Jordan Peccia

Yale University | YU · Department of Chemical & Environmental Engineering

This is an account that should be heard of an important struggle: the struggle of a large group of experts who came together at the beginning of the Covid-19 pandemic to warn the world about the risk of airborne transmission and the consequences of ignoring it. We alerted the World Health Organization (WHO) about the potential significance of the a...

Effectively monitoring the spread of SARS-CoV-2 mutants is essential to efforts to counter the ongoing pandemic. Predicting lineage abundance from wastewater, however, is technically challenging. We show that by sequencing SARS-CoV-2 RNA in wastewater and applying algorithms initially used for transcriptome quantification, we can estimate lineage a...

Monitoring the progression of SARS-CoV-2 outbreaks requires accurate estimation of the unobservable fraction of the population infected over time in addition to the observed numbers of COVID-19 cases, as the latter present a distorted view of the pandemic due to changes in test frequency and coverage over time. The objective of this report is to de...

Exhaled respiratory droplets and aerosols can carry infectious viruses and are an important mode of transmission for COVID-19. Recent studies have been successful in detecting airborne SARS-CoV-2 RNA in indoor settings using active sampling methods. The cost, size, and maintenance of these samplers, however, limit their long-term monitoring ability...

We assessed the relationship between municipality COVID-19 case rates and SARS-CoV-2 concentrations in the primary sludge of corresponding wastewater treatment facilities. Over 1,700 daily primary sludge samples were collected from six wastewater treatment facilities with catchments serving 18 cities and towns in the State of Connecticut, USA. Samp...

Effectively monitoring the spread of SARS-CoV-2 variants is essential to efforts to counter the ongoing pandemic. Wastewater monitoring of SARS-CoV-2 RNA has proven an effective and efficient technique to approximate COVID-19 case rates in the population. Predicting variant abundances from wastewater, however, is technically challenging. Here we sh...

Synechococcus elongatus UTEX 2973 has one of the fastest measured doubling time of cyanobacteria making it an important candidate for metabolic engineering. Traditional genetic engineering methods, which rely on homologous recombination, however, are inefficient, labor-intensive, and time-consuming due to the oligoploidy or polyploidy nature of cya...

Intensive building energy efficiency improvements can reduce emissions from energy use, improving outdoor air quality and human health, but may also affect ventilation and indoor air quality. This study examines the effects of highly ambitious, yet feasible, building energy efficiency upgrades in the United States. Our energy efficiency scenarios,...

Monitoring the progression of SARS-CoV-2 outbreaks requires accurate estimates of infection rates. Estimation methods based on observed cases are biased due to changes in testing over time. Here we report an approach based upon scaling daily concentrations of SARS-CoV-2 RNA in wastewater to infections that produces representative estimates due to t...

We assessed the relationship between municipality COVID-19 case rates and SARS-CoV-2 concentrations in the primary sludge of corresponding wastewater treatment facilities. Over 1,000 daily primary sludge samples were collected from six wastewater treatment facilities with catchments serving 18 cities and towns in the State of Connecticut, USA. Samp...

Dampness or water damage in buildings and human exposure to the resultant mold growth is an ever-present public health concern. This study provides quantitative evidence that the airborne fungal ecology of homes with known mold growth ("moldy") differs from the normal airborne fungal ecology of homes with no history of dampness, water damage, or vi...

This commentary is intended to provide a research roadmap for utilizing recent chemical and molecular-biological technological advances for addressing dampness and mold in buildings. The perspective is unique in that both the mold industry practitioners and academic researchers drive the questions. Research needs were derived from a 2018 internatio...

Background Schools represent high occupancy environments and well-documented high-risk locations for the transmission of respiratory viruses. The goal of this study was to report on the area density, occurrence, and type of respiratory viruses on desks in primary school classrooms. Methods Quantitative reverse transcription polymerase chain reacti...

