Advertisement

Extremophiles

, Volume 23, Issue 3, pp 337–346 | Cite as

Sedimentary Marl mudstone as a substrate in a xeric environment revealed by microbiome analysis

  • Oksana Koryachenko
  • Ruben Girsowicz
  • Yaron Dekel
  • Tirza Doniger
  • Yosef SteinbergerEmail author
Original Paper

Abstract

The sedimentary Marl mudstone soil is composed primarily of CaCO3, and is an important pedologic and geomorphologic element known as Marl, extensively dispersed in slopes and ridges in the northern Negev Desert, Israel. The wide Marl soil-layer areas are barren, with well-developed streamsides and no perennial vegetation cover. Soil systems in the Negev Desert have been widely studied, yet very little information was collected on Marl soils, and even less on the microbiome present in the Negev. Thus, an evaluation of the microbial-community inhabitants in a Marl soil layer was conducted in an attempt to distinguish between Marl with surface green mat and bare Marl soil layer. Our objective was to investigate the microbiome and abiotic components of the upper layer (0–5 cm) of Marl and Marl-with-green-mat soil collected in the Negev Desert. Plate-counting enabled the estimation of fungal and bacterial population size, while nested polymerase chain reaction (nPCR) and Ion Torrent sequencing were used to analyze biological diversity. The results indicate significant differences in microbial biomass and microbial-community diversity between Marl and Marl-green mat, despite similar pH levels. Further study is needed to enhance understanding of the activity of the biotic components and their contribution to slope stabilization.

Keywords

Marl Bacterial diversity Soil environment Soil layer Desert 

Notes

Acknowledgements

We thank Ms. Sharon Victor for preparing the manuscript for publication.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

792_2019_1087_MOESM1_ESM.pptx (89 kb)
Supplementary file1 (PPTX 88 kb)

