María-Eugenia Guazzaroni

University of São Paulo | USP · Departamento de Biologia (Ribeirão Preto)

In response to the escalating demand for sustainable agricultural methodologies, the utilization of microbial volatile organic compounds (VOCs) as antagonists against phytopathogens has emerged as a viable eco-friendly alternative. Microbial volatiles exhibit rapid diffusion rates, facilitating prompt chemical interactions. Moreover, microorganisms...

Currently, industrial bioproducts are less competitive than chemically produced goods due to the shortcomings of conventional microbial hosts. Thus, is essential developing robust bacteria for improved cell tolerance to process-specific parameters. In this context, metagenomic approaches from extreme environments can provide useful biological parts...

Microbial fuel cells (MFCs) offer sustainable solutions for various biotechnological applications and are a crucial area of research in biotechnology. MFCs can effectively treat various refuse, such as wastewater and biodiesel waste by decomposing organic matter and generating electricity. Certain Pseudomonas species possess extracellular electron...

Biotechnological processes at biorefineries are considered one of the most attractive alternatives for valorizing biomasses by converting them into bioproducts, biofuels, and bioenergy. For example, biodiesel can be obtained from oils and grease but generates glycerol as a byproduct. Glycerol recycling has been studied in several bioprocesses, with...

The ability of some bacteria to perform Extracellular Electron Transfer (EET) has been explored in bioelectrochemical systems (BES) to obtain energy or chemicals from pure substances or residual substrates. Here, a new pyoverdine-producing Pseudomonas aeruginosa strain was isolated from an MFC biofilm oxidizing glycerol, a by-product of biodiesel p...

Microbial fuel cells (MFCs) offer sustainable solutions for various biotechnological applications and are a crucial area of research in biotechnology. MFCs can effectively treat wastewater and biodiesel waste by decomposing organic matter and generating electricity. Certain Pseudomonas species possess extracellular electron transfer (EET) pathways,...

The ability of some bacteria to perform Extracellular Electron Transfer (EET) has been explored in bioelectrochemical systems (BES) to obtain energy or chemicals from pure substances or residual substrates. Here, a new pyoverdine-producing Pseudomonas aeruginosa strain was isolated from a MFC biofilm oxidizing glycerol, a by-product of biodiesel pr...

Currently, industrial bioproducts are less competitive than chemically produced goods due to the shortcomings of conventional microbial hosts. Metagenomic approaches from extreme environments can provide useful biological parts to improve bacterial robustness to process-specific parameters. Here, in order to build synthetic genetic circuits that in...

Transcriptional terminators are key players in the flow of genetic information, but are often overlooked in circuit design. In this work, we used the Standard European Vector Architecture (SEVA) as a scaffold to investigate the effects of different terminators in the output of a reporter construct expressed in two bacterial species, and found that...

Pseudomonas aeruginosa can produce pigments, which mediate external electron transfer (EET). Depending on the mediator, this species can be explored in bioelectrosystems to harvest energy or to obtain chemicals from residual organic compounds. This study has compared the performance of microbial fuel cells (MFCs) inoculated with a Pseudomonas aerug...

One major limitation of function-driven metagenomics is the ability of the host to express the metagenomic DNA correctly. Differences in the transcriptional, translational, and post-translational machinery between the organism to which the DNA belongs and the host strain are all factors that influence the success of a functional screening. For this...

Innovations in obtaining products from lignocellulosic biomass have been largely based on the improvement of microorganisms and enzymes capable of degrading these materials. To complete the whole process, microorganisms must be able to ferment the resulting sugars and tolerate high concentrations of product, osmotic pressure, ion toxicity, temperat...

Land-use conversion changes soil properties and their microbial communities, which, combined with the overuse of antibiotics in human and animal health, promotes the expansion of the soil resistome. In this context, we aimed to profile the resistome and the microbiota of soils under different land practices. We collected eight soil samples from dif...

Synthetic biology (SynBio) is a rapidly advancing multidisciplinary field in which South American countries such as Chile, Argentina, and Brazil have made notable contributions and have established leadership positions in the region. In recent years, efforts have strengthened SynBio in the rest of the countries, and although progress is significant...

The demand for robust microbial cell factories that produce valuable biomaterials while resisting stresses imposed by current bioprocesses is rapidly growing. Rhodosporidium toruloides is an emerging host that presents desirable features for bioproduction, since it can grow in a wide range of substrates and tolerate a variety of toxic compounds. To...

