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

Microbial Community Structure in the Taklimakan Desert: The Importance of Nutrient Levels in Medium and Culture Methods

Although the Taklimakan Desert lacks the necessary nutrients and conditions to support an extensive ecosystem, it is a treasure trove of extremophile resources with special structures and functions. We analyzed the bacterial communities using oligotrophic medium and velvet cloth replicate combined with an extended culture duration. We isolated numerous uncultured microorganisms and rare microorganisms belonging to genera not often isolated or recently described, such as Aliihoeflea, Halodurantibacterium, and Indioceanicola. A total of 669 strains were isolated from the soil of the Taklimakan Desert, which were classified into 5 phyla, 7 classes, 25 orders, 42 families, 83 genera, and 379 species. Among them, 148 strains were potential new species. Our data show that even when working with samples from extreme environments, simple approaches are still useful for cultivating stubborn microbes. Through comparing the isolation effects of different nutrient levels on microbial diversity and abundance, the results show that reducing the nutrient level of the medium was more conducive to improving the culturability of microorganisms in low-nutrient environments, while the high-nutrient medium was more suitable for the isolation of dominant fast-growing strains. This study helps to better reflect the diversity of microbial resources and lays a foundation for the further research and utilization of soil microbial resources in the Taklimakan Desert.

Paracoccus actinidiae sp.nov., a novel bacterium isolated from kiwi tree rhizosphere soil

Strain M09T was isolated from the rhizoshere of kiwi fruit trees from an orchard located in Fangshan, Beijing, PR China (39° 49' 25.1″ N, 116° 4' 44.5″ E,). It is a short rod-shaped, Gram-stain-negative, facultatively anaerobic bacterium that tests positive for both oxidase and catalase. The strain exhibited growth within the temperature range of 15-45 °C (optimal growth at 30 °C) and the pH range of 4.0-10.0 (optimal growth at pH 7.0) and without NaCl. It also grew in a sodium chloride-free nutrient agar (NA) medium. The results of phylogenetic analysis of the 16S rRNA gene sequences indicated that M09T represents a member of the genus Paracoccus and shares high similarity with Paracoccus everestensis S8-55T (98.46%) and Paracoccus aerius 011410T (97.58%). The average nucleotide identity values between M09T and P. everestensis S8-55T, P. aerius 011410T, Paracoccus marinaquae X HP0099T and Paracoccus fontiphilus MVW-1T were 95.56, 84.51, 79.83 and 83.68%, respectively. The digital DNA-DNA hybridisation values between between M09T and P. everestensis S8-55T, P. aerius 011410T, P. marinaquae X HP0099T and P. fontiphilus MVW-1T were 56.40, 29.30, 21.60 and 28.60%, respectively. The major fatty acids identified were C10 : 0 3-OH (51.8%) and C18 : 1ω7c (35.5%). The major respiratory quinone was Q-10, with Q-8 present as a minor component. Polar lipids were mainly comprised of diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylcholine (PC), and phosphatidylethanolamine (PE). Genome sequencing revealed that the strain has a DNA G+C content of 64.31 mol%. On the basis of this comprehensive taxonomic characterisation data, M09T represents a novel species within the genus Paracoccus and has been named Paracoccus actinidiae sp. nov. The type strain is designated as M09T (=GDMCC 1.4157T=KCTC 8143T).

Genomic Functional Analysis of Novel Radiation-Resistant Species of Knollia sp. nov. S7-12T from the North Slope of Mount Everest

Radiation protection is an important field of study, as it relates to human health and environmental safety. Radiation-resistance mechanisms in extremophiles are a research hotspot, as this knowledge has great application value in bioremediation and development of anti-radiation drugs. Mount Everest, an extreme environment of high radiation exposure, harbors many bacterial strains resistant to radiation. However, owing to the difficulties in studying them because of the extreme terrain, many remain unexplored. In this study, a novel species (herein, S7-12T) was isolated from the moraine of Mount Everest, and its morphology and functional and genomic characteristics were analyzed. The strain S7-12T is white in color, smooth and rounded, non-spore-forming, and non-motile and can survive at a UV intensity of 1000 J/m2, showing that it is twice as resistant to radiation as Deinococcus radiodurans. Radiation-resistance genes, including IbpA and those from the rec and CspA gene families, were identified. The polyphasic taxonomic approach revealed that the strain S7-12T (=KCTC 59114T =GDMCC 1.3458T) is a new species of the genus Knoellia and is thus proposed to be named glaciei. The in-depth study of the genome of strain S7-12T will enable us to gain further insights into its potential use in radiation resistance. Understanding how microorganisms resist radiation damage could reveal potential biomarkers and therapeutic targets, leading to the discovery of potent anti-radiation compounds, thereby improving human resistance to the threat of radiation.

Purification and Characterization of a Novel Fibrinolytic Enzyme from Marine Bacterium Bacillus sp. S-3685 Isolated from the South China Sea

A novel fibrinolytic enzyme, BSFE1, was isolated from the marine bacterium Bacillus sp. S-3685 (GenBank No.: KJ023685) found in the South China Sea. This enzyme, with a molecular weight of approximately 42 kDa and a specific activity of 736.4 U/mg, exhibited its highest activity at 37 °C in a phosphate buffer at pH 8.0. The fibrinolytic enzyme remained stable over a pH range of 7.5 to 10.0 and retained about 76% of its activity after being incubated at 37 °C for 2 h. The Km and Vmax values of the enzyme at 37 °C were determined to be 2.1 μM and 49.0 μmol min-1 mg-1, respectively. The fibrinolytic activity of BSFE1 was enhanced by Na+, Ba2+, K+, Co2+, Mn2+, Al3+, and Cu2+, while it was inhibited by Fe3+, Ca2+, Mg2+, Zn2+, and Fe2+. These findings indicate that the fibrinolytic enzyme isolated in this study exhibits a strong affinity for fibrin. Moreover, the enzyme we have purified demonstrates thrombolytic enzymatic activity. These characteristics make BSFE1 a promising candidate for thrombolytic therapy. In conclusion, the results obtained from this study suggest that our work holds potential in the development of agents for thrombolytic treatment.

