Antibiotics Producing Soil Microorganisms

Bioprospecting of soil-borne microorganisms and chemical dereplication of their anti-microbial constituents with the aid of UPLC-QTOF-MS and molecular networking approach

Due to the emergence of drug-resistant microorganisms, the search for broad-spectrum antimicrobial compounds has become extremely crucial. Natural sources like plants and soils have been explored for diverse metabolites with antimicrobial properties. This study aimed to identify microorganisms from agricultural soils exhibiting antimicrobial effects against known human pathogens, and to highlight the chemical space of the responsible compounds through the computational metabolomics-based bioprospecting approach. Herein, bacteria were extracted from soil samples and their antimicrobial potential was measured via the agar well diffusion method. Methanolic extracts from the active bacteria were analyzed using the liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) technique, and the subsequent data was further analyzed through molecular networking approach which aided in identification of potential anti-microbial compounds. Furthermore, 16S rRNA gene sequencing enabled identification of the active bacterial isolates, where isolate 1 and 2 were identified as strains of Bacillus pumilus, whilst isolate 3 was found to be Bacillus subtilis. Interestingly, isolate 3 (Bacillus subtilis) displayed wide-ranging antimicrobial activity against the tested human pathogens. Molecular networking revealed the presence of Diketopiperazine compounds such as cyclo (D-Pro-D-Leu), cyclo (L-Tyr-L-Pro), cyclo (L-Pro-D-Phe), and cyclo (L-Pro-L-Val), alongside Surfactin C, Surfactin B, Pumilacidin E, and Isarrin D in the Bacillus strains as the main anti-microbial compounds. The application of the molecular networking approach represents an innovation in the field of bio-guided bioprospection of microorganisms and has proved to be an effective and feasible towards unearthing potent antimicrobial compounds. Additionally, the (computational metabolomics-based) approach accelerates the discovery of bioactive compounds and isolation of strains which offer a promising avenue for discovering new clinical antimicrobials. Finally, soil microbial flora could serve an alternative source of anti-microbial compounds which can assist in the fight against emergence of multi-drug resistance bacterial pathogens.

Soil microbiome influences human health in the context of climate change

Soil microbiomes continue to evolve and shape the human microbiota according to external anthropogenic and climate change effects. Ancient microbes are being exposed as a result of glacier melting, soil erosion and poor agricultural practices. Soil microbes subtly regulate greenhouse gas emissions and undergo profound alterations due to poor soil maintenance. This review highlights how the soil microbiome influences human digestion processes, mineral and vitamin production, mental health and mood stimulation. Although much about microbial functions remains unknown, increasing evidence suggests that beneficial soil microbes are vital for enhancing human tolerance to diseases and pathogens. Further research is essential to delineate the specific role of the soil microbiome in promoting human health, especially in light of the increasing anthropogenic pressures and changing climatic conditions.

Isolation, antibacterial screening, and identification of bioactive cave dwelling bacteria in Fiji

Bacteria are well known producers of bioactive secondary metabolites, including some of the most effective antibiotics in use today. While the caves of Oceania are still largely under-explored, they form oligotrophic and extreme environments that are a promising source for identifying novel species of bacteria with biologically active compounds. By using selective media that mimicked a cave environment, and pretreatments that suppressed the growth of fast-growing bacteria, we have cultured genetically diverse bacteria from a limestone cave in Fiji. Partial 16S rRNA gene sequences from isolates were determined and compared with 16S rRNA gene sequences in EzBioCloud and SILVA data bases. Fifty-five isolates purified from culture had Actinomycete-like morphologies and these were investigated for antibacterial activity. Initial screening using a cross streak test with pathogenic bacteria indicated that 34 of the isolates had antibacterial properties. The best matches for the isolates are bacteria with potential uses in the manufacture of antibiotics and pesticides, in bioremediation of toxic waste, in biomining, in producing bioplastics, and in plant growth promotion. Nineteen bacteria were confirmed as Actinomycetes. Thirteen were from the genus Streptomyces and six from genera considered to be rare Actinomycetes from Pseudonocardia, Kocuria, Micromonospora, Nonomuraea. Ten isolates were Firmicutes from the genera Bacillus, Lysinbacillus, Psychrobacillus and Fontibacillus. Two were Proteobacteria from the genera Mesorhizobium and Cupriavidus. Our findings identify a potentially rich source of microbes for applications in biotechnologies.

