Purple Sulfur Bacteria Dominate Microbial Community in Brazilian Limestone Cave

The mineralogical composition of caves makes the environment ideal for inhabitation by microbes. However, the bacterial diversity in the cave ecosystem remains largely unexplored. In this paper, we described the bacterial community in an oxic chamber of the Sopradeira cave, an iron-rich limestone cave, in the semiarid region of Northeast Brazil. The microbial population in the cave samples was studied by 16S rDNA next-generation sequencing. A type of purple sulfur bacteria (PSB), Chromatiales, was found to be the most abundant in the sediment (57%), gravel-like (73%), and rock samples (96%). The predominant PSB detected were Ectothiorhodospiraceae, Chromatiaceae, and Woeseiaceae. We identified the PSB in a permanently aphotic zone, with no sulfur detected by energy-dispersive X-ray (EDX) spectroscopy. The absence of light prompted us to investigate for possible nitrogen fixing (nifH) and ammonia oxidizing (amoA) genes in the microbial samples. The nifH gene was found to be present in higher copy numbers than the bacterial-amoA and archaeal-amoA genes, and archaeal-amoA dominated the ammonia-oxidizing community. Although PSB dominated the bacterial community in the samples and may be related to both nitrogen-fixing and ammonia oxidizing bacteria, nitrogen-fixing associated gene was the most detected in those samples, especially in the rock. The present work demonstrates that this cave is an interesting hotspot for the study of ammonia-oxidizing archaea and aphotic PSB.