Trends in the Systematics of Bacteria and Fungi

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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
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