Ecophysiological Diversity Research Articles

Response of Soil Microbiota, Enzymes, and Plants to the Fungicide Azoxystrobin.

The present study was aimed at assessing the impact of azoxystrobin-a fungicide commonly used in plant protection against pathogens (Amistar 250 SC)-on the soil microbiota and enzymes, as well as plant growth and development. The laboratory experiment was conducted in three analytical terms (30, 60, and 90 days) on sandy clay (pH-7.0). Azoxystrobin was applied to soil in doses of 0.00 (C), 0.110 (F) and 32.92 (P) mg kg-1 d.m. of soil. Its 0.110 mg kg-1 dose stimulated the proliferation of organotrophic bacteria and actinobacteria but inhibited that of fungi. It also contributed to an increase in the colony development index (CD) and a decrease in the ecophysiological diversity index (EP) of all analyzed groups of microorganisms. Azoxystrobin applied at 32.92 mg kg-1 reduced the number and EP of microorganisms and increased their CD. PP952051.1 Bacillus mycoides strain (P), PP952052.1 Prestia megaterium strain (P) bacteria, as well as PP952052.1 Kreatinophyton terreum isolate (P) fungi were identified in the soil contaminated with azoxystrobin, all of which may exhibit resistance to its effects. The azoxystrobin dose of 0.110 mg kg-1 stimulated the activity of all enzymes, whereas its 32.92 mg kg-1 dose inhibited activities of dehydrogenases, alkaline phosphatase, acid phosphatase, and urease and stimulated the activity of catalase. The analyzed fungicide added to the soil at both 0.110 and 32.92 mg kg-1 doses inhibited seed germination and elongation of shoots of Lepidium sativum L., Sinapsis alba L., and Sorgum saccharatum L.

Influence of biodestructors on sequestration of labile carbon compounds in the soil

Ukraine stands as a testament to agricultural wealth due to its fertile soils, most notably, its significant share of the world’s chornozem. Rich soil is fundemantal to agricultural production, and therefore the success of the agricultural industry heavily relies on the fertility of the soil. However, modern agricultural practices in Ukraine, have led to increased anthropogenic impact on soils, affecting their biodiversity and humus content. In this regard, it is becoming increasingly important to perform comprehensive studies of microbiological, biochemical and chemical processes in the soil in response to different agricultural interventions. The urgent need to restore natural ecosystems to preserve their biodiversity and ensure ecological stability poses new scientific challenges, emphasizing the importance of urgent measures aimed at protecting the environment from pollution and degradation. This research aims to explore the effects of biodestructors on the deposition of labile carbon compounds in the soil during long-term consistent corn cultivation. The research was conducted during 2020–2023 within the framework of a stationary field experiment of the scientific research department of the «Druzhba Nova» in Varva village, Chernihiv region. The soil is a typical low-humus chornozem with the experiment focusing on a monoculture corn crop rotation. The DKC 4351 corn hybrid was sown at a density of 82 thousand units per hectare, employing a three-part experiment design: 1) a UAN control at 32–28 l/ha, 2) Ecostern Classic at 2 l/ha combined with UAN 32–28 l/ha, and 3) Ecostern Bacterial at 2 l/ha alongside Ecostern Trichoderma at 1 l/ha and UAN 32–28 l/ha. In the present study, the influence of biodestructors on soil’s agrochemical and microbiological indicators, as well as corn yield was evaluated. In a long-term stationary field experiment conducted on a typical low-humus chornozem, we investigated the influence of microbial preparations — plant residue biodestructors — on the deposition of labile carbon compounds in the soil under continuos corn cultivation. The application of Ecostern Classic and a combination of Ecostern Bacterial + Ecostern Trichoderma biodestructors resulted in an increase of labile carbon content by 0.11% and 0.18%, respectively, compared to the control. The aim of further analysis was to determinate the dynamics of the organic matter transformation coefficient, which is a marker of enhanced microbiological activity in the soil and a predominance of organic matter synthesis over its mineralization. In treatments utilizing biodestructors, this indicator was significantly higher than control values throughout the study. The survival of the fungal bioagent from Ecostern Classic and Ecostern Trichoderma bioproducts in the soil was monitored by assessing the population dynamics of the Trichoderma genus species. Results demonstrated an increase by an average of 19 thousand CFU/g with Ecostern Classic and by 34 thousand CFU/g with the combined use of Ecostern Bacterial with Ecostern Trichoderma, compared to 28 thousand CFU/g in control soil samples. This may indirectly indicate a successful colonization of the bioagent in treated soils. Using BIOTREX technology to evaluate the soil’s ecophysiological diversity, we found that the diversity index increased from 3.66 in control samples to between 4.87 and 5.61 in treatments with biodestructors. According to the further BIOTREX assessment, the use of biodestructors not only increased soil biodiversity, but also improved soil health. The application of these biodestructors also significantly boosted corn grain yield with an increase of 0.32 t/ha with Ecostern Classic treatment and 0.18 t/ha with the combined use of Ecostern Bacterial with Ecostern Trichoderma, compared to control.

