Search Results (36)

Cold-active lipolytic enzymes enable low-temperature biocatalysis, but remain underexplored in Antarctic actinomycetes. Here, we report the discovery and first-step characterization of a CALB-like cold-active lipolytic enzyme (PanLip) from Pseudonocardia antarctica. Sequence and structure analyses revealed a canonical α/β-hydrolase fold with a conserved Ser–Asp–His triad and short helical elements around the pocket reminiscent of CALB’s α5/α10 lid. Mature PanLip was expressed primarily as inclusion bodies in E. coli; an N-terminally truncation (PanLipΔN) improved solubility and PanLipΔN was purified by Ni–NTA. Far-UV CD confirmed a folded α/β architecture. PanLipΔN favored short-chain substrates (p-NPA, k_cat/K_M = 2.4 × 10⁵ M⁻¹·s⁻¹) but also showed measurable hydrolytic activity toward natural triglycerides, consistently with a lipase-family esterase. The enzyme showed an activity optimum near 25 °C and pH 8.0. The enzyme tolerated low salt (maximal at 0.1 M NaCl), mild glycerol, and selected organic solvents (notably n-hexane), but was inhibited by high salt, Triton X-100, and SDS. AlphaFold predicted high local confidence for the catalytic core; DALI placed PanLip closest to fungal lipases (AFLB/CALB). Temperature-series MD and CABS-flex indicated enhanced surface breathing and flexible segments adjacent to the active site—including a region topologically matching CALB α10—supporting a flexibility-assisted access mechanism at low temperature. Structure-based MSAs did not support a cold adaptation role for the reported VDLPGRS motif. Taken together, these findings position PanLip as a promising cold-active catalyst with CALB-like access control and potential for low-temperature biocatalysis. Full article

Actinobacteria play major roles in human health and soil nutrient biogeochemical cycles, which are important for environmental protection. On the northern Qinghai–Tibet Plateau, the Qiangtang Alpine Grasslands have recently become degraded to varying degrees due to global climate changes and human disturbances. Here, we compared the community diversity, composition, and potential metabolic functions of Actinobacteria in soil from different degradation conditions through Illumina MiSeq sequencing. The soil Actinobacteria community structure in the Qiangtang Alpine Grasslands of northern Tibet was dominated by Nocardioides, Gaiella, Solirubrobacter, and Pseudonocardia, with evidence of previously unidentified taxa. Compared with non-degraded and severely degraded grasslands, the moderately degraded grassland had the highest soil Actinobacteria alpha-diversity, and the community composition showed significant differences between degraded grasslands with different degrees of degradation. The interactions between Actinobacteria and KO functions predominantly show negative correlations, but significant positive correlations outnumber significant negative ones. This study showed that Actinobacteria diversity and potential ecological functions in the alpine grasslands of northern Tibet decreased with grassland degradation due to the loss of vegetation cover. Therefore, it is necessary to effectively manage and protect the Qiangtang Alpine Grasslands on the northern Tibetan Plateau. Full article

Drought stress poses a significant threat to olive cultivation in Mediterranean regions. This study investigated the resilience and functional adaptation of root-associated and rhizosphere soil microorganisms of four olive cultivars under contrasting water regimes (irrigated vs. drought) across seasons. Using a combination of amplicon-targeted metagenomics, phylogenetic analysis, and text mining of the scientific literature, we identified a conserved core microbiome and revealed that drought stress significantly alters the structure of root-associated—but not rhizosphere soil—bacterial communities. Potential functional profiling indicated that drought conditions enriched for genes involved in stress response pathways, including branched-chain amino acid transport, glutathione S-transferase activity, thioredoxin reductase, and chemotaxis. Text mining co-occurrence networks highlighted strong associations between some key bacterial genera and plant growth-promoting functions like phytohormone production and biocontrol. Furthermore, we identified Solirubrobacter, Microvirga, and Pseudonocardia as the primary contributors to these drought-resilience functions. The stability of the soil microbiome suggests functional redundancy, whereas the restructuring of the root endophytic compartment indicates active plant selection for beneficial microbes. Our findings provide a foundation for developing tailored microbial consortia (SynComs) to enhance drought tolerance in olive trees and support sustainable agriculture in water-limited environments. Full article

