Blastococcus atacamensis sp. nov., a novel strain adapted to life in the Yungay core region of the Atacama Desert

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.

Analysis of Microbial Community Heterogeneity and Carbon Fixation Capabilities in Oil-Contaminated Soils in Chinese Onshore Oilfields

This study selected 27 soil samples from four representative horizontally distributed onshore oilfields in China to explore the diversity of soil microbial communities and their carbon fixation capacity, with a focus on the potential interaction between pollution and carbon fixation under oil pollution stress. The analysis of the soil physicochemical properties and microbial community structures from these oilfield samples confirmed a clear biogeographic isolation effect, indicating spatial heterogeneity in the microbial communities. Additionally, the key factors influencing microbial community composition differed across regions. The dominant bacterial phyla of soil microorganisms under soil pollution stress were Proteobacteria, Actinobacteriota, Chloroflexi, Acidobacteriota, Firmicutes, Bacteroidota, and Gemmatimonadota. A correlation network analysis identified Immundisolibacter, Acinetobacter, Blastococcus, Truepera, and Kocuria as key players in the microbial network, with most showing positive correlations. The results of the KEGG database functional annotation showed that degradation and carbon fixation metabolic pathways coexist in soil samples and maintain a balanced relative abundance. These metabolic pathways highlight the functional diversity of microorganisms. Among them, prokaryotic and eukaryotic carbon fixation pathways, along with benzoate degradation pathways, are predominant. These findings establish a theoretical basis for further exploration of the synergistic mechanisms underlying pollution reduction and carbon sequestration by microorganisms in petroleum-contaminated soils.

Blastococcus montanus sp. nov., a multi-stress-resistant and bacteriostatic-producing bacterium isolated from the Flaming Mountain, Xinjiang,China

A bacterial strain designated HT6-4T was isolated from soil samples collected from the Flaming Mountain, Xinjiang, PR China. The purpose of this study was to describe a novel species and its characteristics, through genome sequencing and analysis of the relationship between the members of the genus Blastococcus, and explore the antiradiation, antioxidation and antibacterial capabilities of strain HT6-4T. The polyphasic study confirmed the affiliation of strain HT6-4T with the genus Blastococcus. Strain HT6-4T was aerobic, Gram-stain-positive, non-budding, non-motile, catalase-positive and oxidase-negative. It grew at 10-37 °C, pH 5.0-8.0 and 0-4% (w/v) NaCl. Colonies were circular, smooth and bright orange in colour. In addition, strain HT6-4T was drought tolerant. The predominant menaquinone was MK-9, with MK-8 as the minor component. The polar lipids of strain HT6-4T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, phospholipids, an unidentified aminolipid and two unidentified phospholipids. Whole-cell hydrolysates contain meso-diaminopimelic acid as the diagnostic diamino acid and ribose and galactose as diagnostic sugars. Its major fatty acids were iso-C16 :  0, C17 :  1 ω8c and C18 :  1 ω9c. The genome of strain HT6-4T was 4.30 Mb in the whole-genome shotgun project. The G+C content was 73.9 mol%. The phylogenetic analysis based on the 16S rRNA gene sequence showed that strain HT6-4T was closely related to Blastococcus jejuensis KST3-10T(97.9%), Blastococcus capsensis BMG 804T(97.8%), Blastococcus aggregatus DSM 4725T(97.5%), Blastococcus saxobsidens BC 444T(97.5%), Blastococcus xanthinilyticus BMG 862T(97.5%) and Blastococcus litoris GP-S2-8T(97.5%). The average nucleotide identity (OrthoANI) and digital DNA-DNA hybridization (dDDH) values among strain HT6-4T and B. jejuensis KST3-10T, B. capsensis BMG 804T, B. aggregatus DSM 4725T, B. saxobsidens BC 444T, B. xanthinilyticus BMG 862T and B. litoris GP-S2-8T were below the species delimitation thresholds. The genome of strain HT6-4T contained antiradiation genes, antioxidant genes and antibacterial genes. Based on its morphological, physiological and chemical taxonomic characteristics, strain HT6-4T (=KCTC 59234T =GDMCC 1.4386T) should be classified as a novel species of the genus Blastococcus with the proposed name Blastococcus montanus sp. nov.