Effect of sulcotrione and terbuthylazine on biological characteristics of soil

Excessive and inappropriate use of herbicides in crop protection can lead to soil contamination and thus to changes in this environment, which involves a serious ecological problem. A pot experiment was, a study was conducted to determine how individual and combined application of sulcotrione and terbuthylazine affect the population, diversity and structure of bacterial and fungal communities, soil enzyme activity, as well as growth and development of Zea mays L. These parameters were evaluated during a plant pot experiment conducted in a soil classified to the Eutric Cambisols type. Amending the soil with 0.115 mg kg−1 sulcotrione and 0.165 mg kg−1 terbuthylazine (whether separately or in tandem) did not significantly impact biological activity in the soil. Only the application of sulcotrione in the amount of 1.15 mg kg−1 and terbuthylazine in the amount of 1.65 mg kg−1 disturbed the microbiological and biochemical balance of the soil. Both sulcotrione alone and the sulcotrione-terbuthylazine mixture reduced the number of organotrophic bacteria and actinobacteria, whereas terbuthylazine alone increased the number of fungi. The two chemicals boosted the activity of catalase and acidic phosphatase, while also reducing the dry matter yields of maize. Dehydrogenases activity decreased under the mixture of sulcotrione-terbuthylazine. Terbuthylazine and the sulcotrione-terbuthylazine mixture additionally decreased the SPAD greenness index in maize leaves. The chemicals also affected values of the microbial colony development index and the ecophysiological diversity index. There were also shifts in the structure of bacteria from phyla Actinobacteriota and Proteobacteria, as well as fungi from phyla Ascomycota and Mortiellomycota, though the extent of these changes varied across different soils samples. It can be concluded that microbiological and enzymatic properties of soil are suitable indicators used in diagnosing the quality of soil ecosystems. Bacteria and fungi identified in soil contaminated with sulcotrione and terbuthylazine may have high potential in inactivating these chemicals. The conducted research allowed us to assess the functioning of the soil environment under the influence of single and combined use of sulcotrione and terbuthylazine. They filled the gap regarding the impact of single and combined use of sulcotrione and terbuthylazine on the number and structure of bacterial and fungal communities, enzyme activity and the growth and development of Zea mays L.

Sensitivity of Zea mays and Soil Microorganisms to the Toxic Effect of Chromium (VI).

Chromium is used in many settings, and hence, it can easily enter the natural environment. It exists in several oxidation states. In soil, depending on its oxidation-reduction potential, it can occur in bivalent, trivalent or hexavalent forms. Hexavalent chromium compounds are cancerogenic to humans. The aim of this study was to determine the effect of Cr(VI) on the structure of bacteria and fungi in soil, to find out how this effect is modified by humic acids and to determine the response of Zea mays to this form of chromium. A pot experiment was conducted to answer the above questions. Zea mays was sown in natural soil and soil polluted with Cr(VI) in an amount of 60 mg kg-1 d.m. Both soils were treated with humic acids in the form of HumiAgra preparation. The ecophysiological and genetic diversity of bacteria and fungi was assayed in soil under maize (not sown with Zea mays). In addition, the following were determined: yield of maize, greenness index, index of tolerance to chromium, translocation index and accumulation of chromium in the plant. It has been determined that Cr(VI) significantly distorts the growth and development of Zea mays, while humic acids completely neutralize its toxic effect on the plant. This element had an adverse effect on the development of bacteria of the genera Cellulosimicrobium, Kaistobacter, Rhodanobacter, Rhodoplanes and Nocardioides and fungi of the genera Chaetomium and Humicola. Soil contamination with Cr(VI) significantly diminished the genetic diversity and richness of bacteria and the ecophysiological diversity of fungi. The negative impact of Cr(VI) on the diversity of bacteria and fungi was mollified by Zea mays and the application of humic acids.

Effect of Separate and Combined Toxicity of Bisphenol A and Zinc on the Soil Microbiome.