Anthropization in terrestrial environments commonly leads to land use transformation, changing soil properties and their microbial communities. This, combined with the exacerbated use of antibiotics in human and animal health promotes the expansion of the soil resistome. Considering the urgent need for surveillance of antimicrobial resistance (AMR)...

The demand for robust microbial cell factories that can produce valuable biomaterials while being resistant to stresses imposed by current bioprocesses is rapidly growing. R. toruloides is an emerging host that presents desirable features for bioproduction, since it can grow in a wide range of substrates and tolerate a variety of toxic compounds. I...

We correlated clinical, epidemiological, microbiological, and genomic data of an outbreak with polymyxin B (PB)- and carbapenem-resistant Klebsiella pneumoniae during the COVID-19 pandemic. Twenty-six PB- and carbapenem-resistant K. pneumoniae were isolated from patients in the COVID-19 ICU (Intensive Care Unit), non-COVID-19 ICU (Intensive Care Un...

Acetate and p-coumaric acid, which inhibit fermentation, are important byproducts from the sugarcane biomass pretreatment and hydrolysis steps. At the same time, organic and phenolic acids are valuable substrates to produce bioelectricity in Microbial Fuel Cells (MFCs). Here, we operated an MFC with a synthetic non-fermentable fraction of sugarcane...

Fast and accurate identification of pathogens is an essential task in healthcare settings. Second-generation sequencing platforms such as Illumina have greatly expanded the capacity with which different organisms can be detected in hospital samples, and third-generation nanopore-driven sequencing devices such as Oxford Nanopore's minION have recent...

Fast and accurate identification of pathogens is an essential task in healthcare settings. Next generation sequencing platforms such as Illumina have greatly expanded the capacity with which different organisms can be detected in hospital samples, and third-generation nanopore-driven sequencing devices such as Oxford Nanopore's minION have recently...

(1) Background: The rise of multi-antibiotic resistant bacteria represents an emergent threat to human health. Here, we investigate antibiotic resistance mechanisms in bacteria of several species isolated from an intensive care unit in Brazil. (2) Methods: We used whole-genome analysis to identify antibiotic resistance genes (ARGs) and plasmids in...

Interest in chitin-degrading enzymes has grown over the years, and microbial chitinases are the most attractive and promising candidates for the control of plant pests (fungi and insects). Currently, there are many studies on chitinases produced by cultivable microorganisms; however, almost none of them have achieved acceptable applicability as a b...

The rise of multi-antibiotics resistant bacteria represents an emergent threat to human health. Here, we investigate antibiotic resistance mechanisms in bacteria of several species isolated from an intensive care unit in Brazil. We used whole-genome analysis to identify antibiotic resistance genes (ARGs) and plasmids in 35 strains of Gram-negative...

Adoption of microorganisms as platforms for sustainable biobased production requires host cells to be able to withstand harsh industrial conditions, which are usually far from the ones where these organisms are naturally adapted to thrive. However, novel survival mechanisms unearthed by the study of microbiomes from extreme habitats may be exploite...

The present energy and the waste accumulation crisis make the development of bioelectrochemical systems each day more important as a technology for coupled waste-treatment, electricity production, and biorefinement, whilst closing the circular economy loop. However, its application is still hampered by the complexity of its biocatalysts. This study...

Adoption of microorganisms as platforms for sustainable biobased production requires host cells to be able to withstand harsh industrial conditions, which are usually far from the ones where these organisms are naturally adapted to thrive. However, novel survival mechanisms unearthed by the study of microbiomes from extreme habitats may be exploite...

Diminutos pero con un metabolismo versátil, los microorganismos son la base de procesos biotecnológicos “revolucionarios” en áreas de salud y alimentación, entre otras. Son pequeñas fábricas de productos que buscan mejoran la calidad de vida —entre ellos, la ampicilina o la insulina humana para tratamientos de diabetes—, potenciados con algunas her...

Hospital-associated infections (HAIs) are a leading cause of morbidity and mortality in intensive care units (ICUs) and neonatal intensive care units (NICUs). Organisms causing these infections are often present on surfaces around the patient. Given that microbiota may vary across different ICUs, the HAI-related microbial signatures within these un...

Article Metagenomics approaches have been of high relevance for providing enzymes used in diverse industrial applications. In the current study, we have focused on the prospection of protease and glycosyl hydrolase activities from a soil sample by using the lacZα -based plasmid pSEVA232. For this, we used a functional screen based on skimmed milk a...

