scholarly journals Comparison of Preservation and Extraction Methods on Five Taxonomically Disparate Coral Microbiomes

2021 ◽  
Vol 8 ◽  
Author(s):  
Zoe A. Pratte ◽  
Christina A. Kellogg

All animals are host to a multitude of microorganisms that are essential to the animal’s health. Host-associated microbes have been shown to defend against potential pathogens, provide essential nutrients, interact with the host’s immune system, and even regulate mood. However, it can be difficult to preserve and obtain nucleic acids from some host-associated microbiomes, making studying their microbial communities challenging. Corals are an example of this, in part due to their potentially remote, underwater locations, their thick surface mucopolysaccharide layer, and various inherent molecular inhibitors. This study examined three different preservatives (RNAlater, DNA/RNA Shield, and liquid nitrogen) and two extraction methods (the Qiagen PowerBiofilm kit and the Promega Maxwell RBC kit with modifications) to determine if there was an optimum combination for examining the coral microbiome. These methods were employed across taxonomically diverse coral species, including deep-sea/shallow, stony/soft, and zooxanthellate/azooxanthellate: Lophelia pertusa, Paragorgia johnsoni, Montastraea cavernosa, Porites astreoides, and Stephanocoenia intersepta. Although significant differences were found between preservative types and extraction methods, these differences were subtle, and varied in nature from coral species to coral species. Significant differences between coral species were far more profound than those detected between preservative or extraction method. We suggest that the preservative types presented here and extraction methods using a bead-beating step provide enough consistency to compare coral microbiomes across various studies, as long as subtle differences in microbial communities are attributed to dissimilar methodologies. Additionally, the inclusion of internal controls such as a mock community and extraction blanks can help provide context regarding data quality, improving downstream analyses.

2021 ◽  
Author(s):  
J. K. M. Appah ◽  
E. Dillane ◽  
A. Lim ◽  
R. O ’Riordan ◽  
L. O’Reilly ◽  
...  

Abstract In the Porcupine Bank Canyon, Lophelia pertusa and Madrepora oculata are the main framework-forming corals producing three dimensional structures which provide a home for a range of benthic fauna and microbial communities. To understand the roles and functions that microbes perform in coral health in the Porcupine Bank Canyon, three groups of samples (corals, sediment and water) were collected between 600–800 m depth. DNA was extracted from these samples and metabarcoding was performed on the V3-V4 region of the 16S RNA gene using Illumina technology. The coral microbiome showed greater microbial diversity than both the surrounding sediment and water communities. The genera Pseudomonas, Pseudoalteramonas and Photobacterium were the bacterial communities conserved at 100% coverage of coral samples whereas at the order-level classification Clostridiales, Bacteroidales, Flavobacteriales, Rhodobacterales and Rickettsiales were in high abundance in all the coral samples. A disproportionate distribution of probiotic and pathogenic bacterial groups at the different levels of classification was observed on the corals. Corals do not appear, at present, to be stressed by climate induced changing environmental conditions in the upper Porcupine Bank Canyon. Overall, the corals in the Porcupine Bank Canyon are in a healthy state despite the detection of pathogenic bacterial groups. However, the current trend of climate change and subsequent deep-sea warming could shift the bacterial composition towards a more dominant pathogenic bacterial community, with serious implications for coral health and stability of this important ecosystem.


2018 ◽  
Vol 17 (1) ◽  
pp. 37-49 ◽  
Author(s):  
Abdolrazagh Hashemi Shahraki ◽  
Subba Rao Chaganti ◽  
Daniel Heath

Abstract The characterization of microbial community dynamics using genomic methods is rapidly expanding, impacting many fields including medical, ecological, and environmental research and applications. One of the biggest challenges for such studies is the isolation of environmental DNA (eDNA) from a variety of samples, diverse microbes, and widely variable community compositions. The current study developed environmentally friendly, user safe, economical, and high throughput eDNA extraction methods for mixed aquatic microbial communities and tested them using 16 s rRNA gene meta-barcoding. Five different lysis buffers including (1) cetyltrimethylammonium bromide (CTAB), (2) digestion buffer (DB), (3) guanidinium isothiocyanate (GITC), (4) sucrose lysis (SL), and (5) SL-CTAB, coupled with four different purification methods: (1) phenol-chloroform-isoamyl alcohol (PCI), (2) magnetic Bead-Robotic, (3) magnetic Bead-Manual, and (4) membrane-filtration were tested for their efficacy in extracting eDNA from recreational freshwater samples. Results indicated that the CTAB-PCI and SL-Bead-Robotic methods yielded the highest genomic eDNA concentrations and succeeded in detecting the core microbial community including the rare microbes. However, our study recommends the SL-Bead-Robotic eDNA extraction protocol because this method is safe, environmentally friendly, rapid, high-throughput and inexpensive.


