Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function

Publisher's version (útgefin grein).For decades, researchers have lacked the ability to rapidly correlate microbial identity with bacterial metabolism. Since specialized metabolites are critical to bacterial function and survival in the environment, we designed a data acquisition and bioinformatics technique (IDBac) that utilizes in situ matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze protein and specialized metabolite spectra recorded from single bacterial colonies picked from agar plates. We demonstrated the power of our approach by discriminating between two Bacillus subtilis strains in 99% sequence similarity in the 16S rRNA gene. Finally, we used IDBac to simultaneously extract protein and specialized metabolite MS profiles from unidentified Lake Michigan sponge-associated bacteria isolated from an agar plate. In just 3 h, we created hierarchical protein MS groupings of 11 environmental isolates (10 MS replicates each, for a total of 110 spectra) that accurately mirrored phylogenetic groupings. We further distinguished isolates within these groupings, which share nearly identical 16S rRNA gene sequence identity, based on interspecies and intraspecies differences in specialized metabolite production. IDBac is an attempt to couple in situ MS analyses of protein content and specialized metabolite production to allow for facile discrimination of closely related bacterial colonies.We thank the following contributors: Russel Cuhel and crew of R. V. Neeskay (University of Milwaukee Wisconsin) for assistance with sediment collection; Keith Jung for collection of the freshwater sponge; Dr. Amanda Bulman (Bruker) for assistance with MALDI-TOF MS protein acquisition parameters; Dr. Terry Moore and Dr. Atul Jain for recrystallizing alpha-cyano-4-hydroxycinnamic acid matrix (CHCA); and Dr. Darrell McCaslin (University of Wisconsin Madison) for testing our method on legacy instruments. This work was supported by National Institute of Child Health and Human Development Grant K12HD055892; the National Institutes of Health Office of Research on Women’s Health; National Geographic Grant CP-044R17; Icelandic Research Fund Grant 152336-051; and University of Illinois at Chicago startup funds.Peer Reviewe

Stable isotope analyses of rock hyrax faecal pellets, hyraceum and associated vegetation in southern Africa: Implications for dietary ecology and palaeoenvironmental reconstructions

Rock hyrax middens are important palaeoenvironmental archives in southern Africa. Carbon and nitrogen isotope measurements on middens (hyraceum) are key components of climate reconstructions, but their interpretations require refinement Although delta N-15 in hyraceum often correlates with independent proxies for palaeo-aridity, the impacts of dietary and physiological controls on hyraceum delta N-15 remain to be resolved. We analyse delta C-13 and delta N-15 in plant foliage, hyrax faecal pellets and hyraceum from 21 sites across southern Africa. Faeces are generally depleted in C-13 (delta C-13 typically < -20 parts per thousand), suggesting significant browsing. Grazing is rarely dominant and probably occurs only when palatable grass is available. Variability in faecal and foliar delta N-15 is large, but foliar delta N-15 is positively correlated with faecal delta N-15. The diet-faeces delta N-15 offset is uncorrelated with climate (aridity), but is correlated with %N in faeces. Faecal delta N-15 is positively correlated with modem hyraceum delta N-15, and the relationships with aridity index for foliar and faecal (body tissue) delta N-15 are comparable. These observations implicate diet as a significant control on hyraceum delta N-15 and we observe no strong evidence for metabolic controls on hyraceum delta N-15. More data are required to refine these relationships, but these observations are consistent with current palaeoenvironmental interpretations of midden delta N-15 and delta C-13. (C) 2016 Elsevier Ltd. All rights reserved

A multiscale framework for disentangling the roles of evenness, density, and aggregation on diversity gradients

Ecology published by Wiley Periodicals LLC on behalf of Ecological Society of America Disentangling the drivers of diversity gradients can be challenging. The Measurement of Biodiversity (MoB) framework decomposes scale-dependent changes in species diversity into three components of community structure: species abundance distribution (SAD), total community abundance, and within-species spatial aggregation. Here we extend MoB from categorical treatment comparisons to quantify variation along continuous geographic or environmental gradients. Our approach requires sites along a gradient, each consisting of georeferenced plots of abundance-based species composition data. We demonstrate our method using a case study of ants sampled along an elevational gradient of 28 sites in a mixed deciduous forest of the Great Smoky Mountains National Park, USA. MoB analysis revealed that decreases in ant species richness along the elevational gradient were associated with decreasing evenness and total number of species, which counteracted the modest increase in richness associated with decreasing spatial aggregation along the gradient. Total community abundance had a negligible effect on richness at all but the finest spatial grains, SAD effects increased in importance with sampling effort, and the aggregation effect had the strongest effect at coarser spatial grains. These results do not support the more-individuals hypothesis, but they are consistent with a hypothesis of stronger environmental filtering at coarser spatial grains. Our extension of MoB has the potential to elucidate how components of community structure contribute to changes in diversity along environmental gradients and should be useful for a variety of assemblage-level data collected along gradients

