Genomic characterization of a polyvalent hydrocarbonoclastic bacterium Pseudomonas sp. strain BUN14

Bioremediation offers a viable alternative for the reduction of contaminants from the environment, particularly petroleum and its recalcitrant derivatives. In this study, the ability of a strain of Pseudomonas BUN14 to degrade crude oil, pristane and dioxin compounds, and to produce biosurfactants, was investigated. BUN14 is a halotolerant strain isolated from polluted sediment recovered from the refinery harbor on the Bizerte coast, north Tunisia and capable of producing surfactants. The strain BUN14 was assembled into 22 contigs of 4,898,053 bp with a mean GC content of 62.4%. Whole genome phylogeny and comparative genome analyses showed that strain BUN14 could be affiliated with two validly described Pseudomonas Type Strains, P. kunmingensis DSM 25974T and P. chloritidismutans AW-1T. The current study, however, revealed that the two Type Strains are probably conspecific and, given the priority of the latter, we proposed that P. kunmingensis DSM 25974 is a heteronym of P. chloritidismutans AW-1T. Using GC-FID analysis, we determined that BUN14 was able to use a range of hydrocarbons (crude oil, pristane, dibenzofuran, dibenzothiophene, naphthalene) as a sole carbon source. Genome analysis of BUN14 revealed the presence of a large repertoire of proteins (154) related to xenobiotic biodegradation and metabolism. Thus, 44 proteins were linked to the pathways for complete degradation of benzoate and naphthalene. The annotation of conserved functional domains led to the detection of putative genes encoding enzymes of the rhamnolipid biosynthesis pathway. Overall, the polyvalent hydrocarbon degradation capacity of BUN14 makes it a promising candidate for application in the bioremediation of polluted saline environments

Morphological and Molecular Evolution Are Not Linked in Lamellodiscus (Plathyhelminthes, Monogenea)

Lamellodiscus Johnston & Tiegs 1922 (Monogenea, Diplectanidae) is a genus of common parasites on the gills of sparid fishes. Here we show that this genus is probably undergoing a fast molecular diversification, as reflected by the important genetic variability observed within three molecular markers (partial nuclear 18S rDNA, Internal Transcribed Spacer 1, and mitonchondrial Cytochrome Oxidase I). Using an updated phylogeny of this genus, we show that molecular and morphological evolution are weakly correlated, and that most of the morphologically defined taxonomical units are not consistent with the molecular data. We suggest that Lamellodiscus morphology is probably constrained by strong environmental (host-induced) pressure, and discuss why this result can apply to other taxa. Genetic variability within nuclear 18S and mitochondrial COI genes are compared for several monogenean genera, as this measure may reflect the level of diversification within a genus. Overall our results suggest that cryptic speciation events may occur within Lamellodiscus, and discuss the links between morphological and molecular evolution

Approaches in biotechnological applications of natural polymers

Natural polymers, such as gums and mucilage, are biocompatible, cheap, easily available and non-toxic materials of native origin. These polymers are increasingly preferred over synthetic materials for industrial applications due to their intrinsic properties, as well as they are considered alternative sources of raw materials since they present characteristics of sustainability, biodegradability and biosafety. As definition, gums and mucilages are polysaccharides or complex carbohydrates consisting of one or more monosaccharides or their derivatives linked in bewildering variety of linkages and structures. Natural gums are considered polysaccharides naturally occurring in varieties of plant seeds and exudates, tree or shrub exudates, seaweed extracts, fungi, bacteria, and animal sources. Water-soluble gums, also known as hydrocolloids, are considered exudates and are pathological products; therefore, they do not form a part of cell wall. On the other hand, mucilages are part of cell and physiological products. It is important to highlight that gums represent the largest amounts of polymer materials derived from plants. Gums have enormously large and broad applications in both food and non-food industries, being commonly used as thickening, binding, emulsifying, suspending, stabilizing agents and matrices for drug release in pharmaceutical and cosmetic industries. In the food industry, their gelling properties and the ability to mold edible films and coatings are extensively studied. The use of gums depends on the intrinsic properties that they provide, often at costs below those of synthetic polymers. For upgrading the value of gums, they are being processed into various forms, including the most recent nanomaterials, for various biotechnological applications. Thus, the main natural polymers including galactomannans, cellulose, chitin, agar, carrageenan, alginate, cashew gum, pectin and starch, in addition to the current researches about them are reviewed in this article.. }To the Conselho Nacional de Desenvolvimento Cientfíico e Tecnológico (CNPq) for fellowships (LCBBC and MGCC) and the Coordenação de Aperfeiçoamento de Pessoal de Nvíel Superior (CAPES) (PBSA). This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit, the Project RECI/BBB-EBI/0179/2012 (FCOMP-01-0124-FEDER-027462) and COMPETE 2020 (POCI-01-0145-FEDER-006684) (JAT)

Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016

Gonadal cycle of the dwarf oyster Ostreola stentina from the south of the Gulf of Hammamet on the eastern coast of Tunisia

