Fatty acid patterns of phospholipids and lipopolysaccharides in the characterisation of microbial communities in soil: A review

Biology and Fertility of Soils

Volumn 29, Issue 2, 1999, Pages 111-129

  Zelles, L ^a  

^a INSTITUTE OF EPIDEMIOLOGY   (Germany)

Author keywords

Fatty acid profile; Lipopolysaccharides; Microbial biomass; Phospholipids; Soil microbial communities

Indexed keywords

BIOMASS PRODUCTION; FATTY ACID METABOLISM; LIPOPOLYSACCHARIDE; MICROBE METABOLISM; MICROBIAL CONTAMINATION; PHOSPHOLIPID; PRINCIPAL COMPONENT ANALYSIS; SOIL POLLUTION;

EID: 0032946688     PISSN: 01782762     EISSN: None     Source Type: Journal    
DOI: 10.1007/s003740050533     Document Type: Review

References (81)

1. Albers BP (1994) Mikrobiologie von Bodenaggregaten eines Pelosols: Abhängigkeit von Aggregatgröße, Wasserpotential und Substratverfügbarkeit. PhD thesis, Bayreuth University. Shaker, Aachen
2. Albers B, Zelles L, Bai QY, Lörinci G, Hartmann A, Beese F (1994) Fettsäuremuster von Phospholipiden und Lipopolysacchariden als Indikatoren für Struktur von Microorganismengesellschaften in Böden. In: Alef K, Fiedler H, Hutzinger O (eds) Proceedings of Ecoinforma 1994, Viena Umweltbundesamt, Vienna, pp 297-312
3. Alugupalli S, Laneelle M-A, Larsson L, Daffe M (1995) Chemical characterisation of the ester-linked 3-hydroxy fatty acyl-containing lipids in Mycobacterium tuberculosis. J Bacteriol 177:4566-4570
4. Amann R, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiology Rev 59:143-149
5. Bååth E, Frostegård A, Fritze H (1992) Soil bacterial biomass, activity, phospholipid fatty acid pattern, and pH tolerance in an area polluted with alkaline dust deposition. Appl Environ Microbiol 58:4026-4031
6. Bai Q, Gattinger A, Zelles L (1999) Characterisation of microbial consortia in paddy soil by analysis of phospholipid fatty acids. FEMS Microbiol Ecol (in press)
7. Balkwill DL, Leach FR, Wilson JT, McNabb JF, White DC (1988) Equivalence of microbial biomass measures based on membrane lipid and cell wall components, adenosine triphosphate, and direct counts in subsurface aquifer sediments. Microbiol Ecol 16:73-84
8. Balkwill DL, Drake GR, Reeves RH, Fredrickson JK, White DC, Ringelberg DB, Chandler DP, Romine MF, Kennedy DW, Spadoni CM (1997) Taxonomic study of aromatic-degrading bacteria from deep-terrestrial-subsurface sediments and description of Sphingomonas aromaticivorans sp. nov., Sphingomonas subterranea sp. nov., and Sphingomonas stygia sp. nov. Int J Syst Bactriol 47:191-201
9. Bardgett RD, Leemans DK, Cook R, Hobbs PJ (1997) Seasonality of the soil biota of grazed and ungrazed hill grasslands. Soil Biol Biochem 29:1285-1294
10. Bligh EG, Dyer WJ (1959) A rapid method of total lipid extraction and purification. Can J Biochem Physiol 37:911-917
11. Borgå P, Nilsson M, Tunlid A (1994) Bacterial communities in peat in relation to botanical composition as revealed by phospholipid fatty acids analysis. Soil Biol Biochem 26:841-848
12. Bossio DA, Scow KM (1998) Impacts of carbon and flooding on soil microbial communities: phospholipid fatty acid profiles and substrate utilisation patterns Microbiol Ecol 35:265-278
13. Bowman JP, Sly LI, Nichols PD, Hayward AC (1993) Revised taxonomy of the methanotrophs: description of Methylobacter gen. nov., emendation of Methylococcus, validation of Methylosinus and Methylocystis species, and a proposal that the family Methylococcaceae includes only the group I methanotrophs. Int J Syst Bacteriol 43:735-753
14. Brennan PJ (1988) Mycobacterium and other actinomycetes. In: Ratledge C, Wilkinson SG (eds) Microbial lipids, vol 1. Academic Press, London, pp 204-298
15. Cavigelli MA, Robertson GP, Klug MJ (1995) Fatty acid methyl esters (FAME) profiles as measures of soil microbial community structure. In: Collins HP, Robertson GP, Klug MJ (eds) The significance and regulation of soil biodiversity. Kluwer, Dordrecht, pp 99-113
16. Dobbs FC, Guckert JB (1988) Callianassa trilobata (Crustacea: thalassinidea) influences abundance of meiofauna and biomass, composition, and physiologic state of microbial communities within its burrow. Mar Ecol Prog Ser 45:69-79
