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Life that inhabits deep within the continental crust remained enigmatic, and scientifically less explored. Recent scientific drilling of 3000-meter-deep scientific borehole at the Koyna seismogenic zone of the Deccan Traps, India provided an unprecedented opportunity to investigate the nature of life that evolved and existed within the extreme environment of Archean granitic basement. Rock core samples recovered from deep (up to ~2910 meter below surface), progressively hot (up to 74 °C), high pressure, alkaline, oligotrophic biosphere were analyzed through amplicon sequencing, metagenomics, and cultivation-based approaches. 16S rRNA gene amplicon sequencing showed considerable bacterial diversity. A significant proportion (50-63 %) of the microbial community, represented by the members of Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Bacilli and Clostridia was identified as endemic or core microbiome of this extreme realm. Relative abundance of different taxa of the core microbiome varied with depth in response to prevailing lithology and geochemistry. Ecological modeling depicted a major role dispersal limitation in explaining community variability suggesting the greater impact of stochasticity on the community assembly. Co-occurrence network analysis elucidated close interactions among autotrophic and organotrophic bacteria. Shotgun metagenomics revealed a major role of autotrophic carbon fixation via the Wood-Ljungdahl pathway and Rnf complex for energy and carbon metabolism. Presence of other mechanisms of energy generation such as ATPase, H2, CO, CH4 or sulfur oxidation system and the possibility of coupling of electron donors to NO3−/SO42− reduction illustrated the metabolic versatility of these organisms in terms of utilizing diverse resources. Deeper analysis suggested the existence of an ‘acetate switch’, coordinating biosynthesis and cellular homeostasis. Reactivation of the rock-hosted microbiome using different nutrients (carbon source, e- donor and acceptor) and at elevated temperatures (up to 70-degree C) and anaerobic conditions showed patterns of differential taxa recruitment for utilizing different substrate regimes. Enrichment of strict anaerobic members of taxa Peptococcaceae, Clostridiaceae Family XIV, Clostridiaceae 2 and Moraxellaceae in H2+CO2 condition corroborated well with their ability for acetogenesis. Universal enrichment of Burkholderiaceae, Bacillaceae and Sphingomonadaceae suggested their abilities to use diverse substrates. Our data provided deeper insights into microbial life and its mechanisms of carbon and energy metabolism within the nutrient- and energy-limiting deep granitic crust.

This study reports deep biosphere related outcomes of the scientific drilling into the seismogenic zones of Koyna (India) and South African gold mine and presents a comparative account of microbial ecology across the continental settings (by including geomicrobiological data from Fennoscandian and SAFOD deep drilling / biosphere sites as well). ICDP DSeis project (SA) and Ministry of Earth Sciences (India) - ICDP Koyna scientific drilling allowed us to drill and recover Archean granitic rock cores from deep Earth crust (~3-4 km) and investigate the patterns of deep biosphere microbial ecosystems. Deep crystalline rock hosted microbial communities are elucidated by sequencing the 16S rRNA genes from extracted total DNA of the rock samples. Two rock core samples obtained from borehole B (~3330 meter below surface; representing quartzite from the Babrasco Formation) drilled at the Moab Khotsong Gold mine and several rock samples obtained from various depths of Koyna exploratory and pilot boreholes are used. Microbial taxa affiliated to Burkholderiace dominated (>30% relative abundance) the SA deep rocks. Predominance of multiple hydrogen metabolizing genera such as Comamonas, Ralstonia, Burkholderia-Caballeronia-Paraburkholderia, Enhydrobacter, extremotolerant Corynebacterium and C1- compound metabolizing Methylobacterium could be noted. In contrast, the deep biosphere of Koyna (down to 2910 meter below surface) is found to be constituted by multiple taxa with relatively lower abundance. Abundance of extremotolerant Actinobacteria (Micrococcaceae and Corynebacteriace), Pseudomonadaceae, Burkholderiaceae and Opitutaceae is noted. WPGMA based clustering suggests that microbial communities of Deccan trap subsurface are significantly different from its South African counterparts; and the latter are somewhat similar to microbial communities previously reported from Fennoscandian deep biosphere. Presence of several unique taxa is identified in each of these habitats. Members of Thermoactinomycetaceae, Planococcaceae, Babeliaceae, Thermomonosporaceae and several Clostridial families are found as unique taxa in SA deep biosphere, while Thermoanerobaculaceae, Cyclobacteriaceae, Acidothermaceae, Thioalkalispiraceae, etc. represented those of the deep biosphere underneath the Deccan. The study highlights the pattern of deep granitic crust hosted microbial communities and reinforces the need to develop and adopt more universal sampling and experimental approaches in deep life research.

