Papers by Manuel Gustavo Ferrer
Methods in Molecular Biology, 2010
Laccases are multi-copper oxidoreductases (benzenediol:oxygen oxidoreductases, EC 1.10.3.2) able ... more Laccases are multi-copper oxidoreductases (benzenediol:oxygen oxidoreductases, EC 1.10.3.2) able to oxidise a wide variety of phenolic and non-phenolic compounds. They are useful enzymes for a variety of applications, including bioremediation and craft pulp bio-bleaching as the most significant ones. There is a considerable interest to find new laccases through the exploration of biological diversity. Laccases have been found in plants, insects, and bacteria but predominantly in fungi: these enzymes have been documented in about 60 fungal strains. Microbial diversity constitutes a largely unexplored treasure chest with new laccases with a good potential for basic science and biotechnology. At present, due to our inability to cultivate most microbes, the only means of accessing the resources of the microbial world is to harvest genetic resources ("metagenomes"), which can further on be subjected to extensive screening programs. In this chapter, we provide an overview of screening methods to identify laccase-encoding genes from environmental resources.
Methods in Molecular Biology, 2010
Microbes, which constitute a major fraction of the total biomass, are the main source of biodiver... more Microbes, which constitute a major fraction of the total biomass, are the main source of biodiversity on our Planet and play an essential role in maintaining global processes, which ultimately regulate the functioning of the Biosphere. Recent emergence of "metagenomics" allows for the analysis of microbial communities without tedious cultivation efforts. Metagenomics approach is analogous to the genomics with the difference that it does not deal with the single genome from a clone or microbe cultured or characterized in laboratory, but rather with that from the entire microbial community present in an environmental sample; it is the community genome. Global understanding by metagenomics depends essentially on the possibility of isolating the entire bulk DNA and identifying the genomes, genes, and proteins more relevant to each of the environmental sample under investigation. Following on this, in this chapter, we provide an analysis of methods available to isolate environmental DNA and to establish metagenomic libraries that can further be used for extensive activity screens.
Encyclopedia of Metagenomics, 2015
Encyclopedia of Metagenomics, 2013
Journal of Chemical Technology & Biotechnology, 2007
Biotechnology, in terms of exploitation of catalytic activities for industrial applications, is i... more Biotechnology, in terms of exploitation of catalytic activities for industrial applications, is increasingly recognized as one of the pillars of the knowledge-based economy that we are heading for. Comprehensive knowledge of enzymology should be of practical importance for effective intervention on whole cell processes and enzymatic networks. Over the last decade metagenome-based technologies have been developed to take us farther and deeper into the enzyme universe from uncultivable microbes. This sophisticated platform, which identifies new enzymes from vast genetic pools available, and assesses their potential for novel chemical applications, should be increasingly important in the discovery of advanced biotechnological resources.
Biotechnology and Bioengineering, 1999
The enzymatic synthesis of 6-O-lauroylsucrose and 6-O-palmitoylsucrose was performed by transeste... more The enzymatic synthesis of 6-O-lauroylsucrose and 6-O-palmitoylsucrose was performed by transesterification of sucrose with the corresponding vinyl esters in a medium constituted by two solvents. More specifically, the acylation was carried out in 2-methyl-2-butanol (tert-amyl alcohol) containing a low percentage (not higher than 20%) of dimethyl sulfoxide. Several lipases were able to catalyze the transesterification, but that from Humicola lanuginosa (adsorbed on diatomaceous earth) was particularly useful. We optimized the synthesis of 6-O-lauroylsucrose varying the percentage and nature of the cosolvent, the molar ratio sucrose/vinyl laurate, the nature of bulk solvent and the enzyme content. Under the best conditions (2-methyl-2-butanol/DMSO 4:1 v/v), a sucrose conversion of 70% to 6-O-lauroylsucrose was achieved in 24 h using 50 mg biocatalyst/mL. As a side process, a low percentage (<5% in 24 h) of the initial sucrose is converted into the diesters 6,1'-di-O-lauroylsucrose and 6,6'-di-O-lauroylsucrose. The above methodology was also extended to the synthesis of 6-O-palmitoylsucrose. The acylation process was even faster, giving rise to an 80% conversion to monoester in 48 h using 25 mg biocatalyst/mL. This study shows that the use of two-solvent mixtures may become a feasible alternative for the synthesis of sucrose esters, allowing to exploit the catalytic potential of lipases.
Metagenomics and Complementary Approaches, 2011
A common biological pathway reconstruction approach-as implemented by many automatic biological p... more A common biological pathway reconstruction approach-as implemented by many automatic biological pathway services (such as the KAAS and RAST servers) and the functional annotation of metagenomic sequences-starts with the identification of protein functions or families (e.g., KO families for the KEGG database and the FIG families for the SEED database) in the query sequences, followed by a direct mapping of the identified protein families onto pathways. Given a predicted patchwork of individual biochemical steps, some metric must be applied in deciding what pathways actually exist in the genome or metagenome represented by the sequences. Commonly, and straightforwardly, a complete biological pathway can be identified in a dataset if at least one of the steps associated with the pathway is found. We report, however, that this naïve mapping approach leads to an inflated estimate of biological pathways, and thus overestimates the functional diversity of the sample from which the DNA sequences are derived. We developed a parsimony approach, called MinPath (Minimal set of Pathways), for biological pathway reconstructions using protein family predictions, which yields a more conservative, yet more faithful, estimation of the biological pathways for a query dataset. MinPath identified far fewer pathways for the genomes collected in the KEGG database-as compared to the naïve mapping approach-eliminating some obviously spurious pathway annotations. Results from applying MinPath to several metagenomes indicate that the common methods used for metagenome annotation may significantly overestimate the biological pathways encoded by microbial communities. Citation: Ye Y, Doak TG (2009) A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes. PLoS Comput Biol 5(8): e1000465.
