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A multitude of concurrent biological and physical processes contribute to microbial community turnover, especially in highly dynamic coastal environments. Characterizing what factors contribute most to shifts in microbial community structure and the specific organisms that correlate with changes in the products of photosynthesis improves our understanding of nearshore microbial ecosystem functions. We conducted high frequency sampling in nearshore Southern California in order to capture sub-weekly microbial community dynamics. Microbial communities were characterized by flow cytometry and 16S rRNA gene sequencing, and placed in the context of physicochemical parameters. Within our time-series, season and nutrient availability corresponded to changes in dominant microbial community members. Concurrent aseasonal drivers with overlapping scales of variability were also apparent when we used network analysis to assess the microbial community as subsets of the whole. Our analyses revealed the microbial community as a mosaic, with overlapping groups of taxa that varied on different timescales and correlated with unique abiotic and biotic factors. Specifically, a subnetwork associated with chlorophyll a exhibited rapid turnover, indicating that ecologically important subsets of the microbial community can change on timescales different than and in response to factors other than those that govern turnover of most members of the assemblage.

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.

Phytoplankton blooms can cause acute effects on marine ecosystems due either to their production of endogenous toxins or to their enormous biomass leading to major impacts on local economies and public health. Despite years of effort, the causes of these Harmful Algal Blooms are still not fully understood. Our hypothesis is that bacteria that produce photoactive siderophores may provide a bioavailable source of iron for phytoplankton which could in turn stimulate algal growth and support bloom dynamics. Here we correlate iron concentrations, phytoplankton cell counts, bacterial cell abundance, and copy numbers for a photoactive siderophore vibrioferrin biosynthesis gene in water samples taken from 2017 cruises in the Gulf of California, and the Pacific Ocean off the coast of northern Baja California as well as during a multiyear sampling at Scripps Pier in San Diego, CA. We find that bacteria producing the photoactive siderophore vibrioferrin, make up a surprisingly high percentage of total bacteria in Pacific/Gulf of California coastal waters (up to 9%). Vibroferrin's unique properties and the widespread prevalence of its bacterial producers suggest that it may contribute significantly to generating bioavailability of iron via photoredox reactions.

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

Phakopsora pachyrhizi is an obligate pathogen that causes Asian soybean rust. Asian soybean rust has an unusually broad host range and infects by direct penetration through the leaf cuticle. In order to understand the early events in the infection process, it is important to identify and characterize proteins in P. pachyrhizi. Germination of the urediniospore is the first stage in the infection process and represents a critical life stage applicable to studies with this obligate pathogen. We have applied a 2-DE and MS approach to identify 117 proteins from the National Center of Biotechnology Information nonredundant protein database and a custom database of Basidiomycota EST sequences. Proteins with roles in primary metabolism, energy transduction, stress, cellular regulation and signaling were identified in this study. This data set is accessible at http://world-2dpage.expasy.org/repository/database=0018.

