Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics.

Members of microbial communities can substantially overlap in substrate use. However, what enables functionally redundant microorganisms to coassemble or even stably coexist remains poorly understood. Here, we show that during unstable successional dynamics on complex, natural organic matter, functionally redundant bacteria can coexist by partitioning low-concentration substrates even though they compete for one simple, dominant substrate. We allowed ocean microbial communities to self-assemble on leachates of the brown seaweed Fucus vesiculosus and then analyzed the competition among 10 taxonomically diverse isolates representing two distinct stages of the succession. All, but two isolates, exhibited an average of 90% ± 6% pairwise overlap in resource use, and functional redundancy of isolates from the same assembly stage was higher than that from between assembly stages, leading us to construct a simpler four-isolate community with two isolates from each of the early and late stages. We found that, although the short-term dynamics of the four-isolate communities in F. vesiculosus leachate was dependent on initial isolate ratios, in the long term, the four isolates stably coexist in F. vesiculosus leachate, albeit with some strains at low abundance. We therefore explored the potential for nonredundant substrate use by genomic content analysis and RNA expression patterns. This analysis revealed that the four isolates mainly differed in peripheral metabolic pathways, such as the ability to degrade pyrimidine, leucine, and tyrosine, as well as aromatic substrates. These results highlight the importance of fine-scale differences in metabolic strategies for supporting the frequently observed coexistence of large numbers of rare organisms in natural microbiomes.

An untargeted exometabolomics approach to characterize dissolved organic matter in groundwater of the Samail Ophiolite.

The process of serpentinization supports life on Earth and gives rise to the habitability of other worlds in our Solar System. While numerous studies have provided clues to the survival strategies of microbial communities in serpentinizing environments on the modern Earth, characterizing microbial activity in such environments remains challenging due to low biomass and extreme conditions. Here, we used an untargeted metabolomics approach to characterize dissolved organic matter in groundwater in the Samail Ophiolite, the largest and best characterized example of actively serpentinizing uplifted ocean crust and mantle. We found that dissolved organic matter composition is strongly correlated with both fluid type and microbial community composition, and that the fluids that were most influenced by serpentinization contained the greatest number of unique compounds, none of which could be identified using the current metabolite databases. Using metabolomics in conjunction with metagenomic data, we detected numerous products and intermediates of microbial metabolic processes and identified potential biosignatures of microbial activity, including pigments, porphyrins, quinones, fatty acids, and metabolites involved in methanogenesis. Metabolomics techniques like the ones used in this study may be used to further our understanding of life in serpentinizing environments, and aid in the identification of biosignatures that can be used to search for life in serpentinizing systems on other worlds.

Traceback of the Psoroptes outbreak in British Columbian bighorn sheep (Ovis Canadensis).

Psoroptes are a non-burrowing, ectoparasitic, mange-causing mite that has been documented in American bighorn sheep populations throughout the 19th and 20th centuries; however, it was not seen on Canadian bighorn sheep until 2006. The aim of this study was to determine the potential source of the Psoroptes outbreak in Canadian bighorn sheep. Morphological and molecular analyses were used to compare mites recovered from outbreak-associated bighorn sheep, pet rabbits in Canada, and on historically infested bighorn sheep in the USA. The results revealed that Psoroptes acquired from the Canadian and outbreak-associated American bighorn sheep were morphologically more similar to those collected from rabbits than mites on historically infested bighorn sheep. Outer opisthosomal setae lengths measured an average of 81.7 µm (±7.7 µm) in outbreak associated bighorn mites, 88.9 µm (±12.0 µm) in rabbit mites and 151.2 µm (±16.6 µm) in historically infested bighorn mites. The opisthosomal lobe morphology of bighorn mites in the outbreak herds was also more similar to that of rabbit mites, previously described as P. cuniculi, than historically infested bighorn mites, which match previous descriptions of P. ovis. This finding was supported by DNA sequence data of the mitochondrial cytochrome B gene. This is the first report of Psoroptes of the rabbit ecotype on bighorn sheep. The morphological and molecular data therefore support the hypothesis that the source of Psoroptes outbreak in Canadian bighorn sheep represented a disease spillover event from rabbits rather than transmission from infested American bighorn sheep populations.

AutoTuner: High Fidelity and Robust Parameter Selection for Metabolomics Data Processing.