The following study explores how measured ventilation rates influence bacterial and fungal community structure and concentrations in the indoor air of homes ventilated by leakage-based airflow. The dynamics of bacterial and fungal communities were quantified from homes within the Cherokee Nation in North Eastern, Oklahoma, USA, where seasonal air e...

Dampness and fungal (mold) growth in buildings is a persistent environmental health problem. This study sought to determine the extent to which fungi grown on damp materials are distributed throughout a single family home. Samples were collected from fungi growing directly on building materials in the basement (direct mold), and, as a proxy for ind...

Phthalate esters are present at elevated concentrations in floor dust, and resuspension of dust represents a major source for human exposure to chemicals. Biodegradation of phthalates occurs in aquatic systems and soils but has not been demonstrated in house dust. The goal of this study was to quantify indoor phthalate ester degradation through bot...

Background: The goal of this study was to test for associations between adenosine triphosphate (ATP) content and microbial concentrations on desk surfaces in school classrooms. Methods: ATP bioluminescence and quantitative polymerase chain reaction (qPCR) techniques were employed to measure total bacterial, fungal, and human cell concentrations...

Aims The goal of this study was to quantify the indoor microbiome dynamics of bacterial and fungal communities on school desk surfaces during a cleaning intervention. Methods and Results Quantitative PCR and DNA sequenced‐based approaches were employed to describe microbial community dynamics on ten desk surfaces, spread across three schools, loca...

Waste-streams containing nitrogen (commonly as NH3/NH4⁺) have been promoted as a means to lower the energy burden and improve the overall sustainability of microalgae-based fuel and chemical production. However, beyond a concentration threshold, ammonia (NH3) is toxic to many microalgae. This study investigated the ammonia tolerances of oleaginous...

Under sustained, elevated building moisture conditions, bacterial and fungal growth occurs. The goal of this study was to characterize microbial growth in floor dust at variable equilibrium relative humidity (ERH) levels. Floor dust from one home was embedded in coupons cut from a worn medium pile nylon carpet and incubated at 50, 80, 85, 90, 95, a...

Background: Allergic and nonallergic asthma severity in children can be affected by microbial exposures. Objective: We sought to examine associations between exposures to household microbes and childhood asthma severity stratified by atopic status. Methods: Participants (n = 196) were selected from a cohort of asthmatic children in Connecticut...

Variations in home characteristics, such as moisture and occupancy, affect indoor microbial ecology as well as human exposure to microorganisms. Our objective was to determine how indoor bacterial and fungal community structure and diversity are associated with the broader home environment and its occupants. Next-generation DNA sequencing was used...

This study quantifies the influence of ventilation and indoor emissions on concentrations and particle sizes of airborne indoor allergenic fungal taxa and further examines geographical variability, each of which may affect personal exposures to allergenic fungi. Quantitative PCR and multiplexed DNA sequencing were employed to count and identify all...

Microbial contamination of growth reactors is a major concern for microalgal biofuel production. In this study, the oleaginous, CO2-tolerant microalga Scenedesmus dimorphus was combined with a wastewater-derived microbial community and grown in replicated sequencing batch photobioreactors. The reactors were sparged with either ambient air or 20% v/...

Aerodynamic diameter is an important determinant of the physical processes that act upon airborne fungi. Processes include gravitational settling, respiratory deposition, penetration into buildings, resuspension from surfaces into air, and long-range transport. This study combined next-generation DNA sequencing (NGS) with quantitative PCR (qPCR) to...

Unlabelled: Baseline information on size-resolved bacterial, fungal, and particulate matter (PM) indoor air concentrations and emission rates is presented for six school classrooms sampled in four countries. Human occupancy resulted in significantly elevated airborne bacterial (81 times on average), fungal (15 times), and PM mass (nine times) conc...

Resuspension of particles indoors increases the risk of consequent exposure through inhalation and non-dietary ingestion. Studies have been conducted to characterize indoor particle resuspension but results do not always agree, and there are still many open questions in this field. This paper reviews the recent research of indoor resuspension and s...

