BAYESIAN STATISTICAL METHODS IN GENE-ENVIRONMENT AND GENE-GENE INTERACTION STUDIES

Complex diseases such as cancer result from multiple genetic changes and environmental exposures. Due to the rapid development of genotyping and sequencing technologies, we are now able to more accurately assess causal effects of many genetic and environmental factors. Genome-wide association studies have been able to localize many causal genetic variants predisposing to certain diseases. However, these studies only explain a small portion of variations in the heritability of diseases. More advanced statistical models are urgently needed to identify and characterize some additional genetic and environmental factors and their interactions, which will enable us to better understand the causes of complex diseases. In the past decade, thanks to the increasing computational capabilities and novel statistical developments, Bayesian methods have been widely applied in the genetics/genomics researches and demonstrating superiority over some regular approaches in certain research areas. Gene-environment and gene-gene interaction studies are among the areas where Bayesian methods may fully exert its functionalities and advantages. This dissertation focuses on developing new Bayesian statistical methods for data analysis with complex gene-environment and gene-gene interactions, as well as extending some existing methods for gene-environment interactions to other related areas. It includes three sections: (1) Deriving the Bayesian variable selection framework for the hierarchical gene-environment and gene-gene interactions; (2) Developing the Bayesian Natural and Orthogonal Interaction (NOIA) models for gene-environment interactions; and (3) extending the applications of two Bayesian statistical methods which were developed for gene-environment interaction studies, to other related types of studies such as adaptive borrowing historical data. We propose a Bayesian hierarchical mixture model framework that allows us to investigate the genetic and environmental effects, gene by gene interactions (epistasis) and gene by environment interactions in the same model. It is well known that, in many practical situations, there exists a natural hierarchical structure between the main effects and interactions in the linear model. Here we propose a model that incorporates this hierarchical structure into the Bayesian mixture model, such that the irrelevant interaction effects can be removed more efficiently, resulting in more robust, parsimonious and powerful models. We evaluate both of the 'strong hierarchical' and 'weak hierarchical' models, which specify that both or one of the main effects between interacting factors must be present for the interactions to be included in the model. The extensive simulation results show that the proposed strong and weak hierarchical mixture models control the proportion of false positive discoveries and yield a powerful approach to identify the predisposing main effects and interactions in the studies with complex gene-environment and gene-gene interactions. We also compare these two models with the 'independent' model that does not impose this hierarchical constraint and observe their superior performances in most of the considered situations. The proposed models are implemented in the real data analysis of gene and environment interactions in the cases of lung cancer and cutaneous melanoma case-control studies. The Bayesian statistical models enjoy the properties of being allowed to incorporate useful prior information in the modeling process. Moreover, the Bayesian mixture model outperforms the multivariate logistic model in terms of the performances on the parameter estimation and variable selection in most cases. Our proposed models hold the hierarchical constraints, that further improve the Bayesian mixture model by reducing the proportion of false positive findings among the identified interactions and successfully identifying the reported associations. This is practically appealing for the study of investigating the causal factors from a moderate number of candidate genetic and environmental factors along with a relatively large number of interactions. The natural and orthogonal interaction (NOIA) models of genetic effects have previously been developed to provide an analysis framework, by which the estimates of effects for a quantitative trait are statistically orthogonal regardless of the existence of Hardy-Weinberg Equilibrium (HWE) within loci. Ma et al. (2012) recently developed a NOIA model for the gene-environment interaction studies and have shown the advantages of using the model for detecting the true main effects and interactions, compared with the usual functional model. In this project, we propose a novel Bayesian statistical model that combines the Bayesian hierarchical mixture model with the NOIA statistical model and the usual functional model. The proposed Bayesian NOIA model demonstrates more power at detecting the non-null effects with higher marginal posterior probabilities. Also, we review two Bayesian statistical models (Bayesian empirical shrinkage-type estimator and Bayesian model averaging), which were developed for the gene-environment interaction studies. Inspired by these Bayesian models, we develop two novel statistical methods that are able to handle the related problems such as borrowing data from historical studies. The proposed methods are analogous to the methods for the gene-environment interactions on behalf of the success on balancing the statistical efficiency and bias in a unified model. By extensive simulation studies, we compare the operating characteristics of the proposed models with the existing models including the hierarchical meta-analysis model. The results show that the proposed approaches adaptively borrow the historical data in a data-driven way. These novel models may have a broad range of statistical applications in both of genetic/genomic and clinical studies.

