Bacteria

Seagrasses represent the unique re-colonization of the marine ecosystem by angiosperms. As their terrestrial relatives, seagrasses are important habitat providers but in contrast, their microbiomes are still poorly known. The microbial community associated with terrestrial plants is intensively studied and plays an important role in plant fitness. The close relation of seagrasses to terrestrial plants suggests a resemblance in survival strategies, including the creation of a microbiome distinct of the surrounding environment. To obtain more knowledge regarding seagrass microbiomes and their intra- and interspecies differentiation, samples of three tropical seagrass species occurring around the island of Curaçao, the invasive Halophila stipulacea and the natives Halodule wrightii and Thalassia testudinum, were collected. Root and leaf-associated microbes were separately analyzed using high throughput Illumina sequencing of the region V5-V7 of the 16S rRNA gene. Sequences were aligned and clustered into Operational Taxonomic Units (OTUs). Results displayed the occurrence of a seagrass-specific microbiome, distinct from that of the surrounding seawater and sediment. The existence of a species and tissue (root/leaf) specific bacterial community and structure was detected, along with a bacterial community that was shared among the seagrasses. OTUs belonging to the shared seagrass community were mostly of the orders rhizobiales. Desulfobacterales was the most abundant order associated with the roots and Rhodobacterales with the leaves of the three seagrass species. Species-specific bacteria are represented mostly by OTUs of the same orders as the common OTUs, along with a few species-specific orders. The high abundant and widespread bacterial OTUs were identified to be mostly associated with sulfur and nitrogen cycling, which point towards the importance of these processes in seagrass fitness.

Comparative studies on the distribution of archaeal versus bacterial communities associ- ated with the surface mucus layer of corals have rarely taken place. It has therefore remained enigmatic whether mucus-associated archaeal and bacterial communities exhibit a similar specificity towards coral hosts and whether they vary in the same fashion over spa- tial gradients and between reef locations. We used microbial community profiling (terminal- restriction fragment length polymorphism, T-RFLP) and clone library sequencing of the 16S rRNA gene to compare the diversity and community structure of dominant archaeal and bacterial communities associating with the mucus of three common reef-building coral spe- cies (Porites astreoides, Siderastrea siderea and Orbicella annularis) over different spatial scales on a Caribbean fringing reef. Sampling locations included three reef sites, three reef patches within each site and two depths. Reference sediment samples and ambient water were also taken for each of the 18 sampling locations resulting in a total of 239 samples. While only 41% of the bacterial operational taxonomic units (OTUs) characterized by T- RFLP were shared between mucus and the ambient water or sediment, for archaeal OTUs this percentage was 2-fold higher (78%). About half of the mucus-associated OTUs (44% and 58% of bacterial and archaeal OTUs, respectively) were shared between the three coral species. Our multivariate statistical analysis (ANOSIM, PERMANOVA and CCA) showed that while the bacterial community composition was determined by habitat (mucus, sediment or seawater), host coral species, location and spatial distance, the archaeal com- munity composition was solely determined by the habitat. This study highlights that mucus- associated archaeal and bacterial communities differ in their degree of community turnover over reefs and in their host-specificity. 

Marine organism are often kept, cultured, and experimented on in running seawater aquaria. However, surprisingly little attention is given to the nutrient composition of the water owing through these systems, which is generally assumed to equal
in situ conditions, but may change due to the presence of biofouling organisms. Signi cantly lower bacterial abundances and higher inorganic nitrogen species (nitrate, nitrite, and ammonium) were measured in aquarium water when biofouling organisms were present within a 7-year old inlet pipe feeding a tropical reef running seawater aquaria system, compared with aquarium water fed by a new, biofouling-free inlet pipe. These water quality changes are indicative of the feeding activity and waste production of the suspension- and lter-feeding communities found in the old pipe, which included sponges, bivalves, barnacles, and ascidians. To illustrate the physiological consequences of these water quality changes on a model organism kept in the aquaria system, we investigated the in uence of the presence and absence of the biofouling community on the functioning of the lter-feeding sponge Halisarca caerulea, by determining its choanocyte ( lter cell) proliferation rates. We found a 34% increase in choanocyte proliferation rates following the replacement of the inlet pipe (i.e., removal of the biofouling community). This indicates that the physiological functioning of the sponge was compromised due to suboptimal food conditions within the aquarium resulting from the presence of the biofouling organisms in the inlet pipe. This study has implications for the husbandry and performance of experiments with marine organisms in running seawater aquaria systems. Inlet pipes should be checked regularly, and replaced if necessary, in order to avoid excessive biofouling and to approach in situ water quality. 

This study investigates the relationship between yellow band disease (YBD) infected Montastrea annularis coral colonies and its potential to spread by contact with transect tapes, as commonly used in research. M. annularis plays an important role in maintaining reef complexity and diversity in Bonaire as it is a structural reef-building coral, yet the recent spread of YBD has created an degrading the reefs (Bruckner 2006). The study has two primary goals, to investigate whether the use of transect lines had the potential to transfer YBD from one coral to another, and whether a simple cleaning protocol can reduce this transfer. Transects placed on the YBD infected colonies of M. annularis had the most percent bacterial growth, though not statistically significant. It also showed that even though specific species of bacteria were unable to be identified, the transect lines are indeed capable of carrying bacteria. Although the difference was not significant in this study, cleansing treatments may have an effect on lessening the growth of bacteria.

