Srijak Bhatnagar

Srijak Bhatnagar
Athabasca University · Faculty of Science and Technology

Professor

About

82
Publications
13,268
Reads
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3,873
Citations
Additional affiliations
August 2021 - present
Athabasca University
Position
  • Professor (Assistant)
August 2017 - August 2021
University of Calgary
Position
  • PostDoc Position
July 2008 - September 2011
University of California, Davis
Position
  • Bioinformatician
Education
September 2011 - August 2017
University of California, Davis
Field of study
  • Microbiology
September 2011 - August 2017
University of California, Davis
Field of study
  • Microbiology
August 2006 - December 2007
Georgia Institute of Technology
Field of study
  • Bioinformatics

Publications

Publications (82)
Article
Full-text available
Background Understanding factors associated with antimicrobial resistance (AMR) distribution across populations is a necessary step in planning mitigation measures. While associations between AMR and socioeconomic-status (SES), including employment and education have been increasingly recognized in low- and middle-income settings, connections are l...
Article
Full-text available
Background Approximately 3.7 billion years ago, microbial life may have emerged in phosphate-rich salty ponds. Surprisingly, analogs of these environments are present in alkaline lake systems, recognized as highly productive biological ecosystems. In this study, we investigate the microbial ecology of two Canadian soda lake sediment systems charact...
Preprint
Full-text available
Permanently cold deep-sea sediments (2500-3500 m water depth) with or without indications of thermogenic hydrocarbon seepage were exposed to naphtha to examine the presence and potential of aerobic hydrocarbon-degrading microbial populations. Monitoring these microcosms for volatile hydrocarbons by GC-MS revealed sediments without in situ hydrocarb...
Preprint
Full-text available
Understanding factors associated with antimicrobial resistance (AMR) distribution across populations is a necessary step in planning optimal mitigation measures. While associations between AMR and socioeconomic-status (SES), including factors like income, employment, education, have been increasingly recognized in low- and middle-income settings, t...
Preprint
Full-text available
Approximately 3.7 billion years ago, microbial life may have emerged in phosphate-rich salty ponds. Surprisingly, analogs of these environments are present in alkaline lake systems, recognized as highly productive biological ecosystems. Investigating the microbial ecology of two Canadian soda lake sediment systems characterized by naturally high ph...
Article
Wastewater-based surveillance (WBS) has been established as a powerful tool that can guide health policy at multiple levels of government. However, this approach has not been well assessed at more granular scales, including large work sites such as University campuses. Between August 2021 and April 2022, we explored the occurrence of SARS-CoV-2 RNA...
Preprint
Antimicrobial resistance (AMR) is an ever-increasing threat to global health. Wastewater-based surveillance is an emerging methodology that objectively enables an inclusive and comprehensive assessment of population AMR in an observed sewershed. Here we compared the resistome of two tertiary-care hospitals with two separate neighborhoods, using com...
Preprint
Wastewater-based surveillance (WBS) has been established as a powerful tool that can guide health policy at multiple levels of government. However, this technology has not been well assessed at more granular scales, including large work sites such as University campuses. Between August 2021-April 2022, we explored the occurrence of SARS-CoV-2 RNA i...
Chapter
Declining sea ice is resulting in accelerating maritime and industrial activity in the Arctic Ocean, with an attendant increase in the risk of offshore oil spills or fuel spills. Remediation efforts in this harsh, cold, and remote environment will be challenging and expensive, such that relying on marine oil-degrading bacteria as “emergency first r...
Article
Full-text available
Background WW surveillance enables real time monitoring of SARS-CoV-2 burden in defined sewer catchment areas. Here, we assessed the occurrence of total, Delta and Omicron SARS-CoV-2 RNA in sewage from three tertiary-care hospitals in Calgary, Canada. Methods Nucleic acid was extracted from hospital (H) WW using the 4S-silica column method. H-1 an...
Article
Full-text available
Background We sought to compare WW SARS-CoV-2 RNA detection across a range of sites and scales using RTqPCR and RTddPCR. Figure. Methods Composite-24h WW was collected from a WW treatment plant (WTP; n=18), a neighborhood (Nb1; n=12) and three hospitals; H-1, H-2, and H-3 (3-sites; A-C)(n=84). RNA was extracted using the 4S-silica column method. R...