Scientific drilling within the deep continental crust provides the unique opportunity for characterizing subsurface microorganisms from deep crystalline rocks and is of major scientific interest owing to the crucial role of these microorganism in global carbon cycles. Scientific drilling in Koyna seismogenic zone enables characaterization of deep Earth crust microbiome and provides a new insight into their biogeochemical role. In this study, we investigated the microbial populations reactivated (enriched) from the deep [1679 - 2908 meters below surface (mbs)] granitic rocks underneath the Deccan Traps with inorganic [CO2 (+H2)/ HCO3- ] and organic carbon (CH4 / Organic carbon mix/ Polymeric carbon mix) sources under hot (50°C), anaerobic conditions (180 days). Estimation of total protein, ATP and 16S rRNA gene qPCR suggested considerable microbial growth in all the enrichment setups. 16S rRNA gene amplicon sequencing showed a depth-wide distribution of diverse chemolithotrophic (and a few fermentative) organisms in the inorganic enrichments, whereas a substrate specific response was observed under the heterotrophic conditions with organic carbon sources. Comamonas, Burkholderia-Caballeronia-Paraburkholderia, Ralstonia, Klebsiella, unclassified Burkholderiaceae and Enterobacteriaceae were reactivated as dominant organisms from the enrichments of the deeper rocks (2335 - 2908 mbs) with both CO2 and HCO3-. From shallower depths, organisms of varied taxa were enriched. Pseudomonas, Rhodanobacter, Methyloversatilis, and Thaumarchaeota were major CO2 (+H2) utilizers, while Nocardioides, Sphingomonas, Aeromonas responded towards HCO3-. Enrichments with CH4 reactivated Actinophytocola, Pseudomonas, Methylobacterium, Nocardiodes members, while with the organic carbons, Bacillus and Thermoactinomyces were the most abundant taxa. Gemella, Pseudomonas and Nocardiodes got enriched with the polymeric carbon mix. Interestingly, enrichment of Cyanobacteria were observed mostly with CO2 (+H2), CH4 and polymeric carbon mix, which could be attributed to their ecological versatility, potential for H2-based lithoautotrophic metabolism and their ability to switch to fermentative lifestyle. Statistical analyses depicted depth-wise and substrate-wise distinct cladding of chemolithotrophic and chemoorganotrophic microbial communities, respectively. Phylogenetic analyses of the operational taxonomic units, showed similarities with sequences retrieved from other extreme deep subsurface environments. Co-occurrence networks suggested close interaction between chemolithototrophic and chemoorganotrophic/fermentative organisms. Predictive metabolic profiling revealed the presence of various genes for carbon and energy metabolisms as well as for valuable chemicals. The subsurface microorganisms showed the potential for answering the fundamental questions of deep life and for their exploitation as resources of valuable chemicals.

