Search Results (63)

Dryland soils of the Caspian region of western Kazakhstan are exposed to environmental stress, including drought, alkalinity, low soil organic matter content, and anthropogenic pressure. In this preliminary study, bacterial communities were investigated in 18 soil samples collected from six sampling groups across Makat (M1, M2), Isatay (I1, I2), and Beyneu (B1, B2) districts. Soil physicochemical properties were measured, and bacterial diversity was analyzed using 16S rRNA gene sequencing of the V3–V4 region. Community composition analysis indicated spatial heterogeneity among the sampled groups. M1 and I1 showed the highest taxon richness, whereas B2 contained the highest number of unique taxa. Genus-level profiles showed that B1 and M2 were mainly associated with Rubrobacter and related actinobacterial taxa; B2 contained higher proportions of Marinobacter, Tychonema, Qipengyuania, and Halomonas; and I2 was enriched with Antarcticibacterium, Salinimicrobium, Rhodococcus, Gillisia, Marinobacter, Dietzia, and Pontibacter. Correlation analysis showed that several bacterial taxa were associated with soil organic matter content, total nitrogen, total phosphorus, exchangeable cations, and pH, although the overall Mantel relationship between soil properties and community structure was not significant. FAPROTAX-based prediction indicated differences in putative heterotrophic, nitrogen-related, sulfur-related, and hydrocarbon-associated functional categories among sites. Because FAPROTAX predictions are based on taxonomic composition, these results should be interpreted only as putative functional potential and not as evidence of actual microbial metabolic activity. These findings suggest that the sampled Caspian dryland soils contain distinct bacterial assemblages and taxa with potential ecological relevance; however, their role in dryland soil resilience or bioremediation should be verified through future culture-based, metagenomic, and functional validation studies. Full article

Soil salinization is a challenge for global agriculture and can affect the yield of staple crops such as maize. Plant growth-promoting rhizobacteria (PGPR) are known to play a pivotal role in enhancing plant growth and stress resilience. However, no studies so far have reported plant growth-promoting (PGP) activity in members of the genus Marinobacter. In this study, a novel strain of Marinobacter sp. ZP-590, was identified as a PGPR based on a polyphasic taxonomic analysis, which was isolated from the rhizosphere soil of Tamarix chinensis Lour. Genomic analysis revealed that ZP-590 possesses 5370 protein-coding genes, including core metabolic, catalytic, and transport functions essential for bacterial survival and plant interactions, along with multiple genes potentially associated with PGP traits such as phosphate solubilization, nitrogen fixation, and the production of siderophore and exopolysaccharide (EPS), tryptophan (a prerequisite for IAA synthesis), and amylase. These genomic predictions were functionally validated through in vitro assays confirming all predicted PGP activities. Pot experiment results suggested that inoculation with ZP-590 enhanced maize growth under saline conditions. Compared to the non-inoculated controls, the treatment significantly increased root fresh weight (14.25%; p < 0.05) and stem fresh weight (125.04%; p < 0.01), while shoot height and leaf fresh weight showed no significant changes. Metabolomic profiling revealed that ZP-590 inoculation was associated with systemic metabolic changes in maize under saline conditions. A total of 394, 262, and 601 differentially accumulated metabolites in the root, stem, and leaf, respectively. These changes were characterized by a substantial up-regulation of antioxidant compounds, notably flavonoids, and changes in carbohydrate and lipid metabolism pathways. The changes in carbohydrate and lipid metabolism pathways may contribute to the supply of energy and structural components for stress adaptation. Meanwhile, the accumulation of antioxidant compounds significantly mitigated saline-induced oxidative damage by reducing the levels of superoxide anion (O₂⁻) in leaves. In this study, Marinobacter sp. ZP-590 is characterized as a PGPR that promotes maize growth under saline conditions. These findings provide a foundation for investigating the molecular mechanisms underlying the interaction between ZP-590 and maize under saline conditions. Full article

