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Phyla
Kinds of Phyla Selected AbstractsBook Review: On the Origin of Phyla.BIOESSAYS, Issue 7 2005Jeffrey S. Levinton No abstract is available for this article. [source] Tobacco blue mould disease caused by Peronospora hyoscyami f. sp. tabacinaMOLECULAR PLANT PATHOLOGY, Issue 1 2010ORLANDO BORRÁS-HIDALGO SUMMARY Blue mould [Peronospora hyoscyami f. sp. tabacina (Adam) Skalicky 1964] is one of the most important foliar diseases of tobacco that causes significant losses in the Americas, south-eastern Europe and the Middle East. This review summarizes the current knowledge of the mechanisms employed by this oomycete pathogen to colonize its host, with emphasis on molecular aspects of pathogenicity. In addition, key biochemical and molecular mechanisms involved in tobacco resistance to blue mould are discussed. Taxonomy: Kingdom: Chromista (Straminipila); Phylum: Heterokontophyta; Class: Oomycete; Order: Peronosporales; Family: Peronosporaceae; Genus: Peronospora; Species: Peronospora hyoscyami f. sp. tabacina. Disease symptoms: The pathogen typically causes localized lesions on tobacco leaves that appear as single, or groups of, yellow spots that often coalesce to form light-brown necrotic areas. Some of the leaves exhibit grey to bluish downy mould on their lower surfaces. Diseased leaves can become twisted, such that the lower surfaces turn upwards. In such cases, the bluish colour of the diseased plants becomes quite conspicuous, especially under moist conditions when sporulation is abundant. Hence the name of the disease: tobacco blue mould. Infection process: The pathogen develops haustoria within plant cells that are thought to establish the transfer of nutrients from the host cell, and may also act in the delivery of effector proteins during infection. Resistance: Several defence responses have been reported to occur in the Nicotiana tabacum,P. hyoscyami f. sp. tabacina interaction. These include the induction of pathogenesis-related genes, and a correlated increase in the activities of typical pathogenesis-related proteins, such as peroxidases, chitinases, ,-1,3-glucanases and lipoxygenases. Systemic acquired resistance is one of the best characterized tobacco defence responses activated on pathogen infection. [source] Identification of Lmo1 as part of a Hox-dependent regulatory network for hindbrain patterningDEVELOPMENTAL DYNAMICS, Issue 9 2007Christelle Matis Abstract The embryonic functions of Hox proteins have been extensively investigated in several animal phyla. These transcription factors act as selectors of developmental programmes, to govern the morphogenesis of multiple structures and organs. However, despite the variety of morphogenetic processes Hox proteins are involved in, only a limited set of their target genes has been identified so far. To find additional targets, we used a strategy based upon the simultaneous overexpression of Hoxa2 and its cofactors Pbx1 and Prep in a cellular model. Among genes whose expression was upregulated, we identified LMO1, which codes for an intertwining LIM-only factor involved in protein,DNA oligomeric complexes. By analysing its expression in Hox knockout mice, we show that Lmo1 is differentially regulated by Hoxa2 and Hoxb2, in specific columns of hindbrain neuronal progenitors. These results suggest that Lmo1 takes part in a Hox paralogue 2,dependent network regulating anteroposterior and dorsoventral hindbrain patterning. Developmental Dynamics 236:2675,2684, 2007. © 2007 Wiley-Liss, Inc. [source] A new dimension in combining data?ACTA ZOOLOGICA, Issue 1 2010The use of morphology, phylogenomic data in metazoan systematics Abstract Giribet, G. 2010. A new dimension in combining data? The use of morphology and phylogenomic data in metazoan systematics. ,Acta Zoologica (Stockholm) 91: 11,19 Animal phylogenies have been traditionally inferred by using the character state information derived from the observation of a diverse array of morphological and anatomical features, but the incorporation of molecular data into the toolkit of phylogenetic characters has shifted drastically the way researchers infer phylogenies. A main reason for this is the ease at which molecular data can be obtained, compared to, e.g., traditional histological and microscopical techniques. Researchers now routinely use genomic data for reconstructing relationships among animal phyla (using whole genomes or Expressed Sequence Tags) but the amount of morphological data available to study the same phylogenetic patterns has not grown accordingly. Given the disparity between the amounts of molecular and morphological data, some authors have questioned entire morphological programs. In this review I discuss issues related to the combinability of genomic and morphological data, the informativeness of each set of characters, and conclude with a discussion of how morphology could be made scalable by utilizing new techniques that allow for non-intrusive examination of large amounts of preserved museum specimens. Morphology should therefore remains a strong field in evolutionary and comparative biology, as it continues to provide information for inferring phylogenetic patterns, is an important complement for the patterns derived from the molecular data, and it is the common nexus that allows studying fossil taxa with large data sets of molecular data. [source] Some aspects of spiralian developmentACTA ZOOLOGICA, Issue 1 2010Claus Nielsen Abstract Nielsen, C. 2010. Some aspects of spiralian development. ,Acta Zoologica (Stockholm) 91: 20,28 Spiralian development is not only a characteristic early cleavage pattern, with shifting orientations of the cleavage planes, but also highly conserved cell lineages, where the origin of several organs can be traced back to identifiable cells in the lineage. These patterns are well documented in annelids, molluscs, nemertines, and platyhelminths and are considered ancestral of a bilaterian clade including these phyla. Spiral cleavage has not been documented in ecdysozoans, and no trace of the spiral development pattern is seen in phoronids and brachiopods. Origin of the spatial organization in spiralian embryos is puzzling, but much of the information appears to be encoded in the developing