Stratified lakes and ponds featuring steep oxygen gradients are significant net sources of greenhouse gases and hotspots in the carbon cycle. Despite their significant biogeochemical roles, the microbial communities, especially in the oxygen depleted compartments, are poorly known. Here, we present a comprehensive dataset including 267 shotgun metagenomes from 41 stratified lakes and ponds mainly located in the boreal and subarctic regions, but also including one tropical reservoir and one temperate lake. For most lakes and ponds, the data includes a vertical sample set spanning from the oxic surface to the anoxic bottom layer. The majority of the samples were collected during the open water period, but also a total of 29 samples were collected from under the ice. In addition to the metagenomic sequences, the dataset includes environmental variables for the samples, such as oxygen, nutrient and organic carbon concentrations. The dataset is ideal for further exploring the microbial taxonomic and functional diversity in freshwater environments and potential climate change impacts on the functioning of these ecosystems.

Six reservoirs of Puerto Rico were monitored over a 32-month period to establish relationships between their nutrient concentration status and different thresholds of ecological impairment. The selected reservoirs embody the productivity spectrum of reservoirs on the island. Median concentrations of total phosphorus (TP) for epilimnion waters (1 m) were as follows: Cerrillos, 10 µg/L; Cidra, 33 µg/L; Guajataca, 10 µg/L; La Plata, 49 µg/L; Patillas, 6 µg/L; and Toa Vaca, 22 µg/L. Likewise, median concentrations of total nitrogen (TN) were:Cerrillos, 0.22 mg/L; Cidra, 0.74 mg/L; Guajataca, 0.28 mg/L; La Plata, 0.55 mg/L; Patillas, 0.23 mg/L; and Toa Vaca, 0.34 mg/L. Strong positive correlations were observed between nutrients and chlorophyll a (Chl-a). Correlation coefficients were 0.74 for the relationship between TP and Chl-a, and 0.66 for TN vs. Chl-a. Increases in algal biomass (as measured by Chl-a) diminished the depth of light penetration into the water column (i.e., Seechi depth) (r = -0.70). A biological threshold indicative of designated use impairment was established at a Chl-a concentration of 24 µg/L based on evidence demonstrating that the extent of reduced light penetration at that Chl-a level (due to excessive phytoplankton biomass productivity) hindered the reservoirs' capacity to comply with the aquatic life criteria. Total phosphorus and TN concentrations associated with the Chl-a impairment threshold (i.e., 24 µg/L) were established based on a change-point analysis of the data. The resulting values, 0.035 mg/L for TP and 0.43 mg/L for TN, can be considered nutrient thresholds associated with impairment. To protect against impairment, a margin of safety was added based on concentrations defining the lower 5% confidence interval of the bootstrap distribution of values associated with the Chl-a impairment threshold (i.e., p<0.05-one tail probability). The resulting criteria, 0.026 mg/L for TP and 0.41 mg/L for TN, are proposed as basis for establishing the nutrient standards for reservoirs of Puerto Rico. Significant differences in the maximum depth of compliance with the USEPA aquatic life criteria (i.e., DO = 5.0 mg/L) were observed between data points below and above the proposed numeric criteria. These differences, which can be critical to the sustainablllty of fish populations in reservoirs on the Island, attest to the importance of maintaining the nutritional status of waters in our reservoirs at levels below the specified thresholds. The zooplankton community was characterized by a mix of species already known under similar environmental conditions in the Neotropical region. Sixty-five zooplanktonic taxa were identified. Rotlfera was the richest group with 37 taxa. Cladocerans were represented by 20 taxa; Copepoda by eight taxa. Absolute abundances of rotifers showed an increase with the increase of several eutrophication indexes. A segmented curved analysis was used to describe the relationship between Brachionus rotifers (#ind/L) and phosphorus (lnTP). The relationship yielded a change-point value of 26.58 µg/L for total phosphorus, which coincides with the proposed numeric criteria value. In addition, a change-point of 1.16 meters was obtained for the relationship between Brachionus rotifers (#ind/L) and Seechi depth (m), which can be considered as another impairment index for reservoirs on the island.

