Magnetosome chain arrangement and stability in magnetotactic cocci

We have studied the disposition of chains of magnetosomes inside magnetotactic cocci with light and electron microscopy. Light microscopy of isolated cocci indicated that the chains of magnetosomes are disposed on opposite sides of the cell. Electron spectroscopic imaging of whole unprocessed bacteria, showed the magnetosome chains in the cells. Freeze-etching of the cell surface allowed the observation of the close association of the chain with the cell surface. During the replication process of the freeze-etching, the magnetosome chains remained attached to the replicas, which indicates that chains were very close to the cell surface before freezing. We provide evidence that the large area of the contact faces between magnetosomes in a chain may provide an extra mechanical stability that helps keep the magnetosomes in chains even after isolation from the bacteria. Comparison with pointed magnetosomes from different cocci present in the same samples showed that the maintenance of linear chains is more difficult to be achieved because of the geometry of the crystals.     

Envelope ultrastructure of uncultured naturally occurring magnetotactic cocci

Magnetotactic bacteria are microorganisms that respond to magnetic fields. We studied the surface ultrastructure of uncultured magnetotactic cocci collected from a marine environment by transmission electron microscopy using freeze-fracture and freeze-etching. All bacteria revealed a Gram-negative cell wall. Many bacteria possessed extensive capsular material and a S-layer formed by particles arranged with hexagonal symmetry. No indication of a metal precipitation on the surface of these microorganisms was observed. Numerous membrane vesicles were observed on the surface of the bacteria. Flagella were organized in bundles originated in a depression on the surface of the cells. Occasionally, a close association of the flagella with the magnetosomes that remained attached to the replica was observed. Capsules and S-layers are common structures in magnetotactic cocci from natural sediments and may be involved in inhibition of metal precipitation on the cell surface or indirectly influence magnetotaxis.     

Intracellular amorphous Ca-carbonate and magnetite biomineralization by a magnetotactic bacterium affiliated to the Alphaproteobacteria

Bacteria synthesize a wide range of intracellular submicrometer-sized inorganic precipitates of diverse chemical compositions and structures, called biominerals. Their occurrences, functions and ultrastructures are not yet fully described despite great advances in our knowledge of microbial diversity. Here, we report bacteria inhabiting the sediments and water column of the permanently stratified ferruginous Lake Pavin, that have the peculiarity to biomineralize both intracellular magnetic particles and calcium carbonate granules. Based on an ultrastructural characterization using transmission electron microscopy (TEM) and synchrotron-based scanning transmission X-ray microscopy (STXM), we showed that the calcium carbonate granules are amorphous and contained within membrane-delimited vesicles. Single-cell sorting, correlative fluorescent in situ hybridization (FISH), scanning electron microscopy (SEM) and molecular typing of populations inhabiting sediments affiliated these bacteria to a new genus of the Alphaproteobacteria. The partially assembled genome sequence of a representative isolate revealed an atypical structure of the magnetosome gene cluster while geochemical analyses indicate that calcium carbonate production is an active process that costs energy to the cell to maintain an environment suitable for their formation. This discovery further expands the diversity of organisms capable of intracellular Ca-carbonate biomineralization. If the role of such biomineralization is still unclear, cell behaviour suggests that it may participate to cell motility in aquatic habitats as magnetite biomineralization does.Subject terms: Phylogenetics, Biodiversity, Biogeochemistry, Water microbiology     

'Type' in morphology and phylogeny

Comparative morphologists, developmental biologists, as well as paleontologists, recognize the existence of 'types,' or 'Baupl?ne,' in nature, marked out by a certain 'sameness' of structure that prevails through all variation in shape and function. The 'sameness' that marks out 'types' is one of structural correspondence (topology and connectivity), which is believed to be causally rooted in ontogeny (developmental constraints). In an evolutionary context, the structural relations that mark out 'types' are explained as relations of homology. The use of concepts such as 'type' or 'Bauplan' has been criticized from a 'populational thinking' point of view as being incompatible with current evolutionary theory. The present article explores the contrasting viewpoints, and concludes that current evolutionary theory can accommodate the concept of a 'type' in the sense of a 'homeostatic property cluster natural kind.' The 'homeostatic property cluster natural kind' is a nonessentialistic concept that allows the kind to be historically delimited.     

