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Microbiology Resource Announcements Apr 2024In the present work, we present the draft genome sequence of a new putative species associated with the tomato rhizosphere.
In the present work, we present the draft genome sequence of a new putative species associated with the tomato rhizosphere.
PubMed: 38517186
DOI: 10.1128/mra.01220-23 -
PeerJ 2024Biochar amendments enhance crop productivity and improve agricultural quality. To date, studies on the correlation between different amounts of biochar in pakchoi ( L.)...
BACKGROUND
Biochar amendments enhance crop productivity and improve agricultural quality. To date, studies on the correlation between different amounts of biochar in pakchoi ( L.) quality and rhizosphere soil microorganisms are limited, especially in weakly alkaline soils. The experiment was set up to explore the effect of different concentrations of biochar on vegetable quality and the correlation between the index of quality and soil bacterial community structure changes.
METHODS
The soil was treated in the following ways via pot culture: the blank control (CK) without biochar added and with biochar at different concentrations of 1% (T1), 3% (T2), 5% (T3), and 7% (T4). Here, we investigatedthe synergistic effect of biochar on the growth and quality of pakchoi, soil enzymatic activities, and soil nutrients. Microbial communities from pakchoi rhizosphere soil were analyzed by Illumina MiSeq.
RESULTS
The results revealed that adding 3% biochar significantly increased plant height, root length, and dry weight of pakchoi and increased the contents of soluble sugars, soluble proteins, Vitamin C (VC), cellulose, and reduced nitrate content in pakchoi leaves. Meanwhile, soil enzyme activities and available nutrient content in rhizosphere soil increased. This study demonstrated that the the microbial community structure of bacteria in pakchoi rhizosphere soil was changed by applying more than 3% biochar. Among the relatively abundant dominant phyla, , , and were reduced, and , , , and relative abundance increased. Furthermore, adding 3% biochar reduced the relative abundance of s and increased the relative abundances of , , , , and . The nitrate content was positively correlated with the abundance of and the nitrate content was significantly negatively correlated with the relative abundance of . Carbohydrate transport and metabolism in the rhizosphere soil of pakchoi decreased, and lipid transport and metabolism increased after biochar application.
CONCLUSION
Overall, our results indicated that applying biochar improved soil physicochemical states and plant nutrient absorption, and affected the abundance of dominant bacterial groups (, and ), these were the main factors to increase pakchoi growth and promote quality of pakchoi. Therefore, considering the growth, quality of pakchoi, and soil environment, the effect of using 3% biochar is better.
Topics: Soil; Rhizosphere; Nitrates; Soil Microbiology; Microbiota; Bacteria; Plants; Charcoal
PubMed: 38515457
DOI: 10.7717/peerj.16733 -
Journal of Hazardous Materials May 2024Most current researches focus solely on reducing soil chromium availability. It is difficult to reduce soil Cr(VI) concentration below 5.0 mg kg using single...
Most current researches focus solely on reducing soil chromium availability. It is difficult to reduce soil Cr(VI) concentration below 5.0 mg kg using single remediation technology. This study introduced a sustainable soil Cr(VI) reduction and stabilization system, Penicillium oxalicum SL2-nanoscale zero-valent iron (nZVI), and investigated its effect on Cr(VI) reduction efficiency and microbial ecology. Results showed that P. oxalicum SL2-nZVI effectively reduced soil total Cr(VI) concentration from 187.1 to 3.4 mg kg within 180 d, and remained relatively stable at 360 d. The growth curve of P. oxalicum SL2 and microbial community results indicated that γ-ray irradiation shortened the adaptation time of P. oxalicum SL2 and facilitated its colonization in soil. P. oxalicum SL2 colonization activated nZVI and its derivatives, and increased soil iron bioavailability. After restoration, the negative effect of Cr(VI) on soil microorganisms was markedly alleviated. Cr(VI), Fe(II), bioavailable Cr/Fe, Eh, EC and urease (SUE) were the key environmental factors of soil microbiota. Notably, Penicillium significantly stimulated the growth of urease-positive bacteria, Arthrobacter, Pseudarthrobacter, and Microvirga, synergistically reducing soil chromium availability. The combination of P. oxalicum SL2 and nZVI is expected to form a green, economical and long-lasting Cr(VI) reduction stabilization strategy.
