The formation of carbonate minerals in laboratory and environmental settings

Microbial sulfate reduction, couple to organic matter oxidation or methane oxidation, is one of the key processes driving the formation of sedimentary carbonate minerals. While some work has been done exploring the formation of carbonate minerals via microbial sulfate reduction, less attention has been given to the detailed processes involved in this microbially induced carbonate mineral formation and how the carbonate minerals form may transform and change over time. In this thesis, I investigated the role that microbial sulfate reduction has on the types of calcium carbonate polymorphs precipitated. For this, I grew sulfate-reducing bacteria (Desulfovibrio bizertensis) in media with varying Mg/Ca and different types of seeding materials. My results suggest that sulfate-reducing bacteria induce carbonate precipitation and serve as a nucleation for the growing carbonate minerals. In media where the Mg/Ca is greater than 2, a crystalline monohydrocalcite is the primary carbonate mineral produced. In addition, I examine the role of different seeding materials such as calcite and kaolinite have on the generation of alkalinity and microbial growth in the incubation experiments. My results show higher alkalinity production and rates of sulfate reduction in samples with kaolinite seeds. I suggest this is due to the fact that bacteria grow better in the presence of clay minerals that have a higher surface area. In the final chapter of my thesis, I extend my research from the laboratory setting to the field, in the Norfolk saltmarshes. Using an incubation approach of the saltmarsh sediment allows high-resolution monitoring of the evolution of pore fluid chemistry and thus the stability of siderite in conditions that mimic the saltmarsh. My incubation results suggest that the formation of siderite nodule can be very rapid (within weeks) after burial when there is a substantial iron source. My research thus explores the mineralisation of carbonate through microbial processes and how the diversity of carbonate minerals may be explained and examined in the geological record.ERC StG 307582 to AVT (CARBONSINK), SLAI (Skim Latihan Akademik IPTA) scholarshi

The microbially driven formation of siderite in salt marsh sediments

We employ complementary field and laboratory‐based incubation techniques to explore the geochemical environment where siderite concretions are actively forming and growing, including solid‐phase analysis of the sediment, concretion, and associated pore fluid chemistry. These recently formed siderite concretions allow us to explore the geochemical processes that lead to the formation of this less common carbonate mineral. We conclude that there are two phases of siderite concretion growth within the sediment, as there are distinct changes in the carbon isotopic composition and mineralogy across the concretions. Incubated sediment samples allow us to explore the stability of siderite over a range of geochemical conditions. Our incubation results suggest that the formation of siderite can be very rapid (about two weeks or within 400 hr) when there is a substantial source of iron, either from microbial iron reduction or from steel material; however, a source of dissolved iron is not enough to induce siderite precipitation. We suggest that sufficient alkalinity is the limiting factor for siderite precipitation during microbial iron reduction while the lack of dissolved iron is the limiting factor for siderite formation if microbial sulfate reduction is the dominant microbial metabolism. We show that siderite can form via heated transformation (at temperature 100°C for 48 hr) of calcite and monohydrocalcite seeds in the presence of dissolved iron. Our transformation experiments suggest that the formation of siderite is promoted when carbonate seeds are present

A baseline study on groundwater quality of the tourist island, Pulau Tiga, Sabah, Malaysia.

Pulau Tiga is a group of small islands located at Kimanis Bay off the western coast of Sabah. This preliminary study on groundwater of Pulau Tiga is undertaken to provide guidance and baseline data for future references. An understanding of the chemistry and behavior of water in the island aquifer is crucial for the determination of the availability of freshwater, and also to create a platform for considering proper management and successful remediation of groundwater resources on island to prevent over exploitation of such limited resources. Groundwater samples were collected from five wells on Pulau Tiga to understand the groundwater chemistry based on various ion composition (Ca2+, Mg2+, Na+, K+, HCO3-, SO42-, Cl-, NO3-), in situ parameters such as DO (Dissolved oxygen), EC (Electrical conductivity), TDS (Total dissolved solids), pH, salinity and temperature. Even though groundwater in Pulau Tiga was constantly subject to abstraction activities for its tourism purposes, preliminary results showed that the groundwater still remains freshwater type. The Piper diagram suggested that the groundwater facies generally range from Ca-HCO3 to Ca-Cl waters type. The processes influencing the groundwater chemistry are mainly dissolution of minerals

Stability behavior and Thermodynamic States of Iron and Manganese in Sandy Soil Aquifer, Manukan Island, Malaysia.

