Re-vitalizing wastewater: Nutrient recovery and carbon capture through microbe-algae synergy using omics-biology.

Increasing amounts of wastewater is the most pervasive and challenging environmental problem globally. Conventional treatment methods are costly and entail huge energy, carbon consumption and greenhouse gas emissions. Owing to their unique ability of carbon capturing and resource recovery, microalgae-microbiome based treatment is a potential approach and is widely used for carbon-neutral wastewater treatment. Microalgae-bacteria synergy (i.e., the functionally beneficial microbial synthetic communities) performs better and enhances carbon-sequestration and nutrient recovery from wastewater treatment plants. This review presents a comprehensive information regarding the potential of microalgae-microbiome as a sustainable agent for wastewater and discusses synergistic approaches for effective nutrient removal. Moreover, this review discusses, the role of omics-biology and Insilco approaches in unravelling and understanding the algae-microbe synergism and their response toward wastewater treatment. Finally, it discusses various microbiome engineering approaches for developing the effective microalgae-bacteria partners for carbon sequestration and nutrient recovery from wastewater, and summarizes future research perspectives on microalgae-microbiome based bioremediation.

Modeling and optimization of chlorpyrifos and glyphosate biodegradation using RSM and ANN: Elucidating their degradation pathways by GC-MS based metabolomics.

Ongoing and extensive use of pesticides negatively impact the environment and human health. Microbe-based remediation bears importance as it is an eco-friendly and cost-effective technique. The present study investigated chlorpyrifos (CHL) and glyphosate (GLY) degrading potential of Bacillus cereus AKAD 3-1, isolated from the soybean rhizosphere. Optimization and validation of different process variables were carried out by response surface methodology (RSM) and artificial neural network (ANN). Critical parameters which affect the degradation process are initial pesticide concentration, pH, and inoculum size. At optimum conditions, the bacterial strain demonstrated 94.52% and 83.58% removal of chlorpyrifos and glyphosate, respectively. Both Central-composite design (CCD-RSM) and ANN approaches proved to perform well in modeling and optimizing the growth conditions. The optimum ANN-GA model resulted in R2 ≥ 0.99 for chlorpyrifos and glyphosate, while in the case of RSM, the obtained R2 value was 0.96 and 0.95, respectively. Results indicated that the process variables significantly (p < 0.05) impact chlorpyrifos and glyphosate biodegradation. Moreover, the predicted RSM model had a "lack of fit p-value" of "0.8849" and "0.2502" for chlorpyrifos and glyphosate, respectively. GC-MS analysis revealed that the strain first converted chlorpyrifos into 3,5,6-trichloro pyridin-2-ol & O, O-diethyl O-hydrogen phosphorothiate. Later, these intermediate metabolites were broken and completely mineralized into non-toxic by-products. Similarly, glyphosate was first converted into 2-(methylamino) acetic acid and amino-oxyphosphonic acid, which were further mineralized without any toxic by-products. Taken together, the results of this study clarify the biodegradation pathways and highlights the promising potential of B. cereus AKAD 3-1 in the bioremediation of chlorpyrifos and glyphosate-polluted environments.

Pesticide pestilence: Global scenario and recent advances in detection and degradation methods.

Increased anthropogenic activities are confronted as the main cause for rising environmental and health concerns globally, presenting an indisputable threat to both environment and human well-being. Modern-day industrialization has given rise to a cascade of concurrent environmental and health challenges. The global human population is growing at an alarming rate, posing tremendous pressure on future food security, and healthy and environmentally sustainable diets for all. To feed all, the global food production needs to increase by 50% by 2050, but this increase has to occur from the limited arable land, and under the present-day climate variabilities. Pesticides have become an integral component of contemporary agricultural system, safeguarding crops from pests and diseases and their use must be reduce to fulfill the SDG (Sustainable Development Goals) agenda . However, their indiscriminate use, lengthy half-lives, and high persistence in soil and aquatic ecosystems have impacted global sustainability, overshot the planetary boundaries and damaged the pure sources of life with severe and negative impacts on environmental and human health. Here in this review, we have provided an overview of the background of pesticide use and pollution status and action strategies of top pesticide-using nations. Additionally, we have summarized biosensor-based methodologies for the rapid detection of pesticide residue. Finally, omics-based approaches and their role in pesticide mitigation and sustainable development have been discussed qualitatively. The main aim of this review is to provide the scientific facts for pesticide management and application and to provide a clean, green, and sustainable environment for future generations.

