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Bacterial motility is a widespread characteristic that can provide several advantages for the cell, allowing it to move towards more favorable conditions and enabling host-associated processes such as colonization. There are different bacterial motility types, and their expression is highly regulated by the environmental conditions. Because of this, methods for studying motility under realistic experimental conditions are required. A wide variety of approaches have been developed to study bacterial motility. Here, we present the most common techniques and recent advances and discuss their strengths as well as their limitations. We classify them as macroscopic or microscopic and highlight the advantages of three-dimensional imaging in microscopic approaches. Lastly, we discuss methods suited for studying motility in bacterial-host interactions, including the use of the zebrafish model.

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The host microbiome plays an essential role in health and disease. Microbiome modification by pathogens or probiotics has been poorly explored especially in the case of probiotic yeasts. Next-generation sequencing currently provides the best tools for their characterization. Debaryomyces hansenii 97 (D. hansenii 97) and Yarrowia lipolytica 242 (Y. lipolytica 242) are yeasts that protect wildtype zebrafish (Danio rerio) larvae against a Vibrio anguillarum (V. anguillarum) infection, increasing their survival rate. We investigate the effect of these microorganisms on the microbiome and neutrophil response (inflammation) in zebrafish larvae line Tg(Bacmpx:GFP) i114. We postulated that preinoculation of larvae with yeasts would attenuate the intestinal neutrophil response and prevent modification of the larval microbiome induced by the pathogen. Microbiome study was performed by sequencing the V3-V4 region of the 16S rRNA gene and prediction of metabolic pathways by Piphillin in conventionally raised larvae. Survival and the neutrophil response were both evaluated in conventional and germ-free conditions. V. anguillarum infection resulted in higher neutrophil number in the intestinal area compared to non-infected larvae in both conditions. In germ-free conditions, infected larvae pre-inoculated with yeasts showed fewer neutrophil numbers than infected larvae. In both conditions, only D. hansenii 97 increased the survival of infected larvae. Beta diversity of the microbiota was modified by V. anguillarum and both yeasts, compared to non-inoculated larvae. At 3 days post-infection, V. anguillarum modified the relative abundance of 10 genera, and pre-inoculation with D. hansenii 97 and Y. lipolytica 242 prevented the modification of 5 and 6 of these genera, respectively. Both yeasts prevent the increase of Ensifer and Vogesella identified as negative predictors for larval survival (accounting for 40 and 27 of the variance, respectively). In addition, yeast pre-inoculation prevents changes in some metabolic pathways altered by V. anguillarum's infection. These results suggest that both yeasts and V. anguillarum can shape the larval microbiota configuration in the early developmental stage of D. rerio. Moreover, modulation of key taxa or metabolic pathways of the larval microbiome by yeasts can be associated with the survival of infected larvae. This study contributes to the understanding of yeast-pathogen-microbiome interactions, although further studies are needed to elucidate the mechanisms involved.

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Vital traits of woody species in High Andean forest edges of the Cogua Forest Reserve (Colombia). The Cogua Forest Reserve was studied throughout eight months to detect the existence of functional species-groups associated with edge wood forest. A second goal was to determine which species were the most successful in edge areas and their particular vital traits. The regeneration and growth of the forest patches to the adjacent matrix depends on the establishment of these species and their tolerance to both habitats. Three types of High Andean edge forest were studied. Two forest patches were chosen for each of the three edge types: Chusquea scandens edge, "paramune" and old-edge; the name of the latter was given because of its advanced successional state. in each patch, the vegetation was evaluated in two 60 m transects perpendicular to the edge and along the matrix-edge-interior gradient of the forest. All woody species were identified and counted to determine their abundance. A total of nine species were chosen as representative of High Andean forest edges in the reserve, because of their high abundance in this environment, their presence in both patches of each edge type and their ability to colonize the adjacent matrix. Each species was evaluated using 20 vital attributes of individual, leaf, and reproductive traits. Six species groups were found through a Correspondence Analysis. However, all nine species have high variation and plasticity levels for the attributes, even inside the groups. This trend suggests that while they are not clearly differentiated functional groups, they probably are representing different strategies within a single functional group of great plasticity. Tibouchina grossa and Pentacalia Pulchella are found in all edge and matrix types; the other species are found in all edge types, except by Gaiadendron punctatum and Weinmannia tomentosa, absent in the Chusquea scandens edge. All nine species are important elements in the restoration of forest edges, mainly where they are more abundant, evidencing their success in the particular conditions of an edge type. Miconia ligustrina and M. squamulosa are the most relevant species in the Chusquea scandens edge and matrix; while G. punctatum, P. pulchella, W. tomentosa, W. balbisiana and especially Macleania rupestris, are more important in the paramune edge and matrix; Hedyosmum bonplandianum is more important in the edge than in the matrix regeneration, while T. grossa is the most successful edge and matrix regeneration species, because it is the most abundant and has high levels of tolerance, vegetative reproduction and litter production. These features are related with a high rate of tissue replacement, as well as a persistent seed bank with smaller and more numerous seeds, evidence of its high fecundity. Rev. Biol. Trop. 56 (2): 705-720. Epub 2008 June 30.