References

  1. Aislabie JM, Chhour KL, Saul DJ, Miyauchi S, Ayton J, Paetzold RF, Balks MR (2006) Dominant bacteria in soils of Marble Point and Wright Valley, Victoria Land, Antarctica. Soil Biol Biochem 38:3041–3056CrossRefGoogle Scholar
  2. Anderson JPE, Domsch KH (1978) Physiological method for quantitative measurement of microbial biomass in soils. Soil Biol Biochem 10:215–221CrossRefGoogle Scholar
  3. Aref MAM, Abou El Safa MM (2006) Classification and interpretation of the Quaternary gypsum crust (Gypcrete) in Ayun Mousa area, West Sinai, Egypt. In: Proceedings of the 8th international conference on the geology of the Arab world, vol 8. Geology Arab World, Cairo UniversityGoogle Scholar
  4. Beck MW, Templin EH (1926) Soil survey of Navarro County, Texas. In: Soil survey report (United States, Bureau of Chemistry and Soils), no 20. Washington, DC, p 20Google Scholar
  5. Bernardet JF, Segers P, Vancanneyt M, Berthe F, Kersters K, Vandamme P (1996) Cutting a Gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 46:128–148CrossRefGoogle Scholar
  6. Bernardet JF, Nakagawa Y, Holmes B (2002) Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049–1070Google Scholar
  7. Black CA (1965) Methods of Soil analysis: part 1 physical and mineralogical properties, including statistics of measurement and sampling. American Society of Agronomy, MadisonGoogle Scholar
  8. Campbell CD, Chapman SJ, Cameron CM, Davidson MS, Potts JM (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 Microbiol 69:3593–3599CrossRefGoogle Scholar
  9. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Tumbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336.  https://doi.org/10.1038/nmeth.f.303 CrossRefGoogle Scholar
  10. Chakrabarti G, Shome D (2010) Interaction of microbial communities with clastic sedimentation during Palaeoproterozoic time—An example from basal Gulcheru Formation, Cuddapah basin, India. Sediment Geol 226:22–28CrossRefGoogle Scholar
  11. Delgado-Baquerizo M, Oliverio AM, Brewer TE, Benavent-Gonzalez A, Eldridge DJ, Bardgett RD, Maestre FT, Singh BK, Fierer N (2018) A global atlas of the dominant bacteria found in soil. Science 359:320–325.  https://doi.org/10.1126/science.aap9516 CrossRefGoogle Scholar
  12. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72:5069–5072CrossRefGoogle Scholar
  13. Dreimanis A (1962) Quantitative gasometric determination of calcite and dolomite by using Chittick apparatus. J Sediment Res.  https://doi.org/10.2210/jsr.33.235 Google Scholar
  14. Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461.  https://doi.org/10.1093/bioinformatics/btq461 CrossRefGoogle Scholar
  15. Einsele G (1982) Limestone-marl cycles (periodites); diagnosis, significance, causes—a review. In: Einsele G, Seilacher A (eds) Cyclic and event etratification. Springer-Verlag, Berlin, Heidelberg, New YorkCrossRefGoogle Scholar
  16. Eriksson P, Mourkas E, González-Acuna D, Olsen B, Ellström P (2017) Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species. Infect Ecol Epidemiol 1386536:7.  https://doi.org/10.1080/20008686.2017.1386536 Google Scholar
  17. Eswaran H, Reich PF, Kimble JM, Beinroth FH, Padnamanbhan E, Moncharoen P (2000) Global carbon stocks. In: Lal R, Kimble JM, Eswaran H, Stewart BA (eds) Global climate change and pedogenic carbonates. CRC Press, Boca RatonGoogle Scholar
  18. Evenari ME, Shanan L, Tadmor W (1982) The Negev: the challenge of a desert, 2nd edn. Harvard University Press, CambridgeCrossRefGoogle Scholar
  19. Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford MA, Knight R (2012) Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J 6:1007–1017CrossRefGoogle Scholar
  20. Frank R, Buchbinder B, Benjamini C (2010) The mid-Cretaceous carbonate system of northern Israel: facies evolution, tectono-sedimentary configuration and global control on the central Levant margin of the Arabian Plate. Geol Soc Spec Publ 341:133–169.  https://doi.org/10.1144/SP341.7 CrossRefGoogle Scholar
  21. Hamdali H, Smirnov A, Esnault C, Ouhdouch Y, Virolle MJ (2010) Physiological studies and comparative analysis of rock phosphate solubilization abilities of Actinomycetales originating from Moroccan phosphate mines and of Streptomyces lividans. Appl Soil Ecol 44:24–31CrossRefGoogle Scholar
  22. Jeanbille M, Buee M, Bach C, Cebron A, Frey-Klett P, Turpault MP, Uroz S (2016) Soil parameters drive the structure, diversity and metabolic potentials of the bacterial communities across temperate beech forest soil sequences. Microb Ecol 71:482–493CrossRefGoogle Scholar
  23. Jung C, Bobet A, Siddiki N (2011) Simple method to identify marl soils. Transp Res Rec 2232:76–84CrossRefGoogle Scholar
  24. Kabisch A, Otto A, Konig S, Becher D, Albrecht D, Schuler M, Teeling H, Amann RI, Schweder T (2014) Functional characterization of polysaccharide utilization loci in the marine Bacteroidetes 'Gramella forsetii' KT0803. ISME J 8:1492–1502CrossRefGoogle Scholar
  25. Kelts K, Hsu KJ (1978) Freshwater carbonate sedimentation. In: Lerman A (ed) Lakes: chemistry, geology, and physics. Springer-Verlag, BerlinGoogle Scholar
