First visual occurrence data for deep-sea cnidarians in the South-western Colombian Caribbean.

BACKGROUND: Attention to the deep-sea environment has increased dramatically in the last decade due to the rising interest in natural resource exploitation. Although Colombia holds a large submerged territory, knowledge of the seabed and its biodiversity beyond 1,000 m depth is very limited. During 2015-2017, Anadarko Colombia Company (ACC) carried out hydrocarbon exploratory activities in the South-western Colombian Caribbean, at depths between 375 m and 2,565 m. NEW INFORMATION: Capitalising on available data resources from these activities, several cnidarian species were observed in ROV and towed camera surveys. We analysed over nine hours of video and 5,066 still images from these surveys, identifying organisms to the lowest possible taxonomic level. The images and associated data presented here correspond to 108 observations of deep-sea cnidarians, including seven new records for the Colombian Caribbean. Given the paucity of research and funding to explore the deep-sea in Colombia, the present dataset comprises the largest deep-sea Cnidaria imagery inventory to date for the Colombian Caribbean.

Genetic diversity of the entomopathogenic fungus Cordyceps tenuipes in forests and butterfly gardens in Quindío, Colombia.

Cordyceps tenuipes is an entomopathogenic fungus that infects mostly pupae of several lepidopteran families. In Colombia the species has been reported in non-disturbed tropical rain forests and more recently in butterfly gardens. The aim of this study was to assess the genetic diversity in populations of C. tenuipes present in natural (forests) and artificial (e.g. butterfly gardens) environments in the department of Quindío, Colombia, using three molecular nuclear markers ITS, TEF-1α and RPB1. All the samples evaluated corresponded morphologically and phylogenetically to C. tenuipes. The butterfly garden of Quindio Botanical Garden (QBG) showed the highest genetic diversity among all sampling localities and was very similar to that of its adjacent forest. The Amaranta Butterfly Garden (ABG), located north of QBG, showed lower genetic diversity as well as little genetic differentiation with QBG, consistent with the hypothesis of a pathogen transfer from QBG to ABG. Higher FST values were observed for TEF-1α and ITS, revealing genetic differentiation between all demes and the southern forest population. Our research constitutes the first study of the intraspecific diversity of C. tenuipes in Colombia and can serve as the first step in identifying diversity reservoirs and management of epizootic episodes caused by this fungal species.

Worldwide exploration of the microbiome harbored by the cnidarian model, Exaiptasia pallida (Agassiz in Verrill, 1864) indicates a lack of bacterial association specificity at a lower taxonomic rank.

Examination of host-microbe interactions in early diverging metazoans, such as cnidarians, is of great interest from an evolutionary perspective to understand how host-microbial consortia have evolved. To address this problem, we analyzed whether the bacterial community associated with the cosmopolitan and model sea anemone Exaiptasia pallida shows specific patterns across worldwide populations ranging from the Caribbean Sea, and the Atlantic and Pacific oceans. By comparing sequences of the V1-V3 hypervariable regions of the bacterial 16S rRNA gene, we revealed that anemones host a complex and diverse microbial community. When examined at the phylum level, bacterial diversity and abundance associated with E. pallida are broadly conserved across geographic space with samples, containing largely Proteobacteria and Bacteroides. However, the species-level makeup within these phyla differs drastically across space suggesting a high-level core microbiome with local adaptation of the constituents. Indeed, no bacterial OTU was ubiquitously found in all anemones samples. We also revealed changes in the microbial community structure after rearing anemone specimens in captivity within a period of four months. Furthermore, the variation in bacterial community assemblages across geographical locations did not correlate with the composition of microalgal Symbiodinium symbionts. Our findings contrast with the postulation that cnidarian hosts might actively select and maintain species-specific microbial communities that could have resulted from an intimate co-evolution process. The fact that E. pallida is likely an introduced species in most sampled localities suggests that this microbial turnover is a relatively rapid process. Our findings suggest that environmental settings, not host specificity, seem to dictate bacterial community structure associated with this sea anemone. More than maintaining a specific composition of bacterial species some cnidarians associate with a wide range of bacterial species as long as they provide the same physiological benefits towards the maintenance of a healthy host. The examination of the previously uncharacterized bacterial community associated with the cnidarian sea anemone model E. pallida is the first global-scale study of its kind.

Defining the phylogenetic position of Amanita species from Andean Colombia.

