New papers on Microbiology of the Built Environment, November 19, 2016

Microbes in the city

Microbial Community Patterns Associated with Automated Teller Machine Keypads in New York City – Holly M. Bik – mSphere (OA). News coverage at EurekAlert, ScienceDaily, and NYMagazine.

Relative abundances of bacterial/archaeal groups in 16S rRNA data set.
Relative abundances of bacterial/archaeal groups in 16S rRNA data set.

(…) Here we carried out a baseline study of automated teller machine (ATM) keypads in New York City (NYC). Our goal was to describe the biodiversity and biogeography of both prokaryotic and eukaryotic microbes in an urban setting while assessing the potential source of microbial assemblages on ATM keypads. Microbial swab samples were collected from three boroughs (Manhattan, Queens, and Brooklyn) during June and July 2014, followed by generation of Illumina MiSeq datasets for bacterial (16S rRNA) and eukaryotic (18S rRNA) marker genes. (…)  Our results suggest that ATM keypads amalgamate microbial assemblages from different sources, including the human microbiome, eukaryotic food species, and potentially novel extremophilic taxa adapted to air or surfaces in the built environment. DNA obtained from ATM keypads may thus provide a record of both human behavior and environmental sources of microbes.

ReviewAirborne particulate matter pollution in urban China: A chemical mixture perspective from sources to impacts – Ling Jin – National Science Review (OA)

 Scope of the review covering key scientific issues surrounding PM mixtures
Scope of the review covering key scientific issues surrounding PM mixtures

Rapid urban and industrial development has resulted in severe air pollution problems in developing countries such as China, especially in highly industrialized and populous urban clusters. Dissecting the complex mixtures of airborne particulate matter (PM) has been a key scientific focus in the last two decades, leading to significant advances in understanding physicochemical compositions for comprehensive source apportionment. (…) The microbiome, an integral dimension of the PM mixture, is an unexplored frontier in terms of identities and functions in atmospheric processes and human health. In this review, we identify the major gaps in addressing these issues, and recommend a holistic framework for evaluating the sources, processes, and impacts of atmospheric PM pollution. (…)

Review: Monitoring of airborne biological particles in outdoor atmosphere. Part 2: Metagenomics applied to urban environments – Andrés Núñez – International Microbiology (OA)

 Volumetric Hirst-type spore trap for fungi and pollen collection employed in aerobiological studies
Volumetric Hirst-type spore trap for fungi and pollen collection
employed in aerobiological studies

The air we breathe contains microscopic biological particles such as viruses, bacteria, fungi and pollen, some of them with relevant clinic importance.(…) Currently, metagenomics and next-generation sequencing (NGS) may resolve this shortage of information and have been recently applied to metropolitan areas. Although the procedures and methods are not totally standardized yet, the first studies from urban air samples confirm the previous results obtained by culture and microscopy regarding abundance and variation of these biological particles. (…) Here, we review the procedures, results and perspectives of the recent works that apply NGS to study the main biological particles present in the air of urban environments.

Thesis: The Phyllosphere of Phoenix’s Urban Forest: Insights from a Publicly-Funded Microbial Environment – Benjamin C. MacNeille – Arizona State University (no access for me)

Sissoo tree, Moon Valley Nurseries, Arizona
Sissoo tree, Moon Valley Nurseries, Arizona

(…)  phyllosphere dynamics are not well understood in urban environments, and this environment has never been studied in the City of Phoenix, which maintains roughly 92,000 city trees. The phyllosphere will grow if the City of Phoenix is able to achieve its goal of 25% canopy coverage by 2030, but this begs the question: How and where should the urban canopy expand? I addressed this question from a phyllosphere perspective by sampling city trees of two species, Ulmus parvifolia (Chinese Elm) and Dalbergia sissoo (Indian Rosewood) in parks and on roadsides. (…) Roadside trees had fewer bacteria (10 OTUs) that were significantly more abundant when compared to park trees, but several have been linked to the remediation of petroleum combustion by-products. These findings, that were not available prior to this study, may inform the City of Phoenix as it is designing its future urban forests.