Meta-analysis of biodynamic (BD) preparations reveal the bacterial population involved in improving soil health, crop yield and quality

BACKGROUND

Bacterial community found in biodynamic preparations (BD500-BD507) can help improve soil health, plant development, yield, and quality. The current work describes a metagenomic investigation of these preparations to identify the bacterial communities along with the functional diversity present within them.

RESULTS

Metagenome sequencing was performed using the Illumina MiSeq platform, which employs next-generation sequencing (NGS) technology, to provide an understanding of the bacterial communities and their functional diversity in BD preparations. NGS data of BD preparations revealed that maximum operational taxonomic units (OTUs) of the phylum Proteobacteria were present in BD506 (23429) followed by BD505 (22712) and BD501 (21591), respectively. Moreover, unclassified phylum (16657) and genus (16657) were also highest in BD506. Maximum alpha diversity was reported in BD501 (1095 OTU) and minimum in BD507 (257 OTU). Further, the OTUs for five major metabolic functional groups viz carbohydrate metabolism, xenobiotic degradation, membrane transport functions, energy metabolism, and enzyme activities were abundant in BD506 and BD501.

CONCLUSION

The bacterial communities in BD506 and BD501 are found to be unique and rare; they belong to functional categories that are involved in enzyme activity, membrane transport, xenobiotic degradation, and carbohydrate metabolism. These preparations might therefore be thought to be more effective. The investigation also found a highly varied population of bacteria, which could explain why BD preparations work well in the field. In view of this, the BD preparations may be utilized for unexploited bacterial communities for sustainable agriculture production.

A novel UV-resistant bacterium Sphingomonas endolithica sp. nov., and genomic analysis, isolated from the north slope of Mount Everest

Gram-stain-negative, aerobic, rod-shaped, non-motile bacterium strain ZFBP2030T was isolated from a rock on the North slope of Mount Everest. This strain contained a unique ubiquinone-10 (Q-10) as a predominant respiratory quinone. Among the tested fatty acids, the strain contained summed feature 8, C14:0 2OH, and C16:0, as major cellular fatty acids. The polar lipid profile contained phosphatidyl glycerol, phosphatidyl ethanolamine, three unidentified phospholipids, two unidentified aminolipids, and six unidentified lipids. The cell-wall peptidoglycan was a meso-diaminopimelic acid, and cell-wall sugars were ribose and galactose. Phylogenetic analyses based on 16S rRNA gene sequence revealed that strain ZFBP2030T was a member of the genus Sphingomonas, exhibiting high sequence similarity to the 16S rRNA gene sequences of Sphingomonas aliaeris DH-S5T (97.9%), Sphingomonas alpina DSM 22537T (97.3%) and Sphingomonas hylomeconis CCTCC AB 2013304T (97.0%). The 16S rRNA gene sequence similarity between ZFBP2030T and other typical strains was less than 97.0%. The average amino acid identity values, average nucleotide identity, and digital DNA-DNA hybridization values between strain ZFBP2030T and its highest sequence similarity strains were 56.9-79.9%, 65.1-82.2%, and 19.3-25.8%, respectively. The whole-genome size of the novel strain ZFBP2030T was 4.1 Mbp, annotated with 3838 protein-coding genes and 54 RNA genes. Moreover, DNA G + C content was 64.7 mol%. Stress-related functions predicted in the subsystem classification of the strain ZFBP2030T genome included osmotic, oxidative, cold/heat shock, detoxification, and periplasmic stress responses. The overall results of this study clearly showed that strain ZFBP2030T is a novel species of the genus Sphingomonas, for which the name Sphingomonas endolithica sp. nov. is proposed. The type of strain is ZFBP2030T (= EE 013T = GDMCC 1.3123T = JCM 35386T).

Building the taxonomic profile of the Riniaie Marwah hot spring of Kishtwar in Jammu and Kashmir: the first high-throughput sequencing-based metagenome study

Background and Objectives

Rinaie Marwah hot spring Kishtwar (RMHSK) is one of the geothermal springs located at 33°51'51″N 75°32'07″E with an elevation of 2134 meters above sea level in Jammu and Kashmir, India. We aimed to study the microbial diversity of this geothermal spring using metagenomics.

Materials and Methods

In the present study, physiochemical parameters including temperature (65-75°C), pH (6. 9-8. 8), hardness (250 ppm), and mineral content was measured along with the microbial diversity using Illumina MiSeq metagenome-based 16s amplicon sequencing (V3-V4). The sequence reads were classified taxonomically into 31 phyla, 71 classes, 152 orders, 256 families, 410 genus, and 665 species. QIIME 2 (Quantitative Insights into Microbial Ecology), an extensible, powerful, and decentralized analytical tool, was used for taxonomic analysis.

