Raman spectroscopy of newberyite Mg(PO3OH)•3H2O – a cave mineral

Newberyite Mg(PO3OH)•3H2O is a mineral found in caves such as from Moorba cave, Jurien Bay, Western Australia, the Skipton Lava tubes (SW of Ballarat, Victoria, Australia) and in the Petrogale Cave (Madura , Eucla, Western Australia). Because these minerals contain oxyanions, hydroxyl units and water, the minerals lend themselves to spectroscopic analysis. Raman spectroscopy can investigate the complex paragenetic relationships existing between a number of ‘cave’ minerals. The intense sharp band at 982 cm-1 is assigned to the PO43- ν1 symmetric stretching mode. Low intensity Raman bands at 1152, 1263 and 1277 cm-1 are assigned to the PO43- ν3 antisymmetric stretching vibrations. Raman bands at 497 and 552 cm-1 are attributed to the PO43- ν4 bending modes. An intense Raman band for newberyite at 398 cm-1 with a shoulder band at 413 cm-1 is assigned to the PO43- ν2 bending modes. The values for the OH stretching vibrations provide hydrogen bond distances of 2.728Å (3267 cm-1), 2.781Å (3374cm-1), 2.868Å (3479 cm-1), and 2.918Å (3515 cm-1). Such hydrogen bond distances are typical of secondary minerals. Estimates of the hydrogen-bond distances have been made from the position of the OH stretching vibrations and show a wide range in both strong and weak bonds.

Raman spectroscopy of stercorite H(NH4)Na(PO4)•4H2O – a cave mineral from Petrogale Cave, Madura, Eucla, Western Australia

Raman spectroscopy complimented with infrared spectroscopy has been used to characterise the mineral stercorite H(NH4)Na(PO4)·4H2O. The mineral stercorite originated from the Petrogale Cave, Madura, Eucla, Western Australia. This cave is one of many caves in the Nullarbor Plain in the South of Western Australia. These caves have been in existence for eons of time and have been dated at more than 550 million years old. The mineral is formed by the reaction of bat guano chemicals on calcite substrates. A single Raman band at 920 cm−1 defines the presence of phosphate in the mineral. Antisymmetric stretching bands are observed in the infrared spectrum at 1052, 1097, 1135 and 1173 cm−1. Raman spectroscopy shows the mineral is based upon the phosphate anion and not the hydrogen phosphate anion. Raman and infrared bands are found and assigned to PO43−, H2O, OH and NH stretching vibrations. The detection of stercorite by Raman spectroscopy shows that the mineral can be readily determined; as such the application of a portable Raman spectrometer in a ‘cave’ situation enables the detection of minerals, some of which may remain to be identified.

Whole-proteome phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model

Background The vast sequence divergence among different virus groups has presented a great challenge to alignment-based analysis of virus phylogeny. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignment could not be directly applied to the whole-genome comparison and phylogenomic studies of viruses. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. Among the alignment-free methods, a dynamical language (DL) method proposed by our group has successfully been applied to the phylogenetic analysis of bacteria and chloroplast genomes. Results In this paper, the DL method is used to analyze the whole-proteome phylogeny of 124 large dsDNA viruses and 30 parvoviruses, two data sets with large difference in genome size. The trees from our analyses are in good agreement to the latest classification of large dsDNA viruses and parvoviruses by the International Committee on Taxonomy of Viruses (ICTV). Conclusions The present method provides a new way for recovering the phylogeny of large dsDNA viruses and parvoviruses, and also some insights on the affiliation of a number of unclassified viruses. In comparison, some alignment-free methods such as the CV Tree method can be used for recovering the phylogeny of large dsDNA viruses, but they are not suitable for resolving the phylogeny of parvoviruses with a much smaller genome size.

Are the ‘cave’ minerals archerite (K,NH4)H2PO4 and biphosphammite (K,NH4)H2PO4 identical? A molecular structural study

The molecular structure of the mineral archerite ((K,NH4)H2PO4) has been determined and compared with that of biphosphammite ((NH4,K)H2PO4). Raman spectroscopy and infrared spectroscopy has been used to characterise these ‘cave’ minerals. Both minerals originated from the Murra-el-elevyn Cave, Eucla, Western Australia. The mineral is formed by the reaction of the chemicals in bat guano with calcite substrates. Raman and infrared bands are assigned to H2PO4-, OH and NH stretching vibrations. The Raman band at 981 cm-1 is assigned to the HOP stretching vibration. Bands in the 1200 to 1800 cm-1 region are associated with NH4+ bending modes. The molecular structure of the two minerals appear to be very similar, and it is therefore concluded that the two minerals are identical.