Microbes in the hospital

Molecular epidemiology of Staphylococcus epidermidis in neonatal intensive care units –  Hiie Soeorg – APMIS ($6 to rent, $38 to own).

Baby at a Neonatal Intensive Care Unit. Source: Wikipedia
Baby at a Neonatal Intensive Care Unit. Source: Wikipedia

Late-onset sepsis (LOS) in preterm neonates is increasingly reported to be associated with gut-colonizing Staphylococcus epidermidis. We aimed to describe the molecular epidemiology of S. epidermidis colonizing the gut of neonates hospitalized in two neonatal intensive care units. S. epidermidis from rectal swabs were typed by multilocus variable-number tandem-repeat analysis (MLVA), randomly chosen isolates of predominant MLVA types additionally by multilocus sequence typing. (…)  Overall, the prevalence of mecA, icaA, IS256, and ACME was 91.4%, 28.1%, 64%, and 77%, respectively. Of the mecA-positive isolates (n = 127), 43.9% carried SCCmec type IV. Of eight episodes of LOS, four were caused by ST2 and two by ST5. Preventing gut colonization with nosocomial epidemic S. epidermidis in hospitalized neonates could contribute to the prevention of LOS.

Microbes in drinking water

Exposure to Contaminated Drinking Water and Health Disparities in North Carolina – Frank Stillo – American Journal of Public Health ($22).

Water well drilling rig, West Virginia, USA. Source: Wikipedia.
Water well drilling rig, West Virginia, USA. Source: Wikipedia.

Objectives: To examine drinking water quality in majority Black periurban neighborhoods in Wake County, North Carolina, that are excluded from nearby municipal water service and to estimate the health benefits of extending water service. We tested 3 samples collected July through December 2014 in 57 private wells for microbial contaminants. (…) An estimated 22% of 114 annual emergency department visits for acute gastrointestinal illness could be prevented by extending community water service. Predominantly Black periurban neighborhoods excluded from municipal water service have poorer quality drinking water than do adjacent neighborhoods with municipal services. These disparities increase the risk of emergency department visits for acute gastrointestinal illness.

Microbes and recreational water

The Microbiota of Recreational Freshwaters and the Implications for Environmental and Public Health – Chang Soo Lee – Frontiers in Microbiology (OA)

Locations of the study sites. (A) East Fork Lake, (B) Delaware Lake, and (C) Madison Lake in Ohio.
Locations of the study sites. (A) East Fork Lake, (B) Delaware Lake, and (C) Madison Lake in Ohio.

The microbial communities in recreational freshwaters play important roles in both environmental and public health perspectives. In this study, the bacterial community structure and its associations with freshwater environments were investigated by analyzing the summertime microbiomes of three beach waters in Ohio (East Fork, Delaware, and Madison lakes) together with environmental and microbial water quality parameters. From the swimming season of 2009, 21 water samples were collected from the three freshwater beaches. (…) unique distributions of the genera Enterococcus, Staphylococcus, Streptococcus, Bacteroides, Clostridium, Finegoldia, Burkholderia, and Klebsiella, together with a high density of fecal indicator Escherichia coli, were markedly observed in the sample from Madison Lake on July 13, suggesting a distinctly different source of bacterial loading into the lake, possibly fecal contamination. In conclusion, deep sequencing-based microbial community analysis can provide detailed profiles of bacterial communities and information on potential public health risks at freshwater beaches.

Microbes, pesticides, and pollution

Human Oral Buccal Microbiomes Are Associated with Farmworker Status And Azinphos-methyl Agricultural Pesticide Exposure – Ian B. Stanaway – Applied and Environmental Microbiology ($25 for 1 day access). News coverage by UPI and ASM.

Buccal swab sampling. Source: WiseGeek.com
Buccal swab sampling. Source: WiseGeek.com

In a longitudinal agricultural community cohort sampling of 65 farmworker and 52 non-farmworker adults, we investigated agricultural pesticide exposure associated changes in the oral buccal microbiota. We found a seasonally persistent association between the detected blood concentration of the insecticide Azinphos-methyl and the taxonomic composition of the buccal swab oral microbiome. (…)  The spring/summer ‘exposed’ microbiome cluster with significantly less bacterial diversity was enriched for farmworkers and contained 27 of the 30 individuals who also had Azinphos-methyl agricultural pesticide exposure detected in the blood.