This study utilized pyrosequencing-based phylogenetic library results to assess bacterial communities on the hands of women in Tanzania and compared these communities with bacteria assemblages on the hands of U.S. women. Bacterial population profiles and phylogenetically-based ordinate analysis demonstrated that the bacterial communities on hands w...

Improvements in DNA sequencing technology provide unprecedented opportunities to explore fungal diversity, but also present challenges in data analysis due to the large number of sequences generated. Here, we describe an open source software program "FHiTINGS" that utilizes the output of a BLASTn (blastall) search to rapidly identify, classify, and...

We examined fungal communities associated with the PM10 mass of Rehovot, Israel outdoor air samples collected in the spring and fall seasons. Fungal communities were described by 454 pyrosequencing of the internal transcribed spacer (ITS) region of the fungal ribosomal RNA encoding gene. To allow for a more quantitative comparison of fungal exposur...

This study investigated analytical parameters that are inherently relevant to identifying and quantifying fungal communities based on PCR amplicons. Specifically, we evaluated the accuracy of the BLASTn-based identification for internal transcribed spacer (ITS) sequences generated from pure cultures, and quantified the reproducibility of relative a...

Unlabelled: Dampness and visible mold in homes are associated with asthma development, but causal mechanisms remain unclear. The goal of this research was to explore associations among measured dampness, fungal exposure, and childhood asthma development without the bias of culture-based microbial analysis. In the low-income, Latino CHAMACOS birth...

Elevated sewage sludge concentrations of polybrominated diphenyl ethers (PBDEs) are due to their broad utilization in textiles and polymers, their resistance to biological degradation, and also their hydrophobic nature-which drives partitioning into wastewater solids. This study estimated the total U.S. emissions of PBDE due to sewage sludge land a...

Two freshwater and two marine microalgae species were grown under nitrogen replete and deplete conditions evaluating the impact on total biomass yield and biomolecular fractions (i.e. starch, protein, and lipid). A life cycle assessment was performed to evaluate varying species/growth conditions considering each biomass fraction and final product s...

Exposures to particulate matter (PM) re-suspended by traffic from paved roads are ubiquitous, but little is known about the variability in composition of paved road dust (PRD). This knowledge gap hinders estimates of exposure to PM components near roadways. Respirable fractions of PRD collected from multiple U.S. regions and site types were analyze...

Commercial hardwood biochars ranging in N2 specific surface area of 0.1-427 m(2)·g(-1) were added to an agricultural soil at 0, 1, or 2% levels to determine whether they would predictably reduce the pore water concentration of sulfamethazine (SMT). The soil and biochar-soil mixtures were preweathered under mild (2 d, 20 °C) or more severe (28 d, 40...

Increased susceptibility to allergies has been documented in the Western world in recent decades. However, a comprehensive understanding of its causes is not yet available. It is therefore essential to understand trends and mechanisms of allergy-inducing agents, such as fungal conidia. In this study we investigated the hypothesis that environmental...

Favorable growth characteristics continue to generate interest in using triacylglycerides (TAGs) produced from microalgae for biodiesel feedstocks. In this opinion article, we suggest that due to the energy consumption associated with the production of external nitrogen fertilizers, the manner in which nitrogen is supplied to microalgae biorefineri...

Human adenovirus diversity in sewage sludge was assessed by Ion Torrent sequencing and annotation of partial adenovirus hexon genes. The most abundant species identified were HAdV-C (average 78%) and -B (average 20%), which are associated with respiratory infections. These findings reinforce the necessity to consider aerosol exposure to sewage-deri...

The large diversity of viruses that exist in human populations are potentially excreted into sewage collection systems and concentrated in sewage sludge. In the US, the primary fate of processed sewage sludge (class B biosolids) is application to agricultural land as a soil amendment. To characterize and understand infectious risks associated with...

The objective of this work was to evaluate methanogenesis in relation to the changes in performance and microbial diversity of cellulose-fed microbial fuel cells (MFCs). Replicate MFCs were inoculated with a ruminal microbial consortium and operated under 20 (R(20Ω)) or 100Ω (R(100Ω)) external resistances. During the first week of operation, 0.31 a...