Bioremediation, the use of living or dead microorganism to degrade or remove the waste, has been practised since humans first populated the world and had to dispose of their trash. Heavy metals can be extremely toxic as they damage organs and block functional groups of vital enzymes. Zinc is one of the most important heavy metals often found in effluents discharged and travels via bioaccumulation. The study was aimed in screening of zinc resistant/accumulator bacterial strains isolated from metal contaminated sites and determining the Zn (II) resistance/accumulation performance of selected bacterial strain as a new biosorbent. The maximum removal of Zn (II) at pH 7.0 was found to be 607 nmol/mg proteins at initial Zn (II) ion concentration of 1.0 mM and the Km value was 0.76mM. Competitive uptake experiments were performed with zinc in the presence of copper, cadmium, chromium, cobalt and nickel ions simultaneously and the zinc uptake was not much affected by these ions. Sensitivity of Zn (II) towards sodium azide, zinc cyanide 0.5% glucose and heat suggested that the process was metabolically inactive. The nature of the possible cell–metal ions interactions was evaluated by chemical and instrumental analysis including X-Ray diffraction and FTIR spectroscopy and revealed the involvement of cellular phosphate and carboxyl groups in zinc binding by the bacterial biomass. Almost 61% of biomass-bound Zn could be recovered using H2SO4 as the desorbing agent. In natural environment some bacterial strains develop resistance mechanisms that lead to the selection of metal resistant strains tolerating high zinc concentration.

Deep terrestrial subsurface represents a huge repository of global prokaryotic biomass. Given its vastness and importance, microbial life within the deep subsurface continental crust remains under-represented in global studies. We characterize the microbial communities of deep, extreme and oligotrophic realm hosted by crystalline Archaean granitic rocks underneath the Deccan Traps, through sampling via 3000 m deep scientific borehole at Koyna, India through metagenomics, amplicon sequencing and cultivation-based analyses. Gene sequences 16S rRNA (7.37 × 10

Microbial community analysis of crude oil containing sludge collected from Duliajan oil field, Assam, India, showed the predominance of hydrocarbon-degrading bacteria such as Pseudomonas (20.1%), Pseudoxanthomonas (15.8%), Brevundimonas (1.6%), and Bacillus (0.8%) alongwith anaerobic, fermentative, nitrogen-fixing, nitrate-, sulfate-, and metal-reducing, syntrophic bacteria, and methanogenic archaea. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis indicated gene collection for potential hydrocarbon degradation, lipid, nitrogen, sulfur, and methane metabolism. The culturable microbial community was predominated by Pseudomonas and Bacillus with the metabolic potential for utilizing diverse hydrocarbons, crude oil, and actual petroleum sludge as sole carbon source during growth and tolerating various environmental stresses prevailing in such contaminated sites. More than 90% of the isolated strains could produce biosurfactant and exhibit catechol 2,3-dioxygenase activity. Nearly 30% of the isolates showed alkane hydroxylase activity with the maximum specific activity of 0.54 μmol min-1 mg-1. The study provided better insights into the microbial diversity and functional potential within the crude oil containing sludge which could be exploited for in situ bioremediation of contaminated sites.

Acid mine drainage (AMD) harbors all three life forms in spite of its toxic and hazardous nature. In comparison to bacterial diversity, an in-depth understanding of the archaeal diversity in AMD and their ecological significance remain less explored. Archaeal populations are known to play significant roles in various biogeochemical cycles within the AMD ecosystem, and it is imperative to have a deeper understanding of archaeal diversity and their functional potential in AMD system. The present study is aimed to understand the archaeal diversity of an AMD sediment of Malanjkhand Copper Project, India through archaea specific V6 region of 16S rRNA gene amplicon sequencing. Geochemical data confirmed the acidic, toxic, heavy metal-rich nature of the sample. Archaea specific V6-16S rRNA gene amplicon data showed a predominance of Thermoplasmata (BSLdp215, uncultured Thermoplasmata, and Thermoplasmataceae) and Nitrososphaeria (Nitrosotaleaceae) members constituting ~ 95% of the archaeal community. Uncultured members of Bathyarchaeia, Group 1.1c, Hydrothermarchaeota, and Methanomassiliicoccales along with Methanobacteriaceae, Methanocellaceae, Haloferaceae, Methanosaetaceae, and Methanoregulaceae constituted the part of rare taxa. Analysis of sequence reads indicated that apart from their close ecological relevance, members of the Thermoplasmata present in Malanjkhand AMD were mostly involved in chemoheterotrophy, Fe/S redox cycling, and with heavy metal resistance, while the Nitrososphaeria members were responsible for ammonia oxidation and fixation of HCO3− through 3-hydroxypropionate/4-hydroxybutyrate cycle at low pH and oligotrophic environment which subsequently played an important role in nitrification process in AMD sediment. Overall, the present study elucidated the biogeochemical significance of archaeal populations inhabiting the toxic AMD environment.