Foliar application of selenium and gibberellins reduce cadmium accumulation in soybean by regulating interplay among rhizosphere soil metabolites, bacteria community and cadmium speciation

Both selenium (Se) and gibberellins (GA3) can alleviate cadmium (Cd) toxicity in plants. However, the application of Se and GA3 as foliar spray to against Cd stress on soybean and its related mechanisms have been poorly explored. Herein, this experiment evaluated the effects of Se and GA3 alone and combined application on soybean rhizosphere microenvironment, Cd accumulation and growth of soybean seedlings. The results revealed that both Se and GA3 can effectively decrease the accumulation of Cd in soybean seedlings. Foliar application of Se, GA3 and their combination reduced Cd contents in soybean seedlings respectively by 21.70 %, 27.53 % and 45.07 % when compared with the control treatment, suggest a synergistic effect of Se and GA3 in decreasing Cd accumulation. Se and GA3 also significantly increased diversity and abundance of the metabolites in rhizosphere, which consequently played an important role in shaping rhizosphere bacteria community and improve rhizosphere soil physicochemical properties of Cd contaminated soil, as well as decreased the Cd available forms contents but enhance the immobilized form levels. Overall, this study affords a novel approach on mitigating Cd accumulation in soybean seedlings which is attributed to Se and GA3 regulated interplay among rhizosphere soil metabolites, bacteria community and cadmium speciation.

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.

Airborne antibiotic and metal resistance genes - A neglected potential risk at e-waste recycling facilities

Heavy metal-rich environments can promote the selection of metal-resistance genes (MRGs) in bacteria, often leading to the simultaneous selection of antibiotic-resistance genes (ARGs) through a process known as co-selection. To comprehensively evaluate the biological pollutants at electronic-waste (e-waste) recycling facilities, air, soil, and river samples were collected at four distinct Swiss e-waste recycling facilities and analyzed for ARGs, MRGs, mobile genetic elements (MGEs), endotoxins, and bacterial species, with correlations drawn to heavy metal occurrence. To our knowledge, the present work marks the first attempt to quantify these bio-pollutants in the air of e-waste recycling facilities, that might pose a significant health risk to workers. Although ARG and MRG's profiles varied among the different sample types, intl1 consistently exhibited high relative abundance rates, identifying it as the predominant MGE across all sample types and facilities. These findings underscore its pivol role in driving diverse bacterial adaptations to extreme heavy metal exposure by selection and dissemination of ARGs and MRGs. All air samples exhibited consistent profiles of ARGs and MRGs, with blaTEM emerging as the predominant ARG, alongside pbrT and nccA as the most prevalent MRGs. However, one facility, engaged in batteries recycling and characterized by exceptionally high concentrations of heavy metals, showcased a more diverse resistance gene profile, suggesting that bacteria in this environment required more complex resistance mechanisms to cope with extreme metal exposure. Furthermore, this study unveiled a strong association between gram-negative bacteria and ARGs and less with MRGs. Overall, this research emphasizes the critical importance of studying biological pollutants in the air of e-waste recycling facilities to inform robust safety measures and mitigate the risk of resistance gene dissemination among workers. These findings establish a solid foundation for further investigations into the complex interplay among heavy metal exposure, bacterial adaptation, and resistance patterns in such distinctive ecosystems.

Blastococcus brunescens sp. nov., a member of the Geodermatophilaceae isolated from sandstone collected from the Sahara Desert in Tunisia

The taxonomic position of strain BMG 8361T, isolated from sandstone collected in the Sahara Desert of Southern Tunisia, was refined through a polyphasic taxonomic investigation. Colonies of BMG 8361T were pale-orange coloured, irregular with a dry surface and produced a diffusible pink or brown pigment depending on media. The Gram-positive cells were catalase-positive and oxidase-negative. The strain exhibited growth at 10-40 °C and pH values ranging from 5.5 to 9.0, with optima at 28-35 °C and pH 6.5-8.0. Additionally, BMG 8361T demonstrated the ability to grow in the presence of up to 1 % NaCl (w/v) concentration. The peptidoglycan of the cell wall contained meso-diaminopimelic acid, glucose, galactose, xylose, ribose, and rhamnose. The predominant menaquinones consisted of MK-9(H4) and MK-9. The main polar lipids were phosphatidylcholine, phosphatidylinositol, glycophosphatidylinositol, diphosphatidylglycerol, phosphatidylethanolamine, and two unidentified lipids. Major cellular fatty acids were iso-C16 : 0, iso-C16 : 1 h, and C17 : 1  ω8c. Phylogenetic analyses based on both the 16S rRNA gene and whole-genome sequences assigned strain BMG 8361T within the genus Blastococcus. The highest pairwise sequence similarity observed in the 16S rRNA gene was 99.5 % with Blastococcus haudaquaticus AT 7-14T. However, when considering digital DNA-DNA hybridization and average nucleotide identity, the highest values, 48.4 and 86.58 %, respectively, were obtained with Blastococcus colisei BMG 822T. These values significantly undershoot the recommended thresholds for establishing new species, corroborating the robust support for the distinctive taxonomic status of strain BMG 8361T within the genus Blastococcus. In conjunction with the phenotyping results, this compelling evidence leads to the proposal of a novel species we named Blastococcus brunescens sp. nov. with BMG 8361T (=DSM 46845T=CECT 8880T) as the type strain.

