The impact of arthropods on fungal community structure in Lascaux Cave

Aims:  To determine the major components of the fungal population present in Lascaux Cave, France. The ceiling, walls, sediments and soil were colonized by Fusarium solani in 2001 and later, in 2006, black stains appeared. However, the origin of the successive fungal invasions is unknown as well as the ecology of the cave.
Methods and Results:  The primers nu-SSU-0817F and nu-SSU-1536R were used for the direct amplification of fungal 18S-rDNA sequences from 11 samples. A total of 607 clones were retrieved. Eight out of the ten most abundant phylotypes corresponded to fungi associated with arthropods and represented about 50% of the clones.
Conclusions:  Entomophilous fungi play an important role in the cave and arthropods contribute to the dispersion of spores and fungal development.
Significance and Impact of the Study:  Choosing appropriate targets for control of fungal dispersal is dependent on knowing the causes of fungal colonization. A control of the arthropod populations seems to be a need in order to protect the rock art paintings in Lascaux Cave.     

Uncovering the evolutionary origin of blue anthocyanins in cereal grains

Functional divergence after gene duplication plays a central role in plant evolution. Among cereals, only Hordeum vulgare (barley), Triticum aestivum (wheat) and Secale cereale (rye) accumulate delphinidin‐derived (blue) anthocyanins in the aleurone layer of grains, whereas Oryza sativa (rice), Zea mays (maize) and Sorghum bicolor (sorghum) do not. The underlying genetic basis for this natural occurrence remains elusive. Here, we mapped the barley Blx1 locus involved in blue aleurone to an approximately 1.13 Mb genetic interval on chromosome 4HL, thus identifying a trigenic cluster named MbHF35 (containing HvMYB4H, HvMYC4H and HvF35H). Sequence and expression data supported the role of these genes in conferring blue‐coloured (blue aleurone) grains. Synteny analyses across monocot species showed that MbHF35 has only evolved within distinct Triticeae lineages, as a result of dispersed gene duplication. Phylogeny analyses revealed a shared evolution pattern for MbHF35 in Triticeae, suggesting that these genes have co‐evolved together. We also identified a Pooideae‐specific flavonoid 3′,5′‐hydroxylase (F3′5′H) lineage, termed here Mo_F35H2, which has a higher amino acid similarity with eudicot F3′5′Hs, demonstrating a scenario of convergent evolution. Indeed, selection tests identified 13 amino acid residues in Mo_F35H2 that underwent positive selection, possibly driven by protein thermostablility selection. Furthermore, through the interrogation of barley germplasm there is evidence that HvMYB4H and HvMYC4H have undergone human selection. Collectively, our study favours blue aleurone as a recently evolved trait resulting from environmental adaptation. Our findings provide an evolutionary explanation for the absence of blue anthocyanins in other cereals and highlight the importance of gene functional divergence for plant diversity and environmental adaptation.     

Anthropization level of Lascaux Cave microbiome shown by regional‐scale comparisons of pristine and anthropized caves

Limestone areas across the world develop karstic caves, which are populated by a wide range of macro‐ and microorganisms. Many of these caves display Paleolithic art or outstanding speleothems, and in the last century they have been subjected to anthropization due to touristic management and intense human frequentation. Despite their cultural importance and associated conservation issues, the impact of anthropization on cave biodiversity is not known. Here, we show that anthropization is associated with specific cave biota modifications. We compared diversity in four pristine caves, four anthropized show caves, and the iconic Lascaux Cave with even stronger anthropization. The predominant microbial higher taxa were the same in all caves, but the most anthropized cave (Lascaux) was unique as it differed from the eight others by a higher proportion of Bacteroidetes bacteria and the absence of Euryarchaeota and Woesearchaeota archaea. Anthropization resulted in lower diversity and altered community structure for bacteria and archaea on cave walls, especially in Lascaux, but with a more limited effect on microeukaryotes and arthropods. Our findings fill a key gap in our understanding of the response of karstic communities to anthropization, by revealing that tourism‐related anthropization impacts on the prokaryotic microbiome rather than on eukaryotic residents, and that it shapes cave biota irrespective of cave natural features.     

Assessment of the relationship between geologic origin of soil, rhizobacterial community composition and soil receptivity to tobacco black root rot in Savoie region (France)

Background and aims

In Morens (Switzerland), soils formed on morainic deposits (which contain vermiculite clay and display particular tobacco rhizobacterial community) are naturally suppressive to Thielaviopsis basicola-mediated tobacco black root rot, but this paradigm was never assessed elsewhere. Here, we tested the relation between geology and disease suppressiveness in neighboring Savoie (France).