Plants endophytes: unveiling hidden agenda for bioprospecting toward sustainable agriculture.

Endophytic microbes are present in nearly all of the plant species known to date but how they enter and flourish inside a host plant and display multiple benefits like plant growth promotion (PGP), biodegradation, and stress alleviation are still unexplored. Until now, the majority of the research has been conducted assuming that the host-endophyte interaction is analogous to the PGP microbes, although, studies related to the mechanisms of their infection, colonization as well as conferring important traits to the plants are limited. It would be fascinating to explore the role of these endophytic microbes in host gene expression, metabolism, and the modulation of phenotypic traits, under abiotic and biotic stress conditions. In this review, we critically focused on the following areas: (i) endophytic lifestyle and the mechanism of their entry into plant tissues, (ii) how endophytes modulate the immune system of plants and affect the genotypic and phenotypic expression of host plants under abiotic and biotic stress condition, and (iii) the role of omics and other integrated genomic approaches in unraveling complex host-endophyte signaling crosstalk. Furthermore, we discussed their role in phytoremediation of heavy metal stress and whole genomic analysis based on an understanding of different metabolic pathways these endophytes utilize to combat stress.

Lipopeptides from Bacillus: unveiling biotechnological prospects-sources, properties, and diverse applications.

Bacillus sp. has proven to be a goldmine of diverse bioactive lipopeptides, finding wide-range of industrial applications. This review highlights the importance of three major families of lipopeptides (iturin, fengycin, and surfactin) produced by Bacillus sp. and their diverse activities against plant pathogens. This review also emphasizes the role of non-ribosomal peptide synthetases (NRPS) as significant enzymes responsible for synthesizing these lipopeptides, contributing to their peptide diversity. Literature showed that these lipopeptides exhibit potent antifungal activity against various plant pathogens and highlight their specific mechanisms, such as siderophore activity, pore-forming properties, biofilm inhibition, and dislodging activity. The novelty of this review comes from its comprehensive coverage of Bacillus sp. lipopeptides, their production, classification, mechanisms of action, and potential applications in plant protection. It also emphasizes the importance of ongoing research for developing new and enhanced antimicrobial agents. Furthermore, this review article highlights the need for future research to improve the production efficiency of these lipopeptides for commercial applications. It recognizes the potential for these lipopeptides to expand the field of biological pest management for both existing and emerging plant diseases.

Metagenomics insights into microbiome and antibiotic resistance genes from free living amoeba in chlorinated wastewater effluents.

