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Whole genome sequence of arsenic (As) reducing, hydrocarbon metabolizing groundwater bacterium Achromobacter sp. KAs 3-5T was explored to understand the genomic basis of its As-ecophysiology and niche adaptation in aquifer environment. The genome (5.6 Mbp, 65.5 G + C mol %) encodes 4840 proteins, 1138 enzymes, 53 tRNAs, 11 rRNAs, 608 signal peptides, and 1.13% horizontally transferred genes. Presence of genes encoding cytosolic As5+-reduction (arsRCBH, ACR3), aromatics utilization (bph, naph, catABC, boxABCD, genACB), Fe-transformation (tonB, achromobactin, FUR, FeR), and denitrification (nar, nap) processes were observed and validated through proteomics. Phylogenomic analysis (

Microbial redox-transformation of arsenic (As) species plays an important role in As-mobilization processes in groundwater of South-East Asian countries, affecting health of millions of people. However, the complete genetic mechanism is still unclear, thus, necessitating the genomic study on As eco-physiology and niche colonization mechanisms to understand the As biogeochemical cycling processes. The present study describes the first genome report on whole genomic attributes of an As-transforming Escherichia coli Cont-1 from As-contaminated groundwater and its eco-physiological provenance. The genome (∼4.9 Mb) of the strain Cont-1 codes for 4982 genes, 103 RNAs, 3652 cluster of orthologous groups (COGs), 1544 enzymes, 459 signal peptides, 1124 trans-membrane proteins, and 78 horizontally transferred genes, with 48.2 G + C mol % content. Taxono-genomic analysis [16S rRNA gene homology, average nucleotide identity (ANI), and DNA-DNA hybridization (DDH)] of strain Cont-1 revealed its highest identity to E. coli K-12 members, confirming its species affiliation to E. coli. The genes for As detoxification (As5+-reduction and -transformation by Ars operon), anaerobic respiration [Fe3+, NO3−, S2O32−, trimethyl-amine oxide (TMAO), dimethyl sulfoxide (DMSO), formate, and fumarate], metal-transportation and -resistance (Fe, Zn, Cu) have been detected. The strain harbours complete operon for glycolysis, fermentative pathways, N- and S- assimilation, and transcriptional regulations, confirmed its eco-physiological versatility and validated the physiological observations. The presence of genes for As/Fe metabolism, signal transduction, transcriptional regulations, mobile elements, and hypothetical proteins within genomic island indicates potential horizontal gene transfer events in its genome, suggesting the niche adaptation and competitive survival strategies of strain Cont-1 in the As-contaminated groundwater.

Scope for developing an engineered bioremediation strategy for the treatment of hydrocarbon-rich petroleum refinery waste was investigated through biostimulation and bioaugmentation approaches. Enhanced (46–55%) total petroleum hydrocarbon (TPH) attenuation was achieved through phosphate, nitrate or nitrate+phosphate amendment in the sludge with increased (upto 12%) abundance of fermentative, hydrocarbon degrading, sulfate-reducing, CO2-assimilating and methanogenic microorganisms (Bacillus, Coprothermobacter, Rhodobacter, Pseudomonas, Achromobacter, Desulfitobacter, Desulfosporosinus, T78, Methanobacterium, Methanosaeta, etc). Together with nutrients, bioaugmentation with biosurfactant producing and hydrocarbon utilizing indigenous Bacillus strains resulted in 57–75% TPH reduction. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis revealed enhanced gene allocation for transporters (0.45–3.07%), ABC transporters (0.38–2.07%), methane (0.16–1.06%), fatty acid (0.018–0.15%), nitrogen (0.07–0.17%), butanoate (0.06–0.35%), propanoate (0.004–0.26%) metabolism and some xenobiotics (0.007–0.13%) degradation. This study indicated that nutrient-induced community dynamics of native microorganisms and their metabolic interplay within oil refinery sludge could be a driving force behind accelerated bioremediation.

