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Keywords = N-fixing bacteria

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16 pages, 2657 KiB  
Article
Degradation of Biodegradable Mulch-Derived Microplastics and Their Effects on Bacterial Communities and Radish Growth in Three Vegetable-Cultivated Purple Soils
by Ruixue Ao, Zexian Liu, Yue Mu, Jiaxin Chen and Xiulan Zhao
Agriculture 2025, 15(14), 1512; https://doi.org/10.3390/agriculture15141512 - 13 Jul 2025
Viewed by 409
Abstract
Biodegradable mulch films (BDMs) are considered a promising solution for mitigating plastic residue pollution in agroecosystems. However, the degradation behavior and ecological impacts of their residues on soil–plant systems remain unclear. Here, a pot experiment was conducted using an acidic purple soil (AS), [...] Read more.
Biodegradable mulch films (BDMs) are considered a promising solution for mitigating plastic residue pollution in agroecosystems. However, the degradation behavior and ecological impacts of their residues on soil–plant systems remain unclear. Here, a pot experiment was conducted using an acidic purple soil (AS), a neutral purple soil (NS), and a calcareous purple soil (CS) to investigate the degradation of 1% (w/w) microplastics derived from polyethylene mulch film (PE-MPs) and polybutylene adipate terephthalate/polylactic acid (PBAT/PLA) mulch film (Bio-MPs), as well as their effects on soil properties, bacterial communities, and radish growth. PE-MPs degraded slightly, while the degradation of Bio-MPs followed the order of NS > CS > AS. PE-MPs and Bio-MPs enhanced the nitrification and radish growth in AS but had no significant effects on soil properties and radish growth in CS. Bio-MPs notably increased the relative abundance of PBAT/PLA degradation-related bacteria, such as Ramlibacter, Bradyrhizobium, and Microbacterium, across the three soils. In NS, Bio-MPs raised soil pH and enriched nitrogen-fixing and denitrifying bacteria, leading to a decrease in NO3-N content and radish biomass. Overall, the effects of Bio-MPs on soil–plant systems varied with soil properties, which are closely related to their degradation rates. These findings highlight the need to assess the ecological risks of BDM residues before their large-scale use in agriculture. Full article
(This article belongs to the Section Agricultural Soils)
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16 pages, 7038 KiB  
Article
Responses of Different Soil Microbial Communities to the Addition of Nitrogen into the Soil of Larix gmelinii var. principis-rupprechtii (Mayr) Pilg. Plantations
by Yanlong Jia, Ziyi Wang, Hongna Cui, Liu Yang, Jinping Lu, Jiaojiao Ma, Zhongqi Xu and Honglin He
Forests 2025, 16(7), 1096; https://doi.org/10.3390/f16071096 - 2 Jul 2025
Viewed by 190
Abstract
The increasing rate of atmospheric nitrogen (N) deposition caused by human activities is a global concern. A rise in N deposition can alter the soil microbial community, as demonstrated by most long-term N addition experiments. Nevertheless, it remains unknown how short-term N addition [...] Read more.
The increasing rate of atmospheric nitrogen (N) deposition caused by human activities is a global concern. A rise in N deposition can alter the soil microbial community, as demonstrated by most long-term N addition experiments. Nevertheless, it remains unknown how short-term N addition influences the early succession of the soil microbial community in forests. In this study, the responses of the soil microbial community to multi-level and short-term (one-year) N addition in the soil of Larix gmelinii var. principis-rupprechtii (Mayr) Pilg. plantations in the Yanshan Mountains were explored. We used high-throughput sequencing technology to analyze the 16S rRNA of bacteria, the ITS gene of fungi, and the nifH functional gene of N-fixing bacteria. The results revealed a decrease in N-fixing functional gene abundance (such as nifH) and a slight rise in fungal and bacterial copy number due to N addition. N addition influenced the N-fixing bacterial community but had no influence on the fungal and bacterial communities in general. It drastically decreased the diversity of N-fixing microbial communities while having little impact on the diversity of fungi and bacteria. The NO3-N concentration exhibited a negative connection with the Shannon–Wiener index of the N-fixing microbial community when it exceeded a specific limit. Actinomycetes and N-fixing bacteria were significantly negatively correlated. The changes in soil NO3-N concentration and abundance of actinomycetes were the main reasons for the decrease in N-fixing microbial community diversity. The results of this study set the groundwork for exploring the initial succession mechanisms of soil microorganisms after N addition. This study offers a scientific theoretical basis for precise management of plantations under N deposition. Full article
(This article belongs to the Section Forest Ecology and Management)
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20 pages, 550 KiB  
Review
Molecular Mechanisms Underlying Root Nodule Formation and Activity
by Katarzyna Nuc and Przemysław Olejnik
Agronomy 2025, 15(7), 1552; https://doi.org/10.3390/agronomy15071552 - 26 Jun 2025
Viewed by 624
Abstract
Symbiotic interactions between legumes and a group of soil bacteria, known as rhizobia, lead to the formation of a specialized organs called root nodules. Inside them, atmospheric nitrogen (N2) is fixed by bacteria and reduced to forms available to plants, catalyzed [...] Read more.
