Matthew D. Collins

The Phylogeny of the Genus Clostridium: Proposal of Five New Genera and Eleven New Species Combinations

The 16S rRNA gene sequences of 34 named and unnamed clostridial strains were determined by PCR direct sequencing and were compared with more than 80 previously determined clostridial sequences and the previously published sequences of representative species of other low- G + C-content gram-positive genera, thereby providing an almost complete picture of the genealogical interrelationships of the clostridia. The results of our phylogenetic analysis corroborate and extend previous findings in showing that the genus Clostridium is extremely heterogeneous, with many species phylogenetically intermixed with other spore-forming and non-spore-forming genera. The genus Clostridium is clearly in need of major revision, and the rRNA structures defined in this and previous studies may provide a sound basis for future taxonomic restructuring. The problems and different possibilities for restructuring are discussed in light of the phenotypic and phylogenetic data, and a possible hierarchical structure for the clostridia and their close relatives is presented. On the basis of phenotypic criteria and the results of phylogenetic analyses the following five new genera and 11 new combinations are proposed: Caloramator gen. nov., with Caloramator fervidus comb. nov.; Filifactor gen. nov., with Filifactor villosus comb. nov.; Moorella gen. nov., with Moorella thermoacetica comb. nov. and Moorella thermoautotrophica comb. nov.; Oxobacter gen. nov., with Oxobacter pfennigii comb. nov.; Oxalophagus gen. nov., with Oxalophagus oxalicus comb. nov.; Eubacterium barkeri comb. nov.; Paenibacillus durum comb. nov.; Thermoanaerobacter kivui comb. nov.; Thermoanaerobacter thermocopriae comb. nov.; and Thermoanerobacterium thermosaccharolyticum comb. nov.

Quantification of modelling uncertainties in a large ensemble of climate change simulations.

Comprehensive global climate models are the only tools that account for the complex set of processes which will determine future climate change at both a global and regional level. Planners are typically faced with a wide range of predicted changes from different models of unknown relative quality, owing to large but unquantified uncertainties in the modelling process. Here we report a systematic attempt to determine the range of climate changes consistent with these uncertainties, based on a 53-member ensemble of model versions constructed by varying model parameters. We estimate a probability density function for the sensitivity of climate to a doubling of atmospheric carbon dioxide levels, and obtain a 5–95 per cent probability range of 2.4–5.4 °C. Our probability density function is constrained by objective estimates of the relative reliability of different model versions, the choice of model parameters that are varied and their uncertainty ranges, specified on the basis of expert advice. Our ensemble produces a range of regional changes much wider than indicated by traditional methods based on scaling the response patterns of an individual simulation.

Uncertainty in predictions of the climate response to rising levels of greenhouse gases.

The range of possibilities for future climate evolution needs to be taken into account when planning climate change mitigation and adaptation strategies. This requires ensembles of multi-decadal simulations to assess both chaotic climate variability and model response uncertainty. Statistical estimates of model response uncertainty, based on observations of recent climate change, admit climate sensitivities—defined as the equilibrium response of global mean temperature to doubling levels of atmospheric carbon dioxide—substantially greater than 5 K. But such strong responses are not used in ranges for future climate change because they have not been seen in general circulation models. Here we present results from the ‘climateprediction.net’ experiment, the first multi-thousand-member grand ensemble of simulations using a general circulation model and thereby explicitly resolving regional details. We find model versions as realistic as other state-of-the-art climate models but with climate sensitivities ranging from less than 2 K to more than 11 K. Models with such extreme sensitivities are critical for the study of the full range of possible responses of the climate system to rising greenhouse gas levels, and for assessing the risks associated with specific targets for stabilizing these levels.

Improved general circulation models of the Martian atmosphere from the surface to above 80 km

We describe a set of two “new generation” general circulation models of the Martian atmosphere derived from the models we originally developed in the early 1990s. The two new models share the same physical parameterizations but use two complementary numerical methods to solve the atmospheric dynamic equations. The vertical resolution near the surface has been refined, and the vertical domain has been extended to above 80 km. These changes are accompanied by the inclusion of state-of-the-art parameterizations to better simulate the dynamical and physical processes near the surface (boundary layer scheme, subgrid-scale topography parameterization, etc.) and at high altitude (gravity wave drag). In addition, radiative transfer calculations and the representation of polar processes have been significantly improved. We present some examples of zonal-mean fields from simulations using the model at several seasons. One relatively novel aspect, previously introduced by Wilson [1997], is that around northern winter solstice the strong pole to pole diabatic forcing creates a quasi-global, angular-momentum conserving Hadley cell which has no terrestrial equivalent. Within such a cell the Coriolis forces accelerate the winter meridional flow toward the pole and induce a strong warming of the middle polar atmosphere down to 25 km. This winter polar warming had been observed but not properly modeled until recently. In fact, thermal inversions are generally predicted above one, and often both, poles around 60–70 km. However, the Mars middle atmosphere above 40 km is found to be very model-sensitive and thus difficult to simulate accurately in the absence of observations.

Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small-subunit-ribosomal RNA sequences

The small‐subunit rRNA sequences of 51 species of Bacillus were determined by reverse transcription to elucidate the phylogenetic structure of the genus. Comparative analysis of the sequence data revealed five phylogenetically distinct clusters. Group 1 (Bacillus sensu stricto) included B. subtilis the type species of the genus and 27 other species. Group 2 consisted of B. sphaericus and five other bacilli and Sporosarcina ureae clustered within the confines of this group. Group 3 consisted of a phylogenetically coherent group of 10 species whereas groups 4 and 5 comprised two and three species respectively. It is evident that the genus Bacillus in genetically extremely heterogeneous and requires extensive taxonomic revision. The rRNA structures defined in the present study will provide a firm basis for the division of Bacillus into several phylogenetically distinct genera.

Projected increase in continental runoff due to plant responses to increasing carbon dioxide

In addition to influencing climatic conditions directly through radiative forcing, increasing carbon dioxide concentration influences the climate system through its effects on plant physiology. Plant stomata generally open less widely under increased carbon dioxide concentration, which reduces transpiration and thus leaves more water at the land surface. This driver of change in the climate system, which we term ‘physiological forcing’, has been detected in observational records of increasing average continental runoff over the twentieth century. Here we use an ensemble of experiments with a global climate model that includes a vegetation component to assess the contribution of physiological forcing to future changes in continental runoff, in the context of uncertainties in future precipitation. We find that the physiological effect of doubled carbon dioxide concentrations on plant transpiration increases simulated global mean runoff by 6 per cent relative to pre-industrial levels; an increase that is comparable to that simulated in response to radiatively forced climate change (11 ± 6 per cent). Assessments of the effect of increasing carbon dioxide concentrations on the hydrological cycle that only consider radiative forcing will therefore tend to underestimate future increases in runoff and overestimate decreases. This suggests that freshwater resources may be less limited than previously assumed under scenarios of future global warming, although there is still an increased risk of drought. Moreover, our results highlight that the practice of assessing the climate-forcing potential of all greenhouse gases in terms of their radiative forcing potential relative to carbon dioxide does not accurately reflect the relative effects of different greenhouse gases on freshwater resources.

Comparative analysis of Bacillus anthracis, Bacillus cereus, and related species on the basis of reverse transcriptase sequencing of 16S rRNA

The primary structures of the 16S rRNAs of Bacillus anthracis, Bacillus cereus, Bacillus mycoides, and Bacillus thuringiensis were determined by using the reverse transcription-dideoxy sequencing method. All of the strains exhibited very high levels of sequence similarity (greater than 99%) that were consistent with the close relationships shown by previous DNA hybridization studies. The sequences of B. anthracis Sterne and B. cereus emetic strain NCTC 11143 were found to be identical for a continuous stretch of 1,446 bases and differed from the sequence of B. cereus NCDO 1771T (T = type strain) by only a single nucleotide. The 16S rRNA sequences of B. mycoides and B. thuringiensis differed from each other and from the sequences of B. anthracis and B. cereus by four to nine nucleotides.

Gastrointestinal Microflora Studies in Late-Onset Autism

Some cases of late-onset (regressive) autism may involve abnormal flora because oral vancomycin, which is poorly absorbed, may lead to significant improvement in these children. Fecal flora of children with regressive autism was compared with that of control children, and clostridial counts were higher. The number of clostridial species found in the stools of children with autism was greater than in the stools of control children. Children with autism had 9 species of Clostridium not found in controls, whereas controls yielded only 3 species not found in children with autism. In all, there were 25 different clostridial species found. In gastric and duodenal specimens, the most striking finding was total absence of non-spore-forming anaerobes and microaerophilic bacteria from control children and significant numbers of such bacteria from children with autism. These studies demonstrate significant alterations in the upper and lower intestinal flora of children with late-onset autism and may provide insights into the nature of this disorder.

UNDERSTANDING EL NIÑO IN OCEAN-ATMOSPHERE GENERAL CIRCULATION MODELS Progress and Challenges

Determining how El Nino and its impacts may change over the next 10 to 100 years remains a difficult scientific challenge. Ocean-atmosphere coupled general circulation models (CGCMs) are routinely used both to analyze El Nino mechanisms and teleconnections and to predict its evolution on a broad range of time scales, from seasonal to centennial. The ability to simulate El Nino as an emergent property of these models has largely improved over the last few years. Nevertheless, the diversity of model simulations of present-day El Nino indicates current limitations in our ability to model this climate phenomenon and to anticipate changes in its characteristics. A review of the several factors that contribute to this diversity, as well as potential means to improve the simulation of El Nino, is presented.

Health and climate change: policy responses to protect public health

The 2015 Lancet Commission on Health and Climate Change has been formed to map out the impacts of climate change, and the necessary policy responses, in order to ensure the highest attainable stand ...