Improving the prediction of plant species distribution and community composition by adding edaphic to topo-climatic variables

Questions Soil properties have been widely shown to influence plant growth and distribution. However, the degree to which edaphic variables can improve models based on topo-climatic variables is still unclear. In this study, we tested the roles of seven edaphic variables, namely (1) pH; (2) the content of nitrogen and of (3) phosphorus; (4) silt; (5) sand; (6) clay and (7) carbon-to-nitrogen ratio, as predictors of species distribution models in an edaphically heterogeneous landscape. We also tested how the respective influence of these variables in the models is linked to different ecological and functional species characteristics. Location The Western Alps, Switzerland. Methods With four different modelling techniques, we built models for 115 plant species using topo-climatic variables alone and then topo-climatic variables plus each of the seven edaphic variables, one at a time. We evaluated the contribution of each edaphic variable by assessing the change in predictive power of the model. In a second step, we evaluated the importance of the two edaphic variables that yielded the largest increase in predictive power in one final set of models for each species. Third, we explored the change in predictive power and the importance of variables across plant functional groups. Finally, we assessed the influence of the edaphic predictors on the prediction of community composition by stacking the models for all species and comparing the predicted communities with the observed community. Results Among the set of edaphic variables studied, pH and nitrogen content showed the highest contributions to improvement of the predictive power of the models, as well as the predictions of community composition. When considering all topo-climatic and edaphic variables together, pH was the second most important variable after degree-days. The changes in model results caused by edaphic predictors were dependent on species characteristics. The predictions for the species that have a low specific leaf area, and acidophilic preferences, tolerating low soil pH and high humus content, showed the largest improvement by the addition of pH and nitrogen in the model. Conclusions pH was an important predictor variable for explaining species distribution and community composition of the mountain plants considered in our study. pH allowed more precise predictions for acidophilic species. This variable should not be neglected in the construction of species distribution models in areas with contrasting edaphic conditions.

Accuracy of plant assemblage predictions from species distribution models varies along environmental gradients

Aim: Climatic niche modelling of species and community distributions implicitly assumes strong and constant climatic determinism across geographic space. This assumption had however never been tested so far. We tested it by assessing how stacked-species distribution models (S-SDMs) perform for predicting plant species assemblages along elevation. Location: Western Swiss Alps. Methods: Using robust presence-absence data, we first assessed the ability of topo-climatic S-SDMs to predict plant assemblages in a study area encompassing a 2800 m wide elevation gradient. We then assessed the relationships among several evaluation metrics and trait-based tests of community assembly rules. Results: The standard errors of individual SDMs decreased significantly towards higher elevations. Overall, the S-SDM overpredicted far more than they underpredicted richness and could not reproduce the humpback curve along elevation. Overprediction was greater at low and mid-range elevations in absolute values but greater at high elevations when standardised by the actual richness. Looking at species composition, the evaluation metrics accounting for both the presence and absence of species (overall prediction success and kappa) or focusing on correctly predicted absences (specificity) increased with increasing elevation, while the metrics focusing on correctly predicted presences (Jaccard index and sensitivity) decreased. The best overall evaluation - as driven by specificity - occurred at high elevation where species assemblages were shown to be under significant environmental filtering of small plants. In contrast, the decreased overall accuracy in the lowlands was associated with functional patterns representing any type of assembly rule (environmental filtering, limiting similarity or null assembly). Main Conclusions: Our study reveals interesting patterns of change in S-SDM errors with changes in assembly rules along elevation. Yet, significant levels of assemblage prediction errors occurred throughout the gradient, calling for further improvement of SDMs, e.g., by adding key environmental filters that act at fine scales and developing approaches to account for variations in the influence of predictors along environmental gradients.

Impact of preoperative risk factors on morbidity after esophagectomy: is there room for improvement?

