Culturing the desert microbiota

Harnessing the Ecological and Genomic Adaptability of the Bacterial Genus Massilia for Environmental and Industrial Applications

The bacterial genus Massilia was first described in 1998, and since then has attracted growing interest due to its ecological plasticity and biotechnological promise. Certain species of the genus Massilia inhabit a variety of ecosystems, from arid deserts to polar glaciers, and exhibit unique adaptations such as resistance to cold and heat. In contaminated environments, some members of Massilia contribute significantly to the detoxification of heavy metals and the degradation of organic pollutants, presenting them as promising agents for bioremediation. In addition, Massilia species improve plant resistance and facilitate pollutant absorption in phytoremediation strategies. New research also highlights their potential as bioindicators of environmental health, given their abundance in anthropogenically influenced ecosystems and airborne microbial communities. In addition to their ecological roles, some Massilia species have potential in biotechnological applications by producing biopolymers and secondary metabolites. Here, we integrate findings across various habitats to present a comprehensive overview of the ecological and biotechnological importance of the genus Massilia. We highlight critical knowledge gaps and propose future research directions to fully harness the potential of this not fully explored bacterial genus to address environmental challenges, including contamination.

Bioactive Metabolites from Radioresistant Bacterium Kocuria sp. TMM 11 and Their Role in Prevention of Ultraviolet-Induced Photodamages

A radioresistant bacterium identified as Kocuria sp.TMM 11 was isolated from Thal desert. Kocuria sp.TMM11 demonstrated resistance (57.3% survival rate) to an ultraviolet B radiations dose of 4.1 × 103 J/m2, 61.5% survival rate to hydrogen peroxide (60 mM) and 57.1% survivability to mitomycin C (6 μg/mL). An orange carotenoid pigment from strain TMM 11 was extracted using solvent mixture of methanol, ethyl acetate and acetone (7:5:3), subsequently purified using C18 cartridge column. The purified fraction was analyzed by liquid chromatography mass spectrometry and compounds identified were rhodovibrin, phytoene, 4'-Hydroxy-4,4'-diaponeurosporene-4-oic acid and 3,4,3',4'-Tetrahydrospirilloxanthin. The purified fraction with mixture of carotenoid compounds, was evaluated for its antioxidant activity, total flavonoids, phenolic content and radio protective potential. These assessments were conducted in relation to its ability to prevent protein and lipids oxidation, as well as DNA strand breaks in vitro. The fraction showed strong antioxidant activity, as indicated by its ability to scavenge super oxides, with an IC50 value of 50.8 μg/mL. Additionally, it displayed 75.76% iron chelation activity. The purified fraction strongly inhibited oxidative damage to proteins and lipids, comparable to the activity of standard ascorbic acid. The total phenolic and flavonoid contents in extract were measured 11.6 and 9.8 μg in terms of gallic acid and quercetin equivalents per milligram of dried mass. Hence, it is concluded that the carotenoid mixture from Kocuria sp.TMM 11 not only inhibited DNA strands from UV mediated photo damages but also protected lipid and protein peroxidation and therefore could be a good candidate in radio protective drugs and as sunscreen.

Ecogenomic insights into the resilience of keystone Blastococcus Species in extreme environments: a comprehensive analysis

BACKGROUND

The stone-dwelling genus Blastococcus plays a key role in ecosystems facing extreme conditions such as drought, salinity, alkalinity, and heavy metal contamination. Despite its ecological significance, little is known about the genomic factors underpinning its adaptability and resilience in such harsh environments. This study investigates the genomic basis of Blastococcus's adaptability within its specific microniches, offering insights into its potential for biotechnological applications.

RESULTS

Comprehensive pangenome analysis revealed that Blastococcus possesses a highly dynamic genetic composition, characterized by a small core genome and a large accessory genome, indicating significant genomic plasticity. Ecogenomic assessments highlighted the genus's capabilities in substrate degradation, nutrient transport, and stress tolerance, particularly on stone surfaces and archaeological sites. The strains also exhibited plant growth-promoting traits, enhanced heavy metal resistance, and the ability to degrade environmental pollutants, positioning Blastococcus as a candidate for sustainable agriculture and bioremediation. Interestingly, no correlation was found between the ecological or plant growth-promoting traits (PGPR) of the strains and their isolation source, suggesting that these traits are not linked to their specific environments.

CONCLUSIONS

This research highlights the ecological and biotechnological potential of Blastococcus species in ecosystem health, soil fertility improvement, and stress mitigation strategies. It calls for further studies on the adaptation mechanisms of the genus, emphasizing the need to validate these findings through wet lab experiments. This study enhances our understanding of microbial ecology in extreme environments and supports the use of Blastococcus in environmental management, particularly in soil remediation and sustainable agricultural practices.

Metagenome Analysis Identified Novel Microbial Diversity of Sandy Soils Surrounded by Natural Lakes and Artificial Water Points in King Salman Bin Abdulaziz Royal Natural Reserve, Saudi Arabia

BACKGROUND

Soil microbes play a vital role in the ecosystem as they are able to carry out a number of vital tasks. Additionally, metagenomic studies offer valuable insights into the composition and functional potential of soil microbial communities. Furthermore, analyzing the obtained data can improve agricultural restoration practices and aid in developing more effective environmental management strategies.