Free living amoeba (FLA) are among the organisms commonly found in wastewater and are well-established hosts for diverse microbial communities. Despite its clinical significance, there is little knowledge on the FLA microbiome and resistome, with previous studies relying mostly on conventional approaches. In this study we comprehensively analyzed the microbiome, antibiotic resistome and virulence factors (VFs) within FLA isolated from final treated effluents of two wastewater treatment plants (WWTPs) using shotgun metagenomics. Acanthamoeba has been identified as the most common FLA, followed by Entamoeba. The bacterial diversity showed no significant difference (p > 0.05) in FLA microbiomes obtained from the two WWTPs. At phylum level, the most dominant taxa were Proteobacteria, followed by Firmicutes and Actinobacteria. The most abundant genera identified were Enterobacter followed by Citrobacter, Paenibacillus, and Cupriavidus. The latter three genera are reported here for the first time in Acanthamoeba. In total, we identified 43 types of ARG conferring resistance to cephalosporins, phenicol, streptomycin, trimethoprim, quinolones, cephalosporins, tigecycline, rifamycin, and kanamycin. Similarly, a variety of VFs in FLA metagenomes were detected which included flagellar proteins, Type IV pili twitching motility proteins (pilH and rpoN), alginate biosynthesis genes AlgI, AlgG, AlgD and AlgW and Type VI secretion system proteins and general secretion pathway proteins (tssM, tssA, tssL, tssK, tssJ, fha, tssG, tssF, tssC and tssB, gspC, gspE, gspD, gspF, gspG, gspH, gspI, gspJ, gspK, and gspM). To the best of our knowledge, this is the first study of its kind to examine both the microbiomes and resistome in FLA, as well as their potential pathogenicity in treated effluents. Additionally, this study showed that FLA can host a variety of potentially pathogenic bacteria including Paenibacillus, and Cupriavidus that had not previously been reported, indicating that their relationship may play a role in the spread and persistence of antibiotic resistant bacteria (ARBs) and antibiotic resistance genes (ARGs) as well as the evolution of novel pathogens.

GC-MS based untargeted metabolomics reveals the metabolic response of earthworm (Eudrilus eugeniae) after chronic combinatorial exposure to three different pesticides.

In this study GC-MS-based untargeted metabolomics was used to identify the metabolic response of earthworm; Eudrilus eugeniae exposed to sub-lethal concentrations of chlorpyrifos-CHL, cypermethrin-CYP, Glyphosate-GLY, and Combined-C (all three pesticides) at the concentrations of 3, 6, and 12 mg/kg. Principal component analysis of the obtained datasets revealed a clear distinction between the control and treatment groups. The mean weight of the worms in the treated groups decreased significantly (p < 0.05). Among the identified metabolites, oleic acid (~ 93.47%), lysine (~ 92.20%), glutamic acid (~ 91.81%), leucine (~ 90.20%), asparagine (~ 94.20%), methionine (~ 92.27%), malic acid (~ 93.37%), turanose (~ 95.04%), maltose (~ 92.36%), cholesta-3,5-diene (~ 86.11%), galactose (~ 93.20%), cholesterol (~ 91.56%), tocopherol (~ 85.09%), decreased significantly (p < 0.05), whereas myoinositol (~ 83%) and isoleucine (78.09%) increased significantly (p < 0.05) upon exposure to the CHL, CYP, GLY, and C. Overall, the findings suggest that earthworms might be a new entry point for the pesticides into the food chain. The present study highlights that metabolomics can be a reliable approach to understand the effect of different xenobiotics including pesticides on the metabolic response of earthworms.

Metagenomic analysis displays the potential predictive biodegradation pathways of the persistent pesticides in agricultural soil with a long record of pesticide usage.

