Initial nitrogen enrichment conditions determines variations in nitrogen substrate utilization by heterotrophic bacterial isolates

Background The nitrogen (N) cycle consists of complex microbe-mediated transformations driven by a variety of factors, including diversity and concentrations of N compounds. In this study, we examined taxonomic diversity and N substrate utilization by heterotrophic bacteria isolated from streams under complex and simple N-enrichment conditions. Results Diversity estimates differed among isolates from the enrichments, but no significant composition were detected. Substrate utilization and substrate range of bacterial assemblages differed within and among enrichments types, and not simply between simple and complex N-enrichments. Conclusions N substrate use patterns differed between isolates from some complex and simple N-enrichments while others were unexpectedly similar. Taxonomic composition of isolates did not differ among enrichments and was unrelated to N use suggesting strong functional redundancy. Ultimately, our results imply that the available N pool influences physiology and selects for bacteria with various abilities that are unrelated to their taxonomic affiliation. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-0993-7) contains supplementary material, which is available to authorized users

Advancing river corridor science beyond disciplinary boundaries with an inductive approach to catalyze hypothesis generation

A unified conceptual framework for river corridors requires synthesis of diverse site-, method- and discipline-specific findings. The river research community has developed a substantial body of observations and process-specific interpretations, but we are still lacking a comprehensive model to distill this knowledge into fundamental transferable concepts. We confront the challenge of how a discipline classically organized around the deductive model of systematically collecting of site-, scale-, and mechanism-specific observations begins the process of synthesis. Machine learning is particularly well-suited to inductive generation of hypotheses. In this study, we prototype an inductive approach to holistic synthesis of river corridor observations, using support vector machine regression to identify potential couplings or feedbacks that would not necessarily arise from classical approaches. This approach generated 672 relationships linking a suite of 157 variables each measured at 62 locations in a 5th order river network. Eighty four percent of these relationships have not been previously investigated, and representing potential (hypothetical) process connections. We document relationships consistent with current understanding including hydrologic exchange processes, microbial ecology, and the River Continuum Concept, supporting that the approach can identify meaningful relationships in the data. Moreover, we highlight examples of two novel research questions that stem from interpretation of inductively-generated relationships. This study demonstrates the implementation of machine learning to sieve complex data sets and identify a small set of candidate relationships that warrant further study, including data types not commonly measured together. This structured approach complements traditional modes of inquiry, which are often limited by disciplinary perspectives and favor the careful pursuit of parsimony. Finally, we emphasize that this approach should be viewed as a complement to, rather than in place of, more traditional, deductive approaches to scientific discovery

MOONS: a Multi-Object Optical and Near-infrared Spectrograph for the VLT

MOONS is a new conceptual design for a Multi-Object Optical and Near-infrared Spectrograph for the Very Large Telescope (VLT), selected by ESO for a Phase A study. The baseline design consists of 1000 fibers deployable over a field of view of 500 square arcmin, the largest patrol field offered by the Nasmyth focus at the VLT. The total wavelength coverage is 0.8um-1.8um and two resolution modes: medium resolution and high resolution. In the medium resolution mode (R=4,000-6,000) the entire wavelength range 0.8um-1.8um is observed simultaneously, while the high resolution mode covers simultaneously three selected spectral regions: one around the CaII triplet (at R=8,000) to measure radial velocities, and two regions at R=20,000 one in the J-band and one in the H-band, for detailed measurements of chemical abundances. The grasp of the 8.2m Very Large Telescope (VLT) combined with the large multiplex and wavelength coverage of MOONS - extending into the near-IR - will provide the observational power necessary to study galaxy formation and evolution over the entire history of the Universe, from our Milky Way, through the redshift desert and up to the epoch of re-ionization at z>8-9. At the same time, the high spectral resolution mode will allow astronomers to study chemical abundances of stars in our Galaxy, in particular in the highly obscured regions of the Bulge, and provide the necessary follow-up of the Gaia mission. Such characteristics and versatility make MOONS the long-awaited workhorse near-IR MOS for the VLT, which will perfectly complement optical spectroscopy performed by FLAMES and VIMOS.Comment: 9 pages, 5 figures. To appear in the proceedings of the SPIE Astronomical Instrumentation + Telescopes conference, Amsterdam, 201

Global Patterns and Controls of Nutrient Immobilization On Decomposing Cellulose In Riverine Ecosystems

