Alcaligenes faecalis ZD02, a Novel Nematicidal Bacterium with an Extracellular Serine Protease Virulence Factor

Rhizosphere bacteria G-H27 significantly promoted the degradation of chlorpyrifos and fosthiazate

Microbial remediation of polluted environments is the most promising and significant research direction in the field of bioremediation. In this study, chlorpyrifos and fosthiazate were selected as representative organophosphorus pesticides, wheat was the tested plant, and fluorescently labeled degrading Bacillus cereus G-H27 were the film-forming bacteria. Exogenous strengthening technology was used to establish degrading bacterial biofilms on the root surface of wheat. The influence of root surface-degrading bacterial biofilms on the enrichment of chlorpyrifos and fosthiazate in wheat was comprehensively evaluated. First, the fluorescently-labeled degrading bacteria G-H27 was constructed, and its film-forming ability was investigated. Second, the growth- promoting characteristics and degradation ability of the bacteria G-H27 were investigated. Finally, the degradation effect of the root surface-degrading bacterial biofilm on chlorpyrifos and fosthiazate was determined. The above research provides an important material basis and method for the bioremediation of pesticide-contaminated soil.

3-(Methylthio)Propionic Acid from Bacillus thuringiensis Berliner Exhibits High Nematicidal Activity against the Root Knot Nematode Meloidogyne incognita (Kofoid and White) Chitwood

Root knot nematodes cause serious damage to global agricultural production annually. Given that traditional chemical fumigant nematicides are harmful to non-target organisms and the environment, the development of biocontrol strategies has attracted significant attention in recent years. In this study, it was found that the Bacillus thuringiensis Berliner strain NBIN-863 exhibits strong fumigant nematicidal activity and has a high attraction effect on Meloidogyne incognita (Kofoid and White) Chitwood. Four volatile organic compounds (VOCs) produced by NBIN-863 were identified using solid-phase microextraction and gas chromatography-mass spectrometry. The nematicidal activity of four VOCs, namely, N-methylformamide, propenamide, 3-(methylthio)propionic acid, and phenylmalonic acid, was detected. Among these compounds, 3-(methylthio)propionic acid exhibited the highest direct contact nematicidal activity against M. incognita, with an LC50 value of 6.27 μg/mL at 24 h. In the fumigant bioassay, the mortality rate of M. incognita treated with 1 mg/mL of 3-(methylthio)propionic acid for 24 h increased to 69.93%. Furthermore, 3-(methylthio)propionic acid also exhibited an inhibitory effect on the egg-hatching of M. incognita. Using chemotaxis assays, it was determined that 3-(methylthio)propionic acid was highly attractive to M. incognita. In pot experiments, the application of 3-(methylthio)propionic acid resulted in a reduction in gall numbers, decreasing the number of galls per gram of tomato root from 97.58 to 6.97. Additionally, the root length and plant height of the treated plants showed significant increases in comparison with the control group. The current study suggests that 3-(methylthio)propionic acid is a novel nematicidal virulence factor of B. thuringiensis. Our research provides evidence for the potential use of NBIN-863 or its VOCs in biocontrol against root knot nematodes.

Diversity of bioprotective microbial organisms in Upper Region of Assam and its efficacy against Meloidogyne graminicola

