Search Results (24)

The present study investigated the impact of genetic engineering strategies to produce a cell-free xylanase for applications in the baking industry. The xynA1 gene from the nonpathogenic bacterium Caulobacter vibrioides was integrated into the pAS22 vector with a xylose-inducible promoter and introduced back into the bacteria, resulting in the creation of the BS-xynA1. This construct exhibited substantial secreted xylanase 1 (XynA1) activity, reaching 17.22 U/mL, and a specific activity of 278.64 U/mg after an 18 h growth period with 0.3% (v/v) xylose plus 0.2% (w/v) corn straw. RT-qPCR analysis confirmed that higher xylanase activity in C. vibrioides cells was correlated with increased transcription of the xynA1 gene in the induction medium. Moreover, BS-xynA1 cells coexpress other enzymes, including xylanase 2 (XynA2), cellulase, pectinase, α-amylase, β-glucosidase, β-xylosidase, and α-L-arabinosidase, at low levels (≤2 U/mL). In vitro comparison of cell-free xylanases from BS-xynA1 with three commercially available xylanase-containing mixtures commonly utilized in baking protocols revealed its superior specific activity (163.4 U/mg) across a broad temperature range (30–100 °C), with optimal performance at 50 °C. In practical baking tests, the addition of cell-free XynA1 led to a reduction in dough kneading time and increase in bread height compared to those of the control. Notably, the incorporation of XynA1 resulted in enhanced alveolar structure formation within the bread crumb. Specifically, the following changes were observed in the mass parameters compared to those of the control: an increase in extensibility, elasticity, and deformation energy, and subsequent improvements in strength. Additionally, XynA1 addition led to a reduction in toughness and toughness/elasticity index, indicating a reduction in the mass stiffness of the enzyme-treated bread. To date, this is the first successful application of recombinant XynA1 from C. vibrioides in biotechnological processes related to baking, underscoring the potential and prospects in the food industry. Full article

In view of the increasing environmental pollution caused by bisphenol A (BPA), understanding its impact on the microbiological properties of soil, which play a key role in maintaining soil fertility and consequently ecosystem stability, is particularly important. Therefore, the aim of this study was to assess the sensitivity of the soil microbiome to this xenobiotic and to evaluate the potential of organic materials such as starch (St), grass compost (Co), and fermented bark (B) to restore the balance of soil cultivated with Zea mays. The negative effects of BPA on the abundance, diversity, and structure of bacterial and fungal communities in soil contaminated with 500 and 1000 mg kg⁻¹ d.m. of soil were confirmed. Changes in the phospholipid profile, including phosphatidylethanolamine (PE), phosphatidylcholine (PC), phosphatidylglycerol (PG), and ergosterol (E), were also assessed. BPA applied at 1000 mg kg⁻¹ d.m. of soil inhibited the proliferation of organotrophic bacteria and actinomycetes, while stimulating fungal growth. This xenobiotic’s impact is also reflected by a decrease in PC and PG levels in soil under BPA pressure. Through amplification of the V3-V4 16S rRNA region (for bacteria) and the ITS1 region (for fungi), the dominant bacterial phylum Proteobacteria was identified, with genera including Cellulosimicrobium, Caulobacter, Rhodanobacter, Sphingomonas, Mucilaginibacter, and Pseudomonas. Among fungi, Ascomycota dominated, primarily represented by the genus Penicillium. Of all the organic materials tested for mitigating BPA’s negative effects, grass compost was identified as the most promising, not only restoring soil homeostasis but also enhancing the growth and development of Zea mays cultivated in BPA-contaminated soil. Full article

Interactions between bacteria and bacteriophages are important for the maintenance of soil communities. In this study, we characterized the giant bacteriophages found within diverse soil bacteria and 14 additional phages isolated directly from soil samples. Based on their genome sizes and genetic composition, we concluded that these phages belong to the Dolichocephalovirinae subfamily. In addition, we used pulsed-field gel electrophoresis to show that the genomes of these phages were present as episomal pseudolysogens in the cytoplasm of their host cells. These findings suggest that episomal phages are important components of soil microbial ecosystems. Understanding the interactions between bacteriophages and bacteria is essential for microbial ecology, as they influence nutrient cycling, community composition, and host evolution. Furthermore, these phage-bacteria dynamics offer potential applications in plant disease control, as bacteriophages could serve as biocontrol agents against soilborne pathogens, promoting sustainable agricultural practices. Full article

