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Tara Pacific 16S rRNA ASV table for bacterial communities of crustose coralline algae from the Tuamotu archipelago (French Polynesia)

This data is the result of the primary analysis of the 16S rRNA gene sequencing data collected from the CCA samples collected  during the Tara Pacific expedition. The analysis was conducted using cutadapt/snakemake/dada2 and usearch. A full README is contained within the parent data upload (<a href="https://doi.org/10.5281/zenodo.4451892">https://doi.org/10.5281/zenodo.4451892</a>).

opencc-by-4.0Mar 2023View details →

SI Figure 2: Compositional differences among bacterial microinvertebrate external and internal microbiomes as well as mats they were isolated from using Bray Curtis distance matrix visualized with a NMDS ordination. Circles indicate each community and stars show centroids of microbiome types for each animal host. All host microbiomes (internal and external) are distinct from mat communities (P<0.05), but external microbiomes are more similar to mats than internal microbiomes are to mats. in External and internal microbiomes of Antarctic nematodes are distinct, but more similar to each other than the surrounding environment

SI Figure 2: Compositional differences among bacterial microinvertebrate external and internal microbiomes as well as mats they were isolated from using Bray Curtis distance matrix visualized with a NMDS ordination. Circles indicate each community and stars show centroids of microbiome types for each animal host. All host microbiomes (internal and external) are distinct from mat communities (P<0.05), but external microbiomes are more similar to mats than internal microbiomes are to mats.

Figure 3 in Metagenomic study of the communities of bacterial endophytes in the desert plant Senna Italica and their role in abiotic stress resistance in the plant

Figure 3. Alfa rarefaction curve observed based on observed species (OTUs) value. The curve has shown flatter to the right, which indicates the comparatively high species richness of the senna italica samples. Roots samples: Roots.1, Roots.2, and Roots.3. Leaves samples: Leaves.1, Leaves.2, and Leaves.3 are associated with Senna italica.

Figure 1 in Metagenomic study of the communities of bacterial endophytes in the desert plant Senna Italica and their role in abiotic stress resistance in the plant

Figure 1. (A) Results of clustering: Assembling a group of organisms (The organisms in the same group are similar). (B) The number of OTUs generated for each sample. The Root.1 sample had the most OTUs of 24, while the Leave.1 sample had the fewest of 13. Roots samples: Roots.1, Roots.2, and Roots.3. Leaves samples: Leaves.1, Leaves.2, and Leaves.3 are associated with Senna italica.

Figure 6. A in Metagenomic study of the communities of bacterial endophytes in the desert plant Senna Italica and their role in abiotic stress resistance in the plant

Figure 6. A. The phylum level in Bacteria (bar chart), the bacterial composition of the different samples was similar, while the distribution of each phylum varied in all samples. Based on the V3-V4 region of the 16S rRNA region. Bacterial communities at the phylum classification among the samples (pie chart), as a percentage of the total bacteria isolated from roots and leaves endophyte region. Based on the full-length 16S rRNA sequences. (B) The number of Actinobacteria among the samples. (C) The number of Proteobacteria among the samples. (D) The number of unclassified phyla among the samples. (E) The number of Firmicutes phyla among the samples. (F) The number of Cyanobacteria/Chloroplast among the samples. Roots samples: Roots.1, Roots.2, and Roots.3. Leaves samples: Leaves.1, Leaves.2, and Leaves.3 are associated with Senna italica.

Figure 5 in Metagenomic study of the communities of bacterial endophytes in the desert plant Senna Italica and their role in abiotic stress resistance in the plant

Figure 5. Phylogenetic tree based on 16S rRNA gene sequences representing the diversity of endophytic bacterial communities associated with the leaves and roots from the desert medicinal plant Senna italica "at the Phylum level". The tree was constructed using the "one-click" mode in Phylogeny.fr.(Dereeper et al., 2008).

opencc-by-4.0Jul 2018View details →

Data from: Rhizosphere bacterial community composition depends on plant species identity and soil legacy effects

This record contains supplementary information for the article "Rhizosphere bacterial community composition depends on plant diversity legacy in soil and plant species identity". Supplemental Table S1. The table contains the annotation for all the samples sequenced and analyzed. Supplemental Table S2. The table contains all primer sequences used in the study. Supplemental Table S3. The zip-file contains a table with the taxonomic annotation of the operational taxonomic units (OTUs) identified in the study. Supplemental Table S4.  The zip-file contains a table with sequence counts of the operational taxonomic units (OTUs) identified in the study. Supplemental Table S5. The workbook contains a sheet with the number of operational taxonomic units (OTUs) exhibiting differential abundance in any of the contrasts tested in this study. Note that “down/up” indicates whether the OTU was less (“down”) or more (“up”) abundant in the first group of the contrast. For example, given the contrast “PH_mix_vs_mon_”, “down” corresponds to higher abundance in the pots from the monoculture plant history. Conversely, “up” refers to higher abundance in the pots from the mixed culture plant history. In addition, the workbook contains one sheet per contrast with the logBaseMean (log2 of the average normalized abundance across all samples), the logFC (log2 of the fold-change), the P-value, and the adjusted P-value (FDR). Only OTUs with a P-value <= 0.05 or an adjusted P-value (FDR) <= 0.1 are given. Supplemental Table S6. The table contains the number of bacterial OTUs annotated with a given bacterial phylum. Supplemental Table S7. The table contains all phyla tested for enrichment/depletion in the set of OTUs with an increased abundance in monoculture and mixed culture soils respectively. “Total counts (all OTUs)” corresponds to the total number of all OTUs annotated with a given phyla (reference set). “Observed” corresponds to the number of OTUs annotated with a given phyla in the set OTUs with increased abundance in monoculture/mixed culture soils (test set). "Expected" gives the number of OTUs which would be expected to be annotated with a given phyla if the test set were randomly sampled from the reference set. Supplemental File S1. The zip-file contains a fasta file with the 10'205 OTU sequences identified in the study.

