Abstract
We study the microbiome of sea water collected from two locations of the Barbadian coral reefs. The two sites differ in several environmental and ecological variables including their endogenous benthic community and their proximity to urban development and runoffs from inland watersheds. The composition of the microbial communities was estimated using whole genome DNA shotgun sequencing with adjuvant measurements of chemical and environmental qualities. Although both sites exhibit a similar degree of richness, the less urbanized site (Maycocks reef at Hangman’s Bay) has a strong concentration of phototrophs whereas the more urbanized location (Bellairs reef at Folkstone) is enriched for copiotrophs, macroalgal symbionts and marine-related disease-bearing organisms from taxa scattered across the tree of life. Our results are concordant with previous profiles of warm ocean surface waters, suggesting our approach captures the state of each coral reef site, setting the stage for longitudinal studies of marine microbiome dynamics in Barbados.
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Introduction
The capacity of fragile reef ecosystems to maintain key economic, social and environmental services for coastal human societies has been severely challenged by a global decline in coral reef cover of at least 50% (Eddy et al. 2021). The reef system of Barbados (Jackson et al. 2014) and many other small island states in the Caribbean (Burke et al. 2011) have also witnessed comparable coral loss since the 1970s. Documented drivers of coral loss in Barbados include local factors such as sedimentation, eutrophication (Hunte and Wittenberg 1992; Bell and Tomascik 1993) and overfishing (Gill et al. 2019). Regional factors include hurricane damage (Mah and Stearn 1986) and the loss of a keystone grazer (Hunte et al. 1986). Global factors include temperature-induced bleaching due to sea surface warning (Oxenford and Vallès 2016). The relative contribution of these factors to coral loss in Barbados remains unresolved (Wittenberg and Hunte 1992) and likely fluctuates as the reef deteriorates.
The status of the Barbados reef system has been monitored since 1982, providing observational data of widely-used indicators of reef ecological integrity including coral diversity, percent coral and algal cover, and urchin and fish abundance at multiple sites along the west coast of the island (Cermes 2018). However funding constraints limit monitoring to 5 year cycles, a too infrequent interval to inform on reef change in a rapidly evolving global environment, for example, in response to the recent Sargassum invasions (Langin 2018). One motivation of our study here is the need for monitoring techniques that are accessible for small island states such as Barbados (Vallès et al. 2019).
Since microbiomes influence and reflect the environment they inhabit, an understanding of the natural variability and shifts in community gradients of the coral reef waters may provide a more sensitive measure of reef health and allow for the precise identification of environmental disturbances, in turn suggesting prophylactic measures that could be taken to cull negative influences (Glasl et al. 2019; Weber et al. 2020). We profile for the first time the microbiome of reef water at two locations in the Barbadian reef system using whole genome DNA sequencing. These locations were chosen because they lie along a gradient of increasing eutrophication on the west coast of the island and because they have been previously regularly monitored (Bell and Tomascik 1993; Tosic et al. 2009). We ask whether it is possible to identify differences in microbiome composition that reflect differences in eutrophication and other variables that may be used to develop markers which accurately estimate overall reef health, and compare these sites to other oceanic microbial communities (Sunagawa et al. 2015).
Methods
Water samples were collected from the Bellairs reef at Folkestone Marine Reserve (13°11′30.2″N, 59° 38′ 29.2″ W) and the Maycocks reef at Hangman’s Bay (13° 17′ 32.9″ N, 59° 39′ 47.5″ W) at 13:00–15:00 on January 30 and 31, 2018, respectively. Bellairs is a nearshore fringing reef within the no-take area of Folkstone Marine Reserve in relatively shallow waters (~ 10 m). It lies ~ 100 m from Holetown, a densely populated area with tourism and other urban infrastructure (Helmer et al. 2008). The reef has historically suffered from higher levels of eutrophication (Bell and Tomascik 1993) and episodic run-off during the wet season (Tosic et al. 2009).
