Microbial communities associated with phosphogenic sediments and phosphoclast-associated DNA of the Benguela upwelling system

Roman Zoss, Fernando Medina Ferrer, Beverly E. Flood, Daniel S. Jones, Deon C. Louw, Jake Bailey

Research output: Contribution to journalArticlepeer-review

7 Scopus citations


The processes that lead to the precipitation of authigenic calcium phosphate minerals in certain marine pore waters remain poorly understood. Phosphogenesis occurs in sediments beneath some oceanic upwelling zones that harbor polyphosphate-accumulating bacteria. These bacteria are believed to concentrate phosphate in sediment pore waters, creating supersaturated conditions with respect to apatite precursors. However, the relationship between microbes and phosphorite formation is not fully resolved. To further study this association, we examined microbial community data generated from two sources: sediment cores recovered from the shelf of the Benguela upwelling region where phosphorites are currently forming, and DNA preserved within phosphoclasts recovered from a phosphorite deposit along the Benguela shelf. iTag and clone library sequencing of the 16S rRNA gene showed that many of our sediment-hosted communities shared large numbers of phylotypes with one another, and that the same metabolic guilds were represented at localities across the shelf. Sulfate-reducing bacteria and sulfur-oxidizing bacteria were particularly abundant in our datasets, as were phylotypes that are known to carry out nitrification and the anaerobic oxidation of ammonium. The DNA extracted from phosphoclasts contained the signature of a distinct microbial community from those observed in the modern sediments. While some aspects of the modern and phosphoclast communities were similar, we observed both an enrichment of certain common microbial classes found in the modern phosphogenic sediments and a relative depletion of others. The phosphoclast-associated DNA could represent a relict signature of one or more microbial assemblages that were present when the apatite or its precursors precipitated. While these taxa may or may not have contributed to the precipitation of the apatite that now hosts their genetic remains, several groups represented in the phosphoclast extract dataset have the genetic potential to metabolize polyphosphate, and perhaps modulate phosphate concentrations in pore waters where carbonate fluorapatite (or its precursors) are known to be precipitating.

Original languageEnglish (US)
Pages (from-to)76-90
Number of pages15
Issue number1
StatePublished - Jan 2019

Bibliographical note

Funding Information:
We gratefully acknowledge the assistance of the staff and students of the RGNO Discovery Camp, the University of Namibia, the Namibian Ministry of Fisheries and Marine Resources, Chibo Chikwililwa (SANUMARC of UNAM), Daniel Montlucon and Kurt Hanselmann (ETH Z?rich), Richard Horaeb and Bronwen Currie (NatMIRC, Namibia), and the crew of the R/V Mirabilis. This work was supported by a grant from the Simons Foundation (341838 J.B.), and by a grant from the National Science Foundation (EAR-1057119), and by the Regional Graduate Network in Oceanography Discovery Camp that is funded by the Agouron Institute, the Simons Foundation and the Scientific Committee for Oceanographic Research (SCOR). FFM was supported by a Fulbright fellowship #15150776 and CONICYT folio-72160214. The authors acknowledge the University of Minnesota Genomics Center (UMGC) for supporting sequencing efforts that contributed to the research results reported in this paper.

Publisher Copyright:
© 2018 John Wiley & Sons Ltd


  • phosphorite
  • polyphosphate
  • sulfur bacteria
  • upwelling


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