Stable isotope probing: Technical considerations when resolving ¹⁵N-labeled RNA in gradients

RNA based stable isotope probing (SIP) facilitates the detection and identification of active members of microbial populations that are involved in the assimilation of an isotopically labeled compound. ¹⁵N-RNA-SIP is a new method that has been discussed in recent literature but has not yet been tested. Herein, we define the limitations to using ¹⁵N-labeled substrates for SIP and propose modifications to compensate for some of these shortcomings. We have used ¹⁵N-RNA-SIP as a tool for analysing mixed bacterial populations that use nitrogen substrates. After incubating mixed microbial communities with ¹⁵N-ammonium chloride or ¹⁵N₂ we assessed the fractionation resolution of ¹⁵N-RNA by isopycnic centrifugation in caesium trifluoroacetate (CsTFA) gradients. We found that the more isotopic label incorporated, the further the buoyant density (BD) separation between ¹⁵N- and ¹⁴N-RNA, however it was not possible to resolve the labeled from unlabeled RNA definitively through gradient fractionation. Terminal-restriction fragment length polymorphism (T-RFLP) analysis of the extracted RNA and fluorescent in situ hybridisation (FISH) analysis of the enrichment cultures provided some insight into the organisms involved in nitrogen fixation. This approach is not without its limitations and will require further developments to assess its applicability to other nitrogen-fixing environments

Contingent and created: the significance of the concept of createdness for a theology in dialogue with science, with special reference to the works of Colin E. Gunton

In the first half of the last century, Michael B. Foster argued that the initial impetus for the development of modern science derived from the implicit or explicit Christian convictions of a number of early scientists. More specifically, aspects of the doctrine of creation gave these scientists confidence in the possibility and value of experimental investigation of the natural order. This argument was developed further, notably by Thomas F. Torrance, in two directions. First, this historical connection between natural science and the doctrine of creation was reinterpreted as a continuing methodological reliance of the natural sciences upon the created status of the natural order. Second, those properties of the natural order which are prerequisites for this ongoing reliance and which derive from its created status were identified as rationality and contingency, or the rational contingency of the natural order. In this thesis we develop this argument further by attempting to demonstrate the necessity of the concepts of the created status - the createdness -and rational contingency of the natural order for the interaction of science and theology. First, we argue that createdness is an essential aspect of Christian theology. Second, we argue that createdness and rational contingency are either held together or lost together in interactions between science and theology. Ultimately, we aim to demonstrate that there can be no interaction between science and theology as coherent disciplines in their own right except where the scientific contribution relies on rational contingency and the theological contribution articulates the createdness of the natural order.We begin by developing a grammar of createdness, based on the theology of Colin E. Gunton, to enable us to describe theologically the createdness of the natural order and entities within it. Moreover, this allows us to identify the theological motifs that safeguard and endanger the concept of createdness. Key motifs in support include the divine prevenience, trinitarian divine action in the form of divine action-in-relation, and a conceptualisation of the God-world relationship as a divine gifting of the world with the personal 'space' for existing in creaturely integrity.In the second section, we test our grammar by determining the createdness of the evolutionary process in the theology of Pierre-Marie-Joseph Teilhard de Chardin. We conclude that Teilhard's understanding of evolution disregards its rational contingency, and we trace this back to a failure to safeguard the createdness of the process. For example, Teilhard inadequately secures the divine prevenience, which leads him to introduce an evolutionary Christology and eschatology.In the third section, we apply our grammar to contemporary discussions of divine action at the science-theology interface and also from within popular science. We determine that despite the existence of some fruitful work on the inherent dynamism and potential of the evolutionary process, the createdness and the rational contingency of evolution are not preserved theologically or scientifically. Specifically, in both the science-theology material and the popular science material, there is an assumption that governing divine action is superfluous and undesirable. We finish by illustrating the importance of rational contingency and createdness for science-theology interaction by sketching a model of divine action in evolution that accounts for both

Effect of long-term starvation on the survival, recovery, and carbon utilization profiles of a bovine Escherichia coli O157:H7 isolate from New Zealand

