Kai Jiang

This paper reports the isolation of strain 10bf12 from Daihai Lake. The complete genome of strain 10bf12 is 3,452,620 bp in size, with a G + C content of 42.59%. Cultivation experiments revealed that strain 10bf12 is adaptable to high-salinity environments with potential industrial value.

A novel aerobic, Gram-stain-positive, non-motile, non-spore-forming, short rod-shaped strain X10-3^T, was isolated from Daihai Lake, Inner Mongolia, China. The strain formed circular, smooth, transparent, orange-colored colonies with convex elevation and entire margins, which measured approximately 1.0–4.0 mm in diameter after 48 h of incubation on Luria-Bertani agar at 32 °C. The strain was able to grow at pH levels between 6.5 and 9.0 (optimal at 7.5-8.0), temperatures from 4 to 40 °C (optimal at 37 °C), and in 0–13% (optimal at 2–3%, w/v) NaCl. The complete genome of strain X10-3^T comprises 3,244,194 bp with a DNA G + C content of 45.9%. Phylogenetic analysis revealed the closest relationship to members of the genus Planococcus, showing 16S rRNA gene sequence similarities of 99.2% with P. salinarum DSM 23820^T, 98.8% with P. wigleyi Sa1BUA13^T, 98.6% with P. koreense JG07^T, and 98.6% with P. halotolerans SCU63^T. The average nucleotide identity between strain X10-3^T and the species within the genus Planococcus fell below the species delineation thresholds of 95%, and the digital DNA-DNA hybridization values were lower than 70%. Chemotaxonomic analysis revealed that the predominant cellular fatty acids of strain X10-3^T were anteiso-C_15:0 and C_16:1 ω7c alcohol. The primary cellular polar lipids included phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol, while the predominant isoprenoid quinones were menaquinone-8 and menaquinone-7. Based on these comprehensive analyses, strain X10-3^T represents a new species of the genus Planococcus, for which the name Planococcus daihaiensis sp. nov. is proposed. The type strain is X10-3^T (= CGMCC 1.60163^T = KCTC 43688^T).

We isolated a strain of the genus Alkalibacterium from Daihai Lake in Inner Mongolia. The complete genome size is 2,614,554 bp, with a genomic DNA G + C content of 39.3%. Metabolic pathway analysis indicates that strain f15 is a potential lactic acid-fermenting bacterium with industrial applications in lactate fermentation.

Groundwater harbors phylogenetically diverse Candidate Phyla Radiation (CPR) bacteria, representing an ideal ecosystem for studying this microbial dark matter. However, no CPR strains have been successfully isolated from groundwater, severely limiting further research. This study employed a multi-metagenome approach, integrating time-resolved sampling, antibiotic/nutrient interventions, and microbial correlation networks to unravel CPR ecological roles in groundwater and provide insights into their subsequent cultivation. Through 36 metagenomes from a groundwater system containing at least 68 CPR phyla, we revealed the time-sensitive collapse of CPR communities: total abundance plummeted from 7.9% to 0.15% within 48 h post-sampling, driven by competition with rapidly dividing non-CPR bacteria, such as members of Pseudomonadota. Ampicillin (100 mg/L) stabilized CPR communities by suppressing competitors, whereas low-nutrient conditions paradoxically reversed this effect. Long-term enrichment (14 months) recovered 63 CPR phyla (0.35% abundance), revealing their survival resilience despite nutrient deprivation. Correlation networks prioritized Actinomyces, a novel Acidimicrobiaceae genus, Aestuariivirga, Baekduia and Caedimonadaceae as potential CPR partners, providing actionable targets for co-culture trials. Here, we propose actionable recommendations spanning groundwater sampling, activation status, identification of CPR symbiotic partners, and optimization of culture conditions, which bypass traditional blind cultivation and are critical for future efforts to cultivate CPR bacterial strains from groundwater. Cultivating CPR bacteria will contribute to clarifying their diversity, ecological roles, evolutionary mechanisms, metabolic pathways, and genetic potential.

Locoweeds, including Oxytropis and Astragalus species, are globally recognized as plants containing swainsonine (SW), a neurotoxic alkaloid that induces neurological dysfunction and growth inhibition in livestock. SW is produced by endophytic fungi in plants; the pyrroline-5-carboxylate reductase (P5CR) gene is critical in the fungal SW biosynthetic pathway. In this study, a P5CR gene knockout mutant (ΔP5CR) was constructed from the endophytic fungus Alternaria oxytropis OW7.8 isolated from Oxytropis glabra. Compared to the wild-type strain (A. oxytropis OW7.8), the SW content in the ΔP5CR mycelia was significantly reduced, indicating that the P5CR gene plays a crucial role in promoting SW biosynthesis. Compared to the wild-type strain A. oxytropis OW7.8, the ΔP5CR mutant exhibited distinct morphological alterations in both colony and mycelial structures. The transcriptomic analysis of A. oxytropis OW7.8 and ΔP5CR revealed the downregulation of six genes associated with SW biosynthesis. Metabolomic profiling further demonstrated altered levels of six metabolites linked to SW synthesis. These findings provide foundational insights into the molecular mechanisms and metabolic pathways underlying SW biosynthesis in fungi. They hold significant value for future strategies to control SW in Oxytropis glabra and contribute positively to the protection and sustainable development of grassland ecosystems.