Meloidogyne graminicola has a well-established negative impact on rice yield in transplanted and direct-seeded rice, resulting in yield losses of up to 20 to 90 percent. Studies were undertaken to isolate potential native strains of bio-control agents to manage the devastating Rice Root Knot Nematode (M. graminicola). Eighteen bacterial strains and eleven fungal strains were isolated from the rhizosphere of crops like rice, okra, ash gourd, chili, beans and cucumber, enveloping diverse soil types from the Upper Brahmaputra Valley region of Assam. Six bacterial strains were gram-positive according to morphological results, while twelve others stained negatively. Fifteen bacteria were rod-shaped, two were coccus and one was diplococcus, and all the bacterial isolates showed signs of movement. All the bacterial strains exhibited positivity for gelatin hydrolysis and catalase test. Seven bacteria showed positive, while eleven showed negative reactions to possess the ability to deduce carbon and energy from citrate. The study of the in vitro efficacy of the twenty-nine bacterial and fungal isolates tested against second-stage juveniles (J₂) of Meloidogyne graminicola revealed that all the bacterial and fungal isolates potentially inhibited the test organism and caused significant mortality over sterile water treatment. The promising bacterial and fungal isolates that exhibited mortality above 50% were identified as BSH8, BTS4, BTS5, BJA15, FJB 11 and FSH5. The strain BSH8 exhibited the best result of mortality, with 80.79% mortality against J₂ of M. graminicola. The strain BTS4 and BTS5 expressed mortality of 71.29% and 68.75% under in-vitro conditions and were significant. The effective and promising bioagents were identified using the 16 S rRNA sequencing as Bacillis subtilis (BSH8), Bacillus velezensis (BTS4), Alcaligenes faecalis (BTS5), Rhizobium pusense (BJA15), Talaromyces allahabadensis (FSH5) and Trichoderma asperellum (FJB11). These results indicated the microorganism's potential against M. graminicola and its potential for successful biological implementation. Further, the native strains could be tested against various nematode pests of rice in field conditions. Its compatibility with various pesticides and the implication of the potential strains in integrated pest management can be assessed.

'A plant's major strength in rhizosphere': the plant growth promoting rhizobacteria

Human activities, industrialization and civilization have deteriorated the environment which eventually has led to alarming effects on plants and animals by heightened amounts of chemical pollutants and heavy metals in the environment, which create abiotic stress. Environmental conditions like drought, salinity, diminished macro-and micro-nutrients also contribute in abiotic stress, resulting in decrement of survival and growth of plants. Presence of pathogenic and competitive microorganisms, as well as pests lead to biotic stress and a plant alone can not defend itself. Thankfully, nature has rendered plant's rhizosphere with plant growth promoting rhizobacteria which maintain an allelopathic relationship with host plant to defend the plant and let it flourish in abiotic as well as biotic stress situations. This review discusses the mechanisms behind increase in plant growth via various direct and indirect traits expressed by associated microorganisms in the rhizosphere, along with their current scenario and promising future for sustainable agriculture. It also gives details of ten such bacterial species, viz. Acetobacter, Agrobacterium, Alcaligenes, Arthrobacter, Azospirillum, Azotobacter, Bacillus, Burkholderia, Enterobacter and Frankia, whose association with the host plants is famed for enhancing plant's growth and survival.

Towards Understanding the Function of Aegerolysins

Aegerolysins are remarkable proteins. They are distributed over the tree of life, being relatively widespread in bacteria and fungi, but also present in some insects, plants, protozoa, and viruses. Despite their abundance in cells of certain developmental stages and their presence in secretomes, only a few aegerolysins have been studied in detail. Their function, in particular, is intriguing. Here, we summarize previously published findings on the distribution, molecular interactions, and function of these versatile aegerolysins. They have very diverse protein sequences but a common fold. The machine learning approach of the AlphaFold2 algorithm, which incorporates physical and biological knowledge of protein structures and multisequence alignments, provides us new insights into the aegerolysins and their pore-forming partners, complemented by additional genomic support. We hypothesize that aegerolysins are involved in the mechanisms of competitive exclusion in the niche.

Genomic and resistome analysis of Alcaligenes faecalis strain PGB1 by Nanopore MinION and Illumina Technologies

Background

Drug-resistant bacteria are important carriers of antibiotic-resistant genes (ARGs). This fact is crucial for the development of precise clinical drug treatment strategies. Long-read sequencing platforms such as the Oxford Nanopore sequencer can improve genome assembly efficiency particularly when they are combined with short-read sequencing data.

Results

Alcaligenes faecalis PGB1 was isolated and identified with resistance to penicillin and three other antibiotics. After being sequenced by Nanopore MinION and Illumina sequencer, its entire genome was hybrid-assembled. One chromosome and one plasmid was assembled and annotated with 4,433 genes (including 91 RNA genes). Function annotation and comparison between strains were performed. A phylogenetic analysis revealed that it was closest to A. faecalis ZD02. Resistome related sequences was explored, including ARGs, Insert sequence, phage. Two plasmid aminoglycoside genes were determined to be acquired ARGs. The main ARG category was antibiotic efflux resistance and β-lactamase (EC 3.5.2.6) of PGB1 was assigned to Class A, Subclass A1b, and Cluster LSBL3.

