Aerobic anoxygenic photosynthesis genes and operons in uncultured bacteria in the Delaware River

Abstract

Photosynthesis genes and operons of aerobic anoxygenic photosynthetic (AAP) bacteria have been examined in a variety of marine habitats, but genomic information about freshwater AAP bacteria is lacking. The goal of this study was to examine photosynthesis genes of AAP bacteria in the Delaware River. In a fosmid library, we found two clones bearing photosynthesis gene clusters with unique gene content and organization. Both clones contained 37 open reading frames, with most of those genes encoding known AAP bacterial proteins. The genes in one fosmid were most closely related to those of AAP bacteria in the Rhodobacter genus. The genes of the other clone were related to those of freshwater beta-proteobacteria. Both clones contained the acsF gene, which is required for aerobic bacteriochlorophyll synthesis, suggesting that these bacteria are not anaerobes. The beta-proteobacterial fosmid has the puf operon B-A-L-M-C and is the first example of an uncultured bacterium with this operon structure. The alpha-3-proteobacterial fosmid has a rare gene order (Q-B-A-L-M-X), previously observed only in the Rhodobacter genus. Phylogenetic analyses of photosynthesis genes revealed a possible freshwater cluster of AAP beta-proteobacteria. The data from both Delaware River clones suggest there are groups of freshwater or estuarine AAP bacteria distinct from those found in marine environments.

Bacteriochlorophyll and community structure of aerobic anoxygenic phototrophic bacteria in a particle-rich estuary

“…However, these anaerobic counterparts of AAP bacteria do not seem to be abundant in oxic estuarine waters like the ones we examined (Crump et al, 2007;Waidner and Kirchman, 2008). On the basis of metagenomic sequence analysis of photosynthesis genes and operons, pufM-bearing bacteria in the Delaware Bay lack the anaerobic versions of the hemF and acsF genes, but do possess the acsF gene, which is indicative of aerobic metabolism (Waidner and Kirchman, 2005). In addition, the PCR primers for pufM gene, which we used, should amplify the pufM genes of anaerobic AAP bacteria, including some that are facultative anaerobes, but these were not observed.…”

“…Sequences from site 8 belonged to Groups E, G, I and sequences from site 12 belonged to those plus group K that includes Gammaproteobacteria (Table 2). Notably, pufM Group I includes a 40-kb DNA fragment from a metagenomic library from the nearby Delaware estuary (Waidner and Kirchman, 2005).…”

Diversity of Arctic pelagic <i>Bacteria</i> with an emphasis on photoheterotrophs: a review

“…Wider polymerase chain reaction (PCR) primers targeting puf M gene encoding the M subunit of bacterial photosynthetic reaction centers were then used to expand AAP bacterial diversity in various environments (Yutin et al, 2005). Diverse AAP bacteria were also retrieved in metagenomes from the Atlantic and Pacific oceans Venter et al, 2004;Waidner and Kirchman, 2005;Yutin et al, 2007). Further studies indicated that AAP communities can be structured differently according to geographical location Jiao et al, 2007;Lehours et al, 2010).…”

Metagenomic analysis of uncultured Cytophaga and beta-1,4 glycanases in marine consortia

“…We also surveyed the Delaware River for pufL and pufM genes, which encode AAP reaction center proteins, in a fosmid library of bacterial genomic DNA. Two fosmid clones containing AAP photosynthetic operons were found, completely sequenced by JGI, and annotated (Waidner and Kirchman 2005).…”

“…Results from this part of the project were discussed in detail in our last report. We have also continued work on the aerobic anoxygenic photosynthesizing (AAP) bacteria (Cottrell et al in press;Waidner and Kirchman 2005). Finally, we examined the role of Cytophaga-like bacteria in degrading high molecular weight organic material and stumbled on a cautionary tale about using sequence data for identifying genes from metagenomic libraries (Cottrell et al 2005b).…”