oocyte. Fertilization and "pseudofertilization" apparently provides the information defining the secondary, anterior-posterior body axis in many species. The central nervous system consists of three components: an apical organ, derived from the apical blastomeres 1a111 -1d111, which degenerates before or at metamorphosis; the cerebral ganglia derived from other blastomeres of the first micromere quartet and retained in the adult as a preoral part of the brain; and the originally circumblastoporal nerve cord, which has become differentiated into a perioral part of the brain, the paired or secondarily fused ventral nerve cords, and a small perianal nerve ring. [source] The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genesENVIRONMENTAL MICROBIOLOGY, Issue 5 2010David L. Kirchman Summary Bacterial communities in the surface layer of the oceans consist of a few abundant phylotypes and many rare ones, most with unknown ecological functions and unclear roles in biogeochemical processes. To test hypotheses about relationships between abundant and rare phylotypes, we examined bacterial communities in the western Arctic Ocean using pyrosequence data of the V6 region of the 16S rRNA gene. Samples were collected from various locations in the Chukchi Sea, the Beaufort Sea and Franklin Bay in summer and winter. We found that bacterial communities differed between summer and winter at a few locations, but overall there was no significant difference between the two seasons in spite of large differences in biogeochemical properties. The sequence data suggested that abundant phylotypes remained abundant while rare phylotypes remained rare between the two seasons and among the Arctic regions examined here, arguing against the ,seed bank' hypothesis. Phylotype richness was calculated for various bacterial groups defined by sequence similarity or by phylogeny (phyla and proteobacterial classes). Abundant bacterial groups had higher within-group diversity than rare groups, suggesting that the ecological success of a bacterial lineage depends on diversity rather than on the dominance of a few phylotypes. In these Arctic waters, in spite of dramatic variation in several biogeochemical properties, bacterial community structure was remarkably stable over time and among regions, and any variation was due to the abundant phylotypes rather than rare ones. [source] Gradients of coastal fish farm effluents and their effect on coral reef microbesENVIRONMENTAL MICROBIOLOGY, Issue 9 2008Melissa Garren Summary Coastal milkfish (Chanos chanos) farming may be a source of organic matter enrichment for coral reefs in Bolinao, Republic of the Philippines. Interactions among microbial communities associated with the water column, corals and milkfish feces can provide insight into the ecosystem's response to enrichment. Samples were collected at sites along a transect that extended from suspended milkfish pens into the coral reef. Water was characterized by steep gradients in the concentrations of dissolved organic carbon (70,160 ,M), total dissolved nitrogen (7,40 ,M), chlorophyll a (0.25,10 ,g l,1), particulate matter (106,832 ,g l,1), bacteria (5 × 105,1 × 106 cells ml,1) and viruses (1,7 × 107 ml,1) that correlated with distance from the fish cages. Particle-attached bacteria, which were observed by scanning laser confocal microscopy, increased across the gradient from < 0.1% to 5.6% of total bacteria at the fish pens. Analyses of 16S rRNA genes by denaturing gradient gel electrophoresis and environmental clone libraries revealed distinct microbial communities for each sample type. Coral libraries had the greatest number of phyla represented (range: 6,8) while fish feces contained the lowest number (3). Coral libraries also had the greatest number of ,novel' sequences (defined as < 93% similar to any sequence in the NCBI nt database; 29% compared with 3% and 5% in the feces and seawater libraries respectively). Despite the differences in microbial community composition, some 16S rRNA sequences co-occurred across sample types including Acinetobacter sp. and Ralstonia sp. Such patterns raise the question of whether bacteria might be transported from the fish pens to corals or if microenvironments at the fish pens and on the corals select for the same phylotypes. Understanding the underlying mechanisms of effluent,coral interactions will help predict the ability of coral reef ecosystems to resist and rebound from organic matter enrichment. [source] Active bacterial community structure along vertical redox gradients in Baltic Sea sedimentENVIRONMENTAL MICROBIOLOGY, Issue 8 2008Anna Edlund Summary Community structures of active bacterial populations were investigated along a vertical redox profile in coastal Baltic Sea sediments by terminal-restriction fragment length polymorphism (T-RFLP) and clone library analysis. According to correspondence analysis of T-RFLP results and sequencing of cloned 16S rRNA genes, the microbial community structures at three redox depths (179, ,64 and ,337 mV) differed significantly. The bacterial communities in the community DNA differed from those in bromodeoxyuridine (BrdU)-labelled DNA, indicating that the growing members of the community that incorporated BrdU were not necessarily the most dominant members. The structures of the actively growing bacterial communities were most strongly correlated to organic carbon followed by total nitrogen and redox potentials. Bacterial identification by sequencing of 16S rRNA genes from clones of BrdU-labelled DNA and DNA from reverse transcription polymerase chain reaction showed that bacterial taxa involved in nitrogen and sulfur cycling were metabolically active along the redox profiles. Several sequences had low similarities to previously detected sequences, indicating that novel lineages of bacteria are present in Baltic Sea sediments. Also, a high number of different 16S rRNA gene sequences representing different phyla were detected at all sampling depths. [source] Proteorhodopsin photosystem gene clusters exhibit co-evolutionary trends and shared ancestry among diverse marine microbial phylaENVIRONMENTAL MICROBIOLOGY, Issue 4 2007Jay McCarren Summary Since the recent discovery of retinylidene proteins in marine bacteria (proteorhodopsins), the