Article
Full-text available
Background New tools capable of dynamic assessment of the varying burden of Clostridioides difficile infections are required to mitigate increased patient morbidity, mortality, and health costs. Wastewater (WW)-based epidemiology (WBE) is an emerging science, enabling comprehensive, inclusive, and unbiased assessment of populations, spatially and t...
Article
Full-text available
Wastewater‐based SARS‐CoV‐2 surveillance enables unbiased and comprehensive monitoring of defined sewersheds. We performed real‐time monitoring of hospital wastewater that differentiated Delta and Omicron variants within total SARS‐CoV‐2‐RNA, enabling correlation to COVID‐19 cases from three tertiary‐care facilities with >2100 inpatient beds in Cal...
Preprint
Full-text available
Petroleum reservoirs within the deep biosphere are extreme environments inhabited by diverse microbial communities creating biogeochemical hotspots in the subsurface. Despite their ecological and industrial importance, systematic studies of core microbial taxa and associated genomic attributes of the oil reservoir microbiome are limited. This study...
Article
Full-text available
The deep biosphere is the largest microbial habitat on Earth and features abundant bacterial endospores. Whereas dormancy and survival at theoretical energy minima are hallmarks of microbial physiology in the subsurface, ecological processes such as dispersal and selection in the deep biosphere remain poorly understood. We investigated the biogeogr...
Article
Full-text available
Wastewater-based epidemiology (WBE) is an emerging surveillance tool that has been used to monitor the ongoing COVID-19 pandemic by tracking SARS-CoV-2 RNA shed into wastewater. WBE was performed to monitor the occurrence and spread of SARS-CoV-2 from three wastewater treatment plants (WWTP) and six neighborhoods in the city of Calgary, Canada (pop...
Article
Full-text available
Many pathways for hydrocarbon degradation have been discovered, yet there are no dedicated tools to identify and predict the hydrocarbon degradation potential of microbial genomes and metagenomes. Here we present the Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD), a database of 37 HMMs of marker genes involved in anaerobic...
Preprint
Full-text available
Wastewater-based epidemiology (WBE) is an emerging surveillance tool that has been used to monitor the ongoing COVID-19 pandemic by tracking SARS-CoV-2 RNA shed into wastewater. WBE was performed to monitor the occurrence and spread of SARS-CoV-2 from three wastewater treatment plants (WWTP) and six neighborhoods in the city of Calgary, Canada (pop...
Preprint
Full-text available
paragraph The deep biosphere is the largest microbial habitat on Earth and features abundant bacterial endospores 1,2 . Whereas dormancy and survival at theoretical energy minima are hallmarks of subsurface microbial populations ³ , the roles of fundamental ecological processes like dispersal and selection in these environments are poorly understoo...
Article
Full-text available
Extracellular DNA is a major macromolecule in global element cycles, and is a particularly crucial phosphorus, nitrogen and carbon source for microorganisms in the seafloor. Nevertheless, the identities, ecophysiology and genetic features of DNA-foraging microorganisms in marine sediments are largely unknown. Here, we combined microcosm experiments...
Preprint
Full-text available
Discovery of microbial hydrocarbon degradation pathways has traditionally relied on laboratory isolation and characterization of microorganisms. Although many metabolic pathways for hydrocarbon degradation have been discovered, the absence of tools dedicated to their annotation makes it difficult to identify the relevant genes and predict the hydro...
Article
Full-text available
SARS-CoV-2 has been detected in wastewater and its abundance correlated with community COVID-19 cases, hospitalizations and deaths. We sought to use wastewater-based detection of SARS-CoV-2 to assess the epidemiology of SARS-CoV-2 in hospitals. Between August and December 2020, twice-weekly wastewater samples from three tertiary-care hospitals (tot...
Preprint
Full-text available
Background: SARS-CoV-2 has been detected in wastewater and its abundance correlated with community COVID-19 cases, hospitalizations and deaths. We sought to use wastewater-based detection of SARS-CoV-2 to assess the epidemiology of SARS-CoV-2 in hospitals. Methods: Between August and December 2020, twice-weekly wastewater samples from three tertiar...
