthesis report. Intergovernmental Panel on Climate Change, Cambridge
37. Pan GX, Li LQ, Wu LS, Zhang XH (2003) Storage and sequestration potential of topsoil organic carbon in China's paddy soils. Glob Chang Boil 10:79-2 CrossRef
38. Pan GX, Wu LS, Li LQ, Zhang XH, Gong W, Wood Y (2008) Organic carbon stratification and size distribution of three typical paddy soils from Taihu Lake region, China. J Environ Sci 20:456-63 CrossRef
39. Priha O, Smolander A (1999) Nitrogen transformations in soil under / Pinus sylvestris, / Picea abies and / Betula pendula at two forest sites. Soil Biol Biochem 31:965-77 CrossRef
40. Selesi D, Schmid M, Hartmann A (2005) Diversity of green–like and red–like ribulose-,5–bisphosphate carboxylase/oxygenase large–subunit genes ( / cbbL) in differently managed agricultural soils. Appl Environ Microbiol 71:175-84 CrossRef
41. Selesi D, Pattis I, Schmid M, Kandeler E, Hartmann A (2007) Quantification of bacterial RubisCO genes in soils by / cbbL targeted real-time PCR. J Microbiol Meth 69:497-03 CrossRef
42. Shively JM, van Keulen G, Meijer WF (1998) Something from almost nothing: carbon dioxide fixation in chemoautotrophs. Annu Rev Microbiol 52:191-30 CrossRef
43. Stanley EH, Johnson MD, Ward AK (2003) Evaluating the influence of macrophytes on algal and bacterial production in multiple habitats of a freshwater wetland. Limnol Oceanogr 48:1101-111 CrossRef
44. Tabita FR (1999) Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: a different perspective. Photosynth Res 60:1-8 CrossRef
45. Takai K, Campbell BJ, Cary SC, Suzuki M, Oida H, Nunoura T, Hirayama H, Nakagawa S, Suzuki Y, Inagaki F, Horikoshi K (2005) Enzymatic and genetic characterization of carbon and energy metabolisms by deep-sea hydrothermal chemolithoautotrophic isolates of / Epsilonproteobacteria. Appl Environ Microbiol 71:7310-320 CrossRef
46. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-599 CrossRef
47. Tcherkez GGB, Farquhar GD, Andrews TJ (2006) Despite slow catalysis and confused substrate specificity, all ribulose bisphosphate carboxylases may be nearly perfectly optimized. Proc Natl Acad Sci USA 103:7246-251
48. Tolli J, King GM (2005) Diversity and structure of bacterial chemolithotrophic communities in pine forest and agroecosystem soils. Appl Environ Microbiol l71:8411-418 CrossRef
49. Watanabe A, Machida N, Takahashi K, Kitamura S, Kimura M (2004) Flow of photosynthesized carbon from rice plants into the paddy soil ecosystem at different stages of rice growth. Plant Soil 258:151-60 CrossRef
50. Williams MA, Myrold DD, Bottomley PJ (2006) Carbon flow from 13C-labeled straw and root residues into the phospholipid fatty acids of a soil microbial community under field conditions. Soil Biol Biochem 38:759-68 CrossRef
51. World Meteorological Organization (2009) The state of greenhouse gases in the atmosphere using global observations through 2008. WMO Greenhouse Gas Bulletin, Switzerland
52. Wu J, O'Donnell AG (1997) Procedure for the simultaneous analysis of total and radioactive carbon in soil and plant materials. Soil Biol Biochem 29:199-02 CrossRef
53. Wu J, Joergensen RG, Pommerening B, Chaussod R, Brookes PC (1990) Measurement of soil microbial biomass C by fumigation–extraction—an automated procedure. Soil Biol Biochem 22:1167-169 CrossRef
54. Yuan HZ, Ge TD, Chen CY, O'Donnel AG, Wu JS (2012a) Microbial autotrophy plays a significant role in the sequestration of soil carbon. Appl Environ Microbiol 78:2328-336 CrossRef
55. Yuan HZ, Ge TD, Wu XH, Liu SL, Tong CL, Qin HL, Wu MN, Wei WX, Wu JS (2012b) Long-term field fertilization alters the diversity of autotrophic bacteria based on the ribulose-1,5-biphosphate carboxylase/oxygenase (RubisCO) large-subunit genes in paddy soil. Appl Microbiol Biotechnol 95:1061-071 CrossRef - 作者单位：Xiaohong Wu (1) (2)
Tida Ge (1) (2) (5)
Hongzhao Yuan (1)
Baozhen Li (1) (2)
Hanhua Zhu (1)
Ping Zhou (1) (2)
Fanggong Sui (3)
Anthony G. O’Donnell (2) (4)
Jinshui Wu (1) (2) (5)
1. Changsha Research Station for Agricultural and Environmental Monitoring and Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, 410125, China
2. ISA-CAS and UWA Joint Laboratory for Soil Systems Biology, Hunan, 410125, China
5. Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, 410125, China
3. School of Resource and Environment, Qingdao Agricultural University, Qingdao, 266109, China
4. Institute of Agriculture, Faculty of Science, University of Western Australia, Crawley, WA, 6009, Australia - ISSN：1432-0614
文摘
Soils were incubated continuously in an atmosphere of 14CO2 and the distribution of labeled C into soil organic carbon (14C-SOC) was determined at 0-, 1-, and 5-7?cm down the profile. Significant amounts of 14C-SOC were measured in paddy soils with a mean of 1,180.6?±-05.2?mg?kg- at 0-?cm and 135.3?±-7.1?mg?kg? at 1-?cm. This accounted for 5.9?±-.7?% and 0.7?±-.2?%, respectively, of the total soil organic carbon at these depths. In the upland soils, the mean 14C-SOC concentrations were 43 times (0-?cm) and 11 times (1-?cm) lower, respectively, than those in the paddy soils. The amounts of 14C incorporated into the microbial biomass (MBC) were also much lower in upland soils (5.0?±-.6?% and 2.9?±-.9?% at 0- and 1-?cm, respectively) than in paddy soils (34.1?±-2.4?% and 10.2?±-.1?% at 0- and 1-?cm, respectively). Similarly, the amount of 14C incorporated into the dissolved organic carbon (DOC) was considerably higher in paddy soils (26.1?±-.9?% and 6.9?±-.3?% at 0- and 1-?cm, respectively) than in upland soils (6.0?±-.7?% and 4.3?±-.2?%, respectively). The observation that the majority of the fixed 14C-SOC, RubisCO activity and cbbL gene abundance were concentrated at 0-?cm depth and the fact that light is restricted to the top few millimeters of the soil profiles highlighted the importance of phototrophs in CO2 fixation in surface soils. Phylogenetic analysis of the cbbL genes showed that the potential for CO2 fixation was evident throughout the profile and distributed between both photoautotrophic and chemoautotrophic bacteria such as Rhodopseudomonas palustris, Bradyrhizobium japonicum, Rubrivivax gelatinosus and Ralstonia eutropha.