Polyphenols show promising application prospects as a novel natural disinfectant for drinking water. This study employed a simulated pipe network system to investigate the effects of tea polyphenols at an initial concentration of 5 mg/L on the characteristics of biofilm on pipe walls and microbial community succession patterns under different water ages (12–48 h). The results showed that with increasing water age, the tea polyphenol residual concentration gradually decreased, and the biofilm structure significantly evolved: the surface roughness increased from 5.57 nm to 32.8 nm, and the biofilm thickness increased from 40 nm to 150 nm. Microbial community diversity exhibited a trend of first increasing and then decreasing, with the Shannon index reaching its peak (2.847) at a water age of 36 h and remaining significantly higher than the control group (1.336) at all stages. High-throughput sequencing revealed a transition from a single dominant genus of Methylophilus (54.41%) at a water age of 12 h to a multi-genus coexistence pattern at a water age of 48 h, with Methylophilus (24.33%), unclassified_Saprospiraceae (21.70%), and Hydrogenophaga (16.52%) as the main dominant groups. Functional bacterial groups exhibited temporal changes, with biofilm colonization-related genera (Caulobacter, Sphingobium) reaching their peaks at 36 h, while special metabolic genera (Methylophilus, Hydrogenophaga) dominated at 48 h. Potential pathogens in the tea polyphenol treatment groups were effectively controlled at low levels (<0.21%), except for a temporary increase in Legionella (6.50%) at 36 h. Tea polyphenols’ selective inhibition mechanism helps suppress the excessive proliferation of specific genera and reduces the risk of potential pathogen outbreaks. This has important implications for ensuring the microbiological safety of drinking water. Full article

Bacteriophages grown on Caulobacter vibrioides strain CB15 have reduced plating efficiency on other Caulobacter strains. To determine the cause of this reduced plating efficiency, we performed a series of experiments that demonstrated that the reduced plating efficiency is due to a novel set of restriction and modification (RM) enzymes that are present in most of the Caulobacter strains that we tested. We then demonstrated that one of these RM systems recognizes the nucleotide sequence 5′-ATNNAT-3′. A careful inspection of the genome nucleotide sequences of each of the strains revealed that the genes coding for these RM enzymes have not been annotated or identified, suggesting that the proteins may differ from the common types of bacterial restriction and modification enzymes. In addition, the host strain NA1000 contains a 26 kb mobile element that provides resistance to incoming phages. Full article

Members of the Dolichocephalovirinae subfamily are giant viruses with an elongated head and a flexible tail that is used to infect Caulobacter strains. In this paper, we describe the isolation and characterization of nine newly isolated phages and present evidence that seven of these phages represent a new Dolichocephalovirinae genus that has significant differences from the four previously described Dolichocephalovirinae genera. In addition, since these new phages were isolated from a single sampling site over the course of three years, a comparison of their genome sequences reveals a low level of within-population diversity resulting from both single-nucleotide polymorphisms and insertions or deletions. A comparison of the host ranges of these phages suggests that differences in host susceptibility may be an important factor in maintaining this diversity. Full article

To explore how microbial interactions within the rhizosphere influence the diversity and functional roles of bacterial communities, we isolated 21 bacterial strains from soil samples collected near Rocky Branch Creek on the University of South Carolina campus. Our findings revealed that a significant proportion of the isolated bacterial strains are lysogenic. Contrary to predictions of a narrow host range, most of the bacteriophages derived from these lysogenic bacteria demonstrated the ability to infect a broad range of bacterial strains. These results suggest that the bacterial community shares a complex phage community, creating an intricate web of interactions. This study enhances our understanding of the relationships between phages and their bacterial hosts in soil ecosystems, with implications for ecological balance and agricultural practices aimed at improving plant health through microbial management strategies. Full article

Mine-tailing dumps are one of the leading sources of environmental degradation, often with public health and ecological consequences. Due to the complex ecosystems generated, they are ideal sites for exploring the bacterial diversity of specially adapted microorganisms. We investigated the concentrations of trace metals in solid copper (Cu) mine tailings from the Ovejería Tailings Dam of the National Copper Corporation of Chile and used high-throughput sequencing techniques to determine the microbial community diversity of the tailings using 16S rRNA gene-based amplicon sequence analysis. The concentrations of the detected metals were highest in the following order: iron (Fe) > Cu > manganese (Mn) > molybdenum (Mo) > lead (Pb) > chromium (Cr) > cadmium (Cd). Furthermore, 16S rRNA gene-based sequence analysis identified 12 phyla, 18 classes, 43 orders, 82 families, and 154 genera at the three sampling points. The phylum Proteobacteria was the most dominant, followed by Chlamydiota, Bacteroidetes, Actinobacteria, and Firmicutes. Genera, such as Bradyrhizobium, Aquabacterium, Paracoccus, Caulobacter, Azospira, and Neochlamydia, showed high relative abundance. These genera are known to possess adaptation mechanisms in high concentrations of metals, such as Cd, Cu, and Pb, along with nitrogen-fixation capacity. In addition to their tolerance to various metals, some of these genera may represent pathogens of amoeba or humans, which contributes to the complexity and resilience of bacterial communities in the studied Cu mining tailings. This study highlights the unique microbial diversity in the Ovejería Tailings Dam, including the discovery of the genus Neochlamydia, reported for the first time for heavy metal resistance. This underscores the importance of characterizing mining sites, particularly in Chile, to uncover novel bacterial mechanisms for potential biotechnological applications. Full article

