Integrating microbial ecology into ecosystem models: challenges and priorities

Microbial communities can potentially mediate feedbacks between global change and ecosystem function, owing to their sensitivity to environmental change and their control over critical biogeochemical processes. Numerous ecosystem models have been developed to predict global change effects, but most do not consider microbial mechanisms in detail. In this idea paper, we examine the extent to which incorporation of microbial ecology into ecosystem models improves predictions of carbon (C) dynamics under warming, changes in precipitation regime, and anthropogenic nitrogen (N) enrichment. We focus on three cases in which this approach might be especially valuable: temporal dynamics in microbial responses to environmental change, variation in ecological function within microbial communities, and N effects on microbial activity. Four microbially-based models have addressed these scenarios. In each case, predictions of the microbial-based models differ—sometimes substantially—from comparable conventional models. However, validation and parameterization of model performance is challenging. We recommend that the development of microbial-based models must occur in conjunction with the development of theoretical frameworks that predict the temporal responses of microbial communities, the phylogenetic distribution of microbial functions, and the response of microbes to N enrichment.     

Parents and offspring in an evolutionary game: the effect of supply on demand when costs of care vary

Current models of parent-offspring communication do not explicitly predict the effect of parental food supply on offspring demand (ESD). However, existing theory is frequently interpreted as predicting a negative ESD, such that offspring beg less when parental supply is high. While empirical evidence largely supports this interpretation, several studies have identified the opposite case, with well-fed offspring begging more than those in poorer condition. Here, we show that signalling theory can give rise to either a negative or a positive ESD depending on the precise form of costs and benefits. Introducing variation among parents in the cost of care, we show that the ESD may change sign depending upon the quantitative relation between two effects: (i) decreased supply leads to increased begging because of an increase in marginal fitness benefit of additional resources to offspring, (ii) decreased supply leads to reduced begging because it is associated with a decrease in parental responsiveness, rendering begging less effective. To illustrate the interplay between these two effects, we show that Godfray's seminal model of begging yields a negative ESD when care is generally cheap, because the impact of supply on the marginal benefits of additional resources then outweighs the associated changes in parental responsiveness to begging. By contrast, the same model predicts a positive ESD when care is generally costly, because the impact of care costs on parental responsiveness then outweighs the change in marginal benefits.     

Diversification in the Mexican horned lizard Phrynosoma orbiculare across a dynamic landscape

The widespread montane Mexican horned lizard Phrynosoma orbiculare (Squamata: Phrynosomatidae) represents an ideal species to investigate the relative impacts of Neogene vicariance and Quaternary climate change on lineage diversification across the Mexican highlands. We used mitochondrial DNA to examine the maternal history of P. orbiculare and estimate the timing and tempo of lineage diversification. Based on our results, we inferred 11 geographically structured, well supported mitochondrial lineages within this species, suggesting P. orbiculare represents a species complex. Six divergences between lineages likely occurred during the Late Miocene and Pliocene, and four splits probably happened during the Pleistocene. Diversification rate appeared relatively constant through time. Spatial and temporal divergences between lineages of P. orbiculare and co-distributed taxa suggest that a distinct period of uplifting of the Transvolcanic Belt around 7.5-3 million years ago broadly impacted diversification in taxa associated with this mountain range. To the north, several river drainages acting as filter barriers differentially subdivided co-distributed highland taxa through time. Diversification patterns observed in P. orbiculare provide additional insight into the mechanisms that impacted differentiation of highland taxa across the complex Mexican highlands.     

Selection of line-transect methods for estimating the density of group-living animals: lessons from the primates

We review the four major contemporary methods for estimating density of group-living animals from line-transect sampling: perpendicular modelling of group centers, perpendicular modelling of center of measurable individuals, strip transects and animal-observer distance. The efficacy of each method is evaluated to produce a simple selection guide. We review the literature and use field data from the Udzungwa Mountains, Tanzania. The review is relevant to all group-living animals; however, examples are drawn from the primates. Perpendicular methods have better mathematical justification than non-perpendicular methods. For perpendicular methods using detection function models, it is preferable to measure group location using center of measurable individuals, as group centers are hard to estimate. The assumptions of detection function models are often broken in poor visibility habitats or with unhabituated animals. Alternatively strip transects may be used where there are reliable data on group spread and/or visibility. Strip transects are also the most practical, along with the animal-observer method; however, the latter lacks mathematical justification. We conclude that there are arguments for continued use of all four methods. In certain situations the use of raw encounter rates may also be considered. The appropriate method is determined by minimizing bias and considering time, resources and field conditions.     