The research objective was established by taking into account common sources of soil contamination with bisphenol A (B) and zinc (Zn2+), as well as the scarcity of data on the effect of metabolic pathways involved in the degradation of organic compounds on the complexation of zinc in soil. Therefore, the aim of this study was to determine the spectrum of soil homeostasis disorders arising under the pressure of both the separate and combined toxicity of bisphenol A and Zn2+. With a broad pool of indicators, such as indices of the effect of xenobiotics (IFX), humic acid (IFH), plants (IFP), colony development (CD), ecophysiological diversity (EP), the Shannon–Weaver and the Simpson indices, as well as the index of soil biological fertility (BA21), the extent of disturbances was verified on the basis of enzymatic activity, microbiological activity, and structural diversity of the soil microbiome. A holistic character of the study was achieved, having determined the indicators of tolerance (IT) of Sorghum Moench (S) and Panicum virgatum (P), the ratio of the mass of their aerial parts to roots (PR), and the SPAD leaf greenness index. Bisphenol A not only failed to perform a complexing role towards Zn2+, but in combination with this heavy metal, had a particularly negative effect on the soil microbiome and enzymatic activity. The NGS analysis distinguished certain unique genera of bacteria in all objects, representing the phyla Actinobacteriota and Proteobacteria, as well as fungi classified as members of the phyla Ascomycota and Basidiomycota. Sorghum Moench (S) proved to be more sensitive to the xenobiotics than Panicum virgatum (P).

Hydraulic Function Analysis of Conifer Xylem Based on a Model Incorporating Tracheids, Bordered Pits, and Cross-Field Pits

Wood has a highly complex and anisotropic structure. Its xylem characteristics are key in determining the hydraulic properties of plants to transport water efficiently and safely, as well as the permeability in the process of wood impregnation modification. Previous studies on the relationship between the xylem structure and hydraulic conductivity of conifer have mainly focused on tracheids and bordered pits, with only a few focusing on the conduction model of cross-field pits which connect tracheids and rays. This study takes the xylem structure of conifer as an example, drawing an analogy between water flow under tension and electric current, and extends the model to the tissue scale, including cross-field pits by establishing isometric scaling. The structure parameters were collected by scanning electron microscopy and transmission electron microscopy. The improved model can quantify the important hydraulic functional characteristics of xylem only by measuring the more easily obtained tracheid section size. Then, this model was applied to quantify the relationship between the xylem anatomical structure and hydraulic properties in the pine (Pinus sylvestris L. var. mongholica Litv.) and the spruce (Picea koraiensis Nakai), and also to evaluate the effects of the number and size of cross-field pits on xylem conduction. The results showed that the growth ring conduction value of the pine was more than twice that of the spruce for the two tree species with similar growth widths in this study. The tracheid wall resistance of the pine reflected the result of the interaction of the size and number of cross-field pits, in comparison, the wall resistance of the spruce was more sensitive to the number of cross-field pits. Finally, the calculation output of the new model was cross-validated with the literature, which verified the accuracy and effectiveness of the model. This study provides an effective and complete solution for xylem conductivity measurement and the study of wood ecophysiological diversity and processing.

Bisphenol A—A Dangerous Pollutant Distorting the Biological Properties of Soil

Bisphenol A (BPA), with its wide array of products and applications, is currently one of the most commonly produced chemicals in the world. A narrow pool of data on BPA–microorganism–plant interaction mechanisms has stimulated the following research, the aim of which has been to determine the response of the soil microbiome and crop plants, as well as the activity of soil enzymes exposed to BPA pressure. A range of disturbances was assessed, based on the activity of seven soil enzymes, an abundance of five groups of microorganisms, and the structural diversity of the soil microbiome. The condition of the soil was verified by determining the values of the indices: colony development (CD), ecophysiological diversity (EP), the Shannon–Weaver index, and the Simpson index, tolerance of soil enzymes, microorganisms and plants (TIBPA), biochemical soil fertility (BA21), the ratio of the mass of aerial parts to the mass of plant roots (PR), and the leaf greenness index: Soil and Plant Analysis Development (SPAD). The data brought into sharp focus the adverse effects of BPA on the abundance and ecophysiological diversity of fungi. A change in the structural composition of bacteria was noted. Bisphenol A had a more beneficial effect on the Proteobacteria than on bacteria from the phyla Actinobacteria or Bacteroidetes. The microbiome of the soil exposed to BPA was numerously represented by bacteria from the genus Sphingomonas. In this object pool, the highest fungal OTU richness was achieved by the genus Penicillium, a representative of the phylum Ascomycota. A dose of 1000 mg BPA kg−1 d.m. of soil depressed the activity of dehydrogenases, urease, acid phosphatase and β-glucosidase, while increasing that of alkaline phosphatase and arylsulfatase. Spring oilseed rape and maize responded significantly negatively to the soil contamination with BPA.

Perna canaliculus as an Ecological Material in the Removal of o-Cresol Pollutants from Soil.

