The influence of flint stones on a soil microbial community in the northern Negev Desert

Haggai Wasserstrom; Vered Elias Ben-Ezra; Chen Sherman; Adrian Unc; Yosef Steinberger; Haggai Wasserstrom; Vered Elias Ben-Ezra; Chen Sherman; Adrian Unc; Yosef Steinberger

doi:10.3934/microbiol.2017.3.580

AIMS Microbiology

2017, Volume 3, Issue 3: 580-595. doi: 10.3934/microbiol.2017.3.580

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Research article

The influence of flint stones on a soil microbial community in the northern Negev Desert

1.
The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
2.
School of Science and the Environment, Memorial University of Newfoundland, Corner Brook, NL A2H 5G4, Canada

Received: 22 May 2017 Accepted: 03 July 2017 Published: 10 July 2017

In the Negev Desert ecosystems, flint-stone cover on slopes acts as a barrier against water flow. As a result, soil moisture increases and organic matter accumulates under the stone and in the immediate surroundings, both affecting the duration of soil microbial activity. On the other hand, during the dry season (characterized by approximately 210 dew nights), flint-stone cover plays an important role in the formation of dew, which eventually trickles down beneath the stone, correspondingly enhancing biological activity. The present study examined the possible role of flint stones as hotspots for soil microbial-community activity and diversity. The results were compared with those obtained from the adjacent stone-free soils in the open spaces (OS), which served as controls. Microbial activity (respiration and biomass) and functional diversity were determined by the MicroResp^TM method. In addition, estimates of genetic diversity and viable counts of bacteria and fungi [colony-forming units (CFUs)] were obtained. The soil was significantly wetter and contained more organic matter beneath the flint stones (BFS). As hypothesized, biological activity was enhanced under the stones, as described by CO₂ evolution, microbial-community biomass functional diversity, and fungal phylogenetic diversity. BFS environments favored a greater range of catabolic functions. Taxa generally known for their stress resilience were found in the OS habitats. The results of this study elucidate the importance of flint-stone cover to soil microbial biomass, community activity, and functional diversity in the northern Negev Desert.
- flint stone; microbial community; functional diversity; beneath-stone microbial activity; desert environment
Citation: Haggai Wasserstrom, Vered Elias Ben-Ezra, Chen Sherman, Adrian Unc, Yosef Steinberger. The influence of flint stones on a soil microbial community in the northern Negev Desert[J]. AIMS Microbiology, 2017, 3(3): 580-595. doi: 10.3934/microbiol.2017.3.580

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Abstract

In the Negev Desert ecosystems, flint-stone cover on slopes acts as a barrier against water flow. As a result, soil moisture increases and organic matter accumulates under the stone and in the immediate surroundings, both affecting the duration of soil microbial activity. On the other hand, during the dry season (characterized by approximately 210 dew nights), flint-stone cover plays an important role in the formation of dew, which eventually trickles down beneath the stone, correspondingly enhancing biological activity. The present study examined the possible role of flint stones as hotspots for soil microbial-community activity and diversity. The results were compared with those obtained from the adjacent stone-free soils in the open spaces (OS), which served as controls. Microbial activity (respiration and biomass) and functional diversity were determined by the MicroResp^TM method. In addition, estimates of genetic diversity and viable counts of bacteria and fungi [colony-forming units (CFUs)] were obtained. The soil was significantly wetter and contained more organic matter beneath the flint stones (BFS). As hypothesized, biological activity was enhanced under the stones, as described by CO₂ evolution, microbial-community biomass functional diversity, and fungal phylogenetic diversity. BFS environments favored a greater range of catabolic functions. Taxa generally known for their stress resilience were found in the OS habitats. The results of this study elucidate the importance of flint-stone cover to soil microbial biomass, community activity, and functional diversity in the northern Negev Desert.

