Contrasting effects of ocean acidification on tropical fleshy and calcareous algae

Despite the heightened awareness of ocean acidification (OA) effects on marine organisms, few studies empirically juxtapose biological responses to CO2 manipulations across functionally distinct primary producers, particularly benthic algae. Algal responses to OA may vary because increasing CO2 has the potential to fertilize photosynthesis but impair biomineralization. Using a series of repeated experiments on Palmyra Atoll, simulated OA effects were tested across a suite of ecologically important coral reef algae, including five fleshy and six calcareous species. Growth, calcification and photophysiology were measured for each species independently and metrics were combined from each experiment using a meta-analysis to examine overall trends across functional groups categorized as fleshy, upright calcareous, and crustose coralline algae (CCA). The magnitude of the effect of OA on algal growth response varied by species, but the direction was consistent within functional groups. Exposure to OA conditions generally enhanced growth in fleshy macroalgae, reduced net calcification in upright calcareous algae, and caused net dissolution in CCA. Additionally, three of the five fleshy seaweeds tested became reproductive upon exposure to OA conditions. There was no consistent effect of OA on algal photophysiology. Our study provides experimental evidence to support the hypothesis that OA will reduce the ability of calcareous algae to biomineralize. Further, we show that CO2 enrichment either will stimulate population or somatic growth in some species of fleshy macroalgae. Thus, our results suggest that projected OA conditions may favor non-calcifying algae and influence the relative dominance of fleshy macroalgae on reefs, perpetuating or exacerbating existing shifts in reef community structure.

Impact of changing carbonate chemistry, temperature, and salinity on growth and test degradation of the benthic foraminifer Ammonia aomoriensis

The present study investigated the combined effects of ocean acidification, temperature, and salinity on growth and test degradation of Ammonia aomoriensis. This species is one of the dominant benthic foraminifera in near-coastal habitats of the southwestern Baltic Sea that can be particularly sensitive to changes in seawater carbonate chemistry. To assess potential responses to ocean acidification and climate change, we performed a fully crossed experiment involving three temperatures (8, 13, and 18°C), three salinities (15, 20, and 25) and four pCO2 levels (566, 1195, 2108, and 3843 µatm) for six weeks. Our results highlight a sensitive response of A. aomoriensis to undersaturated seawater with respect to calcite. The specimens continued to grow and increase their test diameter in treatments with pCO2 <1200 µatm, when Omega calc >1. Growth rates declined when pCO2 exceeded 1200 µatm (Omega calc <1). A significant reduction in test diameter and number of tests due to dissolution was observed below a critical Omega calc of 0.5. Elevated temperature (18°C) led to increased Omega calc, larger test diameter, and lower test degradation. Maximal growth was observed at 18°C. No significant relationship was observed between salinity and test growth. Lowered and undersaturated Omega calc, which results from increasing pCO2 in bottom waters, may cause a significant future decline of the population density of A. aomoriensis in its natural environment. At the same time, this effect might be partially compensated by temperature rise due to global warming.

Data base on pelagic ciliates grazing and growth rate as a function of size, prey size and type compiled from the literature

Microzooplankton (the 20 to 200 µm size class of zooplankton) is recognised as an important part of marine pelagic ecosystems. In terms of biomass and abundance pelagic ciliates are one of the important groups of organism in microzooplankton. However, their rates - grazing and growth - , feeding behaviour and prey preferences are poorly known and understood. A set of data was assembled in order to derive a better understanding of pelagic ciliates rates, in response to parameters such as prey concentration, prey type (size and species), temperature and their own size. With these objectives, literature was searched for laboratory experiments with information on one or more of these parameters effect studied. The criteria for selection and inclusion in the database included: (i) controlled laboratory experiment with a known ciliates feeding on a known prey; (ii) presence of ancillary information about experimental conditions, used organisms - cell volume, cell dimensions, and carbon content. Rates and ancillary information were measured in units that meet the experimenter need, creating a need to harmonize the data units after collection. In addition different units can link to different mechanisms (carbon to nutritive quality of the prey, volume to size limits). As a result, grazing rates are thus available as pg C/(ciliate*h), µm**3/(ciliate*h) and prey cell/(ciliate*h); clearance rate was calculated if not given and growth rate is expressed as the growth rate per day.

