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Rathayibacter toxicus is Gram-positive bacterium causing gummosis of forage grasses, and it produces a corynetoxin responsible for livestock poisonings in Australia. R. toxicus is a USDA APHIS-listed Select Agent, threatening seed and livestock production areas in the U.S. We therefore are developing diagnostic assays to prepare for the introduction of the pathogen into the U.S. Using proteomic data, we identified proteins expressed in R. toxicus but not in other Rathayibacter spp. Recombinant proteins corresponding to extracellular domains of candidate proteins were used to raise polyclonal and monoclonal antibodies. Antibodies were evaluated for sensitivity and specificity in immunoassays against a panel of Rathayibacter spp. and near-neighbours. Polyclonal and monoclonal antibodies exhibited high sensitivity and specificity for R. toxicus in assays with cultured bacteria. The highest-performing immunoreagents were identified for further testing with field samples collected in Australia and for eventual development of an immunoassay for bacterial detection in grass samples.

Phytoplankton blooms create organic matter that stimulates entire marine ecosystems, including other components of the microbial community. How the ecosystem responds varies depending on the intensity, duration, and composition of the bloom. When the bloom has a direct or indirect negative impact on the ecosystem, it is termed a harmful algal bloom (HAB). HAB frequency is expected to increase in response to changing oceanic conditions and coastal nutrient supply. Characterizing the response of the bacterial and archaeal communities to HABs will improve our understanding of the ecological impacts of these phenomena. We utilized time series of chlorophyll a, phaeophytin, dissolved oxygen, flow cytometry cell counts, and microbial community structure (assessed via 16S rRNA gene sequences) maintained by several observing programs to investigate how the microbial community was affected by an exceptional bloom of Lingulodinium polyedra in coastal Southern California. These multi-year datasets allowed us to compare the microbial community response to past events, such as a smaller L. polyedra bloom the previous year. We demonstrated that the bacterial and archaeal response to the 2020 bloom was unique taxonomically, with many novel heterotrophs, and higher trophic state variance. The measured heterotrophic response to the bloom resulted in massive oxygen drawdown and may have impacted the length of the bloom and contributed to a secondary diatom bloom following the main HAB event. Taken together, these data illustrate how the massive 2020 L. polyedra bloom created unique ecological conditions for coastal Southern California.

As harmful algae blooms are increasing in frequency and magnitude, one goal of a new generation of higher spectral resolution satellite missions is to improve the potential of satellite optical data to monitor these events. A satellite-based algorithm proposed over two decades ago was used for the first time to monitor the extent and temporal evolution of a massive bloom of the dinoflagellate Lingulodinium polyedra off Southern California during April and May 2020. The algorithm uses ultraviolet (UV) data that have only recently become available from the single ocean color sensor on the Japanese GCOM-C satellite. Dinoflagellates contain high concentrations of mycosporine-like amino acids and release colored dissolved organic matter, both of which absorb strongly in the UV part of the spectrum. Ratios 1, consistent with historical observations showing a sharp transition from dinoflagellate- to diatom-dominated waters in these areas. UV bands are thus potentially useful in the remote sensing of phytoplankton blooms but are currently available only from a single ocean color sensor. As several new satellites such as the NASA Plankton, Aerosol, Cloud, and marine Ecosystem mission will include UV bands, new algorithms using these bands are needed to enable better monitoring of blooms, especially potentially harmful algal blooms, across large spatiotemporal scales.

Published baseline data on biotoxin exposure in cetaceans is sparse but critical for interpreting mortality events as harmful algal blooms increase in frequency and duration. We present the first synthesis of domoic acid (DA), saxitoxin (STX), okadaic acid (OA), and microcystin detections in the feces and urine of stranded and bycaught southern California cetaceans, over an 18 year period (2001–2018), along with corresponding stomach content data. DA was detected in 13 out of 19 cetacean species, most often in harbor porpoise (Phocoena phocoena) (81.8%, n = 22) and long-beaked common dolphins (Delphinus delphis bairdii) (74%, n = 231). Maximum DA concentrations of 324,000 ng/g in feces and 271, 967 ng/ml in urine were observed in D. d. bairdii. DA was detected more frequently and at higher concentrations in male vs. female D. d. bairdii. Higher fecal DA concentrations in D. d. bairdii were associated with a greater proportion of northern anchovy (Engraulis mordax) in the diet, indicating it may be a primary vector of DA. Fecal DA concentrations for D. d. bairdii off Point Conception were greater than those from animals sampled off Los Angeles and San Diego counties, reflecting greater primary productivity and higher Pseudo-nitzschia spp. abundance in that region and a greater abundance of E. mordax in the diet. STX was detected at low levels (fecal max = 7.5 ng/g, urine max = 17 ng/ml) in 3.6% (n = 165) of individuals from 3 out of 11 species. The occurrence of E. mordax in 100% of the 3 examined stomachs suggests this species could be a primary vector of the detected STX. OA was detected in 2.4% of tested individuals (n = 85) at a maximum fecal concentration of 422.8 ng/g. Microcystin was detected in 14.3% (n = 7) of tested individuals with a maximum liver concentration of 96.8 ppb.