BACKGROUND: Despite progress in multidisciplinary treatment of esophageal cancer, oncologic esophagectomy is still the cornerstone of therapeutic strategies. Several scoring systems are used to predict postoperative morbidity, but in most cases they identify nonmodifiable parameters. The aim of this study was to identify potentially modifiable risk factors associated with complications after oncologic esophagectomy. METHODS: All consecutive patients with complete data sets undergoing oncologic esophagectomy in our department during 2001-2011 were included in this study. As potentially modifiable risk factors we assessed nutritional status depicted by body mass index (BMI) and preoperative serum albumin levels, excessive alcohol consumption, and active smoking. Postoperative complications were graded according to a validated 5-grade system. Univariate and multivariate analyses were used to identify preoperative risk factors associated with the occurrence and severity of complications. RESULTS: Our series included 93 patients. Overall morbidity rate was 81 % (n = 75), with 56 % (n = 52) minor complications and 18 % (n = 17) major complications. Active smoking and excessive alcohol consumption were associated with the occurrence of severe complications, whereas BMI and low preoperative albumin levels were not. The simultaneous presence of two or more of these risk factors significantly increased the risk of postoperative complications. CONCLUSIONS: A combination of malnutrition, active smoking and alcohol consumption were found to have a negative impact on postoperative morbidity rates. Therefore, preoperative smoking and alcohol cessation counseling and monitoring and improving the nutritional status are strongly recommended.

Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis.

The mutualistic symbiosis involving Glomeromycota, a distinctive phylum of early diverging Fungi, is widely hypothesized to have promoted the evolution of land plants during the middle Paleozoic. These arbuscular mycorrhizal fungi (AMF) perform vital functions in the phosphorus cycle that are fundamental to sustainable crop plant productivity. The unusual biological features of AMF have long fascinated evolutionary biologists. The coenocytic hyphae host a community of hundreds of nuclei and reproduce clonally through large multinucleated spores. It has been suggested that the AMF maintain a stable assemblage of several different genomes during the life cycle, but this genomic organization has been questioned. Here we introduce the 153-Mb haploid genome of Rhizophagus irregularis and its repertoire of 28,232 genes. The observed low level of genome polymorphism (0.43 SNP per kb) is not consistent with the occurrence of multiple, highly diverged genomes. The expansion of mating-related genes suggests the existence of cryptic sex-related processes. A comparison of gene categories confirms that R. irregularis is close to the Mucoromycotina. The AMF obligate biotrophy is not explained by genome erosion or any related loss of metabolic complexity in central metabolism, but is marked by a lack of genes encoding plant cell wall-degrading enzymes and of genes involved in toxin and thiamine synthesis. A battery of mycorrhiza-induced secreted proteins is expressed in symbiotic tissues. The present comprehensive repertoire of R. irregularis genes provides a basis for future research on symbiosis-related mechanisms in Glomeromycota.

Promise for plant pest control: root-associated pseudomonads with insecticidal activities.

Insects are an important and probably the most challenging pest to control in agriculture, in particular when they feed on belowground parts of plants. The application of synthetic pesticides is problematic owing to side effects on the environment, concerns for public health and the rapid development of resistance. Entomopathogenic bacteria, notably Bacillus thuringiensis and Photorhabdus/Xenorhabdus species, are promising alternatives to chemical insecticides, for they are able to efficiently kill insects and are considered to be environmentally sound and harmless to mammals. However, they have the handicap of showing limited environmental persistence or of depending on a nematode vector for insect infection. Intriguingly, certain strains of plant root-colonizing Pseudomonas bacteria display insect pathogenicity and thus could be formulated to extend the present range of bioinsecticides for protection of plants against root-feeding insects. These entomopathogenic pseudomonads belong to a group of plant-beneficial rhizobacteria that have the remarkable ability to suppress soil-borne plant pathogens, promote plant growth, and induce systemic plant defenses. Here we review for the first time the current knowledge about the occurrence and the molecular basis of insecticidal activity in pseudomonads with an emphasis on plant-beneficial and prominent pathogenic species. We discuss how this fascinating Pseudomonas trait may be exploited for novel root-based approaches to insect control in an integrated pest management framework.

