Bacterial chemolithotroph population structure has been investigated in Lowes Cove marine intertidal mudflat and Damariscotta Lake, Maine. A 492 to 495 fragment of the cbbL gene, coding for the large subunit of Form I ribulose-1,5- bisphosphate carboxylase/oxygenase (rubisco) was amplified from lake surface (upper 2 mm) sediments and mudflat surface (upper 2 mm), subsurface (5-7 cm), and Mya arenaria burrow wall sediments, as well as sulfide-oxidizing bacterial mat samples. Amplified DNA was used to construct cbbL clone libraries. Phylogenetic analysis showed that Damariscotta Lake cbbL clones were mainly of the 1C type, indicating a facultative carbon monoxide/hydrogen-oxidizing community. Conversely, clones constructed from Lowes Cove sediments were dominated by Form 1A cbbL-containing chemolithotrophs that were most closely related to cbbL genes of sulfur-oxidizing bacteria. This suggested that the chemolithotroph community structure in lake sediments differs greatly from marine sediments. Phylogenetic P-tests of Lowes Cove sediments indicated that surface, subsurface and burrow wall sediments contain significant phylogenetic differences. AMOVA and LIBSHUFF statistical analyses of Lowes Cove sediment cbbL libraries suggested that Mya arenaria burrow wall sediments did not harbor distinct communities when compared to mudflat surface and subsurface libraries. However, Lowes Cove surface and subsurface cbbL libraries displayed moderate genetic difference by AMOVA analyses and were observed to contain distinct chemolithotroph communities by LIBSHUFF analysis of homologous and heterologous coverages
