Chapter 1 Introduction and Literature Review

НазваниеChapter 1 Introduction and Literature Review
Дата конвертации12.02.2013
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7.2 References

Barbieri, E., Guidi, C., Bertaux, J., Frey-Klett, P., Garbaye, J., Ceccaroli, P., Saltarelli, R., Zambonelli, A., and Stocchi, V. 2007. Accurance and diversity of bacterial communities in Tuber magnatum during truffle maturation. Environmental Microbiology 9, 2234–2246.

Feng, X., Simpson, A. J., and Simpson, M. J. 2005. Chemical and mineralogical controls on humic acid sorption to clay mineral surfaces. Organic Geochemistry 36, 1553–1566.

Feng, X., Simpson, A. J., and Simpson, M. J. 2006. Investigating the role of mineral-bound humic acid in phenanthrene sorption. Environmental Science and Technology 40, 3260–3266.

Kaiser, K., Guggenberger, G., Haumaier, L., and Zech, W. 2001. Seasonal variation in the chemical composition of dissolved organic matter in organic forest floor layer leachates of old-growth Scots pine (Pinus sylvestris L.) and European beech (Fagus sylvatica L.) stands in northeastern Bavaria, Germany. Biochemistry 55, 103–143.

Kelleher, B. P., Simpson, M. J., and Simpson, A. J. 2006. Assessing the fate and transformation of plant residues in the terrestrial environment using HR-MAS NMR Spectroscopy. Geochimica et Cosmochimica Acta 70, 4080–4094.

Knicker, H. 2000. Biogenic nitrogen in soils as revealed by solidstate carbon-13 and nitrogen-15 nuclear magnetic resonance spectroscopy. Journal of Environmental Quality 29, 715–723.

Knicker., H., Scaroni, A. W., and Hatcher, P. G. 1996. 13C and 15N NMR spectroscopic investigation on the formation of fossil algal residues. Organic Geochemistry 24, 661–669.

Mopper, K., Zhou, X., Kieber, R. J., Kieber, D. I., Sikorski, R. J., and Jones, R. D. 1991. Photochemical degradation of dissolved organic carbon and its impact on oceanic carbon cycle. Nature 353, 60–62.

Otto, A., Chubashini, S., and Simpsom, M. J. 2005. A comparison of plant and microbial biomarkers in grassland soils from the Prairie Ecozone of Canada. Organic Geochemistry 36, 425–448.

Schulze, W. X. 2005. Protein analysis in dissolved organic matter: what proteins from organic debris, soil leachate and surface water can tell us – a prospective. Biogeosciences 2, 75–86.

Schulze, W. X., Gleixner, G., and Kaiser, K. 2005. A proteomic fingerprint of dissolve organic carbon of soil particles. Oecologia 142, 335–343.

Simpson, A. J., Simpson, M. J., Kingery, W, L., Lefebvre, B. A., Moser, A., Williams, A. J., Kvasha, M., and Kelleher, B. P. 2006. The application of 1H high-resolution magic-angle spinning NMR for the study of clay–organic associations in natural and synthetic complexes. Langmuir 22, 4498–4508.

Simpson, A. J., Simpson, M. J., Smith, E., and Kelleher, B. P. 2007. Microbially derived inputs to soil organic matter: are current estimates too low? Environmental Science and Technology 41, 8070–8076.

Tréguer, P., Nelson, D. M., and Van Bennekom, A. J. 1995. The silica balance in the world ocean: a reestimate. Science 268, 375–379.


List of abbreviations

(15NH4)2SO4 heavy nitrogen isotope labelleg ammonium sulphate

(E) trans

(Z) cis

[(CH2)n] C polymethylenic carbon

~ approximately

°2θ two degrees theta

‰ per mil

1°2θ/min one degree two theta per minute

13C HSQC heavy carbon isotope Heteronuclear Single-Quantum Correlation spectroscopy

