Sulfate-reducing bacteria unearthed: ecological functions of the diverse prokaryotic group in terrestrial environments.

Sulfate-reducing prokaryotes (SRPs) are essential microorganisms that play crucial roles in various ecological processes. Even though SRPs have been studied for over a century, there are still gaps in our understanding of their biology. In the past two decades, a significant amount of data on SRP ecology has been accumulated. This review aims to consolidate that information, focusing on SRPs in soils, their relation to the rare biosphere, uncultured sulfate reducers, and their interactions with other organisms in terrestrial ecosystems. SRPs in soils form part of the rare biosphere and contribute to various processes as a low-density population. The data reveal a diverse range of sulfate-reducing taxa intricately involved in terrestrial carbon and sulfur cycles. While some taxa like Desulfitobacterium and Desulfosporosinus are well studied, others are more enigmatic. For example, members of the Acidobacteriota phylum appear to hold significant importance for the terrestrial sulfur cycle. Many aspects of SRP ecology remain mysterious, including sulfate reduction in different bacterial phyla, interactions with bacteria and fungi in soils, and the existence of soil sulfate-reducing archaea. Utilizing metagenomic, metatranscriptomic, and culture-dependent approaches will help uncover the diversity, functional potential, and adaptations of SRPs in the global environment.

Bioinoculant mediated regulation of signalling cascades in various stress responses in plants.

Bio-inoculation involves the association of plant with some beneficial microorganisms, and among these microbiotas, those bacteria which can promote plant growth and development are known as Plant Growth Promoting Rhizobacteria (PGPR). It can help a plant directly or indirectly, which includes root development, biological nitrogen (N2) fixation, stress tolerance, cell division and elongation, solubilization of Zinc, Phosphate, Potassium, soil health improvement and many more. PGPR have gained attention as it can be used as biofertilizers and helpful in bioremediation techniques, which in turn can reduce the chemical dependency in agriculture. PGPR mediated plant growth and stress management is developed by the virtue of the interaction of plant and microbial signalling pathways. On the other hand, environmental stresses are something to which a plant is always exposed irrespective of other factors. The present review is all about the better understanding of the convergence strategies of these signalling molecules and the ambiguities of signalling activities occurring in the host due to the interaction with PGPR under environmental stressed conditions.

Biochar and metal-tolerant bacteria in alleviating ZnO nanoparticles toxicity in barley.

The constant use of zinc oxide nanoparticles (ZnO NPs) in agriculture could increase their concentration in soil, and cause a threat to sustainable crop production. The present study was designed to determine the role of spore-forming and metal-tolerant bacteria, and biochar in alleviating the toxic effects of a high dose of ZnO NPs (2000 mg kg-1) spiked to the soil (Haplic Chernozem) on barley (Hordeum sativum L). The mobile compounds of Zn in soil and their accumulation in H. sativum tissues were increased significantly. The addition of biochar (2.5% of total soil) and bacteria (1010 CFU kg-1) separately and in combination showed a favorable impact on H. sativum growth in ZnO NPs polluted soil. The application of bacteria (separately) to the contaminated soil reduced the mobility of Zn compounds by 7%, due to loosely bound Zn compounds, whereas only biochar inputs lowered Zn mobile compounds mobility by 33%, even the combined application of biochar and bacteria also suppressed the soil Zn mobile compounds. Individual application of biochar and bacteria reduced the Zn plant uptake, i.e., underground parts (roots) by 44% and 20%, and in the above-ground parts of H. sativum plants by 39% and 13%, respectively, compared to ZnO NPs polluted soil treatments. Biochar, both separately and in combination with bacteria improved the root length by 48 and 85%, and plant height by 53 and 40%, respectively, compared to the polluted control. The root length and plant height decreased by 52 and 40% in ZnO NPs spiked soil compared clean soil treatments. Anatomical results showed an improvement in the structural organization of cellular-sub-cellular tissues of root and leaf. The changes in ultrastructural organization of assimilation tissue cells were noted all treatments due to the toxic effects of ZnO NPs compared with control treatment. The results indicate that metal-tolerant bacteria and biochar could be effective as a soil amendment to reduce metal toxicity, enhance crop growth, and improve soil health.

Microbiological status of natural and anthropogenic soils of the Taganrog Bay coast at different levels of combined pollution with heavy metals and PAHs.

