Molecules are more than markers: new directions in molecular microbial ecology

Macromolecules such as DNA, RNA, and proteins are widely used to quantify diversity in natural communities, to monitor the dispersal of organisms and their genes, and to trace phylogenetic relationships among organisms. With such widespread use of molecules as markers, it is easy to forget that they perform functions that are integral to the survival of organisms. The structural and functional properties of macromolecules have been intensively studied in genetics, biochemistry, and physiology. These fields, however, have not generally focused on the ecological significance of molecular variation, but instead have used defective variants as tools for identifying structure and function. Understanding the significance of molecular variation for organismal success or failure is a central problem in ecology, one whose solution will require the integration of diverse approaches and perspectives from ecology, molecular biology, genetics, physiology, and evolutionary biology. I review several studies of bacterial populations evolving in simple environments that have begun to integrate these approaches and perspectives in order to examine the consequences of molecular variation for ecological performance.     

Geographical and taxonomic biases in invasion ecology

Invasive alien species come from most taxonomic groups, and invasion biology is searching for robust cross-taxon generalizations and principles. An analysis of 2,670 papers dealing with 892 invasive species showed that all major groups of invaders are well studied, but that most information on the mechanisms of invasion has emerged from work on a limited number of the most harmful invaders. A strong geographical bias, with Africa and Asia understudied, inhibits a balanced understanding of invasion, because we might be lacking knowledge of specific invasion mechanisms from poorly studied, regionally specific habitats. International cooperation is required to achieve a more geographically balanced picture of biological invasions. Invasive species with the greatest impact are best studied, but more studies of species that are naturalized but not (yet) invasive are needed to improve understanding of the mechanisms acting during the naturalization phase of invasions and leading to successful invasion.     

Time,space and ecology: why some clades have more species than others

Aim We seek biotic and abiotic explanations for differences in lineage sizes of Afromontane sedges (Cyperaceae, Carex) and buttercups (Ranunculaceae, Ranunculus). Location Mountains of sub‐Saharan Africa and Madagascar. Methods We investigated differences in the species richness and diversification rates of 18 lineages of the pan‐temperate plant groups Carex and Ranunculus, established by long‐distance dispersal on African sky islands. We built generalized linear models to test the individual and the cumulative power of biotic and abiotic factors for predicting variation in the size of lineages. Tested variables were: ages of the lineages, their geographic distributions, number of mountain systems occupied, isolation/distance from ancestral areas, elevation range, number of vegetation zones and habitat types in which lineages are found, light requirement and water availability for each lineage, and the sum of the habitat factors, representing habitat heterogeneity. Habitat conservatism was measured by the overlap in habitats among the species within each lineage. Diversification rate changes were investigated using ‘laser’ in R. Results The number of Carex and Ranunculus lineages on the African mountains accumulated gradually through time. The size of these lineages could best be explained by a model combining age and distribution together with a measure of environmental heterogeneity (either elevation and water availability or habitat heterogeneity). Extensive overlap in environmental characteristics and distribution ranges among the species indicates a relatively high degree of conservatism of these characters. Main conclusions Lineages that are species‐rich are those that have the ability and time to occupy many mountain regions and a wide range of habitats. If allopatric or ecological speciation plays a role, then secondary dispersal and/or niche expansion soon obscures the patterns that may have existed at the point of speciation.     

A plea for more ecology in phytoplankton ecology

When looking for a pattern of phytoplankton behaviour across trophic gradients, we need to cross the boundaries between different disciplinary areas, from autoecology to systems ecology, because eutrophication is a complex process which involves different time scales and different levels of community structure. Thus, we submit our observations to the muddled conceptual world of assemblage ecology. These inaccuracies arise, for example, from both species and community arguments; eutrophication as a fertilization or a metabolic phenomenon; and the notions frequently interwoven of pattern, process and rules. We suggest that it is advantageous to tackle this issue from the perspective of general ecology, rather than from a specifically planktonic orientation. In this way, useful general ecological tools, for example, time series and assembly-rule studies, can be used. Time-series study allows the dynamics of any variable to be described or to show that long term variable fluctuations may sometimes be unregulated, in response to some exogenous factor. Rules of assembly help us to resolve which traits are selectively involved during the eutrophication process. In this context, we advocate (1) the use of traits instead of morphospecies in phytoplankton studies, (2) looking for the dynamic patterns of phytoplankton with eutrophication, (3) the use of time series techniques to study phytoplankton trajectories, (4) the use of assembly rules to discern patterns in the formation of multispecies assemblages, (5) the consideration of the pelagic food-web in studies of phytoplankton dynamics and, as an overall suggestion, to borrow knowledge and inspiration from general ecology.     

Livestock grazing: A matter of ecology

Summary   Agricultural ecology is the study of agricultural systems, their component parts (particularly the ecological components) and their internal and external interactions. This paper explores how we, as a family of graziers, employ ecological principles in agricultural land management, specifically livestock grazing, and illustrates this with some specific farm management practices. Implications are explored for natural resource management policy and practice that endeavours to engage land mangers adept at the practical application of ecological principles in managing their grazing businesses.     

