Genetic Analysis of Bacterial Gene Variations in Sulfidic Springs and the Influence on Geochemistry

Culture-independent methods have revolutionized environmental microbiology and geomicrobiology studies and next-generation sequencing and metagenomics techniques continue to reveal the vast genetic diversity of microorganisms. But, these approaches provide comparatively little quantitative information about the roles that naturally occurring microbial gene variations play in local biogeochemical cycling. The goal of this study was to identify how the physical distribution and genetic diversity of microbial genes within a habitat impact environmental geochemistry by examining the biogeography of 16S rRNA genes and bacterial sulfur oxidation (Sox) genes in terrestrial sulfidic springs. 16S rRNA gene pyrosequences were obtained from microbial mats inhabiting eight sulfidic springs in the United States. Pyrosequences were clustered to determine occurrence patterns and the results found that most of the 16S rRNA genes were unique to the springs from which they were retrieved. The occurrence of microbial populations at each spring correlated to specific geochemical conditions, particularly among putative sulfur-oxidizing bacterial groups. Closer examination of a single outflow channel from Rattlesnake Spring in Oklahoma (USA) using twenty-five samples revealed that the distribution of microbial populations were locally distributed and correlated to geochemical conditions. However, cluster-based genetic analysis from this site indicated that inherent biases associated with point sampling affect interpretations of microbial biogeographic patterns. Evaluation of soxB genes from the Rattlesnake Spring outflow channel indicated that the occurrences and distribution patterns of the genes correlated to geochemical conditions within the spring, like the 16S rRNA genes. However, analysis of the translated soxB gene amino acid sequences suggested that the SoxB enzymes could be functionally different. The spatial distribution of the soxB gene variants along the outflow channel could indicate niche partitioning among the bacteria that oxidize reduced sulfur compounds within the spring because the genes could be optimized to specific geochemical conditions and/or reduced sulfur substrates. The identification of gene variations that potentially encode for functionally different enzymes implies that it may be inappropriate to infer function based on DNA or amino acid sequence similarity.