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Biology May 2024The agricultural sector is currently encountering significant challenges due to the effects of climate change, leading to negative consequences for crop productivity and...
The Impact of Nitrogen-Fixing Bacteria-Based Biostimulant Alone or in Combination with Commercial Inoculum on Tomato Native Rhizosphere Microbiota and Production: An Open-Field Trial.
The agricultural sector is currently encountering significant challenges due to the effects of climate change, leading to negative consequences for crop productivity and global food security. In this context, traditional agricultural practices have been inadequate in addressing the fast-evolving challenges while maintaining environmental sustainability. A possible alternative to traditional agricultural management is represented by using beneficial micro-organisms that, once applied as bioinoculants, may enhance crop resilience and adaptability, thereby mitigating the adverse effects of environmental stressors and boosting productivity. Tomato is one of the most important crops worldwide, playing a central role in the human diet. The aim of this study was to evaluate the impact of a nitrogen-fixing bacterial-based biostimulant ( sp., sp., and sp.) in combination or not with a commercial inoculum Micomix (, , , , and ) (MYC) on the native rhizosphere communities and tomato production. Bacterial populations in the different samples were characterized using an environmental metabarcoding approach. The bioinocula effect on the native rhizosphere microbiota resulted in significant variation both in alpha and beta diversity and in a specific signature associated with the presence of biostimulants.
PubMed: 38927280
DOI: 10.3390/biology13060400 -
Environmental Science and Pollution... Jun 2024Azotobacter chroococcum and Bacillus subtilis were selected as fermentation strains, and biogas residue after anaerobic digestion of kitchen waste and residual sludge...
Azotobacter chroococcum and Bacillus subtilis were selected as fermentation strains, and biogas residue after anaerobic digestion of kitchen waste and residual sludge was used as fermentation substrate. A single factor optimization test was used to optimize the solid-state fermentation parameters of biogas residue with the number of viable bacteria and the number of spores as indexes. The results showed that the optimum inoculation conditions involved the following: 55% initial moisture content, 15% initial inoculation amount, 30 ℃, and 1:1 initial inoculation ratio for 13 days. Pot experiment showed that the prepared three kinds of bacterial fertilizers could not only effectively promote the growth of white clover, improve the composition of soil nutrients, but also change the structure of soil bacterial community, which is of great significance to the health of soil ecosystem in white clover.
PubMed: 38918298
DOI: 10.1007/s11356-024-33924-4 -
Frontiers in Microbiology 2024Variability in microbial residues within soil aggregates are becoming progressively essential to the nutritive and sustainability of soils, and are therefore broadly...
INTRODUCTION
Variability in microbial residues within soil aggregates are becoming progressively essential to the nutritive and sustainability of soils, and are therefore broadly regarded as an indispensable part of soil organic matter. It is unexplored how the widespread implementation of microbial fertilisers in agricultural production impacts soil organic nutrients, in particular the microbial residue fraction.
METHODS
We performed a three-year field experiment to verify the distinct impacts of microbial and organic fertilizers on carbon accumulation in soil microbial leftovers among aggregate fractions.
RESULTS
Microbial residual carbon was shown to decrease insignificantly during the application of microbial fertilizer and to rise marginally afterwards with the utilization of organic fertilizer. However, the combined effects of the two fertilizers had substantial impacts on the accumulation of microbial residual carbon. Changes in the structure of the fungi and bacteria shown in this study have implications for the short-term potential of microbial fertilizer shortages to permanent soil carbon sequestration. Additionally, our findings revealed variations in microbial residue accumulation across the microbial fertilizers, with fertilizer being preferable to fertilizer due to its higher efficiency. In this scenario of nutrient addition, fungal residues may serve as the primary binding component or focal point for the production of new microaggregates, since the quantity of SOC provided by fungal residues increased while that supplied by bacterial residues decreased.
DISCUSSION
Our findings collectively suggested that the mechanisms behind the observed bacterial and fungal MRC (microbial residue carbon) responses to microbial fertilizer or organic fertilizer in bamboo forest soils are likely to be distinct. The application of microbial fertilizers for a limited duration led to a decline soil stable carbon pool, potentially influencing the regulation of soil nutrients in such hilly bamboo forests.
PubMed: 38915301
DOI: 10.3389/fmicb.2024.1291947 -
Nature Chemical Biology Jun 2024Biological nitrogen fixation requires substantial metabolic energy in form of ATP as well as low-potential electrons that must derive from central metabolism. During...
Biological nitrogen fixation requires substantial metabolic energy in form of ATP as well as low-potential electrons that must derive from central metabolism. During aerobic growth, the free-living soil diazotroph Azotobacter vinelandii transfers electrons from the key metabolite NADH to the low-potential ferredoxin FdxA that serves as a direct electron donor to the dinitrogenase reductases. This process is mediated by the RNF complex that exploits the proton motive force over the cytoplasmic membrane to lower the midpoint potential of the transferred electron. Here we report the cryogenic electron microscopy structure of the nitrogenase-associated RNF complex of A. vinelandii, a seven-subunit membrane protein assembly that contains four flavin cofactors and six iron-sulfur centers. Its function requires the strict coupling of electron and proton transfer but also involves major conformational changes within the assembly that can be traced with a combination of electron microscopy and modeling.