Untargeted metabolomics experiments provide a snapshot of cellular metabolism but remain challenging to interpret due to the computational complexity involved in data processing and analysis. Prior to any interpretation, raw data must be processed to remove noise and to align mass-spectral peaks across samples. This step requires selection of dataset-specific parameters, as erroneous parameters can result in noise inflation. While several algorithms exist to automate parameter selection, each depends on gradient descent optimization functions. In contrast, our new parameter optimization algorithm, AutoTuner, obtains parameter estimates from raw data in a single step as opposed to many iterations. Here, we tested the accuracy and the run-time of AutoTuner in comparison to isotopologue parameter optimization (IPO), the most commonly used parameter selection tool, and compared the resulting parameters' influence on the properties of feature tables after processing. We performed a Monte Carlo experiment to test the robustness of AutoTuner parameter selection and found that AutoTuner generated similar parameter estimates from random subsets of samples. We conclude that AutoTuner is a desirable alternative to existing tools, because it is scalable, highly robust, and very fast (∼100-1000× speed improvement from other algorithms going from days to minutes). AutoTuner is freely available as an R package through BioConductor.

Carbon Assimilation Strategies in Ultrabasic Groundwater: Clues from the Integrated Study of a Serpentinization-Influenced Aquifer.

Serpentinization is a low-temperature metamorphic process by which ultramafic rock chemically reacts with water. Such reactions provide energy and materials that may be harnessed by chemosynthetic microbial communities at hydrothermal springs and in the subsurface. However, the biogeochemistry mediated by microbial populations that inhabit these environments is understudied and complicated by overlapping biotic and abiotic processes. We applied metagenomics, metatranscriptomics, and untargeted metabolomics techniques to environmental samples taken from the Coast Range Ophiolite Microbial Observatory (CROMO), a subsurface observatory consisting of 12 wells drilled into the ultramafic and serpentinite mélange of the Coast Range Ophiolite in California. Using a combination of DNA and RNA sequence data and mass spectrometry data, we found evidence for several carbon fixation and assimilation strategies, including the Calvin-Benson-Bassham cycle, the reverse tricarboxylic acid cycle, the reductive acetyl coenzyme A (acetyl-CoA) pathway, and methylotrophy, in the microbial communities inhabiting the serpentinite-hosted aquifer. Our data also suggest that the microbial inhabitants of CROMO use products of the serpentinization process, including methane and formate, as carbon sources in a hyperalkaline environment where dissolved inorganic carbon is unavailable.IMPORTANCE This study describes the potential metabolic pathways by which microbial communities in a serpentinite-influenced aquifer may produce biomass from the products of serpentinization. Serpentinization is a widespread geochemical process, taking place over large regions of the seafloor and at continental margins, where ancient seafloor has accreted onto the continents. Because of the difficulty in delineating abiotic and biotic processes in these environments, major questions remain related to microbial contributions to the carbon cycle and physiological adaptation to serpentinite habitats. This research explores multiple mechanisms of carbon fixation and assimilation in serpentinite-hosted microbial communities.

Misleading and dangerous: the use of the precautionary principle in foreign policy debates.

Recent scholarly research has suggested that the Bush Administration embraced the Precautionary Principle (PP) to formulate its policy on Iraq before the coalition invasion in 2003. The article below challenges this argument. Demonstrating the Bush Administration's antipathy--and at times hostility--to the PP in environmental politics, the article outlines the similarities and differences between usage of the PP in foreign policy debates on the one hand, and the established risk strategies of pre-emption and prevention on the other. The article examines the Bush Administration's reaction to Saddam's alleged weapons of mass destruction (WMD) programme by drawing on earlier conceptual work of the PP in international affairs: an acceptance of the limits of the usefulness of intelligence assessments; an openness to alternative solutions; proportionality of response; and reversing the onus of persuasion. Based on these four strands the article argues that the Bush Administration's decision to invade Iraq was based less on the PP and more on the idea of fighting a preventive war.

The management of risk in foreign and defence policy: the precautionary principle and decisions on war.

This article develops a concept that originated in environmental risk decision making, and investigates whether the Precautionary Principle (PP) may be usefully deployed by policymakers in the realm of foreign and defence matters. Drawing on the literature on precaution in the environmental arena, and in its weaker form, we develop an operational model of the PP, which has four main characteristics: an acceptance of the limits of knowledge on a given issue; an openness to alternative solutions; proportionality of response; and reversing the onus of proof. It concludes that the Precautionary Principle is a more inclusive way of deliberating on decisions on war, and the model we propose might provide a useful guideline for policy-makers in today's uncertain world.