Mobile Elements in a Single-Filament Orange Guaymas Basin Beggiatoa (“Candidatus Maribeggiatoa”) sp. Draft Genome: Evidence for Genetic Exchange with Cyanobacteria

Abstract

The draft genome sequence of a single orange Beggiatoa ("Candidatus Maribeggiatoa") filament collected from a microbial mat at a hydrothermal site in Guaymas Basin (Gulf of California, Mexico) shows evidence of extensive genetic exchange with cyanobacteria, in particular for sensory and signal transduction genes. A putative homing endonuclease gene and group I intron within the 23S rRNA gene; several group II catalytic introns; GyrB and DnaE inteins, also encoding homing endonucleases; multiple copies of sequences similar to the fdxN excision elements XisH and XisI (required for heterocyst differentiation in some cyanobacteria); and multiple sequences related to an open reading frame (ORF) (00024_0693) of unknown function all have close non-Beggiatoaceae matches with cyanobacterial sequences. Sequences similar to the uncharacterized ORF and Xis elements are found in other Beggiatoaceae genomes, a variety of cyanobacteria, and a few phylogenetically dispersed pleiomorphic or filamentous bacteria. We speculate that elements shared among filamentous bacterial species may have been exchanged in microbial mats and that some of them may be involved in cell differentiation.

Rapid Redox Signal Transmission by “Cable Bacteria” beneath a Photosynthetic Biofilm

“…These microorganisms constantly readjust their depth distribution in response to diel oscillations in light and redox conditions in order to maintain optimal positions for their growth (17). Gliding motility in the family Beggiatoaceae was acquired by horizontal gene transfer from cyanobacteria, and it has been proposed that the close physical proximity of these organisms within microbial mats over evolutionary time scales favored the gene transfer (19,20). This highlights that strong selective pressures exist across widely divergent taxa for acquiring motility in environments where there are steep and fluctuating chemical gradients (21).…”

Biosphere frontiers of subsurface life in the sedimented hydrothermal system of Guaymas Basin

“…In situ temperature measurements in and beneath these oxygen- and nitrate-dependent sulfur-oxidizing mats indicate cool temperatures (near 10–15°C) right at the sediment surface within the mat, although the temperatures within the underlying sediments rise quickly and can reach >100°C within 30 cm depth (McKay et al, 2012). Genome sequencing of individual filaments supports a sulfur-oxidizing, nitrate-respiring metabolism with both autotrophic and heterotrophic capabilities (MacGregor et al, 2013a,b,c). …”

Visualizing Evolutionary Relationships of Multidomain Proteins: An Example from Receiver (REC) Domains of Sensor Histidine Kinases in the Candidatus Maribeggiatoa str. Orange Guaymas Draft Genome

“…There are complete or near-complete genome sequences for Beggiatoa alba B18LD (BegalDRAFT; Lucas et al, unpublished), Beggiatoa leptomitiformis D-420 (Fomenkov et al, 2015), Thioploca ingrica (THII; Kojima et al, 2015), and Cand . Maribeggiatoa “Orange Guaymas” (MacGregor et al, 2013a,b,c); a partial sequence for Cand . Thiomargarita nelsonii (Mußmann et al, unpublished); and one partial ( Cand .…”

“…Orange Guaymas (BOGUAY) single-filament draft genome contains potential mobile genetic elements of several types (introns, inteins, and possible excision elements) with close relatives among the phylogenetically distant Cyanobacteria, suggesting a history of genetic exchange between these groups (MacGregor et al, 2013c). As identified by the top five BLASTP matches, the largest single category of potentially exchanged genes was for sensory and signal transduction proteins, raising the question of what environmental conditions these might respond to, what other genes they might interact with, and which lineages may have contributed (or received) which functions.…”