Measurement of Biodiversity (MoB): A method to separate the scale-dependent effects of species abundance distribution, density, and aggregation on diversity change

Little consensus has emerged regarding how proximate and ultimate drivers such as productivity, disturbance and temperature may affect species richness and other aspects of biodiversity. Part of the confusion is that most studies examine species richness at a single spatial scale and ignore how the underlying components of species richness can vary with spatial scale. We provide an approach for the measurement of biodiversity that decomposes changes in species rarefaction curves into proximate components attributed to: (a) the species abundance distribution, (b) density of individuals and (c) the spatial arrangement of individuals. We decompose species richness by comparing spatial and nonspatial sample- and individual-based species rarefaction curves that differentially capture the influence of these components to estimate the relative importance of each in driving patterns of species richness change. We tested the validity of our method on simulated data, and we demonstrate it on empirical data on plant species richness in invaded and uninvaded woodlands. We integrated these methods into a new r package (mobr). The metrics that mobr provides will allow ecologists to move beyond comparisons of species richness in response to ecological drivers at a single spatial scale toward a dissection of the proximate components that determine species richness across scales

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

Publisher's version (útgefin grein)In order to visualize the relationship between bacterial phylogeny and specialized metabolite production of bacterial colonies growing on nutrient agar, we developed IDBac-a low-cost and high-throughput matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDITOF MS) bioinformatics pipeline. IDBac software is designed for non-experts, is freely available, and capable of analyzing a few to thousands of bacterial colonies. Here, we present procedures for the preparation of bacterial colonies for MALDI-TOF MS analysis, MS instrument operation, and data processing and visualization in IDBac. In particular, we instruct users how to cluster bacteria into dendrograms based on protein MS fingerprints and interactively create Metabolite Association Networks (MANs) from specialized metabolite data.This work was supported by National Institute of General Medical Sciences Grant R01 GM125943, National Geographic Grant CP-044R-17; Icelandic Research Fund Grant 152336-051; and University of Illinois at Chicago startup funds. Also, we thank the following contributors: Dr. Amanda Bulman for assistance with MALDI-TOF MS protein acquisition parameters; Dr. Terry Moore and Dr. Atul Jain for recrystallizing alpha-cyano-4-hydroxycinnamic acid matrix (CHCA).Peer Reviewe