estimated abundance and diversity of this gene family has expanded rapidly. To explore proteorhodopsin photosystem evolutionary and distributional trends, we identified and compared 16 different proteorhodopsin-containing genome fragments recovered from naturally occurring bacterioplankton populations. In addition to finding several deep-branching proteorhodopsin sequences, proteorhodopsins were found in novel taxonomic contexts, including a betaproteobacterium and a planctomycete. Approximately one-third of the proteorhodopsin-containing genome fragments analysed, as well as a number of recently reported marine bacterial whole genome sequences, contained a linked set of genes required for biosynthesis of the rhodopsin chromophore, retinal. Phylogenetic analyses of the retinal biosynthetic genes suggested their co-evolution and probable coordinated lateral gene transfer into disparate lineages, including Euryarchaeota, Planctomycetales, and three different proteobacterial lineages. The lateral transfer and retention of genes required to assemble a functional proteorhodopsin photosystem appears to be a coordinated and relatively frequent evolutionary event. Strong selection pressure apparently acts to preserve these light-dependent photosystems in diverse marine microbial lineages. [source] Microbial community dynamics in a humic lake: differential persistence of common freshwater phylotypesENVIRONMENTAL MICROBIOLOGY, Issue 6 2006Ryan J. Newton Summary In an effort to better understand the factors contributing to patterns in freshwater bacterioplankton community composition and diversity, we coupled automated ribosomal intergenic spacer analysis (ARISA) to analysis of 16S ribosomal RNA (rRNA) gene sequences to follow the persistence patterns of 46 individual phylotypes over 3 years in Crystal Bog Lake. Additionally, we sought to identify linkages between the observed phylotype variations and known chemical and biological drivers. Sequencing of 16S rRNA genes obtained from the water column indicated the presence of phylotypes associated with the Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, TM7 and Verrucomicrobia phyla, as well as phylotypes with unknown affiliation. Employment of the 16S rRNA gene/ARISA method revealed that specific phylotypes varied independently of the entire bacterial community dynamics. Actinobacteria, which were present on greater than 95% of sampling dates, did not share the large temporal variability of the other identified phyla. Examination of phylotype relative abundance patterns (inferred using ARISA fragment relative fluorescence) revealed a strong correlation between the dominant phytoplankton succession and the relative abundance patterns of the majority of individual phylotypes. Further analysis revealed covariation among unique phylotypes, which formed several distinct bacterial assemblages correlated with particular phytoplankton communities. These data indicate the existence of unique persistence patterns for different common freshwater phylotypes, which may be linked to the presence of dominant phytoplankton species. [source] Niche heterogeneity determines bacterial community structure in the termite gut (Reticulitermes santonensis)ENVIRONMENTAL MICROBIOLOGY, Issue 7 2005Hong Yang Summary Differences in microenvironment and interactions of microorganisms within and across habitat boundaries should influence structure and diversity of the microbial communities within an ecosystem. We tested this hypothesis using the well characterized gut tract of the European subterranean termite Reticulitermes santonensis as a model. By cloning and sequencing analysis and molecular fingerprinting (terminal restriction fragment length polymorphism), we characterized the bacterial microbiota in the major intestinal habitats , the midgut, the wall of the hindgut paunch, the hindgut fluid and the intestinal protozoa. The bacterial community was very diverse (> 200 ribotypes) and comprised representatives of several phyla, including Firmicutes (mainly clostridia, streptococci and Mycoplasmatales -related clones), Bacteroidetes, Spirochaetes and a number of Proteobacteria, all of which were unevenly distributed among the four habitats. The largest group of clones fell into the so-called Termite group 1 (TG-1) phylum, which has no cultivated representatives. The majority of the TG-1 clones were associated with the protozoa and formed two phylogenetically distinct clusters, which consisted exclusively of clones previously retrieved from the gut of this and other Reticulitermes species. Also the other clones represented lineages of microorganisms that were exclusively recovered from the intestinal tract of termites. The termite specificity of these lineages was underscored by the finding that the closest relatives of the bacterial clones obtained from R. santonensis were usually derived also from the most closely related termites. Overall, differences in diversity between the different gut habitats and the uneven distribution of individual phylotypes support conclusively that niche heterogeneity is a strong determinant of the structure and spatial organization of the microbial community in the termite gut. [source] Effect of humic material on the bacterioplankton community composition in boreal lakes and mesocosmsENVIRONMENTAL MICROBIOLOGY, Issue 5 2005Kaisa Haukka Summary The bacterioplankton community composition in two Finnish forest lakes with different content of humic substances was studied by denaturing gradient gel electrophoresis (DGGE) and sequencing of the major bands. The same dominant bacterial phylotypes were detected in the bacterioplankton communities of clear-water Lake Ahvenlammi and humic Lake Sammalisto. For 4 years, in every water layer, Actinobacteria was the dominant and Verrucomicrobia the second most common phylum. In the hypolimnion, other dominant phyla were also found. We set up a mesocosm experiment to assess the effect of a sudden load of allochthonous humus extract to the bacterioplankton community composition. Changes in the bacterial communities were followed in four control and four humus extract-added mesocosms for 50 days. In the humic mesocosms the phylotypes of allochthonous Proteobacteria arriving with the humus extract were