Viruses in extreme environments

The tolerance limits of extremophiles in term of temperature, pH, salinity, desiccation, hydrostatic pressure, radiation, anaerobiosis far exceed what can support non-extremophilic organisms. Like all other organisms, extremophiles serve as hosts for viral replication. Many lines of evidence suggest that viruses could no more be regarded as simple infectious “fragments of life” but on the contrary as one of the major components of the biosphere. The exploration of niches with seemingly harsh life conditions as hypersaline and soda lakes, Sahara desert, polar environments or hot acid springs and deep sea hydrothermal vents, permitted to track successfully the presence of viruses. Substantial populations of double-stranded DNA virus that can reach 10⁹ particles per milliliter were recorded. All these viral communities, with genome size ranging from 14 kb to 80 kb, seem to be genetically distinct, suggesting specific niche adaptation. Nevertheless, at this stage of the knowledge, very little is known of their origin, activity, or importance to the in situ microbial dynamics. The continuous attempts to isolate and to study viruses that thrive in extreme environments will be needed to address such questions. However, this topic appears to open a new window on an unexplored part of the viral world. Marc Le Romancer and Mélusine Gaillard contributed equally to this work.     

Archaeal diversity in naturally occurring and impacted environments from a tropical region

AIMS: To evaluate archaeal diversity in natural and impacted habitats from Rio de Janeiro state, Brazil, a tropical region of South America. METHODS AND RESULTS: 16S rRNA gene was amplified directly by polymerase chain reaction (PCR) from genomic DNA, extracted from Guanabara Bay (GB) water, halomarine sediment (HS), municipal landfill leachate, agricultural soil and wastewater treatment (WT) system. Five archaeal 16S rDNA clone libraries were constructed. A total of 123 clones, within the five libraries analysed, were clustered into 29 operational taxonomic units, related to cultivated (24%) and uncultivated (76%) organisms. Rarefaction analysis showed that the libraries contained different levels of diversity. PCR-denaturing gradient gel electrophoresis (DGGE) of 16S-23S intergenic spacer regions confirmed the presence of a dominant phylotype, revealed by the WT system clone library. CONCLUSIONS: Archaeal communities of impacted environments seem to be confined to specific ecosystems with similar physicochemical properties, while communities from natural environments appear to be widely distributed. The presence of a high number of phylotypes related to uncultivated organisms suggests new archaeal lineages. SIGNIFICANCE AND IMPACT OF THE STUDY: This study reports, for the first time, the analysis of archaeal diversity in tropical environments from Brazil, and adds sequences from this region to the developing database of 16S rRNA clone libraries from environmental samples.     

Molecular quantification of environmental DNA using microfluidics and digital PCR

Real-time PCR has been widely used to evaluate gene abundance in natural microbial habitats. However, PCR-inhibitory substances often reduce the efficiency of PCR, leading to the underestimation of target gene copy numbers. Digital PCR using microfluidics is a new approach that allows absolute quantification of DNA molecules. In this study, digital PCR was applied to environmental samples, and the effect of PCR inhibitors on DNA quantification was tested. In the control experiment using λ DNA and humic acids, underestimation of λ DNA at 1/4400 of the theoretical value was observed with 6.58ngμL(-1) humic acids. In contrast, digital PCR provided accurate quantification data with a concentration of humic acids up to 9.34ngμL(-1). The inhibitory effect of paddy field soil extract on quantification of the archaeal 16S rRNA gene was also tested. By diluting the DNA extract, quantified copy numbers from real-time PCR and digital PCR became similar, indicating that dilution was a useful way to remedy PCR inhibition. The dilution strategy was, however, not applicable to all natural environmental samples. For example, when marine subsurface sediment samples were tested the copy number of archaeal 16S rRNA genes was 1.04×10(3)copies/g-sediment by digital PCR, whereas real-time PCR only resulted in 4.64×10(2)copies/g-sediment, which was most likely due to an inhibitory effect. The data from this study demonstrated that inhibitory substances had little effect on DNA quantification using microfluidics and digital PCR, and showed the great advantages of digital PCR in accurate quantifications of DNA extracted from various microbial habitats.     