Biostimulation and microbial community profiling reveal insights on RDX transformation in groundwater – Dongping Wang – Microbiology Open (OA)

Location of TA-16 and other Laboratory technical areas at Los Alamos National Laboratory
Location of TA-16 and other Laboratory technical areas at Los Alamos National Laboratory

Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a high explosive released to the environment as a result of weapons manufacturing and testing worldwide. At Los Alamos National Laboratory, the Technical Area (TA) 16 260 Outfall discharged high-explosives-bearing water from a high-explosives-machining facility to Cañon de Valle during 1951 through 1996. These discharges served as a primary source of high-explosives and inorganic-element contamination in the area. (…)  In this study, we examined the microbial diversity in a monitoring well completed in perched-intermediate groundwater contaminated by RDX, and examined the response of the microbial population to biostimulation under varying geochemical conditions. (…) The results suggest that strict anaerobic conditions are needed to stimulate RDX degradation under the TA-16 site-specific conditions.

Screening and In Situ Monitoring of Potential Petroleum Hydrocarbon Degraders in Contaminated Surface Water – Bulent Icgen – Clean Soil Air Water ($6 to rent, $38 to own).

Bioremediation. Source: http://bioremediationremedies.tumblr.com/
Bioremediation. Source: http://bioremediationremedies.tumblr.com/

Incomplete combustion of fossil fuels and other anthropogenic activities result in contamination of surface water by petroleum hydrocarbons. These pollutants can have severe effects on aquatic life and human health. In petroleum bioremediation, oil degrading microorganisms are utilized to remove petroleum hydrocarbons from polluted water. However, monitoring and identifying microorganisms capable of degrading petroleum hydrocarbons is very challenging. In the current study, bacteria isolated from a river alongside a petroleum refinery were assessed for their petroleum hydrocarbon degradation abilities. (…) The results revealed that species of Acinetobacter successfully populate the polluted surface water and have high potential for petroleum bioremediation.

Microbes in space

A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space – Luis Zea – PLOS ONE (OA). News coverage at AL.com.

Astronaut Mike Hopkins operating one of the GAPs containing the AES-1 experiment onboard ISS (Photo credit: NASA).
Astronaut Mike Hopkins operating one of the GAPs containing the AES-1 experiment onboard ISS (Photo credit: NASA, source: PLOS ONE).

Bacteria behave differently in space, as indicated by reports of reduced lag phase, higher final cell counts, enhanced biofilm formation, increased virulence, and reduced susceptibility to antibiotics. These phenomena are theorized, at least in part, to result from reduced mass transport in the local extracellular environment, where movement of molecules consumed and excreted by the cell is limited to diffusion in the absence of gravity-dependent convection. However, to date neither empirical nor computational approaches have been able to provide sufficient evidence to confirm this explanation. Molecular genetic analysis findings, conducted as part of a recent spaceflight investigation, support the proposed model. This investigation indicated an overexpression of genes associated with starvation, the search for alternative energy sources, increased metabolism, enhanced acetate production, and other systematic responses to acidity—all of which can be associated with reduced extracellular mass transport.

 

Leave a Reply

Elisabeth Bik

After receiving my PhD at Utrecht University in The Netherlands, I worked at the Dutch National Institute for Health and the St. Antonius Hospital in Nieuwegein. In 2001, I joined the Department of Microbiology and Immunology at Stanford, where I have worked on the characterization of the microbiome of human oral, gastric, and intestinal samples, as well as samples from marine mammals. Since November 2016, I am the new Science Editor at uBiome, a microbiome genomics company enabling citizen science. But you might also find me working on the detection of science misconduct, at my blog Microbiome Digest , an almost daily compilation of scientific papers in the rapidly growing microbiome field, on Twitter at @MicrobiomDigest.