Trait-based analysis of the human skin microbiome

The past decade of microbiome research has concentrated on cataloging the diversity of taxa in different environments. The next decade is poised to focus on microbial traits and function. Most existing methods for doing this perform pathway analysis using reference databases. This has both benefits and drawbacks. Function can go undetected if reference databases are coarse-grained or incomplete. Likewise, detection of a pathway does not guarantee expression of the associated function. Finally, function cannot be connected to specific microbial constituents, making it difficult to ascertain the types of organisms exhibiting particular traits—something that is important for understanding microbial success in specific environments. A complementary approach to pathway analysis is to use the wealth of microbial trait information collected over years of lab-based, culture experiments.https://doi.org/10.1186/s40168-019-0698-

Exploring the functional composition of the human microbiome using a hand-curated microbial trait database

Even when microbial communities vary wildly in their taxonomic composition, their functional composition is often surprisingly stable. This suggests that a functional perspective could provide much deeper insight into the principles governing microbiome assembly. Much work to date analyzing the functional composition of microbial communities, however, relies heavily on inference from genomic features. Unfortunately, output from these methods can be hard to interpret and often suffers from relatively high error rates. We built and analyzed a domain-specific microbial trait database from known microbe-trait pairs recorded in the literature to better understand the functional composition of the human microbiome. Using a combination of phylogentically conscious machine learning tools and a network science approach, we were able to link particular traits to areas of the human body, discover traits that determine the range of body areas a microbe can inhabit, and uncover drivers of metabolic breadth. Domain-specific trait databases are an effective compromise between noisy methods to infer complex traits from genomic data and exhaustive, expensive attempts at database curation from the literature that do not focus on any one subset of taxa. They provide an accurate account of microbial traits and, by limiting the number of taxa considered, are feasible to build within a reasonable time-frame. We present a database specific for the human microbiome, in the hopes that this will prove useful for research into the functional composition of human-associated microbial communities.https://doi.org/10.1186/s12859-021-04216-

Depositional architecture, provenance, and tectonic/eustatic modulation of Miocene submarine fans in the Shikoku Basin: Results from Nankai Trough Seismogenic Zone Experiment

Seismostratigraphy, coring, and logging while drilling during Integrated Ocean Drilling Program Expeditions 319, 322, and 333 (Sites C0011/C0012) show three Miocene submarine fans in the NE Shikoku Basin, with broadly coeval deposits at Ocean Drilling Program Site 1177 and Deep Sea Drilling Project Site 297 (NW Shikoku Basin). The sediment dispersal patterns have major implications for paleogeographies at that time. The oldest, finer-grained (Kyushu) fan has sheet-like geometry; quartz-rich flows were fed mostly from an ancestral landmass in the East China Sea. During prolonged hemipelagic mud deposition at C0011-C0012 (~12.2 to 9.1 Ma), sand supply continued at Sites 1177 and 297. Sand delivery to much of the Shikoku Basin halted during a phase of sinistral strike slip to oblique plate motion, after which the Daiichi Zenisu Fan (~9.1 to 8.0 Ma) was fed by submarine channels. The youngest fan (Daini Zenisu; ~8.0 to 7.6 Ma) has sheet-like geometry with thick-bedded, coarse-grained pumiceous sandstones. The pumice fragments were fed from a mixed provenance that included the collision zone of the Izu-Bonin and Honshu Arcs. The shift from channelized to sheet-like flows was favored by renewal of relatively rapid northward subduction, which accentuated the trench as a bathymetric depression. Increased sand supply appears to correlate with long-term eustatic lowstands of sea level. The stratigraphic position and 3-D geometry of the sandbodies have important implications for subduction-related processes, including the potential for focused fluid flow and fluid overpressures above and below the plate boundary fault: In sheet-like sands, pathways for fluid flow have greater horizontal permeability compared with those in channel sands

The dynamical control of subduction parameters on surface topography

he long-wavelength surface deflection of Earth's outermost rocky shell is mainly controlled by large-scale dynamic processes like isostasy or mantle flow. The largest topographic amplitudes are therefore observed at plate boundaries due to the presence of large thermal heterogeneities and strong tectonic forces. Distinct vertical surface deflections are particularly apparent at convergent plate boundaries mostly due to the convergence and asymmetric sinking of the plates. Having a mantle convection model with a free surface that is able to reproduce both realistic single-sided subduction and long-wavelength surface topography self-consistently, we are now able to better investigate this interaction. We separate the topographic signal into distinct features and quantify the individual topographic contribution of several controlling subduction parameters. Results are diagnosed by splitting the topographic signal into isostatic and residual components, and by considering various physical aspects like viscous dissipation during plate bending. Performing several systematic suites of experiments, we are then able to quantify the topographic impact of the buoyancy, rheology, and geometry of the subduction-zone system to each and every topographic feature at a subduction zone and to provide corresponding scaling laws. We identify slab dip and, slightly less importantly, slab buoyancy as the major agents controlling surface topography at subduction zones on Earth. Only the island-arc high and the back-arc depression extent are mainly controlled by plate strength. Overall, his modeling study sets the basis to better constrain deep-seated mantle structures and their physical properties via the observed surface topography on present-day Earth and back through time

