A modern system of Fusarium taxonomy

A modern system of Fusarium taxonomy is proposed, based on the study over 30 years, of the morphology and growth characteristics of fungi of this genus, and their variability under a wide range of conditions. The system proposed here comprises 13 sections, 33 species and 14 varieties. It differs from systems published by other authors mainly in the sections Eupionnotes, Sporotrichiella, Arthrosporiella, Gibbosum, Discolor, Macroconia and Martiella.     

A new genomic taxonomy system for the Synechococcus collective

Cyanobacteria of the genus Synechococcus are major contributors to global primary productivity and are found in a wide range of aquatic ecosystems. This Synechococcus collective (SC) is metabolically diverse, with some lineages thriving in polar and nutrient-rich locations and others in tropical or riverine waters. Although many studies have discussed the ecology and evolution of the SC, there is a paucity of knowledge on its taxonomic structure. Thus, we present a new taxonomic classification framework for the SC based on recent advances in microbial genomic taxonomy. Phylogenomic analyses of 1085 cyanobacterial genomes demonstrate that organisms classified as Synechococcus are polyphyletic at the order rank. The SC is classified into 15 genera, which are placed into five distinct orders within the phylum Cyanobacteria: (i) Synechococcales (Cyanobium, Inmanicoccus, Lacustricoccus gen. Nov., Parasynechococcus, Pseudosynechococcus, Regnicoccus, Synechospongium gen. nov., Synechococcus and Vulcanococcus); (ii) Cyanobacteriales (Limnothrix); (iii) Leptococcales (Brevicoccus and Leptococcus); (iv) Thermosynechococcales (Stenotopis and Thermosynechococcus) and (v) Neosynechococcales (Neosynechococcus). The newly proposed classification is consistent with habitat distribution patterns (seawater, freshwater, brackish and thermal environments) and reflects the ecological and evolutionary relationships of the SC.     

Chemosystematics of theRutaceae: Suggestions for a more natural taxonomy and evolutionary interpretation of the family

The chemosystematics ofRutaceae is reviewed on the basis of updated surveys of various secondary metabolites and their biosynthetic derivation. A comparison of these data with the morphological and geographical differentiation clearly shows that the current taxonomic arrangement of the family is to a large extent artificial and needs improvement. Starting from obviously natural groups of genera (or single genera) as basic taxonomic entities a new system with informal tribal names is suggested. In particular, the subfamilyToddalioideae is broken up altogether and its former members are rearranged among several of the 17 provisional tribes within the subfamilyRutoideae s. lat. Phylogenetic progressions can be recognized from parallel changes of morphological characters and biosynthetic pathways to secondary metabolites. As a general trend, a stepwise replacement of benzylisoquinolines by simple and complex anthranilic acid derived alkaloids, and eventually by coumarins and/or limonoids is confirmed. The available data are summarized in a discussion of the possible evolutionary relationships among theRutaceae, with theZanthoxylum- andEvodia-tribes in a central position.     

Rational engineering of natural polyhydroxyalkanoates producing microorganisms for improved synthesis and recovery

Microbial production of biopolymers derived from renewable substrates and waste streams reduces our heavy reliance on petrochemical plastics. One of the most important biodegradable polymers is the family of polyhydroxyalkanoates (PHAs), naturally occurring intracellular polyoxoesters produced for decades by bacterial fermentation of sugars and fatty acids at the industrial scale. Despite the advances, PHA production still suffers from heavy costs associated with carbon substrates and downstream processing to recover the intracellular product, thus restricting market positioning. In recent years, model-aided metabolic engineering and novel synthetic biology approaches have spurred our understanding of carbon flux partitioning through competing pathways and cellular resource allocation during PHA synthesis, enabling the rational design of superior biopolymer producers and programmable cellular lytic systems. This review describes these attempts to rationally engineering the cellular operation of several microbes to elevate PHA production on specific substrates and waste products. We also delve into genome reduction, morphology, and redox cofactor engineering to boost PHA biosynthesis. Besides, we critically evaluate engineered bacterial strains in various fermentation modes in terms of PHA productivity and the period required for product recovery.     

The austral cordgrass Spartina densiflora Brong.: its taxonomy, biogeography and natural history

Aim During the last 20 years, the austral cordgrass Spartina densiflora has been recorded aggressively invading estuarine environments in the USA, Spain and Morocco. Whereas this species is one of the three most widely distributed worldwide, it is among the least studied within the genus. The objective of this work is to integrate baseline information about the taxonomy, global distribution, centre of origin, and general ecology of S. densiflora in native and invaded marshes worldwide in order to help to strengthen management efforts currently directed at controlling or eradicating it from locations where it has been introduced. Location World‐wide. Methods I review, update and discuss relevant information about S. densiflora published in peer‐reviewed papers, including those in journals with limited international distribution. I also review theses and major technical reports containing critical up‐to‐date information. Results This work indicates that, although S. densiflora remains in need of thorough scientific attention, key information on its taxonomy, distribution and invasive biology has been overlooked because it was published in languages other than English, and/or in journals with restricted distribution. Main conclusions Spartina densiflora seems to have originated along the east coast of South America; today, however, many other regions worldwide serve as donors for this invasive species, including Chile, the USA, Spain and Morocco. Spartina densiflora is a bioengineer organism, tolerant of a broad spectrum of environmental conditions and able to re‐shape the structure of invaded communities not just in mudflats, but also on sandy, muddy, and rocky shores as well as on cobble beaches. Only by integrating local‐scale research conducted in different geographical regions will we be able to understand the between‐site variations of its biological cycle, which in turn will aid in the design of more effective conservation strategies.     

