Exploring untapped potential of Streptomyces spp. in Gurbantunggut Desert by use of highly selective culture strategy

Response of microbial diversity and function to the degradation of Barkol Saline Lake

Barkol Lake, a shrinking hypersaline lake situated in the northeast of Xinjiang, China, has experienced the exposure of its riverbed and the gradual drying up of its original sediment due to climate change and human activities, resulting in the formation of alkaline soils. These changes have correspondingly altered the physicochemical characteristics of the surrounding environment. Microorganisms play a crucial role, with special functioning involved in various nutrient cycling and energy transfer in saline lake environments. However, little is known about how the microbial community dynamics and metabolic functions in this shrinking saline lake relate to the degradation process. To address this knowledge gap, a cultivation-independent method of amplicon sequencing was used to identify and analyze the microbial community and its potential ecological functions in the sediment and degraded area. The microbial community diversity was found to be significantly lower in the degraded areas than in the sediment samples. The Pseudomonadota was dominant in Barkol Saline Lake. The abundance of Desulfobacterota and Bacillota in the degraded areas was lower than in the lake sediment, while Pseudomonadota, Acidobacteriota, and Actinobacteriota showed an opposite trend. The βNTI showed that microbial community assembly was primarily associated with deterministic processes in Barkol Saline Lake ecosystems and stochastic processes at the boundary between sediment and degraded areas. Functional predictions showed that sulfur metabolism, particularly sulfate respiration, was much higher in sediment samples than in the degraded areas. Overall, these findings provided a possible perspective for us to understand how microorganisms adapt to extreme environments and their role in saline lakes under environmental change.

Aridity drives the variability of desert soil microbiomes across north-western China

Dryland covers >35 % of the terrestrial surface and the global extent of dryland increases due to the forecasted increase in aridity driven by climate change. Due to the climate change-driven aridity ecosystems, deserts provide one of the most hostile environments for microbial life and survival. Therefore, a detailed study was carried out to explore the deserts with different aridity levels (exposed to severe climate change) influence on microbial (bacteria, fungi, and protist) diversity patterns, assembly processes, and co-occurrence. The results revealed that the aridity (semi-arid, arid, and hyper-arid) patterns caused distinct changes in environmental heterogeneity in desert ecosystems. Similarly, microbial diversities were also reduced with increasing the aridity pattern, and it was found that environmental heterogeneity is highly involved in affecting microbial diversities under different ecological niches. Interestingly, it was found that certain microbes, including bacterial (Firmicutes), fungal (Sordariomycetes), and protistan (Ciliophora) abundance increased with increasing aridity levels, indicating that these microbes might possess the capability to tolerate the environmental stress conditions. Moreover, microbial community turnover analysis revealed that bacterial diversities followed homogenous selection, whereas fungi and protists were mostly driven by the dispersal limitation pattern. Co-occurrence network analysis showed that hyper-arid and arid conditions tightened the bacterial and fungal communities and had more positive associations compared to protistan. In conclusion, multiple lines of evidence were provided to shed light on the habitat specialization impact on microbial (bacteria, fungi, and protists) communities and composition under different desert ecosystems.

Telluribacter roseus sp. nov., Isolated from the Kumtag Desert Soil

A pink-pigmented bacterium, designated as strain SYSU D00476T, was isolated from sandy soil collected from the Kumtag Desert in China. Colonies were opaque, smooth and of a slight convexity with a clearly defined border. Cells were rod-shaped, Gram-stain-negative, catalase- and oxidase-positive. Growth occurred at 4-45 ℃ (optimum at 28-30 ℃), pH 6.0-8.0 (optimum at 7.0), and with 0-3.0% NaCl (w/v, optimum at 0-2.0%). Major fatty acids (> 10%) were C16:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), iso-C17:0 3-OH and iso-C15:0. Polar lipids comprised of three unidentified polar aminolipids (ALs), two unidentified aminophosphoglycolipids (APLs), one unidentified glycolipid (GL) and three unidentified phospholipids (PLs). The predominant respiratory quinone was MK-7. The genomic DNA G + C content was 50.5%. The low digital DNA-DNA hybridization (dDDH, 27.4%) and average nucleotide identity (ANI, 85%) values between strain SYSU D00476T and Telluribacter humicola KCTC 42819T indicated that SYSU D00476T represent a distinct species. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SYSU D00476T belonged to the genus Telluribacter, showing 97.5% similarity with T. humicola KCTC 42819T. All these data support that strain SYSU D00476T represent a novel species of the genus Telluribacter within the family Spirosomataceae, named as Telluribacter roseus sp. nov. The type strain is SYSU D00476T (= KCTC 82285T = CGMCC 1.18647T = MCCC 1K04983T).