Geochemical and physical sediment properties of sediment cores from the Portuguese shelf

Marine sediments from the Portuguese shelf are influenced by environmental changes in the surrounding continental and marine environment. These are largely controlled by the North Atlantic Oscillation, but additional impacts may arise from episodic tsunamis. In order to investigate these influences, a high resolution multi-proxy study has been carried out on a 5.4 m long gravity core and five box cores from the Tagus prodelta on the western Portuguese margin, incorporating geochemical (Corg/Ntotal ratios, d13Corg, d15N, d18O, Corg and CaCO3 content) and physical sediment properties (magnetic susceptibility, grain-size). Subsurface data of the five box cores indicate no major effect of early postdepositional alteration. Surface data show a higher fraction of terrigenous organic material close to the river mouth and in the southern prodelta. Gravity core GeoB 8903 covers the last 3.2 kyrs with a temporal resolution of at least 0.1 cm/yr. Very high sedimentation rates between 69 and 140 cm core depth indicate a possible disturbance of the record by the AD1755 tsunami, although no evidence for a disturbance is observed in the data. Sea surface temperature and salinity on the prodelta, the local budget of marine NO3- as well as the provenance of organic matter remained virtually constant during the past 3.2 kyrs. A positive correlation between magnetic susceptibility (MS) and North Atlantic Oscillation (NAO) is evident for the past 250 years, coinciding with a negative correlation between mean grain-size and NAO. This is assigned to a constant riverine supply of fine material with high MS, which is diluted by the riverine input of a coarser, low-MS component during NAO negative, high-precipitation phases. End-member modelling of the lithic grain-size spectrum supports this, revealing a third, coarse lithic component. The high abundance of this coarse end-member prior to 2 kyr BP is interpreted as the result of stronger bottom currents, concentrating the coarse sediment fraction by winnowing. As continental climate was more arid prior to 2 kyr BP (Subboreal), the coarse end-member may also consist of dust from local sources. A decrease in grain-size and CaCO3 content after 2 kyr BP is interpreted as a result of decreasing wind strength. The onset of a fining trend and a further decrease in CaCO3 around AD900 occurs simultaneous to climatic variations, reconstructed from eastern North Atlantic records. A strong increase in MS between AD1400 and AD1500 indicates higher lithic terrigenous input, caused by deforestation in the hinterland.

Inorganic carbon and geochemistry measurements from landfast sea ice in Resolute Passage, Nunavut, Canada, as part of the Arctic-ICE project, May - June 2010

We conducted a six-week investigation of the sea ice inorganic carbon system during the winter-spring transition in the Canadian Arctic Archipelago. Samples for the determination of sea ice geochemistry were collected in conjunction with physical and biological parameters as part of the 2010 Arctic-ICE (Arctic - Ice-Covered Ecosystem in a Rapidly Changing Environment) program, a sea ice-based process study in Resolute Passage, Nunavut. The goal of Arctic-ICE was to determine the physical-biological processes controlling the timing of primary production in Arctic landfast sea ice and to better understand the influence of these processes on the drawdown and release of climatically active gases. The field study was conducted from 1 May to 21 June, 2010.