Conclusions

The present study identified the newly isolated bacterium A. faecalis PGB1 and systematically annotated its genome sequence and ARGs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08507-7.

Microbial proteases: ubiquitous enzymes with innumerable uses

Proteases are ubiquitous enzymes, having significant physiological roles in both synthesis and degradation. The use of microbial proteases in food fermentation is an age-old process, which is today being successfully employed in other industries with the advent of ‘omics’ era and innovations in genetic and protein engineering approaches. Proteases have found application in industries besides food, like leather, textiles, detergent, waste management, agriculture, animal husbandry, cosmetics, and pharmaceutics. With the rising demands and applications, researchers are exploring various approaches to discover, redesign, or artificially synthesize enzymes with better applicability in the industrial processes. These enzymes offer a sustainable and environmentally safer option, besides possessing economic and commercial value. Various bacterial and fungal proteases are already holding a commercially pivotal role in the industry. The current review summarizes the characteristics and types of proteases, microbial source, their current and prospective applications in various industries, and future challenges. Promoting these biocatalysts will prove significant in betterment of the modern world.

Whole-Genome Sequencing of Alcaligenes faecalis HZ01, with Potential to Inhibit Nontuberculous Mycobacterial Growth

Alcaligenes faecalis is a Gram-negative rod that is ubiquitous in the environment and is an opportunistic human pathogen. Here, we report the whole-genome sequencing analysis of A. faecalis HZ01, which presents mycobacterial growth inhibitory activity and was isolated from a contaminated culture of Mycobacterium chubuense ATCC 27278.

Complete genome sequence and analysis of Alcaligenes faecalis strain Mc250, a new potential plant bioinoculant

Here we present and analyze the complete genome of Alcaligenes faecalis strain Mc250 (Mc250), a bacterium isolated from the roots of Mimosa calodendron, an endemic plant growing in ferruginous rupestrian grasslands in Minas Gerais State, Brazil. The genome has 4,159,911 bp and 3,719 predicted protein-coding genes, in a single chromosome. Comparison of the Mc250 genome with 36 other Alcaligenes faecalis genomes revealed that there is considerable gene content variation among these strains, with the core genome representing only 39% of the protein-coding gene repertoire of Mc250. Mc250 encodes a complete denitrification pathway, a network of pathways associated with phenolic compounds degradation, and genes associated with HCN and siderophores synthesis; we also found a repertoire of genes associated with metal internalization and metabolism, sulfate/sulfonate and cysteine metabolism, oxidative stress and DNA repair. These findings reveal the genomic basis for the adaptation of this bacterium to the harsh environmental conditions from where it was isolated. Gene clusters associated with ectoine, terpene, resorcinol, and emulsan biosynthesis that can confer some competitive advantage were also found. Experimental results showed that Mc250 was able to reduce (~60%) the virulence phenotype of the plant pathogen Xanthomonas citri subsp. citri when co-inoculated in Citrus sinensis, and was able to eradicate 98% of juveniles and stabilize the hatching rate of eggs to 4% in two species of agricultural nematodes. These results reveal biotechnological potential for the Mc250 strain and warrant its further investigation as a biocontrol and plant growth-promoting bacterium.

Rare but Fatal Case of Cavitary Pneumonia Caused by Alcaligenes Faecalis

Alcaligenes faecalis is a gram-negative bacterium that is commonly found in the environment. This pathogen is usually transmitted in the form of droplets through ventilation equipment and nebulizers, but transmission through direct contact has also been documented in few case reports. This pathogen can cause rare but fatal infections including appendicitis, abscesses, meningitis, bloodstream infection, endocarditis, and post-operative endophthalmitis. Pan drug resistance to all commercially available antibiotics has been emerging globally. We present the case of a 66-year-old male who had respiratory failure along with multiple comorbidities. A large cavitary lesion caused by pan drug-resistant Alcaligenes faecalis was found on chest imaging. Despite the treatment with broad-spectrum antibiotics, the clinical outcome was very poor.

