Halites, which are typically found in various Atacama locations, are evaporitic rocks that are considered as micro-scaled salterns. Both structural and functional metagenomic analyses of halite nodules were performed. Structural analyses indicated that the halite microbiota is mainly composed of NaCl-adapted microorganisms. In addition, halites appear to harbor a limited diversity of fungal families together with a biodiverse collection of protozoa. Functional analysis indicated that the halite microbiome possesses the capacity to make an extensive contribution to carbon, nitrogen, and sulfur cycles, but possess a limited capacity to fix nitrogen. The halite metagenome also contains a vast repertory of carbohydrate active enzymes (CAZY) with glycosyl transferases being the most abundant class present, followed by glycosyl hydrolases (GH). Amylases were also present in high abundance, with GH also being identified. Thus, the halite microbiota is a potential useful source of novel enzymes that could have biotechnological applicability. This is the first metagenomic report of fungi and protozoa as endolithobionts of halite nodules, as well as the first attempt to describe the repertoire of CAZY in this community. In addition, we present a comprehensive functional metagenomic analysis of the metabolic capacities of the halite microbiota, providing evidence for the first time on the sulfur cycle in Atacama halites.

Recently, studies were initiated to investigate the metagenome, which represents the genomes of cultured and uncultured microbes, as a rich source for isolation of many novel genes. The metagenomic approach originated from the molecular analysis of microbial communities, which revealed that the majority of microorganisms in nature were not cultivable by standard culturing techniques. Therefore, most microorganisms in nature have not been characterized. Although numerous methods have been reported for direct DNA isolation and purification from microorganisms in soil, the sample preparation procedures and experimental conditions used in different studies vary widely. Soils are therefore one of the most challenging environmental matrices from which to obtain microbial DNA that will support PCR. The Papaloapan River is the second largest river basin in México. For the climatic conditions of this region, there is great diversity in plants, animals and microorganisms. In the Papaloapan region different fruits are grown, however, the main crops are sugarcane and pineapple. In this work the extraction of DNA from soils of sugarcane cultivation was performed. We used PCR tests to assess the quality of DNA extracted from soil by amplifying the 16S rDNA gene. Changes in both protocols were performed; satisfactory results were obtained as to the quality of DNA and gene amplification. These results will allow continuing the metagenomic studies, such as sequencing, library construction and identification of enzymes cellulase and amylase activity. It is the first time these studies were performed in the Papaloapan region.

La metagenómica utiliza técnicas de biología molecular para analizar la diversidad de los genomas microbianos (metagenomas). La diversidad de los metagenomas se ha analizado mediante marcadores moleculares para clasificar bacterias y arqueas en grupos taxonómicos a nivel de género. Entre los marcadores moleculares más utilizados se encuentran los genes ribosomales, genes que codifican subunidades del citocromo C y algunos genes constitutivos (gyrB, rpoB, rpoD, recA, atpD, infB, groEL, pmoA, sodA). El marcador más utilizado es el gen 16S rRNA para clasificar bacterias y arqueas de muestras metagenómicas, aunque no permite clasificar de forma adecuada algunas secuencias. Sin embargo, con la secuenciación del gen completo 16S rRNA se identifican todas las secuencias de las regiones hipervariables, por lo que se ha logrado clasificar hasta nivel taxonómico de especie con este marcador molecular. La secuenciación de próxima generación, también llamada secuenciación masiva o de alto rendimiento ha ayudado a describir metagenomas complejos como los de muestras ambientales, con importancia ecológica, así como metagenomas que crecen en ambientes extremos. También han ayudado a estudios relacionados con sanidad animal y en humanos, y en el ámbito agroalimentario. Específicamente, tanto el uso del marcador molecular 16S rRNA como la secuenciación de alta eficiencia combinadas con el uso de las herramientas bioinformáticas para el análisis metagenómico se han usado para describir el metagenoma ruminal, una comunidad microbiana de gran importancia debido a que está involucrada en la producción animal de carne y leche. A pesar de los muchos estudios que se han realizado en este campo, aún faltan microorganismos por descubrir y caracterizar.