High-resolution multi-proxy record of the last interglacial period from Lake Van, eastern Anatolian high plateau, Turkey

A high-resolution multi-proxy record from Lake Van, eastern Anatolia, derived from a lacustrine sequence cored at the 357 m deep Ahlat Ridge (AR), allows a comprehensive view of paleoclimate and environmental history in the continental Near East during the last interglacial (LI). We combined paleovegetation (pollen), stable oxygen isotope (d18Obulk) and XRF data from the same sedimentary sequence, showing distinct variations during the period from 135 to 110 ka ago leading into and out of full interglacial conditions. The last interglacial plateau, as defined by the presence of thermophilous steppe-forest communities, lasted ca. 13.5 ka, from ~129.1-115.6 ka BP. The detailed palynological sequence at Lake Van documents a vegetation succession with several climatic phases: (I) the Pistacia zone (ca. 131.2-129.1 ka BP) indicates summer dryness and mild winter conditions during the initial warming, (II) the Quercus-Ulmus zone (ca. 129.1-127.2 ka BP) occurred during warm and humid climate conditions with enhanced evaporation, (III) the Carpinus zone (ca. 127.2-124.1 ka BP) suggest increasingly cooler and wetter conditions, and (IV) the expansion of Pinus at ~124.1 ka BP marks the onset of a colder/drier environment that extended into the interval of global ice growth. Pollen data suggest migration of thermophilous trees from refugial areas at the beginning of the last interglacial. Analogous to the current interglacial, the migration documents a time lag between the onset of climatic amelioration and the establishment of an oak steppe-forest, spanning 2.1 ka. Hence, the major difference between the last interglacial compared to the current interglacial (Holocene) is the abundance of Pinus as well as the decrease of deciduous broad-leaved trees, indicating higher continentality during the last interglacial. Finally, our results demonstrate intra-interglacial variability in the low mid-latitudes and suggest a close connection with the high-frequency climate variability recorded in Greenland ice cores.

Territory and Infrastructure : Strategic Identification and Project Pondering

El Territorio hoy es visto como una totalidad organizada que no puede ser pensada separando cada uno de los elementos que la componen; cada uno de ellos es definido por su relación con los otros elementos. Así, un pensamiento que integra diferentes disciplinas y saberes comienza a manejar una realidad que lejos está de definir certezas inamovibles, y comienza a vislumbrar horizontes estratégicos. La adaptación a la no linealidad de las relaciones que se dan sobre el territorio, y la diferencia de velocidades en las que actúan los distintos actores, nos exige hacer de la flexibilidad una característica esencial de la metodología de planificación estratégica. La multi-causalidad de los fenómenos que estructuran el territorio nos obliga a construir criterios cualitativos, entendiendo que nos es imposible la medición de estas cadenas causales y su reconstrucción completa en el tiempo; sin dejar por ello de edificar un marco profundo de acción y transformación que responda a una realidad cierta y veraz. Los fenómenos producidos sobre el territorio nunca actúan de manera aislada, lo que implica una responsabilidad a la hora de comprender las sinergias y la restricción que afectan los resultados de los procesos desatados. La presente ponencia corresponde a la Segunda Fase del proceso de identificación estratégica de los proyectos Plan Estratégico Territorial (PET) que se inició en el año 2005; dicho Plan es llevada a cabo por la Subsecretaría de Planificación Territorial del Ministerio de Planificación Federal y fue abordado sobre la base de tres pretensiones: institucionalizar el ejercicio del pensamiento estratégico, fortalecer la metodología de trabajo transdisciplinaria y multisectorial, y diseñar un sistema de ponderación de proyectos estratégicos de infraestructura, tanto a nivel provincial como nacional, con una fuerte base cualitativa. Este proceso dio como resultado una cartera ponderada de proyectos de infraestructura conjuntamente con una metodología que permitió consolidar los equipos provinciales de planificación, tanto en su relación con los decisores políticos como con los actores de los múltiples sectores del gobierno, y en estos resultados consolidar y reforzar una cultura del pensamiento estratégico sobre el territorio

