Cycad Coralloid Roots Contain Bacterial Communities Including Cyanobacteria and Caulobacter spp. That Encode Niche-Specific Biosynthetic Gene Clusters.

Cycads are the only early seed plants that have evolved a specialized root to host endophytic bacteria that fix nitrogen. To provide evolutionary and functional insights into this million-year old symbiosis, we investigate endophytic bacterial sub-communities isolated from coralloid roots of species from Dioon (Zamiaceae) sampled from their natural habitats. We employed a sub-community co-culture experimental strategy to reveal both predominant and rare bacteria, which were characterized using phylogenomics and detailed metabolic annotation. Diazotrophic plant endophytes, including Bradyrhizobium, Burkholderia, Mesorhizobium, Rhizobium, and Nostoc species, dominated the epiphyte-free sub-communities. Draft genomes of six cyanobacteria species were obtained after shotgun metagenomics of selected sub-communities. These data were used for whole-genome inferences that suggest two Dioon-specific monophyletic groups, and a level of specialization characteristic of co-evolved symbiotic relationships. Furthermore, the genomes of these cyanobacteria were found to encode unique biosynthetic gene clusters, predicted to direct the synthesis of specialized metabolites, mainly involving peptides. After combining genome mining with detection of pigment emissions using multiphoton excitation fluorescence microscopy, we also show that Caulobacter species co-exist with cyanobacteria, and may interact with them by means of a novel indigoidine-like specialized metabolite. We provide an unprecedented view of the composition of the cycad coralloid root, including phylogenetic and functional patterns mediated by specialized metabolites that may be important for the evolution of ancient symbiotic adaptations.

Estimation of genetic variation in closely related cycad species in Ceratozamia (Zamiaceae: Cycadales) using rapds markers / Variación genética en especies de cícadas estrechamente relacionadas en Ceratozamia (Zamiaceae: Cycadales) mediante el uso de RAPDs

AbstractThe Ceratozamianorstogii complex from Southern Mexico is made up of four closely related taxa and occurs in similar habitats (Quercus forest). All have linear-lanceolate leaflets with great similarity between them, especially in juvenile stages, but differentiate with age. There has been debate regarding delimitation of species due to character loss in herbarium specimens. The aim of this study was to determine the genetic variation, and to measure genetic similarity between the four taxa. We studied populations in Cintalapa (Chiapas) for C. alvarezii and C. norstogii; the Sierra Atravesada (Oaxaca) for C. chimalapensis, and Villa Flores (Chiapas) for C. mirandae. One population for each taxon was sampled (only one population is known for C. alvarezii) 11-15 randomly chosen adult individuals were sampled. Twenty-eight primers were tested of which five were polymorphic using the RAPD'S technique. The data were analyzed using Bayesian methods. Results revealed low genetic diversity, and a differentiation was found between species, suggesting a recent divergence. A previous morphological and anatomical study on the complex has found the taxa to be distinct. However, the results of this study have shown that the C. norstogii species complex is in a divergence process, probably through genetic drift and founder effects. Rev. Biol. Trop. 65 (1): 305-319. Epub 2017 March 01.

ResumenLos cuatro taxa que componen el complejo Ceratozamia norstogii de especies en el sur de México están estrechamente relacionados y se dan en hábitats similares (bosque de Quercus). Todos tienen folíolos linear-lanceolados con gran similitud entre ellos, sobre todo en las etapas juveniles, pero se diferencian con la edad. Ha habido un debate en relación con la delimitación de especies debido a la pérdida de caracteres en especímenes de herbario. Los objetivos de este estudio son determinar la variación genética y medir la similitud genética entre los cuatro taxones en el complejo. Las poblaciones estudiadas están en; Cintalapa, Chiapas para C. alvarezii y C. norstogii, la Sierra Atravesada, Oaxaca para C. chimalapensis y Villa Flores, Chiapas para C. mirandae. Se tomaron muestras de una población de cada taxón (sólo una población es conocida para C. alvarezii) 11-15 individuos adultos elegidos al azar fueron muestreados. Veintiocho primers fueron probados, de los cuales cinco fueron polimórficos mediante la técnica RAPD's. Los datos fueron analizados utilizando métodos bayesianos. Los resultados revelaron baja diversidad genética y la diferenciación encontrada entre las especies sugiere una divergencia reciente. Un estudio morfológico y anatómico anterior en el complejo encontró que los taxa son distintos. Sin embargo, los resultados del presente estudio han demostrado que el complejo C. norstogii aun se encuentra en un proceso de divergencia, probablemente a través de deriva genética y efectos de fundador.

Estimation of genetic variation in closely related cycad species in Ceratozamia (Zamiaceae: Cycadales) using RAPDs markers.

