Downscaling global ocean climate models improves estimates of exposure regimes in coastal environments.

Climate change is expected to warm, deoxygenate, and acidify ocean waters. Global climate models (GCMs) predict future conditions at large spatial scales, and these predictions are then often used to parameterize laboratory experiments designed to assess biological and ecological responses to future change. However, nearshore ecosystems are affected by a range of physical processes such as tides, local winds, and surface and internal waves, causing local variability in conditions that often exceeds global climate models. Predictions of future climatic conditions at local scales, the most relevant to ecological responses, are largely lacking. To fill this critical gap, we developed a 2D implementation of the Regional Ocean Modeling System (ROMS) to downscale global climate predictions across all Representative Concentration Pathway (RCP) scenarios to smaller spatial scales, in this case the scale of a temperate reef in the northeastern Pacific. To assess the potential biological impacts of local climate variability, we then used the results from different climate scenarios to estimate how climate change may affect the survival, growth, and fertilization of a representative marine benthic invertebrate, the red abalone Haliotis rufescens, to a highly varying multi-stressor environment. We found that high frequency variability in temperature, dissolved oxygen (DO), and pH increases as pCO2 increases in the atmosphere. Extreme temperature and pH conditions are generally not expected until RCP 4.5 or greater, while frequent exposure to low DO is already occurring. In the nearshore environment simulation, strong RCP scenarios can affect red abalone growth as well as reduce fertilization during extreme conditions when compared to global scale simulations.

Climate-related, long-term faunal changes in a california rocky intertidal community.

Changes in the invertebrate fauna of a California rocky intertidal community between the period 1931 to 1933 and the period 1993 to 1994 indicate that species' ranges shifted northward, consistent with predictions of change associated with climate warming. Of 45 invertebrate species, the abundances of eight of nine southern species increased and the abundances of five of eight northern species decreased. No trend was evident for cosmopolitan species. Annual mean shoreline ocean temperatures at the site increased by 0.75 degrees C during the past 60 years, and mean summer maximum temperatures from 1983 to 1993 were 2.2 degrees C warmer than for the period 1921 to 1931.

Oligonucleotide sequencing using guanine-specific methylation and electrospray ionization ion trap mass spectrometry.

This paper describes a novel method to map guanine bases in short oligonucleotides using a simple chemical modification reaction and subsequent analysis by electrospray ionization ion trap mass spectrometry (ITMS). In situ guanine-specific methylation followed by gas-phase fragmentation permits the determination of the positions of all guanine residues. Collision-induced dissociation (CID) of the monomethylated oligonucleotide strand promotes rapid depurination and further collision (MS3) of the apurinic oligonucleotide leads to preferential cleavage of the backbone at the site of depurination. The mass of the resulting complementary product ions verifies the position of each guanine base in the sequence. The utility of this methodology is demonstrated for oligonucleotide sequences up to 10 bases in length. In addition, this technique successfully illustrates the use of selective fragmentation for sequencing oligonucleotides by ITMS.

Distribution of enteric bacteria in Antarctic seawater surrounding a sewage outfall.

The spatial distribution and movement of the sewage plume from McMurdo Station, Antarctica, was investigated in the ocean under the early summer sea ice. Ocean currents were also examined to determine their effect on the movement of the plume. Samples of sea water were obtained via holes drilled through the ice and analyzed for coliform bacteria. Coliform densities in ice cores were also determined. Densities of coliform bacteria as high as 10(5)/100 ml were found along the c. 1 km shoreline of McMurdo Station and the plume extended 200-300 m seaward. The relocation of the outfall from a surface configuration to the subsurface (11 m deep) had little influence on the distribution of the plume that sometimes reached the seawater intake station, 400 m to the south. Ocean current measurements in the study area confirmed that, while the prevailing advection was to the north and away from the intake area, episodic reversals of flow at some current meter stations coincided with pulses of sewage that moved to the intake. These findings support the use of bacterial indicators as one means to map the distribution and movement of recent sewage contamination in cold (-1.8 degrees C) sea water and provide evidence that the disposal and movement of domestic wastes deserves attention in coastal [correction of costal] polar environments.

Phylogenetic affinity of a wide, vacuolate, nitrate-accumulating Beggiatoa sp. from Monterey Canyon, California, with Thioploca spp.