Article
Full-text available
Background Lagoons are common along coastlines worldwide and are important for biogeochemical element cycling, coastal biodiversity, coastal erosion protection and blue carbon sequestration. These ecosystems are frequently disturbed by weather, tides, and human activities. Here, we investigated a shallow lagoon in New England. The brackish ecosyste...
Article
Full-text available
Improved sequencing and analytical techniques allow for better resolution of microbial communities; however, the agriculture field lacks an updated analysis surveying the fecal microbial populations of dairy cattle in California. This study is a large-scale survey to determine the composition of the bacterial community present in the feces of lacta...
Preprint
Full-text available
Phototrophic microbial mats commonly contain multiple phototrophic lineages that coexist based on their light, oxygen and nutrient preferences. Here we show that similar coexistence patterns and ecological niches can occur in suspended phototrophic blooms of an organic-rich estuary. The water column showed steep gradients of oxygen, pH, sulfate, su...
Article
Plants are associated with a complex microbiota that contributes to nutrient acquisition, plant growth, and plant defense. Nitrogen-fixing microbial associations are efficient and well characterized in legumes but are limited in cereals, including maize. We studied an indigenous landrace of maize grown in nitrogen-depleted soils in the Sierra Mixe...
Article
Full-text available
Plants are associated with a complex microbiota that contributes to nutrient acquisition, plant growth, and plant defense. Nitrogen-fixing microbial associations are efficient and well characterized in legumes but are limited in cereals, including maize. We studied an indigenous landrace of maize grown in nitrogen-depleted soils in the Sierra Mixe...
Data
Taxonomic distribution at the family level of the 25 most abundant bacterial families in (A) rRNA gene libraries and (B) whole-genome shotgun libraries. (EPS)
Data
Proportion of nitrogen derived from biological N2 fixation (%Ndfa) in Sierra Mixe maize. Plants grown in Sierra Mixe during 2010 (light gray bars), 2011 (dark grey bars), and 2012 (black bars) were evaluated for %Ndfa; values were calculated using δ15N values in Table 1. Bar = standard error of the mean. %Ndfa, percent of nitrogen derived from the...
Data
δN15 (‰) distribution in root and shoot samples. Data are from a single sampling date (May 2012) in Sierra Mixe maize, with 30 replicates analyzed for each sample reported. (DOCX)
Data
Shoot and root height and diameter measurements for field trials in Sierra Mixe in 2016 and 2017. Numbers followed by different letters are significantly different based on Least Significant difference at p = 0.05. (DOCX)
Data
Soil analyses for samples taken at 0–60 cm before planting for fields in Sierra Mixe, Mexico. (A) Macroelements and soil characteristics. (B) Microelements for fields in 2017. (DOCX)
Data
Heat map showing the hierarchal complete linkage clustering of samples. The heat map depicts the abundances of (A) 1,000 most abundant SVs and (B) 20 most abundant SVs in the dataset that were transformed using variance-stabilizing transformation in DESeq2. The libraries are Mucilage (Blue; OLMC00, OLMD00, OLMV00, OLMX00), Aerial Root (Gray; OLAR00...
Data
Nitrogenase (acetylene reduction) activity in different organs of Sierra Mixe maize. Significant nitrogenase activity was only found on aerial roots with mucilage. (EPS)
Data
Aerial root development in teosinte, Sierra Mixe maize, and a conventional variety, Hickory King grown in the field in Madison, USA. (A) Number of nodes with aerial roots and (B) number of aerial roots observed on teosinte, Sierra Mixe maize, and Hickory King after 14 weeks. Bar = standard error of the mean. Different letters indicate statistically...
Data
Effect of reconstituted mucilage on oxygen diffusion and acetylene reduction. (A) Oxygen measured at 3 depths in Fahraeus medium with (black bars) or without (gray bars) 0.2% agar. (B) Effect of the different sugars present in the mucilage on the ability of H. seropedicae, (C) A. brasilense, and (D) B. unamae to reduce acetylene. (EPS)
Data
Box plot indicating the alpha diversity as calculated by Phyloseq using (A) Simpson index and (B) Shannon index. (EPS)
Data
Reference plants sampled in the Fields 3 and 4 in Sierra Mixe in 2011 and 2012 and summarized in Table 2B. (DOCX)
Data
δ15N (‰) was determined in Sierra Mixe maize, and reference plants sampled from three 10 × 10 m locations were randomly selected from farmers’ fields in Sierra Mixe. From each location, 6 leaf samples were randomly sampled from Sierra Mixe maize plants and 6 leaf samples from each of 2 reference plants. The third emergent leaf of each maize plant w...