17. Fay L, Richli U (1991) Location of double bonds in polyunsaturated fatty acids by gas chromatography-mass spectrometry after 4,4-dimethyloxazoline derivatization. J Chromatogr 541:89-98
18. Federle TW (1986) Microbial distribution in soil - new techniques. In Megusar F, Ganthar M (eds) Perspectives in microbial ecology. Slovene Society for Microbiology, Ljubljana, pp 493-498
19. Findlay R (1996) The use of phospholipid fatty acids to determine microbial community structure. In: Akkermanns ADL, Elsas JD van, Bruijn F de (eds) Molecular microbial ecology manual. Kluwer, Dordrecht, section 4, pp 1-17
20. Fritze H, Pennanen T, Vanhala P (1997) Impact of fertilizer on the humus layer microbial community of Scots Pine stands growing along a gradient of heavy metal pollution. In: Insam H, Rangger A (eds) Microbial communities functional versus structural approaches. Springer, Berlin Heidelberg New York, pp 68-83
21. Frostegård A, Petersen SO, Bååth E, Nielsen TH (1997) Dynamics of a microbial community associated with manure hot spots as revealed by phospholipid fatty acid analysis. Appl Environ Microiol 63:2224-2231
22. Frostegård A (1995) Phospholipid fatty acid analysis to detect changes in soil microbial community structure. PhD thesis. Lund University, Sweden
23. Frostegård A, Tunlid A, Bååth E (1996) Changes in microbial community structure during long-term incubation in two soils experimentally contaminated with metals. Soil Biol Biochem 28:55-63
24. Frostegård A, Tunlid A, Bååth E (1991) Microbial biomass measured as total lipid phosphate in soils of different organic content. J Microbiol Meth 14:151-163
25. Frostegård A, Bååth E. Tunlid A (1993a) Shifts in the structure of soil microbial communities in limed forests as revealed by phospholipid fatty acid analysis. Soil Biol Biochem 25:723-730
26. Frostegård A, Tunlid A, Bååth E (1993b) Phospholipid fatty acid composition, biomass, and activity of microbial communities from two soil types experimentally exposed to different heavy metals. Appl Environ Microbiol 59:3605-3617
27. Frostegård A, Bååth E (1996) The use of phospholipid analysis to estimate bacterial and fungal biomass in soils. Biol Fertil Soils 22:59-65
28. Galbraith L, Wilkinson SG (1991) Polar lipids and fatty acids of Pseudomonas caryophylli, Pseudomonas gladioli and Pseudomonas pickettii. J Gen Microbiol 137:197-202
29. Haack SK, Garchow H, Odelson DA, Forney LJ, Klug MJ (1994) Accuracy, reproducibility, and interpretation of fatty acid methyl ester profiles of model bacterial communities. Appl Environ Microbiol 60:2483-2493
30. Harwood JL, Russel NJ (1984) Lipids in plants and microbes. Allen and Unwin, London
31. Hitchcock C (1975) Structure and distribution of plant acyl lipids. In: Galliard T, Mercer EI (eds) Recent advances in the chemistry and biochemistry of plant lipids. Academic Press, London, pp 1-19
32. Ibekwe AM, Kennedy AC (1998) Phospholipid fatty acid profiles and carbon utilization patterns for analysis of microbial community structure under field and greenhouse conditions. FEMS Microbiol Ecol 26:151-163
33. Kroppenstedt RM (1992) The genus Nocardiopsis. In: Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH (eds) The prokaryotes 2. Springer, Berlin Heidelberg New York, pp 1139-1156
34. Laczko E, Rudaz A, Aragno A (1997) Diversity of anthropogenically influenced or disturbed soil microbial communities. In: Insam H. Rangger A (eds) Microbial communities, functional versus structural approaches. Springer, Berlin Heidelberg New York, pp 57-67
35. Lechevalier MP (1989) Lipids in bacterial taxonomy. In: O'Leary WM (ed) Practical handbook of microbiology. CRC, Boca Raton, Fla., pp 455-561
36. Lechevalier H, Lechevalier MP (1988) Chemotaxonomic use of lipids - an overview. In: Ratledge C, Wilkinson SG (eds) Microbial lipids, vol 1. Academic Press, London, pp 869-902
37. Lösel DM (1988) Fungal lipids. In: Ratledge C, Wilkinson SG (eds) Microbial lipids, vol 1. Academic Press, London, pp 699-806
38. Mayberry WR, Lane JR (1993) Sequential alkaline saponification/acid hydrolysis/esterification: a one-tune method with enhanced recovery of both cyclopropane and hydroxylated fatty acids. J Microbiol Meth 18:21-32