Metagenomic-based surveillance systems for antibiotic resistance in non-clinical settings

The success of antibiotics as a therapeutic agent has led to their ineffectiveness. The continuous use and misuse in clinical and non-clinical areas have led to the emergence and spread of antibiotic-resistant bacteria and its genetic determinants. This is a multi-dimensional problem that has now become a global health crisis. Antibiotic resistance research has primarily focused on the clinical healthcare sectors while overlooking the non-clinical sectors. The increasing antibiotic usage in the environment - including animals, plants, soil, and water - are drivers of antibiotic resistance and function as a transmission route for antibiotic resistant pathogens and is a source for resistance genes. These natural compartments are interconnected with each other and humans, allowing the spread of antibiotic resistance via horizontal gene transfer between commensal and pathogenic bacteria. Identifying and understanding genetic exchange within and between natural compartments can provide insight into the transmission, dissemination, and emergence mechanisms. The development of high-throughput DNA sequencing technologies has made antibiotic resistance research more accessible and feasible. In particular, the combination of metagenomics and powerful bioinformatic tools and platforms have facilitated the identification of microbial communities and has allowed access to genomic data by bypassing the need for isolating and culturing microorganisms. This review aimed to reflect on the different sequencing techniques, metagenomic approaches, and bioinformatics tools and pipelines with their respective advantages and limitations for antibiotic resistance research. These approaches can provide insight into resistance mechanisms, the microbial population, emerging pathogens, resistance genes, and their dissemination. This information can influence policies, develop preventative measures and alleviate the burden caused by antibiotic resistance.

Observations on the interaction between plant growth-promoting bacteria and the root-knot nematode Meloidogyne javanica

Pseudomonas fluorescens, strains L124, L228, L321, and the positive control strain F113 used in this study, produce compounds associated with plant growth promotion, biocontrol, antimicrobial and antiviral activity, and adaptation to stresses. These bacterial strains were tested in vitro and in vivo in tomato plants, to determine their potential role in Meloidogyne javanica suppression. In laboratory experiments, only 2% of M. javanica eggs hatched when exposed to the metabolites of each bacterial strain. Additionally, 100% M. javanica J2 mortality was recorded when nematodes were exposed to the metabolites of F113 and L228. In greenhouse experiments, M. javanica infected tomato plants, which were also inoculated with the bacterial strains F113 and L124, displayed the highest biomass (height, number of leaves, fresh and dry weight) of all bacterial treatments tested. Results from the development and induced systemic resistance experiments indicated that the bacterial strains F113 and L321 had the most effective biocontrol capacity over nematode infection, delayed nematode development (J3/J4, adults and galls), and reduced nematode fecundity. In addition, these results indicated that the bacterial strain L124 is an effective plant growth promoter of tomato plants. Furthermore, it was determined that the bacterial strain L321 was capable of M. javanica biocontrol. P. fluorescens F113 was effective at both increasing tomato plant biomass and M. javanica biocontrol. In an agricultural context, applying successional drenches with these beneficial plant growth promoting rhizobacteria would ensure bacteria viability in the rhizosphere of the plants, encourage positive plant bacterial interactions and increase biocontrol against M. javanica.

