The molecular ecology of Microcystis sp. blooms in the San Francisco Estuary

Harmful blooms of the cyanobacterium Microcystis sp. have become increasingly pervasive in the San Francisco Estuary Delta (USA) since the early 2000s and their rise has coincided with substantial decreases in several important fish species. Direct and indirect effects Microcystis blooms may have on the Delta food web were investigated. The Microcystis population was tracked for 2 years at six sites throughout the Delta using quantitative PCR. High-throughput amplicon sequencing and colony PCR sequencing revealed the presence of 10 different strains of Microcystis, including 6 different microcystin-producing strains. Shotgun metagenomic analysis identified a variety of Microcystis secondary metabolite pathways, including those for the biosynthesis of: aeruginosin, cyanopeptolin, microginin, microviridin and piricyclamide. A sizable reduction was observed in microbial community diversity during a large Microcystis bloom (H′ = 0.61) relative to periods preceding (H′ = 2.32) or following (H′ = 3.71) the bloom. Physicochemical conditions of the water column were stable throughout the bloom period. The elevated abundance of a cyanomyophage with high similarity to previously sequenced isolates known to infect Microcystis sp. was implicated in the bloom's collapse. Network analysis was employed to elucidate synergistic and antagonistic relationships between Microcystis and other bacteria and indicated that only very few taxa were positively correlated with Microcystis

Estimating juvenile copepod growth rates: corrections, inter-comparisons and recommendations

The 2 most common experimental methods used to estimate rates of juvenile growth in marine copepods are the molt rate (MR) method, and the artificial cohort (AC) method. Recently, we showed the equations used in the MR method to be incorrect, and proposed a modified molt rate (MMR) method. Here, using statistical and model approaches, we compare the AC and MMR methods under various scenarios to quantify their errors. Although the AC and MMR methods both use a combination of field sampling and simulated in situ incubations to estimate somatic growth, they differ in several important characteristics. The AC method determines growth by the change in mean weight during incubation. Mean weight of copepods in the samples can be determined directly, or inferred from mean weight by life stage or from length–weight regressions. We show that substantial error is avoided only if weights are measured directly (ACdirect). The ACdirect method is insensitive to variable age within stage due to mortality or variable recruitment in the sampled population, an important advantage over the MMR method. However, the ACdirect method is sensitive to variation in growth rate during incubation, which does not affect the MMR method. We therefore recommend that most experimental estimates of growth rate should apply the ACdirect method, with the MMR as a suitable alternative provided its biases are considered. An indirect method based on life stage is biased and we no longer recommend it, and an indirect method based on length–weight regression provides an intermediate level of bias

The sensitivity of California water resources to climate change scenarios

Using the latest available General Circulation Model (GCM) results we present an assessment of climate change impacts on California hydrology and water resources. The approach considers the output of two GCMs, the PCM and the HadCM3, run under two different greenhouse gas (GHG) emission scenarios: the high emission A1fi and the low emission B1. The GCM output was statistically downscaled and used in the Variable Infiltration Capacity (VIC) macroscale distributed hydrologic model to derive inflows to major reservoirs in the California Central Valley. Historical inflows used as inputs to the water resources model CalSim II were modified to represent the climate change perturbed conditions for water supply deliveries, reliability, reservoir storage and changes to variables of environmental concern. Our results show greater negative impacts to California hydrology and water resources than previous assessments of climate change impacts in the region. These impacts, which translate into smaller streamflows, lower reservoir storage and decreased water supply deliveries and reliability, will be especially pronounced later in the 21st Century and south of the San Francisco bay Delta. The importance of considering how climate change impacts vary for different temporal, spatial, and institutional conditions in addition to the average impacts is also demonstrated

Trends in NE Atlantic landings (southern Portugal): identifying the relative importance of fisheries and environmental variables

Time series of commercial landings from the Algarve (southern Portugal) from 1982 to 1999 were analyzed using min/max autocorrelation factor analysis (MAFA) and dynamic factor analysis (DFA). These techniques were used to identify trends and explore the relationships between the response variables (annual landings of 12 species) and explanatory variables [sea surface temperature, rainfall, an upwelling index, Guadiana river (south-east Portugal) flow, the North Atlantic oscillation, the number of licensed fishing vessels and the number of commercial fishermen]. Landings were more highly correlated with non-lagged environmental variables and in particular with Guadiana river flow. Both techniques gave coherent results, with the most important trend being a steady decline over time. A DFA model with two explanatory variables (Guadiana river flow and number of fishermen) and three common trends (smoothing functions over time) gave good fits to 10 of the 12 species. Results of other models indicated that river flow is the more important explanatory variable in this model. Changes in the mean flow and discharge regime of the Guadiana river resulting from the construction of the Alqueva dam, completed in 2002, are therefore likely to have a significant and deleterious impact on Algarve fisheries landings