Papers by Bharath Prithiviraj
Additional file 2: Figure S2. Discriminant function analysis. Ordination plots of variables resul... more Additional file 2: Figure S2. Discriminant function analysis. Ordination plots of variables resulting from the first (CAN1) and second (CAN2) canonical functions for different plant tissue types (a) and media (b). The variables were generated based on the total populations from different plant tissues (leaf, stem and root) and media (HTM, NFM and MM).
Additional file 1: Figure S1. Culturable endophytic bacteria densities in various Jatropha tissue... more Additional file 1: Figure S1. Culturable endophytic bacteria densities in various Jatropha tissues. Surface-sterilized tissues (roots, stems and leaves) were grinded into fine powder; diluted in water in series and plated on to different media. Values shown are the average of three individual plants originating from the same germplasm collection. (a) Germplasm from Indonesia, (b) Germplasm from China and (c) Germplasm from India. Each value represents the mean ± SD, n = 3.
Microbiome, 2016
The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortiu... more The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is a novel, interdisciplinary initiative comprised of experts across many fields, including genomics, data analysis, engineering, public health, and architecture. The ultimate goal of the MetaSUB Consortium is to improve city utilization and planning through the detection, measurement, and design of metagenomics within urban environments. Although continual measures occur for temperature, air pressure, weather, and human activity, including longitudinal, cross-kingdom ecosystem dynamics can alter and improve the design of cities. The MetaSUB Consortium is aiding these efforts by developing and testing metagenomic methods and standards, including optimized methods for sample collection, DNA/ RNA isolation, taxa characterization, and data visualization. The data produced by the consortium can aid city planners, public health officials, and architectural designers. In addition, the study will continue to lead to the discovery of new species, global maps of antimicrobial resistance (AMR) markers, and novel biosynthetic gene clusters (BGCs). Finally, we note that engineered metagenomic ecosystems can help enable more responsive, safer, and quantified cities.
Authors: Jai Ram Rideout1, Antonio Gonzalez2, Andrew Cochran?, Damien Coy1, Michael Dwan1, Andrew... more Authors: Jai Ram Rideout1, Antonio Gonzalez2, Andrew Cochran?, Damien Coy1, Michael Dwan1, Andrew King3, Logan Knecht1, Dan Knights4,5, Justin Kuczynski6, Levi McCracken1, Jessica Metcalf2, Laura Parfrey2, Bharath Prithiviraj2, Michael S. Robeson7, Will Van Treuren2, Jose Carlos Clemente8, Rob Knight2, J. Gregory Caporaso1,9 Microbial ecology studies are increasing in scope and complexity. As more samples are being taken across temporal, spatial, and environmental gradients, there is an increasing need for tested, reliable biogeographical statistical methods in the field of microbial ecology. Many biogeographical methods have been used in traditional macro-scale ecology for years to address these types of study designs. However, these methods have not been properly evaluated on microscale ecological data, where sample sizes are bigger, there are often more observations (e.g., sequences), and scales are different, to verify that biologically meaningful results are obtained. We presen...
Over a period of eleven days, size segregated aerosols were collected in consecutive 24 hour samp... more Over a period of eleven days, size segregated aerosols were collected in consecutive 24 hour sampling campaigns; these were concurrently executed upwind and downwind of a conventional activated sludge wastewater treatment plant. Airborne particulate matter was separated by mean aerodynamic diameter and continually impacted on polycarbonate filters, which were subsequently extracted with ethanol and chloroform to isolate and purify DNA. As judged by analyses of 16s rDNA sequences from an Illumina Miseq platform, airborne bacteria immediately downwind from the aeration basin was enriched with Actinomycetes when compared to the airborne microbes recovered upwind of this site. Concurrent DNA analyses of the activated sludge suggest that the aerated wastewater was the source of airborne Actinomycetes, and that selected genera were selectively partitioning into a local bioaerosol which included, but was not limited to, Mycobacteria spp., Saccaropolyspora spp., and Streptomyces spp.. These...
Abstract Indoor microbiome studies seek to understand the ecological signatures of airborne micro... more Abstract Indoor microbiome studies seek to understand the ecological signatures of airborne microbial communities, and the associated potential to affect human and animal health. A recent study using high-throughput sequencing has determined that the diversity and composition of microbes within commercial office buildings qualify to be compared to complex ecosystems. Indoor bacterial diversity can be comprised of a multitudes of microbial taxa that may interact with each other, with humans and the indoor infrastructure (Green et al. 2012). Culture-independent methods, such as high-throughput molecular sequencing that leverages robust data analysis tools (e.g., QIIME & MGRAST) have transformed research on the human microbiome and the microbial ecology of aquatic and terrestrial ecosystems (Turnbaugh et al., 2007; Caporaso et al. 2010; Nemergut et al., 2011). Until recently, there have been few attempts to comprehensively survey the microbiome associated with the built environment (Ri...
