DOI: https://doi.org/10.56669/HXMU5377
ABSTRACT
A large portion of the Earth’s surface is covered by dry and semi-dry regions, where conditions are often challenging. Nevertheless, these regions are rich in microbes that live in close association with plants, supporting their growth and helping them withstand stress. Some of the most helpful microbes are called plant growth-promoting microorganisms (PGPMs). They help plants by making nutrients easier to absorb, producing natural plant hormones, and protecting them from diseases. Research done in deserts around the world has found many useful groups of microbes. Among bacteria, Proteobacteria, Actinobacteria, and Bacteroidetes are common, while Ascomycota and Basidiomycota are the main groups of fungi. One well-known bacterial group, Bacillus, has shown many benefits for plant growth. Studying the microbes that live in deserts gives us hope for better and more sustainable farming, especially in places where the climate is very tough. This article takes another perspective on the different microbes found in deserts across the world and discusses how they can help increase crop production even under extreme environments and uncertain weather conditions.
Keywords: PGPM, Arid climate, Disease resistance, Sustainability
INTRODUCTION
In the 21st century, agriculture is facing significant challenges like environmental pollution, climate change, the rise of drug-resistant microbes, and the growing shortage of land, water, and food (FAO, 2022). A primary reason behind these problems is the rapid increase in the world’s population, which has caused a noticeable drop in the amount of cultivable land. Because of these limitations, arid and desert regions covering more than 46 million square kilometers around the world are now being looked at for their possible use in agriculture, even though they face very tough conditions such as extreme heat, poor soil, and very little rain (Osborne et al., 2020). These dry areas are divided into three types hyper-arid, arid, and semi-arid based on the Aridity Index. Many of these areas are becoming deserts even faster and are home to more than two billion people (Alsharif et al., 2020). Despite the harsh environment, these regions support unique forms of life plants, animals, and microbes that have special adaptations to survive strong sunlight, salty soils, low organic content, and large temperature swings. Among these, microbes are very important because they help ecosystems function properly. They assist in recycling nutrients, breaking down organic materials, reducing stress in plants, and supporting plant growth.

Strict environmental conditions mostly influence the types of microbes in deserts. These conditions tend to favor bacteria that can survive in extreme settings. Earlier, it was challenging to study these microbes because scientists mainly used culture-based methods, which only showed a small part of the actual microbial community. But now, with new tools in molecular biology, like gene sequencing, DNA fingerprinting, and metagenomics, scientists can study microbes more effectively in labs without needing to grow them. We now know that although desert soils harbor fewer types of microbes than other regions, those present possess unique traits that enable them to survive under difficult conditions. Considerable international efforts like the Earth Microbiome Project and the use of next-generation sequencing (NGS) have made it possible to discover new kinds of microbes and learn how they might help with sustainable farming (Delgado-Baquerizo et al., 2018). Interestingly, desert microbes can provide helpful features such as drought resistance, nutrient breakdown, protection against harmful organisms, and hormone production for plants. These abilities can be used to create bioinoculants products made from beneficial microbes that help plants grow better in dry areas. A new way of thinking, explained by the holobiont and hologenome theories, shows that plants and microbes evolve together and support each other. This partnership improves plant health, increases stress resistance, and helps them adapt to the environment.
Still, there is more to learn. Even though scientists have studied the genetic information of desert microbes, there’s a gap in turning this knowledge into real-world farming solutions. To fill up the gap, we need combined research that includes genetics, environmental studies, and testing on farms (Mandakovic et al., 2018). As the world looks for farming methods that are sustainable and can handle climate change, using desert microbes in agriculture looks like an up-and-coming option. They could help increase food production, restore damaged lands, and build farming systems that can cope with environmental challenges in the future.
Adaptive strategies of dryland flora
Desert ecosystems have very tough living conditions. They have very limited water, strong sunlight, and poor soil with few nutrients. To survive in such environments, dryland plants have developed many changes in their structure, body functions, and even at the genetic level (Evelin et al., 2019). Some physical changes (morphological traits) include having small leaves, leaves that grow upright, thick outer layers (cuticles), and short plant height. These features help reduce water loss and protect from heat. In terms of body functions (physiology), plants use special methods like Crassulacean Acid Metabolism (CAM), which helps save water. They also improve the efficiency of water use during transpiration and produce special compounds called phenolics that help them deal with stress (Umair et al., 2023).
At the genetic and biochemical level (molecular level), desert plants produce more of specific proteins like heat shock proteins, enzymes that fight harmful molecules (antioxidative enzymes), and substances that protect cells from drying out (osmoprotectants). These help the plants survive in harsh conditions (Gupta et al., 2020; Sharma et al., 2021). Plant hormones such as abscisic acid, cytokinins, and jasmonates also play an essential role in managing how plants respond to drought (Evelin et al., 2019). The structure of the roots is another crucial adaptation. Desert plants often have fibrous roots, deep roots, or roots with a covering called a rhizosheath. These features help them absorb more water and allow helpful microbes to live near the roots (Najafi et al., 2021; Kour et al., 2021). Rhizosheaths, formed by microbes, help retain water and facilitate nutrient uptake.
Beneficial microbes, especially plant growth-promoting bacteria (PGPB), are very important in desert soils. They help plants by making nutrients easier to absorb, producing growth hormones, and protecting against harmful microbes (Sharma et al., 2021). Desert plants also host many types of microbes, not just in the soil around roots (rhizosphere), but also on leaves (phyllosphere), inside roots (endosphere), and within the rhizosheath. These microbial communities depend on the plant type, climate, and soil conditions (Saad et al., 2020; Trivedi et al., 2020). Some of these beneficial microbes, called PGPMs, can be used in agriculture as eco-friendly options for fertilizers and pest control (Alsharif et al., 2020; Bashan et al., 2021). A list of commonly studied PGPMs and their respective growth-promoting mechanisms is presented in Table 1.
Table 1. Plant growth-promoting microorganisms and their mechanism of actions
Sr. No.
|
Plant growth promoting microorganism (PGPM)
|
Growth promotion mechanism
|
1
|
Azospirillum, Azotobacter, Achromobacter, Bradyrhizobium, Beijerinckia, Rhizobium, Clostridium, Klebsiella., Anabaena., Nostoc, Frankia
|
Nitrogen fixation- through the reduction of nitrogen gas (N2) to ammonia (NH3).
|
2
|
Bacillus, Pseudomonas, Rhizobium, Achromobacter, Burkholderia, Microccocus, Agrobacterium, Erwinia sp., Penicillium sp. and Aspergillus sp.
|
Phosphate solubilization- transforms and solubilizes inorganic phosphorus into forms capable of being absorbed by plants, such as monobasic (H2PO4-) or dibasic phosphate (HPO4−2).
|
3
|
Burkholderia, Enterobacter, Grimontella and Pseudomonas
|
Siderophore production- improves plant nutrition and inhibits phytopathogens through iron sequestration from the environment.
|
4
|
Bacillus and Aspergillus
|
Potassium solubilization- produces organic and inorganic acids, acidolysis, chelation, and exchange reactions which are capable of solubilizing potassium.
|
5
|
Rhizophagus irregularis and Funneliformis mosseae
|
Phytoextraction and stabilization- Fungi that extract Cd and enhanced phytostabilization of Cd and Zn respectively.
|
6
|
Pseudomonas sp. and Bacillus
|
Auxin secretion- promote plants growth by increase auxin and ACC (Amino-cyclopropane-carboxylate)-deaminase.
|
7
|
Sphingomonas SaMR12, Phyllobacterium myrsinacearum RC6b
|
IAA- Indole-Acetic –Acid production and root promotion.
|
8
|
Bacillus spp.
|
Exopolysaccharides- forms a protective biofilm on root surface.
|
9
|
Proteus penneri, P. aeruginosa, and Alcaligenes faecalis
|
Exopolysaccharides- alleviate water stress and improve plant biomass under drought stress.
|
10
|
Burkholderia sp.
|
Metabolism- increases plant tolerance against low temperature by modifying carbohydrate metabolism.
|
11
|
Pseudomonas fluorescens
|
Osmoprotectants solutes and enzymes- promote plant tolerance by increasing the activity of catalase and peroxidase, and the accumulation of proline.
|
Structure of desert micro-communities
Bacterial communities in arid ecosystems
Microorganisms, especially plant growth-promoting bacteria (PGPB), are vital in deserts. They help plants by making nutrients more available, producing growth hormones, and protecting against diseases (Sharma et al., 2021). Desert plants also host diverse communities of microbes in different parts like their roots (rhizosphere and rhizosheath), leaves (phyllosphere), and even inside their tissues (endosphere). These microbial groups are influenced by the plant type, soil, and climate (Saad et al., 2020; Trivedi et al., 2020). Some of these microbes-known as Plant Growth-Promoting Microorganisms (PGPMs)-are promising tools for sustainable farming. They can act as natural fertilizers and pest controllers, especially in arid lands (Alsharif et al., 2020; Bashan et al., 2021).
