Diversity of 16S rRNA genes from bacteria of sugarcane rhizosphere soil

Sugarcane is an important agricultural product of Brazil, with a total production of more than 500 million tons. Knowledge of the bacterial community associated with agricultural crops and the soil status is a decisive step towards understanding how microorganisms influence crop productivity. However, most studies aim to isolate endophytic or rhizosphere bacteria associated with the plant by culture-dependent approaches. Culture-independent approaches allow a more comprehensive view of entire bacterial communities in the environment. In the present study, we have used this approach to assess the bacterial community in the rhizosphere soil of sugarcane at different times and under different nitrogen fertilization conditions. At the high taxonomic level, few differences between samples were observed, with the phylum Proteobacteria (29.6%) predominating, followed by Acidobacteria (23.4%), Bacteroidetes (12.1%), Firmicutes (10.2%), and Actinobacteria (5.6%). The exception was the Verrucomicrobia phylum whose prevalence in N-fertilized soils was approximately 0.7% and increased to 5.2% in the non-fertilized soil, suggesting that this group may be an indicator of nitrogen availability in soils. However, at low taxonomic levels a higher diversity was found associated with plants receiving nitrogen fertilizer. Bacillus was the most predominant genus, accounting for 19.7% of all genera observed. Classically reported nitrogen-fixing and/or plant growth-promoting bacterial genera, such as Azospirillum, Rhizobium, Mesorhizobium, Bradyrhizobium, and Burkholderia were also found although at a lower prevalence.

Evolutionary Origin and Maintenance of Sociality in the Small Carpenter Bees

Many arthropods exhibit behaviours precursory to social life, including adult longevity, parental care, nest loyalty and mutual tolerance, yet there are few examples of social behaviour in this phylum. The small carpenter bees, genus Ceratina, provide important insights into the early stages of sociality. I described the biology and social behaviour of five facultatively social species which exhibit all of the preadaptations for successful group living, yet present ecological and behavioural characteristics that seemingly disfavour frequent colony formation. These species are socially polymorphic with both / solitary and social nests collected in sympatry. Social colonies consist of two adult females, one contributing both foraging and reproductive effort and the second which remains at the nest as a passive guard. Cooperative nesting provides no overt reproductive benefits over solitary nesting, although brood survival tends to be greater in social colonies. Three main theories explain cooperation among conspecifics: mutual benefit, kin selection and manipulation. Lifetime reproductive success calculations revealed that mutual benefit does not explain social behaviour in this group as social colonies have lower per capita life time reproductive success than solitary nests. Genetic pedigrees constructed from allozyme data indicate that kin selection might contribute to the maintenance of social nesting -, as social colonies consist of full sisters and thus some indirect fitness benefits are inherently bestowed on subordinate females as a result of remaining to help their dominant sister. These data suggest that the origin of sociality in ceratinines has principal costs and the great ecological success of highly eusociallineages occurred well after social origins. Ecological constraints such as resource limitation, unfavourable weather conditions and parasite pressure have long been considered some of the most important selective pressures for the evolution of sociality. I assessed the fitness consequences of these three ecological factors for reproductive success of solitary and social colonies and found that nest sites were not limiting, and the frequency of social nesting was consistent across brood rearing seasons. Local weather varied between seasons but was not correlated with reproductive success. Severe parasitism resulted in low reproductive success and total nest failure in solitary nests. Social colonies had higher reproductive success and were never extirpated by parasites. I suggest that social nesting represents a form of bet-hedging. The high frequency of solitary nests suggests that this is the optimal strategy when parasite pressure is low. However, social colonies have a selective advantage over solitary nesting females during periods of extreme parasite pressure. Finally, the small carpenter bees are recorded from all continents except Antarctica. I constructed the first molecular phylogeny of ceratinine bees based on four gene regions of selected species covering representatives from all continents and ecological regions. Maximum parsimony and Bayesian Inference tree topology and fossil dating support an African origin followed by an Old World invasion and New World radiation. All known Old World ceratinines form social colonies while New World species are largely solitary; thus geography and phylogenetic inertia are likely predictors of social evolution in this genus. This integrative approach not only describes the behaviour of several previously unknown or little-known Ceratina species, bu~ highlights the fact that this is an important, though previously unrecognized, model for studying evolutionary transitions from solitary to social behaviour.