Maycocks, which lies north of Bellairs, is a bank reef located in deeper water (~ 20 m) approximately 1.5 km away from a sparsely populated coastline with little coastal development (Fig. 1A, B). This site is subject to relatively low levels of chronic eutrophication (Bell and Tomascik 1993) and is too far offshore to be affected by run-off. Maycocks exhibits a higher abundance and more uniform distribution of corals, significantly more hard corals, less filamentous algae, fewer dead corals and greater average fish biomass (Cermes 2018) (Supplemental Table 1A).
At time of sampling the ocean current was flowing in a northwestern direction (Fig. 1C). Sea water was collected at ~ 1 m above the reefs. For each sample (2 per location), 7 L of seawater was sequentially filtered through a 50 μm pore mesh, followed by filtering to discard organisms larger than 3 μm and smaller than 0.22 μm (polycarbonate Sterivex filter, Durapore; Millipore Inc.) consistent with the Tara Oceans project (Sunagawa et al. 2015). Filters were preserved in RNAlater at − 80 °C until processing. DNA was extracted from the Sterivex filter after thawing on ice and RNAlater was removed. The filters were rinsed twice with a sucrose-based lysis buffer and given 1.8 mL of lysis buffer. Filters were then treated with 100 μL of 125 mg mL−1 lysozyme and 20 μL of 10 μg mL−1 RNAse A and left to rotate at 37 °C for 1 h. Then, after incubation, 100 μL of 10 mg mL−1 proteinase K and 100 μL of 20% SDS were added. Filters were rotated for 2 h at 55 °C and the lysate removed. Protein was then precipitated and removed with 0.583 volumes of MPC protein Precipitation Reagent (Epicentre Inc.) and centrifugation at 10,000 × g at 4 °C for 10 min. The supernatant was transferred to a clean tube. The DNA was precipitated with cold isopropanol and resuspended in low TE buffer.
For whole genome sequencing, DNA was prepared (Nextera DNA Library Kit FC-131-1086, Illumina Inc.) and sequenced on an Illumina NovaSeq PE 150 platform (2 × 150 bp reads). Kraken2 version 2.1.0 (Wood and Salzberg 2014) and Bracken 2.6.0 (Lu et al. 2017) were used for alignment and classification with NCBI downloads (restricted to all single cell organisms), the MAR reference database (Klemetsen et al. 2018) and the NCBI Taxonomy database (3/31/2020). Reads mapped to non-microbial taxa were removed from this study. The final microbial dataset after filtering and quality control consists of 4.5 M and 9.2 M reads at Bellairs and Maycocks, respectively (Supplemental Table 1C). Oxygen, seawater temperature and salinity were measured with an EXO2 multiparameter sonde (YSI Inc.; 3 × each per site). Nitrates were measured using the cadmium reduction method with a HACH NitraVer 5 nitrate reagent (3 reps); nitrites were measured using the diazotization method (3 reps; HACH NitriVer 3 nitrite reagent); phosphates were measured using the ascorbic acid method (3 × reps; HACH PhosVer phosphate reagent). All readings were performed with a HACH DR3900 spectrophotometer. Turbidity was measured using a HACH 2100P turbidity meter (3×). Counts of organisms were generated via epifluorescence microscopy as described in (Dinsdale et al. 2008).
The Kruskal–Wallis (KW) test was used to measure significance between the frequencies of child taxa (e.g., genera) within a specific ancestral taxa from the first site versus the frequencies of these same child taxa at the second site. When the KW test was significant, Dunn’s test was used to determine which specific child taxa were significantly different. In some instances we asked if the distribution of observed genera were enriched in a specific ancestral taxa (e.g., clades or phyta); towards this end we used the hypergeometric test where bins correspond to the ancestral taxa and bin size was obtained from our NCBI database above. Clustering was performed by first identifying the most abundant taxa for each sample (Supplemental Information 4), and then transforming their abundances to ranks before use of the Kendall τ distance metric with Ward’s algorithm to construct two dimensional hierarchical clusters.
