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Despite the ubiquity of the genus Citrobacter in clinical, industrial, and environmental scenarios, a large number of Citrobacter strains have not been explored at the genome-scale level. In this study, accurate taxonomic assignment of strain AAK_AS5 isolated from activated sludge was achieved by in-silico genomic comparison using Overall Genome-based Relatedness Indices (ANI(OAT): 97.55%, ANIb:97.28%, and ANIm: 97.83%) that indicated its closest identity to the related strain Citrobacter portucalensis A60

In the present study biodegradation of Polycyclic Aromatic Hydrocarbon (PAH) compound Naphthalene by four bacterial cultures Bacillus subtilis PD6, Bacillussp. PD9, Enterobactersp. PD11 and Bacillussp. PD14 has been targeted. Biodegradation of Naphthalene by these four selected bacterial cultures was analysed by HPLC (High Performance Liquid Chromatography) technique. HPLC analysis revealed biodegradation of naphthalene by all the four bacterial cultures within a span of six days. Highest biodegradation 78.1% has been shown by Bacillus subtilis PD6 while other bacterial cultures Bacillus sp. PD9 has shown 77.90%, Enterobacter sp. PD11 showed 74.4% and Bacillus sp. PD14 exhibited 73.5% biodegradation of naphthalene.

Occurrence of Harmful Algal Blooms (HABs) creates a threat to aquatic ecosystem affecting the existing flora and fauna. Hence, the mitigation of HABs through an eco-friendly approach remains a challenge for environmentalists. The present study provides the genomic insights of Rhizobium strain AQ_MP, an environmental isolate that showed the capability of degrading Microcystis aeruginosa (Cyanobacteria) through lytic mechanisms. Genome sequence analysis of Rhizobium strain AQ_MP unraveled the algal lytic features and toxin degradative pathways in it. Functional genes of CAZymes such as glycosyltransferases (GT), glycoside hydrolases (GH), polysaccharide lyases (PL) which supports algal polysaccharide degradation (lysis) were present in Rhizobium strain AQ_MP. Genome analysis also clarified the presence of the glutathione metabolic pathway, which is the biological detoxification pathway responsible for toxin degradation. The conserved region mlrC, a microcystin toxin-degrading gene was also annotated in the genome. The study illustrated that Rhizobium strain AQ_MP harbored a wide range of mechanisms for the lysis of Microcystis aeruginosa cells and its toxin degradation. In future, this study finds promiscuity for employing Rhizobium strain AQ_MP species for bioremediation, based on its physiological and genomic analysis.

For decades, bacterial natural products have served as valuable resources for developing novel drugs to treat several human diseases. Recent advancements in the integrative approach of using genomic and functional tools have proved beneficial in obtaining a comprehensive understanding of these biomolecules. This study presents an in-depth characterization of the anti-diabetic activity exhibited by a bacterial isolate SW1, isolated from an effluent treatment plant. As a primary screening, we assessed the isolate for its potential to inhibit alpha-amylase and alpha-glucosidase enzymes. Upon confirmation, we further utilized LC-MS, ESI-MS/MS, and NMR spectroscopy to identify and characterize the biomolecule. These efforts were coupled with the genomic assessment of the biosynthetic gene cluster involved in the anti-diabetic compound production. Our investigation discovered that the isolate SW1 inhibited both α-amylase and α-glucosidase activity. The chemical analysis suggested the production of acarbose, an anti-diabetic biomolecule, which was further confirmed by the presence of biosynthetic gene cluster "acb" in the genome. Our in-depth chemical characterization and genome mining approach revealed the potential of bacteria from an unconventional niche, an effluent treatment plant. To the best of our knowledge, it is one of the first few reports of acarbose production from the genus Arthrobacter.