Comparative study of seasonal and intradiurnal variation of airborne herbaceous pollen in urban and rural areas

The content of herbaceous pollen in the atmosphere depends on the vegetal cover, climate and the weather and geographical conditions. The aim of the study reported here was to compare aerobiological data obtained from pollen monitoring stations located at sites differing with respect to their flora and microclimate – i.e. a town and a rural area. A volumetric method was used for sampling. In each microscopic preparation 12 vertical strips corresponding with 2-h intervals were analysed. A 90% method was used to determine the pollen season. The results were statistically verified using the u test and the Kolmogorov-Smirnov, Spearman and Wilcoxon tests. Higher values of the Seasonal Pollen Index (SPI), higher daily average concentrations and higher peak values were recorded in the rural area. An analysis of intradiurnal variations of airborne pollen showed that apart from the Poaceae the number of pollen grains in the air began to increase earlier in the day in the rural area; in the case of Rumex and Ambrosia, the maximum values also appeared a few hours earlier. For all the taxa investigated, the analysis of correlation showed a significant association between the daily average concentrations at both sites. The weakest association occurred for Plantago lanceolata; for all other taxa, the determination coefficients (R ²) were high. The results of the Wilcoxon test showed that, despite the strong positive association between daily concentrations of the pollen types investigated, there were differences in mean pollen concentrations in the overlapping pollen season. Mean concentrations of Poaceae and Rumex airborne pollen were significantly higher in the rural area in both years, and those of Urtica and P. lanceolata were significantly higher only in 2002.     

Systematic placement and biogeographical relationships of the monotypic genera Gypothamnium and Oxyphyllum (Asteraceae: Mutisioideae) from the Atacama Desert

Gypothamnium and Oxyphyllum (Asteraceae) are two monotypic genera endemic to the Atacama Desert of northern Chile. We performed a phylogenetic analysis using published sequences of the plastid rbcL and ndhF genes, the trnL‐trnF region and the nuclear ribosomal internal transcribed spacer (ITS) to assess the systematic placement of the two genera within Mutisioideae. On the basis of the phylogenetic results, we constructed area cladograms to explore the biogeographical relationships and origin of the genera. The phylogenetic analysis showed that Gypothamnium is closely related to Aphylloclados, Plazia, Urmenetia, Lycoseris and Onoseris, whereas Oxyphyllum is closely related to Leucheria, Moscharia, Polyachyrus and, with low support, Jungia. These results do not differ substantially from those proposed in previous treatments based on morphological characters. The biogeographical analysis suggests that Gypothamnium in the coastal Atacama Desert is related to taxa that are currently distributed in eastern subtropical South America and in the Puna. Oxyphyllum may have originated from central Chile and other areas in southern South America, but its sister group (Leucheria + Polyachyrus) also reaches the Puna and the coastal Atacama Desert. Both groups show ancestral affinities with elements currently distributed in north‐western South America and Mesoamerica. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159 , 32–51.     

Does global warming induce segregation among alien and native beetle species in a mountain-top?

The last few centuries have seen an increase in the mean air temperature of the planet, a phenomenon that is called “global warming”. One of the most sensitive habitats to the effects of global warming is the high-elevation mountain environments, because these habitats are characterized by low temperature. Cushion plants are one of the best-adapted growth forms in this habitat, generating more suitable sites for other plants and insects. In the present study, we experimentally evaluated the effects of global warming by open-top chambers on the abundance and interaction of two ladybirds at 3,600 m, growing over cushions of the Azorella monantha species in the Andes of central Chile. Additionally, we measured variation in temperature, water content, and food availability by the presence of open-top chambers as possible mechanisms of spatial segregation between ladybirds. Without open-top chambers, the abundance of native and alien beetles was similar; but with open-top chambers, the native beetle species is spatially segregated by alien species, decreasing in abundance. The open-top chambers increase temperature and food availability, but not water content. We suggest that under the global warming scenario, the native insects will decrease in abundance or become extinct by the presence of alien insects, at least in the high-elevation mountain environments.     