Epsilon Metal Summary Report FY 2011

The Epsilon-metal ({var_epsilon}-metal) phase was selected in FY 2009 as a potential waste form to for immobilizing the noble metals found in the undissolved solids + aqueous stream, and the soluble Tc from ion-exchange process, each resulting from proposed aqueous reprocessing. {var_epsilon}-metal phase is observed in used nuclear fuel and the natural reactors of Oklobono in Gabon, where the long-term corrosion behavior was demonstrated. This makes {var_epsilon}-metal a very attractive waste form. Last fiscal year, {var_epsilon}-metal was successfully fabricated by combining the five-metals, Mo, Ru, Rh, Pd and Re (surrogate for Tc), into pellets followed by consolidation with an arc melter. The arc melter produced fully dense samples with the epsilon structure. However, some chemistry differences were observed in the microstructure that resulted in regions rich in Re and Mo, and others rich in Pd, while Ru and Rh remained fairly constant throughout. This year, thermal stability (air), and corrosion testing of the samples fabricated by arc melting were the main focus for experimental work. Thermal stability was measured with a differential scanning calorimeter - thermogravimetric analyzer, by both ramp heating as well as step heating. There is clear evidence during the ramp heating experiment of an exothermic event + a weight loss peak both beginning at {approx}700 C. Step heating showed an oxidation event at {approx}690 C with minimal weight gain that occurs just before the weight loss event at 700 C. The conclusion being that the e-metal begins to oxidize and then become volatile. These findings are useful for considering the effects of voloxidation process. Three different pellets were subjected to electrochemical testing to study the corrosion behavior of the epsilon-metal phase in various conditions, namely acidic, basic, saline, and inert. Test was done according to an interim procedure developed for the alloy metal waste form. First an open circuit potential was measured, followed by linear polarization sweeps. The linear polarization sweep range was the Tafel equation was fit to the linear polarization sweep data to determine the corrosion rate of each pellet in each test solution. The average calculated corrosion rates of the three pellets according to solution conditions were: -1.91 x 10{sup -4} mm/yr (0.001 M NaOH), -1.48 x 10{sup -3} mm/yr (0.01 M NaCl), -8.77 x 10{sup -4} mm/yr (0.001 M H{sub 2}SO{sub 4}), -2.09 x 10{sup -3} mm/yr (0.001 M NaOH + 0.01 M NaCl), and -1.54 x 10{sup -3} mm/yr (0.001 M H{sub 2}SO{sub 4} + 0.01 M NaCl). Three single-pass flow through (SPFT) test were conducted at a flow rate of 10 ml/day, at 90 C, and pH of 2.5, 7.0, and 9.0 for up to 322 days. Results of the tests indicate that dissolution rates were 5 x 10{sup -4} g m{sup 2} d{sup -1} at pH 9.0, 1.2 x 10{sup -4} g m{sup -2} d{sup -1} at pH 7.0, and 2 x 10{sup -4} g m{sup -2} d{sup -1} at pH 2.5. The sample used for the pH 7.0 SPFT test contains extra Re compared to samples used for the other two SPFT test, which came from a single pellet. The corrosion data measured this year indicate that the {var_epsilon}-metal phase is chemically durable. The two chemically different phases, but structurally the same, behave differently during dissolution according to the microstructure changes observed in both the electrochemical and in SPFT test. Characterization of the test specimens after testing suggests that the dissolution is complex and involves oxidative dissolution followed by precipitation of both oxide and metallic phases. These data suggest that the dissolution in the electrochemical and SPFT tests is different; a process that needs further investigation

Ecological correlates of risk and incidence of West Nile virus in the United States

West Nile virus, which was recently introduced to North America, is a mosquito-borne pathogen that infects a wide range of vertebrate hosts, including humans. Several species of birds appear to be the primary reservoir hosts, whereas other bird species, as well as other vertebrate species, can be infected but are less competent reservoirs. One hypothesis regarding the transmission dynamics of West Nile virus suggests that high bird diversity reduces West Nile virus transmission because mosquito blood-meals are distributed across a wide range of bird species, many of which have low reservoir competence. One mechanism by which this hypothesis can operate is that high-diversity bird communities might have lower community-competence, defined as the sum of the product of each species’ abundance and its reservoir competence index value. Additional hypotheses posit that West Nile virus transmission will be reduced when either: (1) abundance of mosquito vectors is low; or (2) human population density is low. We assessed these hypotheses at two spatial scales: a regional scale near Saint Louis, MO, and a national scale (continental USA). We found that prevalence of West Nile virus infection in mosquito vectors and in humans increased with decreasing bird diversity and with increasing reservoir competence of the bird community. Our results suggest that conservation of avian diversity might help ameliorate the current West Nile virus epidemic in the USA

Synthesis reveals approximately balanced biotic differentiation and homogenization

This work was supported by the German Research Foundation (FZT 118, to S.A.B., T.E., A.S., R.v.K., W.-B.X., and J.M.C.) and ERC GA 101044975 and the Leverhulme Centre for Anthropocene Biodiversity (to M.D.). This work was also supported by the German Research Foundation (DFG) project “Establishment of the National Research Data Infrastructure (NFDI)” in the consortium NFDI4Biodiversity (project number 442032008) (to T.E.), European Union Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 894644 (to I.S.M.), USDA Hatch grant MAFES #1011538 and NSF EPSCOR Track II grant #2019470 (to B.M.), and NSF Track II grant #2019470 (to N.J.G.).It is commonly thought that the biodiversity crisis includes widespread declines in the spatial variation of species composition, called biotic homogenization. Using a typology relating homogenization and differentiation to local and regional diversity changes, we synthesize patterns across 461 metacommunities surveyed for 10 to 91 years, and 64 species checklists (13 to 500+ years). Across all datasets, we found that no change was the most common outcome, but with many instances of homogenization and differentiation. A weak homogenizing trend of a 0.3% increase in species shared among communities/year on average was driven by increased numbers of widespread (high occupancy) species and strongly associated with checklist data that have longer durations and large spatial scales. At smaller spatial and temporal scales, we show that homogenization and differentiation can be driven by changes in the number and spatial distributions of both rare and common species. The multiscale perspective introduced here can help identify scale-dependent drivers underpinning biotic differentiation and homogenization.Peer reviewe