The species concept for prokaryotes

The species concept is a recurrent controversial issue that preoccupies philosophers as well as biologists of all disciplines. Prokaryotic species concept has its own history and results from a series of empirical improvements parallel to the development of the techniques of analysis. Among the microbial taxonomists, there is general agreement that the species concept currently in use is useful, pragmatic and universally applicable within the prokaryotic world. However, this empirically designed concept is not encompassed by any of the, at least, 22 concepts described for eukaryotes. The species could be described as 'a monophyletic and genomically coherent cluster of individual organisms that show a high degree of overall similarity in many independent characteristics, and is diagnosable by a discriminative phenotypic property'. We suggest to refer it as a phylo-phenetic species concept. Here, we discuss the validity of the concept in use which we believe is more pragmatic in comparison with those concepts described for eukaryotes.     

A molecular phylogeny of enteric bacteria and implications for a bacterial species concept

A molecular phylogeny for seven taxa of enteric bacteria (Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Hafnia alvei, Klebsiella oxytoca, Klebsiella pneumoniae, and Serratia plymuthica) was made from multiple isolates per taxa taken from a collection of environmental enteric bacteria. Sequences from five housekeeping genes (gapA, groEL, gyrA, ompA, and pgi) and the 16S rRNA gene were used to infer individual gene trees and were concatenated to infer a composite molecular phylogeny for the species. The isolates from each taxa formed tight species clusters in the individual gene trees, suggesting the existence of 'genotypic' clusters that correspond to traditional species designations. These sequence data and the resulting gene trees and consensus tree provide the first data set with which to assess the utility of the recently proposed core genome hypothesis (CGH). The CGH provides a genetically based approach to applying the biological species concept to bacteria.     

Evolution of the bacterial species Lactobacillus delbrueckii: a partial genomic study with reflections on prokaryotic species concept

The species Lactobacillus delbrueckii consists at present of three subspecies, delbrueckii, lactis and bulgaricus, showing a high level of DNA-DNA hybridization similarity but presenting markedly different traits related to distinct ecological adaptation. The internal genetic heterogeneity of the bacterial species L. delbrueckii was analyzed. Phenotypic and several genetic traits were investigated for 61 strains belonging to this species. These included 16S rDNA sequence mutations, expression of beta-galactosidase and of the cell wall-anchored protease, the characterization of the lactose operon locus and of the sequence of lacR gene, galactose metabolism, and the distribution of insertion sequences. The high genetic heterogeneity of taxa was confirmed by every trait investigated: the lac operon was completely deleted in the subsp. delbrueckii, different mutation events in the repressor gene of the operon led to a constitutive expression of lacZ in the subsp. bulgaricus. Structural differences in the same genetic locus were probably due to the presence of different IS elements in the flanking regions. The different expression of the cell wall-anchored protease, constitutive in the subsp. bulgaricus, inducible in the subsp. lactis, and absent in the subsp. delbrueckii was also a consequence of mutations at the gene level. The galT gene for galactose metabolism was found only in the subsp. lactis, while no specific amplification product was detected in the other two subspecies. All these data, together with the absence of a specific IS element, ISL6, from the major number of strains belonging to the subsp. bulgaricus, confirmed a deep internal heterogeneity among the three subspecies. Moreover, this evidence and the directional mutations found in the 16S rDNA sequences suggested that, of the three subspecies, L. delbrueckii subsp. lactis is the taxon closer to the ancestor. Limitations of the current prokaryotic species definition were also discussed, based on presented evidences. Our results indicate the need for an accurate investigation of internal heterogeneity of bacterial species. This study has consequences on the prokaryotic species concept, since genomic flexibility of prokaryotes collides with a stable classification, necessary from a scientific and applied point of view.     