Biodiversity of amoebae and amoebae-resisting bacteria in a drinking water treatment plant

The complex ecology of free-living amoebae (FLA) and their role in spreading pathogenic microorganisms through water systems have recently raised considerable interest. In this study, we investigated the presence of FLA and amoebae-resisting bacteria (ARB) at various stages of a drinking water plant fed with river water. We isolated various amoebal species from the river and from several points within the plant, mostly at early steps of water treatment. Echinamoeba- and Hartmannella-related amoebae were mainly recovered in the drinking water plant whereas Acanthamoeba- and Naegleria-related amoebae were recovered from the river water and the sand filtration units. Some FLA isolates were recovered immediately after the ozonation step, thus suggesting resistance of these microorganisms to this disinfection procedure. A bacterial isolate related to Mycobacterium mucogenicum was recovered from an Echinamoeba-related amoeba isolated from ozone-treated water. Various other ARB were recovered using co-culture with axenic Acanthamoeba castellanii, including mycobacteria, legionella, Chlamydia-like organisms and various proteobacteria. Noteworthy, a new Parachlamydia acanthamoebae strain was recovered from river water and from granular activated carbon (GAC) biofilm. As amoebae mainly multiply in sand and GAC filters, optimization of filter backwash procedures probably offers a possibility to better control these protists and the risk associated with their intracellular hosts

Importance of sequences adjacent to the terminal tripeptide in the import of a peroxisomal Candida tropicalis protein in plant peroxisomes.

The peroxisome targeting signal (PTS) required for import of the rat acyl-CoA oxidase (AOX; EC 1.3.3.6) and the Candida tropicalis multifunctional protein (MFP) in plant peroxisomes was assessed in transgenic Arabidopsis thaliana (L.) Heynh. The native rat AOX accumulated in peroxisomes in A. thaliana cotyledons and targeting was dependent on the presence of the C-terminal tripeptide S-K-L. In contrast, the native C. tropicalis MFP, containing the consensus PTS sequence A-K-I was not targeted to plant peroxisomes. Modification of the carboxy terminus to the S-K-L tripeptide also failed to deliver the MFP to peroxisomes while addition of the last 34 amino acids of the Brassica napus isocitrate lyase, containing the terminal tripeptide S-R-M, enabled import of the fusion protein into peroxisomes. These results underline the influence of the amino acids adjacent to the terminal tripeptide of the C. tropicalis MFP on peroxisomal targeting, even in the context of a protein having a consensus PTS sequence S-K-L.

The endodermis--development and differentiation of the plant's inner skin.

Controlling external compound entrance is essential for plant survival. To set up an efficient and selective sorting of nutrients, free diffusion via the apoplast in vascular plants is blocked at the level of the endodermis. Although we have learned a lot about endodermal specification in the last years, information regarding its differentiation is still very limited. A differentiated endodermal cell can be defined by the presence of the "Casparian strip" (CS), a cell wall modification described first by Robert Caspary in 1865. While the anatomical description of CS in many vascular plants has been very detailed, we still lack molecular information about the establishment of the Casparian strips and their actual function in roots. The recent isolation of a novel protein family, the CASPs, that localizes precisely to a domain of the plasma membrane underneath the CS represents an excellent point of entry to explore CS function and formation. In addition, it has been shown that the endodermis contains transporters that are localized to either the central (stele-facing) or peripheral (soil-facing) plasma membranes. These features suggest that the endodermis functions as a polar plant epithelium.

Recent plant diversity changes on Europe's mountain summits.

In mountainous regions, climate warming is expected to shift species' ranges to higher altitudes. Evidence for such shifts is still mostly from revisitations of historical sites. We present recent (2001 to 2008) changes in vascular plant species richness observed in a standardized monitoring network across Europe's major mountain ranges. Species have moved upslope on average. However, these shifts had opposite effects on the summit floras' species richness in boreal-temperate mountain regions (+3.9 species on average) and Mediterranean mountain regions (-1.4 species), probably because recent climatic trends have decreased the availability of water in the European south. Because Mediterranean mountains are particularly rich in endemic species, a continuation of these trends might shrink the European mountain flora, despite an average increase in summit species richness across the region.

