Development of a microbial test suite and data integration method for assessing microbial health of contaminated soil

Cerium oxide nanoparticles (nCeO2) exert minimal adverse effects on microbial communities in soils with and without biosolids amendment

Increased use of nano-cerium oxide (nCeO₂) in an array of industrial applications has raised environmental concerns due to potential increased loadings to the soil environment. This research investigated the potential adverse effects of nCeO₂ (10-30 nm) on the soil microbial community in two exposure scenarios: direct application to soil, and indirect application to soil through chemical spiking of biosolids, followed by mixing into soil. Total Ce in test soils without, and with biosolids amendment, ranged from 44 to 770, and 73 to 664 mg Ce kg^-1 soil, respectively. In order to help distinguish whether observed effects were elicited by the solid-phase colloids or the activity of dissolved Ce, a soluble Ce salt (Ce (NO₃)₃) treatment was included in select assays. A suite of tests was used to investigate effects on critical processes: microbial growth (heterotrophic plate count), microbial activity (organic matter (OM) decomposition, enzyme activity and, nitrification) and diversity (structural and functional). Although results showed significant inhibition on microbial growth in soil without biosolids amendment at ≥ 156 mg Ce kg^-1 soil by week 5, these results were inconsistent and non-significant thereafter. In general, nCeO₂ showed no evidence of consistent adverse effects on OM decomposition, nitrification, soil enzyme activities and functional diversity. Leucine aminopeptidase showed significant (p< 0.05) stimulatory effects over time at ≥ 44 mg Ce kg^-1 in soils without biosolids, which was not observed in soils with biosolids amendment. The lack of inhibitory effects of nCeO₂ may be attributed to its low solubility; Ce in soil extracts (0.01 M CaCl₂) were all below detection (< 0.003 mg kg^-1) in the nCeO₂-spiked soils, but detectable in the Ce (NO₃)₃ samples. In contrast, soluble Ce at 359 mg Ce kg^-1 showed a significant reduction in OM decomposition and effects on microbial genomic diversity based on the 16S rDNA data in soils with and without biosolids amendment (359 and 690 mg Ce kg^-1). The nCeO₂ behaviour and effects information described herein are expected to help fulfill data gaps for the characterization of this priority nanomaterial.

Isolation and Characterization of Oil-Degrading Enterobacter sp. from Naturally Hydrocarbon-Contaminated Soils and Their Potential Use against the Bioremediation of Crude Oil

The contamination of crude oil in soil matrices is a persistent problem with negative repercussions because of the recalcitrant, hazardous, and mutagenic properties of its constituents. To mitigate the effect of crude oil contamination in soil, the use of microorganisms is a cheap and feasible option. In the current study, bacterial species from numerous polluted oil field surfaces were isolated and examined for their ability to degrade crude oil. Random soil samples polluted with hydrocarbons were collected and various bacterial isolates were isolated. Results revealed that 40% of total isolates had potential use for hydrocarbon biodegradation, the synthesis of exopolysaccharides and the solubilization of phosphorous. Following isolation and characterization to degrade crude oil, a pot trial was conducted using maize inoculated with the four best strains—i.e., S1 (PMEL-63), S2 (PMEL-67), S3 (PMEL-80), and S4 (PMEL-79)—in artificially hydrocarbon-polluted soil with concentrations of crude oil of 0, 1000, and 2000 ppm. Results revealed that S4 (PMEL-79) had significant potential to degrade hydrocarbon in polluted soils. The root length, shoot length, and fresh biomass of maize were increased by 65%, 45%, and 98%, respectively, in pots inoculated with S4 (PMEL-79) Enterobacter cloacae subsp., whereas the lowest root length was observed where no strain was added and the concentration of crude oil was at maximum. Moreover, S4 (PMEL-79) Enterobacter cloacae subsp. was found to be the most effective strain in degrading crude oil and increasing maize growth under polluted soil conditions. It was concluded that the isolation of microorganisms from oil-contaminated sites should be considered in order to identify the most effective microbial consortium for the biodegradation of naturally hydrocarbon-contaminated soils.

Ecotoxicological effects of copper oxide nanoparticles (nCuO) on the soil microbial community in a biosolids-amended soil

This study represents a holistic approach in assessing the effects of copper oxide nanoparticles (nCuO) on microbial health and community structure in soil amended with municipal biosolids. The biosolids were amended with nCuO (<50 nm) and mixed into a sandy loam soil at measured Cu concentrations of 27, 54, 123, 265 and 627 mg Cu kg^-1 soil. A suite of tests were used to assess the potential impact of nCuO on microbial growth, activity, and diversity. Microbial growth was determined by the heterotrophic plate count (HPC) method, while microbial diversity was assessed using both community level physiological profiling (CLPP) and 16S ribosomal DNA (rDNA) sequencing. Microbial activity was assessed by examining soil nitrification, organic matter decomposition, soil respiration (basal and substrate induced) and soil enzyme assays for dehydrogenase, phosphatase and β-glucosidase activities. As a readily soluble positive control, copper sulfate (CuSO₄) was used at measured Cu concentrations of 65, 140, 335 and 885 mg Cu kg^-1 soil for select tests, and at the highest concentration for the remaining tests. Analysis on Cu bioavailability revealed that extractable Cu²⁺ was higher in CuSO₄-spiked soils than nCuO-spiked soils. At a nCuO exposure concentration of ≤265 mg Cu kg^-1 soil, stimulatory effects were observed in nitrification, β-glucosidase and community level physiological profiling (CLPP) tests. nCuO showed no significant inhibitory effects on the soil microbial growth, activity or diversity at the highest concentration (i.e. 627 mg Cu kg^-1 soil), with the exception of the dehydrogenase (i.e. ≥27 mg Cu kg^-1 soil) and phosphatase (i.e. 627 mg Cu kg^-1 soil) enzyme activities. In contrast, inhibition from CuSO₄ at 885 mg Cu kg^-1 soil was observed in all tests with the exception of β-glucosidase enzyme activity. The growth of a Cu tolerant bacterium, Rhodanobacter sp., was observed at 885 mg Cu kg^-1 soil (CuSO₄).