Étude du polymorphisme intra- et inter-spécifique du gène β-tubuline chez des espèces de champignons mycorhiziens à arbuscules en vue de développer des marqueurs moléculaires

Les champignons mycorhiziens à arbuscules (CMA), classés dans le phylum Glomeromycota, ne peuvent pas être facilement identifiés par la morphologie de leurs spores et leurs mycélia à l'intérieur ou à l'extérieur des racines de leurs hôtes. Ce problème fondamental d'identification rend l'étude de leur diversité, en particulier dans leur habitat naturel (sol et racine) extrêmement difficile. Les gènes ribosomaux ont été largement utilisés pour développer des amorces spécifiques et en inférer des arbres phylogénétiques. Cependant, ces gènes sont très polymorphes et existent en plusieurs copies dans le génome des CMA, ce qui complique l’interprétation des résultats. Dans notre étude, nous avons étudié le polymorphisme intra- et inter-spécifique du gène β-tubuline, présent en faible nombre de copies dans le génome des CMA, afin d’obtenir de nouvelles séquences nucléotidiques pour développer des marqueurs moléculaires. Les gènes β-tubuline amplifiés à partir de l'ADN génomique de cinq espèces du genre Glomus ont été clonés et séquencés. L’analyse des séquences indique un polymorphisme intraspécifique chez trois espèces de CMA. Deux séquences paralogues très variables ont été nouvellement identifiées chez les G. aggregatum, G. fasciculatum et G. cerebriforme. Aucun polymorphisme n’a été détecté chez les G. clarum et G. etunicatum. Toutes les séquences montrent la présence de deux introns hautement variables. La majorité des substitutions ont été localisées dans les exons et sont synonymes à 90%. La conservation des acides aminés suggère un niveau élevé de sélection négative sur le gène β-tubuline et nous permet de confirmer que les CMA représentent un ancien groupe fongique (400 million d’années). L’analyse phylogénétique, réalisée avec vingt et une séquences nucléotidiques du gène β-tubuline, a révélé que les séquences des Glomaceae forment un groupe monophylétique bien supporté, avec les Acaulosporaceae et Gigasporaceae comme groupe frère. Les séquences paralogues nouvellement identifiées chez les G. aggregatum et G. fasciculatum n'ont pas été monophylétiques au sein de chaque espèce. Les oligonucléotides ont été choisis sur la base des régions variables et conservées du gène β-tubuline. Le test PCR des amorces β-Tub.cerb.F/ β-Tub.cerb.R a révélé des bandes spécifiques de 401 pb pour les séquences paralogues du G. cerebriforme. Deux paires d’amorces ont été développées afin d’identifier les séquences du groupe nommé Tub.1. Les tests PCR nous ont permis d’identifier certaines séquences du groupe Tub.1. Une paire d’amorce β-Tub.2.F/ β-Tub.2.R nous a permis d’identifier certaines séquences paralogues du groupe nommé Tub.2. L’analyse d’autres gènes combinée à celle du gène β-tubuline permettra le développement de marqueurs moléculaires plus spécifiques pour l’identification de CMA.