Territory and Infrastructure : Strategic Identification and Project Pondering

El Territorio hoy es visto como una totalidad organizada que no puede ser pensada separando cada uno de los elementos que la componen; cada uno de ellos es definido por su relación con los otros elementos. Así, un pensamiento que integra diferentes disciplinas y saberes comienza a manejar una realidad que lejos está de definir certezas inamovibles, y comienza a vislumbrar horizontes estratégicos. La adaptación a la no linealidad de las relaciones que se dan sobre el territorio, y la diferencia de velocidades en las que actúan los distintos actores, nos exige hacer de la flexibilidad una característica esencial de la metodología de planificación estratégica. La multi-causalidad de los fenómenos que estructuran el territorio nos obliga a construir criterios cualitativos, entendiendo que nos es imposible la medición de estas cadenas causales y su reconstrucción completa en el tiempo; sin dejar por ello de edificar un marco profundo de acción y transformación que responda a una realidad cierta y veraz. Los fenómenos producidos sobre el territorio nunca actúan de manera aislada, lo que implica una responsabilidad a la hora de comprender las sinergias y la restricción que afectan los resultados de los procesos desatados. La presente ponencia corresponde a la Segunda Fase del proceso de identificación estratégica de los proyectos Plan Estratégico Territorial (PET) que se inició en el año 2005; dicho Plan es llevada a cabo por la Subsecretaría de Planificación Territorial del Ministerio de Planificación Federal y fue abordado sobre la base de tres pretensiones: institucionalizar el ejercicio del pensamiento estratégico, fortalecer la metodología de trabajo transdisciplinaria y multisectorial, y diseñar un sistema de ponderación de proyectos estratégicos de infraestructura, tanto a nivel provincial como nacional, con una fuerte base cualitativa. Este proceso dio como resultado una cartera ponderada de proyectos de infraestructura conjuntamente con una metodología que permitió consolidar los equipos provinciales de planificación, tanto en su relación con los decisores políticos como con los actores de los múltiples sectores del gobierno, y en estos resultados consolidar y reforzar una cultura del pensamiento estratégico sobre el territorio

Territory and Infrastructure : Strategic Identification and Project Pondering

El Territorio hoy es visto como una totalidad organizada que no puede ser pensada separando cada uno de los elementos que la componen; cada uno de ellos es definido por su relación con los otros elementos. Así, un pensamiento que integra diferentes disciplinas y saberes comienza a manejar una realidad que lejos está de definir certezas inamovibles, y comienza a vislumbrar horizontes estratégicos. La adaptación a la no linealidad de las relaciones que se dan sobre el territorio, y la diferencia de velocidades en las que actúan los distintos actores, nos exige hacer de la flexibilidad una característica esencial de la metodología de planificación estratégica. La multi-causalidad de los fenómenos que estructuran el territorio nos obliga a construir criterios cualitativos, entendiendo que nos es imposible la medición de estas cadenas causales y su reconstrucción completa en el tiempo; sin dejar por ello de edificar un marco profundo de acción y transformación que responda a una realidad cierta y veraz. Los fenómenos producidos sobre el territorio nunca actúan de manera aislada, lo que implica una responsabilidad a la hora de comprender las sinergias y la restricción que afectan los resultados de los procesos desatados. La presente ponencia corresponde a la Segunda Fase del proceso de identificación estratégica de los proyectos Plan Estratégico Territorial (PET) que se inició en el año 2005; dicho Plan es llevada a cabo por la Subsecretaría de Planificación Territorial del Ministerio de Planificación Federal y fue abordado sobre la base de tres pretensiones: institucionalizar el ejercicio del pensamiento estratégico, fortalecer la metodología de trabajo transdisciplinaria y multisectorial, y diseñar un sistema de ponderación de proyectos estratégicos de infraestructura, tanto a nivel provincial como nacional, con una fuerte base cualitativa. Este proceso dio como resultado una cartera ponderada de proyectos de infraestructura conjuntamente con una metodología que permitió consolidar los equipos provinciales de planificación, tanto en su relación con los decisores políticos como con los actores de los múltiples sectores del gobierno, y en estos resultados consolidar y reforzar una cultura del pensamiento estratégico sobre el territorio