The effect of heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) pollution on the microbiological status of soils on the coast of the Taganrog Bay and adjacent areas was studied. The content of total and exchangeable forms of HMs, the content of 16 priority PAHs and the abundance of several groups of culturable microorganisms was determined, namely copiotrophic, prototrophic, aerobic spore-forming bacteria, actinomycetes, molds and yeasts. The content of total and exchangeable forms of HMs in urban coastal soils in industrial zone significantly exceeded that in non-urban soils. The maximum concentrations of total forms of Mn, Cr, Ni, Cu, Zn, Pb and Cd are 1821, 871, 143, 89, 1390, 317 and 10 mg/kg, respectively. The median value of the total content of 16 PAHs in urban soils is 3 times higher than in the soils of natural areas and reached 4309 ng/g. The lowest numbers of copiotrophic bacteria, prototrophic bacteria and aerobic spore-forming bacteria were found in the soils of industrial zone: 6.8, 13.8 and 0.63 million CFU g-1 dry soil, respectively. The largest numbers of copiotrophic bacteria, prototrophic bacteria and aerobic spore-forming bacteria were recorded in the soils of natural areas-72.5, 136 and 5.73 million CFU g-1 dry soil, respectively. It was found that the abundance of copiotrophs, prototrophs, and aerobic spore-forming bacteria is more affected by the urbanization of coastal soils including the pollution of HMs and PAHs. Other groups of microorganisms (actinomycetes, molds and yeasts) turned out to be more resistant to anthropogenic factors.

Quorum-Sensing Inhibition by Gram-Positive Bacteria.

The modern paradigm assumes that interspecies communication of microorganisms occurs through precise regulatory mechanisms. In particular, antagonism between bacteria or bacteria and fungi can be achieved by direct destruction of the targeted cells through the regulated production of antimicrobial metabolites or by controlling their adaptive mechanisms, such as the formation of biofilms. The quorum-quenching phenomenon provides such a countermeasure strategy. This review discusses quorum-sensing suppression by Gram-positive microorganisms, the underlying mechanisms of this process, and its molecular intermediates. The main focus will be on Gram-positive bacteria that have practical applications, such as starter cultures for food fermentation, probiotics, and other microorganisms of biotechnological importance. The possible evolutionary role of quorum-quenching mechanisms during the development of interspecies interactions of bacteria is also considered. In addition, the review provides possible practical applications for these mechanisms, such as the control of pathogens, improving the efficiency of probiotics, and plant protection.

Soil organic matter and biological activity under long-term contamination with copper.

Organic matter (OM) and enzymes activity can act as indicators of the time and level of soil contamination with heavy metal. The goal of this study is evaluation of the effect of chronic long-term soil contamination with Cu on OM and biological activity in Spolic Technosols. The monitoring plot is located in the zone of industrial wastewater storage and sludge reservoirs in the Seversky Donets River flood plain. The total amount of Cu in the investigated soils varied greatly from 52 to 437 mg/kg. The results of Cu sequential fractionation the contaminated soil have shown that the chemical fraction composition of metal changed when the soil contamination level increased. The amount of Cu compounds associated with OM and Fe and Mn oxides was also higher. Fractions of OM from the humic and fulvic acids groups were studied. Soil was subjected to extraction with cold and hot water, and the content of water-soluble OM (WSOM) was determined. An increased solubility of humic and fulvic acids as well as elevated content of cold and hot extraction WSOM was established. The cold-extracted amount of WSOM increased with an enhance in the Cu content. The long-term contamination of soil with Cu leads to an adaptation of microorganisms to this adverse environmental factor, and this adaptation is manifested in the WSOM content increase. The effect of Cu contamination on microbiological activity was assessed by plate-counting culturable microorganisms and determining urease and dehydrogenase enzymatic activity. A high level of soil contamination with Cu showed a noticeable negative effect on the number of soil bacteria; however, active and potentially active bacteria were observed even in the highly contaminated soils. The changes in soil OM and microbial communities caused by Cu pollution can lead to disruption of ecosystem functioning.

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.

The influence of application of biochar and metal-tolerant bacteria in polluted soil on morpho-physiological and anatomical parameters of spring barley.

