Different composition of plant residues as a driver of microbial community structure and soil organic matter composition: a microcosm study.

Soil organic matter (SOM) is the main pathway of carbon (C) input to the soil with the decomposition of shoot residues, roots and their exudates. The objective was to evaluate the contribution of different vegetal composition and plant parts of Caatinga species and the effects of introducing a grass in the soil microbial community structure and biochemical composition of SOM. A trial was conducted under controlled conditions (120 days) using, separately, the shoot and roots residues of native species from the herbaceous (HERB) and shrub-arboreal (ARB) strata and a grass (GRASS). Megathyrsus maximum, which is native from Africa, but well adapted to the semi-arid conditions of Brazil, was used. Combinations of these species in different proportions were also evaluated: (i) 55 % shrub and trees + 45 % grass (MIX1) and (ii) 75 % shrub and trees + 25 % grass (MIX2). At the end of incubation, soil samples were collected to evaluate the microbial community structure through the phospholipid fatty acids (PLFA). Physical fractioning of SOM into particulate organic matter (POM) and mineralassociated organic matter (MAOM) was also performed, followed by biochemical characterization of these fractions by thermochemolysis analysis. The ARB shoot residue resulted in a 181.5 % increase (p < 0.05) in total PLFA biomass in the soil. A significant increase (p < 0.05) in the abundance of fungi and bacteria was observed with the incorporation of shoot residues. MAOM was characterized by a higher abundance of aliphatic (31.6 ± 5.0 %) and nitrogen-bearing compounds (21.0 ± 2.0 %), while higher lignin derivatives were observed in POM (18.0 ± 0.6 %). The ground cover provided a diversity of compounds in the SOM, thus regulating the structure of the microbial community. These results highlight the importance of conserving biodiversity, both in natural ecosystems and in agroecosystems in the semi-arid environment

Enlarged vascular foramina and lytic lesions in vertebral bodies: a diagnostic dilemma

Among the skeletal material from the sites of Alghero, Mesumundu and Sant’Antioco di Bisarcio (Sassari, Sardinia) and dated back to the period comprises between the 13th and the late 16th century 5 subadult individuals aged between 5 and 15 years and a mature male showed peculiar osteolytic phenomena of the vertebral bodies. These lesions have the appearance of enlarged vascular foramina, affecting several vertebrae mainly of the thoracic and lumbar spine, sometimes with involvement of the sacrum; on the same vertebral body several lesions are generally visible. In the literature similar features have been attributed to brucellosis or tuberculosis. As for the Sardinian skeletal material, an imaging study on the vertebrae of the adult individual was carried out in order to evaluate the appearance of the lesions within the body. Computed Tomography evidenced internal irregular elongated cavitations, sometimes joined together; erosive rounded lesions, whose presence is not detectable externally, were also showed. The molecular analysis has so far been performed on the subadult from Sant’Antioco di Bisarcio, but at initial analysis the DNA resulted degraded. Therefore, the nature of these lesions remains unclear, as it is not sure if they should be referred to tuberculosis, brucellosis or other pathological conditions [hemolytic anemias (eg. Thalassemia), lymphomas, multiple myeloma and infection by Echinococcus]. Further molecular analyses will be carried out on the remains belonging to the other five individuals in an attempt to clarify the etiology of the above mentioned lesions

Enlarged vascular foramina and lytic lesions in vertebral bodies: a diagnostic dilemma

Among the skeletal material from the sites of Alghero, Mesumundu and Sant’Antioco di Bisarcio (Sassari, Sardinia) and dated back to the period comprises between the 13th and the late 16th century 5 subadult individuals aged between 5 and 15 years and a mature male showed peculiar osteolytic phenomena of the vertebral bodies. These lesions have the appearance of enlarged vascular foramina, affecting several vertebrae mainly of the thoracic and lumbar spine, sometimes with involvement of the sacrum; on the same vertebral body several lesions are generally visible. In the literature similar features have been attributed to brucellosis or tuberculosis. As for the Sardinian skeletal material, an imaging study on the vertebrae of the adult individual was carried out in order to evaluate the appearance of the lesions within the body. Computed Tomography evidenced internal irregular elongated cavitations, sometimes joined together; erosive rounded lesions, whose presence is not detectable externally, were also showed. The molecular analysis has so far been performed on the subadult from Sant’Antioco di Bisarcio, but at initial analysis the DNA resulted degraded. Therefore, the nature of these lesions remains unclear, as it is not sure if they should be referred to tuberculosis, brucellosis or other pathological conditions [hemolytic anemias (eg. Thalassemia), lymphomas, multiple myeloma and infection by Echinococcus]. Further molecular analyses will be carried out on the remains belonging to the other five individuals in an attempt to clarify the etiology of the above mentioned lesions

A genomic and historical synthesis of plague in 18th century Eurasia

Plague continued to afflict Europe for more than five centuries after the Black Death. Yet, by the 17th century, the dynamics of plague had changed, leading to its slow decline in Western Europe over the subsequent 200 y, a period for which only one genome was previously available. Using a multidisciplinary approach, combining genomic and historical data, we assembled Y. pestis genomes from nine individuals covering four Eurasian sites and placed them into an historical context within the established phylogeny. CHE1 (Chechnya, Russia, 18th century) is now the latest Second Plague Pandemic genome and the first non-European sample in the post-Black Death lineage. Its placement in the phylogeny and our synthesis point toward the existence of an extra-European reservoir feeding plague into Western Europe in multiple waves. By considering socioeconomic, ecological, and climatic factors we highlight the importance of a noneurocentric approach for the discussion on Second Plague Pandemic dynamics in Europe