initially prevalent but disappeared during the first weeks. After this the Actinobacteria -dominated communities resembled the bacterioplankton communities of the control mesocosms and Lake Ahvenlammi. Towards the end of the experiment the community patterns in all the mesocosms started to change slightly because of erratic occurrence of new proteobacterial phylotypes. Thus the effects of a sudden load of allochthonous humic material and bacteria to the bacterioplankton community composition were transient. [source] The effect of cleaning and disinfecting the sampling well on the microbial communities of deep subsurface water samplesENVIRONMENTAL MICROBIOLOGY, Issue 1 2005Odile Basso Summary Our knowledge of the microbial characteristics of deep subsurface waters is currently very limited, mainly because of the methods used to collect representative microbial samples from such environments. In order to improve this procedure, a protocol designed to remove the unspecific, contaminant biofilm present on the walls of an approximately 800 m deep well is proposed. This procedure included extensive purges of the well, a mechanical cleaning of its wall, and three successive chlorine injections to disinfect the whole line before sampling. Total bacterial counts in water samples decreased from 2.5 × 105 to 1.0 × 104 per millilitre during the cleaning procedure. Culture experiments showed that the first samples were dominated by sulfate-reducers and heterotrophs, whereas the final sample was dominated by oligotrophic and hydrogenotrophic bacteria. Community structures established on the diversity of the 16S rRNA genes and data analysis revealed that the water sample collected, after a purge without removal of the biofilm, was characterized by numerous phyla which are not representative of the deep subsurface water. On the other hand, several bacterial phyla were only detected after the full cleaning of the well, and were considered as important components of the subsurface ecosystem which would have been missed in the absence of well cleaning. [source] In situ studies of the phylogeny and physiology of filamentous bacteria with attached growthENVIRONMENTAL MICROBIOLOGY, Issue 7 2002Trine Rolighed Thomsen Summary Among the filamentous bacteria occasionally causing bulking problems in activated sludge treatment plants, three morphotypes with attached microbial growth are common, Eikelboom Type 0041, Type 1851 and Type 1701. A better knowledge of the phylogeny and physiology of these filamentous bacteria is necessary in order to develop control strategies for bulking. In this study we have used a combination of fluorescence in situ hybridization (FISH) and microautoradiography (MAR) to investigate the identity and in situ physiology of the Type 0041-morphotype and its attached bacteria in two wastewater treatment plants. Identification and enumeration of Type 0041 using group-specific 16S rRNA-targeted FISH probes revealed that approximately 15% of the filaments hybridized with a gene probe specific for the TM7 group, a recently recognized major lineage in the bacterial domain. All other filaments morphologically identified as Type 0041 only hybridized to the general bacterial EUB338-probe, indicating that they probably do not belong to commonly isolated bacterial phyla such as the Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes, for which group-specific probes were used. The phylogenetic heterogeneity of Type 0041 again highlights the inadequacy of a morphology-based classification system. Like the filaments, most of the attached microbial cells were not identified beyond their affiliation to the Bacteria using the group-specific FISH probes. However, several different bacterial phyla were represented in the identified fraction suggesting that the attached microorganisms are phylogenetically diverse. The study of the in situ physiology of Type 0041 using MAR-FISH revealed that both the filaments and the attached bacteria on Type 0041 were versatile in the use of organic substrates and electron acceptors. It was observed that all Type 0041 could consume glucose, but none of the filaments were able to consume acetate under any conditions tested, in contrast to some of the attached bacteria. No significant physiological differences were found between TM7,positive and TM7,negative Type 0041 filaments, and only minor differences were observed between the two treatment plants tested. These are the first data on the physiology of the almost entirely uncharacterized TM7 phylum and show that TM7 filamentous bacteria can uptake carbon substrates under aerobic and anaerobic conditions. [source] Odorant specificity of three oscillations and the DC signal in the turtle olfactory bulbEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 3 2003Ying-Wan Lam Abstract The odour-induced population response in the in vivo turtle (Terepene sp.) olfactory bulb consists of three oscillatory components (rostral, middle and caudal) that ride on top of a DC signal. In an initial step to determine the functional role of these four signals, we compared the signals elicited by different odorants. Most experiments compared isoamyl acetate and cineole, odorants which have very different maps of input to olfactory bulb glomeruli in the turtle and a different perceptual quality for humans. We found substantial differences in the response to the two odours in the rise-time of the DC signal and in the latency of the middle oscillation. The rate of rise for cineole was twice as fast as that for isoamyl acetate. Similarly, the latency for the middle oscillation was about twice as long for isoamyl acetate as it was for cineole. On the other hand, a number of characteristics of the signals were not substantially different for the two odorants. These included the latency of the rostral and caudal oscillation, the frequency and envelope of all three oscillations and their locations and spatial extents. A smaller number of experiments were carried out with hexanone and hexanal; the oscillations elicited by these odorants did not appear to be different from those elicited by isoamyl acetate and cineole. Qualitative differences between the oscillations in the turtle and those in two invertebrate phyla suggest that different odour processing