Biogas production from agricultural residues represents an effective and sustainable option for handling vast quantities of lignocellulosic waste for meeting the global energy demand. However, the recalcitrance of lignocellulosic biomass due to the presence of cellulose and hemicellulose in a structurally complex lignocellulosic matrix, and the crystallinity of cellulose create a hindrance in biogas production by restricting the availability of fermentable sugars to microbial action. This paper assesses the different pretreatment strategies adopted for making the lignocellulosic biomass amenable to anaerobic digestion by altering the structure of lignocellulose and eliminating lignin, thus increasing the accessibility of microbes to the easily degradable components. The review highlights the advantages and limitations of each technology—physical for size reduction (chipping, milling, extrusion, cavitation), thermal for breaking down of hydrogen bonds (conventional heating, steam explosion, microwave irradiation, hydrothermal), chemical for decreasing the crystallinity and polymerization degree of cellulose (alkalis, acids, gases, oxidizing agents, various solvents), biological for enhancing the digestibility (microbial, enzymatic), and their effect on improving the degradation efficiency and biogas yield. Further, the review discusses the role of some emerging technologies and other less explored options which may require optimization at higher scale so that the confidence in the translation of this knowledge can be increased and this abundantly available raw material can be effectively utilized. With the goal of improving the applicability of pretreatment technologies, some recommendations are put forth so that the efficiency of anaerobic digestion can be increased and the development of pretreatment technologies can be promoted on a large scale.

Huge quantum of agricultural crop residue from agrarian economies like India is disposed of improperly by open land burning contributing to particulate and gaseous pollutants thereby severely impacting the environment and human health. There is an overwhelming need for sustainable utilization of this misplaced resource as feedstock in biofuel production through anaerobic digestion. Substrate composition influences the digestibility of the substrate and underlying microbial plasticity involved in anaerobic digestion. In this study, anaerobic inoculum was subjected to enrichment in the presence of agricultural residues with different lignin content whose influence on biogas production, and differential modulation/ reorganization of microbial communities was explored. BMP assay emphasized the inverse proportionality between lignin content and biogas yield, with highest biogas yield of 622 mL/g VS added in case of rice straw (lowest lignin, 16.9%), followed by wheat straw—556 mL/g VS (18.12% lignin), sugar cane leaves—451 mL/g VS (21.87% lignin), and lowest biogas yield of 411 mL/g VS added in case of cotton crop waste (highest lignin, 23.97%). Biogas production efficiency was correlated with the selection and shift of microbial communities to key hemicellulolytic (Bacteroides, Clostridium, Prevotella, Thermotoga, Cytophaga) and lignocellulolytic (Bacillus, Geobacter, Flavobacterium, Spirochaeta, Klebsiella, Escherichia, Pseudomonas, Burkholderia) genotypes in comparison to initial anaerobic inoculum. Study highlighted that the variable lignin content resulted in genomic reorganization and created a scenario for high biogas production by selectively enriching different methanogenic pathways such as hydrogenotrophic pathways in rice straw metagenome (lowest lignin) and acetoclastic pathways in cotton crop waste metagenome (highest lignin).

The commercial production of bioethanol from lignocellulosic biomass is challenged by the repression of cell growth and compromised fermentation conditions. However, employing Saccharomyces cerevisiae is an economically feasible process resulting in the effective conversion of fermentable sugars to bioethanol. S. cerevisiae’s high productive feature is contributed by robust alcohol dehydrogenase and the ability to tolerate various stresses during the fermentation process. The present review employs various bioinformatics pipeline to assess the structural insights of ADH and interaction among the tolerance genes. Docking of S. cerevisiae’s ADH interaction shows the high binding affinity of − 2.81 Kcal/mol with acetaldehyde contributed by four zinc fingers. In inhibitor tolerance capacity of S. cerevisiae was explored. The STRING platform sheds light on the mechanism and interaction of ASR1 and other stress-responsive elements playing a pivotal role in ethanol tolerance. The stress-responsive genes such as HSPs and MSN2/4 provide balanced physiology under various stress conditions. The present review unravels the complex mechanism behind the inhibitor and ethanol tolerance, directing to several bottlenecks for the improvisation of S. cerevisiae’s performance.

Recently discovered Lytic Polysaccharide Mono-Oxygenase (LPMO) enhances the enzymatic deconstruction of complex polysaccharide by oxidation. The present study demonstrates the agricultural waste hydrolyzing capabilities of Paenibacillus dendritiformis CRN18, which exhibits the enzyme activity of exo-glucanase, β-glucosidase, β-glucuronidase, endo-1, 4 β-xylanases, arabinosidase, and α–galactosidase as 0.1U/ml, 0.3U/ml, 0.09U/ml, 0.1U/ml, 0.05U/ml, and 0.41U/ml, respectively. The genome analysis of strain reveals the presence of four LPMO genes, along with lignocellulolytic genes. The gene structure of LPMO and its phylogenetic analysis shows the evolutionary relatedness with the Bacillus LPMO gene. Gene position of LPMOs in the genome of strains shows the close association of two LPMOs with chitin active enzyme GH18, and the other two are associated with hemicellulases (GH39, GH23). Protein-protein interaction and gene networking of LPMO sheds light on the co-occurrence, neighborhood, and interaction of LPMOs with chitinase and xylanase enzymes. Structural prediction of LPMOs unravels the information of the LPMO's binding site. Although the LPMO has been explored for its oxidative mechanism, a little light has been shed on its gene structure. This study provides insights into the LPMO gene structure in P. dendritiformis CRN18 and its potential in lignocellulose hydrolysis.