Danxiaibacter flavus gen. nov., sp. nov., a novel bacterium of the family Chitinophagaceae isolated from forest soil on Danxia Mountain

A Gram-stain-negative, aerobic, short rod-shaped, yellow bacterium, designated SYSU DXS3180T, was isolated from forest soil of Danxia Mountain in PR China. Growth occurred at 15-37 °C (optimum, 28-30 °C), pH 6.0-10.0 (optimum, pH 7.0-8.0) and with 0-2.0 % NaCl (optimum, 0-0.5 %, w/v). Strain SYSU DXS3180T was positive for hydrolysis of Tween 20, Tween 60, Tween 80 and starch, but negative for urease, H2S production, nitrate reduction, Tween 40 and gelatin. Phylogenetic analysis based on 16S rRNA gene and genome sequences showed that SYSU DXS3180T belonged to the family Chitinophagaceae. The closely related members were Foetidibacter luteolus YG09T (94.2 %), Limnovirga soli KCS-6T (93.9 %) and Filimonas endophytica SR 2-06T (93.7 %). The genome of strain SYSU DXS3180T was 7287640 bp with 5782 protein-coding genes, and the genomic DNA G+C content was 41.4 mol%. The main respiratory quinone was MK-7 and the major fatty acids (>10 %) were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. The major polar lipids consisted of phosphatidylethanolamine, two unidentified aminolipids and two unidentified polar lipids. Based on the phylogenetic, phenotypic and chemotaxonomic characteristics, strain SYSU DXS3180T is proposed to represent a novel species of a novel genus named Danxiaibacter flavus gen. nov., sp. nov., within the family Chitinophagaceae. The type strain is SYSU DXS3180T (=KCTC 92895T=GDMCC 1.3825 T).

Rufibacter roseolus sp. nov. and Rufibacter aurantiacus sp. nov., isolated from desert soil

Two novel bacterial strains, designated as SYSU D00344T and SYSU D00433T, were isolated from soil of Gurbantunggut Desert in Xinjiang, north-west PR China. Cells of both strains were Gram-stain-negative, aerobic, short-rod-shaped, catalase-positive and non-motile. Oxidase activities of SYSU D00344T and SYSU D00433T were negative and positive, respectively. Optimal growth occurred at 30 °C, with 0-0.5 % (w/v) NaCl and at pH 7.0. The results of phylogenetic analysis of 16S rRNA gene sequences indicated that they represented members of the genus Rufibacter and were closely related to Rufibacter hautae NBS58-1T. The results of phylogenomic analysis indicated that the two strains formed two independent and robust branches distinct from all reference type strains. The analyses of average nucleotide identity (ANI), digital DNA-DNA hybridisation (dDDH) values and 16S rRNA gene similarities between the two strains and their relatives further demonstrated that SYSU D00344T and SYSU D00433T represented two different novel genospecies. The polar lipids consisted of phosphatidylethanolamine, one unidentified glycolipid, two unidentified aminophospholipids, and two or four unidentified lipids. MK-7 was the only respiratory quinone. The major fatty acids (>10 %) for both strains were identified as iso-C15 : 0, anteiso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), as well as summed feature 4 (anteiso-C17 : 1B and/or iso-C17 : 1I) for SYSU D00344T and C16 : 1ω5c for SYSU D00433T. On the basis of the phylogenetic, phenotypic, chemotaxonomic and genotypic characteristics, we propose Rufibacter roseolus sp. nov. and Rufibacter aurantiacus sp. nov. as two novel species in the genus Rufibacter. The type strains are SYSU D00344T (=CGMCC 1.8625T=MCCC 1K04971T=KCTC 82274T) and SYSU D00433T (=CGMCC 1.8617T=MCCC 1K04982T=KCTC 82277T), respectively.

Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis

Deserts occupy one-third of the Earth's terrestrial surface and represent a potentially significant reservoir of microbial biodiversity, yet the majority of desert microorganisms remain uncharacterized and are seen as "microbial dark matter". Here, we introduce a multi-omics strategy, culturomics-based metagenomics (CBM) that integrates large-scale cultivation, full-length 16S rRNA gene amplicon, and shotgun metagenomic sequencing. The results showed that CBM captured a significant amount of taxonomic and functional diversity missed in direct sequencing by increasing the recovery of amplicon sequence variants (ASVs) and high/medium-quality metagenome-assembled genomes (MAGs). Importantly, CBM allowed the post hoc recovery of microbes of interest (e.g., novel or specific taxa), even those with extremely low abundance in the culture. Furthermore, strain-level analyses based on CBM and direct sequencing revealed that the desert soils harbored a considerable number of novel bacterial candidates (1941, 51.4%), of which 1095 (from CBM) were culturable. However, CBM would not exactly reflect the relative abundance of true microbial composition and functional pathways in the in situ environment, and its use coupled with direct metagenomic sequencing could provide greater insight into desert microbiomes. Overall, this study exemplifies the CBM strategy with high-resolution is an ideal way to deeply explore the untapped novel bacterial resources in desert soils, and substantially expands our knowledge on the microbial dark matter hidden in the vast expanse of deserts.

