Influence of the Antibiotic Oxytetracycline on the Morphometric Characteristics and Endophytic Bacterial Community of Lettuce (Lactuca sativa L.).

Antibiotics enter the soil with compost prepared from livestock manures and other sources. There is concern that they may influence plant growth and cause antibiotic resistance in soil and plant endospheric microbiomes. In the present work, lettuce plants were cultivated in soil and hydroponics spiked with oxytetracycline (0, 15, and 300 mg × kg-1 and 0, 15, and 50 mg × L-1, respectively) during a 28-day greenhouse experiment. It was revealed that the antibiotic reduced the chlorophyll content, the biomass, and the length of the roots and stems by 1.4-4.7, 1.8-39, 2.5-3.2, and 1.8-6.3 times in soil and in hydroponics. The copy numbers of the tet(A) and tet(X) genes were revealed to be 4.51 × 103-1.58 × 105 and 8.36 × 106-1.07 × 108 copies × g-1, respectively, suggesting the potential migration of these genes from soil/hydroponics to plant roots and leaves. According to a non-metric multidimensional scaling (NMDS) analysis of the 16S rRNA amplicon sequencing data, endospheric bacterial communities were similar in leaves and roots independent of the growing substrate and antibiotic concentration. While soil bacterial communities were unaffected by the presence of antibiotics, hydroponic communities exhibited dependency, likely attributable to the absence of the mitigating effect of soil particle absorption.

Bioremediation of contaminated soil and groundwater by in situ biostimulation.

Bioremediation by in situ biostimulation is an attractive alternative to excavation of contaminated soil. Many in situ remediation methods have been tested with some success; however, due to highly variable results in realistic field conditions, they have not been implemented as widely as they might deserve. To ensure success, methods should be validated under site-analogous conditions before full scale use, which requires expertise and local knowledge by the implementers. The focus here is on indigenous microbial degraders and evaluation of their performance. Identifying and removing biodegradation bottlenecks for degradation of organic pollutants is essential. Limiting factors commonly include: lack of oxygen or alternative electron acceptors, low temperature, and lack of essential nutrients. Additional factors: the bioavailability of the contaminating compound, pH, distribution of the contaminant, and soil structure and moisture, and in some cases, lack of degradation potential which may be amended with bioaugmentation. Methods to remove these bottlenecks are discussed. Implementers should also be prepared to combine methods or use them in sequence. Chemical/physical means may be used to enhance biostimulation. The review also suggests tools for assessing sustainability, life cycle assessment, and risk assessment. To help entrepreneurs, decision makers, and methods developers in the future, we suggest founding a database for otherwise seldom reported unsuccessful interventions, as well as the potential for artificial intelligence (AI) to assist in site evaluation and decision-making.

Novel Biodegradable Chelating Agents for Micronutrient Fertilization.

Serious concerns about the negative impact of ethylenediaminetetraacetic acid (EDTA) on the environment resulted in severe restrictions imposed on this compound in many countries. One of the main concerns is related to the use of EDTA in agriculture as a chelator in microelement fertilizers: being introduced directly into the sawing fields, it penetrates into groundwater, with no chance to be captured/recycled. Respectively, there is an active search for environmentally friendly, biodegradable alternatives for this chelator. In this study, we proposed a biodegradable chelating agent, 2-((1,2-dicarboxyethyl)amino)pentanedioic acid (IGSA). It was synthesized in accordance with the principles of "green chemistry" from readily available nonhazardous precursors using water as a solvent; in addition, the method yields literally no waste. The synthesized chelator in the form of the crude reaction mixture was further used for preparing a multicomponent micronutrient fertilizer (B, Zn, Fe, Cu, Mn, and Mo). The fertilizer was shown to be highly biodegradable (72% in 28 days), while the EDTA-based product degraded only by 13%. The plant growing efficiency was tested on lettuce in the greenhouse experiments. The results were compared against the known commercial fertilizers based on EDTA and iminodisuccinic acid (IDS). The newly developed IGSA-based fertilizer significantly outperformed the EDTA-based fertilizer in lettuce biomass (1.4 and 1.6 times for root and foliar application, respectively). The total mineral uptake was almost two times higher (1.9 and 1.8 times for root and foliar treatments, respectively) compared to the EDTA-based complex and even slightly higher (1.2 and 1.1 times, respectively) compared to the IDS-based complex. Our work opens the doors for the industrial scale production and application of this fully "green", inexpensive microelement fertilizer that has the potential to replace the EDTA-based products.