Molecules,morphology, and phylogeny

A complicated, almost conflicting situation exists in contemporary biology, i.e., there are two scientific concepts in existence that solve some phylogenetic problems in a different way. These concepts are evolutionary morphology and molecular biology. Modern biology urgently needs these contradictions to be examined and removed.     

Characterization of a homogeneous taxonomic group of marine magnetotactic cocci within a low tide zone in the China Sea

Magnetotactic bacteria are a heterologous group of motile prokaryotes, ubiquitous in aquatic habitats and cosmopolitan in distribution. Here, we studied the diversity of magnetotactic bacteria in a seawater pond within an intertidal zone at Huiquan Bay in the China Sea. The pond is composed of a permanently submerged part and a low tide subregion. The magnetotactic bacteria collected from the permanently submerged part display diversity in morphology and taxonomy. In contrast, we found a virtually homogenous population of ovoid-coccoid magnetotactic bacteria in the low tide subregion of the pond. They were bilophotrichously flagellated and exhibited polar magnetotactic behaviour. Almost all cells contained two chains of magnetosomes composed of magnetite crystals. Intriguingly, the combination of restriction fragment length polymorphism analysis (RFLP) and sequencing of cloned 16S rDNA genes from the low tide subregion samples as well as fluorescence in situ hybridization (FISH) revealed the presence of a homogenous population. Moreover, phylogenetic analysis indicated that the Qingdao Huiquan low tide magnetotactic bacteria belong to a new genus affiliated with the α-subclass of Proteobacteria . This finding suggests the adaptation of the magnetotactic bacterial population to the marine tide.     

Stachybotrys from soil in China, identified by morphology and molecular phylogeny

Four Stachybotrys strains were isolated from soil in China. One was identified as a novel species by morphological characters of phialides and conidia. It produced cylindrical conidia with irregular striations and smooth, hyaline conidiophores. Phylogenetic analysis of three DNA markers, the internal transcribed spacer region of rDNA (ITS1–5.8S–ITS2), the translation elongation factor 1 alpha (tef1) and RNA polymerase II subunit (rpb2), supported the morphological results. The correlation between morphological and molecular-based clustering demonstrated that the studied isolate was a new species. Two other isolates were identified as S. cf. elegans.     

Angiosperm phylogeny,floral morphology and pollination ecology

Summary The different aspects of floral evolution—Angiosperm descent, floral morphology and pollination ecology—are discussed on the basis of the anthocorm theory of the angiospermous flower. Opposed ideas are critically compared and rejected mainly on account of several inconsistencies and flaws in old floral concepts. Floral evolution passed from a very early phase of dicliny, anemophily and aphananthy of the anthocorm to a phase of incipient entomophily soon associated with a partial sex reversal within the anthocorm. This second phase culminated in the monoclinous and primarily zoophilous flower types, whereas other floral types, more particularly the primarily anemophilous, diclinous flowers, are the direct descendants of the anthocorms of the initial phase. The second phase (to be differentiated in phase II and phase IIA) gave rise to at least two morphologically different flower types and two separate semophyletic lines of floral evolution (phase III and III A), in each of which the primary zoophily is almost always associated with the development of intrafloral semaphylls (petals) usually (at least in dicotyledonous groups) of androecial derivation. Early flower types were aphananthous and clearly anthocormoid (a condition still approximately represented by the so-called inflorescences of theSaururaceae) and assumed the morphology and other characteristics of a true flower by contractions, condensations, readjustments, oligomerisations, reductions and modifications (semaphylls!) leading to the great variety of adaptive floral patterns.

