The microbiota of technosols resembles that of a nearby forest soil three years after their establishment

A method for evaluating the effects of gentle remediation options (GRO) on soil health: Demonstration at a DDX-contaminated tree nursery in Sweden

Healthy soils provide valuable ecosystem services (ES), but soil contamination can inhibit essential soil functions (SF) and pose risks to human health and the environment. A key advantage of using gentle remediation options (GRO) is the potential for multifunctionality: to both manage risks and improve soil functionality. In this study, an accessible, scientific method for soil health assessment directed towards practitioners and decision-makers in contaminated land management was developed and demonstrated for a field experiment at a DDX-contaminated tree nursery site in Sweden to evaluate the relative effects of GRO on soil health (i.e., the 'current capacity' to provide ES). For the set of relevant soil quality indicators (SQI) selected using a simplified logical sieve, GRO treatment was observed to have highly significant effects on many SQI according to statistical analysis due to the strong influence of biochar amendment on the sandy soil and positive effects of nitrogen-fixing leguminous plants. The SQI were grouped within five SF and the relative effects on soil health were evaluated compared to a reference state (experimental control) by calculating quantitative treated-SF indices. Multiple GRO treatments are shown to have statistically significant positive effects on many SF, including pollutant attenuation and degradation, water cycling and storage, nutrient cycling and provisioning, and soil structure and maintenance. The SF were in turn linked to soil-based ES to calculate treated-ES indices and an overall soil health index (SHI), which can provide simplified yet valuable information to decision-makers regarding the effectiveness of GRO. The experimental GRO treatment of the legume mix with biochar amendment and grass mix with biochar amendment are shown to result in statistically significant improvements to soil health, with overall SHI values of 141 % and 128 %, respectively, compared to the reference state of the grass mix without biochar (set to 100 %).

Effect of chicken manure on soil microbial community diversity in poultry keeping areas

The poultry industry is generating a significant amount of waste from chicken droppings that are abundant in microbes as well as macro- and micronutrients suitable for manure. It has the potential to improve the microbial activity and nutrient dynamics in the soil, ultimately improving soil fertility. The present study aimed to investigate the effect of chicken droppings manure (CDM) on the diversity of the soil microbiome in the free walking chicken's area located in Stefanidar, Rostov Region, Russia. The data obtained were compared with 16 s rRNA from control samples located not far from the chicken's free-walking area, but not in direct contact with the droppings. Effect of CDM on the physicochemical characteristics of the soil and changes in its microbial diversity were assessed by employing the metagenomic approaches and 16 s rRNA-based taxonomic assessment. The alpha and beta diversity indices revealed that the application of the CDM significantly improved the soil microbial diversity. The 16S taxonomical analysis confirmed Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Planctomycetes as abundant bacterial phylum. It also revealed the increase in the total number of the individual operational taxonomic unit (OTU) species, a qualitative indicator of the rich microbial community. The alpha diversity confirmed that the significant species richness of the soil is associated with the CDM treatment. The increased OTUs represent the qualitative indicator of a community that has been studied up to the depth of 5-20 cm of the CDM treatment range. These findings suggested that CDM-mediated microbial richness are believed to confer the cycling of carbon, nitrogen, and sulfur, along with key soil enzymes such as dehydrogenases and catalase carbohydrate-active enzymes. Hence, the application of CDM could improve soil fertility by nutrient cycling caused by changes in soil microbial dynamics, and it could also be a cost-effective sustainable means of improving soil health.

The effect of combined pollution by PAHs and heavy metals on the topsoil microbial communities of Spolic Technosols of the lake Atamanskoe, Southern Russia

The contamination with organic and inorganic pollutants changes significantly soil microbial community structure. These shifts indicate anthropogenic pressure and help to discover new possibilities for soil remediation. In this study, the microbial community structure of Spolic Technosols formed at the territory of a former industrial sludge reservoir near the Kamensk-Shakhtinsky (Southern Russia) was studied using a metagenomics approach. The studied soils contain high concentrations of heavy metals (HM) (up to 72,900 mg kg^-1) and 16 priority polycyclic aromatic hydrocarbons (PAHs) (up to 6670 mg kg^-1). Its microbial communities demonstrate an excellent adaptability level reflected in their complexity and diversity. As shown by the high values of alpha diversity indices (Shannon values up to 10.1, Chao1 values from 1430 to 4273), instead of decreasing quantitatively and qualitatively on the systemic level, microbial communities tend to undergo complex redistribution. Regardless of contamination level, the share of Actinobacteria and Proteobacteria was consistently high and varied from 20 to 50%. Following the results of the Mann-Whitney U test, there were significant changes of less abundant phyla. The abundance of oligotrophic bacteria from Gemmatimonadetes and Verrucomicrobia phyla and autotrophic bacteria (e.g., Nitrospira) decreased due to the high PAH's level. And abundance of Firmicutes and amoebae-associated bacteria such as TM6 and soil Chlamydia increased in highly contaminated plots. In the Spolic Technosols studied, the influence of factors on the microbial community composition decreased from PAHs concentration to soil characteristics (organic carbon content) and phylum-phylum interactions. The high concentrations of HMs influenced weakly on the microbial community composition.