strategies may be used. [source] THE IMPORTANCE OF PREADAPTED GENOMES IN THE ORIGIN OF THE ANIMAL BODYPLANS AND THE CAMBRIAN EXPLOSIONEVOLUTION, Issue 5 2010Charles R. Marshall The genomes of taxa whose stem lineages branched early in metazoan history, and of allied protistan groups, provide a tantalizing outline of the morphological and genomic changes that accompanied the origin and early diversifications of animals. Genome comparisons show that the early clades increasingly contain genes that mediate development of complex features only seen in later metazoan branches. Peak additions of protein-coding regulatory genes occurred deep in the metazoan tree, evidently within stem groups of metazoans and eumetazoans. However, the bodyplans of these early-branching clades are relatively simple. The existence of major elements of the bilaterian developmental toolkit in these simpler organisms implies that these components evolved for functions other than the production of complex morphology, preadapting the genome for the morphological differentiation that occurred higher in metazoan phylogeny. Stem lineages of the bilaterian phyla apparently required few additional genes beyond their diploblastic ancestors. As disparate bodyplans appeared and diversified during the Cambrian explosion, increasing complexity was accommodated largely through changes in cis -regulatory networks, accompanied by some additional gene novelties. Subsequently, protein-coding genic richness appears to have essentially plateaued. Some genomic evidence suggests that similar stages of genomic evolution may have accompanied the rise of land plants. [source] TESTS OF SEX ALLOCATION THEORY IN SIMULTANEOUSLY HERMAPHRODITIC ANIMALSEVOLUTION, Issue 6 2009Lukas Schärer Sex allocation is a crucial life-history parameter in all sexual organisms. Over the last decades a body of evolutionary theory, sex allocation theory, was developed, which has yielded capital insight into the evolution of optimal sex allocation patterns and adaptive evolution in general. Most empirical work, however, has focused on species with separate sexes. Here I review sex allocation theory for simultaneous hermaphrodites and summarize over 50 empirical studies, which have aimed at evaluating this theory in a diversity of simultaneous hermaphrodites spanning nine animal phyla. These studies have yielded considerable qualitative support for several predictions of sex allocation theory, such as a female-biased sex allocation when the number of mates is limited, and a shift toward a more male-biased sex allocation with increasing numbers of mates. In contrast, many fundamental assumptions, such as the trade-off between male and female allocation, and numerous predictions, such as brooding limiting the returns from female allocation, are still poorly supported. Measuring sex allocation in simultaneously hermaphroditic animals remains experimentally demanding, which renders evaluation of more quantitative predictions a challenging task. I identify the main questions that need to be addressed and point to promising avenues for future research. [source] Evolution of astacin-like metalloproteases in animals and their function in developmentEVOLUTION AND DEVELOPMENT, Issue 2 2006Frank Möhrlen SUMMARY Astacin-like metalloproteases are ubiquitous in the animal kingdom but their phylogenetic relationships and ancient functions within the Metazoa are unclear. We have cloned and characterized four astacin-like cDNAs from the marine hydroid Hydractinia echinata and performed a database search for related genes in the draft genome sequence of the sea anemone Nematostella vectensis. These sequences and those of higher animals' astacins were subjected to phylogenetic analysis revealing five clusters within the Eumetazoa. The bone morphogenetic protein-1/tolloid-like astacins were represented in all eumetazoan phyla studied. The meprins were only found in vertebrates and cnidarians. Two clusters were taxon-specific, and one cluster represented astacins, which probably evolved after the split of the Cnidaria. Interestingly, grouping of astacins according to the protease catalytic domain alone resulted in clusters of proteins with similar overall domain architecture. The Hydractinia astacins were expressed in distinct cells during metamorphosis and some also during wound healing. Previously characterized cnidarian astacins also act during development. Based on our phylogeny, however, we propose that the developmental function of most of them is not homologous to the developmental function assigned to higher animals' astacins. [source] Thyroid hormones determine developmental mode in sand dollars (Echinodermata: Echinoidea)EVOLUTION AND DEVELOPMENT, Issue 6 2004Andreas Heyland Summary Evolutionary transitions in larval nutritional mode have occurred on numerous occasions independently in many marine invertebrate phyla. Although the evolutionary transition from feeding to nonfeeding development has received considerable attention through both experimental and theoretical studies, mechanisms underlying the change in life history remain poorly understood. Facultative feeding larvae (larvae that can feed but will complete metamorphosis without food) presumably represent an intermediate developmental mode between obligate feeding and nonfeeding. Here we show that an obligatorily feeding larva can be transformed into a facultative feeding larva when exposed to the thyroid hormone thyroxine. We report that larvae of the subtropical sand dollar Leodia sexiesperforata (Echinodermata: Echinoidea) completed metamorphosis without exogenous food when treated with thyroxine, whereas the starved controls (no thyroxine added) did not. Leodia sexiesperforata juveniles from the thyroxine treatment were viable after metamorphosis but were significantly smaller and contained less energy than sibling juveniles reared with exogenous food. In a second starvation experiment, using an L. sexiesperforata female whose eggs were substantially larger than in the first experiment (202±5 vs. 187±5 ,m), a small percentage of starved L. sexiesperforata larvae completed metamorphosis in the absence of food. Still, thyroxine-treated larvae in this experiment completed metamorphosis faster and in much higher