13C heavy carbon isotope

13C-13C 13C-13C Chemical Shift

14C radiogenic carbon isotope

1525r 1525 reverse

15N heavy nitrogen isotope

16S rRNA 16S ribosomal ribonucleic acid

1-D 13C NMR one-dimensional carbon Nuclear Magnetic Resonance

1-D 1H one-dimensional proton Nuclear Magnetic Resonance

1H HR-MAS proton High resolution Magic Angle Spinning

1H NMR proton Nuclear Magnetic Resonance

1H-13C 1H-13C Chemical Shift

1H-15N 1H-15N Chemical Shift

1O2 singlet oxygen

1x TAE 1x concentration Tris-acetate-EDTA

1x 1x concentration

27f 27 forward

2-D 13C NMR two-dimensional carbon Nuclear Magnetic Resonance

2-D 15N NMR two-dimensional nitrogen Nuclear Magnetic Resonance

2-D HSQC two-dimensional Heteronuclear Single-Quantum Correlation spectroscopy

3’- 3 prime

31P NMR phosphorus Nuclear Magnetic Resonance

3-D three dimensional

5’- 5 prime

Å Angstrom

ACCA α-cyano-4-hydroxycinnamic acid

ACD Advanced Chemistry Development

ADEQUATE Abundance Double Quantum Transfer Experiment

ADP adenosine diphosphate

AHY acid hydrolysis

Arg (R) argentine

ATP adenosine triphosphate

BLAST Basic Local Alignment Search Tool

BSA Bovine Serum Albumen

BSTFA N,O-bis-(trimethylsilyl)trifluoroacetamide

Bt Bacillus thuringiensis

c cis

C=O carbonyl group

CEC cationic exchange capacity

CH2 methylene

CH3 methyl

Cmax carbon maximum

CMS Clay Mineral Society

COO- carboxylate ion

CP MAS Cross Angle Polymerization Magic Angle Spinning

C-P carbon-phosphorus linkage

Cu-Kα cupper-Kalpha

Cys (C) cysteine

Cys–Cys cysteine

d(001) basal reflection

D2O deuterated water

D-Asp (D) D-aspartic acid

DE-NMR Diffusion Edited Nuclear magnetic Resonance

D-Glu (E) D-glutamic acid

D-Gly (G) D-glycine

D-His (H) D-histidine

D-Ile (I) D-isoleucine

D-Leu (L) D-leucine

D-Lys (K) D-lysine

DMSO-d6 deuterated Dimethyl sulfoxide

DNA deoxyribonucleic acid

DNB dilute nutrient broth

dNTPs deoxynucleotides

DOC dissolved organic carbon

DOM dissolved organic matter

D-Phe (F) D-phenylalanine

D-Pro (P) D-proline

D-Ser (S) D-serine

D-Thr (T) D-threonine

DTT 1,4-dithio-DL-threitol

D-Tyr (Y) D-tyrosine

D-Val (V) D-valine

EDTA ethylenediaminetetraacetic acid

EDTANa2·H2O sodium ethylenediaminetetraacetic acid·monohydrate

EI electron ionization

EPS extracellular polymeric substances

ESI electrospray ionization

EU European Union

eV electron voltave

Fe2+ ferrous ion

FT-IR Fourier Transform Infrared

GC-IR-MS gas chromatography isotope ratio mass spectrometry

GC-MS gas chromatography mass spectrometry

Glu (E) glutamic acid

Gt gigatons

HMQC Heteronuclear Multiple-Quantum Correlation spectroscopy

HS humic substances

HSQC Heteronuclear Single Quantum Coherence

i.d. identification

INADEQUATE Incredible Natural Abundance Double Quantum Transfer Experiment

IPCC Intergovernmental Panel on Climate Change

Kb Kilo base

kDa kilo Dalton

keV electron voltage

kV kilo voltage

LB Lysogeny broth/Luria broth/Luria-Bertani broth

LC-TOF/MS liquid chromatography time of flight mass spectrometry

Lys (K) lysine

m/z mass-to-charge ration

mA milliamps

MALDI-TOF/MS matrix assisted laser desorption ionization time of flight mass spectrometry

MS mass spectra

MS/MS mass spectrometer coupled mass spectrometer

MSD mass selective detector

MSDB Mass Spectra Database

n- normal

N number of replicates

Na2SO4 sodium sulphate

NaOH-EDTA sodium hydroxide- ethylenediaminetetraacetic acid

NCBI National Centre for Biotechnology Information

NIST National Institute of Standards and Technology

NJ Neighbour Joining

NMR Nuclear Magnetic Resonance

OM organic matter

PAUP Phylogenetic Analysis Using Parsimony

PCR Polymerase Chain Reaction

PG N-acetyl peptidoglycan

Phe (F) phenylalanine

Pi inorganic orthophosphate

pI isoelectric point

PL phospholipids

PLFAs phospholipid fatty acids

PMF peptide mass fingerprinting

POM particulate organic matter

PPE terminal phosphorus in the polyphosphate chain

PUFA poly unsaturated fatty acid

PVDF Polyvinylidene Fluoride

RDP Ribosomal Database Project

RNA ribonucleic acid

RP-HPLC Reversed Phase High Performance Liquid Chromatography

RT room temperature

S sulfer

S_ab binary association coefficient

SDS-PAGE sodium dodecyl sulfate polyacrylamide gel electrophoresis

SEM-EDS scanning electron microscopy energy dispersive X-ray s pectrometer

SOM soil organic matter

spp. species

T Telsa

t trans

THCL Teagasc heavy clay-loam

TIC total ion chromatogram

TlCL Teagasc light clay-loam

TMS Tetra Methyl Silane

TMS trimethylsilyl

TOCSY Total Correlation Spectroscopy

TPPI Time-Proportional Phase Incrementation

Tris-HCL Tris-hydrochloric acid

Trp (W) tryptophan

Tyr (Y) tyrosine

U units

UV-A ultraviolet-A

UV-B ultraviolet-B

v/v volume to volume

wt/vol weight to volume

xg gravity

XRD X-ray diffraction

α- alpha

β - beta

γ- gama

Δ double bon position as enumerated from the carboxyl end

δ13C isotopic signature/delta notation

ω- omega

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