Micromonospora parastrephiae sp. nov. and Micromonospora tarensis sp. nov., isolated from the rhizosphere of a Parastrephia quadrangularis plant growing in the Salar de Tara region of the Central Andes in Chile

Two novel Micromonospora strains, STR1-7T and STR1S-6T, were isolated from the rhizosphere of a Parastrephia quadrangularis plant growing in the Salar de Tara region of the Atacama Desert, Chile. Chemotaxonomic, cultural and phenotypic features confirmed that the isolates belonged to the genus Micromonospora. They grew from 20 to 37 °C, from pH7 to 8 and in the presence of up to 3 %, w/v NaCl. The isolates formed distinct branches in Micromonospora gene trees based on 16S rRNA gene sequences and on a multi-locus sequence analysis of conserved house-keeping genes. A phylogenomic tree generated from the draft genomes of the isolates and their closest phylogenetic neighbours showed that isolate STR1-7T is most closely related to Micromonospora orduensis S2509T, and isolate STR1S-6 T forms a distinct branch that is most closely related to 12 validly named Micromonospora species, including Micromonospora saelicesensis the earliest proposed member of the group. The isolates were separated from one another and from their closest phylogenomic neighbours using a combination of chemotaxonomic, genomic and phenotypic features, and by low average nucleotide index and digital DNA-DNA hybridization values. Consequently, it is proposed that isolates STR1-7T and STR1S-6T be recognized as representing new species in the genus Micromonospora, namely as Micromonospora parastrephiae sp. nov. and Micromonospora tarensis sp. nov.; the type strains are STR1-7T (=CECT 9665T=LMG 30768T) and STR1S-6T (=CECT 9666T=LMG 30770T), respectively. Genome mining showed that the isolates have the capacity to produce novel specialized metabolites, notably antibiotics and compounds that promote plant growth, as well as a broad-range of stress-related genes that provide an insight into how they cope with harsh abiotic conditions that prevail in high-altitude Atacama Desert soils.

Blastococcus carthaginiensis sp. nov., isolated from a monument sampled in Carthage, Tunisia

A comprehensive polyphasic investigation was conducted to elucidate the taxonomic position of an actinobacterium, designated BMG 814T, which was isolated from the historic ruins of Carthage city in Tunisia. It grew as pink-orange pigmented colonies and displayed versatile growth capabilities, thriving within a temperature range of 20-40 °C, across a pH spectrum ranging from pH 5.5 to 10 and in the presence of up to 4 % NaCl. Chemotaxonomic investigations unveiled specific cell components, including diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol, glycophosphatidylinositol, an unidentified aminoglycophospholipid, six unidentified aminolipids, two unidentified phospholipids and one unidentified lipid in its polar lipid profile. Furthermore, galactose, glucose and ribose were identified as the primary cell-wall sugars. Major menaquinones identified were MK-9(H4), MK-9(H2) and MK-9, while major fatty acids comprised iso-C15 : 0, iso-C16 : 0, C17 : 1  ω8c and C18 : 1  ω9c. Through phylogenetic analysis based on the 16S rRNA gene sequence, the strain was positioned within the genus Blastococcus, with Blastococcus capsiensis BMG 804T showing the closest relationship (99.1 %). In light of this, draft genomes for both strains, BMG 814T and BMG 804T, were sequenced in this study, and comparative analysis revealed that strain BMG 814T exhibited digital DNA-DNA hybridization and average nucleotide identity values below the recommended thresholds for demarcating new species with all available genomes of type strains of validly names species. Based on the polyphasic taxonomy assessment, strain BMG 814T (=DSM 46848T=CECT 8878T) was proposed as the type strain of a novel species named Blastococcus carthaginiensis sp. nov.

Description of Two Fungal Endophytes Isolated from Fragaria chiloensis subsp. chiloensis f. patagonica: Coniochaeta fragariicola sp. nov. and a New Record of Coniochaeta hansenii

Prospection of the endosphere of the native plant Fragaria chiloensis subsp. chiloensis f. patagonica from the foothills of the Chilean Andes led to the isolation of two strains of the genus Coniochaeta. We addressed the taxonomic placement of these strains based on DNA sequencing data using the ITS and LSU genetic markers, morphological features, and biochemical traits. One of these strains was identified as Coniochaeta hansenii, for which the anamorph and teleomorph states were described. The second strain did not seem to match any of the currently described species of this genus; therefore, we propose the name Coniochaeta fragariicola sp. nov.