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Zusammenfassung Die drei Aspekte der Evolution der Blüte — die Abstammungsgeschichte der Angiospermen, Blütenmorphologie und Bestäubungsökologie — werden, ausgehend von der Anthokormtheorie der Angiospermenblüte, eingehend besprochen. Entgegengesetzte Meinungen werden kritisch verglichen und hauptsächlich auf Grund mehrerer Strittigkeiten und Fehler der älteren blütenmorphologischen Axiomen abgelehnt. Die Evolution der Blüte fing an mit einer frühen Phase mit Diklinie, Anemophilie und Aphananthie des Anthokorms und schritt allmählich weiter in die Richtung von beginnender Entomophilie, bald mit einer partiellen Geschlechtsinversion innerhalb des Anthokorms zusammengehend. Diese zweite Phase kulminierte in den monoklinen und primär zoophilen Blütentypen, während andere Blütengestalten, besonders die primär anemophilen und diklinen Angiospermenblüten, die unmittelbaren Abkömmlinge der Initialphase des Anthokorms sind. Aus der zweiten Phase (in den Phasen II und II A unterzuteilen) entwickelten sich wenigstens zwei morphologisch differenzierte Blütenformen und auch zwei geschiedene Blütensemophylesen (die Phasen III und III A), in jeder die primäre Zoophilie fast immer verbunden ist mit der Entwicklung von intrafloralen und (wenigstens bei Dikotylen) meistens von Staubblättern angeleiteten Semaphyllen (Kronblätter). Die frühen Blütentypen waren aphanantisch und anfänglich noch deutlich anthokormoid (ein Zustand der heutzutage noch von der sogenannten Infloreszenz der Saururaceen annähernd vertreten wird) und nahmen allmählich die entgültige Gestalt von einer der vielen adaptiven Blütentypen an durch eine Verkürzung der Blütenachse, und durch ein Zusammendrängen, Oligomerisation und (Semaphylle!) Abänderung der Blütenteile.

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Résumé Divers aspects de l'évolution de la fleur — à savoir la descendance des Angiospermes, la morphologie de la fleur, et l'écologie de la pollination — sont discutés à partir de l'hypothèse florale de l'anthocorme. Les opinions opposées, après d'être comparées et critisées, sont rejetées principalement à cause des inconséquences et inconsistances des anciens théorèmes morphologiques concernant l'origine de la fleur. L'évolution de la fleur commençait avec une phase d'antan de diclinie, anémophilie et aphananthie, et s'avançait graduellement dans la direction d'une phase entomophilique initiale, bientôt accompagnée d'un renversement de sexe partiel à l'intérieur de l'anthocorm. La deuxième phase culminait vers les types florals monoclines avec zoophilie primaire pendant que des autres types florals, particulièrement les fleurs diclines avec anémophilie primaire, sont les descendants directs du stade initiale de l'anthocorme. A partir de la phase II (se divisant aux stades II et II A), au moins deux types florals différents et aussi deux sémophylèses florals séparés (les phases III et III A) se développaient. Dans chacun de ses phases III et III A la zoophilie primaire est presque toujours accouplée avec l'origine des sémaphylles intrafloraux (pétales) le plus souvent (du moins chez les dicotylédones) dérivés des étamines. Les anciens types des fleurs ayant été aphanantique et au début encore nettement anthocormoïdes (quelle condition est maintenant toujours représentée par la soi-disante inflorescence des Saururacées), graduellement prenaient la forme d'une des plusieurs types floraux adaptifs par une contraction de l'axe florale et par l'entassement, l'oligomérisation et (sémaphylles!) la modification des pièces de la fleur.

     

New insights into Paleozoic charophyte morphology and phylogeny

Examination of Paleozoic charophyte fructifications using microscopy and high-resolution x-ray synchrotron microtomography has revealed that most of them have a utricle that forms a supplementary calcified cover around the gyrogonite. All Paleozoic families with utricles have been assigned to the Sycidiales. We consider the Moellerinaceae to occupy a central position in the phylogeny of the Charophyta. From these, one group of descendants constitutes the gyrogonites inside the utricles of the Sycidiales; a second descendant goup is thought to be the utricle-free ancestors of the Charales prior to inversion of spiralization and reduction in cell number. The Sycidiales have a multilayered wall and an internal vesicle, but their families are distinguished by diversity in orientation of external cells, complexity of the utricle wall, and in presence or absence of antheridia. The solidly packed structure of the utricle is believed to be an organ protecting the zygote against dessication. We interpret the morphological similarities between Paleozoic Sycidiales and Mesozoic Clavatoraceae, both with a utricle, as homoplasous rather than expressing a true phylogenetic relationship. We confirm that some umbellids might correspond to utricles of charophytes.     

