Environmental Adaptation: Genomic Analysis of the Piezotolerant and Psychrotolerant Deep-Sea Iron Reducing Bacterium Shewanella piezotolerans WP3

Shewanella species are widespread in various environments. Here, the genome sequence of Shewanella piezotolerans WP3, a piezotolerant and psychrotolerant iron reducing bacterium from deep-sea sediment was determined with related functional analysis to study its environmental adaptation mechanisms. The genome of WP3 consists of 5,396,476 base pairs (bp) with 4,944 open reading frames (ORFs). It possesses numerous genes or gene clusters which help it to cope with extreme living conditions such as genes for two sets of flagellum systems, structural RNA modification, eicosapentaenoic acid (EPA) biosynthesis and osmolyte transport and synthesis. And WP3 contains 55 open reading frames encoding putative c-type cytochromes which are substantial to its wide environmental adaptation ability. The mtr-omc gene cluster involved in the insoluble metal reduction in the Shewanella genus was identified and compared. The two sets of flagellum systems were found to be differentially regulated under low temperature and high pressure; the lateral flagellum system was found essential for its motility and living at low temperature

A MOLECULAR GENETIC ANALYSIS OF FLAGELLAR FUNCTION IN ESCHERICHIA COLI (CHEMOTAXIS, MOTILITY).

A MOLECULAR GENETIC ANALYSIS OF FLAGELLAR FUNCTION IN ESCHERICHIA COLI (CHEMOTAXIS, MOTILITY)

Identification of Free-living and Particle-Associated Microbial Communities Present in Hadal regions of the Mariana Trench

Relatively few studies have described the microbial populations present in ultra-deep hadal environments, largely as a result of difficulties associated with sampling. Here we report Illumina-tag V6 16S rRNA sequence-based analyses of the free-living and particle-associated microbial communities recovered from locations within two of the deepest hadal sites on Earth, the Challenger Deep (10,918 meters below surface-mbs) and the Sirena Deep (10,667 mbs) within the Mariana Trench, as well as one control site (Ulithi Atoll, 761 mbs). Seawater samples were collected using an autonomous lander positioned ~1m above the seafloor. The bacterial populations within the Mariana Trench bottom water samples were dissimilar to other deep-sea microbial communities, though with overlap with those of diffuse flow hydrothermal vents and deep-subsurface locations. Distinct particle-associated and free-living bacterial communities were found to exist. The hadal bacterial populations were also markedly different from one another, indicating the likelihood of different chemical conditions at the two sites. In contrast to the bacteria, the hadal archaeal communities were more similar to other less deep datasets and to each other due to an abundance of cosmopolitan deep-sea taxa. The hadal communities were enriched in thirty four bacterial and four archaeal operational taxonomic units (OTUs) including members of the Gammaproteobacteria, Epsilonproteobacteria, Marinimicrobia, Cyanobacteria, Deltaproteobacteria, Gemmatimonadetes, Atribacteria, Spirochaetes, and Euryarchaeota. Sequences matching cultivated piezophiles were notably enriched in the Challenger Deep, especially within the particle-associated fraction, and were found in higher abundances than in other hadal studies, where they were either far less prevalent or missing. Our results indicate the importance of heterotrophy, sulfur-cycling, and methane and hydrogen utilization within the bottom waters of the deeper regions of the Mariana Trench, and highlight novel community features of these extreme habitats

Growth curve of WP3 and its mutant.

<p>The growth of WP3 and the WP3Δorf2 mutant under different temperature and pressure conditions were monitered by measuring the optical density of the cultutes at 0D₆₀₀. For each measurement, triplicate cultures were measured simultaneously, and the average value was recorded. A: Growth of the strains at 0.1 MPa and 20 MPa. Wild type WP3 was grown at 0.1 MPa (□), or at 20 MPa (▪); WP3Δorf2 mutant grown at 0.1 MPa (▴) or 20 MPa(Δ); B: Growth of the strains at 4°C and 20°C. Wild type WP3 was grown at 4°C (□), or at 20°C (▪); WP3Δorf2 mutant grown at 4°C (▴) or 20°C (Δ).</p

Motility and growth assays of the WP3 strains.

<p>The motility assays for WP3 and the mutants (WP3Δ1508 has defect in polar flagellum; WP3Δ5118, WP3Δ5125 defect in lateral flagellum) were conducted on 0.3% agar plates at 20°C (A) or 4°C (B). Triplicates of each strain were spotted onto the soft agar, the motile ability of the strains were compared by observing the movements of the strains after 3 days at 20°C, or 7 days at 4°C. The growth of WP3 and the mutants at 4°C was monitered by measuring the optical density of the cultutes at 0D₆₀₀. The mean values with standard deviations (indicated by vertical bars) from triplicate experiments are given. Δ represents the wild type WP3; • mutant WP3Δ1508; ○WP3Δ5118 ▾WP3Δ5125.</p

Phylogenetic tree based on 16S rRNA (A) and whole proteome analysis (B).

<p>The phylogenetic tree of the 16S rRNA gene sequences from various <i>Shewnaella</i> species was constructed by neighbor-joining method using the programs of MEGA package. 1000 trial of bootstrap analysis was used to provide confident estimates for phylogenetic tree topologies. The phylogenetic tree based on the whole proteome sequences of the strains was constructed as described in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001937#s3" target="_blank">materials and methods</a> with 100 trial of bootstrap.</p

General features of two <i>Shewanella</i> genomes.

<p>General features of two <i>Shewanella</i> genomes.</p