Bacterial poly(A) polymerases (PAPs) play an important role in RNA metabolism but remain poorly characterized outside Gammaproteobacteria. Here, we cloned and biochemically characterized the first PAP from Alphaproteobacteria, specifically from Marinobacter lipolyticus (Mli PAP). Using homology-based screening against E. coli PAP-1, we identified Mli PAP, sharing 54.8% sequence identity with its E. coli counterpart. The enzyme was expressed in E. coli but formed insoluble inclusion bodies; the active enzyme was purified as a fusion protein with the DsbA protein and used for functional assays. Mli PAP exhibited optimal activity at 30 °C and similar thermostability to E. coli PAP-1. ATP was the preferred substrate, with K_m comparable to E. coli PAP-1 (1.61 mM and 1.70 mM, respectively), and Mg²⁺ (10 mM) was identified as the optimal cofactor. Mli PAP displayed salt-dependent activity, with the most effective polyadenylation in KCl and inhibition by NaCl and ammonium salts, contrasting with the halophilic nature of its host. This study provides the first functional insights into PAPs from Alphaproteobacteria, broadening the understanding of PAP diversity and biochemical properties, as well as the potential applications of PAPs in biotechnology. Full article

To reduce dependence on oceanic resources, poultry-based ingredients and fortified feeds have become valid alternatives to fish meal (FM) and fish oil (FO). While their impact on growth performance is well established, effects on host-associated microbiota remain less characterized. This study examines the gut microbiota of European sea bass (Dicentrarchus labrax) following FM and FO replacement with poultry- and additive-based diets, applying machine learning (ML) to evaluate diet and genotype effects. A secondary analysis of microbial profiles from two prior trials employed classification models to determine associations between microbial abundance and categorical groupings, and regression models to assess the predictive power of ingredient variations on microbial abundance. Regressors showed limited predictive capacity, whereas classifiers performed better, particularly when genotype was considered. For poultry-based diets, average accuracy was approximately 0.4 for synergistic effects, 0.6 for diet effects, and 0.8 for genotype effects; for fortified-feed diets, average accuracy was approximately 0.2, 0.4, and 0.5, respectively. Feature selection detected microbial genera encompassing beneficial (Brevundimondas, Clostridium, Idiomarina, Lactobacillus, Marinobacter, Pseudoalteromonas, Salinisphaera), neutral (Enterovibrio, Flavobacterium, Photobacterium), opportunistic (Acinetobacter, Escherichia-Shigella, Streptococcus), and undercharacterized (Acholeplasma, Cutibacterium, Enhydrobacter, Micrococcus, Peptoniphilus, Salegentibacter) taxa. ML techniques thus reveal diet- and genotype-specific signatures, underlining the importance of integrated computational-microbiological pipelines. Full article

This study aimed to induce a shift in a bacterial community by adding substrate into a biofloc system to characterize this shift and estimate its benefits in improving water quality and aquatic animal growth. We compared the bacterial communities between two biofloc systems, either with (sB treatment) or without (nB treatment) the addition of substrate (elastic solid packing filler), and we also analyzed the effects of the shift on the water quality and growth performance of shrimp (Litopenaeus vannamei). Beta diversity analysis indicated that the bacterial communities in the two treatments were significantly different (Jaccard index 0.94 ± 0.01, pseudo-F = 3.96, p = 0.001). The addition of substrate showed significant positive effects on bacterial alpha diversity indices (Shannon, Heip, Pielou, and Simpson; p < 0.05) and the abundances of beneficial genera (e.g., Arenimonas, Arthrobacter, Exiguobacterium, Leadbetterella, Luteolibacter, Marinobacter, Nitratireductor, Novosphingobium, Thermomonas, Plesiocystis, and Rubrivivax; p < 0.05). In addition, the substrate also showed significant positive effects on water quality parameters (TAN, TSS, turbidity, biofloc volume, pH, and carbonate alkalinity; p < 0.05), and it also significantly improved shrimp zootechnical performance indices (survival rate, feed conversion ratio, and productivity; p < 0.05). Redundancy analysis revealed that 94.25–98.58% of the variation in the water quality and the shrimp growth performance between the two treatments could be attributed to the shift in bacterial composition and diversity induced by the addition of substrate. These findings characterize the shift in the microbial community in the biofloc system induced by the substrate, and demonstrate how this shift could be beneficial to the water quality and the growth performance of shrimp. Full article