The ability to maintain a dual lifestyle of colonizing the ruminant gut and surviving in nonhost environments once shed is key to the success of Escherichia coli O157:H7 as a zoonotic pathogen. Both physical and biological conditions encountered by the bacteria are likely to change during the transition between host and nonhost environments. In this study, carbon starvation at suboptimal temperatures in nonhost environments was simulated by starving a New Zealand bovine E. coli O157:H7 isolate in phosphate-buffered saline at 4 and 15°C for 84 days. Recovery of starved cells on media with different nutrient availabilities was monitored under aerobic and anaerobic conditions. We found that the New Zealand bovine E. coli O157:H7 isolate was able to maintain membrane integrity and viability over 84 days and that the level of recovery depended on the nutrient level of the recovery medium as well as the starvation temperature. In addition, a significant difference in carbon utilization was observed between starved and nonstarved cells

Effect of long-term starvation on the survival, recovery, and carbon utilization profiles of a bovine Escherichia coli O157:H7 isolate from New Zealand

The ability to maintain a dual lifestyle of colonizing the ruminant gut and surviving in nonhost environments once shed is key to the success of Escherichia coli O157:H7 as a zoonotic pathogen. Both physical and biological conditions encountered by the bacteria are likely to change during the transition between host and nonhost environments. In this study, carbon starvation at suboptimal temperatures in nonhost environments was simulated by starving a New Zealand bovine E. coli O157:H7 isolate in phosphate-buffered saline at 4 and 15°C for 84 days. Recovery of starved cells on media with different nutrient availabilities was monitored under aerobic and anaerobic conditions. We found that the New Zealand bovine E. coli O157:H7 isolate was able to maintain membrane integrity and viability over 84 days and that the level of recovery depended on the nutrient level of the recovery medium as well as the starvation temperature. In addition, a significant difference in carbon utilization was observed between starved and nonstarved cells

Characterisation of bacterioplankton communities in the meltwater ponds of Bratina Island, Victoria Land, Antarctica

A unique collection of Antarctic aquatic environments (meltwater ponds) lies in close proximity on the rock and sediment-covered undulating surface of the McMurdo Ice Shelf, near Bratina Island (Victoria Land, Antarctica). During the 2009–10 mid-austral summer, sets of discrete water samples were collected across the vertical geochemical gradients of five meltwater ponds (Egg, P70E, Legin, Salt and Orange) for geochemical and microbial community structure analysis. Bacterial DNA fingerprints (using Automated Ribosomal Intergenic Spacer Analysis) statistically clustered communities within ponds based on ANOSIM (R = 0.766, P = 0.001); however, one highly stratified pond (Egg) had two distinct depth-related bacterial communities (R = 0.975, P = 0.008). 454 pyrosequencing at three depths within Egg also identified phylum level shifts and increased diversity with depth, Bacteroidetes being the dominant phyla in the surface sample and Proteobacteria being dominant in the bottom two depths. BEST analysis, which attempts to link community structure and the geochemistry of a pond, identified conductivity and pH individually, and to a lesser extent Ag109, NO2 and V51 as dominant influences to the microbial community structure in these ponds. Increasing abundances of major halo-tolerant OTUs across the strong conductivity gradient reinforce it as the primary driver of community structure in this stud

Evidence of global-scale aeolian dispersal and endemism in isolated geothermal microbial communities of Antarctica

New evidence in aerobiology challenges the assumption that geographical isolation is an effective barrier to microbial transport. However, given the uncertainty with which aerobiological organisms are recruited into existing communities, the ultimate impact of microbial dispersal is difficult to assess. To evaluate the ecological significance of global-scale microbial dispersal, molecular genetic approaches were used to examine microbial communities inhabiting fumarolic soils on Mt. Erebus, the southernmost geothermal site on Earth. There, hot, fumarolic soils provide an effective environmental filter to test the viability of organisms that have been distributed via aeolian transport over geological time. We find that cosmopolitan thermophiles dominate the surface, whereas endemic Archaea and members of poorly understood Bacterial candidate divisions dominate the immediate subsurface. These results imply that aeolian processes readily disperse viable organisms globally, where they are incorporated into pre-existing complex communities of endemic and cosmopolitan taxa

Benthic microbial communities of coastal terrestrial and ice shelf Antarctic meltwater ponds.