PubMed: 38890433
DOI: 10.1038/s41589-024-01641-1 -
Applied Microbiology and Biotechnology Jun 2024Non-symbiotic N-fixation would greatly increase the versatility of N-biofertilizers for sustainable agriculture. Genetic modification of diazotrophic bacteria has...
Non-symbiotic N-fixation would greatly increase the versatility of N-biofertilizers for sustainable agriculture. Genetic modification of diazotrophic bacteria has successfully enhanced NH release. In this study, we compared the competitive fitness of A. vinelandii mutant strains, which allowed us to analyze the burden of NH release under a broad dynamic range. Long-term competition assays under regular culture conditions confirmed a large burden for NH release, exclusion by the wt strain, phenotypic instability, and loss of the ability to release NH. In contrast, co-inoculation in mild autoclaved soil showed a much longer co-existence with the wt strain and a stable NH release phenotype. All genetically modified strains increased the N content and changed its chemical speciation in the soil. This study contributes one step forward towards bridging a knowledge gap between molecular biology laboratory research and the incorporation of N from the air into the soil in a molecular species suitable for plant nutrition, a crucial requirement for developing improved bacterial inoculants for economic and environmentally sustainable agriculture. KEY POINTS: • Genetic engineering for NH excretion imposes a fitness burden on the culture medium • Large phenotypic instability for NH-excreting bacteria in culture medium • Lower fitness burden and phenotypic instability for NH-excreting bacteria in soil.
Topics: Soil Microbiology; Azotobacter vinelandii; Ammonium Compounds; Nitrogen Fixation; Nitrogen; Genetic Fitness; Phenotype; Soil; Culture Media; Genetic Engineering
PubMed: 38888816
DOI: 10.1007/s00253-024-13231-1 -
Investigative Ophthalmology & Visual... Jun 2024The current study evaluated the lid margin microbiome of keratinized lid margins of patients with chronic Stevens-Johnson syndrome (SJS) and compared it with healthy...
PURPOSE
The current study evaluated the lid margin microbiome of keratinized lid margins of patients with chronic Stevens-Johnson syndrome (SJS) and compared it with healthy controls and historically reported lid margin microbiome of patients with meibomian gland dysfunction (MGD).
METHODS
Eyelid margin swabs of 20 asymptomatic adults (mean age = 29 ± 12 years) and 10 patients with chronic SJS (mean age = 31.2 ± 14 years) with lid margin keratinization were sequenced using next generation of 16S rDNA V3 to V4 variable region. Within SJS, the keratinized lid margin microbiome was compared with adjacent eyelid skin.
RESULTS
All patients had obstructive MGD, and mean Schirmer I value was 2.8 ± 1.9 mm. The phyla were similar in two groups, whereas at the genera level, an increase in the relative abundance of Corynebacterium, Haemophilus, Azotobacter, and Afipia and a decrease of Acinetobacter was noted in SJS compared to healthy lid margins. SJS-associated microbiota displayed lesser diversity and more heterogeneity than healthy controls. The Principal Components Analysis (PCA) plot revealed wide separation in the SJS and the control groups. Correlational network analysis revealed Corynebacterium and Sphingomonas forming a major hub of negative interactions with other bacterial genera in the SJS group. Significant differences exist in the prevalent genera between keratinized lid margins and historically reported meibum microbiome of patients with MGD. In addition, the eyelid skin of patients with SJS had predominant Staphylococcus, whereas Corynebacterium and Pseudomonas were more in the keratinized lid margins compared to the eyelid skin microbiome.
CONCLUSIONS
Lid margin microbiome is significantly altered in the keratinized lid margins of patients with SJS compared to the eyelid skin of patients with SJS, normal lid margins, and patients with MGD.
Topics: Humans; Male; Female; Adult; Microbiota; Dry Eye Syndromes; Eyelids; Stevens-Johnson Syndrome; Middle Aged; Young Adult; Bacteria; RNA, Ribosomal, 16S; DNA, Bacterial; Adolescent; Meibomian Glands; Meibomian Gland Dysfunction; Keratins
PubMed: 38888283
DOI: 10.1167/iovs.65.6.28 -
MBio Jun 2024Life depends on a conserved set of chemical energy currencies that are relics of early biochemistry. One of these is ATP, a molecule that, when paired with a divalent...