39. Muyzer GE, Waal C de, Uitterlinden A (1993) Profiling of complex microbial populations by denaturating gradient gel electrophoresis of polymerase chain reaction-amplified genes encoding for 16 S rRNA. Appl Environ Microbiol 59:695-700
40. Nichols PD, White DC (1989) Accumulation of poly-β-hydroxibutyrate in methane enriched, halogenated hydrocarbon-degrading soil columns: implications for microbial community structure and nutritional status. Hydrobiologia 176/ 177:369-377
41. Nichols PD, Guckert JB, White DC (1986) Determination of monounsaturated fatty acid double-bond position and geometry for microbial monocultures and complex consortia by capillary GC-MS of their dimethyl disulphide adducts. J Microbiol Meth 5:49-55
42. Nohynek LJ, Nurmiaho-Lassila EL, Suhonen EL, Busse H-J, Mohammadi M, Hantula J, Rainey F, Salkinoja-Salonen MS (1996) Description of chlorophenol-degrading Pseudomonas sp. strains kf1, kf3, and nkf1 as a new species of the genus Sphingomonas, Sphingomonas subarctica sp. nov. Int J Syst Bacteriol 46:1042-1055
43. O'Leary WM, Wilkinson SG (1988) Gram-positive bacteria. In: Ratledge C, Wilkinson SG (eds) Microbial lipids. vol 1. Academic Press, London, pp 117-202
44. Parker JH, Smith GA, Fredrickson HL, Vestal JR, White DC (1982) Sensitive assay, based on hydroxy fatty acids from lipopolysaccharide lipid A, for Gram-negative bacteria in sediments. Appl Environ Microbiol 44:1170-1177
45. Parkes RJ (1987) Analysis of microbial communities within sediments using biomarkers. In: Flatscher M, Gray TMG, Johns G (eds) Ecology of microbial communities. Cambridge University Press, London, pp 147-177
46. Pennanen T, Frostegård A, Fritze H, Bååth E (1996) Phospholipid fatty acid composition and heavy metal tolerance of soil microbial communities along two heavy metal-polluted gradients in coniferous forests. Appl Environ Microbiol 62:420-428
47. Petersen SO, Klug MJ (1994) Effects of sieving, storage, and incubation temperature on the phospholipid fatty acid profile of a soil microbial community. Appl Environ Microbiol 60:2421-2430
48. Petersen SO, Henriksen K, Blackburn TH, King GM (1991) A comparison of phospholipid and chloroform fumigation analyses for biomass in soil: potentials and limitations. FEMS Microbiol Ecol 85:257-268
49. Rackwitz R (1997) Modelluntersuchungen zur Stickstoffdynamik in Schwarzerden mit unterschiedlicher Düngungsgeschichte. PhD thesis. Technical University of Munich, Shaker, Aachen
50. Ratledge C, Wilkinson SG (1988) Microbial lipids. Academic Press, London
51. Reichardt W, Mascarina G, Padre B, Doll J (1997) Microbial communities of continuously cropped, irrigated rice fields. Appl Environ Microbiol 63:233-238
52. Saddler JN, Wardlaw AC (1980) Extraction, distribution and biodegradation of bacterial lipopolysaccharides in estuarine sediments. Anton Leeuw J Microbiol 46:27-39
53. Schloter M, Zelles L, Hartmann A, Munch JC (1998) New quality of assessment of microbial diversity in arable soils using molecular and biochemical methods. Z Pflanzenernaehr Bodenkd 161:425-431
54. Shah HN (1992) The genus Bacteroides and related taxa. In: Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH (eds) The prokaryotes. Springer, Berlin Heidelberg New York, pp 3593-3608
55. Steinberger Y, Zelles L, Bai QY, Lützow M von, Munch JC (1999) Phospholipid fatty acid profiles as indicators for microbial community structure and biodiversity in soils along a climatic transect in the Judean desert. Biol Fertil Soils 28:292-300
56. Sundh I, Nilsson M, Borgå P (1997) Variation in microbial community structure in two boreal peatlands as determined by analysis of phospholipid fatty acid profiles. Appl Environ Microbiol 63:1476-1482
57. 14C-labelled phosphalidyl choline in soil. Soil Biol Biochem 15:145-148
58. Toriyama S, Yano I, Masui M, Kusunose M, Kusunose E, Akimori N (1980) Regulation of cell wall mycolic acid biosynthesis in acid-fast bacteria. J Biochem 88:211-221
59. Torsvik V, Goksoyr J, Daae FL (1990) High diversity in DNA of soil bacteria. Appl Environ Microbiol 56:78-87
