Diversity of the ribulose bisphosphate carboxylase/oxygenase form I gene (rbcL) in natural phytoplankton communities

Abstract

The phytoplankton of the world's oceans play an integral part in global carbon cycling and food webs by conversion of carbon dioxide into organic carbon. They accomplish this task through the action of the Calvin cycle enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Here we have investigated the phylogenetic diversity in the form I rbcL locus in natural phytoplankton communities of the open ocean and representative clones of marine autotrophic picoplankton by mRNA or DNA amplification and sequencing of a 480 to 483 bp internal fragment of this gene. Five gene sequences were recovered from nucleic acids of natural phytoplankton communities of the Gulf of Mexico. The rbcL genes of two Prochlorococcus isolates and one Synechococcus strain (WH8007) were also sequenced. Sequences were aligned with the database of rbcL genes and subjected to both neighbor-joining and parsimony analyses. The five sequences from the natural phytoplankton community spanned nearly the entire diversity of characterized form I rbcL genes, with some sequences closely related to isolates such as Synechococcus and Prochlorococcus (forms IA and I) and prymnesiophyte algae (form ID), while other sequences were deeply rooted. Unexpectedly, the deep euphotic zone contained an organism that possesses a transcriptionally active rbcL gene closely related to that of a recently characterized manganese-oxidizing bacterium, suggesting that such chemoautotrophs may contribute to the diversity of carbon-fixing organisms in the marine euphotic zone.

Kinetic isotope effect and biochemical characterization of form IA RubisCO from the marine cyanobacterium Prochlorococcus marinus MIT9313

“…Form II is found scattered throughout the Proteobacteria and in some dinoflagellates (Tabita 1999), whereas form III is present in Archaea (Finn and Tabita 2003). In accordance with the broad distribution of form I RubisCOs among phytoplankton, when RubisCO genes are amplified from plankton collections, forms IA, IB, IC, and ID are present (Pichard et al 1997).…”

The twelfth Tansley Lecture. Small is beautiful: the picophytoplankton

“…Fossil evidence on this point is ambiguous: while the oldest known fossil cyanobacteria (3·45 billion years old) are filamentous with individual cells larger than 2 µm diameter (see Falkowski & Raven 1997;Raven 1997c), the identification of structures of picophytoplankton size as the remains of living organisms is problematic (Bradley, Harvey & McSween 1997;McKay et al 1997). Molecular phylogenetic analyses (Douglas & Carr 1988;Palenik & Haselkorn 1992;Urbach, Robertson & Chisholm 1992;Pichard, Campbell & Paul 1997;Watson & Tabita 1997) are consistent with Synechococcus and Prochlorococcus both being derived from larger-celled ancestors. The (divinyl)chlorophylls a-and b-containing marine Prochlorococcus arose from Synechococcus-like ancestors (Hess et al 1996;La Roche et al 1996;Partensky et al 1997).…”

Isotope discrimination by form IC RubisCO from Ralstonia eutropha and Rhodobacter sphaeroides, metabolically versatile members of ‘Proteobacteria’ from aquatic and soil habitats

“…ε values for form IC RubisCOs have yet to be determined. Form IC RubisCO gene sequences are commonly detected in samples collected from soil, lakes, rivers and estuaries (Selesi et al, 2005;Tolli and King, 2005;Nigro and King, 2007;Brauer et al, 2011;Yuan et al, 2012;Wu et al, 2014;Alfreider et al, 2017;Lynn et al, 2017) as well as the open ocean (Caspi et al, 1996;Pichard et al, 1997). Facultative autotrophs with form IC RubisCOs are commonly cultivated from soil, lake and river samples; these Alpha-proteobacteria and Beta-proteobacteria may be responsible for the molecular detection of form IC enzymes from these habitats (e.g., Brauer et al, 2011).…”