Symbiotic interactions between legumes and a group of soil bacteria, known as rhizobia, lead to the formation of a specialized organs called root nodules. Inside them, atmospheric nitrogen (N2) is fixed by bacteria and reduced to forms available to plants, catalyzed by the nitrogenase enzyme complex. The development of a symbiotic relationship between legumes and nodule bacteria is a multi-stage, precisely regulated process, characterized by a high specificity of partner selection. Nodulation involves the enhanced expression of certain plant genes, referred to as early- and late-nodulin genes. Many nodulin genes encode hydroxyproline-rich glycoproteins (HRGPs) and proline-rich proteins (PRPs) which are involved in various processes, including infection thread formation, cell signaling, and defense responses, thereby affecting nodule formation and function. Cyclophilins (CyPs) belong to a family of proteins with peptidyl-prolyl cistrans isomerase activity. Proteins with cyclophilin domain can be found in the cytoplasm, endoplasmic reticulum, nucleus, chloroplast, and mitochondrion. They are involved in various processes, such as protein folding, cellular signaling, mRNA maturation, and response to biotic and abiotic stress. In this review, we aim to summarize the molecular processes involved in the development of symbiosis and highlight the potential role of cyclophilins (peptidyl-prolyl cis-trans isomerases) in this process. Full article
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18 pages, 3168 KiB  
Article
Ammonium-Generating Microbial Consortia in Paddy Soil Revealed by DNA-Stable Isotope Probing and Metatranscriptomics
by Chao-Nan Wang, Yoko Masuda and Keishi Senoo
Microorganisms 2025, 13(7), 1448; https://doi.org/10.3390/microorganisms13071448 - 21 Jun 2025
Viewed by 515
Abstract
Rice paddy fields are sustainable agricultural systems as soil microorganisms help maintain nitrogen fertility through generating ammonium. In these soils, dissimilatory nitrate reduction to ammonium (DNRA), nitrogen fixation, and denitrification are closely linked. DNRA and denitrification share the same initial steps and nitrogen [...] Read more.
Rice paddy fields are sustainable agricultural systems as soil microorganisms help maintain nitrogen fertility through generating ammonium. In these soils, dissimilatory nitrate reduction to ammonium (DNRA), nitrogen fixation, and denitrification are closely linked. DNRA and denitrification share the same initial steps and nitrogen gas, the end product of denitrification, can serve as a substrate for nitrogen fixation. However, the microorganisms responsible for these three reductive nitrogen transformations, particularly those focused on ammonium generation, have not been comprehensively characterized. In this study, we used stable isotope probing with 15NO3, 15N2O, and 15N2, combined with 16S rRNA high-throughput sequencing and metatranscriptomics, to identify ammonium-generating microbial consortia in paddy soils. Our results revealed that several bacterial families actively contribute to ammonium generation under different nitrogen substrate conditions. Specifically, Geobacteraceae (N2O and +N2), Bacillaceae (+NO3 and +N2), Rhodocyclaceae (+N2O and +N2), Anaeromyxobacteraceae (+NO3 and +N2O), and Clostridiaceae (+NO3 and +N2) were involved. Many of these bacteria participate in key ecological processes typical of paddy environments, including iron or sulfate reduction and rice straw decomposition. This study revealed the ammonium-generating microbial consortia in paddy soil that contain several key bacterial drivers of multiple reductive nitrogen transformations and suggested their diverse functions in paddy soil metabolism. Full article
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20 pages, 3021 KiB  
Article
Foliar Epichloë gansuensis Endophyte and Root-Originated Bacillus subtilis LZU7 Increases Biomass Accumulation and Synergistically Improve Nitrogen Fixation in Achnatherum inebrians
by Yuanyuan Jin, Zhenjiang Chen, Kamran Malik and Chunjie Li
J. Fungi 2025, 11(7), 466; https://doi.org/10.3390/jof11070466 - 20 Jun 2025
Viewed by 413
Abstract
Although drunken horse grass (Achnatherum inebrians) can be simultaneously infected by the foliar endophyte Epichloë gansuensis and colonized by Bacillus subtilis, it remains unclear whether Epichloë endophyte symbiosis influences B. subtilis colonization, as well as how their interaction affects nitrogen [...] Read more.
