Soil bacterial community associated with the dioecious Acanthosicyos horridus in the Namib Desert
- 76 Downloads
Plant clusters govern soil microbiology in desert systems. Female Acanthosicyos horridus plants in the Namib Desert are preferentially accessed by grazers, especially during fruit availability. We hypothesized that this differential grazing affects the taxonomic diversity of soil bacterial populations. Sampling was carried out at three locations on a northwest-to-southeast transect starting at the Kuiseb Delta, near the shores of the Atlantic in the western Namib Desert, and extending inland over a distance of 140 km. Analyses of the soil samples showed that proximity to the sea had a strong impact on soil salinity. Soil pH and organic matter content were generally not significantly correlated with the presence or absence of plants and varied little and non-uniformly along the transect. A. horridus presence led to distinct under-canopy bacterial-community diversity in contrast with the non-vegetated spaces between shrubs. However, plant gender has only a marginal, statistically insignificant impact on the bacterial-diversity properties, thus not supporting our hypothesis. Therefore, the taxonomic diversity of the bacterial community in Namib Desert soils vegetated with A. horridus is primarily governed by the presence or absence of plants and by proximity to the ocean.
KeywordsSoil microbial community Namib Desert Acanthosicyos horridus Plant gender
Special thanks to Mrs. Sharon Victor for her useful comments and Ms. Tea Colin for her assistance in the laboratory work. We thank the members of the Soil Ecology Lab at Bar-Ilan University for valuable discussions and technical assistance.
This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
Our research did not involve human participants or animals. All authors agree to the submission of this manuscript.
- Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169Google Scholar
- Anderson MJ (2005) PERMANOVA: a FORTRAN computer program for permutationl multivariate analysis of variance. Department of Statistics, University of Auckland, New ZealandGoogle Scholar
- Berry C (2003) Aspects of phenology and condition of inland and coastal !Nara plants in the Namib-Naukluft Park, Namibia. Dinteria 28:1–18Google Scholar
- 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
- Coleman D, Crossley D (2004) Fundamentals of soil ecology. Academic Press, New YorkGoogle Scholar
- Ding GC, Piceno YM, Heuer H, Weinert N, Dohrmann AB, Carrillo A, Andersen GL, Castellanos T, Tebbe CC, Smalla K (2013) Changes of soil bacterial diversity as a consequence of agricultural land use in a semi-arid ecosystem. PLoS One 8:e59497. https://doi.org/10.1371/journal.pone.0059497 CrossRefGoogle Scholar
- Dowd SE, Callaway TR, Wolcott RD, Sun Y, McKeehan T, Hagevoort RG, Edrington TS (2008) Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). BMC Microbiol 8:125. https://doi.org/10.1186/1471-2180-8-125
- Eldridge DJ (2003) Biological soil crusts and water relations in Australian deserts. In: Belnap J, Lange OL (eds) Biological soil crusts: structure, function, and management. Springer, BerlinGoogle Scholar
- Fierer N, Breitbart M, Nulton J, Salamon P, Lozupone C, Jones R, Robeson M, Edwards RA, Felts B, Rayhawk S, Knight R, Rohwer F, Jackson RB (2007) Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol 73:7059–7066CrossRefGoogle Scholar
- Goodfellow M (2015) Actinomycetales. In: Whitman WB, Rainey F, Kämpfer P, Trujillo M, Chun J, DeVos P, Hedlund B, Dedysh S (eds) Bergey’s manual of systematics of archaea and bacteria. https://doi.org/10.1002/9781118960608.obm00005
- Hammer Ø, Harper DAT, Ryan PD (2001) Past: paleontological statistics software package for education and data analysis. Palaeontol Electron 4(1):4. http://palaeo-electronica.org/2001_1/past/issue1_01.htm
