Chemistry and Microbial Functional Diversity Differences in Biofuel Crop and Grassland Soils in Multiple Geographies

Bioenergy Research

Volumn 6, Issue 2, 2013, Pages 601-619

  Watrud, Lidia S ^a   Reichman, Jay R ^a   Bollman, Michael A ^a   Smith, Bonnie M ^a   Lee, E Henry ^a   Jastrow, Julie D ^b   Casler, Michael D ^c   Collins, Harold P ^d   Fransen, Steven ^e   Mitchell, Robert B ^f   Owens, Vance N ^g   Bean, Brent ^h   Rooney, William L ⁱ   Tyler, Donald D ^j   King, George A ^k  

^a U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

^b ARGONNE NATIONAL LABORATORY   (United States)

^c AGRICULTURAL RESEARCH SERVICE   (United States)

^d U S DEPARTMENT OF AGRICULTURE   (United States)

^e WASHINGTON STATE UNIVERSITY   (United States)

^f UNIVERSITY OF NEBRASKA LINCOLN   (United States)

^g SOUTH DAKOTA STATE UNIVERSITY   (United States)

^h TEXAS A AND M UNIVERSITY   (United States)

ⁱ TEXAS A AND M UNIVERSITY   (United States)

^j UNIVERSITY OF TENNESSEE   (United States)

^k DYNAMAC CORPORATION   (United States)

more..

Author keywords

Functional gene array; GeoChip; Soil ecosystem services; Sorghum; Switchgrass

Indexed keywords

FUNCTIONAL GENES; GEOCHIP; SOIL ECOSYSTEMS; SORGHUM; SWITCHGRASS;

BIOFUELS; CROPS; CULTIVATION; ECOSYSTEMS; GENES; PLANTS (BOTANY);

SOILS;

BACTERIA (MICROORGANISMS); PANICUM VIRGATUM; SORGHUM BICOLOR;

EID: 84877003703     PISSN: 19391234     EISSN: 19391242     Source Type: Journal    
DOI: 10.1007/s12155-012-9279-y     Document Type: Article

References (56)