The numerous perennial meltwater ponds distributed throughout Antarctica represent diverse and productive ecosystems central to the ecological functioning of the surrounding ultra oligotrophic environment. The dominant taxa in the pond benthic communities have been well described however, little is known regarding their regional dispersal and local drivers to community structure. The benthic microbial communities of 12 meltwater ponds in the McMurdo Sound of Antarctica were investigated to examine variation between pond microbial communities and their biogeography. Geochemically comparable but geomorphologically distinct ponds were selected from Bratina Island (ice shelf) and Miers Valley (terrestrial) (<40 km between study sites), and community structure within ponds was compared using DNA fingerprinting and pyrosequencing of 16S rRNA gene amplicons. More than 85% of total sequence reads were shared between pooled benthic communities at different locations (OTU0.05), which in combination with favorable prevailing winds suggests aeolian regional distribution. Consistent with previous findings Proteobacteria and Bacteroidetes were the dominant phyla representing over 50% of total sequences; however, a large number of other phyla (21) were also detected in this ecosystem. Although dominant Bacteria were ubiquitous between ponds, site and local selection resulted in heterogeneous community structures and with more than 45% of diversity being pond specific. Potassium was identified as the most significant contributing factor to the cosmopolitan community structure and aluminum to the location unique community based on a BEST analysis (Spearman's correlation coefficient of 0.632 and 0.806, respectively). These results indicate that the microbial communities in meltwater ponds are easily dispersed regionally and that the local geochemical environment drives the ponds community structure

Influence of soil properties on archaeal diversity and distribution in the McMurdo Dry Valleys, Antarctica

Archaea are the least understood members of the microbial community in Antarctic mineral soils. Although their occurrence in Antarctic coastal soils has been previously documented, little is known about their distribution in soils across the McMurdo Dry Valleys, Victoria Land. In this study, terminal-restriction fragment length polymorphism (t-RFLP) analysis and 454 pyrosequencing were coupled with a detailed analysis of soil physicochemical properties to characterize archaeal diversity and identify environmental factors that might shape and maintain archaeal communities in soils of the three southern most McMurdo Dry Valleys (Garwood, Marshall, and Miers Valley). Archaea were successfully detected in all inland and coastal mineral soils tested, revealing a low overall richness (mean of six operational taxonomic units [OTUs] per sample site). However, OTU richness was higher in some soils and this higher richness was positively correlated with soil water content, indicating water as a main driver of archaeal community richness. In total, 18 archaeal OTUs were detected, predominately Thaumarchaeota affiliated with Marine Group 1.1b (> 80% of all archaeal sequences recovered). Less abundant OTUs (2% of all archaeal sequences) were loosely related to members of the phylum Euryarchaeota. This is the first comprehensive study showing a widespread presence and distribution of Archaea in inland Antarctic soils

Multilingualism and Academic Writing: A Match Made in Heaven or a Disastrous Combination?

There has long been a tradition of international students studying in the United Kingdom. Despite a dip in the most recently published statistics, Indian students continue to make up a high proportion of UK’s international student population. The majority of Indian students are multilingual and this raises potential problems for them with regards to academic writing, such as grammar, structuring, and vocabulary. This article presents a largely empirical study which examines the experiences of, and issues faced by seven postgraduate research students in the Faculty of Computing, Engineering and the Built Environment at Birmingham City University. Samples of academic writing of each participant were analysed and semi structured interviews were also conducted with the participants. Lessons from these experiences, such as the difference between participants’ actual and perceived academic writing ability, and the tendency of some students to think in their native language and then translate their thoughts into English, are discussed and proposals made as to how multilingual students can be better supported in their academic writing within the Faculty