References

[1]	Evenari ME, Shanan L, Tadmor W (1982) The Negev: The Challenge of a Desert, 2 Eds., Cambridge, MA: Harvard University Press, 345.
[2]	Noy-Meir I (1973) Desert ecosystems: Environment and producers. Ann Rev Ecol Syst 4: 25–51. doi: 10.1146/annurev.es.04.110173.000325
[3]	Lahav I, Steinberger Y (2001) The contribution of stone cover to biological activity in the Negev Desert, Israel. Land Degrad Dev 12: 35–43. doi: 10.1002/ldr.422
[4]	Meeting B (1991) Biological surface features of semiarid lands and deserts, In: Skujins J, Editor, Semiarid Lands and Deserts Soil Resource and Reclamation, NY: Marcel Dekker, 257–293.
[5]	Berner T, Evenari M (1978) Influence of temperature and light penetration on abundance of hypolithic algae in Negev Desert of Israel. Oecologia 33: 255–260. doi: 10.1007/BF00344852
[6]	Sparling GP, Williams BL (1986) Microbial biomass in organic soils: Estimation of biomass C, and effect of glucose or cellulose amendments on the amounts of N and P released by fumigation. Soil Biol Biochem 18: 507–513. doi: 10.1016/0038-0717(86)90008-8
[7]	Schimel J, Balser TC, Wallenstein M (2007) Microbial stress-response physiology and its implications for ecosystem function. Ecology 88: 1386–1394. doi: 10.1890/06-0219
[8]	Makhalanyane TP, Valverde A, Gunnigle E, et al. (2015) Microbial ecology of hot desert edaphic systems. FEMS Microbiol Rev 39: 203–221. doi: 10.1093/femsre/fuu011
[9]	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. doi: 10.1016/0016-7061(93)90138-B
[10]	Yechieli A, Oren A (1994) The effect of direct rainfall and runoff on microbial activities along an arid hillslope, northern Negev, Israel. J Arid Environ 23: 209–220.
[11]	Black CA (1965) Methods of Soil Analysis: Part 1. Physical and Mineralogical Properties, Including Statistics of Measurement and Sampling, Madison, WI: American Society of Agronomy.
[12]	Rowell DL (1994) Soil Science: Methods and Applications, London: Longman Group UK Ltd.
[13]	SFAS (1995) Manual-San Plus Analyzer, The Netherlands: SKALAR Analytical.
[14]	Anderson JPE, Domsch KH (1978) Physiological method for quantitative measurement of microbial biomass in soils. Soil Biol Biochem 10: 215–221. doi: 10.1016/0038-0717(78)90099-8
[15]	Anderson TH, Domsch KH (1990) Application of ecophysiological quotients (qCO₂ and qD) on microbial biomasses from soils of different cropping histories. Soil Biol Biochem 22: 251–255. doi: 10.1016/0038-0717(90)90094-G
[16]	Anderson TH, Domsch KH (1993) The metabolic quotient for CO₂ (qCO₂) as a specific activity parameter to assess the effects of environmental conditions, such as pH, on the microbial biomass of forest soils. Soil Biol Biochem 25: 393–395. doi: 10.1016/0038-0717(93)90140-7
[17]	Campbell CD, Chapman SJ, Cameron CM, et al. (2003) A rapid microtiter plate method to measure carbon dioxide evolved from carbon substrate amendments so as to determine the physiological profiles of soil microbial communities by using whole soil. Appl Environ Microb 69: 3593–3599. doi: 10.1128/AEM.69.6.3593-3599.2003
[18]	Zak JC, Willig MR, Moorhead DL, et al. (1994) Functional diversity of microbial communities: a quantitative approach. Soil Biol Biochem 26: 1101–1108. doi: 10.1016/0038-0717(94)90131-7
[19]	Muyzer G, Ramsing NB (1995) Molecular methods to study the organization of microbial communities. Water Sci Technol 32: 1–9.
[20]	Vasileiadis S, Puglisi E, Arena M, et al. (2012) Soil bacterial diversity screening using single 16S rRNA gene V regions coupled with multi-million read generating sequencing technologies. PloS One 7: e42671. doi: 10.1371/journal.pone.0042671
[21]	Gardes M, Bruns TD (1993) ITS primers with enhanced specificity for basidiomycetes-application to the identification of mycorrhizae and rusts. Mol Ecol 2: 113–118. doi: 10.1111/j.1365-294X.1993.tb00005.x
[22]	White TJ, Bruns T, Lee S, et al. (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics, In: Innis MA, Gelfand DH, Sninsky JJ, et al., Editors, PCR protocols: a guide to methods and applications, San Diego: Academic Press, 315–322.
