Current Genomics

This part brings three interesting articles which are very unique and enlightening reviews on important areas of plantmicrobe interaction. The parts I and II have been able to present extensive insights into plant-microbe interactions in various fields which is in continuation in this part too [1, 2]. This part puts light on Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 (CRISPR-associated protein 9) Era plant-microbe interaction, translational research on Fusarium Head Blight (FHB) in Wheat and plant-virus interaction with reference to viral effector proteins. Beginning with the article by Prabhukarthikeyan and co-authors, it presents the emerging CRISPR/Cas9 approach which has gained immense attention in the last few years [3]. The authors here have started with a brief introduction about the plantmicrobe interactions and the CRISPR/Cas9 technique and continued with descriptive but precise mention of the use of this technique for resistance against fungal, bacterial and viral disease. Apart from these, the use of CRISPR/Cas9 technique in case of beneficial microbes and phytopathogens is also discussed. Collections of information from earlier studies have been collated into a table to highlight the target genes. The table mentioned very important genes such as WRKY, eIF4E, etc. which are wellknown to be the regulators of many important signaling pathways in various crops. The authors have pointed the fact that despite this powerful technique in our hands for a time, it has only been extensively used in validating the previously identified genes/pathways and still need to be employed in the successful development of durable resistance in crops against multiple pathogens. Teli et al. discuss a major threat to most cereal crops such as wheat and barley, commonly known as Fusarium head blight or scab [4]. The pathogenic strains of Fusarium are generally devastating for the host plants due to their adaptability and multifaceted nature [5]. History of FHB has documented evidences of most threatening epidemics during the years 1917, 1919, 1928, 1932, and 1935 in the United States [6]. The authors have provided a comprehensive delineation on FHB along with its symptoms, complexity and survivability. There are figures to illustrate the predominance of FHB associated pathogens worldwide, biochemical foundation of host-pathogen interaction in FHB and cutting-edge techniques such as RNA interference (RNAi) and CRISPR to remodel the host defence. There are two tables presenting the information regarding the RNA and CRISPR interference mediated defense against FHB. Extensive description about various strategies such as the conventional breeding, molecular marker, transgenic and non-transgenic genome engineering approaches has been well-documented in this article to offer insights into host-pathogen interaction in FHB. The third article by Marwal and Gaur describes specifically the plant-virus interactions and viral effector proteins [7]. Plant defense machinery is very difficult to understand as it behaves differently depending upon the type of pathogen attack. It is even more critical in case of virus infection as all viruses infecting plants can augment their transmission leading to damaging the host plants. The authors have provided a schematic illustration of R gene mediated resistance in plants, signaling molecule induction, plant antiviral pathways and viral counter-defenses as well as virus effector proteins in plant resistance development. Detailed understanding of R-Avr interactions and mode of their actions can lead to unravel the mystery of plant-virus interactions and this article aimed for providing available information in a brief and precise way to help broaden our knowledge in this regard.

In continuation with part I, this part describes the use of genetically modified microbes, rhizospheric microbial communities, various molecular techniques and omics approaches to shed the light on understanding plant-microbe interactions [1]. Due to the long ongoing controversies regarding the use of application of genetically engineered microbial inoculants in the field, it has been a hot topic since the last two decades. The authors have been able to provide descriptive information regarding the same with special application towards plant-microbe interactions. A bright study carried out with the help of omics technologies, especially bioinformatics approaches to understand the microbial communities in coal samples. Sudheer and co-authors presented a mini-review on engineered microbes and their applications in sustainable agriculture [2]. Authors emphasized especially on methods to shape the rhizosphere zone, which can ultimately promote the beneficial microbial population in the soil. Microbial communities in the soil can be diverse and a deeper understanding of their nature can help plants to provide enhanced stress tolerance, disease resistance, nutrient acquisition and also many other important factors. There are various efficient genetic engineering/molecular techniques which are available and being used to attain better plant health and yield. The authors provided a simpler version of understanding plant-microbe interaction and how the networks work in the soil. Also mentioned briefly about the microbial inoculants and their function as biofertilizers, biocontrol agents, and in biotic and abiotic stress tolerance. Though the application of genetically engineered microbial inoculants in the field is still not approved fully, the