Shifts in Microbial Community and Its Correlation with Degradative Efficiency in a Wastewater Treatment Plant

Designing Knowledge-Based Bioremediation Strategies Using Metagenomics

Functional capacities for bioremediation are governed by metabolic mechanisms of inhabiting microbial communities at polluted niches. Process fluctuations lead to stress scenarios where microbes evolve continuously to adapt to sustain the harsh conditions. The biological wastewater treatment (WWT) process harbors the potential of these catabolic microbes for the degradation of organic molecules. In a typical biological WWT or soil bioremediation process, several microbial species coexist which code for enzymes that degrade complex compounds.High throughput DNA sequencing techniques for microbiome analysis in bioremediation processes have led to a powerful paradigm revealing the significance of metabolic functions and microbial diversity. The present chapter describes techniques in taxonomy and functional gene analysis for understanding bioremediation potential and novel strategies built on in silico analysis for the improvisation of existing aerobic wastewater treatment methods. Methods explaining comparative metagenomics by Metagenome Analysis server (MG-RAST) are described with successful case studies by focusing on industrial wastewaters and soil bioremediation studies.

Identification of heavy metals tolerant Brevundimonas sp. from rhizospheric zone of Saccharum munja L. and their efficacy in in-situ phytoremediation

Heavy metals phytoremediation from pulp and paper industry (PPI) sludge was conducted by employing root-associated Brevundimonas sp (PS-4 MN238722.1) in rhizospheric zone of Saccharum munja L. for its detoxification. The study was aimed to investigate the efficiency of Saccharum munja L. for the removal of heavy metals along with physico-chemical parameters through bacterial interactions. Physico-chemical examination of PPI sludge showed biochemical oxygen demand (8357 ± 94 mg kg^-1), electrical conductivity (2264 ± 49 μmhoscm^-1), total phenol (521 ± 24 mg kg^-1), total dissolve solid (1547 ± 23 mg kg^-1), total nitrogen (264 ± 2.13 mg kg^-1), pH (8.2 ± 0.11), chemical oxygen demand (34756 ± 214 mg kg^-1), color (2434 ± 45 Co-Pt), total suspended solid (76 ± 0.67 mg kg^-1), sulphate (2462 ± 13 mg kg^-1), chlorolignin (597 ± 13.01 mg kg^-1), K⁺ (21.04 ± 0.26 mg kg^-1), total solid (1740 ± 54 mg kg^-1), phosphorous, Cl^-, and Na⁺. Heavy metals, such as Fe followed by Zn, Mn, Cd, Cu, Ni, Pb, As, Cr and Hg were above the permissible limit. Root and shoot of Saccharum munja L. revealed highest concentrations of Cd followed by Mn, Ni, Fe, Zn, Cu, As, Cr, Hg, and Pb. Tested metals (Fe, Mn, Pb, Cd, Cr, Cu, Zn, Ni, As, and Hg) bioaccumulation and translocation factors were also revealed to be < 1 and >1, respectively, demonstrating that these plants have considerable absorption and translocation abilities. Plant growth-promoting activity, such as ligninolytic enzymes, hydrolytic enzymes, indole acetic acid, and siderophore production activity of Brevundimonas sp. (PS-4 MN238722.1) were also noted to be higher. These findings support the use of Brevundimonas sp (PS-4 MN238722.1) in combination with Saccharum munja L. plant as interdisciplinary management of industrial sludge at polluted areas for the prevention of soils near the industrial site.

Metagenomic Insights in Activated Biomass Treating Industrial Wastewater at Different DO Levels

Dissolved oxygen (DO) is an imperative parameter of the activated sludge process (ASP) for wastewater bioremediation. The effect of DO on microbial communities and corresponding metabolic functions in wastewater bioremediation was investigated using next-generation analysis techniques in this study. Illumina-based whole genome sequencing was applied to analyze the composition of the microbial community along with their functional diversity in activated sludge systems operating at three different DO levels. Activated biomass was collected from lab-scale reactors maintained at 1, 2, and 4 mg/L DO levels. Metagenomes were sequenced on an Illumina platform and analyzed using various tools. Results revealed that Proteobacteria phylum and Pseudomonas, Nitrobacter, Thauera, and Alicyclipilus genera were abundant in all reactor samples. Despite distinct DO levels, the microbial communities were conserved and consisted of a common population forming the core group governing the metabolic functions. However, higher diversity was observed at functional level indicating that microbes evolve and adapt to serve their role in a typical ASP. Metabolic pathway related to benzoate dominated at 1 mg/L DO level, while pathways for degradation of aromatic compounds like phenol, toluene, and biphenyl via central metabolic pathway were found dominating at 4 mg/L DO level. Pathways corresponding to homogentisate, naphthalene, cresol, and salicylate degradation enriched at 2 mg/L DO level.