- Heulin T, Barakat M, Christen R, Lesourd M, Sutra L, De Luca G, Achouak W (2003) Ramlibacter tataouinensis gen. nov., sp nov., and Ramlibacter henchirensis sp nov., cyst-producing bacteria isolated from subdesert soil in Tunisia. Int J Syst Evol Microbiol 53:589–594. https://doi.org/10.1099/ijs.0.02482-0 CrossRefGoogle Scholar
- Huson DH, Beier S, Flade I, Gorska A, El-Hadidi M, Mitra S, Ruscheweyh HJ, Tappu R (2016) MEGAN community edition—interactive exploration and analysis of large-scale microbiome sequencing data Plos Comput Biol 12. doi: https://doi.org/10.1371/journal.pcbi.1004957,
- Logan NA, Vos PD (2015) Bacillus. In: Whitman WB, Rainey F, Kämpfer P, Trujillo M, Chun J, Vos PD, Hedlund B, Dedysh S (eds) Bergey’s manual of systematics of archaea and bacteria. https://doi.org/10.1002/9781118960608.gbm00530
- Louw GN, Seely MK (1982) Ecology of desert organisms. Longman Group Ltd., LondonGoogle Scholar
- Maun MA (2004) Burial of plants as a selective force in sand dunes. In: Martinez ML, Psuty NP (eds) Coastal dunes ecology and conservation. Springer, BerlinGoogle Scholar
- Maun MA (2009) The biology of coastal sand dunes. Oxford University Press, OxfordGoogle Scholar
- McBride MJ, Liu W, Lu X, Zhu Y, Zhang W (2014) The family Cytophagaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The prokaryotes: other major lineages of Bacteria and the Archaea. Springer, BerlinGoogle Scholar
- Neilson JW, Quade J, Ortiz M, Nelson WM, Legatzki A, Tian F, LaComb M, Betancourt JL, Wing RA, Soderlund CA, Maier RM (2012) Life at the hyperarid margin: novel bacterial diversity in arid soils of the Atacama Desert, Chile. Extremophiles 16:553–566. https://doi.org/10.1007/s00792-012-0454-z CrossRefGoogle Scholar
- Norris PR (2015) Acidimicrobiales. In: Whitman WB, Rainey F, Kämpfer P, Trujillo M, Chun J, Vos PD, Hedlund B, Dedysh S (eds) Bergey’s manual of systematics of archaea and bacteria. https://doi.org/10.1002/9781118960608.obm00004
- Noy-Meir I (1973) Desert ecosystems: environment and producers. Ann Rev Ecol Syst 4:25–51. https://doi.org/10.1146/annurev.es.04.110173.000325 CrossRefGoogle Scholar
- Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, Minchin PR, O’Hara B, Simpson GL, Solymos P, Stevens MHH, Szoecs E, Wagner H (2017) Vegan: community ecology package. R package version 2.4-5. https://CRAN.R-project.org/package=vegan
- Olsson PA, Jakobsen I, Wallander H (2003) Foraging and resource allocation strategies of mycorrhizal fungi in a patchy environment. In: van der Heijden MGA, Sanders IR (eds) Mycorrhizal ecology. Springer, BerlinGoogle Scholar
- Rosenberg E (2014) The family Chitinophagaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The prokaryotes: other major lineages of Bacteria and the Archaea. Springer, BerlinGoogle Scholar
- Soil and Plant Analysis Council Inc. (1999) Soil analysis handbook of reference methods. CRC Press, Boca RatonGoogle Scholar
- St'ovicek A, Azatyan A, Soares MIM, Gillor O (2017) The impact of hydration and temperature on bacterial diversity in arid soil mesocosms. Front Microbiol 8. doi: https://doi.org/10.3389/fmicb.2017.01078
- Turner S, Pryer KM, Miao VPW, Palmer JD (1999) Investigating deep phylogenetic relationships among cyanobacteria and plastids by small submit rRNA sequence analysis. J Eukaryot Microbiol 46:327–338. https://doi.org/10.1111/j.1550-7408.1999.tb04612.x CrossRefGoogle Scholar
- van der Waal C, Kool A, Meijer SS, Kohi E, Heitkonig IMA, de Boer WF, van Langevelde F, Grant RC, Peel MJS, Slotow R, de Knegt HJ, Prins HHT, de Kroon H (2011) Large herbivores may alter vegetation structure of semi-arid savannas through soil nutrient mediation. Oecologia 165:1095–1107. https://doi.org/10.1007/s00442-010-1899-3 CrossRefGoogle Scholar
- Whitford WG (2002) Ecology of desert systems. Academic Press, New YorkGoogle Scholar