Experimental and observational evidence reveals that predators in natural environments do not regulate their prey: They are passengers,not drivers

Among both ecologists and the wider community there is a tacit assumption that predators regulate populations of their prey. But there is evidence from a wide taxonomic and geographic range of studies that predators that are adapted to co-evolved prey generally do not regulate their prey. This is because predators either cannot reproduce as fast as their prey and/or are inefficient hunters unable to catch enough prey to sustain maximum reproduction. The greater capacity of herbivores to breed successfully is, however, normally restricted by a lack of enough food of sufficient quality to support reproduction. But whenever this shortage is alleviated by a large pulse of food, herbivores increase their numbers to outbreak levels. Their predators are unable to contain this increase, but their numbers, too, surge in response to this increase in food. Eventually both their populations will crash once the food supply runs out, first for the herbivores and then for the predators. Then an “over-run” of predators will further depress the already declining prey population, appearing to be controlling its abundance. This latter phenomenon has led many ecologists to conclude that predators are regulating the numbers of their prey. However, it is the same process that is revealed during outbreaks that limits populations of both predator and prey in “normal” times, although this is usually not readily apparent. Nevertheless, as all the diverse cases discussed here attest, the abundance of predators and their co-evolved prey are both limited by their food: the predators are passengers, not drivers.     

Bottom‐up proteome analysis of E. coli using capillary zone electrophoresis‐tandem mass spectrometry with an electrokinetic sheath‐flow electrospray interface

The Escherichia coli proteome was digested with trypsin and fractionated using SPE on a C18 SPE column. Seven fractions were collected and analyzed by CZE‐ESI‐MS/MS. The separation was performed in a 60‐cm‐long linear polyacrylamide‐coated capillary with a 0.1% v/v formic acid separation buffer. An electrokinetic sheath‐flow electrospray interface was used to couple the separation capillary with an Orbitrap‐Velos operating in higher‐energy collisional dissociation mode. Each CZE‐ESI‐MS/MS run lasted 50 min and total MS time was 350 min. A total of 23 706 peptide spectra matches, 4902 peptide IDs, and 871 protein group IDs were generated using MASCOT with false discovery rate less than 1% on the peptide level. The total mass spectrometer analysis time was less than 6 h, the sample identification rate (145 proteins/h) was more than two times higher than previous studies of the E. coli proteome, and the amount of sample consumed (<1 μg) was roughly fourfold less than previous studies. These results demonstrate that CZE is a useful tool for the bottom‐up analysis of prokaryote proteomes.     

Effects of environmental stress cascade up through four trophic levels in a salt marsh study system

1. Although in recent years there have been a number of studies demonstrating trophic cascades in terrestrial systems, it is still unclear what environmental conditions enable or enhance such cascades, especially among four trophic levels. 2. In this study, the influence of environmental stress (increased soil pore water salinity) on a four trophic level study system in a Florida salt marsh was examined by experimentally increasing soil pore water salinity. Effects of increased salinity on the quality of the host plant, Batis maritima, were assessed, as were resulting effects on the lepidopteran herbivore Ascia monuste, and the primary parasitoids and hyperparasitoids of its caterpillars. 3. Increased salinity altered host‐plant quality, which subsequently affected the consumer species. These effects of altered plant quality cascaded up through the herbivore and primary parasitoid to the hyperparasitoid Hypopteromalus inimicus, influencing its density, sex ratio, body size, and initial egg load. 4. These results demonstrate how heterogeneity in environmental stress can result in effects that cascade up through four trophic levels. We suggest that such strong effects at higher trophic levels may be more likely in systems in which relationships are more specific and intimate such as those among hosts, parasitoids, and hyperparasitoids.     

Spatial patterns and predictors of trophic control in marine ecosystems

A key question in ecology is under which conditions ecosystem structure tends to be controlled by resource availability vs. consumer pressure. Several hypotheses derived from theory, experiments and observational field studies have been advanced, yet a unified explanation remains elusive. Here, we identify common predictors of trophic control in a synthetic analysis of 52 observational field studies conducted within marine ecosystems across the Northern Hemisphere and published between 1951 and 2014. Spatial regression analysis of 45 candidate variables revealed temperature to be the dominant predictor, with unimodal effects on trophic control operating both directly (r² = 0.32; P < 0.0001) and indirectly through influences on turnover rate and quality of primary production, biodiversity and omnivory. These findings indicate that temperature is an overarching determinant of the trophic dynamics of marine ecosystems, and that variation in ocean temperature will affect the trophic structure of marine ecosystems through both direct and indirect mechanisms.     

Investigation of solubilization and digestion methods for microsomal membrane proteome analysis using data-independent LC-MSE

To evaluate the implementation of various denaturants and their efficacy in bottom-up membrane proteomic methods using LC-MS analysis, microsomes isolated from tomato roots were treated with MS-compatible surfactants (RapiGest SF Surfactant from Waters and PPS Silent Surfactant from Protein Discovery), a chaotropic reagent (guanidine hydrochloride), and an organic solvent (methanol). Peptides were analyzed in triplicate sample and technical replicates by data-independent LC-MS(E) analysis. Overall, 2333 unique peptides matching to 662 unique proteins were detected with the order of denaturant method efficacy being RapiGest SF Surfactant, PPS Silent Surfactant, guanidine hydrochloride, and methanol. Using bioinformatic analysis, 103 proteins were determined to be integral membrane proteins. When normalizing the data as a percentage of the overall number of peptides and proteins identified for each method, the order for integral membrane protein identification efficacy was methanol, guanidine hydrochloride, RapiGest SF Surfactant, and PPS Silent Surfactant. Interestingly, only 8% of the proteins were identified in all four methods with the silent surfactants having the greatest overlap at 17%. GRAVY analysis at the protein and peptide level indicated that methanol and guanidine hydrochloride promoted detection of hydrophobic proteins and peptides, respectively; however, trypsin activity in the presence of each denaturant was determined as a major factor contributing to peptide identification by LC-MS(E) . These results reveal the complementary nature of each denaturant method, which can be used in an integrated approach to provide a more effective bottom-up analysis of membrane proteomes than can be achieved using only a single denaturant.     

