No abstract

The complex interactions between trees and soil microbes in forests as well as their inherent seasonal and spatial variations are poorly understood. In this study, we analyzed the effects of major European tree species (Fagus sylvatica L. and Picea abies (L.) Karst) on soil bacterial and fungal communities. Mineral soil samples were collected from different depths (0–10, 10–20 cm) and at different horizontal distances from beech or spruce trunks (0.5, 1.5, 2.5, 3.5 m) in early summer and autumn. We assessed the composition of soil bacterial and fungal communities based on 16S rRNA gene and ITS DNA sequences. Community composition of bacteria and fungi was most strongly affected by soil pH and tree species. Different ectomycorrhizal fungi (e.g., Tylospora) known to establish mutualistic associations with plant roots showed a tree species preference. Moreover, bacterial and fungal community composition showed spatial and seasonal shifts in soil surrounding beech and spruce. The relative abundance of saprotrophic fungi was higher at a depth of 0–10 vs. 10–20 cm depth. This was presumably a result of changes in nutrient availability, as litter input and organic carbon content decreased with soil depth. Overall bacterial community composition showed strong variations under spruce with increasing distance from the tree trunks, which might be attributed in part to higher fine root biomass near spruce trunks. Furthermore, overall bacterial community composition was strongly affected by season under deciduous trees.

Crop wild relatives that have experienced multiple and independent domestication events provide an excellent model for understanding adaptation processes in crop populations and a first and relevant aspect to investigate is the geographic origin of landraces. The aim of this research was to establish the origin of Mesoamerican and Andean Lima bean (Phaseolus lunatus L.) landraces by analyzing chloroplast DNA and ITS polymorphisms in a sample of 59 wild and 50 landrace accessions. According to seed size, genetic distance analyses, and haplotype networks, at least two independent domestication events are proposed. The first one would have taken place in the Andes of southern Ecuador–northwestern Peru and would have given rise to the large‐seeded landraces collectively known as the “Big Lima” cultivars. The second one would have taken place in central–western Mexico, more likely in the area to the north and northwest of the Isthmus of Tehuantepec. This event, along with post‐domestication migrations of landraces in South America, would have given rise to the great variety of small‐seeded Mesoamerican landraces that exist today. We did not find any evidence supporting the existence of two discrete groups within Mesoamerican landraces that might correspond to the previously proposed “Sieva” and “Potato” cultigroups. A severe reduction in genetic diversity because of domestication, known as the “founder effect”, was detected, which may have implications for the conservation of genetic resources in this species.

Mobile genetic elements, including plasmids, drive the evolution of prokaryotic genomes through the horizontal transfer of genes allowing genetic exchange between bacteria. Moreover, plasmids carry accessory genes, which encode functions that may offer an advantage to the host. Thus, it is expected that in a certain ecological niche, plasmids are enriched in accessory functions, which are important for their hosts to proliferate in that niche. Puquio de Campo Naranja is a high-altitude lake from the Andean Puna exposed to multiple extreme conditions, including high UV radiation, alkalinity, high concentrations of arsenic, heavy metals, dissolved salts, high thermal amplitude and low O 2 pressure. Microorganisms living in this lake need to develop efficient mechanisms and strategies to cope under these conditions. The aim of this study was to characterize the plasmidome of microbialites from Puquio de Campo Naranja, and identify potential hosts and encoded functions using a deep-sequencing approach. The potential ecological impact of the plasmidome, including plasmids from cultivable and non-cultivable microorganisms, is described for the first time in a lake representing an extreme environment of the Puna. This study showed that the recovered genetic information for the plasmidome was novel in comparison to the metagenome derived from the same environment. The study of the total plasmid population allowed the identification of genetic features typically encoded by plasmids, such as resistance and virulence factors. The resistance genes comprised resistances to heavy metals, antibiotics and stress factors. These results highlight the key role of plasmids for their hosts and impact of extrachromosomal elements to thrive in a certain ecological niche.

Phosphorus (P) is a key element involved in numerous cellular processes and essential to meet global food demand. Phosphatases play a major role in cell metabolism and contribute to control the release of P from phosphorylated organic compounds, including phytate. Apart from the relationship with pathogenesis and the enormous economic relevance, phosphatases/phytases are also important for reduction of phosphorus pollution. Almost all known functional phosphatases/phytases are derived from cultured individual microorganisms. We demonstrate here for the first time the potential of functional metagenomics to exploit the phosphatase/phytase pools hidden in environmental soil samples. The recovered diversity of phosphatases/phytases comprises new types and proteins exhibiting largely unknown characteristics, demonstrating the potential of the screening method for retrieving novel target enzymes. The insights gained into the unknown diversity of genes involved in the P cycle highlight the power of function-based metagenomic screening strategies to study Earth’s phosphatase pools.

The release of phosphate from inorganic and organic phosphorus compounds can be mediated enzymatically. Phosphate-releasing enzymes, comprising acid and alkaline phosphatases, are recognized as useful biocatalysts in applications such as plant and animal nutrition, bioremediation and diagnostic analysis. Metagenomic approaches provide access to novel phosphatase-encoding genes. Here, we describe a function-based screening approach for rapid identification of genes conferring phosphatase activity from small-insert and large-insert metagenomic libraries derived from various environments. This approach bears the potential for discovery of entirely novel phosphatase families or subfamilies and members of known enzyme classes hydrolyzing phosphomonoester bonds such as phytases. In addition, we provide a strategy for efficient heterologous phosphatase gene expression.

Pseudomonas balearica strain EC28 is an iron-oxidizing bacterium isolated from corroded steel at a floating production storage and offloading facility in Australia. Here, we report its complete genome sequence, which comprises 4,642,566 bp with a GC content of 64.43%. The genome harbors 4,164 predicted protein-encoding genes.

Here, we describe the genome of Shewanella chilikensis strain DC57, a facultatively anaerobic bacterium isolated from corroded seal rings at a floating oil production system in Australia. The genome of strain DC57 has a size of 4.91 Mbp and harbors 4,178 predicted protein-encoding genes.