Topics: Chromium; Environmental Restoration and Remediation; Iron; Penicillium; Soil; Urease; Water Pollutants, Chemical
PubMed: 38508106
DOI: 10.1016/j.jhazmat.2024.134058 -
ISME Communications Jan 2024Northern peatlands contain ~30% of terrestrial carbon (C) stores, but in recent decades, 14% to 20% of the stored C has been lost because of conversion of the peatland...
Northern peatlands contain ~30% of terrestrial carbon (C) stores, but in recent decades, 14% to 20% of the stored C has been lost because of conversion of the peatland to cropland. Microorganisms are widely acknowledged as primary decomposers, but the keystone taxa within the bacterial community regulating C loss from cultivated peatlands remain largely unknown. In this study, we investigated the bacterial taxa driving peat C mineralization during rice cultivation. Cultivation significantly decreased concentrations of soil organic C, dissolved organic C (DOC), carbohydrates, and phenolics but increased C mineralization rate (CMR). Consistent with the classic theory that phenolic inhibition creates a "latch" that reduces peat C decomposition, phenolics were highly negatively correlated with CMR in cultivated peatlands, indicating that elimination of inhibitory phenolics can accelerate soil C mineralization. Bacterial communities were significantly different following peatland cultivation, and co-occurrence diagnosis analysis revealed substantial changes in network clusters of closely connected nodes (modules) and bacterial keystone taxa. Specifically, in cultivated peatlands, bacterial modules were significantly negatively correlated with phenolics, carbohydrates, and DOC. While keystone taxa , , and can regulate bacterial modules and promote carbon mineralization. Those observations indicated that changes in bacterial modules can promote phenolic decomposition and eliminate phenolic inhibition of labile C decomposition, thus accelerating soil organic C loss during rice cultivation. Overall, the study provides deeper insights into microbe-driven peat C loss during rice cultivation and highlights the crucial role of keystone bacterial taxa in the removal of phenolic constraints on peat C preservation.
PubMed: 38500699
DOI: 10.1093/ismeco/ycae022 -
Journal, Genetic Engineering &... Mar 2024Choline oxidase, a flavoprotein, is an enzyme that catalyzes the reaction which converts choline into glycine betaine. Choline oxidase started its journey way back in...
BACKGROUND
Choline oxidase, a flavoprotein, is an enzyme that catalyzes the reaction which converts choline into glycine betaine. Choline oxidase started its journey way back in 1933. However, the impact of the high temperature on its structure has not been explored despite the long history and availability of its crystal structure. Both choline oxidase and its product, glycine betaine, have enormous applications spanning across multiple industries. Understanding how the 3D structure of the enzyme will change with the temperature change can open new ways to make it more stable and useful for industry.
PROCESS
This research paper presents the in-silico study and analysis of the structural changes of A. globiformis choline oxidase at temperatures from 25 °C to 60 °C. A step-wise process is depicted in Fig. 1.
RESULTS
Multiple sequence alignment (MSA) of 11 choline oxidase sequences from different bacteria vs Arthrobacter globiformis choline oxidase showed that active site residues are highly conserved. The available crystal structure of A. globiformis choline oxidase with cofactor Flavin Adenine Dinucleotide (FAD) in the dimeric state (PDB ID: 4MJW) was considered for molecular dynamics simulations. A simulated annealing option was used to gradually increase the temperature of the system from 25 °C to 60 °C. Analysis of the conserved residues, as well as residues involved in Flavin Adenine Dinucleotide (FAD) binding, substrate binding, substate gating, and dimer formationwas done. At high temperatures, the formation of the inter-chain salt bridge between Arg50 and Glu63 was a significant observation near the active site of choline oxidase.
CONCLUSION
Molecular dynamics studies suggest that an increase in temperature has a significant impact on the extended Flavin Adenine Dinucleotide (FAD) binding region. These changes interfere with the entry of substrate to the active site of the enzyme and make the enzyme inactive.