1. Ragauskas AJ, Williams CK, Davison BH, Britovsek G, Cairney J, Eckert CA et al (2006) The path forward for biofuels and biomaterials. Sci 311(5760): 484-489. doi: 10. 1126/science. 1114736.
2. Fargione J, Hill J, Tilman D, Polasky S, Hawthorne P (2008) Land clearing and the biofuel carbon debt. Sci 319(5867): 1235-1238. doi: 10. 1126/science. 1152747.
3. Carroll A, Somerville C (2009) Cellulosic biofuels. Annual Rev Plant Biology 60(1): 165-182. doi: 10. 1146/annurev. arplant. 043008. 092125.
4. Davis SC, Anderson-Teixeira KJ, DeLucia EH (2009) Life-cycle analysis and the ecology of biofuels. Trends Plant Sci 14(3): 140-146.
5. Tilman D, Socolow R, Foley JA, Hill J, Larson E, Lynd L et al (2009) Beneficial biofuels-the food, energy, and environment trilemma. Sci 325(5938): 270-271. doi: 10. 1126/science. 1177970.
6. Moon HS, Abercrombie JM, Kausch AP, Stewart CN Jr (2010) Sustainable use of biotechnology for bioenergy feedstocks. Environ Manag 46(4): 531-538. doi: 10. 1007/s00267-010-9503-5.
7. Hill J, Nelson E, Tilman D, Polasky S, Tiffany D (2006) Environmental, economic, and energetic costs and benefits of biodiesel and ethanol biofuels. PNAS 103(30): 11206-11210. doi: 10. 1073/pnas. 0604600103.
8. Tilman D, Wedin D, Knops J (1996) Productivity and sustainability influenced by biodiversity in grassland ecosystems. Nat 379(6567): 718-720.
9. Hooper DU, Vitousek PM (1997) The effects of plant composition and diversity on ecosystem processes. Sci 277(5330): 1302-1305.
10. Tilman D, Hill J, Lehman C (2006) Carbon-negative biofuels from low-input high-diversity grassland biomass. Sci 314(5805): 1598-1600. doi: 10. 1126/science. 1133306.
11. Dale VH, Kline KL, Wiens J, Fargione J (2010) Biofuels: implications for land use and biodiversity. Ecological Society of America, Washington, DC.
12. Maestre FT, Quero JL, Gotelli NJ, Escudero A, Ochoa V, Delgado-Baquerizo M et al (2012) Plant species richness and ecosystem multifunctionality in global drylands. Sci 335(6065): 214-218. doi: 10. 1126/science. 1215442.
13. Midgley GF (2012) Biodiversity and ecosystem function. Sci 335(6065): 174-175. doi: 10. 1126/science. 1217245.
14. Tilman D, Knops J, Wedin D, Reich P, Ritchie M, Siemann E (1997) The influence of functional diversity and composition on ecosystem processes. Sci 277(5330): 1300-1302. doi: 10. 1126/science. 277. 5330. 1300.
15. Dobranic JK, Zak JC (1999) A microtiter plate procedure for evaluating fungal functional diversity. Mycologia 91(5): 756-765.
16. Bossio DA, Girvan MS, Verchot L, Bullimore J, Borelli T, Albrecht A et al (2005) Soil microbial community response to land use change in an agricultural landscape of western Kenya. Microb Ecol 49(1): 50-62. doi: 10. 1007/s00248-003-0209-6.
17. He Z, Gentry TJ, Schadt CW, Wu L, Liebich J, Chong SC et al (2007) GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J 1(1): 67-77, http://www. nature. com/ismej/journal/v1/n1/suppinfo/ismej20072s1. html.
18. Yergeau E, Kang S, He Z, Zhou J, Kowalchuk GA (2007) Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect. ISME J 1(2): 163-179, http://www. nature. com/ismej/journal/v1/n2/suppinfo/ismej200724s1. html.
19. Zhang Y, Zhang X, Liu X, Xiao Y, Qu L, Wu L et al (2007) Microarray-based analysis of changes in diversity of microbial genes involved in organic carbon decomposition following land use/cover changes. FEMS Microbiol Lett 266(2): 144-151. doi: 10. 1111/j. 1574-6968. 2006. 00511. x.
20. Zhou J, Kang S, Schadt CW, Garten CT Jr (2008) Spatial scaling of functional gene diversity across various microbial taxa. PNAS 105(22): 7768-7773. doi: 10. 1073/pnas. 0709016105.
21. Berthrong ST, Schadt CW, Piñeiro G, Jackson RB (2009) Afforestation alters the composition of functional genes in soil and biogeochemical processes in South American grasslands. Appl Environ Microbiol 75(19): 6240-6248. doi: 10. 1128/aem. 01126-09.