Prophylactic usage and high persistent nature of several antibiotics have put selective pressure on the native microbial population that led to the emergence, propagation, and persistence of antibiotic resistance in nature. The surveillance of antibiotic resistome pattern and identification of points of intervention throughout the different environmental habitats will help to break the flow of antibiotic resistance from environmental bacteria to human pathogens. The present study compares the occurrence, diversity, and abundance of ARGs in industrial sludge, wetland sludge, and sediment sample contaminated with pharmaceutical discharge. Metagenomes were mined for the presence of ARGs against the ResFinder 3.2 database using BLASTn program. Pharmaceutical sample (2.52%) showed high degree of ARG abundance and richness as compared with ETP sludge (2.28%) and wetland sludge samples (1.29%). The modern resistome pattern represented by critically important resistance genes against tetracycline (tetA, tetC, tetW, tetT, and tetS/M) and quinolone (qnrS, qnrVC, and qnrD) was identified in pharmaceutical sediment sample. However, effluent treatment plant (ETP) sludge sample showed abundance of multidrug efflux pumps indicating the presence of primitive resistome profile. In conclusion, the indiscriminate distribution pattern of antibiotic resistance genes in three selected environmental sites suggests enrichment and distribution of environmental niche–driven resistance. The study also suggests effluent discharge site from pharmaceutical industries and ETPs as pivotal points of intervention for the mitigation of antibiotic resistance.

Cellulose is the most abundant natural polymer present on Earth in the form of agriculture waste. Hydrolysis of agriculture waste for simple fermentable reducing sugars is the bottleneck in the area of biofuel generation and other value-added products. The present study aims to utilize the camel rumen as a bioreactor for potent cellulolytic and hemicellulolytic bacteria by altering the feed types with varying cellulosic concentrations. A total of 6716 bacterial cultures were subjected to three layers of screening, where plate zymography and chromophoric substrate screening served as primary screening method for cellulolytic and hemicellulolytic potential. The potential isolates were genetically grouped using RAPD, and 51 representative isolates from each group were subjected to molecular identification through 16S rDNA sequencing, followed by quantification of various cellulolytic and hemicellulolytic enzymes. Out of 51 potent isolates, 5 isolates had high endoglucanase activity ranging from 0.3 to 0.48 U/ml. The selected five key isolates identified as Pseudomonas, Paenibacillus, Citrobacter, Bacillus subtilis, and Enterobacter were employed for hydrolyzing the various agriculture residues and resulted in approximately 0.4 mg/ml of reducing sugar. Furthermore, the metaculturomics approach was implemented to deduce the total cultured diversity through 16S rRNA amplicon library sequencing. The metaculturomics data revealed the dominance of proteobacteria and unidentified bacterial population in all four feed types, which indicates the possibility of culturing novel cellulose-deconstructing bacteria. Moreover, the presence of diverse hydrolytic enzymes in cultured isolates supports the usage of these bacteria in bio-processing of agriculture waste residues and obtaining the biofuels and other value-added products.

In addition to a wide variety of anaerobic and facultative anaerobic bacteria, camel rumen also harbors a diverse of eukaryotic organisms. In the present study, the eukaryotic communities of camel rumen were characterized using 18S rRNA amplicon sequencing. Metagenomic DNA was isolated from rumen samples of fourteen adult Bikaneri and Kachchhi breeds of camel fed different diets containing Jowar, Bajra, Maize, and Guar. Illumina sequencing generated 27,161,904 number of reads corresponding to 1543 total operational taxonomic units (OTUs). Taxonomic classification of community metagenome sequences from all the samples revealed the presence of 92 genera belonging to 16 different divisions, out of which Ciliophora (73%), Fungi (13%) and Streptophyta (9%) were found to be the most dominant. Notably, the abundance of Ciliophora was significantly higher in the case of Guar feed, while Fungi was significantly higher in the case of Maize feed, indicating the influence of cellulose and hemicellulose content of feedstuff on the composition of eukaryotes. The results suggest that the camel rumen eukaryotes are highly dynamic and depend on the type of diet given to the animal. Pearson's correlation analysis suggested the ciliate protozoa and fungi were negatively correlated with each other. To the best of our knowledge, this is first systematic study to characterize camel rumen eukaryotes, which has provided newer information regarding eukaryotic diversity patterns amongst camel fed on different diets.