This study explores the potential of two marine-derived bacteria, Cytobacillus kochii and Marinobacter, through in silico analysis of their catechol 2,3-dioxygenase (C23O) enzymes. Molecular docking simulations were conducted using AutoDock Vina to assess the binding interactions between C23O enzymes and ten hydrocarbon pollutants, including monocyclic and polycyclic aromatic hydrocarbons (PAHs). Binding affinities ranged from −4 to −8.7 kcal/mol for Cytobacillus kochii, with the highest affinity observed for fluoranthene (−8.7 kcal/mol), followed by pyrene (−8.5 kcal/mol) and phenanthrene (−8.2 kcal/mol). In comparison, Marinobacter’s C23O showed binding affinities between −4.1 and −8 kcal/mol, with fluoranthene (−8 kcal/mol) and phenanthrene (−7.9 kcal/mol) being top performers. Despite slightly lower affinity, Marinobacter exhibits superior environmental resilience under high salinity and temperature, making it valuable for application in fluctuating marine conditions. Structural interaction analysis revealed consistent pi-pi stacking and hydrogen bonding within the active sites, further supporting enzyme–substrate compatibility. These computational findings underscore Cytobacillus kochii ’s superior catalytic potential and Marinobacter’s ecological robustness. The integration of both strains into a microbial consortium offers a promising synergistic approach, combining enzymatic efficiency and environmental adaptability for effective hydrocarbon degradation. While these computational assessments offer valuable predictive insights, further validation through in vitro and in vivo experiments would be beneficial to determine the actual hydrocarbon degradation efficiencies. Full article

Recirculating aquaculture systems (RAS) address pollution, disease, and sustainability in commercial fish farming, but marine RAS are limited by biofilter maturation and nitrification. This study investigated the effects of air nanobubbles on water quality, fish growth, and bacterial communities in marine RAS stocked with juvenile Malabar red snapper, barramundi and saline-tolerant hybrid tilapia. Flow cytometry was evaluated as a rapid management tool for non-culturable microbes, finding viable bacterial counts 30–100 times higher than conventional total plate counts. There were no significant differences in fish growth, survival, or Feed Conversion Ratio between groups, likely due to low stocking densities (<20 kg/m³) and high water exchange rates (>100%/hour), indicating low system stress. Air nanobubbles did not significantly increase dissolved oxygen levels. While bacterial abundance in water was consistently higher in nanobubble-treated RAS (RAS-N), tank walls showed less biofilm. RAS-N also exhibited a higher abundance of nitrifying bacteria like Nitrospira and Marinobacter, leading to improved nitrogenous waste breakdown and lower nitrite levels. Future research should investigate nanobubbles’ benefits at higher stocking densities and longer durations to fully assess their impact on intensive aquaculture. Full article

Tropical sandy beaches are dynamic ecosystems where microbial communities play crucial roles in biogeochemical processes and tracking human impact. Despite their importance, these habitats remain underexplored. Here, using amplicon-based sequencing of bacterial (V3-V4 16S rRNA) and fungal (ITS2) markers, we first describe microbial communities inhabiting supralittoral–intertidal sediments of two contrasting sandy beaches in the Tadjoura Gulf (Djibouti Republic): Sagallou-Kalaf (SK, rural, siliceous sand) and Siesta Plage (SP, urban, calcareous sand). Sand samples were collected at low tide along 10 m transects perpendicular to the shoreline. Bacterial communities differed significantly between sites and along the sea-to-land gradient, suggesting an influence from both anthropogenic activity and sediment granulometry. SK was dominated by Escherichia-Shigella, Staphylococcus, and Bifidobacterium, associated with human and agricultural sources. SP showed higher richness, with enriched marine-associated genera such as Hoeflea, Xanthomarina, and Marinobacter, also linked to hydrocarbon degradation. Fungal diversity was less variable, but showed significant shifts along transects. SK communities were dominated by Kluyveromyces and Candida, while SP hosted a broader fungal assemblage, including Pichia, Rhodotorula, and Aureobasidium. The higher richness at SP suggests that calcium-rich sands, possibly due to their buffering capacity and greater moisture retention, offer more favorable conditions for microbial colonization. Full article

The study is devoted to the analysis of the physicochemical parameters of formation waters, the metagenomic composition of the microbial community and the characteristics of bacterial isolates from the oil fields of Western Kazakhstan to assess their potential in microbial-enhanced oil recovery (MEOR) technologies. Analyses revealed an adaptation of local microorganisms to extreme conditions of high salinity, temperature and pressure, with the dominant presence of Proteobacteria, including the genus Marinobacter. Screening isolates for biosurfactant synthesis showed a high activity of strains M22-7, M93-8C and M142-2, capable of reducing surface tension to 28.81 ± 0.6 mN/m and forming emulsions. Genetic analysis confirmed the presence of key genes (srfAA, srfp) responsible for surfactin synthesis, but the absence of lchAA and rhlAA indicates that the synthesis of other types of biosurfactants is limited. The results highlight the promise of developing microbial consortia and using biosurfactants in high-salinity environments to enhance oil recovery. Full article

