The microBEnet blog

New papers on Microbiology of the Built Environment, October 21, 2016

Microbes indoors

How do we make indoor environments and healthcare settings healthier? – Jack A. Gilbert – Microbial Biotechnology (OA)

Microbial Biotechnology cover
Microbial Biotechnology cover

It is now well accepted that our modern lifestyle has certain implications for our health (Schaub et al., 2006), mainly as a result of our willingness to remove ourselves from the biological diversity of our natural environments (Roduit et al., 2016), while still being drawn inextricably to interact with it (Kellert and Wilson, 1995). Much of our interaction with the biological world is shaped by our interaction with the microbiological world. The bacteria, fungi, viruses, archaea and protists that comprise the microbiome of this planet, are also key to the development and normal functioning of our bodies. Our immune system is built to shepherd our microbial exposure, ensuring that microbial organisms that we need are kept close (but not too close), and that less-desirable organisms are expelled or killed before they can do too much damage. By moving from a life interacting with nature on a regular basis, to a life in which we isolate ourselves physically from natural microbial exposure, we may have instigated one of the great plagues of the 21st century; chronic immune disorders.

High temporal variability in airborne bacterial diversity and abundance inside single-family residences – Joanne B. Emerson – Indoor Air ($6 to rent, $38 to own)

Bacterial abundances as determined via qPCR.
Bacterial abundances as determined via qPCR.

Our homes are microbial habitats, and although the amounts and types of bacteria in indoor air have been shown to vary substantially across residences, temporal variability within homes has rarely been characterized. Here, we sought to quantify the temporal variability in the amounts and types of airborne bacteria in homes, and what factors drive this variability. We collected filter samples of indoor and outdoor air in 15 homes over one year (approximately 8 time points per home, 2 per season), and we used culture-independent DNA sequencing approaches to characterize bacterial community composition. (…) Although all homes had highly variable indoor air communities, homes with the most temporally variable communities had more stable, lower average microbial loads than homes with less variable communities.

Microbes and clothing

Forensic analysis using microbial community between skin bacteria and fabrics – So-Yeon Lee – Toxicology and Environmental Health Sciences ($39.95)

Taxonomic composition analysis at the genus level.
Taxonomic composition analysis at the genus level.

Microorganisms flourish on and in the human body and skin surfaces are the largest. The skin surface microbiota can be transferred to an object upon touch. This has forensic implications. This study explored the hypothesis that residual skin bacteria left on fabrics could be valuable for forensic analysis. A nonculture based approach was used, since it can reveal a more diverse microbiome than culture-based methods. Fabrics examined were 100% cotton, 55% cotton – 45% polyester fabric, and 100% polyester. Three volunteers firmly grasped each fabric, and the DNA of all the samples was extracted and analyzed for the 16S rRNA gene. The 454-Next generation sequencing was used to observe the microbiome community relation between the individual and the fabrics in dendrogram and PCoA graph analyses. The analyses confirmed that the touched fabrics retained microorganisms from the individual. The study reveals the potential value of the approach in forensic examinations.

Microbes and plants in the city

Diversity and hydrocarbon-degrading potential of epiphytic microbial communities on Platanus x acerifolia leaves in an urban area – Isabella Gandolfi – Environmental Pollution ($35.95)

Graphical Abstract
Graphical Abstract

(…) In this work, bacterial communities hosted by urban Platanus x acerifolia leaves were taxonomically characterized using high throughput sequencing of 16S rRNA gene, and their temporal and spatial variability was assessed by comparing samples collected from different locations in the city of Milan (Italy) and in different months. (…) Results revealed that temporal changes, which are related to seasonality, acted as a stronger driver both on Platanus phyllospheric community structure and on alkB phylotype diversity than sampling location. Biodiversity of bacterial communities decreased along the growing season, leading to a strong dominance by the genus Stenotrophomonas. (…)

Impact of urban land use on the bacterial phyllosphere of ivy (Hedera sp.) – Wenke Smets – Atmospheric Environment ($35.95)

Relative abundances of the 20 most abundant OTUs in the different plants
Relative abundances of the 20 most abundant OTUs in the different plants

(…) In this study, we investigated the effect of an urban environment on the bacterial composition of phyllosphere communities. We performed a passive biomonitoring experiment in which leaves were sampled from ivy (Hedera sp.), a common evergreen climber species, in urban and non-urban locations. Exposure to traffic-generated particulate matter was estimated using leaf biomagnetic analyses. The bacterial community composition was determined using 16S rRNA gene sequencing on the Illumina MiSeq. (…)  The results of this study indicate that an urban environment can greatly affect the local phyllosphere community composition. Although other urban-related factors cannot be ruled out, the relative abundance of most of the dominant taxa was significantly correlated with exposure to traffic-generated PM.

Meeting: Chemistry of Microbiomes in Human Environments – 11/9/16

November 9 Seminar: The Chemistry of Microbiomes in Human Environments

Hosted by the Chemical Sciences Roundtable

Wednesday, November 9
2pm – 5pm EDT

When most people think about microbes, they think disease. For well over 100 years the medical community’s mantra has been that “the only good bug is a dead bug.” But the functions of the human body rely not only on our own cells, but on the intricate interplay between complex communities of bacteria, archaea, viruses and microscopic eukaryotes living within us. Its overall health and wellbeing is a reflection of the interactions and balance among these many microbial mini-ecosystems and the host.