Multifaceted Physiological Response Allows Yeast to Adapt to the Loss of the Signal Recognition Particle-dependent Protein-targeting PathwayD⃞

Translational control has recently been recognized as an important facet of adaptive responses to various stress conditions. We describe the adaptation response of the yeast Saccharomyces cerevisiae to the loss of one of two mechanisms to target proteins to the secretory pathway. Using inducible mutants that block the signal recognition particle (SRP) pathway, we find that cells demonstrate a physiological response to the loss of the SRP pathway that includes specific changes in global gene expression. Upon inducing the loss of the SRP pathway, SRP-dependent protein translocation is initially blocked, and cell growth is considerably slowed. Concomitantly, gene expression changes include the induction of heat shock genes and the repression of protein synthesis genes. Remarkably, within hours, the efficiency of protein sorting improves while cell growth remains slow in agreement with the persistent repression of protein synthesis genes. Our results suggest that heat shock gene induction serves to protect cells from mislocalized precursor proteins in the cytosol, whereas reduced protein synthesis helps to regain efficiency in protein sorting by reducing the load on the protein translocation apparatus. Thus, we suggest that cells trade speed in cell growth for fidelity in protein sorting to adjust to life without SRP.

Selective adsorption of l- and d-amino acids on calcite: Implications for biochemical homochirality

The emergence of biochemical homochirality was a key step in the origin of life, yet prebiotic mechanisms for chiral separation are not well constrained. Here we demonstrate a geochemically plausible scenario for chiral separation of amino acids by adsorption on mineral surfaces. Crystals of the common rock-forming mineral calcite (CaCO3), when immersed in a racemic aspartic acid solution, display significant adsorption and chiral selectivity of d- and l-enantiomers on pairs of mirror-related crystal-growth surfaces. This selective adsorption is greater on crystals with terraced surface textures, which indicates that d- and l-aspartic acid concentrate along step-like linear growth features. Thus, selective adsorption of linear arrays of d- and l-amino acids on calcite, with subsequent condensation polymerization, represents a plausible geochemical mechanism for the production of homochiral polypeptides on the prebiotic Earth.

Haploinsufficiency of Sox9 results in defective cartilage primordia and premature skeletal mineralization

In humans, SOX9 heterozygous mutations cause the severe skeletal dysmorphology syndrome campomelic dysplasia. Except for clinical descriptions, little is known about the pathogenesis of this disease. We have generated heterozygous Sox9 mutant mice that phenocopy most of the skeletal abnormalities of this syndrome. The Sox9+/− mice died perinatally with cleft palate, as well as hypoplasia and bending of many skeletal structures derived from cartilage precursors. In embryonic day (E)14.5 heterozygous embryos, bending of radius, ulna, and tibia cartilages was already prominent. In E12.5 heterozygotes, all skeletal elements visualized by using Alcian blue were smaller. In addition, the overall levels of Col2a1 RNA at E10.5 and E12.5 were lower than in wild-type embryos. We propose that the skeletal abnormalities observed at later embryonic stages were caused by delayed or defective precartilaginous condensations. Furthermore, in E18.5 embryos and in newborn heterozygotes, premature mineralization occurred in many bones, including vertebrae and some craniofacial bones. Because Sox9 is not expressed in the mineralized portion of the growth plate, this premature mineralization is very likely the consequence of allele insufficiency existing in cells of the growth plate that express Sox9. Because the hypertrophic zone of the heterozygous Sox9 mutants was larger than that of wild-type mice, we propose that Sox9 also has a role in regulating the transition to hypertrophic chondrocytes in the growth plate. Despite the severe hypoplasia of cartilages, the overall organization and cellular composition of the growth plate were otherwise normal. Our results suggest the hypothesis that two critical steps of the chondrocyte differentiation pathway are sensitive to Sox9 dosage. First, an early step presumably at the stage of mesenchymal condensation of cartilage primordia, and second, a later step preceding the transition of chondrocytes into hypertrophic chondrocytes.

Particles move along actin filament bundles in nerve growth cones.

Organelle movement along actin filaments has been demonstrated in dissociated squid axoplasm [Kurznetsov, S. A., Langford, G.M. & Weiss, D. G. (1992) Nature (London) 356, 722-725 and Bearer, E.L., DeGiorgis, J.A., Bodner, R.A., Kao, A.W. & Reese, T.S. (1993) Proc. Natl. Acad. Sci. USA 90, 11252-11256] but has not been shown to occur in intact neurons. Here we demonstrate that intracellular transport occurs along actin filament bundles in intact neuronal growth cones. We used video-enhanced differential interference contrast microscopy to observe intracellular transport in superior cervical ganglion neurons cultured under conditions that enhance the visibility of actin bundles within growth cone lamellipodia. Intracellular particles, ranging in size from < 0.5-1.5 microns, moved along linear structures (termed transport bundles) at an average maximum rate of 0.48 micron/sec. After particle movement had been viewed, cultures were preserved by rapid perfusion with chemical fixative. To determine whether particle transport occurred along actin, we then used fluorescence microscopy to correlate this movement with actin and microtubule distributions in the same growth cones. The observed transport bundles colocalized with actin but not with microtubules. The rates of particle movement and the association of moving particles with actin filament bundles suggest that myosins may participate in the transport of organelles (or other materials) in intact neurons.