Metabolic syndrome is a global health crisis. However, there are no effective therapeutic strategies for metabolic syndrome. Therefore, this study was conducted to find out a novel silkworm-based metabolic syndrome model that bridges microbial ecology and metabolic dysregulation by integrating hemolymph lipids and midgut microbiota. Our results showed that the levels of HDL-C in the hemolymph of the lean silkworm strain were significantly higher than that in the obese silkworm strain. Furthermore, correlation analysis revealed that Lactococcus and Oceanobacillus were positively related to HDL-C levels, while SM1A02 and Pseudonocardia were negatively associated with HDL-C levels. These relationships between the identified bacteria in the midgut and HDL-C, known as the “good” lipid, in the hemolymph could help guide the development of new treatments for obesity and metabolic problems like high cholesterol in humans. Overall, our results not only established a framework for understanding microbiota-driven lipid dysregulation in silkworms but also offered potential probiotic targets and a bacterial biomarker for obesity and metabolic dysfunction intervention in humans. Full article

Petroleum-derived contaminants pose a significant threat to the soil microbiome. Therefore, it is essential to explore materials and techniques that can restore homeostasis in disturbed environments. The aim of the study was to assess the response of the soil microbiome to contamination with diesel oil (DO) and gasoline (G) and to determine the capacity of sorbents, vermiculite (V), dolomite (D), perlite (P) and agrobasalt (A), to enhance the activity of microorganisms under Zea mays cultivation conditions in pot experiments. The restoration and activity of the soil microbiome were evaluated based on the abundance and diversity of bacteria and fungi, using both classical microbiological methods and Next Generation Sequencing (NGS). Bioinformatic tools were employed to calculate the physicochemical properties of proteins. DO increased the abundance of cultured microorganisms, whereas G significantly reduced it. Both DO and G increased the number of ASVs of Proteobacteria and decreased the relative abundance of Gemmatimonadetes, Chloroflexi, Acidobacteria, Verrucomicrobia, Planctomycetes, and fungal OTUs. These contaminants stimulated the growth of bacteria from the genera Rhodanobacter, Sphingomonas, Burkholderia, Sphingobium, and Mycobacterium, as well as fungi belonging to the Penicillium genus. Conversely, they had a negative effect on Kaistobacter, Rhodoplanes, and Ralstonia, as well as the fungi Chaetomium, Pseudaleuria, and Mortierella. DO caused greater changes in microbial alpha diversity than G. The stability of microbial proteins was higher at 17 °C than at −1 °C. The most stable proteins were found in bacteria and fungi identified within the core soil microbiome. These organisms exhibited greater diversity and more compact RNA secondary structures. The application of sorbents to contaminated soil altered the composition of bacterial and fungal communities. All sorbents enhanced the growth of organotrophic bacteria (Org) and fungi (Fun) in DO-contaminated soils, and actinobacteria (Act) and fungi in G-contaminated soils. V and A had the most beneficial effects on cultured microorganisms. In DO-contaminated soils, all sorbents inhibited the growth of Rhodanobacter, Parvibaculum, Sphingomonas, and Burkholderia, while stimulating Salinibacterium and Penicillium. In G-contaminated but otherwise unamended soils, all sorbents negatively affected the growth of Burkholderia, Sphingomonas, Kaistobacter, Rhodoplanes, Pseudonocardia, and Ralstonia and increased the abundance of Gymnostellatospora. The results of this study provide a valuable foundation for developing effective strategies to remediate soils contaminated with petroleum-derived compounds. Full article