Geomicrobiology of mine tailing from Asia’s largest open-cast Cu mine at Malanjkhand was established, emphasizing the roles of microorganisms in acidification process using 16S rRNA gene amplicon a...

Scientific deep drilling of the Koyna pilot borehole into the continental crust up to a depth of 3000 m below the surface at the Deccan Traps, India, provided a unique opportunity to explore microbial life within the deep granitic bedrock of the Archaean Eon. Microbial communities of the returned drilling fluid (fluid returned to the mud tank from the underground during the drilling operation; designated here as DF) sampled during the drilling operation of the Koyna pilot borehole at a depth range of 1681–2908 metres below the surface (m b.s.) were explored to gain a glimpse of the deep biosphere underneath the continental crust. Change of pH to alkalinity, reduced abundance of Si and Al, but enrichment of Fe, Ca and SO42- in the samples from deeper horizons suggested a gradual infusion of elements or ions from the crystalline bedrock, leading to an observed geochemical shift in the DF. Microbial communities of the DFs from deeper horizons showed progressively increased abundance of Firmicutes, Gammaproteobacteria and Actinobacteria as bacterial taxa and members of Euryarchaeota as the major archaeal taxa. Microbial families, well known to strive in strictly anaerobic and extremophilic environments, (e.g. Thermoanaerobacteraceae, Clostridiaceae, Bacillaceae, Carnobacteriaceae, Ruminococcaceae), increased in the samples obtained at a depth range of 2000 to 2908 m b.s. Phylogenetic analysis of common and unique operational taxonomic units (OTUs) of DF samples indicated signatures of extremophilic and deep subsurface relevant bacterial genera (Mongoliitalea, Hydrogenophaga, Marinilactibacillus, Anoxybacillus, Symbiobacterium, Geosporobacter, Thermoanaerobacter). Thermophilic, obligatory anaerobic sulfate-reducing bacterial taxa known to inhabit the deep subsurface were enriched from DF samples using sulfate as a terminal electron acceptor. This report on the geomicrobiology of the DF obtained during drilling of the deep subsurface of the Deccan Traps showed new opportunities to investigate deep life from terrestrial, granite-rock-hosted habitats.

Over 50 million people are affected by groundwater arsenic (As) contamination beyond the prescribed safe limit of 10 µg/L across various regions in the Ganga-Brahmaputra basin of India. Among all, south-eastern Asiatic countries especially India and Bangladesh are most severely affected. Rice is the staple food for millions of people of this region and among many other crops, rice grains are champion in accumulating very high As. Irrigation of As-contaminated groundwater for rice cultivation has resulted in high deposition of As in topsoil and uptake in rice grain posing a serious threat to the sustainable agriculture. In addition, cooking and parboiling with As-contaminated water increases the As burden through dietary intake along with processed food items. Studies have shown that various factors like As solubility, bioavailability, microbial colonization, and uptake in the rice rhizosphere decides the fate of As transportation in rice. In this context, the use of plant growth promoting (PGP) microbial community members having both plant beneficial properties (increased production of phytohormone, enzymes, Siderophore, N2 fixation, P solubilization, disease resistance, mineral solubilization, etc.) and As amelioration or detoxification activities (biosorption, accumulation, volatilization, enhanced adsorption) can be a suitable alternative for sustainable rice farming in As-hotspots.

