Soil Biodiversity Digital Exhibition

PART III – Soil biodiversity in the desert and UAE

World distribution of soil biodiversity

Estimated global distribution of soil biodiversity. Orgiazzi et al (2016) Publications Office of the European Union (https://www.sciencedirect.com/science/article/pii/B9780128096659098220)

There is a long-standing view in ecology that species richness is maximal in the tropics and gradually declines towards the poles. However, it appears that this is only true for aboveground diversity. Belowground (in the soil), clear relationships between latitude and species richness do not seem to be so clear. Furthermore, there are 27% areas of mismatch between aboveground and soil biodiversity. Indeed, a single soil profile may contain equivalent diversity to that found aboveground within an entire ecosystem.

Wow factor: The mushroom-forming ‘honey’ fungus Armillaria ostoyae is the largest living organism on the planet by area, estimated by scientists as a contiguous specimen found in the Oregon, USA covering 965 hectares (2,385 acres), equivalent to 1,350 soccer fields. The mycelium of Armillaria ostoyae grows and spreads primarily in the soil, out of sight. This fungus causes Armillaria root disease in a number of trees, particularly Douglas-fir, grand fir and subalpine fir. Wow!

Desert soil and biocrusts

Desert soil is mostly sandy (90-95%). It is very arid due to the strong wind erosion, sedimentation, daily temperature fluctuations, water deprivation and high levels of solar radiation. Most desert soils are classified as Aridisols (or less commonly Entisols), and possess very low nitrogen content and organic matter (often unevenly distributed), are slightly alkaline, and contain high amounts of salt ions, phosphate, calcium carbonate, and magnesium carbonate. Desert soils are variable in color but often light brown, gray, or yellowish. Life in the desert is profoundly challenged by these cumulative, harsh and abiotic conditions.

Biological soil crusts (or biocrusts) are assemblages of organisms on the soil surface of arid and semi-arid ecosystems; up to 70% of semiarid and arid zones are covered by biocrusts. They are composed of soil particles and filamentous cyanobacteria, lichens, mosses, and fungi in varying proportions. These consortia of soil organisms are present in a cohesive form, providing protection against water and wind erosion and enhancing the soil physical structure via the formation of soil aggregates. Biocrusts also help improving the water holding capacity of the soil and assist with nourishing the soil by capturing nutrient rich dust. In addition, carbon and nitrogen fixed from the atmosphere by microbes are released into the dry surrounding soils in forms that can be utilized by other organisms. The cohesive nature of biocrusts is due to the formation of a polysaccharide sheath on the soil surface by some of the microbial community members (e.g., filamentous cyanobacteria). Microbial activity in desert soils is highly dependent on temperature, moisture and the availability of organic carbon. Of these, it appears that moisture is the major constraint affecting soil microbial biodiversity, community structure and activity.

Did you know? There are 22 deserts in the world. More specifically, 19% (27.6×106 km2) of the global land is arid deserts and 14.6% (21.2×106 km2) is semi-arid deserts (excluding Antarctica). That’s one third of the Earth’s land surface. Estimates based on current global warming trends suggest that drylands will constitute more than half of land surfaces by the end of the century.

Typical biocrust types. (a) Light or thin cyanobacterial crust. Filamentous cyanobacteria (Microcoleus sp. ) dominate this crust, which is only a few millimeters thick. Patches of bare soil are visible. (b) Dark or thick cyanobacterial crust. Besides the filamentous species of Microcoleus, also coccoid species ( Nostoc colonies) and other filamentous cyanobacteria ( Phormidium ) form this up to 5 mm thick biocrust. (c) Crustose “rugose” cyanolichen biocrust. Different Collema species or other cyanolichens dominate this crust type, but free-living cyanobacteria and green algae occur as well. (d) Rugose moss crust. Moss stems grow mainly embedded within the uppermost centimeters of soil. Only the uppermost leaves or the fruiting bodies rise over the soil surface. (e) Rolling chlorolichen crust. Mainly crustose and squamulose chlorolichens on top of the soil with rhizines penetrating deep into the soil dominate this crust type. Other components like cyanobacteria or green algae are also free living in this biocrust. (f) Rolling “thick” moss crust. Up to 5 cm thick moss carpets and cushions with cyanobacteria and green algae living on top of or in between the stems. (g) Pinnacled crust. Turret-like structures are elevated over the ground surface where organisms prevent soil erosion.

