Aquatic Hyphomycete Species Are Screened by the Hyporheic Zone of Woodland Streams

Aquatic hyphomycetes strongly contribute to organic matter dynamics in streams, but their abilities to colonize leaf litter buried in streambed sediments remain unexplored. Here, we conducted field and laboratory experiments (slow-filtration columns and stream-simulating microcosms) to test the following hypotheses: (i) that the hyporheic habitat acting as a physical sieve for spores filters out unsuccessful strategists from a potential species pool, (ii) that decreased pore size in sediments reduces species dispersal efficiency in the interstitial water, and (iii) that the physicochemical conditions prevailing in the hyporheic habitat will influence fungal community structure. Our field study showed that spore abundance and species diversity were consistently re- duced in the interstitial water compared with surface water within three differing streams. Significant differences occurred among aquatic hyphomycetes, with dispersal efficiency of filiform-spore species being much higher than those with compact or branched/tetraradiate spores. This pattern was remarkably consistent with those found in laboratory experiments that tested the influence of sediment pore size on spore dispersal in microcosms. Furthermore, leaves inoculated in a stream and incubated in slow-filtration columns exhibited a fungal assemblage dominated by only two species, while five species were codominant on leaves from the stream-simulating microcosms. Results of this study highlight that the hyporheic zone exerts two types of selec- tion pressure on the aquatic hyphomycete community, a physiological stress and a physical screening of the benthic spore pool, both leading to drastic changes in the structure of fungal community

Updating known distribution models for forecasting climate change impact on endangered species

To plan endangered species conservation and to design adequate management programmes, it is necessary to predict their distributional response to climate change, especially under the current situation of rapid change. However, these predictions are customarily done by relating de novo the distribution of the species with climatic conditions with no regard of previously available knowledge about the factors affecting the species distribution. We propose to take advantage of known species distribution models, but proceeding to update them with the variables yielded by climatic models before projecting them to the future. To exemplify our proposal, the availability of suitable habitat across Spain for the endangered Bonelli’s Eagle (Aquila fasciata) was modelled by updating a pre-existing model based on current climate and topography to a combination of different general circulation models and Special Report on Emissions Scenarios. Our results suggested that the main threat for this endangered species would not be climate change, since all forecasting models show that its distribution will be maintained and increased in mainland Spain for all the XXI century. We remark on the importance of linking conservation biology with distribution modelling by updating existing models, frequently available for endangered species, considering all the known factors conditioning the species’ distribution, instead of building new models that are based on climate change variables only.Ministerio de Ciencia e Innovación and FEDER (project CGL2009-11316/BOS

Search for rare quark-annihilation decays, B --> Ds(*) Phi

We report on searches for B- --> Ds- Phi and B- --> Ds*- Phi. In the context of the Standard Model, these decays are expected to be highly suppressed since they proceed through annihilation of the b and u-bar quarks in the B- meson. Our results are based on 234 million Upsilon(4S) --> B Bbar decays collected with the BABAR detector at SLAC. We find no evidence for these decays, and we set Bayesian 90% confidence level upper limits on the branching fractions BF(B- --> Ds- Phi) Ds*- Phi)<1.2x10^(-5). These results are consistent with Standard Model expectations.Comment: 8 pages, 3 postscript figues, submitted to Phys. Rev. D (Rapid Communications

Complex dynamics of defective interfering baculoviruses during serial passage in insect cells