Environmental factors and available nutrients influence microbial communities, and with that, there exists a dynamic shift in community structure and hierarchy in wastewater treatment systems. Of the various factors, the availability and gradient of oxygen selectively enrich a typical microbial community and also form the community stratification which could be established through metagenomics studies. In recent years, metagenomics with various sets of bioinformatics tools has assisted in exploration and better insight into the organization and relation of the taxonomical and functional composition and associate physiological intelligence of the microbial communities. The microbial communities, under defined conditions acquire a typical hierarchy with flexible but active network of the metabolic route, which ensures the survival needs of every member residing in that community and their abundance. This knowledge of community functional organization defines the rule in designing and improving biodegradation processes in case of both aerobic and anaerobic systems.

Reconstruction of genomes from environmental metagenomes offers an excellent prospect for studying the metabolic potential of organisms resilient to isolation in laboratory conditions. Here, we assembled 12 high-quality metagenome-assembled genomes (MAGs) with an estimated completion of ≥ 90% from cow and buffalo rumen metagenomes. Average nucleotide identity (ANI) score-based screening with an existing database suggests the novelty of these genomes. Gene prediction led to the identification of 30,359 protein-encoding genes (PEGs) across 12 genomes, of which only 44.8% were annotated against a specific functional attribute. Further analysis revealed the presence of 985 carbohydrate-active enzymes (CAZymes) from more than 50 glycoside hydrolase families, of which 90% do not have a proper match in the CAZy database. Genome mining revealed the presence of a high frequency of plant biomass deconstructing genes in Bacteroidetes MAGs compared to Firmicutes. The results strongly indicate that the rumen chamber harbors high numbers of deeply branched and as-yet uncultured microbes that encode novel CAZymes, candidates for prospective usage in plant biomass-hydrolyzing and biofuels industries. KEY POINTS: • Genome binning plays a crucial role in revealing the metabolic potential of uncultivable microbes. • Assembled 12 novel genomes from cow and buffalo rumen metagenome datasets. • High frequency of plant biomass deconstructing genes identified in Bacteroidetes MAGs.

Genome sequencing of Klebsiella pneumoniae PVN-1, isolated from effluent treatment plant (ETP), generates a 5.064 Mb draft genome with 57.6% GC content. The draft genome assembled into 19 contigs comprises 4783 proteins, 3 rRNA, 44 tRNA, 8 other RNA, 4911 genes, and 73 pseudogenes. Genome information revealed the presence of phosphate metabolism/solubilizing, potassium solubilizing, auxin production, and other plant benefiting attributes like enterobactin and pyrroloquinoline quinone biosynthesis genes. Presence of gcd and pqq genes in K. pneumoniae PVN-1 genome validates the inorganic phosphate solubilizing potential (528.5 mg/L). Pangenome analysis identified a unique 5ʹ-Nucleotidase that further assists in enhanced phosphate acquisition. Additionally, the genetic potential for complete benzoate, catechol, and phenylacetate degradation with stress response and heavy metal (Cu, Zn, Ni, Co) resistance was identified in K. pneumoniae PVN-1. Functioning of annotated plant benefiting genes validates by the metabolic activity of auxin production (7.40 µg/mL), nitrogen fixation, catalase activity, potassium solubilization (solubilization index—3.47), and protease activity (proteolytic index—2.27). In conclusion, the K. pneumoniae PVN-1 genome has numerous beneficial qualities that can be employed to enhance plant growth as well as for phytoremediation. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-03020-2.

