Trends in the Systematics of Bacteria and Fungi

Methods in microbial systematics have developed and changed significantly in the last 40 years. This has resulted in considerable change in both the defining of microbial species and the methods required to make reliable identifications. Developments in information technology have enabled ready access to vast amounts of new and historic data online. Establishing both the relevance and the most appropriate use of this data is now a major consideration when undertaking identifications and systematic research. This book provides some insights into how current methods and resources are being used in microbial systematics, together with some thoughts and suggestions as to how both methodologies and concepts may develop in the future. It includes coverage of: The philosophy and changes in microbial systematics, including the relevance of names, new concepts of species, and the issues encountered with species that cannot be grown in culture. The application of new identification technologies, specifically those based on nucleic acids and complex chemo-taxonomic methods. The challenges of using published databases and other data resources in arriving at an identification appropriate to current species concepts. The practical requirements of an identification: obtaining and verifying reference cultures and data, and the type and level of identification required by different users. This book is suitable for academic researchers, scientists involved with identification or survey, microbiologists, students and extension workers. Cover Trends in the Systematics of Bacteria and Fungi Copyright Contents List of Figures List of Tables List of Authors Preface 1 Bridging 200 Years of Bacterial Classification Introduction The Historical Perspective The changing consideration of bacterial taxonomic assessment The early era A witness of scientific progress: Bergey’s Manual of Determinative Bacteriology The dawn of unravelling the evolution of Prokaryotes Reconciliation of bacterial taxonomy Changing gear: Bergey’s Manual of Systematic Bacteriology Some Considerations on Taxonomy and the Misunderstandings The Paramount Relevance of the Genomic Data Recent Innovations Taxonomy Needs to Change Its Path Conclusions: Reconciliation or Divorce Acknowledgements References 2 Identification of Fungi: Background, Challenges and Prospects Introduction Fungi and Fungi The Identification Process Challenges of Identifying Fungi Prospects for Addressing Challenges Conclusion References 3 Names of Microorganisms and Data Resources to Retrieve Information About Published Names Introduction The International Code of Nomenclature of Prokaryotes (the Prokaryotic Code) Resources from Which Information About Names of Prokaryotic Taxa Can Be Retrieved The ‘official’ sources of information: articles and lists in the IJSB/IJSEM Online Resources that Provide Information on Validly Published Names of Taxa of Prokaryotes List of Prokaryotic names with Standing in Nomenclature (LPSN) (Euzéby, 1997; Parte, 2014, 2018) Prokaryotic Nomenclature Up-to-Date (Leibniz Institute DSMZ, 2019) NamesforLife (Garrity, 2010) Names of Prokaryotes Effectively but not Validly Published Names of Candidatus Taxa of Prokaryotes The Special Status of the Cyanobacteria/Cyanophyta Names of Fungi and Related Digital Resources Effective Publication Under the ICN Chapter F of the ICN Typification Priority, starting-point dates and hemihomonyms Registration of nomenclatural acts Pleomorphic life cycles – One fungus: one name Lists of approved and rejected names Naming cryptic diversity eDNA Linking names to DNA, and DNA to names Data Standards and Databases Digital Resources Names Taxa Descriptive data Sequence-related databases Conclusion References 4 Preserving the Reference Strains Rationale Introduction Handling Samples from the Environment to the Laboratory DNA Sample Preparation and Storing Sample Acquisition and Authentication Preservation Techniques Approaches to Testing Stability in Storage mBRC Management: Adopting an Appropriate Standard Conclusion References 5 Can Older Fungal Sequence Data be Useful? Introduction Data Available Placing mOTUs in Beauveria ‘Fishing’ for New Sequences ‘Clustering’ for New Sequences Outcome Mislabelled Sequences Limitations in the Methodology ITS Cut-off values Duplicated sequences Limitations of names and labels Species Complexes Conclusion References 6 Data Resources: Role and Services of Culture Collections Introduction The Importance of Reliable Data Desired Function of a Modern Culture Collections Management System Reliable and Useful Data Supporting Fungal Taxonomy Standards and Open Access Conclusion References 7 MALDI-TOF MS and Currently Related Proteomic Technologies in Reconciling Bacterial Systematics Introduction Proteins in Microbial Systematics Arrival of MALDI-TOF MS in Microbiology Establishing MALDI-TOF MS in Clinical Microbiology MALDI-TOF MS in the Non-clinical Laboratory and its Role in Searching for New Diversity MALDI-TOF MS in Subspecies Identification, Typing and Screening for Genetic Variants: Implication for Systematics MALDI-TOF MS in Microbial Systematics; a Case Study Involving Cutibacterium acnes Brief biology of Cutibacterium acnes MALDI-TOF MS delineates three proteotypes Correlation of proteotypes with whole-genome sequencing MALDI-TOF MS and the Future Interest of MS Companies Use of MALDI-TOF MS in a Clinical Laboratory Limitations of MALDI-TOF MS as currently used Retaining the Interest of Mass Spectrometry Companies Potential to Identify the Biomarker Peaks in a MALDI-TOF MS Spectrum: Towards a MALDI-TOF MS Global Database High-resolution forms of MS that may be used to deduce peptide/protein taxon-specific signatures From linear MALDI-TOF MS to tandem LC-MS/MS: unravelling the proteome of microbial species and future implications for bacterial systematics Case study: use of tandem LC-MS/MS during a major disease outbreak of pathogenic E. coli and taxonomic implications Nature of the outbreak Proteomics and systematics in