Cultivation strategies for prokaryotes from extreme environments

The great majority of microorganisms are as-yet-uncultivated, mostly found in extreme environments. High-throughput sequencing provides data-rich genomes from single-cell and metagenomic techniques, which has enabled researchers to obtain a glimpse of the unexpected genetic diversity of "microbial dark matter." However, cultivating microorganisms from extreme environments remains essential for dissecting and utilizing the functions of extremophiles. Here, we provide a straightforward protocol for efficiently isolating prokaryotic microorganisms from different extreme habitats (thermal, xeric, saline, alkaline, acidic, and cryogenic environments), which was established through previous successful work and our long-term experience in extremophile resource mining. We propose common processes for extremophile isolation at first and then summarize multiple cultivation strategies for recovering prokaryotic microorganisms from extreme environments and meanwhile provide specific isolation tips that are always overlooked but important. Furthermore, we propose the use of multi-omics-guided microbial cultivation approaches for culturing these as-yet-uncultivated microorganisms and two examples are provided to introduce how these approaches work. In summary, the protocol allows researchers to significantly improve the isolation efficiency of pure cultures and novel taxa, which therefore paves the way for the protection and utilization of microbial resources from extreme environments.

Rubellimicrobium arenae sp. nov., isolated from desert soil

Two Gram-stain-negative strains, designated as SYSU D00286^T and SYSU D00782, were isolated from a sand sample collected from the Kumtag Desert in Xinjiang, north-west China. Cells were aerobic, non-motile and positive for both oxidase and catalase. Growth occurred at 4-37 °C (optimum, 28-30 °C), pH 6.0-7.0 (optimum, pH 7.0) and NaCl concentration of 0-1.5 % (w/v; optimum, 0%). Growth was observed on Reasoner's 2A agar and nutrient agar, but not on Luria-Bertani agar and trypticase soy agar. The polar lipids were identified as diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, three unidentified aminolipids, one unidentified glycolipid and two unidentified phospholipids. The major respiratory quinone was ubiquinone-10 and the major fatty acids (>10 %) were C_16 : 0 and summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c). The 16S rRNA gene sequence similarity between strains SYSU D00286^T and SYSU D00782 was 100%, and their average nucleotide identity (ANI), average amino acid identity and (AAI) digital DNA-DNA hybridization (dDDH) values were all 100.0 %. Phylogenetic analysis indicated that these two strains belong to the same species of the genus Rubellimicrobium and show the highest sequence similarity to Rubellimicrobium rubrum KCTC 72461^T (98.2 %) and Rubellimicrobium roseum CCTCC AA 208029^T (97.5 %). The ANI, AAI and dDDH values between SYSU D00286^T (as well as SYSU D00782) and the other five Rubellimicrobium type strains were all less than or equal to 83.2, 80.1 and 23.6 %, respectively. Based on their phylogenetic, phenotypic and chemotaxonomical features, strains SYSU D00286^T and SYSU D00782 represent a novel species of the genus Rubellimicrobium, for which the name Rubellimicrobium arenae sp. nov. is proposed. The type strain is SYSU D00286^T (=MCCC 1K04981^T=CGMCC 1.8626^T=KCTC 82271^T).

Shaoyao-Gancao-Tang regulates the T-helper-type 1/T-helper-type 2 ratio in the lung and gut and alters gut microbiota in rats with ovalbumin-induced asthma

ETHNOPHARMACOLOGICAL RELEVANCE

Shaoyao-Gancao Tang (SGT) is a traditional Chinese medicine formulation. It has been used to treat kinds of pain and to alleviate asthma in clinic. However, the mechanism of action is not known.

AIM OF THE STUDY

To investigate the anti-asthma effect of SGT involving modulation of the T-helper type 1 (Th1) Th1/Th2 ratio in the gut-lung axis and alteration of the gut microbiota (GM) in rats with ovalbumin (OVA)-induced asthma.

MATERIALS AND METHODS

The main constituents of SGT were analyzed by high-performance liquid chromatography (HPLC). A model of asthma was established in rats by OVA-induced allergen challenge. Rats suffering from asthma (RSAs) were treated with SGT (2.5, 5.0 and 10.0 g/kg), dexamethasone (1 mg/kg) or physiologic saline for 4 weeks. The level of immunoglobulin (Ig)E in bronchoalveolar lavage fluid (BALF) and serum was determined by enzyme-linked immunosorbent assay. Histology of lung and colon tissues was investigated using staining (hematoxylin and eosin and periodic acid-Schiff). The Th1/Th2 ratio and levels of cytokines (interferon (IFN)-γ and interleukin (IL)-4) in the lung and colon were detected by immunohistochemistry. The GM in fresh feces was analyzed by 16 S rRNA gene sequencing.