Soil contamination with cresol is a problem of the 21st century and poses a threat to soil microorganisms, humans, animals, and plants. The lack of precise data on the potential toxicity of o-cresol in soil microbiome and biochemical activity, as well as the search for effective remediation methods, inspired the aim of this study. Soil is subjected to four levels of contamination with o-cresol: 0, 0.1, 1, 10, and 50 mg o-cresol kg−1 dry matter (DM) of soil and the following are determined: the count of eight groups of microorganisms, colony development index (CD) and ecophysiological diversity index (EP) for organotrophic bacteria, actinobacteria and fungi, and the bacterial genetic diversity. Moreover, the responses of seven soil enzymes are investigated. Perna canaliculus is a recognized biosorbent of organic pollutants. Therefore, microbial biostimulation with Perna canaliculus shells is used to eliminate the negative effect of the phenolic compound on the soil microbiome. Fungi appears to be the microorganisms most sensitive to o-cresol, while Pseudomonas sp. is the least sensitive. In o-cresol-contaminated soils, the microbiome is represented mainly by the bacteria of the Proteobacteria and Firmicutes phyla. Acid phosphatase, alkaline phosphatase and urease can be regarded as sensitive indicators of soil disturbance. Perna canaliculus shells prove to be an effective biostimulator of soil under pressure with o-cresol.

Energetic Value of Elymus elongatus L. and Zea mays L. Grown on Soil Polluted with Ni2+, Co2+, Cd2+, and Sensitivity of Rhizospheric Bacteria to Heavy Metals

Plants, and microorganisms associated with them, offer an effective tool for removing pollutants, such as heavy metals, from the soil environment. The aim of this study was to determine changes caused by Ni2+, Co2+, and Cd2+ in the genetic diversity of soil-populating bacteria and the effect these heavy metals on the heating value of elongated coach grass (Elymus elongatus L.) and maize (Zea mays L.). Microorganisms support plants in removing heavy metals from soil. These plants can then be used for energetic purposes. The study aim was accomplished by determining counts of microorganisms and their resistance (RS) to Ni2+, Co2+, Cd2+, their colony development index (CD), ecophysiological diversity index (EP), and diversity established with the next generation sequencing (NGS) method. Further analyses aimed to establish test plants resistance to pollution with heavy metals and their heating value. Organotrophic bacteria turned out to be the most resistant to Co2+, whereas actinobacteria—to Cd2+ effects. At all taxonomic levels, the genetic diversity of bacteria was most adversely influenced by Cd2+ in the soil sown with Zea mays L. Bacteria belonging to Arthrobacter, Rhodoplanes, Kaistobacter, Devosia, Phycicoccus, and Thermomonas genera showed high tolerance to soil pollution with Ni2+, Co2+, and Cd2+, hence they should be perceived as potential sources of microorganisms useful for bioaugmentation of soils polluted with these heavy metals. Ni2+, Co2+, and Cd2+ had no effect on the heating value of Elymus elongatus L. and Zea mays L. The heating value of 1 kg of air-dry biomass of the tested plants was relatively high and ranged from 14.6 to 15.1 MJ. Elymus elongatus L. proved more useful in phytoremediation than Zea mays L.

The Response of the Soil Microbiome to Contamination with Cadmium, Cobalt and Nickel in Soil Sown with Brassica napus

Soil fertility is determined by biological diversity at all levels of life, from genes to entire biocenoses. The aim of this study was to evaluate bacterial diversity in soil contaminated with Cd2+, Co2+ and Ni2+ and sown with Brassica napus. This is an important consideration because soil-dwelling microorganisms support phytoremediation and minimize the adverse effects of heavy metals on the environment. Microbial counts, the influence (IFHM) of Cd2+, Co2+ and Ni2+ on microorganisms, the colony development (CD) index, the ecophysiological diversity (EP) index and genetic diversity of bacteria were determined under controlled conditions. Soil contamination with Cd2+, Co2+ and Ni2+ significantly influenced microbial diversity and increased the values of CD and EP indices. The tested heavy metals decreased the genetic diversity of bacteria, in particular in the phyla Actinobacteria and Proteobacteria. Bacteria of the genera Arthrobacter, Devosia, Kaistobacter, Paenibacillus, Phycicoccus, Rhodoplanes and Thermomonas were identified in both contaminated and non-contaminated soil. These bacteria are highly resistant to soil contamination with Cd2+, Co2+ and Ni2+.

Microbiological Study in Petrol-Spiked Soil.