Bacterial species capable of performing both nitrification and denitrification in a single vessel under similar conditions have gained significance in the wastewater treatment scenario considering their unique character of performing the above reactions under heterotrophic and aerobic conditions respectively. Such a novel strategy often referred to as simultaneous nitrification and denitrification (SND) has a tremendous potential in dealing with various wastewaters having low C : N content, considering that the process needs very little or no external carbon source and oxygen supply thus adding to its cost-effective and environmentally friendly nature. Though like other micro-organisms, heterotrophic nitrifiers and aerobic denitrifiers convert inorganic or organic nitrogen-containing substances into harmless dinitrogen gas in the wastewater, their ecophysiological role in the global nitrogen cycle is still not fully understood. Attempts to highlight the role played by the heterotrophic nitrifiers and aerobic denitrifiers in dealing with nitrogen pollution under various environmental operating conditions will help in developing a mechanistic understanding of the SND process to address the issues faced by the traditional methods of aerobic autotrophic nitrification-anaerobic heterotrophic denitrification.

Improving enzymatic saccharification of lignocellulosic biomass is the major bottle neck in the area of second generation biofuel production. Metalloenzyme lytic polysaccharide monooxygenase (LPMO) has the capability to oxidize the complex lignocellulose in the crystalline area and thus acts as a catalyst in the process of lignocellulosic deconstruction. The present review undermines the importance of LPMO in biofuel sectors. It emphasizes evolutionary relationship, structure, mechanism, and synergistic action of LPMOs. A radial phylogram of 168 LPMO genes from archaea to terrestrial plant infers their evolution in different domains. The existence of LPMOs in extreme environmental condition and structural insights of these LPMOs show the conservation in active copper center and flat surface for substrate binding. This finding may open a new way for the isolation of active LPMOs from different environmental condition and their optimization to withstand the industrial parameters. The synergistic action of LPMO with different cellulase and hemicellulase may help in lowering the catalytic load which ultimately may reduce the cost of pretreatment steps. This review therefore sums up the recent findings concerning the LPMO’s mechanism of action and identifies issues and questions to be addressed in the future.

Generation of biowastes is increasing rapidly and its uncontrolled, slow and persistent fermentation leads to the release of Green-house gases (GHGs) into the environment. Exploration and exploitation of microbial diversity for degrading biowastes can result in producing diverse range of bioactive molecules, which can act as a source of bioenergy, biopolymers, nutraceuticals and antimicrobials. The whole process is envisaged to manage biowastes, and reduce their pollution causing capacity, and lead to a sustainable society. A strategy has been proposed for: (1) producing bioactive molecules, and (2) achieving a zero-pollution emission by recycling of the GHGs through biological routes.

Rumen microbial community harbors a distinct genetic reservoir of potent carbohydrate-active enzymes (CAZyme) that functions efficiently for the deconstruction of plant biomass. Based on this premise, metagenomics approach was applied to characterize the rumen microbial community and identify carbohydrate-active genes of Bos taurus (cow) and Bubalus bubalis (buffalo) fed on green or dry roughage. Metadata was generated from the samples: green roughage-fed cow (NDC_GR), buffalo (NDB_GR) and dry roughage-fed cow (NDC_DR), buffalo (NDB_DR). Phylogenetic analysis revealed the dominance of Bacteroidetes, Firmicutes, Proteobacteria, Actinobacteria and Fibrobacter in all the four samples, covering 90-96% of the total bacterial population. On finer resolution, higher abundance of bacterial genera Fibrobacter, Bacteroides, Clostridium, Prevotella and Ruminococcus involved in plant biomass hydrolysis was observed in NDB_DR. Functional annotation using dbCAN annotation algorithm identified 28.13%, 8.08% 10.93% and 12.53% of the total contigs as putatively carbohydrate-active against NDC_GR, NDB_GR, NDC_DR and NDB_DR, respectively. Additional profiling of CAZymes revealed an over representation and diversity of putative glycoside hydrolases (GHs) in the animals fed on dry roughage with substantial enrichments of genes encoding GHs from families GH2, GH3, GH13 and GH43. GHs of families GH45, GH12, GH113, GH128, GH54 and GH27 were observed exclusively in NDB_DR metagenome. A higher abundance of cellulases, hemicellulases, debranching and oligosaccharide hydrolyzing enzymes was revealed in NDB_DR metagenome. Accordingly, it can be concluded that buffalo rumen microbiome are more efficient in plant biomass hydrolysis. The present study provides a deep understanding of the shifts in microbial community and plant polysaccharide deconstructing capabilities of rumen microbiome in response to changes in the feed type and host animal. Activity-specific microbial consortia procured from these animals can be used further for efficient plant biomass hydrolysis. The study also establishes the utility of rumen microbiome as a unique resource for mining diverse lignocellulolytic enzymes.