Geomicrobiological details of the interactions between groundwater microbiome (GWM) and arsenic (As)-rich aquifer sediment of Bengal basin was investigated through microcosm incubations. Role of key microorganisms and their specific interactions with As-bearing minerals was demarcated under organic carbon- amended and -unamended conditions. Acinetobacter (50.8 %), Brevundimonas (7.9 %), Sideroxydans (3.4 %), Alkanindiges (3.0 %) dominated the GWM. The microbiome catalysed considerable alterations in As-bearing mineral [Fe-(hydr)oxide and aluminosilicate] phases resulting in substantial changes in overall geochemistry and release of As (65 μg/L) and Fe (118 μg/L). Synergistic roles of autotrophic, NH4+-oxidizing Archaea (Thaumarchaeota) and chemoheterotrophic bacteria (Stenotrophomonas, Pseudomonas, Geobacter) of diverse metabolic abilities (NH4+-oxidizing, NO3−, As/Fe-reducing) were noted for observed changes. Organic carbon supported enhanced microbial growth and As mobilization (upto 403.2 μg As/L) from multiple mineral phases (hematite, magnetite, maghemite, biotite, etc.). In presence of high organic carbon, concerted actions of anaerobic, hydrocarbon-utilizing, As-, Fe-reducing Rhizobium, fermentative Escherichia, anaerobic Bacillales, metal-reducing and organic acid-utilizing Pseudomonas and Achromobacter were implicated in altering sediment mineralogy and biogeochemistry. Increase in abundance of arrA, arsC, bssA genes, and dissolution of Fe, Ca, Mg, Mn confirmed that dissimilatory-, cytosolic-As reduction, and mineral weathering fuelled by anaerobic (hydro)carbon metabolism are the predominant mechanisms of As release in aquifers of Bengal basin.

Intrinsic biodegradation potential of bacteria from petroleum refinery waste was investigated through isolation of cultivable strains and their characterization. Pseudomonas and Bacillus spp. populated the normal cultivable taxa while prolonged enrichment with hydrocarbons and crude oil yielded hydrocarbonoclastic bacteria of genera Burkholderia, Enterobacter, Kocuria, Pandoraea, etc. Strains isolated through enrichment showed assemblages of superior metabolic properties: utilization of aliphatic (C6-C22) and polyaromatic compounds, anaerobic growth with multiple terminal electron acceptors and higher biosurfactant production. Biodegradation of dodecane was studied thoroughly by GC-MS along with detection of gene encoding alkane hydroxylase (alkB). Microcosms bioaugmented with Enterobacter, Pandoraea and Burkholderia strains showed efficient biodegradation (98% TPH removal) well fitted in first order kinetic model with low rate constants and decreased half-life. This study proves that catabolically efficient bacteria resides naturally in complex petroleum refinery wastes and those can be useful for bioaugmentation based bioremediation.

Metal resistance and uranium (U) sequestration abilities of bacteria residing in subsurface U ore was investigated using 122 pure culture strains isolated through enrichment. The cumulative frequencies of isolates resistant to each metal tested were as follows: As(V), 74%; Zn, 58%; Ni, 53%; Cd, 47%; Cr(VI), 41%; Co, 40%; Cu, 20%; and Hg, 4%. 16S rRNA gene analysis revealed that isolated bacteria belonged to 14 genera with abundance of Arthrobacter, Microbacterium, Acinetobacter and Stenotrophomonas. Cobalt did not interfere with the growth of most of the bacterial isolates belonging to different groups while U allowed growth of four different genera of which Stenotrophomonas and Microbacterium showed high U tolerance. Interestingly, tolerance to Ni, Zn, Cu, and Hg was observed only in Microbacterium, Arthrobacter, Paenibacillus¸ and Acinetobacter, respectively. However, Microbacterium was found to be dominant when isolated from other five different metal enrichments including U. Uranium removal study showed that 84% of the test bacteria could remove more than 50mgUg(-1) dry weight from 80 or 160mgL(-1) U within 48h. In general, Microbacterium, Arthrobacter and Acinetobacter could remove a higher amount of U. High resolution transmission electron microscopy (HRTEM) study of U exposed cells revealed that accumulated U sequestered mostly around the cell periphery. The study highlights that indigenous U ore deposit bacteria have the potential to interact with U, and thus could be applied for bioremediation of U contaminated sites or wastes.

Impact of uranium (U) ore and soluble uranium (at pH 4.0) contamination on agricultural soil bacterial diversity was assessed by using laboratory microcosms for one year. Diversity and abundance of metabolically active bacterial populations in periodically collected microcosm’s samples were analyzed by extracting total RNA and preparation of cDNA followed by analysis of 16S rRNA gene by DGGE and real time PCR. DGGE analysis revealed prominent shift of soil bacterial population due to uranium ore contamination within 12 months while uranium ore along with soluble U completely destroyed the soil bacterial diversity within first six months. Real time PCR based analysis indicated 100–200 folds increase in 16S rRNA gene copies of total as well as individual bacterial taxa in both U ore amended and unamended soils in first six months while increase in incubation period upto 12 months showed reduction of the same only in U ore amended soil. Antagonistic effect of U ore contamination on soil bacterial diversity indicated the severe impact of U mining likely to have on nearby ecosystems. Role of U at acidic pH in destroying the diversity completely is noteworthy as it corroborated the disastrous consequence of acid mine drainage generated from U mine sites.