The pollution of arable lands and water with petroleum-derived products is still a valid problem, mainly due the extensive works aimed to improve their production technology to reduce fuel consumption and protect engines. An example of the upgraded fuels is the BP 98 unleaded petrol with Active technology. A pot experiment was carried out in which Eutric Cambisol soil was polluted with petrol to determine its effect on the microbiological and biochemical properties of this soil. Analyses were carried out to determine soil microbiome composition—with the incubation and metagenomic methods, the activity of seven enzymes, and cocksfoot effect on hydrocarbon degradation. The following indices were determined: colony development index (CD); ecophysiological diversity index (EP); index of cocksfoot effect on soil microorganisms and enzymes (IFG); index of petrol effect on soil microorganisms and enzymes (IFP); index of the resistance of microorganisms, enzymes, and cocksfoot to soil pollution with petrol (RS); Shannon–Weaver’s index of bacterial taxa diversity (H); and Shannon–Weaver’s index of hydrocarbon degradation (IDH). The soil pollution with petrol was found to increase population numbers of bacteria and fungi, and Protebacteria phylum abundance as well as to decrease the abundance of Actinobacteria and Acidobacteria phyla. The cultivation of cocksfoot on the petrol-polluted soil had an especially beneficial effect mainly on the bacteria belonging to the Ramlibacter, Pseudoxanthomonas, Mycoplana, and Sphingobium genera. The least susceptible to the soil pollution with petrol and cocksfoot cultivation were the bacteria of the following genera: Kaistobacter, Rhodoplanes, Bacillus, Streptomyces, Paenibacillus, Phenylobacterium, and Terracoccus. Cocksfoot proved effective in the phytoremediation of petrol-polluted soil, as it accelerated hydrocarbon degradation and increased the genetic diversity of bacteria. It additionally enhanced the activities of soil enzymes.

Microbiological and Biochemical Properties in Eutric/Dystric Brunic Arenosols, Eutric/Endocalcaric Cambisols, and Haplic/Albic Luvisols Soils

To understand the role of microorganisms in the functioning of forest ecosystems, the structure of bacterial communities and the enzymatic activity were determined in forest soils representing the following soil subtypes: Eutric/Dystric Brunic Arenosols (A), Eutric/Endocalcaric Cambisols (C), and Haplic/Albic Luvisols (L). Their microbiological and biochemical properties were compared based on bacterial counts and diversity, and activities of seven soil enzymes: dehydrogenases, catalase, urease, acid phosphatase, alkaline phosphatase, arylsulfatase, and β-glucosidase. Organotrophic bacteria and actinobacteria were the most abundant and featured the highest values of the EP (ecophysiological diversity index) in the Haplic/Albic Luvisol soil. In turn, the CD (colony development index) values of these bacterial groups were the highest in the Eutric/Endocalcaric Cambisols. The OTU number of bacteria allowed concluding that, at the class level, the Eutric/Dystric Brunic Arenosols and Haplic/Albic Luvisols were predominated by Alphaproteobacteria belonging to Proteobacteria, whereas the Eutric/Endocalcaric Cambisols by Actinobacteria. At the family rank, the Eutric/Dystric Brunic Arenosols were colonized in the highest numbers by Mycobacteriaceae, Rhodospirillaceae, Koribacteriaceae, and Acidobacteriaceae; the Eutric/Endocalcaric Cambisols by Nocardiaceae, Bradyrhizobiaceae, and Mycobacteriaceae, whereas Haplic/Albic Luvisols by Sinobacteriaceae and Rhodospirillaceae. Four bacterial genera, i.e., Rhodoplanes, Burkholderia belonging to Proteobacteria, Mycobacterium belonging to Actinobacteria, and Candidatus Solibacter belonging to Acidobacteria, were identified in all soils tested. The genetic diversity of bacteria was proved the highest in Eutric/Endocalcaric Cambisols. In turn, the highest enzymatic activity was found for Haplic/Albic Luvisols, while the lowest one for Eutric/Endocalcaric Cambisols. The present study results point out to significant differences between the soil types analyzed in terms of the diversity and structure of their bacterial communities and their enzymatic properties.

Phylogenetic Divergence and Ecophysiological Variation in the DisjunctKalmia buxifolia(Sand-myrtle, Ericaceae)