Morphologie évolutive et fonctionnelle des hémichordés

L’embranchement Hemichordata regroupe les classes Enteropneusta et Pterobranchia. Hemichordata constitue, avec l’embranchement Echinodermata, le groupe-frère des chordés. Les entéropneustes sont des organismes vermiformes solitaires qui vivent sous ou à la surface du substrat et s’alimentent généralement par déposivorie, alors que les ptérobranches sont des organismes coloniaux filtreurs habitant dans un réseau de tubes appelé coenecium. Ce mémoire présente trois études dont le point commun est l’utilisation des hémichordés actuels pour répondre à des questions concernant l’évolution des hémichordés, des chordés, et du super-embranchement qui les regroupe, Deuterostomia. Notre première étude démontre que les fentes pharyngiennes, l’organe pré-oral cilié (POCO) et le pharynx de l’entéropneuste Protoglossus graveolens sont utilisés pour l’alimentation par filtration. Le système de filtration de P. graveolens permet la capture de particules jusqu’à 1.3 um, à un débit de 4.05 mm.s-1, pour une demande énergétique de 0.009 uW. Les similarités structurales et fonctionnelles avec le système de filtration des céphalochordés suggèrent que la filtration pharyngienne est ancestrale aux deutérostomes. Lors de notre deuxième étude, nous avons exploré l’hypothèse selon laquelle le POCO des entéropneustes, une structure ciliée pré-buccale au rôle possiblement chémorécepteur, serait homologue au « wheel organ » des céphalochordés et à l’adénohypophyse des vertébrés. Pour cela, nous avons déterminé par immunohistochimie l’expression de Pit-1, un facteur de transcription spécifique à ces deux structures, chez l’entéropneuste Saccoglossus pusillus. Pit-1 est exprimé dans des cellules sensorielles du POCO, mais aussi dans des cellules épithéliales distribuées dans le proboscis, collet et tronc. Ce patron d’expression ne permet pas de confirmer ou rejeter l’homologie du POCO et de l’adénohypophyse des vertébrés. Lors de notre troisième étude, nous avons caractérisé l’ultrastructure du coenecium des ptérobranches Cephalodiscus hodgsoni, Cephalodiscus nigrescens et Cephalodiscus densus par microscopie électronique à transmisison et à balayage. Cephalodiscus est le groupe frère de Graptolithina, un groupe qui inclut les graptolithes éteints ainsi que les ptérobranches du genre Rhabdopleura. Nous avons décrit les types de fibrilles de collagène présents, leur taille et leur organisation, ainsi que l’organisation globale du coenecium. Nous avons ainsi démontré la présence chez Cephalodiscus d’une organisation similaire au paracortex, pseudocortex et eucortex des graptolithes. La présence chez Cephalodiscus de ce type d’organisation suggère que le cortex est ancestral à la classe Pterobranchia. Ces trois études illustrent plusieurs axes importants de la recherche sur les hémichordés, qui en intégrant des données morphologiques, fonctionnelles et moléculaires permet de reconstruire certains évènements clés de l’évolution des deutérostomes.

Comparative mitochondrial genomics toward understanding genetics and evolution of arbuscular mycorrhizal fungi