Russian thistle or tumbleweed (Salsola tragus L.) is an introduced invasive weed in N. America. It is widely distributed in the US and is a target of biological control efforts. The fungus Colletotrichum gloeosporioides (Penz.) Penz. & Sacc. in Penz. f. sp. salsolae (CGS) is a facultative parasite under evaluation for classical biological control of this weed. Host-range tests were conducted with CGS in quarantine to determine whether the fungus is safe to release in N. America. Ninetytwo accessions were analyzed from 19 families: Aizoaceae, Alliaceae, Amaranthaceae, Apiaceae, Asteraceae, Brassicaceae, Cactaceae, Campanulaceae, Chenopodiaceae, Cucurbitaceae, Cupressaceae, Fabaceae, Malvaceae, Nyctaginaceae, Phytolaccaceae, Poaceae, Polygonaceae, Sarcobataceae, and Solanaceae and 10 tribes within the Chenopodiaceae: Atripliceae, Beteae, Camphorosmeae, Chenopodieae, Corispermeae, Halopepideae, Polycnemeae, Salicornieae, Salsoleae, and Suaedeae. These included 62 genera and 120 species. To facilitate interpretation of results, disease reaction data were combined with a relationship matrix derived from internal transcribed spacer DNA sequences and analyzed with mixed model equations to produce Best Linear Unbiased Predictors (BLUPs) for each species. Twenty-nine species (30 accessions) from seven closely-related Chenopodiaceae tribes had significant levels of disease severity as indicated by BLUPs, compared to six species determined to be susceptible with least squares means estimates. The 29 susceptible species were: 1 from Atripliceae, 4 from Camphorosmeae, 1 from Halopepideae, 2 from Polycnemeae, 6 from Salicornieae, 8 from Salsolae, and 7 from Suaedeae. Most species in the genus Salsola, which are all introduced and weedy, were very susceptible and damaged by CGS. Statistical comparisons and contrasts of BLUPs indicated that these Salsola species were significantly more susceptible than non-target species, including 15 species from relatives in the closely-related genera Bassia (=Kochia), Nitrophila, Salicornia, Sarcocornia, and Suaeda. Of the 29 susceptible species, 10 native or commercially important species in N. America were identified as needing additional tests to determine the extent of any damage caused by infection.

Surface chlorophyll (CHL) measured at the Scripps Pier in the Southern California Bight (SCB) for 18 years (1983–2000) reveals that the spring bloom occurs with irregular timing and intensity each year, unlike sea-surface temperature (SST), which is dominated by a regular seasonal cycle. In the 1990s, the spring bloom occurred earlier in the year and with larger amplitudes compared to those of the 1980s. Seasonal anomalies of the Pier CHL have no significant correlation with local winds, local SST, or upwelling index, which implies that classical coastal upwelling is not directly responsible for driving chlorophyll variations in nearshore SCB. The annual mean Pier CHL exhibits an increasing trend, whereas the Pier SST has no evident concomitant trend during the CHL observation period. The interannual variation of the Pier CHL is not correlated with tropical El Nino or La Nina conditions over the entire observing period. However, the Pier CHL was significantly influenced by El Nino/Southern Oscillation during the 1997/1998 El Nino and 1998/1999 La Nina transition period. The Pier CHL is highly coherent at long periods (3–7 years) with nearby offshore in situ surface CHL at the CalCOFI (California Cooperative Fisheries Investigations) station 93.27.

Oil-spill fate and transport modeling may be used to evaluate water column hydrocarbon concentrations, potential exposure to organisms, and impacts of oil spills with and without dispersant use. Important inputs to transport modeling for such analyses are current velocities and turbulent dispersion coefficients. Fluorescein dye studies off San Diego, California, were used to calibrate an oil transport model by hindcasting movement and dispersion of dye. The oil spill model was then used to predict subsurface hydrocarbon concentrations and potential water column impacts if oil were to be dispersed into the water column under similar conditions. Field-collected data included surface currents calculated from high-frequency radar data (HF-Radar), near-surface currents from drifter measurements drogued at several depths (1m, 2m, 4m or 5m), dye concentrations measured by fluorescence, spreading and dye intensity measurements based on aerial photography, and water density profiles from CTD casts. As the dye plume quickly extended throughout an upper mixed layer (7–15m), the horizontal dye movements were better indicated by the drifters drogued to a depth near the middle of that layer than the HF-Radar, which measured surface (∼top 50 cm) currents (including wind drift). Diffusion rates were estimated based on dye spreading measured by aerial photography and fluorescence-depth profiles. The model used these data as inputs, modeling of wind-forced surface water turbulence and drift as a function of wind speed and direction (based on published results of fluid dynamics studies), and Stokes law for droplet rise/sinking rates, to predict oil transport and dispersion rates within the water column. Use of such diffusion rate data in an oil fate model can provide estimates of likely dispersed oil concentrations under similar conditions, which may be used to evaluate potential impacts on water column biota. However, other conditions with different patterns of current shear (due to background currents, tidal currents, and wind stress) should be examined before these results can be generalized.

