Geodermatophilus chilensis sp. nov., from soil of the Yungay core-region of the Atacama Desert,Chile

A polyphasic study was undertaken to establish the taxonomic status of three representative Geodermatophilus strains isolated from an extreme hyper-arid Atacama Desert soil. The strains, isolates B12^T, B20 and B25, were found to have chemotaxonomic and morphological properties characteristic of the genus Geodermatophilus. The isolates shared a broad range of chemotaxonomic, cultural and physiological features, formed a well-supported branch in the Geodermatophilus 16S rRNA gene tree in which they were most closely associated with the type strain of Geodermatophilus obscurus. They were distinguished from the latter by BOX-PCR fingerprint patterns and by chemotaxonomic and other phenotypic properties. Average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between the whole genome sequences of isolate B12^T and G. obscurus DSM 43160^T were 89.28%, 87.27% and 37.4%, respectively, metrics consistent with its classification as a separate species. On the basis of these data, it is proposed that the isolates be assigned to the genus Geodermatophilus as Geodermatophilus chilensis sp. nov. with isolate B12^T (CECT 9483^T = NCIMB 15089^T) as the type strain. Analysis of the whole genome sequence of G. chilensis B12^T with 5341 open reading frames and a genome size of 5.5 Mb highlighted genes and gene clusters that encode for properties relevant to its adaptation to extreme environmental conditions prevalent in extreme hyper-arid Atacama Desert soils.     

Biogeographic diversification in Nolana （Solanaceae）, a ubiquitous member of the Atacama and Peruvian Deserts along the western coast of South America

The present paper reconstructs the biogeographic diversification for Nolana L.f. （Solanaceae）, a genus of 89 endemic species largely restricted to fog-dependent desert lomas formations of coastal Peru and Chile. Previous efforts have reconstructed a phylogenetic estimate for Nolana using a combination of molecular markers. Herein, we expand on those results to examine hypotheses of biogeographic origins and diversification patterns. Nolana occupies habitats within a continuous coastal desert and forms a terrestrial archipelago of discrete ＂islands＂ unique in size, topography, and species composition. Each locality contains at least one Nolana species and many contain multiple species in sympatry. The genus has a Chilean origin, with the basal clades confined to Chile with wide geographic and ecological distributions. Peru contains two strongly supported clades, suggesting two introductions with subsequent radiation. A Chilean clade of shrubby, small-flowered species appears to have had its origins from the same ancestors of the second line that radiated in Peru and northern Chile. Nolana galapagensis is endemic to the Islas Galapagos, with origins traced to Peruvian taxa with a divergence time of 0.35 mya. Rates of diversification over the past 4.02 mya in Nolana, in one of the driest habitats on Earth, suggest rapid adaptive radiation in several clades. Success in Nolana may be attributed to characters that confer a competitive advantage in unpredictable and water-dependent environments, such as succulent leaf anatomy and ecophysiology, and the reproductive mericarp unique to Nolana. The processes affecting or shaping the biota of western South America are discussed.     

Phylogenetic Profiling and Diversity of Bacterial Communities in the Death Valley,an Extreme Habitat in the Atacama Desert

The Atacama Desert, one of the driest deserts in the world, represents a unique extreme environmental ecosystem to explore the bacterial diversity as it is considered to be at the dry limit for life. A 16S rRNA gene (spanning the hyper variable V3 region) library was constructed from an alkaline sample of unvegetated soil at the hyperarid margin in the Atacama Desert. A total of 244 clone sequences were used for MOTHUR analysis, which revealed 20 unique phylotypes or operational taxonomic units (OTUs). V3 region amplicons of the 16S rRNA were suitable for distinguishing the bacterial community to the genus and specie level. We found that all OTUs were affiliated with taxa representative of the Firmicutes phylum. The extremely high abundance of Firmicutes indicated that most bacteria in the soil were spore-forming survivors. In this study we detected a narrower diversity as compared to other ecological studies performed in other areas of the Atacama Desert. The reported genera were Oceanobacillus (representing the 69.5 % of the clones sequenced), Bacillus, Thalassobacillus and Virgibacillus. The present work shows physical and chemical parameters have a prominent impact on the microbial community structure. It constitutes an example of the communities adapted to live in extreme conditions caused by dryness and metal concentrations .

Electronic supplementary material

The online version of this article (doi:10.1007/s12088-015-0539-3) contains supplementary material, which is available to authorized users.     

