The presence of emerging contaminants in the environment, such as pharmaceuticals, is a growing global concern. The excessive use of medication globally, together with the recalcitrance of pharmaceuticals in traditional wastewater treatment systems, has caused these compounds to present a severe environmental problem. In recent years, the increase in their availability, access and use of drugs has caused concentrations in water bodies to rise substantially. Considered as emerging contaminants, pharmaceuticals represent a challenge in the field of environmental remediation; therefore, alternative add-on systems for traditional wastewater treatment plants are continuously being developed to mitigate their impact and reduce their effects on the environment and human health. In this review, we describe the current status and impact of pharmaceutical compounds as emerging contaminants, focusing on their presence in water bodies, and analyzing the development of bioremediation systems, especially mycoremediation, for the removal of these pharmaceutical compounds with a special focus on fungal technologies.

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Understanding plant-microbe interactions with the possibility to modulate the plant’s microbiome is essential to design new strategies for a more productive and sustainable agriculture and to maintain natural ecosystems. Therefore, a key question is how to design bacterial consortia that will yield the desired host phenotype. This work was designed to identify the potential genomic features involved in the interaction between Micromonospora and known host plants. Seventy-four Micromonospora genomes representing diverse environments were used to generate a database of all potentially plant-related genes using a novel bioinformatic pipeline that combined screening for microbial-plant related features and comparison with available plant host proteomes. The strains were recovered in three clusters, highly correlated with several environments: plant-associated, soil/rhizosphere, and marine/mangrove. Irrespective of their isolation source, most strains shared genes coding for commonly screened plant growth promotion features, while differences in plant colonization related traits were observed. When Arabidopsis thaliana plants were inoculated with representative Micromonospora strains selected from the three environments, significant differences were in found in the corresponding plant phenotypes. Our results indicate that the identified genomic signatures help select those strains with the highest probability to successfully colonize the plant and contribute to its wellbeing. These results also suggest that plant growth promotion markers alone are not good indicators for the selection of beneficial bacteria to improve crop production and the recovery of ecosystems.

An important number of Micromonospora strains have been reported from nitrogen fixing root nodules of legume and actinorhizal plants. However, the question of whether this bacterium can also be found in other parts of these plants remains unanswered. Over 150 strains were recovered from different Lupinus angustifolius and Pisum sativum tissues including leaves, stems, roots, and nodules. Ninety-seven percent of the isolates were identified by 16S rRNA gene sequence in the target genus and were associated with 27 different Micromonospora species. Plant-polymer degrading enzymes are suspected to play a role in the colonization of plants. To this end, bacterial enzymatic activity assays for amylases, cellulases, chitinases, pectinases and xylanases were determined. All strains produced xylanases and pectinases, while 98.6%, 98%, and 94.6% of them produced amylases, cellulases, and chitinases, respectively. The most productive strains included seven isolates from P. sativum and one from L. angustifolius. Strain Micromonospora lupini ML01-gfp was used to determine its capacity to reach and colonize different plant organs using P. sativum as the plant model. Stem and leaf samples were monitored by optical and fluorescence microscopy to locate the tagged strain. These results strongly suggest that Micromonospora is able, not only to infect nitrogen-fixing nodules, but also of reaching other parts of the host plant, especially the leaves.

Six actinobacterial strains isolated from diverse legume tissues collected in various locations in Spain were characterized to determine their taxonomic status. Using 16S rRNA gene sequencing, the strains were primarily identified as members of the genus Micromonospora with more than 99 % similarity. Digital DNA–DNA hybridization values and average nucleotide identities between the six strains and the nearest type strains confirmed that each strain represented a novel species. Genome sequences were analysed to infer their metabolic profiles, their potential to produce secondary metabolites and plant growth promoting features. Chemotaxonomic and physiological studies were carried out to complete the phenotypic characterization and to distinguish the new Micromonospora species. The genomic and phenotypic characterization of the Micromonospora strains strongly support their classification as representatives of new species with the following names: Micromonospora alfalfae sp. nov., Micromonospora cabrerizensis sp. nov., Micromonospora foliorum sp. nov., Micromonospora hortensis sp. nov., Micromonospora salmantinae sp. nov. and Micromonospora trifolii sp. nov., with the type strains MED01T, LAH09T, PSH25T, NIE111T, PSH03T and NIE79T, respectively.