The swnN gene in the endophytic fungus Alternaria oxytropis OW 7.8 isolated from Oxytropis glabra was identified, and the gene knockout mutant ΔswnN was first constructed in this study. Compared with A. oxytropis OW 7.8, the ΔswnN mutant exhibited altered colony and mycelia morphology, slower growth rate, and no swainsonine (SW) in mycelia. SW was detected in the gene function complementation strain ΔswnN/swnN, indicating that the function of the swnN gene promoted SW biosynthesis. Six differentially expressed genes (DEGs) closely associated with SW synthesis were identified by transcriptomic analysis of A. oxytropis OW 7.8 and ΔswnN, with P5CR, swnR, swnK, swnH2, and swnH1 down-regulating, and sac up-regulating. The expression levels of the six genes were consistent with the transcriptomic analysis results. Five differential metabolites (DEMs) closely associated with SW synthesis were identified by metabolomic analysis, with L-glutamate, α-ketoglutaric acid, and L-proline up-regulating, and phosphatidic acid (PA) and 2-aminoadipic acid down-regulating. The SW biosynthetic pathways in A. oxytropis OW 7.8 were predicted and refined. The results lay the foundation for in-depth elucidation of molecular mechanisms and the SW synthesis pathway in fungi. They are also of importance for the prevention of locoism in livestock, the control and utilization of locoweeds, and the protection and sustainable development of grassland ecosystems.

A novel aerobic, Gram-staining-negative, non-motile, short-rod-shaped strain, designated f23^T, was obtained from Daihai Lake, Inner Mongolia, Republic of China. 16S rRNA gene sequences analysis showed that f23^T belongs to the genus Orrella and is most closely related to Orrella marina H-Z20^T with 98.35% sequence similarity. The strain was oxidase positive, catalase positive and had well growth at pH 6.5–8.5, at temperature 28–40 °C and at 0–4.5% (w/v) NaCl. Colonies incubated at 37 °C on marine 2216 agar for 3 days were white, smooth, transparent, circular and less than 1.0 mm in diameter. The total genome size of f23^T was 2,803,849 bp with a G + C content of 52.79%. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain f23^T and O. marina H-Z20^T were 69.62% and 20.5%, which both below the species delineation threshold. Chemotaxonomic analysis showed that C_16:0, cyclo-C_17:0, C_18:0, Sum Feature 3 (C_16:1ω7c and/or C_16:1ω6c) and Sum Feature 8 (C_18:1ω6c and C_18:1ω7c) as the major fatty acids, ubiquinone-8 as the major isoprenoid quinone, phosphatidylethanolamine as the major cellular polar lipids. Based on the polyphasic analysis, f23^T represents a novel species within the genus Orrella, for which the name Orrella daihaiensis sp. nov. is proposed. The type strain is f23^T (= CGMCC 1.18761 ^T = KCTC 82425 ^T).

A novel Gram-negative strain, designated X100-76^T, was isolated from Daihai Lake in Inner Mongolia, Republic of China. The strain was non-motile, non-spore-forming, long-rod-shaped, oxidase positive and catalase positive. Colonies incubated at 33 °C on 2216 marine agar medium for 3 days were circular, smooth, transparent, convex with clear edges, orange-red in colour and approximately 1.0 mm in diameter. Growth occurred at pH 6.5–12 (optimum pH 7.5), in 0–5.0% (w/v) NaCl (optimum 1.5%, w/v) and at 4–40 °C (optimum 28–33 °C). Phylogenetic analysis based on 16S rRNA gene sequences showed that X100-76^T belongs to the genus Mongoliitalea and is most closely related to Mongoliitalea lutea MIM18^T with 98.3% sequence similarity. The total genome size of X100-76^T was 4,816,617 bp with a G + C content of 39.6%. The digital DNA–DNA hybridization and average nucleotide identity values between strain X100-76^T and M. lutea MIM18^T were both below the recommended cut-off values. Chemotaxonomic analysis revealed iso-C_15:0, Sum Feature 4 (anteiso-C_17:1 B and/or iso-C_17:1 I), C_15:1ω6c, Sum Feature 9 (C_16:0 10-methyl and/or iso-C_17:1ω9c), C_16:0 and iso-C_15:1 G as the major fatty acids, menaquinone MK-7 as the major isoprenoid quinone, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and phosphatidylinositol as the major cellular polar lipids. The results of polyphasic analysis demonstrated that X100-76^T represents a novel species within the genus Mongoliitalea, for which the name Mongoliitalea daihaiensis sp. nov. is proposed. The type strain is X100-76^T (= CGMCC 1.18762^T = KCTC 82458^T).