Results and discussion
We found striking and consistent differences between Bellairs and Maycocks in many dimensions. Maycocks had higher concentrations of dissolved oxygen whereas Bellairs had higher concentrations of nitrate (Supplemental Table 1B). In total, 97% of the genera were identified at both sites through analysis of the sequencing data (Supplemental Table 1C and Supplemental Information 1 for richness analyses). However, the relative frequency of taxa is very different between the two sites. For example, Maycocks exhibits a relative enrichment of Bacteria and Chlorophyta whereas Bellairs contains more eukaryotic (primarily fungal) and archaeal taxa (Fig. 1D; all p << 0.01, Pearson’s \(\chi\)2). Then within the bacterial superkingdom, there are more pronounced differences in the distribution across phyla (Fig. 1E). For example, Maycocks has a strong preference for the Terrabacteria group (37% B vs 69% M; KW test, p << 0.01), whereas Bellairs has a preference for Proteobacteria, specifically the Alpha class. We explore these differences below.
Maycocks is highly enriched for phototrophic microbes including the autotrophic genera Prochlorococcus and Synechococcus which account for over 98% of all Cyanobacteria identified in our study, a fact consistent with the oligotrophic nature of the Barbadian marine environment (Biller et al. 2015). This is consistent with our microscopy imaging which suggests that Maycocks has a tendency towards smaller organisms (Supplemental Fig. 1). Prochlorococcus is typically more prevalent in nutrient poor water while Synechococcus is more prevalent in eutrophic water and coastal plumes of rivers (Wawrik et al. 2003). This is consistent with our data where we observe a 3.7:1 Prochlorococcus to Synechococcus ratio at Bellairs, but a 5.3:1 ratio at Maycocks. The observed frequencies of both genera at Maycocks are more extreme than all other locations world-wide, including nearby Curacao (Weber et al. 2020). Candidatus Pelagibacter, which belongs to the ubiquitous marine SAR11 clade, is also significantly shifted towards Maycocks and is one of the most abundant genera identified in our study (KW test, p << 0.01, Fig. 2A). These small free-living heterotrophic species thrive in low-nutrient environments and play a significant role in carbon cycling (Dinasquet et al. 2019).
The enrichment of phototrophs at Maycocks also holds in the Archaea superkingdom. This includes euryarchaeota such as Candidatus Poseidoniales, which contains some of the most abundant planktonic archaeons in ocean surface waters. It is a motile photoheterotroph capable of degrading proteins and lipids (Rinke et al. 2019) (Fig. 2C). Although the two sites have a similar percentage of Eukaryota, it is the Viridiplantae which exhibit the largest enrichment at Maycocks (21% B vs. 32% M). Some 99% of these reads map to the autotrophic green algae Chlorophyta (Fig. 2D). This includes Micromonas pusilla and M. commoda which are photosynthetic picoeukaryotes known to thrive globally in tropical marine environments and play a key role in the primary production within the euphotic zone (Šlapeta et al. 2006).
Bellairs is enriched for copiotrophs from taxa scattered across the tree of life, an observation consistent with its proximity to urban development and inland run-offs. There is a significant enrichment of Proteobacteria at Bellairs (Fig. 2A), with emphasis on the Alpha class which are major contributors of bacterioplankton to ocean waters (Dunn’s test, p << 0.01; Fig. 2B). The majority of genera within Rhodobacteraceae show a general trend towards the Bellairs site (KW test, p << 0.01), highlighting Dinoroseobacter, Tateyamaria and Jannaschia. Dinorosebacter are aerobic anoxygenic phototrophic bacteria, highly abundant in marine turf algae. Tateyamaria is a genus of coastal aerobic bacteria which can thrive under acidification conditions (Huggett et al. 2018). Jannaschia are aerobic anoxygenic phototrophic bacteria and some species play a role in nitrate reduction (Moran et al. 2007). Bellairs is also slightly enriched for several species of the highly abundant Vibrio genus, of which many species play a significant causative role in coral diseases (Munn 2015) (Supplemental Information 2).