Study of Boraginaceae plants for phytoremediation of oil-contaminated soil.

Long-term field observations of the natural vegetation cover in industrial and adjacent areas has revealed that the Boraginaceae was one of the main plant family representatives of which were noted in oil-contaminated area. In this study against the background of the previously well characterized plant families Poaceae and Fabaceae, the phytoremediation potential of Boraginaceae plants was investigated under the field conditions and described. Among the members of this family, Lithospermum arvense, Nonea pulla, Asperugo procumbens, Lappula myosotis, and Echium vulgare were the most common in oil-contaminated areas. N. pulla was the most tolerant to hydrocarbons and, along with L. arvense and E. vulgare, actively stimulated the soil microorganisms, including hydrocarbon-oxidizing ones, in their rhizosphere. A comparative assay confirmed that the plants of the Fabaceae family as a whole more efficiently enrich the soil both with available nitrogen and with pollutant degradation genes. Nevertheless, the comparatively high ammonium nitrogen content in the rhizosphere of N. pulla and E. vulgare allows these species to be singled out to explain their high rhizosphere effect, and to suggest their remediation potential for oil-contaminated soil.Novelty statement Against the background of the previously well characterized plant families Poaceae and Fabaceae, the remediation potential of Boraginaceae plants was described for the first time. Overall, this study contributes to understanding the differences in remediation potential of plants at the family level and suggests the monitoring pollutant degradation genes as an informative tool to the search for plant promising for use in the cleanup of oil-contaminated soil.

Response of bacterial and fungal communities to high petroleum pollution in different soils.

Petroleum pollution of soils is a major environmental problem. Soil microorganisms can decompose a significant fraction of petroleum hydrocarbons in soil at low concentrations (1-5%). This characteristic can be used for soil remediation after oil pollution. Microbial community dynamics and functions are well studied in cases of moderate petroleum pollution, while cases with heavy soil pollution have received much less attention. We studied bacterial and fungal successions in three different soils with high petroleum contents (6 and 25%) in a laboratory experiment. The proportion of aliphatic and aromatic compounds decreased by 4-7% in samples with 6% pollution after 120 days of incubation but remained unchanged in samples with 25% hydrocarbons. The composition of the microbial community changed significantly in all cases. Oil pollution led to an increase in the relative abundance of bacteria such as Actinobacteria and the candidate TM7 phylum (Saccaribacteria) and to a decrease in that of Bacteroidetes. The gene abundance (number of OTUs) of oil-degrading bacteria (Rhodococcus sp., candidate class TM7-3 representative) became dominant in all soil samples, irrespective of the petroleum pollution level and soil type. The fungal communities in unpolluted soil samples differed more significantly than the bacterial communities. Nonmetric multidimensional scaling revealed that in the polluted soil, successions of fungal communities differed between soils, in contrast to bacterial communities. However, these successions showed similar trends: fungi capable of lignin and cellulose decomposition, e.g., from the genera Fusarium and Mortierella, were dominant during the incubation period.

Response of soil bacterial communities to high petroleum content in the absence of remediation procedures.

Oil spills are events that frequently lead to petroleum pollution. This pollution may cause stress to microbial communities, which require long adaption periods. Soil petroleum pollution is currently considered one of the most serious environmental problems. In the present work, processes occurring in the bacterial communities of three soil samples with different physicochemical characteristics, artificially polluted with 12% of crude oil, were investigated in 120-day laboratory experiment. It was found that the total petroleum hydrocarbon content did not decrease during this time; however, the proportion of petroleum fractions was altered. Petroleum pollution led to a short-term decrease in the bacterial 16S rRNA gene copy number. On the basis of amplicon sequencing analysis, it was concluded that bacterial community successions were similar in the three soils investigated. Thus, the phyla Actinobacteria and Proteobacteria and candidate TM7 phylum (Saccaribacteria) were predominant with relative abundances ranging from 35 to 58%, 25 to 30%, and 15 to 35% in different samples, respectively. The predominant operational taxonomic units (OTUs) after pollution belonged to the genera Rhodococcus and Mycobacterium, families Nocardioidaceae and Sinobacteraceae, and candidate class ТМ7-3. Genes from the alkIII group encoding monoxygenases were the most abundant compared with other catabolic genes from the alkI, alkII, GN-PAH, and GP-PAH groups, and their copy number significantly increased after pollution. The copy numbers of expressed genes involved in the horizontal transfer of catabolic genes, FlgC, TraG, and OmpF, also increased after pollution by 11-33, 16-63, and 11-71 times, respectively. The bacterial community structure after a high level of petroleum pollution changed because of proliferation of the cells that initially were able to decompose hydrocarbons, and in the second place, because proliferation of the cells that received these catabolic genes through horizontal transfer.