Climate change effects on animal and plant phylogenetic diversity in southern Africa

Much attention has been paid to the effects of climate change on species' range reductions and extinctions. There is however surprisingly little information on how climate change driven threat may impact the tree of life and result in loss of phylogenetic diversity (PD). Some plant families and mammalian orders reveal nonrandom extinction patterns, but many other plant families do not. Do these discrepancies reflect different speciation histories and does climate induced extinction result in the same discrepancies among different groups? Answers to these questions require representative taxon sampling. Here, we combine phylogenetic analyses, species distribution modeling, and climate change projections on two of the largest plant families in the Cape Floristic Region (Proteaceae and Restionaceae), as well as the second most diverse mammalian order in Southern Africa (Chiroptera), and an herbivorous insect genus (Platypleura) in the family Cicadidae to answer this question. We model current and future species distributions to assess species threat levels over the next 70years, and then compare projected with random PD survival. Results for these animal and plant clades reveal congruence. PD losses are not significantly higher under predicted extinction than under random extinction simulations. So far the evidence suggests that focusing resources on climate threatened species alone may not result in disproportionate benefits for the preservation of evolutionary history.

Shifts in species richness, herbivore specialization, and plant resistance along elevation gradients.

Environmental gradients have been postulated to generate patterns of diversity and diet specialization, in which more stable environments, such as tropical regions, should promote higher diversity and specialization. Using field sampling and phylogenetic analyses of butterfly fauna over an entire alpine region, we show that butterfly specialization (measured as the mean phylogenetic distance between utilized host plants) decreases at higher elevations, alongside a decreasing gradient of plant diversity. Consistent with current hypotheses on the relationship between biodiversity and the strength of species interactions, we experimentally show that a higher level of generalization at high elevations is associated with lower levels of plant resistance: across 16 pairs of plant species, low-elevation plants were more resistant vis-à-vis their congeneric alpine relatives. Thus, the links between diversity, herbivore diet specialization, and plant resistance along an elevation gradient suggest a causal relationship analogous to that hypothesized along latitudinal gradients.

Variation in habitat suitability does not always relate to variation in species' plant functional traits.

Habitat suitability models, which relate species occurrences to environmental variables, are assumed to predict suitable conditions for a given species. If these models are reliable, they should relate to change in plant growth and function. In this paper, we ask the question whether habitat suitability models are able to predict variation in plant functional traits, often assumed to be a good surrogate for a species' overall health and vigour. Using a thorough sampling design, we show a tight link between variation in plant functional traits and habitat suitability for some species, but not for others. Our contrasting results pave the way towards a better understanding of how species cope with varying habitat conditions and demonstrate that habitat suitability models can provide meaningful descriptions of the functional niche in some cases, but not in others.

Computer-assisted placement technique in hip resurfacing arthroplasty: improvement in accuracy?

Freehand positioning of the femoral drill guide is difficult during hip resurfacing and the surgeon is often unsure of the implant position achieved peroperatively. The purpose of this study was to find out whether, by using a navigation system, acetabular and femoral component positioning could be made easier and more precise. Eighteen patients operated on by the same surgeon were matched by sex, age, BMI, diagnosis and ASA score (nine patients with computer assistance, nine with the regular ancillary). Pre-operative planning was done on standard AP and axial radiographs with CT scan views for the computer-assisted operations. The final position of implants was evaluated by the same radiographs for all patients. The follow-up was at least 1 year. No difference between both groups in terms of femoral component position was observed (p > 0.05). There was also no difference in femoral notching. A trend for a better cup position was observed for the navigated hips, especially for cup anteversion. There was no additional operating time for the navigated hips. Hip navigation for resurfacing surgery may allow improved visualisation and hip implant positioning, but its advantage probably will be more obvious with mini-incisions than with regular incision surgery.

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita.

Plant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them are sorely needed. We report the draft genome sequence of the root-knot nematode Meloidogyne incognita, a biotrophic parasite of many crops, including tomato, cotton and coffee. Most of the assembled sequence of this asexually reproducing nematode, totaling 86 Mb, exists in pairs of homologous but divergent segments. This suggests that ancient allelic regions in M. incognita are evolving toward effective haploidy, permitting new mechanisms of adaptation. The number and diversity of plant cell wall-degrading enzymes in M. incognita is unprecedented in any animal for which a genome sequence is available, and may derive from multiple horizontal gene transfers from bacterial sources. Our results provide insights into the adaptations required by metazoans to successfully parasitize immunocompetent plants, and open the way for discovering new antiparasitic strategies.