Search Results (138)

The nursery phase is vital for forest regeneration, yet studies on plant growth-promoting (PGP) bacteria to enhance sustainable nursery production in forest species are scarce. This study explores whether endophytic bacteria from disease-resistant Pinus pinea L. can improve germination and seedling quality in susceptible Pinus radiata D. Don. Root endophytes were isolated, screened for PGP traits, and identified via 16S rRNA gene sequencing. Bacterial formulations were applied to P. radiata seeds to determine their impact on germination and plant quality indicators (photosynthetic pigments and other metabolites). Paenibacillaceae (19%) and Bacillaceae (13%) were predominant among 68 isolates, with 94% producing indole-3-acetic acid, and Burkholderiaceae showing the broadest PGP trait diversity. Seedlings inoculated with formulation C3 (Caballeronia R.M3R3, Rhodococcus T.M4R4, and Mesorhizobium R.M1R2) displayed an improved germination rate (89% compared to 71% from the uninoculated control), while those inoculated with formulation P4 (Paenibacillus T.M5R4, Bacillus R.M2R7, Acinetobacter T.M2R22, and Paraburkholderia R.M1R3) showed an improved germination rate (81%), increased amount of starch (0.4-fold), and free amino acids (1.5-fold). This study presents a comprehensive approach, from endophyte isolation to in vivo tests, highlighting two bacterial formulations as candidates for further proof-of-concept nursery trials. Ultimately, these bioinoculants represent eco-friendly strategies to enhance forest seedling establishment and support sustainable forest management. Full article

Extracellular polymeric substances (EPS) are multifunctional biopolymers that have significant biotechnological potential. In this study, forty-seven strains of Rhodococcus actinomycetes were screened for EPS production and the content of its main components: carbohydrates, lipids, proteins, and nucleic acids. The Rhodococcus strains produced lipid-rich EPS (15.6 mg·L⁻¹ to 71.7 mg·L⁻¹) with carbohydrate concentrations varying from 0.6 mg·L⁻¹ to 58.2 mg·L⁻¹ and low amounts of proteins and nucleic acids. Biofilms of R. ruber IEGM 231 were grown on nitrocellulose filters in the presence of n-hexane, n-hexadecane, or diesel fuel. The distribution of β-polysaccharides, glycoconjugates, and proteins between cells and the extracellular matrix was examined using fluorescence microscopy. The observed release of β-polysaccharides into the biofilm matrix in the presence of n-hexane and diesel fuel was regarded as an adaptation to the assimilation of these toxic hydrocarbons by Rhodococcus cells. Atomic force microscopy of the dried EPS film revealed adhesion forces between 1.0 and 20.0 nN, while some sites were highly adhesive (F_a ≥ 20.0 nN). EPS biosynthetic genes were identified, with two glycosyltransferases correlating with an increase in carbohydrate production. The production of EPS by Rhodococcus cells exhibited strain-specific rather than species-specific patterns, reflecting a high genetic diversity of these bacteria. Full article

There is a lack of research on screening new strains of high-efficiency ammonia nitrogen degrading bacteria and treating high-concentration ammonia nitrogen aquaculture wastewater using immobilized composite bacteria. In this study, two strains capable of degrading ammonia nitrogen and nitrite were isolated from surface water. The species of the strains were accurately identified using ITS sequencing technology. Scp1 was identified as Pseudomonas and Scr1 as Rhodococcus erythropolis. Both strains were preserved. When the initial concentration of ammonia nitrogen was 1.50 mg/L, the degradation efficiency of ammonia nitrogen after 4 days of inoculation with Scp1, Scr1, and a combination of Scp1 and Scr1 was 90%, 93.3%, and 99.99%, respectively. Similarly, when the initial concentration of nitrite was 0.25 mg/L, the degradation efficiency after 4 days of inoculation with Scp1, Scr1, and a combination of Scp1 and Scr1 was 60%, 82%, and 97.2%, respectively. In addition, when the initial concentration of COD was 20 mg/L, the degradation efficiency after 6 days of inoculation with Scp1, Scr1, and a combination of Scp1 and Scr1 was 59%, 59.4%, and 93.75%, respectively. The results demonstrated that the combined bacteria, Scp1 and Scr1, had a better degradation effect on ammonia nitrogen, nitrite, and COD. Furthermore, a degradation test was conducted in a Penaeus vannamei breeding base, which showed good degradation effects. These findings provide theoretical support for the treatment of high ammonia nitrogen wastewater in aquaculture and have important practical applications. Full article

