New biotechnology applications require in-depth preliminary studies of biodiversity. The methods of massive sequencing using metagenomics and bioinformatics tools offer us sufficient and reliable knowledge to understand environmental diversity, to know new microorganisms, and to take advantage of their functional genes. Villa Luz caves, in the southern Mexican state of Tabasco, are fed by at least 26 groundwater inlets, containing 300–500 mg L−1 H2S and <0.1 mg L−1 O2. We extracted environmental DNA for metagenomic analysis of collected samples in five selected Villa Luz caves sites, with pH values from 2.5 to 7. Foreign organisms found in this underground ecosystem can oxidize H2S to H2SO4. These include: biovermiculites, a bacterial association that can grow on the rock walls; snottites, that are whitish, viscous biofilms hanging from the rock walls, and sacks or bags of phlegm, which live within the aquatic environment of the springs. Through the emergency food assistance program (TEFAP) pyrosequencing, a total of 20,901 readings of amplification products from hypervariable regions V1 and V3 of 16S rRNA bacterial gene in whole and pure metagenomic DNA samples were generated. Seven bacterial phyla were identified. As a result, Proteobacteria was more frequent than Acidobacteria. Finally, acidophilic Proteobacteria was detected in UJAT5 sample.

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A rapid bioassay is presented for determining acute toxicity directly in soil. Modifying the Organisation for Economic Cooperation and Development (OECD) protocol 207, it uses a thin layer of moistened soil laid directly in the bottom of the bioassay jar into which the earthworms are placed and incubated. Examples are presented in comparisons between the soil contact bioassay vs. the filter paper bioassay run on Toxicity Characteristic Leaching Procedure (TCLP) extracts of pesticide contaminated soil and petroleum drilling cuttings. In 2,4-dichlorophenoxyacetic acid (2,4-D) contaminated soil (300mg/Kg), no mortality was found in soil extracts, but 100% mortality was found when exposed directly to soil. Treatment with the Daremend® product in five anaerobic/aerobic cycles slowly reduced the 24 h mortality (0%) but still showed 100% mortality at 48 h. However, severe sub-lethal effects (expulsion of celomic/bloody fluids) were reduced from 50% to 37%, and further treatment may reduce the toxicity to acceptable levels. The petroleum drilling cuttings treated by chemical oxidation (1.3% H 2 O 2 , w/w) and bioremediation (simulation of biopiles), showed a similar response, where 0% mortality in soil extracts was found, but 100% mortality with soil contact. Post-treatment with chemical oxidation resulted in a reduction in the soil contact bioassay to 3% and 13% mortality, within the accepted range (10%) of the OECD protocol. Observations are presented with respect to moisture control to prevent earthworm desiccation and recommendation for confirmation using the sub-chronic test in the OECD protocol but by testing the contaminated/treated soil itself rather than artificial soil.

Tropical gar (Atractosteus tropicus) is freshwater and estuarine fish, inhabiting the Earth since the Mesozoic era and undergoing limited physiological variation ever since. Besides its recognized cultural andscientific relevance, the species has seen remarkable growth in its economic impact due to pisciculture. In this study, we present the first report of the whole taxonomic composition of microbial communities in gut contents in juveniles and adults of A. tropicus, by sex and origin (wild and cultivated). For this study, 508 genera were identified, with the most and least abundant being Cetobacterium and Paludibacter, respectively. Fusobacteria, Proteobacteria, Firmicutes, and Bacteroidetes phyla are the core gut microbiome of A. tropicus juvenile and adult by sex and origin. Deinococcus-Thermus phylum sequence was only identified in wild-type males. In the phylogenetic trees reconstruction Lactococcus lactis strains CAU929 and CAU6600, Cp6 and CAU9951,Cetobacterium strain H69, Aeromonas hydrophila strain P5 and WR-5-3-2, Aeromonas sobria strain CP DC28 and Aeromonas hydrophila were identified, some of them with probiotic potential within the three dominant phyla in core gut microbiome in A. tropicus adults, especially in wild-type organisms. Myroides genus was recognized in microbiota gut of the cultivated juvenile A. tropicus. Nevertheless, Alpha diversity indicated that the highest gut microbiota abundance and richness is found in cultivated juvenile and wild-type adult A. tropicus female, rather than adult wild-type males and the least gut microbiota abundance and richness is found in a cultivated adult of A. tropicus for both sexes.

Microorganisms that are adapted to extremely acidic conditions, known as extreme acidophiles, are catalysts for rock weathering, metal cycling, and mineral formation in naturally acidic environments. They are also important drivers of large-scale industrial processes such as biomining and contaminant remediation.