Les champignons mycorhiziens arbusculaires (CMA) sont très répandus dans le sol où ils forment des associations symbiotiques avec la majorité des plantes appelées mycorhizes arbusculaires. Le développement des CMA dépend fortement de la plante hôte, de telle sorte qu'ils ne peuvent vivre à l'état saprotrophique, par conséquent ils sont considérés comme des biotrophes obligatoires. Les CMA forment une lignée évolutive basale des champignons et ils appartiennent au phylum Glomeromycota. Leurs mycélia sont formés d’un réseau d’hyphes cénocytiques dans lesquelles les noyaux et les organites cellulaires peuvent se déplacer librement d’un compartiment à l’autre. Les CMA permettent à la plante hôte de bénéficier d'une meilleure nutrition minérale, grâce au réseau d'hyphes extraradiculaires, qui s'étend au-delà de la zone du sol explorée par les racines. Ces hyphes possèdent une grande capacité d'absorption d’éléments nutritifs qui vont être transportés par ceux-ci jusqu’aux racines. De ce fait, les CMA améliorent la croissance des plantes tout en les protégeant des stresses biotiques et abiotiques. Malgré l’importance des CMA, leurs génétique et évolution demeurent peu connues. Leurs études sont ardues à cause de leur mode de vie qui empêche leur culture en absence des plantes hôtes. En plus leur diversité génétique intra-isolat des génomes nucléaires, complique d’avantage ces études, en particulier le développement des marqueurs moléculaires pour des études biologiques, écologiques ainsi que les fonctions des CMA. C’est pour ces raisons que les génomes mitochondriaux offrent des opportunités et alternatives intéressantes pour étudier les CMA. En effet, les génomes mitochondriaux (mt) publiés à date, ne montrent pas de polymorphismes génétique intra-isolats. Cependant, des exceptions peuvent exister. Pour aller de l’avant avec la génomique mitochondriale, nous avons besoin de générer beaucoup de données de séquençages de l’ADN mitochondrial (ADNmt) afin d’étudier les méchanismes évolutifs, la génétique des population, l’écologie des communautés et la fonction des CMA. Dans ce contexte, l’objectif de mon projet de doctorat consiste à: 1) étudier l’évolution des génomes mt en utilisant l’approche de la génomique comparative au niveau des espèces proches, des isolats ainsi que des espèces phylogénétiquement éloignées chez les CMA; 2) étudier l’hérédité génétique des génomes mt au sein des isolats de l’espèce modèle Rhizophagus irregularis par le biais des anastomoses ; 3) étudier l’organisation des ADNmt et les gènes mt pour le développement des marqueurs moléculaires pour des études phylogénétiques. Nous avons utilisé l’approche dite ‘whole genome shotgun’ en pyroséquençage 454 et Illumina HiSeq pour séquencer plusieurs taxons de CMA sélectionnés selon leur importance et leur disponibilité. Les assemblages de novo, le séquençage conventionnel Sanger, l’annotation et la génomique comparative ont été réalisés pour caractériser des ADNmt complets. Nous avons découvert plusieurs mécanismes évolutifs intéressant chez l’espèce Gigaspora rosea dans laquelle le génome mt est complètement remanié en comparaison avec Rhizophagus irregularis isolat DAOM 197198. En plus nous avons mis en évidence que deux gènes cox1 et rns sont fragmentés en deux morceaux. Nous avons démontré que les ARN transcrits les deux fragments de cox1 se relient entre eux par épissage en trans ‘Trans-splicing’ à l’aide de l’ARN du gene nad5 I3 qui met ensemble les deux ARN cox1.1 et cox1.2 en formant un ARN complet et fonctionnel. Nous avons aussi trouvé une organisation de l’ADNmt très particulière chez l’espèce Rhizophagus sp. Isolat DAOM 213198 dont le génome mt est constitué par deux chromosomes circulaires. En plus nous avons trouvé une quantité considérable des séquences apparentées aux plasmides ‘plasmid-related sequences’ chez les Glomeraceae par rapport aux Gigasporaceae, contribuant ainsi à une évolution rapide des ADNmt chez les Glomeromycota. Nous avons aussi séquencé plusieurs isolats de l’espèces R. irregularis et Rhizophagus sp. pour décortiquer leur position phylogénéque et inférer des relations évolutives entre celles-ci. La comparaison génomique mt nous montré l’existence de plusieurs éléments mobiles comme : des cadres de lecture ‘open reading frames (mORFs)’, des séquences courtes inversées ‘short inverted repeats (SIRs)’, et des séquences apparentées aux plasimdes ‘plasmid-related sequences (dpo)’ qui impactent l’ordre des gènes mt et permettent le remaniement chromosomiques des ADNmt. Tous ces divers mécanismes évolutifs observés au niveau des isolats, nous permettent de développer des marqueurs moléculaires spécifiques à chaque isolat ou espèce de CMA. Les données générées dans mon projet de doctorat ont permis d’avancer les connaissances fondamentales des génomes mitochondriaux non seulement chez les Glomeromycètes, mais aussi de chez le règne des Fungi et les eucaryotes en général. Les trousses moléculaires développées dans ce projet peuvent servir à des études de la génétique des populations, des échanges génétiques et l’écologie des CMA ce qui va contribuer à la compréhension du rôle primorial des CMA en agriculture et environnement.

Taxonomy, Bionomics and Biofouling of Bryozoans from the Coasts of India and the Antarctic Waters

The study of bryozoans, an important group of coelomates in the marine environment is an integral part of faunistic investigations. Bryozones are an ancient, aberrant phylum of microscopic but fascinating and often beautiful animals that build intricate colonies sometimes resembling minicolonies. In this study taxonomy, bionomics and biofouling of bryozoans from the coasts of India and the Antarctic waters. The marine biofouling is found to be hazardous. Bryozoans are microscopic , sessile,colonical coelomates that are permanently fastened in exoskeletal cases or gelatinous material of their own secretion.It is hoped that this work would help the future researchers to devote attention on microbenthos of the continental shelf of India when samples are made available through collections conducted by any ocean going vessel. In the present work an extensive study on the bryozoan foulers that occur at five selected sites of the cochin estury had to be examined and since the hydrographic parameters such as salinity, temperature, pH and dissolved oxygen in the estury,vary greatly from that in the open ocean, a frequent monitoring of these parameters was essential.