Results

Bacteroidota (32. 57%) was the dominant phylum, Bacteroidia (32. 51%) the dominant class, Bacteroidales (16. 6%) the dominant order, and Lentimicrobiaceae (14. 23%) was the dominant family per the abundance analysis. Shannon (2. 28) and Chao 1 (87. 0) diversity indices support the existence of higher microbial diversity in RMHSK (50717 OTUs).

Conclusion

The microbial diversity of RMHSK is reported for the first time through a metagenomic study. Identification of microorganisms with characteristics that are relevant to industries.

Ecology and resistance to UV light and antibiotics of microbial communities on UV cabins in the dermatology service of a Spanish hospital

Microorganisms colonize all possible ecological habitats, including those subjected to harsh stressors such as UV radiation. Hospitals, in particular the UV cabins used in phototherapy units, constitute an environment in which microbes are intermittently subjected to UV irradiation. This selective pressure, in addition to the frequent use of antibiotics by patients, may represent a threat in the context of the increasing problem of antimicrobial resistance. In this work, a collection of microorganisms has been established in order to study the microbiota associated to the inner and outer surfaces of UV cabins and to assess their resistance to UV light and the antibiotics frequently used in the Dermatology Service of a Spanish hospital. Our results show that UV cabins harbor a relatively diverse biocenosis dominated by typically UV-resistant microorganisms commonly found in sun-irradiated environments, such as Kocuria, Micrococcus or Deinococcus spp., but also clinically relevant taxa, such as Staphylococcus or Pseudomonas spp. The UV-radiation assays revealed that, although some isolates displayed some resistance, UV is not a major factor shaping the biocenosis living on the cabins, since a similar pool of resistant microorganisms was identified on the external surface of the cabins. Interestingly, some Staphylococcus spp. displayed resistance to one or more antibiotics, although the hospital reported no cases of antibiotic-resistance infections of the patients using the cabins. Finally, no association between UV and antibiotic resistances was found.

Gillisia lutea sp. nov., isolated from marine aluminium residues from the Mediterranean sea

A novel Gram-reaction-negative, facultatively anaerobic, rod-shaped, non-motile, non-spore forming, orange-pigmented bacterium identified as M10.2AT, was isolated from marine residues submerged on the Malva-rosa beach (València, Spain), on the western coast of the Mediterranean Sea. This strain was catalase-positive and oxidase-negative and grew under mesophilic, neutrophilic and halophilic conditions. With respect to the 16S rRNA gene sequences, M10.2AT showed similarities with Gillisia mitskevichiae DSM 19839T and Gillisia hiemivida IC154T (97.57 and 97.50 % gene sequence similarity, respectively). The genome of M10.2AT was sequenced and has been deposited in the DDBJ/ENA/GenBank databases under the accession code JAKGTH000000000. The genomic DNA G+C content was 36.13 %. Its adscription to a novel species of the genus Gillisia was confirmed by the genomic indexes average nucleotide identity by blast (ANIb) and digital DNA-DNA hybridisation (dDDH). The major fatty acids were iso-C15 : 0, iso-C15 : 1G, iso-C16 : 0 3-OH, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c). According to the results of this polyphasic study, strain M10.2AT represents a novel species of the genus Gillisia, for which name Gillisia lutea sp. nov. (type strain M10.2AT = CECT 30308T = DSM 112385T) is proposed.

Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles

More than 20,000 species of prokaryotes (less than 1% of the estimated number of Earth's microbial species) have been described thus far. However, the vast majority of microbes that inhabit extreme environments remain uncultured and this group is termed "microbial dark matter." Little is known regarding the ecological functions and biotechnological potential of these underexplored extremophiles, thus representing a vast untapped and uncharacterized biological resource. Advances in microbial cultivation approaches are key for a detailed and comprehensive characterization of the roles of these microbes in shaping the environment and, ultimately, for their biotechnological exploitation, such as for extremophile-derived bioproducts (extremozymes, secondary metabolites, CRISPR Cas systems, and pigments, among others), astrobiology, and space exploration. Additional efforts to enhance culturable diversity are required due to the challenges imposed by extreme culturing and plating conditions. In this review, we summarize methods and technologies used to recover the microbial diversity of extreme environments, while discussing the advantages and disadvantages associated with each of these approaches. Additionally, this review describes alternative culturing strategies to retrieve novel taxa with their unknown genes, metabolisms, and ecological roles, with the ultimate goal of increasing the yields of more efficient bio-based products. This review thus summarizes the strategies used to unveil the hidden diversity of the microbiome of extreme environments and discusses the directions for future studies of microbial dark matter and its potential applications in biotechnology and astrobiology.

Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons

In terms of the number and diversity of living units, the prokaryotic empire is the most represented form of life on Earth, and yet it is still to a significant degree shrouded in darkness. This microbial "dark matter" hides a great deal of potential in terms of phylogenetically or metabolically diverse microorganisms, and thus it is important to acquire them in pure culture. However, do we know what microorganisms really need for their growth, and what the obstacles are to the cultivation of previously unidentified taxa? Here we review common and sometimes unexpected requirements of environmental microorganisms, especially soil-harbored bacteria, needed for their replication and cultivation. These requirements include resuscitation stimuli, physical and chemical factors aiding cultivation, growth factors, and co-cultivation in a laboratory and natural microbial neighborhood.