With respect to Archaea, Bellairs is strong enriched for thaumarchaeota involved in nitrification. (23% B versus 3% M, Dunn’s test, p << 0.01; Fig. 2C, Fig. 3A). The chemolithoautotrophic Nitrosopumilus maritimus species is a dominant contributor to nitrification in marine environments (Sánchez-Quinto and Falcón 2019) and Candidatus Nitrosopelagicus is a planktonic pelagic ammonia-oxidizing thaumarchaeon involved in nitrogen and carbon fixation (Santoro et al. 2015).
With respect to Eukaryota, Bellairs is enriched for benthic epiphytes growing on coral and algae. Many species of Stramenopiles within the SAR clade are observed uniquely at Bellairs (Fig. 3B denoted by a yellow star, 11 of all 34 uniquely identified organisms identified at Bellairs (hypergeometric binned by eukaryotic phyta, p << 0.01). This is not likely due to the depth of sequencing alone given that Maycocks in fact received 1.57 fold more reads than Bellairs and analysis in Supplemental Information 1). Several marine diatoms were identified including Licmophora, Cylindrotheca, Seminavis, and others which contribute species that grow on algae and corals or feed on diatoms in eutrophic environments and are causal in brown and red tides. Supplemental Information 3 provides a more detailed investigation of the SAR clade. Analogous to the Stramenopiles, the Foraminifera contribute a surprising number of uniquely identified genera (9 of 34; p << 0.01, hypergeometric binned by clades; Fig. 3B).
We asked how our sites compare to other ocean waters previously profiled by the Tara Oceans (N = 68 epipelagic and mesopelagic locations) (Sunagawa et al. 2015). After normalizing our data with Tara Oceans’ and applying unsupervised clustering of genera frequencies, we see that both sites co-cluster with samples harvested from the surface and deep chlorophyll maximum layers (SRF, DCM respectively) of the trade and coastal biomes (Fig. 3C). This is consistent with the finding from Sunagawa et al. that depth is the most important factor that determines species abundance. Both Bellairs and Maycocks are closest to Red Sea and Indian Ocean samples. Although concentrations of nitrates NO2 and PO4 at Maycocks are similar to levels of its neighbors in the clustering, nitrate levels of Bellairs are higher and more similar to mesopelagic layers. The right subtree of Fig. 4 is enriched for autotrophs consistent with the hot, oligotrophic waters of Barbados.
Although it is infeasible to draw definitive conclusions from only two sites, the microbiome-level profiles are consistent with a shift from coral to macroalgae between Maycocks and Bellairs. This observation is further supported by our chemical/environmental and microscopy data, in addition to documentation of the benthic communities and with known differences in stressors between the two sites. However, our microbiome approach here provides potentially more mechanistic insight into the global effects of some stressors (e.g., run-off) on the state of reef health than standard monitoring efforts (e.g., benthic communities), as it identifies ~ 100 distinct differentially abundant genera which may interact with different dimensions of the reef ecology. As such, the findings here may influence, for example, the design and feasibility of coral rehabilitation projects and, more generally, our capacity to identify microbiome changes consistent with known stressors and states of eutrophication. This sets the stage for systematic studies using microbiome-based markers of the rate of change to reef health along many variables (e.g., geographic location, degree of urbanization, seasonal change). Our approach here should have relevance to other small islands in the vicinity of Barbados with similar reef systems and stressors.
Data availability
Raw sequencing data is available at NCBI SRA accession PRJNA685579. Normalized data is available at JGI GOLD with study ID Gs0136136. Code is available via GitHub https://github.com/hallettmiket/barbadian-reef which links to data, code and analyses at Zenodo.