RESULTS

Twelve main constituents (gallic acid, albiflorin, paeoniflorin, liquiritin apioside, liquiritin, benzoic acid, isoliquiritin apioside, isoliquiritin, liquiritigenin, glycyrrhizic acid, isoliquiritigenin and glycyrrhetinic acid) of SGT were simultaneously determined by HPLC. SGT treatment (5.0 and 10.0 g/kg) was found to reduce the IgE level (a vital marker of hyper-responsiveness) in BALF and serum, improve typical morphological changes (inflammatory-cell infiltration and goblet cell metaplasia) in the lung and colon, alleviate airway remodeling (including bronchiostenosis and basement membrane-thickening) in the lung, significantly decrease the IL-4 level and increase the IFN-γ level in the lung and colon, which led to restoration of the IFN-γ/IL-4 ratio. The dysbiosis and dysfunction of GM in RSAs were modulated by SGT. The abundance of bacteria of the genera Ethanoligenens and Harryflintia was increased in RSAs and was decreased upon SGT treatment. The abundance of Family_XIII_AD3011_group was decreased in RSAs and increased upon SGT treatment. Moreover, SGT therapy increased the abundance of bacteria of the genera Ruminococcaceae_UCG-005 and Candidatus_Sacchrimonas, and decreased that of Ruminococcus_2 and Alistipes.

CONCLUSIONS

SGT ameliorated rats with OVA-induced asthma via regulation of the Th1/Th2 ratio in the lung and gut, and modulated the GM.

Salinibacterium sedimenticola sp. nov., Isolated from Tidal Flat Sediment

An actinobacterium, designated as SYSU T00001^T, was isolated from a tidal flat sediment sample from Guangdong province, China. Cells were Gram-stain-positive, aerobic, motile and short rod-shaped. Colonies on marine agar 2216 were smooth, yellow-pigmented, and circular with low convexity. The isolate was able to grow at the temperature range 4-37 °C (optimum 30 °C), at pH 4.0-10.0 (optimum 7.0) and in the presence of 0-10% (w/v) NaCl. The major menaquinones were MK-11 and MK-10. The cell wall contained alanine, glutamic acid, lysine and ornithine. The major fatty acids were C_19:0 cyclo ω8c (35.7%) and anteiso C_15:0 (26.0%). The polar lipids consisted of one diphosphatidyl glycerol, one unidentified glycolipid and one unknown lipid. Whole genome sequencing of strain SYSU T00001^T revealed 2,837,702 bp with a DNA G + C content of 67.8%. Phylogenetic analyses clearly demonstrated that strain SYSU T00001^T belonged to the genus Salinibacterium, and the highest 16S rRNA gene similarity to Salinibacterium hongtaonis 194^T (97.8%). The ANI and dDDH values of strain SYSU T00001^T relative to Salinibacterium hongtaonis 194^T were 74.5% and 19.5%, respectively. According to our data, strain SYSU T00001^T represents a novel species of the genus Salinibacterium, for which the name Salinibacterium sedimenticola sp. nov. is proposed, the type strain is SYSU T00001^T (= GDMCC 1.3283^T = KCTC 49758^T).

Effects of UV-B radiation on epiphytic bacterial communities on male and female Sargassum thunbergii

The effects of increased UV-B radiation on macroalgae have been widely studied, but knowledge concerning the response of communities of algal epiphytic bacteria to increased UV-B radiation and differences between male and female algae is still lacking. Via 16S rDNA high-throughput sequencing technology, changes in the epiphytic bacterial communities on male and female S. thunbergii under increased UV-B radiation were studied in the lab. Under different UV-B radiation intensities, although the α diversity and community composition of epiphytic bacteria changed little, the β diversity indicated that the community structure of bacteria on S. thunbergii was obviously clustered, and the relative abundance of dominant bacteria and indicator species changed considerably. There were unique bacteria in each experimental group, and the bacteria whose abundance obviously changed were members of groups related to environmental resistance or adaptability. The variation in the abundance of epiphytic bacteria was different in male and female S. thunbergii, and the bacteria whose abundance greatly changed were mainly related to algal growth and metabolism. The abundance of genes with predicted functions related to metabolism, genetic information processing, environmental adaptation and infectious diseases changed with increased UV-B radiation, and those variations differed between epiphytic bacteria on male and female S. thunbergii. This study found that the algal epiphytic bacteria were influenced by the increase in UV-B radiation and underwent certain adaptations through adjustments to community structure and function, and this response was also affected by the sex of the macroalgae. These results are expected to serve as experimental basis and provide reference for further understanding of the response of algae epiphytic bacteria to enhanced UV-B radiation caused by the thinning of the ozone layer and the resulting changes in the relationship between algae and bacteria, which may change the community of the marine ecosystem and affect important marine ecological process.