Methods

Two morainic and two sandstone soils from Savoie were compared based on disease receptivity (T. basicola inoculation tests on tobacco), clay mineralogy (X-ray diffraction), tobacco rhizobacterial community composition (16S rRNA gene-based taxonomic microarray) and phlD ⁺ Pseudomonas populations involved in 2,4-diacetylphloroglucinol production (real-time PCR and tRFLP).

Results

Unlike in Morens, in Savoie the morainic soils were receptive to disease whereas T. basicola inoculation did not increase disease level in the sandstone soils. Vermiculite was not present in Savoie soils. The difference in rhizobacterial community composition between Savoie morainic and sandstone soils was significant but modest, and there was little agreement in bacterial taxa discriminating soils of different disease receptivity levels when comparing Morens versus Savoie soils. Finally, phlD ⁺ rhizosphere pseudomonads were present at levels comparable to those in Morens soils, but with different diversity patterns.

Conclusions

The morainic model of black root rot suppressiveness might be restricted to the particular type of moraine occurring in the Morens region, and the low disease receptivity of sandstone soils in neighboring Savoie might be related to other plant-protection mechanisms.     

Uncovering interactions in the frequency domain

Oscillatory activity plays a critical role in regulating biological processes at levels ranging from subcellular, cellular, and network to the whole organism, and often involves a large number of interacting elements. We shed light on this issue by introducing a novel approach called partial Granger causality to reliably reveal interaction patterns in multivariate data with exogenous inputs and latent variables in the frequency domain. The method is extensively tested with toy models, and successfully applied to experimental datasets, including (1) gene microarray data of HeLa cell cycle; (2) in vivo multi-electrode array (MEA) local field potentials (LFPs) recorded from the inferotemporal cortex of a sheep; and (3) in vivo LFPs recorded from distributed sites in the right hemisphere of a macaque monkey.     

Palaeoceanographic differences of early Late Aptian black shale events in the Vocontian Basin (SE France)

A high-resolution study focussing on the distribution of calcareous nannofossils and carbon isotopes was carried out to improve the understanding of mid-Cretaceous black shale formation. The studied interval of the early Late Aptian is characterized by two major black shale couplets, the Niveau Noire 4 (NN4) and Niveau Noire Calcaire 2 (NNC2), of the Serre Chaitieu section in the Vocontian Basin (SE France; Bréhéret, 1997). This interval occurs within a long-term negative carbon isotope excursion of > 1.5‰ following the Early Aptian Oceanic Anoxic Event 1a (OAE1a). In contrast to the local NN4 black shales, the black shales of NNC2 are of regional significance and occur at the end of the major negative carbon isotope excursion of the early Late Aptian. Time equivalent black shales are suggested to be coeval with black shales found in the Western Tethys and Atlantic Ocean (Herrle et al., 2004). Calcareous nannofossil analyses and carbon isotopes indicate higher surface water productivity (mesotrophic), warmer surface water, and higher sea-level during the formation of the NN4 black shales. In contrast, the formation of the NNC2 black shales took place during a cooler phase, lower surface water productivity, and lower sea-level. A sea-level fall may cause a restriction of water mass exchange between the open-marine Western Tethys and the Vocontian Basin. This resulted in a longer residence time of the bottom water, decreased ventilation and less mixing of surface waters and thus enhanced preservation of organic matter at the sea floor. Our results indicate that the black shale formation of NN4 and NNC2 was caused by different processes such as increased surface water productivity and enhanced preservation of organic matter at the sea floor. Thus, we emphasize the role of different forcing factors which control the formation of local and regional black shales. The most important factors are sea-level fluctuations, increasing productivity, and changes in precipitation and evaporation rates.     

Uncovering adaptive evolution in the human lineage

Background

The recent increase in human polymorphism data, together with the availability of genome sequences from several primate species, provides an unprecedented opportunity to investigate how natural selection has shaped human evolution.

Results

We compared human branch-specific substitutions with variation data in the current human population to measure the impact of adaptive evolution on human protein coding genes. The use of single nucleotide polymorphisms (SNPs) with high derived allele frequencies (DAFs) minimized the influence of segregating slightly deleterious mutations and improved the estimation of the number of adaptive sites. Using DAF ≥ 60% we showed that the proportion of adaptive substitutions is 0.2% in the complete gene set. However, the percentage rose to 40% when we focused on genes that are specifically accelerated in the human branch with respect to the chimpanzee branch, or on genes that show signatures of adaptive selection at the codon level by the maximum likelihood based branch-site test. In general, neural genes are enriched in positive selection signatures. Genes with multiple lines of evidence of positive selection include taxilin beta, which is involved in motor nerve regeneration and syntabulin, and is required for the formation of new presynaptic boutons.