Heavy metal sequestration by a multimetal resistant Pseudomonas strain isolated from a uranium mine was characterized for its potential application in metal bioremediation. 16S rRNA gene analysis revealed phylogenetic relatedness of this isolate to Pseudomonas fluorescens. Metal uptake by this bacterium was monophasic, fast saturating, concentration and pH dependent with maximum loading of 1048 nmol Ni2+ followed by 845 nmol Co2+, 828 nmol Cu2+ and 700 nmol Cd2+ mg−1 dry wt. Preferential metal deposition in cell envelope was confirmed by TEM and cell fractionation. FTIR spectroscopy and EDX analysis revealed a major role of carboxyl and phosphoryl groups along with a possible ion exchange mechanism in cation binding. Binary system demonstrated selective metal binding affinity in the order of Cu2+ > Ni2+ > Co2+ > Cd2+. A comparison with similar metal uptake reports considering live bacteria strongly indicated the superiority of this strain in metal sequestration, which could be useful for developing efficient metal removal system.

A Pseudomonas strain, characterized as part of a project to develop a biosorbent for removal of toxic radionuclides from nuclear waste streams, was a potent accumulator of uranium (VI) and thorium (IV), with the metal sequestration process being unaffected by culture age, presence of carbon/energy source and metabolic inhibitor but sensitive to the composition of the growth medium. Further characterization of radionuclide biosorption using lyophilized biomass revealed rapid cation binding of >90% within 1– 10 min of contact and complete removal of U and Th was observed at initial concentrations up to 100 mg l −1 . Initial solution pH strongly affected radionuclide biosorption with an optimum at pH 4.0–5.0. High affinity, efficient and high capacity uranium and thorium binding was indicated, with maximum loading of 541 mg U g −1 dry mass or 430 mg Th g −1 dry mass. Good conformity of sorption data with the Langmuir model suggests monolayered U and Th binding. Sorption in presence of several interfering cations and anions indicates a specific U and Th binding by the biomass with significant antagonism offered only by iron (III). Transmission electron microscopy and energy dispersive X-ray fluorescence analysis of metal loaded biomass revealed intracellular U and Th sequestration. More than 90% of biomass-bound radionuclide was recovered using sodium or calcium carbonate. For continuous process application an immobilized biomass system was developed and tested with multiple cycles of sorption–desorption. Overall, the biosorbent appeared suitable for realistic bioremediation.

Biosorption of nickel (Ni2+) and copper (Cu2+) by lyophilized Pseudomonas aeruginosa cells was investigated based on Freundlich isotherm. Bacterial biomass showed significant sorption of both Ni (265 mg g−1) or Cu (137.6 mg g−1), and was also superior over the cation exchanger, IRA 400 (98 mg Ni g−1 or 26.6 mg Cu g−1). Metal binding by the test organism was a fast saturating, pH-dependent process. The optimum pH for Cu adsorption was 7.0 and for Ni 8.0. X-ray diffraction studies revealed that both cations were deposited on the cell predominantly as phosphide crystals. The participation of carboxyl, carbonyl, and phosphoryl groups along with H-bonding in metal sorption was evident in IR spectra. Biomass pretreatment by agents like NaOH, NH4OH or toluene enhanced the metal loading capacity, whereas, oven heating (80°C), autoclaving (120°C, 15 lb (in.2)−1), acid, detergent and acetone treatments were inhibitory. In bimetallic combination, Na, K or Ca increased sorption of Ni as well as Cu in contrast to Cd or Pb. Mineral acids (HCl, H2SO4 and HNO3) and NTA could recover more than 75% (on average) Ni or Cu adsorbed on the biomass. Calcium carbonate (10 mM) was efficient in Ni desorption (71%) compared to Cu (57%). Noticeably sodium carbonate remained specific for Cu remobilization (88%) than Ni (21%). The data are in favour of deployment of the test biomass as an efficient metal removal/recovery system.