[23]	Schloss PD, Gevers D, Westcott SL (2011) Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PloS One 6: e27310. doi: 10.1371/journal.pone.0027310
[24]	Schloss PD, Westcott SL, Ryabin T, et al. (2009) Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microb 75: 7537–7541.
[25]	Pruesse E, Quast C, Knittel K, et al. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188–7196. doi: 10.1093/nar/gkm864
[26]	Wang QG, Garrity M, Tiedje JM, et al. (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microb 73: 5261–5267. doi: 10.1128/AEM.00062-07
[27]	Koljalg U, Nilsson RH, Abarenkov K, et al. (2013) Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol 22: 5271–5277. doi: 10.1111/mec.12481
[28]	Hughes JB, Hellmann JJ, Ricketts TH, et al. (2001) Counting the uncountable: Statistical approaches to estimating microbial diversity. Appl Environ Microb 67: 4399–4406. doi: 10.1128/AEM.67.10.4399-4406.2001
[29]	Huson DH, Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23: 254–267.
[30]	Daly MJ, Gaidamakova EK, Matrosova VY, et al. (2004) Accumulation of Mn(II) in Deinococcus radiodurans facilitates gamma-radiation resistance. Science 306: 1025–1028. doi: 10.1126/science.1103185
[31]	Hugenholtz P, Stackebrandt E (2004) Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description). Int J Syst Evol Micr 54: 2049–2051. doi: 10.1099/ijs.0.03028-0
[32]	DeBruyn JM, Nixon LT, Fawaz MN, et al. (2011) Global biogeography and quantitative seasonal dynamics of Gemmatimonadetes in soil. Appl Environ Microb 77: 6295–6300. doi: 10.1128/AEM.05005-11
[33]	Lee KCY, Dunfield PF, Stott MB (2014) The Phylum Armatimonadetes, In: Rosenberg E, DeLong EF, Lory S, et al., Editors, The Prokaryotes: Other Major Lineages of Bacteria and the Archaea, Berlin, Heidelberg: Springer, 447–458.
[34]	Fierer N, Bradford MA, Jackson RB (2007) Toward an ecological classification of soil bacteria. Ecology 88: 1354–1364. doi: 10.1890/05-1839
[35]	Petersen PM (1985) The ecology of Danish soil inhabiting Pezizales with emphasis on edaphic conditions. Opera Bot 77: 1–38.
[36]	Weber HA, Gloer JB (1991) The preussomerins: novel antifungal metabolites from the coprophilous fungus Preussia isomera Cain. J Org Chem 56: 4355–4360. doi: 10.1021/jo00014a007
[37]	Foissner W, Agatha S, Berger H (2002) Soil Ciliates (Protozoa, Ciliophora) from Namibia (Southwest Africa) with Emphasis on Two Contrasting Environments, the Etosha Region and the Namib Desert, Linz, Austria: Oberosterreichisches Landesmuseum.
[38]	Huxman TE, Snyder KA, Tissue D, et al. (2004) Precipitation pulses and carbon fluxes in semiarid and arid ecosystems. Oecologia 141: 254–268. doi: 10.1007/s00442-004-1682-4
[39]	Belnap J, Welter JR, Grimm NB, et al. (2005) Linkages between microbial and hydrologic processes in arid and semiarid watersheds. Ecology 86: 298–307. doi: 10.1890/03-0567
[40]	Temina M, Kidron GJ (2015) The effect of dew on flint and limestone lichen communities in the Negev Desert. Flora 213: 77–84. doi: 10.1016/j.flora.2015.04.005
[41]	Kidron GJ (2010) The effect of substrate properties, size, position, sheltering and shading on dew: An experimental approach in the Negev Desert. Atmos Res 98: 378–386. doi: 10.1016/j.atmosres.2010.07.015
[42]	Clark J, Campbell J, Grizzle H, et al. (2009) Soil microbial community response to drought and precipitation variability in the Chihuahuan Desert. Microbial Ecol 57: 248–260. doi: 10.1007/s00248-008-9475-7
[43]	Bamforth SS (2004) Water film fauna of microbiotic crusts of a warm desert. J Arid Environ 56: 413–423. doi: 10.1016/S0140-1963(03)00065-X
[44]	Massimo NC, Devan MMN, Arendt KR, et al. (2015) Fungal endophytes in aboveground tissues of desert plants: Infrequent in culture, but highly diverse and distinctive symbionts. Microbial Ecol 70: 61–76. doi: 10.1007/s00248-014-0563-6

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