22. Da C Jesus E, Susilawati E, Smith S, Wang Q, Chai B, Farris R et al (2010) Bacterial communities in the rhizosphere of biofuel crops grown on marginal lands as evaluated by 16S rRNA gene pyrosequences. BioEnergy Res 3(1): 20-27.
23. Lu Z, Deng Y, van Nostrand JD, He Z, Voordeckers J, Zhou A et al (2012) Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume. ISME J 6(2): 451-460, http://www. nature. com/ismej/journal/vaop/ncurrent/suppinfo/ismej201191s1. html.
24. DeSantis T, Brodie E, Moberg J, Zubieta I, Piceno Y, Andersen G (2007) High-density universal 16S rRNA Microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb Ecol 53(3): 371-383. doi: 10. 1007/s00248-006-9134-9.
25. Cole JR, Chai B, Farris RJ, Wang Q, Kulam SA, McGarrell DM et al (2005) The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res 33(suppl 1): D294-D296. doi: 10. 1093/nar/gki038.
26. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ et al (2009) The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37(suppl 1): D141-D145. doi: 10. 1093/nar/gkn879.
27. McGrath KC, Mondav R, Sintrajaya R, Slattery B, Schmidt S, Schenk PM (2010) Development of an environmental functional gene microarray for soil microbial communities. Appl Environ Microbiol 76(21): 7161-7170. doi: 10. 1128/aem. 03108-09.
28. Horneck DA, Hart JM, Topper K, Koepsell B (1989) Methods of soil analysis used in the Soil Testing Laboratory at Oregon State University. Agricultural Experiment Station, Oregon State University, Corvallis.
29. Ingham ER, Klein DA (1984) Soil fungi: relationships between hyphal activity and staining with fluorescein diacetate. Soil Biol Biochem 16(3): 273-278. doi: 10. 1016/0038-0717(84)90014-2.
30. Schnürer J, Rosswall T (1982) Fluorescein diacetate hydrolysis as a measure of total microbial activity in soil and litter. Appl Environ Microbiol 43(6): 1256-1261.
31. van Veen JA, Ladd JN, Frissel MJ (1984) Modelling C and N turnover through the microbial biomass in soil. Plant Soil 76(1): 257-274. doi: 10. 1007/bf02205585.
32. Hazen TC, Dubinsky EA, DeSantis TZ, Andersen GL, Piceno YM, Singh N et al (2010) Deep-sea oil plume enriches indigenous oil-degrading bacteria. Sci 330(6001): 204-208. doi: 10. 1126/science. 1195979.
33. He Z, Deng Y, van Nostrand JD, Tu Q, Xu M, Hemme CL et al (2010) GeoChip 3. 0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity. ISME J 4(9): 1167-1179, http://www. nature. com/ismej/journal/v4/n9/suppinfo/ismej201046s1. html.
34. Wu L, Liu X, Schadt CW, Zhou J (2006) Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification. Appl Environ Microbiol 72(7): 4931-4941. doi: 10. 1128/aem. 02738-05.
35. Liang Y, He Z, Wu L, Deng Y, Li G, Zhou J (2010) Development of a common oligonucleotide reference standard for microarray data normalization and comparison across different microbial communities. Appl Environ Microbiol 76(4): 1088-1094. doi: 10. 1128/aem. 02749-09.
36. He Z, Xu M, Deng Y, Kang S, Kellogg L, Wu L et al (2010) Metagenomic analysis reveals a marked divergence in the structure of belowground microbial communities at elevated CO2. Ecol Lett 13(5): 564-575. doi: 10. 1111/j. 1461-0248. 2010. 01453. x.
37. Girvan MS, Bullimore J, Pretty JN, Osborn AM, Ball AS (2003) Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Appl Environ Microbiol 69(3): 1800-1809. doi: 10. 1128/aem. 69. 3. 1800-1809. 2003.
38. Bezemer TM, Lawson CS, Hedlund K, Edwards AR, Brook AJ, Igual JM et al (2006) Plant species and functional group effects on abiotic and microbial soil properties and plant-soil feedback responses in two grasslands. J Ecol 94(5): 893-904. doi: 10. 1111/j. 1365-2745. 2006. 01158. x.
39. Pereira e Silva MC, Poly F, Guillaumaud N, van Elsas JD, Falcao Salles J (2012) Fluctuations in ammonia oxidizing communities across agricultural soils are driven by soil structure and pH. Front Microbiol 3. doi: 10. 3389/fmicb. 2012. 00077.