The structure of microbial communities in sponge-sand filters, used for the treatment of real domestic sewage with elevated ammonium nitrogen concentrations (approximately 155 mg·dm⁻³), was characterized using 16S rRNA gene sequencing. Analyses using the Illumina technique allowed us to perform a comparison of filters by layer (two or three layers) and type of fill (waste PUR foams with 95% open porosity, sand). Proteobacteria, actinobacteria, and firmicutes were shown to be the most abundant phyla. The number and type of fill layers had a significant impact on the diversity of nitrifying bacteria. The presence of Nitrosomonas and Nitrospira was observed in every sponge fill sample, but the abundance of autotrophic nitrifiers was negligible in the two-layer filter. The conditions there proved more favorable for the growth of aerobic heterotrophic bacteria. Also in the Schmutzdecke layer, a dominance of heterotrophic nitrifiers was found. The abundance of bacteria with nitrifying activity (AOB, comammox, HNAD) in the biomass of spongy fill placed in casings was 1.7 times lower than in foams without casings. In addition, anammox bacteria (unidentified Planctomycetes), found mainly in the sponge fill and Schmutzdecke of the three-layer filters, may have been responsible for NH4⁺-N removal exceeding 70%. In the case of the two-layer filter, the removal of this pollutant reached 92%. Burkholderia and Sphingopyxis were identified as the predominant denitrifying bacteria. The foam-filled filter in the casings showed an increase in o_Caldilineaceae, involved in nitrate removal as non-denitrifiers. Actinomycetes Pseudonocardia and Amycolatopsis, as well as Proteobacteria Devosia, Acinetobacter, and Bdellovibrio, were found to be involved in phosphorus removal in the waste PUR foams. Full article

Background/Objectives: The evidence regarding the efficacy of probiotics in chronic rhinosinusitis (CRS) is very limited, prompting the EPOS2020 steering group to advise against their use in CRS treatment. Therefore, further research to evaluate the impact of probiotics on microbial communities is particularly important. This study aimed to assess the influence of probiotic nasal rinses on nasal microbiota profiles in patients with primary CRS, granulomatosis with polyangiitis (GPA), and nasal septal perforation (NSP) using 16S rRNA sequencing. Methods: Thirty-six patients with nasal mucosal diseases, including sixteen with primary CRS, eleven with GPA, and nine with NSP, were randomly assigned to either a study group receiving nasal rinses with probiotics containing Lactobacillus plantarum and Bifidobacterium animalis, or a control group using nasal rinses with saline. Metagenomic analysis targeting the V3–V4 hypervariable region of the 16S rRNA gene was performed to characterize bacterial and archaeal populations. Results: At the genus level, the most abundant co-colonizers included Staphylococcus, Streptococcus, and Haemophilus. After one month of probiotic rinsing, a decrease in abundance of the genera Finegoldia (p = 0.010), Haemophilus (p = 0.020), Streptococcus (p = 0.027), Staphylococcus (p = 0.033), Micrococcus (p = 0.035), Corynebacterium (p = 0.049), Gemella (p = 0.055), Rubrobacter (p = 0.055), and Pseudonocardia (p = 0.058) was observed. Conversely, the abundance of probiotic species Lactobacillus plantarum and Bifidobacterium animalis increased. Moreover, increases in the genera Dolosigranulum and Stenotrophomonas were observed, although they did not reach statistical significance. Conclusions: Probiotic nasal rinses may contribute to restoring microbial homeostasis by reducing genera associated with inflammatory dysbiosis in nasal inflammatory diseases, warranting further research on their clinical benefits. Full article

This study developed a semi-passive treatment system for manganese (Mn)- and zinc (Zn)-containing mine water by repurposing a neutralization tank into a biologically active stirred reactor. Laboratory-scale experiments demonstrated efficient removal of Mn²⁺ (>97%) and Zn²⁺ (>80%) with hydraulic retention times (HRTs) as short as 6 h—significantly faster than traditional passive systems. XRD and XANES analyses identified the predominant formation of birnessite, a layered Mn oxide, during Mn²⁺ oxidation, with Zn co-treatment promoting the precipitation of Zn-containing carbonates. Despite decreasing crystallinity of birnessite over time, microbial activity, dominated by Mn-oxidizing genera, such as Sphingomonas, Pseudonocardia, Sphingopyxis, Nitrospira, and Rhodobacter, persisted in the presence of Zn²⁺, ensuring system stability. Importantly, the low leachability of Mn and Zn from the resulting sludge in TCLP tests confirmed its environmental safety and potential for reuse. By leveraging existing infrastructure and microbial biomineralization, this system bridges the gap between passive and active treatments, significantly reducing treatment footprints and operational costs. These findings highlight the potential of repurposing mine water treatment tanks as a scalable, cost-effective solution for sustainable mine water remediation. Full article