Fungal communities in arid and semi-arid ecosystems
Fungi that live in dry and semi-dry regions have adapted well to survive in tough conditions like extreme heat, dryness, and strong sunlight. These fungi are important for breaking down organic material, recycling nutrients, and supporting interactions between plants and microbes, which helps maintain healthy soil and functioning ecosystems (Tedersoo et al., 2020). In deserts, fungi can live in many ways. They may act as decomposers (saprophytes), cause disease (pathogens), live off of other organisms (parasites), live inside plants without causing harm (endophytes), or form helpful partnerships (mutualists). Instead of having very complex survival systems, these fungi often rely on strategies like producing spores, staying dormant during extreme weather, and using very few resources (Egidi et al., 2019). Many types of fungi have been found in desert soils, such as yeasts, thread-like (filamentous) fungi, micro-colonial fungi, and arbuscular mycorrhizal fungi (AMF) (Egidi et al., 2019; Tedersoo et al., 2020). Studies show that Ascomycota is the most common fungal group in deserts. Within this group, classes like Dothideomycetes, Pezizomycetes, and Sordariomycetes are especially abundant (Durán et al., 2021). These findings come from both lab culture methods and modern DNA sequencing done in different parts of the world, including Saudi Arabia, Jordan, Australia, and North America (Egidi et al., 2019; Tedersoo et al., 2020). Among these fungi, arbuscular mycorrhizal fungi (AMF) are beneficial for plants. They improve the plant’s ability to take up water and nutrients—especially phosphorus—by expanding the plant’s root reach into dry soil (Fallah et al., 2021; Chandrasekaran et al., 2022). A global study found that the Glomeraceae family is the most common AMF in deserts, followed by families like Claroideoglomeraceae, Diversisporaceae, and Acaulosporaceae (Vasar et al., 2021). Besides supporting plant growth, AMF also help restore degraded land and stabilize soils. This makes them key contributors to the long-term health and recovery of dryland ecosystems (Zhang et al., 2023).
Archaea in arid and semi-arid ecosystems
Archaea are renowned for their resilience in extreme environments, including arid and hyperarid zones characterized by desiccation, nutrient scarcity, and high salinity. In desert ecosystems, these microorganisms play crucial roles in biogeochemical cycling, particularly in nitrogen and carbon transformations (Zhou et al., 2020; Tripathi et al., 2020; Siles et al., 2023). Although less abundant in mesic environments, archaeal taxa are frequently detected in desert soils, often dominated by chemolithoautotrophic members of the phylum Thaumarchaeota, which are central to desert archaeal communities (Lehtovirta-Morley, 2018). Halotolerant Euryarchaeota, especially Halobacteria from the orders Halobacteriales, Haloferacales, and Natrialbales, are also widely reported and noted for their metabolic flexibility and salinity adaptation (Lv et al., 2022; Bachran et al., 2019). Interestingly, uncultured or unclassified archaeal lineages account for nearly 40% of desert archaeal communities, pointing to vast unexplored diversity (Bachran et al., 2019; Wang et al., 2021). Recent isolations of novel genera such as Halorubrum and Haloparvum exemplify archaeal adaptability to extreme arid niches, while the detection of Crenarchaeota in deserts such as Tataouine further highlights their phylogenetic diversity (Taffner et al., 2022). Despite growing evidence of their ecological significance, desert archaeal communities remain poorly studied, and comprehensive metagenomic and functional analyses are needed to better understand their physiological adaptations and ecosystem roles (Tripathi et al., 2020; Siles et al., 2023; Taffner et al., 2022).
Viral communities in arid and semi-arid ecosystems
Viruses, especially bacteriophages (viruses that infect bacteria), are now being recognized as important but less-studied members of desert microbial communities. Recent studies using metaviromic techniques in extremely dry areas like the Namib and Atacama Deserts have found many different and new types of viruses. The most common among them are tailed bacteriophages, including families such as Myoviridae, Siphoviridae, and Podoviridae (Rout et al., 2023; Chen et al., 2021). These viruses seem to adapt to harsh conditions like very low water levels, changes in soil pH, and high salinity. When comparing viruses from cold deserts like Antarctica with those from hot deserts, researchers found fewer free viruses in hyper-arid soils. However, they also discovered many unknown viruses that don’t match any known genomes in current databases (Rout et al., 2023). This suggests that deserts could hold a large number of undiscovered viruses, which might be important for ecology and biotechnology. So far, most research has focused on bacteriophages, while plant-related viruses in deserts have received less attention. Still, recent studies in dry farming areas have detected harmful plant viruses, such as begomoviruses and tobamoviruses, affecting crops like tomato, watermelon, and cucurbits—even in very dry conditions (Maruthi et al., 2022). These discoveries highlight the urgent need for more virus research in desert farming systems to understand their roles and impacts.
Microbial Communities in Deserts Across the Globe
Deserts of South and North America
Despite their harsh climates, the deserts of North and South America are home to a wide variety of tough and adaptable microbes. In North America, the Chihuahuan Desert has a rich mix of bacteria, especially in gypsum soils. Major bacterial groups found here include Actinobacteria, Proteobacteria, and Cyanobacteria, along with beneficial microbes that live around cactus roots, like Bacillus and Sordariomycetes (Mascot-Gómez et al., 2021; Vega-Flores et al., 2022).
The Sonoran Desert contains many types of bacteria in both the soil and plant root zones (rhizosphere), such as Planctomycetes and Chloroflexi, along with archaea like Euryarchaeota (Lopez-Robles et al., 2023). In the Mojave Desert, the biological soil crusts are mainly made up of Cyanobacteria like Phormidium, although helpful fungi (arbuscular mycorrhizal fungi) are found in smaller numbers (Gonzalez-Torres et al., 2021). Even cold deserts like the Colorado Plateau have many Cyanobacteria and nitrogen-fixing microbes like Nostoc and Scytonema, which play an important role in soil health (Huang et al., 2024). In South America, the Atacama Desert one of the driest places on Earth—has microbes that survive extreme dryness and intense UV rays. Common types here include fungi like Ascomycota and Basidiomycota, and bacteria such as Rubrobacterales and Actinobacteria, especially around plant roots (Zhang et al., 2022). Likewise, the dry Patagonian Desert contains groups like Rhizobiales and Actinomycetales, along with airborne fungi such as Cladosporium and Alternaria. These microbes are influenced by soil moisture and wind (Perez-Moreno et al., 2023).
Thar and cold deserts of India
The Thar Desert, spread across over 200,000 square kilometers in Rajasthan and Gujarat, is the 18th largest desert in the world. It experiences very hot daytime temperatures, sometimes reaching up to 55 °C, along with strong winds. Even in such extreme conditions, many types of microbes can survive. Studies have found that sand dunes here contain between 150 and 50,000 bacteria per gram, with nearly half being actinomycetes. Advanced methods like 16S r-RNA sequencing have helped scientists identify important bacterial genera, such as Streptomyces, Nocardiopsis, Saccharomonospora, and Actinoalloteichus (Kumar et al., 2021). Fungi are also present, including the Basidiomycete Broomeia congregata (Gehlot et al., 2020), and heat-tolerant endophytes like Aspergillus, Alternaria, Chaetomium, Penicillium, and Nigrospora, which can grow at 40–45°C and support plant growth under drought conditions (Ilyas et al., 2021). Researchers have also found root-associated bacteria in desert plants. For example, species like Pseudomonas pseudoalcaligenes, Azospirillum brasilense, and Rhizobium were isolated from the roots of Lasiurus sindicus, a native desert grass. The Central Arid Zone Research Institute (CAZRI) in Jodhpur has been working for over 20 years to identify useful microbes from desert areas. They have discovered many potential biofertilizers and biocontrol agents, such as Bacillus firmus, B. tequilensis, Streptomyces mexicanus, Aspergillus versicolor, A. nidulans, Trichoderma harzianum, and T. longibrachiatum (Mawar et al., 2017; Lodha et al., 2019; Mawar et al., 2021a, 2021b). In comparison, the cold deserts in northern India, like Ladakh, support microbes called psychrophiles that thrive in low temperatures. These include Exiguobacterium indicum, Paenibacillus glacialis, Janthinobacterium lividum, Sphingobacterium antarcticus, Psychrobacter valli, Alishewanella species, and Brevundimonas species. These organisms produce useful cold-active enzymes, pigments, and antifreeze substances that have potential applications in high-altitude farming and biotechnology.
Deserts of China
Taklamakan Desert (346,905 km², Northwest China): The Taklamakan Desert, the largest sandy desert in China, has a surprisingly rich microbial community despite being extremely dry. Research shows that the main types of bacteria in its soils include Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidetes (Wang et al., 2020a). Scientists have discovered new types of endophytic Actinobacteria (bacteria that live inside plants) from native desert plants, including genera like Prauserella, Nesterenkonia, Labedella, and Aeromicrobium (Li et al., 2019a, 2019b). These microbes may carry genes that help plants survive stress and could also be helpful in producing valuable compounds.