Culturing the desert microbiota

Over the last 30 years, the description of microbial diversity has been mainly based on culture-independent approaches (metabarcoding and metagenomics) allowing an in-depth analysis of microbial diversity that no other approach allows. Bearing in mind that culture-dependent approaches cannot replace culture-independent approaches, we have improved an original method for isolating strains consisting of "culturing" grains of sand directly on Petri dishes (grain-by-grain method). This method allowed to cultivate up to 10% of the bacteria counted on the surface of grains of the three sites studied in the Great Western Erg in Algeria (Timoudi, Béni Abbès, and Taghit), knowing that on average about 10 bacterial cells colonize each grain. The diversity of culturable bacteria (collection of 290 strains) predicted by 16S rRNA gene sequencing revealed that Arthrobacter subterraneus, Arthrobacter tecti, Pseudarthrobacter phenanthrenivorans, Pseudarthrobacter psychrotolerans, and Massilia agri are the dominant species. The comparison of the culture-dependent and -independent (16S rRNA gene metabarcoding) approaches at the Timoudi site revealed 18 bacterial genera common to both approaches with a relative overestimation of the genera Arthrobacter/Pseudarthrobacter and Kocuria, and a relative underestimation of the genera Blastococcus and Domibacillus by the bacterial culturing approach. The bacterial isolates will allow further study on the mechanisms of tolerance to desiccation, especially in Pseudomonadota (Proteobacteria).

Diversity and antibacterial potential of the Actinobacteria associated with Apis mellifera ligustica

Insect-associated Actinobacteria are a potentially rich source of novel natural products with antibacterial activity. Here, the community composition of Actinobacteria associated with Apis mellifera ligustica was investigated by integrated culture-dependent and independent methods. A total of 61 strains of Streptomyces genera were isolated from the honeycomb, larva, and different anatomical parts of the honeybee's body using the culture-dependent method. Amplicon sequencing analyses revealed that the actinobacterial communities were dominated by the family of Bifidobacteriaceae and Microbacteriaceae in the honeybee gut, and Nocardiaceae and Pseudonocardiaceae in the honeycomb, whereas only Streptomyces genera were isolated by the culture-dependent method. Culture-independent analyses showed more diverse actinobacterial communities than those of culture-dependent methods. The antibacterial bioassay showed that most crude extracts of representative isolates exhibited antibacterial activities. Among them, the crude extract of Streptomyces sp. FCF01 showed the best antibacterial activities against Staphylococcus aureus, Micrococcus tetragenus, and Pseudomonas syringae pv. actinidiae (Psa) with the disc diameter of inhibition zone diameter (IZD) of 23.00, 15.00, and 13.33 mm, respectively. Chemical analysis of Streptomyces sp. FCF01 led to the isolation of three secondary metabolites, including mayamycin (1), mayamycin B (2), and N-(2-Hydroxyphenyl) acetamide (3). Among them, compound 1 displayed strong antibacterial activity against S. aureus, M. tetragenus, and Psa with minimum inhibitory concentrations (MIC) values of 6.25, 12.5, and 6.25 μg/ml, respectively. In addition, two novel derivative compounds 1a and 1b were synthesized by acetylation of compound 1. Both compounds 1a and 1b displayed similar antibacterial activities with those of metabolite 1. These results indicated that Streptomyces species associated with honeybees had great potential in finding antibiotics.

Effects of Isolated LAB on Chemical Composition, Fermentation Quality and Bacterial Community of Stipa grandis Silage

This study aimed to screen and identify lactic acid bacteria (LAB) strains from the Stipa grandis and naturally fermented silage, and assess their effects on the silage quality and bacterial community of Stipa grandis after 60 days of the fermentation process. A total of 38 LAB were isolated, and strains ZX301 and YX34 were identified as Lactiplantibacillus plantarum and Pediococcus pentosaceus using 16S rRNA sequences; they can normally grow at 10−30 °C, with a tolerance of pH and NaCl from 3.5 to 8.0 and 3 to 6.5%, respectively. Subsequently, the two isolated LAB and one commercial additive (Lactiplantibacillus plantarum) were added to Stipa grandis for ensiling for 60 days and recorded as the ZX301, YX34, and P treatments. The addition of LAB was added at 1 × 105 colony-forming unit/g of fresh weight, and the same amount of distilled water was sprayed to serve as a control treatment (CK). Compared to the CK treatment, the ZX301 and YX34 treatments exhibited a positive effect on pH reduction. The water-soluble carbohydrate content was significantly (p < 0.05) increased in ZX301, YX34, and P treatments than in CK treatment. At the genus level, the bacterial community in Stipa grandis silage involves a shift from Pantoea to Lactiplantibacillus. Compared to the CK treatment, the ZX301, YX34, and P treatments significantly (p < 0.05) increase the abundance of Pediococcus and Lactiplantibacillus, respectively. Consequently, the results indicated that the addition of LAB reconstructed microbiota and influenced silage quality. The strain ZX301 could improve the ensiling performance in Stipa grandis silage.