Isolation and identification of promising antibiotic-producing bacteria

Multiple stresses in waste dumpsite soils can drive antibiotic production as one of the strategies for survival. Bacteria are the most prolific producers of antibiotics. This study investigated the antibiotic production potential of bacteria isolated from Bahir Dar city municipal solid waste dumpsite (MSWDS). Bacteria were isolated from soil collected from the dumpsite on starch casein or nutrient agar. The isolates were carefully screened for antimicrobial activity against six pathogenic bacterial test strains. Minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were also determined from cell-free metabolites of the most promising isolates. Isolates showing antimicrobial activity were identified using cultural and biochemical methods. A total of 143 distinctive colonies were obtained and tentatively identified to 13 bacterial genera. Twenty-six (18.18%) of the isolates (six Bacillus and 20 actinobacteria related) demonstrated antimicrobial activities at least against one of the tested bacterial strains. These isolates were related to two actinobacterial and 11 other bacterial genera. Seven out of 26 isolates showed a broad-spectrum of antibiotic activities. Two isolates, which showed a wide spectrum, were selected for the MIC and MBC tests against Escherichia coli and Staphylococcus aureus. The MIC and MBC of the isolates were recorded to be 250–500 µg/mL against the test strains. Bahir Dar city MSWDS contained a high incidence of antibiotic-producing bacteria. Strain level identification of the isolates and detailed characterization of the metabolites will give a good insight into the antimicrobial production potential in the waste dumpsite.

Naturalized Escherichia coli in Wastewater and the Co-evolution of Bacterial Resistance to Water Treatment and Antibiotics

Antibiotic resistance represents one of the most pressing concerns facing public health today. While the current antibiotic resistance crisis has been driven primarily by the anthropogenic overuse of antibiotics in human and animal health, recent efforts have revealed several important environmental dimensions underlying this public health issue. Antibiotic resistant (AR) microbes, AR genes, and antibiotics have all been found widespread in natural environments, reflecting the ancient origins of this phenomenon. In addition, modern societal advancements in sanitation engineering (i.e., sewage treatment) have also contributed to the dissemination of resistance, and concerningly, may also be promoting the evolution of resistance to water treatment. This is reflected in the recent characterization of naturalized wastewater strains of Escherichia coli-strains that appear to be adapted to live in wastewater (and meat packing plants). These strains carry a plethora of stress-resistance genes against common treatment processes, such as chlorination, heat, UV light, and advanced oxidation, mechanisms which potentially facilitate their survival during sewage treatment. These strains also carry an abundance of common antibiotic resistance genes, and evidence suggests that resistance to some antibiotics is linked to resistance to treatment (e.g., tetracycline resistance and chlorine resistance). As such, these naturalized E. coli populations may be co-evolving resistance against both antibiotics and water treatment. Recently, extraintestinal pathogenic strains of E. coli (ExPEC) have also been shown to exhibit phenotypic resistance to water treatment, seemingly associated with the presence of various shared genetic elements with naturalized wastewater E. coli. Consequently, some pathogenic microbes may also be evolving resistance to the two most important public health interventions for controlling infectious disease in modern society-antibiotic therapy and water treatment.

Impact of spent engine oil contamination on the antibiotic resistome of a tropical agricultural soil

Profiling of hydrocarbon-contaminated soils for antibiotic resistance genes (ARGs) is becoming increasingly important due to emerging realities of their preponderance in hydrocarbon-inundated matrices. In this study, the antibiotic resistome of an agricultural soil (1S) and agricultural soil contaminated with spent engine oil (AB1) were evaluated via functional annotation of the open reading frames (ORFs) of their metagenomes using the comprehensive antibiotic database (CARD) and KEGG KofamKOALA. CARD analysis of AB1 metagenome revealed the detection of 24 AMR (antimicrobial resistance) gene families, 66 ARGs, and the preponderance (69.7%) of ARGs responsible for antibiotic efflux in AB1 metagenome. CARD analysis of 1S metagenome revealed four AMR gene families and five ARGs. Functional annotation of the two metagenomes using KofamKOALA showed 171 ARGs in AB1 and 29 ARGs in 1S, respectively. Majority of the detected ARGs in AB1 (121; 70.8%) and 1S (16; 55.2%) using KofamKOALA are responsible for antibiotic efflux while ARGs for other resistance mechanisms were also detected. All the five major antibiotic efflux pump systems were detected in AB1 metagenome, though majority of the ARGs for antibiotic efflux belong to the RND (resistance-nodulation-cell division) and MFS (major facilitator superfamily) efflux systems. Significant differences observed in the ARGs recovered from 1S and AB1 metagenomes were statistically validated (P < 0.05). SEO contamination is believed to be responsible for ARGs increase in AB1 metagenome via mechanisms of cross-resistance especially with efflux pumps. The detection of these ARGs is of great public health concern in this era of multidrug resistant isolates resurgence.

