Abstract
The Negev Desert is characterized by low soil–water availability and organic matter content, as well as important factors significantly influencing soil biological activity. In order to overcome the xeric environment, plant and soil biota have evolutionarily developed, over time, ecophysiological abilities that help them fulfill their biological role and function. Microorganisms are known as a major part of the ecosystem’s total biomass and play an important role in decomposition processes and the nutrient cycle. Perennial shrubs have been found to play an important role as organic matter suppliers and as a physical barrier prolonging biological activity of microbial communities. Soil samples were collected monthly, from November 2006 to November 2007, from a 0 to 10-cm depth under the canopies of Reaumuria negevensis and from open areas (control) in order to evaluate abiotic components and microbial variables on a temporal basis. H′ values, evenness, and β diversity (Sørensen’s similarity) were determined by a molecular method based on sequencing. Water availability, organic matter content, and total soluble nitrogen were higher in soil samples collected in the vicinity of R. negevensis than in samples collected in open areas. Our study also indicated that, in spite of the similarity between H′ values of soil samples collected in the vicinity of R. negevensis and the open area, a low percentage of similarity was found between the soil bacterial populations. These results support the hypothesis that distribution of resources in the environment under R. negevensis shrubs varies in space and time and also influences soil microbial diversity and the abiotic environmental role.
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References
Alexander M (1967) Introduction to soil microbiology. Wiley, Inc
Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
Ayres E, Dromph KM, Bardgett RD (2006) Do plant species encourage soil biota that specialise in the rapid decomposition of their litter? Soil Biol Biochem 38:183–186
Berg N, Steinberger Y (2008) Role of perennial plants in determining the activity of the microbial community in a Negev Desert ecosystem. Soil Biol Biochem 40:2686–2695
Bolton H Jr, Fredrickson JK, Elliott LF (1994) Microbial ecology of the rhizosphere. In: Metting FB Jr (ed) Soil microbial ecology. Marcel Dekker, Inc., New York, pp 27–63
Bowen GD, Rovira AD (1991) The rhizosphere—the hidden half of the hidden half. In: Waisel Y, Eshel A, Kafkafi U (eds) Plant roots—the hidden half. Marcel Dekker, New York, pp 641–649
Broughton LC, Gross KL (2000) Patterns of diversity in plant and soil microbial communities along a productivity gradient in a Michigan old-field. Oecologia 125:420–427
Buckley DH, Schmidt TM (2003) Diversity and dynamics of microbial communities in soils from agro-ecosystems. Environ Microbiol 5:441–452
Burke IC, Yonker CM, Parton WJ, Cole CV, Flach K, Schimel DS (1989) Texture, climate, and cultivation effects on soil organic matter content in US grassland soils. Soil Sci Soc Am J 53:800–805
Buyanovsky G, Dicke M, Berwick P (1982) Soil environment and activity of soil microflora in the Negev Desert. J Arid Environ 5:13–28
Carney KM, Matson PA (2005) Plant communities, soil microorganisms, and soil carbon cycling: does altering the world belowground matter to ecosystem functioning? Ecosystems 8:928–940
Charley JL, West NE (1975) Plant-induced soil chemical patterns in some shrub-dominated semi-desert ecosystems in Utah. J Ecol 63:945–964
Coleman DC (1994) The microbial loop concept as used in terrestrial soil ecology studies. Microb Ecol 28:245–250
Coleman DC (1985) Through a ped darkly: an ecological assessment of root-soil-microbial-faunal interactions. In: Fitter AH, Atkinson D, Read DJ, Usher MB (eds) Ecological interactions in soil. Blackwell, Cambridge, pp 1–21