A total of 20 soil samples were collected from 10 boreholes constructed in the low lying area, which included ancillary samples taken from the high elevation area. Redox processes were investigated in the soil as well as groundwater in the shallow groundwater aquifer of Manukan Island, Sabah, Malaysia. Groundwater samples (n = 10) from each boreholes were also collected in the low lying area to understand the concentrations and behaviors of Fe and Mn in the dissolved state. This study strives to obtain a general understanding of the stability behaviors on Fe and Mn at the upper unsaturated and the lower-saturated soil horizons in the low lying area of Manukan Island as these elements usually play a major role in the redox chemistry of the shallow groundwater. Thermodynamic calculations using PHREEQC showed that the groundwater samples in the study area are oversaturated with respect to goethite, hematite, Fe(OH)3 and undersaturated with respect to manganite and pyrochroite. Low concentrations of Fe and Mn in the groundwater might be probably due to the lack of minerals of iron and manganese oxides, which exist in the sandy aquifer. In fact, high organic matters that present in the unsaturated horizon are believed to be responsible for the high Mn content in the soil. It was observed that the soil samples collected from high elevation area (BK) comprises considerable amount of Fe in both unsaturated (6675.87 mg/kg) and saturated horizons (31440.49 mg/kg) compared to the low Fe content in the low lying area. Based on the stability diagram, the groundwater composition lies within the stability field for Mn2+ and Fe2+ under suboxic condition and very close to the FeS/Fe2+ stability boundary. This study also shows that both pH and Eh values comprise a strong negative value thus suggesting that the redox potential is inversely dependent on the changes of pH

Assessment of selected chemical and microbial parameters in groundwater of Pulau Tiga, Sabah, Malaysia

Ambient groundwater samples collected from five wells in Pulau Tiga have been studied for selected physico-chemical and biological parameters to understand general water quality of the island. This preliminary study on groundwater of Pulau Tiga was undertaken to provide guidance and baseline data for future references. Two field works were undertaken in August and November 2007 to collect the groundwater samples. Groundwater samples were collected from five representatives wells at the low lying area of Pulau Tiga in order to study the in-situ parameters such as DO (dissolved oxygen), EC (electrical conductivity), TDS (total dissolved solids), pH, salinity and temperature. In general, groundwater in Pulau Tiga is moderate in conductivity (330 μS/cm – 1005 μS/cm), and serves as a vital freshwater source to both tourists and local inhabitants. However, bacteriological analysis showed that the groundwater quality was poor, with fecal coliform counts exceeding the WHO permissible limits for drinking water. Through this study, human factor was to be blame for the fecal contamination coliform where the polluted ground water might be originated from sanitation facilities located too close to the wells. The occurrence of total and fecal coliform bacteria in counts suggests poor sanitary handling and warns of the potential presence of disease-causing organisms

Groundwater assessment at Manukan Island, Sabah : multidisciplinary approaches.

A rapid increase in the number of tourists has placed a heavy demand for freshwater on Manukan Island, a small island located offcoast of Kota Kinabalu, Sabah. Hydrochemical and numerical approaches have been applied in this study to evaluate the groundwater quality of unconfined aquifer lying in Manukan Island, Sabah, East Malaysia. This is vital to enhance better understanding about groundwater management. Hydrochemical analysis output indicated NaCl water type in sampling locations. Seawater intrusion is marked by its relatively high Na + , Mg 2+ , Cl À and SO 4 2À concentrations. Hydrochemical analysis output clearly showed the influence of seawater in groundwater of Manukan Island. The numerical model output proved the influence of seawater in groundwater of Manukan Island by indicating the upconing process at the beneath of the pumping well. Current status of sea-water intrusion in Manukan Island is about 14.6% of freshwater and seawater mixing ratio in low lying area of Manukan Island as simulated by SEAWAT-2000 model output. Numerical model SEAWAT-2000 output showed clearly that the upconing process is the possible route of seawater to influence the fresh groundwater aquifer chemistry in Manukan Island. The results have enhanced the current understanding of seawater intrusion in the study area. Future studies will focus on using numerical models to simulate and suggest suitable groundwater management plans in Manukan Island