2013 ◽  
Vol 10 (5) ◽  
pp. 3269-3283 ◽  
Author(s):  
J. Felden ◽  
A. Lichtschlag ◽  
F. Wenzhöfer ◽  
D. de Beer ◽  
T. Feseker ◽  
...  

Abstract. The Amon mud volcano (MV), located at 1250 m water depth on the Nile deep-sea fan, is known for its active emission of methane and non-methane hydrocarbons into the hydrosphere. Previous investigations showed a low efficiency of hydrocarbon-degrading anaerobic microbial communities inhabiting the Amon MV center in the presence of sulfate and hydrocarbons in the seeping subsurface fluids. By comparing spatial and temporal patterns of in situ biogeochemical fluxes, temperature gradients, pore water composition, and microbial activities over 3 yr, we investigated why the activity of anaerobic hydrocarbon degraders can be low despite high energy supplies. We found that the central dome of the Amon MV, as well as a lateral mud flow at its base, showed signs of recent exposure of hot subsurface muds lacking active hydrocarbon degrading communities. In these highly disturbed areas, anaerobic degradation of methane was less than 2% of the methane flux. Rather high oxygen consumption rates compared to low sulfide production suggest a faster development of more rapidly growing aerobic hydrocarbon degraders in highly disturbed areas. In contrast, the more stabilized muds surrounding the central gas and fluid conduits hosted active anaerobic hydrocarbon-degrading microbial communities. The low microbial activity in the hydrocarbon-vented areas of Amon MV is thus a consequence of kinetic limitations by heat and mud expulsion, whereas most of the outer MV area is limited by hydrocarbon transport.


2017 ◽  
Vol 32 (1) ◽  
pp. 11
Author(s):  
IVONNE LUNA ORTEGA ◽  
VICENCIO DE LA CRUZ FRANCISCO

Las macroalgas son abundantes en el arrecife Oro Verde, Veracruz pero, hasta ahora, se desconocía su riqueza taxonómica, y se presume que presentan asentamientos en los corales escleractinios hermatípicos. Por ello el presente trabajo investigó qué especies de corales presentaron colonizaciones algales; además, se determinó la composición taxonómica y la similitud de los ensambles de macroalgas entre las especies de corales escleractinios. Se establecieron diez puntos de muestreo de manera sistemática en el arrecife; en cada lugar de estudio se colocó un transecto de banda de 50 x 2 m para localizar y recolectar macroalgas en superficies muertas de corales escleractinios. La frecuencia de aparición de las algas se estimó con base en el total de corales estudiados, así como para cada especie coral. Para explicar similitudes y diferencias significativas de la composición de ensamblajes macroalgales entre especies de corales se aplicaron análisis de similitud y ordenación. Los corales escleractinios con ensambles de algas fueron Siderastrea siderea, Montastraea cavernosa, Pseudodiploria strigosa, Colpophylia natans, Stephanocoenia intersepta, Porites astreoides, Orbicella annularis, Orbicella faveolata. De un total de 100 colonias coralinas revisadas se determinaron 32 especies de macroalgas, las cuales están representadas en tres divisiones, 10 órdenes y 15 familias. Las macroalgas corticadas, foliosas corticadas y filamentosas fueron las más representadas en especies. Las algas de mayor frecuencia sobre los corales masivos fueron Laurencia obtusa, Amphiroa rigida y Caulerpa chemnitzia. Los corales masivos con mayor número de registros de algas fueron S. siderea (9 especies), M. cavernosa (19) y P. strigosa (17). Los ensambles algales en los corales masivos presentaron baja similitud, sin embargo no se detectaron grupos significativamente disimiles. Solamente S. siderea y M. cavernosa son ligeramente parecidos en la composición ficológica. Los resultados sugieren que los corales masivos del arrecife Oro Verde son vulnerables a la colonización de algas, pero es necesario indagar qué condiciones preceden al asentamiento algal.Macroalgal assemblages on dead surfaces of scleractinian corals (Anthozoa: Scleractinia) in the Oro Verde reef, Veracruz, MexicoBenthic macroalgae are abundant in the Oro Verde reef but their taxonomic richness was hitherto unknown and it is presumed to present settlements on the massive corals. For this reason, the present work investigated which species of massive corals show algal colonization. Also, their taxonomic composition was determined, and the similarity of the algal assemblages between species of scleractinian corals was measured. Ten sampling points were systematically established in the reef, where a transect band of 50 x 2 m at each site was placed to locate and collect algae fron the dead surfaces of scleractinian corals. The frequency of occurrence of algae species was estimated based on the total number of coral species studied, as well as on each coral species. Similarity and ordination analysis were applied in order to explain similarities and significant differences of the phycological composition among the coral species. Scleractinian corals with algal assemblages were: Siderastrea siderea, Montastraea cavernosa, Pseudodiploria strigosa, Colpophylia natans, Stephanocoenia intersepta, Porites astreoides, Orbicella annularis, Orbicella faveolata. Thirty-two species of algae were identified from a total of 100 revised coral colonies which are represented in 3 divisions, 10 orders and 15 families. The corticated, foliose corticated and filamentous macroalgae were the most represented species. The most frequent algae on massive corals were Laurencia obtusa, Amphiroa rigida and Caulerpa chemnitzia. Massive corals with higher algal records were S. siderea (9 species), M. cavernosa (19 species) and P. strigosa (17 species). The algal assemblages on the massive corals presented low similarity. However, no significant dissimilar groups were detected. Only S. siderea and M. cavernosa are relatively similar in phycological composition. The results suggest that the massive corals of the Oro Verde reef are vulnerable to the colonization of algae, but it is necessary to investigate the conditions preceding algal settlement.


