Phylogenetic conservation of soil bacterial responses to simulated global changes.

Soil bacterial communities are altered by anthropogenic drivers such as climate change-related warming and fertilization. However, we lack a predictive understanding of how bacterial communities respond to such global changes. Here, we tested whether phylogenetic information might be more predictive of the response of bacterial taxa to some forms of global change than others. We analysed the composition of soil bacterial communities from perturbation experiments that simulated warming, drought, elevated CO2 concentration and phosphorus (P) addition. Bacterial responses were phylogenetically conserved to all perturbations. The phylogenetic depth of these responses varied minimally among the types of perturbations and was similar when merging data across locations, implying that the context of particular locations did not affect the phylogenetic pattern of response. We further identified taxonomic groups that responded consistently to each type of perturbation. These patterns revealed that, at the level of family and above, most groups responded consistently to only one or two types of perturbations, suggesting that traits with different patterns of phylogenetic conservation underlie the responses to different perturbations. We conclude that a phylogenetic approach may be useful in predicting how soil bacterial communities respond to a variety of global changes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'

Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change

We acknowledge funding from the US DOE Genomic Science Program, BER, Office of Science project DE-SC0016410. We thank Bin Wang for discussion and inputs on trait-based modelling.Peer reviewedPublisher PD

Concentrations and ratios of particulate organic carbon, nitrogen, and phosphorus in the global ocean

Knowledge of concentrations and elemental ratios of suspended particles are important for understanding many biogeochemical processes in the ocean. These include patterns of phytoplankton nutrient limitation as well as linkages between the cycles of carbon and nitrogen or phosphorus. To further enable studies of ocean biogeochemistry, we here present a global dataset consisting of 100,605 total measurements of particulate organic carbon, nitrogen, or phosphorus analyzed as part of 70 cruises or time-series. The data are globally distributed and represent all major ocean regions as well as different depths in the water column. The global median C:P, N:P, and C:N ratios are 163, 22, and 6.6, respectively, but the data also includes extensive variation between samples from different regions. Thus, this compilation will hopefully assist in a wide range of future studies of ocean elemental ratios

Differential Response of Bacterial Microdiversity to Simulated Global Change

ACKNOWLEDGMENTS UC Irvine and the LRGCE are located on the ancestral homelands of the Indigenous Kizh and Acjachemen nations. We thank Alejandra Rodriguez Verdugo, Katrine Whiteson, Kendra Walters, Cynthia Rodriguez, Kristin Barbour, Alberto Barron Sandoval, Joanna Wang, Joia Kai Capocchi, Pauline Uyen Phuong Nguyen, Khanh Thuy Huynh, and Clara Barnosky for their input on analyses and previous drafts and for laboratory help. This work was supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research grants DE-SC0016410 and DE-SC0020382.Peer reviewedPublisher PD

C : N : P stoichiometry at the Bermuda Atlantic Time-series Study station in the North Atlantic Ocean

Nitrogen (N) and phosphorus (P) availability, in addition to other macro- and micronutrients, determine the strength of the ocean's carbon (C) uptake, and variation in the N : P ratio of inorganic nutrient pools is key to phytoplankton growth. A similarity between C : N : P ratios in the plankton biomass and deep-water nutrients was observed by Alfred C. Redfield around 80 years ago and suggested that biological processes in the surface ocean controlled deep-ocean chemistry. Recent studies have emphasized the role of inorganic N : P ratios in governing biogeochemical processes, particularly the C : N : P ratio in suspended particulate organic matter (POM), with somewhat less attention given to exported POM and dissolved organic matter (DOM). Herein, we extend the discussion on ecosystem C : N : P stoichiometry but also examine temporal variation in stoichiometric relationships. We have analyzed elemental stoichiometry in the suspended POM and total (POM + DOM) organic-matter (TOM) pools in the upper 100 m and in the exported POM and subeuphotic zone (100–500 m) inorganic nutrient pools from the monthly data collected at the Bermuda Atlantic Time-series Study (BATS) site located in the western part of the North Atlantic Ocean. C : N and N : P ratios in TOM were at least twice those in the POM, while C : P ratios were up to 5 times higher in TOM compared to those in the POM. Observed C : N ratios in suspended POM were approximately equal to the canonical Redfield ratio (C : N : P = 106 : 16 : 1), while N : P and C : P ratios in the same pool were more than twice the Redfield ratio. Average N : P ratios in the subsurface inorganic nutrient pool were ~ 26 : 1, squarely between the suspended POM ratio and the Redfield ratio. We have further linked variation in elemental stoichiometry to that of phytoplankton cell abundance observed at the BATS site. Findings from this study suggest that elemental ratios vary with depth in the euphotic zone, mainly due to different growth rates of cyanobacterial cells. We have also examined the role of the Arctic Oscillation on temporal patterns in C : N : P stoichiometry. This study strengthens our understanding of the variability in elemental stoichiometry in different organic-matter pools and should improve biogeochemical models by constraining the range of non-Redfield stoichiometry and the net relative flow of elements between pools