a high-containment laboratory Conclusion References 8 MALDI-TOF MS and its Requirements for Fungal Identification Introduction Principles of MALDI-TOF MS and its Application in Fungal Taxonomy Examples of the Use of MALDI-TOF MS Technique in Fungal Identification Limitations to the Use of MALDI-TOF MS Technique in Fungal Identification MALDI-TOF MS for Cryptic and Dimorphic Fungal Identification MALDI-TOF MS Databases and Data Analysis in Fungal Identification Current situation of each different commercial database dedicated to fungal identification In-house MALDI-TOF MS databases for fungal identification Conclusion Acknowledgements References 9 The Strength of Chemotaxonomy Introduction Background and History of Chemotaxonomic Biomarkers Cell wall components Lipids Polyamines Applications of Chemotaxonomy to Bacterial Systematics Winds of Change: Chemotaxonomy in the Era of Omics Conclusion: Chemotaxonomy and What Lies Ahead References 10 Microbial Genomic Taxonomy Introduction Genomic Microbial Taxonomy In silico Phenotyping Suggestions for a Genome-based Taxonomy Challenges Ahead for Microbial Taxonomy in the Context of Microbial Ecology Challenges in the Taxonomy of the Cyanobacteria Phylum Conclusion References 11 Navigating Bacterial Taxonomy in a World of Unchartered Microbial Organisms Introduction Determining Taxonomy in Metabarcoding Experiments Approaches for Assigning OTUs to Amplicon Sequences Emergence of Amplicon Sequence Variants (ASVs) Assigning Taxonomy to MAGS The Disconnect Between MAGs and Metabarcoding Approaches Conclusion References 12 Sequence-based Identification and Classification of Fungi Introduction The ITS Region as a Universal Barcode for Fungal Identification: Advantages and Limitations Secondary DNA Barcode Regions as Adjuncts to (or Replacements for) ITS Quality of Reference Sequence Libraries The Problem of Sequences Without Names: ‘Dark Taxa’ Implications for Fungal Taxonomy and Nomenclature Conclusion References 13 Identification and Classification of Prokaryotes Using Whole-genome Sequences Introduction Genome-based Classification: Advantages What Did Whole-genome Sequencing Reveal About Traditional Taxonomic Practices? Genome-based Classification: Limitations Genome Classification Resources Available Unculturable Taxa: Genome-based Classification is the Only Way Forward Tips for Genome-based Classification of an Unknown Query Genome Acknowledgements References 14 Genomic Sequences for Fungi Introduction The Species Concept in the Next-generation Sequencing (NGS) Era Methodology Sequencing technologies De novo, resequencing and targeted sequencing RNA sequencing (RNA-Seq) Epigenetics Genomic variation and mutation detection Data analysis and interpretation Experimental design and generation of data Analysis Interpretation Visualization and reporting Techniques Comparative genomics Genome sequences to link genetics with biological traits From biochemistry to genomics Metagenomics Technology and Fungal Systematics Saccharomyces Penicillium Aspergillus Fusarium Colletotrichum Discussion and Conclusion Acknowledgements References 15 What can Genome Analysis Offer for Bacteria? Introduction Schools of Taxonomic Thought and Associated Methods of Analysis Methodological Issues in Polyphasic Taxonomy Causes of Conflict Between Taxonomic Classifications and Genome-scale Analyses Assigning Taxonomic Ranks Using Genome-scale or Other Data Conclusion References 16 Genomes Reveal the Cohesiveness of Bacterial Species Taxa And Provide a Path Towards Describing All of Bacterial Diversity Introduction How Taxonomy Demarcates Bacterial Species A Genome-based Species Taxonomy Substituting a type genome sequence for a type strain Demarcating genomes into new species Describing the phenotype of novel species Is There Something Real About Species? Recombination Does Not Prevent Ecological Divergence Between Bacterial Populations Periodic Selection as a Force of Cohesion in Bacterial Species Ecotypes as Species-like Lineages Enriching Bacterial Systematics with Ecotypes Recombination as a Force of Cohesion Among Ecologically Distinct Lineages A Force of Cohesion That is Limited to Species Taxa Across Much of Life Conclusion References 17 Are Species Concepts Outdated for Fungi? Intraspecific Variation in Plant-pathogenic Fungi Illustrates the Need for Subspecific Categorization Introduction Difficulties in Applying Species Concepts in Fungi Phylogenetic Species Concept and Molecular Data Structured Case Summaries Rhizoctonia solani Colletotrichum Fusarium oxysporum Verticillium Redefinition of species in Verticillium Intraspecific diversity in Verticillium species and its phytopathological relevance Conclusion References 18 Where to Now? Introduction Progress in Mycological Systematics Species Concepts Diverging Developments in Bacterial Classification Bacterial Nomenclature in the Future Reference Materials for Mycology Herbarium resources Curating the names Networking Microbial Strain Information Systematics in the Post-Nagoya Era Conclusion References Appendix Abbreviations and Acronyms List Abbreviations and Acronyms List Chapters 1–10 Chapters 11–17 Index Back Cover There are fundamental differences between the current levels of genomic and proteomic knowledge for bacteria and fungi. With multiple growth forms and over 100,000 known species, the fungi probably present a more complex situation, but genomic studies are hindered by the lack of reliable reference data for many species. As activities such as environmental sampling, and genomic and proteomic profiling, become more important in extending our understanding of ecosystems, there is an increasing imperative for researchers in microbial systematics to develop the methods and concepts required to interpret the information being generated. This volume presents a collection of chapters that provide some insights into how current methods and resources are being used in microbial systematics, together with some thoughts and suggestions about how both methodologies and concepts may develop in the future