Genotype-phenotype correlations within the Geodermatophilaceae

The integration of genomic information into microbial systematics along with physiological and chemotaxonomic parameters provides for a reliable classification of prokaryotes. In silico analysis of chemotaxonomic traits is now being introduced to replace characteristics traditionally determined in the laboratory with the dual goal of both increasing the speed of the description of taxa and the accuracy and consistency of taxonomic reports. Genomics has already successfully been applied in the taxonomic rearrangement of Geodermatophilaceae (Actinomycetota) but in the light of new genomic data the taxonomy of the family needs to be revisited. In conjunction with the taxonomic characterisation of four strains phylogenetically located within the family, we conducted a phylogenetic analysis of the whole proteomes of the sequenced type strains and established genotype-phenotype correlations for traits related to chemotaxonomy, cell morphology and metabolism. Results indicated that the four isolates under study represent four novel species within the genus Blastococcus. Additionally, the genera Blastococcus, Geodermatophilus and Modestobacter were shown to be paraphyletic. Consequently, the new genera Trujillonella, Pleomorpha and Goekera were proposed within the Geodermatophilaceae and Blastococcus endophyticus was reclassified as Trujillonella endophytica comb. nov., Geodermatophilus daqingensis as Pleomorpha daqingensis comb. nov. and Modestobacter deserti as Goekera deserti comb. nov. Accordingly, we also proposed emended descriptions of Blastococcus aggregatus, Blastococcus jejuensis, Blastococcus saxobsidens and Blastococcus xanthilyniticus. In silico chemotaxonomic results were overall consistent with wet-lab results. Even though in silico discriminatory levels varied depending on the respective chemotaxonomic trait, this approach is promising for effectively replacing and/or complementing chemotaxonomic analyses at taxonomic ranks above the species level. Finally, interesting but previously overlooked insights regarding morphology and ecology were revealed by the presence of a repertoire of genes related to flagellum synthesis, chemotaxis, spore production and pilus assembly in all representatives of the family. A rich carbon metabolism including four different CO2 fixation pathways and a battery of enzymes able to degrade complex carbohydrates were also identified in Blastococcus genomes.

Blastococcus tunisiensis sp. nov., isolated from limestone collected in Tunisia

A new actinobacterium strain, designated BMG 823T, was isolated from a limestone sample collected in Tunisia. Its taxonomic position was scrutinized using a polyphasic approach. Colonies of strain BMG 823T were pink orange-coloured, regular and had a moist surface. Cells are Gram-stain-positive, catalase-negative and oxidase-negative. The strain grew at pH 5.5–9, 10–40 °C and in presence of up to 4 % NaCl (w/v). Chemotaxonomically, strain BMG 823T was characterized by cell-wall type III containing meso-diaminopimelic acid as diamino acid, glucose, ribose and rhamnose as whole-cell sugars, MK-9(H4) as predominant menaquinone, and phosphatidylcholine, diphosphadidylglycerol, phosphatidethanolamine, phosphatidylcholine, phosphatidylinositol, unidentified glycolipid, unidentified aminophospholipids and unidentified glycophospholipid as major polar lipids. The fatty acid profile consisted of iso-C16 : 0 and iso-C17 : 1  ω9. Phylogenetic trees based on 16S rRNA gene and genome sequences placed strain BMG 823T within the genus Blastococcus and separated it from all type strains of validly published species. Comparison of 16S rRNA gene sequence similarity, digital DNA–DNA hybridization and average nucleotide identity indicated that strain BMG 823T was most closely related to Blastococcus litoris DSM 106127T and Blastococcus colisei BMG 822T with pairwise values well below the species differentiation thresholds. The distinct phenotypic and genotypic features of strain BMG 823T (=DSM 46838T=CECT 8881T) within the genus Blastococcus warrant its recognition as the type strain for the new species for which we propose the name Blastococcus tunisiensis sp. nov.

Responses of Cyanobacterial Crusts and Microbial Communities to Extreme Environments of the Stratosphere

How microbial communities respond to extreme conditions in the stratosphere remains unclear. To test this effect, cyanobacterial crusts collected from Tengger Desert were mounted to high balloons and briefly exposed (140 min) to high UV irradiation and low temperature in the stratosphere at an altitude of 32 km. Freezing and thawing treatments were simulated in the laboratory in terms of the temperature fluctuations during flight. Microbial community composition was characterized by sequencing at the level of DNA and RNA. After exposure to the stratosphere, the RNA relative abundances of Kallotenue and Longimicrobium increased by about 2-fold, while those of several dominant cyanobacteria genera changed slightly. The RNA relative abundances of various taxa declined after freezing, but increased after thawing, whereas cyanobacteria exhibited an opposite change trend. The DNA and RNA relative abundances of Nitrososphaeraceae were increased by 1.4~2.3-fold after exposure to the stratosphere or freezing. Exposure to stratospheric environmental conditions had little impact on the total antioxidant capacity, photosynthetic pigment content, and photosynthetic rate, but significantly increased the content of exopolysaccharides by 16%. The three treatments (stratospheric exposure, freezing, and thawing) increased significantly the activities of N-acetyl-β-D-glucosidase (26~30%) and β-glucosidase (14~126%). Our results indicated cyanobacterial crust communities can tolerate exposure to the stratosphere. In the defense process, extracellular organic carbon degradation and transformation play an important role. This study makes the first attempt to explore the response of microbial communities of cyanobacterial crusts to a Mars-like stratospheric extreme environment, which provides a new perspective for studying the space biology of earth communities.