Microbes are crucial in removing various xenobiotics, including pesticides, from the environment, specifically by mineralizing these hazardous pollutants. However, the specific procedure of microbe-mediated pesticide degradation and its consequence on the environment remain elusive owing to limitations in culturing techniques. Therefore, in this study, we have investigated i) the physicochemical and elemental compositions of PCAS (pesticide-contaminated agricultural soils) and NS (natural soils); ii) the bacterial communities and degradation pathways, as well as some novel biodegradation genes (BDGs) and pesticide degradation genes (PDGs) across two different landscapes (PCAS and NS) by applying high-throughput sequencing. The chemical and elemental composition analyses showed that all nutrients (P, K, N, S, Mn, B, and Zn) were significantly higher in PCAS than in NS (p ≤ 0.05). The results of the 16S rRNA amplicon sequencing analysis of pesticide-contaminated (PCAS-1, PCAS-2, PCAS-3, PCAS-4) samples showed that the relative abundance of the phylum Proteobacteria (30-36%) > Actinobacteria (15-20%) > Firmicutes (13-14%) > Bacteroidetes (7-13%), were higher compared to the natural soil (NS-1, NS2). Consistent with this, a phylogenetic shift was observed with (alpha, beta, and gamma Proteobacteria) being abundant in PCAS, whereas delta and epsilon groups were more prevalent in NS. The functional characterization of the PCAS and NS by PICRUSt2 revealed that bacterial communities play a significant role in pesticide metabolism. Predictive metagenome analysis of contaminated soils showed the role of core degrading genes in membrane transport, stress response, regulatory genes, resource transport, and environmental sensing. Furthermore, 14 BDGs and 30 PDGs were examined, with a relative abundance of 0.081-1.029 % and 0.107-0.8903 % in each PCAS, respectively. The major BDGs and PDGs, with the compounds they hydrolyze, include ppo (polyphenol oxidase and laccase), CYP (cytochrome p450 protein), lip gene (lignin peroxidase), similarly, among the PDGs mhel (carbendazim), opd (organophosphate), mpd (methyl parathion), atzA, atzB, atzD, atzF and trzN (atrazine), chd (chlorothalonil), hdx (metamitron), hdl-1 (isoproturon) and fmo (nicosulfuron). Overall, our findings demonstrated the significance of utilizing metagenomic methods to predict microbial aided degradation in the ecology of contaminated environments.

Taxonomical and functional bacterial community profiling in disease-resistant and disease-susceptible soybean cultivars.

Highly varied bacterial communities inhabiting the soybean rhizosphere perform important roles in its growth and production; nevertheless, little is known about the changes that occur in these communities under disease-stress conditions. The present study investigated the bacterial diversity and their metabolic profile in the rhizosphere of disease-resistant (JS-20-34) and disease-susceptible (JS-335) soybean (Glycine max (L.) Merr.) cultivars using 16S rRNA amplicon sequencing and community-level physiological profiling (CLPP). In disease-resistant soybean (AKADR) samples, the most dominating phyla were Actinobacteria (40%) followed by Chloroflexi (24%), Proteobacteria (20%), and Firmicutes (12%), while in the disease-susceptible (AKADS) sample, the most dominating phyla were Proteobacteria (35%) followed by Actinobacteria (27%) and Bacteroidetes (17%). Functional profiling of bacterial communities was done using the METAGENassist, and PICRUSt2 software, which shows that AKADR samples have more ammonifying, chitin degrading, nitrogen-fixing, and nitrite reducing bacteria compared to AKADS rhizosphere samples. The bacterial communities present in disease-resistant samples were significantly enriched with genes involved in nitrogen fixation, carbon fixation, ammonification, denitrification, and antibiotic production. Furthermore, the CLPP results show that carbohydrates and carboxylic acids were the most frequently utilized nutrients by the microbes. The principal component analysis (PCA) revealed that the AKADR soils had higher functional activity (strong association with the Shannon-Wiener index, richness index, and hydrocarbon consumption) than AKADS rhizospheric soils. Overall, our findings suggested that the rhizosphere of resistant varieties of soybean comprises of beneficial bacterial population over susceptible varieties.

Emerging frontiers in microbe-mediated pesticide remediation: Unveiling role of omics and In silico approaches in engineered environment.

The overuse of pesticides for augmenting agriculture productivity always comes at the cost of environment, biodiversity, and human health and has put the land, water, and environmental footprints under severe threat throughout the globe. Underpinning and maximizing the microbiome functions in pesticide-contaminated environments has become a prerequisite for a sustainable environment and resilient agriculture. It is imperative to elucidate the metabolic network of the microbial communities and environmental variables at the contaminated site to predict the best strategy for remediation and soil microbe-pesticide interactions. High throughput next-generation sequencing and in silico analysis allow us to identify and discern the members and characteristics of core microbiomes at the contaminated site. Integration of modern high throughput multi-omics investigations and informatics pipelines provide novel approaches and pathways to capitalize on the core microbiomes for enhancing environmental functioning and mitigation. The role of eco-genomics tools in visualising the microbial network, taxonomy, functional potential, and environmental variables in contaminated habitats is discussed in this review. The integrated role of the potential microbe identification as individual or consortia, mechanistic approach for pesticide degradation, identification of responsible enzymes/genes, and in silico approach is emphasized for the prospects of the area.

