title: Deciphering the prokaryotic community and metabolisms in South African deep-mine biofilms through antibody microarrays and graph theory.
abstract: 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.
authors.affiliation: Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir, km 4, Torrejón de Ardoz, 28850, Madrid, Spain.
authors.forename: Yolanda
authors.initials: Y
authors.lastname: Blanco
authors.affiliation: Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir, km 4, Torrejón de Ardoz, 28850, Madrid, Spain.
authors.forename: Luis A
authors.initials: LA
authors.lastname: Rivas
authors.affiliation: TIA/UFS Metagenomics Platform, Department of Biotechnology, University of the Free State, P. O. Box 339, Bloemfontein, 9300, South Africa.
authors.forename: Antonio
authors.initials: A
authors.lastname: García-Moyano
authors.affiliation: Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir, km 4, Torrejón de Ardoz, 28850, Madrid, Spain.
authors.forename: Jacobo
authors.initials: J
authors.lastname: Aguirre
authors.affiliation: Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir, km 4, Torrejón de Ardoz, 28850, Madrid, Spain.
authors.forename: Patricia
authors.initials: P
authors.lastname: Cruz-Gil
authors.affiliation: Centro de Biotecnología y Genómica de Plantas, Campus de Montegancedo, Autopista M40, km 38, 28223, Pozuelo de Alarcón, Madrid, Spain.
authors.forename: Arantxa
authors.initials: A
authors.lastname: Palacín
authors.affiliation: TIA/UFS Metagenomics Platform, Department of Biotechnology, University of the Free State, P. O. Box 339, Bloemfontein, 9300, South Africa.
authors.forename: Esta
authors.initials: E
authors.lastname: van Heerden
authors.affiliation: Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir, km 4, Torrejón de Ardoz, 28850, Madrid, Spain.
authors.forename: Víctor
authors.initials: V
authors.lastname: Parro
mesh_terms: D019844:Antibodies, Archaeal / Q000378:metabolism; D000907:Antibodies, Bacterial / Q000378:metabolism; D001105:Archaea / Q000235:genetics / Q000276:immunology / Q000378:metabolism* / Q000502:physiology; D001419:Bacteria / Q000235:genetics / Q000276:immunology / Q000378:metabolism*; D018407:Bacterial Physiological Phenomena; D018441:Biofilms / Q000254:growth & development*; D003196:Computer Graphics; D006046:Gold; D007118:Immunoassay; D008906:Mining; D010100:Oxygen / Q000378:metabolism; D010802:Phylogeny; D040081:Protein Array Analysis; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D013019:South Africa
chemical_list: D019844:Antibodies, Archaeal; D000907:Antibodies, Bacterial; D012336:RNA, Ribosomal, 16S; D006046:Gold; D010100:Oxygen