potential of these cannot be denied. Upon more research and better as well as safe practices, these can be used as huge assets to achieve sustainable agriculture. In addition, a review is presented on genomics approaches to provide insights into the role of rhizospheric microbial communities in plant-microbe synergy for enhanced phytoremediation [3]. This review aims at drawing an understanding of genetic approach integrated with bioremediation of contaminated sites. Authors have described extensively on phytoremediation and the role of predominant rhizospheric microbial communities in it. In the later part, the application of genetically modified plants and microbes for phytoremediation has been described. The cutting-edge genomic approaches such as CRISPR (clustered regularly interspaced short palindromic repeats) technology was illustrated in plant-microbe synergy. Authors also presented a table containing various plants, microbes, target pollutants and their enhanced effect on phytoremediation. Another review by Sharma and co-authors provided insights into overall omics technologies for plant-microbe interaction [4]. The review tries to bring together important aspects such as plant growth promotion, nitrogen fixation, stress suppressions and metabolic interactions along with the recent studies on various advanced omics approaches. The basics of various types of plant-microbe interactions have been stated briefly with a vivid description of various molecular techniques. It continues with an extensive discussion of applications of next generation sequencing techniques and meta-omics approaches in unravelling plant-microbe interaction understandings. The authors also discussed the research gaps and future prospects of omics approaches with respect to plant-microbe interaction studies. Jha and team carried out bioinformatics analyses of the metagenomic data obtained from the West Jharia coal seam, Moonidih, Jharkhand [5]. Pyrosequencing was performed on DNA extracted from the coal samples following by bioinformatics analyses which are taxonomic assignment and functional analysis. The upshot of the study helped in revealing important information regarding biodiversity such as the dominance of hyperthermophilic archaea Pyrococcus furiosus along with Thermococcus kodakarensis present in the underground coal mines of Jharia. The results also revealed the presence of dissimilatory sulfite reductase and formylmethanofuran dehydrogenase enzymes involved in sulfite reduction and methanogenesis processes respectively. Much information about real efficiency of coal degrading microbes is still hidden. The study has been able to provide preliminary as well as extensive insight into meta-genomic information such as taxonomic and functional diversity of the microbial communities in coal mines.

In the present scenario, increasing pollution and green house effect on climate are serious concerns that lead to extreme environment conditions. Therefore, the major aim of scientist is to resolve environmental issues in an economic and sustainable way. To deal with extreme conditions, extremophiles are safer option for scientist or industries. In industries, most of possesses are completed in extreme environment like temperature, pH, pressure etc. However, the majority of enzymes used in industrial process are derived from mesophilic microbes, few are from extremophiles. The mesophilic enzymes are unable to perform at extreme conditions in industrial processes [1]. Thus, the need of extrmophilic enzymes is increasing globally to meet out the industrial requirements. In addition, industrial processes are also performed with chemical compounds or enzymes, which are very cost effective and harmful. In this context, extremophilic microbes can be used directly as a cell or enzymes (extremozymes) to carry out chemical reaction in an eco-friendly manner [2]. Extremophiles are used in food, pharmaceutical, textile, beverages and agricultural industries. Extremophilic microbes possess different types of enzymes and metabolites, which can work on harsh condition and make them perfect for the industrial purposes. These microbes are used at different physical conditions i.e. elevated level of extreme temperature, pH, heavy metal contamination, organic solvents etc [3]. We can improve the efficiency of extremophiles by using modern technologies such as genetic engineering and protein engineering. The demand of extremophilic products is very large in global market. The fulfilling of this demand requires recombinant technology for large scale production and also purification [3]. However, there is still need to explore multiple extremophilic microbes that can be used for society. In continuation to first part of this special issue, this part describes different extremophilic microbes and their role in biofuel production, industrial dye degradation and abiotic stress tolerance. Topic is also included on metagenomic analysis of plastic degrading bacteria. In this sense, a review article by Fongaro et al. [4] described the importance of muiti-omics tools including (genomics, transcriptomics, proteiomics and metabolomics) in exploitation of extremophile microorganism and their novel metabolites for bioenergitic application. Authors discussed about different types of extremozymes including, thermophilic, psychrophilic, piezophilic, acidophilic and halophilic in details. In another review, Purohit et al. [5] documented about metagenomic approach for exploration of microbial population involved