A pervasive denigration of natural history misconstrues how biodiversity inventories and taxonomy underpin scientific knowledge

Embracing comparative biology, natural history encompasses those sciences that discover, decipher and classify unique (idiographic) details of landscapes, and extinct and extant biodiversity. Intrinsic to these multifarious roles in expanding and consolidating research and knowledge, natural history endows keystone support to the veracity of law-like (nomothetic) generalizations in science. What science knows about the natural world is governed by an inherent function of idiographic discovery; characteristic of natural history, this relationship is exemplified wherever an idiographic discovery overturns established wisdom. This nature of natural history explicates why inventories are of such epistemological importance. Unfortunately, a Denigration of Natural History weakens contemporary science from within. It expresses in the prevalent, pervasive failure to appreciate this pivotal role of idiographic research: a widespread disrespect for how natural history undergirds scientific knowledge. Symptoms of this Denigration of Natural History present in negative impacts on scientific research and knowledge. One symptom is the failure to appreciate and support the inventory and monitoring of biodiversity. Another resides in failures of scientiometrics to quantify how taxonomic publications sustain and improve knowledge. Their relevance in contemporary science characteristically persists and grows; so the temporal eminence of these idiographic publications extends over decades. This is because they propagate a succession of derived scientific statements, findings and/or conclusions - inherently shorter-lived, nomothetic publications. Widespread neglect of natural science collections is equally pernicious, allied with disregard for epistemological functions of specimens, whose preservation maintains the veracity of knowledge. Last, but not least, the decline in taxonomic expertise weakens research capacity; there are insufficient skills to study organismal diversity in all of its intricacies. Beyond weakening research capacities and outputs across comparative biology, this Denigration of Natural History impacts on the integrity of knowledge itself, undermining progress and pedagogy throughout science. Unprecedented advances in knowledge are set to follow on consummate inventories of biodiversity, including the protists. These opportunities challenge us to survey biodiversity representatively—detailing the natural history of species. Research strategies cannot continue to ignore arguments for such an unprecedented investment in idiographic natural history. Idiographic shortcuts to general (nomothetic) insights simply do not exist. The biodiversity sciences face a stark choice. No matter how charismatic its portrayed species, an incomplete ‘Brochure of Life’ cannot match the scientific integrity of the ‘Encyclopedia of Life’.     

Flavonoids and the taxonomy of Cercis

Flavonoids of 11 samples of Cercis, comprising seven species, were isolated and identified. Only 3-O-monoglycosides of kaempferol, quercetin and myricetin were obtained. Bauhinia (the largest genus in tribe Cercideae) is akin to Cercis because flavones are rarely found in the former. On the other hand, species of Bauhinia often present glycosides of isorhamnetin and a wider diversity of glycosides, and only rarely present myricetin. The frequent occurrence of this flavonol and the simpler flavonoid profile of Cercis may reflect a greater antiquity of Cercis as compared with Bauhinia. With the exception of C. canadensis var. mexicana, Cercis taxa from xerophytic habitats did not yield kaempferol glycosides in detectable amounts, as opposed to taxa from mesophytic habitats. The results obtained are consistent with proposals of merging C. reniformis into synonymy of C. occidentalis, as well as the recognition of two North American species, C. canadensis and C. occidentalis, and the recognition of the Asian C. gigantea.     

Chemistry and taxonomy of the cunoniaceae

The inclusion of the Cunoniaceae within a rosalean alliance is unquestioned, but its position in such an alliance is uncertain. In respect of proanthocyanidins, flavonols, ellagitannins and absence of iridoids the most closely similar taxa are Saxifragaceae-Saxifragoideae and Rosaceae-Rosoideae, but in their xerophytic, arborescent habit and present and past southern hemisphere distribution the Cunoniaceae are very different from either. In these (but not in chemical) respects an analogy can be found in the Proteaceae, and a detached position similar to that assigned to this family in Dahlgren's system seems appropriate for the Cunoniaceae.     

Integrative taxonomy,or iterative taxonomy?

The recently introduced term ‘integrative taxonomy’ refers to taxonomy that integrates all available data sources to frame species limits. We survey current taxonomic methods available to delimit species that integrate a variety of data, including molecular and morphological characters. A literature review of empirical studies using the term ‘integrative taxonomy’ assessed the kinds of data being used to frame species limits, and methods of integration. Almost all studies are qualitative and comparative – we are a long way from a repeatable, quantitative method of truly ‘integrative taxonomy’. The usual methods for integrating data in phylogenetic and population genetic paradigms are not appropriate for integrative taxonomy, either because of the diverse range of data used or because of the special challenges that arise when working at the species/population boundary. We identify two challenges that, if met, will facilitate the development of a more complete toolkit and a more robust research programme in integrative taxonomy using species tree approaches. We propose the term ‘iterative taxonomy’ for current practice that treats species boundaries as hypotheses to be tested with new evidence. A search for biological or evolutionary explanations for discordant evidence can be used to distinguish between competing species boundary hypotheses. We identify two recent empirical examples that use the process of iterative taxonomy.     

Impediments to taxonomy and users of taxonomy: accessibility and impact evaluation

There has been much discussion of the “taxonomic impediment”. This phrase confuses two kinds of impediment: an impediment to end users imposed by lack of reliable information; and impediments to taxonomy itself, which vary from insufficient funding to low citation rates of taxonomic monographs. In order to resolve both these types of impediment, taxonomy needs to be revitalized through funding and training taxonomists, as well as investing in taxonomic revisions and monographs rather than technological surrogates such as DNA barcoding.
© The Willi Hennig Society 2011.     

A specification of numerical taxonomy: Thermodynamical taxonomy

Thermodynamic taxonomy (ThT) is established from both a theoretical and pragmatical point of view. An application of thermodynamic taxonomy is given.