Abstract

Bacteria extracellular vesicles (BEVs), characterized as the lipid bilayer membrane-surrounded nanoparticles filled with molecular cargo from parent cells, play fundamental roles in the bacteria growth and pathogenesis, as well as facilitating essential interaction between bacteria and host systems. Notably, benefiting from their unique biological functions, BEVs hold great promise as novel nanopharmaceuticals for diverse biomedical potential, attracting significant interest from both industry and academia. Typically, BEVs are evaluated as promising drug delivery platforms, on account of their intrinsic cell-targeting capability, ease of versatile cargo engineering, and capability to penetrate physiological barriers. Moreover, attributing to considerable intrinsic immunogenicity, BEVs are able to interact with the host immune system to boost immunotherapy as the novel nanovaccine against a wide range of diseases. Towards these significant directions, in this review, we elucidate the nature of BEVs and their role in activating host immune response for a better understanding of BEV-based nanopharmaceuticals’ development. Additionally, we also systematically summarize recent advances in BEVs for achieving the target delivery of genetic material, therapeutic agents, and functional materials. Furthermore, vaccination strategies using BEVs are carefully covered, illustrating their flexible therapeutic potential in combating bacterial infections, viral infections, and cancer. Finally, the current hurdles and further outlook of these BEV-based nanopharmaceuticals will also be provided.

Introduction

Vesiculation is a crucial and fundamental process across all kinds of species to produce the extracellular vesicles that serve as essential mediators of basic physiological events [1]. These nanovesicles are filled with molecular patterns originated from parent cells, including metabolites, nucleic acids, proteins, and signaling molecules, to maintain cell growth and homeostasis [2, 3]. Biological regulation by extracellular vesicles is widespread across both prokaryotes and eukaryotes [4]. Notably, bacteria, as one of the major inhabitants in the human body, establish intricate relationships with host health and disease, wherein bacterial extracellular vesicles (BEVs) are indispensably involved in these processes [5, 6]. With the increasing and deep understanding of their biological function, BEVs are found to influence various cellular behaviors, including the transport of genetic information, phage infection, mediation of metabolism, as well as interaction between bacteria-bacteria and bacteria-host [7, 8].

Particularly, BEVs are characterized as nanosized nanoparticles, surrounded by lipid-bilayer membranes, ranging from 20 to 400 nm in diameter [7]. In account of the diversity of bacterial types and biogenesis mechanisms, the BEVs could carry versatile cargos inherited from mother cells, such as lipopolysaccharides (LPS), endotoxins, genetic information, cytosolic and membrane proteins [9]. By thanking the unique structure and intrinsic properties of BEVs, these naturally occurring nanovesicles attract the research interest to be developed as novel nanopharmaceuticals, prompting further exploration of their biomedical applications [10, 11]. Generally, BEVs are widely evaluated as biotherapeutics in different forms. Firstly, these nanovesicles with hollow structures could serve as novel drug delivery platforms, facilitating the transport of diverse bioactive molecules and therapeutic cargo to the recipient cells at the lesion site [12]. Thanks to the stability of naturally-occurring membrane structure, the BEVs-based drug delivery platform could carry the therapeutic genetic tools (e.g. siRNA, CRISPR-Cas9, etc.), protecting them from enzymatic degradation or hydrolysis in the complex physiological environment [13, 14]. Besides, benefiting from the ease of modification, BEVs-based drug delivery platforms could efficiently load the small molecular therapeutics [14], or directly produce the synthetic cargo (e.g. antigens, enzymes, therapeutic proteins, etc.) on the BEVs by editing the desired gene in parent bacteria. The BEVs-based drug carriers are also featured in their capability for targeting delivery toward the disease area to enhance drug accumulation and availability [15]. Moreover, the BEVs drug delivery platform can integrate with functional materials, to facilitate combinational therapy (e.g. photodynamic therapy, photothermal therapy, etc.) and maximize the synergistic therapeutic efficiency [16].

Conclusion and further perspective

In this review, we comprehensively summarize the development of BEV-based nanopharmaceuticals to facilitate disparate biomedical applications in recent years. Amongst the unique advantages and functions of BEVs, we demonstrated the tremendous potential of applying these naturally occurring nanovesicles to establish a myriad of innovative therapeutic strategies for new-generation pharmaceuticals evolution, especially in the versatile bioactive cargo delivery and powerful vaccination approaches.

