Molecular ecology techniques reveal both spatial and temporal variations in the diversity of archaeal communities within the athalassohaline environment of Rambla Salada, Spain.

We have studied the distribution of the archaeal communities in Rambla Salada (Murcia, Spain) over three different seasons and observed the influence upon them of the environmental variables, salinity, pH, oxygen and temperature. Samples were collected from three representative sites in order to gain an insight into the archaeal population of the rambla as a whole. Denaturing gradient gel electrophoresis patterns and diversity indexes indicate that the diversity of the archaeal community in Rambla Salada changed mainly according to the season. We found no significant differences between the types of sample studied: watery sediments and soils. The upwelling zone showed most diversity in its archaeal community. The overall archaeal community was composed mainly of Halobacteriales and Thermoplasmatales, accounting for 72.6 and 12.1 % of the total, respectively. Haloarcula was the most abundant genus, being present at all three sites during all three seasons. Some few Crenarchaeota were always found, mainly at low-salinity levels. Ordination canonical correspondence analysis demonstrated that salinity affected the structure of the community significantly, whilst pH, oxygen and temperature did so to a lesser extent. Most Halobacteriales correlated positively with salinity and pH, whilst Thermoplasmatales correlated negatively with both salinity and pH and positively with temperature and oxygen. The archaeal community with the highest diversity was sampled during June 2006, the season with the highest salt concentration. Catalyzed reporter deposition-fluorescence in situ hybridization showed that the percentage of archaea in Rambla Salada compared to the total number of microorganisms (as measured by DAPI) ranged from 11.1 to 16.7 %. Our research group had isolated the most abundant taxon, Haloarcula, previously in Rambla Salada using classical culture techniques, but on this occasion, using culture-independent methods, we were also able to identify some phylotypes, Halorubrum, Methanolobus, Natronomonas, Halomicrobium, Halobacterium, Halosimplex, uncultured Thermoplasmatales and uncultured Crenarchaeota, that had remained undetected during our earlier studies in this habitat.

Study of Bacterial Community Composition and Correlation of Environmental Variables in Rambla Salada, a Hypersaline Environment in South-Eastern Spain.

We studied the bacterial community in Rambla Salada in three different sampling sites and in three different seasons and the effect of salinity, oxygen, and pH. All sites samples had high diversity and richness (Rr > 30). The diversity indexes and the analysis of dendrograms obtained by DGGE fingerprint after applying Pearson's and Dice's coefficient showed a strong influence of sampling season. The Pareto-Lorenz (PL) curves and Fo analysis indicated that the microbial communities were balanced and despite the changing environmental conditions, they can preserve their functionality. The main phyla detected by DGGE were Bacteroidetes (39.73%), Proteobacteria (28.43%), Firmicutes (8.23%), and Cyanobacteria (5.14%). The majority of the sequences corresponding to uncultured bacteria belonged to Bacteroidetes phylum. Within Proteobacteria, the main genera detected were Halothiobacillus and Roseovarius. The environmental factors which influenced the community in a higher degree were the salinity and oxygen. The bacteria belonging to Bacteroidetes and Proteobacteria were positively influenced by salinity. Nevertheless, bacteria related to Alpha- and Betaproteobacteria classes and phylum Firmicutes showed a positive correlation with oxygen and pH but negative with salinity. The phylum Cyanobacteria were less influenced by the environmental variables. The bacterial community composition of Rambla Salada was also studied by dilution-to-extinction technique. Using this method, 354 microorganisms were isolated. The 16S sequences of 61 isolates showed that the diversity was very different to those obtained by DGGE and with those obtained previously by using classic culture techniques. The taxa identified by dilution-to-extinction were Proteobacteria (81.92%), Firmicutes (11.30%), Actinobacteria (4.52%), and Bacteroidetes (2.26%) phyla with Gammaproteobacteria as predominant class (65.7%). The main genera were: Marinobacter (38.85%), Halomonas (20.2%), and Bacillus (11.2%). Nine of the 61 identified bacteria showed less than 97% sequence identity with validly described species and may well represent new taxa. The number of bacteria in different samples, locations, and seasons were calculated by CARD-FISH, ranging from 54.3 to 78.9% of the total prokaryotic population. In conclusion, the dilution-to-extinction technique could be a complementary method to classical culture based method, but neither gets to cultivate the major taxa detected by DGGE. The bacterial community was influenced significantly by the physico-chemical parameters (specially the salinity and oxygen), the location and the season of sampling.

Diversity and distribution of Halomonas in Rambla Salada, a hypersaline environment in the southeast of Spain.

We have studied the diversity and distribution of Halomonas populations in the hypersaline habitat Rambla Salada (Murcia, southeastern Spain) by using different molecular techniques. Denaturing gradient gel electrophoresis (DGGE) using specific primers for the 16S rRNA gene of Halomonas followed by a multivariate analysis of the results indicated that richness and evenness of the Halomonas populations were mainly influenced by the season. We found no significant differences between the types of samples studied, from either watery sediments or soil samples. The highest value of diversity was reached in June 2006, the season with the highest salinity. Furthermore, canonical correspondence analysis (CCA) demonstrated that both salinity and pH significantly affected the structure of the Halomonas community. Halomonas almeriensis and two denitrifiers, H. ilicicola and H. ventosae were the predominant species. CARD-FISH showed that the percentage of Halomonas cells with respect to the total number of microorganisms ranged from 4.4% to 5.7%. To study the functional role of denitrifying species, we designed new primer sets targeting denitrification nirS and nosZ genes. Using these primers, we analyzed sediments from the upwelling zone collected in June 2006, where we found the highest percentage of denitrifiers (74%). Halomonas ventosae was the predominant denitrifier in this site.