Land application of sewage sludge: Response of soil microbial communities and potential spread of antibiotic resistance

The effect of land application of sewage sludge on soil microbial communities and the possible spread of antibiotic- and metal-resistant strains and resistance determinants were evaluated during a 720-day field experiment. Enzyme activities, the number of oligotrophic bacteria, the total number of bacteria (qPCR), functional diversity (BIOLOG) and genetic diversity (DGGE) were established. Antibiotic and metal resistance genes (ARGs, MRGs) were assessed, and the number of cultivable antibiotic- (ampicillin, tetracycline) and heavy metal- (Cd, Zn, Cu, Ni) resistant bacteria were monitored during the experiment. The application of 10 t ha^-1 of sewage sludge to soil did not increase the organic matter content and caused only a temporary increase in the number of bacteria, as well as in the functional and structural biodiversity. In contrast to expectations, a general adverse effect on the tested microbial parameters was observed in the fertilized soil. The field experiment revealed a significant reduction in the activities of alkaline and acid phosphatases, urease and nitrification potential. Although sewage sludge was identified as the source of several ARGs and MRGs, these genes were not detected in the fertilized soil. The obtained results indicate that the effect of fertilization based on the recommended dose of sewage sludge was not achieved.

CoMA - an intuitive and user-friendly pipeline for amplicon-sequencing data analysis

In recent years, there has been a veritable boost in next-generation sequencing (NGS) of gene amplicons in biological and medical studies. Huge amounts of data are produced and need to be analyzed adequately. Various online and offline analysis tools are available; however, most of them require extensive expertise in computer science or bioinformatics, and often a Linux-based operating system. Here, we introduce "CoMA-Comparative Microbiome Analysis" as a free and intuitive analysis pipeline for amplicon-sequencing data, compatible with any common operating system. Moreover, the tool offers various useful services including data pre-processing, quality checking, clustering to operational taxonomic units (OTUs), taxonomic assignment, data post-processing, data visualization, and statistical appraisal. The workflow results in highly esthetic and publication-ready graphics, as well as output files in standardized formats (e.g. tab-delimited OTU-table, BIOM, NEWICK tree) that can be used for more sophisticated analyses. The CoMA output was validated by a benchmark test, using three mock communities with different sample characteristics (primer set, amplicon length, diversity). The performance was compared with that of Mothur, QIIME and QIIME2-DADA2, popular packages for NGS data analysis. Furthermore, the functionality of CoMA is demonstrated on a practical example, investigating microbial communities from three different soils (grassland, forest, swamp). All tools performed well in the benchmark test and were able to reveal the majority of all genera in the mock communities. Also for the soil samples, the results of CoMA were congruent to those of the other pipelines, in particular when looking at the key microbial players.

Soil Microbial Community Profiling and Bacterial Metabolic Activity of Technosols as an Effect of Soil Properties following Land Reclamation: A Case Study from the Abandoned Iron Sulphide and Uranium Mine in Rudki (South-Central Poland)

The aims of the study were (1) to recognize the structure of bacteria diversity in Technosols developed from mine spoils containing iron (Fe) sulphides with the use of culture-independent technique, and (2) to determine microbial metabolic activities, in the context of their potential to be an adequate indicators of soil properties being the consequence of land reclamation. The study site was located in the vicinity of the abandoned Fe sulphide and uranium mine in Rudki village (Holy Cross Mts., Poland). Three soil profiles with different chemical properties (pH, content of carbonates, soil salinity, content of total organic carbon and total nitrogen) were studied. Biodiversity was determined with the use of meta-barcoding of 16S rRNA community profiling analysis based on the hypervariable V3-V4 region of 16S rRNA gene (MiSeq, Illumina). The catabolic fingerprinting of soil microbial communities was evaluated with the use of Biolog®EcoPlates™ System. It was evidenced that changes in microbial structure and their metabolic activity were the consequence of a combined effect of both the soil depth and soil chemical properties being the final result of reclamation process. Consequently, microbial indicators (from phyla to genera level) indirectly testifying about success or ineffectiveness of reclamation in technogenic soils were recommended. To our best knowledge, the present study is the first insight into Polish Technosols biodiversity and catabolic activity.