40. Di Giovanni GD, Watrud LS, Seidler RJ, Widmer F (1999) Comparison of parental and transgenic alfalfa rhizosphere bacterial communities using biolog GN metabolic fingerprinting and enterobacterial repetitive intergenic consensus sequence-PCR (ERIC-PCR). Microb Ecol 37(2): 129-139. doi: 10. 1007/s002489900137.
41. Grayston SJ, Wang S, Campbell CD, Edwards AC (1998) Selective influence of plant species on microbial diversity in the rhizosphere. Soil Biol Biochem 30(3): 369-378. doi: 10. 1016/s0038-0717(97)00124-7.
42. Latour X, Corberand T, Laguerre G, Allard F, Lemanceau P (1996) The composition of fluorescent pseudomonad populations associated with roots is influenced by plant and soil type. Appl Environ Microbiol 62(7): 2449-2456.
43. Ben-Hammouda M, Kremer RJ, Minor HC (1995) Phytotoxicity of extracts from sorghum plant components on wheat seedlings. Crop Sci 35(6): 1652-1656.
44. Czarnota MA, Paul RN, Dayan FE, Nimbal CI, Weston LA (2001) Mode of action, localization of production, chemical nature, and activity of sorgoleone: a potent PSII inhibitor in Sorghum spp. root exudates. Weed Technol 15(4): 813-825.
45. Weston LA, Harmon R, Mueller S (1989) Allelopathic potential of sorghum-sudangrass hybrid (sudex). J Chem Ecol 15(6): 1855-1865.
46. Coelho MRR, Marriel IE, Jenkins SN, Lanyon CV, Seldin L, O'Donnell AG (2009) Molecular detection and quantification of nifH gene sequences in the rhizosphere of sorghum (Sorghum bicolor) sown with two levels of nitrogen fertilizer. Appl Soil Ecol 42(1): 48-53. doi: 10. 1016/j. apsoil. 2009. 01. 010.
47. Hai B, Diallo NH, Sall S, Haesler F, Schauss K, Bonzi M et al (2009) Quantification of key genes steering the microbial nitrogen cycle in the rhizosphere of sorghum cultivars in tropical agroecosystems. Appl Environ Microbiol 75(15): 4993-5000. doi: 10. 1128/aem. 02917-08.
48. Coelho MRR, Da Mota FF, Carneiro NP, Marriel IE, Paiva E, Rosado AS et al (2007) Diversity of Paenibacillus spp. in the rhizosphere of four sorghum (Sorghum bicolor) cultivars sown with two contrasting levels of nitrogen fertilizer assessed by rpoB-based PCR-DGGE and sequencing analysis. J Microbiol Biotechnol 17(5): 753-760.
49. Mao Y, Yannarell AC, Mackie RI (2011) Changes in N-transforming Archaea and bacteria in soil during the establishment of bioenergy crops. PLoS One 6(9): 12. doi: 10. 1371/journal. pone. 0024750, e24750.
50. Culman SW, DuPont ST, Glover JD, Buckley DH, Fick GW, Ferris H et al (2010) Long-term impacts of high-input annual cropping and unfertilized perennial grass production on soil properties and belowground food webs in Kansas, USA. Agr Ecosyst Environ 137(1-2): 13-24, 10. 1016/j. agee. 2009. 11. 008.
51. Liang C, EdC J, Duncan DS, Jackson RD, Tiedje JM, Balser TC (2012) Soil microbial communities under model biofuel cropping systems in southern Wisconsin, USA: impact of crop species and soil properties. Appl Soil Ecol 54: 24-31. doi: 10. 1016/j. apsoil. 2011. 11. 015.
52. Arriola PE, Ellstrand NC (1996) Crop-to-weed gene flow in the genus Sorghum (Poaceae): spontaneous interspecific hybridization between johnsongrass, Sorghum halepense, and crop sorghum. S Bicolor American J Botany 83(9): 1153-1159.
53. Skinner K, Smith L, Rice PM (2000) Using noxious weed lists to prioritize targets for developing weed management strategies. Weed Sci 48(5): 640-644.
54. Warwick SI, Black LD (1983) The biology of Canadian weeds. 61. Sorghum halepense (L.) Pers. Canadian J Plant Sci 63(4): 997-1014.
55. Callaway RM, Thelen GC, Rodriguez A, Holben WE (2004) Soil biota and exotic plant invasion. Nat 427(6976): 731-733.
56. Reinhart KO, Callaway RM (2006) Soil biota and invasive plants. New Phytol 170(3): 445-457. doi: 10. 1111/j. 1469-8137. 2006. 01715. x.