Simple rules describe bottom-up and top-down control in food webs with alternative energy pathways

Many human influences on the world's ecosystems have their largest direct impacts at either the top or the bottom of the food web. To predict their ecosystem-wide consequences we must understand how these impacts propagate. A long-standing, but so far elusive, problem in this endeavour is how to reduce food web complexity to a mathematically tractable, but empirically relevant system. Simplification to main energy channels linking primary producers to top consumers has been recently advocated. Following this approach, we propose a general framework for the analysis of bottom-up and top-down forcing of ecosystems by reducing food webs to two energy pathways originating from a limiting resource shared by competing guilds of primary producers (e.g. edible vs. defended plants). Exploring dynamical models of such webs we find that their equilibrium responses to nutrient enrichment and top consumer harvesting are determined by only two easily measurable topological properties: the lengths of the component food chains (odd-odd, odd-even, or even-even) and presence vs. absence of a generalist top consumer reconnecting the two pathways (yielding looped vs. branched webs). Many results generalise to other looped or branched web structures and the model can be easily adapted to include a detrital pathway.     

Context‐dependent effects of mycorrhizae on herbivore density and parasitism in a tritrophic coastal study system

1. Stressful abiotic conditions and mycorrhizal fungi have both been shown to influence plant quality significantly, yet the interactive effects of these factors on relationships among plants, herbivores, and natural enemies remain unclear. 2. In this study, the results of a factorial field experiment are reported in which the effects of plant stress and mycorrhizae on density and parasitism of three herbivores of Baccharis halimifolia L. were examined. 3. Plant stress was increased by adding salt to the soil, and association with mycorrhizal fungi was increased by inoculating plant roots. 4. Inoculation with mycorrhizal fungi resulted in increased density of all three herbivore species, but the effects of mycorrhizae on parasitism varied by species and with soil salinity levels. For the gall maker Neolasioptera lathami Gagne, mycorrhizae decreased parasitism regardless of soil salinity levels. For the leaf miners Amauromyza maculosa Malloch and Liriomyza trifolii Burgess, mycorrhizae effectively negated the decrease in parasitism resulting from increased salinity. 5. The results of this study show that the effects of mycorrhizae on parasitism may be context dependent, and can be positive or negative depending upon species and environmental conditions.     

Over 4100 protein identifications from a Xenopus laevis fertilized egg digest using reversed‐phase chromatographic prefractionation followed by capillary zone electrophoresis–electrospray ionization–tandem mass spectrometry analysis

A tryptic digest generated from Xenopus laevis fertilized embryos was fractionated by RPLC. One set of 30 fractions was analyzed by 100‐min CZE‐ESI‐MS/MS separations (50 h total instrument time), and a second set of 15 fractions was analyzed by 3‐h UPLC‐ESI‐MS/MS separations (45 h total instrument time). CZE‐MS/MS produced 70% as many protein IDs (4134 versus 5787) and 60% as many peptide IDs (22 535 versus 36 848) as UPLC‐MS/MS with similar instrument time (50 h versus 45 h) but with 50 times smaller total consumed sample amount (1.5 μg versus 75 μg). Surprisingly, CZE generated peaks that were 25% more intense than UPLC for peptides that were identified by both techniques, despite the 50‐fold lower loading amount; this high sensitivity reflects the efficient ionization produced by the electrokinetically pumped nanospray interface used in CZE. This report is the first comparison of CZE‐MS/MS and UPLC‐MS/MS for large‐scale eukaryotic proteomic analysis. The numbers of protein and peptide identifications produced by CZE‐ESI‐MS/MS approach those produced by UPLC‐MS/MS, but with nearly two orders of magnitude lower sample amounts.     

Simulation of water colors in a shallow acidified lake, Lake Onneto, Japan, using colorimetric analysis and bio-optical modeling

Lake Onneto has unusually brilliant water colors, such as blue-green, green, and greenish yellow. We investigated the coloration mechanism in this lake by measuring the radiometric water color and inherent optical properties (IOPs), such as attenuation, absorption, and scattering coefficients of color-producing agents (CPAs) in the lake. The hue of the water body was determined using colorimetric analysis. In addition, the radiometric water color of the lake was simulated using bio-optical modeling. Results showed that the hues of the water body were different between two sampling stations (blue-green and green at 3.1 and 5.5 m of bottom depth, respectively). However, the total suspended solids (TSS) concentrations were almost identical between the two stations (0.47 and 0.42 mg l⁻¹, respectively). In addition, the attenuation and absorption coefficients showed that the CPAs in the water body were only inorganic suspended solids (ISS) more than 0.7 μm in diameter, and specific CPAs, such as dissolved mineral ions and aqueous colloids, were not observed in the lake. Simulation of the radiometric water color showed that the radiation around 600 nm of wavelength (yellow region) steeply increased with decreasing bottom depth, indicating that the water colors of Lake Onneto are strongly governed by the light reflection from yellowish bottom sediments.