Interleukin 1 beta suppresses transforming growth factor-induced inorganic pyrophosphate (PPi) production and expression of the PPi-generating enzyme PC-1 in human chondrocytes.

Articular cartilage chondrocytes have the unique ability to elaborate large amounts of extracellular pyrophosphate (PPi), and transforming growth factor beta (TGF beta) appears singular among cartilage regulatory factors in stimulating PPi production. TGF beta caused a time and dose-dependent increase in intracellular and extracellular PPi in human articular chondrocyte cultures. TGF beta and interleukin 1 beta (IL-1 beta) antagonistically regulate certain chondrocyte functions. IL-1 beta profoundly inhibited basal and TGF beta-induced PPi elaboration. To address mechanisms involved with the regulation of PPi synthesis by IL-1 beta and TGF beta, we analyzed the activity of the PPi-generating enzyme NTP pyrophosphohydrolase (NTPPPH) and the PPi-hydrolyzing enzyme alkaline phosphatase. Human chondrocyte NTPPPH activity was largely attributable to plasma cell membrane glycoprotein 1, PC-1. Furthermore, TGF beta induced comparable increases in the activity of extracellular PPi, intracellular PPi, and cellular NTPPPH and in the levels of PC-1 protein and mRNA in chondrocytes as well as a decrease in alkaline phosphatase. All of these TGF beta-induced responses were completely blocked by IL-1 beta. Thus, IL-1 beta may be an important regulator of mineralization in chondrocytes by inhibiting TGF beta-induced PPi production and PC-1 expression.

(Table 8.4, Page 220-223) Chemical composition of different growth structures of manganese nodules, SONNE cruise SO78

In the nodule field of the Peru Basin, situated south of the zone of high bioproductivity, a relatively high flux of biogenic matter explains a distinct redox boundary at about 10 cm depth separating very soft oxic surface sediments from stiffer suboxic sediments. Maximum abundance (50 kg/m**2) of diagenetic nodules is found near the calcite compensation depth (CCD), currently at 4250 m. There, the accretion rate of nodules is much higher (100 mm/Ma) than on ridges (5 mm/Ma). Highest accretion rates are found at the bottom of large nodules that repeatedly sink to a level immediately above the redox boundary. There, distinct diagenetic growth conditions prevail and layers of dense laminated Mn oxide of very pure todorokite are formed. The layering of nodules is mainly the result of organisms moving nodules within the oxic surface sediment from diagenetic to hydrogenetic environments. The frequency of such movements is much higher than that of climatic changes. Two types of nodule burial occur in the Peru Basin. Large nodules are less easily moved by organisms and become buried. Consequently, buried nodules generally are larger than surface nodules. This type of burial predominates in basins. At ridges where smaller nodules prevail, burial is mainly controlled by statistical selection where some nodules are not moved up by organisms.

(Table 2) Aragonite, high and low magnesium calcite, major elements, bioclast and planktic foraminifera from ODP Hole 133-817A

Investigation of the Middle Miocene-Pleistocene succession in cores at ODP Site 817A (Leg 133), drilled on the slope south of the Queensland Plateau, identified the various material fluxes contributing to sedimentation and has determined thereby the paleogeographic events which occurred close to the studied area and influenced these fluxes. To determine proportions of platform origin and of plankton origin of carbonate mud, two reference sediments were collected: (1) back-reef carbonate mud from the Young Reef area (Great Barrier Reef); and (2) Late Miocene chalk from the Loyalty Basin, off New Caledonia. Through their biofacies and mineralogical and geochemical characters, these reference sediments were used to distinguish the proportions of platform and basin components in carbonate muds of 25 core samples from Hole 817A. Two "origin indexes" (i1 and i2) relate the proportion in platform and basin materials. The relative sedimentation rate is inferred from the high-frequency cycles determined by redox intervals in the cores. Bulk carbonate deposited in each core has been calculated in two ways with close results: (1) from calcimetric data available in the Leg 133 preliminary reports (Davies et al., 1991); and (2) from average magnetic susceptibility of cores, a value negatively correlated to the average carbonate content. Vertical changes in sedimentation rates, in carbonate content, in origin indexes and in "linear fluxes" document the evolution of sediment origins from platform carbonates, planktonic carbonates and insoluble material through time. These data are augmented with the variations in organic-matter content through the 817A succession. The observed changes and their interpretation are not modified by compaction, and are compatible with major paleogeographic events including drowning of the Queensland Plateau (Middle Miocene-Early Pliocene) and the renewal of shallow carbonate production, (1) during the Late Pliocene, and (2) from the Early Pleistocene. The birth and growth of the Great Barrier Reef is also recorded from 0.5 Ma by a strengthening of detrital carbonate deposition and possibly by a lack of clay minerals in the 4 upper cores, a response to trapping of terrigenous material behind this barrier. In addition, a maximum of biological silica production is displayed in the Middle Miocene. These changes constrain the time of events and the sequence-stratigraphy framework some components of which are transgression surface, maximum flooding surface and low-stand turbidites. Sedimentation rates and material fluxes show cycles lasting 1.75 Myr. Whatever their origin (climatic and/or eustatic) these cycles affected the planktonic production primarily. The changes also show that major carbonate variations in the deposits are due to a dilution effect by insoluble material (clay, biogenic silica and volcanic glasses) and that plankton productivity, controlling the major fraction of carbonate sedimentation, depends principally on terrigenous supplies, but also on deep-water upwelling. Accuracy of the method is reduced by redeposition, reworking, and probable occurrence of hiatuses.

