Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica
Abstract
:1. Introduction
2. Results
2.1. Variation in Holobiont PalA Levels Across Ascidian Colonies and Collection Sites
2.2. Characterization of Host-Associated Cultivated Bacteria
2.3. Synoicum Adareanum Microbiome (SaM)
2.4. ASV Co-Occurrences, and Relationship to PalA
2.5. Culture Collection: Microbiome and Bacterioplankton Comparisons
2.6. Microbiome: Bacterioplankton Comparisons
3. Discussion
3.1. Core Microbiome
3.2. Secondary Metabolite Distributions and Bioaccumulation in Marine Biota
3.3. The Biosynthetic Potential of the Core
4. Conclusions
5. Materials and Methods
5.1. Cultivation-Dependent Effort
5.2. Field Sample Collections for Cultivation-Independent Efforts
5.3. Palmerolide A Screening
5.4. S. Adareanum-Associated Microbial Cell Preparation
5.5. DNA Extractions
5.6. The 16S rRNA Gene Sequencing
5.7. Bioinformatic Analysis of 16S rRNA Gene tag Sequences
5.8. Statistical Analyses
5.9. Biosynthetic Gene Cluster Analysis
5.10. Data Availability
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Phlya or Class | Whole Community | Core80 | Dynamic50 | Variable |
---|---|---|---|---|
Proteobacteria | ||||
Gammaproteobacteria | 71.990 ± 6.640 | 73.280 ± 6.330 | 51.300 ± 23.160 | 43.710 ± 23.630 |
Alphaproteobacteria | 22.900 ± 5.390 | 23.830 ± 5.930 | 23.830 ± 19.700 | |
Deltaproteobacteria | 0.170 ± 0.100 | 0.160 ± 0.100 | 1.110 ± 2.000 | |
Bacteroidetes | 2.830 ± 2.140 | 0.790 ± 0.690 | 46.550 ± 22.910 | 17.40 ± 14.690 |
Verrucomicrobia | 1.560 ± 2.800 | 1.590 ± 2.930 | 2.830 ± 3.970 | |
Nitrospirae | 0.270 ± 0.230 | 0.290 ± 0.240 | 0.020 ± 0.170 | |
Planctomycetes | 0.120 ± 0.130 | 2.150 ± 3.060 | 4.600 ± 12.840 | |
Actinobacteria | 0.100 ± 0.080 | 0.050 ± 0.050 | 3.150 ± 3.530 | |
Patescibacteria | 0.020 ± 0.090 | 0.840 ± 2.050 | ||
Dadabacteria | 0.020 ± 0.003 | 1.220 ± 2.030 | ||
Uncl. Bacteria | 0.009 ± 0.017 | 0.720 ± 1.530 | ||
Dependentiae | 0.004 ± 0.018 | 0.340 ± 1.990 | ||
Chlamydiae | 0.002 ± 0.006 | 0.190 ± 0.830 | ||
Acidobacteria | 0.000 ± 0.003 | 0.020 ± 0.130 | ||
Chloroflexi | 0.000 ± 0.003 | 0.020 ± 0.130 | ||
Epsilonbacteraeota | 0.000 ± 0.001 | 0.010 ± 0.070 |
ASV_ID | Phylum, Highest Taxonomic Assignment | Average Relative Abundance (%) | Rank | Nearest Neighbor % Identity | NRP BGC | PKS BGC | Combined NRP-PKS |
---|---|---|---|---|---|---|---|
SaM_ASV1, 2, 4, 5, 10, 17, 18 | Proteobacteria, Microbulbifer | 77.54 ± 21.86 | 1, 2, 4, 5, 8, 9, 10 | 97.42 | + | + | - |
SaM_ASV7 | Proteobacteria, Endozoicomonas | 0.47 ± 0.51 | 13 | 96.71 | + | + | - |
SaM_ASV13 | Proteobacteria, Nitrosomonas | 0.46 ± 0.35 | 14 | 99.77 | + | + | + |
SaM_ASV3 | Proteobacteria, Pseudovibrio | 19.92 ± 4.74 | 3 | 98.75 | + | + | + |
SaM_ASV6 | Proteobacteria, Hoeflea | 1.59 ± 1.36 | 6 | 99.25 | + | + | + |
SaM_ASV16 | Proteobacteria, Halocynthiibacter | 0.63 ± 0.64 | 11 | 99.75 | + | - | - |
SaM_ASV11 | Nitrospirota/Nitrospirae, Nitrospira | 0.27 ± 0.23 | 15 | 98.32 | + | + | + |
SaM_ASV12 | Bacteroidota/Bacteroidetes, Lutibacter | 0.50 ± 0.55 | 12 | 94.54 | + | - | + |
SaM_ASV14 | Verrucomicrobiota/Verrucomicrobia, Lentimonas | 0.16 ± 0.22 | 19 | 99.77 | + | - | + |
Sam_ASV21 | Proteobacteria, Rhodobacteraceae | 0.18 ± 0.26 | 18 | 98.75 | - | - | - |
SaM_ASV8 | Proteobacteria, Rhodospirillales | 0.22 ± 0.22 | 17 | 86.60 | - | - | - |
SaM_ASV9 | Bdellovibrionota/Proteobacteria, Bdellovibrionaceae | 0.15 ± 0.09 | 20 | 90.35 | - | - | - |
SaM_ASV19 | Bacteroidetes, Cryomorphaceae | 0.24 ± 0.23 | 16 | 89.10 | - | - | - |
SaM_ASV15 | Verrucomicrobiota/Verrucomicrobia, Opitutaceae | 1.34 ± 2.77 | 7 | 90.14 | - | - | - |
SaM_ASV20 | Actinobacteria, Solirubrobacterales | 0.05 ± 0.05 | 21 | 91.80 | - | - | - |
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Murray, A.E.; Avalon, N.E.; Bishop, L.; Davenport, K.W.; Delage, E.; Dichosa, A.E.K.; Eveillard, D.; Higham, M.L.; Kokkaliari, S.; Lo, C.-C.; et al. Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica. Mar. Drugs 2020, 18, 298. https://doi.org/10.3390/md18060298
Murray AE, Avalon NE, Bishop L, Davenport KW, Delage E, Dichosa AEK, Eveillard D, Higham ML, Kokkaliari S, Lo C-C, et al. Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica. Marine Drugs. 2020; 18(6):298. https://doi.org/10.3390/md18060298
Chicago/Turabian StyleMurray, Alison E., Nicole E. Avalon, Lucas Bishop, Karen W. Davenport, Erwan Delage, Armand E.K. Dichosa, Damien Eveillard, Mary L. Higham, Sofia Kokkaliari, Chien-Chi Lo, and et al. 2020. "Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica" Marine Drugs 18, no. 6: 298. https://doi.org/10.3390/md18060298