Wastewater (WW) treatment using biofilms harboring bacteria and microalgae is considered a promising polishing solution to improve current treatment technologies present in wastewater treatment plants (WWTPs), but their interaction in a sessile community remains to be understood. In this work, multi-species biofilms of Chlorella vulgaris, Chlorella sorokiniana, or Scenedesmus obliquus were selected as representative microalgae species of interest for WW bioremediation, and Rhodococcus fascians, Acinetobacter calcoaceticus, or Leucobacter sp. were selected as the bacteria for co-cultivation in a synthetic WW since they are normally found in WW treatment processes. The attached consortia were developed in specific carriers (K5 carriers) for 168 h, and their biofilm formation ability was evaluated in a profilometer and via scanning electron microscopy (SEM) imaging. From the selected microorganisms, C. sorokiniana was the microalga that adapted best to co-cultivation with R. fascians and A. calcoaceticus, developing a thicker biofilm in these two consortia (3.44 ± 0.5 and 4.51 ± 0.8 µm, respectively) in comparison to the respective axenic cultures (2.55 ± 0.7 µm). In contrast, Leucobacter sp. did not promote biofilm growth in association with C. vulgaris and C. sorokiniana, while S. obliquus was not disturbed by the presence of this bacterium. Some bacterial clusters were observed through SEM, especially in A. calcoaceticus cultures in the presence of microalgae. In some combinations (especially when C. vulgaris was co-cultivated with bacteria), the presence of bacteria was able to increase the number of microalga cells adhered to the K5 carrier. This study shows that biofilm development was distinctly dependent on the co-cultivated species, where synergy in biofilm formation was highly dependent on the microalgae and bacteria species. Moreover, profilometry appears to be a promising method for biofilm analyses. Full article

This research aimed to characterise hydrocarbonoclastic bacteria isolated from naturally hydrocarbon-contaminated springs and the surrounding soils in the Agri Valley (Southern Italy) and to assess the effectiveness of bioaugmentation using a four-strain microbial consortium for removing hydrocarbons from artificially diesel-contaminated lake waters in mesocosm experiments. Four novel bacterial strains were selected for the experimentation: Gordonia amicalis S2S5, Rhodococcus erythropolis S2W2, Acinetobacter tibetensis S2S8, and Acinetobacter puyangensis S1W1. The four isolates can use diesel oil as their sole carbon source, and some exhibited a relatively high emulsifying capacity and ability to adhere to hydrocarbons. Furthermore, genome analyses revealed the presence of genes associated with the degradation, detoxification, and transport of various contaminants. Mesocosm experiments demonstrated that the bioaugmentation enhanced the capacities of the native lake microbial communities to remove hydrocarbons, although drastic changes in their composition (analysed through Next-Generation Sequencing—NGS) were observed. Taken together, these results suggest that naturally contaminated environments can serve as a valuable reservoir of microorganisms with significant biotechnological potential, particularly in the field of bioremediation. However, a complete understanding of the ability of the isolated bacterial strains to efficiently degrade contaminants requires further research to fully assess their capabilities and limitations across different settings. Full article

Alkane-oxidizing bacteria play a crucial role in the global carbon cycle. Rhodococcus species are well-known hydrocarbon degraders, distinguished by the harboring of multiple homologs of AlkB family alkane monooxygenases. Although different types of rhodococcal AlkBs have been described, the overall picture of their diversity remains unclear, leaving gaps in the current classification. We conducted a phylogenetic analysis of all AlkBs identified in Rhodococcus (sensu lato) and examined the genomic context of the corresponding genes. The sequence clustering was well aligned with genomic neighborhoods, allowing both features to be used as criteria for proposing AlkB types that form distinct phylogenetic groups and have characteristic genomic contexts. Our approach allowed us to revise the classification of previously described AlkBs, identifying eight types on their basis, and to propose three new ones. Alkane monooxygenases whose genes are co-localized with rubredoxin genes can be considered a generalized AlkBR type, the most common among all Rhodococcus. In the AlkB0 type, which is a paralog of AlkBR, violations of conservativity in known alkane monooxygenase signature motifs were found. Our findings provide a more consistent classification framework for rhodococcal AlkB that prevents the over-reporting of “novel” types and contributes to a deeper understanding of alkane monooxygenase diversity. Full article