Previous studies have identified diverse bacteriophages that infect Caulobacter vibrioides strain CB15 ranging from small RNA phages to four genera of jumbo phages. In this study, we focus on 20 bacteriophages whose genomes range from 40 to 60 kb in length. Genome comparisons indicated that these diverse phages represent six Caulobacter phage genera and one additional genus that includes both Caulobacter and Brevundimonas phages. Within species, comparisons revealed that both single base changes and inserted or deleted genetic material cause the genomes of closely related phages to diverge. Among genera, the basic gene order and the orientation of key genes were retained with most of the observed variation occurring at ends of the genomes. We hypothesize that the nucleotide sequences of the ends of these phage genomes are less important than the need to maintain the size of the genome and the stability of the corresponding mRNAs. Full article

Reductive soil disinfestation (RSD) and chemical soil fumigation (CSF) comprise the most popular pre-planting soil management strategies. Their efficiency in suppressing several plant diseases in agricultural production systems has been compared. However, the disease-control effect of these methods on Fusarium wilt disease in Dioscorea batatas Decne (D. batatas) remains unclear. Importantly, dissimilarities in the impact of their bio-predictors on plant health have not been well characterized. Herein, four treatments, including no treatment (CK), RSD with gran chaff (GC-RSD) and molasses (MO-RSD), and CSF with dazomet (DA-CSF), were performed in a pot experiment using D. batatas-diseased soil. Compared with the CK treatment, the Fusarium oxysporum population significantly decreased by 88.89–97.78% following the DA-CSF, GC-RSD, and MO-RSD treatments. The bacterial community and functional composition of the soil were considerably altered by these treatments. However, the incidence of Fusarium wilt disease in D. batatas was significantly decreased in the two RSD-treated soils, rather than in DA-CSF-treated soils. Bacterial α-diversity and population as well as some key nitrogen-related functional gene expressions as bio-predictors were significantly lower in DA-CSF-treated soil than in RSD-treated soil. In particular, the core (e.g., Azotobacter, Phenylobacterium, Clostridium, Bradyrhizobium, Microvirga, and Caulobacter) and unique (e.g., Pseudomonas, Brevundimonas, Flavobacterium, Ochrobactrum, and Sphingobacterium) functional microbiomes in RSD-treated soil exerted a positive impact on soil functional composition of the soil and plant growth. Taken together, our results indicate that RSD outperformed CSF in promoting plant health by regulating the bacterial community and functional composition. Full article

Tuberculosis, caused by Mycobacterium tuberculosis (Mtb), is a serious and devastating infectious disease worldwide. Approximately a quarter of the world population harbors latent Mtb infection without pathological consequences. Exposure of immunocompetent healthy individuals with Mtb does not result in active disease in more than 90% individuals, suggesting a defining role of host immunity to prevent and/or clear early infection. However, innate immune stimulation strategies have been relatively underexplored for the treatment of tuberculosis. In this study, we used cell culture and mouse models to examine the role of a heat-killed form of a non-pathogenic microbe, Caulobacter crescentus (HKCC), in inducing innate immunity and limiting Mtb infection. We also examined the added benefits of a distinct chemo-immunotherapeutic strategy that incorporates concurrent treatments with low doses of a first-line drug isoniazid and HKCC. This therapeutic approach resulted in highly significant reductions in disseminated Mtb in the lungs, liver, and spleen of mice compared to either agent alone. Our studies demonstrate the potential of a novel innate immunotherapeutic strategy with or without antimycobacterial drugs in controlling Mtb infection in mice and open new avenues for the treatment of tuberculosis in humans. Full article

Although the important role of microbes in freshwater is well understood, studies on phage–host systems in such environments during ice cover are completely lacking. Here, we describe the isolation and characterization of three new bacteriophages infecting Xylophilus sp., Caudobacter sp., and Polaromonas sp. from freshwater samples taken under the ice cover of Lake Konnevesi, Finland. Lumi, Kuura, and Tiera bacteriophages have tailed icosahedral virions and double-stranded DNA. Lumi is a siphophage with a genome of 80,496 bp, and Kuura and Tiera are podophages, and their genomes are 43,205 and 45,327 bp in length, resembling viruses in the class Caudoviricetes. Their host ranges were very limited among the winter-isolated bacterial strains from Konnevesi, each infecting only their own hosts. They can infect efficiently at 4 °C, showing that they are adapted to living in lake water under ice cover. Analysis of the viral genome sequences showed that a significant number of the gene products of each virus are unique, indicating that there is unexplored viral diversity in freshwaters. To our knowledge, Lumi and Tiera are the first phages isolated on the Xylophilus sp. and Polaromonas sp. strains, allowing their exploitation in further studies of freshwater bacterial–phage interactions. Full article