Gurbantunggut Desert (Xinjiang, China): In the Gurbantunggut Desert, specialized soil layers known as biological soil crusts (biocrusts) form daily. These crusts are composed of algae, lichens, mosses, and fungi, particularly from fungal groups such as Ascomycota, Lecanoromycetes, Eurotiomycetes, and Dothideomycetes (Zhang et al., 2018). Temporal changes in these communities are influenced by soil salinity and organic matter content. Commonly occurring fungi include Heteroplacidium and Endocarpon. Additionally, salt-tolerant bacteria such as Bacillus endophyticus, B. tequilensis, Planococcus rifietoensis, Variovorax paradoxus, and Arthrobacter agilis have been isolated from the halophyte Salicornia europaea, suggesting their potential role in enhancing plant tolerance to harsh desert conditions.
Gobi Desert (around 2.3 million km², Northern China and Southern Mongolia): The Gobi Desert, stretching across northern China and southern Mongolia, contains diverse microbial life. Actinobacteria, Acidobacteria, Chloroflexi mainly populate its soils, and several types of Proteobacteria (Maki et al., 2017). When dust storms occur, the number of Firmicutes and Bacteroidetes temporarily increases. Archaea, including Thaumarchaeota and Euryarchaeota, are also present, but in small amounts. Scientists have also isolated fungi living inside the roots of Stipa species in the Gobi grasslands. Most of these fungi belong to the group Ascomycota, and the most common types were Curvularia and Rhizopus.
Deserts of Africa
Sahara Desert: The Sahara Desert is the largest hot desert in the world, covering more than 9 million square kilometers. A recent research using advanced high-throughput sequencing methods has shown that the main types of bacteria found in Egyptian desert soils belong to the groups Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. Among these, the most common bacterial genera include Ochrobactrum, Rhodococcus, and Bacillus, while other groups like Gemmatimonadetes and Planctomycetes are present in smaller numbers. Scientists have also studied the bacteria living inside the tissues of the date palm (Phoenix dactylifera L.). These endophytic bacteria include Pseudomonas species that show strong resistance to drought and can help plants grow better under stress conditions (Kalam et al., 2020). In addition, some types of actinomycetes found in the Sahara, such as Streptomyces rochei PTL2 and Nocardiopsis dassonvillei MB22, have been found to work well as biocontrol agents. These strains help protect plants by fighting against harmful soil-borne pathogens (Allali et al., 2019).
Namib Desert: The Namib Desert, which stretches about 2,000 kilometers from Angola to South Africa, is one of the oldest deserts in the world. Research on microbial diversity in this region has found that bacteria from the groups Actinobacteria, Proteobacteria, and Bacteroidetes are common. In a study of Tylosema esculentum, a local plant that does not belong to the legume family, scientists discovered many plant growth-promoting (PGP) endophytic bacteria. These included Rhizobium, Massilia, Burkholderia, Sphingomonas, Microbacterium, and Chitinophaga, showing that various bacteria have adapted to survive in the extremely dry conditions of the Namib (Chimwamurombe et al., 2016).
Kalahari Desert: The Kalahari Desert, which stretches across parts of Botswana, Namibia, and South Africa, is one of the largest areas of continuous sand in the world. Studies on its microbes have found that halophilic (salt-loving) archaea are common, especially those from the Halobacteria group. Among bacteria, groups like Acetothermia, Gemmatimonadetes, and Firmicutes are often found. Earlier research on vesicular-arbuscular mycorrhizae (VAM) showed that they provided plant-specific benefits to native species like Vangueria infausta, though newer studies on this topic are still few. In addition to helpful microbes, some harmful fungi have also been found. Pathogenic fungi such as Curvularia, Alternaria, and Trichoderma have been observed in desert trees like Aloe and Acacia, suggesting that fungi also play a role in causing diseases in desert plants (Chimwamurombe et al., 2016).
Karoo Desert: The Karoo, a semi-arid region in South Africa, is home to fungal communities that can survive in harsh conditions. Scientists have found endophytic fungi, those that live inside plants, such as Aspergillus, Cladosporium, Fusarium, and Talaromyces, in a salt-tolerant plant called Sesuvium portulacastrum, which grows in the Succulent Karoo zone. These fungi may help the plant survive in environments with high salt levels and low water availability (Jacob et al., 2016).
Deserts of Arabia
The Arabian Desert, which spreads across parts of Saudi Arabia, Yemen, and the Persian Gulf, is home to many types of microbes that are well adapted to survive in extremely dry conditions. The most common bacterial groups found here are Actinobacteria, Proteobacteria, Firmicutes, and Gemmatimonadetes. These bacteria play important roles in the soil, helping with nutrient cycling and helping other organisms deal with environmental stress (Khan et al., 2020). Researchers have also found specific groups of bacteria with special functions. These include Cyanobacteria and Rhodoplanes, which perform photosynthesis, Rhizobium and Bradyrhizobium, which fix nitrogen, and Candidatus nitrososphaera, which helps in the oxidation of ammonia. This shows that the desert supports a complex and ecologically important microbial community. Fungi are also found in the dust and soil of the Arabian Desert. Some of the common ones include Alternaria, Penicillium, Phoma, and Mortierella. These fungi may cause allergies or help break down organic materials (Alsheikh et al., 2021). In addition, new types of fungi have been discovered in Saudi desert soils, such as previously unidentified species of Chaetomium. These findings point to a hidden wealth of fungal diversity in the region that may have future uses in biotechnology (Alotaibi et al., 2022).
Desert Region
|
Dominant Bacteria
|
Dominant Fungi
|
Key Functional Traits
|
Thar Desert (India)
|
Bacillus, Streptomyces
|
Aspergillus, Trichoderma
|
Thermotolerance, PGPR, biocontrol
|
Atacama (Chile)
|
Actinobacteria, Rubrobacter
|
Ascomycota
|
UV resistance, N-fixation
|
Namib (Africa)
|
Proteobacteria, Bacteroidetes
|
-
|
Soil crust formation, PGP
|
Gobi (China)
|
Firmicutes, Actinobacteria
|
Curvularia
|
Spore-forming, drought resilience
|
CONCLUSION
Deserts and arid lands, once considered lifeless, are actually full of microbial life that has developed special abilities to survive in harsh conditions. Microorganisms such as bacteria, fungi, archaea, and viruses play key roles in important ecological functions like breaking down organic matter, recycling nutrients, and helping plants tolerate stress. With the help of modern scientific tools like metagenomics and next-generation sequencing, scientists have discovered a wide variety of plant-friendly microbes, known as plant growth-promoting microorganisms (PGPMs). These microbes are found in deserts around the world and have useful traits like fixing nitrogen, dissolving phosphate, surviving drought, and producing growth hormones for plants. Our understanding of how plants and microbes work together has also improved, thanks to new perspectives like the “holobiont” and “hologenome” concepts. These explain how plants and their associated microbes form a team works together to improve plant health and resistance to environmental stress. Desert plants also have their own structural and chemical adaptations that help them survive. When combined with the help of beneficial microbes, these plants become even more capable of thriving in tough conditions. However, many desert microbes, especially certain archaea and viruses, are still unknown and have not yet been studied in the lab. To fully unlock the potential of these desert microorganisms, future research must bring together genetics, environmental science, and agriculture. This will help us use desert microbes to grow better crops, restore damaged land, and support food security in a warming and drying world.
REFERENCES
Allali, K., Sekhsokh, Y., & Elabed, S. (2019). Antagonistic activity of Streptomyces rochei PTL2 against Fusarium oxysporum. Moroccan Journal of Agricultural Sciences, 4(2), 12–19.
Alotaibi, M. O., Alsheikh, H. M., & Al-Jurayyan, A. (2022). Diversity of fungi in Saudi Arabian desert soils. Saudi Journal of Biological Sciences, 29(1), 45–54.
Alsharif, K., Hobbs, M., & Gornall, J. (2020). Desertification trends and challenges in the 21st century. Environmental Research Letters, 15(10), 104001.
Alsheikh, H. M., Alotaibi, M. O., & Al-Jurayyan, A. (2021). Fungal diversity in dust samples from arid regions of Saudi Arabia. Environmental Monitoring and Assessment, 193(5), 281.
Bachran, M., Kirk, M. F., & Flynn, T. M. (2019). Archaeal community structure in salt-dominated desert environments. Environmental Microbiology Reports, 11(1), 70–78.
Bashan, Y., de-Bashan, L. E., Prabhu, S. R., & Hernandez, J. P. (2021). Advances in plant growth-promoting bacterial inoculants for agriculture: A perspective for the future. Bioengineered, 12(1), 1160–1173.
Chen, Y., Li, Y., Liu, Y., & He, J. (2021). Viral diversity and community structure in desert soils of northern China. Virus Research, 293, 198297.
Chimwamurombe, P. M., Valentine, A. J., & Steyn, C. (2016). Rhizosphere and endophytic bacteria associated with Tylosema esculentum, a drought-tolerant desert legume. South African Journal of Botany, 104, 57–62.
Delgado-Baquerizo, M., Reith, F., Dennis, P. G., Hamonts, K., Powell, J. R., Young, A., & Singh, B. K. (2018). Ecological drivers of soil microbial diversity and biological functions across the Atacama Desert. Scientific Reports, 8(1), 888.