Modelling the effect of soil moisture on germination and emergence of wheat and sugar beet with the minimum number of parameters

Soil moisture and temperature, sowing depth and penetration resistance affect the time and percentage of seedling emergence, which are crucial for the simulation of drought‐limited crop production. The aim of this research was to measure the effect of soil water potential on germination and emergence, shoot and root elongation rates (SER and RER) of two different seed/crop types. Sugar beet and durum wheat seeds were sown into two soils (clay and loam), submitted to five matric potentials (?0.01, ?0.1, ?0.2, ?0.4 and ?0.8 MPa) and incubated at constant temperature (25°C) and humidity. Cumulative count analysis was used to estimate parameters of the distribution of germination or emergence times for each box of beet or wheat seeds and to derive estimates for base potentials (ψ_b), hydrothermal times (H) and numbers of viable units. In a second experiment, NaCl solution was used to mimic the soil matric potentials to estimate potential RER and SER. Germination of sugar beet was slightly more sensitive to matric potential than durum wheat (ψ_b of ?1.13 and ?1.23 MPa, respectively). H_(g) was longer for sugar beet than for durum wheat (67 vs 47 MPa °Cd). For emergence ψ_b was similar for both seed types and soils but hydrothermal times (H_(e)) were 40 MPa °Cd higher for sugar beet than for wheat. Emergence was about 20 MPa °Cd earlier in loam than in clay. SER measured in soils were similar for both crops and for durum wheat it agreed with those determined in NaCl solution. RER and SER fell with decreasing osmotic potential to approximately 20% of their maximum values (1.03 mm h^?1 and 0.57 mm h^?1, respectively). Seedling viability decreased with decreasing matric potential and more in clay than in loam soil and more for sugar beet than durum wheat. Seed and soil aggregate size are discussed with respect to the effects of water diffusion and soil–seed contact on germination and emergence modelling.     

The effect of type of shade on physiology,behaviour and performance of grazing steers

Research has addressed the issue of type of shade mainly on feedlots and high-producing dairy farms, but more studies are needed on the impact of shade on grazing beef cattle in a low-to-medium plane of nutrition. A 63-day grazing study using 24 British steers (268±4 kg) was undertaken in Uruguay (33°14'S, 54°15'W) to determine the effect of type of artificial shade on tympanic temperature (TT), behaviour and performance during summer. Cattle were allocated to six paddocks with an area of 2.5 ha each (four steers/paddock) continuously grazed. Treatments (two paddocks/treatment) were unshaded (US) and shaded with either 35% (35S) or 80% (80S) blockage of solar radiation. TT was recorded during 12 days placing an automatic device near the tympanic membrane inside the animal’s ear. Animal behaviours were measured by live observations of animals every 15 min from 1100 to 1600 h six times during the experimental period. According to the temperature–humidity index (THI), cattle was in the ‘normal’ category (THI<70, absence of heat stress) during 50% of the time, the rest being exposed to some degree of heat stress including 15% of the time with environmental conditions. Black globe temperature and surface soil temperature decreased as solar protection increased under the shade structure. Steers spent more time under the 80S structure than under the 35S between 1100 and 1600 h (83% and 49% of the time, respectively). Average 24-h TT did not differ among treatments (mean±s.e. 38.79±0.04ºC). Minimum TT was registered at 0700 h for all treatments (37.92±0.08ºC), whereas maximum TT was reached at 1700 h for both control group (39.73±0.18ºC) and 35% shade (39.48±0.12ºC) and at 1900 h for 80% shade (39.57±0.15ºC). Neither the provision nor the type of shade affected animal performance (0.622±0.060 kg/a per day), indicating the ability of cattle to acclimate and/or compensate for eventually short-term severe heat stress events. The results of this experiment suggest that the provision of shade with either 35% or 80% of blockage of solar radiation is recommended for the improvement of cattle well-being (expressed through changes in behaviour) without significantly affecting animal performance and TT. However, the overall results of the 63 days of the study can mask or dilute punctual effects of short heat stress events on cattle. More powerful experimental designs are required to address this issue in temperate regions.     

Effects of crop residues,soil type and temperature on emergence and early growth of wheat

Summary Two controlled environment experiments were conducted to examine the germination and early growth of wheat (Triticum aestivum L. cv. Songlen) growing under crop residues of rape, sorghum, field pea and wheat. Additional treamments also included were soil type (Lithic Vertic Ustochrept and Plinthustalf) and temperature (8°C and 24°C to simulate winter and autumn sowing conditions). At low temperature, wheat and sorghum residues produced the most adverse effects on germination with all residues reducing emergence at high temperatures. Shoot lengths were also reduced by most residues at high temperatures whilst root lengths and shoot and root dry weights were unaffected by residue treatments. These results suggest major phytotoxic effects of residues during early growth (up to 14 days after sowing) with, in general, few interactions with soil type or temperature.     