Amino acid in Deep Sea Drilling Project cores

Several amino acid diagenetic reactions, which take place in the deep-sea sedimentary environment, were investigated, using various Deep Sea Drilling Project (DSDP) cores. Initially it was found that essentially all the amino acids in sediments are bound in peptide linkages; but, with increasing age, the peptide bonds undergo slow hydrolysis that results in an increasingly larger fraction of amino acids in the free state. The hydrolysis half-life in calcareous sediments was estimated to be ~1-2 million years, while in non-carbonate sediment the hydrolysis rate may be considerably slower. The amino acid compositions and the extent of racemization of several amino acids were determined in various fractions isolated from the sediments. These analyses demonstrated that the mechanism, kinetics, and rate of amino acid diagenesis are highly dependent upon the physical state (i.e., free, bound, etc.) in which the amino acids exist in the sedimentary environment. In the free state, serine and threonine were found to decompose primarily by a dehydration reaction, while in the bound state (residue or HCl-insoluble fraction) a reversible aldol-cleavage reaction is the main decomposition pathway of these amino acids. The change in amino acid composition of the residue fraction with time was suggested to be due to the hydrolysis of peptide bonds, while in foraminiferal tests the compositional changes over geological time are the result of various decomposition reactions. Reversible first-order racemization kinetics are not observed for free amino acids in sediments. The explanation for these anomalous kinetics involves a complex reaction series which includes the hydrolysis of peptide bonds and the very rapid racemization of free amino acids. The racemization rates of free amino acids in sediments were found to be many orders of magnitude faster than those predicted from elevated temperature experiments using free amino acids in aqueous solution. The racemization rate enhancement of free amino acids in sediments may be due to the catalysis of the reaction by trace metals. Reversible first-order kinetics are followed for amino acids in the residue fraction isolated from sediments; the rate of racemization in this fraction is slower than that predicted for protein-bound amino acids. Various applications of amino acid diagenetic reactions are discussed. Racemization and the decomposition reaction of serine and threonine can both be used, with certain limitations, to make rough age estimates of deep-sea sediments back to several million years. The extent of racemization in foraminiferal tests which have been dated by some other independent technique can be used to estimate geothermal gradients, and thus heat flows, and to evaluate the bottom water temperature history in certain oceanic areas.

Multi-temporal mapping of seagrass cover, species and biomass of the Eastern Banks, Moreton Bay, Australia, with links to shapefiles

The spatial and temporal dynamics of seagrasses have been studied from the leaf to patch (100 m**2) scales. However, landscape scale (> 100 km**2) seagrass population dynamics are unresolved in seagrass ecology. Previous remote sensing approaches have lacked the temporal or spatial resolution, or ecologically appropriate mapping, to fully address this issue. This paper presents a robust, semi-automated object-based image analysis approach for mapping dominant seagrass species, percentage cover and above ground biomass using a time series of field data and coincident high spatial resolution satellite imagery. The study area was a 142 km**2 shallow, clear water seagrass habitat (the Eastern Banks, Moreton Bay, Australia). Nine data sets acquired between 2004 and 2013 were used to create seagrass species and percentage cover maps through the integration of seagrass photo transect field data, and atmospherically and geometrically corrected high spatial resolution satellite image data (WorldView-2, IKONOS and Quickbird-2) using an object based image analysis approach. Biomass maps were derived using empirical models trained with in-situ above ground biomass data per seagrass species. Maps and summary plots identified inter- and intra-annual variation of seagrass species composition, percentage cover level and above ground biomass. The methods provide a rigorous approach for field and image data collection and pre-processing, a semi-automated approach to extract seagrass species and cover maps and assess accuracy, and the subsequent empirical modelling of seagrass biomass. The resultant maps provide a fundamental data set for understanding landscape scale seagrass dynamics in a shallow water environment. Our findings provide proof of concept for the use of time-series analysis of remotely sensed seagrass products for use in seagrass ecology and management.

