Multiplication of microbes below 0.690 water activity: implications for terrestrial and extraterrestrial life

Since a key requirement of known life forms is available water (water activity; aw), recent searches for signatures of past life in terrestrial and extraterrestrial environments have targeted places known to have contained significant quantities of biologically available water. However, early life on Earth inhabited high-salt environments, suggesting an ability to withstand low water-activity. The lower limit of water activity that enables cell division appears to be ∼ 0.605 which, until now, was only known to be exhibited by a single eukaryote, the sugar-tolerant, fungal xerophile Xeromyces bisporus. The first forms of life on Earth were, though, prokaryotic. Recent evidence now indicates that some halophilic Archaea and Bacteria have water-activity limits more or less equal to those of X. bisporus. We discuss water activity in relation to the limits of Earth's present-day biosphere; the possibility of microbial multiplication by utilizing water from thin, aqueous films or non-liquid sources; whether prokaryotes were the first organisms able to multiply close to the 0.605-aw limit; and whether extraterrestrial aqueous milieux of ≥ 0.605 aw can resemble fertile microbial habitats found on Earth.

Evolution of Precambrian life in the Brazilian geological record

Precambrian rocks comprise nearly one-quarter of the surface of Brazil and range from Paleoarchean (ca. 3.6 Ga) to the latest Ediacaran (0.542 Ga) in age. Except for controversial phosphatized 'embryo-like' microfossils like those from the lower Ediacaran Doushantuo Formation, China and complex rangeomorphs, Brazilian research has revealed all major categories of Precambrian life forms described elsewhere - microbialites, biomarkers, silicified microfossils, palynomorphs, vase-shaped microfossils, macroalgae, metazoans, vendobionts and ichnofossils - but the paleobiological significance of this record has been little explored. At least four occurrences of these fossils offer promise for increased understanding of the following aspects of Precambrian biospheric evolution: (i) the relationship of microbialites in 2.1-2.4 Ga old carbonates of the Minas Supergroup in the Quadrilatero Ferrifero, Minas Gerais (the oldest Brazilian fossils) to the development of the early oxygenic atmosphere and penecontemporaneous global tectonic and climatic events; (ii) the evolutionary and biostratigraphic significance of Mesoproterozoic to Ediacaran organic-walled microfossils in central-western Brazil; (iii) diversity and paleoecological significance of vase-shaped heterotrophic protistan microfossils in the Urucum Formation (Jacadigo Group) and possibly the Bocaina Formation (Corumba Group), of Mato Grosso do Sul; and (iv) insights into the record of skeletogenesis and paleoecology of latest Ediacaran metazoans as represented by the abundant organic carapaces of Corumbella and calcareous shells of the index fossil Cloudina, of the Corumba Group, Mato Grosso do Sul. Analysis of the Brazilian Precambrian fossil record thus holds great potential for augmenting paleobiological knowledge of this crucial period on Earth and for developing more robust hypotheses regarding possible origins and evolutionary pathways of biospheres on other planets. Received 26 February 2012, accepted 17 May 2012, first published online 18 June 2012

The importance of plant life form on spatial associations along a subtropical coastal dune gradient

Questions Does the spatial association between isolated adult trees and understorey plants change along a gradient of sand dunes? Does this association depend on the life form of the understorey plant? Location Coastal sand dunes, southeast Brazil. Methods We recorded the occurrence of understorey plant species in 100 paired 0.25 m2 plots under adult trees and in adjacent treeless sites along an environmental gradient from beach to inland. Occurrence probabilities were modelled as a function of the fixed variables of the presence of a neighbour, distance from the seashore and life form, and a random variable, the block (i.e. the pair of plots). Generalized linear mixed models (GLMM) were fitted in a backward step-wise procedure using Akaike's information criterion (AIC) for model selection. Results The occurrence of understorey plants was affected by the presence of an adult tree neighbour, but the effect varied with the life form of the understorey species. Positive spatial association was found between isolated adult neighbour and young trees, whereas a negative association was found for shrubs. Moreover, a neutral association was found for lianas, whereas for herbs the effect of the presence of an adult neighbour ranged from neutral to negative, depended on the subgroup considered. The strength of the negative association with forbs increased with distance from the seashore. However, for the other life forms, the associational pattern with adult trees did not change along the gradient. Conclusions For most of the understorey life forms there is no evidence that the spatial association between isolated adult trees and understorey plants changes with the distance from the seashore, as predicted by the stress gradient hypothesis, a common hypothesis in the literature about facilitation in plant communities. Furthermore, the positive spatial association between isolated adult trees and young trees identified along the entire gradient studied indicates a positive feedback that explains the transition from open vegetation to forest in subtropical coastal dune environments.