Taking the unique merits of nanovesicles, the structural stability, ease of cargo loading, promising penetration across physiological barriers, and specific targeting capabilities endow the BEVs application to be beneficial in delivery for a wide range of therapeutics. Particularly, the naturally occurring membrane structure of BEVs enables targeting delivery of therapeutic genetic tools (e.g., siRNA, DNA, CRISPR-Cas9, etc.) in the physiological, preserving stability and bioactivity, thus enhancing gene therapy. Leveraging the ease of genetic modification in parent bacteria, protein cargo, such as enzymes and antigens, can also be directly expressed within BEVs, optimizing loading efficiency compared to conventional delivery platforms. Furthermore, advancements in nanotechnology and material science have witnessed the integration of functional materials with BEV delivery platforms to achieve combinational therapy, thereby further improving the synergistic therapeutic efficacy.

Abstract

Introduction

Wastewater in area of focus

Nanotechnology in water purifcation

Nano‑adsorption

Microbial agent

Nanocomposites

Types of nanocomposites

Synthesis modes for nanocomposites

Graphene oxide‑based composites as a disinfectant

Zinc oxide nanocomposites as disinfectant

Copper oxide nanocomposites

Silver/silver oxide nanocomposites

Titanium oxide nanocomposites

Discussion

Conclusion

References

Abstract

     Water is crucial for the existence of life. The world, however, is facing a global water crisis. There are variety of microorganisms, gases and other toxins responsible for water contamination. Various types of nanomaterials exist that have enormous potential to treat contaminated water (water containing metal toxins or specific organic or inorganic impurities) due to their unique properties such as a high surface area and their ability to work effectively even at low concentrations. In recent years, scientists have been giving considerable attention to the application of nanocomposites for water purification, wastewater treatment, microorganism elimination, chemical contaminants, heavy metals removal and so forth. The incorporation of different nanofillers such as carbon nanotubes, graphene oxide, 2D materials, zinc oxide, titanium dioxide, copper and silver nanoparticles into polymeric materials has facilitated important advances, such as suppressing the accumulation of pollutants and foulants, improving the hydrophilicity, increasing the efficiency and improving the mechanical properties. This review discusses leading advances in the development of nanocomposites for antimicrobial and wastewater treatment with the aim of providing an improved understanding of nanocomposites and their applications in antimicrobial and wastewater treatment.

Introduction

     Water is a basic requirement for human life. However, we are far from meeting global requirements for clean water, and this issue will continue to grow over the time (Hillie and Hlophe 2007; Elwakeel et al. 2020b). The demand of clean drinking water is rising as a result of the deterioration of water quality, global climate change and population growth (Tchobanoglous et al. 1991; Elwakeel et al. 2020d). Emissions of organic dyes and heavy metal ions from the paper, leather and textile industries are a serious problem, as they are potentially mutagenic and carcinogenic. To meet environmental requirements, wastewater contaminated with these organic and inorganic species need to be treated before being discharged (Santhosh et al. 2016; Elwakeel et al. 2021). Heavy metals are widely used in various industries for many purposes, including mining and pigment production. Synthetic dyes are also an important type of pollutant, and their sources for water contamination include the textile, pulp and paper, tinting, printing, painting and tanning industries. The removal of dye from such wastewater is a challenging task, as pigments and synthetic dyes are biodegradation-resistant and remain in the environment for a long time. The destruction and handling of organic dyes is therefore an important issue, and a cost-efective method for removing dye substances from wastewater has been developed (Santhosh et al. 2016; Elwakeel et al. 2018).