STUDIES ON TAXONOMY, DISTRIBUTION, ECOLOGY AND REPRODUCTIVE POTENTIAL OF ROTIFERS FROM SELECTED CENTRES IN COCHIN BACKWATER SYSTEM, KERALA

The studies were conducted in nine stations with varying ecological characteristics along Cochin backwaters and adjoining canals. Many workers opined that the distribution of rotifers is cosmopolitan. The significance of rotifers as first food for early larvae was indicated by Fujita. Aquaculture is a fast growing field in fisheries sector and it is gaining more importance as the fish landings and supply are getting irregular. A consistent supply of fish/shellfish can only be achieved through aquaculture. The success of any culture activity depends on the timely production of seeds of finfishes/shellfishes. The availability of wild seed is seasonal and erratic. So, a dependable source of seed of fishes and shellfishes is possible only through large scale production in hatchery. A successful seed production activity depends on the availability of a variety of suitable live feed organisms in sufficient quantities at the proper time for use in the larval stages. As the live feeds promote high growth rates, easy digestion, assimilation and the quality of not contaminating the culture water when compared to other artificial feeds, make the culture of live feed organisms the principal means of providing food for the larvae of finfishes and shellfishes. Rotifers are considered to be an excellent and indispensable food for larvae of many finfishes and crustaceans. It (1960) was the first to culture Brachionus plicatilis for feeding marine fish larvae, and now it is being extensively used as live feed in hatcheries all over the world. They are a group of microscopic organisms coming under the Phylum Rotifera which comprises of about 2000 species. Their slow swimming habits, ability to tolerate a wide range of salinities, parthenogenetic mode of reproduction and ability to get enriched easily, make rotifers an ideal live feed organism. The major factors such as temperature, salinity and food that influence the reproductive potential and thereby the population size of rotifer, Salinity is one of the most important aspect influencing the reproductive rate of rotifers. The feed type and feed concentration play a vital role in influencing the reproductive rate of rotifers. For culture of rotifers, the commonly used micro algae belong to Chlorella, Nannochloropsis, Isochrysis and Tetraselmis. While some studies have suggested that, algal diet has little effect on reproductive rates in 1979 while using the rotifer, Brachionus plicatilis as feed for the larvae of red sea bream, Pagrus major. It is generally accepted that rotifers play a pivotal role in the successful rearing of marine fish larvae.

Studies on the taxonomy of interstitial Fauna of some prominent beaches of Kerala

The oceans in their expanse cover, seven - tenths of the Earth surface. Despite being restricted in size, the littoral zone or the intertidal zone (beach) has the greatest variation in environment factors of any marine area .Stemming from this variation ,a treamendous diversity of life, which may be great as or greater than that found in the more extensive sub tidal habits exist in this realm. the study beaches harbour diverse and abundant assemblage of marine organisms. Besides macro funna, microscopic organisms belonging to the lower and higher invertebrate taxa profusely inhabit these beaches. The ecological realm where these animals exist is known as the interstitial environment, which in principle includes the pore spaces in between the sand grains containing copious supply of nutrient rich oxygenated seawater. An astonishing diversity of taxa could be found within the interstitial fauna.

