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Our knowledge of zoosporic fungal phylogeny, physiology, and ecological functions, in particular their role in aquatic food web dynamics and biogeochemistry, is limited. The recent discovery of numerous dark matter fungi (DMF), i.e., uncultured and poorly known taxa belonging to early diverging branches of the fungal tree (namely the Rozellomycota and Chytridiomycota) calls for reconsideration of the phylogeny and ecology of zoosporic fungi. In this opinion paper, we summarize the exploration of new, recently discovered lineages of DMF and their implications for the ecology, evolution, and biogeography of the rapidly growing fungal tree. We also discuss possible ecological roles of zoosporic fungi in relation to recent methodological developments including single cell genomics and cultivation efforts. Finally, we suggest linking explorative with experimental research to gain deeper insights into the physiology and ecological functioning of zoosporic fungi DMF in aquatic habitats. (C) 2015 Elsevier Ltd and The British Mycological Society. All rights reserved.
Microcystins do not necessarily lower the sensitivity of Microcystis aeruginosa to tannic acid
(2016)
Different phytoplankton strains have been shown to possess varying sensitivities towards macrophyte allelochemicals, yet the reasons for this are largely unknown. To test whether microcystin (MC) is responsible for strain-specific sensitivities of Microcystis aeruginosa to macrophyte allelochemicals, we compared the sensitivity of 12 MC- and non-MC-producing M. aeruginosa strains, including an MC-deficient mutant and its wild type, to the polyphenolic allelochemical tannic acid (TA). Non-MC-producing strains showed a significantly higher sensitivity to TA than MC-producing strains, both in Chlorophyll a concentrations and quantum yields of photosystem II. In contrast, an MC-deficient mutant displayed a higher fitness against TA compared to its wild type. These results suggest that the resistance of M. aeruginosa to polyphenolic allelochemicals is not primarily related to MCs per se, but to other yet unknown protective mechanisms related to MCs.
This work is devoted to the convergence analysis of a modified Runge-Kutta-type iterative regularization method for solving nonlinear ill-posed problems under a priori and a posteriori stopping rules. The convergence rate results of the proposed method can be obtained under a Holder-type sourcewise condition if the Frechet derivative is properly scaled and locally Lipschitz continuous. Numerical results are achieved by using the Levenberg-Marquardt, Lobatto, and Radau methods.
Landscapes can be viewed as spatially heterogeneous areas encompassing terrestrial and aquatic domains. To date, most landscape carbon (C) fluxes have been estimated by accounting for terrestrial ecosystems, while aquatic ecosystems have been largely neglected. However, a robust assessment of C fluxes on the landscape scale requires the estimation of fluxes within and between both landscape components. Here, we compiled data from the literature on C fluxes across the air–water interface from various landscape components. We simulated C emissions and uptake for five different scenarios which represent a gradient of increasing spatial heterogeneity within a temperate young moraine landscape: (I) a homogeneous landscape with only cropland and large lakes; (II) separation of the terrestrial domain into cropland and forest; (III) further separation into cropland, forest, and grassland; (IV) additional division of the aquatic area into large lakes and peatlands; and (V) further separation of the aquatic area into large lakes, peatlands, running waters, and small water bodies These simulations suggest that C fluxes at the landscape scale might depend on spatial heterogeneity and landscape diversity, among other factors. When we consider spatial heterogeneity and diversity alone, small inland waters appear to play a pivotal and previously underestimated role in landscape greenhouse gas emissions that may be regarded as C hot spots. Approaches focusing on the landscape scale will also enable improved projections of ecosystems’ responses to perturbations, e.g., due to global change and anthropogenic activities, and evaluations of the specific role individual landscape components play in regional C fluxes. WIREs Water 2016, 3:601–617. doi: 10.1002/wat2.1147
The central rift of the Red Sea has 25 brine pools with different physical and geochemical characteristics. Atlantis II (ATIID), Discovery Deeps (DD) and Chain Deep (CD) are characterized by high salinity, temperature and metal content. Several studies reported microbial communities in these brine pools, but few studies addressed the brine pool sediments. Therefore, sediment cores were collected from ATIID, DD, CD brine pools and an adjacent brine-influenced site. Sixteen different lithologic sediment sections were subjected to shotgun DNA pyrosequencing to generate 1.47 billion base pairs (1.47 x 10(9) bp). We generated sediment-specific reads and attempted to annotate all reads. We report the phylogenetic and biochemical uniqueness of the deepest ATIID sulfur-rich brine pool sediments. In contrary to all other sediment sections, bacteria dominate the deepest ATIID sulfur-rich brine pool sediments. This decrease in virus-to-bacteria ratio in selected sections and depth coincided with an overrepresentation of mobile genetic elements. Skewing in the composition of viruses-to-mobile genetic elements may uniquely contribute to the distinct microbial consortium in sediments in proximity to hydrothermally active vents of the Red Sea and possibly in their surroundings, through differential horizontal gene transfer.
