Erosion of functional independence early in the evolution of a microbial mutualism.

Many species have evolved to function as specialized mutualists, often to the detriment of their ability to survive independently. However, there are few, if any, well-controlled observations of the evolutionary processes underlying the genesis of new mutualisms. Here, we show that within the first 1,000 generations of initiating independent syntrophic interactions between a sulfate reducer (Desulfovibrio vulgaris) and a hydrogenotrophic methanogen (Methanococcus maripaludis), D. vulgaris frequently lost the capacity to grow by sulfate respiration, thus losing the primary physiological attribute of the genus. The loss of sulfate respiration was a consequence of mutations in one or more of three key genes in the pathway for sulfate respiration, required for sulfate activation (sat) and sulfate reduction to sulfite (apsA or apsB). Because loss-of-function mutations arose rapidly and independently in replicated experiments, and because these mutations were correlated with enhanced growth rate and productivity, gene loss could be attributed to natural selection, even though these mutations should significantly restrict the independence of the evolved D. vulgaris. Together, these data present an empirical demonstration that specialization for a mutualistic interaction can evolve by natural selection shortly after its origin. They also demonstrate that a sulfate-reducing bacterium can readily evolve to become a specialized syntroph, a situation that may have often occurred in nature.

Model organisms retain an "ecological memory" of complex ecologically relevant environmental variation.

Although tractable model organisms are essential to characterize the molecular mechanisms of evolution and adaptation, the ecological relevance of their behavior is not always clear because certain traits are easily lost during long-term laboratory culturing. Here, we demonstrate that despite their long tenure in the laboratory, model organisms retain "ecological memory" of complex environmental changes. We have discovered that Halobacterium salinarum NRC-1, a halophilic archaeon that dominates microbial communities in a dynamically changing hypersaline environment, simultaneously optimizes fitness to total salinity, NaCl concentration, and the [K]/[Mg] ratio. Despite being maintained under controlled conditions over the last 50 years, peaks in the three-dimensional fitness landscape occur in salinity and ionic compositions that are not replicated in laboratory culturing but are routinely observed in the natural hypersaline environment of this organism. Intriguingly, adaptation to variations in ion composition was associated with differential regulation of anaerobic metabolism genes, suggesting an intertwined relationship between responses to oxygen and salinity. Our results suggest that the ecological memory of complex environmental variations is imprinted in the networks for coordinating multiple cellular processes. These coordination networks are also essential for dealing with changes in other physicochemically linked factors present during routine laboratory culturing and, hence, retained in model organisms.

Propagation-inside-layer-expansion method combined with physical optics for scattering by coated cylinders, a rough layer, and an object below a rough surface.

In this article, the fields scattered by coated cylinders, a rough layer, and an object below a rough surface are computed by the efficient propagation-inside-layer-expansion (PILE) method combined with the physical optics (PO) approximation to accelerate the calculation of the local interactions on the non-illuminated scatterer, which is assumed to be perfectly conducting. The PILE method is based on the method of moments, and the impedance matrix of the two scatterers is then inverted by blocks from a Taylor series expansion of the inverse of the Schur complement. Its main interest is that it is rigorous, with a simple formulation and a straightforward physical interpretation. In addition, one of the advantages of PILE is to be able to hybridize methods (rigorous or asymptotic) valid for a single scatterer. Then, in high frequencies, the hybridization with PO allows us to significantly reduce the complexity in comparison to a direct lower-upper inversion of the impedance matrix of the two scatterers without loss in accuracy.

Polarized infrared reflectivity of one-dimensional Gaussian sea surfaces with surface reflections.

Sea surface infrared reflectivity is an important parameter in maritime remote sensing. Usually, single reflection by the sea surface is considered. However, a loss of energy is then reported for large zenith observation angles (θ>50°) with a peak of about 4% for θ≈80°, because of the neglect of the multiple surface reflections. This paper presents calculations for the polarized infrared reflectivity of one-dimensional sea surfaces (2D problems) with two surface reflections, by introducing a bistatic illumination function with two reflections. The results show good agreement with the ones obtained by a Monte Carlo ray-tracing method. It is also shown that the energy conservation criterion is better satisfied after considering two surface reflections.