The Korean fir (Abies koreana), a native coniferous tree species mainly found on Mt. Halla in Jeju, South Korea, is suffering from continuous population decline and has been declared an endangered species. Research efforts have focused on the possible abiotic causes behind this worrying decline. However, the potential link between tree vitality and the rhizosphere microbiome remains unclear. In this study, a comparative metagenomic 16S rRNA sequence analysis was used to investigate the composition of the rhizosphere microbiota of samples collected from healthy and die-back-affected trees on Mt. Halla. The results indicated a significant reduction in the richness and diversity of microbiota in the rhizosphere of die-back-affected trees. Moreover, the relative abundance of Proteobacteria, Actinobacteria, and Bacteroidetes were significantly higher in healthy trees than in standing dead trees. Many bacterial genera were significantly more abundant in the rhizosphere of healthy trees, including those known for promoting plant growth and tolerance to biotic and abiotic stresses (e.g., Bradyrhizobium, Rhizomicrobium, Caulobacter, Nitrosospira, Rhizobacter, Paraburkholderia, Rhizobium, Devosia, Caballeronia, Niveispirillum, Dyella, Herbaspirillum, Frankia, Streptomyces, Actinoallomurus, Lysobacter, Luteibacter, Mucilaginibacter, and Variovorax). To our knowledge, this is the first report on rhizosphere bacterial microbiome dysbiosis in die-back-affected Korean fir trees, suggesting that the influence of rhizosphere microbiota should be considered to save this endangered species by investigating possible intervention strategies in future work. Full article

The nucleoid-associated protein GapR found in Caulobacter crescentus is crucial for DNA replication, transcription, and cell division. Associated with overtwisted DNA in front of replication forks and the 3′ end of highly-expressed genes, GapR can stimulate gyrase and topo IV to relax (+) supercoils, thus facilitating the movement of the replication and transcription machines. GapR forms a dimer-of-dimers structure in solution that can exist in either an open or a closed conformation. It initially binds DNA through the open conformation and then undergoes structural rearrangement to form a closed tetramer, with DNA wrapped in the central channel. Here, we show that the DNA binding domain of GapR (residues 1–72, GapR^ΔC17) exists as a dimer in solution and adopts the same fold as the two dimer units in the full-length tetrameric protein. It binds DNA at the minor groove and reads the spatial distribution of DNA phosphate groups through a lysine/arginine network, with a preference towards AT-rich overtwisted DNA. These findings indicate that the dimer unit of GapR has an intrinsic DNA binding preference. Thus, at the initial binding step, the open tetramer of GapR with two relatively independent dimer units can be more efficiently recruited to overtwisted regions. Full article

Vachellianilotica (L.) Willd. Ex Del. is a multipurpose leguminous tree that is common in grassland and savanna ecosystems in southern and eastern Africa. These ecosystem soils are reported to be acidic and nutrient-limited, specifically with regards to nitrogen (N) and phosphorus (P). The presence of this plant in these terrestrial ecosystems improves soil fertility benefiting the surrounding vegetation due to its ability to fix atmospheric N. This study seeks to understand the N-fixing bacteria symbiosis and physiological adaptations of V. nilotica in these acidic and nutrient-deficient KwaZulu-Natal soils. The soils used for this study were collected from the Ukulinga Grassland Nutrient Experiment located at the Ukulinga research farm of the University of KwaZulu-Natal, Pietermaritzburg, South Africa. Due to long-term soil nutrient addition treatments, these soils offered a diverse nutrient variation for better understanding the effects of acidity and nutrient variation on microbial symbiosis, plant nutrition, and biomass accumulation of V. nilotica. V. nilotica was able to maintain growth by relying on both atmospheric and soil-derived N across all treatments decreasing carbon (C) growth costs. There was an increased reliance on atmospheric-derived N of un-nodulated high N-treated plants. The plants grown in high N + P soils were able to nodulate with various species from the Mesorhizobium genus, which resulted in increased biomass compared to other plants. The results of this study show that V. nilotica can alter N sources to reduce C growth costs. In addition, both nodulating and free-living soil N₂ fixing bacteria such as Caulobacter rhizosphaerae, Sphingomonas sp. and Burkholderia contaminans identified in the experimental soils may play an important role under P-deficient conditions. Full article