Use of environmental DNA in assessment of fish functional and phylogenetic diversity

Assessing the impact of global changes and protection effectiveness is a key step in monitoring marine fishes. Most traditional census methods are demanding or destructive. Nondisturbing and nonlethal approaches based on video and environmental DNA are alternatives to underwater visual census or fishing. However, their ability to detect multiple biodiversity factors beyond traditional taxonomic diversity is still unknown. For bony fishes and elasmobranchs, we compared the performance of eDNA metabarcoding and long-term remote video to assess species’ phylogenetic and functional diversity. We used 10 eDNA samples from 30 L of water each and 25 hr of underwater videos over 4 days on Malpelo Island (pacific coast of Colombia), a remote marine protected area. Metabarcoding of eDNA detected 66% more molecular operational taxonomic units (MOTUs) than species on video. We found 66 and 43 functional entities with a single eDNA marker and videos, respectively, and higher functional richness for eDNA than videos. Despite gaps in genetic reference databases, eDNA also detected a higher fish phylogenetic diversity than videos; accumulation curves showed how 1 eDNA transect detected as much phylogenetic diversity as 25 hr of video. Environmental DNA metabarcoding can be used to affordably, efficiently, and accurately census biodiversity factors in marine systems. Although taxonomic assignments are still limited by species coverage in genetic reference databases, use of MOTUs highlights the potential of eDNA metabarcoding once reference databases have expanded.     

Specificity between Neotropical tree seedlings and their fungal mutualists leads to plant-soil feedback

A growing body of evidence obtained largely from temperate grassland studies suggests that feedbacks occurring between plants and their associated soil biota are important to plant community assemblage. However, few studies have examined the importance of soil organisms in driving plant-soil feedbacks in forested systems. In a tropical forest in central Panama, we examined whether interactions between tree seedlings and their associated arbuscular mycorrhizal fungi (AMF) lead to plant-soil feedback. Specifically, do tropical seedlings modify their own AMF communities in a manner that either favors or inhibits the next cohort of conspecific seedlings (i.e., positive or negative feedback, respectively)? Seedlings of two shade-tolerant tree species (Eugenia nesiotica, Virola surinamensis) and two pioneer tree species (Luehea seemannii, Apeiba aspera) were grown in pots containing identical AMF communities composed of equal amounts of inoculum of six co-occurring AMF species. The different AMF-host combinations were all exposed to two light levels. Under low light (2% PAR), only two of the six AMF species sporulated, and we found that host identity did not influence composition of AMF spore communities. However, relative abundances of three of the four AMF species that produced spores were influenced by host identity when grown under high light (20% PAR). Furthermore, spores of one of the AMF species, Glomus geosporum, were common in soils of Luehea and Eugenia but absent in soils of Apeiba and Virola. We then conducted a reciprocal experiment to test whether AMF communities previously modified by Luehea and Apeiba differentially affected the growth of conspecific and heterospecific seedlings. Luehea seedling growth did not differ between soils containing AMF communities modified by Luehea and Apeiba. However, Apeiba seedlings were significantly larger when grown with Apeiba-modified AMF communities, as compared to Apeiba seedlings grown with Luehea-modifed AMF communities. Our experiments suggest that interactions between tropical trees and their associated AMF are species-specific and that these interactions may shape both tree and AMF communities through plant-soil feedback.     

Urbanization and small household agricultural land use choices in the Brazilian Amazon and the role for the water chemistry of small streams

Many small watersheds and streams in the Brazilian Amazon have been impacted by agriculture and urban development, often due to household economic needs and migration processes. This study examined the relationships between land use, soil type, and household factors on stream water chemistry in and near the city of Altamira, Pará, Brazil, in 2008–2009. While soil weathering and stream discharge may have affected several stream water ion concentrations, agriculture and especially urban development were associated with high dissolved nitrogen concentrations, high water temperatures, and low dissolved oxygen concentrations in streams. Younger interviewed households were generally associated with these watersheds, and many urban residents reported disposing of household waste directly into streams. In contrast, older households were generally associated with forest and cocoa agriculture, along with lower water temperatures and higher dissolved oxygen concentrations in streams. These conditions persisted despite reported uses of herbicides and fertilizers by some residents.     