Data
Fig. S1. Visualization of assembled contigs of the six metagenomes (Oxy‐1, Oxy‐2, Nit‐1, Nit‐2, Con‐1, Con‐2) after binning. Bins A‐R are indicated with capital letters. Letters in parentheses show large bins that were detected, but had assembled better in another sample. Refer to this graph to link the metatranscriptomic contig identifier (Dataset...
Article
Full-text available
Agrobacterium tumefaciens biovar 1 strain 186 was isolated from a walnut tree expressing crown gall symptoms. The draft genome sequence of this strain harbored genes for crown gall formation and will be useful for understanding its virulence on Paradox, the predominant hybrid rootstock used for the cultivation of English walnut in California.
Article
Full-text available
For the anaerobic remineralization of organic matter in marine sediments, sulfate reduction coupled to fermentation plays a key role. Here, we enriched sulfate-reducing/fermentative communities from intertidal sediments under defined conditions in continuous culture. We transiently exposed the cultures to oxygen or nitrate twice daily and investiga...
Article
Full-text available
For the anaerobic remineralization of organic matter in marine sediments, sulfate reduction coupled to fermentation plays a key role. Here, we enriched sulfate-reducing/fermentative communities from intertidal sediments under defined conditions in continuous culture. We transiently exposed the cultures to oxygen or nitrate twice daily and investiga...
Article
Full-text available
Here, we present the complete genome sequence of Streptomyces sp. strain CCM_MD2014 (phylum Actinobacteria ), isolated from surface soil in Woods Hole, MA. Its single linear chromosome of 8,274,043 bp in length has a 72.13% G+C content and contains 6,948 coding sequences.
Article
Full-text available
Here, we present the 3,443,800-bp complete genome sequence of Curtobacterium sp. strain MR_MD2014 (phylum Actinobacteria ). This strain was isolated from soil in Woods Hole, MA, as part of the 2014 Microbial Diversity Summer Program at the Marine Biological Laboratory in Woods Hole, MA.
Article
Full-text available
Here, we present the complete 2,003,803-bp genome of a sulfate-reducing thermophilic bacterium, Thermodesulfovibrio yellowstonii strain DSM 11347T. FOOTNOTES Address correspondence to Jonathan A. Eisen, jaeisen{at}ucdavis.edu. ↵* Present address: Hoda M. Khouri, Independent Consultant, Bethesda, Maryland, USA. Citation Bhatnagar S, Badger JH, Madup...
Article
Full-text available
Here, we present the complete genome sequence of Thermodesulfobacterium commune DSM 2178T of the phylum Thermodesulfobacteria. FOOTNOTES Address correspondence to Jonathan A. Eisen, jaeisen{at}ucdavis.edu. ↵* Present address: Hoda M. Khouri, Independent Consultant, Bethesda, Maryland, USA. Citation Bhatnagar S, Badger JH, Madupu R, Khouri HM, O’Con...
Article
Full-text available
Significance Land plants continuously contact beneficial, commensal, and pathogenic microbes in soil via their roots. There is limited knowledge as to how the totality of root-associated microbes (i.e., the microbiome) is shaped by various factors or its pattern of acquisition in the root. Using rice as a model, we show that there exist three diffe...
Conference Paper
Full-text available
Actinomycetes are ubiquitous Gram (+) bacteria commonly found to have high G+C content and best known for their metabolic by-products and novel enzymes [1]. Isolates CCMMD2014 & MRMD2014 were co-cultured from soil impacted by a rusty fire hydrant in Woods Hole, MA. The Streptomyces sp. and Curtobacterium sp. isolates were identified by marker genes...
Article
Full-text available
Helicobacter pylori uses natural competence and homologous recombination to adapt to the dynamic environment of the stomach mucosa and maintain chronic colonization. Although H. pylori competence is constitutive, its rate of transformation is variable, and little is known about factors that influence it. To examine this, we first determined the tra...