Amanita is a worldwide-distributed fungal genus, with approximately 600 known species. Most species within the genus are ectomycorrhizal (ECM), with some saprotrophic representatives. In this study, we constructed the first comprehensive phylogeny including ECM species from Colombia collected in native Quercus humboldtii forests and in introduced Pinus patula plantations. We included 8 species (A. brunneolocularis, A. colombiana, A. flavoconia, A. fuligineodisca, A. muscaria, A. rubescens, A. sororcula, and A. xylinivolva) out of 16 species reported for the country, two new reports: A. citrina and A. virosa, and a new variety A. brunneolocularis var. pallida. Morphological taxonomic keys together with a phylogenetic approach using three nuclear gene regions: partial nuc rDNA 28S nuc rDNA internal transcribed spacers ITS1 and ITS2 and partial translation elongation factor 1-α gene (TEF1), were used to classify the specimens. Several highly supported clades were obtained from the phylogenetic hypotheses obtained by Bayesian inference and maximum likelihood approaches, allowing us to position the Colombian collections in a coherent infrageneric level and to contribute to the knowledge of local Amanita diversity.

Elucidating the evolutionary relationships of the Aiptasiidae, a widespread cnidarian-dinoflagellate model system (Cnidaria: Anthozoa: Actiniaria: Metridioidea).

Sea anemones of the family Aiptasiidae sensu Grajales and Rodríguez (2014) are conspicuous members of shallow-water environments, including several species widely used as model systems for the study of cnidarian-dinoflagellate symbiosis and coral bleaching. Although previously published phylogenetic studies of sea anemones recovered Aiptasiidae as polyphyletic, they only included a sparse sample in terms of its taxonomic diversity and membership of the family had not been yet revised. This study explores the phylogenetic relationships of this family using five molecular markers and including newly collected material from the geographical distribution of most of the currently described genera and species. We find a monophyletic family Aiptasiidae. All the currently proposed genera were recovered as monophyletic units, a finding also supported by diagnostic morphological characters. Our results confirm Bellactis and Laviactis as members of Aiptasiidae, also in agreement with previous morphological studies. The monophyly of the group is congruent with the morphological homogeneity of the members of this family. The obtained results also allow discussing the evolution of morphological characters within the family. Furthermore, we find evidence for and describe a new cryptic species, Exaiptasia brasiliensis sp. nov., based on molecular data, geographical distribution, and the identity of its endosymbiotic dinoflagellate.

Symbiont type influences trophic plasticity of a model cnidarian-dinoflagellate symbiosis.

The association between cnidarians and photosynthetic dinoflagellates within the genus Symbiodinium is a prevalent relationship in tropical and subtropical marine environments. Although the diversity of Symbiodinium provides a possible axis for niche diversification, increased functional range and resilience to physical stressors such as elevated temperature, how such diversity relates to the physiological balance between autotrophy and heterotrophy of the host animal remains unknown. Here, we experimentally show interspecific and intraspecific variability of photosynthetic carbon fixation and subsequent translocation by Symbiodinium to the model cnidarian host Aiptasia pallida. By using a clonal anemone line harboring different species of Symbiodinium, we determined that symbiont identity influences trophic plasticity through its density, capacity to fix carbon, quantity of translocated carbon and ultimately the host's capacity to ingest and digest prey. Symbiont carbon translocation and host prey ingestion were positively correlated across symbiont combinations that consisted of different isoclonal lines of Symbiodinium minutum, while a combination with type D4-5 Symbiodinium displayed lower carbon translocation, and prey capture and digestion more similar to Aiptasia lacking symbionts. The absence of a shift toward greater heterotrophy when carbon translocation is low suggests that the metabolic demand of feeding and digestion may overwhelm nutritional stores when photosynthesis is reduced, and amends the possible role of animal feeding in resistance to or recovery from the effects of climate change in more obligate symbioses such as reef-building corals.

Morphological revision of the genus Aiptasia and the family Aiptasiidae (Cnidaria, Actiniaria, Metridioidea).

Sea anemones of the genus Aiptasia Gosse, 1858 are conspicuous members of shallow-water environments worldwide and serve as a model system for studies of cnidarian-dinoflagellate symbiosis. However, to date there have been no comprehensive analyses investigating the systematics of the group. In addition, previously published phylogenetic studies of sea anemones have shown that the genus is not monophyletic. Herein we revise the genus Aiptasia and the family Aiptasiidae Carlgren, 1924 using newly-collected material. We find that the formerly-named A. pallida (Agassiz in Verrill, 1864) (now Exaiptasia pallida comb. nov.) encompasses a single, widespread species from the tropics and subtropics; we erect a new genus, Exaiptasia gen. nov., for this species primarily based on cnidae, mode of asexual reproduction and symbionts. We also find morphological evidence that supports splitting A. mutabilis into two species: A. couchii (Cocks, 1851) and A. mutabilis. In addition, we find Bellactis Dube, 1983 (formerly placed within Sagartiidae Gosse, 1858) and Laviactis gen. nov. (formerly known Ragactis Andres, 1883, whose familial placement was previously uncertain) belonging within Aiptasiidae. Aiptasiidae is a morphologically homogeneous family whose members (those species in genera Aiptasia, Aiptasiogeton Schmidt, 1972, Bartholomea Duchassaing de Fombressin & Michelotti, 1864, Bellactis, Exaiptasia gen. nov., and Laviactis gen. nov.) are characterized by ectodermal longitudinal muscles in the distal column, rows of cinclides in mid-column, microbasic b-mastigophores in the column, and acontia with basitrichs and microbasic p-amastigophores.