Development of an appropriate bioremediation strategy for acid mine drainage (AMD) impacted environment is imperative for sustainable mining but remained critically challenged due to the paucity of knowledge on desired microbiological factors and their nutrient requirements. The present study was conducted to utilize the potential of an anaerobic, acid-tolerant, Fe

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 (

Paddy soil is a heterogenous ecosystem that harbours diverse microbial communities critical for maintaining ecosystem sustainability and crop yield. Considering the importance of soil in crop production and recent reports on its contamination with arsenic (As) across the South East Asia, its microbial community composition and biogeochemical functions remained inadequately studied. We have characterized the microbial communities of rice soil from eleven paddy fields of As-contaminated sites from West Bengal (India), through metagenomics and amplicon sequencing. 16S rRNA gene sequencing showed considerable bacterial diversity [over 0.2 million Operational Taxonomic Units (OTUs)] and abundance (upto 1.6 × 10

Arsenic (As) mobilization in alluvial aquifers is facilitated by microbially catalyzed redox transformations that depend on the availability of electron acceptors (EAs). In this study, the response of an As-contaminated groundwater microbial community from West Bengal, India towards varied EAs was elucidated through microcosm based 16S rRNA gene amplicon sequencing. Acinetobacter, Deinococcus, Nocardioides, etc., and several unclassified bacteria (Ignavibacteria) and archaea (Bathyarchaeia, Micrarchaeia) previously not reported from As-contaminated groundwater of West Bengal, characterized the groundwater community. Distinct shifts in community composition were observed in response to various EAs. Enrichment of operational taxonomic units (OTUs) affiliated to Denitratisoma (NO3-), Spirochaetaceae (Mn4+), Deinococcus (As5+), Ruminiclostridium (Fe3+), Macellibacteroides (SO42-), Holophagae-Subgroup 7 (HCO3-), Dechloromonas and Geobacter (EA mixture) was noted. Alternatively, As3+ amendment as electron donor allowed predominance of Rhizobium. Taxonomy based functional profiling highlighted the role of chemoorganoheterotrophs capable of concurrent reduction of NO3-, Fe3+, SO42-, and As biotransformation in As-contaminated groundwater of West Bengal. Our analysis revealed two major aspects of the community, (a) taxa selective toward responding to the EAs, and (b) multifaceted nature of taxa appearing in abundance in response to multiple substrates. Thus, the results emphasized the potential of microbial community members to influence the biogeochemical cycling of As and other dominant anions/cations.

Anaerobic enrichment of As5+ reducing bacteria in the presence and/or absence of organic carbon (OC) and As5+ from As contaminated soil of Brahmaputra river basin (BRB) (Jorhat, Assam) was performe...

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.

Exploration of community structures, habitations, and potential plant growth promoting (PGP) attributes of endophytic bacteria through next generation sequencing (NGS) is a prerequisite to culturing PGP endophytic bacteria for their application in sustainable agriculture. The present study unravels the taxonomic abundance and diversity of endophytic bacteria inhabiting in vitro grown root, shoot and callus tissues of two aromatic rice cultivars through 16S rRNA gene-based Illumina NGS. Wide variability in the number of bacterial operational taxonomic units (OTUs) and genera was observed between the two samples of the root (55, 14 vs. 310, 76) and shoot (26, 12 vs. 276, 73) but not between the two callus samples (251, 61 vs. 259, 51), indicating tissue-specific and genotype-dependent bacterial community distribution in rice plant, even under similar gnotobiotic growth conditions. Sizes of core bacteriomes of the selected two rice genotypes varied from 1 to 15 genera, with Sphingomonas being the only genus detected in all six samples. Functional annotation, based upon the abundance of bacterial OTUs, revealed the presence of several PGP trait-related genes having variable relative abundance in tissue-specific and genotype-dependent manners. In silico study also documented a higher abundance of certain genes in the same biochemical pathway, such as nitrogen fixation, phosphate solubilization and indole acetic acid production; implying their crucial roles in the biosynthesis of metabolites leading to PGP. New insights on utilizing callus cultures for isolation of PGP endophytes aiming to improve rice crop productivity are presented, owing to constancy in bacterial OTUs and genera in callus tissues of both the rice genotypes.