The role of microbial sulfate reduction in calcium carbonate polymorph selection

Microbial sulfate reduction is a dominant metabolism in many marine sedimentary environments. The influence of this metabolism on the kinetics of CaCO3 growth, as well as the dominant polymorphs precipitated, is poorly understood. To investigate the role of microbial metabolism on CaCO3 precipitation and polymorph selection, we conducted growth experiments with the sulfate reducing bacteria (D. bizertensis) in media with varying Mg/Ca and different seeding materials (calcite and kaolinite). Our results suggest that sulfate reducing bacteria both induce carbonate mineral precipitation through an increase in alkalinity and serve as a nucleation sites for the growing carbonate mineral; the majority of the carbonate minerals produced were on cell material rather than mineral seeds. We also find the Mg/Ca and presence of phosphate in the media play a key role in controlling the rates of carbonate mineral precipitation and calcium carbonate polymorph selection. In media where the Mg/Ca is greater than 2, crystalline monohydrocalcite (MHC) is the primary carbonate mineral produced. Although phosphate concentrations have a lesser effect on which polymorph initially precipitates, a series of transformation experiments suggests that the presence of phosphate stabilizes MHC crystals and prevents its transformation to more stable calcium carbonate polymorphs. Collectively, these results suggest that the polymorph of microbially-mediated calcium carbonate cements is determined by the solution chemistry upon nucleation.Ministry of Education Malaysia, SLAI (Skim Latihan Akademik IPTA) scholarship to CY

Calcium isotope fractionation during microbially induced carbonate mineral precipitation

We report the calcium isotope fractionation during the microbially-induced precipitation of calcium carbonate minerals in pure cultures of the marine sulfate-reducing bacterium Desulfovibrio bizertensis. These data are used to explore how the calcium isotope fractionation factor during microbially-induced carbonate mineral precipitation differs from the better-constrained calcium isotope fractionation factors during biogenic or abiotic carbonate mineral precipitation. Bacterial growth was then modulated with antibiotics, and the evolution of δ44Ca in solution was monitored under different microbial growth rates. The faster the microbial growth rate, the larger the calcium isotope fractionation during carbonate mineral precipitation, with Δ44Ca(s-f) ranging from −1.07‰ to −0.48‰. The reported calcium isotope fractionation can help us understand the link between calcium isotope fractionation and microbial metabolism in carbonate minerals precipitated during sedimentary diagenesis

Assessment of heavy metals contamination in Mamut river sediments using sediment quality guidelines and geochemical indices

This paper describes the concentration of selected heavy metals (Co, Cu, Ni, Pb, and Zn) in the Mamut river sediments and evaluate the degree of contamination of the river polluted by a disused copper mine. Based on the analytical results, copper showed the highest concentration in most of the river samples. A comparison with Interim Canadian Sediment Quality Guidelines (ICSQG) and Germany Sediment Quality Guidelines (GSQG) indicated that the sediment samples in all the sampling stations, except Mamut river control site (M1), exceeded the limit established for Cu, Ni, and Pb. On the contrary, Zn concentrations were reported well below the guidelines limit (ICSQG and GSQG). Mineralogical analysis indicated that the Mamut river sediments were primarily composed of quartz and accessory minerals such as chalcopyrite, pyrite, edenite, kaolinite, mica, and muscovite, reflected by the geological character of the study area. Enrichment factor (EF) and geo accumulation index (Igeo) were calculated to evaluate the heavy metal pollution in river sediments. Igeo values indicated that all the sites were strongly polluted with the studied metals in most sampling stations, specifically those located along the Mamut main stream. The enrichment factor with value greater than 1.5 suggested that the source of heavy metals was mainly derived from anthropogenic activity such as mining. The degree of metal changes (δfold) revealed that Cu concentration in the river sediments has increased as much as 20 to 38 folds since the preliminary investigation conducted in year 2004

Numerical modelling of seawater intrusion in Manukan Island's aquifer

A numerical model SEAWAT-2000 was developed to investigate the current seawater intrusion status in the low lying area of Manukan Island. SEAWAT-2000 output indicated that there is about 1.4% of freshwater and seawater mixing ratio at sea level in low lying area of Manukan Island illustrates the seawater intrusion problem. Upconing process simulated by SEAWAT-2000 showed the current status of seawater intrusion in Manukan Island is about 14.6% of freshwater and seawater mixing ratio at the beneath of pumping well (W6). The improved understanding of current seawater intrusion status is crucial for groundwater management by adjustments pumping schemes to protect groundwater