To date, the nitrogen metabolism pathways and salt-tolerance mechanisms of halophilic denitrifying bacteria have not been fully studied, and full-scale engineering trials with saline fly ash-washing wastewater have not been reported. In this study, we isolated and screened a halophilic denitrifying bacterium (Marinobacter sp.), GH-1, analyzed its nitrogen metabolism pathways and salt-tolerance mechanisms using whole-genome data, and explored its nitrogen removal characteristics under both aerobic and anaerobic conditions at different salinity levels. GH-1 was then applied in a full-scale engineering project to treat saline fly ash-washing leachate. The main results were as follows: (1) Based on the integration of whole-genome data, it is preliminarily hypothesized that the strain possesses complete nitrogen metabolism pathways, including denitrification, a dissimilatory nitrate reduction to ammonium (DNRA), and ammonium assimilation, as well as the following three synergistic strategies through which to counter hyperosmotic stress: inorganic ion homeostasis, organic osmolyte accumulation, and structural adaptations. (2) The strain demonstrated effective nitrogen removal under aerobic, anaerobic, and saline conditions (3–9%). (3) When applied in a full-scale engineering system treating saline fly ash-washing wastewater, it improved nitrate nitrogen (NO₃⁻-N), total nitrogen (TN), and chemical oxygen demand (COD) removal efficiencies by 31.92%, 25.19%, and 31.8%, respectively. The proportion of Marinobacter sp. increased from 0.73% to 3.41% (aerobic stage) and 2.86% (anoxic stage). Overall, halophilic denitrifying bacterium GH-1 can significantly enhance the nitrogen removal efficiency of saline wastewater systems, providing crucial guidance for biological nitrogen removal treatment. Full article

Robust strains with high simultaneous nitrification and denitrification (SND) capabilities in hypersaline wastewater, particularly those containing different oxysalts, are rarely reported. Here, an isolated oxysalt-tolerant bacterium, Marinobacter sp. Y2, showed excellent nitrogen removal capabilities of around 98% at 11% salinity of NaCl or oxysalts such as Na₂SO₄, Na₂HPO₄, NaHCO₃, and NaNO₃ through response surface methodology optimization. At >5% salinities, Marinobacter sp. Y2 showed superior nitrogen removal performance in oxysalt-laden wastewater compared to chloride-based wastewater. In contrast, other SND strains, including Pseudomonas sp. and Halomonas sp., experienced significant activity inhibition and even bacterial demise in oxysalt-rich wastewater, despite their high halotolerance to NaCl. The excellent SND activities of the oxysalt-tolerant strain were further validated using single and mixed nitrogen sources at 11% Na₂SO₄ salinity. Moreover, the amplification of nitrogen removal functional genes and the corresponding enzyme activities elucidated the nitrogen metabolism pathway of the strain in harsh oxysalt environments. Full article

This study investigates the bioremediation potential of Marinobacter-hydrocarbonoclasticus SDK644, a strain that has been isolated from petroleum-contaminated environments, for the degradation of the herbicide metribuzin and the treatment of slaughterhouse effluent. The strain’s bacterial growth and degradation capacity were assessed under varying conditions, including different metribuzin concentrations, pH values, temperatures, and inoculum sizes. The strain demonstrated optimal growth at a metribuzin concentration of 20 mg/L, with an optical density (OD600) of 0.408 after 96 h. At this concentration, 80% of the chemical oxygen demand (COD) was reduced over 144 h. The optimal growth conditions for M. hydrocarbonoclasticus SDK644 were identified as a pH of 7 and a temperature of 30 °C, where the enzymatic activity and degradation efficiency were maximized. Additionally, the treatment of slaughterhouse effluent showed significant reductions in organic pollution, with the COD and biochemical oxygen demand (BOD₅) decreasing by 80% (from 1900 mg/L to 384 mg/L) and 81% (from 1700 mg/L to 320 mg/L), respectively, within seven days. The strain also facilitated ammonium removal and promoted nitrification, indicating its suitability for treating high-organic-load wastewater. Notably, the visual transformation of the effluent, from a dark red color to a clear state, further highlighted the efficiency of the treatment process. This research highlights the adaptability of M. hydrocarbonoclasticus SDK644 to a wide range of environmental conditions and its efficiency in biodegrading metribuzin and treating complex wastewater. The findings demonstrate the strain’s potential as a sustainable solution for mitigating organic pollution in agricultural runoff, pesticide-contaminated water, and industrial effluents. Full article

