title: A survey of the microbial community in the rhizosphere of two dominant shrubs of the Negev Desert highlands, Zygophyllum dumosum (Zygophyllaceae) and Atriplex halimus (Amaranthaceae), using cultivation-dependent and cultivation-independent methods.
abstract: OBJECTIVE
  Plant roots comprise more than 50% of the plant's biomass. Part of that biomass includes the root microbiome, the assemblage of bacteria and fungi living in the 1-3 mm region adjacent to the external surface of the root, the rhizosphere. We hypothesized that the microorganisms living in the rhizosphere and in bulk soils of the harsh environment of the Negev Desert of Israel had potential for use as plant-growth-promoting bacteria (PGPB) to improve plant productivity in nutrient-poor, arid soils that are likely to become more common as the climate changes. •
  
  
  METHODS
  We used cultivation-dependent methods including trap experiments with legumes to find nitrogen-fixing rhizobia, specialized culture media to determine iron chelation via siderophores and phosphate-solubilizing and cellulase activities; cultivation-independent methods, namely 16S rDNA cloning and sequencing; and also community-level physiological profiling to discover soil microbes associated with the Negev desert perennials Zygophyllum dumosum and Atriplex halimus during the years 2009-2010. •
  
  
  RESULTS
  We identified a number of PGPB, both epiphytes and endophytes, which fix nitrogen, chelate iron, solubilize phosphate, and secrete cellulase, as well as many other bacteria and some fungi, thereby providing a profile of the microbiomes that support the growth of two desert perennials. •
  
  
  CONCLUSIONS
  We generated a snapshot of the microbial communities in the Negev Desert, giving us an insight in its natural state. This desert, like many arid environments, is vulnerable to exploitation for other purposes, including solar energy production and dry land farming.
authors: Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus Midreshet Ben-Gurion 84990, Israel.
authors: Drora
authors: D
authors: Kaplan
authors: Maskit
authors: M
authors: Maymon
authors: Christina M
authors: CM
authors: Agapakis
authors: Andrew
authors: A
authors: Lee
authors: Andrew
authors: A
authors: Wang
authors: Barry A
authors: BA
authors: Prigge
authors: Mykola
authors: M
authors: Volkogon
authors: Ann M
authors: AM
authors: Hirsch
mesh_terms: D000383:Agriculture; D027466:Atriplex / Q000382:microbiology*; D001419:Bacteria / Q000145:classification / Q000302:isolation & purification*; D044822:Biodiversity; D018533:Biomass; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D003889:Desert Climate; D017753:Ecosystem; D005658:Fungi / Q000145:classification / Q000302:isolation & purification*; D007557:Israel; D009584:Nitrogen / Q000378:metabolism; D018517:Plant Roots / Q000382:microbiology*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D058441:Rhizosphere; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology; D013559:Symbiosis; D032445:Zygophyllum / Q000382:microbiology*
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D009584:Nitrogen
keywords: Atriplex halimus; Zygophyllum dumosum; cultivation-dependent and -independent analysis; desert rhizosphere; trap experiments