Colesie et al (2016) Biological Soil Crusts: An Organizing Principle in Drylands (https://link.springer.com/chapter/10.1007%2F978-3-319-30214-0_9)

The biotic composition of desert soils

Microbial community structure of global desert soils. Leung et al (2020) mSystems (https://msystems.asm.org/content/5/2/e00495-19)

The introduction of culture-dependent and -independent methods have recently shed light on the composition of microbial communities associated with desert plants. Recent data has demonstrated that deserts are usually dominated by heterotrophic Actinobacteria, Proteobacteria, and Chloroflexi (all bacterial organisms). Heterotrophic organisms require organic compounds produced elsewhere as their nutritional support. In the harsh desert environments, heterotrophs may face extreme starvation for their preferred organic energy and carbon sources. Thus, some of these organisms have evolved to reversibly enter a metabolically less active state termed dormancy during periods of environmental pressures. The state of dormancy increases cellular resistance to external stresses while reducing energy expenditure.

Interesting: Desert soil microbiota appear to take advantage of brief “water pulses”, such as occasional precipitation, condensation of dew or fog, and ice or snow melts (in polar deserts) to generate biomass and accumulate reserve compounds in preparation for long periods of water scarcity. In the desert environment, water is commonly provided in the form of early-morning dew, which is followed by desiccation as temperatures rise and relative humidity declines during the day. Some biocrust microbes must therefore rapidly respond to a dew event by activating respiration and photosynthesis for biomass production and then rapidly shut these systems off. This is known as the “energy reserve hypothesis”. Another hypothesis recently put forward (but not mutually exclusive), the “continual energy harvesting hypothesis”, suggests that heterotrophic microbes in desert ecosystems possess hidden metabolic flexibility. They may meet energy demands during starvation by continually harvesting atmospheric trace gases (lithoheterotrophy) or sunlight (photoheterotrophy) as alternative energy sources.

Soil biodiversity of the Arabian deserts

The Middle East and North Africa (MENA) comprises some of the largest sandy deserts in the planet, which includes the Sahara (in Northern Africa) and the Rub' al Khali (or Empty Quarter; in the Arabian Peninsula, encompassing areas of Saudi Arabia, Oman, the United Arab Emirates and Yemen). The DARWIN21 project was launched some years ago to generate a global knowledge base of the biodiversity of the Arabian desert rhizosphere and to study their potential use for sustainable agricultural systems in arid lands. DARWIN21 is an initiative by the King Abdullah University of Science and Technology with partners such as the International Center for Biosaline Agriculture in the United Arab Emirates and academic institutions in Europe.

The bacterial composition of the rhizosphere of four plants, including a desert grass (Panicum turgidum) and three Zygophyllaceae species (Tribulus terrestris, Tribulus pentandum and Zygophyllum simplex), and of a soil sample of the Jizan desert (southern Saudi Arabia) was analyzed in a recent study. More than 3,500 operational taxonomic units (OTUs) were found – in Biology, an OTU defines a cluster of closely related individuals based on DNA similarity. In the plant samples, the most abundant organisms belonged to the Proteobacteria and Bacteroidetes phyla, while in the soil sample displayed an abundance of organisms from the Firmicutes phylum, particularly Bacillus. This study was further expanded to include the microbial composition not only of the rhizosphere (soil close to the root surface) but also the root endosphere (within root tissues) of desert plant samples in the Jizan area and in the Al Wahbah crater (Western Saudi Arabia). Actinobacteria and Proteobacteria dominated both the rhizosphere and endosphere of all samples, but the bacterial distribution from the Jizan and Al Wahbah areas were significantly different. The authors went on to cultivate more than 100 of bacterial isolates from these samples and observed that there were substantial differences in nutrient acquisition, hormone production and growth under stress conditions. More importantly, eleven of the isolated strains helped the plant model Arabidopsis thaliana to tolerate high salt conditions, suggesting a potential utilization of these microbes as natural enhancers of agriculture yield in the desert. Similar beneficial effects for various crop traits of alfalfa were observed for root-adhering bacteria isolated from the rhizosphere of plants from Hada Al Sham in Saudi Arabia. In the Al Jouf region (Northern Saudi Arabia), an Actinobacteria was obtained from the rhizosphere of a desert grass that was able to alleviate the effects of drought stress on maize. Finally, a recent study has determined that there is a considerable fungal biodiversity in sand samples from Saudi Arabia and Jordan deserts, which included culturable species from the genera Fusarium, Chaetomium and Albifimbria. These are simply some examples; similar examinations of the soil biodiversity (mainly bacterial diversity) of the Arabian desert have been conducted.

