Typing method for N2-fixing bacteria based on PCR-F — application to the characterization of Frankia strains

DNA sequences of an intergenic spacer (IGS) and parts of genes in the nif cluster were amplified by the polymerase chain reaction (PCR) using two primers derived from nifD -and nifK -conserved sequences. The PCR products were cleaved by ten 4–base cutting restriction enzymes and the restriction patterns were used as fingerprints to type Frankia strains. The feasability of this PCR-RFLP method for typing Frankia strains was investigated on Frankia reference strains belonging mainly to the Elaeagnaceae infectivity group but also on new Frankia isolates and on other N₂-fixing microorganisms. By modulating the stringency of the amplifications, we showed the method allowed to target either Frankia strains or the whole N₂-fixing microbial community. DNA digestion patterns were used to estimate the sequence divergence between the Frankia nifD-K fragment. The estimated relationships deduced from these genotypic data correlated well with established Frankia taxonomic schemes.     

A phylogenetic analysis of the monogenomic Triticeae (Poaceae) based on morphology

A cladistic analysis, primarily based on morphology, is presented from 40 diploid taxa representing the 24 monogenomic genera of the Triticeae. General problems related to the treatment of hybrids and supposedly allopolyploid heterogenomic taxa are highlighted. Special emphasis is given to taxa not traditionally included in Aegilops s.J. Most of the 33 characters used in the analysis are coded as binary. The only four multistate characters in the matrix are treated as unordered. Three diploid species of Bromus are used as outgroup. The number of equally parsimonious trees found is very large (approx. 170000; length = 107, ci = 0.36, ri = 0.75) and the strict consensus tree has an expectedly low level of resolution. However, most of the equally parsimonious trees owe their existence to an unresolved Aegilops clade. If this clade is replaced by its hypothetical ancestor, the number of equally parsimonious trees drops dramatically (48; length = 78, ci = 0.45, ri = 0.76). When trees for which more highly resolved compatible trees exist are excluded, only two trees remain. Bremer support is used as a measure of branch support. The trees based on morphology and on molecular data are largely incongruent.     

Landscape genetics, historical isolation and cross-Andean gene flow in the wax palm, Ceroxylon echinulatum (Arecaceae)

Knowledge of the role of landscapes in shaping genetic connectivity and divergence is essential for understanding patterns of biogeography and diversity. This is particularly relevant for the Andes region, a major biodiversity hotspot of relatively recent origin. We examined the phylogeography and landscape genetics of the Andean wax palm Ceroxylon echinulatum (Arecaceae) that occurs in two narrow bands of montane forests on each side of the Andes in Ecuador and northeastern Peru. First, we tested the hypothesis of C. echinulatum being a geographic cline species crossing the Andes in the Amotape–Huancabamba zone (AHZ) of southern Ecuador/northern Peru, as indicated by observations on fruit morphology. Second, we assessed the timeframe of cross-Andean divergence, and third, we investigated the impact of contemporary and historical landscape features on observed spatio-genetic patterns. Individual-based Bayesian clustering (BC) identified a northeastern, southeastern, southwestern, and northwestern cluster, with areas of genetic discontinuity coinciding with the Andes and the Giron–Paute deflection. F -statistics derived from BC suggested an east-to-west dispersal history. Population-based analyses revealed strong genetic structuring at both small and large geographic scales. Interpopulation relationships and Mantel tests strongly supported the cline model with cross-Andean dispersal in the AHZ. Along the cline, gene flow measured as F _ST was mainly limited by distance, with less but significant impact of climatic friction. Coalescent analysis revealed that cross-Andean divergence took place during the Quaternary. Significant historical isolation ( R _ST >  F _ST) was found in the southwestern population. The current study illustrates a joint effect of founder dynamics, divergence by distance and historical isolation on patterns of Andean diversity and distribution.     