Two-year systematic investigation reveals alterations induced on chemical and bacteriome profile of PM2.5 by African dust incursions to the Mediterranean atmosphere

PM_2.5 atmospheric samples were regularly collected between January 2013 and March 2015 at a central location of Eastern Mediterranean (Island of Crete) during African dust events (DES) and periods of absence of such episodes as controls (CS). The elemental composition and microbiome DES and CS were thoroughly investigated. Fifty-six major and trace elements were determined by inductively coupled plasma-mass spectrometry. Relative mass abundances (RMA) of major crustal elements and lanthanoids were higher in DES than in CS. Conversely in CS, RMAs were higher for most anthropogenic transition metals. Lanthanum-to-other lanthanoids concentration ratios for DES approached the corresponding reference values for continental crust and several African dust source regions, while in CS they exceeded these values. USEPA's UNMIX receptor model, applied in all PM_2.5 samples, established that African dust is the dominant contributing source (by 80%) followed by road dust/fuel oil emissions (17%) in the receptor area. Potential source contribution function (PSCF) identified dust hotspots in Tunisia, Libya and Egypt. The application of 16S rRNA gene amplicon sequencing revealed high variation of bacterial composition and diversity between DES and CS samples. Proteobacteria, Actinobacteria and Bacteroides were the most dominant in both DES and CS samples, representing ~88% of the total bacterial diversity. Cutibacterium, Tumebacillus and Sphingomonas dominated the CS samples, while Rhizobium and Brevundimonas were the most prevalent genera in DES. Mutual exclusion/co-occurrence network analysis indicated that Sphingomonas and Chryseobacterium exhibited the highest degrees of mutual exclusion in CS, while in DES the corresponding species were Brevundimonas, Delftia, Rubellimicrobium, Flavobacterium, Blastococcus, and Pseudarthrobacter. Some of these microorganisms are emerging global opportunistic pathogens and an increase in human exposure to them as a result of environmental changes, is inevitable.

Actinobacteria From Desert: Diversity and Biotechnological Applications

Deserts, as an unexplored extreme ecosystem, are known to harbor diverse actinobacteria with biotechnological potential. Both multidrug-resistant (MDR) pathogens and environmental issues have sharply raised the emerging demand for functional actinobacteria. From 2000 to 2021, 129 new species have been continuously reported from 35 deserts worldwide. The two largest numbers are of the members of the genera Streptomyces and Geodermatophilus, followed by other functional extremophilic strains such as alkaliphiles, halotolerant species, thermophiles, and psychrotolerant species. Improved isolation strategies for the recovery of culturable and unculturable desert actinobacteria are crucial for the exploration of their diversity and offer a better understanding of their survival mechanisms under extreme environmental stresses. The main bioprospecting processes involve isolation of target actinobacteria on selective media and incubation and selection of representatives from isolation plates for further investigations. Bioactive compounds obtained from desert actinobacteria are being continuously explored for their biotechnological potential, especially in medicine. To date, there are more than 50 novel compounds discovered from these gifted actinobacteria with potential antimicrobial activities, including anti-MDR pathogens and anti-inflammatory, antivirus, antifungal, antiallergic, antibacterial, antitumor, and cytotoxic activities. A range of plant growth-promoting abilities of the desert actinobacteria inspired great interest in their agricultural potential. In addition, several degradative, oxidative, and other functional enzymes from desert strains can be applied in the industry and the environment. This review aims to provide a comprehensive overview of desert environments as a remarkable source of diverse actinobacteria while such rich diversity offers an underexplored resource for biotechnological exploitations.