Paphiopedilum micranthum, an IUCN Red List species, is discontinuously distributed in the karst limestone mountain of southwest China and exhibits ecological specialization, typically through lithophytic and terrestrial ecotypes. Whether the distribution of rhizosphere bacteria and fungi in these different habitats is random or reflects soil preferences requires further investigation. A total of 73 samples from the core distribution areas in China, representing all habitats in two sites, were analyzed for soil differences by comparing edaphic properties and microbial community structure based on high-throughput sequencing of bacterial 16S rRNA genes and fungal ITS region sequences, alongside soil physiochemical data. The results showed no significant differences in microbial community richness and diversity across the heterogeneous habitats. However, significant differences in taxa were observed across various habitats. Dominant bacterial phyla included Actinobacteriota, Proteobacteria and Acidobacteriota, with dominant genera such as Crossiella, Pseudonocardia, 67-14, Mycobacterium and RB41. The primary fungal phyla were Basidiomycota and Ascomycota, featuring prominent genera such as Phlegmacium, Archaeorhizomyces, Trechispora, and Lepiota. There were 16 bacterial genera and 13 fungal genera associated with nitrogen transformation and fixation. Alkali-hydrolyzed nitrogen (AN) was identified as a main driver of soil bacterial and fungal community variation. Based on an analysis of soil physicochemical properties, ammonium nitrogen content was consistently higher than nitrate nitrogen across different habitats. Furthermore, across all heterogeneous habitats, P. micranthum showed no significant differences in nitrate nitrogen, ammonium nitrogen, or their ratio. The nitrogen-use efficiency of P. micranthum ranged from 7.73% to 9.87%, with the highest efficiency observed in the terrestrial habitat of Shedu. These results suggest that P. micranthum prefers habitats rich in organic matter and nitrogen, showing a preference for ammonium nitrogen uptake in natural conditions. Heterogeneous habitats affect plant nitrogen-use efficiency as well as changes in microbial community composition. Full article

To explore and utilize the abundant soil microorganisms and their beneficial functions, high-throughput sequencing technology was used to analyze soil microbial compositions in the rhizosphere of red and green amaranth varieties. The results showed that significant differences in soil microbial composition could be found in the rhizosphere of amaranth plants with different color phenotypes. Firstly, soil bacterial compositions in the rhizosphere were significantly different between red and green amaranths. Among them, Streptomyces, Pseudonocardia, Pseudolabrys, Acidibacter, norank_ f_ Micropepsaceae, Bradyrhizobium, and Nocardioides were the unique dominant soil bacterial genera in the rhizosphere of red amaranth. In contrast, Conexibacter, norank_f_norank_o_norank_c_TK10, and norank_f_ norank_o_ norank_ c_AD3 were the special dominant soil bacterial genera in the rhizosphere of green amaranth. Additionally, even though the soil fungal compositions in the rhizosphere were not significantly different between red and green amaranths, the abundance of the dominant soil fungal genera in the rhizosphere showed significant differences between red and green amaranths. For example, unclassified_k__Fungi, Fusarium, Cladophialophora, unclassified_c__Sordariomycetes and unclassified_p__Chytridiomycota significantly enriched as the dominant soil fungal genera in the rhizosphere of the red amaranth. In contrast, Aspergillues only significantly enriched as the dominant soil fungal genus in the rhizosphere of green amaranth. All of the above results indicated that amaranth with various color phenotypes exactly recruited different microorganisms in rhizosphere, and the enrichments of soil microorganisms in the rhizosphere could be speculated in contributing to amaranth color formations. Full article