Protein engineering emerged as a powerful approach to generate more robust and efficient biocatalysts for bio-based economy applications, an alternative to ecologically toxic chemistries that rely on petroleum. On the quest for environmentally friendly technologies, sustainable and low-cost resources such as lignocellulosic plant-derived biomass ar...

Protein engineering emerged as a powerful approach to generate more robust and efficient biocatalysts for bio-based economy applications, an alternative to ecologically toxic chemistries that rely on petroleum. On the quest for environmentally friendly technologies, sustainable and low-cost resources such as lignocellulosic plant-derived biomass ar...

A key challenge for domesticating alternative cultivable microorganisms with biotechnological potential lies in the development of innovative technologies. Within this framework, a myriad of genetic tools has flourished, allowing the design and manipulation of complex synthetic circuits and genomes to become the general rule in many laboratories ra...

In this work, we used a systems biology approach to map new regulatory interactions in Trichoderma reesei controlling the expression of genes encoding cellulase and hemicellulase. By integrating transcriptomics related to complex biomass degradation, we were able to identify a novel transcriptional regulator which is able to activate the expression...

Hospital-associated infections (HAIs) are the leading cause of morbidity and mortality in intensive care units (ICUs) and neonatal intensive care units (NICUs). Organisms causing these infections are often present on surfaces around the patient. Given that microbiotas may vary across different ICUs, the HAI-related microbial signatures within these...

We report on the nearly complete genome sequence of Clostridium beijerinckii strain Br21, formerly isolated from a sugarcarne vinasse wastewater treatment plant. The resulting genome is ca. 5.9 Mbp in length and resembles the size of previously published C. beijerinckii genomes. We annotated the genome sequence and predicted a total of 5323 genes....

All biosensing platforms rest on two pillars: specific biochemical recognition of a particular analyte and transduction of that recognition into a readily detectable signal. Most existing biosensing technologies utilize proteins that passively bind to their analytes and therefore require wasteful washing steps, specialized reagents, and expensive i...

Details about the strains shown in Figure 1.

Genes encoding for glycosyl hydrolases identified in the C. beijerinckii strain Br21 genome.

Scanning electron micrograph of C. beijerinckii strain Br21 during the logarithmic growth phase.

Extended description of the procedures followed for species level assignment of strain Br21.

Complete results from the Genome-to-Genome Distance Calculator and OrthoANIu.

Genes encoding for enzymes and electron carriers related to biofuel and chemical production identified in the C. beijerinckii strain Br21 genome.

Maximum-likelihood phylogeny with 168 markers for the genome sequences of all clostridia deposited in the NCBI RefSeq database

Details about the genomes used for strain identification using genome-wide information.

As the field of synthetic biology moves towards the utilization of novel bacterial chassis, there is a growing need for biological parts with enhanced performance in a wide number of hosts. Is not unusual that biological parts (such as promoters and terminators), initially characterized in the model bacteria Escherichia coli, do not perform well wh...

The introduction of new high-throughput technologies has profoundly impacted the development of modern science outside the gene-centered understanding perceived in the earlier genomic era [1, 2]. Thus, low-cost platforms known as Next Generation Sequencing (NGS) technologies can pro- duce millions of sequences of DNA molecules with different yields...

Beta-glucosidases are key enzymes involved in lignocellulosic biomass degradation for bioethanol production, which complete the final step during cellulose hydrolysis by converting cellobiose into glucose. Currently, industry requires enzymes with improved catalytic performance or tolerance to process-specific parameters. In this sense, metagenomic...

When recombinant DNA technology was developed more than 40 years ago, no one could have imagined the impact it would have on both society and the scientific community. In the field of genetic engineering, the most important tool developed was the plasmid vector. This technology has been continuously expanding and undergoing adaptations. Here, we pr...

Carbohydrate binding modules (CBMs) are non-catalytic domains within larger multidomain polypeptides. The CelH from Ruminoclostridium (Clostridium) thermocellum contains a family 11 CBM (RtCBM11) with high binding affinity for the linear polysaccharide β-glucan, and low affinity for the branched xyloglucan. Screening a random RtCBM11 mutant phage l...

Bacterial transcriptional factors (TFs) and their target promoters are key devices for engineering of complex circuits in many biotechnological applications. Yet, there is a dearth of well characterized inducer-responsive TFs that could be used in the context of an animal or human host. In this work we have deciphered the inducer recognition mechan...