Crassulacean acid metabolism contributes significantly to the in situ carbon budget in a population of the invasive aquatic macrophyte Crassula helmsii

1. The ecophysiological significance of Crassulacean acid metabolism (CAM) in the invasive aquatic macrophyte Crassula helmsii was studied in an English soft‐water lake. The extent and the contribution of CAM to the carbon budget was examined in spring (April) and summer (July) along a depth gradient (0.5–2.2 m), covering the growth range of C. helmsii in the lake. 2. Significant in situ CAM activity (30–80 meq kg⁻¹ FW) was present in all specimens, although it decreased with depth and hence correlated with the decline in photon irradiance. Potential CAM activity (60–161 meq kg⁻¹ FW), measured after exposure to low concentrations of CO₂ in the day and high concentrations at night, were on average 2.7‐times greater than in situ CAM activity. Overall CAM activity increased from April to July, which is consistent with higher potential carbon limitation caused by increased temperature and light availability. 3. CAM activity in C. helmsii appeared to be carbon‐limited at night because night‐time carbon‐fixation increased at raised, compared to ambient, concentrations of CO₂. 4. The high in situ CAM activity in C. helmsii was reflected in the contribution of CAM to the total carbon budget which, independent of depth and season, ranged from 18% to 42%. The amount of CO₂ taken up in the night via CAM was 0.74 to 2.94 times the amount of CO₂ lost in respiration, thus emphasizing the importance of CAM in refixation of potentially lost respiratory CO₂. 5. The onset of decarboxylation in the morning appeared to be under circadian control as there was a delay of up to 5.5 h between the start of the light period and a decline in cell acidity level. 6. There was little variation in δ¹³C content (−21.69 to 23.49‰) with season or depth suggesting, along with the estimated contribution to the carbon‐budget, that CAM is important for the whole population of C. helmsii. CAM may confer a competitive advantage in relation to growth, which may be one of the reasons for the invasiveness of this species.     

Climate change and plant distribution: local models predict high-elevation persistence

Mountain ecosystems will likely be affected by global warming during the 21st century, with substantial biodiversity loss predicted by species distribution models (SDMs). Depending on the geographic extent, elevation range, and spatial resolution of data used in making these models, different rates of habitat loss have been predicted, with associated risk of species extinction. Few coordinated across-scale comparisons have been made using data of different resolutions and geographic extents. Here, we assess whether climate change-induced habitat losses predicted at the European scale (10 × 10' grid cells) are also predicted from local-scale data and modeling (25 m × 25 m grid cells) in two regions of the Swiss Alps. We show that local-scale models predict persistence of suitable habitats in up to 100% of species that were predicted by a European-scale model to lose all their suitable habitats in the area. Proportion of habitat loss depends on climate change scenario and study area. We find good agreement between the mismatch in predictions between scales and the fine-grain elevation range within 10 × 10' cells. The greatest prediction discrepancy for alpine species occurs in the area with the largest nival zone. Our results suggest elevation range as the main driver for the observed prediction discrepancies. Local-scale projections may better reflect the possibility for species to track their climatic requirement toward higher elevations.     

The nodular endophytes of Coriaria spp. form a distinct lineage within the genus Frankia

Repeated attempts at isolating the Frankia endophyte of Coriaria spp. have not yielded infective microbial cultures that could fulfil Koch's postulates. In order to circumvent the critical isolation step, nodule endophytes of Coriaria were characterized directly by means of specific amplification of nodule DNA (PCR) followed by sequencing of part of the 16S rDNA gene. Three closely related sequences were obtained from nodules originating from France, Mexico and New Zealand, containing unique sequences different from all other Frankia strains characterized so far. The sequences obtained were closest (with 5 or 6 substitutions) to those of Frankia alni and those of Casuarina-infective Frankia strains, respectively. Two nucleotides unique to the Coriaria endophyte sequences were used to define specific primers, resulting in a hybridization test that could discriminate between Frankia DNAs originating from Coriaria nodules and those recovered from all cultured Frankia strains tested. The endophytes of Coriaria thus appear to form a distinct Frankia lineage.     