Costa R, Gotz M, Mrotzek N, Lottmann J, Berg G, Smalla K (2006) Effects of site and plant species on rhizosphere community structure as revealed by molecular analysis of microbial guilds. FEMS Microbiol Ecol 56:236–249
Di Cello F, Bevivino A, Chiarini L, Fani R, Paffetti D, Tabacchioni S, Dalmastri C (1997) Biodiversity of a Burkholderia cepacia population isolated from the maize rhizosphere at different plant growth stages. Appl Environ Microbiol 63:4485–4493
Evenari M (1981) Ecology of the Negev Desert: a critical review of our knowledge. In: Shuval H (ed) Developments in arid zone ecology and environmental quality. Balaban ISS, Philadelphia, pp 1–33
Evenari ME, Shanan L, Tadmor W (1982) The Negev: the challenge of a desert. Harvard University Press, Cambridge
Flowers TJ, Troke PF, Yeo AR (1977) Mechanism of salt tolerance in halophytes. Annu Rev Plant Physiol Plant Mol Biol 28:89–121
Garner W, Steinberger Y (1989) A proposed mechanism for the formation of ‘Fertile Island’ in the desert ecosystem. J Arid Environ 16:257–262
Germida JJ, Siciliano SD (2001) Taxonomic diversity of bacteria associated with the roots of modern, recent and ancient wheat cultivars. Biol Fertil Soils 33:410–415
Germida JJ, Siciliano SD, de Freitas JR, Seib AM (1998) Diversity of root-associated bacteria associated with field-grown canola (Brassica napus L.) and wheat (Triticum aestivum L.). FEMS Microbiol Ecol 26:43–50
Grayston SJ, Wang S, Campbell CD, Edwards AC (1998) Selective influence of plant species on microbial diversity in the rhizosphere. Soil Biol Biochem 30:369–378
Haichar FE, Marol C, Berge O, Rangel-Castro JI, Prosser JI, Balesdent J, Heulin T, Achouak W (2008) Plant host habitat and root exudates shape soil bacterial community structure. ISME J 2:1221–1230
Hertenberger G, Zampach P, Bachmann G (2002) Plant species affect the concentration of free sugars and free amino acids in different types of soil. J Plant Nutr Soil Sci 165:557–565
Hodgson DA (2000) Primary metabolism and its control in Streptomycetes: a most unusual group of bacteria. Adv Microb Physiol 42:47–238
Johnson MJ, Lee KY, Scow KM (2003) DNA fingerprinting reveals links among agricultural crops, soil properties, and the composition of soil microbial communities. Geoderma 114:279–303
Katterer T, Andren O (2001) The ICBM family of analytically solved models of soil carbon, nitrogen and microbial biomass dynamics descriptions and application examples. Ecol Modell 136:191–207
Kell DB, Kaprelyants AS, Weichart DH, Harwood CR, Barer MR (1998) Viability and activity in readily culturable bacteria: a review and discussion of the practical issues. Antonie van Leeuwenhoek Int J Gen Mol Microbiol 73:169–187
Kennedy AC, Smith KL (1995) Soil microbial diversity and the sustainability of agricultural soils. Plant Soil 170:75–86
Kieft TL, Soroker E, Firestone MK (1987) Microbial biomass response to a rapid increase in water potential when dry soil is wetted. Soil Biol Biochem 19:119–126
Kuske CR, Barns SM, Busch JD (1997) Diverse uncultivated bacterial groups from soils of the arid southwestern United States that are present in many geographic regions. Appl Environ Microbiol 63:3614–3621
Lahav I, Steinberger Y (2001) Soil bacterial functional diversity in a potato field. Eur J Soil Biol 37:59–67
Larson WE, Pierce FJ (1994) The dynamics of soil quality as measure of sustainable management. In: Doran DW, Coleman DC, Bendicek DF, Stewart BA (eds) Defining soil quality for sustainable environment. Soil Science Society of America Inc. and American Society of Agronomy Inc., Madison, pp 37–51
Latour X, Corberand TS, 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 62:2449–2456
Li GY, Cai FJ, Zhang Q, Mahbub A, Lei TW (2003) Effects of irrigation interval and nitrogen application on soil moisture, salt distribution and cotton growth under plastic mulch drip irrigation. J Exp Bot 54(suppl 1):34–35