Over the past thirty years, since the dawn of metagenomic studies, a completely new (micro) universe was revealed, with the potential to have profound impacts on many aspects of the society. Remarkably, the study of human microbiome provided a new perspective on a myriad of human traits previously regarded as solely (epi-) genetically encoded, such...

Bacteria are a source of a large number of secondary metabolites with several biomedical and biotechnological applications. In recent years, there has been tremendous progress in the development of novel synthetic biology approaches both to increase the production rate of secondary metabolites of interest in native producers and to mine and reconst...

Although functional metagenomics has been widely employed for the discovery of genes relevant to biotechnology and biomedicine, its potential for assessing the diversity of transcriptional regulatory elements of microbial communities has remained poorly explored. Here, we experimentally mined novel constitutive promoter sequences in metagenomic lib...

Engineering microbial systems allows the generation of new technologies having significant impact in the biotechnological industry and on human health. In the past few years, several synthetic biology approaches have been implemented in bacteria to allow precise engineering of novel regulatory circuits for several applications. The advent of high-t...

Although functional metagenomics has been widely employed for the discovery of genes relevant to biotechnology and biomedicine, its potential for assessing the diversity of transcriptional regulatory elements of microbial communities has remained poorly explored. Here, we have developed a novel framework for prospecting, characterising and estimati...

The vast biochemical repertoire found in microbial communities from a wide-range of environments allows screening and isolation of novel enzymes with improved catalytic features. In this sense, metagenomics approaches have been of high relevance for providing enzymes used in diverse industrial applications. For instance, glycosyl hydrolases, which...

Bioactive compounds and enzymes with tolerance to process-specific parameters or improved catalytic performance play a crucial role in the development of applications in the chemical and pharmaceutical industry or energy production. Metagenomics takes advantage of the wealth of biochemical diversity present in the genomes of microorganisms found in...

Efflux pumps were found to be the most efficient mechanism of hydrocarbon tolerance in several bacterial strains resistant to solvents and other toxic chemicals. This involves an energy-dependent process that ensures the active removal of toxic compounds from the bacterial cytoplasm to the external medium. In order to achieve the maximal response o...

Algal biomass is a promising raw material for production of third-generation biohydrogen. Few studies have investigated how the concentration of galactose, the main monosaccharide of algae biomass, affects fermentative production of H2. We isolated a new culture of H2-producing bacterium from an anaerobic sludge. This culture was identified as Clos...

Filamentous fungi are remarkable organisms naturally specialized in deconstructing plant biomass and this feature has a tremendous potential for biofuel production from renewable sources. The past decades have been marked by a remarkable progress in the genetic engineering of fungi to generate industry-compatible strains needed for some biotech app...

Recognition of cis-regulatory elements by transcription factors (TF) at target promoters is crucial to gene regulation in bacteria. In this process, binding of TFs to their cognate sequences depends on a set of physical interactions between these proteins and specific nucleotides in the operator region. Previously, we showed that in silico optimiza...

There is a growing demand for enzymes with improved catalytic performance or tolerance to process-specific parameters, and biotechnology plays a crucial role in the development of biocatalysts for use in industry, agriculture, medicine and energy generation. Metagenomics takes advantage of the wealth of genetic and biochemical diversity present in...

The understanding of how the architecture of cis-regulatory elements at bacterial promoters determines their final output is of central interest in modern biology. In this work, we attempt to gain insight into this process by analysing complex promoter architectures in the model organism Escherichia coli. By focusing on the relationship between dif...

In this work, we report the in silico identification of the cis-regulatory elements for XYR1 and CRE1 proteins in the filamentous fungus Trichoderma reesei, two regulators that play a central role in the expression of cellulase genes. Using four datasets of condition-dependent genes from RNA-seq and RT-qPCR experiments, we performed unsupervised mo...

Herein, we applied a community genomic approach using a naphthalene-enriched community (CN1) to isolate a versatile esterase (CN1E1) from the α/β-hydrolase family. The protein shares low-to-medium identity (≤ 57%) with known esterase/lipase-like proteins. The enzyme is most active at 25-30°C and pH 8.5; it retains approximately 55% of its activity...

Ubiquitous bacteria from the genus Oleispira drive oil degradation in the largest environment on Earth, the cold and deep sea. Here we report the genome sequence of Oleispira antarctica and show that compared with Alcanivorax borkumensis-the paradigm of mesophilic hydrocarbonoclastic bacteria-O. antarctica has a larger genome that has witnessed mas...