Petroleum oil refinery sludge is a complex of mixture of aliphatic and aromatic hydrocarbons, heavy metals, asphaltenes, etc., which is generated in huge amounts by related industries all over the world. Remediation strategies of such wastes are further complicated by their hydrophobic nature and nutritionally imbalanced state. Ecofriendly and cost-effective bioremediation strategy has been identified as an effective technology for the treatment of pollutants. The native microbial community composition and function in the petroleum-contaminated environments have been an area of active research and advancements in next-generation sequencing technologies have revealed the diversity and metabolic function of native resident microorganisms from a plethora of hydrocarbon-contaminated environments. Natural attenuation of such contaminated environments by native microorganisms is a slow process, which is greatly regulated by prevalent environmental conditions and can be affected severely by minimal changes in environmental parameters. Therefore biostimulation (BS) and bioaugmentation (BA) of indigenous microbial communities, the two main bioremediation strategies, have gained popularity in the restoration of contaminated environments. BS entails balancing the physicochemical or nutritional regime within the environment to stimulate the growth and/or activity of native microorganisms, while BA includes extraneous addition of specialist microbes (exogenous or endogenous) to accelerate the remediation process. These techniques have been recommended as site-specific bioremediation strategies for the treatment of various hydrocarbon-contaminated environments.

Additional file 2.

Additional file 1.

Acid mine drainage (AMD) is considered to be one of the major environmental problems faced by the mining industries due to its toxic and lethal impact on the ecosystem. Generation of million tons of mine wastes like tailings, slags, waste rocks/ore bodies, etc. are the major sources of AMD generation in metalliferous/coal mine, due to the biologically mediated oxidation of sulfidic waste. Low pH and high heavy metal and sulfate concentration are the major characteristic features of the AMD environment and considered to be lethal than single-factor pollutants. Owing to its toxic effects, development of both preventive and treatment options remain the main focus of scientific research for decades. Prevention is a better option than complex treatment processes; however, due to several environmental factors preventive measures are limited from its application in several mining locations. In order to minimize the impact of AMD on ecosystem, several remediation technologies have been developed including chemical and biological treatment options. Due to the high capital investment and other reasons, chemical technologies are less preferred over biological treatments. Nowadays, several studies have been conducted to develop promising biological treatment system to attenuate AMD and recover metals from such environment. The present chapter discusses the cause and generation of AMD, available prevention measures, and treatment technologies using metabolic capacities of sulfate-reducing bacteria (SRB), which is the main player of biological treatment system.

Molecular and eco-physiological characterization of arsenic (As)-transforming and hydrocarbon-utilizing Achromobacter type strain KAs 3–5T has been investigated in order to gain an insight into As-...

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.

The deep biosphere is often characterized by multiple extreme physical–chemical conditions, of which pressure is an important parameter that influences life but remains less studied. This geomicrobiology study was designed to understand the response of a subterranean microbial community of the Deccan traps to high-pressure conditions and to elucidate their genomic properties. Groundwater from a deep basaltic aquifer of the Deccan traps was used to ascertain the community response to 25 MPa and 50 MPa pressure following enrichment in high-salt and low-salt organic media. Quantitative PCR data indicated a decrease in bacterial and archaeal cell numbers with increasing pressure. 16S rRNA gene sequencing displayed substantial changes in the microbial community in which Acidovorax appeared to be the most dominant genus in the low-salt medium and Microbacteriaceae emerged as the major family in the high-salt medium under both pressure conditions. Genes present in metagenome-associated genomes which have previously been associated with piezotolerance include those related to nutrient uptake and extracytoplasmic stress (omp, rseC), protein folding and unfolding (dnaK, groEL and others), and DNA repair mechanisms (mutT, uvr and others). We hypothesize that these genes facilitate tolerance to high pressure by certain groups of microbes residing in subsurface Deccan traps.

