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Deep continental subsurface hosts diverse microbial ecosystems that are primarily driven by chemolithoautotrophy. In this study, we investigated deep continental igneous rock-hosted bacterial populations enriched under microoxic (ME) and anoxic (AE) conditions. Metataxonomic, metagenomics and metabolomics approaches, along with physiological analyses, were performed to elucidate community composition, CO 2 utilization and possible bioconversion potential of subsurface rock enrichment cultures under chemolithoautotrophic conditions. Following prolonged incubation, ME enrichments resulted in higher microbial growth with greater species diversity than the AE cultures. Ralstonia and unclassified Comamonadaceae were predominant in both the enrichment conditions. On the other hand, Cellulomonas , Phenylobacterium , Deinococcus , Desulfurispora , etc. were relatively abundant in ME, and Solimonas , Curvibacter , Caulobacter , Novosphingobium , Anaeromyxobacter , unclassified Clostridia, etc. were abundant in AE communities. CO 2 /H 2 utilization and organic acids production were greater in ME enrichments. Shotgun metagenomics and predictive metabolic profiling revealed CBB cycle as the predominant carbon fixation pathway in ME, whereas WL pathway was prominent in AE. Genes for hydrogen, sulfur, and nitrogen metabolisms were observed in both the enrichment cultures. HRLC-MS based untargeted metabolomics indicated the presence of valuable metabolites (organic acids, osmolytes, lipids/amides) in rock cultures, reflecting the potential of deep subsurface microorganisms for CO 2 utilization and possible bioconversion to valuable biomolecules.

Reductive transformation of toxic arsenic (As) species by As reducing bacteria (AsRB) is a key process in As-biogeochemical-cycling within the subsurface aquifer environment. In this study, we have characterized a Gram-stain-negative, non-spore-forming, rod-shaped As reducing bacterium designated KAs 5-3T, isolated from highly As-contaminated groundwater of India. Strain KAs 5-3T displayed high 16S rRNA gene sequence similarity to the members of the genus Pseudoxanthomonas, with P. mexicana AMX 26BT (99.25% similarity), P. japonensis 12-3T (98.9 0%), P. putridarboris WD-12T (98.02%), and P. indica P15T (97.27%) as closest phylogenetic neighbours. DNA-DNA hybridization study unambiguously indicated that strain KAs 5-3T represented a novel species that was separate from reference strains of P. mexicana AMX 26BT (35.7%), P. japonensis 12-3T (35.5%), P. suwonensis 4M1T (35.5%), P. wuyuanensis XC21-2T (35.0%), P. indica P15T (32.5%), P. daejeonensis TR6-08T (32.0%), and P. putridarboris WD12T (22.1%). The DNA G+C content of strain KAs 5-3T was 64.9 mol %. The predominant fatty acids were C15:0 (37.4%), C16:0 iso (12.6%), C17:1 iso ω9c (10.5%), C15:0 anteiso (9.5%), C11:0 iso 3-OH (8.5%), and C16:1 ω7c/ C16:1 ω6c (7.5%). The major polar lipids were diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylcholine, and two unknown phospholipids (PL1, PL2). Ubiquinone 8 (Q8) was the predominant respiratory quinone and spermidine was the major polyamine of the strain KAs 5-3T. Cells of strain KAs 5-3T showed the ability to use O2, As5+, NO3-, NO2-, and Fe3+ as terminal electron acceptors as well as to reduce As5+ through the cytosolic process under aerobic incubations. Genes encoding arsenate reductase (arsC) for As-detoxification, nitrate- and nitrite reductase (narG and nirS) for denitrification were detected in the strain KAs 5-3T. Based on taxonomic and physiological data, strain KAs 5-3T is described as a new representative member of the genus Pseudoxanthomonas, for which the name Pseudoxanthomonas arseniciresistens sp. nov. is proposed. The type strain is KAs 5-3T (= LMG 29169T = MTCC 12116T = MCC 3121T).

In this work, morphology-dependent antibacterial property of zinc oxide nanoparticles (ZNPs) has been studied and an attempt has been made to investigate the reactive oxygen species generation potential of these nanoparticles. The antibacterial properties of ZnO nanorods with two different sizes have been quantitatively studied and their Minimum Inhibitory Concentration (MIC) has been determined against E.coli, a gram negative bacteria. It has been observed that ZNPs with smaller size exhibit better bacteriostatic and bactericidal properties. Furthermore, optical analysis has revealed that the smaller nanoparticles having greater efficiency to inhibit cell growth have higher density of surface defects and greater availability of free electrons and holes which leads to the generation of reactive oxygen species (ROS). To develop an insight into the oxidative microenvironment and the consequential cellular response, we have done the transcriptional analysis of oxidative stress gene sodA in ZNPs treated bacterial samples. Expression profile of the gene has been found to be ZNPs concentration dependent. An increase in the concentration of nanoparticles till MIC increased the expression level in a concentration dependent fashion. However beyond the MIC, the expression level of the gene is unexpectedly down-regulated reflecting the detrimental effect of higher levels of ROS on cellular components and metabolic activities. Thus through this study, we have tried to investigate the correlation between the surface morphology of ZNPs, production of ROS, growth-inhibiting activity and cellular response in this condition.