Hidden among sea anemones: the first comprehensive phylogenetic reconstruction of the order Actiniaria (Cnidaria, Anthozoa, Hexacorallia) reveals a novel group of hexacorals.

Sea anemones (order Actiniaria) are among the most diverse and successful members of the anthozoan subclass Hexacorallia, occupying benthic marine habitats across all depths and latitudes. Actiniaria comprises approximately 1,200 species of solitary and skeleton-less polyps and lacks any anatomical synapomorphy. Although monophyly is anticipated based on higher-level molecular phylogenies of Cnidaria, to date, monophyly has not been explicitly tested and at least some hypotheses on the diversification of Hexacorallia have suggested that actiniarians are para- or poly-phyletic. Published phylogenies have demonstrated the inadequacy of existing morphological-based classifications within Actiniaria. Superfamilial groups and most families and genera that have been rigorously studied are not monophyletic, indicating conflict with the current hierarchical classification. We test the monophyly of Actiniaria using two nuclear and three mitochondrial genes with multiple analytical methods. These analyses are the first to include representatives of all three currently-recognized suborders within Actiniaria. We do not recover Actiniaria as a monophyletic clade: the deep-sea anemone Boloceroides daphneae, previously included within the infraorder Boloceroidaria, is resolved outside of Actiniaria in several of the analyses. We erect a new genus and family for B. daphneae, and rank this taxon incerti ordinis. Based on our comprehensive phylogeny, we propose a new formal higher-level classification for Actiniaria composed of only two suborders, Anenthemonae and Enthemonae. Suborder Anenthemonae includes actiniarians with a unique arrangement of mesenteries (members of Edwardsiidae and former suborder Endocoelantheae). Suborder Enthemonae includes actiniarians with the typical arrangement of mesenteries for actiniarians (members of former suborders Protantheae, Ptychodacteae, and Nynantheae and subgroups therein). We also erect subgroups within these two newly-erected suborders. Although some relationships among these newly-defined groups are still ambiguous, morphological and molecular results are consistent enough to proceed with a new higher-level classification and to discuss the putative functional and evolutionary significance of several morphological attributes within Actiniaria.

Genomes-based phylogeny of the genus Xanthomonas.

BACKGROUND: The genus Xanthomonas comprises several plant pathogenic bacteria affecting a wide range of hosts. Despite the economic, industrial and biological importance of Xanthomonas, the classification and phylogenetic relationships within the genus are still under active debate. Some of the relationships between pathovars and species have not been thoroughly clarified, with old pathovars becoming new species. A change in the genus name has been recently suggested for Xanthomonas albilineans, an early branching species currently located in this genus, but a thorough phylogenomic reconstruction would aid in solving these and other discrepancies in this genus. RESULTS: Here we report the results of the genome-wide analysis of DNA sequences from 989 orthologous groups from 17 Xanthomonas spp. genomes available to date, representing all major lineages within the genus. The phylogenetic and computational analyses used in this study have been automated in a Perl package designated Unus, which provides a framework for phylogenomic analyses which can be applied to other datasets at the genomic level. Unus can also be easily incorporated into other phylogenomic pipelines. CONCLUSIONS: Our phylogeny agrees with previous phylogenetic topologies on the genus, but revealed that the genomes of Xanthomonas citri and Xanthomonas fuscans belong to the same species, and that of Xanthomonas albilineans is basal to the joint clade of Xanthomonas and Xylella fastidiosa. Genome reduction was identified in the species Xanthomonas vasicola in addition to the previously identified reduction in Xanthomonas albilineans. Lateral gene transfer was also observed in two gene clusters.