Development of an efficient bioremediation strategy for the mitigation of low pH (3.21), high dissolved SO42− (6285 mg/L), and Fe (7292 mg/kg)-rich acid mine drainage–impacted soil (AIS) was investigated through amendment of readily available organic carbon substrates (rice husk, compost, leaf litter, and grass clippings). An organic carbon mixture (OCM) formulated by mixing the test substrates was used to biostimulate microbial processes (SO42−/Fe3+reduction) necessary for efficient attenuation of the hazards imposed by AIS. OCM amendment in calcium carbonate–treated AIS enhanced reductive processes and removed dissolved SO42− and Fe3+ considerably raising the pH close to neutrality. 16S rRNA gene amplicon sequencing performed with total DNA and RNA elucidated the microbial population dynamics of treated AIS. Metabolically active populations comprised of fermentative (Clostridium sensu stricto 1 and Fonticella), iron-reducing (Acidocella, Anaeromyxobacter, and Clostridium sensu stricto 1), and sulfate-reducing (Desulfovibrio, Desulfotomaculum, Desulfosporosinus, and Desulfobacteraceae) bacteria. Microbial guilds obtained highlighted the synergistic role of cellulolytic, fermentative, and SO42−/Fe3+-reducing bacteria in attenuation of hazardous contaminants. Quantitative PCR analysis well supported the role of OCM in stimulating the indigenous bacterial populations, including those harboring the dissimilatory sulfite reductase (dsrB) gene and involved actively in SO42− reduction. The study demonstrated the suitability of locally available organic substrates as a low-cost and efficient biostimulation agent for in situ bioremediation of acid mine drainage (AMD)–impacted soil system.

Deep biosphere represents an unexplored realm of planetary life residing underneath the continental and oceanic crusts that constitutes majorly of prokaryotic life forms bacteria and archaea. Microbial communities which reside within various deep subsurface environments form a significant but largely unknown portion of the Earth’s biosphere. While the shallow aquifer and sedimentary rock microbiome might get access to the nutrient pool available above ground, deep subterranean habitats hosted by crystalline rocks are severely constrained by the availability of photosynthetically derived nutrients. Deep subsurface microbiome underneath the continental crusts not only showed variations based on their geographic locations but also with respect to the abundance of various microbial populations and their metabolic properties. It is estimated that the deep biosphere microorganisms represent the largest pool of carbon, nitrogen, and phosphorous and constitute a critical component of biogeochemical engine of our planet. The aphotic deep dark microbial realm that has evolved possibly billions of years ago has developed unique metabolic repertoire for their survival. The deep biosphere microbiome is considered to be a portion of planetary life with extraordinary life-supporting system that works beyond our notion about biological and physical constraints. Advancement of techniques in microbial ecology has enabled us to decipher deep subsurface microbiome which resides up to several kilometers below the surface using both cultivation-dependent and cultivation-independent techniques. In this chapter, we have summarized our understanding of the deep biosphere microbiome within terrestrial subsurface. Habitability of life within the deep subsurface has been discussed considering the major metabolic routes deployed by the microorganisms. Cultivation-dependent and cultivation-independent studies and their requirement and outcome from various exploratory researches have been documented. Techniques used for sampling the subsurface microbiome are discussed, highlighting the role of possible contamination during drilling and subsequent postcore extraction processes. Lastly, applications of deep subsurface microbiome research in achieving better sustainability and biotechnological innovations are discussed.