Red Sea Atlas of Coral-Associated Bacteria Highlights Common Microbiome Members and Their Distribution across Environmental Gradients-A Systematic Review

The Red Sea is a suitable model for studying coral reefs under climate change due to its strong environmental gradient that provides a window into future global warming scenarios. For instance, corals in the southern Red Sea thrive at temperatures predicted to occur at the end of the century in other biogeographic regions. Corals in the Red Sea thrive under contrasting thermal and environmental regimes along their latitudinal gradient. Because microbial communities associated with corals contribute to host physiology, we conducted a systematic review of the known diversity of Red Sea coral-associated bacteria, considering geographic location and host species. Our assessment comprises 54 studies of 67 coral host species employing cultivation-dependent and cultivation-independent techniques. Most studies have been conducted in the central and northern Red Sea, while the southern and western regions remain largely unexplored. Our data also show that, despite the high diversity of corals in the Red Sea, the most studied corals were Pocillopora verrucosa, Dipsastraea spp., Pleuractis granulosa, and Stylophora pistillata. Microbial diversity was dominated by bacteria from the class Gammaproteobacteria, while the most frequently occurring bacterial families included Rhodobacteraceae and Vibrionaceae. We also identified bacterial families exclusively associated with each of the studied coral orders: Scleractinia (n = 125), Alcyonacea (n = 7), and Capitata (n = 2). This review encompasses 20 years of research in the Red Sea, providing a baseline compendium for coral-associated bacterial diversity.

Coupling of metataxonomics and culturing improves bacterial diversity characterization and identifies a novel Rhizorhapis sp. with metal resistance potential in a multi-contaminated waste sediment

Long-term contaminated environments have been recognized as potential hotspots for bacterial discovery in taxonomic and functional terms for bioremediation purposes. Here, bacterial diversity in waste sediment collected from a former industrial dumpsite and contaminated with petroleum hydrocarbon and heavy metals was investigated through the parallel application of culture-independent (16S rRNA gene amplicon sequencing) and -dependent (plate culturing followed by colony picking and identification of isolates by 16S rRNA gene Sanger sequencing) approaches. The bacterial diversities retrieved by both approaches greatly differed. Bacteroidetes and Proteobacteria were dominant in the culture-independent community, while Firmicutes and Actinobacteria were the main culturable groups. Only 2.7% of OTUs (operational taxonomic units) in the culture-independent dataset were cultured. Most of the culturable OTUs were absent or in very low abundances in the culture-independent dataset, revealing that culturing is a useful tool to study the rare bacterial biosphere. One culturable OTUs (comprising only the isolate SPR117) was identified as a potential new species in the genus Rhizorhapis (class Alphaproteobacteria) and was selected for further characterization. Phytopathogenicity tests showed that Rhizorhapis sp. strain SPR117 (ATCC TSD-228) is not pathogenic to lettuce, despite the only described species in this genus, Rhizorhapis suberifaciens, is causal agent of the lettuce corky root disease. The genome of the strain SPR117 was sequenced, assembled in 256 contigs, with a length of 4,419,522 bp and a GC content of 59.9%, and its further annotation revealed the presence of genes related to the resistance to arsenic, copper, iron, and mercury, among other metals. Therefore, the coupling of metataxonomics and culturing is a useful tool to obtain not only an improved description of bacterial communities in contaminated environments, but also to isolate microorganisms with bioremediation potential.

Culturomics of Bacteria from Radon-Saturated Water of the World's Oldest Radium Mine

Balneotherapeutic water springs, such as those with thermal, saline, sulfur, or any other characteristics, have recently been the subject of phylogenetic studies with a closer focus on the description and/or isolation of phylogenetically novel or biotechnologically interesting microorganisms. Generally, however, most such microorganisms are rarely obtained in pure culture or are even, for now, unculturable under laboratory conditions. In this culture-dependent study of radioactive water springs of Jáchymov (Joachimstahl), Czech Republic, we investigated a combination of classical cultivation approaches with those imitating sampling source conditions. Using these environmentally relevant cultivation approaches, over 1,000 pure cultures were successfully isolated from 4 radioactive springs. Subsequent dereplication yielded 121 unique taxonomic units spanning 44 genera and 9 taxonomic classes, ~10% of which were identified as hitherto undescribed taxa. Genomes of the latter were sequenced and analyzed, with a special focus on endogenous defense systems to withstand oxidative stress and aid in radiotolerance. Due to their origin from radioactive waters, we determined the resistance of the isolates to oxidative stress. Most of the isolates were more resistant to menadione than the model strain Deinococcus radiodurans DSM 20539T. Moreover, isolates of the Deinococcacecae, Micrococcaceae, Bacillaceae, Moraxellaceae, and Pseudomonadaceae families even exhibited higher resistance in the presence of hydrogen peroxide. In summary, our culturomic analysis shows that subsurface water springs contain diverse bacterial populations, including as-yet-undescribed taxa and strains with promising biotechnological potential. Furthermore, this study suggests that environmentally relevant cultivation techniques increase the efficiency of cultivation, thus enhancing the chance of isolating hitherto uncultured microorganisms. IMPORTANCE The mine Svornost in Jáchymov (Joachimstahl), Czech Republic is a former silver-uranium mine and the world's first and for a long time only radium mine, nowadays the deepest mine devoted to the extraction of water which is saturated with radon and has therapeutic benefits given its chemical properties. This healing water, which is approximately 13 thousand years old, is used under medical supervision for the treatment of patients with neurological and rheumatic disorders. Our culturomic approach using low concentrations of growth substrates or the environmental matrix itself (i.e., water filtrate) in culturing media combined with prolonged cultivation time resulted in the isolation of a broad spectrum of microorganisms from 4 radioactive springs of Jáchymov which are phylogenetically novel and/or bear various adaptive or coping mechanisms to thrive under selective pressure and can thus provide a wide spectrum of capabilities potentially exploitable in diverse scientific, biotechnological, or medical disciplines.