Diversity of growth performance and rumen microbiota vary with feed types

Diet is a major factor in influencing the growth performance and the microbial community of lambs. This study aimed to investigate how diverse diets influence their growth performance and rumen microbiota. Ninety male lambs were randomly allocated into three groups in a completely randomized design with equal lambs: non-pelleted native grass hay (HA) as the control diet and pelleted native grass hay (GP) and pelleted native grass hay with concentrate (GPC) as experimental diets. The rumen fluid samples of the lambs in the HA, GP, and GPC groups were used to study rumen microbiota diversity through 16S rDNA high-throughput sequencing. In the present study, the final body weight, dry matter intake, and average daily gain differed significantly (p &lt; 0.05) among the HA, GP, and GPC groups. Compared to the HA group, higher final body weight, dry matter intake, and average daily gain were found in the GP group. Similarly, better animal performance was observed in the GPC group than in the GP group. The principal coordinates analysis displayed that the composition of the rumen microbiota in the three groups was distinctly separated from each other. Bacteroidetes and Firmicutes were the dominant members of the community in the HA and GP groups, while Bacteroidetes, Firmicutes, and Proteobacteria became the predominant members in the GPC group. The comparison among these groups showed significant (p &lt; 0.05) differences in Rikenellaceae_RC9_gut_group, Prevotella_1, Ruminococcaceae_NK4A214_group, and Succiniclasticum. These results suggest that the GP and GPC diets are more beneficial for growth performance than the HA diet and also indicate that the rumen microbiota varied in response to different feed types. In conclusion, these results could provide strategies to influence rumen microbiota for better growth and a healthier ecosystem on the Mongolian Plateau and lay the theoretical groundwork for feeding the pelleted native grass diet.

Longitalea arenae gen. nov., sp. nov. and Longitalea luteola sp. nov., two new members of the family Chitinophagaceae isolated from desert soil

Two strains designated as SYSU D01084^T and SYSU D00799^T, were isolated from a sandy soil sample collected from Gurbantunggut Desert in Xinjiang, north-west China. Cells of both strains were Gram-stain-negative, strictly aerobic, long-rod-shaped, oxidase- and catalase-negative, motile or non-motile. Colonies were circular, translucent, convex, smooth and light-yellow in color on R2A agar. The two isolates were found to grow at 4-50 ºC, at pH 6.0-8.0 and with 0-1.0% (w/v) NaCl. Analysis of their 16S rRNA gene sequences indicated that they belonged to the family Chitinophagaceae, and closely related to the genera Paraflavitalea, Niastella, Pseudoflavitalea and Flavitalea. The two novel strains shared 98.1% 16S rRNA sequence similarity and represent different species on the basis of low average nucleotide identity (ANI, 83.8%) and digital DNA-DNA hybridization (dDDH, 51.4%) values. The genomic DNA G + C contents of strains SYSU D01084^T and SYSU D00799^T were 46.0 and 45.6%, respectively. Phylogenetic trees showed that the two isolates were clustered in an individual lineage and not grouped consistently into any specific genus. The polar lipids contained of phosphatidylethanolamine, four unidentified aminolipids, two unidentified aminoglycolipids, and three or four unidentified lipids. The predominant respiratory quinone was MK-7 and the major fatty acids (> 10%) were identified as iso-C_15:0, iso-C_17:0 3-OH, and iso-C_15:1 G. Based on the combined phenotypic, genomic and phylogenetic analyses, the two strains represent two novel species of a new genus in the family Chitinophagaceae, for which the name Longitalea gen. nov. is proposed, comprising the type species Longitalea arenae sp. nov. (type strain SYSU D01084^T = CGMCC 1.18641^T = MCCC 1K05006^T = KCTC 82283^T) and Longitalea luteola sp. nov. (type strain SYSU D00799^T = MCCC 1K04987^T = KCTC 82282^T = NBRC 114888^T).

Diversity of epiphytic bacterial communities on male and female Sargassum thunbergii

The epiphytic bacteria are the most abundant microorganisms on marine macroalga. However, there are few studies on the distribution of these epiphytic bacteria on male and female Sargassum thunbergii. In this study, the composition and diversity of epiphytic bacterial communities on male and female S. thunbergii were investigated by using the traditional culture-based method and 16S rDNA high-throughput sequencing. The results showed that the dominant bacterial phyla and genera were the same on both male and female S. thunbergii. However, there were significant differences in the relative abundance of epiphytic bacteria at the genus level. Furthermore, male and female S. thunbergii had their own indicative species and specific bacteria. In addition, the predicted functions of the epiphytic bacteria mainly differed in transport and metabolism, environmental adaptation and spore development. This study enriches the baseline knowledge of epiphytic bacteria related to dioecious algae and paves the way for further studies of the relationships between epiphytic microbial communities and the sex of algae.