En la Reserva Forestal de Cogua (Colombia), estudiamos mediante transectos la vegetación leñosa en dos parches de bosque altoandino para tres tipos de borde: chusque, paramizado y antiguo (este último denominado así por presentar un estado sucesional más avanzado). Seleccionamos como especies típicas de borde las que tenían mayor abundancia en esta zona, presentes en ambos parches del borde y capaces de colonizar la matriz adyacente. Se obtuvo un conjunto de nueve especies a las cuales se les evaluaron 20 atributos vitales, generando seis grupos mediante un análisis de agrupamiento (cluster): 1) Weinmannia balbisiana-W. tomentosa, 2) Gaiadendron punctatum-Hedyosmum bonplandianum, 3) Miconia ligustrina-M. squamulosa, 4) Macleania rupestris, 5) Pentacalia pulchella y 6) Tibouchina grossa. La amplia variación y plasticidad de las especies estudiadas en cuanto a los atributos analizados, conduce a pensar que los conjuntos obtenidos no obedecen a grupos funcionales claramente diferenciados, sino más bien a estrategias diferentes y que estas especies podrían hacer parte de un solo grupo funcional de gran plasticidad. T. grossa es la especie de borde más exitosa en la reserva, dados sus altos valores de abundancia, tolerancia fisiológica, reproducción vegetativa, producción de hojarasca y producción de semillas pequeñas, numerosas, formadoras de un banco de semillas persistente que evidencian su alta fecundidad.

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The Cogua Forest Reserve was studied throughout eight months to detect the existence of functional species-groups associated with edge wood forest. A second goal was to determine which species were the most successful in edge areas and their particular vital traits. The regeneration and growth of the forest patches to the adjacent matrix depends on the establishment of these species and their tolerance to both habitats. Three types of High Andean edge forest were studied. Two forest patches were chosen for each of the three edge types: Chusquea scandens edge, "paramune" and old-edge; the name of the latter was given because of its advanced successional state. In each patch, the vegetation was evaluated in two 60 m transects perpendicular to the edge and along the matrix-edge-interior gradient of the forest. All woody species were identified and counted to determine their abundance. A total of nine species were chosen as representative of High Andean forest edges in the reserve, because of their high abundance in this environment, their presence in both patches of each edge type and their ability to colonize the adjacent matrix. Each species was evaluated using 20 vital attributes of individual, leaf, and reproductive traits. Six species groups were found through a Correspondence Analysis. However, all nine species have high variation and plasticity levels for the attributes, even inside the groups. This trend suggests that while they are not clearly differentiated functional groups, they probably are representing different strategies within a single functional group of great plasticity. Tibouchina grossa and Pentacalia Pulchella are found in all edge and matrix types; the other species are found in all edge types, except by Gaiadendron punctatum and Weinmannia tomentosa, absent in the Chusquea scandens edge. All nine species are important elements in the restoration of forest edges, mainly where they are more abundant, evidencing their success in the particular conditions of an edge type. Miconia ligustrina and M. squamulosa are the most relevant species in the Chusquea scandens edge and matrix; while G. punctatum, P. pulchella, W. tomentosa, W. balbisiana and especially Macleania rupestris, are more important in the paramune edge and matrix; Hedyosmum bonplandianum is more important in the edge than in the matrix regeneration, while T. grossa is the most successful edge and matrix regeneration species, because it is the most abundant and has high levels of tolerance, vegetative reproduction and litter production. These features are related with a high rate of tissue replacement, as well as a persistent seed bank with smaller and more numerous seeds, evidence of its high fecundity.

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En este trabajo se caracteriza el sistema de uso, manejo, demanda y oferta potencial de Stenocereus griseus, un cactus columnar muy utilizado por la comunidad indígena Wayúu en la Guajira, Caribe colombiano. Actualmente el uso de S. griseus se restringe a la recolección de madera seca (“yotojoro”) para construcción de viviendas, la recolección de frutos para la alimentación, de tallos jóvenes para alimentos de cabras y para utilizarlos en cercas vivas. Una evaluación de los factores que afectan las poblaciones permitió determinar cinco categorías de daño: las ocasionadas por corte con machete (tipo I), insectos (tipo II), cabras (tipo III), aves (tipo IV) y viento (tipo V). La demanda anual de “yotojoro” está sujeta a la necesidad de construcción de los habitantes del área, que es definida como ocasional. El método actual de cosecha y extracción del mismo no está generando desequilibrio local en el mantenimiento de la especie. La demanda de cardones para cercas vivas y pastoreo es constante durante todo el año y es la que genera el mayor impacto de daño. Finalmente, se discuten los principales problemas de conservación de la especie y se recomienda establecer alternativas de manejo para las actividades de pastoreo.

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