Four new species of mygalomorph spiders (Araneae, Halonoproctidae and Theraphosidae) from the Colombian Pacific region (Bahía Solano, Chocó).

The Colombian Pacific coast is an amazing natural region, immersed in one of the most unknown biodiversity hotspots in the world. An expedition carried out in the north of this area, at the Jardín Botánico del Pacífico (JBP) in Bahía Solano, Chocó, focused on studying the diversity of the mygalomorph spider fauna, allowed us to discover four new species included in the families Halonoproctidae and Theraphosidae. The trapdoor species Ummidiasolanasp. nov., and the theraphosids species Euthycaeluscunampiasp. nov. (Schismatothelinae), Melloinapacificasp. nov. (Glabropelmatinae), and Neischnocolusmecanasp. nov. (Theraphosinae) are illustrated, diagnosed, and described in detail. Photographs of somatic features and copulatory organs and a distribution map are provided. Morphological, taxonomical, and biogeographical aspects are discussed for each species. All these taxonomic novelties represent the first records of these genera for the region, expanding the range of geographic distribution of each of them. This work constitutes the first effort focused on characterizing the community of Mygalomorphae species in the Chocó Biogeographic Region.

Genome sequence of "Candidatus Microthrix parvicella" Bio17-1, a long-chain-fatty-acid-accumulating filamentous actinobacterium from a biological wastewater treatment plant.

"Candidatus Microthrix" bacteria are deeply branching filamentous actinobacteria which occur at the water-air interface of biological wastewater treatment plants, where they are often responsible for foaming and bulking. Here, we report the first draft genome sequence of a strain from this genus: "Candidatus Microthrix parvicella" strain Bio17-1.

Polarized infrared emissivity of one-dimensional Gaussian sea surfaces with surface reflections.

Surface reflection is an important phenomenon that must be taken into account when studying sea surface infrared emissivity, especially at large observation angles. This paper models analytically the polarized infrared emissivity of one-dimensional sea surfaces with shadowing effect and one surface reflection, by assuming a Gaussian surface slope distribution. A Monte Carlo ray-tracing method is employed as a reference. It is shown that the present model agrees well with the reference method. The emissivity calculated by the present model is then compared with measurements. The comparisons show that agreements are greatly improved by taking one surface reflection into account. The Monte Carlo ray-tracing results of sea surface infrared emissivity with two and three reflections are also determined. Their contributions are shown to be negligible.

Unpolarized emissivity of thin oil films over anisotropic Gaussian seas in infrared window regions.

In this paper, we derive the unpolarized infrared (IR) emissivity of thin oil films over anisotropic Gaussian seas from a refined physical surface spectrum model of damping due to oil. Since the electromagnetic wavelength is much smaller than the surface mean curvature radius and than the surface root mean square height, the Kirchhoff-tangent plane approximation, reduced to the geometric optics approximation, can be used. The surface can then be replaced by its local infinite tangent plane at each point of each rough surface. The multiple reflections at each interface are ignored (i.e., for both the upper air/oil interface and the lower oil/sea interface of the contaminated sea). Nevertheless, the multiple reflections between the upper and the lower interfaces of the oil film are taken into account, by assuming a locally flat and planar thin oil film, which forms a local Fabry-Perot interferometer. This means that the Fresnel reflection coefficient of a single interface can be substituted for the equivalent Fresnel reflection coefficient of the air/oil/sea film, calculated by considering an infinite number of reflections inside the layer. Comparisons of the emissivity between a clean sea and a contaminated sea are presented, with respect to emission angle, wind speed, wind direction, oil film thickness, oil type, and wavelength. Thus, oil detection, characterization, and quantization are investigated in the IR window regions.

On the mathematical modelling and data assimilation for air pollution assessment in the Tropical Andes.