Invasive bivalves are known to negatively impact aquatic ecosystems across the globe. Previous research has demonstrated invasive bivalves can shift nutrients from the water column to the sediment, harm native bivalves, and reduce phytoplankton biomass. However, bivalve effects vary with species and the region where the invasion occurs. Therefore, we used mesocosm experiments to examine the impact of invasive Corbicula fluminea on nutrient concentration and phytoplankton biomass in the water column of mesotrophic and eutrophic Puerto Rican reservoirs. We used four treatments to determine the effect of C. fluminea on the water column. We found C. fluminea did not have a significant effect on the ammonium, nitrate, or phosphorus concentration in either the mesotrophic or eutrophic mesocosm experiments. Additionally, C. fluminea presence did not significantly alter phytoplankton biomass, though Synedra dominated the phytoplankton community when C. fluminea were absent. While C. fluminea may not have caused an effect in the water column as it was potentially phytoplankton limited, the mesocosm experiment conditions reflect the natural environment, indicating phytoplankton limitation could be an issue in the reservoirs. Our findings suggest C. fluminea does not have a large effect on nutrient concentration or phytoplankton biomass in eutrophic and mesotrophic Puerto Rican reservoirs. This study represents the first effort to examine the effects of C. fluminea presence on the water column of a tropical reservoir.

1Intensively managed dairy farms in Puerto Rico are suspected of being important contributors of 2 phosphorus (P) in runoff that can reach surface-waters. A whole-farm P balance is a practical 3 tool that can be used to estimate the net amounts of P retained within farms. In addition, 4 knowledge of the internal mass-P cycling within farms (cows, pasture-lagoon, soils and forage) 5 can be used to assess the relative risk of the on-farm agricultural practices to the environment 6 and to identify management practices that reduce P accumulation in soils. Two dairy farms 7 representative of feed and management practices in the Caribbean were assessed to describe 8 internal mass-P cycling and to produce a whole-farm P balance. Farm A with an area of 58 ha 9 had 120 lactating cows that rotationally grazed on improved tropical-grass pastures, and Farm B 10 with an area of 310 ha had 482 lactating cows that were managed in semi-confinement, were fed 11 silage and concentrate during the day, and were grazed only at night. Over 60% (DM basis) of all 12 feeds consumed by dairy cows were imported to the farms, accounting for 71% and 81% of the P 13 consumed in Farms A and B, respectively. The majority of the total P consumed by lactating 14 cows (65% in Farm A and 75% in Farm B) was from commercial dairy grain concentrate, and 15 the remaining P inputs were from grazed and cut pasture. Phosphorus in milk and animals sold 16 (outputs) was 21% of total P inputs in Farm A, and 17.5% in Farm B. Dietary P concentrations, 17 in both farms, exceeded by more than 60% nutritional recommendations of P. On an annual 18 basis, there was an annual surplus (i.e., positive P balance) of 3,132 kg P farm -1 (54 kg P ha -1 ) 19 and 18,290 kg P farm -1 (59 kg P ha -1 ) in Farms A and B, respectively. At current milk production 20 levels the practices with the greatest impact potential for reducing soil P enrichment in dairy 21 farms are reducing P inputs in feeds, improving P recycling by maximizing harvested pasture, 22 and reducing or discontinuing fertilizing P additions to grazed pastures.

Water column profiles of important limnological indicators (temperature, pH, dissolved oxygen, reduction potential, nutrients) were collected at the center section of La Plata reservoir in north-central Puerto Rico during 2008 and 2009. Temperatures at the surface ranged from values close to 25° C during the hemisphere winter months (December-February) to approximately 30° C during summer (June-August). Total nitrogen and phosphorus concentrations at the epilimnion (≤ 3-m depth) averaged 1.06 mg/L and 50 µg/L, respectively. Chlorophyll a values averaged 32.4 µg/L, which altogether with its nutrient status, would place this reservoir within the eutrophic-hypereutrophic categories. The annual average volume-weighed dissolved oxygen concentration for the reservoir was 3.02 mg/L, a reflection of the delicate ecological condition of this reservoir. The reservoir remains stratified during a large portion of the year (≥ eight months), inducing prevailing anoxic conditions at the hypolimnion. However, mixing because of incoming flow associated with intense rain events can be common. As a result, the mixing regime of this reservoir is best classified as discontinuous warm polymictic. Runoff associated with intense rainfall is probably the major contributor of hypolimnion dissolved oxygen and nutrient recharge at this reservoir. The distribution of iron (Fe) and manganese (Mn) is strongly influenced by the redox status of the system. Solid phases containing these metals exert a dominant role in the cycling of phosphate in the system.