Process optimization of cypermethrin biodegradation by regression analysis and parametric modeling along with biochemical degradation pathway.

Pyrethroid pesticides are of great environmental and health concern with regard to neurotoxicity and ubiquitous occurrence. Here, we reported a new bacterial strain identified as Bacillus cereus AKAD 3-1 that degraded 88.1% of 50 mg/l of cypermethrin in an aqueous medium. The biodegradation of cypermethrin was optimized by CCD (central composite design) and validated by ANN-GA (artificial neural network-genetic algorithm). Both the approaches proved to possess good performance in modeling and optimizing the growth conditions. Results indicated that the process variables have a significant (< 0.0001) impact on cypermethrin biodegradation. Moreover, the predicted CCD model had a "lack of fit p-value" of "0.9975." The optimum CCD and ANN model had an R2 value of 0.9703 and 0.9907, indicating that the two models' experimental and predicted values are closely fitted. The isolate successfully converted cypermethrin to CO2 and phenol without producing any toxic metabolite. Finally, a degradation pathway was proposed with the intermediate compounds identified by GC-MS. The present study highlights an important potential application of strain AKAD 3-1 for the in situ bioremediation of cypermethrin-contaminated environments.

Pyrosequencing and phenotypic microarray to decipher bacterial community variation in Sorghum bicolor (L.) Moench rhizosphere.

Different cultivation practices and climatic conditions play an important role in governing and modulating soil microbial communities as well as soil health. This study investigated, for the first time, keystone microbial taxa inhabiting the rhizosphere of sweet sorghum (Sorghum bicolor) under extensive cultivation practices at three different field sites of South Africa (North West-South (ASHSOIL1); Mpumalanga-West - (ASHSOIL2); and Free State-North West - (ASHSOIL3)). Soil analysis of these sites revealed differences in P, K, Mg, and pH. 16S rRNA amplicon sequencing data revealed that the rhizosphere bacterial microbiome differed significantly both in the structure and composition across the samples. The sequencing data revealed that at the phylum level, the dominant group was Cyanobacteria with a relative abundance of 63.3%, 71.8%, and 81.6% from ASHSOIL1, ASHSOIL2, and ASHSOIL3, respectively. Putative metabolic requirements analyzed by METAGENassist software revealed the ASHSOIL1 sample as the prominent ammonia degrader (21.1%), followed by ASHSOIL3 (17.3%) and ASHSOIL2 (11.1%). The majority of core-microbiome taxa were found to be from Cyanobacteria, Bacteroidetes, and Proteobacteria. Functionally, community-level physiological profiling (CLPP) analysis revealed that the metabolic activity of the bacterial community in ASHSOIL3 was the highest, followed by ASHSOIL1 and ASHSOIL2. This study showed that soil pH and nutrient availability and cultivation practices played significant roles in governing the bacterial community composition in the sorghum rhizosphere across the different sites.

Approaches for the amelioration of adverse effects of drought stress on crop plants.

