Computer modelling and estimation of recruitment patterns of non-branching coral colonies at three sites in Wakatobi Marine Park, S.E. Sulawesi, Indonesia; implications for coral reef conservation

We have studied growth and estimated recruitment of massive coral colonies at three sites, Kaledupa, Hoga and Sampela, separated by about 1.5 km in the Wakatobi Marine National Park, S.E. Sulawesi, Indonesia. There was significantly higher species richness (P<0.05), coral cover (P<0.05) and rugosity (P<0.01) at Kaledupa than at Sampela. A model for coral reef growth has been developed based on a rational polynomial function, where dx/dt is an index of coral growth with time; W is the variable (for example, coral weight, coral length or coral area), up to the power of n in the numerator and m in the denominator; a1……an and b1…bm are constants. The values for n and m represent the degree of the polynomial, and can relate to the morphology of the coral. The model was used to simulate typical coral growth curves, and tested using published data obtained by weighing coral colonies underwater in reefs on the south-west coast of Curaçao [‘Neth. J. Sea Res. 10 (1976) 285’]. The model proved an accurate fit to the data, and parameters were obtained for a number of coral species. Surface area data was obtained on over 1200 massive corals at three different sites in the Wakatobi Marine National Park, S.E. Sulawesi, Indonesia. The year of an individual's recruitment was calculated from knowledge of the growth rate modified by application of the rational polynomial model. The estimated pattern of recruitment was variable, with little numbers of massive corals settling and growing before 1950 at the heavily used site, Sampela, relative to the reef site with little or no human use, Kaledupa, and the intermediate site, Hoga. There was a significantly greater sedimentation rate at Sampela than at either Kaledupa (P<0.0001) or Hoga (P<0.0005). The relative mean abundance of fish families present at the reef crests at the three sites, determined using digital video photography, did not correlate with sedimentation rates, underwater visibility or lack of large non-branching coral colonies. Radial growth rates of three genera of non-branching corals were significantly lower at Sampela than at Kaledupa or at Hoga, and there was a high correlation (r=0.89) between radial growth rates and underwater visibility. Porites spp. was the most abundant coral over all the sites and at all depths followed by Favites (P<0.04) and Favia spp. (P<0.03). Colony ages of Porites corals were significantly lower at the 5 m reef flat on the Sampela reef than at the same depth on both other reefs (P<0.005). At Sampela, only 2.8% of corals on the 5 m reef crest are of a size to have survived from before 1950. The Scleractinian coral community of Sampela is severely impacted by depositing sediments which can lead to the suffocation of corals, whilst also decreasing light penetration resulting in decreased growth and calcification rates. The net loss of material from Sampela, if not checked, could result in the loss of this protective barrier which would be to the detriment of the sublittoral sand flats and hence the Sampela village.

Monitoring growth of hard corals as performance indicators for coral reefs

Digital videophotography, computer image analysis and physical measurements have been used to monitor sedimentation rates, coral cover, genera richness, rugosity and estimated recruitment dates of massive corals at three different sites in the Wakatobi Marine National Park, Indonesia, and on the reefs around Discovery Bay, Jamaica. Semi-structured interviews with key stakeholders in the Wakatobi Marine National Park indicated that coral mining was extensively practised, and is responsible for the absence of large non-branching corals on the Sampela reef Blast fishing is also practised in the Wakatobi Marine Park, and the authors, together with students, showed that blast fishing resulted in coral bleaching and not mortality of two Porites lutea colonies. In addition, we showed that monitoring of bleaching in Porites colonies induced by blast fishing could be a useful way of monitoring blast fishing practices in susceptible areas in the Indo-Pacific. The techniques used in this study are appropriate for use by volunteers with sufficient training, and provide excellent projects for dissertation students reading undergraduate degrees.