The more the merrier: Multi-species experiments in ecology

A major objective in ecology is to find general patterns, and to establish the rules and underlying mechanisms that generate those patterns. Nevertheless, most of our current insights in ecology are based on case studies of a single or few species, whereas multi-species experimental studies remain rare. We underline the power of the multi-species experimental approach for addressing general ecological questions, e.g. on species environmental responses or on patterns of among- and within-species variation. We present simulations that show that the accuracy of estimates of between-group differences is increased by maximizing the number of species rather than the number of populations or individuals per species. Thus, the more species a multi-species experiment includes, the more powerful it is. In addition, we discuss some inevitable methodological challenges of multi-species experiments. While we acknowledge the value of single- or few-species experiments, we strongly advocate the use of multi-species experiments for addressing ecological questions at a more general level.     

Variation in the outcome of competition between two aphid species on pecan: plants matter more than predators

The relative importance of resource-mediated competition versus apparent competition was studied in two native aphids, Monellia caryella , and Melanocallis caryaefoliae, on pecan, Carya illinoensis . We compared reproduction and body size of the two aphid species when they were caged on pecan leaves as single or mixed species, and when green lacewing larvae ( Chrysoperla comanche or Chyrsopa nigricornis ) were present or absent. The experiment was repeated two times on mature compound leaves in the field in the autumn of 1997 and summer of 1998 and once in a greenhouse, on young seedlings with simple leaves.
Our results suggest that interspecific competition was variable and asymmetric; in both the Summer 98 experiment and the greenhouse experiment, reproduction of M. caryaefoliae was significantly reduced in the mixed species treatments relative to the single species treatment, while M. caryella reproduction was significantly reduced only in the Summer 98 experiment. No evidence of an effect of competition on reproduction was found in the Autumn 97 experiment. M. caryella body size was reduced in one of the mixed species treatments in the Autumn 97 experiment. Body size of both aphid species was reduced in the mixed species treatments of the greenhouse experiment.
The introduction of green lacewing larvae reduced the reproduction of aphids in two of the three experiments in comparison to controls. However, a significant interaction between aphid and predator treatment ( M. caryella in the greenhouse experiment) was found in only one experiment. Variation in the outcome of competition was more likely to be due to aspects of plant quality, including leaf age and previous aphid feeding.     

Stability structures tropical woody plant diversity more than seasonality: Insights into the ecology of high legume-succulent-plant biodiversity

Phylogenies of legume taxa are ecologically structured along a tropical seasonality gradient, which suggests phylogenetic niche conservatism. This seasonality gradient spans Neotropical wet forests, savannas, and highly seasonal drought-prone woody vegetation known as the succulent biome. Ecological phylogenetic structure was investigated using a community phylogenetic approach. We further analyzed bioclimatic and other independent variables that potentially explained phylogenetic beta diversity among 466 floristic sites that spanned the savanna and succulent biomes in eastern South America. Explanatory variables were selected using variance inflation factors, information criteria, and the ability to explain both species and phylogenetic beta diversity. A model involving annual precipitation suggests that a threshold of < 1200 mm explains community phylogenetic structure along the savanna–succulent biome transition. Variables involving temperatures or measures of seasonality were notably lacking from top-ranked models. The abundance and diversity of legumes across the tropical seasonality gradient suggest that a high nitrogen metabolism confers an advantage in one of two ways, both of which are related to rapid growth rates. Legumes adapted to the succulent biome may be responding to regular post-dry-season leaf-flush opportunities. Legumes adapted to the savanna biome may be responding to intermittent post-disturbance growing opportunities. A seasonal predominance of leaf flushing by woody plants implicates the role of ecological stability in the succulent biome because of the need to recover the cost of regenerating short-lived leaves. Ecological stability may be the fundamental cause of ecological phylogenetic structure across the tropical seasonality gradient and required for maintaining high levels of both leaf-flushing legume and succulent plant biodiversity.     

Irradiation to the young mouse brain impaired white matter growth more in females than in males

Modern therapy cures 80% of all children with brains tumors, but may also cause long-lasting side effects, so called late effects. Radiotherapy is particularly prone to cause severe late effects, such as intellectual impairment. The extent and nature of the resulting cognitive deficits may be influenced by age, treatment and gender, where girls suffer more severe late effects than boys. The reason for this difference between boys and girls is unknown, but very few experimental studies have addressed this issue. Our aim was to investigate the effects of ionizing radiation on the corpus callosum (CC) in both male and female mice. We found that a single dose of 8 Gray (Gy) to the brains of postnatal day 14 mice induced apoptosis in the CC and reduced the number of proliferating cells by one third, as judged by the number of phospho-histone H3 positive cells 6 h after irradiation (IR). BrdU incorporation was reduced (62% and 42% lower in females and males, respectively) and the number of oligodendrocytes (Olig2⁺ cells) was lower (43% and 21% fewer in females and males, respectively) 4 months after IR, so the lack of developing and differentiated cells was more pronounced in females. The number of microglia was unchanged in females but increased in males at this late time point. The density of microvessel profiles was unchanged by IR. This single, moderate dose of 8 Gy impaired the brain growth to some extent (8.1% and 0.4% lower brain/body weight ratio in females and males, respectively) but the CC growth was even more impaired (31% and 19% smaller in females and males, respectively) 4 months after IR compared with non-irradiated mice. In conclusion, this is the first study to our knowledge demonstrating that IR to the young rodent brain affects white matter development more in females than in males.     