Ectoparasites on reintroduced roe deer Capreolus capreolus in Israel

The ectoparasite fauna of reintroduced roe deer (Capreolus capreolus) was surveyed in a Mediterranean forest in Israel. Ectoparasites were collected from four female hand-reared deer during 2004 and 2005. Seasonality, predilection sites of infestation, and the apparent effect of the parasites are presented. This is the first study of roe deer parasites in the East Mediterranean. The ectoparasite fauna included three hippoboscid fly (Lipoptena capreoli, Hippobosca equina, and Hippobosca longipennis), four tick (Rhipicephalus sanguineus, Rhipicephalus turanicus, Rhipicephalus kohlsi, and Hyalomma marginatum), and one unidentified trombiculid mite species. For most of these ectoparasites, this is the first record on roe deer. All ectoparasite species were documented in Israel prior to the reintroduction program; exotic ectoparasites were not detected.     

Two distinct pathways for cyclooxygenase-2 protein degradation

Cyclooxygenases (COX-1 and COX-2) are N-glycosylated, endoplasmic reticulum-resident, integral membrane proteins that catalyze the committed step in prostanoid synthesis. COX-1 is constitutively expressed in many types of cells, whereas COX-2 is usually expressed inducibly and transiently. The control of COX-2 protein expression occurs at several levels, and overexpression of COX-2 is associated with pathologies such as colon cancer. Here we have investigated COX-2 protein degradation and demonstrate that it can occur through two independent pathways. One pathway is initiated by post-translational N-glycosylation at Asn-594. The N-glycosyl group is then processed, and the protein is translocated to the cytoplasm, where it undergoes proteasomal degradation. We provide evidence from site-directed mutagenesis that a 27-amino acid instability motif (27-IM) regulates posttranslational N-glycosylation of Asn-594. This motif begins with Glu-586 8 residues upstream of the N-glycosylation site and ends with Lys-612 near the C terminus at Leu-618. Key elements of the 27-IM include a helix involving residues Glu-586 to Ser-596 with Asn-594 near the end of this helix and residues Leu-610 and Leu-611, which are located in an apparently unstructured downstream region of the 27-IM. The last 16 residues of the 27-IM, including Leu-610 and Leu-611, appear to promote N-glycosylation of Asn-594 perhaps by causing this residue to become exposed to appropriate glycosyl transferases. A second pathway for COX-2 protein degradation is initiated by substrate-dependent suicide inactivation. Suicide-inactivated protein is then degraded. The biochemical steps have not been resolved, but substrate-dependent degradation is not inhibited by proteasome inhibitors or inhibitors of lysosomal proteases. The pathway involving the 27-IM occurs at a constant rate, whereas degradation through the substrate-dependent process is coupled to the rate of substrate turnover.     

Core temperature measurement by microwave radiometry

A ‘double-container model’ was used for core temperature (T_c) measurement by microwave emission radiometry (MR) of warm fluid inside a tube, placed in a container with a cooler fluid. The intensity of microwaves emitted from the warmer fluid inside the tube were measured using a MR metering device, consisting of an antenna linked to a low-noise radio frequency amplifier (bandwidth 500 MHz, centered at 4.0 GHz). Based on the MR measurements, a T_c prediction model was developed for measuring the temperature of fluid inside a tube, achieving a sensitivity of ±0.5 °C at environmental temperature of 33–37 °C.     

The Frequent 5,10-Methylenetetrahydrofolate Reductase C677T Polymorphism Is Associated with a Common Haplotype in Whites, Japanese, and Africans

The common 5,10-methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism causes decreased activity of this enzyme and can be associated with mild-to-moderate hyperhomocysteinemia in homozygotes, particularly when there is folic acid deficiency, as well as with vascular dementia, arterial thrombosis, venous thrombosis, neural-tube defects, and fetal loss. When folic acid intake is sufficient, homozygotes for MTHFR 677T appear to be protected against colon cancer and acute lymphatic leukemia, and fetuses bearing this genotype have an augmented survival. The distribution of MTHFR 677T is worldwide, but its frequency in different populations varies extensively. In the present study, we addressed the question of whether the MTHFR 677T alteration has an ancestral origin or has occurred repeatedly. We analyzed the frequency distribution of the previously described polymorphism A1298C in exon 7 and of three intronic dimorphisms, in white Israelis (Jews and Arabs), Japanese, and Ghanaian Africans. The 677T allele was, remarkably, associated with one haplotype, G-T-A-C, in white and Japanese homozygotes. Among the Africans, analysis of maximum likelihood also disclosed an association with the G-T-A-C haplotype, although none of the 174 subjects examined was homozygous for MTHFR 677T. These results suggest that the MTHFR 677T alteration occurred on a founder haplotype that may have had a selective advantage.