Due to its persistence, glyphosate contamination in soil poses environmental and health risks. Plant growth-promoting bacteria (PGPB) offer a potential solution for mitigating glyphosate pollution. This study assessed the glyphosate degradation capacity of three airborne PGPB isolates (Exiguobacterium indicum AS03, Kocuria sediminis AS04, and Rhodococcus rhodochrous AS33) individually and in a consortium (CS) compared to natural attenuation in microcosms as the control (CTL), where soil autochthonous microorganisms (MS) were present. AS03 exhibited the highest glyphosate degradation (86.3%), followed by AS04 and AS33 at 14 days (61.6% and 64.7%). The consortium accelerated glyphosate removal, reaching 99.7%, while the control treatment removal was 94% at 60 days. Aminomethylphosphonic acid (AMPA) is the main metabolite in glyphosate degradation, and it had a maximum peak in concentration at 28 days in the CS + MS (1072 mg kg⁻¹) and CTL (990 mg kg⁻¹) treatments. Subsequently, a decrease in AMPA concentration was observed at 60 days up to 349 mg kg⁻¹ and 390 mg kg⁻¹, respectively. These results suggested that soil autochthonous microorganisms and their interactions with a consortium have similar biotransformation of glyphosate, but the AMPA conversion to other intermedium metabolites through degradation was slow. A minimum AMPA concentration of 15–45 mg kg⁻¹ over time was detected with the consortium. The microbiome analysis revealed shifts in microbial composition, with an increase in glyphosate-degrading genera like Psychrobacter and Lyzobacter. These changes enhance soil resilience and fertility, demonstrating the potential of airborne PGPB for bioremediation and environmental sustainability. Full article

Phenolic compounds are an extensive group of natural and anthropogenic organic substances of the aromatic series containing one or more hydroxyl groups. The main sources of phenols entering the environment are waste from metallurgy and coke plants, enterprises of the leather, furniture, and pulp and paper industries, as well as wastewater from the production of phenol–formaldehyde resins, adhesives, plastics, and pesticides. Among this group of compounds, phenol is the most common environmental pollutant. One of the cheapest and most effective ways to combat phenol pollution is biological purification. However, the inability of bacteria to decompose high concentrations of phenol is a significant limitation. Due to the uncoupling of oxidative phosphorylation, phenol concentrations above 1 g/L are toxic and inhibit cell growth. This article presents data on the biodegradative potential of Rhodococcus opacus strain 3D. This strain is capable of decomposing a wide range of toxicants, including phenol. In the present study, cell growth with phenol, growth after rest, growth of immobilized cells before and after rest, phase contrast, and scanning microscopy of immobilized cells on fiber were studied in detail. The free-living and immobilized cells can decompose phenol concentrations up to 1.5 g/L and 2.5 g/L, respectively. The decomposition of the toxicant was catalyzed by the enzymes catechol 1,2-dioxygenase and cis,cis-muconate cycloisomerase. The role of protocatechuate 3,4-dioxygenase in biodegradative processes is discussed. In this work, it is shown that the immobilized cells can be stored for a long time (up to 2 years) without significant loss of their degradation activity. An assessment of the induction of genes potentially involved in this process was taken. Based on our investigation, we can conclude that this strain can be considered an effective destructor that is capable of degrading phenol at high concentrations, increases its biodegradative potential during immobilization, and retains this ability for a long storage time. Therefore, the strain can be used in biotechnology for the purification of aqueous samples at high concentrations from phenolic contamination. Full article

The adhesion between dibenzofuran (DF) and degrading bacteria is the first step of DF biodegradation and affects the efficient degradation of DF. However, their efficient adhesion mechanism at the molecular level remains unclear. Therefore, this study first examined the adhesive behaviors and molecular mechanisms of Rhodococcus sp. strain p52 upon exposure to DF. The results showed that the adhesion between strain p52 and DF is mediated by extracellular polymeric substances (EPSs). Compared with sodium acetate as a carbon source, the percentages of glucose and proteins related to electron transfer, toxin–antitoxin, and stress responses were elevated, which were analyzed by polysaccharide composition and proteomics, and the contents of extracellular polysaccharides and proteins were increased. Moreover, biofilm analysis suggested an increase in EPS content, and the change in components increased biofilm yield and promoted loose and porous aggregation between the bacteria; this aggregation caused an increase in the specific surface area in contact with DF. The surface characteristics analysis indicated that the production of EPS reduced the absolute value of the zeta potential and increased the hydrophobicity of strain p52, which was beneficial for the adhesion of strain p52 and DF. These findings help us to enhance the understanding of the adhesion mechanisms and bioremediation of polycyclic aromatic hydrocarbons by degrading bacteria. Full article