An Environment-Sensitive Synthetic Microbial Ecosystem

Microbial ecosystems have been widely used in industrial production, but the inter-relationships of organisms within them haven't been completely clarified due to complex composition and structure of natural microbial ecosystems. So it is challenging for ecologists to get deep insights on how ecosystems function and interplay with surrounding environments. But the recent progresses in synthetic biology show that construction of artificial ecosystems where relationships of species are comparatively clear could help us further uncover the meadow of those tiny societies. By using two quorum-sensing signal transduction circuits, this research designed, simulated and constructed a synthetic ecosystem where various population dynamics formed by changing environmental factors. Coherent experimental data and mathematical simulation in our study show that different antibiotics levels and initial cell densities can result in correlated population dynamics such as extinction, obligatory mutualism, facultative mutualism and commensalism. This synthetic ecosystem provides valuable information for addressing questions in ecology and may act as a chassis for construction of more complex microbial ecosystems

Limits of the seismogenic zone in the epicentral region of the 26 December 2004 great Sumatra-Andaman earthquake: Results from seismic refraction and wide-angle reflection surveys and thermal modeling

The 26 December 2004 Sumatra earthquake (Mw = 9.1) initiated around 30 km depth and ruptured 1300 km of the Indo-Australian Sunda plate boundary. During the Sumatra OBS (ocean bottom seismometer) survey, a wide angle seismic profile was acquired across the epicentral region. A seismic velocity model was obtained from combined travel time tomography and forward modeling. Together with reflection seismic data from the SeaCause II cruise, the deep structure of the source region of the great earthquake is revealed. Four to five kilometers of sediments overlie the oceanic crust at the trench, and the subducting slab can be imaged down to a depth of 35 km. We find a crystalline backstop 120 km from the trench axis, below the fore arc basin. A high velocity zone at the lower landward limit of the raycovered domain, at 22 km depth, marks a shallow continental Moho, 170 km from the trench. The deep structure obtained from the seismic data was used to construct a thermal model of the fore arc in order to predict the limits of the seismogenic zone along the plate boundary fault. Assuming 100C-150C as its updip limit, the seismogenic zone is predicted to begin 530 km from the trench. The downdip limit of the 2004 rupture as inferred from aftershocks is within the 350C 450C temperature range, but this limit is 210-250 km from the trench axis and is much deeper than the fore arc Moho. The deeper part of the rupture occurred along the contact between the mantle wedge and the downgoing plate

Phylogeography of Supralittoral Rocky Intertidal Ligia Isopods in the Pacific Region from Central California to Central Mexico

Ligia isopods are widely distributed in the Pacific rocky intertidal shores from central California to central Mexico, including the Gulf of California. Yet, their biological characteristics restrict them to complete their life cycles in a very narrow range of the rocky intertidal supralittoral. Herein, we examine phylogeographic patterns of Ligia isopods from 122 localities between central California and central Mexico. We expect to find high levels of allopatric diversity. In addition, we expect the phylogeographic patterns to show signatures of past vicariant events that occurred in this geologically dynamic region.We sequenced two mitochondrial genes (Cytochrome Oxidase I and 16S ribosomal DNA). We conducted Maximum Likelihood and Bayesian phylogenetic analyses. We found many divergent clades that, in general, group according to geography. Some of the most striking features of the Ligia phylogeographic pattern include: (1) deep mid-peninsular phylogeographic breaks on the Pacific and Gulf sides of Baja peninsula; (2) within the Gulf lineages, the northern peninsula is most closely related to the northern mainland, while the southern peninsula is most closely related to the central-southern mainland; and, (3) the southernmost portion of the peninsula (Cape Region) is most closely related to the southernmost portion of mainland.Our results shed light on the phylogenetic relationships of Ligia populations in the study area. This study probably represents the finest-scale phylogeographic examination for any organism to date in this region. Presence of highly divergent lineages suggests multiple Ligia species exist in this region. The phylogeographic patterns of Ligia in the Gulf of California and Baja peninsula are incongruent with a widely accepted vicariant scenario among phylogeographers, but consistent with aspects of alternative geological hypotheses and phylo- and biogeographic patterns of several other taxa. Our findings contribute to the ongoing debate regarding the geological origin of this important biogeographic region

Principles of genetic circuit design

Cells navigate environments, communicate and build complex patterns by initiating gene expression in response to specific signals. Engineers seek to harness this capability to program cells to perform tasks or create chemicals and materials that match the complexity seen in nature. This Review describes new tools that aid the construction of genetic circuits. Circuit dynamics can be influenced by the choice of regulators and changed with expression 'tuning knobs'. We collate the failure modes encountered when assembling circuits, quantify their impact on performance and review mitigation efforts. Finally, we discuss the constraints that arise from circuits having to operate within a living cell. Collectively, better tools, well-characterized parts and a comprehensive understanding of how to compose circuits are leading to a breakthrough in the ability to program living cells for advanced applications, from living therapeutics to the atomic manufacturing of functional materials.National Institute of General Medical Sciences (U.S.) (Grant P50 GM098792)National Institute of General Medical Sciences (U.S.) (Grant R01 GM095765)National Science Foundation (U.S.). Synthetic Biology Engineering Research Center (EEC0540879)Life Technologies, Inc. (A114510)National Science Foundation (U.S.). Graduate Research FellowshipUnited States. Office of Naval Research. Multidisciplinary University Research Initiative (Grant 4500000552