Metabolomics Insights into Chemical Convergence in Xanthomonas perforans and Metabolic Changes Following Treatment with the Small Molecule Carvacrol

Microbes are natural chemical factories and their metabolome comprise diverse arrays of chemicals. The genus Xanthomonas comprises some of the most important plant pathogens causing devastating yield losses globally and previous studies suggested that species in the genus are untapped chemical minefields. In this study, we applied an untargeted metabolomics approach to study the metabolome of a globally spread important xanthomonad, X. perforans. The pathogen is difficult to manage, but recent studies suggest that the small molecule carvacrol was efficient in disease control. Bacterial strains were treated with carvacrol, and samples were taken at time intervals (1 and 6 h). An untreated control was also included. There were five replicates for each sample and samples were prepared for metabolomics profiling using the standard procedure. Metabolomics profiling was carried out using a thermo Q-Exactive orbitrap mass spectrometer with Dionex ultra high-performance liquid chromatography (UHPLC) and an autosampler. Annotation of significant metabolites using the Metabolomics Standards Initiative level 2 identified an array of novel metabolites that were previously not reported in Xanthomonas perforans. These metabolites include methoxybrassinin and cyclobrassinone, which are known metabolites of brassicas; sarmentosin, a metabolite of the Passiflora-heliconiine butterfly system; and monatin, a naturally occurring sweetener found in Sclerochiton ilicifolius. To our knowledge, this is the first report of these metabolites in a microbial system. Other significant metabolites previously identified in non-Xanthomonas systems but reported in this study include maculosin; piperidine; β-carboline alkaloids, such as harman and derivatives; and several important medically relevant metabolites, such as valsartan, metharbital, pirbuterol, and ozagrel. This finding is consistent with convergent evolution found in reported biological systems. Analyses of the effect of carvacrol in time-series and associated pathways suggest that carvacrol has a global effect on the metabolome of X. perforans, showing marked changes in metabolites that are critical in energy biosynthesis and degradation pathways, amino acid pathways, nucleic acid pathways, as well as the newly identified metabolites whose pathways are unknown. This study provides the first insight into the X. perforans metabolome and additionally lays a metabolomics-guided foundation for characterization of novel metabolites and pathways in xanthomonad systems.

Bioremediation of arsenic contamination from the environment: New approach to sustainable resource management

Present acceleration of Arsenic [As] exposure leads to severe health problems. Modern scientific approaches look towards potent bio-agents for the removal of such types of contaminations in sustainable ways. Microbes can potentially change the redox potential, solubility, pH by different complex reactions during bioremediation. There are many enzymes present in the microbial system which are involved in methylation such as As (V) reductase, monomethyl arsonic acid reductase, As (III) methyltransferase, and MMA (III) methyltransferase. On the other hand, microbes have As transformation ability and changed into different extractable forms with sulfide minerals such as arsenopyrite (FeAsS), enargite (Cu3AsS4) and realgar (As4S4). In some bacteria, the As-operon machinery thiol group bind with As, itdetoxifies its toxicity. Ars R gene and arsenic reductase enzyme (Ars C) play the key role in the reduction of As (V) to As (III) and detoxify by being transported outside of the cell by Ars AB As chemiosmotic efflux system. In fungi, As (V) is reduced to As (III) by the arsenate reductase and GSH glutathione converted into GSSH glutathione disulfide. In plants, As (III) conjugates with phytochelatin (PC) or GSH glutathione and accumulates in the vacuole or is converted into less toxic forms in the presence of arsenic reductase enzyme. This review focused on the potentiality and mechanisms of different microbes for As-detoxification in a sustainable manner.