Characterization of Nucleotide Misincorporation Patterns in the Iceman's Mitochondrial DNA

BACKGROUND: The degradation of DNA represents one of the main issues in the genetic analysis of archeological specimens. In the recent years, a particular kind of post-mortem DNA modification giving rise to nucleotide misincorporation ("miscoding lesions") has been the object of extensive investigations. METHODOLOGY/PRINCIPAL FINDINGS: To improve our knowledge regarding the nature and incidence of ancient DNA nucleotide misincorporations, we have utilized 6,859 (629,975 bp) mitochondrial (mt) DNA sequences obtained from the 5,350-5,100-years-old, freeze-desiccated human mummy popularly known as the Tyrolean Iceman or Otzi. To generate the sequences, we have applied a mixed PCR/pyrosequencing procedure allowing one to obtain a particularly high sequence coverage. As a control, we have produced further 8,982 (805,155 bp) mtDNA sequences from a contemporary specimen using the same system and starting from the same template copy number of the ancient sample. From the analysis of the nucleotide misincorporation rate in ancient, modern, and putative contaminant sequences, we observed that the rate of misincorporation is significantly lower in modern and putative contaminant sequence datasets than in ancient sequences. In contrast, type 2 transitions represent the vast majority (85%) of the observed nucleotide misincorporations in ancient sequences. CONCLUSIONS/SIGNIFICANCE: This study provides a further contribution to the knowledge of nucleotide misincorporation patterns in DNA sequences obtained from freeze-preserved archeological specimens. In the Iceman system, ancient sequences can be clearly distinguished from contaminants on the basis of nucleotide misincorporation rates. This observation confirms a previous identification of the ancient mummy sequences made on a purely phylogenetical basis. The present investigation provides further indication that the majority of ancient DNA damage is reflected by type 2 (cytosine-->thymine/guanine-->adenine) transitions and that type 1 transitions are essentially PCR artifacts

Quantification of damage in DNA recovered from highly degraded samples – a case study on DNA in faeces

BACKGROUND: Poorly preserved biological tissues have become an important source of DNA for a wide range of zoological studies. Measuring the quality of DNA obtained from these samples is often desired; however, there are no widely used techniques available for quantifying damage in highly degraded DNA samples. We present a general method that can be used to determine the frequency of polymerase blocking DNA damage in specific gene-regions in such samples. The approach uses quantitative PCR to measure the amount of DNA present at several fragment sizes within a sample. According to a model of random degradation the amount of available template will decline exponentially with increasing fragment size in damaged samples, and the frequency of DNA damage (λ) can be estimated by determining the rate of decline. RESULTS: The method is illustrated through the analysis of DNA extracted from sea lion faecal samples. Faeces contain a complex mixture of DNA from several sources and different components are expected to be differentially degraded. We estimated the frequency of DNA damage in both predator and prey DNA within individual faecal samples. The distribution of fragment lengths for each target fit well with the assumption of a random degradation process and, in keeping with our expectations, the estimated frequency of damage was always less in predator DNA than in prey DNA within the same sample (mean λ(predator )= 0.0106 per nucleotide; mean λ(prey )= 0.0176 per nucleotide). This study is the first to explicitly define the amount of template damage in any DNA extracted from faeces and the first to quantify the amount of predator and prey DNA present within individual faecal samples. CONCLUSION: We present an approach for characterizing mixed, highly degraded PCR templates such as those often encountered in ecological studies using non-invasive samples as a source of DNA, wildlife forensics investigations and ancient DNA research. This method will allow researchers to measure template quality in order to evaluate alternate sources of DNA, different methods of sample preservation and different DNA extraction protocols. The technique could also be applied to study the process of DNA decay

DNA antico

DNA antico In biologia molecolare, qualsiasi traccia di DNA proveniente da organismi estinti o estratto da resti scheletrici fossili, per il cui studio a partire dalla seconda metà degli anni Ottanta l'impiego della tecnica della reazione a catena della polimerasi (PCR, Polymerase chain reaction) ha fornito ai ricercatori di paleontologia e di archeologia molecolare un potente strumento di amplificazione genica in vitro

How microbial ancient DNA, found in association with human remains, can be interpreted.

The analysis of the DNA of ancient micro-organisms in archaeological and palaeontological human remains can contribute to the understanding of issues as different as the spreading of a new disease, a mummification process or the effect of diets on historical human populations. The quest for this type of DNA, however, can represent a particularly demanding task. This is mainly due to the abundance and diffusion of bacteria, fungi, yeasts, algae and protozoans in the most diverse environments of the present-day biosphere and the resulting difficulty in distinguishing between ancient and modern DNA. Nevertheless, at least under some special circumstances, by using rigorous protocols, which include an archaeometric survey of the specimens and evaluation of the palaeoecological consistency of the results of DNA sequence analysis, glimpses of the composition of the original microbial flora (e.g. colonic flora) can be caught in ancient human remains. Potentials and pitfalls of this research field are illustrated by the results of research works performed on prehistoric, pre-Columbian and Renaissance human mummies