Egidi, E., Delgado-Baquerizo, M., Plett, J. M., Wang, J., Eldridge, D. J., Bardgett, R. D., & Singh, B. K. (2019). A few Ascomycota taxa dominate soil fungal communities worldwide. Nature Communications, 10(1), 2369.
Evelin, H., Kapoor, R., & Giri, B. (2019). Arbuscular mycorrhizal fungi in alleviation of salt stress: A review. Annals of Botany, 104(7), 1263–1280.
Fallah, N., Aroca, R., & Porcel, R. (2021). AMF-mediated regulation of plant water status and drought signaling under arid conditions. Plant Cell Reports, 40(3), 379–393.
FAO. (2022). The state of the world's land and water resources for food and agriculture – Systems at breaking point (SOLAW 2021). Food and Agriculture Organization of the United Nations.
Gehlot, P., Bohra, N. K., & Purohit, D. K. (2020). Mycological diversity of thermotolerant fungi in Indian arid zone. Journal of Arid Environments, 178, 104161.
Gonzalez-Torres, P., Gutierrez-Moreno, A., & Enciso-Maldonado, A. (2021). Diversity of microbial communities in biological soil crusts of the Mojave Desert. Microbial Ecology, 81(2), 475–486.
Gupta, A., Patil, M., Qamar, A., & Senthil-Kumar, M. (2020). Ath-miR164c influences plant responses to combined drought and bacterial stress in Arabidopsis. Plant Physiology, 182(3), 1661–1679.
Huang, J., Yu, H., Li, S., & Smith, G. (2024). Composition and ecological roles of microbial communities in the Colorado Plateau Desert. Soil Biology and Biochemistry, 185, 109073.
Ilyas, N., Mumtaz, K., Akhtar, N., Yasmin, H., Sayyed, R. Z., & Khan, W. (2021). Drought-tolerant endophytes mitigate stress in arid region plants. Environmental Sustainability, 4, 297–306.
Jacob, A. M., Mariga, A. M., & Chirchir, D. (2016). Endophytic fungi isolated from halophytes of the Succulent Karoo Desert and their potential roles in abiotic stress adaptation. Mycology, 7(1), 24–31.
Kalam, S., Das, S. N., Basu, A., & Podile, A. R. (2020). Endophytic microbiome and plant host interactions in the arid ecosystem. Archives of Microbiology, 202(6), 1443–1454.
Khan, A. L., Waqas, M., Hussain, J., Al-Harrasi, A., & Al-Rawahi, A. (2020). Desert microbial ecology and its role in plant adaptation to climate extremes. Environmental and Experimental Botany, 179, 104209.
Kour, D., Rana, K. L., Yadav, A. N., Yadav, N., Kumar, M., Kumar, V. & Saxena, A. K. (2021). Microbial consortia and drought tolerance: Functional and mechanistic perspectives. Plant Stress, 2, 100020.
Kumar, V., Bhanjana, G., & Sharma, M. (2021). Isolation and characterization of actinomycetes from desert habitats of Rajasthan. Current Research in Microbial Sciences, 2, 100029.
Li, X., Wu, H., Zeng, L., Huang, Y., & Qiu, S. (2019). Endophytic actinobacteria from desert plants and their role in stress tolerance. Frontiers in Microbiology, 10, 1066.
Lodha, S., Mawar, R., & Rathore, R. S. (2019). Application of microbial bio-inoculants for biocontrol and plant growth promotion in arid regions. Arid Land Research and Management, 33(2), 141–152.
Lopez-Robles, D., Iñiguez, C., & Romero, D. (2023). Microbial diversity in rhizosphere and soil crusts of Sonoran Desert ecosystems. Environmental Microbiology, 25(1), 100–115.
Lv, X., Zhang, Y., Wang, F., & Han, T. (2022). Archaeal community composition and metabolic potential in saline deserts. Microbial Ecology, 84(3), 750–762.
Maki, T., Susuki, M., Kobayashi, F., Kakikawa, M., Tobo, Y., Matsuki, A., ... & Hara, K. (2017). Variations in airborne bacterial communities at high altitudes over Asian deserts. Atmospheric Environment, 157, 129–137.
Mandakovic, D., Rojas, C., Maldonado, J., Latorre, M., Travisany, D., Delage, E., ... & González, M. (2018). Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience. Scientific Reports, 8, 5875.
Maruthi, M. N., Bagewadi, S., & Lister, R. (2022). First report of tomato leaf curl virus in watermelon from arid Indian regions. Plant Disease, 106(5), 1585.
Mascot-Gómez, D., Aranda, E., & Blanco, M. (2021). Microbial diversity associated with desert cactus rhizospheres: Adaptation to extreme environments. Microbial Ecology, 82(4), 844–856.
Mawar, R., Lodha, S., & Mathur, B. K. (2017). Development and evaluation of microbial bioformulations for plant growth promotion in arid regions. Journal of Environmental Biology, 38(3), 555–561.
Mawar, R., Lodha, S., & Mathur, B. K. (2021a). Arid zone soil microbes for sustainable agriculture: CAZRI’s contribution. Indian Journal of Dryland Agricultural Research and Development, 36(2), 22–29.
Mawar, R., Lodha, S., & Mathur, B. K. (2021b). Microbial interventions for drought tolerance and plant health in desert agro-ecosystems. Arid Land Research and Management, 35(1), 1–16.
Najafi, M., Ghorbanpour, M., & Kariman, K. (2021). The role of beneficial soil microorganisms in improving drought tolerance of crops. Applied Soil Ecology, 157, 103781.
Osborne, C. P., Saltré, F., Shoemaker, A., Haverd, V., Reich, P. B., Lunt, D., & Griscom, B. (2020). Human impact on terrestrial ecosystems has reached a tipping point. Nature Ecology & Evolution, 4(4), 541–549.
Perez-Moreno, J., Alvarez-Sanchez, M. E., & Morales-Trejo, A. (2023). Fungal dispersion via desert winds in southern Patagonia. Aerobiologia, 39(2), 141–151.
References
Rout, M., Tiwari, O. N., & Singh, A. (2023). Virome profiling in extreme desert ecosystems: Challenges and opportunities. Virus Research, 322, 199987.
Saad, M. M., Eida, A. A., & Hirt, H. (2020). Tailoring plant-associated microbial inoculants in desert agriculture: A roadmap for successful application. Frontiers in Microbiology, 11, 1978.
Sharma, S. B., Sayyed, R. Z., Trivedi, M. H., & Gobi, T. A. (2021). Phosphate solubilizing microbes: Sustainable approach for managing phosphorus deficiency in agricultural soils. Springer.
Siles, J. A., García-Sánchez, M., & Malavasi, V. (2023). Unraveling the desert plant-microbe holobiont: A new frontier in ecological resilience. Frontiers in Ecology and Evolution, 11, 1120451.
Tedersoo, L., Bahram, M., Põlme, S., Kõljalg, U., Yorou, N. S., Wijesundera, R., ... & Abarenkov, K. (2020). Global diversity and geography of soil fungi. Science, 346(6213), 1256688.
Tripathi, P., Kalra, A., & Prakash, A. (2020). Biofilm-forming PGPR for sustainable agriculture in arid regions. Rhizosphere, 14, 100200.
Trivedi, P., Leach, J. E., Tringe, S. G., Sa, T., & Singh, B. K. (2020). Plant–microbiome interactions: From community assembly to plant health. Nature Reviews Microbiology, 18(11), 607–621.
Umair, M., Ali, M., Khalid, M., & Noman, A. (2023). Secondary metabolites of drought-adapted plants: A perspective for plant stress tolerance and microbial interactions. Plant Stress, 3, 100072.
Uroz, S., Buée, M., Murat, C., Frey-Klett, P., & Martin, F. (2022). Pyrosequencing reveals a core fungal community in forest soil. Microbial Ecology, 83(1), 95–106.
Vasar, M., Andreson, R., Davison, J., Jairus, T., & Moora, M. (2021). Arbuscular mycorrhizal fungal communities in desert habitats: Drivers of diversity and functionality. Fungal Ecology, 50, 101041.
Vega-Flores, D., González-Pérez, J. A., & Cañizares, M. C. (2022). Rhizosphere microbiome assembly and functions in desert legumes. Plant and Soil, 481(1), 59–75.
Wang, H., Liu, Y., Chen, W., & Hu, C. (2020a). Effects of cyanobacterial inoculation on soil microbial community structure in desert environments. Soil Biology and Biochemistry, 143, 107739.
Zhang, Q., Liu, Z., Cao, L., & Wang, D. (2022). The influence of drought on desert plant-associated microbiomes and soil functionality. Journal of Arid Environments, 200, 104707.
Zhang, X., Zhou, X., & Wang, X. (2023). Desert viromes and their ecological implications in arid soils. Frontiers in Microbiology, 14, 1136789.
Zhang, Y., Wang, X., Zhang, Z., & Li, J. (2018). Distribution and diversity of soil microbial communities in arid desert ecosystems of China. Applied Soil Ecology, 124, 284–292.