A minimal gene set for cellular life derived by comparison of complete bacterial genomes.

The recently sequenced genome of the parasitic bacterium Mycoplasma genitalium contains only 468 identified protein-coding genes that have been dubbed a minimal gene complement [Fraser, C.M., Gocayne, J.D., White, O., Adams, M.D., Clayton, R.A., et al. (1995) Science 270, 397-403]. Although the M. genitalium gene complement is indeed the smallest among known cellular life forms, there is no evidence that it is the minimal self-sufficient gene set. To derive such a set, we compared the 468 predicted M. genitalium protein sequences with the 1703 protein sequences encoded by the other completely sequenced small bacterial genome, that of Haemophilus influenzae. M. genitalium and H. influenzae belong to two ancient bacterial lineages, i.e., Gram-positive and Gram-negative bacteria, respectively. Therefore, the genes that are conserved in these two bacteria are almost certainly essential for cellular function. It is this category of genes that is most likely to approximate the minimal gene set. We found that 240 M. genitalium genes have orthologs among the genes of H. influenzae. This collection of genes falls short of comprising the minimal set as some enzymes responsible for intermediate steps in essential pathways are missing. The apparent reason for this is the phenomenon that we call nonorthologous gene displacement when the same function is fulfilled by nonorthologous proteins in two organisms. We identified 22 nonorthologous displacements and supplemented the set of orthologs with the respective M. genitalium genes. After examining the resulting list of 262 genes for possible functional redundancy and for the presence of apparently parasite-specific genes, 6 genes were removed. We suggest that the remaining 256 genes are close to the minimal gene set that is necessary and sufficient to sustain the existence of a modern-type cell. Most of the proteins encoded by the genes from the minimal set have eukaryotic or archaeal homologs but seven key proteins of DNA replication do not. We speculate that the last common ancestor of the three primary kingdoms had an RNA genome. Possibilities are explored to further reduce the minimal set to model a primitive cell that might have existed at a very early stage of life evolution.

Storytelling beyond the anthropocene : a quest through the crises of ecocide toward new ecological paradigms

This project is a passionate and sometimes enraged thrust toward a biodiverse future. Weaving stories with deep thinking beyond the limits of the anthropocene, I am trying to recall myself in a more-than-human world. Our planet is suffering human induced ecocide which is a global crisis threatening the existence of multiple life forms. The alchemical mix of storytelling and ecological thinking could be part remedy for humanity's adaptation: a transformational mix to re-pattern the crisis into an opportunity and shift anthropocentric structures toward networks of dynamic relationships. The purpose of this project is to explore this cultural remedy. This is a quest, a search for tools that can germinate the hypothesis: storytelling in relation to ecological thinking manifests human potential in a more-than-human world. The practice-led research is guided by the philosophy and practice of Mythology, Deep ecology and Transdisciplinarity. Further navigation is sourced from Systems Thinking, Indigenous Methodologies, Biomimicry, and Quantum Physics. The journey unfolds by reawakening the Artist's function as caretaker of Mythology and pattern inciter for the collective. The resounding discovery of this adventure is Quantum Narratives: a storytelling tool for today's world, a method to connect multiple ways of knowing and diverse languages with the purpose of engaging, relating and working with living knowledge. Quantum Narratives are used to test the field study research into the Future of Water in context of Coal Seam Gas Mining in the Murray-Darling Basin and to materialise the collaborative results as the Water Stories. This thesis is a Living Script, full of imagination and complexity. Within its folds are strategies for systemic change ready to be adapted by policy and planning brokers and those who hold power for widespread remedial action.

