Characterization of Microbial Diversity in Decayed Wood from a Spanish Forest: An Environmental Source of Industrially Relevant Microorganisms.

Rotting wood is inhabited by a large diversity of bacteria, fungi, and insects with complex environmental relationships. The aim of this work was to study the composition of the microbiota (bacteria and fungi) in decaying wood from a northwest Spanish forest as a source of industrially relevant microorganisms. The analyzed forest is situated in a well-defined biogeographic area combining Mediterranean and temperate macrobioclimates. Bacterial diversity, determined by metagenome analyses, was higher than fungal heterogeneity. However, a total of 194 different cultivable bacterial isolates (mainly Bacillaceae, Streptomycetaceae, Paenibacillaceae, and Microbacteriaceae) were obtained, in contrast to 343 fungal strains (mainly Aspergillaceae, Hypocreaceae, and Coniochaetaceae). Isolates traditionally known as secondary metabolite producers, such as Actinobacteria and members of the Penicillium genus, were screened for their antimicrobial activity by the detection of antibiotic biosynthetic clusters and competitive bioassays against fungi involved in wood decay. In addition, the ability of Penicillium isolates to degrade cellulose and release ferulic acid from wood was also examined. These results present decaying wood as an ecologically rich niche and a promising source of biotechnologically interesting microorganisms.

Microbial Isolation and Characterization of New Antibiotic-Producing Strains from Decayed Wood.

Microbial drug resistance is increasing over the last years, becoming one of the most important health concerns in the twenty-first century. It encourages the discovery of new antibiotics. Thus, novel antibiotics discovered by exploring different environments that previously have been left out of the scientific focus is a realistic opportunity. One of these habitats can be forest deadwood, which is a specific niche inside of the forest that provides shelter and nutrition to a great variety of organisms, such as fungi, bacteria, or saproxylic insects. Different studies have found the existence of complex antagonisms and symbiotic interactions among them, which points at decayed wood as a competitive environment. Besides, it is an interesting niche to look for new antibiotic producer microorganisms and active chemicals. This chapter describes isolation and screening methods of novel producers of antimicrobial compounds from decayed wood.

Screening of Antibiotic Gene Clusters in Microorganisms Isolated from Wood.

The biosphere of Earth is made up of a variety of ecosystems governed by complex biological interactions, some of them mediated by microbial bioactive secondary metabolites. These metabolites such as antibiotics (e.g., polyketides and nonribosomal peptides) have been receiving increasing attention, due to their multiple pharmaceutical uses. Besides, antibiotic resistance is on the rise, and it is currently regarded as one of the greatest threats to global human health. The screening of novel antimicrobial polyketides and nonribosomal peptides in poorly studied ecosystems is an interesting alternative to address the problem of antibiotic resistance. This chapter updates a molecular method to identify antibiotics gene clusters and their subsequent production and activity validation. On the one hand, a PCR method based on degenerated primers for nonribosomal peptide synthases (NRPS) and the polyketide synthases (PKS) genes is used as an initial fast screening. On the other hand, a bioassay-based method is the protocol selected for the production confirmation and antibacterial effect estimation. These methods are applied to screen Actinobacteria and Penicillium species as main antibiotic producers isolated from wood.