Actinobacteria Community and Their Antibacterial and Cytotoxic Activity on the Weizhou and Xieyang Volcanic Islands in the Beibu Gulf of China

Weizhou Island and Xieyang Island are two large and young volcanic sea islands in the northern part of the South China Sea. In this study, high-throughput sequencing (HTS) of 16S rRNA genes was used to explore the diversity of Actinobacteria in the Weizhou and Xieyang Islands. Moreover, a traditional culture-dependent method was utilized to isolate Actinobacteria, and their antibacterial and cytotoxic activities were detected. The alpha diversity indices (ACE metric) of the overall bacterial communities for the larger island (Weizhou) were higher than those for the smaller island (Xieyang). A beta diversity analysis showed a more dispersive pattern of overall bacterial and actinobacterial communities on a larger island (Weizhou). At the order level, Frankiales, Propionibacteriales, Streptomycetales, Micrococcales, Pseudonocardiales, Micromonosporales, Glycomycetales, Corynebacteriales, and Streptosporangiales were the predominant Actinobacteria. A total of 22.7% of the OTUs shared 88%–95% similarity with some known groups. More interestingly, 15 OTUs formed a distinct and most predominant clade, and shared identities of less than 95% with any known families. This is the first report about this unknown group and their 16S rRNA sequences obtained from volcanic soils. A total of 268 actinobacterial strains were isolated by the culture-dependent method. Among them, 55 Streptomyces species were isolated, representing that 76.6% of the total. S. variabilis and S. flavogriseus were the most abundant. Moreover, some rare Actinobacteria were isolated. These included Micromonospora spp., Nocardia spp., Amycolatopsis spp., Tsukamurella spp., Mycobacterium spp., and Nonomuraea spp. Among them, eight Streptomyces spp. exhibited antibacterial activity against Bacillus cereus. Only three strains inhibited the growth of Escherichia coli. Four strains showed good activity against aquatic pathogenic bacterial strains of Streptococcus iniae. The cytotoxicity assay results showed that 27 strains (10.07%) exhibited cytotoxic activity against HeLa and A549 cell lines. Many actinobacterial strains with cytotoxic activity were identified as rare Actinobacteria, which illustrated that volcanic islands are vast reservoirs for Actinobacteria with promising antibacterial and cytotoxic activity. This study may significantly improve our understanding of actinobacterial communities on volcanic islands. The isolated Actinobacteria showed promising prospects for future use.

Microvirga roseola sp. nov. and Microvirga lenta sp. nov., isolated from Taklamakan Desert soil

Two Gram-negative, rod-shaped, non-spore-forming bacteria, designated SM9T and SM2T, were isolated from Taklamakan Desert soil samples. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strains SM9T and SM2T had the highest sequence similarity to the type strains Microvirga indica BCRC 80972T and Microvirga soli NBRC 112417T with similarity values of 98.2 and 97.7 %, respectively, and Microvirga was among the predominant genera in the desert soil. The draft genomes of these two strains were 4.56 Mbp (SM9T) and 5.08 Mbp (SM2T) long with 65.1 mol% (SM9T) and 63.5 mol% (SM2T) G+C content. To adapt to the desert environment, these two strains possessed pathways for the synthesis of stress metabolite trehalose. The major fatty acids (>5 %) included C18 : 1 ω9c in SM2T, but C16 : 0, C18 : 0 and C19 : 0 cyclo ω8c in SM9T, while the major menaquinone was ubiquinone 10 in both strains. The major polar lipids of SM9T and SM2T were phosphatidylglycerol, phosphatidylethanolamine and phospholipid. The average nucleotide identity and digital DNA–DNA hybridization results further indicated that strains SM9T and SM2T were distinguished from phylogenetically related species and represented two novel species within the genus Microvirga , for which the names Microvirga roseola sp. nov. (type strain SM2T=KCTC 72792T=CGMCC 1.17776T) and Microvirga lenta sp. nov. (type strain SM9T=KCTC 82729T=CCTCC AB 2021131T) are proposed.

Bioprospecting of the novel isolate Microbacterium proteolyticum LA2(R) from the rhizosphere of Rauwolfia serpentina

The study aimed to assess the proficiency of secondary metabolites (SMs) synthesized by actinobacteria isolated from the rhizospheric soil of Rauwolfia serpentina for its antimicrobial and anti-biofilm activity. After morphological and biochemical identification of actinobacteria, primary and secondary screening was done for specific metabolite production. The secondary metabolites were then tested for their antioxidant, antibacterial, and antibiofilm potential. Out of 29 bacterial colonies isolated, only one emerged as a novel isolate, Microbacterium LA2(R). Partial 16S rRNA gene sequence of the isolate LA2(R) was deposited in NCBI GenBank with accession number MN560041. The highest antioxidant capacity of the methanolic extract the novel isolate was found to be 474.183 µL AAE/mL and 319.037 µL AAE/mL by DPPH assay and ABTS assay respectively; three folds higher than the control. These results were further supported by the high total phenolic (194.95 gallic acid equivalents/mL) and flavonoid contents (332.79 µL quercetin equivalents/mL) of the methanolic extract. GC–MS analysis revealed the abundance of antibacterial compounds; where, n-Hexadecanoic acid was found to be the major compound present with a peak of 14 min retention time (RT) and 95% similarity index. MIC value of the metabolite was noted to be around 132.28 ± 84.48 μg/mL. The IC₅₀ value was found to be 74.37, 71.33, 66.28 and 84.48 μg/mL against Escherichia coli, Staphylococcus aureus, Klebsiella pneumonia, and Salmonella abony, respectively. Treatment with IC₅₀ of the extract decreased the biofilm formation up to 70%–80% against pathogenic strains viz. Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae and Salmonella abony. These significant activities of Microbacterium sp. LA2(R) suggests that it could be utilized for antibiotic production for human welfare and in various important industrial applications.