Aislamiento y caracterización de dos cepas de Fusarium oxysporum causantes de la pudrición seca en Solanum tuberosum en Colombia / Isolation and characterization of two strains of Fusarium oxysporum causing potato dry rot in Solanum tuberosum in Colombia

resumen(AU)

Background. Fusarium oxysporum has worldwide distribution and causes severe vascular wilt or root rot in many plants. Strains are classified into formae speciales based on their high degree of host specificity, of which multilocus sequence typing provides a fairly good estimate. Aims. The main aim of this study was to identify the causal agent of an infected potato tuber in Colombia. Methods. Two F. oxysporum isolates were recovered from a potato tuber showing symptoms of dry rot. Both macroscopic and microscopic morphology differences were observed between the two isolates. Koch's postulates were verified and in quantitative tuber pathogenecity trials, both isolates induced moderate dry rot. Ribosomal internal transcribed spacer (ITS) and partial intergenic spacer region (IGS) sequences were PCR-amplified, sequenced and shown to be identical for the two isolates. A maximum parsimony phylogeny was created using F. oxysporum IGS sequences available in the Genebank database, which does not include sequences from the formae speciales tuberosi. Results. Our two isolates were most closely related to a red clover (Trifolium pratense) pathogenic isolate and two non-pathogenic F. oxysporum isolates from birdsfoot trefoil (Lotus corniculatus) and Lycopersicon sp. rhyzosphere (99% identity). Conclusions. These experiments showed that our isolates are not restricted to potato and that a molecular marker is needed to differentiate the formae speciales since the IGS and EF-1alpha do not have the power to do it(AU)

Isolation and characterization of two strains of Fusarium oxysporum causing potato dry rot in Solanum tuberosum in Colombia.

BACKGROUND: Fusarium oxysporum has worldwide distribution and causes severe vascular wilt or root rot in many plants. Strains are classified into formae speciales based on their high degree of host specificity, of which multilocus sequence typing provides a fairly good estimate. AIMS: The main aim of this study was to identify the causal agent of an infected potato tuber in Colombia. METHODS: Two F. oxysporum isolates were recovered from a potato tuber showing symptoms of dry rot. Both macroscopic and microscopic morphology differences were observed between the two isolates. Koch's postulates were verified and in quantitative tuber pathogenecity trials, both isolates induced moderate dry rot. Ribosomal internal transcribed spacer (ITS) and partial intergenic spacer region (IGS) sequences were PCR-amplified, sequenced and shown to be identical for the two isolates. A maximum parsimony phylogeny was created using F. oxysporum IGS sequences available in the Genebank database, which does not include sequences from the formae speciales tuberosi. RESULTS: Our two isolates were most closely related to a red clover (Trifolium pratense) pathogenic isolate and two non-pathogenic F. oxysporum isolates from birdsfoot trefoil (Lotus corniculatus) and Lycopersicon sp. rhyzosphere (99% identity). CONCLUSIONS: These experiments showed that our isolates are not restricted to potato and that a molecular marker is needed to differentiate the formae speciales since the IGS and EF-1α do not have the power to do it.

Genetic diversity of Phytophthora infestans in the Northern Andean region.

BACKGROUND: Phytophthora infestans (Mont.) de Bary, the causal agent of potato late blight, is responsible for tremendous crop losses worldwide. Countries in the northern part of the Andes dedicate a large proportion of the highlands to the production of potato, and more recently, solanaceous fruits such as cape gooseberry (Physalis peruviana) and tree tomato (Solanum betaceum), all of which are hosts of this oomycete. In the Andean region, P. infestans populations have been well characterized in Ecuador and Peru, but are poorly understood in Colombia and Venezuela. To understand the P. infestans population structure in the Northern part of the Andes, four nuclear regions (ITS, Ras, ß-tubulin and Avr3a) and one mitochondrial (Cox1) region were analyzed in isolates of P. infestans sampled from different hosts in Colombia and Venezuela. RESULTS: Low genetic diversity was found within this sample of P. infestans isolates from crops within several regions of Colombia and Venezuela, revealing the presence of clonal populations of the pathogen in this region. We detected low frequency heterozygotes, and their distribution patterns might be a consequence of a high migration rate among populations with poor effective gene flow. Consistent genetic differentiation exists among isolates from different regions. CONCLUSIONS: The results here suggest that in the Northern Andean region P. infestans is a clonal population with some within-clone variation. P. infestans populations in Venezuela reflect historic isolation that is being reinforced by a recent self-sufficiency of potato seeds. In summary, the P. infestans population is mainly shaped by migration and probably by the appearance of variants of key effectors such as Avr3a.

Discovery of Phytophthora infestans genes expressed in planta through mining of cDNA libraries.