Sediment quality assessment of Beasley Lake: bioaccumulation and effects of pesticides in Hyalella azteca

Beasley Lake is a Conservation Effects Assessment Program (CEAP) watershed in the intensively cultivated Mississippi Delta, USA. Lake sediment quality at three sites was evaluated in 2004 and 2008 for biological impairment and uptake (animal tissue pesticide residues) from 14 pesticides and three metabolites using Hyalella azteca (Saussure). Eleven pesticides and three metabolites were detected in sediment among the three sites in 2004 and all 17 compounds examined were detected among the three sites in 2008, with the herbicide atrazine having the greatest concentrations. Twenty-eight-day H. azteca survival and growth (mg w/w) indicated no survival effects at any site for either year, but growth impairment occurred in H. azteca exposed to sediments in 2004, whereas growth enhancement occurred in H. azteca exposed to sediments at one site in 2008. Pesticides observed in animal tissue pesticide residues occurred more frequently and in greater concentrations in 2004 compared with 2008. Thirteen pesticides were detected in animal tissue pesticide residues in 2004, with chlorpyrifos occurring in the greatest concentrations, and six pesticides were detected in 2008, with p,p′-DDT occurring in the greatest concentrations. H. azteca tissue pesticide residues of seven pesticides, two herbicides, three insecticides, one insecticide metabolite, and p,p′-DDT, were associated with growth.     

Transport of Sewage Sludge From the 106-Mile Site - Results From an October Survey

Abstract

Approximately 8 million tons of sewage sludge were disposed of annually at the 106-Mile Deepwater Municipal Sludge Dump Site (106-Mile Site) between 1987 and 1990. Beginning in 1988 and continuing to the present, the focus of monitoring at the 106-Mile Site moved towards improved understanding of the fate of the sludge. A survey conducted in October 1989 was designed to (1) detect the presence of any sludge particles that settle rapidly following disposal, (2) determine if sludge could be detected in the surface waters at locations away from the immediate disposal site, and (3) determine if water quality was degraded, by assessing whether the Environmental Protection Agency's marine water quality criteria were being exceeded.

The survey showed that the sludge does have a rapidly settling component composed of organic floc. mineral grains, and other heavy, gritlike particles, all of which are relatively large. These particles may settle at rates of between 8 and 180 m h^?1 and may reach the sea floor within 1 to 13 days following disposal. Even though a rapidly settling component is present in the sludge, a significant fraction of the sludge was detectable in the form of intact sludge plumes in the upper 35 m of the water column at least 15 km from the Site. in addition, unique tracers of sludge such as xylem tracheids and Clostridium perfringens plus elevated total suspended solids and trace metals concentrations, were found at locations up to 40 km from the Site. the presence of these tracers correspond with in situ transmissometry data suggesting that a fraction of the sludge was remaining in the near-surface waters above the seasonal pycnocline. Concentrations of metals were below EPA chronic marine water quality criteria, which indicates that the water quality downstream of the Site was not impaired. the detection of sludge downstream of the 106-Mile Site is consistent with the southwestward movement of the surface water mass during the survey, as recorded by satellite-tracked surface drifters and current vectors derived from a current meter moored at 100-m depth immediately west of the Site. Near-surface transport was generally towards the southwest at a speed of approximately 22 cm s^?1?.     

Oxidative stress-mediated cardiac mast cell degranulation

Pulmonary mast cell degranulation is a well-characterized response to diesel exhaust exposure. A primary constituent of fossil fuel combustion is sulfur dioxide (SO₂). SO₂ was shown to induce mast cell degranulation in an immortalized cell line secondary to induction of intracellular oxidative stress; however, it is not known whether SO₂-induced oxidative stress directly triggers the activation of cardiac mast cells. Accordingly, this study sought to determine whether Na₂SO₃ induces degranulation of cardiac mast cells, and furthermore whether cardiac mast cell activation may be prevented by inhibition of oxidative stress. To this end, cardiac mast cells were isolated from epicardial surface of the heart and incubated with increasing concentrations of Na₂SO₃ (0, 0.5, or 5 mM). Antioxidant compounds targeting different mechanisms of free radical generation, including ebselen, diphenyleneiodonium (DPI), or α-tocopherol, were incubated with 5 mM of Na₂SO₃ in order to determine their efficacy in preventing mast cell degranulation. Na₂SO₃ induced a significant concentration-dependent histamine release from cardiac mast cells ranging from 8.87% to 18.86%, which was prevented by ebselen. No effect was observed with DPI and α-tocopherol under these conditions. In conclusion, these findings indicate that SO₂ is capable of producing cardiac mast cell degranulation in vitro; however, the variable effectiveness of the three antioxidants evaluated is indicative of a multifactorial mechanism mediating SO₂-induced cardiac mast cell degranulation. The particular effectiveness of ebselen in preventing mast cell degranulation may be related to its multiple mechanisms of preventing oxidative stress.     