The paper presents the results of the model experiment on spring barley (Hordeum vulgare L.) grown in polluted soil. The influence of separate and combined application of wood biochar and heavy metal-tolerant bacteria on morpho-physiological, anatomical and ultrastructural parameters of H. vulgare L. has been studied. The joint application of biochar and bacteria increased the shoot length by 2.1-fold, root length by 1.7-fold, leaf length by 2.3-fold and dry weight by threefold compared to polluted variant, bringing the plant parameters to the control level. The maximal quantum yield of photosystem II decreased by 8.3% in H. vulgare L. grown in contaminated soil, whereas this decrease was less in biochar (7%), bacteria (6%) and in combined application of bacteria and biochar (5%). As for the transpiration rate, the H. vulgare L. grown in polluted soil has shown a decrease in transpiration rate by 26%. At the same time, the simultaneous application of biochar and bacteria has led to a significant improvement in the transpiration rate (14%). The H. vulgare L. also showed anatomical (integrity of epidermal, vascular bundles, parenchymal and chlorenchymal cells) and ultrastructural (chloroplasts, thylakoid system, plastoglobules, starch grains, mitochondria, peroxisomes, ribosomes, endoplasmic reticulum, vacuoles) changes, revealed by light-optical and transmission electron microscopy of leaf sections. The effects were most prominent in H. vulgare L., grown in polluted soil but gradually improved with application of biochar, bacteria and their combination. The use of biochar in combination with metal-tolerant bacteria is an efficient tool for remediation of soils, contaminated with heavy metals. The positive changes caused by the treatment can be consistently traced at all levels of plant organization.

The influence of long-term Zn and Cu contamination in Spolic Technosols on water-soluble organic matter and soil biological activity.

Potentially toxic elements (PTE) pollution has a pronounced negative effect on the soil and its components. The characteristics of soil organic matter and the activity of soil enzymes can serve as sensitive indicators of the degree of changes occurring in the soil. This study aims to assess the effect of long-term severe soil contamination with Zn and Cu on water-soluble organic matter (WSOM) and the associated changes in the biochemical activity of microorganisms. The total content of Zn and Cu in the studied soils varies greatly: Zn from 118 to 65,311 mg/kg, Cu from 52 to 437 mg/kg. The content of WSOM was determined using cold and hot extraction. It was revealed that the WSOM, extracted with cold water is a sensitive indicator reflecting the nature of the interaction of Zn and Cu with it. With an increase in the Cu and Zn content, the amount of WSOM extracted with cold water increases due to rise in the complex-bound metal compounds associated with it. The content of complex-bound compounds Zn in Spolic Technosols reaches 50% of the total metal content. It is shown that one of the biogeochemical mechanisms of microorganisms' adaptation to metal contamination is clearly manifested by the increase in the content of WSOM. The precipitation of metal carbonates develops in the soil which reduces the mobility and toxicity of PTE. Due to this mechanism, a decrease in the activity of dehydrogenases and urease was not prominent in all studied soils, despite the very high level of pollution and the transformation of organic matter. The study of the relationship of PTE with the most easily transformed part of WSOM and the activity of soil enzymes is of great importance for an objective assessment of possible environmental risks.

Assessing the toxicity and accumulation of bulk- and nano-CuO in Hordeum sativum L.

The effects of bulk- and nano-CuO were monitored on barley (Hordeum sativum L.) in hydroponic conditions. The anatomical and cyto-/morphometric parameters of plants, exposed to both types of CuO in different doses (300 and 2000 mg/L) were recorded. The germination rate, root and shoot lengths decreased in a dose-dependent manner. Exposure to nano-CuO significantly increased Cu content in the H. sativum roots; however, the translocation rates of dissolved Cu were low and showed less accumulation in above-ground tissues. The differences between nano- and bulk-CuO treated plants were sufficiently evident, but at lower concentrations, these differences were non-significant. The relative seed germination inhibition was noted up to 11% and 22% under the high dose of bulk- and nano-CuO, respectively; however, at low dose, it was non-significant. The relative root length was reduced 3.6 fold by bulk- and 1.5 fold by nano-CuO, and shoot lengths decreased 1.6 fold by bulk- and 1.4 fold by nano-CuO under the high dose after growth of 30 days. It indicated more morphological effects on H. sativum caused by bulk- than the nano-CuO. The cytomorphometric analysis indicated the average cortex cell, total cortex, and total central cylinder areas of root cells and the average areas of chlorenchyma leaf cells were increased as compared to control in both bulk- and nano-CuO treated plants. It showed destructive effects of nano- and bulk-CuO on cellular organizations of H. sativum anatomy. Thus, at the low dose, the minimal effects of nano-CuO were observed than the bulk. Therefore, the finding could be interest for the safe application of nano-CuO.