International Journal of PIXE, 2011
Lichens have been used extensively as biomonitors of air quality (Richardson 1992; Seaward 1995, ... more Lichens have been used extensively as biomonitors of air quality (Richardson 1992; Seaward 1995, 2005). Lichen thalli lack a protective layer and hence accumulate airborne pollutants and particulate matter from the environment by wet and dry deposition (Nash 1996). The elements accumulated on lichen thalli can be quantitatively analysed using techniques such as Proton Induced X-ray Emission (PIXE) and Electron probe microanalysis. These techniques yield two-dimensional, quantitative element information with micron-level spatial resolution. This study used Scanning Electron Microscopy-Energy Dispersive X-ray (SEM-EDX) and PIXE to quantify elements accumulated on lichen thalli of selected species collected from polluted and unpolluted areas of the Madukkarai – Walayar forests. Thalli of selected lichen species from the study site (polluted and unpolluted) were irradiated using 1.7 MV tandem accelerator with Proton beam energy of 2 MeV. The ion induced X-rays were detected by Si ( Li ) semiconductor detector. The morphological analysis and localization of elements accumulated on these lichen samples were also carried out with the use of a SEM-EDX microanalysis using environmental scanning electron microscopy (ESEM) as supporting evidence. PIXE spectral elemental output revealed the presence of elements such as As , Ba , Br , Ca , Cu , Fe , K , Mn , Zn , Cl , Ti , Cr and Pd with the incidence of increased Calcium levels. IAEA 336 lichen reference material was used for standardization.
PLoS ONE, 2011
Background: Soil bacteria are important drivers for nearly all biogeochemical cycles in terrestri... more Background: Soil bacteria are important drivers for nearly all biogeochemical cycles in terrestrial ecosystems and participate in most nutrient transformations in soil. In contrast to the importance of soil bacteria for ecosystem functioning, we understand little how different management types affect the soil bacterial community composition. Methodology/Principal Findings: We used pyrosequencing-based analysis of the V2-V3 16S rRNA gene region to identify changes in bacterial diversity and community structure in nine forest and nine grassland soils from the Schwäbische Alb that covered six different management types. The dataset comprised 598,962 sequences that were affiliated to the domain Bacteria. The number of classified sequences per sample ranged from 23,515 to 39,259. Bacterial diversity was more phylum rich in grassland soils than in forest soils. The dominant taxonomic groups across all samples (.1% of all sequences) were Acidobacteria, Alphaproteobacteria, Actinobacteria, Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Firmicutes. Significant variations in relative abundances of bacterial phyla and proteobacterial classes, including Actinobacteria, Firmicutes, Verrucomicrobia, Cyanobacteria, Gemmatimonadetes and Alphaproteobacteria, between the land use types forest and grassland were observed. At the genus level, significant differences were also recorded for the dominant genera Phenylobacter, Bacillus, Kribbella, Streptomyces, Agromyces, and Defluviicoccus. In addition, soil bacterial community structure showed significant differences between beech and spruce forest soils. The relative abundances of bacterial groups at different taxonomic levels correlated with soil pH, but little or no relationships to management type and other soil properties were found. Conclusions/Significance: Soil bacterial community composition and diversity of the six analyzed management types showed significant differences between the land use types grassland and forest. Furthermore, bacterial community structure was largely driven by tree species and soil pH.
Journal of Plant Biochemistry and Biotechnology, 2008
Roccella montagnei Bél emend Awas and R. belangeriana Awas were keyed out as distinct species bas... more Roccella montagnei Bél emend Awas and R. belangeriana Awas were keyed out as distinct species based on their reproductive strategies. These two species are similar in their morphology and secondary chemistry. The phylogenetic relationship analysis using maximum parsimony method based on ITS sequences of the nuclear ribosomal DNA clustered these two species in a single clade with a bootstrap value of 100 indicating that these two species are the same.