References
Bell PR, Tomascik T (1993) The demise of the fringing coral reefs of Barbados and of regions in the Great Barrier Reef lagoon - impacts of eutrophication. Colloq Glob Asp Coral Reefs 319–325
Biller SJ, Berube PM, Lindell D, Chisholm SW (2015) Prochlorococcus: the structure and function of collective diversity. Nat Rev Microbiol 13:13–27
Burke L, Reytar K, Spalding M, Perry A (2011) Reefs at risk revisited. World Resources Institute
Cermes (2018) The Barbados Coral Reef Monitoring Programme: Changes in Coral Reef Communities on the West and South Coasts 2007–2012. 81
Dinasquet J, Landa M, Obernosterer I (2019) High contribution of Pelagibacterales to bacterial community composition and activity in spring blooms off Kerguelen Island (Southern Ocean). bioRxiv 633925
Dinsdale EA, Pantos O, Smriga S, Edwards RA, Angly F, Wegley L, Hatay M, Hall D, Brown E, Haynes M, Krause L, Sala E, Sandin SA, Thurber RV, Willis BL, Azam F, Knowlton N, Rohwer F (2008) Microbial Ecology of Four Coral Atolls in the Northern Line Islands. PLoS ONE 3:e1584
Eddy TD, Lam VWY, Reygondeau G, Cisneros-Montemayor AM, Greer K, Palomares MLD, Bruno JF, Ota Y, Cheung WWL (2021) Global decline in capacity of coral reefs to provide ecosystem services. One Earth 4:1278–1285
Gill DA, Oxenford HA, Turner RA, Schuhmann PW (2019) Making the most of data-poor fisheries: Low cost mapping of small island fisheries to inform policy. Mar Policy 101:198–207
Glasl B, Bourne DG, Frade PR, Thomas T, Schaffelke B, Webster NS (2019) Microbial indicators of environmental perturbations in coral reef ecosystems. Microbiome 7:94
Helmer EH, Kennaway TA, Pedreros DH, Clark ML, Marcano-Vega H, Tieszen LL, Schill SR, Carrington CMS (2008) Land cover and forest formation distributions for St. Kitts, Nevis, St. Eustatius, Grenada and Barbados from decision tree classification of cloud-cleared satellite imagery. Caribbean Journal of Science. 44(2):175–198. Caribb J Sci 442175–198 44:175–198
Huggett MJ, McMahon K, Bernasconi R (2018) Future warming and acidification result in multiple ecological impacts to a temperate coralline alga. Environ Microbiol 20:2769–2782
Hunte W, Wittenberg M (1992) Effects of eutrophication and sedimentation on juvenile corals: II. Settlement Mar Biol 114:625–631
Hunte W, Cöté I, Tomascik T (1986) On the dynamics of the mass mortality of Diadema antillarum in Barbados. Coral Reefs 4:135–139
Jackson J, Donovan M, Cramer K, Lam W (2014) Status and trends of Caribbean coral reefs: 1970–2012. Gland, Switzerland
Klemetsen T, Raknes IA, Fu J, Agafonov A, Balasundaram SV, Tartari G, Robertsen E, Willassen NP (2018) The MAR databases: development and implementation of databases specific for marine metagenomics. Nucleic Acids Res 46:D692–D699
Langin K (2018) Seaweed masses assault Caribbean islands. Science 360:1157–1158
Lu J, Breitwieser FP, Thielen P, Salzberg SL (2017) Bracken: estimating species abundance in metagenomics data. PeerJ Comput Sci 3:e104
Mah AJ, Stearn CW (1986) The effect of Hurricane Allen on the Bellairs fringing reef, Barbados. Coral Reefs 4:169–176
Moran MA, Belas R, Schell MA, González JM, Sun F, Sun S, Binder BJ, Edmonds J, Ye W, Orcutt B, Howard EC, Meile C, Palefsky W, Goesmann A, Ren Q, Paulsen I, Ulrich LE, Thompson LS, Saunders E, Buchan A (2007) Ecological Genomics of Marine Roseobacters. Appl Environ Microbiol 73:4559–4569