PubMed: 38494262
DOI: 10.1016/j.jgeb.2023.100348 -
Journal of Dairy Science Mar 2024To evaluate the sodium chloride content effect on microbiological, biochemical, physicochemical and sensorial characteristics, Munster cheeses were prepared from...
To evaluate the sodium chloride content effect on microbiological, biochemical, physicochemical and sensorial characteristics, Munster cheeses were prepared from pasteurized milk seeded with 3 yeasts (Kluyveromyces marxianus, Debaryomyces hansenii, Geotrichum candidum) and 5 ripening bacteria (Arthrobacter arilaitensis, Brevibacterium aurantiacum, Corynebacterium casei, Hafnia alvei, and Staphylococcus equorum). Experiments were performed under 1.0%, 1.7% and 2.4% NaCl levels in cheese in triplicate. Ripening (d2 - d27) was carried under 12°C and 96% RH. These kinetics were both reproducible and repeatable at 99% confidence level. For each microbial, biochemical and physicochemical parameter, 2 kinetic descriptors (maximal or minimal rate and its occurrence time) were defined. On d2 the physicochemical variables (water activity, dry matter, water content) were strongly dependent on the salting level. From d2 to d27 K. lactis was insensitive to salt while D. hansenii was stimulated. G. candidum growth appeared very sensitive to salt in cheese: at 1.0% NaCl G. candidum exhibited overgrowth, negatively impacting rind appearance, underrind consistency and thickness and off-flavor flaws. Salt concentration of 2.4% induced death of G. candidum. Four bacteria (A. arilaitensis, B. aurantiacum, C. casei, and H. alvei) were moderately sensitive to salt while S. equorum was insensitive to it. Salt level in cheese had a significant effect on carbon substrate consumption rates. Lactate consumption rate in 1.0% salted cheeses was approximately twice higher than under 2.4% NaCl. Data analysis of microorganism, biochemical, and physicochemical kinetics and sensory analysis showed that the best salt level in Munster-type cheeses to achieve an optimum balance between cheese characteristics, sensory qualities and marketability was 1.7% NaCl.
PubMed: 38490552
DOI: 10.3168/jds.2024-24307 -
Plants (Basel, Switzerland) Feb 2024The application of biostimulants has been proven to be an advantageous tool and an appropriate form of management towards the effective use of natural resources, food... (Review)
Review
The application of biostimulants has been proven to be an advantageous tool and an appropriate form of management towards the effective use of natural resources, food security, and the beneficial effects on plant growth and yield. Plant-growth-promoting rhizobacteria (PGPR) are microbes connected with plant roots that can increase plant growth by different methods such as producing plant hormones and molecules to improve plant growth or providing increased mineral nutrition. They can colonize all ecological niches of roots to all stages of crop development, and they can affect plant growth and development directly by modulating plant hormone levels and enhancing nutrient acquisition such as of potassium, phosphorus, nitrogen, and essential minerals, or indirectly via reducing the inhibitory impacts of different pathogens in the forms of biocontrol parameters. Many plant-associated species such as , , , , , and can increase plant growth by improving plant disease resistance, synthesizing growth-stimulating plant hormones, and suppressing pathogenic microorganisms. The application of biostimulants is both an environmentally friendly practice and a promising method that can enhance the sustainability of horticultural and agricultural production systems as well as promote the quantity and quality of foods. They can also reduce the global dependence on hazardous agricultural chemicals. Science Direct, Google Scholar, Springer Link, CAB Direct, Scopus, Springer Link, Taylor and Francis, Web of Science, and Wiley Online Library were checked, and the search was conducted on all manuscript sections in accordance with the terms , , , , , , , , Biostimulants, Plant growth promoting rhizobactera, and . The aim of this manuscript is to survey the effects of plant-growth-promoting rhizobacteria by presenting case studies and successful paradigms in various agricultural and horticultural crops.
PubMed: 38475460
DOI: 10.3390/plants13050613 -
Microbiology Resource Announcements Apr 2024Ruchi a temperate, AS1 subcluster bacteriophage isolated in Lumpkin County, Georgia using host , possesses a genome of 38,571 bp and 67.7% GC. Annotation of this virus...
