Deciphering the prokaryotic community and metabolisms in South African deep-mine biofilms through antibody microarrays and graph theory

• Published in: PloS one Vol. 9; no. 12; p. e114180
• Main Authors: Blanco, Yolanda, Rivas, Luis A, García-Moyano, Antonio, Aguirre, Jacobo, Cruz-Gil, Patricia, Palacín, Arantxa, van Heerden, Esta, Parro, Víctor
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 22.12.2014; Public Library of Science (PLoS)
• Subjects: Anaerobic microorganisms; Antibodies; Antibodies, Archaeal - metabolism; Antibodies, Bacterial - metabolism; Antibody microarrays; Antigens; Archaea - genetics; Archaea - immunology; Archaea - metabolism; Archaea - physiology; Bacteria - genetics; Bacteria - immunology; Bacteria - metabolism; Bacterial Physiological Phenomena; Biofilms; Biofilms - growth & development; Biology and Life Sciences; Biomarkers; Communities; Computer Graphics; Cross-reactivity; Deoxyribonucleic acid; DNA; DNA microarrays; Earth Sciences; Ecology and Environmental Sciences; Environmental monitoring; Evolution; Fermentation; Fractures; Galleries; Gene sequencing; Genomes; Geobiology; Gold; Gold mines & mining; Graph theory; Immunoassay; Immunoglobulins; Immunology; Intersections; Medical research; Methanogenesis; Methanogenic bacteria; Microbial activity; Microorganisms; Mines; Mining; Monitoring methods; Nitrate reduction; Open systems; Oxidation; Oxidizing agents; Oxygen; Oxygen - metabolism; Phylogeny; Protein Array Analysis; Proteins; RNA; RNA, Ribosomal, 16S - genetics; rRNA 16S; Seepage; Sequence Analysis, DNA; South Africa; Storage conditions; Studies; Sulfate; Sulfates; Sulfur; South Africa
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0114180

In the South African deep mines, a variety of biofilms growing in mine corridor walls as water seeps from intersections or from fractures represents excellent proxies for deep-subsurface environments. However, they may be greatly affected by the oxygen inputs through the galleries of mining activities. As a consequence, the interaction between the anaerobic water coming out from the walls with the oxygen inputs creates new conditions that support rich microbial communities. The inherent difficulties for sampling these delicate habitats, together with transport and storage conditions may alter the community features and composition. Therefore, the development of in situ monitoring methods would be desirable for quick evaluation of the microbial community. In this work, we report the usefulness of an antibody-microarray (EMChip66) immunoassay for a quick check of the microbial diversity of biofilms located at 1.3 km below surface within the Beatrix deep gold mine (South Africa). In addition, a deconvolution method, previously described and used for environmental monitoring, based on graph theory and applied on antibody cross-reactivity was used to interpret the immunoassay results. The results were corroborated and further expanded by 16S rRNA gene sequencing analysis. Both culture-independent techniques coincided in detecting features related to aerobic sulfur-oxidizers, aerobic chemoorganotrophic Alphaproteobacteria and metanotrophic Gammaproteobacteria. 16S rRNA gene sequencing detected phylotypes related to nitrate-reducers and anaerobic sulfur-oxidizers, whereas the EMChip66 detected immunological features from methanogens and sulfate-reducers. The results reveal a diverse microbial community with syntrophic metabolisms both anaerobic (fermentation, methanogenesis, sulphate and nitrate reduction) and aerobic (methanotrophy, sulphur oxidation). The presence of oxygen-scavenging microbes might indicate that the system is modified by the artificial oxygen inputs from the mine galleries.