Climate change, water scarcity, population growth, and food shortage are some of the threatening challenges being faced in today's world. Among different types of stresses, drought stress presents a persistent challenge for global food production, however, its harshness and intensity are supposed to expand in the imminent future. The most striking effects of drought stress on plants are stunted growth, severe damage to photosynthetic apparatus, reduction in photosynthesis, reduction in seed germination, and nutrient uptake. To deal with the destructive effect of drought stress on plants, it is necessary to consider its effects, mechanisms of action, the agronomic and genetic basis for sustainable management. Therefore, there is an urgent need for sustainable solutions to cope up with the negative impact of drought stress. This review focuses on the detrimental effects of drought stress on plants' morphological, physiological, and biochemical characteristics and recommends suitable drought management techniques to reduce the severity of drought stress. We summarize the effect of drought stress on physiological and biochemical parameters (such as germination, photosynthesis, biomass, water status, and nutrient uptake) and yield. Overall, in this article, we have reviewed the role of different phytohormones, osmolytes, exogenous compounds, proteins, plant growth-promoting microbes (PGPM), omics approaches, and genome editing technologies like clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (CRISPR-Cas9) in alleviating drought effects in plants. We also proposed that developing drought-tolerant plant varieties requires the combined use of biotechnological and agronomic approaches and cutting-edge genome editing (GE) tools.

With Corona Outbreak: Nature Started Hitting the Reset Button Globally.

Considering the potential threat and the contagious nature of the Covid-19 pandemic, lockdowns have been implemented worldwide to stop the spread of this novel virus. The coronavirus pandemic has hit the world severely, representing the most severe threat to human health in more than a century. The environment from local to global scales has witnessed apparent positive and negative impacts. Global lockdowns have drastically altered the patterns of energy demand and have caused an economic downturn but at the same time, have provided an upside-cleaner global environment. Such immense unintended advantages offer opportunities for unprecedented insights into the dynamics of our natural and built environments that can lead to viable paths for the conservation and perpetuation of the recovered environments and through sensible policies and practices that can help to create new recovery pathways. Knowledge gained from the studies suggests that a substantial relationship exists between the contingency measures and environmental health. Here in this review, the authors discussed the impact of coronavirus pandemic on human life, healthcare organizations, and the environment. The parallels between the Covid-19 and other diseases are mentioned. Finally, the impact of Covid-19 on society and the global environment has also been highlighted.

Complete Genome Sequence of Lactobacillus plantarum Strain JDARSH, Isolated from Sheep Milk.

Lactobacillus plantarum strain JDARSH, a potential probiotic with a wide range of functions, was isolated from sheep milk. Here, we report the whole-genome sequence of this bacterium. The draft genome yielded a 3.20-Mb genome and 2,980 protein-coding sequences.

Exploring the Human Microbiome: The Potential Future Role of Next-Generation Sequencing in Disease Diagnosis and Treatment.

The interaction between the human microbiome and immune system has an effect on several human metabolic functions and impacts our well-being. Additionally, the interaction between humans and microbes can also play a key role in determining the wellness or disease status of the human body. Dysbiosis is related to a plethora of diseases, including skin, inflammatory, metabolic, and neurological disorders. A better understanding of the host-microbe interaction is essential for determining the diagnosis and appropriate treatment of these ailments. The significance of the microbiome on host health has led to the emergence of new therapeutic approaches focused on the prescribed manipulation of the host microbiome, either by removing harmful taxa or reinstating missing beneficial taxa and the functional roles they perform. Culturing large numbers of microbial taxa in the laboratory is problematic at best, if not impossible. Consequently, this makes it very difficult to comprehensively catalog the individual members comprising a specific microbiome, as well as understanding how microbial communities function and influence host-pathogen interactions. Recent advances in sequencing technologies and computational tools have allowed an increasing number of metagenomic studies to be performed. These studies have provided key insights into the human microbiome and a host of other microbial communities in other environments. In the present review, the role of the microbiome as a therapeutic agent and its significance in human health and disease is discussed. Advances in high-throughput sequencing technologies for surveying host-microbe interactions are also discussed. Additionally, the correlation between the composition of the microbiome and infectious diseases as described in previously reported studies is covered as well. Lastly, recent advances in state-of-the-art bioinformatics software, workflows, and applications for analysing metagenomic data are summarized.