Loranger-Merciris G, Barthes L, Gastine A, Leadley P (2006) Rapid effects of plant species diversity and identity on soil microbial communities in experimental grassland ecosystems. Soil Biol Biochem 38:2336–2343
Maloney PE, van Bruggen AHC, Hu S (1997) Bacterial community structure in relation to the carbon environment in lettuce and tomato rhizosphere and in bulk soil. Microb Ecol 34:109–117
Marschner P, Yang CH, Lieberei R, Crowley DE (2001) Soil and plant specific effects on bacterial community composition in the rhizosphere. Soil Biol Biochem 33:1437–1445
McCaig AE, Glover LA, Prosser JI (1999) Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures. Appl Environ Microbiol 65:1721–1730
Mills AJ, Wasser RA (1980) Aspects of diversity measurement for microbial communities. Appl Environ Microbiol 41:578–586
Mondini C, Cayuela ML, Sanchez-Monedero MA, Roig A, Brookes PC (2006) Soil microbial biomass activation by trace amounts of readily available substrate. Biol Fertil Soils 42:542–549
Nadeem SM, Zahir ZA, Naveed M, Arshad M (2007) Preliminary investigations on inducing salt tolerance in maize through inoculation with rhizobacteria containing ACC deaminase activity. Can J Microbiol 53:1141–1149
Noy-Meir I (1973) Desert ecosystems: environment and producers. Ann Rev Ecol Syst 4:25–51
Noy-Meir I (1974) Desert ecosystems: higher trophic levels. Ann Rev Ecol Syst 5:195–214
Nunan N, Daniell TJ, Singh BK, Papert A, McNicol JW, Prosser JI (2005) Links between plant and rhizoplane bacterial communities in grassland soils, characterized using molecular techniques. Appl Environ Microbiol 71:6784–6792
Pankhurst CE, Hawke BG, McDonald HJ, Kirkby CA, Buckerfield JC, Michelsen P, O’Brien KA, Gupta VVSR, Doube BM (1995) Evaluation of soil biological properties as potential bioindicators of soil health. Aust J Exp Agric 35:1015–1028
Pankratov TA, Serkebaeva YM, Kulichevskaya IS, Liesack W, Dedysh SN (2008) Substrate-induced growth and isolation of Acidobacteria from acidic Sphagnum peat. ISME J 2:551–560
Parker LW, Santos PF, Phillips J, Whitford WG (1984) Carbon and nitrogen dynamics during the decomposition of litter and roots of a Chihuahuan desert annual, Leupedium lasiocarpum. Ecol Monogr 54:339–360
Patra AK, Le Roux X, Grayston SJ, Loiseau P, Louault F (2008) Unraveling the effects of management regime and plant species on soil organic carbon and microbial phospholipid fatty acid profiles in grassland soils. Bioresour Technol 99:3545–3551
Pen-Mouratov S, Rakhimbaev M, Steinberger Y (2006) Spatio-temporal effect on soil respiration in fine-scale patches in a desert ecosystem. Pedosphere 16:1–9
Pielou EC (1966) The measurement of diversity in different types of biological collections. Statistical Research Service, Canada Department of Agriculture, Ottawa
Porter J, Deere D, Hardman M, Edwards C, Pickup R (1997) Go with the flow—use of flow cytometry in environmental microbiology. FEMS Microbiol Ecol 24:93–101
Quaiser A, Ochsenreiter T, Lanz C, Schuster SC, Treusch AH, Eck J, Schleper C (2003) Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics. Mol Microbiol 50:563–575
Ronn R, McCaig AE, Griffiths BS, Prosser JI (2002) Impact of protozoan grazing on bacterial community structure in soil microcosms. Appl Environ Microbiol 68:6094–6105
Rowell DL (1994) Soil science: methods and applications. Longman Group UK Ltd., London
S.F.A.S. (1995) Manual-San Plus Analyzer. SKALAR Analytical, The Netherlands
Sarig S, Barness G, Steinberger Y (1994) Annual plant-growth and soil characteristics under desert halophyte canopy. Acta Oecol 15:521–527
Sarig S, Fliessbach A, Steinberger Y (1999) Soil microbial biomass under the canopy of coastal sand dune shrubs. Arid Soil Res Rehabil 13:75–80
Sarig S, Steinberger Y (1993) Immediate effect of wetting event on microbial biomass and carbohydrate production mediated aggregation in desert soil. Geoderma 56:599–607
Sarig S, Steinberger Y (1994) Microbial biomass response to seasonal fluctuation in soil salinity under the canopy of desert halophytes. Soil Biol Biochem 26:1405–1408