Sphingomonas arenae sp. nov., isolated from desert soil

Two bacterial strains, designated as SYSU D00720T and SYSU D00722, were isolated from a desert sandy soil sample collected from Gurbantunggut Desert in Xinjiang, north-west China. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped, oxidase-positive and catalase-negative. Colonies were circular, opaque, convex, smooth, orange on Reasoner's 2A (R2A) agar. The isolates were found to grow at 4-45 °C (optimum, 28-30 °C), at pH 6.0-7.0 (optimum, 7.0) and with 0-1.5 % (w/v) NaCl (optimum, 0%). Growth was observed on R2A agar, Luria-Bertani agar and nutrient agar, but not on trypticase soy agar. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid, two unidentified aminolipids, one unidentified glycolipid, one unidentified aminoglycolipid, one unidentified aminophospholipid, one unidentified phospholipid and two unidentified lipids. The main fatty acids (>10%) were C17 : 1  ω6c, summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c) and C16 : 0. The major respiratory quinone was ubiquinone-10 and the major polyamine was sym-homospermidine. The genomic DNA G+C content was 66.0 mol%. Strains SYSU D00720T and SYSU D00722 were nearly identical with a 16S rRNA gene sequence similarity of 99.6 %, and 100.0 % average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values. Phylogenetic analyses clearly demonstrated that these two strains belonged to the same species of the genus Sphingomonas, and had highest sequence similarity to Sphingomonas lutea KCTC 23642T (97.3 %). The ANI, AAI and dDDH values of strains SYSU D00720T and SYSU D00722 to S. lutea KCTC 23642T were both 73.2, 69.9 and 19.2 %, respectively. Based on phylogenetic, phenotypic and chemotaxonomic distinctiveness, strains SYSU D00720T and SYSU D00722 represent a novel species of the genus Sphingomonas, for which the name Sphingomonas arenae sp. nov. is proposed. The type strain is SYSU D00720T (=MCCC 1K05154T=NBRC 115061T).

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.

Microbial Community and Fermentation Characteristics of Native Grass Prepared Without or With Isolated Lactic Acid Bacteria on the Mongolian Plateau

This study aimed to isolate and identify lactic acid bacteria (LAB) from the native grass and naturally fermented silage from the Mongolian Plateau. The effect of selected strains on bacterial community and quality of native grass silage was also studied. Strains XM2, 265, and 842 could grow normally at 15°C–30°C, pH 4.0–8.0, and NaCl 3 and 6.5%; they were identified as Lactiplantibacillus plantarum subsp. plantarum, Pediococcus acidilactici, and Latilactobacillus graminis, by sequencing 16S rRNA, respectively. The three strains (XM2, 265, and 842) and one commercial additive (L) were used as inoculants and singularly added to the native grass. Compared to the control, the dry matter content was significantly (p < 0.05) lower in L and XM2 groups. The water-soluble carbohydrate content was significantly (p < 0.05) higher in control than in other groups. Compared with the control, the crude protein and ammonia nitrogen contents were significantly (p < 0.05) higher and lower in the LAB-treated groups, and the acid and detergent fiber contents were significantly (p < 0.05) reduced in the L and XM2 groups than those in other groups. There was a significant (p < 0.05) difference in the pH value, lactic acid content, and lactic acid-to-acetic acid ratio in L and XM2 groups than in other groups. Compared with the control, the number of LAB was significantly (p < 0.05) higher in LAB-treated silages, whereas no significant (p > 0.05) differences were observed in yeast and aerobic bacteria in all groups. Compared to the control, the Shannon index was significantly (p < 0.05) reduced. Simpson and Chao1 were significantly (p < 0.05) increased. Principal coordinate analysis based on the unweighted UniFrac distance showed clear separation of the bacterial community in fresh materials and LAB-treated silages. Besides, compared to the control, the principal coordinate analysis of LAB-treated silages was also separate. After 30 days of fermentation, the relative abundance of Firmicutes increased and was the primary phylum in all silages. Compared with the control, the abundance of Firmicutes and Proteobacteriawas significantly (p < 0.05) higher and lower in L and XM2 groups. In contrast, no significant differences were observed among control, 265, and 842 groups. At the genus level, the relative abundance of Lactobacillus, Enterobacter, Pediococcus, and Weissella was increased and dominated the native grass fermentation. Compared with the control, the abundance of Lactobacillus was significantly (p < 0.05) higher in L, XM2, and 842 groups, while no significant (p > 0.05) differences were observed between the control and 265 groups. The abundance of Pediococcus was higher than that in other groups. Consequently, the results demonstrated that LAB significantly influenced silage fermentation by reconstructing microbiota, and Lactobacillus was the dominant genus in the native grass silages. Furthermore, the results showed that strain XM2 could effectively improve the silage quality, and it is considered a potential starter for the native grass silage.