Australopithecine taxonomy and phylogeny in light of facial morphology

The beginning of specialization characterizing the robust australopithecines is manifested in almost every aspect of the masticatory system of Australopithecus africanus. Of particular significance is the presence of two massive bony columns on both sides of the nasal aperture that support the anterior portion of the palate. These columns--the anterior pillars--are viewed as a structural response to the greater occlusal load stemming from the beginning stages of molarization of the premolars and exerted on the more anterior part of the dental arcade. In A. africanus the molarization process is, indeed, just in its initial phase, but the still considerable protrusion of the palate relative to the more peripheral facial frame increases the need for pillars. The anterior pillars and the advancement of the inferior part of the infraorbital plate (the origin of the masseter) play a major role in molding the facial topography of A. africanus. The absence of the pillars and the common position of the masseteric origin lead us to define the face of A. afarensis as the most primitive of the australopithecines and allow us to discriminate between its facial morphology and that of A. africanus. The presence of anterior pillars in the face of the latter places it clearly in the robust australopithecine clade.     

Evolution and phylogeny of gonad morphology in bony fishes

Gonad morphology at the gross anatomical or histological levelshas long been studied by fisheries biologists to identify annualreproductive cycles and length of breeding season, among othergoals. Comparative surveys across vertebrate taxa have not beendetailed enough, however, to describe fully the differencesand similarities among gonads of bony fishes and other vertebrates,and to use gonad morphology in phylogenetic systematic analyses.An emerging constant among vertebrates is the presence of agerminal epithelium composed of somatic and germ cells in bothmales and females. In females, the germinal epithelium linesthe ovarian lamellae. In males, arrangement of the germinalepithelium into compartments varies among osteichthyans: basaltaxa have an anastomosing tubular testis, whereas derived taxahave a lobular testis. The lobular testis is proposed as a synapomorphyof the Neoteleostei. The annual reproductive cycle is hypothesizedto be the source of morphological variation among testis types.Elongation of germinal compartments during early maturationmay result in a transition from anastomosing tubular to lobulartestes. In all male atherinomorphs surveyed, spermatogonia arerestricted to the distal termini of lobules rather than beingdistributed along the lobule; there is an epithelioid arrangementof Sertoli and germ cells rather than a germinal epithelium.Arrest of the maturation-regression phases is hypothesized tolead to formation of the atherinomorph testis. Atherinomorphsalso have a distinctive egg with fluid, rather than granular,yolk. Variation among germinal epithelia is interpreted in adeveloping phylogenetic framework to understand evolution ofgonad morphology and to propose gonad characters for phylogeneticanalyses.     

Floral morphology and phylogeny of the Disinae (Orchidaceae)

Previous classification of the Disinae has been based almost entirely on floral morphological data. These data are critically assessed by various methods to determine to what extent they support a classification resolved to sectional level. The variation in the characters relative to the sections and genera is mapped, homologies are established by careful morphological observation and ontogenetic studies, and finally hypotheses of homology are tested by congruence in several cladistic analyseS. It is found that although floral morphology allows the recognition of some groups, for others the results are ambiguouS. Floral morphological data are clearly inadequate to establish the taxonomy of the Disinae on a sound footing.     

Pollen morphology and phylogeny of the Alyxieae (Apocynaceae)

The pollen of the tribe Alyxieae, including Alyxia , Chilocarpus , Condylocarpon , Lepinia , Lepiniopsis , Plectaneia and Pteralyxia , has been studied with light, scanning electron and transmission electron microscopy. It is characterised by relatively large, irregularly disposed and - unequal-sized pores. 2-porate grains are most common in the Alyxieae, and occur in all genera except for Condylocarpon . 1-, 3-, 4- and 5-porate pollen grains are less common. The orientation of the polar axis and the equatorial plane could not be determined in any of the genera. Within the Alyxieae, Chilocarpus and Plectaneia are the nearest to other Apocynaceae, showing an essentially similar exine ultrastructure. Alyxia , Lepinia , Lepiniopsis and Pteralyxia make up a derived group, characterised by large pollen grain size and a remarkable nexine structure. Pollen of Lepinia and Lepiniopsis might be derived on the basis of their fossulate-verrucate ornamentation. Condylocarpon pollen shows a deviating set of pollen features (tetrads, inaperturate, reduced exine) that suggest it to be neotenic. Pollen morphology supports preliminary results of cladistic analyses of chloroplast data, in which the tribe is a monophyletic group nested in a 3-colporate environment, Chilocarpus and Condylocarpon are sisters at the base of the tree, Plectaneia is sister to a clade made up by Alyxia , Pteralyxia , Lepinia and Lepiniopsis , of which Lepinia and Lepiniopsis are the most derived.     