Life depends on a conserved set of chemical energy currencies that are relics of early biochemistry. One of these is ATP, a molecule that, when paired with a divalent metal ion such as Mg, can be hydrolyzed to support numerous cellular and molecular processes. Despite its centrality to extant biochemistry, it is unclear whether ATP supported the function of ancient enzymes. We investigate the evolutionary necessity of ATP by experimentally reconstructing an ancestral variant of the N-reducing enzyme nitrogenase. The Proterozoic ancestor is predicted to be ~540-2,300 million years old, post-dating the Great Oxidation Event. Growth rates under nitrogen-fixing conditions are ~80% of those of wild type in . In the extant enzyme, the hydrolysis of two MgATP is coupled to electron transfer to support substrate reduction. The ancestor has a strict requirement for ATP with no other nucleotide triphosphate analogs (GTP, ITP, and UTP) supporting activity. Alternative divalent metal ions (Fe, Co, and Mn) support activity with ATP but with diminished activities compared to Mg, similar to the extant enzyme. Additionally, it is shown that the ancestor has an identical efficiency in ATP hydrolyzed per electron transferred to the extant of two. Our results provide direct laboratory evidence of ATP usage by an ancient enzyme.IMPORTANCELife depends on energy-carrying molecules to power many sustaining processes. There is evidence that these molecules may predate the rise of life on Earth, but how and when these dependencies formed is unknown. The resurrection of ancient enzymes provides a unique tool to probe the enzyme's function and usage of energy-carrying molecules, shedding light on their biochemical origins. Through experimental reconstruction, this research investigates the ancestral dependence of a nitrogen-fixing enzyme on the energy carrier ATP, a requirement for function in the modern enzyme. We show that the resurrected ancestor does not have generalist nucleotide specificity. Rather, the ancestor has a strict requirement for ATP, like the modern enzyme, with similar function and efficiency. The findings elucidate the early-evolved necessity of energy-yielding molecules, delineating their role in ancient biochemical processes. Ultimately, these insights contribute to unraveling the intricate tapestry of evolutionary biology and the origins of life-sustaining dependencies.
PubMed: 38869277
DOI: 10.1128/mbio.01271-24 -
Microorganisms May 2024To optimize the application of plant growth-promoting rhizobacteria (PGPR) in field trials, tracking methods are needed to assess their shelf life and to determine the...
To optimize the application of plant growth-promoting rhizobacteria (PGPR) in field trials, tracking methods are needed to assess their shelf life and to determine the elements affecting their effectiveness and their interactions with plants and native soil microbiota. This work developed a real-time PCR (qtPCR) method which traces and quantifies bacteria when added as microbial consortia, including five PGPR species: , , , , and Through a literature search and in silico sequence analyses, a set of primer pairs which selectively tag three bacterial species (, and ) was retrieved. The primers were used to trace these microbial species in a field trial in which the consortium was tested as a biostimulant on two wheat varieties, in combination with biochar and the mycorrhizal fungus . The qtPCR assay demonstrated that the targeted bacteria had colonized and grown into the soil, reaching a maximum of growth between 15 and 20 days after inoculum. The results also showed biochar had a positive effect on PGPR growth. In conclusion, qtPCR was once more an effective method to trace the fate of supplied bacterial species in the consortium when used as a cargo system for their delivery.
PubMed: 38792831
DOI: 10.3390/microorganisms12051002 -
Foods (Basel, Switzerland) May 2024Due to climate change and exacerbated population growth, the search for new sustainable strategies that allow for greater food productivity and that provide greater...
Due to climate change and exacerbated population growth, the search for new sustainable strategies that allow for greater food productivity and that provide greater nutritional quality has become imperative. One strategy for addressing this problem is the combined use of fertilization with a reduced dose of nitrogen and biostimulants. Celery processing produces a large amount of waste with its concomitant pollution. Therefore, it is necessary to address the valorization of its byproducts. Our results revealed reductions in the biomass, Na, P, Mn, B, sugars, and proteins in the byproducts and increased lipid peroxidation, Fe (all celery parts), and K (byproducts) when the N supplied was reduced. Plants inoculated with obtained a greater biomass, a higher accumulation of K (byproducts), a build-up of sugars and proteins, reduced concentrations of P, Cu, Mn, B, Fe (petioles), and Zn (byproducts), and reduced lipid peroxidation. The application of Se at 8 μM reinforced the beneficial effect obtained after inoculation with . In accordance with our results, edible celery parts are recommended as an essential ingredient in the daily diet. Furthermore, the valorization of celery byproducts with health-promoting purposes should be considered.
PubMed: 38790737
DOI: 10.3390/foods13101437 -
Biochimica Et Biophysica Acta.... Aug 2024Azotobacter vinelandii is a genetically tractable Gram-negative proteobacterium able to fix nitrogen (N2) under aerobic growth conditions. This narrative describes how... (Review)
Review
Azotobacter vinelandii is a genetically tractable Gram-negative proteobacterium able to fix nitrogen (N2) under aerobic growth conditions. This narrative describes how biochemical-genetic approaches using A. vinelandii to study nitrogen fixation led to the formulation of the "scaffold hypothesis" for the assembly of both simple and complex [Fe-S] clusters associated with biological nitrogen fixation. These studies also led to the discovery of a parallel, but genetically distinct, pathway for maturation of [Fe-S] proteins that support central metabolic processes.
Topics: Azotobacter vinelandii; Iron-Sulfur Proteins; Nitrogen Fixation; Bacterial Proteins
PubMed: 38762171
DOI: 10.1016/j.bbamcr.2024.119750