Microbes play a critical role in plant litter decomposition and influence the fate of carbon in rivers and riparian zones. When decomposing low-nutrient plant litter, microbes acquire nitrogen (N) and phosphorus (P) from the environment (i.e., nutrient immobilization), and this process is potentially sensitive to nutrient loading and changing climate. Nonetheless, environmental controls on immobilization are poorly understood because rates are also influenced by plant litter chemistry, which is coupled to the same environmental factors. Here we used a standardized, low-nutrient organic matter substrate (cotton strips) to quantify nutrient immobilization at 100 paired stream and riparian sites representing 11 biomes worldwide. Immobilization rates varied by three orders of magnitude, were greater in rivers than riparian zones, and were strongly correlated to decomposition rates. In rivers, P immobilization rates were controlled by surface water phosphate concentrations, but N immobilization rates were not related to inorganic N. The N:P of immobilized nutrients was tightly constrained to a molar ratio of 10:1 despite wide variation in surface water N:P. Immobilization rates were temperature-dependent in riparian zones but not related to temperature in rivers. However, in rivers nutrient supply ultimately controlled whether microbes could achieve the maximum expected decomposition rate at a given temperature

The Science Performance of JWST as Characterized in Commissioning

This paper characterizes the actual science performance of the James Webb Space Telescope (JWST), as determined from the six month commissioning period. We summarize the performance of the spacecraft, telescope, science instruments, and ground system, with an emphasis on differences from pre-launch expectations. Commissioning has made clear that JWST is fully capable of achieving the discoveries for which it was built. Moreover, almost across the board, the science performance of JWST is better than expected; in most cases, JWST will go deeper faster than expected. The telescope and instrument suite have demonstrated the sensitivity, stability, image quality, and spectral range that are necessary to transform our understanding of the cosmos through observations spanning from near-earth asteroids to the most distant galaxies

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure

Diversity of Fungi, Bacteria, and Actinomycetes on Leaves Decomposing in a Stream

Although fungi, bacteria, and specific bacterial taxa, such as the actinomycetes, have been studied extensively in various habitats, few studies have examined them simultaneously, especially on decomposing leaves in streams. In this study, sugar maple and white oak leaves were incubated in a stream in northeastern Ohio for 181 days during which samples were collected at regular intervals. Following DNA extraction, PCR-denaturing gradient gel electrophoresis (DGGE) was performed using fungus-, bacterium-, and actinomycete-specific primers. In addition, fungal and bacterial biomass was estimated. Fungal biomass differed on different days but not between leaves of the two species and was always greater than bacterial biomass. There were significant differences in bacterial biomass through time and between leaf types on some days. Generally, on the basis of DGGE, few differences in community structure were found for different leaf types. However, the ribotype richness of fungi was significantly greater than those of the bacteria and actinomycetes, which were similar to each other. Ribotype richness decreased toward the end of the study for each group except bacteria. Lack of differences between the two leaf types suggests that the microorganisms colonizing the leaf biofilm were primarily generalists that could exploit the resources of the leaves of either species equally well. Thus, we conclude that factors, such as the ecological role of the taxa (generalists versus specialists), stage of decay, and time of exposure, appeared to be more important determinants of microbial community structure than leaf quality

Pharmaceutical Compounds and Ecosystem Function: An Emerging Research Challenge for Aquatic Ecologists

ABSTRACT The number of anthropogenic compounds that occur in aquatic ecosystems today is in the thousands, many at trace concentrations. One group of compounds that has captured the interest of both the scientific community and the general public is pharmaceutical and personal care products (PPCPs), for example, hormones, chemotherapy drugs, antihistamines, stimulants, antimicrobials and various cosmetic additives. Toxicology of some PPCPs is currently understood, but their effect on ecological structure and function of aquatic ecosystems is largely unknown. We review sources and fates of these compounds in aquatic ecosystems and discuss how methods developed to study aquatic ecosystem ecology can contribute to our understanding of the influence of PPCPs on aquatic ecosystems. We argue that aquatic ecology has a well-developed tool kit for measuring the transformation, fate, and transport of solutes using assays and experiments and that these methods could be employed to investigate how PPCPs impact ecological function. We discuss the details of these approaches and conclude that application of existing ecological methods to the study of this issue could substantially improve our understanding of the effect of these compounds in aquatic ecosystems