The myth of bacterial species and speciation

The Tree of Life hypothesis frames the evolutionary process as a series of events whereby lineages diverge from one another, thus creating the diversity of life as descendent lineages modify properties from their ancestors. This hypothesis is under scrutiny due to the strong evidence for lateral gene transfer between distantly related bacterial taxa, thereby providing extant taxa with more than one parent. As a result, one argues, the Tree of Life becomes confounded as the original branching structure is gradually superseded by reticulation, ultimately losing its ability to serve as a model for bacterial evolution. Here we address a more fundamental issue: is there a Tree of Life that results from bacterial evolution without considering such lateral gene transfers? Unlike eukaryotic speciation events, lineage separation in bacteria is a gradual process that occurs over tens of millions of years, whereby genetic isolation is established on a gene-by-gene basis. As a result, groups of closely related bacteria, while showing robust genetic isolation as extant lineages, were not created by an unambiguous series of lineage-splitting events. Rather, a temporal fragmentation of the speciation process results in cognate genes showing different genetic relationships. We argue that lineage divergence in bacteria does not produce a tree-like framework, and inferences drawn from such a framework have the potential to be incorrect and misleading. Therefore, the Tree of Life is an inappropriate paradigm for bacterial evolution regardless of the extent of gene transfer between distantly related taxa.     

The 3Cs provide a novel concept of bacterial species: messages from the genome as illustrated by Salmonella

A key issue troubling bacterial taxonomy and systematics is the lack of a biological species definition. Criteria to be used for defining bacterial species on genetic and biological bases should be able to reveal clear-cut boundaries among clusters of bacteria. To date, DNA–DNA re-association assays and ribosomal RNA sequence comparison have been useful in determining relative evolutionary distances among bacteria but the data are continuous and thus cannot define bacterial clusters as taxonomic units to be called species. Using Salmonella as models, we have looked for definite genetic and biologic uniqueness of clusters of bacteria. Based on our findings that each Salmonella lineage has a unique genome structure shared by strains of the same lineage but not overlapping with strains of other Salmonella lineages, we conclude that this is a result of genetic isolation following divergence of the bacteria. We propose that there should be genetic boundaries between different species of bacteria at the genomic level, which awaits further genomic information for validation.     

The bacterial species definition in the genomic era

The bacterial species definition, despite its eminent practical significance for identification, diagnosis, quarantine and diversity surveys, remains a very difficult issue to advance. Genomics now offers novel insights into intra-species diversity and the potential for emergence of a more soundly based system. Although we share the excitement, we argue that it is premature for a universal change to the definition because current knowledge is based on too few phylogenetic groups and too few samples of natural populations. Our analysis of five important bacterial groups suggests, however, that more stringent standards for species may be justifiable when a solid understanding of gene content and ecological distinctiveness becomes available. Our analysis also reveals what is actually encompassed in a species according to the current standards, in terms of whole-genome sequence and gene-content diversity, and shows that this does not correspond to coherent clusters for the environmental Burkholderia and Shewanella genera examined. In contrast, the obligatory pathogens, which have a very restricted ecological niche, do exhibit clusters. Therefore, the idea of biologically meaningful clusters of diversity that applies to most eukaryotes may not be universally applicable in the microbial world, or if such clusters exist, they may be found at different levels of distinction.     

Genomics and the bacterial species problem

Whether or not bacteria have species is a perennially vexatious question. Given what we now know about variation among bacterial genomes, we argue that there is no intrinsic reason why the processes driving diversification and adaptation must produce groups of individuals sufficiently coherent in their genetic and phenotypic properties to merit the designation 'species' - although sometimes they might.     

细菌性阴道病的细菌因素研究进展

细菌性阴道病是妇科常见疾病,对女性、胎儿和新生儿的健康构成严重威胁.阴道微生物群落中产H2O2的乳酸杆菌与厌氧菌数量发生转换为其主要特征,具体机制不清.本文系统综述了近年来细菌性阴道病的细菌因素研究进展.     