A little movement orientated to the geomagnetic field makes a big difference in strong flows

Whilst a range of animals have been shown to respond behaviourally to components of the Earth’s magnetic field, evidence of the value of this sensory perception for small animals advected by strong flows (wind/ocean currents) is equivocal. We added geomagnetic directional swimming behaviour for North Atlantic loggerhead turtle hatchlings (Caretta caretta) into a high-resolution (1/4°) global general circulation ocean model to simulate 2,925-year-long hatchling trajectories comprising 355,875 locations. A little directional swimming (1–3 h per day) had a major impact on trajectories; simulated hatchlings travelled further south into warmer water. As a result, thermal elevation of hatchling metabolic rates was estimated to be between 63.3 and 114.5% after 220 days. We show that even small animals in strong flows can benefit from geomagnetic orientation and thus the potential implications of directional swimming for other taxa may be broad.     

Response of hydrothermal vent vestimentiferan <Emphasis Type="Italic">Riftia pachyptila</Emphasis> to differences in habitat chemistry

Vestimentiferan tubeworms, which rely on intracellular sulfide-oxidizing autotrophic bacteria for organic carbon, flourish at deep-sea hydrothermal vents despite the erratic nature of their habitat. To assess the degree to which differences in habitat chemistry (sulfide, pH/CO₂) might impact host and symbiont metabolic activity, Riftia pachyptila tubeworms were collected from habitats with low (H₂S < 0.0001 mM) and high (up to 0.7 mM) sulfide concentrations. The elemental sulfur content of the symbiont-containing trophosome organ was lower in specimens collected from the low-sulfide site. Symbiont abundance, RubisCO activity, and trophosome carbon fixation rates were not significantly different for individuals collected from low- versus high-sulfide habitats. Carbonic anhydrase activities were higher in the anterior gas exchange organs of R. pachyptila from the low-sulfide habitat. Despite large differences in habitat chemistry, symbiont abundance and autotrophic potential were consistent, while the host appears to tailor carbonic anhydrase activity to environmental CO₂ availability.     

Impacts of cyclone Hamish at One Tree Reef: integrating environmental and benthic habitat data

The southern Great Barrier Reef (GBR), a region that rarely experiences cyclones, was impacted by tropical cyclone (TC) Hamish in March 2009. We documented on-reef physical and habitat conditions before, during and after the cyclone at One Tree Reef (OTR) using data from environmental sensor instrumentation and benthic surveys. Over 5 years of monitoring, ocean mooring data revealed that OTR experienced large swells (4–8 m) of short duration (10–20 min) not associated with a cyclone in the area. These swells may have contributed to the physical disturbance of benthic biota and decline in coral cover recorded prior to and after TC Hamish. During the cyclone, OTR sustained southeasterly gale force winds (>61.2 km h⁻¹) for 18.5 h and swells >6 m in height for 4 h. Benthic surveys of exposed sites documented a 20% drop in live coral cover, 30% increase in filamentous algae cover and the presence of dislodged corals and rubble after the storm. Leeward sites were largely unaffected by the cyclone. Benthic cover did not change in the lagoon sites. Significant rubble movement and infill of the lagoon occurred. Two years after the cyclone, algal cover remained high and laminar corals had not recovered. Total coral cover at impacted sites had continued to decline. Environmental conditions and habitat surveys supported Puotinen’s (Int J Geogr Inf Sci 21:97–120, 2007) model for cyclone conditions that cause reef destruction. While TC Hamish had a major impact on the reef, change in benthic cover over several years was due to multiple stressors. This on-reef scale integration of physical and biological data provided a rare opportunity to assess impacts of a major storm and other disturbances, showing the importance of considering multiple stressors (short-lived and sustained) in assessing change to reef habitats.