Nitrification in a packed bed bioreactor integrated into amarine recirculating maturation system under different substrate concentrations and flow rates

BACKGROUND: A packed bed bioreactor (PBBR) activated with an indigenous nitrifying bacterial consortia was developed and commercialized for rapid establishment of nitrification in brackish water and marine hatchery systems in the tropics. The present study evaluated nitrification in PBBR integrated into a Penaeus monodon recirculating maturation system under different substrate concentrations and flow rates. RESULTS:Instantnitrificationwasobservedafter integration ofPBBRinto thematuration system.TANandNO2-Nconcentrations were always maintained below0.5 mg L−1 during operation. The TANandNO2-N removalwas significant (P < 0.001) in all the six reactor compartments of the PBBR having the substrates at initial concentrations of 2, 5 and 10 mg L−1. The average volumetric TAN removal rates increased with flow rates from 43.51 (250 L h−1) to 130.44 (2500 L h−1) gTAN m−3 day−1 (P < 0.05). FISH analysis of the biofilms after 70 days of operation gave positive results with probes NSO 190 ((β ammonia oxidizers), NsV 443 (Nitrosospira spp.) NEU (halophilic Nitrosomonas), Ntspa 712 (Phylum Nitrospira) indicating stability of the consortia. CONCLUSION: The PBBR integrated into the P. monodon maturation system exhibited significant nitrification upon operation for 70 days as well as at different substrate concentrations and flow rates. This system can easily be integrated into marine and brackish water aquaculture systems, to establish instantaneous nitrification

Molecular characterization of the nitrifying bacterial consortia employed for the activation of bioreactors used in brackish and marine aquaculture systems

The addition of commercial nitrifying bacterial products has resulted in significant improvement of nitrification efficiency in recirculating aquaculture systems (RAS). We developed two nitrifying bacterial consortia (NBC) from marine and brackish water as start up cultures for immobilizing commercialized nitrifying bioreactors for RAS. In the present study, the community compositions of the NBC were analyzed by universal 16S rRNA gene and bacterial amoA gene sequencing and fluorescence in situ hybridization (FISH). This study demonstrated that both the consortia involved autotrophic nitrifiers, denitrifiers as well as heterotrophs. Abundant taxa of the brackish water heterotrophic bacterial isolates were Paenibacillus and Beijerinckia spp. whereas in the marine consortia they were Flavobacterium, Cytophaga and Gramella species. The bacterial amoA clones were clustered together with high similarity to Nitrosomonas sp. and uncultured beta Proteobacteria. FISH analysis detected ammonia oxidizers belonging to b subclass of proteobacteria and Nitrosospira sp. in both the consortia, and Nitrosococcus mobilis lineage only in the brackish water consortium and the halophilic Nitrosomonas sp. only in the marine consortium. However, nitrite oxidizers, Nitrobacter sp. and phylum Nitrospira were detected in both the consortia. The metabolites from nitrifiers might have been used by heterotrophs as carbon and energy sources making the consortia a stable biofilm.

PvRON2, a new Plasmodium vivax rhoptry neck antigen

Background: Rhoptries are specialized organelles from parasites belonging to the phylum Apicomplexa; they secrete their protein content during invasion of host target cells and are sorted into discrete subcompartments within rhoptry neck or bulb. This distribution is associated with these proteins’ role in tight junction (TJ) and parasitophorous vacuole (PV) formation, respectively. Methods: Plasmodium falciparum RON2 amino acid sequence was used as bait for screening the codifying gene for the homologous protein in the Plasmodium vivax genome. Gene synteny, as well as identity and similarity values, were determined for ron2 and its flanking genes among P. falciparum, P. vivax and other malarial parasite genomes available at PlasmoDB and Sanger Institute databases. Pvron2 gene transcription was determined by RT-PCR of cDNA obtained from the P. vivax VCG-1 strain. Protein expression and localization were assessed by Western blot and immunofluorescence using polyclonal anti-PvRON2 antibodies. Co-localization was confirmed using antibodies directed towards specific microneme and rhoptry neck proteins. Results and discussion: The first P. vivax rhoptry neck protein (named here PvRON2) has been identified in this study. PvRON2 is a 2,204 residue-long protein encoded by a single 6,615 bp exon containing a hydrophobic signal sequence towards the amino-terminus, a transmembrane domain towards the carboxy-terminus and two coiled coil a-helical motifs; these are characteristic features of several previously described vaccine candidates against malaria. This protein also contains two tandem repeats within the interspecies variable sequence possibly involved in evading a host’s immune system. PvRON2 is expressed in late schizonts and localized in rhoptry necks similar to what has been reported for PfRON2, which suggests its participation during target cell invasion. Conclusions: The identification and partial characterization of the first P. vivax rhoptry neck protein are described in the present study. This protein is homologous to PfRON2 which has previously been shown to be associated with PfAMA-1, suggesting a similar role for PvRON2.