Plant Disease Management: Leveraging on the Plant-Microbe-Soil Interface in the Biorational Use of Organic Amendments

Agriculture is faced with many challenges including loss of biodiversity, chemical contamination of soils, and plant pests and diseases, all of which can directly compromise plant productivity and health. In addition, inadequate agricultural practices which characterize conventional farming play a contributory role in the disruption of the plant-microbe and soil-plant interactions. This review discusses the role of organic amendments in the restoration of soil health and plant disease management. While the use of organic amendments in agriculture is not new, there is a lack of knowledge regarding its safe and proper deployment. Hence, a biorational approach of organic amendment use to achieve sustainable agricultural practices entails the deployment of botanicals, microbial pesticides, and organic minerals as organic amendments for attaining plant fitness and disease suppression. Here, the focus is on the rhizosphere microbial communities. The role of organic amendments in stimulating beneficial microbe quorum formation related to the host-plant-pathogen interactions, and its role in facilitating induced systemic resistance and systemic-acquired resistance against diseases was evaluated. Organic amendments serve as soil conditioners, and their mechanism of action needs to be further elaborated to ensure food safety.

Characterization of two relacidines belonging to a novel class of circular lipopeptides that act against Gram-negative bacterial pathogens

The development of sustainable agriculture and the increasing antibiotic resistance of human pathogens call for novel antimicrobial compounds. Here, we describe the extraction and characterization of a class of cationic circular lipopeptides, for which we propose the name relacidines, from the soil bacterium Brevibacillus laterosporus MG64. Relacidines are composed of a fatty acid side chain (4‐methylhexanoic acid) and 13 amino acid residues. A lactone ring is formed by the last five amino acid residues and three positively charged ornithines are located in the linear fragment. Relacidines selectively combat Gram‐negative pathogens, including phytopathogens and human pathogens. Further investigation of the mode of action revealed that relacidine B binds to the lipopolysaccharides but does not form pores in the cell membrane. We also provide proof to show that relacidine B does not affect the biosynthesis of the cell wall and RNA. Instead, it affects the oxidative phosphorylation process of cells and diminishes the biosynthesis of ATP. Transcription of relacidines is induced by plant pathogens, which strengthens the potential of B. laterosporus MG64 to be used as a biocontrol agent. Thus, we identified a new group of potent antibiotic compounds for combating Gram‐negative pathogens of plants or animals.

Unravelling the antibiotic and heavy metal resistome of a chronically polluted soil

The antibiotic and heavy metal resistome of a chronically polluted soil (3S) obtained from an automobile workshop in Ilorin, Kwara State, Nigeria was deciphered via functional annotation of putative ORFs (open reading frames). Functional annotation of antibiotic and heavy metal resistance genes in 3S metagenome was conducted using the Comprehensive Antibiotic Resistance Database (CARD), Antibiotic Resistance Gene-annotation (ARG-ANNOT) and Antibacterial Biocide and Metal Resistance Gene Database (BacMet). Annotation revealed detection of resistance genes for 15 antibiotic classes with the preponderance of beta lactamases, mobilized colistin resistance determinant (mcr), glycopepetide and tetracycline resistance genes, the OqxBgb and OqxA RND-type multidrug efflux pumps, among others. The dominance of resistance genes for antibiotics effective against members of the Enterobacteriaceae indicate possible contamination with faecal materials. Annotation of heavy metal resistance genes revealed diverse resistance genes responsible for the uptake, transport, detoxification, efflux and regulation of copper, zinc, cadmium, nickel, chromium, cobalt, mercury, arsenic, iron, molybdenum and several others. Majority of the antibiotic and heavy metal resistance genes detected in this study are borne on mobile genetic elements, which facilitate their spread and dissemination in the polluted soil. The presence of the heavy metal resistance genes is strongly believed to play a major role in the proliferation of antibiotic resistance genes. This study has established that soil is a huge repertoire of antibiotic and heavy metal resistome and due to the intricate link between human, animals and the soil environment, it may be a major contributor to the proliferation of multidrug-resistant clinical pathogens.