Additional file 8: of Comparative genomic analysis reveals the evolution and environmental adaptation strategies of vibrios

Figure S6. Genes related to the chitin-degrading process in 20 vibrios with complete genomes. Each column indicates a chitin metabolism-related gene family, with the family name indicating the predicted function. The number in the box indicates the copy number of that gene family in the corresponding genome. (PDF 282 kb

Data_Sheet_2_Sediment Depth-Dependent Spatial Variations of Bacterial Communities in Mud Deposits of the Eastern China Marginal Seas.CSV

<p>The mud sediments of the eastern China marginal seas (ECMS) are deposited under different hydrodynamic conditions with different organic matter sources. These events have been demonstrated to exert significant influences on microbial communities and biogeochemical processes in surface sediments. However, the extent to which such effects occur in subsurface microbial communities remains unclear. In this study, both horizontal and vertical (five sites, each for eight layers) distributions of bacterial abundance and community composition in mud deposits of the South Yellow Sea (SYS) and East China Sea (ECS) were investigated by quantitative PCR and Illumina sequencing of the 16S rRNA gene. Both bacterial abundance and diversity were higher in the ECS than in the SYS, and tended to be higher in up than in deep layers. Proteobacteria (JTB255 marine benthic group), Acidobacteria and Bacteroidetes were dominant in the upper layers, whereas Lactococcus, Pseudomonas, and Dehalococcoidia were enriched in the deep layers. The bacterial communities in surface and subsurface sediments showed different inter-taxa relationships, indicating contrasting co-occurrence patterns. The bacterial communities in the upper layer samples clustered in accordance with mud zones, whereas those in the deep layer samples of all sites tended to cluster together. TOC δ¹³C and TON δ¹⁵N significantly affected the bacterial community composition, suggesting that the abundance and composition of organic matter played critical roles in shaping of sedimentary bacterial communities. This study provides novel insights into the distribution of subsurface bacterial communities in mud deposits of the ECMS, and provides clues for understanding the biogeochemical cycles in this area.</p

Additional file 5: of Comparative genomic analysis reveals the evolution and environmental adaptation strategies of vibrios

Figure S3. Pan genome tree. The tree was created based on the presence or absence of gene clusters in the 20 complete Vibrio genomes. The number at each node denotes the bootstrap value based on 1000 replicates. The color red and yellow are corresponding to the core genome tree, suggesting the discrepancy between core and pan genome trees. (PDF 194 kb

Additional file 6: of Comparative genomic analysis reveals the evolution and environmental adaptation strategies of vibrios

Figure S4. Neighbor-joining phylogenetic tree of the 20 vibrios genomes based on 16S rRNA gene. The number at each node denotes the bootstrap value based on 1000 replicates. S. denitrificans OS217 was used as the outgroup. Bar, 0.01 substitutions per site. (PDF 186 kb

Additional file 1: of Comparative genomic analysis reveals the evolution and environmental adaptation strategies of vibrios

Table S1. General features of the 20 complete genomes of Vibrio species analyzed. (DOCX 48 kb

Struttura complessa di servizio urbano sull’asse flaminio a Roma: modalità di integrazione nell’ambito di un sistema cardo-decumano attrezzato, quale ipotesi alternativa al sistema direzionale tangenziale previsto dal PRG del 1962, 1972.

(1972, Contributo in rivista / Ricerca progettuale). “Struttura complessa di servizio urbano sull’asse flaminio a Roma: modalità di integrazione nell’ambito di un sistema cardo-decumano attrezzato, quale ipotesi alternativa al sistema direzionale tangenziale previsto dal PRG del 1962”, 1972. Un contributo (test dimostrativo, prova di studio, arrangiamento virtuale, esperimento di trasposizione, trasferimento di senso), formulato attraverso il riutilizzo e la trascrizione di due serie di elaborati estratte rispettivamente dalla Tesi di laurea di Luigi Calcagnile (figg. 5-10, pp. 80-82), e dalla Tesi di laurea di Rosalba Pillai (figg. 11-14, p. 83), traslocate e montate in libera successione, con una breve nota di presentazione (p. 79), inserito nel saggio critico di Antonino Terranova, “Note su alcune esperienze di composizione architettonica” (pp. 49-75/103), in Università degli Studi di Roma-Facoltà di Ingegneria, Rassegna dell’Istituto di Architettura e Urbanistica, a. VIII, n. 22-23 - agosto 1972

Additional file 7: of Comparative genomic analysis reveals the evolution and environmental adaptation strategies of vibrios

Figure S5. Heatmap presentation of pairwise average nucleotide identity of the 19 Vibrio species with complete genomes. The genomes are hierarchical clustered according to the values of rows. The clusters present in blue and orange are corresponding to the core genome tree. (PDF 212 kb

Primers used for <i>fliC</i> deletion and complementation.

a<p>Nucleotides in bold represent restriction enzyme sites added to the 5′ region of the primer.</p>b<p>Nucleotides underlined represent 15-bp overlap sequences.</p

Characterization of <i>E. tarda</i> strains.

**<p>, P<0.01.</p

Transmission electron microscopy of <i>E. tarda</i> strains.

<p>A: Electron micrographs of 10,000× magnification; B: Electron micrographs of 100,000× magnification to show flagella filaments.</p