Interesting facts: Plant growth promoting rhizobacteria (PGPR) are a group of naturally-occurring bacteria that proliferate in the plant rhizosphere and stimulate plant physiological processes and biomass production. This includes enhancing plant growth, remediating degraded wastelands, controlling pesticide pollution, nitrogen, and phosphorous runoff, and increasing resistance to pathogens. For example, PGPR found in the desert soil are evolutionarily well adapted to the harsh abiotic conditions of those ecosystems and help plants to thrive in the extreme conditions. Thus, these organisms have been applied as “biofertilizers” in agricultural settings to enhance productivity.

Photograph courtesy of John A. Kelly, USDA-NRCS

Soils of the UAE

The United Arab Emirates (UAE) occupies about 82,880 km2 from which the Abu Dhabi Emirate represents more than 85% of the UAE’s mainland territory. The desert landscape of the UAE encompasses plains, sand sheets, sand dunes, sabkhas (supratidal salt flats formed by the precipitation of evaporites), burqas and mesas (burqas and mesas are rocky outcrops and small mountains found in the western region). These desert soils are a central component of the cultural heritage of the UAE. UAE soils are composed of 2 orders called Aridisol and Entisol. A soil survey revealed that these 2 orders could be subdivided into 6 suborders, 10 great groups, 41 sub-groups and 74 series in the UAE. The 10 great groups of soils found in the UAE are Aquisalids, Calcigypsids, Haplocalcids, Haplocambids, Haplogypsids, Haplosalids, Petrocalcids, Petrogypsids, Torriorthents, and Torripsamments. More information can be found on the website of the Emirates Soil Museum (http://www.emiratessoilmuseum.org/uae-soil-map).

Did you know? It has been estimated that about 2/3 of the soil in the UAE are unsuitable for irrigated agriculture while approximately 1/3 is marginally (27%) to moderately suitable (5%); only 0.04% of the soils in the UAE soils highly suitable for irrigated agriculture. Some of the policies that have been proposed to address the issues that the UAE faces in terms of soil quality include integrated soil salinity management, irrigation using brackish water, selection of salt-tolerant plants, understanding nutrient cycling in desert environments, controlled grazing, and fundamental scientific research.

Soil biodiversity in the UAE

Vegetation of the UAE that has been shown to interact with biotic components of the soil.
Left: Salt cedar (https://www.dm.gov.ae/rakws_animal_listing/salt-cedar/)
Middle: White saxaul (https://connectwithnature.ae/knowledge-hub/white-saxaul)
Right: Ghaf tree and longhorn beetle (Ajmal Hasan 2014. https://outdooruae.com/outdoor-activity/otheractivities/beetling-about-…)

More than 800 species of plants (including multiple halophytic plants), 48 species of wild mammals, 440 species of birds, 72 species of reptiles and amphibians, along with rich coral reef areas have been recorded in the UAE. This includes trees such as the ghaf, samur, salt cedar and Arabian gum tree, shrubs as rimth and ghada, birds such as the greater hoopoe-lark, black-crowned sparrow-lark, crested lark, southern grey shrike and cream-colored courser, and various other animals such as the sand cat, Arabian oryx, sand gazelle, Arabian tahr, red fox, caracal, horned viper, camel spider, black fat-tailed scorpion and many others. We know that the salt cedar dramatically increases the salinity of the surface of the soil around them, making it inhospitable to other plant species. We also know that the white saxaul (ghada) possesses an extensive root system, which helps stabilize sandy soil and reduce desertification. We know that the larvae of longhorn beetles live for long periods of time in the soil near ghaf trees, boring into roots or rhizomes before they become mature and live inside holes in the tree. Despite these examples, the soil biodiversity of the UAE remains largely uncharted. Future directions should include the exploration of the biodiversity of the UAE soils to better understand their dynamics and guide favorable soil management strategies.

Abu Dhabi sabkha

A specific soil type, rich in anhydrite (anhydrous calcium sulfate; chemical formula: CaSO4) was described in a coastal sabkha south of Abu Dhabi. X-ray diffraction confirmed that anhydrite is the dominant mineral in coastal sabkha soils, with the absence of gypsum. Sabkhas are flat areas rich in minerals that resulted from evaporite precipitation. This sabkha is the only one in the world that contains the four main distinctive layers of this type of salt flat: lagoon mud (subtidal), microbial mat (intertidal), gypsum mud and anhydrite nodules (supratidal). Interestingly, sabkhas have been proposed as analogs of a potential Mars ecosystem.