The influence of climate variability on hydrological processes and surface and groundwater hydrochemistry : the tropical upper roper river catchment, Northern Territory, Australia

The Upper Roper River is one of the Australia’s unique tropical rivers which have been largely untouched by development. The Upper Roper River catchment comprises the sub-catchments of the Waterhouse River and Roper Creek, the two tributaries of the Roper River. There is a complex geological setting with different aquifer types. In this seasonal system, close interaction between surface water and groundwater contributes to both streamflow and sustaining ecosystems. The interaction is highly variable between seasons. A conceptual hydrogeological model was developed to investigate the different hydrological processes and geochemical parameters, and determine the baseline characteristics of water resources of this pristine catchment. In the catchment, long term average rainfall is around 850 mm and is summer dominant which significantly influences the total hydrological system. The difference between seasons is pronounced, with high rainfall up to 600 mm/month in the wet season, and negligible rainfall in the dry season. Canopy interception significantly reduces the amount of effective rainfall because of the native vegetation cover in the pristine catchment. Evaporation exceeds rainfall the majority of the year. Due to elevated evaporation and high temperature in the tropics, at least 600 mm of annual rainfall is required to generate potential recharge. Analysis of 120 years of rainfall data trend helped define “wet” and “dry periods”: decreasing trend corresponds to dry periods, and increasing trend to wet periods. The period from 1900 to 1970 was considered as Dry period 1, when there were years with no effective rainfall, and if there was, the intensity of rainfall was around 300 mm. The period 1970 – 1985 was identified as the Wet period 2, when positive effective rainfall occurred in almost every year, and the intensity reached up to 700 mm. The period 1985 – 1995 was the Dry period 2, with similar characteristics as Dry period 1. Finally, the last decade was the Wet period 2, with effective rainfall intensity up to 800 mm. This variability in rainfall over decades increased/decreased recharge and discharge, improving/reducing surface water and groundwater quantity and quality in different wet and dry periods. The stream discharge follows the rainfall pattern. In the wet season, the aquifer is replenished, groundwater levels and groundwater discharge are high, and surface runoff is the dominant component of streamflow. Waterhouse River contributes two thirds and Roper Creek one third to Roper River flow. As the dry season progresses, surface runoff depletes, and groundwater becomes the main component of stream flow. Flow in Waterhouse River is negligible, the Roper Creek dries up, but the Roper River maintains its flow throughout the year. This is due to the groundwater and spring discharge from the highly permeable Tindall Limestone and tufa aquifers. Rainfall seasonality and lithology of both the catchment and aquifers are shown to influence water chemistry. In the wet season, dilution of water bodies by rainwater is the main process. In the dry season, when groundwater provides baseflow to the streams, their chemical composition reflects lithology of the aquifers, in particular the karstic areas. Water chemistry distinguishes four types of aquifer materials described as alluvium, sandstone, limestone and tufa. Surface water in the headwaters of the Waterhouse River, the Roper Creek and their tributaries are freshwater, and reflect the alluvium and sandstone aquifers. At and downstream of the confluence of the Roper River, river water chemistry indicates the influence of rainfall dilution in the wet season, and the signature of the Tindall Limestone and tufa aquifers in the dry. Rainbow Spring on the Waterhouse River and Bitter Spring on the Little Roper River (known as Roper Creek at the headwaters) discharge from the Tindall Limestone. Botanic Walk Spring and Fig Tree Spring discharge into the Roper River from tufa. The source of water was defined based on water chemical composition of the springs, surface and groundwater. The mechanisms controlling surface water chemistry were examined to define the dominance of precipitation, evaporation or rock weathering on the water chemical composition. Simple water balance models for the catchment have been developed. The important aspects to be considered in water resource planning of this total system are the naturally high salinity in the region, especially the downstream sections, and how unpredictable climate variation may impact on the natural seasonal variability of water volumes and surface-subsurface interaction.

Vibrational spectroscopy of synthetic stercorite H(NH4)Na(PO4)•4H2O – a comparison with the natural cave mineral

In order to mimic the chemical reactions in cave systems, the analogue of the mineral stercorite H(NH4)Na(PO4)•4H2O has been synthesised. X-ray diffraction of the stercorite analogue matches the stercorite reference pattern. A comparison is made with the vibrational spectra of synthetic stercorite analogue and the natural Cave mineral. The mineral in nature is formed by the reaction of bat guano chemicals on calcite substrates. A single Raman band at 920 cm-1 (Cave) and 922 cm-1 (synthesised) defines the presence of hydrogen phosphate in the mineral. In the synthetic stercorite analogue, additional bands are observed and are attributed to the dihydrogen and phosphate anions. The vibrational spectra of synthetic stercorite only partly match that of the natural stercorite. It is suggested that natural stercorite is more pure than that of synthesised stercorite. Antisymmetric stretching bands are observed in the infrared spectrum at 1052, 1097, 1135 and 1173 cm-1. Raman spectroscopy shows the stercorite mineral is based upon the hydrogen phosphate anion and not the phosphate anion. Raman and infrared bands are found and assigned to PO43-, H2O, OH and NH stretching vibrations. Raman spectroscopy shows the synthetic analogue is similar to the natural mineral. A mechanism for the formation of stercorite is provided.