With the omics tool, the challenges in understanding the microbial community functions are becoming more intriguing. It is the environment created scenario, which demands alignment of the different members of the community for the desired output leading to common condition for their survival. The resultant community pathways provide a broad umbrella of metabolic options giving the desired plasticity, which plays decision making role in the adaptation process. The initial step in community characterization must involve the discovery of key and core member of the community and monitoring the fluctuations in functional abundance over the space and time. The concept of entropy and metabolic fluxes must reflect the inner metabolic machinery of the taxon selection and route of functional operation in a community. The segregation of member based on their functional role and hierarchical level in the community must be an essential step to be followed by interaction mapping and measurement of metabolic fluxes to derive the flow of metabolites within the community. This conceptual framework and integrated omics tools with supported statistical modeling algorithm can help in bringing out finer details in the process of community functional adaptation in any given scenario.

Activated sludge, a microbial ecosystem at industrial wastewater treatment plants, is an active collection of diverse gene pool that creates the intelligence required for coexistence at the cost of pollutants. This study has analyzed one such ecosystem from a site treating wastewater pooled from over 200 different industries. The metagenomics approach used could predict the degradative pathways of more than 30 dominating molecules commonly found in wastewater. Results were extended to design a bioremediation strategy using 4-methylphenol, 2-chlorobenzoate, and 4-chlorobenzoate as target compounds. Catabolic potential required to degrade four aromatic families, namely benzoate family, PAH family, phenol family, and PCB family, was mapped. Results demonstrated a network of diverse genera, where a few phylotypes were seen to contain diverse catabolic capacities and were seen to be present in multiple networks. The study highlights the importance of looking more closely at the microbial community of activated sludge to harness its latent potential. Conventionally treated as a black box, the activated biomass does not perform at its full potential. Metagenomics allows a clearer insight into the complex pathways operating at the site and the detailed documentation of genes allows the activated biomass to be used as a bioresource.

This study aims at designing a consortium using rumen bacterial isolates for enhancing the hydrolysis of sugarcane bagasse (SB) for efficient biofuel formation. The microbial population was screened through biochemical and molecular tools along with enzymatic activity to obtain potential isolates for diverse cellulolytic and hemicellulolytic carbohydrate active enzyme (CAZyme). Five strains (Paenibacillus, Bacillus, Enterobacter, and Microbacterium) were selected for designing the consortium NDMC-1. The hydrolytic efficiency of NDMC-1 was determined based on cellulase production with simultaneous rise in monosaccharides, oligosaccharides, and soluble chemical oxygen demand (sCOD) concentration. Cellulolytic machinery of these isolates was further explored using genome sequencing. The isolates selected for consortia NDMC-1 interacted synergistically leading to enhanced cellulase production. Maximal endoglucanase (1.67 μmol ml−1 min−1), exoglucanase (0.69 μmol ml−1 min−1), and β-glucosidase (2.03 μmol ml−1 min−1) activity were achieved with SB as a sole carbon source after 48 h of incubation. Enhancement in SB hydrolysis employing NDMC-1 was evident by the increase in sCOD from 609 to 2589 mg/l and release of 1295 mg/l reducing sugar, comprising 59.8%, 8.23%, and 6.16% of glucose, cellobiose, and cellotriose, respectively, which resulted in 5.5-fold rise in biogas production. On genome annotation, total 472 contigs from glycoside hydrolase family: 84 from Microbacterium arborescens ND21, 72 from Enterobacter cloacae ND22, 61 from Bacillus subtilis ND23, 116 from Paenibacillus polymyxa ND24, and 140 from Paenibacillus polymyxa ND25 were identified. On further analysis, total 33 cellulases, 59 hemicellulases, and 48 esterases were annotated in the reported genomes. This work proposes the application of consortia-based bioprocessing systems over the conventionally favorable single organism approach for efficient hydrolysis of cellulosic substrates to fermentable sugars.