numbers than in the starved controls. Furthermore, starved larvae of the sand dollar Mellita tenuis, which developed from much smaller eggs (100±2 ,m), did not complete metamorphosis either with or without excess thyroxine. Based on these data, and from recent experiments with other echinoids, we hypothesize that thyroxine plays a major role in echinoderm metamorphosis and the evolution of life history transitions in this group. We discuss our results in the context of current life history models for marine invertebrates, emphasizing the role of egg size, juvenile size, and endogenous hormone production for the evolution of nonfeeding larval development. [source] Deuterostome evolution: early development in the enteropneust hemichordate, Ptychodera flavaEVOLUTION AND DEVELOPMENT, Issue 6 2001Jonathan Q. Henry SUMMARY Molecular and morphological comparisons indicate that the Echinodermata and Hemichordata represent closely related sister-phyla within the Deuterostomia. Much less is known about the development of the hemichordates compared to other deuterostomes. For the first time, cell lineage analyses have been carried out for an indirect-developing representative of the enteropneust hemichordates, Pty- chodera flava. Single blastomeres were iontophoretically labeled with DiI at the 2- through 16-cell stages, and their fates followed through development to the tornaria larval stage. The early cleavage pattern of P. flava is similar to that of the direct-developing hemichordate, Saccoglossus kowalevskii, as well as that displayed by indirect-developing echinoids. The 16-celled embryo contains eight animal "mesomeres," four slightly larger "macromeres," and four somewhat smaller vegetal "micromeres." The first cleavage plane was not found to bear one specific relationship relative to the larval dorsoventral axis. Although individual blastomeres generate discrete clones of cells, the appearance and exact locations of these clones are variable with respect to the embryonic dorsoventral and bilateral axes. The eight animal mesomeres generate anterior (animal) ectoderm of the larva, which includes the apical organ; however, contributions to the apical organ were found to be variable as only a subset of the animal blastomeres end up contributing to its formation and this varies from embryo to embryo. The macromeres generate posterior larval ectoderm, and the vegetal micromeres form all the internal, endomesodermal tissues. These blastomere contributions are similar to those found during development of the only other hemichordate studied, the direct-developing enteropneust, S. kowalevskii. Finally, isolated blastomeres prepared at either the two- or the four-cell stage are capable of forming normal-appearing, miniature tornaria larvae. These findings indicate that the fates of these cells and embryonic dorsoventral axial properties are not committed at these early stages of development. Comparisons with the developmental programs of other deuterostome phyla allow one to speculate on the conservation of some key developmental events/mechanisms and propose basal character states shared by the ancestor of echinoderms and hemichordates. [source] Molecular and functional characterization of a novel splice variant of ANKHD1 that lacks the KH domain and its role in cell survival and apoptosiscFEBS JOURNAL, Issue 16 2005Melissa C. Miles Multiple ankyrin repeat motif-containing proteins play an important role in protein,protein interactions. ANKHD1 proteins are known to possess multiple ankyrin repeat domains and a single KH domain with no known function. Using yeast two-hybrid system analysis, we identified a novel splice variant of ANKHD1. This splice variant of ANKHD1, which we designated as HIV-1 Vpr-binding ankyrin repeat protein (VBARP), does not contain the signature KH domain, and codes for only a single ankyrin repeat motif. We characterized VBARP by molecular and functional analysis, revealing that VBARP is ubiquitously expressed in different tissues as well as cell lines of different lineage. In addition, blast searches indicated that orthologs and homologs to VBARP exist in different phyla, suggesting that VBARP might be evolutionarily conserved, and thus may be involved in basic cellular function(s). Furthermore, biochemical analysis revealed the presence of two VBARP isoforms coding for 69 and 49 kDa polypeptides, respectively, that are primarily localized in the cytoplasm. Functional analysis using short interfering RNA approaches indicate that this gene product is essential for cell survival through its regulation of caspases. Taken together, these results indicate that VBARP is a novel splice variant of ANKHD1 and may play a role in cellular apoptosis (antiapoptotic) and cell survival pathway(s). [source] Abundance, diversity, and activity of microbial assemblages associated with coral reef fish guts and fecesFEMS MICROBIOLOGY ECOLOGY, Issue 1 2010Steven Smriga Abstract Feces and distal gut contents were collected from three coral reef fish species. Bacteria cell abundances, as determined via epifluorescence microscopy, ranged two orders of magnitude among the fishes. Mass-specific and apparent cell-specific hydrolytic enzyme activities in feces from Chlorurus sordidus were very high, suggesting that endogenous fish enzymes were egested into feces. Denaturing gradient gel electrophoresis profiles of 16S rRNA genes were more similar among multiple individuals of the surgeonfish Acanthurus nigricans than among individuals of the parrotfish C. sordidus or the snapper Lutjanus bohar. Analyses of feces-derived 16S rRNA gene clones revealed that at least five bacterial phyla were present in A. nigricans and that Vibrionaceae comprised 10% of the clones. Meanwhile, C. sordidus contained at least five phyla and L. bohar three, but Vibrionaceae comprised 71% and 76% of the clones, respectively. Many sequences clustered phylogenetically to cultured Vibrio spp. and Photobacterium spp. including Vibrio ponticus and Photobacterium damselae. Other Vibrionaceae -like sequences comprised a distinct phylogenetic group that may represent the presence of ,feces-specific' bacteria. The observed differences among fishes may reflect native gut microbiota and/or bacterial assemblages associated with ingested