Buddenbrockia is a Cnidarian worm

A major evolutionary divide occurs in the animal kingdom between the so-called radially symmetric animals, which includes the cnidarians, and the bilaterally symmetric animals, which includes all worm phyla. Buddenbrockia plumatellae is an active, muscular, parasitic worm that belongs to the phylum Myxozoa, a group of morphologically simplified microscopic endoparasites that has proved difficult to place phylogenetically. Phylogenetic analyses of multiple protein-coding genes demonstrate that Buddenbrockia is a cnidarian. This active muscular worm increases the known diversity in cnidarian body plans and demonstrates that a muscular, wormlike form can evolve in the absence of overt bilateral symmetry.

Orphan worms and, homeless parasites enhance bilaterian diversity

Microscopic endoparasites belonging to the Phylum Myxozoa provide a striking example of how much there is still to be learned about the diversity of the Metazoa. Recent research on myxozoans has provided new insights into evolution within the Bilateria, revealing unparalleled levels of morphological simplification associated with parasitism, a home for an orphan worm, and a hypothesis of the endosymbiotic origin(s) for extrusible intracellular organelles in myxozoans and cnidarians. In addition, discovery of the source of a devastating disease of salmonid fish has enabled researchers to identify two ancient clades within the Myxozoa, and has exposed new mysteries concerning myxozoan life-cycle evolution and evolutionary diversification. This plethora of new insights exemplifies the fundamental value of studying obscure organisms.

What do we mean when we refer to Bacteroidetes populations in the human gastrointestinal microbiota?

Recent large-scale cloning studies have shown that the ratio of Bacteroidetes to Firmicutes may be important in the obesity-associated gut microbiota, but the species these phyla represent in this ecosystem has not been examined. The Bacteroidetes data from the recent Turnbaugh study were examined to determine those members of the phylum detected in human faecal samples. In addition, FISH analysis was performed on faecal samples from 17 healthy, nonobese donors using probe Bac303, routinely used by gut microbiologists to enumerate BacteroidesPrevotella populations in faecal samples, and another probe (CFB286) whose target range has some overlap with that of Bac303. Sequence analysis of the Turnbaugh data showed that 23/519 clones were chimeras or erroneous sequences; all good sequences were related to species of the order Bacteroidales, but no one species was present in all donors. FISH analysis demonstrated that approximately one-quarter of the healthy, nonobese donors harboured high numbers of Bacteroidales not detected by probe Bac303. It is clear that Bacteroidales populations in human faecal samples have been underestimated in FISH-based studies. New probes and complementary primer sets should be designed to examine numerical and compositional changes in the Bacteroidales during dietary interventions and in studies of the obesity-associated microbiota in humans and animal model systems.

Anaerofustis stercorihominis gen. nov., sp nov., from human faeces

Phenotypic and phylogenetic studies were performed on an unidentified Gram-positive, strictly anaerobic, non-spore-forming, rod-shaped bacterium isolated from human feces. The organism was catalase-negative, resistant to 20% bile, produced acetic and butyric acids as end products of glucose metabolism, and possessed a G + C content of approximately 70 mol %. Comparative 16S rRNA gene sequencing demonstrated that the unidentified bacterium was a member of the Clostridium sub-phylum of the Gram-positive bacteria, and formed a loose association with rRNA cluster XV. Sequence divergence values of 12% or greater were observed between the unidentified bacterium and all other recognized species within this and related rRNA clusters. Treeing analysis showed the unknown anaerobe formed a deep line branching near to the base of rRNA cluster XV and phylogenetically represents a hitherto unknown taxon, distinct from Acetobacterium, Eubacterium sensu stricto, Pseudoramibacter and other related organisms. Based on both phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium from feces be classified in a new genus Anaerofustis, as Anaerofustis stercorihominis sp. nov. The type strain of Anaerofustis stercorihominis is ATCC BAA-858(T) = CCUG 47767(T). (C) 2003 Elsevier Ltd. All rights reserved.