METHODOLOGY

In November 2023, sandy soil samples were collected from ten sites of different geographical areas surrounding natural lakes and artificial water points in the Tubaiq conservation area of King Salman Bin Abdulaziz Royal Natural Reserve (KSRNR), Saudi Arabia. In addition, genomic DNA was extracted from the collected soil samples, and 16S rRNA sequencing was conducted using high-throughput Illumina technology. Several computational analysis tools were used for gene prediction and taxonomic classification of the microbial groups.

RESULTS

In this study, sandy soil samples from the surroundings of natural and artificial water resources of two distinct natures were used. Based on 16S rRNA sequencing, a total of 24,563 OTUs were detected. The metagenomic information was then categorized into 446 orders, 1036 families, 4102 genera, 213 classes, and 181 phyla. Moreover, the phylum Pseudomonadota was the most dominant microbial community across all samples, representing an average relative abundance of 34%. In addition, Actinomycetes was the most abundant class (26%). The analysis of clustered proteins assigned to COG categories provides a detailed understanding of the functional capabilities and adaptation of microbial communities in soil samples. Amino acid metabolism and transport were the most abundant categories in the soil environment.

CONCLUSIONS

Metagenome analysis of sandy soils surrounding natural lakes and artificial water points in the Tubaiq conservation area of KSRNR (Saudi Arabia) has unveils rich microbial activity, highlighting the complex interactions and ecological roles of microbial communities in these environments.

Atacama desert actinomycetes: taxonomic analysis, drought tolerance and plant growth promoting potential

This study was designed to recover representative culturable actinomycetes from the Atacama Desert, and to detect their ability to promote plant growth under drought conditions. Environmental samples were taken from three Atacama Desert habitats, namely, from the Aguas Calientes, Lomas Bayas and Yungay core regions. With one exception higher actinomycete counts were obtained when isolation media were inoculated with mineral particles than with corresponding aliquots of serial dilution. Comparative 16S rRNA gene sequencing showed that representative isolates belonged to thirteen genera including putative novel Blastococcus, Kocuria, Micromonospora, Pseudonocardia, Rhodococcus and Streptomyces species. Representative isolates produced indole-3-acetic acid, siderophore and solubilized phosphate as well as displaying an ability to grow under drought conditions. In conclusion, the current findings open up exciting prospects for the promising potential of actinomycetes from the Atacama Desert to be used as bioinoculants to promote plant growth in arid and semi-arid biomes.

Interplay between desiccation and oxidative stress responses in iron-oxidizing acidophilic bacteria

Variations in water availability represent a foremost stress factor affecting the growth and survival of microorganisms. Acidophilic bioleaching bacteria are industrially applied for releasing metals from mineral sulphides, and they are considered extremely tolerant to oxidative conditions prevailing in acidic bioleaching environments. Such processes usually are performed in heaps and thus these microorganisms are also exposed to intermittent desiccations or high osmolarity periods that reduce the water availability. However, the tolerance to water stress and the molecular basis of adaptation to it are still largely unknown. The aim of this work was to determine the cellular response to desiccation stress and establish its relationship to oxidative stress response in the acidophilic iron-oxidizing bacteria Acidithiobacillus ferrooxidans ATCC 23270 and Leptospirillum ferriphilum DSM 14647. Results showed that the exposure of cell cultures to desiccation (0-120 min) led to a significant reduction in cell growth, and to an increase in content in reactive oxygen species in both bacteria. However, Leptospirillum ferriphilum turned out to be more tolerant than Acidithiobacillus ferrooxidans. In addition, the pre-treatment of the cell cultures with compatible solutes (trehalose and ectoine), and antioxidants (glutathione and cobalamin) restored all stress parameters to levels exhibited by the control cultures. To evaluate the role of the osmotic and redox homeostasis mechanisms in coping with desiccation stress, the relative expression of a set of selected genes was approached by RT-qPCR experiments in cells exposed to desiccation for 30 min. Results showed a generalized upregulation of genes that code for mechanosensitive channels, and enzymes related to the biosynthesis of compatible solutes and oxidative stress response in both bacteria. These data suggest that acidophiles show variable tolerance to desiccation and allow to establish that water stress can trigger oxidative stress, and thus anti-oxidative protection capability can be a relevant mechanism when cells are challenged by desiccation or other anhydrobiosis states.

Impacts of sulfamethoxazole stress on vegetable growth and rhizosphere bacteria and the corresponding mitigation mechanism

Antibiotics are an important pharmaceutical class excessively used by humans. Its presence in the soil can impact plant growth and induce antibiotic resistance. This research studies the effect of sulfamethoxazole (SMX) on plant growth, rhizosphere bacteria composition, and resistance genes. Two sets of vegetables (basil, cilantro, and spinach) were treated separately with water and SMX solution. The plant growth data and soil samples were collected and analyzed. The results revealed that SMX increased spinach leaf length (34.0%) while having no significant impacts on basil and cilantro. On the other hand, SMX improved the bacterial diversity in all samples. The shifts in the abundance of plant growth-promoting bacteria could indirectly affect vegetable stem and leaf length. SMX also significantly increased the abundance of resistance genes Sul1 and Sul2. A further study into the correlation between bacteria highlights the importance of Shingomonas and Alfipia for inhibiting the spread of key resistance gene hosts, namely, Pseudomonas, Stenotrophomonas, and Agrobacterium. This research provides insight into SMX's impact on vegetable growth and microbial diversity. It also points out important microbial interactions that could potentially be utilized to mitigate ARG proliferation.