Evaluating the efficacy of planktonic foraminifer calcite and 18O data for sea surface temperature reconstruction for the Late Miocene

This study examines the efficacy of published δ18O data from the calcite of Late Miocene surface dwelling planktonic foraminifer shells, for sea surface temperature estimates for the pre-Quaternary. The data are from 33 Late Miocene (Messinian) marine sites from a modern latitudinal gradient of 64°N to 48°S. They give estimates of SSTs in the tropics/subtropics (to 30°N and S) that are mostly cooler than present. Possible causes of this temperature discrepancy are ecological factors (e.g. calcification of shells at levels below the ocean mixed layer), taphonomic effects (e.g. diagenesis or dissolution), inaccurate estimation of Late Miocene seawater oxygen isotope composition, or a real Late Miocene cool climate. The scale of apparent cooling in the tropics suggests that the SST signal of the foraminifer calcite has been reset, at least in part, by early diagenetic calcite with higher δ18O, formed in the foraminifer shells in cool sea bottom pore waters, probably coupled with the effects of calcite formed below the mixed layer during the life of the foraminifera. This hypothesis is supported by the markedly cooler SST estimates from low latitudes—in some cases more than 9 °C cooler than present—where the gradients of temperature and the δ18O composition of seawater between sea surface and sea bottom are most marked, and where ocean surface stratification is high. At higher latitudes, particularly N and S of 30°, the temperature signal is still cooler, though maximum temperature estimates overlap with modern SSTs N and S of 40°. Comparison of SST estimates for the Late Miocene from alkenone unsaturation analysis from the eastern tropical Atlantic at Ocean Drilling Program (ODP) Site 958—which suggest a warmer sea surface by 2–4 °C, with estimates from oxygen isotopes at Deep Sea Drilling Project (DSDP) Site 366 and ODP Site 959, indicating cooler than present SSTs, also suggest a significant impact on the δ18O signal. Nevertheless, much of the original SST variation is clearly preserved in the primary calcite formed in the mixed layer, and records secular and temporal oceanographic changes at the sea surface, such as movement of the Antarctic Polar Front in the Southern Ocean. Cooler SSTs in the tropics and sub-tropics are also consistent with the Late Miocene latitude reduction in the coral reef belt and with interrupted reef growth on the Queensland Plateau of eastern Australia, though it is not possible to quantify absolute SSTs with the existing oxygen isotope data. Reconstruction of an accurate global SST dataset for Neogene time-slices from the existing published DSDP/ODP isotope data, for use in general circulation models, may require a detailed re-assessment of taphonomy at many sites.

Evaluating the efficacy of planktonic foraminifer calcite and 18O data for sea surface temperature reconstruction for the Late Miocene

This study examines the efficacy of published δ18O data from the calcite of Late Miocene surface dwelling planktonic foraminifer shells, for sea surface temperature estimates for the pre-Quaternary. The data are from 33 Late Miocene (Messinian) marine sites from a modern latitudinal gradient of 64°N to 48°S. They give estimates of SSTs in the tropics/subtropics (to 30°N and S) that are mostly cooler than present. Possible causes of this temperature discrepancy are ecological factors (e.g. calcification of shells at levels below the ocean mixed layer), taphonomic effects (e.g. diagenesis or dissolution), inaccurate estimation of Late Miocene seawater oxygen isotope composition, or a real Late Miocene cool climate. The scale of apparent cooling in the tropics suggests that the SST signal of the foraminifer calcite has been reset, at least in part, by early diagenetic calcite with higher δ18O, formed in the foraminifer shells in cool sea bottom pore waters, probably coupled with the effects of calcite formed below the mixed layer during the life of the foraminifera. This hypothesis is supported by the markedly cooler SST estimates from low latitudes—in some cases more than 9 °C cooler than present—where the gradients of temperature and the δ18O composition of seawater between sea surface and sea bottom are most marked, and where ocean surface stratification is high. At higher latitudes, particularly N and S of 30°, the temperature signal is still cooler, though maximum temperature estimates overlap with modern SSTs N and S of 40°. Comparison of SST estimates for the Late Miocene from alkenone unsaturation analysis from the eastern tropical Atlantic at Ocean Drilling Program (ODP) Site 958—which suggest a warmer sea surface by 2–4 °C, with estimates from oxygen isotopes at Deep Sea Drilling Project (DSDP) Site 366 and ODP Site 959, indicating cooler than present SSTs, also suggest a significant impact on the δ18O signal. Nevertheless, much of the original SST variation is clearly preserved in the primary calcite formed in the mixed layer, and records secular and temporal oceanographic changes at the sea surface, such as movement of the Antarctic Polar Front in the Southern Ocean. Cooler SSTs in the tropics and sub-tropics are also consistent with the Late Miocene latitude reduction in the coral reef belt and with interrupted reef growth on the Queensland Plateau of eastern Australia, though it is not possible to quantify absolute SSTs with the existing oxygen isotope data. Reconstruction of an accurate global SST dataset for Neogene time-slices from the existing published DSDP/ODP isotope data, for use in general circulation models, may require a detailed re-assessment of taphonomy at many sites.

