Single-cell Sequencing of Thiomargarita Reveals Genomic Flexibility for Adaptation to Dynamic Redox Conditions

Abstract

Large, colorless sulfur-oxidizing bacteria (LSB) of the family Beggiatoaceae form thick mats at sulfidic sediment surfaces, where they efficiently detoxify sulfide before it enters the water column. The genus Thiomargarita harbors the largest known free-living bacteria with cell sizes of up to 750 μm in diameter. In addition to their ability to oxidize reduced sulfur compounds, some Thiomargarita spp. are known to store large amounts of nitrate, phosphate and elemental sulfur internally. To date little is known about their energy yielding metabolic pathways, and how these pathways compare to other Beggiatoaceae. Here, we present a draft single-cell genome of a chain-forming “Candidatus Thiomargarita nelsonii Thio36”, and conduct a comparative analysis to five draft and one full genome of other members of the Beggiatoaceae. “Ca. T. nelsonii Thio36” is able to respire nitrate to both ammonium and dinitrogen, which allows them to flexibly respond to environmental changes. Genes for sulfur oxidation and inorganic carbon fixation confirmed that “Ca. T. nelsonii Thio36” can function as a chemolithoautotroph. Carbon can be fixed via the Calvin–Benson–Bassham cycle, which is common among the Beggiatoaceae. In addition we found key genes of the reductive tricarboxylic acid cycle that point toward an alternative CO2 fixation pathway. Surprisingly, “Ca. T. nelsonii Thio36” also encodes key genes of the C2-cycle that convert 2-phosphoglycolate to 3-phosphoglycerate during photorespiration in higher plants and cyanobacteria. Moreover, we identified a novel trait of a flavin-based energy bifurcation pathway coupled to a Na+-translocating membrane complex (Rnf). The coupling of these pathways may be key to surviving long periods of anoxia. As other Beggiatoaceae “Ca. T. nelsonii Thio36” encodes many genes similar to those of (filamentous) cyanobacteria. In summary, the genome of “Ca. T. nelsonii Thio36” provides additional insight into the ecology of giant sulfur-oxidizing bacteria, and reveals unique genomic features for the Thiomargarita lineage within the Beggiatoaceae.

Sulfur-oxidizing symbionts without canonical genes for autotrophic CO2fixation

“…Our metabolic model has parallels to free-living thiotrophs (63,64) and to heterotrophic bacteria involved in enhanced biological phosphorus removal (EBPR) from wastewater (65).…”

“…For example, lithomixotrophic giant sulfur bacteria like Thiomargarita and Thioploca survive anoxia by using nitrate stored in vacuoles as an alternative electron acceptor to partially oxidize sulfide to elemental sulfur. They also use polyphosphate for energy and can store assimilated carbon as glycogen or PHA (64,66).…”

Major Bottom Water Ventilation Events Do Not Significantly Reduce Basin-Wide Benthic N and P Release in the Eastern Gotland Basin (Baltic Sea)

“…and Beggiatoa spp. in sediments from the Namibian upwelling system (Schulz and Schulz, 2005;Goldhammer et al, 2010;Winkel et al, 2016). Breakdown of polyphosphates may account for the fact that sediments in the deep basin again acted as a PO 3− 4 source in March 2016 where O 2 in the bottom water had decreased to <40 µM.…”

Metabolic potential and in situ activity of marine Marinimicrobia bacteria in an anoxic water column

“…3B). Clade 1 comprised two of the three ARCTIC96B-7 NarG homologues and one of the PN262000N21 homologues, with these Clade 1 sequences displaying greater than 90% amino acid similarity to one another, and 66% amino acid identity to NarG of Geothrix fermentans, a physiologically characterized denitrifier (Coates et al, 1999;Schulz, 2006;Winkel et al, 2016). All three Clade 1 Marinimicrobia NarG sequences analysed here were positioned on contigs downstream of genes encoding a small cytochrome c protein (CccA) and Fe-S transcriptional regulator (IscR), suggesting conservation of gene organization across subgroups (Fig.…”