60. Tunlid A, White DC (1992) Biochemical analysis of biomass, community structure, nutritional status, and metabolic activity of microbial communities in soil. In: Stotzky G, Bollag JM (eds) Soil biochemistry, vol 7. Dekker, New York, pp 229-262
61. Vestal JR, White DC (1989) Lipid analysis in microbial ecology. Quantitative approaches to the study of microbial communities. Bioscience 39:535-541
62. Von Wirén-Lehr (1997) Mikrobieller Abbau der Herbizide Isoproturon und Glyphosat und ihrer in organischen Bestandesabfällen festgelegten Rückstände in Bodenproben aus unterschiedlichen landwirtschaftlichen Bewirtschaftungssystemen. PhD thesis. Technical University of Munich. Shaker, Aachen
63. Wander MM, Hedrick DS, Kaufman D, Traina SJ, Stinner BR, Kehrmeyer SR, White DC (1995) The functional significance of the microbial biomass in organic and conventional managed soils. Plant Soil 170:87-97
64. Wells GB, Dickson RC, Lester LR (1996) Isolation and composition of inositolphosphorylceramide-type sphingolipids of hyphal forms of Candida albicans. J Bacteriol 178:6223-6226
65. White DC (1994) Is there anything else you need to understand about the microbiota that cannot be derived from analysis of nucleic acids? Microbiol Ecol 28:163-166
66. White DC, Davis WM, Nickels JS, King JD, Bobbie RJ (1979) Determination of the sedimentary microbial biomass by extractable lipid phosphate. Oecologia 40:51-62
67. Yano I, Saito K, Furukawa Y, Kusunose M (1972) Structural analysis of molecular species of nocardomycolic acids from Nocardia erythropolis by the combined system of gas chromatography and mass spectrometry. FEBS Lett 21:215-221
68. Yano I, Kageyama K, Ohno Y, Masui M (1978) Separation and analysis of molecular species of mycolic acids in Nocardia and related taxa by gas chromatography mass spectrometry. Biomed Mass Spectrom 5:14-24
69. 2. Ecol Appl 6:257-262
70. Zelles L (1996) Fatty acid patterns of microbial phospholipids and lipopolysaccharides. In: Schinner F, Öhlinger R, Kandeler E, Margesin R (eds) Methods in soil biology. Springer, Berlin Heidelberg New York, pp 80-93
71. Zelles L (1997) Phospholipid fatty acid profiles in selected members of soil microbial communities. Chemosphere 35:275-294
72. Zelles L (1999) Identification of single cultured micro-organisms based on their whole-community fatty acid profiles, using extended extraction procedure. Chemosphere (in press)
73. Zelles L, Alef K (1995) Biomarkers. In: Alef K, Nannipieri P (eds) Methods in applied soil microbiology and biochemistry. Academic Press, London, pp 422-439
74. Zelles L, Bai QY (1993) Fractionation of fatty acids derived from soil lipids by solid phase extraction and their quantitative analysis by GC-MS. Soil Biol Biochem 25:495-507
75. Zelles L, Bai QY (1994) Fatty acid patterns of phospholipids and lipopolysaccharides in environmental samples. Chemosphere 28:391-411
76. Zelles L, Bai QY, Beck T, Beese F (1992) Signature fatty acids in phospholipids and lipopolysaccharides as indicators of microbial biomass and community structure in agricultural soils. Soil Biol Biochem 24:317-323
77. Zelles L, Bai QY, Ma RX, Rackwitz R, Winter K, Beese F (1994) Microbial biomass, metabolic activity and nutritional status determined from fatty acid patterns and poly-hydroxybutyrate in agriculturally-managed soils. Soil Biol Biochem 26:439-446
78. Zelles L, Bai QY, Rackwitz R, Chadwick D, Beese F (1995a) Determination of phospholipid- and lipopolysaccharide-derived fatty acids as an estimate of microbial biomass and community structure in soils. Biol Fertil Soils 19:115-123
79. Zelles L, Rackwitz R, Bai QY, Beck T, Beese F (1995b) Discrimination of microbial diversity by fatty acid profiles of phospholipids and lipopolysaccharides in differently cultivated soils. Plant Soil 170:115-122
80. Zelles L, Palojärvi A, Kandeler E, Lützow M von, Winter K, Bai QY (1997) Changes in soil microbial properties and phospholipid fatty acid fractions after chloroform fumigation. Soil Biol Biochem 29:1325-1336
81. Zogg GP, Zak DR, Ringelberg DB, MacDonald NW, Pregitzer KS, White DC (1997) Compositional and functional shifts in microbial communities due to soil warming. Soil Sci Soc Am J 61:475-481