in plastic biodegradation. Metagenomic approach helps in harnessing predominant uncultured microbial species and also opens up the scope for mining genes or enzymes (hydrolases, laccase, etc.) engaged in polymer or plastic degradation. The comparative metagenomic study allows us to engineer microbial community to speed up the degradation process. Authors have targeted different metagenomic approach based on 16S V2-V6 regions for identifying plastic degrading microbes from different habitat. In a research article, Ghosh et al. [6], studied the diversity of the psychrotolerant actinomycetes sp. nov., in the Bay of Bengal and recovered cold active industrial and pharmaceutical biomolecules. In this study, authors have isolated cold-adapted actinomycetes from 1200 mts below the surface in Bay-of-Bengal. A total number of 37 novel actinomycetes from 17 distinct groups were characterized on the basis of phenotypic and genotypic level. The major dominant group was Streptomyces. The optimum growth of isolated strains was observed at 15°C to 20°C and also able to survive at 4°C. All the recovered isolates were able to produce extracellular enzymes including amylase, cellulase, lipase, pectinase, and L-asparaginase and also showed antagonistic activity. In another study, Mawad et al. [7] have applied microbial consortium including Pseudomoans aeruginosa and Aspergillus flavus for the degradation of Disperse Blue 64 (DB 64) and Acid Yellow 17 (AY 17) dyes. The consortium was able to possess higher ability to degrade dye even at 300mg/L as compared to individual one. This microbial consortium and their derived metabolites were also able to promote Vicia faba and Triticum vulgaris germination and health of seedlings in in-vitro assay. Chatterjee et al. [8] studied the abiotic stress tolerance mechanism of Cyanobacteria through Alr0765 protein study of Anabaena PCC7120. Alr0765 is a novel CBS-CP12 domain protein that has function to provide protection against stress through involving cellular energy mechanism and iron homeostasis. The gene expression of Alr0765 was found to increase in Anabaena PCC7120 treated under heat, arsenic, cadmium, butachlor, salt, mannitol (drought), UV-B, and methyl viologen stresses. Further study with FTIR confirmed the binding of Alr0765 with ATP, ADP, AMP and NADH. The same protein was also able to accumulate iron in E. coli cells upon heterologous expression. The ROS content and total cellular H2O2 content was reduced when Alr0765 was expressed.

For the last few decades, the constant striving to understand the mechanism of plant-microbe interaction has increased manifold, even though a lot of inaccessible information is yet to unfold. Ingress into such covered information can be a notable aid for mankind, particularly by helping plants fight against pathogens and other stresses. Crops are continuously exposed to many stresses, which may be abiotic or/and biotic. At times the interactivity of microbes with plants assists plants to stand against various environmental stresses; on the contrary, sometimes they act as stresses for plants. Plants are always at higher risks as most of the microbes interact with the plants to feed or to survive [1, 2]. There is an extensive range of beneficial microorganisms which play vital role in plant growth, development and survival [3]. These are most often known as agriculturally important microbes which not only help plants to get proper nutrients but also regulate the plant and other microbe interactions. Knowing the nature of microbe and its connection with particular plants be useful to control diseases in plants. There are several mechanisms for plant-microbe interactions which vary from plant to plant and microbe to microbe as well [4]. The interaction can materialize in any part of the plants, may it be underground or above the soil. It can also be both endophytic and epiphytic, depending on the microbes. In addition to these two major participants, it also relies on the environment neighboring the area where the interaction occurs. Zooming into the high definition resolution of the genomic arrangements with the help of emerging and advanced techniques in the post-genomics era has been of primary focus. Comparative genomics studies have successfully revealed the genetic make-up of both plants and microbes in the past using powerful molecular approaches. In the last few decades, the advancement in the sequencing, as well as data analysis techniques have provided the most efficient way of studying the genetic variation, differential expression, gene regulatory networks, and many more [5]. Microarray technologies created a new world for the scientists which has been almost replaced by the Next generation sequencing (NGS) and before the NGS has been used to even its full capabilities, we have single cell genomics in the picture which promises to provide the genomic resolution up to the single cell level. Technologies such as CRISPR-Cas-9 (Clustered regularly interspaced short palindromic repeats- CRISPRassociated protein 9) have been a boon to the world of research, especially in the field of plant pathology. Keeping in mind all these points, the current issue is aiming at shining light into the current scenario as well as past researches that brought so much useful information to improve crop protection. The review article by Agrahari et al. [6] describes the importance of studying plant-microbe interaction and its use to crop improvement. The article discusses the post-genomic era omics approaches