Desert microbes, crops, and climate change

By Simran Patel

Deserts are one of the harshest environments in the world because of their extreme temperatures, low water levels, high salinity, high solar radiation1 and lack of soil nutrients2. School biology curricula often use desert animals and plants as examples of how life has adapted to places humans considered uninhabitable. However, those examples overlook the microbiome such as endophytic bacteria in plant tissues2 or cyanobacteria in soil crusts1. Desert microorganisms have adapted their metabolism to the unforgiving desert conditions. Apart from ensuring their own survival, desert microbes have evolved to boost the growth of plants and lay the foundation for thriving desert ecosystems. As droughts become more intense and frequent with climate change, these desert plant-microbial interactions are being studied for applications in drought-tolerant agriculture.  

Microbes have adapted to desert life in many ways, and this article will focus on three of them. Firstly, the high-intensity solar radiation deserts receive provide a level of UV light most organisms would not be able to tolerate. Liu et al. found 7 radiation-tolerant bacterial strains in China’s Taklimakan Desert, 6 of which produce colourful pigments that protect these strains from UV-induced damage3. This agrees with previous research by Sajjad et al., who observed yellow, orange, and red bacterial colonies from desert samples in Pakistan and attributed the colours to UV-absorbing pigments4

Secondly, desert microorganisms can fix carbon1 using organic and inorganic methods. While cyanobacteria fix carbon into organic sources using the Calvin cycle5, autotrophic bacteria in China’s Mu Us Desert have been found to mostly use the reductive tricarboxylic acid cycle6.  Alternatively, scientists have found carbonate-containing deposits precipitated out by microbes using inorganic pathways7. The carbon for this mineralisation may be coming from the atmosphere7, raising the possibility of exploiting desert bacteria for carbon sequestration and combatting climate change. 

Thirdly, bacteria have adapted to the nitrogen- and phosphorus-poor soils in deserts. Cyanobacteria and Proteobacteria living in deserts can fix nitrogen8, meaning they can convert atmospheric nitrogen to ammonia for the rest of the desert ecosystem. In fact, farms in arid areas lose these nitrogen fixers because they cannot survive the higher nitrogen levels from fertilisation8. Other bacteria can rely on phosphate rock as their source of phosphate2Pseudomonas and Enterobacter strains can solubilise the phosphate in rocks by producing organic acids, making the phosphate available to other organisms9

Because of these unique abilities, desert bacteria have evolved mutualisms with desert plants. A plant’s microbiome forms a “rhizosheath”, providing plant roots with nutrients and water in a habitat where they are scarce10. It also produces hormones that increase a plant’s own capability to absorb nutrients, by increasing root hair formation.2 This plant growth promoting effect was evident in Nepeta micrantha, which stabilises sand dunes in China’s Gurbantunggut Desert11. When supplied with 80mL or 120mL water per day, the presence of soil microbial communities alone increased above- and below-ground biomass of this plant11. To attract beneficial microorganisms to the rhizosphere, plant roots release sugars, amino acids, and molecules that pretend to be quorum sensing signals1. For example, Artemisia ordosica is a “nurse species” that changes the desert bacterial community to favour nitrogen fixers and phosphate solubilisers12. These bacteria make nitrogen and phosphorus accessible for plants and trigger the next stage of plant succession in deserts, showing how microbes underpin desert ecology12. The importance of plant-microbe mutualism is evident by how early on in life a desert plant microbiome is established – plants coat their seeds in endophytic bacteria in a process called vertical transmission2.  

These mutualisms are the basis of creating drought-tolerant crops by altering their microbiome. Although the planet’s climate has changed, this has not led to a change in political resistance to genetically modified drought-tolerant crops13. Thus, inoculating crops with bacterial consortia may be a way to grow organic crops that are resilient to the droughts, pests and diseases linked to climate change2. Bacteria isolated from deserts have been showed to improve yield of common crops as well as native desert plants. In one experiment, corn was treated with Dietzia cinnamea 55 that was isolated from soil in Negev Desert, Israel14. The treatment led to an increase in shoot length, dry biomass and kernel fresh weight14. In another experiment, wheat was treated with Pseudomonas sp. Strain LTGT-11-2Z from the rhizosphere of a drought-tolerant legume, and the wheat was grown for 7 days without water15. The treated wheat plants looked healthier and had a higher biomass than untreated wheat in drought conditions15. This research proves how desert bacteria can promote plant growth whether or not the plant host is native to the desert2. Introducing stability and scalability into these naturally versatile desert bacteria could make these inoculations commercially viable10