Phytobiomes Journal, 2020
Accelerating the pace of microbiome science to enhance crop productivity and agroecosystem health... more Accelerating the pace of microbiome science to enhance crop productivity and agroecosystem health will require transdisciplinary studies, comparisons among datasets, and synthetic analyses of research from diverse crop management contexts. However, despite the widespread availability of crop-associated microbiome data, variation in field sampling and laboratory processing methodologies, as well as metadata collection and reporting, significantly constrains the potential for integrative and comparative analyses. Here we discuss the need for agriculture-specific metadata standards for microbiome research, and propose a list of “required” and “desirable” metadata categories and ontologies essential to be included in a future minimum information metadata standards checklist for describing agricultural microbiome studies. We begin by briefly reviewing existing metadata standards relevant to agricultural microbiome research, and describe ongoing efforts to enhance the potential for integr...
medRxiv, 2020
SARS-CoV-2 genomic variants impacts the overall sensitivity of COVID-19 diagnosis, leading to fal... more SARS-CoV-2 genomic variants impacts the overall sensitivity of COVID-19 diagnosis, leading to false-negative diagnosis and the continued spread of the virus. Objective: To evaluate how nucleotide variability in target primer binding sites of the SARS-CoV-2 genomes may impact diagnosis using different recommended primer/probe sets, as well as to suggest the best primer/probes for diagnosis. Design: We downloaded 105,118 public SARS-CoV-2 genomes from GISAID (Sept, 25th, 2020), removed genomes of apparent worst quality (genome length <29kb and/or >5% ambiguous bases) and missing metadata, and performed an analysis of complementarity for the 13 most used diagnostic primers/probe sets for RT-PCR detection. We calculated the N rate and % of genome recovery, with all primer/probe-sets considering viral origin and clade. Results: Our findings indicate that currently, the Paris_nCoV-IP2, -IP4 and WHO|E_Sarbeco primer/probe sets for COVID-19, to perform the best diagnostically worldwid...
Environmental Research
In urban ecosystems, microbes play a key role in maintaining major ecological functions that dire... more In urban ecosystems, microbes play a key role in maintaining major ecological functions that directly support human health and city life. However, the knowledge about the species composition and functions involved in urban environments is still limited, which is largely due to the lack of reference genomes in metagenomic studies comprises more than half of unclassified reads. Here we uncovered 732 novel bacterial species from 4728 samples collected from various common surface with the matching materials in the mass transit system across 60 cities by the MetaSUB Consortium. The number of novel species is significantly and positively correlated with the city population, and more novel species can be identified in the skin-associated samples. The in-depth analysis of the new gene catalog showed that the functional terms have a significant geographical distinguishability. Moreover, we revealed that more biosynthetic gene clusters (BGCs) can be found in novel species. The co-occurrence relationship between BGCs and genera and the geographical specificity of BGCs can also provide us more information for the synthesis pathways of natural products. Expanded the known urban microbiome diversity and suggested additional mechanisms for taxonomic and functional characterization of the urban microbiome. Considering the great impact of urban microbiomes on human life, our study can also facilitate the microbial interaction analysis between human and urban environment.
Frontiers in Microbiology
The importance of natural ecosystem processes is often overlooked in urban areas. Green Infrastru... more The importance of natural ecosystem processes is often overlooked in urban areas. Green Infrastructure (GI) features have been constructed in urban areas as elements to capture and treat excess urban runoff while providing a range of ancillary benefits, e.g., ecosystem processes mediated by microorganisms that improve air and water quality, in addition to the associations with plant and tree rhizospheres. The objective of this study was to characterize the bacterial community and diversity in engineered soils (Technosols) of five types of GI in New York City; vegetated swales, right of way bioswales (ROWB; including street-side infiltration systems and enhanced tree pits), and an urban forest. The design of ROWB GI features directly connects with the road to manage street runoff, which can increase the Technosol saturation and exposure to urban contaminants washed from the street and carried into the GI feature. This GI design specifically accommodates dramatic pulses of water that influence the bacterial community composition and diversity through the selective pressure of contaminants or by disturbance. The ROWB had the highest biodiversity, but no significant correlation with levels of soil organic matter and microbially-mediated biogeochemical functions. Another important biogeochemical parameter for soil bacterial communities is pH, which influenced the bacterial community composition, consistent with studies in non-urban soils. Bacterial community composition in GI features showed signs of anthropogenic disturbance, including exposure to animal feces and chemical contaminants, such as petroleum products. Results suggest the overall design and management of GI features with a channeled connection with street runoff, such as ROWB, have a comprehensive effect on soil parameters (particularly organic matter) and the bacterial community. One key consideration for future assessments of GI microbial community would be to determine the source of organic matter and elucidate the relationship between vegetation, Technosol, and bacteria in the designed GI features.