Abstract—Kalmia buxifolia(sand-myrtle, Ericaceae) is disjunctly distributed across the high-elevation rock outcrops of the southern Appalachians, upper monadnocks and pine savannas of the Carolina Piedmont and Coastal Plain, and the New Jersey Pine Barrens. Here, we sampled plants from each region and reconstructed the phylogeographic history ofK.buxifoliato test a rock-outcrop Pleistocene refugium hypothesis, estimate the potential direction(s) and timing of migration, and date divergence from its alpine sister species,K. procumbens. We also assess whether isolation in these different environments has led to variation in intrinsic water-use efficiency. Dating analysis challenges the current hypothesis that rock-outcrop species are relics of Pleistocene refugia (< 18,000 ybp), placing the divergence ofK. buxifoliaandK. procumbensmuch earlier, in the late-Miocene (9.40 Ma). Chloroplast haplotype analysis indicates four potential refugial sites, with the most ancient on Mount LeConte in the Great Smoky Mountains, and point to an Appalachian corridor as the likely Pine Barrens colonization route. The sister species divergence time and population level divergences withinK. buxifoliagenerally coincide with major climatic shifts from the late-Miocene to mid-Pleistocene. Results from carbon isotope discrimination indicate that plant water-use varies geographically withinK. buxifolia, as does leaf morphology, although it is unclear whether this variation is due to genetic adaptation or phenotypic plasticity. These patterns of phylogenetic divergence and resulting ecophysiological diversity withinK. buxifoliaare significant for clarifying long-held questions about the biogeographic history and trait differentiation within this species. Further, our results suggest that high-elevation rock outcrop communities may have been inhabitated by northern-affinity species for much longer than previously assumed, and that subsequent population disjunction and isolation may have resulted in ecophysiological differentiation in these communities.

Genomic and Physiological Characteristics of a Novel Nitrite-Oxidizing Nitrospira Strain Isolated From a Drinking Water Treatment Plant.

Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, which is an important process of the biogeochemical nitrogen cycle and is exploited extensively as a biological nitrogen removal process. Members of the genus Nitrospira are often identified as the dominant NOB in a diverse range of natural and artificial environments. Additionally, a number of studies examining the distribution, abundance, and characterization of complete ammonia oxidation (comammox) Nitrospira support the ecological importance of the genus Nitrospira. However, niche differentiation between nitrite-oxidizing Nitrospira and comammox Nitrospira remains unknown due to a lack of pure cultures. In this study, we report the isolation, physiology, and genome of a novel nitrite-oxidizing Nitrospira strain isolated from a fixed-bed column at a drinking water treatment plant. Continuous feeding of ammonia led to the enrichment of Nitrospira-like cells, as well as members of ammonia-oxidizing genus Nitrosomonas. Subsequently, a microcolony sorting technique was used to isolate a novel nitrite-oxidizing Nitrospira strain. Sequences of strains showing the growth of microcolonies in microtiter plates were checked. Consequently, the most abundant operational taxonomic unit (OTU) exhibited high sequence similarity with Nitrospira japonica (98%) at the 16S rRNA gene level. The two other Nitrospira OTUs shared over 99% sequence similarities with N. japonica and Nitrospira sp. strain GC86. Only one strain identified as Nitrospira was successfully subcultivated and designated as Nitrospira sp. strain KM1 with high sequence similarity with N. japonica (98%). The half saturation constant for nitrite and the maximum nitrite oxidation rate of strain KM1 were orders of magnitude lower than the published data of other known Nitrospira strains; moreover, strain KM1 was more sensitive to free ammonia compared with previously isolated Nitrospira strains. Therefore, the new Nitrospira strain appears to be better adapted to oligotrophic environments compared with other known non-marine nitrite oxidizers. The complete genome of strain KM1 was 4,509,223 bp in length and contained 4,318 predicted coding sequences. Average nucleotide identities between strain KM1 and known cultured Nitrospira genome sequences are 76.7–78.4%, suggesting at least species-level novelty of the strain in the Nitrospira lineage II. These findings broaden knowledge of the ecophysiological diversity of nitrite-oxidizing Nitrospira.

Bioaugmentation of Soil Contaminated with Zinc

An experiment described in this work aimed to establish the role of bioaugmentation in minimizing adverse outcomes of loamy sand contamination with zinc. The bioaugmentation was conducted with the use of microbial strains being most resistant to the action of zinc, which were isolated from the soil contaminated with 1250 mg Zn2+ kg−1 dry matter (DM) of soil after 12-month incubation. The soil was inoculated with 4 strains of bacteria (Bacillus licheniformis KT986159.1, Bacillus sp. KF956639.1, Gordonia amicalis KM113029.1, Leifsonia sp. KJ191763.1) and 4 strains of fungi (Penicillium raperi KC797647.1, Penicillium janthinellum AY373921.1, Penicillium glabrum LT558918.1, Trichoderma harzianum LN714612.1). In the case of the non-contaminated soil, a metal dose of 250 mg Zn2+ kg−1 DM of soil contributed to enhanced proliferation and microorganisms and enzymatic activity. In turn, zinc in its highest dose (1250 mg Zn2+ kg−1 DM of soil) evoked adverse effects, which were manifested in reduced numbers and diversity of microorganisms and suppressed activity of soil enzymes. This contamination rate stimulated only the proliferation of fungi, but their ecophysiological diversity was reduced either. The bioaugmentation treatment minimized adverse effects of zinc. Unfortunately, the use of autochthonous microorganisms failed to reduce zinc bioavailability in the soil.