The abundance of health-associated bacteria is altered in PAH polluted soils-Implications for health in urban areas?

Long-term exposure to polyaromatic hydrocarbons (PAHs) has been connected to chronic human health disorders. It is also well-known that i) PAH contamination alters soil bacterial communities, ii) human microbiome is associated with environmental microbiome, and iii) alteration in the abundance of members in several bacterial phyla is associated with adverse or beneficial human health effects. We hypothesized that soil pollution by PAHs altered soil bacterial communities that had known associations with human health. The rationale behind our study was to increase understanding and potentially facilitate reconsidering factors that lead to health disorders in areas characterized by PAH contamination. Large containers filled with either spruce forest soil, pine forest soil, peat, or glacial sand were left to incubate or contaminated with creosote. Biological degradation of PAHs was monitored using GC-MS, and the bacterial community composition was analyzed using 454 pyrosequencing. Proteobacteria had higher and Actinobacteria and Bacteroidetes had lower relative abundance in creosote contaminated soils than in non-contaminated soils. Earlier studies have demonstrated that an increase in the abundance of Proteobacteria and decreased abundance of the phyla Actinobacteria and Bacteroidetes are particularly associated with adverse health outcomes and immunological disorders. Therefore, we propose that pollution-induced shifts in natural soil bacterial community, like in PAH-polluted areas, can contribute to the prevalence of chronic diseases. We encourage studies that simultaneously address the classic "adverse toxin effect" paradigm and our novel "altered environmental microbiome" hypothesis.

Fungal and bacterial successions in the process of co-composting of organic wastes as revealed by 454 pyrosequencing.

Composting is viewed as one of the primary methods to treat organic wastes. Co-composting may improve the efficiency of this treatment by establishing the most suitable conditions for decomposers than those present in the individual wastes. Given that bacteria and fungi are the driving agents of composting, information about the composition of their communities and dynamics during composting may improve reproducibility, performance and quality of the final compost as well as help to evaluate the potential human health risk and the choice of the most appropriate application procedure. In this study, the co-composting of mixtures containing two similar components (organic fraction of municipal solid waste and sawdust polluted by oil) and one discriminate component (sewage sludges of different origin) were investigated. Bacterial and fungal community successions in the two mixtures were analyzed during the composting process by determining the change in their structural dynamics using qPCR and 454 pyrosequencing methods in a lab experiment for a period of 270 days. During the initial composting stage, the number of 16S bacterial copies was (3.0±0.2) x 106 and (0.4±0.0) x 107 g-1, and the Rhodospiralles and Lactobacialles orders dominated. Fungal communities had (2.9±0.0) x105 and (6.1±0.2) x105 ITS copies g-1, and the Saccharomycetales order dominated. At the end of the thermophilic stage on the 30th day of composting, bacterial and fungal communities underwent significant changes: dominants changed and their relative abundance decreased. Typical compost residents included Flavobacteriales, Chitinophagaceae and Bacterioidetes for bacteria and Microascaceae, Dothideomycetes, Eurotiomycetes, Sordariomycetes, and Agaricomycetes for fungi. During the later composting stages, the dominating taxa of both bacterial and fungal communities remained, while their relative abundance decreased. In accordance with the change in the dominating OTUs, it was concluded that the dynamics of the bacterial and fungal communities were not similar. Analysis by non-metric multidimensional scaling (NMDS) revealed that the bacterial communities of the two composts became progressively more similar; a similar trend was followed by the fungal community.