Although drunken horse grass (Achnatherum inebrians) can be simultaneously infected by the foliar endophyte Epichloë gansuensis and colonized by Bacillus subtilis, it remains unclear whether Epichloë endophyte symbiosis influences B. subtilis colonization, as well as how their interaction affects nitrogen fixation and assimilation. The purpose of the present study was to investigate whether E. gansuensis endophyte infection facilitates the colonization of B. subtilis in the roots of host plants, with a focus on understanding the interaction effects of the E. gansuensis endophyte and B. subtilis on plant growth and nutrient absorption. In this study, we measured the colony growth rate of B. subtilis LZU7 when co-cultured with E. gansuensis strains. In addition to an in vitro test, we investigated the root colonization of Epichloë endophyte-infected plants (E+) and Epichloë endophyte-free plants (E−) with the GFP-tagged B. subtilis LZU7 in an inoculation test. Furthermore, we evaluated the interactions between E. gansuensis endophyte symbiosis and B. subtilis LZU7 colonization on the dry weight, nitrogen fixation, nitrogen converting-enzyme activity, and nutrients for E+ and E− plants by labeling with 15N2. The results showed that the growth rates of B. subtilis LZU7 were altered and increased in a co-culture with the E. gansuensis endophyte. A significantly greater colonization of GFP-tagged B. subtilis LZU7 was detected in the roots of E+ plants compared with the roots of E− plants, suggesting that E. gansuensis endophyte symbiosis enhances the colonization of beneficial microorganisms. The combination of E. gansuensis endophyte symbiosis and B. subtilis LZU7 inoculation significantly altered the expression of the nitrogenase (nifH) gene, thereby promoting increased biological nitrogen fixation (BNF). The E. gansuensis endophyte infection and inoculation with B. subtilis LZU7 significantly increased δ15NAir in plants. Co-inoculation with the E. gansuensis endophyte and B. subtilis LZU7 significantly elevated NH4+ accumulation in the roots, depleted the NH4+ availability in the surrounding soil, and showed no measurable impact on the foliar NH4+ content. The observed alterations in the NH4+ content were linked to nitrogen-fixing microorganisms that promoted nitrogen fixation, thereby enhancing nitrogen uptake and contributing to greater biomass production in A. inebrians. Our findings highlighted the fact that a foliar symbiosis with the E. gansuensis endophyte enhances the recruitment of beneficial bacteria, and that the resulting interaction significantly impacts nitrogen fixation, assimilation, and allocation in host plants. Full article
(This article belongs to the Section Environmental and Ecological Interactions of Fungi)
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13 pages, 828 KiB  
Article
Potential of Bacterial Inoculants to Mitigate Soil Compaction Effects on Gossypium hirsutum Growth
by Fausto Henrique Viera Araújo, Crislaine Alves da Conceição, Adriene Caldeira Batista, Gabriel Faria Parreiras de Andrade, Caique Menezes de Abreu, Paulo Henrique Grazziotti and Ricardo Siqueira da Silva
Plants 2025, 14(12), 1844; https://doi.org/10.3390/plants14121844 - 16 Jun 2025
Viewed by 476
Abstract
Aims: Soil compaction is one of the main challenges in agriculture, negatively affecting cotton growth (Gossypium hirsutum L.), nutrition, and productivity. This study evaluated the efficacy of plant growth-promoting bacteria (PGPB), Exiguobacterium sibiricum, and Pantoea vagans in mitigating the effects of different [...] Read more.
Aims: Soil compaction is one of the main challenges in agriculture, negatively affecting cotton growth (Gossypium hirsutum L.), nutrition, and productivity. This study evaluated the efficacy of plant growth-promoting bacteria (PGPB), Exiguobacterium sibiricum, and Pantoea vagans in mitigating the effects of different soil compaction levels (65%, 75%, 85%, and 95%) on cotton performance. Methods: Parameters such as plant height, stem diameter, number of leaves, shoot dry matter (SDM), and nutrient content in leaves, stems, and roots were assessed. The methodology included variance analysis and mean clustering to identify significant differences among treatments using R software. Results: The results indicated that PGPB inoculation improved plant growth and nutrition even under high compaction levels. Cotton height increased by up to 45% in compacted soils (95%), while stem diameter and SDM also showed significant gains. Foliar nutrient levels of N (37.2 g kg−1), Ca, and Mg remained within the adequate range for cotton cultivation, reflecting the efficiency of PGPB in enhancing nutrient absorption. Under severe compaction, Ca accumulation dropped to 18.2 g kg−1, highlighting the physical constraints imposed on the roots; however, the bacterial action mitigated this impact. Additionally, bacterial strains increased the availability of N and P in the soil due to their ability to fix nitrogen, solubilize phosphates, and produce exopolysaccharides that improve soil structure. Conclusions: In conclusion, inoculation with Exiguobacterium sibiricum and Pantoea vagans is an effective strategy to mitigate the impacts of soil compaction on cotton. These bacteria promote plant growth and nutrition and enhance the soil’s physical and biological properties. Full article
(This article belongs to the Special Issue Beneficial Effects of Bacteria on Plants)
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31 pages, 2910 KiB  
Review
Tyre Wear Particles in the Environment: Sources, Toxicity, and Remediation Approaches
by Jie Kang, Xintong Liu, Bing Dai, Tianhao Liu, Fasih Ullah Haider, Peng Zhang, Habiba and Jian Cai
Sustainability 2025, 17(12), 5433; https://doi.org/10.3390/su17125433 - 12 Jun 2025
Viewed by 1211
Abstract
Tyre wear particles (TWPs), generated from tyre-road abrasion, are a pervasive and under-regulated environmental pollutant, accounting for a significant share of global microplastic contamination. Recent estimates indicate that 1.3 million metric tons of TWPs are released annually in Europe, dispersing via atmospheric transport, [...] Read more.