Aim: The present study is aimed to investigate whether single-nucleotide polymorphism (SNP) of resistin gene (RETN) at −420 and +299 sites, is associated with resistin levels in serum and gingival crevicular fluid (GCF) in periodontally healthy, chronic periodontitis (CP) with and without type 2 diabetes mellitus (T2DM) patients. Materials and Methods: Serum and GCF samples were procured from all the 60 patients (twenty in each group) of the three study groups i.e., periodontally healthy (Group I), CP (Group II) and CP with T2DM patients (Group III) to analyze resistin levels using enzyme-linked immunosorbent assay test and clinical parameters were assessed at baseline and at 3 months after scaling and root planing (SRP). RETN polymorphism at −420 and +299 was genotyped by polymerase chain reaction-restriction fragment length polymorphism technique. Results: Patients with SNP −420 and +299 were positively correlated with increased serum and GCF resistin levels in Group II and Group III patients. SRP led to substantial reduction in the serum and GCF resistin levels. Conclusion: These findings are suggestive of a biologic link between resistin, periodontal diseases, and periodontal diseases with T2DM and RETN SNP at −420 and +299 in imparting increased resistin levels in inflammatory and diabetic conditions.

Membrane biofouling in water purification plants is a serious issue of worldwide concern. Various chemical, physical, and biochemical processes are practised for membrane clean-up. A high-dosage treatment adversely affects the life expectancy of the membrane, and minimum dosage seems unable to deteriorate the biofilms on the membrane. It is reported that quorum quenchers like nitric oxide (NO) disrupt biofilm signals through metabolic rewiring, and also NO is known to be secreted by probiotics (good bacteria). In the present review, it is hypothesized that if probiotic biofilms secreting NO are used, other microbes that aggregate on the filtration membrane could be mitigated. The concept of probiotic administration on filtration membrane seeks to be encouraged because probiotic bacteria will not be hazardous, even if released during filtration. The fundamental motive to present probiotics as a resource for sequestering NO may serve as multifunctional bioweapons for membrane remediation, which will virtually guarantee their long-term sustainability and green approach.

In the present study, the microbial community residing at different depths of the landfill was characterized to assess their roles in serving as a methane sink. Physico-chemical characterization revealed the characteristic signatures of anaerobic degradation of organic matter in the bottom soil (50-60 cm) and, active process of aerobic denitrification in the top soil (0-10 cm). This was also reflected from the higher abundance of bacterial domain in the top soil metagenome represented by dominant phyla Proteobacteria and Actinobacteria which are prime decomposers of organic matter in landfill soils. The multiple fold higher relative abundances of the two most abundant genera; Streptomyces and Intrasporangium in the top soil depicted greater denitrifying taxa in top soil than the bottom soil. Amongst the aerobic methanotrophs, the genera Methylomonas, Methylococcus, Methylocella, and Methylacidiphilum were abundantly found in the top soil metagenome that were essential for oxidizing methane generated in the landfill. On the other hand, the dominance of archaeal domain represented by Methanosarcina and Methanoculleus in the bottom soil highlighted the complete anaerobic digestion of organic components via acetoclasty, carboxydotrophy, hydrogenotrophy, methylotrophy. Functional characterization revealed a higher abundance of methane monooxygenase gene in the top soil and methyl coenzyme M reductase gene in the bottom soil that correlated with the higher relative abundance of aerobic methanotrophs in the top soil while methane generation being the active process in the highly anaerobic bottom soil in the landfill. The activity dependent abundance of endogenous microbial communities in the different zones of the landfill was further validated by microcosm studies in serum bottles which established the ability of the methanotrophic community for methane metabolism in the top soil and their potential to serve as sink for methane. The study provides a better understanding about the methanotrophs in correlation with their endogenous environment, so that these bacteria can be used in resolving the environmental issues related to methane and nitrogen management at landfill site.

In dromedary camels, which are pseudo-ruminants, rumen or C1 section of stomach is the main compartment involved in fiber degradation, as in true ruminants. However, as camels are adapted to the harsh and scarce grazing conditions of desert, their ruminal microbiota makes an interesting target of study. The present study was undertaken to generate the rumen microbial profile of Indian camel using 16S rRNA amplicon and shotgun metagenomics. The camels were fed three diets differing in the source of roughage. The comparative metagenomic analysis revealed greater proportions of significant differences between two fractions of rumen content followed by diet associated differences. Significant differences were also observed in the rumen microbiota collected at different time-points of the feeding trial. However, fraction related differences were more highlighted as compared to diet dependent changes in microbial profile from shotgun metagenomics data. Further, 16 genera were identified as part of the core rumen microbiome of Indian camels. Moreover, glycoside hydrolases were observed to be the most abundant among all Carbohydrate-Active enzymes and were dominated by GH2, GH3, GH13 and GH43. In all, this study describes the camel rumen microbiota under different dietary conditions with focus on taxonomic, functional, and Carbohydrate-Active enzymes profiles.