Article
Full-text available
Helicobacter pylori colonization is highly prevalent among humans and causes significant gastric disease in a subset of those infected. When present, this bacterium dominates the gastric microbiota of humans and induces antimicrobial responses in the host. Since the microbial context of H. pylori colonization influences the disease outcome in a mou...
Data
This excel file contains the taxonomy assigned to each sequence used in this study along with information regarding the host species, location, environment and other information regarding the library each sequence belongs to. Additionally, the composition of each OTU can be determined using the unique OTU identifiers (used in Figures S1, S2, S3, S4...
Data
This file contains the beta-diversity measurements for all possible comparisons between our 20 natural Drosophila samples. (XLSX)
Data
Full-text available
Phylogenetic tree of the Lactobacilli found with Drosophila. Taxa highlighted in red are OTUs identified within this study. Each OTU begins with a unique identifier corresponding to a sequence within the FASTA files available on BioTorrents (http://biotorrents.net/details.php?id=143). The number of libraries and the number of sequences each OTU rep...
Data
Full-text available
Phylogenetic tree of the Enterococci found with Drosophila. Taxa highlighted in red are OTUs identified within this study. Each OTU begins with a unique identifier corresponding to a sequence within the FASTA files available on BioTorrents (http://biotorrents.net/details.php?id=143). The number of libraries and the number of sequences each OTU repr...
Data
Gut bacterial microbiome composition in D. melanogaster strains from different labs. (DOC)
Data
This table describes the samples which Wolbachia and Spiroplasma were found in. Note that samples TRR and TUR were removed from the overall analysis because, after the removal of their Wolbachia sequences, they each were left with too few sequences for analysis. Each of these samples was a D. melanogaster/D. simulans mix collected from citrus fruit...
Data
This file contains the GenBank accession numbers and the RDP identifiers of all the sequences used for tree building in this study. (TXT)
Data
Full-text available
Phylogenetic tree of the Enterobacteriaceae found with Drosophila. Taxa highlighted in red are OTUs identified within this study. Each OTU begins with a unique identifier corresponding to a sequence within the FASTA files available on BioTorrents (http://biotorrents.net/details.php?id=143). The number of libraries and the number of sequences each O...
Data
Diversity of bacterial communities associated with wild flies. (DOC)
Data
Comparison of the wild Drosophila samples in this and previous studies. (DOC)
Data
Comparison between internal and external bacterial microbiome of Drosophila adults (August, 2008) and larvae (July, 2008). (DOC)
Data
Phylogenetic tree of the Acetobacteraceae found with Drosophila. Phylogenetic trees of bacterial groups associated with Drosophila. Taxa highlighted in red are OTUs identified within this study. Each OTU begins with a unique identifier corresponding to a sequence within the FASTA files available on BioTorrents (http://biotorrents.net/details.php?id...
Data
Number of OTUs as a function of genetic distance. Number of OTUs was calculated at all genetic distances from 0 (unique sequences) to 0.37 (the largest distance between any two sequences). Clustering was performed using the average neighbor algorithm in mothur [35]. (TIF)
Data
Diversity of bacterial communities associated with laboratory samples. (DOC)
Data
Taxonomic comparison of the dominant bacterial orders found within Drosophila and mammals. (DOC)
Data
Variation in D. melanogaster bacterial microbiome on rich media at different times within the same laboratory. (DOC)
Data
A more detailed version of Table 1 describing where, when and by whom each sample was collected. (XLS)
Data
Full-text available
Phylogenetic tree of the Enterobacteriaceae Group Orbus found with Drosophila. Taxa highlighted in red are OTUs identified within this study. Each OTU begins with a unique identifier corresponding to a sequence within the FASTA files available on BioTorrents (http://biotorrents.net/details.php?id=143). The number of libraries and the number of sequ...
Data
Proportion of OTUs that are unique to a single library for wild Drosophila and mammals. Calculations done as in Ley et al., 2008a [12]. (TIF)
Data
The composition of all the laboratory diets used in this study are described here along with which libraries are included for each UniFrac comparison. Additionally, a description of the co-occurrence tests that were attempted is included. (DOC)