Temporary Survival Increasing the Diversity of Culturable Heterotrophic Bacteria in the Newly Exposed Moraine at a Glacier Snout

Laohugou Glacier No. 12 is located on the northern slope of the western Qilian Mountains with a temperate continental wet climate and an extremely cold winter. Bacteria in a newly exposed moraine have to cope with various pressures owing to deglaciation at the glacier snout. However, limited information is available regarding the high diversity and temporary survival of culturable heterotrophic bacteria under various environmental stresses. To examine the tolerance of extremophiles against varying environmental conditions in a newly exposed moraine, we simulated environmental stress in bacterial cultures. The results showed that the isolated strains belonged to actinobacteria, Proteobacteria, Bacteroidetes, Deinococcus-Thermus, and Firmicutes. Actinobacteria was the most abundant phylum, followed by Proteobacteria, at both high and low temperatures. Pseudarthrobacter was the most abundant genus, accounting for 14.2% of the total isolates. Although several microorganisms grew at 10 °C, the proportion of microorganisms that grew at 25 °C was substantially higher. In particular, 50% of all bacterial isolates grew only at a high temperature (HT), whereas 21.4% of the isolates grew at a low temperature (LT), and 38.6% of the isolates grew at both HT and LT. In addition, many radiation-resistant extremophiles were identified, which adapted to both cold and oxidative conditions. The nearest neighbors of approximately >90% of bacteria belonged to a nonglacial environment, such as oil-contaminated soil, rocks, and black sand, instead of glacial niches. This study provides insights into the ecological traits, stress responses, and temporary survival of culturable heterotrophic bacteria in a newly exposed moraine with variable environmental conditions and the relationship of these communities with the non-glacial environment. This study may help to understand the evolution, competition, and selective growth of bacteria in the transition regions between glaciers and retreats in the context of glacier melting and retreat owing to global warming.

Genomic Insights into the Radiation-Resistant Capability of Sphingomonas qomolangmaensis S5-59T and Sphingomonas glaciei S8-45T, Two Novel Bacteria from the North Slope of Mount Everest

Mount Everest provides natural advantages to finding radiation-resistant extremophiles that are functionally mechanistic and possess commercial significance. (1) Background: Two bacterial strains, designated S5-59T and S8-45T, were isolated from moraine samples collected from the north slope of Mount Everest at altitudes of 5700m and 5100m above sea level. (2) Methods: The present study investigated the polyphasic features and genomic characteristics of S5-59^T and S8-45^T. (3) Results: The major fatty acids and the predominant respiratory menaquinone of S5-59^T and S8-45^T were summed as feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c) and ubiquinone-10 (Q-10). Phylogenetic analyses based on 16S rRNA sequences and average nucleotide identity values among these two strains and their reference type strains were below the species demarcation thresholds of 98.65% and 95%. Strains S5-59^T and S8-45^T harbored great radiation resistance. The genomic analyses showed that DNA damage repair genes, such as mutL, mutS, radA, radC, recF, recN, etc., were present in the S5-59^T and S8-45^T strains. Additionally, strain S5-59^T possessed more genes related to DNA protection proteins. The pan-genome analysis and horizontal gene transfers revealed that strains of Sphingomonas had a consistently homologous genetic evolutionary radiation resistance. Moreover, enzymatic antioxidative proteins also served critical roles in converting ROS into harmless molecules that resulted in resistance to radiation. Further, pigments and carotenoids such as zeaxanthin and alkylresorcinols of the non-enzymatic antioxidative system were also predicted to protect them from radiation. (4) Conclusions: Type strains S5-59^T (=JCM 35564T =GDMCC 1.3193T) and S8-45^T (=JCM 34749T =GDMCC 1.2715T) represent two novel species of the genus Sphingomonas with the proposed name Sphingomonas qomolangmaensis sp. nov. and Sphingomonas glaciei sp. nov. The type strains, S5-59^T and S8-45^T, were assessed in a deeply genomic study of their radiation-resistant mechanisms and this thus resulted in a further understanding of their greater potential application for the development of anti-radiation protective drugs.

Paracoccus everestensis sp. nov., a novel bacterium with great antioxidant capacity isolated from the north slope of Mount Everest

A bacterial strain, designated S8-55T, was isolated from moraine samples collected from the north slope of Mount Everest at an altitude of 5 500 m above sea level. 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 Paracoccus , and explore the antioxidant capacity of strain S8-55T. The polyphasic study confirmed the affiliation of strain S8-55T with the genus Paracoccus . Strain S8-55T was aerobic, Gram-negative and oxidase- and catalase positive. Cells were orange-pigmented, ellipsoid and had no spore formation, no flagella and no motility. Strain S8-55T grow at 10–37 °C, pH 7–11 and without NaCl. Ubiquinone 10 was its predominant respiratory menaquinone. The polar lipids of strain S8-55T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified phospholipid, an unidentified aminolipid and three unidentified lipids. Its major fatty acids were summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c). The G+C content was 64.3 mol%. The phylogenetic analysis based on the 16S rRNA sequence showed that strain S8-55T was closely related to Paracoccus angustae E6T (97.9 %), Paracoccus aerius 011410T (97.9 %) and Paracoccus hibisci THG-T2.8T (97.8 %). The average nucleotide identity values among strain S8-55T and P. angustae CCTCC AB 2015056T, P. aerius KCTC 42845T and P. hibisci CCTCC AB 2016181T were 84.1, 84.5 and 76.3 %, respectively. The genome of strain S8-55T contained antioxidant genes such as oxyR, recD, katE, recD and rpoH. Based on its morphological, physiological and chemical taxonomic characteristics, strain S8-55T (=JCM 35 227T=GDMCC 1.3026T) should be classified as a novel species of the genus Paracoccus with the proposed name Paracoccus everestensis sp. nov.