This student research was retrieved from Physis: Journal of Marine Science X (Fall 2011)19: 11-15 from CIEE Bonaire.

A lack of sufficient wastewater treatment practices on the island of Bonaire, Dutch Caribbean suggests that contaminated groundwater seepage or runoff could be impacting the health of the coastal habitats and fringing reefs that surround the island. Bonaire does not monitor the health of its coastal waters, although effects of pollution have been observed. This study aims to learn more about the coastal water quality at three stations along the coast of the city of Kralendijk, Bonaire. Both indicator bacteria (coliform bacteria, Escherichia coli, and enterococci) and polychaete assemblages were monitored. IDEXX ColilertTM and EnterolertTM test kits were used to monitor bacteria levels in samples taken over a five-week study period. Polychaetes were identified to the family level from soft sediment samples. Polychaete family abundance, richness, and diversity were compared between stations. Grain size of the soft sediments at each station was measured. Polychaete assemblages varied between stations, but not enough data was gathered to eliminate the possibility of unexpectedly large grain size differences in explaining this variability. Typical water samples from each station showed narrow variability within U.S. Environmental Protection Agency standards for indicator bacteria levels. Two outliers occurred. The Marina station experienced a wider variance in all bacteriological indicator levels than the other two stations, and all surface stations experienced a significant spike in enterococci levels after a heavy rainstorm. If elevated enterococci levels consistently occur during heavy rainstorms, this could present a

This student research was retrieved from Physis: Journal of Marine Science XII (Fall 2012)19: 22-32 from CIEE Bonaire.

The filter feeding mechanism of marine sponges exposes them to water-borne toxins and bacteria, forcing them to evolve immune systems effective in fighting these pathogens. Therefore, antibacterial properties of the sponge’s defense system are effective tools that can be used in medicinal therapies. By modeling sponges’ response to pathogens, advances can be made in human medicine. This study analyzed how the pumping efficiency of the species Aplysina archeri and Aplysina lacunosa affected the antibacterial properties of the sponge. Sponges were sampled from depth ranges of 10 – 12 m, and 16 – 18 m. The pumping efficiency of each sponge was tested using water sampling (In-Ex), determined by comparing the turbidity of water before it entered and as it exited the sponge. Variation in antibacterial properties was analyzed by assembling antibiotic assays from sponge extracts. Using this method, sponges showed no bacterial inhibition. Both A. archeri and A. lacunosa filtered water more efficiently in shallow water, but this trend was not significant. This study sought to introduce information that could be useful when determining what sponge to use in pharmaceutical testing. With such knowledge, pharmaceutical companies can continue to compile qualities to formulate an ideal sponge species they should research for medicinal cures

This student research was retrieved from Physis: Journal of Marine Science XVII (Spring 2015)19: 10-16 from CIEE Bonaire.

In the microbial loop, heterotrophic bacteria utilize dissolved organic matter (DOM) as an energy source. DOM becomes remineralized into inorganic material and nutrients available for primary production. As the amount of nutrients increase, the abundance of each trophic level increases, which is known as the bottom-up effect. This study investigates the effect of the increasing human population density on an intertidal community along the waterfront of Kralendijk, Bonaire. DOM, fecal indicator bacteria (enterococci, Escherichia coli, and coliform bacteria), nutrients (nitrate, phosphate, and ammonia), primary producers (percent cover of macroalgae), and herbivorous consumers (density of sea urchins) were sampled. There was no pattern between the variables and the increase of the adjacent population density. Factors such as rainfall, changes over time, tides, and herbivore grazing may have influenced the results. When graphed over time, rainfall impacted the concentrations of nutrients and fecal indicators. Nitrate, ammonia, and coliform bacteria increased, while phosphate, enterococci, and E. coli decreased. Concentrations of ammonia were found to exceed the threshold for a healthy coral reef ecosystem (6x). No correlation was found between DOM and heterotrophic bacteria, although concentrations of E. coli and nutrients were high at one site. This intertidal ecosystem does not appear to be influenced by bottom-up controls, as there was neither a correlation found between the percent cover macroalgae and nutrients or the density of sea urchins. The site with the highest percent cover of macroalage had the lowest density of urchins and vice versa.

This student research was retrieved from Physis: Journal of Marine Science XIX (Spring 2016)19: 91-99 from CIEE Bonaire.

Abstract:

Emerging infectious diseases are a worldwide problem and are believed to play a major role in coral reef degradation. The study of coral diseases is difficult but the use of culture-independent molecular techniques has been, and will continue to be, useful in a system where a limited number of visible signs are commonly used to define a “coral disease”. We propose that coral “diseases”, with rare exception, are opportunistic infections secondary to exposure to physiological stress (e.g. elevated temperature) that result in reduced host resistance and unchecked growth of bacteria normally benign and non-pathogenic. These bacteria are from the environment, the host, or the coral mucus layer and become opportunistic pathogens. While difficult and time consuming, we do not advocate abandoning the study of disease-causing pathogens in corals. However, these studies should include comprehensive efforts to better understand the relationship between coral diseases and environmental changes, largely anthropogenic in nature, occurring on coral reefs around the world. These environmental insults are the cause of the physiological stress that subsequently leads to coral mortality and morbidity by many mechanisms including overwhelming infections by opportunistic pathogens.