Edaphic influences on plant community adaptation in the Chiquibul forest of Belize

Edaphic variables figure significantly in plant community adaptations in tropical ecosystems but are often difficult to resolve because of the confounding influence of climate. Within the Chiquibul forest of Belize, large areas of Ultisols and Inceptisols occur juxtaposed within a larger zone of similar climate, permitting unambiguous assessment of edaphic contributions to forest composition. Wet chemical analyses, X-ray diffraction and X-ray fluorescence spectroscopy were employed to derive chemical (pH, exchangeable cations, CEC, total and organic C, total trace elements) and physical (texture, mineralogy) properties of four granite-derived Ustults from the Mountain Pine Ridge plateau and four limestone-derived Ustepts from the San Pastor region. The soils of these two regions support two distinct forests, each possessing a species composition reflecting the many contrasting physicochemical properties of the underlying soil. Within the Mountain Pine Ridge forest, species abundance and diversity is constrained by nutrient deficiencies and water-holding limitations imposed by the coarse textured, highly weathered Ultisols. As a consequence, the forest is highly adapted to seasonal drought, frequent fires and the significant input of atmospherically derived nutrients. The nutrient-rich Inceptisols of the San Pastor region, conversely, support an abundant and diverse evergreen forest, dominated by Sabal mauritiiformis, Cryosophila stauracantha and Manilkara spp. Moreover, the deep, fine textured soils in the depressions of the karstic San Pastor landscape collect and retain during the wet season much available water, thereby serving as refugia during particularly long periods of severe drought. To the extent that the soils of the Chiquibul region promote and maintain forest diversity, they also confer redundancy and resilience to these same forests and, to the broader ecosystem, of which they are a central part. (C) 2005 Elsevier B.V. All rights reserved.

The interaction of the Madden-Julian Oscillation with the Maritime Continent in a GCM

Previous studies using the Hadley Centre coupled model (HadCM3) have shown that the islands of the Maritime Continent act as an unrealistic block to the eastward propagation of the Madden-Julian Oscillation (MJO). This blocking effect is investigated using a simplified, aqua-planet version of this GCM, with various idealized configurations of the Maritime Continent islands placed on the equator, and an MJO-like convective signal forced by a propagating sea-surface temperature anomaly dipole. Results suggest that it is the orography of the islands, rather than the presence of the islands themselves, which results in the blocking of the MJO. Although the peak elevation of the orography in the GCM is very much lower than in reality, it appears to act as effective block to the eastward propagation of the low-level Kelvin wave signal which accompanies the MJO. In particular, the representation of Sumatra in the GCM, as a north-south oriented ridge straddling the equator, seems to be particularly effective at blocking the Kelvin wave signal, which in a full GCM would result in the weakening or complete extinction of the MJO signal to the east of the Maritime Continent.

Evolution of microbial virulence: the benefits of stress

Although genome sequencing of microbial pathogens has shed light on the evolution of virulence, the drivers of the gain and loss of genes and of pathogenicity islands (gene clusters), which contribute to the emergence of new disease outbreaks, are unclear. Recent experiments with the bean pathogen Pseudomonas syringae pv. phaseolicola illustrate how exposure to resistance mechanisms acts as the driving force for genome reorganization. Here we argue that the antimicrobial conditions generated by host defences can accelerate the generation of genome rearrangements that provide selective advantages to the invading microbe. Similar exposure to environmental stress outside the host could also drive the horizontal gene transfer that has led to the evolution of pathogenicity towards both animals and plants.