Ecological Engineering
Abstract Green infrastructure (GI) refers to environmental design features or engineered systems ... more Abstract Green infrastructure (GI) refers to environmental design features or engineered systems in an interconnected natural and urban space that provide multifunctional ecosystem services. However, there is great uncertainty and variation in the function of different GI features related to carbon and nitrogen cycling processes that are essential for sustained plant growth and water quality. The objective of this study was to evaluate the effects of GI designs (enhanced tree pits (ETP), street-side infiltration swales (SSIS), and vegetation swales (VS)), including surface area, and watershed area ratio (WAR), on the biogeochemical processes and properties (organic carbon (Corg), total nitrogen (Ntotal), pH, salts, total petroleum hydrocarbons (TPH), Pb, Zn, moisture content (MC), texture, microbial biomass carbon and nitrogen content, potential net nitrogen mineralization and nitrification, microbial respiration, and denitrification potential) of GI engineered soils. Results showed that GI sites did not have significant levels of contamination with metals or TPH and that GI with larger surface area had significantly lower TPH, Pb, and Zn. Microbial biomass and activity were positively correlated with Corg, Ntotal, pH, MC, TPH, and WAR. Denitrification potential was higher in the ETP and SSIS (3 mg N kg−1 h−1) compared to the VS (0.5 mg N kg−1 h−1). Microbial biomass carbon and nitrogen contents were significantly higher in ETP followed by SSIS then VS. These results suggest that relatively young (
Nature, Nov 1, 2017
Our growing awareness of the microbial world's importance and diversity contrasts starkly wit... more Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete ...
Frontiers in microbiology, 2015
Algal biofuels and valuable co-products are being produced in both open and closed cultivation sy... more Algal biofuels and valuable co-products are being produced in both open and closed cultivation systems. Growing algae in open pond systems may be a more economical alternative, but this approach allows environmental microorganisms to colonize the pond and potentially infect or outcompete the algal "crop." In this study, we monitored the microbial community of an outdoor, open raceway pond inoculated with a high lipid-producing alkaliphilic alga, Chlorella vulgaris BA050. The strain C. vulgaris BA050 was previously isolated from Soap Lake, Washington, a system characterized by a high pH (∼9.8). An outdoor raceway pond (200 L) was inoculated with C. vulgaris and monitored for 10 days and then the culture was transferred to a 2,000 L raceway pond and cultivated for an additional 6 days. Community DNA samples were collected over the 16-day period in conjunction with water chemistry analyses and cell counts. Universal primers for the SSU rRNA gene sequences for Eukarya, Bacteri...
The large-scale production of algae for biofuel synthesis has potential to help alleviate current... more The large-scale production of algae for biofuel synthesis has potential to help alleviate current energy problems. The vast majority of research on algal biofuel production has been conducted on single species isolates in closed systems that are costly to maintain. In contrast, open ponds are estimated to be an order of magnitude less expensive to run than closed systems, but overall productivity is typically lower than in closed systems. Use of extremophile alkaliphilic algae may help overcome some of the constraints associated with large-scale biofuel production. Open alkaline systems are not easily colonized by other species because the restrictive environment limits diversity, which allows for better selective control and management of a desired biofuel producing algal species. Characterizing and understanding the microbial ecology and dynamics of an alkaphilic open pond system provides significant insight into control and optimization for biomass production and resource allocat...
The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortiu... more The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is a novel, interdisciplinary initiative comprised of experts across many fields, including genomics, data analysis, engineering, public health, and architecture. The ultimate goal of the MetaSUB Consortium is to improve city utilization and planning through the detection, measurement, and design of metagenomics within urban environments. Although continual measures occur for temperature, air pressure, weather, and human activity, including longitudinal, cross-kingdom ecosystem dynamics can alter and improve the design of cities. The MetaSUB Consortium is aiding these efforts by developing and testing metagenomic methods and standards, including optimized methods for sample collection, DNA/ RNA isolation, taxa characterization, and data visualization. The data produced by the consortium can aid city planners, public health officials, and architectural designers. In addition, the study will continue to lead to the discovery of new species, global maps of antimicrobial resistance (AMR) markers, and novel biosynthetic gene clusters (BGCs). Finally, we note that engineered metagenomic ecosystems can help enable more responsive, safer, and quantified cities.
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Papers by Bharath Prithiviraj