Sphingomonas radiodurans sp. nov., a novel radiation-resistant bacterium isolated from the north slope of Mount Everest

A bacterial strain, designated S9-5T, was isolated from moraine samples collected from the north slope of Mount Everest at an altitude of 5 500 m above sea level. A polyphasic study confirmed the affiliation of the strain with the genus Sphingomonas . Strain S9-5T was an aerobic, Gram-stain-negative, non-spore-forming, non-motile and rod-shaped bacterium that could grow at 10–40 °C, pH 5–8 and with 0–9 % (w/v) NaCl. Q-10 was its predominant respiratory menaquinone. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminophospholipid and eight unidentified lipids comprised the polar lipids of strain S9-5T. Its major fatty acids were summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c) and C16 : 0. The G+C content was 65.75mol%. Phylogenetic analysis based on 16S rRNA sequences showed that strain S9-5T was phylogenetically closely related to Sphingomonas panaciterrae DCY91T (98.17 %), Sphingomonas olei K-1-16T (98.11 %) and Sphingomonas mucosissima DSM 17494T (97.39 %). The average nucleotide identity values among strain S9-5T and Sphingomonas panaciterrae DCY91T, Sphingomonas olei K-1-16T and Sphingomonas mucosissima DSM 17494T were 78.82, 78.87 and 78.29 %, respectively. Based on the morphological, physiological and chemotaxonomic data, strain S9-5T (=JCM 34750T=GDMCC 1.2714T) should represent a novel species of the genus Sphingomonas , for which we propose the name Sphingomonas radiodurans sp. nov.

High Proportions of Radiation-Resistant Strains in Culturable Bacteria from the Taklimakan Desert

Simple Summary

Radiation-resistant extremophiles have frequently been found in the Taklimakan Desert, which is known for its harsh conditions. However, there is no systemic study investigating the diversity and proportion of radiation-resistant strains among culturable bacteria. The results of this study revealed the distribution of culturable bacteria in the Taklimakan Desert and indicated high proportions of radiation-resistant strains in the culturable bacteria. The study helps to better understand the ecological origin of radio-resistance and to quantitatively describe the desert as a common habitat for radiation-resistant extremophiles.

Abstract

The Taklimakan Desert located in China is the second-largest shifting sand desert in the world and is known for its harsh conditions. Types of γ-rays or UV radiation-resistant bacterial strains have been isolated from this desert. However, there is no information regarding the proportions of the radiation-resistant strains in the total culturable microbes. We isolated 352 bacterial strains from nine sites across the Taklimakan Desert from north to south. They belong to Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. The phylum Actinobacteria was the most predominant in abundance and Firmicutes had the highest species richness. Bacteroidetes had the lowest abundance and was found in four sites only, while the other three phyla were found in every site but with different distribution profiles. After irradiating with 1000 J/m² and 6000 J/m² UV-C, the strains with survival rates higher than 10% occupied 72.3% and 36.9% of all culturable bacteria, respectively. The members from Proteobacteria had the highest proportions, with survival rates higher than 10%. After radiation with 10 kGy γ-rays, Kocuria sp. TKL1057 and Planococcus sp. TKL1152 showed higher radiation-resistant capabilities than Deinococcus radiodurans R1. Besides obtaining several radiation-resistant extremophiles, this study measured the proportions of the radiation-resistant strains in the total culturable microbes for the first time. This study may help to better understand the origin of radioresistance, especially by quantitatively comparing proportions of radiation-resistant extremophiles from different environments in the future.

Sagittula salina sp. nov., isolated from marine waste

A novel Gram-stain-negative, non-motile, halophilic bacterium designated strain M10.9X^T was isolated from the inner sediment of an aluminium can collected from the Mediterranean Sea (València, Spain). Cells of strain M10.9X^T were rod-shaped and occasionally formed aggregates. The strain was oxidase-negative and catalase-positive, and showed a slightly psychrophilic, neutrophilic and slightly halophilic metabolism. The phylogenetic analyses revealed that strain M10.9X^T was closely related to Sagittula stellata E-37^T and Sagittula marina F028-2^T. The genomic G+C content of strain M10.9X^T was 65.2 mol%. The average nucleotide identity and digital DNA–DNA hybridization values were 76.6 and 20.9 %, respectively, confirming its adscription to a new species within the genus Sagittula. The major cellular fatty acids were C_18 : 1 ω7c/C_18 : 1 ω6c and C_16 : 0. The polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid, an unidentified glycolipid, an unidentified phospholipid and an unidentified lipid. According to the resuts of a polyphasic study, strain M10.9X^T represents a novel species of the genus Sagittula for which the name Sagittula salina sp. nov. (type strain M10.9X^T=DSM 112301^T=CECT 30307^T) is proposed.

