Genomic sequences for fungi.

This chapter aims to give an overview of the basic knowledge, understanding and perspectives in fungal genomics. It is likely that fungal genome sequencing will soon become simpler and cheaper, and allow most research laboratories to undertake in-house, whole genome sequencing on a regular basis, as sequencers will be accessible to most laboratories. Nonetheless, most of the innovation in the next decade will be driven by theories in innovative perspectives and fields of investigation, rather than in novel technical approaches.

Identification and Classification of Prokaryotes using whole-genome sequences.

This book chapter attempts to summarize the major findings from genome-based taxonomic studies in the past two decades, and briefly describe the major genome-based approaches currently available for species identification and classification with special focus on the 'uncultivated majority' and associated limitations, as well as outlines future directions towards a truly genome-based taxonomy for prokaryotes that will equally encompass cultured and uncultivated taxa. Importantly, the need for a system to catalogue uncultivated taxa is very urgent, because the genomes and ecological/functional data that are becoming available are already overwhelming, and alphanumeric identifiers and synonyms are creating confusion of Babylonian dimensions.

The Strength of Chemotaxonomy.

This book chapter discusses the history and development of chemotaxonomic methods, with examples of the application to different taxa, and with extensive reference to primary literature and reviews. The application of in silico methods utilizing information from the genome and future directions will also be discussed. The delineation of higher taxa at the family level and above may especially be aided by chemotaxonomic criteria, as demonstrated in published minimum standards. Although chemotaxonomic methods have been enormously important in the past with identification and classification schemes, it remains to be seen in what form they will be utilized in the genomic era, and in the suite of methods available in the era of omics.

MALDI-TOF MS and its requirements for fungal identification.

Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is now used as a routine technique for the fast and reliable identification of fungi at the species level and, currently, it represents an important phenotypic methodology based on proteomic profiles. The main limitations to MALDI-TOF MS for fungal identification are related to sample quality (e.g. quality of biological material such as rigidity or pigmentation of cell walls), sample preparation (e.g. the myriad of sample preparation methodologies that deliver different data sets to different MALDI-TOF MS databases) and the databases themselves (e.g. the 'black-box' commercial databases). This chapter presents an overview and discussion of the use of MALDI-TOF MS for fungal identification. The major known limitations of the technique for fungal taxonomy, and how to overcome these, are also discussed.

Names of microorganisms and data resources to retrieve information about published names.

This chapter deals with the process of giving names to newly discovered microorganisms and assigning names to them that are correctly formed in agreement with the rules of the relevant code of nomenclature: the International Code of Nomenclature of Prokaryotes for the prokaryotes (Archaea and Bacteria, including a small number of cyanobacteria), and the International Code of Nomenclature for algae, fungi, and plants for the microfungi and for most cyanobacteria. In-depth discussions will be devoted to the online databases and handbooks, where updated information can be found about all names with standing in the nomenclature.

Microbial Genomic Taxonomy.

This book chapter argues for an open-access catalogue of taxonomic descriptions with prototypes; diagnostic tables; and links to culture collections, to genome and gene sequences, and to other phenotypic and ecological databases. Ideally, the open access taxonomy will be based solely on genome sequences that allow both the phylogenetic allocation of new strains and species in the taxonomic space and the phenotypic/metabolic characterization in open online databases. Careful and thorough annotation of the genome sequences for function and chemotaxonomic data will be required. An alternative Code will be required for the naming strategy of genomes. Current microbial taxonomy is not able to keep up with the pace of development in microbial ecology. Innovative ways of developing microbial taxonomy are, therefore, needed urgently. This novel approach can, for the first time, allow microbial species descriptions using genomes based on ecological and evolutionary theory. One challenge ahead is to leverage the use of genome sequences to obtain insights on the (in silico) phenotypes and ecology of novel taxa.

MALDI-TOF MS and currently related proteomic technologies in reconciling bacterial systematics.

This book chapter presents an overview and discussion of the use of MALDI-TOF MS for fungal identification. The major known limitations of the technique for fungal taxonomy, and how to overcome these, are also discussed. Moreover, this should guarantee that spectra deposited in such MALDI-TOF MS database would remain public, preferably in open free access. To avoid misidentification, these stored spectra must be curated and based on well-established standard operating procedures. The number of spectra available within species needs to be increased to accommodate the diversity and geographic differences, unique strain traits and the varied culture conditions and procedures in order to establish a single public and open access MALDITOF MS database. This could then be used with metadata analysis and artificial intelligence algorithms, to provide reliable fungal identification.

Navigating bacterial taxonomy in a world of unchartered microbial organisms.

This book chapter focuses on state-of-the-art informatics techniques that perform bacterial taxonomic assertions on metabarcoding data sets and MAGs, as well as highlighting some of the advantages and disadvantages of the respective approaches and finishes by exploring why they are yet to be perfectly complementary. Currently, the results of these two approaches can be difficult to compare for the various reasons we highlight, and they are compounded by the fact that the data sets typically have different purposes. Despite the current difficulties, the field is heading in a direction that attempts to harmonize bacterial taxonomy generated by both approaches, ultimately making these comparisons less problematic in the future.

Preserving the reference strains.

It is critical that storage of the living reference strains, on which the names and properties are based and the DNA sequenced to assign a name (the reference genetic resources), are preserved optimally to retain stability. The fact that less than 1% of microbial diversity can be grown sets enormous challenges for repositories (microbial domain biological resource centres or mBRCs). It is most often the case that it is an axenic culture of the reference genetic resource that is preserved but, for those organisms that cannot be grown or where molecular techniques are used to identify the organism, DNA should be stored. This task increases further when the microbiome is being studied, and environmental samples from whole communities are examined; mBRCs need to address how these can be preserved too. This chapter focuses on property retention, selecting the appropriate techniques for longterm survival and stability of characters. It covers the operations of mBRCs and the most appropriate technologies and mechanisms for stability testing and quality assurance. It addresses the preservation of microbial strains of the wide range of archaeal, bacterial (including cyanobacterial), yeast and fungal type and reference strains.

Where to now?

This chapter provides information on the status quo of molecular assessment of prokaryotes, fungi and yeast. The recent developments in sequencing approaches to assess the diversity of cultured and not-as-yet-cultured organisms and metagenomes, together with the most widely applied algorithms for gene annotation and the pros and cons of defining taxon ranks, are outlined and discussed.