Molecular Rationale of Insect-Microbes Symbiosis—From Insect Behaviour to Mechanism

Insects nurture a panoply of microbial populations that are often obligatory and exist mutually with their hosts. Symbionts not only impact their host fitness but also shape the trajectory of their phenotype. This co-constructed niche successfully evolved long in the past to mark advanced ecological specialization. The resident microbes regulate insect nutrition by controlling their host plant specialization and immunity. It enhances the host fitness and performance by detoxifying toxins secreted by the predators and abstains them. The profound effect of a microbial population on insect physiology and behaviour is exploited to understand the host–microbial system in diverse taxa. Emergent research of insect-associated microbes has revealed their potential to modulate insect brain functions and, ultimately, control their behaviours, including social interactions. The revelation of the gut microbiota–brain axis has now unravelled insects as a cost-effective potential model to study neurodegenerative disorders and behavioural dysfunctions in humans. This article reviewed our knowledge about the insect–microbial system, an exquisite network of interactions operating between insects and microbes, its mechanistic insight that holds intricate multi-organismal systems in harmony, and its future perspectives. The demystification of molecular networks governing insect–microbial symbiosis will reveal the perplexing behaviours of insects that could be utilized in managing insect pests.

Modern microbial mats from the Chihuahuan Desert provide insights into ecological stability throughout Earth's history

Microbial mats are complex ecological assemblages that are found in the Precambrian fossil record and in extant extreme environments. Hence, these structures are regarded as highly stable ecosystems. In this work, we assess the ecological stability in a modern, fluctuating, hypersaline pond from the Cuatro Ciénegas Basin. From the 2016 to 2019 metagenomic sampling of this site, we found that this microbial site is sensitive to disturbances, which leads to high taxonomic replacement. Additionally, the mats have shown to be functionally stable throughout time, and could be differentiated between dry and rainy seasonal states. We speculate that this microbial system could represent a modern analog of ancient, hypersaline coastal microbial mats, where functions were preserved over time, whereas taxonomic composition was subject to diversification in the face of local and planetary perturbations.

Degradation of lignocelluloses in straw using AC-1, a thermophilic composite microbial system

In composting, the degradation of lignocellulose in straw is problematic due to its complex structures such as lignin. A common solution to this problem is the addition of exogenous inoculants. AC-1, a stable thermophilic microbial composite, was isolated from high temperature compost samples that can decompose lignocellulose at 50–70 °C. AC-1 had a best degradation efficiency of rice straw at 60 °C (78.92%), of hemicellulose, cellulose and lignin were 82.49%, 97.20% and 20.12%, respectively. It showed degrad-ability on both simple (filter paper, absorbent cotton) and complex (rice straw) cellulose materials. It produced acetic and formic acid during decomposition process and the pH had a trend of first downward then upward. High throughput sequencing revealed the main bacterial components of AC-1 were Tepidimicrobium, Haloplasma, norank-f-Limnochordaceae, Ruminiclostridium and Rhodothermus which provides major theoretical basis for further application of AC-1.

Environmental Occurrence, Toxicity Concerns, and Degradation of Diazinon Using a Microbial System

Diazinon is an organophosphorus pesticide widely used to control cabbage insects, cotton aphids and underground pests. The continuous application of diazinon in agricultural activities has caused both ecological risk and biological hazards in the environment. Diazinon can be degraded via physical and chemical methods such as photocatalysis, adsorption and advanced oxidation. The microbial degradation of diazinon is found to be more effective than physicochemical methods for its complete clean-up from contaminated soil and water environments. The microbial strains belonging to Ochrobactrum sp., Stenotrophomonas sp., Lactobacillus brevis, Serratia marcescens, Aspergillus niger, Rhodotorula glutinis, and Rhodotorula rubra were found to be very promising for the ecofriendly removal of diazinon. The degradation pathways of diazinon and the fate of several metabolites were investigated. In addition, a variety of diazinon-degrading enzymes, such as hydrolase, acid phosphatase, laccase, cytochrome P450, and flavin monooxygenase were also discovered to play a crucial role in the biodegradation of diazinon. However, many unanswered questions still exist regarding the environmental fate and degradation mechanisms of this pesticide. The catalytic mechanisms responsible for enzymatic degradation remain unexplained, and ecotechnological techniques need to be applied to gain a comprehensive understanding of these issues. Hence, this review article provides in-depth information about the impact and toxicity of diazinon in living systems and discusses the developed ecotechnological remedial methods used for the effective biodegradation of diazinon in a contaminated environment.