Defective interfering (DI) viruses are thought to cause oscillations in virus levels, known as the 'Von Magnus effect'. Interference by DI viruses has been proposed to underlie these dynamics, although experimental tests of this idea have not been forthcoming. For the baculoviruses, insect viruses commonly used for the expression of heterologous proteins in insect cells, the molecular mechanisms underlying DI generation have been investigated. However, the dynamics of baculovirus populations harboring DIs have not been studied in detail. In order to address this issue, we used quantitative real-time PCR to determine the levels of helper and DI viruses during 50 serial passages of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) in Sf21 cells. Unexpectedly, the helper and DI viruses changed levels largely in phase, and oscillations were highly irregular, suggesting the presence of chaos. We therefore developed a simple mathematical model of baculovirus-DI dynamics. This theoretical model reproduced patterns qualitatively similar to the experimental data. Although we cannot exclude that experimental variation (noise) plays an important role in generating the observed patterns, the presence of chaos in the model dynamics was confirmed with the computation of the maximal Lyapunov exponent, and a Ruelle-Takens-Newhouse route to chaos was identified at decreasing production of DI viruses, using mutation as a control parameter. Our results contribute to a better understanding of the dynamics of DI baculoviruses, and suggest that changes in virus levels over passages may exhibit chaos.The authors thank Javier Carrera, Just Vlak and Lia Hemerik for helpful discussion. MPZ was supported by a Rubicon Grant from the Netherlands Organization for Scientific Research (NWO, www.nwo.nl) and a 'Juan de la Cierva' postdoctoral contract (JCI-2011-10379) from the Spanish 'Secretaria de Estado de Investigacion, Desarrollo e Innovacion'. JS was supported by the Botin Foundation. SFE was supported by grant BFU2012-30805, also from the Spanish 'Secretaria de Estado de Investigacion, Desarrollo e Innovacion'.Zwart, MP.; Pijlman, G.; Sardanyes Cayuela, J.; Duarte, J.; Januario, C.; Elena Fito, SF. (2013). Complex dynamics of defective interfering baculoviruses during serial passage in insect cells. Journal of Biological Physics. 39(2):327-342. doi:10.1007/s10867-013-9317-9S327342392Von Magnus, P.: Incomplete forms of influenza virus. Adv. Virus. Res. 2, 59–79 (1954)Huang, A.S.: Defective interfering viruses. Annu. Rev. Microbiol. 27, 101–117 (1973)Kool, M., Voncken, J.W., Vanlier, F.L.J., Tramper, J., Vlak, J.M.: Detection and analysis of Autographa californica nuclear polyhedrosis-virus mutants with defective interfering properties. Virology 183, 739–746 (1991)Wickham, T.J., Davis, T., Granados, R.R., Hammer, D.A., Shuler, M.L., Wood, H.A.: Baculovirus defective interfering particles are responsible for variations in recombinant protein-production as a function of multiplicity of infection. Biotechnol. Lett. 13, 483–488 (1991)Pijlman, G.P., van den Born, E., Martens, D.E., Vlak, J.M.: Autographa californica baculoviruses with large genomic deletions are rapidly generated in infected insect cells. Virology 283, 132–138 (2001)Giri, L., Feiss, M.G., Bonning, B.C., Murhammer, D.W.: Production of baculovirus defective interfering particles during serial passage is delayed by removing transposon target sites in fp25k. J. Gen. Virol. 93, 389–399 (2012)King, L.A., Possee, R.D.: The Baculovirus Expression System. University Press, Cambridge (1992)Lee, H.Y., Krell, P.J.: Reiterated DNA fragments in defective genomes of Autographa californica nuclear polyhedrosis virus are competent for AcMNPV-dependent DNA replication. 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Technol. 18, 460–466 (1996)Zwart, M.P., Erro, E., van Oers, M.M., de Visser, J.A.G.M., Vlak, J.M.: Low multiplicity of infection in vivo results in purifying selection against baculovirus deletion mutants. J. Gen. Virol. 89, 1220–1224 (2008)Luckow, V.A., Lee, S.C., Barry, G.F., Olins, P.O.: Efficient generation of infectious recombinant baculoviruses by site-specific transposon-mediated insertion of foreign genes into a baculovirus genome propagated in Escherichia coli. J. Virol. 67, 4566–4579 (1993)Vaughn, J.L., Goodwin, R.H., Tompkins, G.J., McCawley, P.: Establishment of 2 cell lines from insect Spodoptera frugiperda (Lepidoptera, Noctuidae). In Vitro 13, 213–217 (1977)Zwart, M.P., van Oers, M.M., Cory, J.S., van Lent, J.W.M., van der Werf, W., Vlak, J.M.: Development of a quantitative real-time PCR for determination of genotype frequencies for studies in baculovirus population biology. J. Virol. Meth. 148, 146–154 (2008)Zwart, M.P., Hemerik, L., Cory, J.S., de Visser, J.A.G.M., Bianchi, F.J.J.A., van Oers, M.M., Vlak, J.M., Hoekstra, R.F., van der Werf, W.: An experimental test of the independent action hypothesis in virus-insect pathosystems. Proc. R. Soc. B 276, 2233–2242 (2009)Olkin, I., Gleser, L.J., Derman, C.: Probability Models and Applications. Macmillan, New York (1994)Parker, T., Chua, L.: Practical Numerical Algorithms for Chaotic Systems. Springer-Verlag, Berlin (1989)Dieci, L., van Vleck, E.S.: Computation of a few Lyapunov exponents for continuous and discrete dynamical systems. J. Appl. Numer. Math. 17, 275–291 (1995)Matsumoto, T., Chua, L.O., Komuro, M.: The double scroll. IEEE Trans. Circuits Syst. 32, 797–818 (1985)Chua, L.O., Komuro, M., Matsumoto, T.: The double scroll family: rigorous proof of chaos. IEEE Trans. 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Hepatic Abnormalities Associated with Aluminum Loading in Piglets