At the tipping point: Differential influences of warming and deoxygenation on the survival,emergence, and respiration of cosmopolitan clams

Although warming and low dissolved oxygen (DO) levels are co‐occurring significant climatic stressors in the ocean, the combined effects of these stressors on marine benthic animals have not been well established. Here, we tested the effects of elevated temperatures and low dissolved oxygen levels on the survival, emerging behavior from sediment, and the respiration of juvenile cosmopolitan Manila clams (Venerupis philippinarum) by exposing them to two temperatures (20 and 23.5°C) and DO levels (3.5 and 6–7 mg/L). Although within previously described tolerable ranges of temperature and DO, this 3.5°C increase in temperature combined with a 50% decrease in DO had a devastating effect on the survival of clams (85% mortality after 8 days). The mortality of clams under normoxia at 23.5°C appeared to be higher than under the low DO condition at 20°C. On the other hand, more clams emerged from sediment under the low DO condition at 20°C than under any other conditions. Oxygen consumption rates were not significantly affected by different conditions. Our results suggest temperature elevation combined with low oxygen additively increases stress on Manila clams and that warming is at least as stressful as low DO in terms of mortality. However, low DO poses another threat as it may induce emergence from sediment, and, thus increase predation risk. This is the first evidence that a combination of warming and deoxygenation stressors should reduce population survival of clams much more so than changes in a single stressor.     

Effects of gravel size and peat material concentrations on embryo survival and alevin emergence of brown trout,Salmo trutta L.

Embryo survival and alevin emergence pattern of brown trout were studied in simulated redds with different homogeneous gravel sizes and different concentrations of peat material. Optimal survival (95%) occurred in 18 mm gravel and survival decreased with decreasing gravel size. High concentrations (40%) of peat material resulted in low survival (65%). The proportion of premature emerging alevins increased in finer gravels and at high peat concentrations. Premature alevins had a large yolk sac and are probably very vulnerable to predators.     

植物提取物和常用药剂对蚜茧蜂的存活、羽化和寄生的影响

天然源药剂由于具有与环境良好的相容性而日益受到重视。研究测试苍耳XanthiumsibiricumPetr.etWidd.和白蝴蝶SyngoniumpodophyllumSchott的提取物以及几种药剂在田间常用浓度下对蚜茧蜂的影响。结果表明,几种药剂对蚜茧蜂成虫有明显杀伤力,毒性的大小次序是绿福(4.5%高效顺反氯氰菊酯乳油)(稀释3000倍)>0.3%印楝素乳油(稀释2000倍)>0.6%阿维菌素(稀释2000倍),2h内可致半数以上的试虫死亡,2.5%鱼藤酮精(稀释800倍)次之,99.9%机油乳剂(稀释400倍)和两种植物提取物(0.04gDW·ml-1)对成蜂的存活无显著影响;处理僵蚜的结果表明,印楝素乳油和机油乳剂影响较明显,僵蚜羽化率分别比对照降低14.67%和18.67%,而两种植物提取物和其余药剂无显著影响;鱼藤精和印楝素乳油处理后,蚜茧蜂寄生蚜虫的效能明显降低,而机油乳剂和两种植物提取物对蚜茧蜂的寄生作用无明显影响。可以看出,目前使用的一些天然源药剂虽然对害虫有较好的控制作用,但在害虫天敌的某些生长期,其仍存在不利影响,因此应根据田间害虫和天敌的发生情况和不同发育期,有选择性地合理用药;同时,筛选对害虫特异性强,对害虫天敌不利影响小的作用物质,是当前乃至将来筛选和应用天然源物质的目标。     

Biological soil crusts and their microenvironment: Impact on emergence,survival and establishment of seedlings

To elucidate the impact of biological soil crusts (BSCs) on the establishment of habitat-typical vascular plant species, we studied the effects of seed location (surface versus sub-surface), age of crusts (initial versus stable), long rainy periods (continuous versus discontinuous watering) and microenvironment (cracks versus no cracks). In addition, we investigated growth height, phytomass and N-content of one vascular plant species (Phleum arenarium). Initial crusts were compared with older, stable crusts using seven habitat-typical plant species representing different life forms (annuals versus perennials). Our model ecosystem, situated in the temperate zone (but edaphically dry), is characterised by calcareous sand with threatened pioneer vegetation (Koelerion glaucae). We carefully translocated soil monoliths of these crusts and analysed the effects under common garden conditions.     