Diversity and bioprospecting for industrial hydrolytic enzymes of microbial communities isolated from deserted areas of south-east Morocco

The current study aimed to analyze bacterial communities' diversity and abundance in three different deserted areas (Merzouga, Mhamid Elghizlane, and Erg lihoud) located in Moroccan Sahara, as well as to investigate osmotolerant microorganisms producing hydrolytic enzymes. The isolates were taxonomically affiliated using 16S rRNA gene sequencing. Four different hydrolase activities (amylase, lipase, cellulase, and protease) and osmotic stress tolerance were evaluated. The phylogenetic analysis of 364 screened isolates belonged to three phyla (Firmicutes 73%, Proteobacteria 26% and Actinobacteria 1%) and 18 different genera, from Bacillus, Ornithinibacillus, Paenibacillus, Geobacillus, Pseudomonas, Acinetobacter, Agrobacterium, Arthrobacter, Paenarthrobacter, Enterobacter, Staphylococcus, Erwinia, Herbasprillum, Ocuria, Massilia, Planomicrobium, Hodococcus, and Stenotrophomonas. The results detected a high proportion of osmotolerant and enzymes producing bacteria, many isolates can tolerate up to 55 °C (40%, 28%, and 30% in Merzouga, Mhamid Elghizlane, and Erg lihoudi, respectively). Meanwhile, the salinity tolerance reached 12% in some isolates with different proportions in each site, 29% in Merzouga, 24% in Mhamid Elghizlane, and 9% in Erg lihoudi. Furthermore, the enzymatic tests showed the presence of an amylolytic, lipolytic, cellulolytic, proteolytic activities in 20%, 31%, 63% and 72% of total strains, respectively. As a result, the present study is thus a preliminary yet critical step towards identifying the best bacterial candidates for further biotechnological applications.

A Round Trip to the Desert: In situ Nanopore Sequencing Informs Targeted Bioprospecting

Bioprospecting expeditions are often performed in remote locations, in order to access previously unexplored samples. Nevertheless, the actual potential of those samples is only assessed once scientists are back in the laboratory, where a time-consuming screening must take place. This work evaluates the suitability of using Nanopore sequencing during a journey to the Tabernas Desert (Spain) for forecasting the potential of specific samples in terms of bacterial diversity and prevalence of radiation- and desiccation-resistant taxa, which were the target of the bioprospecting activities. Samples collected during the first day were analyzed through 16S rRNA gene sequencing using a mobile laboratory. Results enabled the identification of locations showing the greatest and the least potential, and a second, informed sampling was performed focusing on those sites. After finishing the expedition, a culture collection of 166 strains belonging to 50 different genera was established. Overall, Nanopore and culturing data correlated well, since samples holding a greater potential at the microbiome level also yielded a more interesting set of microbial isolates, whereas samples showing less biodiversity resulted in a reduced (and redundant) set of culturable bacteria. Thus, we anticipate that portable sequencers hold potential as key, easy-to-use tools for in situ-informed bioprospecting strategies.

The Isolation of Culturable Bacteria in Ixodes ricinus Ticks of a Belgian Peri-Urban Forest Uncovers Opportunistic Bacteria Potentially Important for Public Health

Most bacteria found in ticks are not pathogenic to humans but coexist as endosymbionts and may have effects on tick fitness and pathogen transmission. In this study, we cultured and isolated 78 bacteria from 954 Ixodes ricinus ticks collected in 7 sites of a Belgian peri-urban forest. Most isolated species were non-pathogenic environmental microorganisms, and were from the Firmicutes (69.23%), Actinobacteria (17.95%) and Proteobacteria (3.84%) phyla. One bacterium isolate was particularly noteworthy, Cedecea davisae, a rare opportunistic bacterium, naturally resistant to various antibiotics. It has never been isolated from ticks before and this isolated strain was resistant to ampicillin, cefoxitin and colistin. Although cultivable bacteria do not represent the complete tick microbiota, the sites presented variable bacterial compositions and diversities. This study is a first attempt to describe the culturable microbiota of ticks collected in Belgium. Further collections and analyses of ticks of different species, from various areas and using other bacterial identification methods would strengthen these results. However, they highlight the importance of ticks as potential sentinel for opportunistic bacteria of public health importance.

Needles in haystacks: reevaluating old paradigms for the discovery of bacterial secondary metabolites

Covering: up to 2021Natural products research is in the midst of a renaissance ushered in by a modern understanding of microbiology and the technological explosions of genomics and metabolomics. As the exploration of uncharted chemical space expands into high-throughput discovery campaigns, it has become increasingly clear how design elements influence success: (bio)geography, habitat, community dynamics, culturing/induction methods, screening methods, dereplication, and more. We explore critical considerations and assumptions in natural products discovery. We revisit previous estimates of chemical rediscovery and discuss their relatedness to study design and producer taxonomy. Through frequency analyses of biosynthetic gene clusters in publicly available genomic data, we highlight phylogenetic biases that influence rediscovery rates. Through selected examples of how study design at each level determines discovery outcomes, we discuss the challenges and opportunities for the future of high-throughput natural product discovery.

Using Oxidative Electrodes to Enrich Novel Members in the Desulfobulbaceae Family from Intertidal Sediments

Members in the family of Desulfobulbaceae may be influential in various anaerobic microbial communities, including those in anoxic aquatic sediments and water columns, and within wastewater treatment facilities and bioelectrochemical systems (BESs) such as microbial fuel cells (MFCs). However, the diversity and roles of the Desulfobulbaceae in these communities have received little attention, and large portions of this family remain uncultured. Here we expand on findings from an earlier study (Li, Reimers, and Alleau, 2020) to more fully characterize Desulfobulbaceae that became prevalent in biofilms on oxidative electrodes of bioelectrochemical reactors. After incubations, DNA extraction, microbial community analyses, and microscopic examination, we found that a group of uncultured Desulfobulbaceae were greatly enriched on electrode surfaces. These Desulfobulbaceae appeared to form filaments with morphological features ascribed to cable bacteria, but the majority were taxonomically distinct from recognized cable bacteria genera. Thus, the present study provides new information about a group of Desulfobulbaceae that can exhibit filamentous morphologies and respire on the oxidative electrodes. While the phylogeny of cable bacteria is still being defined and updated, further enriching these members can contribute to the overall understanding of cable bacteria and may also lead to identification of successful isolation strategies.