Conclusion

     This paper explores the existing nanocomposites used to extract heavy metal ions and dyes from wastewater as efective adsorbents. This article addressed recent developments in nanomaterials as economical and environmentally sustainable water purifcation adsorbents. This review highlights fve commonly used nanomaterials/nanoparticles that are used in most existing nanocomposites. In this review, we concluded that TiO2-based nanocomposites have been used for photodegradation activity by most of the researchers in the literature. Silver-based nanocomposites are mostly used for antimicrobial activity. Silver and GO-based nanocomposites were used for the removal of green dye, anionic dye and Cu(II). Copper-based nanocomposites are mostly used for adsorption and photodegradation activity. Zinc oxide nanocomposites are used for adsorption, antimicrobial and photodegradation activity. Finally, we concluded that GO also greatly contributes to the improvement of other materials’ efciency. Further, much needs to be done to control the two-dimensional GO sheets for advanced technologies in the future. There are many challenges and obstacles associated with handling wastewater, and many precautions are required to prevent environmental and health problems. Therefore, new modern wastewater treatment equipment should be versatile, low-cost and commercially efective.

1- Introduction

2- Material and methods

3- Results

4- Discussion

5- Conclusion

References

Abstract

Soil microbes play vital roles in energy flow and nutrient cycling and, thus, are important for agricultural production. A better understanding of the complex responses of microbial communities to various organic and inorganic fertilization regimes is critical for sustainable development of agroecosystems. Changes in bacterial and fungal abundance and diversity in fluvo-aquic soil in Northern China were studied under 38-year long-term fertilization strategies: four chemical-fertilization strategies (i.e., no fertilizer, N, NP, or NPK), with or without manure amendment, were investigated by high-throughput sequencing and quantitative polymerase chain reaction-based amplification of bacterial 16S rRNA and fungal internal transcribed spacer (ITS) rRNA genes. Chemical fertilizer plus manure addition clearly increased the soil fertility and was recommended for further optimization of fertilization patterns. Both principal component analysis and partial least-square discriminant analysis showed greater impacts of manure addition than chemical fertilizer on bacterial community distributions, whereas fungal communities were more sensitive to inorganic fertilizer. The linear discriminant analysis effect size method revealed that the number of responding microbes (microbes significantly affected by various fertilizations) in bacterial communities in manure-treated soils was markedly higher than that in chemical fertilizer-treated soils, whereas those of fungal communities showed the opposite trend. In addition, redundancy analysis further illustrated the primary importance of organic matter in shaping community distributions of bacteria, rather than in driving fungal community patterns. These results suggested that organic and inorganic fertilizers, respectively, dominated in shaping bacterial and fungal community distributions in fluvo-aquic soils.

Introduction

Soil microorganisms play vital roles in the maintenance of soil health, productivity, and sustainability, and thus crop production, because of their contributions to soil nutrient transformation, formation and decomposition of organic matter, and stabilization of soil aggregates (Van Der Heijden et al., 2008; Zhao et al., 2014; Singh, 2016; Pan et al., 2018a). Therefore, a profound understanding of soil microbial ecology has become increasingly recognized and emphasized because of the ecological and economic importance of microorganisms (Mele and Crowley, 2008). Due to the increasing concerns regarding food demands and the scarcity of land available for agriculture, high amount of fertilizer is implemented to increase crop productivity (Inselsbacher et al., 2010). The application of organic and inorganic fertilizers can cause detectable changes in nutrient availability to plants, as well as in the diversity and function of microorganisms (Marschner et al., 2003). For example, long-term field experiments involving polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) demonstrated the importance of balanced fertilization in promoting the activities of bacterial communities (Chu et al., 2007a,b; Luo et al., 2015). Nitrogen (N) is regarded as a key limiting factor for soil microbes, and N amendment can alter the activity and diversity of soil organisms (Sarathchandra et al., 2001; Xu et al., 2017; Liu et al., 2019). Organic fertilization exerted no effects on the fungal biomass, while increasing the bacterial biomass by increasing soil organic carbon (Corg) and C/N ratio (Crecchio et al., 2001; Marschner et al., 2003). In addition, manure application promoted soil bacterial communities by enhancing root exudates and also improved plant growth (Bittman et al., 2005). Suzuki et al.