such as next-generation sequencing (NGS) in association with marker assisted selection, cloning and recombination techniques, Genome-wide association studies (GWAS) and also CRISPR-Cas-9 technology. A brief overview of various models such as zig-zag model, invasion model, spatial immunity model, etc. has been provided to understand plant defense responses against various pathogens. To fight against various abiotic and biotic stress conditions, deployment plant-associated microbial population has the potential to help up to a great extent. Last but not the least, the article describes the beneficial microbes and their applications in crop improvement. Another article by Anupriya et al. [7] describes the genomics and molecular aspects of white rust disease along with how the white rust resistance can be transferred in the susceptible varieties of oilseed Mustard. This review broadly defines the nucleotide binding leucine rich repeat receptor (NLR) signaling and its application to exhibit oomycetes resistance in plants with special reference to effector molecules, Albugo candida secretome. It also describes various efficient approaches such as NLR repertoire enrichment, r-avr gene interaction, RNAi, and CRSPR-Cas technologies, which are being used to understand the pathogen-resistance mechanism. Shukla et al., [8] in their article, have reviewed biotechnological approaches for bioremediation of xenobiotics. They specifically discuss potential extremophiles, basically microorganisms living in extreme conditions. This review provides information on the previous studies regarding the extremophiles (microbes) and the pollutants which can been degraded. The use of extremozymes such as amylases, proteases, etc. are highly stable and can act as good novel catalysts. There are reports of more than 3,000 such enzymes which have been isolated from various extremophiles and have immense importance industrial uses.

Survival of life in extreme environments has always caught the attention of scientists and researchers as it can lead to understand several mechanisms leading to humanity. A few groups of organisms, including animals, plants and microorganisms can survive against harsh environmental conditions such as extreme temperature (cold and hot), salt, pressure, pH (acidic and alkaline) and drought. The organisms surviving on these niches are individually called thermophiles, psychrophiles, halophiles, piezophiles, acidophiles, alkaliphiles and xerophiles. The collective term for all these organisms is extremophiles. The study of extremophiles has received significant interest in both environmental and industrial perspectives. It has already been reported that microorganisms are present in a huge diversity in extreme niches. A great interest in the exploration of extreme habitats with a diversity of extremophilic microbes and their survival mechanisms has been shown in recent years. Some microbes represented the very ancient life forms when the environmental conditions were totally different than today, hence studying about these microbial physiology helps to answer the evolution of life. In addition, extremophiles had also shown their role in astrobiology [1]. The genetic and metabolic machinery of these microbes has been adapted for harsh conditions. For instance, thermophiles, psychrophiles and piezophiles have thermostable proteins, cell wall and cell membrane that resist extreme temperature; halophiles and xerophiles possess osmolytes and antioxidants in high concentration and; acidophiles/alkaliphiles have specific ion transporters to pump out excess ions and maintain neutral pH. Extremophiles also maintain their cell membrane fluidity, which protects their genetic material. They have unique genes that produce important metabolites which are stable at extreme environments known as extremozymes. Such types of metabolites, including protein and enzymes, have proven their importance in the field of biotechnology. For example, a DNA polymerase enzyme used in Polymerase Chain Reaction (PCR) technique is extracted from thermophilic bacteria (Thermus aquaticus). A large number of extremozymes approximately 3000 have been recovered from different extremophiles and are being used in several biotechnological and industrial purposes. However, there are so many extreme niches as well as microbes and their metabolites which are needed to be explored and utilized for improving the quality of life. The recent advances in genomics technologies have allowed for the investigation of extremophiles diversity and their survival mechanism as has never been seen before. Such advance genome-based studies will transform our understanding of physiology, genetic basis and genetic mechanisms of extremophiles and will reveal the importance of extremophiles and their products in multiple aspects of biotechnology including medicine, food technology, biofuel production, agriculture, waste management and many more [2]. The first part of this special issue explores genomic aspects of extremophiles including their survival mechanisms, gene expression and their applications in agriculture and other biotechnology purposes. The extremophiles have unique genetic material that is needed to be mined, which may be useful for genetic engineering in mesophillic microbes and their metabolites can be used in industries. The physiology and diversity of extremophiles including halophiles, psychrophiles and heavy metal tolerance will be presented in this special issue. Topics will also include the engineering