Ocean acidification induces multi-generational decline in copepod naupliar production with possible conflict for reproductive resource allocation

Climate change, including ocean acidification (OA), presents fundamental challenges to marine biodiversity and sustained ecosystem health. We determined reproductive response (measured as naupliar production), cuticle composition and stage specific growth of the copepod Tisbe battagliai over three generations at four pH conditions (pH 7.67, 7.82, 7.95, and 8.06). Naupliar production increased significantly at pH 7.95 compared with pH 8.06 followed by a decline at pH 7.82. Naupliar production at pH 7.67 was higher than pH 7.82. We attribute the increase at pH 7.95 to an initial stress response which was succeeded by a hormesis-like response at pH 7.67. A multi-generational modelling approach predicted a gradual decline in naupliar production over the next 100 years (equivalent to approximately 2430 generations). There was a significant growth reduction (mean length integrated across developmental stage) relative to controls. There was a significant increase in the proportion of carbon relative to oxygen within the cuticle as seawater pH decreased. Changes in growth, cuticle composition and naupliar production strongly suggest that copepods subjected to OA-induced stress preferentially reallocate resources towards maintaining reproductive output at the expense of somatic growth and cuticle composition. These responses may drive shifts in life history strategies that favour smaller brood sizes, females and perhaps later maturing females, with the potential to profoundly destabilise marine trophodynamics.

Response of benthic foraminifera to ocean acidification in their natural sediment environment: a long-term culturing experiment

Calcifying foraminifera are expected to be endangered by ocean acidification; however, the response of a complete community kept in natural sediment and over multiple generations under controlled laboratory conditions has not been constrained to date. During 6 months of incubation, foraminiferal assemblages were kept and treated in natural sediment with pCO2-enriched seawater of 430, 907, 1865 and 3247 µatm pCO2. The fauna was dominated by Ammonia aomoriensis and Elphidium species, whereas agglutinated species were rare. After 6 months of incubation, pore water alkalinity was much higher in comparison to the overlying seawater. Consequently, the saturation state of Omega calc was much higher in the sediment than in the water column in nearly all pCO2 treatments and remained close to saturation. As a result, the life cycle (population density, growth and reproduction) of living assemblages varied markedly during the experimental period, but was largely unaffected by the pCO2 treatments applied. According to the size-frequency distribution, we conclude that foraminifera start reproduction at a diameter of 250 µm. Mortality of living Ammonia aomoriensis was unaffected, whereas size of large and dead tests decreased with elevated pCO2 from 285 µm (pCO2 from 430 to 1865 µatm) to 258 µm (pCO2 3247 µatm). The total organic content of living Ammonia aomoriensis has been determined to be 4.3% of CaCO3 weight. Living individuals had a calcium carbonate production rate of 0.47 g/m**2/a, whereas dead empty tests accumulated a rate of 0.27 g /m**2/a. Although Omega calc was close to 1, approximately 30% of the empty tests of Ammonia aomoriensis showed dissolution features at high pCO2 of 3247 µatm during the last 2 months of incubation. In contrast, tests of the subdominant species, Elphidium incertum, stayed intact. Our results emphasize that the sensitivity to ocean acidification of the endobenthic foraminifera Ammonia aomoriensis in their natural sediment habitat is much lower compared to the experimental response of specimens isolated from the sediment.