The California Department of Fish and Game Office of Spill Prevention and Response (CA OSPR) is utilizing oil-spill fate and transport modeling to develop the time and spatial scales, and equipment needs, for a formal Dispersed Oil Monitoring Plan (DOMP). When fully implemented, the DOMP will aid in documenting hydrocarbon concentrations in the water column, potentially exposed organisms (zooplankton), and the impacts of entrained oil and dissolved hydrocarbons with and without dispersant applications. Fluorescein dye studies off San Diego, California (USA) have been completed to test the operational framework for repeated sampling of dispersed oil plumes as outlined in the DOMP, to allow evaluation of high-frequency radar (HP-Radar) for providing surface current input data to oil spill models, and to provide verification of model-predicted movement of subsurface oil (dye) by comparison with drogue movement and measured dye concentrations over three dimensions and time. Aerial photodocumentation, subsurface drogues, dye transport, and HF-Radar were used to measure near-surface current fields at varying depths. High-resolution subsurface dye-plume structure was mapped using an in situ GPS-coupled towed fluorometer equipped with pressure sensors to provide dye concentration data as a function of time, position, and depth. In addition, data from the more traditional Special Monitoring of Applied Response Technology (SMART) protocols utilized by the U.S. Coast Guard (USCG) were compared with the in situ towed-fluorometer measurements, and conventional CTD data were collected to determine the mixed layer depth, an important variable in monitoring dispersion of oil in the water column. As a result of these efforts, significant progress has been made on developing and testing sampling protocols for the DOMP, and nearly continuous and synoptic data have been obtained from seven cruises conducted over a 12-month period. These data sets (available on-line through the Coastal Response Research Center (CRRC) website: http://www.crrc.unh.edu/) are being analyzed and integrated to support oil spill model development and verification with direct applicability to spill response decision making, net environmental benefit analysis, natural resource damage assessments, and educating the spill community and public.

Within California, there are several programs for studying and monitoring harmful algal blooms (HABs); however, these programs have been largely uncoordinated with respect to each other. To address this issue, the California Harmful Algal Bloom Monitoring and Alert Program (CalHABMAP) was established in 2008, the outcome of a community-led meeting and organizational effort. CalHABMAP created an integrated, statewide, harmful algal bloom monitoring and alert network by coordinating organizations and researchers currently collecting HAB data and developing a centralized portal for the dissemination of this information. The main goal of HABMAP is to implement a statewide HAB network and forecasting system for California, and potentially the US West Coast. CalHABMAP has succeeded in highlighting the need for a coordinated network and serves as partner for regional and national efforts led by the NOAA National Ocean Service, the Integrated Ocean Observing System, and the NASA Applied Sciences Program.

Evidence is increasing for a mutualistic relationship between phytoplankton and heterotrophic marine bacteria. It has been proposed that bacteria producing photoactive iron binding compounds known as siderophores could play an important role in such mutualistic associations by producing bioavailable iron utilizable by phytoplankton and in exchange receive autotrophically derived DOM. In order to understand the potential role photoactive siderophores might be playing in bacterial–algal mutualism or marine biogeochemistry in general, it is important to be able to detect and quantify their presence in various environments. One approach to accomplish that end is to make use of high sensitivity genomics technology (qPCR) to search for siderophore biosynthesis genes related to the production of photoactive siderophores. In this way one can access their “biochemical potential” and utilize this information as a proxy for the presence of these siderophores in the marine environment. In this report we studied the correlation of the presence of bacteria producing one of the three photoactive siderophores relative to total bacterial and dinoflagellate numbers from surface water at the Scripps Pier before, during, and after fall bloom of the dinoflagellate Lingulodinium polyedrum. We believe that these findings will aid us in gauging the importance of photoactive siderophores in the marine environment and in harmful algal bloom dynamics in particular.

[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.