Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding.

Our understanding of marine communities and their functions in an ecosystem relies on the ability to detect and monitor species distributions and abundances. Currently, the use of environmental DNA (eDNA) metabarcoding is increasingly being applied for the rapid assessment and monitoring of aquatic species. Most eDNA metabarcoding studies have either focussed on the simultaneous identification of a few specific taxa/groups or have been limited in geographical scope. Here, we employed eDNA metabarcoding to compare beta diversity patterns of complex pelagic marine communities in tropical coastal shelf habitats spanning the whole Caribbean Sea. We screened 68 water samples using a universal eukaryotic COI barcode region and detected highly diverse communities, which varied significantly among locations, and proved good descriptors of habitat type and environmental conditions. Less than 15% of eukaryotic taxa were assigned to metazoans, most DNA sequences belonged to a variety of planktonic "protists," with over 50% of taxa unassigned at the phylum level, suggesting that the sampled communities host an astonishing amount of micro-eukaryotic diversity yet undescribed or absent from COI reference databases. Although such a predominance of micro-eukaryotes severely reduces the efficiency of universal COI markers to investigate vertebrate and other metazoans from aqueous eDNA, the study contributes to the advancement of rapid biomonitoring methods and brings us closer to a full inventory of extant marine biodiversity.

Environmental DNA reveals tropical shark diversity in contrasting levels of anthropogenic impact.

Sharks are charismatic predators that play a key role in most marine food webs. Their demonstrated vulnerability to exploitation has recently turned them into flagship species in ocean conservation. Yet, the assessment and monitoring of the distribution and abundance of such mobile species in marine environments remain challenging, often invasive and resource-intensive. Here we pilot a novel, rapid and non-invasive environmental DNA (eDNA) metabarcoding approach specifically targeted to infer shark presence, diversity and eDNA read abundance in tropical habitats. We identified at least 21 shark species, from both Caribbean and Pacific Coral Sea water samples, whose geographical patterns of diversity and read abundance coincide with geographical differences in levels of anthropogenic pressure and conservation effort. We demonstrate that eDNA metabarcoding can be effectively employed to study shark diversity. Further developments in this field have the potential to drastically enhance our ability to assess and monitor elusive oceanic predators, and lead to improved conservation strategies.

Spatial variability associated with shifting land use: water quality and sediment metals in La Parguera, Southwest Puerto Rico.

Development in southwest Puerto Rico, as in many areas of the Caribbean, is outpacing the ability of upland flora, salt flats, and mangroves to capture sediments and intercept and transform nutrients. A comparative study to examine the effects of development on near-shore water quality in La Parguera, Puerto Rico, was initiated in 1998. Total suspended solids were significantly higher in the vicinity of developing areas compared to reference areas. Chlorophyll-a measurements near of the wastewater treatment plant averaged two times the level of other areas. The overall average concentrations of copper, chromium, nickel, and zinc in sediments collected from salt flats exceeded values reported to cause impairment of biological systems. Marine sediments near more developed locations had the highest metal concentrations, suggesting a greater transport in this area. Natural resources are the primary attraction in this area; therefore, protection of near-shore resources should receive greater attention in land use planning.

Effects of houseboats on organisms of the La Parguera Reserve, Puerto Rico.

As coastal development increases so too does the number of artificial floating and permanent structures. It has been postulated that because of their size, many houseboats are similar to permanent structures in that they shade a significant portion of the benthos and thereby limit production by benthic flora. On the other hand, these structures can benefit biotic communities by providing sites for attachment of organisms in a substrate-limited environment and both habitat and food sources for fish. In this study, we examined whether houseboats benefit or harm the ecological integrity of a typical seagrass dominated system, at La Parguera, Puerto Rico. We performed a benthic survey to compare the diversity and health of seagrasses under houseboats to that at control locations. Species diversity (0-0.79) varied significantly among sites, but this variability was not attributed to the houseboats. Rather, the variability appeared related to the proximity of the study locations to new development along the shoreline. Average seagrass blade density and length were 52.7 blades/m(-2) and 23.6 cm, respectively. Neither parameter differed between houseboat and control areas; however, both varied significantly among sites. In addition, boat hulls were heavily encrusted with invertebrates. The overall averages of species diversity and richness of sessile organisms on hulls of the houseboats were 1.13 and 4.83, respectively. Fish also utilized these structures. Our results indicate that houseboats did not directly harm the seagrass communities at La Parguera primarily because of sound environmental management of wastes and mooring techniques.