prey. [source] Molecular bacterial community analysis of clean rooms where spacecraft are assembledFEMS MICROBIOLOGY ECOLOGY, Issue 3 2007Christine Moissl Abstract Molecular bacterial community composition was characterized from three geographically distinct spacecraft-associated clean rooms to determine whether such populations are influenced by the surrounding environment or the maintenance of the clean rooms. Samples were collected from facilities at the Jet Propulsion Laboratory (JPL), Kennedy Space Flight Center (KSC), and Johnson Space Center (JSC). Nine clone libraries representing different surfaces within the spacecraft facilities and three libraries from the surrounding air were created. Despite the highly desiccated, nutrient-bare conditions within these clean rooms, a broad diversity of bacteria was detected, covering all the main bacterial phyla. Furthermore, the bacterial communities were significantly different from each other, revealing only a small subset of microorganisms common to all locations (e.g. Sphingomonas, Staphylococcus). Samples from JSC assembly room surfaces showed the greatest diversity of bacteria, particularly within the Alpha - and Gammaproteobacteria and Actinobacteria. The bacterial community structure of KSC assembly surfaces revealed a high presence of proteobacterial groups, whereas the surface samples collected from the JPL assembly facility showed a predominance of Firmicutes. Our study presents the first extended molecular survey and comparison of NASA spacecraft assembly facilities, and provides new insights into the bacterial diversity of clean room environments . [source] Genome analysis of microorganisms living in amoebae reveals a melting pot of evolutionFEMS MICROBIOLOGY REVIEWS, Issue 3 2010Claire Moliner Abstract Amoebae-resistant microorganisms exhibit a specific lifestyle. Unlike allopatric specialized intracellular pathogens, they have not specialized because they infect the amoebae via amoebal attack and present a sympatric lifestyle with species from different phyla. In this review, we compare the genomes from bacteria (Legionella pneumophila, Legionella drancourtii, Candidatus,Protochlamydia amoebophila,'Rickettsia bellii, Candidatus,Amoebophilus asiaticus') and a virus (mimivirus) that multiply naturally in amoebae. The objective is to highlight the genomic traits characterizing these microorganisms and their niche by comparison with other specialized pathogens. The genome of intra-amoebal microorganisms is significantly larger than that of their relatives, contradicting the genome reduction theory mostly accepted for intracellular pathogens. This is probably due to the fact that they are not specialized and therefore maintain their genome size. Moreover, the presence of many horizontally transferred genes and mobilomes in their genomes suggests that these microorganisms acquired genetic material from their neighbors and amoebal host, thus increasing their genome size. Important features involved in gene transfer and pathogenicity were thus acquired. These characteristics suggest that amoebae constitute a gene melting pot, allowing diverse microorganisms to evolve by the same pathway characterized by gene acquisition, and then either adapt to the intra-amoebal lifestyle or create new pathogens. [source] Yeast diversity sampling on the San Juan Islands reveals no evidence for the spread of the Vancouver Island Cryptococcus gattii outbreak to this localeFEMS YEAST RESEARCH, Issue 4 2006James A. Fraser Abstract Biological diversity has been estimated for various phyla of life, such as insects and mammals, but in the microbe world is has been difficult to determine species richness and abundance. Here we describe a study of species diversity of fungi with a yeast-like colony morphology from the San Juan Islands, a group of islands that lies southeast of Vancouver Island, Canada. Our sampling revealed that the San Juan archipelago biosphere contains a diverse range of such fungi predominantly belonging to the Basidiomycota, particularly of the order Tremellales. One member of this group, Cryptococcus gattii, is the etiological agent of a current and ongoing outbreak of cryptococcosis on nearby Vancouver Island. Our sampling did not, however, reveal this species. While the lack of recovery of C. gattii does not preclude its presence on the San Juan Islands, our results suggest that the Strait of Juan de Fuca may be serving as a geographical barrier to restrict the dispersal of this primary human fungal pathogen into the United States. [source] Microbial biodiversity in groundwater ecosystemsFRESHWATER BIOLOGY, Issue 4 2009C. GRIEBLER Summary 1. Groundwater ecosystems offer vast and complex habitats for diverse microbial communities. Here we review the current status of groundwater microbial biodiversity research with a focus on Bacteria and Archaea and on the prospects of modern techniques for enhancing our understanding of microbial biodiversity patterns and their relation to environmental conditions. 2. The enormous volume of the saturated terrestrial underground forms the largest habitat for microorganisms on earth. Up to 40% of prokaryotic biomass on earth is hidden within this terrestrial subsurface. Besides representing a globally important pool of carbon and nutrients in organisms, these communities harbour a degree of microbial diversity only marginally explored to date. 3. Although first observations of groundwater microbiota date back to Antonie van Leeuwenhoek in 1677, the systematic investigation of groundwater microbial biodiversity has gained momentum only within the last few decades. These investigations were initiated by an increasing awareness of the importance of aquifer microbiota for ecosystem services and functioning, including the provision of drinking water and the degradation of contaminants. 4. The development of sampling techniques suitable for microbiological investigations as well as the application of both cultivation-based and molecular methods has yielded substantial insights into microbial communities in contaminated aquifers, whereas knowledge of microbial biodiversity in pristine habitats is still poor at present. 