Zhou, J., Jiang, Y., & Xue, K. (2020). Functional potential and stability of microbial communities in desert soils under stress. The ISME Journal, 14(6), 1537–1549.
Unveiling Microbial Richness in Arid Ecosystems: A Pathway to Agricultural Sustainability
DOI: https://doi.org/10.56669/HXMU5377
ABSTRACT
A large portion of the Earth’s surface is covered by dry and semi-dry regions, where conditions are often challenging. Nevertheless, these regions are rich in microbes that live in close association with plants, supporting their growth and helping them withstand stress. Some of the most helpful microbes are called plant growth-promoting microorganisms (PGPMs). They help plants by making nutrients easier to absorb, producing natural plant hormones, and protecting them from diseases. Research done in deserts around the world has found many useful groups of microbes. Among bacteria, Proteobacteria, Actinobacteria, and Bacteroidetes are common, while Ascomycota and Basidiomycota are the main groups of fungi. One well-known bacterial group, Bacillus, has shown many benefits for plant growth. Studying the microbes that live in deserts gives us hope for better and more sustainable farming, especially in places where the climate is very tough. This article takes another perspective on the different microbes found in deserts across the world and discusses how they can help increase crop production even under extreme environments and uncertain weather conditions.
Keywords: PGPM, Arid climate, Disease resistance, Sustainability
INTRODUCTION
In the 21st century, agriculture is facing significant challenges like environmental pollution, climate change, the rise of drug-resistant microbes, and the growing shortage of land, water, and food (FAO, 2022). A primary reason behind these problems is the rapid increase in the world’s population, which has caused a noticeable drop in the amount of cultivable land. Because of these limitations, arid and desert regions covering more than 46 million square kilometers around the world are now being looked at for their possible use in agriculture, even though they face very tough conditions such as extreme heat, poor soil, and very little rain (Osborne et al., 2020). These dry areas are divided into three types hyper-arid, arid, and semi-arid based on the Aridity Index. Many of these areas are becoming deserts even faster and are home to more than two billion people (Alsharif et al., 2020). Despite the harsh environment, these regions support unique forms of life plants, animals, and microbes that have special adaptations to survive strong sunlight, salty soils, low organic content, and large temperature swings. Among these, microbes are very important because they help ecosystems function properly. They assist in recycling nutrients, breaking down organic materials, reducing stress in plants, and supporting plant growth.
Strict environmental conditions mostly influence the types of microbes in deserts. These conditions tend to favor bacteria that can survive in extreme settings. Earlier, it was challenging to study these microbes because scientists mainly used culture-based methods, which only showed a small part of the actual microbial community. But now, with new tools in molecular biology, like gene sequencing, DNA fingerprinting, and metagenomics, scientists can study microbes more effectively in labs without needing to grow them. We now know that although desert soils harbor fewer types of microbes than other regions, those present possess unique traits that enable them to survive under difficult conditions. Considerable international efforts like the Earth Microbiome Project and the use of next-generation sequencing (NGS) have made it possible to discover new kinds of microbes and learn how they might help with sustainable farming (Delgado-Baquerizo et al., 2018). Interestingly, desert microbes can provide helpful features such as drought resistance, nutrient breakdown, protection against harmful organisms, and hormone production for plants. These abilities can be used to create bioinoculants products made from beneficial microbes that help plants grow better in dry areas. A new way of thinking, explained by the holobiont and hologenome theories, shows that plants and microbes evolve together and support each other. This partnership improves plant health, increases stress resistance, and helps them adapt to the environment.
Still, there is more to learn. Even though scientists have studied the genetic information of desert microbes, there’s a gap in turning this knowledge into real-world farming solutions. To fill up the gap, we need combined research that includes genetics, environmental studies, and testing on farms (Mandakovic et al., 2018). As the world looks for farming methods that are sustainable and can handle climate change, using desert microbes in agriculture looks like an up-and-coming option. They could help increase food production, restore damaged lands, and build farming systems that can cope with environmental challenges in the future.
Adaptive strategies of dryland flora
Desert ecosystems have very tough living conditions. They have very limited water, strong sunlight, and poor soil with few nutrients. To survive in such environments, dryland plants have developed many changes in their structure, body functions, and even at the genetic level (Evelin et al., 2019). Some physical changes (morphological traits) include having small leaves, leaves that grow upright, thick outer layers (cuticles), and short plant height. These features help reduce water loss and protect from heat. In terms of body functions (physiology), plants use special methods like Crassulacean Acid Metabolism (CAM), which helps save water. They also improve the efficiency of water use during transpiration and produce special compounds called phenolics that help them deal with stress (Umair et al., 2023).
At the genetic and biochemical level (molecular level), desert plants produce more of specific proteins like heat shock proteins, enzymes that fight harmful molecules (antioxidative enzymes), and substances that protect cells from drying out (osmoprotectants). These help the plants survive in harsh conditions (Gupta et al., 2020; Sharma et al., 2021). Plant hormones such as abscisic acid, cytokinins, and jasmonates also play an essential role in managing how plants respond to drought (Evelin et al., 2019). The structure of the roots is another crucial adaptation. Desert plants often have fibrous roots, deep roots, or roots with a covering called a rhizosheath. These features help them absorb more water and allow helpful microbes to live near the roots (Najafi et al., 2021; Kour et al., 2021). Rhizosheaths, formed by microbes, help retain water and facilitate nutrient uptake.
Beneficial microbes, especially plant growth-promoting bacteria (PGPB), are very important in desert soils. They help plants by making nutrients easier to absorb, producing growth hormones, and protecting against harmful microbes (Sharma et al., 2021). Desert plants also host many types of microbes, not just in the soil around roots (rhizosphere), but also on leaves (phyllosphere), inside roots (endosphere), and within the rhizosheath. These microbial communities depend on the plant type, climate, and soil conditions (Saad et al., 2020; Trivedi et al., 2020). Some of these beneficial microbes, called PGPMs, can be used in agriculture as eco-friendly options for fertilizers and pest control (Alsharif et al., 2020; Bashan et al., 2021). A list of commonly studied PGPMs and their respective growth-promoting mechanisms is presented in Table 1.
Table 1. Plant growth-promoting microorganisms and their mechanism of actions
Sr. No.
Plant growth promoting microorganism (PGPM)
Growth promotion mechanism
1
Azospirillum, Azotobacter, Achromobacter, Bradyrhizobium, Beijerinckia, Rhizobium, Clostridium, Klebsiella., Anabaena., Nostoc, Frankia
Nitrogen fixation- through the reduction of nitrogen gas (N2) to ammonia (NH3).
2
Bacillus, Pseudomonas, Rhizobium, Achromobacter, Burkholderia, Microccocus, Agrobacterium, Erwinia sp., Penicillium sp. and Aspergillus sp.
Phosphate solubilization- transforms and solubilizes inorganic phosphorus into forms capable of being absorbed by plants, such as monobasic (H2PO4-) or dibasic phosphate (HPO4−2).
3
Burkholderia, Enterobacter, Grimontella and Pseudomonas
Siderophore production- improves plant nutrition and inhibits phytopathogens through iron sequestration from the environment.
4
Bacillus and Aspergillus
Potassium solubilization- produces organic and inorganic acids, acidolysis, chelation, and exchange reactions which are capable of solubilizing potassium.
5
Rhizophagus irregularis and Funneliformis mosseae
Phytoextraction and stabilization- Fungi that extract Cd and enhanced phytostabilization of Cd and Zn respectively.
6
Pseudomonas sp. and Bacillus
Auxin secretion- promote plants growth by increase auxin and ACC (Amino-cyclopropane-carboxylate)-deaminase.
7
Sphingomonas SaMR12, Phyllobacterium myrsinacearum RC6b
IAA- Indole-Acetic –Acid production and root promotion.
8
Bacillus spp.
Exopolysaccharides- forms a protective biofilm on root surface.
9
Proteus penneri, P. aeruginosa, and Alcaligenes faecalis
Exopolysaccharides- alleviate water stress and improve plant biomass under drought stress.
10
Burkholderia sp.
Metabolism- increases plant tolerance against low temperature by modifying carbohydrate metabolism.
11
Pseudomonas fluorescens
Osmoprotectants solutes and enzymes- promote plant tolerance by increasing the activity of catalase and peroxidase, and the accumulation of proline.
Structure of desert micro-communities
Bacterial communities in arid ecosystems
Microorganisms, especially plant growth-promoting bacteria (PGPB), are vital in deserts. They help plants by making nutrients more available, producing growth hormones, and protecting against diseases (Sharma et al., 2021). Desert plants also host diverse communities of microbes in different parts like their roots (rhizosphere and rhizosheath), leaves (phyllosphere), and even inside their tissues (endosphere). These microbial groups are influenced by the plant type, soil, and climate (Saad et al., 2020; Trivedi et al., 2020). Some of these microbes-known as Plant Growth-Promoting Microorganisms (PGPMs)-are promising tools for sustainable farming. They can act as natural fertilizers and pest controllers, especially in arid lands (Alsharif et al., 2020; Bashan et al., 2021).