Encyclopedia of Metagenomics, 2015
ABSTRACT The Mediterranean Accretionary Ridge is formed along the rifted margins of Northern Afri... more ABSTRACT The Mediterranean Accretionary Ridge is formed along the rifted margins of Northern Africa and the subducting margins of Southern Europe. This area contains one of the world’s highest abundance of unique geological features called deep-sea hypersaline anoxic lakes (DHALs). Since the discovery of the first Mediterranean DHAL Tyro in 1983, six other salt-related structures have been unveiled in this area in the last decades: l’Atalante, Bannock, Discovery, Medee, Thetis, and Urania, and the existence of many other DHALs has been speculated (Medriff Consortium 1995) (Fig. 1).Fig. 1Location of the deep-sea anoxic hypersaline lakes (DHALs) in the Eastern Mediterranean Sea The hydrologic and geological settings of these fascinating builds likely share the same genesis, i.e., their formation is originated from dissolution of Messinian evaporitic salt deposits that underlie most of the Mediterranean basin. The astonishing amount of evaporites (this subsurface layer can be of up to 1,000–2,000 m ...
Encyclopedia of Metagenomics, 2013
ABSTRACT The Mediterranean Accretionary Ridge is formed along the rifted margins of Northern Afri... more ABSTRACT The Mediterranean Accretionary Ridge is formed along the rifted margins of Northern Africa and the subducting margins of Southern Europe. This area contains one of the world’s highest abundance of unique geological features called deep-sea hypersaline anoxic lakes (DHALs). Since the discovery of the first Mediterranean DHAL Tyro in 1983, six other salt-related structures have been unveiled in this area in the last decades: l’Atalante, Bannock, Discovery, Medee, Thetis, and Urania, and the existence of many other DHALs has been speculated (Medriff Consortium 1995) (Fig. 1).Fig. 1Location of the deep-sea anoxic hypersaline lakes (DHALs) in the Eastern Mediterranean Sea The hydrologic and geological settings of these fascinating builds likely share the same genesis, i.e., their formation is originated from dissolution of Messinian evaporitic salt deposits that underlie most of the Mediterranean basin. The astonishing amount of evaporites (this subsurface layer can be of up to 1,000–2,000 m ...
Microbial Biotechnology, 2009
In recent years, the application of approaches for harvesting DNA from the environment, the so-ca... more In recent years, the application of approaches for harvesting DNA from the environment, the so-called, 'metagenomic approaches' has proven to be highly successful for the identification, isolation and generation of novel enzymes. Functional screening for the desired catalytic activity is one of the key steps in mining metagenomic libraries, as it does not rely on sequence homology. In this mini-review, we survey high-throughput screening tools, originally developed for directed evolution experiments, which can be readily adapted for the screening of large libraries. In particular, we focus on the use of in vitro compartmentalization (IVC) approaches to address potential advantages and problems the merger of cultureindependent and IVC techniques might bring on the mining of enzyme activities in microbial communities.
Microbial Biotechnology, 2009
There is not one path anymore. Twenty years ago, you worked at the clean bench, you isolated new ... more There is not one path anymore. Twenty years ago, you worked at the clean bench, you isolated new microbes able to grow on agar plates, and then you isolated single genes coding single enzymes for particular processes, you optimized them, and you wrote books or articles ...
FEMS Microbiology Reviews, 2009
The world of microorganisms comprises a vast diversity of live organisms, each with its individua... more The world of microorganisms comprises a vast diversity of live organisms, each with its individual set of genes, cellular components and metabolic reactions that interact within the cell and communicate with the environment in many different ways. There is a strong imperative to gain a broader view of the wired and interconnected cellular and environmental processes as a whole via the systems microbiology approach in order to understand and predict ecosystem functioning. On the other hand, currently we experience a rise of metagenomics as an emerging tool to study communities of uncultured microorganisms. In this review, we conducted a survey of important methodologies in metagenomics and describe systems microbiology-like approaches for gaining a mechanistic understanding of complex microbial systems to interrogate compositional, evolutionary and metabolic properties. The review also discusses how metagenomics can be used as a holistic indicator for ecosystem response in terms of matter, nutrient and energy sources and functional networking.
Current Opinion in Microbiology, 2007
Current advances in metagenomics have revolutionized the research in fields of microbial ecology ... more Current advances in metagenomics have revolutionized the research in fields of microbial ecology and biotechnology, enabling not only a glimpse into the uncultured microbial population and mechanistic understanding of possible biogeochemical cycles and lifestyles of extreme organisms but also the high-throughput discovery of new enzymes for industrial bioconversions. Nowadays, the genetic and enzymatic differences across the gradients from 'neutral and pristine' to 'extreme and polluted' environments are well documented. Yet, extremophilic organisms are possibly the least well understood because our ability to study and understand their metabolic potential has been hampered by our inability to isolate pure cultures. There are at least two obstacles for reaping the fruit of the microbial diversity of extremophiles: first, in spite of the recent progress in development of new culturing techniques most extremophiles cannot be cultured using traditional culturing technologies; and second, the problem of the very low biomass densities often occurs under the conditions hostile for life, which often do not yield enough DNA and reduces the effectiveness of cloning.
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Papers by Manuel Gustavo Ferrer