Air pollution assessment in the Tropical Andes requires a multidisciplinary approach. This can be supported from the understanding of the underlying biological dynamics and atmospheric behavior, to the mathematical approach for the proper use of all available information. This review paper touches on several aspects in which mathematical models can help to solve challenging problems regarding air pollution in reviewing the state-of-the-art at the global level and assessing the corresponding state of development as applied to the Tropical Andes. We address the complexities and challenges that modelling atmospheric dynamics in a mega-diverse region with abrupt topography entails. Understanding the relevance of monitoring and facing the problems of data scarcity, we call attention to the usefulness of data assimilation for uncertainty reduction, and how these techniques could help tackle the scarcity of regional monitoring networks to accelerate the implementation and development of modelling systems for air quality in the Tropical Andes. Finally, we suggest a cyberphysical framework for decision-making processes based on the data assimilation of chemical transport models, the forecast of scenarios, and their use in regulation and policy making.

Contribution of mobile genetic elements to Desulfovibrio vulgaris genome plasticity.

The genome of Desulfovibrio vulgaris strain DePue, a sulfate-reducing Deltaproteobacterium isolated from heavy metal-impacted lake sediment, was completely sequenced and compared with the type strain D. vulgaris Hildenborough. The two genomes share a high degree of relatedness and synteny, but harbour distinct prophage and signatures of past phage encounters. In addition to a highly variable phage contribution, the genome of strain DePue contains a cluster of open-reading frames not found in strain Hildenborough coding for the production and export of a capsule exopolysaccharide, possibly of relevance to heavy metal resistance. Comparative whole-genome microarray analysis on four additional D. vulgaris strains established greater interstrain variation within regions associated with phage insertion and exopolysaccharide biosynthesis.

Metabolic modeling of a mutualistic microbial community.

The rate of production of methane in many environments depends upon mutualistic interactions between sulfate-reducing bacteria and methanogens. To enhance our understanding of these relationships, we took advantage of the fully sequenced genomes of Desulfovibrio vulgaris and Methanococcus maripaludis to produce and analyze the first multispecies stoichiometric metabolic model. Model results were compared to data on growth of the co-culture on lactate in the absence of sulfate. The model accurately predicted several ecologically relevant characteristics, including the flux of metabolites and the ratio of D. vulgaris to M. maripaludis cells during growth. In addition, the model and our data suggested that it was possible to eliminate formate as an interspecies electron shuttle, but hydrogen transfer was essential for syntrophic growth. Our work demonstrated that reconstructed metabolic networks and stoichiometric models can serve not only to predict metabolic fluxes and growth phenotypes of single organisms, but also to capture growth parameters and community composition of simple bacterial communities.

Unsupervised fuzzy binning of metagenomic sequence fragments on three-dimensional Barnes-Hut t-Stochastic Neighbor Embeddings.

Shotgun metagenomic studies attempt to reconstruct population genome sequences from complex microbial communities. In some traditional genome demarcation approaches, high-dimensional sequence data are embedded into two-dimensional spaces and subsequently binned into candidate genomic populations. One such approach uses a combination of the Barnes-Hut approximation and the $t -$Stochastic Neighbor Embedding (BH-SNE) algorithm for dimensionality reduction of DNA sequence data pentamer profiles; and demarcation of groups based on Gaussian mixture models within humanimposed boundaries. We found that genome demarcation from three-dimensional BH-SNE embeddings consistently results in more accurate binnings than 2-D embeddings. We further addressed the lack of a priori population number information by developing an unsupervised binning approach based on the Subtractive and Fuzzy c-means (FCM) clustering algorithms combined with internal clustering validity indices. Lastly, we addressed the subject of shared membership of individual data objects in a mixed community by assigning a degree of membership to individual objects using the FCM algorithm, and discriminated between confidently binned and uncertain sequence data objects from the community for subsequent biological interpretation. The binning of metagenome sequence fragments according to thresholds in the degree of membership opens the door for the identification of horizontally transferred elements and other genomic regions of uncertain assignment in which biologically meaningful information resides. The reported approach improves the unsupervised genome demarcation of populations within complex communities, increases the confidence in the coherence of the binned elements, and enables the identification of evolutionary processes ignored in hard-binning approaches in shotgun metagenomic studies.

IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses.

Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the integrated and reference-independent analysis of coupled metagenomic and metatranscriptomic data. IMP incorporates robust read preprocessing, iterative co-assembly, analyses of microbial community structure and function, automated binning, as well as genomic signature-based visualizations. The IMP-based data integration strategy enhances data usage, output volume, and output quality as demonstrated using relevant use-cases. Finally, IMP is encapsulated within a user-friendly implementation using Python and Docker. IMP is available at http://r3lab.uni.lu/web/imp/ (MIT license).

Alignment-free visualization of metagenomic data by nonlinear dimension reduction.

The visualization of metagenomic data, especially without prior taxonomic identification of reconstructed genomic fragments, is a challenging problem in computational biology. An ideal visualization method should, among others, enable clear distinction of congruent groups of sequences of closely related taxa, be applicable to fragments of lengths typically achievable following assembly, and allow the efficient analysis of the growing amounts of community genomic sequence data. Here, we report a scalable approach for the visualization of metagenomic data that is based on nonlinear dimension reduction via Barnes-Hut Stochastic Neighbor Embedding of centered log-ratio transformed oligonucleotide signatures extracted from assembled genomic sequence fragments. The approach allows for alignment-free assessment of the data-inherent taxonomic structure, and it can potentially facilitate the downstream binning of genomic fragments into uniform clusters reflecting organismal origin. We demonstrate the performance of our approach by visualizing community genomic sequence data from simulated as well as groundwater, human-derived and marine microbial communities.

Earthworm symbiont Verminephrobacter eiseniae mediates natural transformation within host egg capsules using type IV pili.

The dense microbial communities commonly associated with plants and animals should offer many opportunities for horizontal gene transfer through described mechanisms of DNA exchange including natural transformation (NT). However, studies of the significance of NT have focused primarily on pathogens. The study presented here demonstrates highly efficient DNA exchange by NT in a common symbiont of earthworms. The obligate bacterial symbiont Verminephrobacter eiseniae is a member of a microbial consortium of the earthworm Eisenia fetida that is transmitted into the egg capsules to colonize the embryonic worms. In the study presented here, by testing for transformants under different conditions in culture, we demonstrate that V. eiseniae can incorporate free DNA from the environment, that competency is regulated by environmental factors, and that it is sequence specific. Mutations in the type IV pili of V. eiseniae resulted in loss of DNA uptake, implicating the type IV pilus (TFP) apparatus in DNA uptake. Furthermore, injection of DNA carrying antibiotic-resistance genes into egg capsules resulted in transformants within the capsule, demonstrating the relevance of DNA uptake within the earthworm system. The ability to take up species-specific DNA from the environment may explain the maintenance of the relatively large, intact genome of this long-associated obligate symbiont, and provides a mechanism for acquisition of foreign genes within the earthworm system.

Genome Sequence of the Thermophilic Cyanobacterium Thermosynechococcus sp. Strain NK55a.

The genome of the unicellular cyanobacterium Thermosynechococcus sp. strain NK55a, isolated from the Nakabusa hot spring, Nagano Prefecture, Japan, comprises a single, circular, 2.5-Mb chromosome. The genome is predicted to contain 2,358 protein-encoding genes, including genes for all typical cyanobacterial photosynthetic and metabolic functions. No genes encoding hydrogenases or nitrogenase were identified.

Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage.

Microbial communities are complex and dynamic systems that are primarily structured according to their members' ecological niches. To investigate how niche breadth (generalist versus specialist lifestyle strategies) relates to ecological success, we develop and apply an integrative workflow for the multi-omic analysis of oleaginous mixed microbial communities from a biological wastewater treatment plant. Time- and space-resolved coupled metabolomic and taxonomic analyses demonstrate that the community-wide lipid accumulation phenotype is associated with the dominance of the generalist bacterium Candidatus Microthrix spp. By integrating population-level genomic reconstructions (reflecting fundamental niches) with transcriptomic and proteomic data (realised niches), we identify finely tuned gene expression governing resource usage by Candidatus Microthrix parvicella over time. Moreover, our results indicate that the fluctuating environmental conditions constrain the accumulation of genetic variation in Candidatus Microthrix parvicella likely due to fitness trade-offs. Based on our observations, niche breadth has to be considered as an important factor for understanding the evolutionary processes governing (microbial) population sizes and structures in situ.