Tyre wear particles (TWPs), generated from tyre-road abrasion, are a pervasive and under-regulated environmental pollutant, accounting for a significant share of global microplastic contamination. Recent estimates indicate that 1.3 million metric tons of TWPs are released annually in Europe, dispersing via atmospheric transport, stormwater runoff, and sedimentation to contaminate air, water, and soil. TWPs are composed of synthetic rubber polymers, reinforcing fillers, and chemical additives, including heavy metals such as zinc (Zn) and copper (Cu) and organic compounds like polycyclic aromatic hydrocarbons (PAHs) and N-(1,3-dimethylbutyl)-N′-phenyl-p-phenylenediamine (6PPD). These constituents confer persistence and bioaccumulative potential. While TWP toxicity in aquatic systems is well-documented, its ecological impacts on terrestrial environments, particularly in agricultural soils, remain less understood despite global soil loading rates exceeding 6.1 million metric tons annually. This review synthesizes global research on TWP sources, environmental fate, and ecotoxicological effects, with a focus on soil–plant systems. TWPs have been shown to alter key soil properties, including a 25% reduction in porosity and a 20–35% decrease in organic matter decomposition, disrupt microbial communities (with a 40–60% reduction in nitrogen-fixing bacteria), and induce phytotoxicity through both physical blockage of roots and Zn-induced oxidative stress. Human exposure occurs through inhalation (estimated at 3200 particles per day in urban areas), ingestion, and dermal contact, with epidemiological evidence linking TWPs to increased risks of respiratory, cardiovascular, and developmental disorders. Emerging remediation strategies are critically evaluated across three tiers: (1) source reduction using advanced tyre materials (up to 40% wear reduction in laboratory tests); (2) environmental interception through bioengineered filtration systems (60–80% capture efficiency in pilot trials); and (3) contaminant degradation via novel bioremediation techniques (up to 85% removal in recent studies). Key research gaps remain, including the need for long-term field studies, standardized mitigation protocols, and integrated risk assessments. This review emphasizes the importance of interdisciplinary collaboration in addressing TWP pollution and offers guidance on sustainable solutions to protect ecosystems and public health through science-driven policy recommendations. Full article
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16 pages, 1464 KiB  
Article
Impact of Fire Severity on Soil Bacterial Community Structure and Its Function in Pinus densata Forest, Southeastern Tibet
by Lei Hou, Jie Chen and Wen Lin
Forests 2025, 16(6), 894; https://doi.org/10.3390/f16060894 - 26 May 2025
Viewed by 394
Abstract
Forest fires are one of the significant factors affecting forest ecosystems globally, with their impacts on soil microbial community structure and function drawing considerable attention. This study focuses on the short-term effects of different fire intensities on soil bacterial community structure and function [...] Read more.
Forest fires are one of the significant factors affecting forest ecosystems globally, with their impacts on soil microbial community structure and function drawing considerable attention. This study focuses on the short-term effects of different fire intensities on soil bacterial community structure and function in Abies (Pinus densata) forests within the Birishen Mountain National Forest Park in southeastern Tibet. High-throughput sequencing technology was employed to analyze soil bacterial community variations under unburned (C), low-intensity burn (L), moderate-intensity burn (M), and high-intensity burn (S) conditions. The results revealed that with increasing fire severity, the dominant phylum Actinobacteriota significantly increased, while Proteobacteria and Acidobacteriota markedly decreased. At the genus level, the relative abundance of Bradyrhizobium declined significantly with higher fire severity, whereas Arthrobacter exhibited a notable increase. Additionally, soil environmental factors such as available phosphorus (AP), dissolved organic carbon (DOC), C/N ratio, and C/P ratio displayed distinct trends: AP content increased with fire severity, while DOC, C/N ratio, and C/P ratio showed decreasing trends. Non-metric Multidimensional Scaling (NMDS) analysis indicated significant differences in soil bacterial community structures across fire intensities. Diversity analysis demonstrated that Shannon and Simpson indices exhibited regular fluctuations correlated with fire severity and were significantly associated with soil C/N ratios. Functional predictions revealed a significant increase in nitrate reduction-related bacterial functions with fire severity, while nitrogen-fixing bacteria declined markedly. These findings suggest that forest fire severity profoundly influences soil bacterial community structure and function, potentially exerting long-term effects on nutrient cycling and ecosystem recovery in forest ecosystems. Full article
(This article belongs to the Special Issue Fire Ecology and Management in Forest—2nd Edition)
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12 pages, 232 KiB  
Article
Yield and Seed Quality of Faba Bean (Vicia faba L. var. minor) as a Result of Symbiosis with Nitrogen-Fixing Bacteria
by Magdalena Serafin-Andrzejewska, Agnieszka Falkiewicz, Wiesław Wojciechowski and Marcin Kozak
Agriculture 2025, 15(9), 960; https://doi.org/10.3390/agriculture15090960 - 28 Apr 2025
Viewed by 642
Abstract
Faba bean is a high-protein legume that can be successfully grown in most climates around the world. It is one of the most popular pulses cultivated in Poland. Its seeds are a source of plant protein, used most often in feed production. Field [...] Read more.