Seawater carbonate chemistry and proportion of different dissolution levels in live juvenile Limacina helicina antarctica from the natural environment and ship-board incubations

The carbonate chemistry of the surface ocean is rapidly changing with ocean acidification, a result of human activities. In the upper layers of the Southern Ocean, aragonite-a metastable form of calcium carbonate with rapid dissolution kinetics-may become undersaturated by 2050. Aragonite undersaturation is likely to affect aragonite-shelled organisms, which can dominate surface water communities in polar regions. Here we present analyses of specimens of the pteropod Limacina helicina antarctica that were extracted live from the Southern Ocean early in 2008. We sampled from the top 200 m of the water column, where aragonite saturation levels were around 1, as upwelled deep water is mixed with surface water containing anthropogenic CO2. Comparing the shell structure with samples from aragonite-supersaturated regions elsewhere under a scanning electron microscope, we found severe levels of shell dissolution in the undersaturated region alone. According to laboratory incubations of intact samples with a range of aragonite saturation levels, eight days of incubation in aragonite saturation levels of 0.94-1.12 produces equivalent levels of dissolution. As deep-water upwelling and CO2 absorption by surface waters is likely to increase as a result of human activities, we conclude that upper ocean regions where aragonite-shelled organisms are affected by dissolution are likely to expand.

Benthic cover map of Heron Reef derived from a high-spatial-resolution multi-spectral satellite image using object based image analysis

Providing accurate maps of coral reefs where the spatial scale and labels of the mapped features correspond to map units appropriate for examining biological and geomorphic structures and processes is a major challenge for remote sensing. The objective of this work is to assess the accuracy and relevance of the process used to derive geomorphic zone and benthic community zone maps for three western Pacific coral reefs produced from multi-scale, object-based image analysis (OBIA) of high-spatial-resolution multi-spectral images, guided by field survey data. Three Quickbird-2 multi-spectral data sets from reefs in Australia, Palau and Fiji and georeferenced field photographs were used in a multi-scale segmentation and object-based image classification to map geomorphic zones and benthic community zones. A per-pixel approach was also tested for mapping benthic community zones. Validation of the maps and comparison to past approaches indicated the multi-scale OBIA process enabled field data, operator field experience and a conceptual hierarchical model of the coral reef environment to be linked to provide output maps at geomorphic zone and benthic community scales on coral reefs. The OBIA mapping accuracies were comparable with previously published work using other methods; however, the classes mapped were matched to a predetermined set of features on the reef.

Phytoplankton responses and associated carbon cycling during shipboard carbonate chemistry manipulation experiments conducted around Northwest European shelf seas

The ongoing oceanic uptake of anthropogenic carbon dioxide (CO2) is significantly altering the carbonate chemistry of seawater, a phenomenon referred to as ocean acidification. Experimental manipulations have been increasingly used to gauge how continued ocean acidification will potentially impact marine ecosystems and their associated biogeochemical cycles in the future; however, results amongst studies, particularly when performed on natural communities, are highly variable, which may reflect community/environment-specific responses or inconsistencies in experimental approach. To investigate the potential for identification of more generic responses and greater experimentally reproducibility, we devised and implemented a series (n = 8) of short-term (2-4 days) multi-level (>=4 conditions) carbonate chemistry/nutrient manipulation experiments on a range of natural microbial communities sampled in Northwest European shelf seas. Carbonate chemistry manipulations and resulting biological responses were found to be highly reproducible within individual experiments and to a lesser extent between geographically separated experiments. Statistically robust reproducible physiological responses of phytoplankton to increasing pCO2, characterised by a suppression of net growth for small-sized cells (<10 µm), were observed in the majority of the experiments, irrespective of natural or manipulated nutrient status. Remaining between-experiment variability was potentially linked to initial community structure and/or other site-specific environmental factors. Analysis of carbon cycling within the experiments revealed the expected increased sensitivity of carbonate chemistry to biological processes at higher pCO2 and hence lower buffer capacity. The results thus emphasise how biogeochemical feedbacks may be altered in the future ocean.