Global and local expression of chirality in serine on the Cu{110} surface

Establishing a molecular-level understanding of enantioselectivity and chiral resolution at the organic−inorganic interfaces is a key challenge in the field of heterogeneous catalysis. As a model system, we investigate the adsorption geometry of serine on Cu{110} using a combination of low-energy electron diffraction (LEED), scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. The chirality of enantiopure chemisorbed layers, where serine is in its deprotonated (anionic) state, is expressed at three levels: (i) the molecules form dimers whose orientation with respect to the substrate depends on the molecular chirality, (ii) dimers of l- and d-enantiomers aggregate into superstructures with chiral (−1 2; 4 0) lattices, respectively, which are mirror images of each other, and (iii) small islands have elongated shapes with the dominant direction depending on the chirality of the molecules. Dimer and superlattice formation can be explained in terms of intra- and interdimer bonds involving carboxylate, amino, and β−OH groups. The stability of the layers increases with the size of ordered islands. In racemic mixtures, we observe chiral resolution into small ordered enantiopure islands, which appears to be driven by the formation of homochiral dimer subunits and the directionality of interdimer hydrogen bonds. These islands show the same enantiospecific elongated shapes those as in low-coverage enantiopure layers.

Application of molecular biological methods for studying probiotics and the gut flora

Increasingly, the microbiological scientific community is relying on molecular biology to define the complexity of the gut flora and to distinguish one organism from the next. This is particularly pertinent in the field of probiotics, and probiotic therapy, where identifying probiotics from the commensal flora is often warranted. Current techniques, including genetic fingerprinting, gene sequencing, oligonucleotide probes and specific primer selection, discriminate closely related bacteria with varying degrees of success. Additional molecular methods being employed to determine the constituents of complex microbiota in this area of research are community analysis, denaturing gradient gel electrophoresis (DGGE)/temperature gradient gel electrophoresis (TGGE), fluorescent in situ hybridisation (FISH) and probe grids. Certain approaches enable specific aetiological agents to be monitored, whereas others allow the effects of dietary intervention on bacterial populations to be studied. Other approaches demonstrate diversity, but may not always enable quantification of the population. At the heart of current molecular methods is sequence information gathered from culturable organisms. However, the diversity and novelty identified when applying these methods to the gut microflora demonstrates how little is known about this ecosystem. Of greater concern is the inherent bias associated with some molecular methods. As we understand more of the complexity and dynamics of this diverse microbiota we will be in a position to develop more robust molecular-based technologies to examine it. In addition to identification of the microbiota and discrimination of probiotic strains from commensal organisms, the future of molecular biology in the field of probiotics and the gut flora will, no doubt, stretch to investigations of functionality and activity of the microflora, and/or specific fractions. The quest will be to demonstrate the roles of probiotic strains in vivo and not simply their presence or absence.

Pathogenicity and other genomic islands in plant pathogenic bacteria

Pathogenicity islands (PAIs) were first described in uropathogenic E. coli. They are now defined as regions of DNA that contain virulence genes and are present in the genome of pathogenic strains, but absent from or only rarely present in non-pathogenic variants of the same or related strains. Other features include a variable G+C content, distinct boundaries from the rest of the genome and the presence of genes related to mobile elements such as insertion sequences, integrases and transposases. Although PAIs have now been described in a wide range of both plant and animal pathogens it has become evident that the general features of PAIs are displayed by a number of regions of DNA with functions other than pathogenicity, such as symbiosis and antibiotic resistance, and the general term genomic islands has been adopted. This review will describe a range of genomic islands in plant pathogenic bacteria including those that carry effector genes, phytotoxins and the type III protein secretion cluster. The review will also consider some medically important bacteria in order to discuss the range, acquisition and stabilization of genomic islands.

Chromium nanostructures formed by dewetting of heteroepitaxial films on W(100)

In this paper, we report the surprising formation of square-based facetted islands with linear dimension of the order of 500 nm upon dewetting of a Cr multilayer onW(100).We show that these square islands are composed of inclined facets surrounding a depressed center such that the facet slopes inward with the outer edges of the islands thicker than the centers. The islands’ shapes do not represent traditional equilibrium crystal shapes as expected for a Wulf construction. In situ UV and x-ray photoelectron emission microscopy allied to spatially resolved spectroscopy throws considerable light on the nature of the dewetting and shows that the metal surface between the islands remains covered by a thin pseudomorphic wetting layer of ∼1 ML. Low-energy electron diffraction and scanning tunneling and atomic force microscopies allow quantification of facet slopes, and we identify a predominance of tilted Cr(100) facets ±5◦ off of the substrate normal bound by (210) planes at ∼26◦. The epitaxial Cr islands adopt the bulk Cr lattice constant but are tilted with respect to the surface normal.We suggest that the Cr crystallite tilting creates a vicinal-like interface structure that determines the island morphology