On display : Ravensthorpe Wildflower Show and the assembly of place

Each September since 1983 in the rural Shire of Ravensthorpe, Western Australia, volunteers collect samples of up to 700 wildfl ower species which are then displayed in the Ravensthorpe Senior Citizens Centre from 9.00 am to 4.00 pm daily over a two-week period. This chapter offers an ethnographic interpretation of this enduring annual event focusing on the 25th show held in 2007. The study contributes to understanding the complex and nuanced role of local wildflower shows in shaping and supporting rural senses of place and of community. Importantly, this particular type of festival, and more specifically this local instance, foregrounds a less-remarked aspect of festivals, namely the (re)production and celebration of place-specific knowledge through validations of, and interconnections between, scientific flower classification and emotive experience. This feature, encapsulated in Laurel Lamperd’s poem above, invites consideration of the ways in which local place knowledge and the simultaneous (re)production of ‘place’ are constituted by a complex layering of rational, objective ways of knowing and those which emphasize emotions, aesthetics and memories. This rural wildflower show not only mobilises both the rational and the emotional in ‘making sense of the world’ for local residents and for tourists, but also offers insights into the production of place as constituted in and through relations between humans and non-human life forms (Cloke & Jones, 2001; Conradson, 2005; see also Chapter 6).

The structural basis of DNA binding by the single-stranded DNA-binding protein from Sulfolobus solfataricus

Canonical single-stranded DNA-binding proteins (SSBs) from the oligosaccharide/oligonucleotide-binding (OB) domain family are present in all known organisms and are critical for DNA replication, recombination and repair. The SSB from the hyperthermophilic crenarchaeote Sulfolobus solfataricus (SsoSSB) has a ‘simple’ domain organization consisting of a single DNA-binding OB fold coupled to a flexible C-terminal tail, in contrast with other SSBs in this family that incorporate up to four OB domains. Despite the large differences in the domain organization within the SSB family, the structure of the OB domain is remarkably similar all cellular life forms. However, there are significant differences in the molecular mechanism of ssDNA binding. We have determined the structure of the SsoSSB OB domain bound to ssDNA by NMR spectroscopy. We reveal that ssDNA recognition is modulated by base-stacking of three key aromatic residues, in contrast with the OB domains of human RPA and the recently discovered human homologue of SsoSSB, hSSB1. We also demonstrate that SsoSSB binds ssDNA with a footprint of five bases and with a defined binding polarity. These data elucidate the structural basis of DNA binding and shed light on the molecular mechanism by which these ‘simple’ SSBs interact with ssDNA.

Genome sequencing of cells that live inside glass cages reveals their past history

One-quarter of the total primary production on earth is contributed by diatoms1. These are photosynthetic, unicellular algae with ornamented silica shells found in all aquatic and moist environments. They form the base of energy-efficient food webs that support all aquatic life forms. More than 250 genera of living diatoms, with as many as 100,000 species are known2. Fossil diatoms are known as early as the Cretaceous, 144–65 m.y. ago3. In India, deposits of diatoms occur in Rajasthan and are known as ‘multani mitti’. Multani mitti or Indian Fuller’s earth or diatomaceous earth as it is called in the West, is applied as a paste on the surface of the skin for 15–20 min and then washed-off. This leaves the skin feeling smooth, soft, moist and rejuvenated. Diatomaceous earth is now being used in the formulation of soaps, cleansing products, face powders and skincare preparations. Diatomaceous earth is a mineral material consisting mainly of siliceous fragments of various species of fossilized remains of diatoms.