The debate about the biological species concept - a review

The importance of the species concept in biology has led to a continuing debate about the definition of species. This paper summarizes the recent literature in relation to the ‘biological species concept’ (MAYR 1942). Among the general attributes demanded, possible limitations of the universality and applicability of a species definition are discussed. Three different areas of criticism of the biological species concept are considered: 1. The impracticability of the criterion of reproductive isolation. The demand for more practical criteria is rejected, because reproductive isolation is seen as the factor that produces and maintains species as discrete entities in nature. 2. The inapplicability to non-bisexual organisms. A brief survey of modes of uniparental reproduction and their relative importance suggests that obligatory apomicts are of little evolutionary significance. 3. The inapplicability to multidimensional situations. Despite practical difficulties, the biological species concept is held to apply to organisms separated in space. The impossibility to delimit species in time by reproductive isolation is recognized. Out of two ways to divide continuous evolutionary lineages in time, the phylogenetic approach, which considers only speciation events (cladogenesis), is preferred as it is more objective. A list of recently published alternative definitions of species, none of which is found acceptable, is given. It is concluded that the biological species concept needs not be changed or dismissed on the basis of the discussed criticisms.     

The impact of species concept on biodiversity studies

Species are defined using a variety of different operational techniques. While discussion of the various methodologies has previously been restricted mostly to taxonomists, the demarcation of species is also crucial for conservation biology. Unfortunately, different methods of diagnosing species can arrive at different entities. Most prominently, it is widely thought that use of a phylogenetic species concept may lead to recognition of a far greater number of much less inclusive units. As a result, studies of the same group of organisms can produce not only different species identities but also different species range and number of individuals. To assess the impact of different definitions on conservation issues, we collected instances from the literature where a group of organisms was categorized both under phylogenetic and nonphylogenetic concepts. Our results show a marked difference, with surveys based on a phylogenetic species concept showing more species (48%) and an associated decrease in population size and range. We discuss the serious consequences of this trend for conservation, including an apparent change in the number of endangered species, potential political fallout, and the difficulty of deciding what should be conserved.     

The (mis)concept of species recognition

To many, the concept of 'species recognition' is integral to the origin and maintenance of species. However, the heuristic value of species recognition is hampered by its reliance on the problematic concept of species. In this paper, we first discuss assumptions associated with prevailing use of the term, including the typological implications of the concept, the false dichotomy of compatibility and mate quality, and the commonly held model of species recognition in which animals determine taxonomic status before mate status. Subsequently, we propose research directions aimed to improve our understanding of the role of courtship behavior in speciation. We propose two complementary research approaches, one addressing the processes that drive the evolution of mate recognition systems and the other addressing the phenotypic architecture of behavioral isolation. Our approach emphasizes the fitness consequences and multidimensional nature of mate choice.     

Editorial and introduction: The species concept in fish biology

Reviews in Fish Biology and Fisheries -     

形象检索法与形象检索表

形象检索法是采用典型的外部形态特征,辅以图片检索,对种及种以下单元进行分类的方法。该方法仅使用典型的外部形态特征对不同分类等级的多歧对应或非对应性状编制检索表,对鉴定所涉及的特征或名词术语辅以简练准确的文字以及典型特征的照片或图片予以说明。主要为非专业人员快速检索而设计。对野生动物的执法、管理、保护教育及知识普及具有理论和实践指导意义。     

The species concept in a long-extinct fossil group,the conodonts

Conodonts are an extinct group of organisms, known from the Upper Cambrian to the Triassic. They have no extant representatives, and tooth-like buccal elements are usually the only remains of the animal found in the sediments. Therefore, most of their taxonomy rests on these elements that are good stratigraphic tools for these ancient periods, due to their rapid morphological evolution. Conodont species are usually described species that are based on either clusters of elements corresponding to an entire apparatus (natural assemblages), or on the most frequently preserved element. These described species are acceptable stratigraphic tools, but hardly consider the dimension of the variation that a biological species can encompass through time and space. In order to tackle temporal, environmental and biogeographical changes, recent studies have shown that morphological variation should be taken into account by quantitative analyses, aiming at getting at the closest of what the former species might have been.