Identifying different types of microorganisms with terahertz spectroscopy

Most microbial detection techniques require pretreatment, such as fluorescent labeling and cultivation processes. Here, we propose novel tools for classifying and identifying microorganisms such as molds, yeasts, and bacteria based on their intrinsic dielectric constants in the THz frequency range. We first measured the dielectric constant of films that consisted of a wide range of microbial species, and extracted the values for the individual microbes using the effective medium theory. The dielectric constant of the molds was 1.24-1.85, which was lower than that of bacteria ranging from 2.75-4.11. The yeasts exhibited particularly high dielectric constants reaching 5.63-5.97, which were even higher than that of water. These values were consistent with the results of low-density measurements in an aqueous environment using microfluidic metamaterials. In particular, a blue shift in the metamaterial resonance occurred for molds and bacteria, whereas the molds have higher contrast relative to bacteria in the aqueous environment. By contrast, the deposition of the yeasts induced a red shift because their dielectric constant was higher than that of water. Finally, we measured the dielectric constants of peptidoglycan and polysaccharides such as chitin, α-glucan, and β-glucans (with short and long branches), and confirmed that cell wall composition was the main cause of the observed differences in dielectric constants for different types of microorganisms.

Nematicidal activity of thermostable alkaline protease produced by Saccharomonospora viridis strain Hw G550

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Isolation and identification of thermo alkaliphilic actinomycetes.

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Obtaining of thermostable alkaline protease enzyme.

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Evaluation of the nematicidal activity of obtained protease.

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Application of thermostable alkaline protease as nemticidal agent.

Application of thermostable alkaline protease to control the harmful nematodes was investigated in the current study. A total of 14 proteolytic actinomycetes were isolated from Egyptian harsh environments. Out of them, isolate G550 exhibited the highest proteolytic activity (528.9 U/ml). Protease from isolate G550 exhibited high nematicidal activity against M. incognita under laboratory conditions and caused hydrolysis of J₂S cuticle. This isolate was identified using molecular techniques and deposited in GenBank under name of Saccharomonospora viridis strain Hw G550 with accession number: MF152631. The G550 protease was extracted, characterized and applied under greenhouse conditions as nematicidal agent. This enzyme exhibited maximum activity and stability at alkaline pH (8) and thermal conditions (50–60 °C). Also, the results showed that, all treatments using protease caused a significant decrease in nematode reproduction and increasing in the plant properties. Finally, the thermo alkaliphilic protease could be used as bio-control agent against RKN.

Bloodstream infection with pandrug-resistant Alcaligenes faecalis treated with double-dose of tigecycline

Introduction

Alcaligenes faecalis is a species of gram-negative, rod-shaped, aerobic bacteria commonly found in the environment. A. faecalis-associated nosocomial infections are common in hospitalized patients, but serious life threatening infections are rare. Here, we report a rare case of BSI with A. faecalis resistant to all available antibiotics; successfully treated with double-dose of tigecycline.

Presentation of case

A 60-year-old female presented with A. faecalis bloodstream infection, where the organism was completely resistant to all commercially available antibiotics including polymyxins and tigecycline. The physical condition of the patient was deteriorating and there were no active antibiotics available to prescribe based on sensitivities. Despite the organism's resistance to tigecycline, double-dose of tigecycline therapy (100 mg twice daily, intravenously after a 200 mg single intravenous loading dose) was prescribed intentionally for the treatment of this infection. The organism was completely eradicated from the bloodstream of that patient within the 5 days of therapy-initiation.

Discussion

Double-dose of tigecycline maintains a higher serum drug concentration rather than the standard dose, and in this case, double-dose of tigecycline completely cleared the pandrug-resistant A. faecalis from the blood where initially, that organism was resistant to tigecycline. Previously, A. faecalis isolates were found resistant to fluoroquinolones, but here it was found very rarely resistant to even reserve antibiotics, polymyxins, carbapenems and tigecycline.

Conclusion

Pandrug-resistant A. faecalis-associated bloodstream infection is a very uncommon case and double-dose of tigecycline may be an effective option to treat it.