The study of the metagenomes of bacterial communities in saline areas is relevant in connection with the global salinization of agricultural lands. The aim of this study was to investigate the biodiversity and structure of rhizobacterial communities associated with the halophyte S. marina from low and moderate sulfate–chloride salinity habitats. The bacterial community of bulk and rhizosphere soil was analyzed using high-throughput sequencing of the V1–V9 region of 16S rRNA by Oxford Nanopore Technologies. Alpha and beta diversity indices were calculated. A total of 55 phyla and 309 genera of bacteria were identified, among which Proteobacteria and Bacteroidetes dominated. The occurrence of Planctomycetes, Verrucomicrobia, and Acidobacteria in the rhizosphere was higher than in the bulk soil. Bacterial alpha diversity in the bulk soil decreased with increasing salinity, while it increased in the rhizosphere. The proportion of the halotolerant bacteria of Flavobacterium and Alteromonas genera significantly grew with increasing salinity both in the bulk and rhizosphere soil. In addition, in the rhizosphere, the percentage of Comamonas, Methylibium, Lysobacter, Planctomyces, Sphingomonas, Stenotrophomonas, and Lewinella genera increased. Among them, several genera included plant growth promoting rhizobacteria (PGPR). In the more saline bulk soil, the proportion of halotolerant genera Bacillus, Salinimicrobium, Marinobacter, Clostridium, Euzebya, KSA1, Marinobacter, Clostridium, Salinimicrobium, and Halorhodospira was also higher compared to the low saline site. Thus, increasing the salinity changed the taxonomic structure of the bacterial communities of both bulk soil and rhizosphere. Full article

Bacterial communities from three different sampling sites of a copper mine tunnel were characterized by 16S rRNA sequencing (NGS). A high presence of halophilic bacteria was confirmed by comparison with literature data and with reference samples from other highly salt-exposed soils. Among others, high read numbers of Gracilimonas, Kangiella, Limibacillus, Marinobacter, Woseia, and uncultivated strains of Actinomarinales, Gammaproteobacterium AT-s16, Actinobacteria 0319-7L14, and Thiotrichaceae were found. The community in a sample from the surface of the copper seam was significantly different from the community composition of a sample from the mine tunnel floor. The specificity in the appearance and in the abundance of special bacterial types (for example, Thiogranum, Thiohalophilus, Sulfuriflexus, Sedimenticolaceae, Desulfomonile, Desulfosporosinus, and Cand. Thiobios) can be partially explained by the different local conditions for sulfur-related metabolisms at the sampling sites. Full article

Biogeochemical redox cycling of iron (Fe) essentially governs various geochemical processes in nature. However, the mechanistic underpinnings of Fe-redox cycling in deep-sea sediments remain poorly understood, due to the limited access to the deep-sea environment. Here, abyssal sediment collected from a depth of 5800 m in the Pacific Ocean was characterized for its elemental, mineralogical, and biological properties. The sedimentary environment was determined to be oligotrophic with limited nutrition, yet contained a considerable amount of trace elements. Fe-redox reactions in sediment progressed through an initial lag phase, followed by a fast Fe(II) reduction and an extended period of Fe(III) oxidation before achieving equilibrium after 58 days. The presence of an external H₂ electron donor significantly increased the extent of Fe(III) bio-reduction by 7.73% relative to an amendment-free control under high pressure of 58 MPa. A similar enhancement of 11.20% was observed following lactate amendment under atmospheric pressure. Fe(II) bio-oxidation occurred after 16 days’ anaerobic culturing, coupled with nitrate reduction. During Fe bio-redox reactions, microbial community composition was significantly shaped by the presence/absence of an electron donor, while the hydrostatic pressure levels were the controlling factor. Shewanella spp. emerged as the primary Fe(III)-reducing microorganisms, and were stimulated by supplemented lactate. Marinobacter hydrocarbonoclasticus was the predominant Fe(II)-oxidizing microorganism across all conditions. Our findings illustrate continuous Fe-redox reactions occurring in the deep-sea environment, with coexisting Fe-redox microorganisms determining the oscillation of Fe valence states within the abyssal sediment. Full article