There is limited research on food safety practices of street foods, particularly food trucks in developed countries. Given this gap, this study explores the safety and sanitation status of food trucks in the highly developed tourist destination of Orlando, Florida, in the United States. A sample of 30 raw and cooked ready-to-eat foods was collected from 24 food trucks located in residential and touristic sites located in Orlando and then held for microbiological analyses (E. coli and Salmonella enterica spp.) to determine pathogen populations of the final products. In addition to lab analyses for coliform bacteria, food safety practices of vendors were evaluated. Although developed countries are believed to have strict safety and quality measures in place, our study results reveal that food prepared in and sold from food trucks can be potential vehicles of clinically relevant E. coli and Salmonella carrying intestinal pathogenic virulence factors or antibiotic resistance genes, which might create a public health hazard or more specifically foodborne illnesses and outbreak. To minimize foodborne illnesses and infection risks, food inspections and monitoring processes should be carefully revised by municipal, county, and state health departments. This is one of the first studies to explore safety of food truck products in the context of a developed country.

Introduction

Street foods are often integral components of local culture and offer diverse opportunities to tourists and locals alike, for unique cultural experiences. Since food and travel are inextricably linked in memorable tourist experiences, travelers often try local cuisine at various types of restaurants or try indigenous foods at street food stalls. The sensual experience of eating and engaging in adventures involving various types of food and cuisines have led to the creation of the term “food porn” by travelers and bloggers (Scott, 2018). According to the Food and Agriculture Organization, 2.5 billion people around the world regularly consume street food and it is considered to be the most common form of public dining (Food and Agriculture Organization, 2007; Kraig and Sen, 2013). Street food also represents one of the most significant sources of employment for low-income families (Bhowmik, 2012; Freese et al., 1998). From time to time, the food service industry has been associated with news related to foodborne illnesses resulting from improper food handling, lack of sanitation, and other problems. Mobile and street food vendors (e.g., food trucks) in particular have been associated with environmental and public health risks. These types of events are attributed to improper food preparation and service, absence of food safety regulations, and improper waste management practices (Alimi, 2016; Food and Agriculture Organization, 2011; Kothe et al., 2016; Liu et al., 2014; Qureshi and Azim, 2016; World Health Organization, 1996). Previous studies on street food and street food vendors have revealed numerous safety, quality, and environmental problems in developing countries (Alimi, 2016; Al Mamun et al., 2013; Campos et al., 2009).

The present study aims to synthesized biomaterial that has antibacterial properties. Currently the surgical implants associated infections are a major cause of implant failure. Synthesis of silver doped hydroxyapatite as an antibacterial agent has potential importance to overcome post-surgical infections in a variety of clinical applications. Five silver doped hydroxyapatite Ca10−xAgx(PO4)6(OH)2 (x = 0, 0.1, 0.3, 0.5, 0.7 M) samples were synthesized by precipitation method and sintered at 900 °C to obtain well crystallized structure. No minor phase developed with silver addition, hexagonal hydroxyapatite (JCPDS# 09-432) was the single phase identified in all silver doped hydroxyapatite samples. The lattice parameter a and c changed with increase in silver concentration. The results of in vitro bioactivity revealed the bone bonding ability of silver doped hydroxyapatite samples. The antibacterial test showed that silver doped hydroxyapatite was sensitive to Staphylococcus aureus bacteria. Addition of silver significantly (P < 0.005) increased the antibacterial activity.