The mechanisms of biochar interactions with microorganisms in soil.

Biochar, a carbonaceous material, is increasingly used in the remediation of the anthropogenically polluted soils and the restoration of their ecological functions. However, the interaction mechanisms among biochar, inorganic and organic soil properties and soil biota are still not very clear. The effect of biochar on soil microorganisms is very diverse. Several mechanisms of these interactions were suggested. However, a well acceptable mechanism of biochar effect on soil microorganisms is still missing. Therefore, efforts were made to examine and proposed a mechanism of the interactions between biochar and microorganisms, as well as existing problems of biochar impacts on main groups of soil enzymes, the composition of the microbiota and the detoxification (heavy metals) and degradation (polycyclic aromatic hydrocarbons) of soil pollutants. The data on the process of biochar colonization by microorganisms and the effect of volatile pyrolysis products released by biochar on the soil microbiota were analysed in detail. The effects of biochar on the physico-chemical properties of soils, the content of mineral nutrients and the response of microbial communities to these changes are also discussed. The information provided here may contribute to the solution of the feasibility, effectiveness and safety of the biochar questions to enhance the soil fertility and to detoxify pollutants in soils.

Interaction of Copper-Based Nanoparticles to Soil, Terrestrial, and Aquatic Systems: Critical Review of the State of the Science and Future Perspectives.

In the past two decades, increased production and usage of metallic nanoparticles (NPs) have inevitably increased their discharge into the different compartments of the environment, which ultimately paved the way for their uptake and accumulation in various trophic levels of the food chain. Due to these issues, several questions have been raised on the usage of NPs in everyday life and have become a matter of public health concern. Among the metallic NPs, Cu-based NPs have gained popularity due to their cost-effectiveness and multifarious promising uses. Several studies in the past represented the phytotoxicity of Cu-based NPs on plants. However, comprehensive knowledge is still lacking. Additionally, the impact of Cu-based NPs on soil organisms such as agriculturally important microbes, fungi, mycorrhiza, nematode, and earthworms is poorly studied. This review article critically analyses the literature data to achieve a more comprehensive knowledge on the toxicological profile of Cu-based NPs and increase our understanding of the effects of Cu-based NPs on aquatic and terrestrial plants as well as on soil microbial communities. The underlying mechanism of biotransformation of Cu-based NPs and the process of their penetration into plants have also been discussed herein. Overall, this review could provide valuable information to design rules and regulations for the safe disposal of Cu-based NPs into a sustainable environment.

The influence of heavy metals, polyaromatic hydrocarbons, and polychlorinated biphenyls pollution on the development of antibiotic resistance in soils.

The minireview is devoted to the analysis of the influence of soil pollution with heavy metals, polyaromatic hydrocarbons (PAHs), and the polychlorinated biphenyls (PCBs) on the distribution of antibiotics resistance genes (ARGs) in soil microbiomes. It is shown that the best understanding of ARGs distribution process requires studying the influence of pollutants on this process in natural microbiocenoses. Heavy metals promote co-selection of genes determining resistance to them together with ARGs in the same mobile elements of a bacterial genome, but the majority of studies focus on agricultural soils enriched with ARGs originating from manure. Studying nonagricultural soils would clear mechanisms of ARGs transfer in natural and anthropogenically transformed environments and highlight the role of antibiotic-producing bacteria. PAHs make a considerable shift in soil microbiomes leading to an increase in the number of Actinobacteria which are the source of antibiotics formation and bear multiple ARGs. The soils polluted with PAHs can be a selective medium for bacteria resistant to antibiotics, and the level of ARGs expression is much higher. PCBs are accumulated in soils and significantly alter the specific structure of soil microbiocenoses. In such soils, representatives of the genera Acinetobacter, Pseudomonas, and Alcanivorax dominate, and the ability to degrade PCBs is connected to horizontal gene transfer (HGT) and high level of genomic plasticity. The attention is also focused on the need to study the properties of the soil having an impact on the bioavailability of pollutants and, as a result, on resistome of soil microorganisms.