Faba bean is a high-protein legume that can be successfully grown in most climates around the world. It is one of the most popular pulses cultivated in Poland. Its seeds are a source of plant protein, used most often in feed production. Field experiments and laboratory seed analyses were carried out in 2022 and 2023 to assess the effect of the application of nitrogen-fixing bacteria on the yield and seed quality of a low-tannin faba bean cultivar. The factor was tested at four levels: control, seed inoculation with Rhizobium leguminosarum bv. viceae, foliar spraying with Methylobacterium symbioticum, and seed inoculation and spraying (double application). The application of N-fixing bacteria had a positive effect on faba bean seed yield. In 2022, plants responded most effectively to a double application, increasing seed yield by 25.4%, while, in 2023, the highest seed yield was obtained after inoculation (12.3% increase). Although the single application of bacteria caused a decrease in seed protein content, the double application (inoculation and spraying) significantly enhanced seed protein content. The protein productivity per hectare was compensated by the higher seed yield and increased by 41.7% in 2022 and 14.9% in 2023 compared to plots where N-fixing bacteria were not applied. This work shows that it is possible to use different strains of N-fixing bacteria in faba bean cultivation and this can significantly improve yields while reducing the need for synthetic nitrogen fertilizers, which supports sustainable production. Full article
(This article belongs to the Special Issue Advances in the Cultivation and Production of Leguminous Plants)
27 pages, 2090 KiB  
Article
Nitrogen-Fixing Bacteria Promote the Growth of Fritillaria taipaiensis P. Y. Li by Regulating Physiological and Biochemical Reactions and Protecting Enzyme System-Related Gene Expression
by Mingyan Ye, Jiaqi Lang, Xiaotian Kong, Zhifen Shi, Fengjie Duan, Guiyong Qin, Hua Zhang, Dongqin Guo and Nong Zhou
Biology 2025, 14(4), 325; https://doi.org/10.3390/biology14040325 - 24 Mar 2025
Cited by 1 | Viewed by 713
Abstract
The widespread application of chemical fertilizers and pesticides has resulted in environmental pollution. With the growing emphasis on ecological agriculture in traditional Chinese medicine, microbial fertilizers are increasingly recognized for their potential. The aim of this study is to investigate the effect of [...] Read more.
The widespread application of chemical fertilizers and pesticides has resulted in environmental pollution. With the growing emphasis on ecological agriculture in traditional Chinese medicine, microbial fertilizers are increasingly recognized for their potential. The aim of this study is to investigate the effect of inoculating nitrogen-fixing bacteria on the soil (yellow loam, river sand, and organic fertilizer in a 2:1:1 ratio) of Fritillaria taipaiensis, with a focus on the leaf changes in terms of physiological parameters, antioxidant enzyme activity, and corresponding gene expression levels. The experiment involved three nitrogen-fixing bacteria, namely Rahnella aquatilis, Pseudomonas chlororaphis, and Paenibacillus stellifer, with a total of eight treatment groups. The objective was to assess how these bacterial treatments influenced physiological parameters, photosynthetic characteristics, pigment content, and both antioxidant enzyme activities and gene expression in the leaves of F. taipaiensis. The experimental results demonstrated statistically significant reductions (p < 0.05) in malondialdehyde (MDA) content and stomatal limitation value (LS) in F. taipaiensis leaves under treatment conditions relative to the control group (CK). The most substantial decreases were observed dual-inoculation with R. aquatilis and P. stellifer (N5), showing reductions of 38.24% and 20.94% in MDA and LS compared to CK values. Additionally, leaf area, leaf thickness, stem thickness, plant height, photosynthetic parameters, pigment content, soluble sugars, soluble proteins, proline levels, and the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) exhibited varying degrees of increase. Compared to the CK group, the SOD, POD, and CAT activities of the N5 group increased by 141.06%, 160.59%, and 106.23%, respectively. The relative gene expression patterns of SOD, POD, and CAT corresponded with the trends observed in their respective antioxidant enzyme activities. Pearson correlation analysis further demonstrated that leaf area and net photosynthetic rate (Pn) were significantly correlated with respect to SOD, POD, and CAT activities, as well as their