Ecology drives a global network of gene exchange connecting the human microbiome

Horizontal gene transfer (HGT), the acquisition of genetic material from non-parental lineages, is known to be important in bacterial evolution. In particular, HGT provides rapid access to genetic innovations, allowing traits such as virulence, antibiotic resistance and xenobiotic metabolism to spread through the human microbiome. Recent anecdotal studies providing snapshots of active gene flow on the human body have highlighted the need to determine the frequency of such recent transfers and the forces that govern these events. Here we report the discovery and characterization of a vast, human-associated network of gene exchange, large enough to directly compare the principal forces shaping HGT. We show that this network of 10,770 unique, recently transferred (more than 99% nucleotide identity) genes found in 2,235 full bacterial genomes, is shaped principally by ecology rather than geography or phylogeny, with most gene exchange occurring between isolates from ecologically similar, but geographically separated, environments. For example, we observe 25-fold more HGT between human-associated bacteria than among ecologically diverse non-human isolates (P = 3.0 × 10(-270)). We show that within the human microbiome this ecological architecture continues across multiple spatial scales, functional classes and ecological niches with transfer further enriched among bacteria that inhabit the same body site, have the same oxygen tolerance or have the same ability to cause disease. This structure offers a window into the molecular traits that define ecological niches, insight that we use to uncover sources of antibiotic resistance and identify genes associated with the pathology of meningitis and other diseases.     

Seismic tremors and magma wagging during explosive volcanism

Volcanic tremor is a ubiquitous feature of explosive eruptions. This oscillation persists for minutes to weeks and is characterized by a remarkably narrow band of frequencies from about 0.5?Hz to 7?Hz (refs 1-4). Before major eruptions, tremor can occur in concert with increased gas flux and related ground deformation. Volcanic tremor is thus of particular value for eruption forecasting. Most models for volcanic tremor rely on specific properties of the geometry, structure and constitution of volcanic conduits as well as the gas content of the erupting magma. Because neither the initial structure nor the evolution of the magma-conduit system will be the same from one volcano to the next, it is surprising that tremor characteristics are so consistent among different volcanoes. Indeed, this universality of tremor properties remains a major enigma. Here we employ the contemporary view that silicic magma rises in the conduit as a columnar plug surrounded by a highly vesicular annulus of sheared bubbles. We demonstrate that, for most geologically relevant conditions, the magma column will oscillate or 'wag' against the restoring 'gas-spring' force of the annulus at observed tremor frequencies. In contrast to previous models, the magma-wagging oscillation is relatively insensitive to the conduit structure and geometry, which explains the narrow band of tremor frequencies observed around the world. Moreover, the model predicts that as an eruption proceeds there will be an upward drift in both the maximum frequency and the total signal frequency bandwidth, the nature of which depends on the explosivity of the eruption, as is often observed.     

De novo cardiomyocytes from within the activated adult heart after injury

A significant bottleneck in cardiovascular regenerative medicine is the identification of a viable source of stem/progenitor cells that could contribute new muscle after ischaemic heart disease and acute myocardial infarction. A therapeutic ideal--relative to cell transplantation--would be to stimulate a resident source, thus avoiding the caveats of limited graft survival, restricted homing to the site of injury and host immune rejection. Here we demonstrate in mice that the adult heart contains a resident stem or progenitor cell population, which has the potential to contribute bona fide terminally differentiated cardiomyocytes after myocardial infarction. We reveal a novel genetic label of the activated adult progenitors via re-expression of a key embryonic epicardial gene, Wilm's tumour 1 (Wt1), through priming by thymosin β4, a peptide previously shown to restore vascular potential to adult epicardium-derived progenitor cells with injury. Cumulative evidence indicates an epicardial origin of the progenitor population, and embryonic reprogramming results in the mobilization of this population and concomitant differentiation to give rise to de novo cardiomyocytes. Cell transplantation confirmed a progenitor source and chromosome painting of labelled donor cells revealed transdifferentiation to a myocyte fate in the absence of cell fusion. Derived cardiomyocytes are shown here to structurally and functionally integrate with resident muscle; as such, stimulation of this adult progenitor pool represents a significant step towards resident-cell-based therapy in human ischaemic heart disease.     

Grass rhizosheaths: associated bacterial communities and potential for nitrogen fixation

Rhizosheaths are structures composed of mucilage secreted from plants and adherent soil particles that form a cylinder around the root. Using scanning electron microscopy (SEM), we observed bacteria associated with rhizosheaths of the grasses Achnatherum hymenoides, Calamovilfa longifolia, Hesperostipa comata, and Pascopyrum smithii from a sand dune area in Harding County in northwestern South Dakota. The greatest numbers of bacteria, observed with SEM (529 mm –2 ), and the greatest number of culturable bacteria (9.9 × 10 7 CFU ? g –1 or 5178 CFU ? mm –2 ) were on rhizosheaths of C. longifolia. Rhizosheaths of all the grasses examined contained a higher density of bacteria than the surrounding soil. Nitrogen fixation, as assayed by reduction of acetylene to ethylene, was present in some rhizosheaths. Bacterial nif H gene sequences amplified from bacteria associated with rhizosheaths were most similar to those from Alcaligenes latus and Mesorhizobium loti .     

Characteristics of mule deer beds

Rocky Mountain mule deer ( Odocoileus hemionus hemionus ) beds were studied in selected plant communities with the purpose of characterizing bedding sites. Six trends exist among the data: (1) deer appeared to prefer bedding under or near conifers, (2) most beds were found on or near game trails, (3) beds in xeric communities were located at higher altitudes and had less overhead cover than in mesic communities, (4) the percentage of uphill cover in xeric areas was greater than in mesic areas, (5) visibility was lower on the north and west sides of deer beds in both community types than on the south and east sides, and (6) the mean size of deer beds was the same in both xeric and mesic communities. These trends, as well as other tendencies in bed locations, are considered from the standpoint of deer thermoregulation and predator avoidance.     

Food of townsend ground squirrels on the Arid Land Ecology Reserve (Washington)

Diets of townsend ground squirrels were quantified from the Arid Land Ecology (ALE) Reserve eastern Washington.