This article may have started with the biology of desert microbes, but it has ended with the usage of that biology in developing drought-tolerant “biofertilisers”1. The carbon sequestration and nutrient mobilisation capabilities of these microorganisms cannot be underestimated in a hotter, drier world. From sand dunes to sorghum, desert plant microbiomes will continue to be a goldmine for understanding desert ecology, extreme metabolism, and climate change adaptation. 


1.         Alsharif W, Saad MM, Hirt H. Desert Microbes for Boosting Sustainable Agriculture in Extreme Environments. Frontiers in Microbiology; 11, (2020, accessed 16 October 2022).

2.         Zhang Q, White JF. Bioprospecting Desert Plants for Endophytic and Biostimulant Microbes: A Strategy for Enhancing Agricultural Production in a Hotter, Drier Future. Biology 2021; 10: 961.

3.         Liu Y, Chen T, Li J, et al. High Proportions of Radiation-Resistant Strains in Culturable Bacteria from the Taklimakan Desert. Biology 2022; 11: 501.

4.         Sajjad W, Khan S, Ahmad M, et al. Effects of Ultra-violet Radiation on Cellular Proteins and Lipids of Radioresistant Bacteria Isolated from Desert Soil. Folia Biologica 2018; 66: 41–52.

5.         Burney J, Ramanathan V. Recent climate and air pollution impacts on Indian agriculture. PNAS 2014; 111: 16319–16324.

6.         Liu Z, Sun Y, Zhang Y, et al. Metagenomic and 13C tracing evidence for autotrophic atmospheric carbon absorption in a semiarid desert. Soil Biology and Biochemistry 2018; 125: 156–166.

7.         Liu Z, Sun Y, Zhang Y, et al. Desert soil sequesters atmospheric CO2 by microbial mineral formation. Geoderma 2020; 361: 114104.

8.         Chen L-F, He Z-B, Zhao W-Z, et al. Soil structure and nutrient supply drive changes in soil microbial communities during conversion of virgin desert soil to irrigated cropland. European Journal of Soil Science2020; 71: 768–781.

9.         Delgado M, Mendez J, Rodríguez-Herrera R, et al. Characterization of phosphate-solubilizing bacteria isolated from the arid soils of a semi-desert region of north-east Mexico. Biological Agriculture & Horticulture2014; 30: 211–217.

10.       Perera I, Subashchandrabose SR, Venkateswarlu K, et al. Consortia of cyanobacteria/microalgae and bacteria in desert soils: an underexplored microbiota. Appl Microbiol Biotechnol 2018; 102: 7351–7363.

11.       Zhao C, Zheng R, Shi X, et al. Soil microbes and seed mucilage promote growth of the desert ephemeral plant Nepeta micrantha under different water conditions. Flora 2021; 280: 151845.

12.       Bai Y, She W, Miao L, et al. Soil microbial interactions modulate the effect of Artemisia ordosica on herbaceous species in a desert ecosystem, northern China. Soil Biology and Biochemistry 2020; 150: 108013.

13.       Matt Reynolds. Europe’s Drought Might Force Acceptance of Gene-Edited Crops. Wired UK, 2022, (2022, accessed 17 October 2022).

14.       Khan N, Martínez-Hidalgo P, Humm EA, et al. Inoculation With a Microbe Isolated From the Negev Desert Enhances Corn Growth. Frontiers in Microbiology; 11, (2020, accessed 17 October 2022).

15.       Zhang L, Zhang W, Li Q, et al. Deciphering the Root Endosphere Microbiome of the Desert Plant Alhagi sparsifolia for Drought Resistance-Promoting Bacteria. Applied and Environmental Microbiology 2020; 86: e02863-19.

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