Prevalence of toxic arsenic (As) oxyanion species in oligotrophic groundwater of south-east Asiatic regions (India and Bangladesh) has threatened the health of millions of people. As-transforming bacteria alter the mobility, speciation and bioavailability of As in the aquifer ecosystem, hence play important roles in the biogeochemical cycling of As. Till date, only 19 cultivable As-transforming bacterial strains have been reported but with no description on their detail genomic and physiological perspective of As homeostasis. In this study, the draft genome (5.7 Mbp) of an As-transforming, aromatic hydrocarbon utilizing and iron disproportioning indigenous groundwater bacterium KAs 3-5 has been obtained by Ion-Torrent sequencing revealed 65% genomic GC content, 5100 protein coding genes, and taxonomic affiliation to the members of genus Achromobacter, with >85% of genomic completeness. Phylogenomic signatures like MLST of 10 house-keeping genes, cut-off of <95% of average nucleotide/amino acid identity (ANI/OrthoANI/AAI), <0.99 of tetra-nucleotide correlations, and <70% value of DNA-DNA homology with nearest phylogenetic neighbors exhibited its species distinctiveness among all the described Achromobacter sp. members. Pan-genomic analysis confirmed the strain’s potential to adapt wide array of environmental stresses with a higher abundance of unique genes for metabolism of amino acids, polyketide, xenobiotics, nitroso compounds, aromatic hydrocarbons and most necessarily complete operon cluster for As-resistance/transformation/detoxification, as well as genes for transport, and signal transduction mechanisms. The genome analysis also highlighted its genetic determinants for loss of functions for antibiotic resistance, pathogenicity regulations, and gain of new/acquired functions for Fe-transport, fatty acids uptake-metabolism, motility, heavy metal (Cu-Zn-Co) metabolism and several putative/hypothetical proteins owing to its capacity to acquired desired traits through horizontal gene transfer events. The ability of the organism to metabolize mono-poly aromatics like benzene, toluene, naphthalene, anthracene, etc. (by catechol, homogentisate pathways) coupled to As reduction (through arsHBC, arsC, ACR3) found to be well validated by genomic observations. X-ray absorption fine structure (XANES) also enabled us to decipher detailed Fe-based reductive As release process from sediment and its interaction. The obtained genome data provide us with a better understanding of sub-surface mechanisms of hydrocarbon (organic matter) driven As release, which may contribute to the future design of rational strategies for bioremediation of As/other heavy metal contaminated environments.

Deep continental subsurface hosts diverse microbial ecosystems that are primarily driven by chemolithoautotrophy. In this study, we investigated deep continental igneous rock-hosted bacterial populations enriched under microoxic (ME) and anoxic (AE) conditions. Metataxonomic, metagenomics and metabolomics approaches, along with physiological analyses, were performed to elucidate community composition, CO utilization and possible bioconversion potential of subsurface rock enrichment cultures under chemolithoautotrophic conditions. Following prolonged incubation, ME enrichments resulted in higher microbial growth with greater species diversity than the AE cultures. Ralstonia and unclassified Comamonadaceae were predominant in both the enrichment conditions. On the other hand, Cellulomonas, Phenylobacterium, Deinococcus, Desulfurispora, etc. were relatively abundant in ME, and Solimonas, Curvibacter, Caulobacter, Novosphingobium, Anaeromyxobacter, unclassified Clostridia, etc. were abundant in AE communities. CO /H utilization and organic acids production were greater in ME enrichments. Shotgun metagenomics and predictive metabolic profiling revealed CBB cycle as the predominant carbon fixation pathway in ME, whereas WL pathway was prominent in AE. Genes for hydrogen, sulfur, and nitrogen metabolisms were observed in both the enrichment cultures. HRLC-MS based untargeted metabolomics indicated the presence of valuable metabolites (organic acids, osmolytes, lipids/amides) in rock cultures, reflecting the potential of deep subsurface microorganisms for CO utilization and possible bioconversion to valuable biomolecules.

A novel arsenic (As)-resistant, arsenate-respiring, alkane-metabolizing bacterium KAs 5-22 T , isolated from As-rich groundwater of West Bengal was characterized by physiological and genomic properties. Cells of strain KAs 5-22 T were Gram-stain-negative, rod-shaped, motile, and facultative anaerobic. Growth occurred at optimum of pH 6.0–7.0, temperature 30 °C. 16S rRNA gene affiliated the strain KAs 5-22 T to the genus Rhizobium showing maximum similarity (98.4 %) with the type strain of Rhizobium naphthalenivorans TSY03b T followed by (98.0 % similarity) Rhizobium selenitireducens B1 T . The genomic G + C content was 59.4 mol%, and DNA–DNA relatedness with its closest phylogenetic neighbors was 50.2 %. Chemotaxonomy indicated UQ-10 as the major quinone; phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol as major polar lipids; C 16:0 , C 17:0 , 2-OH C 10:0 , 3-OH C 16:0 , and unresolved C 18:1 ɷ7C/ɷ9C as predominant fatty acids. The cells were found to reduce O 2 , As 5+ , NO 3 − , SO 4 2− and Fe 3+ as alternate electron acceptors. The strain’s ability to metabolize dodecane or other alkanes as sole carbon source using As 5+ as terminal electron acceptor was supported by the presence of genes encoding benzyl succinate synthase ( bss A like) and molybdopterin-binding site ( mop B) of As 5+ respiratory reductase ( arr A). Differential phenotypic, chemotaxonomic, genotypic as well as physiological properties revealed that the strain KAs 5-22 T is separated from its nearest recognized Rhizobium species. On the basis of the data presented, strain KAs 5-22 T is considered to represent a novel species of the genus Rhizobium , for which the name Rhizobium arsenicireducens sp. nov. is proposed as type strain (=LMG 28795 T =MTCC 12115 T ).