Introduction

Bioceramics is a new class of biomaterials that is used to replace damaged tissues and bones. These bioceramic materials have the ability of direct bonding with host bone tissues [1,2]. Synthetic hydroxyapatite (Ca10 (PO4)6(OH)2) (HA) among these ceramics has been widely used for bone tissue engineering. Bones consist of 22% protein, 70% hydroxyapatite and 8% water. Natural bones are composed of hydroxyapatite nanoparticles having needle-like or rod-like shapes [3,4]. Chemical structure of HA is similar to human bone and it is widely used as coating for metal prosthesis, bone graft, drug [5] and antibiotics [6,7] carrier in bone-implant interface to reduce the bacterial infections. HA crystal is composed of OH−, Ca2+ and PO4 −2 groups, which are closely packed in hexagonal arrangement and had space group of P63/m with lattice parameter a = b = 9.423 Ao and c = 6.875 Ao [8]. Although, hydroxyapatite is the most osteoconductive and biocompatible material among other calcium phosphates, but it has limited antibacterial resistance [9]. Bacterial infections are the main cause of implant failure [10]. To overcome this problem Ag+ is introduced to HA, since past silver has been recognized as strong inhibitor to bacterial growth [5]. Silver exhibits good thermal stability, low volatility, is biocompatible and non-toxic to human cell at low concentration along with superior antibacterial characteristics [11]. Previously, Ag+ doped HA had been synthesized by several precipitation methods [12], microwave refluxing method [3], sol-gel method [13] ultrasonic precipitation method [14] electrostatic spray-pyrolysis process [6] and sintered at different temperatures from 800 to 1200 °C to obtain monophasic fully crystallized silver doped hydroxyapatite. When larger ionic radius (1.28 Å) Ag+ is substituted to smaller ionic radius Ca+2 (0.99 Å) in hydroxyapatite lattice it provokes stress and strain in crystal structure [15]. These strains cause a stability problem in crystal structure. The theoretical limit of the Ag+ substituting Ca+2 is 20% [16], but the practical limit is much lower than this. It is essential to optimize the concentration of dopant and sintering temperature to obtain monophasic hydroxyapatite, previous study show that < 3% concentration of silver [5,6] did not alter the crystalline structure of hydroxyapatite. The aim of the study is to use optimize temperature and dopant concentration to obtain monophasic hydroxyapatite structure. In the present study the inexpensive and conventional precipitation method has been selected to synthesize silver doped hydroxyapatite. To evaluate the antibacterial properties of HA by incorporating Ag+ while maintaining bioactivity, and to demonstrate effects of Ag+ concentration on crystallite size, crystallinity and lattice parameters.

1- Introduction

2- Materials and methods

3- Results

4- Discussion

5- Conclusions

References

Abstract

Self-healing concrete based on calcium carbonate precipitation induced through bacterial activity has been investigated in recent years by teams around the world. For the first time, optimisation of the self-healing performance was considered in terms of the number of bacterial spores required, the concentration and composition of nutrients and precursors, and whether a two-component system was likely to efficiently produce self-healing in concrete. This information is required if efficient and cost-effective self-healing systems based on bacterial activity are to be implemented. For this research, coated expanded perlite was used to immobilise bacterial spores and encapsulate nutrients as two separate components for self-healing concrete. Self-healing capacity was evaluated by imaging and by initial surface absorption of water. The results indicated that healing could be achieved when coated expanded perlite containing self-healing agents was used as a 20% replacement of fine aggregate and if a suitable ratio of spores to calcium acetate was provided. This research is the first to show that self-healing is not simply a requirement of having sufficient healing compounds (e.g. calcium acetate) but that a minimal number of bacterial spores are also required to ensure that sufficient cells take part in the healing process.

Introduction

The effect of some water-borne ions (e.g. chlorides) on the durability of reinforced concrete is well documented, and cracked concrete has been shown to be more susceptible to permeation of these deleterious ions. Consequently, research is being undertaken in an attempt to develop concrete that can self-heal cracks; potentially reducing repair and maintenance costs on key infrastructure [1–3]. One approach to autonomic self-healing is the utilization of microbiologically induced calcite precipitation (MICP). This approach utilises the metabolic activity of bacteria and biomineral precursors embedded within the concrete to form an inorganic compound as a healing material. This is usually calcium carbonate, typically in the form of calcite but sometimes as vaterite [4,5]. This healing material can precipitate in small cracks soon after they form and it has the potential to limit the permeation of water and dissolved ions. Thereby the life of concrete structures can be extended without the need for manual intervention; which can be both costly and dangerous, particularly for structures with poor access. While there have been a number of studies into the feasibility of using MICP for self-healing in concrete, there have not been studies on optimising the self-healing performance through consideration of the number of bacterial spores required, the concentration and composition of nutrients and precursors or whether a twocomponent system is likely to efficiently produce self-healing in concrete.

Abstract

Probiotic based products are associated with many health benefits. However, the main problem is the low survival of these microorganisms in food products and in gastrointestinal tract. Providing probiotics with a physical barrier is an efficient approach to protect microorganisms and to deliver them into the gut. In our opinion, microencapsulation is one of the most efficient methods, and has been under especial consideration and investigation. However, there are still many challenges to overcome with respect to the microencapsulation process. This review focuses mainly on the methodological approach of probiotic encapsulation including materials and results obtained using encapsulated probiotic in food matrices and different pathologies in animal models.