Munn CB (2015) The Role of Vibrios in Diseases of Corals. Microbiol Spectr 3:
Oxenford HA, Vallès H (2016) Transient turbid water mass reduces temperature-induced coral bleaching and mortality in Barbados. PeerJ 4:
Rinke C, Rubino F, Messer LF, Youssef N, Parks DH, Chuvochina M, Brown M, Jeffries T, Tyson GW, Seymour JR, Hugenholtz P (2019) A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.). ISME J 13:663–675
Sánchez-Quinto A, Falcón LI (2019) Metagenome of Acropora palmata coral rubble: Potential metabolic pathways and diversity in the reef ecosystem. PLoS ONE 14:e0220117
Santoro AE, Dupont CL, Richter RA, Craig MT, Carini P, McIlvin MR, Yang Y, Orsi WD, Moran DM, Saito MA (2015) Genomic and proteomic characterization of “Candidatus Nitrosopelagicus brevis”: An ammonia-oxidizing archaeon from the open ocean. Proc Natl Acad Sci U S A 112:1173–1178
Šlapeta J, López-García P, Moreira D (2006) Global Dispersal and Ancient Cryptic Species in the Smallest Marine Eukaryotes. Mol Biol Evol 23:23–29
Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d’Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans coordinators, Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P, Boss E, Bowler C, Follows M, Karp-Boss L, Krzic U, Reynaud EG, Sardet C, Sieracki M, Velayoudon D (2015) Structure and function of the global ocean microbiome. Science 348:1261359–1261359
Tosic M, Bonnell RB, Dutilleul P, Oxenford HA (2009) Runoff Water Quality, Landuse and Environmental Impacts on the Bellairs Fringing Reef, Barbados. In: Yang X (ed) Remote Sensing and Geospatial Technologies for Coastal Ecosystem Assessment and Management. Springer, Berlin, Heidelberg, pp 521–553
Vallès H, Oxenford HA, Henderson A (2019) Switching between standard coral reef benthic monitoring protocols is complicated: proof of concept. PeerJ 7:e8167
Wawrik B, Paul J, Campbell L, Griffin D, Houchin L, Fuentes-Ortega A, Muller-Karger F (2003) Vertical structure of the phytoplankton community associated with a coastal plume in the Gulf of Mexico. Mar Ecol Prog Ser 251:87–101
Weber L, González-Díaz P, Armenteros M, Ferrer VM, Bretos F, Bartels E, Santoro AE, Apprill A (2020) Microbial signatures of protected and impacted Northern Caribbean reefs. Environ Microbiol 22:499–519
Wittenberg M, Hunte W (1992) Effects of eutrophication and sedimentation on juvenile corals: I. Abundance, mortality and community structure. Mar Biol 112:131–138
Wood DE, Salzberg SL (2014) Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol 15:R46
Acknowledgements
We thank the Bellairs Research Institute of McGill University and the Centre for Resource Management and Environmental Studies (CERMES) for their logistical assistance.
Funding
This work was supported Natural Science and Engineering Research Council (Discovery) and the Canadian Research Chairs grants awarded to MH.
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This work was approved by the Coastal Zone Management Unit, of the Ministry of Maritime Affairs and the Blue Economy, of the Government of Barbados CZ01/9/9.
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Simpson, S., Bettauer, V., Ramachandran, A. et al. A metagenomic-based study of two sites from the Barbadian reef system. Coral Reefs 42, 359–366 (2023). https://doi.org/10.1007/s00338-022-02330-y
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DOI: https://doi.org/10.1007/s00338-022-02330-y