Variability in amount and frequency of water supply affects roots but not growth of arid shrubs

Rainfall and soil moisture variability have a strong effect on plant survival and seed germination in arid environments, yet very little is known about the effects on roots and growth of woody seedlings. Here we focused on the effects of variability in both amount and frequency of water supply on juvenile root and leaf functional traits and growth of seven Mediterranean shrub species occurring in arid SE Spain, Anthyllis cytisoides, Atriplex halimus, Ephedra fragilis, Genista umbellata, Lycium intricatum, Retama sphaerocarpa, and Salsola oppositifolia. In a 14-month greenhouse experiment we manipulated water supply expecting that reduced water amount and pulses of watering of different magnitude affected functional traits and seedling growth, even if the amount of water provided was the same. Different watering patterns altered soil drying dynamics, with reduced supply of water amount and frequent watering becoming the driest treatment. We found that roots of all species responded to alterations in water supply by changing biomass allocation patterns (i.e., higher root-to-shoot mass [R:S] ratio in droughted plants), and by altering fine roots diameter, measured in terms of specific root length. Indeed, differences in growth rate among species were significantly linked to fine roots diameter and biomass allocation, which relates to uptake capacity of roots. However, relative growth rate and leaf traits such as specific leaf area were insensitive, likely because prolonged droughts over longer periods of time seem necessary to constraint growth in all these arid shrubs.     

Definition of grassland biomes from phytoliths in West Africa

Aim In order to enhance the effectiveness of comparisons between modelled and empirical data for present and past vegetation, it is important to improve the characterization of tropical grass‐dominated biomes reconstructed from fossil tracers. This study presents a method for assigning phytolith assemblages to tropical grass‐dominated biomes, with the objective of offering a new tool for combining pollen and phytolith data in the reconstruction of tropical biomes. Location The West African latitudinal transect studied here extends from 12° N (southern Senegal) to 23° N (southern Mauritania), passing through the Guinean, Sudanian, Sahelian and Saharan bioclimatic zones. Methods Modern phytolith assemblages were extracted from 59 soil surface samples taken throughout the study area and allocated, a priori, to three current biomes: (1) desert C₄ grassland, (2) short grass savanna, and (3) tall grass savanna. Five out of nine phytolith types identified were used as predictors in a discriminant analysis (with calibration and validation steps) for assigning phytolith assemblages to biomes. In addition, 74 modern pollen spectra from the West African transect, acquired from the African Pollen Database ( http://medias.obs‐mip.fr/apd ), were processed by the biomization method. This mathematical procedure involves assigning palynological taxa to one or more plant functional types, which represent broad classes of plants. The plant functional types, in turn, are combined to define biomes following a specific set of algorithms and rules. The resulting maps of the phytolith biomes thus derived were compared with maps of pollen biomes and of contemporary ecosystem classes. Results In the calibration and validation steps, 91.5% and up to 83%, respectively, of the phytolith samples were assigned to the correct biome. The short grass savanna and tall grass savanna biomes were assigned with similar accuracy by both the phytolith and pollen biomization methods, but the phytolith method gave substantially superior results for the desert C₄ grassland biome, providing seven out of seven correct assignments, compared with just one out of four by pollen biomization. Comparisons between an existing ecosystem map and the maps created from phytolith estimation showed close correspondence for desert C₄ grassland, short grass savanna and tall grass savanna, the latter providing correct assignments in 88, 62 and 91% of cases, respectively. Main conclusions The phytolith discriminant analysis method presented here accurately estimates three C₄ grass‐dominated biomes that are widespread in West Africa. Complementarities between the phytolith method and pollen biomization are highlighted. Combining complementary phytolith and pollen data would provide more accurate assignments of C₄ grass‐dominated biomes than pollen biomization alone.