沙埋与水分对科尔沁沙地主要固沙植物出苗的影响

蒿属半灌木乌丹蒿(Artemisia wudanica)、白沙蒿(A. sphaerocephala)、差不嘎蒿(A. halodendron)是科尔沁沙地的主要固沙植物。其中乌丹蒿和差不嘎蒿是科尔沁沙地的本土植物,白沙蒿为来自于库布齐沙漠、毛乌素沙地的飞播植物。设置了 5个沙埋深度(0.5、1.0、1.5、2.0和3.0 cm)和 4个水分梯度(86、171、257和 342 mL,分别模拟每月25、50、75和100 mm的降雨量),以探讨3种植物幼苗出土对沙埋和水分的响应。结果表明,沙埋与水分均显著影响着3种蒿属植物的幼苗出土(P < 0.001)。3种植物最适沙埋深度在0.5-1.5 cm范围内,萌发出土时适宜水量要高于当地种子萌发期的平均降水量(50 mm/月)。两种固沙先锋植物乌丹蒿和白沙蒿的种子出苗率均显著高于差不嘎蒿,乌丹蒿较白沙蒿也明显为高,尤其在水分缺乏时,表现出两种先锋植物种子出苗对干旱有更好的适应性。协方差分析表明,乌丹蒿幼苗死亡率显著高于白沙蒿和差不嘎蒿(P < 0.05),在达到75 mm/月降水量时,3种植物的出苗较好,但不能满足乌丹蒿幼苗生长对水分的需求,而实际种子萌发期的降水量平均只有50 mm/月。因而降水的缺乏导致乌丹蒿种群更新出现问题,加之飞播植物的竞争,使得近几年科尔沁沙地较多乌丹蒿种群出现衰退。     

Effects of substrate type, moisture and its interactions on soil seed survival of three Rumex species

Background and Aims

Seed bank persistence plays a highly relevant role for population dynamics. The impact of interacting environmental factors on seed longevity has only scarcely been investigated. We aimed to analyse the effects of varied soil substrate type and moisture on soil seed survival.

Methods

Seeds of three Rumex species native to different habitats were buried in pots placed in open-air basins. The factors substrate (sand, loam, mud), water table depth (WTD; high, intermediate, low), time, and their interactions were investigated. Viability was tested after 6, 12, and 18 months.

Results

Seeds of R. acetosella (dry habitat) were short-term persistent with highest survival in low WTD on sand. Survival in R. acetosa (moist habitat) was very strongly reduced after 6 months with highest survival under wet conditions. R. maritimus (wet habitat) had overall long-term seed survival, where ‘substrate type’ had the strongest impact. Significant interactions of ‘substrate type’ and WTD were detected.

Conclusions

Seed bank longevity is not a fixed species trait, but varies with environmental factors. Soil moisture, substrate type and their interactions have different effects on the studied species. Persistence-classifications ought to consider the impact of environmental factors.     

Differential effects of interspecific interactions and water availability on survival, growth and fecundity of three congeneric grassland herbs

Fitness of individual plants and of populations depends on the rates of survival, growth and fecundity. This study tested whether vital rates were differentially affected by biotic interactions and water availability. The effects of manipulations of above-ground competition (through clipping) and water availability (through water addition) on the vital rates of seedlings of three species (Viola elatior Fries, Viola pumila Chaix and Viola stagnina Kit.) were analysed in dry, mesic and wet grasslands. Water addition and grassland type had the largest effects on survival (accounting for 41 and 24% of total variation, respectively) across species. Height growth rate was positively affected by grassland type (19%) and water addition (12%) and varied among species (8%), while leaf accumulation rates and reproduction were affected by grassland type and clipping. The data suggested facilitative effects of the canopy on seedling survival in the dry grassland. This study presents evidence that environmental conditions and biotic interactions may have differential effects on seedling survival, growth and reproduction. The findings highlight the complex interplay between spatial and temporal environmental variation and biotic interactions in structuring plant communities.     

Experimental determination of seed emergence and carry‐over in the soil seed bank of the herbaceous perennial,Trachymene incisa (Apiaceae)