Background The lack of sequenced genomes for oleaginous microalgae limits our understanding of the mechanisms these organisms utilize to become enriched in triglycerides. Here we report the de novo transcriptome assembly and quantitative gene expression analysis of the oleaginous microalga Neochloris oleoabundans, with a focus on the complex intera...

The inactivation of fecal coliforms in anaerobic batch reactors has been investigated at the thermophilic temperatures of 50, 55 and 60 °C. Throughout inactivation experiments at each temperature, individual colonies were isolated and identified by 16S rDNA gene sequencing to illustrate how the diversity of fecal coliforms is affected by thermophil...

Background The k-mer hash length is a key factor affecting the output of de novo transcriptome assembly packages using de Bruijn graph algorithms. Assemblies constructed with varying single k-mer choices might result in the loss of unique contiguous sequences (contigs) and relevant biological information. A common solution to this problem is the cl...

Many fungi may cause allergic reactions and increase asthma symptoms prevalence and severity. One susceptible, vulnerable population subgroup of increasing size in industrialized countries and of public health concern who spends the majority of their time at home is older adults. Older adults diagnosed with chronic obstructive pulmonary disease (CO...

Microbial fuel cells (MFCs) are often inoculated from a single wastewater source. The extent that the inoculum affects community development or power production is unknown. The stable anodic microbial communities in MFCs were examined using three inocula: a wastewater treatment plant sample known to produce consistent power densities, a second wast...

Exposure to specific airborne bacteria indoors is linked to infectious and noninfectious adverse health outcomes. However, the sources and origins of bacteria suspended in indoor air are not well understood. This study presents evidence for elevated concentrations of indoor airborne bacteria due to human occupancy, and investigates the sources of t...

HVAC filtration efficiency. Filtration efficiency was estimated at the HVAC filter—through which indoor return air and outdoor air passes—by placing optical particle counters (size ranges 0.3–0.5 µm, 0.5–1 µm, 1–2.5 µm, 2.5–5 µm, 5–10 µm and >10 µm) before and after the filter. Submicron size particles are inefficiently removed whereas particles bi...

Abundance of dominant (A) and rare (B) bacterial phyla from indoor air (Indoor10), ventilation duct supply air (Duct10), HVAC filter dust (HVAC10), and floor dust (Floor10/37). The dominant phyla represent 93%–98.5% of the sequences recovered. The Cyanobacteria are dominated by chloroplast sequences from plant (Streptophyta) material. The number af...

Sequencing summary table describing the sample type and listing corresponding sample multiplex identifiers (MIDs). MIDs were contained on the forward primer. The key adaptor on both primers was TCAG. (DOC)

Rarefaction curves for samples of indoor air, ventilation duct supply air, HVAC filter dust, and floor dust. Curves are based on samples that contained more than 300 sequences to avoid diversity estimate biases. The inset shows the same plot for one floor dust and one indoor air sample, each containing more than 1350 sequences. Error bars represent...

Fungi are ubiquitous in outdoor air, and their concentration, aerodynamic diameters and taxonomic composition have potentially important implications for human health. Although exposure to fungal allergens is considered a strong risk factor for asthma prevalence and severity, limitations in tracking fungal diversity in air have thus far prevented a...

Airborne fungal spores are an important fraction of atmospheric particulate matter and are major causative agents of allergenic and infectious diseases. Predicting the variability and species of allergy-causing fungal spores requires detailed and reliable methods for identification and quantification. There are diverse methods for their detection i...

The role of human occupancy as a source of indoor biological aerosols is poorly understood. Size-resolved concentrations of total and biological particles in indoor air were quantified in a classroom under occupied and vacant conditions. Per-occupant emission rates were estimated through a mass-balance modeling approach, and the microbial diversity...