Purifying selection and molecular adaptation in the genome of Verminephrobacter, the heritable symbiotic bacteria of earthworms.

While genomic erosion is common among intracellular symbionts, patterns of genome evolution in heritable extracellular endosymbionts remain elusive. We study vertically transmitted extracellular endosymbionts (Verminephrobacter, Betaproteobacteria) that form a beneficial, species-specific, and evolutionarily old (60-130 Myr) association with earthworms. We assembled a draft genome of Verminephrobacter aporrectodeae and compared it with the genomes of Verminephrobacter eiseniae and two nonsymbiotic close relatives (Acidovorax). Similar to V. eiseniae, the V. aporrectodeae genome was not markedly reduced in size and showed no A-T bias. We characterized the strength of purifying selection (ω = dN/dS) and codon usage bias in 876 orthologous genes. Symbiont genomes exhibited strong purifying selection (ω = 0.09 ± 0.07), although transition to symbiosis entailed relaxation of purifying selection as evidenced by 50% higher ω values and less codon usage bias in symbiont compared with reference genomes. Relaxation was not evenly distributed among functional gene categories but was overrepresented in genes involved in signal transduction and cell envelope biogenesis. The same gene categories also harbored instances of positive selection in the Verminephrobacter clade. In total, positive selection was detected in 89 genes, including also genes involved in DNA metabolism, tRNA modification, and TonB-dependent iron uptake, potentially highlighting functions important in symbiosis. Our results suggest that the transition to symbiosis was accompanied by molecular adaptation, while purifying selection was only moderately relaxed, despite the evolutionary age and stability of the host association. We hypothesize that biparental transmission of symbionts and rare genetic mixing during transmission can prevent genome erosion in heritable symbionts.

Spatial and temporal variability in a stratified hypersaline microbial mat community.

Hypersaline microbial mat communities have recently been shown to be more diverse than once thought. The variability in community composition of hypersaline mats, both in terms of spatial and temporal dimensions, is still poorly understood. Because this information is essential to understanding the complex biotic and abiotic interactions within these communities, terminal restriction fragment analysis and 16S rRNA gene sequencing were used to characterize the near-surface community of a hypersaline microbial mat in Guerrero Negro, Mexico. Core samples were analyzed to assay community variability over large regional scales (centimeter to kilometer) and to track depth-related changes in population distribution at 250-microm intervals over a diel period. Significant changes in total species diversity were observed at increasing distances across the mat surface; however, key species (e.g. Microcoleus sp.) were identified throughout the mat. The vertical position and abundance of >50% of the 60 peaks detected varied dramatically over a diel cycle, including Beggiatoa sp., cyanobacteria, Chloroflexus sp., Halochromatium sp., Bacteroidetes sp. and several as-yet-identified bacteria. Many of these migrations correlated strongly with diel changes in redox conditions within the mat, contributing to strong day-night community structure differences.

Scattering from very rough layers under the geometric optics approximation: further investigation.

Scattering from very rough homogeneous layers is studied in the high-frequency limit (under the geometric optics approximation) by taking the shadowing effect into account. To do so, the iterated Kirchhoff approximation, recently developed by Pinel et al. [Waves Random Complex Media17, 283 (2007)] and reduced to the geometric optics approximation, is used and investigated in more detail. The contributions from the higher orders of scattering inside the rough layer are calculated under the iterated Kirchhoff approximation. The method can be applied to rough layers of either very rough or perfectly flat lower interfaces, separating either lossless or lossy media. The results are compared with the PILE (propagation-inside-layer expansion) method, recently developed by Déchamps et al. [J. Opt. Soc. Am. A23, 359 (2006)], and accelerated by the forward-backward method with spectral acceleration. They highlight that there is very good agreement between the developed method and the reference numerical method for all scattering orders and that the method can be applied to root-mean-square (RMS) heights at least down to 0.25lambda.