In Silico Modeling the Effects of Missense Mutations Causing Snyder-Robinson Syndrome and Rescuing the Effects by Small Molecules Binding

Snyder-Robinson Syndrome (SRS) is an X-linked mental retardation disorder. Three missense mutations (G56S, V132G and I150T) on human spermine synthase (SMS) were reported to cause SRS. SMS is an important enzyme which converts spermindine into spermine, both of which are two polyamines controlling the normal cell growth and development. In vitro experiments showed that the dimer conformation played a crucial role on the SMS function. Our in silico studies including energy calculation, pKa calculation and molecular dynamics (MD) simulation based on the available 3D structure of SMS revealed that these mutations affected SMS function by affecting the dimer affinity, monomer stability or hydrogen bond network. One of the above sites, G56S, is accessible from the water phase, thus it provides the opportunity to rescue the disease-causing effect by binding an appropriate small molecule to the vicinity of the mutation site. Currently we run MD simulation to generate multiple receptor conformations and identified two potent binding pockets. Then two programs, Surflex and Autodock Vina, were applied for structure-based virtual screening (SBVS) and a consensus list of about 200 common compounds selected by both of the programs was created, and these compounds were tested experimentally by our collaborators

Development and Bias Assessment of a Method for Targeted Metagenomic Sequencing of Marine Cyanobacteria

Prochlorococcus and Synechococcus are the most abundant photosynthetic organisms in oligotrophic waters and responsible for a significant percentage of the earth's primary production. Here we developed a method for metagenomic sequencing of sorted Prochlorococcus and Synechococcus populations using a transposon-based library preparation technique. First, we observed that the cell lysis technique and associated amount of input DNA had an important role in determining the DNA library quality. Second, we found that our transposon-based method provided a more even coverage distribution and matched more sequences of a reference genome than multiple displacement amplification, a commonly used method for metagenomic sequencing. We then demonstrated the method on Prochlorococcus and Synechococcus field populations from the Sargasso Sea and California Current isolated by flow cytometric sorting and found clear environmentally related differences in ecotype distributions and gene abundances. In addition, we saw a significant correspondence between metagenomic libraries sequenced with our technique and regular sequencing of bulk DNA. Our results show that this targeted method is a viable replacement for regular metagenomic approaches and will be useful for identifying the biogeography and genome content of specific marine cyanobacterial populations

Ethoxyfagaronine, a synthetic analogue of fagaronine that inhibits vascular endothelial growth factor-1, as a new anti-angiogeneic agent

Angiogenesis plays a pivotal role in tumorigenesis and also contributes to the pathogenesis of hematologic malignancies. A number of plant compounds have shown efficacy in preclinical and clinical studies and some of them possess an anti-angiogenic activity. Our present findings report anti-angiogenic activities of ethoxyfagaronine (etxfag), a synthetic derivative of fagaronine. Once determined the non-cytotoxic concentration of etxfag, we showed that the drug inhibits VEGF-induced angiogenesis in a Matrigel™ plug assay and suppresses ex vivo sprouting from VEGF-treated aortic rings. Each feature leading to neovascularization was then investigated and results demonstrate that etxfag prevents VEGF-induced migration and tube formation in human umbilical vein endothelial cells (HUVEC). Moreover, etxfag also suppresses VEGF-induced VEGFR-2 phosphorylation and inhibits FAK phosphorylation at Y-861 as well as focal adhesion complex turnover. Beside these effects, etxfag modifies MT1-MMP localization at the endothelial cell membrane. Finally, immunoprecipitation assay revealed that etxfag decreases VEGF binding to VEGFR-2. As we previously reported that etxfag is able to prevent leukemic cell invasiveness and adhesion to fibronectin, all together our data collectively support the anti-angiogenic activities of etxfag which could represent an additional approach to current anti-cancer therapies

A relative version of Daugavet-points and the Daugavet property

We introduce relative versions of Daugavet-points and the Daugavet property, where the Daugavet-behavior is localized inside of some supporting slice. These points present striking similarities with Daugavet-points, but lie strictly between the notions of Daugavet- and $\Delta$-points. We provide a geometric condition that a space with the Radon--Nikod\'{y}m property must satisfy in order to be able to contain a relative Daugavet-point. We study relative Daugavet-points in absolute sums of Banach spaces, and obtain positive stability results under local polyhedrality of the underlying absolute norm. We also get extreme differences between the relative Daugavet property, the Daugavet property, and the diametral local diameter 2 property. Finally, we study Daugavet- and $\Delta$-points in subspaces of $L_1(\mu)$-spaces. We show that the two notions coincide in the class of all Lipschitz-free spaces over subsets of $\mathbb{R}$-trees. We prove that the diametral local diameter 2 property and the Daugavet property coincide for arbitrary subspaces of $L_1(\mu)$, and that reflexive subspaces of $L_1(\mu)$ do not contain $\Delta$-points. A subspace of $L_1[0,1]$ with a large subset of $\Delta$-points, but with no relative Daugavet-point, is constructed.Comment: 45 pages, 6 figure