Aerobic Anoxygenic Phototrophic (AAP) bacteria are bacteriochlorophyll (BChl) a -containing organisms which use light energy to supplement their predominantly heterotrophic metabolism. Here, we investigated mortality and growth rates of AAP bacteria in three different freshwater lakes in Central Europe: the mountain lake Plesne, the oligo-mesotrophic Lake Stechlin and the forest pond Huntov. The mortality of AAP bacteria was estimated from diel changes of BChl a fluorescence. Net and gross growth rates were calculated from the increases in AAP cell numbers. The gross growth rates of AAP bacteria ranged from 0.38 to 5.6 d(-1), with the highest values observed during summer months. Simultaneously, the rapidly growing AAP cells have to cope with an intense grazing pressure by both zooplankton and protists. The presented results document that during the day, gross growth usually surpased mortality. Our results indicate that AAP bacteria utilize light energy under natural conditions to maintain rapid growth rates, which are balanced by a generally intense grazing pressure.
Climatic controls on debris-flow activity and sediment aggradation: The Del Medio fan, NW Argentina
(2016)
In the Central Andes, several studies on alluvial terraces and valley fills have linked sediment aggradation to periods of enhanced sediment supply. However, debate continues over whether tectonic or climatic factors are most important in triggering the enhanced supply. The Del Medio catchment in the Humahuaca Basin (Eastern Cordillera, NW Argentina) is located within a transition zone between subhumid and arid climates and hosts the only active debris-flow fan within this intermontane valley. By combining Be-10 analyses of boulder and sediment samples within the Del Medio catchment, with regional morphometric measurements of nearby catchments, we identify the surface processes responsible for aggradation in the Del Medio fan and their likely triggers. We find that the fan surface has been shaped by debris flows and channel avulsions during the last 400 years. Among potential tectonic, climatic, and autogenic factors that might influence deposition, our analyses point to a combination of several favorable factors that drive aggradation. These are in particular the impact of occasional abundant rainfall on steep slopes in rock types prone to failure, located in a region characterized by relatively low rainfall amounts and limited transport capacity. These characteristics are primarily associated with the climatic transition zone between the humid foreland and the arid orogen interior, which creates an imbalance between sediment supply and sediment transfer. The conditions and processes that drive aggradation in the Del Medio catchment today may provide a modern analog for the conditions and processes that drove aggradation in other nearby tributaries in the past.
Devising computational methods to accurately reconstruct gene regulatory networks given gene expression data is key to systems biology applications. Here we propose a method for reconstructing gene regulatory networks by simultaneous consideration of data sets from different perturbation experiments and corresponding controls. The method imposes three biologically meaningful constraints: (1) expression levels of each gene should be explained by the expression levels of a small number of transcription factor coding genes, (2) networks inferred from different data sets should be similar with respect to the type and number of regulatory interactions, and (3) relationships between genes which exhibit similar differential behavior over the considered perturbations should be favored. We demonstrate that these constraints can be transformed in a fused LASSO formulation for the proposed method. The comparative analysis on transcriptomics time-series data from prokaryotic species, Escherichia coli and Mycobacterium tuberculosis, as well as a eukaryotic species, mouse, demonstrated that the proposed method has the advantages of the most recent approaches for regulatory network inference, while obtaining better performance and assigning higher scores to the true regulatory links. The study indicates that the combination of sparse regression techniques with other biologically meaningful constraints is a promising framework for gene regulatory network reconstructions.
Fluvial fill terraces preserve sedimentary archives of landscape responses to climate change, typically over millennial timescales. In the Humahuaca Basin of NW Argentina (Eastern Cordillera, southern Central Andes), our 29 new optically stimulated luminescence ages of late Pleistocene fill terrace sediments demonstrate that the timing of past river aggradation occurred over different intervals on the western and eastern sides of the valley, despite their similar bedrock lithology, mean slopes, and precipitation. In the west, aggradation coincided with periods of increasing precipitation, while in the east, aggradation coincided with decreasing precipitation or more variable conditions. Erosion rates and grain size dependencies in our cosmogenic Be-10 analyses of modern and fill terrace sediments reveal an increased importance of landsliding compared to today on the west side during aggradation, but of similar importance during aggradation on the east side. Differences in the timing of aggradation and the Be-10 data likely result from differences in valley geometry, which causes sediment to be temporarily stored in perched basins on the east side. It appears as if periods of increasing precipitation triggered landslides throughout the region, which induced aggradation in the west, but blockage of the narrow bedrock gorges downstream from the perched basins in the east. As such, basin geometry and fluvial connectivity appear to strongly influence the timing of sediment movement through the system. For larger basins that integrate subbasins with differing geometries or degrees of connectivity (like Humahuaca), sedimentary responses to climate forcing are likely attenuated.