5. Several novel phylogenetic lineages have been described from groundwater habitats, but to date no clearly ,endemic' subsurface microbial phyla have been identified. The future will show if the rather low diversity generally found in pristine oligotrophic aquifers is a fact or just a result of low abundances and insufficient resolution of today's methods. Refined approaches complemented by statistically rigorous applications of biodiversity estimates are urgently needed. 6. Factors identified to control microbial diversity in aquifers include spatial heterogeneity, temporal variability and disturbances such as pollution with chemical anthropogenic contaminants. Although first insights into the importance of individual biogeochemical processes may be obtained from surveys of microbial diversity within functional groups, direct links to groundwater ecosystem functioning have rarely been established so far. [source] The biology and ecology of lotic rotifers and gastrotrichsFRESHWATER BIOLOGY, Issue 1 2000Claudia Ricci Summary 1The occurrence of Rotifera and Gastrotricha in the meiobenthos of lotic habitats is reviewed. About 150 rotifer and 30 gastrotrich species are reported in such habitats worldwide. 2The two phyla share some morphological and biological features that might account for their presence in the meiofauna. Small-size, a soft and elongate body, adhesive glands on the posterior body end, movement through cilia, relatively short life cycles, parthenogenesis and dormant stages are common characteristics. 3Most species of both taxa inhabiting the superficial sediments in streams and rivers may move downward into the hyporheos in response to both biotic (predation) and abiotic (spates, erosion, desiccation) disturbances. [source] An evolutionary fast-track to biocalcificationGEOBIOLOGY, Issue 3 2010D. J. JACKSON The ability to construct mineralized shells, spicules, spines and skeletons is thought to be a key factor that fuelled the expansion of multicellular animal life during the early Cambrian. The genes and molecular mechanisms that control the process of biomineralization in disparate phyla are gradually being revealed, and it is broadly recognized that an insoluble matrix of proteins, carbohydrates and other organic molecules are required for the initiation, regulation and inhibition of crystal growth. Here, we show that Astrosclera willeyana, a living representative of the now largely extinct stromatoporid sponges (a polyphyletic grade of poriferan bauplan), has apparently bypassed the requirement to evolve many of these mineral-regulating matrix proteins by using the degraded remains of bacteria to seed CaCO3 crystal growth. Because stromatoporid sponges formed extensive reefs during the Paelozoic and Mesozoic eras (fulfilling the role that stony corals play in modern coral reefs), and fossil evidence suggests that the same process of bacterial skeleton formation occurred in these stromatoporid ancestors, we infer that some ancient reef ecosystems might have been founded on this microbial,metazoan relationship. [source] Microbiology and geochemistry of Little Hot Creek, a hot spring environment in the Long Valley CalderaGEOBIOLOGY, Issue 2 2010T. J. VICK A culture-independent community census was combined with chemical and thermodynamic analyses of three springs located within the Long Valley Caldera, Little Hot Creek (LHC) 1, 3, and 4. All three springs were approximately 80 °C, circumneutral, apparently anaerobic and had similar water chemistries. 16S rRNA gene libraries constructed from DNA isolated from spring sediment revealed moderately diverse but highly novel microbial communities. Over half of the phylotypes could not be grouped into known taxonomic classes. Bacterial libraries from LHC1 and LHC3 were predominantly species within the phyla Aquificae and Thermodesulfobacteria, while those from LHC4 were dominated by candidate phyla, including OP1 and OP9. Archaeal libraries from LHC3 contained large numbers of Archaeoglobales and Desulfurococcales, while LHC1 and LHC4 were dominated by Crenarchaeota unaffiliated with known orders. The heterogeneity in microbial populations could not easily be attributed to measurable differences in water chemistry, but may be determined by availability of trace amounts of oxygen to the spring sediments. Thermodynamic modeling predicted the most favorable reactions to be sulfur and nitrate respirations, yielding 40,70 kJ mol,1 e, transferred; however, levels of oxygen at or below our detection limit could result in aerobic respirations yielding up to 100 kJ mol,1 e, transferred. Important electron donors are predicted to be H2, H2S, S0, Fe2+ and CH4, all of which yield similar energies when coupled to a given electron acceptor. The results indicate that springs associated with the Long Valley Caldera contain microbial populations that show some similarities both to springs in Yellowstone and springs in the Great Basin. [source] The genetic response to Snowball Earth: role of HSP90 in the Cambrian explosionGEOBIOLOGY, Issue 1 2006M. E. BAKER ABSTRACT The events that shaped the Cambrian explosion from 545 to 530 Ma, when multicellular animals suddenly appeared in the fossil record, are not fully understood. It is likely that the evolution of new transcription factors and other signal transduction proteins that regulated developmental networks was important in the emergence of diverse animal phyla seen in the Cambrian. I propose that one or both extensive glaciations that ended about 670 and 635 Ma were important in the evolution of signal transduction proteins in small animals in the Neoproterozoic/Proterozoic. These glaciations have been called Snowball Earth. One consequence of these glaciations is that they increased the expression of genetic diversity in animals due to the effect of extreme climatic stress on heat-shock protein 90 (HSP90). Climatic stress diverted HSP90 from chaperoning the folding and proper intracellular localization of many signal transduction proteins that regulate development in animals. As a result, pre-existing mutant signal transduction proteins and developmental pathways were expressed in animals. Selectively advantageous mutations were fixed in stem group animals and later were a source for the expansion of animal phyla during the Cambrian. [source] | ||||||||||||||||||||||||||||||||||||||||||||||