Comparative morphology and molecular phylogeny of aplanochytrids (Labyrinthulomycota)

Aplanochytrids comprise one of three major subgroups within the Labyrinthulomycota. We have surveyed the diversity of aplanochytrids and have discovered that most isolates are difficult to identify to species because of character plasticity and ambiguity. Ten isolates were studied using molecular phylogenies based on small subunit ribosomal gene sequences (SSU rDNA) and morphological characters derived from light microscopy, SEM and TEM (e.g., colony size, colony shape, colony pattern, agar penetration, cell shape, cell surface patterns, cell inclusion characteristics and ectoplasmic net morphology). Of these isolates, we could positively identify two of them to species, namely Aplanochytrium yorkensis (Perkins, 1973) Leander and Porter, 2000 and A. minuta (Watson and Raper, 1957) Leander and Porter, 2000. We used standardized conditions for growing aplanochytrid isolates in order to minimize environmentally induced phenotypic plasticity in our comparative studies of morphology. By mapping the morphological characters listed above onto a conservative phylogenetic topology derived from SSU rDNA sequences, we were able to identify several synapomorphies (e.g., gross colony characteristics and cell surface patterns) that serve as valuable taxonomic characters for the identification of species and specific clades of aplanochytrids.     

Comparative genomic analysis of magnetotactic bacteria from the Deltaproteobacteria provides new insights into magnetite and greigite magnetosome genes required for magnetotaxis

Magnetotactic bacteria (MTB) represent a group of diverse motile prokaryotes that biomineralize magnetosomes, the organelles responsible for magnetotaxis. Magnetosomes consist of intracellular, membrane‐bounded, tens‐of‐nanometre‐sized crystals of the magnetic minerals magnetite (Fe₃O₄) or greigite (Fe₃S₄) and are usually organized as a chain within the cell acting like a compass needle. Most information regarding the biomineralization processes involved in magnetosome formation comes from studies involving Alphaproteobacteria species which biomineralize cuboctahedral and elongated prismatic crystals of magnetite. Many magnetosome genes, the mam genes, identified in these organisms are conserved in all known MTB. Here we present a comparative genomic analysis of magnetotactic Deltaproteobacteria that synthesize bullet‐shaped crystals of magnetite and/or greigite. We show that in addition to mam genes, there is a conserved set of genes, designated mad genes, specific to the magnetotactic Deltaproteobacteria, some also being present in Candidatus Magnetobacterium bavaricum of the Nitrospirae phylum, but absent in the magnetotactic Alphaproteobacteria. Our results suggest that the number of genes associated with magnetotaxis in magnetotactic Deltaproteobacteria is larger than previously thought. We also demonstrate that the minimum set of mam genes necessary for magnetosome formation in Magnetospirillum is also conserved in magnetite‐producing, magnetotactic Deltaproteobacteria. Some putative novel functions of mad genes are discussed.     

A web-database of mammalian morphology and a reanalysis of placental phylogeny

Background  

Recent publications concerning the interordinal phylogeny of placental mammals have converged on a common signal, consisting of four major radiations with some ambiguity regarding the placental root. The DNA data with which these relationships have been reconstructed are easily accessible from public databases; access to morphological characters is much more difficult. Here, I present a graphical web-database of morphological characters focusing on placental mammals, in tandem with a combined-data phylogenetic analysis of placental mammal phylogeny.     