Identification and Characterization of a Novel pic Gene Cluster Responsible for Picolinic Acid Degradation in Alcaligenes faecalis JQ135

Picolinic acid (PA) is a natural toxic pyridine derivative. Microorganisms can degrade and utilize PA for growth. However, the full catabolic pathway of PA and its physiological and genetic foundation remain unknown. In this study, we identified a gene cluster, designated picRCEDFB4B3B2B1A1A2A3, responsible for the degradation of PA from Alcaligenes faecalis JQ135. Our results suggest that PA degradation pathway occurs as follows: PA was initially 6-hydroxylated to 6-hydroxypicolinic acid (6HPA) by PicA (a PA dehydrogenase). 6HPA was then 3-hydroxylated by PicB, a four-component 6HPA monooxygenase, to form 3,6-dihydroxypicolinic acid (3,6DHPA), which was then converted into 2,5-dihydroxypyridine (2,5DHP) by the decarboxylase PicC. 2,5DHP was further degraded to fumaric acid through PicD (2,5DHP 5,6-dioxygenase), PicE (N-formylmaleamic acid deformylase), PicF (maleamic acid amidohydrolase), and PicG (maleic acid isomerase). Homologous pic gene clusters with diverse organizations were found to be widely distributed in Alpha-, Beta-, and Gammaproteobacteria Our findings provide new insights into the microbial catabolism of environmental toxic pyridine derivatives.IMPORTANCE Picolinic acid is a common metabolite of l-tryptophan and some aromatic compounds and is an important intermediate in organic chemical synthesis. Although the microbial degradation/detoxification of picolinic acid has been studied for over 50 years, the underlying molecular mechanisms are still unknown. Here, we show that the pic gene cluster is responsible for the complete degradation of picolinic acid. The pic gene cluster was found to be widespread in other Alpha-, Beta-, and Gammaproteobacteria These findings provide a new perspective for understanding the catabolic mechanisms of picolinic acid in bacteria.

Genome sequencing and analysis of Alcaligenes faecalis subsp. phenolicus MB207

Bacteria within the genus Alcaligenes, exhibit diverse properties but remain largely unexplored at genome scale. To shed light on the genome structure, heterogeneity and traits of Alcaligenes species, the genome of a tannery effluent isolated Alcaligenes faecalis subsp. phenolicus MB207 was sequenced and assembled. The genome was compared to the whole genome sequences of genus Alcaligenes present in the National Centre for Biotechnology Information database. Core, pan and species specific gene sequences i.e. singletons were identified. Members of this genus did not portray exceptional genetic heterogeneity or conservation and out of 5,166 protein coding genes from pooled genome dataset, 2429 (47.01%) contributed to the core, 1193 (23.09%) to singletons and 1544 (29.88%) to accessory genome. Secondary metabolite forming apparatus, antibiotic production and resistance was also profiled. Alcaligenes faecalis subsp. phenolicus MB207 genome consisted of a copious amount of bioremediation genes i.e. metal tolerance and xenobiotic degrading genes. This study marks this strain as a prospective eco-friendly bacterium with numerous benefits for the environment related research. Availability of the whole genome sequence heralds an opportunity for researchers to explore enzymes and apparatus for sustainable environmental clean-up as well as important compounds/substance production.

Volatile organic compounds from Paenibacillus polymyxa KM2501-1 control Meloidogyne incognita by multiple strategies

Plant-parasitic nematodes (PPNs) cause serious crop losses worldwide. In this study, we investigated the nematicidal factors and the modes and mechanisms of action involved in nematode control by Paenibacillus polymyxa KM2501-1. Treatment of the second-stage juveniles (J2) juveniles of PPN Meloidogyne incognita with the biological control agent KM2501-1 resulted in a mortality of 87.66% in vitro and reduced symptoms on tomato by up to 82.61% under greenhouse conditions. We isolated 11 volatile organic compounds (VOCs) from strain KM2501-1, of which 8 had contact nematicidal activity, 6 had fumigant activity, and 5 acted as stable chemotactic agents to M. incognita. The VOCs provided a comprehensive strategy against PPNs that included "honey-trap", fumigant, attractant and repellent modes. Furfural acetone and 2-decanol functioned as "honey-traps" attracting M. incognita and then killing it by contact or fumigation. Two other VOCs, 2-nonanone and 2-decanone, as well as strain KM2501-1 itself, destroyed the integrity of the intestine and pharynx. Collectively our results indicate that VOCs produced by P. polymyxa KM2501-1 act through diverse mechanisms to control M. incognita. Moreover, the novel "honey-trap" mode of VOC-nematode interaction revealed in this study extends our understanding of the strategies exploited by nematicidal biocontrol agents.