The Ceratozamia norstogii complex from Southern Mexico is made up of four closely related taxa and occurs in similar habitats (Quercus forest). All have linear-lanceolate leaflets with great similarity between them, especially in juvenile stages, but differentiate with age. There has been debate regarding delimitation of species due to character loss in herbarium specimens. The aim of this study was to determine the genetic variation, and to measure genetic similarity between the four taxa. We studied populations in Cintalapa (Chiapas) for C. alvarezii and C. norstogii; the Sierra Atravesada (Oaxaca) for C. chimalapensis, and Villa Flores (Chiapas) for C. mirandae. One population for each taxon was sampled (only one population is known for C. alvarezii) 11-15 randomly chosen adult individuals were sampled. Twenty-eight primers were tested of which five were polymorphic using the RAPD'S technique. The data were analyzed using Bayesian methods. Results revealed low genetic diversity, and a differentiation was found between species, suggesting a recent divergence. A previous morphological and anatomical study on the complex has found the taxa to be distinct. However, the results of this study have shown that the C. norstogii species complex is in a divergence process, probably through genetic drift and founder effects.

Estratificación vertical y preferencia de hospedero de las epífitas vasculares de un bosque nublado de Chiapas, México

Vertical stratification and host preference by vascular epiphytes in a Chiapas, Mexico, cloud forest. The high diversity of vascular epiphytes in neotropical montane forest has been explained as the result of vertical stratification of the forest and specific relationships between epiphytes and their hosts trees at local scales. In a lower montane cloud forest, we studied the vertical stratification and host preferences of vascular epiphytes in a 0.0625 ha plot where 41 trees ≥ of 10 cm DBH were sampled during 12 months in 2001 and 2002. We found 43 epiphyte species growing on 15 tree genera. We tested for vertical strata and host preferences using 19 epiphyte taxa. We found strong evidence that epiphytes divided the canopy, but those epiphyte species dispersed by animals were generalists with respect to hosts and vertical strata. Wind dispersed epiphytes were vertically stratified, with a higher richness in the lowest tree strata. On average the epiphytes preferred 3.5 host species, suggesting low host preference. Two host species, Ardisia and Quercus, were avoided by the majority of the epiphyte species. Our results show that epiphytes divided the canopy horizontally and were stratified vertically, suggesting that host identity could be important determining the abundance of colonizing sites for epiphytes. Rev. Biol. Trop. 56 (4): 2069-2086. Epub 2008 December 12.

En escala local, la alta diversidad de epífitas vasculares en bosques montanos neotropicales ha sido explicada por que logran estratificar verticalmente al dosel y tienen relaciones específicas con sus hospederos. En un bosque de montaña estudiamos la estratificación vertical y las preferencias de hospedero de las epífitas vasculares en un cuadrante de 0.0625 ha en donde muestreamos 41 árboles ≥10 DAP, durante 12 meses en los años 2001 y 2002. Encontramos 43 especies de epífitas en 15 géneros de árboles. Probamos preferencia de estratos verticales o de hospedero con 19 táxones epífitos. Encontramos evidencia de que las epífitas se dividen el dosel; aunque, las epífitas dispersadas por animales tendieron a ser generalistas. Entre las epífitas dispersadas por el viento reconocimos una clara estratificación vertical, concentrando especies en la parte baja de los árboles. En promedio las especies de epífitas prefirieron 3.5 especies de hospederos, sugiriendo una baja preferencia. Dos especies de árboles resultaron ser malos hospederos, Ardisia y Quercus. Nuestros resultados muestran que las epífitas parten el dosel horizontalmente, se estratifican verticalmente y sugieren que la identidad de los hospederos es importante por que puede determinar la abundancia de sitios colonizables para muchas epífitas.

[Vertical stratification and host preference by vascular epiphytes in a Chiapas, Mexico, cloud forest]. / Estratificación vertical y preferencia de hospedero de las epifitas vasculares de un bosque nublado de Chiapas, México.

The high diversity of vascular epiphytes in neotropical montane forest has been explained as the result of vertical stratification of the forest and specific relationships between epiphytes and their hosts trees at local scales. In a lower montane cloud forest, we studied the vertical stratification and host preferences of vascular epiphytes in a 0.0625 ha plot where 41 trees > or = of 10 cm DBH were sampled during 12 months in 2001 and 2002. We found 43 epiphyte species growing on 15 tree genera. We tested for vertical strata and host preferences using 19 epiphyte taxa. We found strong evidence that epiphytes divided the canopy, but those epiphyte species dispersed by animals were generalists with respect to hosts and vertical strata. Wind dispersed epiphytes were vertically stratified, with a higher richness in the lowest tree strata. On average the epiphytes preferred 3.5 host species, suggesting low host preference. Two host species, Ardisia and Quercus, were avoided by the majority of the epiphyte species. Our results show that epiphytes divided the canopy horizontally and were stratified vertically, suggesting that host identity could be important determining the abundance of colonizing sites for epiphytes.