Industrial relevance

he inclusion of probiotics into food matrices is one of the most challenging lines of research in food technology. Probiotics in general, and some strains in particular, have a low resistance to different environmental conditions, such as oxygen, light or temperature. Thus, the protection and isolation of the microorganism from the food matrix and the environmental condition are crucial for the development of new probiotic food. In this sense, microencapsulation has gained an increasing interest, since it has been demonstrated that it could protect the bacteria not only during its production process but also during its incorporation into the food matrix, also with protective effects during storage. In conclusion, microencapsulation is of great interest since it could allow a wider application of probiotics in the food market, actually restricted to fresh or powder products.

Introduction

Wide spread of antibiotic resistance remains a serious clinical problem, which stimulates studies for search of new methods for coping with drug resistance or renews interest in traditionally used and forgotten methods, such as treatment with antibacterial plant extracts and essential oils (EOs) (Ríos and Recio 2005; Fisher and Phillips 2009). Combined therapy is traditionally used to increase antimicrobial activity and reduce toxic effects of agents (Houghton 2009).

Thyme plant is used since ancient times to achieve healing, antiseptic fumigator, food preservation and other useful effects (Stahl-Biskup and Sáez 2002). Nowadays, Thymus vulgaris EO belongs to EOs with the most pronounced antimicrobial activity (Iten et al. 2009). It was shown to be active against many bacteria, viruses and fungi. High antimicrobial activity of thyme oil and its components, first of all thymol and carvacrol, was demonstrated against Staphylococcus aureus (Al-Bayati 2008; Soković et al. 2010; Lević et al. 2011), including methicillin-resistant isolates (Tohidpour et al. 2010), S. epidermidis (Soković et al. 2010), Enterococcus faecalis (Lević et al. 2011), Bacillus cereus (Al-Bayati 2008), Vibrio cholerae (Rattanachaikunsopon and Phumkhachorn 2010), Escherichia coli (Lević et al. 2011), Proteus mirabilis (Soković et al. 2010; Lević et al. 2011), P. vulgaris (Al-Bayati 2008), Pseudomonas aeruginosa (Soković et al. 2010), Salmonella enteritidis (Soković et al. 2010), S. choleraesuis (Lević et al. 2011), S. typhimurium (Soković et al. 2010), and other microorganisms.

Solving real-life optimization problems using conventional methods requires substantial effort and time as the solution lies in the precise quantities associated with the variables which have nonlinear relationships. The variables also have equality and non-equality constraints. The presence of large number of variables and constraints generates an exceptionally wide search space. Classical optimization techniques such as exhaustive search have been found to be inefficient for solving such type of problems. Approximate algorithms based upon the concept of evolution and swarm intelligence have been found to be more efficient in solving high-dimensional problems characterized by the presence of large number of variables and constraints. These algorithms have been found to provide high speedups, easier to implement and provide near optimal solutions by augmenting the current best solution using the principle of randomization. The approximate algorithms are being widely used in multifarious fields of science including computational intelligence, artificial intelligence and soft computing. Many of approximate algorithms are inspired by various phenomena which occur in nature. genetic algorithm (GA), particle swarm optimization (PSO), artificial bee colony (ABC), firefly (FF) algorithm, ant colony optimization (ACO), cuckoo search (CS), gravitational search algorithm (GSA), bacterial foraging (BF), etc. are popular nature-inspired optimization algorithms. These algorithms are being used in the area of civil engineering. Cui and Sheng [1] used genetic algorithm and finite element displacement method to compute reliability index. They found that genetic algorithm relatively took less computation time. Liu et al. [2] used automatic grouping genetic algorithm for optimizing the pile group design. Liu et al. [3] proposed genetic algorithm for determining loadcarrying capacity of composite foundation. Elbeltagia et al. [4] compared PSO with genetic algorithm and other evolutionary techniques and found the PSO algorithm to be more efficient and easy to implement. ANNs have been used to compute the load-carrying capacity of driven piles by a number of researchers [4–6]. Ismail et al. [7] used ANN for load deformation analysis of pile foundation. The ANN was trained first by PSO and then by back propagation by [8, 9]. Ismail et al. [10] analyzed load deformation of pile foundation by PSO-BP hybrid. The input parameters considered by various researchers for the design of pile foundation are given in Table 1. The input parameters used for the study were effective angle of shearing resistance, effective cohesion intercept, modulus of deformation, Poisson’s ratio, unit weight and depth of soil layer. These input parameters were the same as required by the finite element method for the determination of unit skin friction resistance and unit tip bearing capacity of the pile foundation. The ANNs were developed using the input and target data obtained from the finite element method. These input/output data are free from noise which generally characterizes the field observations due to heterogeneous and anisotropic behavior of the soil. The manual and instrumental errors also add to the noise in the field observations. The ANNs so developed in the study reported a high value of coefficient of determination averaging 0.99996.