The Role of Dactylis Glomerata and Diesel Oil in the Formation of Microbiome and Soil Enzyme Activity.

The global demand for petroleum contributes to a significant increase in soil pollution with petroleum-based products that pose a severe risk not only to humans but also to plants and the soil microbiome. The increasing pollution of the natural environment urges the search for effective remediation methods. Considering the above, the objective of this study was to determine the usability of Dactylis glomerata for the degradation of hydrocarbons contained in diesel oil (DO), as well as the effects of both the plant tested and DO on the biochemical functionality and changes in the soil microbiome. The experiment was conducted in a greenhouse with non-polluted soil as well as soil polluted with DO and phytoremediated with Dactylis glomerata. Soil pollution with DO increased the numbers of microorganisms and soil enzymes and decreased the value of the ecophysiological diversity index of microorganisms. Besides, it contributed to changes in the bacterial structure at all taxonomic levels. DO was found to increase the abundance of Proteobacteria and to decrease that of Actinobacteria, Acidobacteria, Chloroflexi, Gemmatimonadetes and Firmicutes. In the non-polluted soil, the core microbiome was represented by Kaistobacter and Rhodoplanes, whereas in the DO-polluted soil, it was represented by Parvibaculum and Rhodococcus. In soil sown with Dactylis glomerata, gasoline fraction (C6–C12) degradation was higher by 17%; mineral oil (C12–C35), by 9%; benzene, by 31%; anthracene, by 12%; chrysene, by 38%; benzo(a)anthracene, by 19%; benzo(a)pyrene, by 17%; benzo(b)fluoranthene, by 15%; and benzo(k)fluoranthene, by 18% than in non-sowed soil. To conclude, Dactylis glomerata proved useful in degrading DO hydrocarbons and, therefore, may be recommended for the phytoremediation of soils polluted with petroleum-based products. It has been shown that the microbiological, biochemical and chemical tests are fast and sensitive in the diagnosis of soil contamination with petroleum products, and a combination of all these tests gives a reliable assessment of the state of soils.

Soil Microbiome Response to Contamination with Bisphenol A, Bisphenol F and Bisphenol S.

The choice of the study objective was affected by numerous controversies and concerns around bisphenol F (BPF) and bisphenol S (BPS)—analogues of bisphenol A (BPA). The study focused on the determination and comparison of the scale of the BPA, BPF, and BPS impact on the soil microbiome and its enzymatic activity. The following parameters were determined in soil uncontaminated and contaminated with BPA, BPF, and BPS: the count of eleven groups of microorganisms, colony development (CD) index, microorganism ecophysiological diversity (EP) index, genetic diversity of bacteria and activity of dehydrogenases (Deh), urease (Ure), catalase (Cat), acid phosphatase (Pac), alkaline phosphatase (Pal), arylsulphatase (Aryl) and β-glucosidase (Glu). Bisphenols A, S and F significantly disrupted the soil homeostasis. BPF is regarded as the most toxic, followed by BPS and BPA. BPF and BPS reduced the abundance of Proteobacteria and Acidobacteria and increased that of Actinobacteria. Unique types of bacteria were identified as well as the characteristics of each bisphenol: Lysobacter, Steroidobacter, Variovorax, Mycoplana, for BPA, Caldilinea, Arthrobacter, Cellulosimicrobium and Promicromonospora for BPF and Dactylosporangium Geodermatophilus, Sphingopyxis for BPS. Considering the strength of a negative impact of bisphenols on the soil biochemical activity, they can be arranged as follows: BPS > BPF > BPA. Urease and arylsulphatase proved to be the most susceptible and dehydrogenases the least susceptible to bisphenols pressure, regardless of the study duration.

Soil Bacterial Community and Soil Enzyme Activity Depending on the Cultivation of Triticum aestivum, Brassica napus, and Pisum sativum ssp. arvense