The ongoing scientific debate on the selection of the best bioindicators to reflect the quality of arable soils indicates both their microbiome and biochemical parameters. Consideration has also been given to the fact that Zea mays has achieved the status of a crop used in the feed industry and for energy purposes, and Triticosecale is attracting increasing interest in this area. Therefore, the aim of this study was to determine the wide range of effects of Zea mays and Triticosecale cultivation on soil microbial and biochemical activity. The assessment of these parameters was based on the determination of microbial abundance, colony development index (CD), ecophysiological index of microbial diversity (EP), soil enzyme activities (dehydrogenases, catalase, urease, acid phosphatase, alkaline phosphatase, β-glucosidase, and arylsulfatase) as well as soil physicochemical properties. The innovative nature of the research was achieved by extending the pool of analyses to include both microbial biodiversity and analysis of soil samples at three depths: 0–20 cm; 21–40 cm; and 41–60 cm. It was found that the highest activities of soil enzymes and the abundance of organotrophic bacteria and fungi, as well as their colony development indices (CD), occurred within the rhizosphere and that their values decreased with increasing depth of the soil profile layers. Two phyla, Actinobacteria and Proteobacteria, representing the microbiome of arable soils, were identified independently of soil management practices. Unique bacterial genera in the soil under Triticosecale cultivation were Pseudonocardia, whereas Rhodoplanes, Nocardioides, and Rhodanobacter were found under Zea mays cultivation. The activity of all enzymes, especially urease and arylsulfatase, was significantly higher in the soil under Triticosecale. This was influenced by the more favorable physicochemical properties of the soil. Full article

Seed endophytes in maize, which facilitate the transmission of microorganisms from one plant generation to the next, may play a crucial role in plant protection and growth promotion. This study aimed to investigate the effects of various maize varieties on the communities of endophytic bacteria in seeds and germinating roots. This study utilized Illumina high-throughput sequencing technology to examine the structural and diversity differences of endophytic bacterial communities within seed maize (BY1507), silage maize (QQ446), and wild maize (Teosinte) in both seeds and germinating roots. The results showed that 416 bacterial genera were detected, with Pantoea, Lachnospiraceae, Pararhizobium, Enterobacteriaceae, Stenotrophomonas, and Pseudonocardia being the most prevalent (relative abundance > 10%) at the genus level. No significant difference was observed in diversity indices (Chao1, ACE, Shannon, and Simpson) of seed endophytes among BY1507, QQ446, and Teosinte. The Shannon and Simpson indices for the germinating root endophyte from the wild variety (Teosinte) were significantly higher than the domesticated varieties (BY1507 and QQ446). PCoA revealed a notable overlap in the endophytic bacterial communities from the seeds of BY1507, QQ446, and Teosinte. Yet, clustering patterns were found. Co-occurrence network analysis showed that BY1507, QQ446, and Teosinte share a notable proportion of shared endophytic bacteria (>30%) between the seeds and germinating roots. This investigation elucidates the characteristics of endophytic microbial communities of seeds and germinating roots with seed maize, silage maize, and wild maize, offering data for future research on the physiological ecological adaptation of these endophytic microbial communities. Full article

Emerging zoonotic diseases are one of the main threats to human and animal health. Among the agents with the potential for zoonoses, those of bacterial origin have great relevance in Public Health. Rodents are considered one of the main reservoirs of pathogens that represent a risk to human health or animal species. We used massive 16S ribosomal RNA gene amplicon sequencing to survey bacteria present in the spleen of six species of rodents in Panama in order to identify bacterial taxa with zoonotic potential in the country. We found 3352 bacterial Amplicon Sequence Variants (ASVs, i.e., phylogenetic species) in the spleen of six rodent species surveyed (Liomys adspersus, Melanomys caliginosus, Mus musculus, Proechimys semispinosus, Rattus rattus, Zygodontomys brevicauda). This bacterial community was represented by 25 phyla, 55 classes, 140 orders, 268 families, and 508 genera. The three predominant phyla were Actinobacteria, Firmicutes, and Proteobacteria, and the five predominant classes were Actinobacteria, Alpha- and Gammaproteobacteria, Bacilli, and Clostridia. There were seven high-abundance genera: Acinetobacter, Bartonella, Cutibacterium, Enterococcus, Sarcina, Staphylococcus, and Wolbachia. Genera found with less abundance included Bradyrhizobium, Chryseobacterium, Clostridium, Corynebacterium, Lactobacillus, Pseudonocardia, Rhodococcus, and Sphingomonas. Some of these genera (high or low abundance) have clinical importance. The identification of bacterial taxa with zoonotic potential in rodent species performed here allows us to have surveillance mechanisms for these pathogens and to be able to recognize localities to be prioritized for prevention of transmission and outbreaks, thus being of value for public health in Panama. Full article