  26. Kirk JL, Beaudette LA, Hart M, Moutoglis P, Khironomos JN, Lee H, Trevors JT (2004) Methods of studying soil microbial diversity. J Microbiol Meth 58:169–188CrossRefGoogle Scholar
  27. Lajtha K, Bloomer SH (1988) Factors affecting phosphate sorption and phosphate retention in a desert ecosystem. Soil Sci 146:160–167CrossRefGoogle Scholar
  28. LaMontagne MG, Michel FC, Holden PA, Reddy CA (2002) Evaluation of extraction and purification methods for obtaining PCR-amplifiable DNA from compost for microbial community analysis. J Microbiol Meth 49:255–264CrossRefGoogle Scholar
  29. Lauber CL, Hamady M, Knight R, Fierer N (2009) Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75:5111–5120.  https://doi.org/10.1128/Aem.00335-09 CrossRefGoogle Scholar
  30. Littmann T (1997) Atmospheric input of dust and nitrogen into the Nizzana sand dune ecosystem, north-western Negev, Israel. J Arid Environ 36:433–457CrossRefGoogle Scholar
  31. Loeppert RH, Suarez DL (1996) Carbonate and gypsum. In: Sparks DL (ed) Methods of soil analysis Part 3, 3rd edn. SSSA, ASA, MadisonGoogle Scholar
  32. Lombard N, Prestat E, van Elsas JD, Simonet P (2011) Soil-specific limitations for access and analysis of soil microbial communities by metagenomics. FEMS Microbiol Ecol 78:31–49CrossRefGoogle Scholar
  33. Maier RM, Drees KP, Neilson JW, Henderson DA, Quade J, Betancourt JL (2004) Microbial life in the Atacama Desert. Science 306:1289–1289CrossRefGoogle Scholar
  34. Martin JP (1950) Use of acid, rose bengal, and streptomycin in the plate method for estimating soil fungi. Soil Sci 52:215–232CrossRefGoogle Scholar
  35. Mayrberger JM (2011) Studies of genera cytophaga-flavobacterium in context of the soil carbon cycle. Michigan State University, East LansingGoogle Scholar
  36. Müller C, Higazi F, Hamdan W, Mroueh M (2010) Revised stratigraphy of the upper Cretaceous and cenozoic series of Lebanon based on nannofossils. In: Homberg C, Bachmann M (eds) Evolution of the levant margin and western arabia platform since the Mesozoic. Geological Society, LondonGoogle Scholar
  37. Navarro-Gonzalez R, Rainey FA, Molina P, Bagaley DR, Hollen BJ, de la Rosa J, Small AM, Quinn RC, Grunthaner FJ, Caceres L, Gomez-Silva B, McKay CP (2003) Mars-like soils in the Atacama Desert, Chile, and the dry limit of microbial life. Science 302:1018–1021CrossRefGoogle Scholar
  38. Offer ZY, Zangvil A, Azmon E (1993) Characterization of airborne dust in Sede Boqer area. Israel J Earth Sci 41:239–245Google Scholar
  39. Offer ZY, Boqer S, Goossens D (2001) Airborne particle accumulation and composition at different locations in the northern Negev desert. Z Geomorphol 45:101–120Google Scholar
  40. Oulas A, Minadakis G, Zachariou M, Sokratous K, Bourdakou M, Spyrou G (2017) Systems bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches. Brief Bioinform.  https://doi.org/10.1093/bib/bbx151 Google Scholar
  41. Rousk J, Baath E, Brookes PC, Lauber CL, Lozupone C, Caporaso JG, Knight R, Fierer N (2010) Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J 4:1340–1351CrossRefGoogle Scholar
  42. Uroz S, Tech JJ, Sawaya NA, Frey-Klett P, Leveau JHJ (2014) Structure and function of bacterial communities in ageing soils: Insights from the Mendocino ecological staircase. Soil Biol Biochem 69:265–274CrossRefGoogle Scholar
  43. Vassilev N, Vassileva M, Nikolaeva I (2006) Simultaneous P-solubilizing and biocontrol activity of microorganisms: potentials and future trends. Appl Microbiol Biotechnol 71:137–144CrossRefGoogle Scholar
  44. Weisskopf L, Heller S, Eberl L (2011) Burkholderia species are major inhabitants of white lupin cluster roots. Appl Environ Microbiol 77:7715–7720CrossRefGoogle Scholar
  45. Wiik E, Bennion H, Sayer CD, Davidson TA, Clarke SJ, McGowan S, Prentice S, Simpson GL, Stone L (2015) The coming and going of a marl lake: multi-indicator palaeolimnology reveals abrupt ecological change and alternative views of reference conditions. Front Ecol Evol 3:82.  https://doi.org/10.3389/fevo.2015.00082 CrossRefGoogle Scholar
  46. EME Wiik 2012Understanding the ecological response of marl lakes to enrichment: a combined limnological and palaeolimnological approach. For submission for a Doctorate of Philosophy, Department of Geography, UCL, UKGoogle Scholar
  47. Yu J, Steinberger Y (2012) Vertical distribution of soil microbial biomass and its association with shrubs from the Negev Desert. J Arid Environ 78:110–118.  https://doi.org/10.1016/j.jaridenv.2011.11.012 CrossRefGoogle Scholar
  48. Zak JC, Willig MR, Moorhead DL, Wildman HG (1994) Functional diversity of microbial communities: a quantitative approach. Soil Biol Biochem 26:1101–1108CrossRefGoogle Scholar

Copyright information

© Springer Japan KK, part of Springer Nature 2019

Authors and Affiliations

  1. 1.The Mina and Everard Goodman Faculty of Life SciencesBar-Ilan UniversityRamat-GanIsrael
  2. 2.Shamir Research InstituteUniversity of HaifaKazerinIsrael

Personalised recommendations