Schlesinger WH, Raikes JA, Hartley AE, Cross AF (1996) On the spatial pattern of soil nutrients in desert ecosystems. Ecology 77:364–374
Shamir I, Steinberger Y (2007) Vertical distribution and activity of soil microbial population in a sandy desert ecosystem. Microb Ecol 53:340–347
Shamir I, Zahavy E, Steinberger Y (2009) Bacterial viability assessment by flow cytometry analysis in soil. Front Biol China 4:424–435
Shannon CE, Weaver W (1949) The mathematical theory of communication. University of Illinois Press, Urbana
Shmida A, Evenari M, Noy-Meir I (1986) Hot desert ecosystems. An integrated view. In: Evenari M, Noy-Meir I, Goodall DW (eds) Ecosystems of the world: hot deserts and arid shrublands. Elsevier Science Publishers, Amsterdam, pp 379–387
Smalla K, Wieland G, Buchner A, Zock A, Parzy J, Kaiser S, Roskot N, Heuer H, Berg G (2001) Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl Environ Microbiol 67:4742–4751
Sørensen T (1948) A method of establishing groups of equal amplitude in plant society based on similarity of species content. K Danske Vidensk Selsk Biol SKR 5:1–34
Steinberger Y, Loboda I (1991) Nematode population dynamics and trophic structure in a soil profile under the canopy of the desert shrub Zygophyllum dumosum. Pedobiologia 35:191–197
Steinberger Y, Whitford WG (1983) The contribution of rodents to decomposition processes in a desert ecosystem. J Arid Environ 6:177–181
Stephan A, Meyer AH, Schmid B (2000) Plant diversity affects culturable soil bacteria in experimental grassland communities. J Ecol 88:988–998
Strickland MS, Lauber C, Fierer N, Bradford MA (2009) Testing the functional significance of microbial community composition. Ecology 90:441–451
ter Braak CJF (1995) Ordination (Chapter 5). In: Jongman RHG, ter Braak CJF, Van Tongeren OFR (eds) Data analysis in community and landscape ecology. Cambridge University Press, Cambridge, pp 91–173
Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J, Barabote RD, Bradley B, Brettin TS, Brinkac LM, Bruce D, Creasy T, Daugherty SC, Davidsen TM, Deboy RT, Detter JC, Dodson RJ, Durkin AS, Ganapathy A, Gwinn-Giglio M, Han CS, Khouri H, Kiss H, Kothari SP, Madupu R, Nelson KE, Nelson WC, Paulsen I, Penn K, Ren QH, Rosovitz MJ, Selengut JD, Shrivastava S, Sullivan SA, Tapia R, Thompson LS, Watkins KL, Yang Q, Yu CH, Zafar N, Zhou LW, Kuske CR (2009) Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Appl Environ Microbiol 75:2046–2056
Wardle DA (1992) A comparative assessment of factors which influence microbial biomass carbon and nitrogen levels in soil. Biol Rev Camb Philos Soc 67:321–358
West NE, Skujins J (1978) Nitrogen in Desert Ecosystems, US/IBP no. 9. Dowden, Hutchinson and Ross, Stroudsburg, PA
Whitford WG (2002) Ecology of desert systems. Academic, London
Winding A, Hund-Rinke K, Rutgers M (2005) The use of microorganisms in ecological soil classification and assessment concepts. Ecotox Environ Safe 62:230–248
Zhou JZ, Davey ME, Figueras JB, Rivkina E, Gilichinsky D, Tiedje JM (1997) Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA. Microbiology-UK 143:3913–3919
Acknowledgements
The authors thank Dr. Dror Minz; his students Lilach Iasur, Hila Elifantz, and Patricia Bucki; and Dr. Einav Mayzlish-Gati for consultation and guidance. Thanks also go to Ms. Sharon Victor for her suggestions and language editing and Dr. Orit Shaul for providing necessary equipment.
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This paper is dedicated to the loving memory of Saul Saul (father of V.S-T.)
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Saul-Tcherkas, V., Steinberger, Y. Soil Microbial Diversity in the Vicinity of a Negev Desert Shrub—Reaumuria negevensis . Microb Ecol 61, 64–81 (2011). https://doi.org/10.1007/s00248-010-9763-x
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DOI: https://doi.org/10.1007/s00248-010-9763-x