Tartary buckwheat is a healthy grain rich in nutrients and medicinal ingredients and consequently is commonly used for Huangjiu brewing. In order to reveal the correlation between microbial succession and higher alcohols production, in this study, Huangjiu fermentation was conducted using Tartary buckwheat as the raw material and wheat Qu as the starter culture. Microbial community dynamics analysis indicated that the bacterial diversity initially decreased rapidly to a lower level and then increased and maintained at a higher level during fermentation. Lactococcus was the dominant bacteria and Ralstonia, Acinetobacter, Cyanobacteria, and Oxalobacteraceae were the bacterial genera with higher abundances. In sharp contrast, only 13 fungal genera were detected during fermentation, and Saccharomyces showed the dominant abundance. Moreover, 18 higher alcohol compounds were detected by GC-MS during fermentation. Four compounds (2-phenylethanol, isopentanol, 1-hexadecanol, and 2-phenoxyethanol) were stably detected with high concentrations during fermentation. The compound 2-ethyl-2-methyl-tridecanol was detected to be of the highest concentration in the later period of fermentation. Correlation analysis revealed that the generation of 2-phenylethanol, isopentanol, 1-hexadecanol, and 2-phenoxyethanol were positively correlated with Granulicatella and Pelomonas, Bacteroides, Pseudonocardia and Pedomicrobium, and Corynebacterium, respectively. The verification fermentation experiments indicated that the improved wheat Qu QT3 and QT4 inoculated with Granulicatella T3 and Acidothermus T4 led to significant increases in the contents of 2-phenylethanol and pentanol, as well as isobutanol and isopentanol, respectively, in the Tartary buckwheat Huangjiu. The findings benefit understanding of higher alcohols production and flavor formation mechanisms in Huangjiu fermentation. Full article

Mangrove ecosystems play curial roles in providing many ecological services and alleviating global climate change. However, they are in decline globally, mainly threatened by human activities and global warming, and organic pollutants, especially PAHs, are among the crucial reasons. Microbial remediation is a cost-effective and environmentally friendly way of alleviating PAH contamination. Therefore, understanding the effects of environmental and nutritional parameters on the biodegradation of polycyclic aromatic hydrocarbons (PAHs) is significant for the bioremediation of PAH contamination. In the present study, five bacterial strains, designated as Bp1 (Genus Rhodococcus), Sp8 (Genus Nitratireductor), Sp13 (Genus Marinobacter), Sp23 (Genus Pseudonocardia), and Sp24 (Genus Mycolicibacterium), have been isolated from mangrove sediment and their ring hydroxylating dioxygenase (RHD) genes have been successfully amplified. Afterward, their degradation abilities were comprehensively evaluated under normal cultural (monoculture and co-culture) and different nutritional (tryptone, yeast extract, peptone, glucose, sucrose, and NPK fertilizer) and environmental (cetyl trimethyl ammonium bromide (CTAB), sodium dodecyl sulfate (SDS)) parameters, as well with different co-contaminants (phenanthrene and naphthalene) and heavy metals (Cd²⁺, Cu²⁺, Fe³⁺, Ni²⁺, Mg²⁺, Mn²⁺, and Co²⁺). The results showed that strain Sp24 had the highest pyrene degradation rate (85%) in the monoculture experiment after being cultured for 15 days. Adding nitrogen- and carbon-rich sources, including tryptone, peptone, and yeast extract, generally endorsed pyrene degradation. In contrast, the effects of carbon sources (glucose and sucrose) on pyrene degradation were distinct for different bacterial strains. Furthermore, the addition of NPK fertilizer, SDS, Tween-80, phenanthrene, and naphthalene enhanced the bacterial abilities of pyrene removal significantly (p < 0.05). Heavy metals significantly reduced all bacterial isolates’ degradation potentials (p < 0.05). The bacterial consortia containing high bio-surfactant-producing strains showed substantially higher pyrene degradation. Moreover, the consortia of three and five bacterial strains showed more degradation efficiency than those of two bacterial strains. These results provide helpful microbial resources for mangrove ecological remediation and insight into optimized culture strategies for the microbial degradation of PAHs. Full article