Conclusions

We combined several methods to detect adaptive evolution in human coding sequences at a genome-wide level. The use of variation data, in addition to sequence divergence information, uncovered previously undetected positive selection signatures in neural genes.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-599) contains supplementary material, which is available to authorized users.     

Uncovering the Nutritional Landscape of Food

Recent progresses in data-driven analysis methods, including network-based approaches, are revolutionizing many classical disciplines. These techniques can also be applied to food and nutrition, which must be studied to design healthy diets. Using nutritional information from over 1,000 raw foods, we systematically evaluated the nutrient composition of each food in regards to satisfying daily nutritional requirements. The nutrient balance of a food was quantified and termed nutritional fitness; this measure was based on the food’s frequency of occurrence in nutritionally adequate food combinations. Nutritional fitness offers a way to prioritize recommendable foods within a global network of foods, in which foods are connected based on the similarities of their nutrient compositions. We identified a number of key nutrients, such as choline and α-linolenic acid, whose levels in foods can critically affect the nutritional fitness of the foods. Analogously, pairs of nutrients can have the same effect. In fact, two nutrients can synergistically affect the nutritional fitness, although the individual nutrients alone may not have an impact. This result, involving the tendency among nutrients to exhibit correlations in their abundances across foods, implies a hidden layer of complexity when exploring for foods whose balance of nutrients within pairs holistically helps meet nutritional requirements. Interestingly, foods with high nutritional fitness successfully maintain this nutrient balance. This effect expands our scope to a diverse repertoire of nutrient-nutrient correlations, which are integrated under a common network framework that yields unexpected yet coherent associations between nutrients. Our nutrient-profiling approach combined with a network-based analysis provides a more unbiased, global view of the relationships between foods and nutrients, and can be extended towards nutritional policies, food marketing, and personalized nutrition.     

Uncovering the mutation-fixation correlation in short lineages

Background  

We recently reported a highly unexpected positive correlation between the fixation probability of nonsynonymous mutations (estimated by ω) and neutral mutation rate (estimated by K _s) in mammalian lineages. However, this positive correlation was observed for lineages with relatively long divergence time such as the human-mouse lineage, and was not found for very short lineages such as the human-chimpanzee lineage. It was previously unclear how to interpret this discrepancy. It may indicate that the positive correlation between ω and K _s in long lineages is a false finding. Alternatively, it may reflect a biologically meaningful difference between various lineages. Finally, the lack of positive correlation in short lineages may be the result of methodological artifacts.     

Uncovering the role of 5-hydroxymethylcytosine in the epigenome

Just over 2 years ago, TET1 was found to catalyse the oxidation of 5-methylcytosine, a well-known epigenetic mark, into 5-hydroxymethylcytosine in mammalian DNA. The exciting prospect of a novel epigenetic modification that may dynamically regulate DNA methylation has led to the rapid accumulation of publications from a wide array of fields, from biochemistry to stem cell biology. Although we have only started to scratch the surface, interesting clues on the role of 5-hydroxymethylcytosine are quickly emerging.     

Application of stains in clinical microbiology

Stains have been used for diagnosing infectious diseases since the late 1800s. The Gram stain remains the most commonly used stain because it detects and differentiates a wide range of pathogens. The next most commonly used diagnostic technique is acid-fast staining that is used primarily to detect Mycobacterium tuberculosis and other severe infections. Many infectious agents grow slowly on culture media or may not grow at all; stains may be the only method to detect these organisms in clinical specimens. In the hands of experienced clinical microscopists, stains provide rapid and cost-effective information for preliminary diagnosis of infectious diseases. A review of the most common staining methods used in the clinical microbiology laboratory is presented here.     

Application of stains in clinical microbiology

Stains have been used for diagnosing infectious diseases since the late 1800s. The Gram stain remains the most commonly used stain because it detects and differentiates a wide range of pathogens. The next most commonly used diagnostic technique is acid-fast staining that is used primarily to detect Mycobacterium tuberculosis and other severe infections. Many infectious agents grow slowly on culture media or may not grow at all; stains may be the only method to detect these organisms in clinical specimens. In the hands of experienced clinical microscopists, stains provide rapid and cost-effective information for preliminary diagnosis of infectious diseases. A review of the most common staining methods used in the clinical microbiology laboratory is presented here.