Biotechnological and Ecological Potential of Micromonospora provocatoris sp. nov., a Gifted Strain Isolated from the Challenger Deep of the Mariana Trench

A Micromonospora strain, isolate MT25^T, was recovered from a sediment collected from the Challenger Deep of the Mariana Trench using a selective isolation procedure. The isolate produced two major metabolites, n-acetylglutaminyl glutamine amide and desferrioxamine B, the chemical structures of which were determined using 1D and 2D-NMR, including ¹H-¹⁵N HSQC and ¹H-¹⁵N HMBC 2D-NMR, as well as high resolution MS. A whole genome sequence of the strain showed the presence of ten natural product-biosynthetic gene clusters, including one responsible for the biosynthesis of desferrioxamine B. Whilst 16S rRNA gene sequence analyses showed that the isolate was most closely related to the type strain of Micromonospora chalcea, a whole genome sequence analysis revealed it to be most closely related to Micromonospora tulbaghiae 45142^T. The two strains were distinguished using a combination of genomic and phenotypic features. Based on these data, it is proposed that strain MT25^T (NCIMB 15245^T, TISTR 2834^T) be classified as Micromonospora provocatoris sp. nov. Analysis of the genome sequence of strain MT25^T (genome size 6.1 Mbp) revealed genes predicted to responsible for its adaptation to extreme environmental conditions that prevail in deep-sea sediments.

Evaluation of Microbial Assemblages in Various Saline-Alkaline Soils Driven by Soluble Salt Ion Components

Land degraded by salinization and alkalization is widely distributed globally and involves a wide range of ecosystem types. However, the knowledge of the indigenous microbial assemblages and their roles in various saline-alkaline soils is limited. This study demonstrated microbial assemblages in various saline-alkaline soils from different regions of Inner Mongolia and revealed the key driving factors to influence microbiome. The correlation network analysis indicates the difference in adaptability of bacterial and fungal communities under stimulation by saline-alkaline stress: fungal community shows higher tolerance, stability, and resilience to various saline-alkaline soils than a bacterial community. The keystone bacteria and fungi that have potential adaptability to various saline-alkaline environments are further identified, and they may confer benefits in restoring saline-alkaline soils by their own effects or assisting plants. For salt-rich soils in different regions, the soluble salt ion components are the major determinant to drive microbial assemblages of different saline-alkaline soils, rather than salinity. Thus, these saline-alkaline soils are clustered into sulfated, chlorinated, and soda-type saline-alkaline soils. Multivariate analysis reveals unique, dominant, and common microbial taxa in three saline-alkaline soils. This result of the conceptual mode indicates that potential roles of unique and dominant microbial taxa on regulating saline-alkaline functions are more vital.

High Culturable Bacterial Diversity From a European Desert: The Tabernas Desert

One of the most diverse ecological niches for microbial bioprospecting is soil, including that of drylands. Drylands are one of the most abundant biomes on Earth, but extreme cases, such as deserts, are considered very rare in Europe. The so-called Tabernas Desert is one of the few examples of a desert area in continental Europe, and although some microbial studies have been performed on this region, a comprehensive strategy to maximize the isolation of environmental bacteria has not been conducted to date. We report here a culturomics approach to study the bacterial diversity of this dryland by using a simple strategy consisting of combining different media, using serial dilutions of the nutrients, and using extended incubation times. With this strategy, we were able to set a large (254 strains) collection of bacteria, the majority of which (93%) were identified through 16S ribosomal RNA (rRNA) gene amplification and sequencing. A significant fraction of the collection consisted of Actinobacteria and Proteobacteria, as well as Firmicutes strains. Among the 254 isolates, 37 different genera were represented, and a high number of possible new taxa were identified (31%), of which, three new Kineococcus species. Moreover, 5 out of the 13 genera represented by one isolate were also possible new species. Specifically, the sequences of 80 isolates held a percentage of identity below the 98.7% threshold considered for potentially new species. These strains belonged to 20 genera. Our results reveal a clear link between medium dilution and isolation of new species, highlight the unexploited bacterial biodiversity of the Tabernas Desert, and evidence the potential of simple strategies to yield surprisingly large numbers of diverse, previously unreported, bacterial strains and species.

Activity and Diversity of Microorganisms in Root Zone of Plant Species Spontaneously Inhabiting Smelter Waste Piles

The aim was to assess plant driven changes in the activity and diversity of microorganisms in the top layer of the zinc and lead smelter waste piles. The study sites comprised two types (flotation waste—FW and slag waste—SW) of smelter waste deposits in Piekary Slaskie, Poland. Cadmium, zinc, lead, and arsenic contents in these technosols were extremely high. The root zone of 8 spontaneous plant species (FW—Thymus serpyllum, Silene vulgaris, Solidago virgaurea, Echium vulgare, and Rumex acetosa; and SW—Verbascum thapsus; Solidago gigantea, Eupatorium cannabinum) and barren areas of each waste deposit were sampled. We observed a significant difference in microbial characteristics attributed to different plant species. The enzymatic activity was mostly driven by plant-microbial interactions and it was significantly greater in soil affected by plants than in bulk soil. Furthermore, as it was revealed by BIOLOG Ecoplate analysis, microorganisms inhabiting barren areas of the waste piles rely on significantly different sources of carbon than those found in the zone affected by spontaneous plants. Among phyla, Actinobacteriota were the most abundant, contributing to at least 25% of the total abundance. Bacteria belonging to Blastococcus genera were the most abundant with the substantial contribution of Nocardioides and Pseudonocardia, especially in the root zone. The contribution of unclassified bacteria was high—up to 38% of the total abundance. This demonstrates the unique character of bacterial communities in the smelter waste.