La biodiversidad microbiana como fuente de productos de interés biotecnológico / No disponible

Introducción: La diversidad microbiana es una fuente importante de productos de interés biotecnológico, tales como antibióticos, enzimas o Polímeros 11,12. Actualmente la biodiversidad está viéndose seriamente afectada por la contaminación y por la intervención del hombre en la naturaleza. La pérdida de microorganismos no solo alterará los ecosistemas sino que supondrá la desaparición de productos de interés biotecnológico. La biodiversidad microbiana permanece aún inexplorada porque con los métodos clásicos de cultivo microbiano sólo aislamos en el laboratorio entre el 0,1 y el 10% de los microorganismos presentes en determinado ecosistema. En cambio la aplicación de herramientas moleculares permite estudiar la diversidad, estructura y la dinámica de comunidades microbianas de diferentes y complejos ambientes, así como detectar la presencia de microorganismos con interés para la industria farmacéutica y la agricultura, entre otras áreas. Objetivo: Analizar y estudiar la diversidad microbiana mediante técnicas moleculares, tanto en ambientes libres de contaminación como es el Parque natural Rambla Salada (Murcia), como en otros hábitatsc ontaminados por las actividades humanas (suelos agrícolas de Motril, Granada)(AU)

Metodología: El estudio de la diversidad microbiana requirió la puesta a punto de una estrategia molecular basada en la amplificación por PCR del gen ribosomal 16S rRNA, a partir del DNA total extraído directamente de las muestras. Posteriormente, se desarrolló la electroforesis en gel con gradiente desnaturalizante (DGGE)1 para la separación de los fragmentos del gen ribosomal 16S ya amplificados, y finalmente se procedió a la secuenciación y comparación de las secuencias obtenidas a partir de los patrones del DGGE con las existentes en las bases de datos. Por otro lado se desarrolló la técnica de hibridación in situ 7 empleando sondas fluorescentes; estas últimas fueron diseñadas para detectar la presencia de microorganismos pertenecientes a los dominios de procariotas Bacteria y Arquea. Discusión y conclusión: Mediante las herramientas moleculares hemos detectado la presencia de arqueas y bacterias no halófilas, halófilas y halotolerantes tanto en todas las zonas analizadas de Rambla Salada como algunas muestras de los suelos agrícolas de Motril. La diversidad microbiana de los suelos agrícolas de Motril es inferior a la de Rambla Salada. Se ha puesto de manifiesto la existencia de una gran diversidad microbiana en Rambla Salada compuesta fundamentalmente por procariotas pertenecientes a los phila Bacteroidetes, Cianobacteria, Proteobacteria, Firmicutes y Actinobacteria cuyos miembros no se aíslan en el laboratorio mediante las técnicas de cultivo empleadas hasta el momento. La presencia de una mayor diversidad microbiana en Rambla Salada indica que los hábitats hipersalinos son una fuente potencial de productos de interés farmacéutico(AU)

Microbial diversity is an important source of products that have potential biotechnological applications, such as antibiotics, enzymes or polymers [1, 2]. The biodiversity is seriously affected by pollution and human impact on natural environments. In this sense, reduction of biodiversity not only alters the ecosystems but also will entail the disappearance of products having biotechnological interest. Microbial biodiversity is not enough known because we have only be able so far to culture between 0.1 and 10% of the microorganisms that exist in nature. Never the less, molecular ecologytechniques represent an opportunity to study the diversity, structure and dynamics of these uncultured microorganisms, both in diverse and complex environments. They also are useful tools to detect Microorganisms that are of interest to pharmaceutical industry and agriculture, among to other areas(AU)

Therefore, the main objective of this work has been to analyse the microbial diversity in different environments using molecular methods. The habitats studied were an hypersaline soil located at Rambla Salada (Murcia), and some agricultural soils from Motril (Granada). We used PCR/DGGE to investigate the microbial diversity; this method is based on the amplification of partial 16S RNAr geneusing the total DNA extracted directly from the sample. Subsequently denaturant gradient gel electrophoresis (DGGE) [3] is developed to separate the amplified fragments of the 16S RNAr gene. Finally the sequences obtained from the DGGE patterns are compared to those available at the database. On the other hand, we used fluorescence in situ hybridization or FISH [4] to detect and quantify microorganisms be longing to the Domain Bacteria and Archaea. According to our results, non halophilic, halophilic, and halotolerant Archaea and Bacteria were present in all the areas analyzed at Rambla Salada, as well as in some samples of the agricultural soils in Motril. Microbial diversity found in the agricultural soils in Motril was lower than in Rambla Salada. Microbial community at Rambla Salada was composed of Prokaryotes belonging to the phyla Bacteroidetes, Cyanobacteria, Proteobacteria, Firmicutes and Actinobacteria, which cannot not so far isolated using methods based on traditional culture techniques(AU)