Decomposition of detritus plays a crucial role in the recycling of nutrients and organic matter (Swift et al. 1979; Moore et al. 2004). Defined as any resource of nonliving organic matter, detritus is considered the basal trophic level of many terrestrial and aquatic food webs (Swift et al. 1979; Moore et al. 2004; Benbow et al. 2015). In terrestrial ecosystems, detritus may consist of plant-derived matter (e.g. leaf litter, dead wood, root exudates), dead microbes, fecal matter and animal tissue (carrion) (Swift et al. 1979). Plantderived detritus comprises the majority of the resources that undergo decomposition in terrestrial ecosystems but they are nutrient poor and very recalcitrant (Swift et al. 1979; Carter et al. 2007). Contrary, carrion is much more nutrient-rich and decomposes at much faster rates than plant detritus, and, as such, its role in nutrient cycling may be highly relevant (Swift et al. 1979; Barton et al. 2013). Indeed, carrion decomposition is usually associated with the activity of microbes, invertebrate and vertebrate detritivores and scavengers (Carter et al. 2007; Barton et al. 2013). The combined activity of microbes and invertebrates increases the nutrients released from the carrion into the soil; however, vertebrates may reduce this contribution by direct consumption or dispersion (Carter et al. 2007; Barton et al. 2013). In terrestrial ecosystems where carrion releases nutrients into the soil, plants may ultimately mobilize these nutrients entering the belowground detrital pathway (Moore et al. 2004; Carter et al. 2007). Despite its potential importance, only very recently the scientific community has started to acknowledge the role of carrion decomposition in nutrient recycling (DeVault et al. 2003; Carter et al. 2007; Wilson and Wolkovich 2011). Detrital inputs enter any ecosystem via allochthonous or autochthonous sources (Moore et al. 2004). Allochthonous inputs are resources that originate in one habitat but move into another, while autochthonous inputs originate and are consumed in the same habitat (Polis et al. 1997). Many ecosystems experience spatial subsidies as regular seasonal events, but subsidies can also result from sporadic episodes of resource superabundance, named resource pulses (Ostfeld and Keesing 2000; Anderson et al. 2008b; Yang et al. 2008). Examples of resource pulses include periodical cicadas’ emergence in North American forests (e.g. Yang 2004, 2008), El Nin˜o rainfalls in arid ecosystems (e.g. Polis et al. 1997; Meserve et al. 2003; Letnic et al. 2005), seed or fruit mast events (e.g. Woff 1996; Curran and Leighton 2000), and massive spawning events by migratory fish (e.g. Woff and Hershey 1999; Yanai and Kochi 2005). Despite their ecological importance, these studies focused mostly on aboveground processes and just a few assessed belowground effects (Yang 2004; Yang et al. 2010).