The Ecobiomics project: Advancing metagenomics assessment of soil health and freshwater quality in Canada

Transformative advances in metagenomics are providing an unprecedented ability to characterize the enormous diversity of microorganisms and invertebrates sustaining soil health and water quality. These advances are enabling a better recognition of the ecological linkages between soil and water, and the biodiversity exchanges between these two reservoirs. They are also providing new perspectives for understanding microorganisms and invertebrates as part of interacting communities (i.e. microbiomes and zoobiomes), and considering plants, animals, and humans as holobionts comprised of their own cells as well as diverse microorganisms and invertebrates often acquired from soil and water. The Government of Canada's Genomics Research and Development Initiative (GRDI) launched the Ecobiomics Project to coordinate metagenomics capacity building across federal departments, and to apply metagenomics to better characterize microbial and invertebrate biodiversity for advancing environmental assessment, monitoring, and remediation activities. The Project has adopted standard methods for soil, water, and invertebrate sampling, collection and provenance of metadata, and nucleic acid extraction. High-throughput sequencing is located at a centralized sequencing facility. A centralized Bioinformatics Platform was established to enable a novel government-wide approach to harmonize metagenomics data collection, storage and bioinformatics analyses. Sixteen research projects were initiated under Soil Microbiome, Aquatic Microbiome, and Invertebrate Zoobiome Themes. Genomic observatories were established at long-term environmental monitoring sites for providing more comprehensive biodiversity reference points to assess environmental change.

Soil exposed to silver nanoparticles reveals significant changes in community structure and altered microbial transcriptional profiles

Anthropogenic activities can disrupt soil ecosystems, normally resulting in reduced soil microbial health. Regulatory agencies need to determine the effects of uncharacterized substances on soil microbial health to establish the safety of these chemicals if they end up in the environment. Previous work has focused on measuring traditional ecotoxicologial endpoints within the categories of microbial biomass, activity, and community structure/diversity. Because these tests can be labor intensive, lengthy to conduct, and cannot measure changes in individual gene functions, we wanted to establish whether metatranscriptomics could be used as a more sensitive endpoint and provide a perspective on community function that is more informative than taxonomic identification of microbes alone. We spiked a freshly collected sandy loam soil (Vulcan, Alberta, Canada) with 0, 60, 145, 347, 833, and 2000 mg kg^-1 of silver nanoparticles (AgNPs), a known antagonist of microorganisms due to its propensity for dissolution of toxic silver ions. Assessments performed in our previous work using traditional tests demonstrated the toxicity of AgNPs on soil microbial processes. We expanded this analysis with genomics-based tests by measuring changes in community taxonomic structure and function using 16S rDNA profiling and metatranscriptomics. In addition to identifying bacterial taxa affected by AgNPs, we found that genes involved in heavy metal resistance (e.g., the CzcA efflux pump) and other toxicity response pathways were highly upregulated in the presence of silver. Dose-response analysis using BMDExpress2 software successfully modeled many physiologically relevant genes responding to low concentrations of AgNPs. We found that the transcriptomic point of departure (BMD₅₀) was lower than the IC50s calculated using the traditional tests in our previous work. These results suggest that dose-response modeling of metatranscriptomic gene expression is a useful tool in soil microbial health assessment. SUMMARY: Genomics-based endpoints for the assessment of soil microbial health can be used to perform quantitative dose-response modeling, and soil-based RNAseq adds functional insights.

Standard methods for the assessment of structural and functional diversity of soil organisms: A review

The lack of standardized methods to study soil organisms prevents comparisons across data sets and the development of new global and regional experiments and assessments. Moreover, standardized methods are needed to evaluate the impact of anthropogenic stressors, such as chemicals, on soil organism communities in the regulatory context. The goal of this contribution is to summarize current methodological approaches to measure structural and functional diversity of soil organisms, and to identify gaps and methodological improvements so as to cross data sets generated worldwide. This is urgently needed because several currently ongoing regional and global soil biodiversity studies are not coordinated with one another in terms of methodology, including database development. Therefore, we evaluated the standard methods to sample, identify, determine, and assess soil organisms currently applied or proposed, using well-accepted criteria such as ecological relevance; practicability of usage in terms of resources, time, and costs; and the level of standardization. Methods addressing both the structure and the functions of soil organisms (populations or communities) are included, with a special focus on new molecular methods based on nucleic acid extraction and further analyses by polymerase chain reaction (PCR)-based approaches for microorganisms and invertebrates. We particularly highlight the activities of the Technical Committee (TC) 190 of the International Organization for Standardization (ISO) because ISO guidelines are legally accredited by many national or international authorities when they put conservation laws and regulations into practice. Finally, we propose detailed recommendations regarding gaps in the available set of standards, in order to identify a list of new methods to be standardized. We propose to organize this whole process under the Global Soil Biodiversity Initiative (GSBI) in order to ensure a truly global approach for the assessment of soil biodiversity. Integr Environ Assess Manag 2018;14:463-479. © 2018 SETAC.