Acosta-Martínez V, Dowd S, Sun Y, Allen V (2008) Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biol Biochem 40:2762-2770

Boon N, De Windt V, Verstraete W, Top EM (2002) Evaluation of nested PCR-DGGE (denaturing gradient gel electrophoresis) with group-specific 16S rRNA primers for the analysis of bacterial communities from different wastewater treatment plants. FEMS Microbiol Ecol 39:101-112

Britschgi TB, Giovannoni SJ (1991) Phylogenetic analysis of a natural marine bacterioplankton population by rRNA gene cloning and sequencing. Appl Environ Microbiol 57:1707-1713 Brosius J, Palmer ML, Kennedy PJ, Noller HF (1978) Complete nucleotide sequence of a 16S

ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci USA 75:4801-4805 Curl EA, Truelove B (1986) The rhizosphere. Springer, Berlin

Curtis TP, Sloan W, Scannell J (2002) Estimating prokaryotic diversity and its limits. Proc Natl

Acad Sci USA 99:10494-10499 De Angelis M, Di Cagno R, Gallo G, Curci M, Siragusa S, Crecchio C, Parente E, Gobbetti M (2007) Molecular and functional characterization of Lactobacillus sanfranciscensis strains isolated from sourdoughs. Int J Food Microbiol 114:69-82 Dunbar J, Takala S, Barns SM, Davis JA, Kuske CR (1999) Levels of bacterial community diversity in four arid soils compared by cultivation and 16rRNA gene cloning. Appl Environ Microbiol 65:1662-1669 Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791

Felske A, Weller R (2004) Cloning 16S rRNA genes and utilization to type bacterial communities. In: Kowalchuk GA, de Bruijn FJ, Head IM, Akkermans ADL, van Elsas JD (eds) Molecular microbial ecology manual, vol 3. Kluwer Academic, Netherlands, pp 523-542 Foereid B, Yearsley JM (2004) Modelling the impact of microbial grazers on soluble rhizodeposit turnover. Plant Soil 267:329-342 Fontaine S, Mariotti A, Abbadie L (2003) The priming effect of organic matter: a question of microbial competition? Soil Biol Biochem 35:837-843 Frackman S, Kephart D (1999) Rapid Ligation for the pGEM®-T and pGEM®-T Easy Vector

Systems. Promega Notes 71:8-12 Frothingham R, Allen RL, Wilson KH (1991) Rapid 16S ribosomal DNA sequencing from a single colony without DNA extraction or purification. Biotechniques 11:40-44 Griffiths RI, Whiteley AS, O'Donnell AG, Bailey MJ (2000) Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA and rRNA-based microbial community composition. Appl Environ Microbiol 66:5488-5491 Hall TA (1999) BIOEDIT: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp 41:95-98 Hassink J, Bouwman LA, Zwart KB, Brussard L (1993) Relationships between habitable pore space, soil biota and mineralisation rates in grassland soils. Soil Biol Biochem 25:47-55 Heuer H, Smalla K (1997) Application of denaturing gradient gel electophoresis and temperature gradient gel electrophoresis for studying soil microbial communities. In: van Elsas JD, Wellington EMH, Trevors JT (eds) Modern soil microbiology. Dekker, New York, pp 353-373 Hill GT, Mitkowski NA, Aldrich-Wolfe L, Emele LR, Jurkonie DD, Ficke A, Maldonado-Ramirez S, Lynch ST, Nelson EB (2000) Methods for assessing the composition and diversity of soil microbial communities. Appl Soil Ecol 15:25-36 Hodge A, Robinson D, Fitter AH (2000) An arbuscular mycorrhizal inoculum enhances root proliferation in, but not nitrogen capture from, nutrient-rich patches in soil. New Phytol 145:575-584

Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic, New York, pp 21-132 Kiem R, Kogel-Knabner I (2003) Contribution of lignin and polysaccharides to the refractory carbon pool in C-depleted arable soils. Soil Biol Biochem 35:101-118 Kindler R, Miltnera A, Richnowb HH, Matthias Kästner M (2006) Fate of gram-negative bacterial biomass in soil-mineralization and contribution to SOM. Soil Biol Biochem 38:2860-2870 Krave AS, Lin B, Braster M, Laverman AM, van Straalen NM, Roäling WFM, van Verseveld HW (2002) Stratification and seasonal stability of diverse bacterial communities in a Pinus merkusii (pine) forest soil in central Java, Indonesia. Environ Microbiol 4:361-373 Kuikman PJ, Jansen AG, van Veen JA, Zehnder AJB (1990a) Protozoan predation and the turnover of soil organic carbon and nitrogen in the presence of plants. Biol Fertil Soils 10:22-28

Kuikman PJ, van Elsas JD, Jansen AG, Burgers SLGE, van Veen JA (1990b) Population dynamics and activity of bacteria and protozoa in relation to their spatial distribution in soil. Soil Biol Biochem 22:1063-1073

Ladd JN, Forster RC, Nannipieri P, Oades JM (1996) Soil structure and biological activity. In:

Stotzky G, Bollag JM (eds) Soil biochemistry. Dekker, New York, pp 23-78 Lagomarsino A, Moscatelli MC, De Angelis P, Greco S (2006) Labile substrates quality as the main driving force of microbial mineralization activity in a poplar plantation soil under elevated CO2 and nitrogen fertilization. Sci Total Environ 372:256-265 Maidak BL, Larsen N, McCaughey MJ, Overbeek R, Olsen GJ, Fogel K, Blandy J, Woese CR