Herein, biochars derived from corn stalks, rice husks, and bamboo powder were modified by nitric acid oxidation and sodium hydroxide alkali activation to identify efficient and cost-effective polycyclic aromatic hydrocarbon-adsorbent and microbial-immobilized carriers. The surface characterization and adsorption investigation results suggested that acid/alkali modification promoted the phenanthrene removal ability in an aqueous solution of biochars via facilitating π–π/n–π electron donor–acceptor interactions, electrostatic interactions, hydrogen bonds, and hydrophobic interactions. Subsequently, the degrading bacteria Rhodococcus sp. DG1 was successfully immobilized on the rice husk-derived biochar with nitric acid oxidation (RBO), which exhibited the maximum phenanthrene adsorption efficiency (3818.99 µg·g⁻¹), abundant surface functional groups, and a larger specific surface area (182.6 m²·g⁻¹) and pore volume (0.141 m³·g⁻¹). Degradation studies revealed that the microorganisms immobilized on RBO by the adsorption method yielded a significant phenanthrene removal rate of 80.15% after 30 days, which was 38.78% higher than that of the control. Conversely, the polymer gel network-based microenvironment in the microorganism-immobilized RBO by the combined adsorption–embedding method restricted the migration and diffusion of nutrients and pollutants in the reaction system. This study thus introduces an innovative modified biochar-based microbial immobilization technology characterized by a simple design, convenient operation, and high adsorption efficiency, offering valuable insights into material selection for PAH contamination bioremediation. Full article

Phenol and its chlorinated derivatives are introduced into the environment with wastewater effluents from various industries, becoming toxic pollutants. Phenol-degrading bacteria are important objects of research; among them, representatives of the genus Rhodoccocus are often highlighted as promising. Strain 7Ba was isolated by enrichment culture. A new isolate was characterized using culturing, biochemistry, high-throughput sequencing, microscopy (including electron microscopy), and functional genome analysis. Rhodococcus erythropolis strain 7Ba is able to grow on phenol and chlorophenols without losing its properties during long-term storage. It was shown that strain 7Ba is able to form viable but nonculturable (VBNC) forms during long-term storage under nutrient limitation, preserving both cell viability and the ability to degrade phenols. The ultrastructural organization of the vegetative forms of cells and VBNC forms was characterized. The following distinctive features were found: modifications (thickening) of cell membranes, cell size reduction, nucleoid condensation. Functional analysis of the genome showed the presence of genes for the degradation of alkanes, and two branches of the β-ketoadipate pathway for the degradation of aromatic compounds. Also, the genome of strain 7Ba contains several copies of Rpf (resuscitation promoting factor) genes, a resuscitation factor of resting bacterial forms. The new isolate strain 7Ba is a promising biotechnological agent that can not only utilize toxic aromatic compounds but also remain viable during long-term storage. For this reason, its further application as an agent for bioremediation can be successful under changing conditions of climate and given the deficiency of nutrient compounds in nature. Minor biostimulation will allow the strain to recover its metabolic activity and effectively degrade pollution. Full article

Soybean meal, renowned for its high yield, cost efficiency, and protein richness, serves as a pivotal plant-based alternative to fish meal. However, high soybean meal inclusion in Larimichthys crocea diets is linked to enteritis and oxidative damage, with unknown mechanisms. Our study aims to elucidate the molecular basis of soybean-meal-induced enteritis and its impact on intestinal microbiota in L. crocea. To this end, four isonitrogenous and isolipidic diets with varying soybean meal levels (0% FM, 15% SBM15, 30% SBM30, and 45% SBM45) were administered to L. crocea for 8 weeks. The results indicated that the SBM30 and SBM45 treatments significantly hindered fish growth, digestive efficiency, and protein utilization. Furthermore, high soybean meal levels (SBM30 and SBM45) activated intestinal Toll-like receptors (TLR2A, TLR2B, TLR5, and TLR22), stimulating C-Rel and mTOR protein expression and elevating ERK phosphorylation. This led to increased pro-inflammatory cytokine production (IL-1β, IL-6, and TNF-α) and decreased anti-inflammatory cytokine expression (IL-4/13A, IL-4/13B, and TGF-β), suggesting a potential signaling pathway for soybean-meal-induced enteritis. Furthermore, enteritis induced by high soybean meal levels led to oxidative damage, evident from increased MDA levels and decreased antioxidant enzyme activities (SOD and CAT). The SBM30 and SBM45 treatments increased Firmicutes and Bacteroidetes abundance in fish gut microbiota, while Proteobacteria abundance decreased. This microbiota shift may enhance soybean meal nutrient utilization, yet high soybean meal concentrations still impair growth. A soybean-meal-rich diet promotes harmful bacteria like Rhodococcus and depletes probiotics like Ralstonia, increasing disease risks. L. crocea has limited tolerance for soybean meal, necessitating advanced processing to mitigate anti-nutritional factors. Ultimately, exploring alternative protein sources beyond soybean meal for fish meal replacement is optimal for L. crocea. Full article