Several members of C-C meta-cleavage product (MCP) hydrolases family demonstrate an unusual ability to hydrolyze esters as well as the MCPs (including those from mono- and bicyclic aromatics). While the molecular mechanisms responsible for such substrate promiscuity are starting to emerge the full understanding of these complex enzymes is far from...

The esterases and lipases from the α/β hydrolase superfamily exhibit an enormous sequence diversity, fold plasticity and activities. Herein, we present the comprehensive sequence and biochemical analyses of seven distinct esterases and lipases from the metagenome of Lake Arreo, an evaporite karstic lake in Spain (42°46' N, 2°59' W; 655 m altitude)....

General features of reported esterases/lipases isolated from metagenomic resources (Table S1); list of primers used in the study (Table S2); percentage of identity between Arreo enzymes, determined by Matcher (EMBOSS package) (Table S3); half-saturation (Michaelis) coefficient (Km), catalytic rate constant (kcat), and catalytic efficiency (kcat/Km)...

Microorganisms that thrive in acidic environments are endowed with specialized molecular mechanisms to survive under this extremely harsh condition. In this work, we performed functional screening of six metagenomic libraries from planktonic and rhizosphere microbial communities of the Tinto River, an extremely acidic environment, to identify genes...

Microbial metabolism in aromatic-contaminated environments has important ecological implications, and obtaining a complete understanding of this process remains a relevant goal. To understand the roles of biodiversity and aromatic-mediated genetic and metabolic rearrangements, we conducted 'OMIC' investigations in an anthropogenically influenced an...

Microbial communities from cow rumen are known for their ability to degrade diverse plant polymers at high rates. In this work, we identified 15 hydrolases through an activity-centred metagenome analysis of a fibre-adherent microbial community from dairy cow rumen. Among them, 7 glycosyl hydrolases (GHs) and 1 feruloyl esterase were successfully cl...

R_09-02, as overexpressed in the active form in E. coli at low temperatures. The quantification of the activity level (A) and optical density (B) of cells expressing R_09-02 was performed at 37, 28 and 22 °C at the indicated time points. Please refer to the Materials and Methods for details of the activity quantification (using pNPβX as the substra...

General structures of the activated and non-activated oligosaccharide substrates for R_09-02. The arrow indicates the putative cleavage site. (PDF)

Annotation of the genes predicted in the fosmid/plasmid clones from the bovine rumen (R) metagenome library. (A) Fosmid r_01, (B) fosmid r_02, (C) fosmid r_03, (D) plasmid r_05, (E) plasmid r_06, (F) plasmid r_07, (G) plasmid r_08 and (H) plasmid r_09. Selected fosmids were sequenced by shotgun sequencing, and the sorted ORFs were annotated by homo...

Summary of the annotation features of the glycosyl- and feruloyl-like coding sequences (CDSs) predicted in the hydrolase-coding DNA fragments from the R library. (PDF)

Temperature optima for the hydrolases recovered from the R library. The enzyme activity was determined as described in the Supporting Materials and Methods using the best substrate and pH (see the details in Table S5) and the enzyme at a concentration of 12 nM. (PDF)

Summary of the characteristics of selected fosmid/plasmid clones from the bovine rumen (R) metagenome library that contains genes encoding glycosyl hydrolases. (PDF)

Complete description of materials and methods and cloning, expression and purification of the plant polymeric-substance hydrolases. (DOC)

Domain organisation of the rumen hydrolases identified in the present work, according to sequence using the Pfam database. The signal peptides predicted using the SignalP server are indicated with a red dot at the N-terminal site. (PDF)

Overall 3-D modelling of the structure of the hydrolases from the R library. The residues belonging to the catalytic core and regions that are suggested to have functional and structural roles are indicated. The following proteins were used as the templates for the homology modelling: β-galactosidase from Bacteroides vulgatus (PDB 3gm8) for R_01-20...

Dendrogram of the compositional sequence similarities, as calculated by the comparison of the frequencies of tetranucleotides in the sequenced DNA fragments, of the r_02 fosmid and bacterial chromosomes. (PDF)

Physical maps of the r_01, r_02, r_03, r_05, r_06, r_07, r_09 fosmid/plasmid from the R library. (PDF)

pH optima for the hydrolases recovered from the R library. The enzyme activity was determined as described in the Supporting Materials and Methods using the best substrate and temperature (see the details in Table S5) and the enzyme at a concentration of 12 nM. (PDF)

Kinetic parameters of the glycosyl and feruloyl hydrolases that were subcloned, expressed, purified and characterised in this study. (PDF)