Adsorption of ionizable compounds by black carbon is poorly characterized. Adsorption of the veterinary antibiotic sulfamethazine (SMT; a.k.a., sulfadimidine; pK(a1) = 2.28, pK(a2) = 7.42) on a charcoal was determined as a function of concentration, pH, inorganic ions, and organic ions and molecules. SMT displayed unconventional adsorption behavior...

Airborne fungal spores are an important fraction of atmospheric particulate matter and are major causative agents of allergenic and infectious diseases. Predicting the variability and species of allergy-causing fungal spores requires detailed and reliable methods for identification and quantification. There are diverse methods for their detection i...

The present study compared the airborne fungi collection performance of a two-stage cyclone sampler (active method) to the performance of the Personal Aeroallergen Sampler (passive method) using quantitative polymerase chain reaction (qPCR) assays. Indoor air concentrations of the common fungal species Alternaria alternata, Cladosporium cladosporio...

Abstract In the present study, we modified an existing surface wipe sampling method for lead and other heavy metals to create a protocol to collect fungi in floor dust followed by real-time quantitative PCR (qPCR)-based detection. We desired minimal inconvenience for participants in residential indoor environmental quality and health studies. Accur...

Common indoor and outdoor environmental fungi such as Aspergillus fumigatus produce asexual spores containing a collection of proteins that can bind IgE antibodies and trigger allergic reactions. We characterized the impact of sporulation temperature on the IgE-binding capacity (allergenicity) of A. fumigatus and explored the links between variable...

The potential for anaerobic digester energy production must be balanced with the sustainability of reusing the resultant biosolids for land application. Mesophilic, thermophilic, temperature-phased, and high temperature (60 or 70 °C) batch pre-treatment digester configurations have been systematically evaluated for net energy production and pathoge...

The science linking processed sewage sludge (biosolids) land application with human health has improved in the last ten years. The goal of this review is to develop a consensus view on the human health impacts associated with land-applying biosolids. Pre-existing risk studies are integrated with recent advances in biosolids pathogen exposure scienc...

The aim of this study was to develop and demonstrate an approach for describing the diversity of human pathogenic viruses in an environmentally isolated viral metagenome. In silico bioinformatic experiments were used to select an optimum annotation strategy for discovering human viruses in virome data sets and applied to annotate a class B biosolid...

This spreadsheet contains the list of annotated KOIs missing in single k -mer assemblies (provided as separate tabs), but present in the clustered assembly obtained by CD-HIT-EST with 1.0 sequence identity.

This spreadsheet contains the list of annotated KOIs missing in the clustered assembly obtained by CD-HIT-EST with 1.0 sequence identity, but present in the corresponding single k -mer assemblies (provided as separate tabs).

This file provides the reader with a representative workflow to generate optimized de novo transcriptome assembly.

This spreadsheet contains the list of annotated KOIs missing in the clustered assembly obtained by Oases multi- k option, but present in the corresponding single k -mer assemblies (provided as separate tabs).

Global pathway level representation of differential gene expression inN. oleoabundans. Central metabolic pathways appear within the top right boxes and pathways associated with the biosynthesis of secondary metabolites are shown bottom right. Module level close-up representation (light gray boxes) of differential regulation are presented for (A) Fa...

This spreadsheet contains the list of annotated KOIs missing in single k -mer assemblies (provided as separate tabs), but present in the clustered assembly obtained by Oases multi- k option.

Biodiesel or ethanol derived from lipids or starch produced by microalgae may overcome many of the sustainability challenges previously ascribed to petroleum-based fuels and first generation plant-based biofuels. The paucity of microalgae genome sequences, however, limits gene-based biofuel feedstock optimization studies. Here we describe the seque...

Real-time quantitative PCR (qPCR) for rapid and specific enumeration of microbial agents is finding increased use in aerosol science. The goal of this study was to determine qPCR accuracy, precision, and method detection limits (MDLs) within the context of indoor and ambient aerosol samples. Escherichia coli and Bacillus atrophaeus vegetative bacte...