of extremophiles and their application in pigment production, waste management and bioenergetic purposes. In this sense, a research article by Mawad et al. [3] explored phenanthrene degrading bacteria Pseudomonas fluorescens AH-40 from oily sludge sample. This bacterium requires less time for degrading complete phenanthrene as compared to previously reported bacterial cultures. Mawadand colleagues quantified the expression of phenathrene degrading genes i.e. naphthalene dioxygenase (nahAc) and catechol 2,3-dioxygenase (C23O) in AH-40 culture and found their increased expression during the degradation process. Authors suggested the role of nahAc and C23O as a marker gene in phenanthrene degradation and recommend to AH-40 culture for bioremediation process. In a review, specific metabolic and genomic features of thermophiles and psychrophiles are discussed by Kohli et al. [4]. Kohli and colleagues reported the role of hydrophobic molecules in cell membrane structure, amino acid composition, tRNA structure, GC content in genomes and many more in the stability of extremophiles under harsh conditions. They also described some examples of different enzymes extracted from both thermophiles and psychrophiles and their applications for industrial purposes. Another review by Usmani et al. [5] described the importance of bioengineering technologies on microbes and their uses for producing microbial pigments using agricultural wastes as substrate. In this review, advance techniques such as Multivariate modular metabolic engineering (MMME) and Multiplex automated genome engineering (MAGE) are reported for modulation in secondary metabolism of extremophiles. These techniques are used for the production of carotenoid and anthocyanin compounds. In addition, use of different agro-wastes such as Apple pomace, Rice powder, Palm date waste, Sugar-beet molasses, Orange waste and many more in production of microbial pigments are reported.

Except for mRNA that encodes proteins, there is another kind of RNA, known as non-coding RNA (ncRNAs), that does not encode proteins. ncRNAs control various levels of gene expression in physiology and development, such as RNA splicing, RNA translation, cell proliferation and apoptosis. Accumulated evidence have demonstrated that ncRNAs are correlated with the progression of a series of diseases. Besides ncRNAs, RNA modification is another layer of epigenetic regulation of gene expression. Since the first modified RNA ribonucleic acid was found in 1957, more than 150 kinds of known RNA modifications have been reported. RNA modifications play critical roles in a series of biological processes, such as RNA degradation, localization and degradation, and even circadian rhythm. Recent studies revealed that RNA modifications are also associated with metabolic diseases, cancer, neurological disorders and cardiovascular diseases. Due to their important roles, more researchers have devoted to the researches on ncRNAs and RNA modification. However, the biological functions and mechanisms of ncRNAs and RNA modification are still unclear. Since experimental methods are cost-ineffective to rapidly and effectively reveal their biological functions, it is highly desirable to develop computational methods which are good complements to experimental techniques for this aim. In recent years, a series of computational methods have been developed to infer the regulatory functions of RNA modification and ncRNA. Therefore, the thematic issue was proposed with the aim to collect a diverse and complementary set of articles that demonstrate new developments and applications of machine learning methods in computational RNA epigenetics. This thematic issue has attracted 6 papers from highly regarded researchers around the world. After the rigorous peer review, 3 of them were accepted for publication. Guan et al. [1] contributed a review article, where they summarized the recent advances in pre-miRNA recognition from the following aspects, namely the benchmark dataset, feature extraction, prediction algorithms, and the evaluation of existing models. The challenges and future perspectives are also discussed. It is believed that this review will provide novel insights into researches on computational identification of miRNA precursors. In a mini review paper contributed by Li et al. [2], the authors reviewed available machine learning based methods for identifying RNA 5-methylcytosine (m5C) sites. Three essential elements, namely dataset, sequence encoding scheme, and machinelearning algorithms, required to constitute a predictor for identifying m5C sites were firstly discussed. More importantly, the bottleneck of those predictors was also pointed out, which should be considered when developing predictors for identifying m5C and even the other kinds of RNA modifications. Govindaraj et al. [3] proposed a novel computational predictor termed as ERT-m6Apred based on extremely randomized tree to identify N6-methyladenosine (m6A), in which a two-step feature selection technique was used to obtain the optimal feature set. Finally, the guest editor would like to thank all the authors who contributed their original works to the thematic issue and to the reviewers for their valuable comments on those works. The guest editor would also like to express sincere gratitude to the Editor in Chief, Dr. Christian Néri, of Current Genomics and the Assistant Manager Publications, Ms. Iqra Shafi for their excellent supports and providing the opportunity to organize the thematic issue.