This study aims to determine the effects of crops and their cultivation regimes on changes in the soil microbiome. Three plant species were selected for the study: Triticum aestivum, Brassica napus, and Pisum sativum ssp. arvense, that were cultivated in soils with a similar particle size fraction. Field experiments were performed on the area of the Iławski Lake District (north-eastern Poland) at the Production and Experimental Station ‘Bałcyny’ (53°35′49″ N, 19°51′20″ E). In soil samples counts, organotrophic bacteria and actinobacteria were quantified, and the colony development index (CD) and ecophysiological diversity index (EP) were computed. In addition, a 16S amplicon sequencing encoding gene was conducted based on the hypervariable region V3–V4. Further analyses included an evaluation of the basic physiochemical properties of the soil and the activities of dehydrogenases, catalase, urease, acid phosphatase, alkaline phosphatase, arylsulfatase, and β-glucosidase. Analyses carried out in the study demonstrated that the rhizosphere of Triticum aestivum had a more beneficial effect on bacteria development than those of Brassica napus and Pisum sativum ssp. arvense, as indicated by the values of the ecophysiological diversity index (EP) and OTU abundance calculated for individual taxa in the soils in which the studied crops were grown. More OTUs of the taxa Alphaproteobacteria, Gammaproteobacteria, Clostridia, Sphingomonadales, Rhodospirillales, Xanthomonadales, Streptomycetaceae, Pseudonocardiaceae, Acetobacteraceae, Solibacteraceae, Kaistobacter, Cohnella, Azospirillum, Cryptosporangium, Rhodoplanes, and Saccharopolyspora were determined in the bacteriome structure of the soil from Triticum aestivum cultivation than in the soils from the cultivation of Brassica napus and Pisum sativum ssp. arvense. Also, the activities of most of the analyzed enzymes, including urease, catalase, alkaline phosphatase, β-glucosidase, and arylsulfatase, were the higher in the soil sown with Triticum aestivum than in those with the other two plant species.

Response of soil microorganisms and enzymes to the foliar application of Helicur 250 EW fungicide on Horderum vulgare L.

The use of fungicides bears the risk of many undesirable outcomes that are manifested in, among other things, changes in the structure and activity of microorganisms. This study aimed at determining the effect of a Helicur 250 EW preparation, used to protect crops against fungal diseases, on the microbiological and biochemical activity of soil and on the development of Horderum vulgare L. The fungicide was sprayed on leaves of spring barley in the following doses (per active substance, i.e. tebuconazole, TEB): 0.046, 0.093, 0.139, 1.395, and 2.790 mg TEB plant-1. The following indices were analyzed in the study: index of microorganisms resistance (RS) to the effects of fungicide, microorganisms colony development index (CD), microorganisms ecophysiological diversity index (EP), genetic diversity of bacteria, enzymatic activity, and effect of the fungicide on spring barley development (IFH). The most susceptible to the effects of the fungicide turned out to be fungi. The metagenomic analysis demonstrated that the bacterial community differed in terms of structure and percentage contribution in the soil exposed to the fungicide from the control soil even at the Phylum level. However, Proteobacteria appeared to be the prevailing taxon in both soils. Bacillus arabhattai, B.soli, and B.simplex occurred exclusively in the control soil, whereas Ramlibacter tataounensis, Azospirillum palatum, and Kaistobacter terrae - exclusively in the soil contaminated with the fungicide. Helicur 250 EW suppressed activities of all soil enzymes except for arylsulfatase. In addition, it proved to be a strong inhibitor of spring barley growth and development.

Role of Festuca rubra and Festuca arundinacea in determinig the functional and genetic diversity of microorganisms and of the enzymatic activity in the soil polluted with diesel oil

The objective of this study was to analyze the effect of two grass species, i.e. red fescue (Festuca rubra) and tall fescue (F. arundinacea), on the functional and genetic diversity of soil-dwelling microorganisms and on the enzymatic activity of soil not polluted and polluted with diesel oil. Grasses were examined for their effectiveness in accelerating degradation of PAHs introduced into soil with diesel oil. A growing experiment was conducted in Kick-Brauckman pots. The soil not polluted and polluted with diesel oil (7 cm3 kg-1 d.m.) was determined for the count of bacteria, colony development index, ecophysiological diversity index, functional diversity (using Biolog system), genetic diversity of bacteria (using NGS), enzymatic activity, and content of hydrocarbons. Study results demonstrated disturbed homeostasis of soil. The toxic effect of diesel oil on grasses alleviate with time since soil pollution. The yield of the first swath of red fescue decreased by 98% and that of tall fescue by 92%, whereas the yields of the second swath decreased by 82% and 89%, and these of the third swath by 50% and 47%, respectively. Diesel oil diminished also the functional and genetic diversity of bacteria. The use of grasses significantly decreased contents of C6-C12 (gasoline total), C12-C35 mineral oils, BTEX (volatile aromatic hydrocarbons), and PAHs in the soil, as well as enabled restoring the microbiological equilibrium in the soil, and increased functional and genetic diversity of bacteria. For this reason, both analyzed grass species, i.e. Festuca rubra and F. arundinacea, may be recommended for the remediation of soil polluted with diesel oil.