Synthetic chemicals including organochlorine pesticides pose environment and health hazard due to persistent and bio-accumulation property. Majority of them are recognized as endocrine disruptors. Fungi are ubiquitous in nature and employs efficient enzymatic machinery for the biotransformation and degradation of toxic, recalcitrant pollutants. This review critically discusses the organochlorine biotransformation process mediated by fungi and highlights the role of enzymatic system responsible for biotransformation, especially distribution of dehalogenase homologs among fungal classes. It also explores the potential use of fungal derived biomaterial, mainly chitosan as an adsorbing biomaterial for pesticides and heavy metals removal. Further, prospects of employing fungus to over-come the existing bioremediation limitations are discussed. The study highlights the potential scope of utilizing fungi for initial biotransformation purposes, preceding final biodegradation by bacterial species under environmental conditions. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-021-00940-8.

Pseudomonas simiae EGD-AQ6 showed utilization of chloroaromatic compound, 2-4-dichlorophenoxyacetic acid (2,4-D) efficiently in its biofilm phenotype. The differential rates of accumulation of intermediate metabolite 4-chlorocatechol (4-CCA) were significant in both planktonic and biofilm phenotypes; also increased number of biofilm cells were observed during 2,4-D utilization. Interestingly, response surface analysis demonstrated the combined positive effects of 2,4-D degradation and 4-CCA accumulations. Also, gene expression profiles showed significant up-regulation of degradative and biofilm genes (particularly pellicle forming genes) in the biofilm phenotypes than their planktonic counterparts, thereby confirming occurrence of phenotype variations of Pseudomonas simiae EGD-AQ6 during chloroaromatic degradation. Furthermore, the sequence similarity of the 2-4-D catabolic genes and biofilm forming proteins (pel ABCDEFG and pga ABCD) which are responsible for building carbohydrate rich extracellular matrix, were significant with the respective organisms as revealed through genome analysis. This is the first report, which endorses this Pseudomonas simiae species to be unique in chloro-aromatic degradation through phenotype variation, thereby proving as a potential candidate in the improvement of bioremediation technologies.

Volatile fatty acids (VFA), the secondary metabolite of microbial fermentation, are used in a wide range of industries for production of commercially valuable chemicals. In this review, the fermentative production of VFAs by both pure as well mixed microbial cultures is highlighted along with the strategies for enhancing the VFA production through innovations in existing approaches. Role of conventionally applied tools for the optimization of operational parameters such as pH, temperature, retention time, organic loading rate, and headspace pressure has been discussed. Furthermore, a comparative assessment of above strategies on VFA production has been done with alternate developments such as co-fermentation, substrate pre-treatment, and in situ removal from fermented broth. The review also highlights the applications of different bioreactor geometries in the optimum production of VFAs and how metagenomic tools could provide a detailed insight into the microbial communities and their functional attributes that could be subjected to metabolic engineering for the efficient production of VFAs.

For decades, bacterial natural products have served as valuable resources for developing novel drugs to treat several human diseases. Recent advancements in the integrative approach of using genomic and functional tools have proved beneficial in obtaining a comprehensive understanding of these biomolecules. This study presents an in-depth characterization of the anti-diabetic activity exhibited by a bacterial isolate SW1, isolated from an effluent treatment plant. As a primary screening, we assessed the isolate for its potential to inhibit alpha-amylase and alpha-glucosidase enzymes. Upon confirmation, we further utilized LC-MS, ESI-MS/MS, and NMR spectroscopy to identify and characterize the biomolecule. These efforts were coupled with the genomic assessment of the biosynthetic gene cluster involved in the anti-diabetic compound production. Our investigation discovered that the isolate SW1 inhibited both α-amylase and α-glucosidase activity. The chemical analysis suggested the production of acarbose, an anti-diabetic biomolecule, which was further confirmed by the presence of biosynthetic gene cluster "acb" in the genome. Our in-depth chemical characterization and genome mining approach revealed the potential of bacteria from an unconventional niche, an effluent treatment plant. To the best of our knowledge, it is one of the first few reports of acarbose production from the genus Arthrobacter.