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Technosols can be used to rehabilitate degraded land and reuse wastes. Ideally, these newly formed soils should also fulfil the main soil functions. In this study, initially, we characterized the physicochemical and microbial properties of different formulations and their ingredients (i.e., dirt from a waste recovery plant, recycled bentonite, sewage sludge). When these technosols were then used for the rehabilitation of a quarry, the evolution of such properties was monitored for three consecutive years. Physicochemical and microbial properties were compared to those of a reference soil from a nearby forest. Diversity and composition of prokaryotes and eukaryotes were determined using 16S and 18S rRNA amplicon sequencing. Three years after establishment, as much as 78.8% and 63.9% of the prokaryotic and eukaryotic orders, respectively, were shared between the technosols and the reference forest soil. Although technosols initially showed lower values of CO2 emission, compaction and functional diversity (Biolog EcoPlates™), at the end of the study these values were similar to those observed in the reference forest soil. It was concluded that the microbiota of the studied technosols resembles that of the nearby forest soil after just three years of establishment.

Livestock manure-derived amendments can be beneficial for agricultural soil quality, as they can increase the content of soil organic matter and nutrients, stimulate microbial activity and biomass, and enhance crop yield. Here, we studied the impact of six different manure-derived amendments, according to the origin (horse manure-derived vs. chicken manure-derived) and type of amendment (fresh vs. composted vs. bokashi), on agricultural soil quality. To this purpose, an experiment was conducted with lettuce plants, paying special attention to amendment-induced changes in soil microbial properties and the abundance and risk of dissemination of antibiotic resistance genes (ARGs) through horizontal gene transfer (HGT). Soils amended with fresh manure showed higher values of microbial biomass and activity. In particular, fresh chicken manure yielded the highest crop yield of lettuce, but also increased the abundance of ARGs considerably. Genes encoding mobile genetic elements (tnpA, intI1) were positively correlated with ARGs, suggesting a risk of dissemination of antibiotic resistance via HGT in agricultural soils, as a result of the application of livestock manure-derived amendments. In order to minimize this risk, we therefore suggest that manure-derived amendments be properly treated and managed prior to their application to agricultural soil.

Studying the dynamics of nitrogen and sulphur cycling bacteria in river surface sediments is essential to better understand their contribution to global biogeochemical cycles. Evaporitic rocks settled at the headwater of the Deba River catchment (northern Spain) lead to high values of sulphate concentration in its waters. Besides, the discharge of effluents from untreated and treated residual (urban and industrial) wastewaters increases the concentration of metals, nutrients and organic compounds in its mid- and low-water courses. The aim of this study was to assess the impact of anthropogenic contamination from untreated and treated residual and industrial wastewaters on the structure and function of bacterial communities present in surface sediments of the Deba River catchment. The application of a quantitative functional approach (qPCR) based on denitrification genes (nir: nirS+nirK; and nosZ), together with a 16S rRNA gene metabarcoding structural analysis, revealed (i) the high relevance of the sulphur cycle at headwater surface sediments (as reflected by the abundance of members of the Syntrophobacterales order, and the Sulfuricurvum and Thiobacillus genera) and (ii) the predominance of sulphide-driven autotrophic denitrification over heterotrophic denitrification. Incomplete heterotrophic denitrification appeared to be predominant in surface sediments strongly impacted by treated and untreated effluents, as reflected by the lower values of the nosZ/nir ratio, thus favouring N2O emissions. Understanding nitrogen and sulphur cycling pathways has profound implications for the management of river ecosystems, since this knowledge can help us determine whether a specific river is acting or not as a source of greenhouse gases (i.e., N2O).

The incorporation of stover into soil can bring beneficial effects in terms of soil fertility, stabilization of soil structure, maintenance of soil organic carbon, etc. We evaluated the effects, after 6 years of consecutive treatment, of corn stover incorporation versus corn stover removal on soil quality, using physicochemical and biological parameters as indicators of soil quality. Throughout the experimental period, soil organic carbon decreased as a result of stover removal (from 20.1 to 14.7 g kg−1). Substrate-induced respiration and bacterial gene abundance decreased by stover removal over the same period (24.0 and 47.6%, respectively). Biolog EcoPlates™ data showed faster rates of d -xylose and D-mannitol utilization by the soil bacterial communities under stover incorporation. 16 S and 18 S rRNA Illumina sequencing data did not show significant differences in terms of microbial diversity and composition between stover incorporation and stover removal treatments. Finally, the incorporation of stover resulted in higher values (27.2% higher) of soil quality, as reflected by the value of a Soil Quality Index, which integrates the values of a variety of microbial indicators of soil quality. In conclusion, incorporation of stover after corn harvest is a beneficial agronomic practice which enhances soil N and C pools and stimulates microbial communities, leading to an increase in soil quality.

To avoid loss of genetic information in environmental DNA (eDNA) field samples, the preservation of nucleic acids during field sampling is a critical step. In the development of standard operating procedures (SOPs) for eDNA-based compliance monitoring, the effect of different routinely used sediment preservations on biological community structures serving as bioindicators has gone untested. We compared eDNA metabarcoding results of marine bacterial communities from sample aliquots that were treated with a nucleic acid preservation solution (treated samples) and aliquots that were frozen without further treatment (non-treated samples). Sediment samples were obtained from coastal locations subjected to different stressors (aquaculture, urbanization, industry). DNA extraction efficiency, bacterial community profiles, and measures of alpha- and beta-diversity were highly congruent between treated and non-treated samples. As both preservation methods provide the same relevant information to environmental managers and regulators, we recommend the inclusion of both methods into SOPs for biomonitoring in marine coastal environments.

8 pages, 1 table, The incursion of High-Throughput Sequencing (HTS) in environmental microbiology brings unique opportunities and challenges. HTS now allows a high-resolution exploration of the vast taxonomic and metabolic diversity present in the microbial world, which can provide an exceptional insight on global ecosystem functioning, ecological processes and evolution. This exploration has also economic potential, as we will have access to the evolutionary innovation present in microbial metabolisms, which could be used for biotechnological development. HTS is also challenging the research community, and the current bottleneck is present in the data analysis side. At the moment, researchers are in a sequence data deluge, with sequencing throughput advancing faster than the computer power needed for data analysis. However, new tools and approaches are being developed constantly and the whole process could be depicted as a fast co-evolution between sequencing technology, informatics and microbiologists. In this work, we examine the most popular and recently commercialized HTS platforms as well as bioinformatics methods for data handling and analysis used in microbial metagenomics. This non-exhaustive review is intended to serve as a broad state-of-the-art guide to researchers expanding into this rapidly evolving field. © 2012 Elsevier B.V., The Department of Biology, University of Oslo, MLSUIO (Molecular Life Science) and ForBio (Norwegian–Swedish Research School in Biosystematics) are acknowledged for financial support, enabling the preparation of this work. R.L. has been financed by a Marie Curie Intra-European Fellowship grant PIEF-GA-2009-235365. T.H.A.H. has been supported with a VISTA/Statoil grant project number 6503

The identification of inteins in viral genomes is becoming increasingly common. Inteins are selfish DNA elements found within coding regions of host proteins. Following translation, they catalyse their own excision and the formation of a peptide bond between the flanking protein regions. Many inteins also display homing endonuclease function. Here, the newly identified coccolithovirus intein is described and is predicted to have both self-splicing and homing endonuclease activity. The biochemical mechanism of its protein splicing activity is hypothesised, and the prevalence of the intein among natural coccolithovirus isolates is tested.