Climate change impacts on northern Australian rangeland livestock carrying capacity: a review of issues

Grazing is a major land use in Australia's rangelands. The 'safe' livestock carrying capacity (LCC) required to maintain resource condition is strongly dependent on climate. We reviewed: the approaches for quantifying LCC; current trends in climate and their effect on components of the grazing system; implications of the 'best estimates' of climate change projections for LCC; the agreement and disagreement between the current trends and projections; and the adequacy of current models of forage production in simulating the impact of climate change. We report the results of a sensitivity study of climate change impacts on forage production across the rangelands, and we discuss the more general issues facing grazing enterprises associated with climate change, such as 'known uncertainties' and adaptation responses (e.g. use of climate risk assessment). We found that the method of quantifying LCC from a combination of estimates (simulations) of long-term (>30 years) forage production and successful grazier experience has been well tested across northern Australian rangelands with different climatic regions. This methodology provides a sound base for the assessment of climate change impacts, even though there are many identified gaps in knowledge. The evaluation of current trends indicated substantial differences in the trends of annual rainfall (and simulated forage production) across Australian rangelands with general increases in most of western Australian rangelands ( including northern regions of the Northern Territory) and decreases in eastern Australian rangelands and south-western Western Australia. Some of the projected changes in rainfall and temperature appear small compared with year-to-year variability. Nevertheless, the impacts on rangeland production systems are expected to be important in terms of required managerial and enterprise adaptations. Some important aspects of climate systems science remain unresolved, and we suggest that a risk-averse approach to rangeland management, based on the 'best estimate' projections, in combination with appropriate responses to short-term (1-5 years) climate variability, would reduce the risk of resource degradation. Climate change projections - including changes in rainfall, temperature, carbon dioxide and other climatic variables - if realised, are likely to affect forage and animal production, and ecosystem functioning. The major known uncertainties in quantifying climate change impacts are: (i) carbon dioxide effects on forage production, quality, nutrient cycling and competition between life forms (e.g. grass, shrubs and trees); and (ii) the future role of woody plants including effects of. re, climatic extremes and management for carbon storage. In a simple example of simulating climate change impacts on forage production, we found that increased temperature (3 degrees C) was likely to result in a decrease in forage production for most rangeland locations (e. g. -21% calculated as an unweighted average across 90 locations). The increase in temperature exacerbated or reduced the effects of a 10% decrease/increase in rainfall respectively (-33% or -9%). Estimates of the beneficial effects of increased CO2 (from 350 to 650 ppm) on forage production and water use efficiency indicated enhanced forage production (+26%). The increase was approximately equivalent to the decline in forage production associated with a 3 degrees C temperature increase. The large magnitude of these opposing effects emphasised the importance of the uncertainties in quantifying the impacts of these components of climate change. We anticipate decreases in LCC given that the 'best estimate' of climate change across the rangelands is for a decline (or little change) in rainfall and an increase in temperature. As a consequence, we suggest that public policy have regard for: the implications for livestock enterprises, regional communities, potential resource damage, animal welfare and human distress. However, the capability to quantify these warnings is yet to be developed and this important task remains as a challenge for rangeland and climate systems science.

Surveillance protocols for management of invasive plants: modelling Chilean needle grass (Nassella neesiana) in Australia

Aim: To develop a surveillance support model that enables prediction of areas susceptible to invasion, comparative analysis of surveillance methods and intensity and assessment of eradication feasibility. To apply the model to identify surveillance protocols for generalized invasion scenarios and for evaluating surveillance and control for a context-specific plant invasion. Location: Australia. Methods: We integrate a spatially explicit simulation model, including plant demography and dispersal vectors, within a Geographical Information System. We use the model to identify effective surveillance protocols using simulations of generalized plant life-forms spreading via different dispersal mechanisms in real landscapes. We then parameterize the surveillance support model for Chilean needle grass [CNG; Nassella neesiana (Trin. & Rupr.) Barkworth], a highly invasive tussock grass, which is an eradication target in south-eastern Queensland, Australia. Results: General surveillance protocols that can guide rapid response surveillance were identified; suitable habitat that is susceptible to invasion through particular dispersal syndromes should be targeted for surveillance using an adaptive seek-and-destroy method. The search radius of the adaptive method should be based on maximum expected dispersal distances. Protocols were used to define a surveillance strategy for CNG, but simulations indicated that despite effective and targeted surveillance, eradication is implausible at current intensities. Main conclusions: Several important surveillance protocols emerged and simulations indicated that effectiveness can be increased if they are followed in rapid response surveillance. If sufficient data are available, the surveillance support model should be parameterized to target areas susceptible to invasion and determine whether surveillance is effective and eradication is feasible. We discovered that for CNG, regardless of a carefully designed surveillance strategy, eradication is implausible at current intensities of surveillance and control and these efforts should be doubled if they are to be successful. This is crucial information in the face of environmentally and economically damaging invasive species and large, expensive and potentially ineffective control programmes.