Cultivated mushrooms are an important food source for many people around the world, with global production estimated at over 10 million tons per year (Food and Agriculture Organization of the United Nations 2014). Over two thirds of the production of edible mushrooms are harvested in mainland China, where mushrooms form a more traditional role in food and medicine than they do in many Western countries, and where they provide a living for over 25 million mushroom farmers (Zhang et al. 2014b). The most important edible mushroom genus grown commercially is Agaricus (mainly Agaricus bisporus, the button mushroom), which makes up about 30% of the global market (Royse 2014). Other important edible genera include Pleurotus (5–6 species of oyster mushrooms that are cultivated commercially), Lentinula (shiitake), Auricularia (3–4 species of woodear mushrooms), Flammulina (enoki), and Volvariella (paddy straw). Edible mushroom production is dominated by a few species where the technology for large-scale industrial cultivation has been optimized (Chang and Miles 2004), but in many countries large numbers of small-scale farms also exist, and there are increasing attempts to domesticate local wild mushrooms for production purposes (Mwai and Muchane 2016). Cultivated mushrooms are saprophytes which grow by degrading natural lignocellulosic substrates, which are commonly available in large volumes as agricultural or industrial byproducts. The methods for commercial cultivation of mushrooms on these substrates can be divided into three broad groups. The first group includes cultivation of many wooddegrading mushrooms that were traditionally grown on wood logs or harvested from trees. Some of these, such as Lentinula, are now grown on artificial logs of compacted, sterilized sawdust, while others, such as Flammulina, Pholiota (nameko), or Auricularia are cultivated on a partly composted mixture of sawdust and other components (bran, straw, corncobs), which is sterilized at high temperature (121 °C) before inoculation with mycelium (Chang and Miles 2004; Sanchez 2010). Because of the rigorous sterilization process, these mushrooms are essentially grown in axenic culture. The second group of cultivation methods either uses uncomposted substrates directly, or uses partially composted substrates that have not been subjected to a rigorous sterilization process. This includes methods commonly used for Pleurotus and Volvariella species, though Pleurotusis also sometimes grown on sterilized sawdust substrates. These are fast-growing and adaptable genera capable of rapid bioconversion of a broad range of substrates (e.g., rice straw, bagasse, cornstalks, waste cotton, stalks, and leaves of bananas (Chang and Miles 2004; Thongklang and Luangharn 2016). The substrates are usually not sterilized before inoculation, though a pasteurization step may be included in the process, and the mushrooms therefore grow in competition with other microorganisms on the substrate. The most industrially complex process is the cultivation of Agaricus, which is grown on a pasteurized straw-based compost which requires lengthy preparation, but allows selective growth of the Agaricus mycelium over competitor organisms.

The main function of mitochondria is the production of ATP in the process of oxidative phosphorylation. The main byproduct that is formed in the course of electron transport in the respiratory chain is superoxide anion radical. Superoxide emerges as a result of one-electron reduction of molecular oxygen in various parts of the respiratory chain, including Complex I (NADH: ubiquinone oxidoreductase), Complex II (succinate dehydrogenase), Complex III (ubiquinol: cytochrome oxidoreductase), and mitochondrial matrix dehydrogenases [Grivennikova and Vinogradov, 2013]. Subsequently, the superoxide gives rise to various reactive oxygen species (ROS). Normally, only 1-2% of the oxygen consumed by the cells are used for ROS formation in mitochondria (mtROS) [Turrens, 2003, Inoue et al., 2003]. Until recently, it was believed that mtROS predominantly play a destructive role causing cell damage and accelerating aging [Harman, 2003]. These views are exemplified by the ideas that are expressed in the work of Huang and co-workers [1997]. It was established that mice with a knockout of cytosolic CuZn-dependent superoxide dismutase gene are viable, while mice with a nonfunctional mitochondrial Mn-dependent superoxide dismutase gene do not survive. Recently, it has been established that mtROS formation is mandatory for the functioning of virtually all organs and tissues, being involved in numerous metabolic pathways and in the regulation of signaling processes [Dan Dunn et al., 2015]. Importantly, mtROS are essential for the functioning of the immune system. However, their influence may be either positive or negative, depending on the quantity of the mtROS involved. From the immunological viewpoint, the positive effects of mtROS are primarily based on their activating influence on antimicrobial immunity, while their negative effects, caused by their excessive production, result in the induction of autoinflammatory [van der Burgh and Boes, 2015] and autoimmune processes [Lee et al., 2016; Lood et al., 2016]. The formation of mtROS plays an important role in the development of the antiviral immunity including the production of proinflammatory cytokines by immune system cells [Kim et al., 2015]. This review is concerned with the analysis of the mtROS role in terms of antibacterial innate immunity.