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141476/1/jpen0293.pd

Compositional analysis of bacterial communities in seawater, sediment, and sponges in the Misool coral reef system, Indonesia

Sponge species have been deemed high microbial abundance (HMA) or low microbial abundance (LMA) based on the composition and abundance of their microbial symbionts. In the present study, we evaluated the richness and composition of bacterial communities associated with one HMA sponge (Xestospongia testudinaria; Demospongiae: Haplosclerida: Petrosiidae), one LMA sponge (Stylissa carteri; Demospongiae: Scopalinida - Scopalinidae), and one sponge with a hitherto unknown microbial community (Aaptos suberitoides; Demospongiae: Suberitida: Suberitidae) inhabiting the Misool coral reef system in the West Papua province of Indonesia. The bacterial communities of these sponge species were also compared with seawater and sediment bacterial communities from the same coastal coral reef habitat. Using a 16S rRNA gene barcoded pyrosequencing approach, we showed that the most abundant phylum overall was Proteobacteria. The biotope (sponge species, sediment or seawater) explained almost 84% of the variation in bacterial composition with highly significant differences in composition among biotopes and a clear separation between bacterial communities from seawater and S. carteri; X. testudinaria and A. suberitoides and sediment. The Chloroflexi classes SAR202 and Anaerolineae were most abundant in A. suberitoides and X. testudinaria and both of these species shared several OTUs that were largely absent in the remaining biotopes. This suggests that A. suberitoides is a HMA sponge. Although similar, the bacterial communities of S. carteri and seawater were compositionally distinct. These results confirm compositional differences between sponge and non-sponge biotopes and between HMA and LMA sponges.publishe

Global Pyrogeography: the Current and Future Distribution of Wildfire

Climate change is expected to alter the geographic distribution of wildfire, a complex abiotic process that responds to a variety of spatial and environmental gradients. How future climate change may alter global wildfire activity, however, is still largely unknown. As a first step to quantifying potential change in global wildfire, we present a multivariate quantification of environmental drivers for the observed, current distribution of vegetation fires using statistical models of the relationship between fire activity and resources to burn, climate conditions, human influence, and lightning flash rates at a coarse spatiotemporal resolution (100 km, over one decade). We then demonstrate how these statistical models can be used to project future changes in global fire patterns, highlighting regional hotspots of change in fire probabilities under future climate conditions as simulated by a global climate model. Based on current conditions, our results illustrate how the availability of resources to burn and climate conditions conducive to combustion jointly determine why some parts of the world are fire-prone and others are fire-free. In contrast to any expectation that global warming should necessarily result in more fire, we find that regional increases in fire probabilities may be counter-balanced by decreases at other locations, due to the interplay of temperature and precipitation variables. Despite this net balance, our models predict substantial invasion and retreat of fire across large portions of the globe. These changes could have important effects on terrestrial ecosystems since alteration in fire activity may occur quite rapidly, generating ever more complex environmental challenges for species dispersing and adjusting to new climate conditions. Our findings highlight the potential for widespread impacts of climate change on wildfire, suggesting severely altered fire regimes and the need for more explicit inclusion of fire in research on global vegetation-climate change dynamics and conservation planning

Testing the Water–Energy Theory on American Palms (Arecaceae) Using Geographically Weighted Regression

Water and energy have emerged as the best contemporary environmental correlates of broad-scale species richness patterns. A corollary hypothesis of water–energy dynamics theory is that the influence of water decreases and the influence of energy increases with absolute latitude. We report the first use of geographically weighted regression for testing this hypothesis on a continuous species richness gradient that is entirely located within the tropics and subtropics. The dataset was divided into northern and southern hemispheric portions to test whether predictor shifts are more pronounced in the less oceanic northern hemisphere. American palms (Arecaceae, n = 547 spp.), whose species richness and distributions are known to respond strongly to water and energy, were used as a model group. The ability of water and energy to explain palm species richness was quantified locally at different spatial scales and regressed on latitude. Clear latitudinal trends in agreement with water–energy dynamics theory were found, but the results did not differ qualitatively between hemispheres. Strong inherent spatial autocorrelation in local modeling results and collinearity of water and energy variables were identified as important methodological challenges. We overcame these problems by using simultaneous autoregressive models and variation partitioning. Our results show that the ability of water and energy to explain species richness changes not only across large climatic gradients spanning tropical to temperate or arctic zones but also within megathermal climates, at least for strictly tropical taxa such as palms. This finding suggests that the predictor shifts are related to gradual latitudinal changes in ambient energy (related to solar flux input) rather than to abrupt transitions at specific latitudes, such as the occurrence of frost