Regeneration ecology and woody species diversity in the remnant natural forest at Wondo Genet, Ethiopia – Potential for landscape restoration

Regeneration ecology, diversity of native woody species and its potential for landscape restoration was studied in the remnant natural forest at the College of Forestry and Natural Resources at Wondo Genet, Ethiopia. The type of forest is Afromontane rainforest , with many valuable tree species like Aningeria adolfi-friederici, and it is an important provider of ecological, social and economical services for the population that lives in this area. The study contains two parts, natural regeneration studies (at the natural forest) and interviews with farmers in the nearby village of the remnant patch. The objective of the first part was to investigate the floristic composition, densitiy and regeneration profiles of native woody species in the forest, paying special attention to woody species that are considered the most relevant (socio-economic). The second part provided information on woody species preferred by the farmers and on multiple uses of the adjacent natural forest, it also provided information and analysed perceptions on forest degradation. Systematic plot sampling was used in the forest inventory. Twenty square plots of 20 x 20 m were assessed, with 38 identified woody species (the total number of species was 45), representing 26 families. Of these species 61% were trees, 13% shrubs, 11% lianas and 16% species that could have both life forms. An analysis of natural regeneration of five important tree species in the natural forest showed that Aningeria adolfi-friederici had the best regeneration results. An analysis of population structure (as determined by height classes) of two commercially important woody species in the forest, Aningeria adolfi-friederici and Podocarpus falcatus, showed a marked difference: Aningeria had a typical “reversed J” frequency distribution, while Podocarpus showed very low values in all height classes. Multi dimensional scaling (MDS) was used to map the sample plots according to their similarity in species composition, using the Sørensen quantitative index, coupled with indicator species analysis .Three groups were identified with respective indicator species: Group 1 – Adhatoda schimperiana, Group 2 – Olea hochstetteri , Group 3 – Acacia senegal and Aningeria adolfi-friederici. Thirty questionnaire interviews were conducted with farmers in the village of Gotu Onoma that use the nearby remant forest patch. Their tree preferences were exotic species such as Eucalyptus globulus for construction and fuelwood and Grevillea robusta for shade and fertility. Considering forest land degradation farmers were aware of the problem and suggested that the governmental institutions address the problem by planting more Eucalyptus globulus. The natural forest seemed to have moderate levels of disturbance and it was still floristically diverse. However, the low rate of natural regeneration of Podocarpus falcatus suggested that this species is threatened and must be a priority in conservation actions. Plantations and agroforestry seem to be possible solutions for rehabilitation of the surrounding degraded lands, thereby decreasing the existent pressure in the remnant natural forest.

Cyclic AMP in Mycobacteria: the second messenger comes first

Cyclic AMP (cAMP) has emerged as a pivotal molecule for signalling in all life forms. Mycobacterial genomes have been found to encode for numerous proteins that are involved in cAMP generation, degradation and utilization. Many of these proteins have domain organizations unique to mycobacteria. This review summarizes recent advances in mechanisms of cAMP synthesis and degradation, focusing on the processes by which cAMP modulates mycobacterial signalling. We explore its impact on the physiology of the organism and on the discourse between M. tuberculosis and its host.