Modestobacter altitudinis sp. nov., a novel actinobacterium isolated from Atacama Desert soil

Three presumptive Modestobacter strains isolated from a high altitude Atacama Desert soil were the subject of a polyphasic study. The isolates, strains 1G4^T, 1G51 and 1G52, were found to have chemotaxonomic and morphological properties that were consistent with their assignment to the genus Modestobacter. They formed a well supported clade in Modestobacter 16S rRNA gene trees and were most closely related to the type strain of 'Modestobacter excelsi' (99.8-99.9% similarity). They were also closely related to the type strains of Modestobacter caceresii (99.6 % similarity), Modestobacter italicus (99.7-99.9% similarity), Modestobacter lacusdianchii (98.4-99.2% similarity), Modestobacter marinus (99.4-99.5% similarity) and Modestobacter roseus (99.3-99.5% similarity), but were distinguished from their closest relatives by a combination of phenotypic features. Average nucleotide identity and digital DNA:DNA hybridization similarities drawn from comparisons of draft genome sequences of isolate 1G4^T and its closest phylogenetic neighbours mentioned above, were well below the threshold used to assign closely related strains to the same species. The close relationship between isolate 1G4^T and the type strain of M. excelsi was showed in a phylogenomic tree containing representative strains of family Geodermatophilaceae. The draft genome sequence of isolate 1G4^T (size 5.18 Kb) was shown to be rich in stress related genes providing further evidence that the abundance of Modestobacter propagules in Atacama Desert habitats reflects their adaptation to the harsh environmental conditions prevalent in this biome. In light of all of these data it is proposed that the isolates be assigned to a novel species in the genus Modestobacter. The name proposed for this taxon is Modestobacter altitudinis sp. nov., with isolate 1G4^T (=DSM 107534^T=PCM 3003^T) as the type strain.

Dark, rare and inspirational microbial matter in the extremobiosphere: 16 000 m of bioprospecting campaigns

The rationale of our bioprospecting campaigns is that the extremobiosphere, particularly the deep sea and hyper-arid deserts, harbours undiscovered biodiversity that is likely to express novel chemistry and biocatalysts thereby providing opportunities for therapeutic drug and industrial process development. We have focused on actinobacteria because of their frequent role as keystone species in soil ecosystems and their unrivalled track record as a source of bioactive compounds. Population numbers and diversity of actinobacteria in the extremobiosphere are traditionally considered to be low, although they often comprise the dominant bacterial biota. Recent metagenomic evaluation of 'the uncultured microbial majority' has now revealed enormous taxonomic diversity among 'dark' and 'rare' actinobacteria in samples as diverse as sediments from the depths of the Mariana Trench and soils from the heights of the Central Andes. The application of innovative culture and screening options that emphasize rigorous dereplication at each stage of the analysis, and strain prioritization to identify 'gifted' organisms, have been deployed to detect and characterize bioactive hit compounds and sought-after catalysts from this hitherto untapped resource. The rewards include first-in-a-class chemical entities with novel modes of action, as well as a growing microbial seed bank that represents a potentially enormous source of biotechnological and therapeutic innovation.

Modestobacter excelsi sp. nov., a novel actinobacterium isolated from a high altitude Atacama Desert soil

A polyphasic study was undertaken to establish the taxonomic status of three Modestobacter strains isolated from a high altitude Atacama Desert soil. The isolates, strains 1G6^T, 1G14 and 1G50, showed chemotaxonomic and morphological properties characteristic of members of the genus Modestobacter. The peptidoglycan contained meso-diaminopimelic acid, the whole cell sugars were glucose and ribose (diagnostic sugars) and arabinose, the predominant menaquinone was MK-9(H₄), polar lipid patterns contained diphosphatidylglycerol, glycophosphatidylinositol, phosphatidylethanolamine (diagnostic component), phosphatidylglycerol and phosphatidylinositol while whole cellular fatty acid profiles consisted of complex mixtures of saturated, unsaturated iso- and anteiso-components. The isolates were shown to have different BOX-PCR fingerprint and physiological profiles. They formed a distinct phyletic line in Modestobacter 16S rRNA gene trees, were most closely related to the type strain of Modestobacter italicus (99.9 % similarity) but were distinguished from this and other closely related Modestobacter type strains using a combination of phenotypic properties. Average nucleotide identity and digital DNA:DNA hybridization similarities between the draft genome sequences of isolate 1G6^T and M. italicus BC 501^T were 90.9 % and 42.3 %, respectively, indicating that they belong to different species. Based on these phenotypic and genotypic data it is proposed that the isolates be assigned to a novel species in the genus Modestobacter, namely as Modestobacter excelsi with isolate 1G6^T (=DSM 107535^T =PCM 3004^T) as the type strain. Analysis of the whole genome sequence of M. excelsi 1G6^T (genome size of 5.26 Mb) showed the presence of genes and gene clusters that encode for properties that are in tune with its adaptation to extreme environmental conditions that prevail in the Atacama Desert biome.