Assessing Fracture Connectivity using Stable and Clumped Isotope Geochemistry of Calcite Cements

Understanding flow path connectivity within a geothermal reservoir is a critical component for efficiently producing sustained flow rates of hot fluids from the subsurface. I present a new approach for characterizing subsurface fracture connectivity that combines petrographic and cold cathodoluminescence (CL) microscopy with stable isotope analysis (δ18O and δ13C) and clumped isotope (Δ47) thermometry of fracture-filling calcite cements from a geothermal reservoir in northern Nevada. Calcite cement samples were derived from both drill cuttings and core samples taken at various depths from wells within the geothermal field. CL microscopy of some fracture filling cements shows banding parallel to the fracture walls as well as brecciation, indicating that the cements are related to fracture opening and fault slip. Variations in trace element composition indicated by the luminescence patterns reflect variations in the composition and source of fluids moving through the fractures as they opened episodically. Calcite δ13C and δ18O results also show significant variation among the sampled cements, reflecting multiple generations of fluids and fracture connectivity. Clumped isotope analyses performed on a subset of the cements analyzed for conventional δ18O and δ13C mostly show calcite growth temperatures around 150°C—above the current ambient rock temperature, which indicates a common temperature trend for the geothermal reservoir. However, calcite cements sampled along faults located within the well field showed both cold (18.7°C) and hot (226.1°C) temperatures. The anomalously cool temperature found along the fault, using estimates from clumped isotope thermometry, suggests a possible connection to surface waters for the geothermal source fluids for this system. This information may indicate that some of the faults within the well field are transporting meteoric water from the surface to be heated at depth, which then is circulated through a complex network of fractures and other faults.

Seismically-Induced Rock-Slope Failure: Numerical Investigation using the Bonded Particle Model

Thesis (Ph.D.)--University of Washington, 2016-06

Aspects of Markov Chains and Particle Systems

Thesis (Ph.D.)--University of Washington, 2016-06

Ultrastructure, aggregation-state, and crystal growth of biogenic nanocrystalline sphalerite and wurtzite

In this study, we investigated the size, submicrometer-scale structure, and aggregation state of ZnS formed by sulfate-reducing bacteria (SRB) in a SRB-dominated biofilm growing on degraded wood in cold (Tsimilar to8degreesC), circumneutral-pH (7.2-8.5) waters draining from an abandoned, carbonate-hosted Pb-Zn mine. High-resolution transmission electron microscope (HRTEM) data reveal that the earliest biologically induced precipitates are crystalline ZnS nanoparticles 1-5 nm in diameter. Although most nanocrystals have the sphalerite structure, nanocrystals of wurtzite are also present, consistent with a predicted size dependence for ZnS phase stability. Nearly all the nanocrystals are concentrated into 1-5 mum diameter spheroidal aggregates that display concentric banding patterns indicative of episodic precipitation and flocculation. Abundant disordered stacking sequences and faceted, porous crystal-aggregate morphologies are consistent with aggregation-driven growth of ZnS nanocrystals prior to and/or during spheroid formation. Spheroids are typically coated by organic polymers or associated with microbial cellular surfaces, and are concentrated roughly into layers within the biofilm. Size, shape, structure, degree of crystallinity, and polymer associations will all impact ZnS solubility, aggregation and coarsening behavior, transport in groundwater, and potential for deposition by sedimentation. Results presented here reveal nanometer- to micrometer-scale attributes of biologically induced ZnS formation likely to be relevant to sequestration via bacterial sulfate reduction (BSR) of other potential contaminant metal(loid)s, such as Pb2+, Cd2+, As3+ and Hg2+, into metal sulfides. The results highlight the importance of basic mineralogical information for accurate prediction and monitoring of long-term contaminant metal mobility and bioavailability in natural and constructed bioremediation systems. Our observations also provoke interesting questions regarding the role of size-dependent phase stability in biomineralization and provide new insights into the origin of submicrometer- to millimeter-scale petrographic features observed in low-temperature sedimentary sulfide ore deposits.