Propagation of the Madden-Julian Oscillation through the Maritime Continent and scale interaction with the diurnal cycle of precipitation

The convectively active part of the Madden-Julian Oscillation (MJO) propagates eastward through the warm pool, from the Indian Ocean through the Maritime Continent (the Indonesian archipelago) to the western Pacific. The Maritime Continent's complex topography means the exact nature of the MJO propagation through this region is unclear. Model simulations of the MJO are often poor over the region, leading to local errors in latent heat release and global errors in medium-range weather prediction and climate simulation. Using 14 northern winters of TRMM satellite data it is shown that, where the mean diurnal cycle of precipitation is strong, 80% of the MJO precipitation signal in the Maritime Continent is accounted for by changes in the amplitude of the diurnal cycle. Additionally, the relationship between outgoing long-wave radiation (OLR) and precipitation is weakened here, such that OLR is no longer a reliable proxy for precipitation. The canonical view of the MJO as the smooth eastward propagation of a large-scale precipitation envelope also breaks down over the islands of the Maritime Continent. Instead, a vanguard of precipitation (anomalies of 2.5 mm day^-1 over 10^6 km^2) jumps ahead of the main body by approximately 6 days or 2000 km. Hence, there can be enhanced precipitation over Sumatra, Borneo or New Guinea when the large-scale MJO envelope over the surrounding ocean is one of suppressed precipitation. This behaviour can be accommodated into existing MJO theories. Frictional and topographic moisture convergence and relatively clear skies ahead of the main convective envelope combine with the low thermal inertia of the islands, to allow a rapid response in the diurnal cycle which rectifies onto the lower-frequency MJO. Hence, accurate representations of the diurnal cycle and its scale interaction appear to be necessary for models to simulate the MJO successfully.

Effects of past climate variability on fire and vegetation in the cerrãdo savanna of the Huanchaca Mesetta, NE Bolivia

Cerrãdo savannas have the greatest fire activity of all major global land-cover types and play a significant role in the global carbon cycle. During the 21st century, temperatures are projected to increase by ∼ 3 ◦C coupled with a precipitation decrease of ∼ 20 %. Although these conditions could potentially intensify drought stress, it is unknown how that might alter vegetation composition and fire regimes. To assess how Neotropical savannas responded to past climate changes, a 14 500-year, high-resolution, sedimentary record from Huanchaca Mesetta, a palm swamp located in the cerrãdo savanna in northeastern Bolivia, was analyzed with phytoliths, stable isotopes, and charcoal. A nonanalogue, cold-adapted vegetation community dominated the Lateglacial–early Holocene period (14 500–9000 cal yr BP, which included trees and C3 Pooideae and C4 Panicoideae grasses. The Lateglacial vegetation was fire-sensitive and fire activity during this period was low, likely responding to fuel availability and limitation. Although similar vegetation characterized the early Holocene, the warming conditions associated with the onset of the Holocene led to an initial increase in fire activity. Huanchaca Mesetta became increasingly firedependent during the middle Holocene with the expansion of C4 fire-adapted grasses. However, as warm, dry conditions, characterized by increased length and severity of the dry season, continued, fuel availability decreased. The establishment of the modern palm swamp vegetation occurred at 5000 cal yr BP. Edaphic factors are the first-order control on vegetation on the rocky quartzite mesetta. Where soils are sufficiently thick, climate is the second-order control of vegetation on the mesetta. The presence of the modern palm swamp is attributed to two factors: (1) increased precipitation that increased water table levels and (2) decreased frequency and duration of surazos (cold wind incursions from Patagonia) leading to increased temperature minima. Natural (soil, climate, fire) drivers rather than anthropogenic drivers control the vegetation and fire activity at Huanchaca Mesetta. Thus the cerrãdo savanna ecosystem of the Huanchaca Plateau has exhibited ecosystem resilience to major climatic changes in both temperature and precipitation since the Lateglacial period.