(1994) The ribosomal database project. Nucleic Acids Res 22:3485-3487 Maidak BL, Olsen GJ, Larsen N, Overbeck R, McCaughey MJ, Woese CR (1997) The ribosomal database project (RDP). Nucleic Acids Res 25:109-110 Muyzer G, de-Waal EC, Uitterlinden AG (1993) Profiling of complex microbial population by denaturating gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695-700 Nannipieri P, Ascher J, Ceccherini MT, Landi L, Pietramellara G, Renella G (2003) Microbial diversity and soil functions. Eur J Soil Sci 54:655-670 Nicolardot B, Recous S, Mary B (2001) Simulation of C and N mineralisation during crop residue decomposition: a simple dynamic model based on the C:N ratio of the residues. Plant Soil 228:83-103

Ogram AV (2000) Soil molecular ecology at age 20: methodological challenges for the future. Soil

Biol Biochem 32:1499-1504 Ogram A, Sayler GS, Barkay T (1987) The extraction and purification of microbial DNA from sediments. J Microbiol Methods 7:57-66 Paustian K, Elliott ET, Killian K (1998) Modeling soil carbon in relation to management and climate change in some agroecosystems in central North America. In: Lal R, Kimble JM, Follett RF, Stewart BA (eds) Soil processes and the carbon cycle. CRC, Boca Raton, FL, pp 459-471

Prosser JI (2002) Molecular and functional diversity in soil micro-organisms. Plant Soil 244:9-17 Rademaker JL, De Bruijn WFJ (2004) Computer-assisted analysis of molecular fingerprint profiles and database construction. In: Kowalchuk GA, de Bruijn FJ, Head IM, Akkermans ADL, van Elsas JD (eds) Molecular microbial ecology manual, vol 7, 2nd edn. Kluwer Academic, Netherlands, pp 1397-1446 Ronaghi M (2001) Pyrosequencing sheds light on DNA sequencing. Genome 11:3-11 Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlin HA (1988) Primed-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487-494

Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phyloge-

netic trees. Mol Biol Evol 4:406-425 Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold

Spring Harbor Laboratory, Cold Spring Harbor, NY Simpson A, Simpson M, Smith E, Kelleher B (2007) Microbially derived inputs to soil organic matter: are current estimates too low? Environ Sci Technol 41:8070-8076 Smit E, Leeflang P, Wernars K (1997) Detection of shifts in microbial community structure and diversity in soil caused by copper contamination using amplified ribosomal DNA restriction analysis. FEMS Microbiol Ecol 23:249-261 Smith JL, Papendick RI, Bezdicek DF, Lynch JM (1993) Soil organic matter dynamics and crop residue management. In: Meetting JFB (ed) Soil microbial ecology. Dekker, New York, pp 65-94

Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680 Torsvik VL (1980) Isolation of bacterial DNA from soil. Soil Biol Biochem 12:15-121

Torsvik V, Ovreas L, Thingstad TF (2002) Prokaryotic diversity: magnitude, dynamics, and controlling factors. Science 296:1064-1066 Toyota K, Kuninaga S (2006) Comparison of soil microbial community between soils amended with or without farmyard manure. Appl Soil Ecol 33:39-48 Trevors JT (1998) Molecular evolution in bacteria: cell division. Microbiol Rev 29:237-245 Van de Peer YR, De Wachter H (1997) Construction of evolutionary distance trees with TREECON for Windows: accounting for variation in nucleotide substitution rate among sites. Comput Appl Biosci 13:227-230 von Lutzow M, Kogel-Knabner I, Ekschmitt K, Matzner E, Guggenberger G, Marschner B, Flessa H (2006) Stabilization of organic matter in temperate soils: mechanisms and their relevance under different soil conditions. Eur J Soil Sci 57:426-445 Wang GCY, Wang Y (1997) Frequency of formation of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes. Appl Environ Microbiol 63:4645-4650 Ward DM, Bateson MM, Weller R, Ruff Roberts AL (1992) Ribosomal RNA analysis of microorganisms as they occur in nature. In: Marshall KC (ed) Advances in microbial ecology. Plenum, New York, pp 219-286 Wertz S, Czarnes S, Batoli F, Renault P, Commeaux C, Guillaumaud N, Clays-Josserand A (2007) Early-stage bacterial colonization between a sterilized remoulded soil clod and natural soil aggregates of the same soil. Soil Biol Biochem 39:3127-3137 Zoetendal EG, Akkermans ADL, de Vos WM (1998) Temperature gradient gel electrophoresis of 16rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl Environ Microbiol 4:3854-3859

Was this article helpful?

0 0
Guide to Alternative Fuels

Guide to Alternative Fuels

Your Alternative Fuel Solution for Saving Money, Reducing Oil Dependency, and Helping the Planet. Ethanol is an alternative to gasoline. The use of ethanol has been demonstrated to reduce greenhouse emissions slightly as compared to gasoline. Through this ebook, you are going to learn what you will need to know why choosing an alternative fuel may benefit you and your future.

Get My Free Ebook

Post a comment