Exploration of activated sludge resistome using metagenomics

Antibiotic resistance is a global problem. In India poor waste management and inadequate sanitary are key factors which encourage the dissemination of antimicrobial resistance. Microbial biodiversity serves as an invaluable source for diverse types of bioactive compounds that encompass most of the pharmaceuticals to date. Therefore, in this study, we used the metagenomic approach for the surveillance of antibiotic resistance genes, drug resistant microbes and mobile-genetic elements in two activated sludge metagenome samples collected from Ankleshwar, Gujarat, India. Proteobacteria were found to be the most abundant bacteria among the metagenome analyzed. Twenty-four genes conferring resistance to antibiotics and heavy metals were found. Multidrug resistant "ESKAPE pathogens" were also abundant in the sludge metagenome. Mobile genetic elements like IncP-1 plasmid pKJK5, IncP-1beta multi resistance plasmid and pB8 were also noticed in the higher abundance. These plasmids play an important role in the spread of antibiotic resistance by the horizontal gene transfer. Statistical analysis of both metagenome using STAMP software confirmed presence of mobile genetic elements such as gene transfer agents, phages, Prophages etc. which also play important role in the dissemination of antibiotic resistant genes.

Detection of Androgenic-Mutagenic Compounds and Potential Autochthonous Bacterial Communities during In Situ Bioremediation of Post-methanated Distillery Sludge

Sugarcane-molasses-based post-methanated distillery waste is well known for its toxicity, causing adverse effects on aquatic flora and fauna. Here, it has been demonstrated that there is an abundant mixture of androgenic and mutagenic compounds both in distillery sludge and leachate. Gas chromatography-mass spectrometry (GC-MS) analysis showed dodecanoic acid, octadecanoic acid, n-pentadecanoic acid, hexadecanoic acid, β-sitosterol, stigmasterol, β-sitosterol trimethyl ether, heptacosane, dotriacontane, lanosta-8, 24-dien-3-one, 1-methylene-3-methyl butanol, 1-phenyl-1-propanol, 5-methyl-2-(1-methylethyl) cyclohexanol, and 2-ethylthio-10-hydroxy-9-methoxy-1,4 anthraquinone as major organic pollutants along with heavy metals (all mg kg^-1): Fe (2403), Zn (210.15), Mn (126.30, Cu (73.62), Cr (21.825), Pb (16.33) and Ni (13.425). In a simultaneous analysis of bacterial communities using the restriction fragment length polymorphism (RFLP) method the dominance of Bacillus sp. followed by Enterococcus sp. as autochthonous bacterial communities growing in this extremely toxic environment was shown, indicating a primary community for bioremediation. A toxicity evaluation showed a reduction of toxicity in degraded samples of sludge and leachate, confirming the role of autochthonous bacterial communities in the bioremediation of distillery waste in situ.

Detection of Bacillus and Stenotrophomonas species growing in an organic acid and endocrine-disrupting chemical-rich environment of distillery spent wash and its phytotoxicity

Sugarcane molasses-based distillery spent wash (DSW) is well known for its toxicity and complex mixture of various recalcitrant organic pollutants with acidic pH, but the chemical nature of these pollutants is unknown. This study revealed the presence of toxic organic acids (butanedioic acid bis(TMS)ester; 2-hydroxysocaproic acid; benzenepropanoic acid, α-[(TMS)oxy], TMS ester; vanillylpropionic acid, bis(TMS)), and other recalcitrant organic pollutants (2-furancarboxylic acid, 5-[[(TMS)oxy] methyl], TMS ester; benzoic acid 3-methoxy-4-[(TMS)oxy], TMS ester; and tricarballylic acid 3TMS), which are listed as endocrine-disrupting chemicals. In addition, several major heavy metals were detected, including Fe (163.947), Mn (4.556), Zn (2.487), and Ni (1.175 mg l^-1). Bacterial community analysis by restriction fragment length polymorphism revealed that Bacillus and Stenotrophomonas were dominant autochthonous bacterial communities belonging to the phylum Firmicutes and γ-Proteobacteria, respectively. The presence of Bacillus and Stenotrophomonas species in highly acidic environments indicated its broad range adaptation. These findings indicated that these autochthonous bacterial communities were pioneer taxa for in situ remediation of this hazardous waste during ecological succession. Further, phytotoxicity assay of DSW with Phaseolus mungo L. and Triticum aestivum revealed that T. aestivum was more sensitive than P. mungo L. in the seed germination test. The results of this study may be useful for monitoring and toxicity assessment of sugarcane molasses-based distillery waste at disposal sites.

Insights in Waste Management Bioprocesses Using Genomic Tools

Microbial capacities drive waste stabilization and resource recovery in environmental friendly processes. Depending on the composition of waste, a stress-mediated selection process ensures a scenario that generates a specific enrichment of microbial community. These communities dynamically change over a period of time while keeping the performance through the required utilization capacities. Depending on the environmental conditions, these communities select the appropriate partners so as to maintain the desired functional capacities. However, the complexities of these organizations are difficult to study. Individual member ratios and sharing of genetic intelligence collectively decide the enrichment and survival of these communities. The next-generation sequencing options with the depth of structure and function analysis have emerged as a tool that could provide the finer details of the underlying bioprocesses associated and shared in environmental niches. These tools can help in identification of the key biochemical events and monitoring of expression of associated phenotypes that will support the operation and maintenance of waste management systems. In this chapter, we link genomic tools with process optimization and/or management, which could be applied for decision making and/or upscaling. This review describes both, the aerobic and anaerobic, options of waste utilization process with the microbial community functioning as flocs, granules, or biofilms. There are a number of challenges involved in harnessing the microbial community intelligence with associated functional plasticity for efficient extension of microbial capacities for resource recycling and waste management. Mismanaged wastes could lead to undesired genotypes such as antibiotic/multidrug-resistant microbes.