Fungal communities in arid and semi-arid ecosystems
Fungi that live in dry and semi-dry regions have adapted well to survive in tough conditions like extreme heat, dryness, and strong sunlight. These fungi are important for breaking down organic material, recycling nutrients, and supporting interactions between plants and microbes, which helps maintain healthy soil and functioning ecosystems (Tedersoo et al., 2020). In deserts, fungi can live in many ways. They may act as decomposers (saprophytes), cause disease (pathogens), live off of other organisms (parasites), live inside plants without causing harm (endophytes), or form helpful partnerships (mutualists). Instead of having very complex survival systems, these fungi often rely on strategies like producing spores, staying dormant during extreme weather, and using very few resources (Egidi et al., 2019). Many types of fungi have been found in desert soils, such as yeasts, thread-like (filamentous) fungi, micro-colonial fungi, and arbuscular mycorrhizal fungi (AMF) (Egidi et al., 2019; Tedersoo et al., 2020). Studies show that Ascomycota is the most common fungal group in deserts. Within this group, classes like Dothideomycetes, Pezizomycetes, and Sordariomycetes are especially abundant (Durán et al., 2021). These findings come from both lab culture methods and modern DNA sequencing done in different parts of the world, including Saudi Arabia, Jordan, Australia, and North America (Egidi et al., 2019; Tedersoo et al., 2020). Among these fungi, arbuscular mycorrhizal fungi (AMF) are beneficial for plants. They improve the plant’s ability to take up water and nutrients—especially phosphorus—by expanding the plant’s root reach into dry soil (Fallah et al., 2021; Chandrasekaran et al., 2022). A global study found that the Glomeraceae family is the most common AMF in deserts, followed by families like Claroideoglomeraceae, Diversisporaceae, and Acaulosporaceae (Vasar et al., 2021). Besides supporting plant growth, AMF also help restore degraded land and stabilize soils. This makes them key contributors to the long-term health and recovery of dryland ecosystems (Zhang et al., 2023).
Archaea in arid and semi-arid ecosystems
Archaea are renowned for their resilience in extreme environments, including arid and hyperarid zones characterized by desiccation, nutrient scarcity, and high salinity. In desert ecosystems, these microorganisms play crucial roles in biogeochemical cycling, particularly in nitrogen and carbon transformations (Zhou et al., 2020; Tripathi et al., 2020; Siles et al., 2023). Although less abundant in mesic environments, archaeal taxa are frequently detected in desert soils, often dominated by chemolithoautotrophic members of the phylum Thaumarchaeota, which are central to desert archaeal communities (Lehtovirta-Morley, 2018). Halotolerant Euryarchaeota, especially Halobacteria from the orders Halobacteriales, Haloferacales, and Natrialbales, are also widely reported and noted for their metabolic flexibility and salinity adaptation (Lv et al., 2022; Bachran et al., 2019). Interestingly, uncultured or unclassified archaeal lineages account for nearly 40% of desert archaeal communities, pointing to vast unexplored diversity (Bachran et al., 2019; Wang et al., 2021). Recent isolations of novel genera such as Halorubrum and Haloparvum exemplify archaeal adaptability to extreme arid niches, while the detection of Crenarchaeota in deserts such as Tataouine further highlights their phylogenetic diversity (Taffner et al., 2022). Despite growing evidence of their ecological significance, desert archaeal communities remain poorly studied, and comprehensive metagenomic and functional analyses are needed to better understand their physiological adaptations and ecosystem roles (Tripathi et al., 2020; Siles et al., 2023; Taffner et al., 2022).
Viral communities in arid and semi-arid ecosystems
Viruses, especially bacteriophages (viruses that infect bacteria), are now being recognized as important but less-studied members of desert microbial communities. Recent studies using metaviromic techniques in extremely dry areas like the Namib and Atacama Deserts have found many different and new types of viruses. The most common among them are tailed bacteriophages, including families such as Myoviridae, Siphoviridae, and Podoviridae (Rout et al., 2023; Chen et al., 2021). These viruses seem to adapt to harsh conditions like very low water levels, changes in soil pH, and high salinity. When comparing viruses from cold deserts like Antarctica with those from hot deserts, researchers found fewer free viruses in hyper-arid soils. However, they also discovered many unknown viruses that don’t match any known genomes in current databases (Rout et al., 2023). This suggests that deserts could hold a large number of undiscovered viruses, which might be important for ecology and biotechnology. So far, most research has focused on bacteriophages, while plant-related viruses in deserts have received less attention. Still, recent studies in dry farming areas have detected harmful plant viruses, such as begomoviruses and tobamoviruses, affecting crops like tomato, watermelon, and cucurbits—even in very dry conditions (Maruthi et al., 2022). These discoveries highlight the urgent need for more virus research in desert farming systems to understand their roles and impacts.
Microbial Communities in Deserts Across the Globe
Deserts of South and North America
Despite their harsh climates, the deserts of North and South America are home to a wide variety of tough and adaptable microbes. In North America, the Chihuahuan Desert has a rich mix of bacteria, especially in gypsum soils. Major bacterial groups found here include Actinobacteria, Proteobacteria, and Cyanobacteria, along with beneficial microbes that live around cactus roots, like Bacillus and Sordariomycetes (Mascot-Gómez et al., 2021; Vega-Flores et al., 2022).
The Sonoran Desert contains many types of bacteria in both the soil and plant root zones (rhizosphere), such as Planctomycetes and Chloroflexi, along with archaea like Euryarchaeota (Lopez-Robles et al., 2023). In the Mojave Desert, the biological soil crusts are mainly made up of Cyanobacteria like Phormidium, although helpful fungi (arbuscular mycorrhizal fungi) are found in smaller numbers (Gonzalez-Torres et al., 2021). Even cold deserts like the Colorado Plateau have many Cyanobacteria and nitrogen-fixing microbes like Nostoc and Scytonema, which play an important role in soil health (Huang et al., 2024). In South America, the Atacama Desert one of the driest places on Earth—has microbes that survive extreme dryness and intense UV rays. Common types here include fungi like Ascomycota and Basidiomycota, and bacteria such as Rubrobacterales and Actinobacteria, especially around plant roots (Zhang et al., 2022). Likewise, the dry Patagonian Desert contains groups like Rhizobiales and Actinomycetales, along with airborne fungi such as Cladosporium and Alternaria. These microbes are influenced by soil moisture and wind (Perez-Moreno et al., 2023).
Thar and cold deserts of India
The Thar Desert, spread across over 200,000 square kilometers in Rajasthan and Gujarat, is the 18th largest desert in the world. It experiences very hot daytime temperatures, sometimes reaching up to 55 °C, along with strong winds. Even in such extreme conditions, many types of microbes can survive. Studies have found that sand dunes here contain between 150 and 50,000 bacteria per gram, with nearly half being actinomycetes. Advanced methods like 16S r-RNA sequencing have helped scientists identify important bacterial genera, such as Streptomyces, Nocardiopsis, Saccharomonospora, and Actinoalloteichus (Kumar et al., 2021). Fungi are also present, including the Basidiomycete Broomeia congregata (Gehlot et al., 2020), and heat-tolerant endophytes like Aspergillus, Alternaria, Chaetomium, Penicillium, and Nigrospora, which can grow at 40–45°C and support plant growth under drought conditions (Ilyas et al., 2021). Researchers have also found root-associated bacteria in desert plants. For example, species like Pseudomonas pseudoalcaligenes, Azospirillum brasilense, and Rhizobium were isolated from the roots of Lasiurus sindicus, a native desert grass. The Central Arid Zone Research Institute (CAZRI) in Jodhpur has been working for over 20 years to identify useful microbes from desert areas. They have discovered many potential biofertilizers and biocontrol agents, such as Bacillus firmus, B. tequilensis, Streptomyces mexicanus, Aspergillus versicolor, A. nidulans, Trichoderma harzianum, and T. longibrachiatum (Mawar et al., 2017; Lodha et al., 2019; Mawar et al., 2021a, 2021b). In comparison, the cold deserts in northern India, like Ladakh, support microbes called psychrophiles that thrive in low temperatures. These include Exiguobacterium indicum, Paenibacillus glacialis, Janthinobacterium lividum, Sphingobacterium antarcticus, Psychrobacter valli, Alishewanella species, and Brevundimonas species. These organisms produce useful cold-active enzymes, pigments, and antifreeze substances that have potential applications in high-altitude farming and biotechnology.
Deserts of China
Taklamakan Desert (346,905 km², Northwest China): The Taklamakan Desert, the largest sandy desert in China, has a surprisingly rich microbial community despite being extremely dry. Research shows that the main types of bacteria in its soils include Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidetes (Wang et al., 2020a). Scientists have discovered new types of endophytic Actinobacteria (bacteria that live inside plants) from native desert plants, including genera like Prauserella, Nesterenkonia, Labedella, and Aeromicrobium (Li et al., 2019a, 2019b). These microbes may carry genes that help plants survive stress and could also be helpful in producing valuable compounds.