opencc-by-4.0Apr 2019View details →

Bacterial Communities Composition across the French National Territory 2

Bacterial Communities Composition across the French National Territory : the dataset is composed of 1798 samples and 1355 bacterial and archaeal genera

Figure 3 in Bacterial community associated with Culex quinquefasciatus Say, 1823 (Diptera: Culicidae) from an urban area in the Amazon, Brazil

Figure 3 Phylogenetic tree based on maximum likelihood method using MEGA 11. The numbers shown next to the branches correspond to the percentage of replicate trees that the taxa were clustered together in the bootstrap test (1000 replicates).

Figure 2 in Bacterial community associated with Culex quinquefasciatus Say, 1823 (Diptera: Culicidae) from an urban area in the Amazon, Brazil

Figure 2 Heatmap of sequences with taxonomic assignment to genus level. The color gradient (yellow to purple) represents abundance. Yellow: higher bacterial abundance. Purple: lowest bacterial abundance. Abundance legend corresponds log10(%).

Figure 1 in Bacterial community associated with Culex quinquefasciatus Say, 1823 (Diptera: Culicidae) from an urban area in the Amazon, Brazil

Figure 1 Bar chart of the relative abundance of each bacterial genus per sample. The black bar comprises the genera that show relative abundance of less than 1%.

Fig. 4. Goods coverage index for each sample using the OTUs. Retained 330,000 in Bacterial community of ticks (Acari: Ixodidae) and mammals from Arauca, Colombian Orinoquia

Fig. 4. Goods coverage index for each sample using the OTUs. Retained 330,000 (49.90%) features in 15 (93.75%) samples at the specified sampling depth (22,000).

Fig. 3 in Bacterial community of ticks (Acari: Ixodidae) and mammals from Arauca, Colombian Orinoquia

Fig. 3. Operational taxonomic units (OTUs) shared at the genus and species level for mammals and ticks. Percentage values are found in the Venn diagrams. (A) Samples of Desmodus rotundus. (B) Samples of Didelphis marsupialis. (C) Samples of Marmosa robinsoni. (D) Samples of Hydrochoerus. hydrochaeris and Amblyomma mixtum. (E) Samples of Odocoileus virginianus cariacou and Rhipicephalus microplus. (F) Samples of Amblyomma mixtum and Riphicephalus microplus.

Fig. 1 in Bacterial community of ticks (Acari: Ixodidae) and mammals from Arauca, Colombian Orinoquia

Fig. 1. Study area. (A) American Continent, (B) Colombia, (C) Department of Arauca, Colombia. Sampled localities in the municipalities of Arauca. (1) Vereda El Socorro, Finca Los Trompillos. (2) Vereda El Socorro, Finca Palmira. (3) Vereda Las Plumas, El Ca˜no. (4) Vereda Las Plumas, Los Iguanitos.

Fig. 2 in Bacterial community of ticks (Acari: Ixodidae) and mammals from Arauca, Colombian Orinoquia

Fig. 2. Relative frequency of OTUs. The bars represent the bacterial communities and the representative families are indicated. (A) OTUs in blood and liver of mammals and ticks (16 samples); bacterial taxa were grouped up to the genus level (6 levels). (B) Relative frequency of OTUs in ticks (3 samples: MH13; MH16 and MH18). Bacterial taxa were grouped at the species level (7 levels). Complete relative frequencies in supplementary material 2.

Fig. 5 in Bacterial communities associated with Megalopyge opercularis (Smith) (Lepidoptera: Megalopygidae): exploring poisonous lepidopterans

Fig. 5. Diversity order profile (Rényi 1961, Hill 1973) and 95% confidence intervals (dotted) for each developmental stage: larvae (caterpillar, black) and adult (moth, red).

Fig. 3 in Bacterial communities associated with Megalopyge opercularis (Smith) (Lepidoptera: Megalopygidae): exploring poisonous lepidopterans

Fig. 3. Dominant bacterial families found in Megalopyge opercularis: (A) corresponds to percentage of bacterial community in caterpillars; (B) corresponds to percentage of bacterial community in moths.

Fig. 2 in Bacterial communities associated with Megalopyge opercularis (Smith) (Lepidoptera: Megalopygidae): exploring poisonous lepidopterans

Fig. 2. Dominant bacterial community found in Megalopyge opercularis. *Inner circle corresponds to percentage of bacterial community in moths. *Outer circle corresponds to percentage of bacterial community in caterpillars.

Fig. 4 in Bacterial communities associated with Megalopyge opercularis (Smith) (Lepidoptera: Megalopygidae): exploring poisonous lepidopterans

Fig. 4. Percentage of bacterial community at genus level in Megalopyge opercularis. Orange bars correspond to caterpillars and blue bars correspond to moths.