Environmentally dominant members of the genus Beggiatoa and Thioploca spp. are united by unique morphological and physiological adaptations (S. C. McHatton, J. P. Barry, H. W. Jannasch, and D. C. Nelson, Appl. Environ. Microbiol. 62:954-958, 1996). These adaptations include the presence of very wide filaments (width, 12 to 160 microm), the presence of a central vacuole comprising roughly 80% of the cellular biovolume, and the capacity to internally concentrate nitrate at levels ranging from 150 to 500 mM. Until recently, the genera Beggiatoa and Thioploca were recognized and differentiated on the basis of morphology alone; they were distinguished by the fact that numerous Thioploca filaments are contained within a common polysaccharide sheath, while Beggiatoa filaments occur singly. Vacuolate Beggiatoa or Thioploca spp. can dominate a variety of marine sediments, seeps, and vents, and it has been proposed (H. Fossing, V. A. Gallardo, B. B. Jorgensen, M. Huttel, L. P. Nielsen, H. Schulz, D. E. Canfield, S. Forster, R. N. Glud, J. K. Gundersen, J. Kuver, N. B. Ramsing, A. Teske, B. Thamdrup, and O. Ulloa, Nature [London] 374:713-715, 1995) that members of the genus Thioploca are responsible for a significant portion of total marine denitrification. In order to investigate the phylogeny of an environmentally dominant Beggiatoa sp., we analyzed complete 16S rRNA gene sequence data obtained from a natural population found in Monterey Canyon cold seeps. Restriction fragment length polymorphism analysis of a clone library revealed a dominant clone, which gave rise to a putative Monterey Beggiatoa 16S rRNA sequence. Fluorescent in situ hybridization with a sequence-specific probe confirmed that this sequence originated from wide Beggiatoa filaments (width, 65 to 85 microm). A phylogenetic tree based on evolutionary distances indicated that the Monterey Beggiatoa sp. falls in the gamma subdivision of the class Proteobacteria and is most closely related to the genus Thioploca. This vacuolate Beggiatoa-Thioploca cluster and a more distantly related freshwater Beggiatoa species cluster form a distinct phylogenetic group.

Detection and identification of benzo[a]pyrene diol epoxide adducts to DNA utilizing capillary electrophoresis-electrospray mass spectrometry.

Capillary zone electrophoresis (CZE) coupled with negative ion electrospray mass spectrometry (ES-MS) is used for the detection and identification of adducts formed from the reaction of DNA with (+/-)-anti-7,8,9,10-tetrahydrobenzo[a]pyrene-7,8-diol 9,10-epoxide (BPDE),an active metabolite of benzo[a]pyrene (BaP). Results presented in this paper demonstrate low nanogram detection limits ( < 10 ng or < 15 pmol) for normal scan spectra and collision-induced dissociation spectra of the main nucleotide adduct formed from this reaction. (BPDE reacts predominantly with the exocyclic amino group of guanine.) Exploitation of selective reaction monitoring (SRM) produces detection limits in the low picogram range ( < 85 pg or < 130 fmol). The application of sample stacking significantly increases the concentration detection limit (to approximately 10(-8) M). Nucleotide adducts are negatively charged at most pHs and are therefore ideally suited to the stacking process used in this research. These techniques have been applied to the analysis of the adducts formed from the in vitro reaction of BPDE with DNA. In addition it is shown that CZE-ES-MS, combined with solid-phase sample cleanup, can detect adducts at levels of four adducts in 10(7) unmodified bases or less.

Development, Temperature Tolerance, and Settlement Preference of Embryos and Larvae of the Articulate Brachiopod Laqueus californianus.

Populations of the articulate brachiopod Laqueus californianus occur in dense single-species aggregations near the continental shelf/slope break (100-200 m) in Monterey Bay, California. The development of embryos and larvae of L. californianus has been examined by scanning electron microscopy. Fertilizable eggs are 130-140 {mu}m in diameter, and sperm are unmodified. Cleavage is holoblastic and radial. At 10{deg}C an up-swimming blastula develops by 18-h, and gastrulation occurs within 24-38 h. The embryo elongates on a new larval axis and the blastopore closes by 72 h. A trilobed articulate brachiopod larva forms by day 3-4, and a metamorphically competent larva with attachment disk is attained in 7 days. Competent larvae swim downwards. Effects of temperature on larval survival and development rate have also been examined. Larvae die within 1 day at 25{deg}C. At 20{deg}C, development appears normal but results in spontaneous abnormal settlement of larvae 5-6 days old. At 15{deg}, 10{deg}, and 5{deg}C, most larvae achieve competence in 5, 7, and 9 days, respectively. Many larvae survive for 71 days at 10{deg} and 15{deg}C. Patterns of larval settlement vary among substrates, but larvae show strong preference for shells of living conspecific adults. Settlement and metamorphosis can occur within 24 h upon exposure of larvae to substrate.