Gurbantunggut Desert (Xinjiang, China): In the Gurbantunggut Desert, specialized soil layers known as biological soil crusts (biocrusts) form daily. These crusts are composed of algae, lichens, mosses, and fungi, particularly from fungal groups such as Ascomycota, Lecanoromycetes, Eurotiomycetes, and Dothideomycetes (Zhang et al., 2018). Temporal changes in these communities are influenced by soil salinity and organic matter content. Commonly occurring fungi include Heteroplacidium and Endocarpon. Additionally, salt-tolerant bacteria such as Bacillus endophyticus, B. tequilensis, Planococcus rifietoensis, Variovorax paradoxus, and Arthrobacter agilis have been isolated from the halophyte Salicornia europaea, suggesting their potential role in enhancing plant tolerance to harsh desert conditions.
Gobi Desert (around 2.3 million km², Northern China and Southern Mongolia): The Gobi Desert, stretching across northern China and southern Mongolia, contains diverse microbial life. Actinobacteria, Acidobacteria, Chloroflexi mainly populate its soils, and several types of Proteobacteria (Maki et al., 2017). When dust storms occur, the number of Firmicutes and Bacteroidetes temporarily increases. Archaea, including Thaumarchaeota and Euryarchaeota, are also present, but in small amounts. Scientists have also isolated fungi living inside the roots of Stipa species in the Gobi grasslands. Most of these fungi belong to the group Ascomycota, and the most common types were Curvularia and Rhizopus.
Deserts of Africa
Sahara Desert: The Sahara Desert is the largest hot desert in the world, covering more than 9 million square kilometers. A recent research using advanced high-throughput sequencing methods has shown that the main types of bacteria found in Egyptian desert soils belong to the groups Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. Among these, the most common bacterial genera include Ochrobactrum, Rhodococcus, and Bacillus, while other groups like Gemmatimonadetes and Planctomycetes are present in smaller numbers. Scientists have also studied the bacteria living inside the tissues of the date palm (Phoenix dactylifera L.). These endophytic bacteria include Pseudomonas species that show strong resistance to drought and can help plants grow better under stress conditions (Kalam et al., 2020). In addition, some types of actinomycetes found in the Sahara, such as Streptomyces rochei PTL2 and Nocardiopsis dassonvillei MB22, have been found to work well as biocontrol agents. These strains help protect plants by fighting against harmful soil-borne pathogens (Allali et al., 2019).
Namib Desert: The Namib Desert, which stretches about 2,000 kilometers from Angola to South Africa, is one of the oldest deserts in the world. Research on microbial diversity in this region has found that bacteria from the groups Actinobacteria, Proteobacteria, and Bacteroidetes are common. In a study of Tylosema esculentum, a local plant that does not belong to the legume family, scientists discovered many plant growth-promoting (PGP) endophytic bacteria. These included Rhizobium, Massilia, Burkholderia, Sphingomonas, Microbacterium, and Chitinophaga, showing that various bacteria have adapted to survive in the extremely dry conditions of the Namib (Chimwamurombe et al., 2016).
Kalahari Desert: The Kalahari Desert, which stretches across parts of Botswana, Namibia, and South Africa, is one of the largest areas of continuous sand in the world. Studies on its microbes have found that halophilic (salt-loving) archaea are common, especially those from the Halobacteria group. Among bacteria, groups like Acetothermia, Gemmatimonadetes, and Firmicutes are often found. Earlier research on vesicular-arbuscular mycorrhizae (VAM) showed that they provided plant-specific benefits to native species like Vangueria infausta, though newer studies on this topic are still few. In addition to helpful microbes, some harmful fungi have also been found. Pathogenic fungi such as Curvularia, Alternaria, and Trichoderma have been observed in desert trees like Aloe and Acacia, suggesting that fungi also play a role in causing diseases in desert plants (Chimwamurombe et al., 2016).
Karoo Desert: The Karoo, a semi-arid region in South Africa, is home to fungal communities that can survive in harsh conditions. Scientists have found endophytic fungi, those that live inside plants, such as Aspergillus, Cladosporium, Fusarium, and Talaromyces, in a salt-tolerant plant called Sesuvium portulacastrum, which grows in the Succulent Karoo zone. These fungi may help the plant survive in environments with high salt levels and low water availability (Jacob et al., 2016).
Deserts of Arabia
The Arabian Desert, which spreads across parts of Saudi Arabia, Yemen, and the Persian Gulf, is home to many types of microbes that are well adapted to survive in extremely dry conditions. The most common bacterial groups found here are Actinobacteria, Proteobacteria, Firmicutes, and Gemmatimonadetes. These bacteria play important roles in the soil, helping with nutrient cycling and helping other organisms deal with environmental stress (Khan et al., 2020). Researchers have also found specific groups of bacteria with special functions. These include Cyanobacteria and Rhodoplanes, which perform photosynthesis, Rhizobium and Bradyrhizobium, which fix nitrogen, and Candidatus nitrososphaera, which helps in the oxidation of ammonia. This shows that the desert supports a complex and ecologically important microbial community. Fungi are also found in the dust and soil of the Arabian Desert. Some of the common ones include Alternaria, Penicillium, Phoma, and Mortierella. These fungi may cause allergies or help break down organic materials (Alsheikh et al., 2021). In addition, new types of fungi have been discovered in Saudi desert soils, such as previously unidentified species of Chaetomium. These findings point to a hidden wealth of fungal diversity in the region that may have future uses in biotechnology (Alotaibi et al., 2022).
Desert Region
Dominant Bacteria
Dominant Fungi
Key Functional Traits
Thar Desert (India)
Bacillus, Streptomyces
Aspergillus, Trichoderma
Thermotolerance, PGPR, biocontrol
Atacama (Chile)
Actinobacteria, Rubrobacter
Ascomycota
UV resistance, N-fixation
Namib (Africa)
Proteobacteria, Bacteroidetes
-
Soil crust formation, PGP
Gobi (China)
Firmicutes, Actinobacteria
Curvularia
Spore-forming, drought resilience
CONCLUSION
Deserts and arid lands, once considered lifeless, are actually full of microbial life that has developed special abilities to survive in harsh conditions. Microorganisms such as bacteria, fungi, archaea, and viruses play key roles in important ecological functions like breaking down organic matter, recycling nutrients, and helping plants tolerate stress. With the help of modern scientific tools like metagenomics and next-generation sequencing, scientists have discovered a wide variety of plant-friendly microbes, known as plant growth-promoting microorganisms (PGPMs). These microbes are found in deserts around the world and have useful traits like fixing nitrogen, dissolving phosphate, surviving drought, and producing growth hormones for plants. Our understanding of how plants and microbes work together has also improved, thanks to new perspectives like the “holobiont” and “hologenome” concepts. These explain how plants and their associated microbes form a team works together to improve plant health and resistance to environmental stress. Desert plants also have their own structural and chemical adaptations that help them survive. When combined with the help of beneficial microbes, these plants become even more capable of thriving in tough conditions. However, many desert microbes, especially certain archaea and viruses, are still unknown and have not yet been studied in the lab. To fully unlock the potential of these desert microorganisms, future research must bring together genetics, environmental science, and agriculture. This will help us use desert microbes to grow better crops, restore damaged land, and support food security in a warming and drying world.
REFERENCES
Allali, K., Sekhsokh, Y., & Elabed, S. (2019). Antagonistic activity of Streptomyces rochei PTL2 against Fusarium oxysporum. Moroccan Journal of Agricultural Sciences, 4(2), 12–19.
Alotaibi, M. O., Alsheikh, H. M., & Al-Jurayyan, A. (2022). Diversity of fungi in Saudi Arabian desert soils. Saudi Journal of Biological Sciences, 29(1), 45–54.
Alsharif, K., Hobbs, M., & Gornall, J. (2020). Desertification trends and challenges in the 21st century. Environmental Research Letters, 15(10), 104001.
Alsheikh, H. M., Alotaibi, M. O., & Al-Jurayyan, A. (2021). Fungal diversity in dust samples from arid regions of Saudi Arabia. Environmental Monitoring and Assessment, 193(5), 281.
Bachran, M., Kirk, M. F., & Flynn, T. M. (2019). Archaeal community structure in salt-dominated desert environments. Environmental Microbiology Reports, 11(1), 70–78.
Bashan, Y., de-Bashan, L. E., Prabhu, S. R., & Hernandez, J. P. (2021). Advances in plant growth-promoting bacterial inoculants for agriculture: A perspective for the future. Bioengineered, 12(1), 1160–1173.
Chen, Y., Li, Y., Liu, Y., & He, J. (2021). Viral diversity and community structure in desert soils of northern China. Virus Research, 293, 198297.
Chimwamurombe, P. M., Valentine, A. J., & Steyn, C. (2016). Rhizosphere and endophytic bacteria associated with Tylosema esculentum, a drought-tolerant desert legume. South African Journal of Botany, 104, 57–62.
Delgado-Baquerizo, M., Reith, F., Dennis, P. G., Hamonts, K., Powell, J. R., Young, A., & Singh, B. K. (2018). Ecological drivers of soil microbial diversity and biological functions across the Atacama Desert. Scientific Reports, 8(1), 888.