Thermal stability of the ‘cave’ mineral ardealite Ca2(HPO4)(SO4)•4H2O

Thermogravimetry combined with evolved gas mass spectrometry has been used to characterise the mineral ardealite and to ascertain the thermal stability of this ‘cave’ mineral. The mineral ardealite Ca2(HPO4)(SO4)•4H2O is formed through the reaction of calcite with bat guano. The mineral shows disorder and the composition varies depending on the origin of the mineral. Thermal analysis shows that the mineral starts to decompose over the temperature range 100 to 150°C with some loss of water. The critical temperature for water loss is around 215°C and above this temperature the mineral structure is altered. It is concluded that the mineral starts to decompose at 125°C, with all waters of hydration being lost after 226°C. Some loss of sulphate occurs over a broad temperature range centred upon 565°C. The final decomposition temperature is 823°C with loss of the sulphate and phosphate anions.

Thermal stability of newberyite Mg(PO3OH)•3H2O – a cave mineral from Skipton lava tubes, Victoria, Australia.

The mineral newberyite Mg(PO3OH)•3H2O is a mineral that has been found in caves such as the Skipton Lava Tubes (SW of Ballarat, Victoria, Australia), Moorba cave, Jurien Bay, Western Australia, and in the Petrogale Cave (Madura , Eucla, Western Australia). Because these minerals contain water, the minerals lend themselves to thermal analysis. The mineral newberyite is found to decompose at 145°C with a water loss of 31.96%, a result which is very close to the theoretical value. The result shows that the mineral is not stable in caves where the temperature exceeds this value. The implication of this result rests with the removal of kidney stones, which have the same composition as newberyite. Point heating focussing on the kidney stone results in the destruction of the kidney stone.

Thermal stability of stercorite H(NH4)Na(PO4)·4H2O – a cave mineral from Petrogale Cave, Madura, Eucla, Western Australia

Thermogravimetric analysis has been used to determine the thermal stability of the mineral stercorite H(NH4)Na(PO4)·4H2O. The mineral stercorite originated from the Petrogale Cave, Madura, Eucla, Western Australia. This cave is one of many caves in the Nullarbor Plain in the South of Western Australia. The mineral is formed by the reaction of bat guano chemicals on calcite substrates. Upon thermal treatment the mineral shows a strong decomposition at 191°C with loss of water and ammonia. Other mass loss steps are observed at 158, 317 and 477°C. Ion current curves indicate a gain of CO2 at higher temperature and are attributed to the thermal decomposition of calcite impurity.

Thermal stability of crandallite CaAl3(PO4)2(OH)5•(H2O) – a ‘cave’ mineral from the Jenolan Caves

Thermogravimetry combined with evolved gas mass spectrometry has been used to characterise the mineral crandallite CaAl3(PO4)2(OH)5•(H2O) and to ascertain the thermal stability of this ‘cave’ mineral. X-ray diffraction proves the presence of the mineral and identifies the products after thermal decomposition. The mineral crandallite is formed through the reaction of calcite with bat guano. Thermal analysis shows that the mineral starts to decompose through dehydration at low temperatures at around 139°C while dehydroxylation occurs over the temperature range 200 to 700°C with loss of OH units. The critical temperature for OH loss is around 416°C and above this temperature the mineral structure is altered. Some minor loss of carbonate impurity occurs at 788°C. This study shows the mineral is unstable above 139°C. This temperature is well above the temperature in caves, which have a maximum temperature of 15°C. A chemical reaction for the synthesis of crandallite is offered and the mechanism for the thermal decomposition is given.

Vibrational spectroscopy of synthetic archerite (K,NH4)H2PO4 : and in comparison with the natural cave mineral

In order to mimic the formation of archerite in cave minerals, the mineral analogue has been synthesised. The cave mineral is formed by the reaction of the chemicals in bat guano with calcite substrates. X-ray diffraction proves that the synthesised archerite analogue was pure. The vibrational spectra of the synthesised mineral are compared with that of the natural cave mineral. Raman and infrared bands are assigned to H2PO4-, OH and NH stretching and bending vibrations. The Raman band at 917 cm-1 is assigned to the HOP stretching vibration of the H2PO4- units. Bands in the 1200 to 1800 cm-1 region are associated with NH4+ bending modes. Vibrational spectroscopy enables the molecular structure of archerite to be analysed.