corresponding gene expression levels. In conclusion, inoculation with nitrogen-fixing bacteria improved the growth and stress tolerance of F. taipaiensis, with the combined application of Rahnella aquatilis and Pseudomonas stellifer yielding the most effective results. This study establishes that different rhizosphere nitrogen-fixing bacteria, either individually or in combination, influence the photosynthetic characteristics, physiological and biochemical parameters, and protective enzyme systems of F. taipaiensis. These findings provide a theoretical foundation for the selection of nitrogen-fixing bacteria as biofertilizers in the artificial cultivation of F. taipaiensis and highlight their potential application in the cultivation of traditional Chinese medicinal materials. Full article
(This article belongs to the Section Genetics and Genomics)
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16 pages, 3231 KiB  
Article
Sulfurimonas microaerophilic sp. nov. and Sulfurimonas diazotrophicus sp. nov.: Two Novel Nitrogen-Fixing and Hydrogen- and Sulfur-Oxidizing Chemolithoautotrophs Within the Campylobacteria Isolated from Mangrove Sediments
by Yangsheng Zhong, Yufei Li, Zhaodi Wang, Liang Cui, Shiwei Lv, Han Zhu, Qing Yuan, Qiliang Lai, Shasha Wang and Lijing Jiang
Microorganisms 2025, 13(4), 713; https://doi.org/10.3390/microorganisms13040713 - 21 Mar 2025
Viewed by 503
Abstract
Two novel marine hydrogen- and sulfur-oxidizing bacteria, designated HSL1-7T and HSL3-1T, were isolated from mangrove sediments from Fujian Province, China. Strain HSL1-7T exhibited Gram-negative, rod-shaped to slightly curved morphology with polar flagellum-driven motility, whereas strain HSL3-1T was Gram-negative, [...] Read more.
Two novel marine hydrogen- and sulfur-oxidizing bacteria, designated HSL1-7T and HSL3-1T, were isolated from mangrove sediments from Fujian Province, China. Strain HSL1-7T exhibited Gram-negative, rod-shaped to slightly curved morphology with polar flagellum-driven motility, whereas strain HSL3-1T was Gram-negative, rod-shaped and non-motile. Strain HSL1-7T and HSL3-1T were obligate chemolithoautotrophs, capable of using molecular hydrogen and thiosulfate as an energy source, and molecular oxygen and elemental sulfur as the electron acceptors for growth. Cellular fatty acid profiles revealed similar predominant components (C16:1ω7c, C16:0, C18:1ω7c, and C14:0) in both strains. Strains HSL1-7T and HSL3-1T were strongly diazotrophic, as demonstrated by 15N2 fixation when a fixed nitrogen source was absent from the growth medium. The DNA G+C contents of strains HSL1-7T and HSL3-1T were determined to be 36.1% and 57.3%, respectively. Based on the 16S rRNA gene sequences, strains HSL1-7T and HSL3-1T exhibited the highest sequence similarities with Sulfurimonas marina B2T (98.5% and 94.45%, respectively). Notably, the 16S rRNA gene sequence similarity between strains HSL1-7T and HSL3-1T was 93.19%, indicating that they represent distinct species within the genus Sulfurimonas. Comparative genomic analyses revealed the presence of diverse metabolic profiles in strains HSL1-7T and HSL3-1T, including carbon fixation, hydrogen oxidation, sulfur oxidation, and nitrogen fixation. The combined phenotypic, chemotaxonomic, and phylogenetic evidence, including average nucleotide identity and in silico DNA-DNA hybridization values, shows that strains HSL1-7T and HSL3-1T represent two novel species of the genus Sulfurimonas for which the names Sulfurimonas microaerophilic sp. nov. and Sulfurimonas diazotrophicus sp. nov. are proposed, with the type strains HSL1-7T (=MCCC 1A18899T = KCTC 25640T) and HSL3-1T (=MCCC 1A18844T), respectively. Full article
(This article belongs to the Section Environmental Microbiology)
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20 pages, 817 KiB  
Article
Effectiveness of Nitrogen-Fixing Bacteria Rhodobacter sphaeroides in Soil–Plant Nitrogen and Rice Performance in Extremely Saline Acid Sulfate Soil over Two Consecutive Seasons
by Nguyen Hoang Anh, Cao Tan Phat, Le Minh Nhut, Le Thi My Thu, Nguyen Duc Trong, Le Thanh Quang, Ly Ngoc Thanh Xuan, Tran Chi Nhan, Ngo Thanh Phong and Nguyen Quoc Khuong
Sustainability 2025, 17(5), 2228; https://doi.org/10.3390/su17052228 - 4 Mar 2025
Viewed by 1166
Abstract
The overuse of chemical fertilizers under adverse conditions endangers the sustainability of agriculture. A biological approach should be investigated to address this issue. Therefore, this study aimed to detect the potency of purple non-sulfur bacteria that can fix nitrogen (N) (PNSB-fN) Rhodobacter sphaeroides [...] Read more.