The irregular appearance of planktonic algae blooms off the coast of southern California has been a source of wonder for over a century. Although large algal blooms can have significant negative impacts on ecosystems and human health, a predictive understanding of these events has eluded science, and many have come to regard them as ultimately random phenomena. However, the highly nonlinear nature of ecological dynamics can give the appearance of randomness and stress traditional methods-such as model fitting or analysis of variance-to the point of breaking. The intractability of this problem from a classical linear standpoint can thus give the impression that algal blooms are fundamentally unpredictable. Here, we use an exceptional time series study of coastal phytoplankton dynamics at La Jolla, CA, with an equation-free modeling approach, to show that these phenomena are not random, but can be understood as nonlinear population dynamics forced by external stochastic drivers (so-called "stochastic chaos"). The combination of this modeling approach with an extensive dataset allows us to not only describe historical behavior and clarify existing hypotheses about the mechanisms, but also make out-of-sample predictions of recent algal blooms at La Jolla that were not included in the model development.

An unusual stem rust infestation occurred in German wheat fields in summer 2013. This study analysed 48 isolates derived from 17 Puccinia graminis f. sp. tritici (Pgt) samples and six races were identified: TKTTF, TKKTF, TKPTF, TKKTP, PKPTF and MMMTF. Infection type and genotypic data confirmed that none of these races belonged to the TTKS (Ug99) race group. German isolates of race TKTTF are phenotypically different to the ones responsible for the stem rust epidemic in Ethiopia in 2013–2014. Forty isolates were genotyped using a custom SNP array. Phylogenetic analysis showed that these 40 isolates represented two distinct lineages (clade IV and clade V). Thirty-eight isolates clustered into clade IV, which previously was defined by Ethiopian isolates of race TKTTF. Race TKKTP is of special concern due to its combined virulence to stem rust resistance genes Sr24, SrTmp and Sr1RSAmigo. The vulnerability to race TKKTP in US and international winter wheat was confirmed as 55% of North American and international cultivars and breeding lines resistant to race TTKSK (Ug99) became susceptible to TKKTP. Races identified in Germany in 2013 confirmed the presence of virulence to important resistance genes that are effective against race TTKSK. This information should be useful for breeders to select diverse and effective resistance genes in order to provide more durable stem rust resistance and reduce the use of fungicides.

Many different atmospheric trace gases have been directly and indirectly linked to biological sources and sinks. Here we assess how atmospheric mixing ratios of a range of halocarbons (CH3Br, CH2Br2, CHBr3, CH3Cl, CHCl3, and CH3I) and COS are causally connected to naturally occurring marine eukaryotic phytoplankton in coastal Southern California. We use a self-organizing map to characterize the abiotic environment and empirical dynamic modeling with convergent cross mapping to identify causal interactions between multiple in situ 8-year time-series, sampled at the Ellen Browning Scripps Pier at Scripps Institution of Oceanography. Our work supports previous findings that halocarbon production is found in a variety of marine phytoplankton taxa and suggests that local phytoplankton may have the ability to affect changes in the mixing ratios of halocarbons in nearshore environments. There were notable links between changes in CH3I and several different diatom taxa and between changes in CHCl3 and a group of phytoplankton during specific ecosystem states. Our results suggest that both seasonal and non-seasonal shifts in eukaryotic phytoplankton structure contribute to small fluctuations in atmospheric halocarbon mixing ratios that exhibit strong seasonality and may occasionally play a larger role in atmospheric mixing ratios of halocarbons that display reduced seasonality.

The nutrient climate on the inner shelf off southern California changed markedly across the 1976–1977 North Pacific climate regime shift. With respect to giant kelp (Macrocystis pyrifera) canopies off southern California, the nitrate climate shifted from relatively replete conditions prior to the regime shift to depleted conditions afterward, and the dynamics of 14 giant kelp forests appeared to change as a result. The response of giant kelp to nutrientreplete years before the regime shift was dampened compared to their response afterward. The sensitivity of these kelp-forest canopies to nutrient limitation appears to have increased since the regime shift. This intensification of physical control after 1977 is evident in the strong correlation of seawater density (st) and M. pyrifera density. The linear fit of the percent of time the 25.1 st isopycnal bathes the inner shelf, accounted for , 71% of the variability in kelp density off Point Loma, and the median depth of this isopycnal has deepened , 5 m since the regime shift. The wave climate also intensified beginning in the early 1970s. The dampened kelp response prior to the regime shift was likely due to greater biological control of kelp canopies via consumer and competitive processes (i.e., biological modulation) or decreased physical control at possibly many trophic levels. Our results

[1] The interaction of alongshore coastal currents with large headlands has been shown to increase the retention of planktonic organisms through the formation of headland eddies or upwelling shadows in their lee. This study investigates the circulation within Bodega Bay (in the lee of a small headland), in an upwelling region, and the potential for retention of plankton. During the upwelling season of 2004, time series of temperature and velocity were recorded throughout Bodega Bay, conductivity-temperature-depth (CTD) surveys were conducted, and surface drifters were released during upwelling, downwelling, and relaxation conditions. Postlarval settlement was monitored daily over two periods coinciding with CTD surveys. Under strong upwelling favorable conditions, wind-driven surface currents were equatorward both offshore and throughout the bay. However, there was significant current shear along the eastern shore of the bay where cold bottom waters move poleward, counter to the direction of the wind-driven surface flow. During downwelling and relaxation conditions, flow was poleward throughout the water column along the eastern shore of the bay. Postlarvae settled during all wind conditions, but greatest settlement was observed at the onset of upwelling favorable conditions. While no “typical” upwelling shadow is evident in the lee of the Bodega headland, subsurface recirculation driven by the alongshore flow past Bodega Head may facilitate the retention of plankton in the bay. Previous studies have generally focused on large headlands; however, it is likely that other small embayments in the lee of small headlands may also provide retention opportunities for planktonic organisms in upwelling regions.