21st century climate change threatens mountain flora unequally across Europe

Continental‐scale assessments of 21st century global impacts of climate change on biodiversity have forecasted range contractions for many species. These coarse resolution studies are, however, of limited relevance for projecting risks to biodiversity in mountain systems, where pronounced microclimatic variation could allow species to persist locally, and are ill‐suited for assessment of species‐specific threat in particular regions. Here, we assess the impacts of climate change on 2632 plant species across all major European mountain ranges, using high‐resolution (ca. 100 m) species samples and data expressing four future climate scenarios. Projected habitat loss is greater for species distributed at higher elevations; depending on the climate scenario, we find 36–55% of alpine species, 31–51% of subalpine species and 19–46% of montane species lose more than 80% of their suitable habitat by 2070–2100. While our high‐resolution analyses consistently indicate marked levels of threat to cold‐adapted mountain florae across Europe, they also reveal unequal distribution of this threat across the various mountain ranges. Impacts on florae from regions projected to undergo increased warming accompanied by decreased precipitation, such as the Pyrenees and the Eastern Austrian Alps, will likely be greater than on florae in regions where the increase in temperature is less pronounced and rainfall increases concomitantly, such as in the Norwegian Scandes and the Scottish Highlands. This suggests that change in precipitation, not only warming, plays an important role in determining the potential impacts of climate change on vegetation.     

Spatial variability in macroinvertebrate assemblages along and among neighbouring equatorial glacier‐fed streams

1. During the past two decades, understanding of the structure and function of glacier‐fed stream ecosystems at temperate latitudes has increased substantially. In contrast, information on their tropical counterparts is very limited. We studied three neighbouring glacier‐fed streams in the tropical Andes of Ecuador. Our main goals were (i) to determine overall longitudinal patterns in density, taxon richness and the composition of macroinvertebrate assemblages and driving factors in equatorial glacial streams and (ii) to examine variability among replicate streams in faunal metrics and assemblages, and stream‐specific effects of supposed environmental key factors. 2. We measured four geographical and 17 environmental factors and collected five Surber samples (500 cm²) of macroinvertebrates at each of nine sites, three sites along three streams. The streams were located 1–5 km apart. In each stream, the three sites were placed at comparable distances from the glacier and were grouped as ‘upper’ (50–200 m), ‘middle’ (1.5 km) and ‘lower’ sites (3.5–5.6 km). 3. In total, 2200 individuals (64% chironomids) were collected and 47 taxa (30 dipterans, 18 of these Chironomidae) identified. Density ranged from 176 to 372 ind. m^?2, and the number of taxa ranged from 2 to 6 at the upper sites and 868–3044 ind. m^?2 and 21–27 taxa at the lower sites. Density, number of taxa, rarefied richness and axis‐1 coordinates from a MDS ordination increased logarithmically with distance from the glacier. These faunal metrics were equally related to altitude and glacier per cent of catchment and correlated with maximum conductivity, mean temperature, mean daily maximum temperature and a channel stability index. As expected, the mean difference in distance decay in similarity was higher at the upper (47% km^?1) than at the lower reaches (20% km^?1) of the streams. 4. The number of taxa varied among sites within the upper and middle groups, but not among the lower sites. In contrast, but in accordance with our expectation, assemblage composition did not differ among upper sites but did so at middle and lower sites, following a supposed decrease in environmental harshness along the streams. Relationships between faunal metrics and the four environmental variables mean temperature, the stability index, chlorophyll a and coarse particulate organic matter also varied among the three streams. Generalised linear model analyses revealed that temperature interacted with stream on macroinvertebrate density, while chlorophyll a had a significant effect on the number of taxa in interaction with stream and stability. 5. The basic predictions of the Milner et al. (2001a) , model regarding longitudinal faunal patterns and temperature and stability as main driving factors were met by our three replicate equatorial glacial streams. Qualitative departures from the model were mainly because of zoogeographical differences. We demonstrated that variability in assemblages between comparable sites in closely situated streams was considerable, and the effect of key environmental factors varied among streams and interacted with other factors. Quantifying spatial variation in benthic assemblages may help us foresee possible consequences for biodiversity as a result of glacial retreat.