The overuse of chemical fertilizers under adverse conditions endangers the sustainability of agriculture. A biological approach should be investigated to address this issue. Therefore, this study aimed to detect the potency of purple non-sulfur bacteria that can fix nitrogen (N) (PNSB-fN) Rhodobacter sphaeroides in soil N fertility, plant N uptake, growth, and rice yield. In brief, an experiment was conducted to check whether the biofertilizer containing PNSB-fN strains can improve rice yield and soil fertility under a highly saline acidic condition. A randomized complete block design was used with four replicates on saline soil in An Bien-Kien Giang, Vietnam. The first factor was the N fertilizer level, i.e., (i) 100%, (ii) 75%, (iii) 50%, and (iv) 0%; the second factor was the PNSB-fN (R. sphaeroides), i.e., (i) the control, (ii) S01, (iii) S06, and (iv) combined S01–S06. In the results, supplying PNSB-fN increased NH4+ compared with the control, i.e., 104.7–112.0 mg NH4+ kg−1 compared with 94.0 mg NH4+ kg−1 in season 1 and 35.9–38.0 mg NH4+ kg−1 compared with 34.2 mg NH4+ kg−1 in season 2. Additionally, by supplying each PNSB-fN strain, the soil Na+ and plant Na in culm leaf and grain were decreased in comparison with those in treatments without PNSB-fN. The total N uptake was also enhanced by the PNSB-fN compared with the control. Moreover, supplying PNSB-fN improved the crop height, panicle length, panicle quantity pot−1, grain quantity panicle−1, filled spikelet rate, and grain yield compared with the control. Ultimately, in extremely saline soil, the mixture of PNSB-fN not only improved soil fertility and reduced soil salinity but also replaced 25% of chemical N fertilizer to ensure sustainable agriculture. This newly developed biofertilizer was potent in not only improving the rice and soil health in the locality but also performing the same under similar conditions around the globe. Full article
(This article belongs to the Section Sustainable Agriculture)
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15 pages, 3717 KiB  
Article
Impact of Karst Rocky Desertification on N-Fixing Tree Species Root System and Bacteria
by Shuzhong Yu, Chunhui Guo and Xianyu Yao
Forests 2025, 16(3), 425; https://doi.org/10.3390/f16030425 - 26 Feb 2025
Viewed by 503
Abstract
The study aimed to investigate the effect of soil textural or soil mineral fraction substrates (loam and gravel) from karst desertification areas on the rhizospheric and root-associated bacterial community structure of Dalbergia odorifera (an N-fixing tree), using high-throughput sequencing techniques, based on treatment [...] Read more.
The study aimed to investigate the effect of soil textural or soil mineral fraction substrates (loam and gravel) from karst desertification areas on the rhizospheric and root-associated bacterial community structure of Dalbergia odorifera (an N-fixing tree), using high-throughput sequencing techniques, based on treatment methods of whole-root and two-chambered split-root systems. Further, this study determined the relative importance of the plant and substrate properties on the rhizospheric, non-rhizospheric and endospheric bacteria composition. The type of substrate exerts a significant influence on both rhizospheric and non-rhizospheric bacterial communities, whereas endophytic communities within the root system are predominantly determined by plant species rather than substrate type. The analysis revealed that endospheric bacterial diversity was considerably lower than that of rhizospheric and non-rhizospheric communities. Cluster analysis indicated that endospheric bacterial samples formed a distinct cluster, while rhizospheric and non-rhizospheric bacteria in the soil substrate grouped into one branch, and those in the gravel substrate formed another branch. In comparison to the gravel treatments, a reduced bacterial abundance was observed in the rhizosphere and non-rhizosphere of nitrogen-fixing plants in soil, potentially due to the interplay of lower nutrient availability and increased porosity in gravel treatments. Proteobacteria, which are involved in the nitrogen cycle, exhibited the highest abundance. In contrast, Acidobacteria, Firmicutes and other bacterial phyla involved in nutrient cycling demonstrated higher abundance, with their presence being more pronounced in extreme environments, such as gravel treatments, compared to soil substrates. These results suggest that nitrogen-fixing plants can respond to extreme environments by increasing bacterial abundance. The findings of this study provide a theoretical basis for the use of D. odorifera for ecosystem recovery and vegetation restoration. Full article
(This article belongs to the Section Forest Biodiversity)
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12 pages, 1481 KiB  
Communication
Biofilm Inhibition: The Role of Fixed Oil from Caryocar coriaceum in Fighting Resistant Bacterial Communities
by José Weverton Almeida-Bezerra, José Thyálisson da Costa Silva, Saulo Almeida Menezes, Gabriel Gonçalves Alencar, Daiany Alves Ribeiro, Bárbara Fernandes Melo, João Pereira da Silva-Junior, Francisca de Fátima Silva de Sousa, Severino Denicio Gonçalves de Sousa, Marcos Aurélio Figueirêdo dos Santos, Dieferson Leandro de Souza, Luiz Neldecílio Alves Vitor, Ademar Maia Filho, Murilo Felipe Felício, Jacqueline Cosmo Andrade-Pinheiro, Viviane Bezerra da Silva, José Jailson Lima Bezerra, Maria Flaviana Bezerra Morais-Braga and Henrique Douglas Melo Coutinho
Bacteria 2025, 4(1), 6; https://doi.org/10.3390/bacteria4010006 - 2 Feb 2025
Viewed by 1251
Abstract
Biofilms, formed by microbial communities that increase resistance to antibiotics, are responsible for chronic infections, making their combat a therapeutic priority. Taking this into account, the fruit Caryocar coriaceum stands out for its potential in the treatment of infectious diseases. The different parts [...] Read more.