Sperm package morphology in scorpions and its relation to phylogeny

Sperm packages are widespread in the order Scorpiones, but absent in the family Buthidae. The morphology of sperm packages is diverse and apparently has phylogenetic information. The objectives of this work were to show diversity of sperm packages and to provide a quantitative basis for using sperm packages’ morphology as a taxonomic character. For this, we conducted a morphological analysis and comparison of the different sperm packages of species of the family Bothriuridae. The seminal content from males of species of Bothriuridae was studied. Specimens from Iuridae, Buthidae, Euscorpiidae, Liochelidae, Scorpionidae, Vaejovidae, Chaerilidae, and Chactidae were used for comparison. Digital images of sperm packages were measured and statistically analysed based on the following variables: total length, head width, head–body angle, total area, and head length. Pairs of variables were also contrasted, and all the variables were correlated with the current phylogenetic hypothesis for Bothriuridae. High morphological diversity and variability in measures was observed. In general, measurements were similar within each genus, but differed amongst genera. Cane‐like sperm packages are very common in species of the family Bothriuridae. Species from Bothriurus show a wide range of sperm package shapes, some of them shared with Timogenes and Vachonia species, supporting the idea of nonmonophyly of the genus. Many species showed sperm package dimorphism inside a single male. Some of the analysed features fit well with the phylogenetic hypothesis in Bothriuridae, and the general package shape shows high correlation with scorpion phylogeny in other families. Bent and round packages are the most common amongst the different families. Sperm packages are not developed in Chaerilidae, as in Buthidae. This is the first morphological and comparative analysis of sperm packages in scorpions, and reveals much greater diversity in this trait than previously known. Our results reinforce the idea that the study of morphology of sperm packages would contribute characters for scorpion phylogeny at different levels. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 161 , 463–483.     

DNA phylogeny, morphology and pathogenicity of Botryosphaeria species on grapevines

Several species of Botr yosphaeria are known to occur on grapevines, causing a wide range of disorders including bud mortality, dieback, brown wood streaking and bunch rot. In this study the 11 Botryosphaeria spp. associated with grapevines growing in various parts of the world, but primarily in South Africa, are distinguished based on morphology, DNA sequences (ITS-1, 5.8S, ITS-2 and EF1-α) and pathological data. Botryosphaeria australis, B. lutea, B. obtusa, B. parva, B. rhodina and a Diplodia sp. are confirmed from grapevines in South Africa, while Diplodia porosum, Fusicoccum viticlavatum and F. vitifusiforme are described as new. Although isolates of B. dothidea and B. stevensii are confirmed from grapevines in Portugal, neither of these species occurred in South Africa, nor were any isolates of B. ribis confirmed from grapevines. All grapevine isolates from Portugal, formerly presumed to be B. ribis, are identified as B. parva based on their EF1-α equence data. From artificial inoculations on grapevine shoots, we conclude that B. australis, B. parva, B. ribis and B. stevensii are more virulent than the other species studied. The Diplodia sp. collected from grapevine canes is morphologically similar but phylogenetically distinct from D. sarmentorum. Diplodia sarmentorum is confirmed as anamorph of Otthia spiraeae, the type species of the genus Otthia (Botryosphaeriaceae). A culture identified as O. spiraeae clustered within Botryosphaeria and thus is regarded as probable synonym. These findings confirm earlier suggestions that the generic concept of Botryosphaeria should be expanded to include genera with septate ascospores and Diplodia anamorphs.     

Taxonomy,morphology, masticatory function and phylogeny of heterodontosaurid dinosaurs

Heterodontosaurids comprise an important early radiation of small-bodied herbivores that persisted for approximately 100 My from Late Triassic to Early Cretaceous time. Review of available fossils unequivocally establishes Echinodon as a very small-bodied, late-surviving northern heterodontosaurid similar to the other northern genera Fruitadens and Tianyulong. Tianyulong from northern China has unusual skeletal proportions, including a relatively large skull, short forelimb, and long manual digit II. The southern African heterodontosaurid genus Lycorhinus is established as valid, and a new taxon from the same formation is named Pegomastax africanusgen. n., sp. n. Tooth replacement and tooth-to-tooth wear is more common than previously thought among heterodontosaurids, and in Heterodontosaurus the angle of tooth-to-tooth shear is shown to increase markedly during maturation. Long-axis rotation of the lower jaw during occlusion is identified here as the most likely functional mechanism underlying marked tooth wear in mature specimens of Heterodontosaurus. Extensive tooth wear and other evidence suggests that all heterodontosaurids were predominantly or exclusively herbivores. Basal genera such as Echinodon, Fruitadens and Tianyulong with primitive, subtriangular crowns currently are known only from northern landmasses. All other genera except the enigmatic Pisanosaurus have deeper crown proportions and currently are known only from southern landmasses.