High Nitrate Concentrations in Vacuolate, Autotrophic Marine Beggiatoa spp.

Massive accumulations of very large Beggiatoa spp. are found at a Monterey Canyon cold seep and at Guaymas Basin hydrothermal vents. Both environments are characterized by high sediment concentrations of soluble sulfide and low levels of dissolved oxygen in surrounding waters. These filamentous, sulfur-oxidizing bacteria accumulate nitrate intracellularly at concentrations of 130 to 160 mM, 3,000- to 4,000-fold higher than ambient levels. Average filament widths range from 24 to 122 (mu)m, and individual cells of all widths possess a central vacuole. These findings plus recent parallel discoveries for Thioploca spp. (H. Fossing, V. A. Gallardo, B. B. Jorgensen, M. Huttel, L. P. Nielsen, H. Schulz, D. E. Canfield, S. Forster, R. N. Glud, J. K. Gundersen, J. Kuver, N. B. Ramsing, A. Teske, B. Thamdrup, and O. Ulloa, Nature (London) 374:713-715, 1995) suggest that nitrate accumulation may be a universal property of vacuolate, filamentous sulfur bacteria. Ribulose bisphosphate carboxylase-oxygenase and 2-oxoglutarate dehydrogenase activities in the Beggiatoa sp. from Monterey Canyon suggest in situ autotrophic growth of these bacteria. Nitrate reductase activity is much higher in the Monterey Beggiatoa sp. than in narrow, laboratory-grown strains of Beggiatoa spp., and the activity is found primarily in the membrane fraction, suggesting that the vacuolate Beggiatoa sp. can reduce nitrate coupled to electron flow through an electron transport system. Nitrate-concentrating and respiration potentials of these chemolithoautotrophs suggest that the Beggiatoa spp. described here are an important link between the sulfur, nitrogen, and carbon cycles at the Monterey Canyon seeps and the Guaymas Basin hydrothermal vents where they are found.

Neutral and nonneutral mitochondrial genetic variation in deep-sea clams from the family vesicomyidae.

Nucleotide sequences at two mitochondrial genes from 57 individuals representing eight species of deep-sea clams (Vesicomyidae) were examined for variation consistent with the neutral model of molecular evolution. One gene, cytochrome oxidase subunit I (COI), deviated from the expectations of neutrality by containing an excess of intraspecific nonsynonymous polymorphism. Additionally, one species, Calyptogena kilmeri, showed a significant excess of rare polymorphism specifically at the COI locus. In contrast, a second mitochondrial gene, the large-subunit 16S ribosomal RNA gene (16S), showed little deviation from neutrality either between or within species. Together, COI and 16S show no deviation from neutral expectations by the HKA test, produce congruent phylogenetic relationships between species, and show correlated numbers of fixed differences between species and polymorphism within species. These patterns of both neutral and nonneutral evolution within the mitochondrial genome are most consistent with a model where intraspecific nonsynonymous polymorphism at COI is near neutrality. In addition to examining the forces of molecular evolution, we extend hypotheses about interspecific relationships within this family for geographical locations previously unexamined by molecular methods including habitats near the Middle Atlantic, the Aleutian Trench, and Costa Rica.

Rapid and early export of Phaeocystis antarctica blooms in the Ross Sea, Antarctica.

The Southern Ocean is very important for the potential sequestration of carbon dioxide in the oceans and is expected to be vulnerable to changes in carbon export forced by anthropogenic climate warming. Annual phytoplankton blooms in seasonal ice zones are highly productive and are thought to contribute significantly to pCO2 drawdown in the Southern Ocean. Diatoms are assumed to be the most important phytoplankton class with respect to export production in the Southern Ocean; however, the colonial prymnesiophyte Phaeocystis antarctica regularly forms huge blooms in seasonal ice zones and coastal Antarctic waters. There is little evidence regarding the fate of carbon produced by P. antarctica in the Southern Ocean, although remineralization in the upper water column has been proposed to be the main pathway in polar waters. Here we present evidence for early and rapid carbon export from P. antarctica blooms to deep water and sediments in the Ross Sea. Carbon sequestration from P. antarctica blooms may influence the carbon cycle in the Southern Ocean, especially if projected climatic changes lead to an alteration in the structure of the phytoplankton community.