Biofilms, formed by microbial communities that increase resistance to antibiotics, are responsible for chronic infections, making their combat a therapeutic priority. Taking this into account, the fruit Caryocar coriaceum stands out for its potential in the treatment of infectious diseases. The different parts of this plant can be used, and the fixed oil extracted from its fruit, rich in fatty acids, is indicated as responsible for its biological activities. Thus, the objective of this study was to evaluate the chemical composition of the fixed oil extracted from the fruits of C. coriaceum (FOCC), in addition to analyzing its action in the inhibition and pre-formed biofilm disruption of bacteria. The fixed oil was extracted from the internal mesocarp through exhaustive extraction with n-hexane, resulting in a yield of 38.29%. For antibiofilm evaluation, multidrug-resistant bacterial strains were exposed to the oil, and the antibiofilm activity was verified through biofilm formation and pre-formed biofilm disruption assays. The chemical analysis of the fixed oil of C. coriaceum (FOCC) identified eight fatty acids, representing 98.2% of the total composition, with a predominance of oleic acid (60.1%) and palmitic acid (33.5%). FOCC demonstrated approximately 70% inhibition of Streptococcus mutans biofilm formation at a concentration of 10 mg/mL and approximately 60% inhibition against Staphylococcus aureus and Pseudomonas aeruginosa. In pre-formed biofilm disruption, FOCC showed low efficacy against S. mutans and P. aeruginosa but showed greater activity against Enterococcus faecalis and S. aureus. These results indicate that FOCC has the potential to prevent biofilms, but its pre-formed biofilm disruption capacity is still limited. Full article
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25 pages, 2187 KiB  
Article
Effect of Herbicide-Resistant Oil-Degrading Bacteria on Plants in Soil Contaminated with Oil and Herbicides
by Tatyana Korshunova, Elena Kuzina, Svetlana Mukhamatdyarova, Milyausha Iskuzhina, Liliya Kulbaeva and Svetlana Petrova
Plants 2024, 13(24), 3560; https://doi.org/10.3390/plants13243560 - 20 Dec 2024
Cited by 1 | Viewed by 887
Abstract
Biological remediation of agricultural soils contaminated with oil is complicated by the presence of residual amounts of chemical plant protection products, in particular, herbicides, which, like oil, negatively affect the soil microbiome and plants. In this work, we studied five strains of bacteria [...] Read more.
Biological remediation of agricultural soils contaminated with oil is complicated by the presence of residual amounts of chemical plant protection products, in particular, herbicides, which, like oil, negatively affect the soil microbiome and plants. In this work, we studied five strains of bacteria of the genera Pseudomonas and Acinetobacter, which exhibited a high degree of oil biodegradation (72–96%). All strains showed resistance to herbicides based on 2,4-D, imazethapyr and tribenuron-methyl, the ability to fix nitrogen, phosphate mobilization, and production of indole-3-acetic acid. The presence of pollutants affected the growth-stimulating properties of bacteria in different ways. The most promising strain P. citronellolis N2 was used alone and together with oat and lupine plants for soil remediation of oil, including herbicide-treated oil-contaminated soil. Combined contamination was more toxic to plants and soil microorganisms. Bacterization stimulated the formation of chlorophyll and suppressed the synthesis of abscisic acid and malonic dialdehyde in plant tissues. The combined use of bacteria and oat plants most effectively reduced the content of hydrocarbons in the soil (including in the presence of herbicides). The results obtained can be used to develop new methods for bioremediation of soils with polychemical pollution. Full article
(This article belongs to the Special Issue Role of Microbial Plant Biostimulants in Abiotic Stress Mitigation)
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