The reproductive cycle of the dwarf oyster Ostreola stentina (Payraudeau 1826) at Monastir in the south of the Gulf of Hammamet on the east coast of Tunisia was studied using condition indices and histological techniques. The species was shown to be a protandric hermaphrodite. Whereas males dominated the small shell length categories (12.45–34.99 mm), females (21.00–47.16 mm) and hermaphroditic individuals (30.00–57.95 mm) become more predominant with increasing size, suggesting that individuals may undergo protandric development. The overall male to female ratio was 1.0:1.7. Gametogenic development begins in February–March for females and in September for males, and spawning occurs during April and July for females and December and July for males. There was a clear relationship between the gonadal condition index and gametogenic stage for both sexes. Values increased from zero in their early stage of development and peaked during ripe and spawning stages, before decreasing in the spent stage. However, the meat condition index did not show any statistical differences between gametogenic stages. Keywords: condition indices, gametogenic cycle, histology, protandrous hermaphroditismAfrican Journal of Marine Science 2012, 34(4): 537–54

Reproductive biology of Klein’s sole, Synapturichthys kleinii (Actinopterygii: Pleuronectiformes: Soleidae), off Tunisian coast (central Mediterranean)

Background. Klein’s sole, Synapturichthys kleinii (Risso, 1827), is a rare fish, included in the IUCN Red List as Data Deficient, and its biology is poorly known. Biological investigations of S. kleinii have been surprisingly rare in Tunisian waters. In the presently reported study, we investigated the reproductive period, size at first sexual maturity, and fecundity of S. kleinii along the Tunisian waters, with the aim of achieving the first complete and comprehensive description of the reproduction of this fish in the Mediterranean Sea. Materials and methods. A total of 294 specimens of S. kleinii were sampled over two years, off the Tunisian coasts. Sex ratio was estimated through the seasons of the year and the size classes. The stage of maturity was determined macroscopically only for females. Monthly gonadosomatic index (GSI), monthly hepatosomatic index (HSI), and condition factor (K) were calculated for males and females of S. kleinii. Size at first maturity was estimated only for females during the spawning season. Eighteen mature females at spawning stage were collected, weighed, and fixed in 4% formaldehyde solution for fecundity estimation. Results. Annual sex ratio showed significant differences between males and females. In specimens exceeding 27 cm in total length females outnumbered males significantly. The Klein’s sole reproduction period started in October and ended in January. The gonadosomatic index reached highest values in November for females and males. Females attained sexual maturity at 20.53 cm total body length (TL). Total fecundity ranged from 3647 to 23 174 eggs. We found a low correlation coefficient between total fecundity and total length, but a high correlation coefficient between eviscerated weight and ovary weight. Conclusion. Our results constitute a preliminary baseline for monitoring changes in the biological indexes linked to the reproduction cycle and length at first sexual maturity of S. kleinii. The presently acquired data will enable biologists to assess the status of this fish and develop culture technology in natural waters and will be useful for the fishery biologists and conservation biologists, for successful development, management, production, and ultimate conservation of this favoured Tunisian food fish

Lamellodiscus (Monogenea : Diplectanidae) parasites of Dentex macrophthalmus (Teleostei : Sparidae) from the North Atlantic coast of Africa, with a redescription of L. dentexi Aljoshkina, 1984, and description of three new species

Lamellodiscus dentexi Aljoshkina, 1984, a gill parasite of Dentex macrophthalmus (Bloch), is redescribed based on new material from the northwest coast of Africa (Senegal and Morocco). Three new species of Lamellodiscus Johnston et Tiegs, 1922 from D. macrophthalmus are described, Lamellodiscus toguebayei sp. n., L. vicinus sp. n., and L. triacies sp. n.. all belonging to the "ignoratus" group. They can be distinguished from all other species of this group by the size and shape of male copulatory organ and sclerotised parts of the haptor. Considering the peculiar morphology of the male copulatory organ (long and thin tube) we propose to put together L. dentexi, L. virgula Euzet et Oliver, 1967 and L. obeliae Oliver, 1973 to form the "elongatus" type within the "elegans" group

Exhaustion of pentachlorophenol in soil microcosms with three Pseudomonas species as detoxification agents

Pentachlorophenol (PCP) is a toxic compound, which is widely used as a wood preservative product and general biocide. It is persistent in the environment and has been classified as a persistent organic pollutant to be reclaimed in many countries. Bioremediation is an emerging approach to rehabilitating areas polluted by recalcitrant xenobiotics. In the present study, we evaluated the potential of three strains of Pseudomonas (P. putida S121, P. rhizophila S211, and P. fuscovagiceae S115) as bioremediation agents in depletion and detoxification of PCP in soil microcosms. PCP removal was effectively optimized using a central-composite experimental design and response surface methodology (RSM). The optimum conditions for maximum PCP removal yield (85 \ub1 5%) were: 500 mg/kg PCP concentration, 108 UFC/g soil inoculum size of each strain and 55 days incubation period. The bacterial strains, P. putida, P. rhizophila, and P. fuscovagiceae, showed good capability to tolerate and degrade PCP so that they could be successfully used in synergistic effect to treat PCP polluted soils