Micro- and macrodiversity in rbcL sequences in ambient phytoplankton populations from the southeastern Gulf of Mexico

Abstract

Ribulose-l,5-diphosphate carboxylase/oxygenase (RuBisCO) large subunit genes (rbcL) were obtained by amplification and cloning of 554 or 614 bp sequences of indigenous phytoplankton populations at 2 stations in the southeastern Gulf of Mexico. One station (Stn 4) was located in a low saiinity, high chlorophyii plume (the 'Green River') which has previously been shown to contain elevated levels of Form IA rbcL mRNA while the other (Stn 7) was in oligotrophic, oceanic water. A diversity of rbcL sequences was obtained, spanning 3 of the 4 evolutionary clades of Form I RuBisCOs. Six nucleotide sequences obtained from Stn 4 were closely related (92 to 96% simiiar) to the Form iAcontaining Prochlorococcus GP2. Flow cytometry and pigment analysis indicated that Prochlorococcus was abundant at this site. Other sequences found included a Form IB rbcL closely related to prasinophytes, and Form ID sequences related to prymnesiophytes, diatoms, and pelagophytes. One sequence was nearly identical to the pelagophyte, Pelagomonas calceolata. At Stn 7, sequences were obtained that were more deeply rooted, and less similar to rbcLs in existing databases (77 to 83 % simiiar), and no Form 1A rbcLs were detected. HPLC pigment signatures and flow cytometry data were consistent with the forms obtained by cloning. The similarity of the 6 Prochlorococcus GP2-like sequences (93 to 98 %) is consistent with the phenomenon of molecular rnicrodiversity as found at other loci in manne (and other environmental) microorganisms.

Phytoplankton community structure in the river‑influenced continental margin of the northern Gulf of Mexico

“…Recent studies have shown the importance of pelagophyte subsurface populations , in some cases accounting for as much as 40% of the total picoeukaryote populations at depth. Besides pelagophytes, prasinophytes belonging to Micro monas and Bathycoccus have also been found to be an important member of picoeukaryote populations at CFM depths and deeper waters of the Gulf of Mexico (Paul et al 2000, Hernandez-Becerril et al 2012. Our results are also consistent with Steinberg et al (2001) and Claustre & Marty (1995), who found the above phytoplankton groups to be a significant part of the community in the chlorophyll maximum and deep populations in the subtropical and tropical North Atlantic.…”

Real-Time PCR Quantification of rbcL (Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase) mRNA in Diatoms and Pelagophytes

“…Picoeukaryotes (including diatoms and pelagophytes) are found throughout the photic zone and numerically dominate the phytoplankton community at the SCM. The diversity of picoeukaryotes at any particular site in the ocean may be quite large; the population may simultaneously include green algae, coccolithophorids, and a great diversity of haptophytes, such as prymnsiophytes, pelagophytes, eustigmatophytes, and diatoms (18,20;Wawrik et al,unpublished). Little is known, however, about the numerical contributions of these groups to oceanic picoplankton communities, nor is there information concerning the relative contributions of these different organisms to primary productivity.…”

“…The genes encoding the small and large subunits are designated rbcS and rbcL, respectively (in proteobacteria they are designated cbbS and cbbL, respectively). Phylogenetic analysis revealed that there are four distinct evolutionary lineages within the form I clade of rbcL sequences (20,32). Form IA is found in most marine picocyanobacteria in the genus Prochlorococcus, as well as some Synechococcus species, while it appears that all green algae and other cyanobacteria contain a form IB rbcL.…”

Phytoplankton community structure and productivity along the axis of the Mississippi River plume in oligotrophic Gulf of Mexico waters

“…DNA sequences were translated into amino acids and translations were aligned with a representative sample of rbcL sequences obtained from GenBank as were all sequences we recovered previously from similar environments (Paul et al 2000, Wawrik et al 2003. Alignment was performed using Omiga 1.1 (Oxford Molecular Group) using a Clustal W pairwise-weighted alignment method.…”