Egidi, E., Delgado-Baquerizo, M., Plett, J. M., Wang, J., Eldridge, D. J., Bardgett, R. D., & Singh, B. K. (2019). A few Ascomycota taxa dominate soil fungal communities worldwide. Nature Communications, 10(1), 2369.
Evelin, H., Kapoor, R., & Giri, B. (2019). Arbuscular mycorrhizal fungi in alleviation of salt stress: A review. Annals of Botany, 104(7), 1263–1280.
Fallah, N., Aroca, R., & Porcel, R. (2021). AMF-mediated regulation of plant water status and drought signaling under arid conditions. Plant Cell Reports, 40(3), 379–393.
FAO. (2022). The state of the world's land and water resources for food and agriculture – Systems at breaking point (SOLAW 2021). Food and Agriculture Organization of the United Nations.
Gehlot, P., Bohra, N. K., & Purohit, D. K. (2020). Mycological diversity of thermotolerant fungi in Indian arid zone. Journal of Arid Environments, 178, 104161.
Gonzalez-Torres, P., Gutierrez-Moreno, A., & Enciso-Maldonado, A. (2021). Diversity of microbial communities in biological soil crusts of the Mojave Desert. Microbial Ecology, 81(2), 475–486.
Gupta, A., Patil, M., Qamar, A., & Senthil-Kumar, M. (2020). Ath-miR164c influences plant responses to combined drought and bacterial stress in Arabidopsis. Plant Physiology, 182(3), 1661–1679.
Huang, J., Yu, H., Li, S., & Smith, G. (2024). Composition and ecological roles of microbial communities in the Colorado Plateau Desert. Soil Biology and Biochemistry, 185, 109073.
Ilyas, N., Mumtaz, K., Akhtar, N., Yasmin, H., Sayyed, R. Z., & Khan, W. (2021). Drought-tolerant endophytes mitigate stress in arid region plants. Environmental Sustainability, 4, 297–306.
Jacob, A. M., Mariga, A. M., & Chirchir, D. (2016). Endophytic fungi isolated from halophytes of the Succulent Karoo Desert and their potential roles in abiotic stress adaptation. Mycology, 7(1), 24–31.
Kalam, S., Das, S. N., Basu, A., & Podile, A. R. (2020). Endophytic microbiome and plant host interactions in the arid ecosystem. Archives of Microbiology, 202(6), 1443–1454.
Khan, A. L., Waqas, M., Hussain, J., Al-Harrasi, A., & Al-Rawahi, A. (2020). Desert microbial ecology and its role in plant adaptation to climate extremes. Environmental and Experimental Botany, 179, 104209.
Kour, D., Rana, K. L., Yadav, A. N., Yadav, N., Kumar, M., Kumar, V. & Saxena, A. K. (2021). Microbial consortia and drought tolerance: Functional and mechanistic perspectives. Plant Stress, 2, 100020.
Kumar, V., Bhanjana, G., & Sharma, M. (2021). Isolation and characterization of actinomycetes from desert habitats of Rajasthan. Current Research in Microbial Sciences, 2, 100029.
Li, X., Wu, H., Zeng, L., Huang, Y., & Qiu, S. (2019). Endophytic actinobacteria from desert plants and their role in stress tolerance. Frontiers in Microbiology, 10, 1066.
Lodha, S., Mawar, R., & Rathore, R. S. (2019). Application of microbial bio-inoculants for biocontrol and plant growth promotion in arid regions. Arid Land Research and Management, 33(2), 141–152.
Lopez-Robles, D., Iñiguez, C., & Romero, D. (2023). Microbial diversity in rhizosphere and soil crusts of Sonoran Desert ecosystems. Environmental Microbiology, 25(1), 100–115.
Lv, X., Zhang, Y., Wang, F., & Han, T. (2022). Archaeal community composition and metabolic potential in saline deserts. Microbial Ecology, 84(3), 750–762.
Maki, T., Susuki, M., Kobayashi, F., Kakikawa, M., Tobo, Y., Matsuki, A., ... & Hara, K. (2017). Variations in airborne bacterial communities at high altitudes over Asian deserts. Atmospheric Environment, 157, 129–137.
Mandakovic, D., Rojas, C., Maldonado, J., Latorre, M., Travisany, D., Delage, E., ... & González, M. (2018). Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience. Scientific Reports, 8, 5875.
Maruthi, M. N., Bagewadi, S., & Lister, R. (2022). First report of tomato leaf curl virus in watermelon from arid Indian regions. Plant Disease, 106(5), 1585.
Mascot-Gómez, D., Aranda, E., & Blanco, M. (2021). Microbial diversity associated with desert cactus rhizospheres: Adaptation to extreme environments. Microbial Ecology, 82(4), 844–856.
Mawar, R., Lodha, S., & Mathur, B. K. (2017). Development and evaluation of microbial bioformulations for plant growth promotion in arid regions. Journal of Environmental Biology, 38(3), 555–561.
Mawar, R., Lodha, S., & Mathur, B. K. (2021a). Arid zone soil microbes for sustainable agriculture: CAZRI’s contribution. Indian Journal of Dryland Agricultural Research and Development, 36(2), 22–29.
Mawar, R., Lodha, S., & Mathur, B. K. (2021b). Microbial interventions for drought tolerance and plant health in desert agro-ecosystems. Arid Land Research and Management, 35(1), 1–16.
Najafi, M., Ghorbanpour, M., & Kariman, K. (2021). The role of beneficial soil microorganisms in improving drought tolerance of crops. Applied Soil Ecology, 157, 103781.
Osborne, C. P., Saltré, F., Shoemaker, A., Haverd, V., Reich, P. B., Lunt, D., & Griscom, B. (2020). Human impact on terrestrial ecosystems has reached a tipping point. Nature Ecology & Evolution, 4(4), 541–549.
Perez-Moreno, J., Alvarez-Sanchez, M. E., & Morales-Trejo, A. (2023). Fungal dispersion via desert winds in southern Patagonia. Aerobiologia, 39(2), 141–151.
References
Rout, M., Tiwari, O. N., & Singh, A. (2023). Virome profiling in extreme desert ecosystems: Challenges and opportunities. Virus Research, 322, 199987.
Saad, M. M., Eida, A. A., & Hirt, H. (2020). Tailoring plant-associated microbial inoculants in desert agriculture: A roadmap for successful application. Frontiers in Microbiology, 11, 1978.
Sharma, S. B., Sayyed, R. Z., Trivedi, M. H., & Gobi, T. A. (2021). Phosphate solubilizing microbes: Sustainable approach for managing phosphorus deficiency in agricultural soils. Springer.
Siles, J. A., García-Sánchez, M., & Malavasi, V. (2023). Unraveling the desert plant-microbe holobiont: A new frontier in ecological resilience. Frontiers in Ecology and Evolution, 11, 1120451.
Tedersoo, L., Bahram, M., Põlme, S., Kõljalg, U., Yorou, N. S., Wijesundera, R., ... & Abarenkov, K. (2020). Global diversity and geography of soil fungi. Science, 346(6213), 1256688.
Tripathi, P., Kalra, A., & Prakash, A. (2020). Biofilm-forming PGPR for sustainable agriculture in arid regions. Rhizosphere, 14, 100200.
Trivedi, P., Leach, J. E., Tringe, S. G., Sa, T., & Singh, B. K. (2020). Plant–microbiome interactions: From community assembly to plant health. Nature Reviews Microbiology, 18(11), 607–621.
Umair, M., Ali, M., Khalid, M., & Noman, A. (2023). Secondary metabolites of drought-adapted plants: A perspective for plant stress tolerance and microbial interactions. Plant Stress, 3, 100072.
Uroz, S., Buée, M., Murat, C., Frey-Klett, P., & Martin, F. (2022). Pyrosequencing reveals a core fungal community in forest soil. Microbial Ecology, 83(1), 95–106.
Vasar, M., Andreson, R., Davison, J., Jairus, T., & Moora, M. (2021). Arbuscular mycorrhizal fungal communities in desert habitats: Drivers of diversity and functionality. Fungal Ecology, 50, 101041.
Vega-Flores, D., González-Pérez, J. A., & Cañizares, M. C. (2022). Rhizosphere microbiome assembly and functions in desert legumes. Plant and Soil, 481(1), 59–75.
Wang, H., Liu, Y., Chen, W., & Hu, C. (2020a). Effects of cyanobacterial inoculation on soil microbial community structure in desert environments. Soil Biology and Biochemistry, 143, 107739.
Zhang, Q., Liu, Z., Cao, L., & Wang, D. (2022). The influence of drought on desert plant-associated microbiomes and soil functionality. Journal of Arid Environments, 200, 104707.
Zhang, X., Zhou, X., & Wang, X. (2023). Desert viromes and their ecological implications in arid soils. Frontiers in Microbiology, 14, 1136789.
Zhang, Y., Wang, X., Zhang, Z., & Li, J. (2018). Distribution and diversity of soil microbial communities in arid desert ecosystems of China. Applied Soil Ecology, 124, 284–292.
Zhou, J., Jiang, Y., & Xue, K. (2020). Functional potential and stability of microbial communities in desert soils under stress. The ISME Journal, 14(6), 1537–1549.