BACKGROUND: Phytophthora infestans (Mont.) de Bary causes late blight of potato and tomato, and has a broad host range within the Solanaceae family. Most studies of the Phytophthora--Solanum pathosystem have focused on gene expression in the host and have not analyzed pathogen gene expression in planta. METHODOLOGY/PRINCIPAL FINDINGS: We describe in detail an in silico approach to mine ESTs from inoculated host plants deposited in a database in order to identify particular pathogen sequences associated with disease. We identified candidate effector genes through mining of 22,795 ESTs corresponding to P. infestans cDNA libraries in compatible and incompatible interactions with hosts from the Solanaceae family. CONCLUSIONS/SIGNIFICANCE: We annotated genes of P. infestans expressed in planta associated with late blight using different approaches and assigned putative functions to 373 out of the 501 sequences found in the P. infestans genome draft, including putative secreted proteins, domains associated with pathogenicity and poorly characterized proteins ideal for further experimental studies. Our study provides a methodology for analyzing cDNA libraries and provides an understanding of the plant--oomycete pathosystems that is independent of the host, condition, or type of sample by identifying genes of the pathogen expressed in planta.

Comparative study of Chalcone synthase promoters across plant families / Estudio Comparativo de Promotores de la Chalcón Sintasa en Diferentes Familias de Plantas

In the post – genomic era the understanding of gene regulation has become a challenge and a research priority. In this research, we performed a comparative study of the regulator sequences of the chalcone synthase gene across plant families. Twenty-two sequences of chalcone synthase promoters were compared considering three regulator Cis elements: G-Box, H-Box and TATA Box. Our results show that these Cis elements are conserved among species and even at the family level. However, in some species all of the Cis elements were not found, showing that the expression and regulation of these promoters via the Cis elements can be variable. Additionally, a comparison between promoters from a species with a chalcone synthase multigene family showed that the duplicate genes are variable in the composition of the Cis elements, suggesting that these genes could be expressing in different ways.

Phylogenetic reconstruction using secondary structures of Internal Transcribed Spacer 2 (ITS2, rDNA): finding the molecular and morphological gap in Caribbean gorgonian corals.

BACKGROUND: Most phylogenetic studies using current methods have focused on primary DNA sequence information. However, RNA secondary structures are particularly useful in systematics because they include characteristics, not found in the primary sequence, that give "morphological" information. Despite the number of recent molecular studies on octocorals, there is no consensus opinion about a region that carries enough phylogenetic resolution to solve intrageneric or close species relationships. Moreover, intrageneric morphological information by itself does not always produce accurate phylogenies; intra-species comparisons can reveal greater differences than intra-generic ones. The search for new phylogenetic approaches, such as by RNA secondary structure analysis, is therefore a priority in octocoral research. RESULTS: Initially, twelve predicted RNA secondary structures were reconstructed to provide the basic information for phylogenetic analyses; they accorded with the 6 helicoidal ring model, also present in other groups of corals and eukaryotes. We obtained three similar topologies for nine species of the Caribbean gorgonian genus Eunicea (candelabrum corals) with two sister taxa as outgroups (genera Plexaura and Pseudoplexaura) on the basis of molecular morphometrics of ITS2 RNA secondary structures only, traditional primary sequence analyses and maximum likelihood, and a Bayesian analysis of the combined data. The latter approach allowed us to include both primary sequence and RNA molecular morphometrics; each data partition was allowed to have a different evolution rate. In addition, each helix was partitioned as if it had evolved at a distinct rate. Plexaura flexuosa was found to group within Eunicea; this was best supported by both the molecular morphometrics and combined analyses. We suggest Eunicea flexuosa (Lamouroux, 1821) comb. nov., and we present a new species description including Scanning Electron Microscopy (SEM) images of morphological characteristics (sclerites). Eunicea flexuosa, E. pallida, E. laxispica and E. mammosa formed a separate clade in the molecular phylogenies, and were reciprocally monophyletic with respect to other Eunicea (Euniceopsis subgenus, e.g. E. tourneforti and E. laciniata) in the molecular morphometrics tree, with the exception of E. fusca. Moreover, we suggest a new diagnostic character for Eunicea, also present in E. flexuosa: middle layer sclerites > 1 mm in length. CONCLUSION: ITS2 was a reliable sequence for intrageneric studies in gorgonian octocorals because of the amount of phylogenetic signal, and was corroborated against morphological characters separating Eunicea from Plexaura. The ITS2 RNA secondary structure approach to phylogeny presented here did not rely on alignment methods such as INDELS, but provided clearly homologous characters for partition analysis and RNA molecular morphometrics. These approaches support the divergence of Eunicea flexuosa comb. nov. from the outgroup Plexaura, although it has been considered part of this outgroup for nearly two centuries because of morphological resemblance.