Transcriptome-Guided Insights Into Plastic Degradation by the Marine Bacterium

Polyethylene terephthalate (PET) is a common single-use plastic that accumulated in the environment because of its non-degradable characteristics. In recent years, microbes from different environments were found to degrade plastics and suggested their capability to degrade plastics under varying environmental conditions. However, complete degradation of plastics is still a void for large-scale implications using microbes because of the lack of knowledge about genes and pathways intricate in the biodegradation process. In the present study, the growth and adherence of marine Bacillus species AIIW2 on PET surface instigating structural deterioration were confirmed through weight loss and hydrophobicity reduction, as well as analyzing the change in bond indexes. The genome-wide comparative transcriptomic analysis of strain AIIW2 was completed to reveal the genes during PET utilization. The expression level of mRNA in the strain AIIW2 was indexed based on the log-fold change between the presence and absence of PET in the culture medium. The genes represent carbon metabolism, and the cell transport system was up-regulated in cells growing with PET, whereas sporulation genes expressed highly in the absence of PET. This indicates that the strain AIIW2 hydrolyzes PET and assimilated via cellular carbon metabolism. A protein–protein interaction network was built to obtain the interaction between genes during PET utilization. The genes traced to degrade PET were confirmed by detecting the hydrolytic product of PET, and genes were cloned to improve PET utilization by microbial system as an eco-friendly solution.

Exploiting Microbes in the Petroleum Field: Analyzing the Credibility of Microbial Enhanced Oil Recovery (MEOR)

Crude oil is a major energy source that is exploited globally to achieve economic growth. To meet the growing demands for oil, in an environment of stringent environmental regulations and economic and technical pressure, industries have been required to develop novel oil salvaging techniques. The remaining ~70% of the world’s conventional oil (one-third of the available total petroleum) is trapped in depleted and marginal reservoirs, and could thus be potentially recovered and used. The only means of extracting this oil is via microbial enhanced oil recovery (MEOR). This tertiary oil recovery method employs indigenous microorganisms and their metabolic products to enhance oil mobilization. Although a significant amount of research has been undertaken on MEOR, the absence of convincing evidence has contributed to the petroleum industry’s low interest, as evidenced by the issuance of 400+ patents on MEOR that have not been accepted by this sector. The majority of the world’s MEOR field trials are briefly described in this review. However, the presented research fails to provide valid verification that the microbial system has the potential to address the identified constraints. Rather than promising certainty, MEOR will persist as an unverified concept unless further research and investigations are carried out.

Understanding Wine through Yeast Interactions

Wine is a product of microbial activities and microbe–microbe interactions. Yeasts are the principal microorganisms responsible for the evolution and fulfillment of alcoholic fermentation. Several species and strains coexist and interact with their environment and with each other during the fermentation course. Yeast–yeast interactions occur even from the early stages of fermentation, determining yeast community structure and dynamics during the process. Different types of microbial interactions (e.g., mutualism and commensalism or competition and amensalism) may exert positive or negative effects, respectively, on yeast populations. Interactions are intimately linked to yeast metabolic activities that influence the wine analytical profile and shape the wine character. In this context, much attention has been given during the last years to the interactions between Saccharomyces cerevisiae (SC) and non-Saccharomyces (NS) yeast species with respect to their metabolic contribution to wine quality. Yet, there is still a significant lack of knowledge on the interaction mechanisms modulating yeast behavior during mixed culture fermentation, while much less is known about the interactions between the various NS species or between SC and Saccharomyces non-cerevisiae (SNC) yeasts. There is still much to learn about their metabolic footprints and the genetic mechanisms that alter yeast community equilibrium in favor of one species or another. Gaining deeper insights on yeast interactions in the grape–wine ecosystem sets the grounds for understanding the rules underlying the function of the wine microbial system and provides means to better control and improve oenological practices.

Presence of Microorganisms and Use of Antimicrobial Agents in Car Seat Fabrics: A Brief Review

The present paper discusses the presence of microorganisms in textile materials, especially in car seats, and the use of antimicrobial agents. We observed that the main agent between the user and the car's microbial system are the seats, due to the direct contact with the users. In addition, the environment in which the car is inserted, the type of car, and the seat fabric-type influence directly the reproduction of the microbial system. Microorganisms found in different parts of cars, especially in seats, could be potential threats to human health. Thus, to combat these microorganisms, it is necessary to study antimicrobial agents aimed at eliminating or inhibiting their reproduction and, consequently, promoting hygiene, ensuring the health and well-being of car users.