Clinician gender is more important than gender concordance in quality of HIV care

Background: Previous studies have examined the impact of physician gender and gender concordance on preventive care, satisfaction, and communication. Less is known about how physician gender and gender concordance affect care for chronic illnesses, including HIV.Objective: This study sought to determine whether patient-clinician gender concordance (patient and clinician are of the same gender) influences receipt of protease inhibitor (PI) therapy and ratings of care among HIV-infected patients.Methods: We reviewed data from 1860 patients and 397 clinicians in the HIV Cost and Services Utilization Study, a nationally representative the association between gender concordance and time to first PI use, and multivariable logistic regression was utilized to examine the association of gender concordance with patients' problems with care and their overall rating of care.Results: Patients who had a male clinician received PIs earlier than those who had a female clinician (adjusted time ratio = 0.69 for having a male vs having a female clinician; P ≤ 0.01). Gender concordance was not a significant predictor of time to PI use. Gender discordance was associated with problems with feeling respected by clinicians. Female patients with a male clinician were most likely, and female patients with female clinicians were least likely, to report a problem with being treated with respect (P ≤ 0.01 for the interaction term). Gender discordance was not associated with other problems with care or with overall ratings of care.Conclusions: Gender discordance was associated with perceived problems of being treated with respect by clinicians, but not with time to receipt of PIs, overall ratings of care, coordination of care, or obtaining information. The perception of not being respected may represent a significant barrier to care that is particularly worse for women, in that most HIV-infected women receive their care from male clinicians.     

Growth depression in socially subordinate rainbow trout Oncorhynchus mykiss: more than a fasting effect

To assess the effects of subordinate social status on digestive function, metabolism, and enzyme activity in salmonid fish, juvenile rainbow trout Oncorhynchus mykiss were paired with size-matched conspecifics (<1.5% difference in fork length) for 5 d. Fish that were fasted for 5 d and fish sampled directly from the holding tank were used as control groups. Both subordinate and fasted fish experienced significant decreases in intestine mass (P = 0.043), and the gall bladder showed marked and significant changes in both size (P = 0.004) and appearance. These findings suggest that the negative effect of social subordination on digestive function reflects in large part a lack of feeding. Hepatic phosphoenolpyruvate carboxykinase activity was significantly higher in subordinate fish relative to dominants, whereas subordinate hepatic pyruvate kinase activity was significantly lower; activities of both enzymes were significantly correlated with plasma cortisol concentrations and behavior scores. Dominant-subordinate differences in the activities of these enzymes were eliminated by administration of the glucocorticoid receptor antagonist RU486, underlining a role for circulating cortisol in eliciting the differences. Significant increases relative to control fish were also detected in red and white muscles from subordinate fish in the activities of protein catabolic enzymes (aspartate aminotransferase, alanine aminotransferase, glutamate dehydrogenase). These differences occurred in the absence of any change in plasma free amino acid or ammonia concentrations, supporting an enhanced turnover of amino acids in muscle in subordinate fish. The results support the hypothesis that changes in metabolism, beyond those elicited by low food consumption, may be responsible at least in part for the low growth rates typical of subordinate fish and that these changes may be related specifically to circulating cortisol levels in subordinate fish.     

Lysosomal cysteine proteases: more than scavengers

Lysosomal cysteine proteases were believed to be mainly involved in intracellular protein degradation. Under special conditions they have been found outside lysosomes resulting in pathological conditions. With the discovery of a series of new cathepsins with restricted tissue distributions, it has become evident that these enzymes must be involved in a range of specific cellular tasks much broader than as simple housekeeping enzymes. It is therefore timely to review and discuss the various physiological roles of mammalian lysosomal papain-like cysteine proteases as well as their mechanisms of action and the regulation of their activity.     

Telomeres: more than chromosomal non-sticking ends

Telomeres are specialized natural ends of eukaryotic chromosomes that, contrary to the ends of broken chromosomes, are stable and do not fuse with the ends of other chromosomes. In addition, telomeres protect chromosomal ends from degradation, facilitate completion of chromosomal DNA replication, and contribute to chromosome positioning within nuclei. Telomeric DNA consists of repetitive sequences and specific associated proteins, including the telomere repeat-binding factors TRF1 and TRF2. A lack of TRF2 enables end-to-end chromosome fusion. A structural disruption of telomeres not only causes chromosomal mechanical instability but also activates a programmed cell death cascade.     

Spindle assembly: more than just microtubules

Do actin dynamics play an active role in mitotic spindle assembly? A new study demonstrates that cortical actin polymerization assists with the earliest phase of spindle pole migration.