Responses of soil microbial communities and their network interactions to saline-alkaline stress in Cd-contaminated soils

Land degradation by salinization and sodification changes soil function, destroys soil health, and promotes bioaccumulation of heavy metals in plants, but little is known about their fundamental mechanisms in shaping microbial communities and regulating microbial interactions. In this study, we explored the impact of saline-alkaline (SA) stress on soil bacterial and fungal community structures in different Cd-contaminated soils of Dezhou, Baoding, Xinxiang, Beijing and Shenyang cities from the North China Plain, China. Increased soil salinity and alkalinity enhanced Cd availability, indicated by significant increases in available Cd²⁺ in soil solution of 34.1%-49.7%, soil extractable Cd of 32.0-51.6% and wheat root Cd concentration of 24.5%-40.2%, as well as decreased activities of antioxidative enzymes of wheat root when compared with CK (no extra neutral or alkaline salts added). Soil bacteria were more active in response to the SA stress than fungi, as the significant structural reorganization of soil bacterial microbiota rather than fungal microbiota between SA and CK treatments was illustrated by principal component analysis. Adding neutral and alkaline salts enriched oligotrophic and haloalkaliphilic taxa in the Sphingobacteriaceae, Cellvibrionaceae, and Caulobacteraceae bacterial families, but decreased some Acidobacteria such as subgroup 6_norank, which was a sensitive biomarker that responded only to Cd contamination in CK-treated soils. Conversely, fungi were more sensitive to soil differences than bacteria: the composition of the fungal community was significantly different among different soil types. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the microbial community structure and network interactions were altered to strengthen the adaptability of microorganisms to SA stress; the changes in structure and network interactions were proposed to contribute to competitive interactions. Most of the keystone genera identified in SA-treated soils, such as Blastococcus, Gemmatimonas, RB41, or Candida, had relatively low abundances (<1%), indicating their disproportionate ecological roles in triggering resistance or tolerance to SA stress and Cd toxicity.

Extreme environments: microbiology leading to specialized metabolites

The prevalence of multidrug-resistant microbial pathogens due to the continued misuse and overuse of antibiotics in agriculture and medicine is raising the prospect of a return to the preantibiotic days of medicine at the time of diminishing numbers of drug leads. The good news is that an increased understanding of the nature and extent of microbial diversity in natural habitats coupled with the application of new technologies in microbiology and chemistry is opening up new strategies in the search for new specialized products with therapeutic properties. This review explores the premise that harsh environmental conditions in extreme biomes, notably in deserts, permafrost soils and deep-sea sediments select for micro-organisms, especially actinobacteria, cyanobacteria and fungi, with the potential to synthesize new druggable molecules. There is evidence over the past decade that micro-organisms adapted to life in extreme habitats are a rich source of new specialized metabolites. Extreme habitats by their very nature tend to be fragile hence there is a need to conserve those known to be hot-spots of novel gifted micro-organisms needed to drive drug discovery campaigns and innovative biotechnology. This review also provides an overview of microbial-derived molecules and their biological activities focusing on the period from 2010 until 2018, over this time 186 novel structures were isolated from 129 representatives of microbial taxa recovered from extreme habitats.

Rare taxa and dark microbial matter: novel bioactive actinobacteria abound in Atacama Desert soils

An "in house" taxonomic approach to drug discovery led to the isolation of diverse actinobacteria from hyper-arid, extreme hyper-arid and very high altitude Atacama Desert soils. A high proportion of the isolates were assigned to novel taxa, with many showing activity in standard antimicrobial plug assays. The application of more advanced taxonomic and screening strategies showed that strains classified as novel species of Lentzea and Streptomyces synthesised new specialised metabolites thereby underpinning the premise that the extreme abiotic conditions in the Atacama Desert favour the development of a unique actinobacterial diversity which is the basis of novel chemistry. Complementary metagenomic analyses showed that the soils encompassed an astonishing degree of actinobacterial 'dark matter', while rank-abundance analyses showed them to be highly diverse habitats mainly composed of rare taxa that have not been recovered using culture-dependent methods. The implications of these pioneering studies on future bioprospecting campaigns are discussed.