The effect of a coating material containing organic photoluminophore (PL) on the growth and development of mustard Brassica juncea L. plants colonized with beneficial associative bacteria Pseudomonas putida KT2442 and Rhodococcus erythropolis X5 was studied in vitro and in vivo. Plants grown with the use of microbial bacterization in combination with a photoluminophore coating (PLC) had significantly faster growth rates in vitro (2.1 times faster, P. putida; 1.8 times faster, R. erythropolis) than those grown using PLC alone (1.2 times faster). The leaves of plants grown with PLC had higher contents of glucose and fructose (28.4 ± 0.3% more glucose and 60.4 ± 0.3% more fructose accumulated compared to plants grown without PLC). It was found that seed weights and seed number increased 1.9-fold and 1.6-fold, respectively, for plants grown with PLC and colonized with beneficial P. putida KT2442 bacteria. The stimulatory effect of PLC on photosynthetic parameters of Photosystem II (PSII) was observed in colonized plants grown in vitro. For the first time, it was shown that providing plants with a PLC for only 4 weeks may make it possible to support further plant growth without PLC to obtain higher yields in the future. Thus, PLCs that convert shorter-wavelength radiation into red light may induce enhancement of biochemical processes not only in plants but also in microorganisms that supply plants with growth regulators and other active compounds. The results indicate the need for further research to understand the mechanisms of photobiological and photoregulatory systems in the interaction of microbes and plants. Full article

Microorganisms from various taxonomic groups play a crucial role in environmental cleanup, specifically in the bioremediation of contaminated soils and aquatic ecosystems by decomposing toxic pollutants or transforming them into less toxic substrates that can be easily recycled. Over 150 cultures were examined for their capability to utilize these substances as the only source of growth in a mineral medium, with phenol concentrations in the medium varying from 0.1 g/L to 2.5 g/L, oil at 1–2%, pinoxaden and toluene up to 0.5%, and carbon tetrachloride up to 10%. It was found that the isolated bacteria belonged to the genera Rhodococcus, Pseudomonas, Peribacillus, Microbacterium, and Bacillus. As a result, strains that can efficiently eliminate various pollutants were isolated and characterized. Full article

Microorganisms harbor catabolic plasmids to tackle refractory organic pollutants, which is crucial for bioremediation and ecosystem health. Understanding the impacts of plasmids on hosts provides insights into the behavior and adaptation of degrading bacteria in the environment. Here, we examined alterations in the physiological properties and gene expression profiles of Rhodococcus sp. strain p52 after losing two conjugative dioxin-catabolic megaplasmids (pDF01 and pDF02). The growth of strain p52 accelerated after pDF01 loss, while it decelerated after pDF02 loss. During dibenzofuran degradation, the expression levels of dibenzofuran catabolic genes on pDF01 were higher compared to those on pDF02; accordingly, pDF01 loss markedly slowed dibenzofuran degradation. It was suggested that pDF01 is more beneficial to strain p52 under dibenzofuran exposure. Moreover, plasmid loss decreased biofilm formation, especially after pDF02 loss. Transcriptome profiling revealed different pathways enriched in upregulated and downregulated genes after pDF01 and pDF02 loss, indicating different adaptation mechanisms. Based on the transcriptional activity variation, pDF01 played roles in transcription and anabolic processes, while pDF02 profoundly influenced energy production and cellular defense. This study enhances our knowledge of the impacts of degradative plasmids on native hosts and the adaptation mechanisms of hosts, contributing to the application of plasmid-mediated bioremediation in contaminated environments. Full article