Ruchi a temperate, AS1 subcluster bacteriophage isolated in Lumpkin County, Georgia using host , possesses a genome of 38,571 bp and 67.7% GC. Annotation of this virus revealed 64 predicted reading frames, no predicted tRNA genes, and a close evolutionary relationship to AS1 phage Basilisk.
PubMed: 38466103
DOI: 10.1128/mra.01224-23 -
Chemosphere Apr 2024Cr(VI) contamination is widely recognized as one of the major environmental hazards. To address the problem of remediation of soil Cr(VI) contamination and utilization...
Cr(VI) contamination is widely recognized as one of the major environmental hazards. To address the problem of remediation of soil Cr(VI) contamination and utilization of waste peanut shells, this study comprehensively investigated the effects of peanut shell-derived biochar loaded with root exudates of hyperaccumulator Leersia hexandra Swartz on Cr(VI) reduction and microbial community succession in soil. This study confirmed that root exudate-loaded peanut shell biochar reduced soil pH while simultaneously increasing DOC, sulfide, and Fe(II) concentrations, thereby facilitating the reduction of Cr(VI), achieving a reduction efficiency of 81.8%. Based on XPS and SEM elemental mapping analyses, Cr(VI) reduction occurred concurrently with the Fe and S redox cycles. Furthermore, the microbial diversity, abundance of the functional genera (Geobacter, Arthrobacter, and Desulfococcus) and the metabolic functions associated with Cr(VI) reduction were enhanced by root exudate-loaded biochar. Root exudate-loaded biochar can promote both direct Cr(VI) reduction mediated by the Cr(VI)-reducing bacteria Arthrobacter, and indirect Cr(VI) reduction through Cr/S/Fe co-transformation mediated by the sulfate-reducing bacteria Desulfococcus and Fe(III)-reducing bacteria Geobacter. This study demonstrates the effectiveness of peanut shell biochar loaded with root exudates of hyperaccumulator Leersia hexandra Swartz to promote soil Cr(VI) reduction, reveals the mechanism how root exudate-loaded biochar shapes functional microbial communities to facilitate Cr(VI) reduction, and proposes a viable strategy for Cr(VI) remediation and utilization of peanut shell.
Topics: Ferric Compounds; Soil; Charcoal; Chromium; Microbiota; Poaceae; Soil Pollutants; Exudates and Transudates
PubMed: 38447895
DOI: 10.1016/j.chemosphere.2024.141636 -
Parasites & Vectors Mar 2024Ticks serve as vectors for a diverse array of pathogens, including viruses responsible for both human and livestock diseases. Symbiotic bacteria hold significant...
BACKGROUND
Ticks serve as vectors for a diverse array of pathogens, including viruses responsible for both human and livestock diseases. Symbiotic bacteria hold significant potential for controlling tick-borne disease. However, the alteration of tick gut bacterial community in response to pathogen infection has not been analyzed for any tick-borne viruses. Here, the impact of severe fever with thrombocytopenia syndrome virus (SFTSV) infection on bacterial diversity in the gut of Haemaphysalis longicornis is investigated.
METHODS
Unfed tick females were artificially infected with SFTSV. The gut samples were collected and the genomic DNA was extracted. We then investigated alterations in gut bacterial composition in response to SFTSV infection through 16S rRNA gene sequencing.
RESULTS
The study found that a reduction in the number of operational taxonomic units (OTUs) in the tick gut following SFTSV infection. However, there were no significant changes in alpha diversity indices upon infection. Four genera, including Corynebacterium, Arthrobacter, Sphingomonas, and Escherichia, were identified as biomarkers for the tick gut without SFTSV infection. Notably, the predicted correlation network indicated that the biomarkers Sphingomonas and Escherichia exhibited positive correlations within the same subcommunity, which was altered upon viral infection.
CONCLUSIONS
These findings revealed that the change in tick gut bacterial composition upon SFTSV infection and could facilitate the discovery new target for tick-borne viral disease control.
Topics: Female; Humans; Animals; Severe Fever with Thrombocytopenia Syndrome; Gastrointestinal Microbiome; Haemaphysalis longicornis; RNA, Ribosomal, 16S; Biomarkers
PubMed: 38444018
DOI: 10.1186/s13071-024-06204-w