Hydrocarbon-Contaminated Sites: Is There Something More Than Exophiala xenobiotica? New Insights into Black Fungal Diversity Using the Long Cold Incubation Method

Human-made hydrocarbon-rich environments are important reservoirs of microorganisms with specific degrading abilities and pathogenic potential. In particular, black fungi are of great interest, but their presence in the environment is frequently underestimated because they are difficult to isolate. In the frame of a biodiversity study from fuel-contaminated sites involving 30 diesel car tanks and 112 fuel pump dispensers (52 diesel and 60 gasoline, respectively), a total of 181 black fungal strains were isolated. The long cold incubation (LCI) of water-suspended samples, followed by plating on Dichloran Rose Bengal Chloramphenicol Agar (DRBC), gave isolation yields up to six times (6.6) higher than those of direct plating on DRBC, and those of enrichment with a phenolic mix. The sequencing of ITS and LSU-rDNA confirmed the dominance of potentially pathogenic fungi from the family Herpotrichiellaceae and Exophiala xenobiotica. Moreover, other opportunistic species were found, including E. opportunistica, E. oligosperma, E. phaeomuriformis, and Rhinocladiella similis. The recurrent presence of E. crusticola, Knufia epidermidis, Aureobasidium melanogenum, Cladosporium spp., and Scolecobasidium spp. was also recorded. Interestingly, 12% of total isolates, corresponding to 50% of taxa found (16/32), represent new species. All the novel taxa in this study were isolated by LCI. These findings suggest that black fungal diversity in hydrocarbon-rich niches remains largely unexplored and that LCI can be an efficient tool for further investigations.

Belnapia mucosa sp. nov. and Belnapia arida sp. nov., isolated from desert biocrust

Two novel Gram-staining-negative, aerobic, cocci-shaped, non-motile, non-spore forming, pink-pigmented bacteria designated strains T6^T and T18^T, were isolated from a biocrust (biological soil crust) sample from the vicinity of the Tabernas Desert (Spain). Both strains were catalase-positive and oxidase-negative, and grew under mesophilic, neutrophilic and non-halophilic conditions. According to the 16S rRNA gene sequences, strains T6^T and T18^T showed similarities with Belnapia rosea CGMCC 1.10758^T and Belnapia moabensis CP2C^T (98.11 and 98.55% gene sequence similarity, respectively). The DNA G+C content was 69.80 and 68.96% for strains T6^T and T18^T, respectively; the average nucleotide identity by blast (ANIb) and digital DNA–DNA hybridization (dDDH) values confirmed their adscription to two novel species within the genus Belnapia. The predominant fatty acids were summed feature 8 (C_{18 : 1}ω7c/C_{18 : 1}ω6c), C_{16 : 0}, C_{18 : 1} 2-OH and summed feature 3 (C_{16 : 1}ω7c/C_{16 : 1}ω6c). According to he results of the polyphasic study, strains T6^T and T18^T represent two novel species in the genus Belnapia (which currently includes only three species), for which names Belnapia mucosa sp. nov. (type strain T6^T = CECT 30228^T=DSM 112073^T) and Belnapia arida sp. nov. (type strain T18^T=CECT 30229^T=DSM 112074^T) are proposed, respectively.

Diversity and plant growth-promoting potential of (un)culturable bacteria in the Hedera helix phylloplane

Background

A diverse community of microbes naturally exists on the phylloplane, the surface of leaves. It is one of the most prevalent microbial habitats on earth and bacteria are the most abundant members, living in communities that are highly dynamic. Today, one of the key challenges for microbiologists is to develop strategies to culture the vast diversity of microorganisms that have been detected in metagenomic surveys.

Results

We isolated bacteria from the phylloplane of Hedera helix (common ivy), a widespread evergreen, using five growth media: Luria–Bertani (LB), LB01, yeast extract–mannitol (YMA), yeast extract–flour (YFlour), and YEx. We also included a comparison with the uncultured phylloplane, which we showed to be dominated by Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Inter-sample (beta) diversity shifted from LB and LB01 containing the highest amount of resources to YEx, YMA, and YFlour which are more selective. All growth media equally favoured Actinobacteria and Gammaproteobacteria, whereas Bacteroidetes could only be found on LB01, YEx, and YMA. LB and LB01 favoured Firmicutes and YFlour was most selective for Betaproteobacteria. At the genus level, LB favoured the growth of Bacillus and Stenotrophomonas, while YFlour was most selective for Burkholderia and Curtobacterium. The in vitro plant growth promotion (PGP) profile of 200 isolates obtained in this study indicates that previously uncultured bacteria from the phylloplane may have potential applications in phytoremediation and other plant-based biotechnologies.

Conclusions

This study gives first insights into the total bacterial community of the H. helix phylloplane, including an evaluation of its culturability using five different growth media. We further provide a collection of 200 bacterial isolates underrepresented in current databases, including the characterization of PGP profiles. Here we highlight the potential of simple strategies to obtain higher microbial diversity from environmental samples and the use of high-throughput sequencing to guide isolate selection from a variety of growth media.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02119-z.