Field photographs from ICBA & EAD Abu Dhabi soil surveys 2006-2009

Field photographs from ICBA & EAD Abu Dhabi soil surveys 2006-2009

The microbial mats of sabkhas are particularly pronounced since the harsh nature of this system limits the occurrence of grazing fauna. These microbial mats form distinctive polygon-shaped, desiccated mounds and are known to become solid rock over geological time scales. The prokaryotic diversity of mats from the Abu Dhabi sabkha has been determined to be mainly formed by Cyanobacteria in the lower intertidal zone, although representatives of Spirochaetes, Proteobacteria, Bacteroidetes, Firmicutes, Acidobacteria and Actinobacteria bacterial phyla, and members of the Archaea, were also found. Microbial community structures appeared to be associated with the intertidal zone and salinity changes. Moreover, it has been suggested that these microbes could be involved in the formation process of the mineral dolomite.

Interesting fact: Sabkhas and their microbial mats have been shown to contain significant pools of carbon.

Furthermore, a recent study investigated the microbial mats of interdune sabkhas among large dunes in the Rub' al Khali (‘Empty Quarter’), more precisely in the Liwa Oasis. Different layers of mats obtained from the collection sites showed a distinct microbial composition: the top and middle layers were dominated by the phylum Bacteroidetes, while the bottom and sediment layers showed a higher fraction of Cyanobacteria and Proteobacteria, respectively.

Close-up of an endoevaporite mat from sabkhas in the Liwa Oasis.

Close-up of an endoevaporite mat from sabkhas in the Liwa Oasis. The uppermost white layer, about 5 mm thick, is the salt crust. Below that is a layer, almost 5 mm thick of pink halophilic bacteria and below that a layer of green photosynthetic organisms. Below the green layer the material is darker in color. McKay et al (2016) PLoS One (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0150342)
 

Current and future work: As microbes collected in sabkhas and other desert landscapes have evolved to tolerate extreme conditions of temperature, salinity, moisture, pH, …), their properties have been pursued for various applications in biotechnology. The field of research in which scientists specifically search for useful products derived from bioresources is called bioprospection.

Can microbes recovered from the mango rhizosphere in the UAE be useful as biological control agents against fungal pests?

The soil biodiversity of the rhizosphere (soil region around the plant roots) of mango plantation in the UAE was studied by Kamil and colleagues. A total of 53 Actinobacteria isolates were isolated from a 30 cm depth under healthy mango trees, 2/3 of which were classified as Streptomyces. Interestingly, 19 of the isolates demonstrated to possess antagonistic activities against the fungus Lasiodiplodia theobromae, a pathogen that afflicts mango plants by causing the mango dieback disease. The strain of L. theobromae used in this study had previously been isolated from diseased tree twigs in Abu Dhabi.

In vivo inhibitory effect of a biological control Streptomyces candidate against Lasiodiplodia theobromae using a mango fruit bioassay.

In vivo inhibitory effect of a biological control Streptomyces candidate against Lasiodiplodia theobromae using a mango fruit bioassay. Adapted from: Kamil et al (2018) Frontiers in Microbiology (https://www.frontiersin.org/articles/10.3389/fmicb.2018.00829/full)
 

From these 19 candidates, three strains from the species Streptomyces samsunensis, Streptomyces cavourensis and Micromonospora tulbaghiae showed the strongest inhibitory effects, and conferred disease protection in mango seedlings infected with L. theobromae in greenhouse experiments. This study showed for the first time that soil Actinobacteria have the potential to counteract an important fungal pathogen, L. theobromae, that causes plant dieback in a variety of hosts, including mango, guava, coconut, papaya, and grapevine.

Antagonistic effect of a biological control Streptomyces candidates against mango dieback disease under greenhouse conditions.

Antagonistic effect of a biological control Streptomyces candidates against mango dieback disease under greenhouse conditions. Adapted from: Kamil et al (2018) Frontiers in Microbiology (https://www.frontiersin.org/articles/10.3389/fmicb.2018.00829/full)
 

How does oil pollution in mangroves of the UAE affect microbial activity in soil sediments?

El-Tarabily reported an analysis of sediment samples from oil-polluted and nonpolluted mangrove sites in the UAE which were analyzed for their microbial activity and composition (for culturable organisms). The total population of bacteria, filamentous fungi and yeast was significantly lower in the oil-polluted sediment in comparison with the nonpolluted sediment. This tendency was further supported by the observation that the addition of water-soluble fractions of the light Arabian crude oil to the nonpolluted sediment caused a reduction in microbial activity.

Additional examples

Images of bacterial cultivations from the rhizosphere of ghaf trees (Prosopis cineraria). Soil depth: 20-30 cm. Gram staining. Image credits: Dr. Sumitha Thushar, Shreya Prajapat, and Sirisha Nuti, International Center for Biosaline Agriculture (ICBA).

Images of bacterial cultivations from the rhizosphere of ghaf trees (Prosopis cineraria).