Abstract Many populations of herbaceous perennial plants contain seeds stored in a soil seed bank. The contribution of seeds to population persistence is an important parameter in population models but germination rates of known‐age seeds are difficult to obtain because individual seeds cannot easily be followed. Although Trachymene incisa Rudge plants produce copious seeds that are dispersed into the soil, the existence of a seed bank has not been confirmed. To quantify the potential for a seed bank fresh seeds of T. incisa were sown into experimental seed banks in the eucalypt‐dominated Agnes Banks Woodland in western Sydney, NSW. A recent fire provided the opportunity to compare germination in the burnt and unburnt vegetation. Density of seed sowing and time of maturation/dispersal of seeds were manipulated in 75 seed cages. Emergence of seeds after 5 months was significantly higher for the earliest planting date but after 1 year, germination of seeds planted in the later weeks increased, and the final germination for all weeks was 28%. Density of sowing and the recent fire did not affect emergence. A second experiment planted over a broader time span (9 weeks instead of 3 weeks) confirmed the effect of planting date but also found significant spatial variation on a scale of tens of metres. Laboratory germination rates of over 70% confirmed that the seeds were viable and non‐dormant when sown in the field cages. The carry‐over of non‐germinated seed in the soil seed bank is estimated to be about 70% after 2 years, implying that a cohort of seeds would not be depleted through germination alone for up to 40 years. The potential for a long‐lived seed bank in this species is interesting because the plants are also capable of resprouting from their rootstock after fire, giving them characteristics of both resprouters and seeders.     

Disrupted phylogeographical microsatellite and chloroplast DNA patterns indicate a vicariance rather than long‐distance dispersal origin for the disjunct distribution of the Chilean endemic Dioscorea biloba (Dioscoreaceae) around the Atacama Desert

Aim The Chilean endemic Dioscorea biloba (Dioscoreaceae) is a dioecious geophyte that shows a remarkable 600 km north–south disjunction in the peripheral arid area of the Atacama Desert. Its restricted present‐day distribution and probable Neogene origin indicate that its populations have a history linked to that of the Atacama Desert, making this an ideal model species with which to investigate the biogeography of the region. Location Chile, Atacama Desert and peripheral arid area. Methods Two hundred and seventy‐five individuals from nine populations were genotyped for seven nuclear microsatellite loci, and plastid trnL–F and trnT–L sequences were obtained for a representative subset of these. Analyses included the estimation of genetic diversity and population structure through clustering, Bayesian and analysis of molecular variance analyses, and statistical parsimony networks of chloroplast haplotypes. Isolation by distance was tested against alternative dispersal hypotheses. Results Microsatellite markers revealed moderate to high levels of genetic diversity within populations, with those from the southern Limarí Valley showing the highest values and northern populations showing less exclusive alleles. Bayesian analysis of microsatellite data identified three genetic groups that corresponded to geographical ranges. Chloroplast phylogeography revealed no haplotypes shared between northern and southern ranges, and little haplotype sharing between the two neighbouring southern valleys. Dispersal models suggested the presence of extinct hypothetical populations between the southern and northern ranges. Main conclusions Our results are consistent with prolonged isolation of the northern and southern groups, mediated by the life‐history traits of the species. Significant isolation was revealed at both large and moderate distances as gene flow was not evident even between neighbouring valleys. Bayesian analyses of microsatellite and chloroplast haplotype diversity identified the southern area of Limarí as the probable area of origin of the species. Our data do not support recent dispersal of D. biloba from the southern range into Antofagasta, but indicate the fragmentation of an earlier wider range, concomitant with the Pliocene–Pleistocene climatic oscillations, with subsequent extinctions of the Atacama Desert populations and the divergence of the peripheral ones as a consequence of genetic drift.     

The impact of global warming on germination and seedling emergence in Alliaria petiolata,a woodland species with dormancy loss dependent on low temperature

• The impact of global warming on seed dormancy loss and germination was investigated in Alliaria petiolata (garlic mustard), a common woodland/hedgerow plant in Eurasia, considered invasive in North America. Increased temperature may have serious implications, since seeds of this species germinate and emerge at low temperatures early in spring to establish and grow before canopy development of competing species.
• Dormancy was evaluated in seeds buried in field soils. Seedling emergence was also investigated in the field, and in a thermogradient tunnel under global warming scenarios representing predicted UK air temperatures through to 2080.
• Dormancy was simple, and its relief required the accumulation of low temperature chilling time. Under a global warming scenario, dormancy relief and seedling emergence declined and seed mortality increased as soil temperature increased along a thermal gradient. Seedling emergence advanced with soil temperature, peaking 8 days earlier under 2080 conditions.
• The results indicate that as mean temperature increases due to global warming, the chilling requirement for dormancy relief may not be fully satisfied, but seedling emergence will continue from low dormancy seeds in the population. Adaptation resulting from selection of this low dormancy proportion is likely to reduce the overall population chilling requirement. Seedling emergence is also likely to keep pace with the advancement of biological spring, enabling A. petiolata to maintain its strategy of establishment before the woodland canopy closes. However, this potential for adaptation may be countered by increased seed mortality in the seed bank as soils warm.