2020 ◽  
Author(s):  
Zexin Li ◽  
Donald Pan ◽  
Guangshan Wei ◽  
Weiling Pi ◽  
Jiang-Hai Wang ◽  
...  

AbstractIn marine ecosystems, viruses exert control on the composition and metabolism of microbial communities, thus influencing overall biogeochemical cycling. Deep sea sediments associated with cold seeps are known to host taxonomically diverse microbial communities, but little is known about viruses infecting these microorganisms. Here, we probed metagenomes from seven geographically diverse cold seeps across global oceans, to assess viral diversity, virus-host interaction, and virus-encoded auxiliary metabolic genes (AMGs). Gene-sharing network comparisons with viruses inhabiting other ecosystems reveal that cold seep sediments harbour considerable unexplored viral diversity. Most cold seep viruses display high degrees of endemism with seep fluid flux being one of the main drivers of viral community composition. In silico predictions linked 14.2% of the viruses to microbial host populations, with many belonging to poorly understood candidate bacterial and archaeal phyla. Lysis was predicted to be a predominant viral lifestyle based on lineage-specific virus/host abundance ratios. Metabolic predictions of prokaryotic host genomes and viral AMGs suggest that viruses influence microbial hydrocarbon biodegradation at cold seeps, as well as other carbon, sulfur and nitrogen cycling via virus-induced mortality and/or metabolic augmentation. Overall, these findings reveal the global diversity and biogeography of cold seep viruses and indicate how viruses may manipulate seep microbial ecology and biogeochemistry.


2021 ◽  
Vol 8 (9) ◽  
pp. 210035
Author(s):  
Amy A. Briggs ◽  
Anya L. Brown ◽  
Craig W. Osenberg

Microbes influence ecological processes, including the dynamics and health of macro-organisms and their interactions with other species. In coral reefs, microbes mediate negative effects of algae on corals when corals are in contact with algae. However, it is unknown whether these effects extend to larger spatial scales, such as at sites with high algal densities. We investigated how local algal contact and site-level macroalgal cover influenced coral microbial communities in a field study at two islands in French Polynesia, Mo'orea and Mangareva. At 5 sites at each island, we sampled prokaryotic microbial communities (microbiomes) associated with corals, macroalgae, turf algae and water, with coral samples taken from individuals that were isolated from or in contact with turf or macroalgae. Algal contact and macroalgal cover had antagonistic effects on coral microbiome alpha and beta diversity. Additionally, coral microbiomes shifted and became more similar to macroalgal microbiomes at sites with high macroalgal cover and with algal contact, although the microbial taxa that changed varied by island. Our results indicate that coral microbiomes can be affected by algae outside of the coral's immediate vicinity, and local- and site-level effects of algae can obscure each other's effects when both scales are not considered.


2018 ◽  
Vol 9 ◽  
Author(s):  
Jueeli D. Vaidya ◽  
Bartholomeus van den Bogert ◽  
Joan E. Edwards ◽  
Jos Boekhorst ◽  
Sanne van Gastelen ◽  
...  

Author(s):  
M SUGIMORI ◽  
K TAKEUCHI ◽  
S FURUKAWA ◽  
H ISHIDA ◽  
Y SHIRAYAMA

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