The ability of these communities to properly perform vital functions, and to recognize and respond to environmental changes both outside and inside the human body depends on molecular networks comprising signaling and target molecules and their biosynthetic and regulatory pathways. These molecular networks including the many chemical molecules necessary for their function remain mostly unknown.

The Human Microbiome Seminar will explore the advances, opportunities and challenges to unveil the “chemical dark matter” of the human microbiome and its role in health and disease. The seminar will be webcast online at Please register to be a webcast participant or to attend in person by clicking this link:

New Sloan Funded Project: The MoBE 2017 Research and Applications Symposium

We received the announcement today that the MoBE 2017 Symposium, chaired by Lynn Schriml at the University of Maryland School of Medicine, Institute for Genome Sciences, has been funded by the Alfred P. Sloan Foundation’s program in the Microbiology of the Built Environment. MoBE 2017 will be co-sponsored by and held at the National Academy of Sciences in Washington, D.C., October 10-12th, 2017. MoBE 2017 will be an historic event, bringing together and engaging leading academic and government researchers with community stakeholders to examine and discuss MoBE program findings pertinent to human health, safe drinking water, healthy built environments and urban design. Join us as we outline the exciting future of the MoBE research field launched by the Alfred P. Sloan Foundation.


Fungal diversity surveys not using ITS amplicons


I was at a meeting a few weeks ago where the topic of fungal diversity surveys was discussed and many people there commented on how ITS based surveys (one of the main approaches for culture independent studies of fungi) had some limitations. ITS stands for the “internal transcribed sequence” and it is a region in between two rRNA genes that is highly variable and has become used as a means to identify fungi from sequence data. One limitation of ITS is that it is so variable that one cannot align many ITS regions to each other and this in turn means that to identify an organism from its ITS sequence the best way to do it is to have a reference database that has information on which ITS sequences map to which taxa. Unfortunately such reference DBS are not available for many fungi of interest. There are also other limitations of ITS approaches. There are benefits to using ITS too, but that is not the issue here – the issue is that there are some disadvantages and thus people are looking for other approaches.

In my lab we have been looking into fungal diversity studies using approaches other than ITS surveys but were not convinced we had found all the examples out there of such work. So I posted to Twitter and Facebook asking for help and got some useful responses. I have collated them together into a Storify. See below:

If you know of any other approaches, please share.

Meeting Report: Microbiomes of the Built Environment #3 – Day 2

Report on Day 2 of the “Microbiomes of the Built Environment: From Research to Application”.  My report and Storify of tweets from Day 1 can be found here.

Session #1 “Beyond Bacteria: Viral and Fungal Ecology in Indoor Environments”

First speaker was Linsey Marr “Viruses in the Built Environment”.  Talking about their work looking at seasonality of viruses in daycare centers, detailed studies of Influenza A, and others.  Interesting finding that viruses were more concentrated outdoors than indoors, and that similar numbers of bacteria and viruses were found.  Described a vertical concentration gradient of particles, but only a 15% difference in exposure between 1 meter and 2 meters from floor. Described how airborne viruses are subject to aerosol dynamics.

Next was John Taylor “Fungi in the Built Environment”.  Started off talking about the Rachel Adams study in student housing at Berkeley where they found that dispersal and geography/season were the primary drivers of fungal populations (not occupant behavior).  Found the reverse for bacteria (affected by occupants).  Showing data that shedding is less important than resuspension of environmental microbes.  Several studies showing that indoor air looks a lot like outdoor air, with some extra bacteria from people.  Talked about practical implications of this work, for example with litigation around poorly maintained buildings.

Session #2 “Built Environment Interventions and the Microbiome: Impacts and Tradeoffs”

Mark Mendell went next with “Changing Indoor Microbial Environments to Benefit Human Health: What Do We Know?”. Started off by saying how much more complicated we have made our knowledge about microbes in the built environment.  Basically reviewed the entire literature on health effects.  He talked about which microbial/environmental factors are correlated with positive or negative health outcomes.  Too hard to summarize here!  See the Storify below for more details, I’m going to try to get his slides to post here.

Then Michael Waring “Bio-walls and Indoor Houseplants: Facts and Fictions”.  He talked about the various claims being made in the world about the cleansing effects of plants.  He then went back to the famous NASA study (that we’ve blogged about in the past) and went through the literature and basically concluded that to have any effect at all you would need more plants per square meter than could possibly fit in the space.  At a high air exchange rate you would need 500 potted plants per square meter!  Then he talked about bio-walls, which he showed could theoretically actually clean air.  However, there are a number of disadvantages of biowalls in terms of emitting other VOCs, humidity concerns, and cost.  His conclusion was that for air cleaning, we’d be better off with just increased ventilation.

Session #3 “Perspectives from Building Design and Commissioning”

Started with Kevin van den Wymelenberg “What the Design Community Needs to Incorporate Consideration of the Microbiomes of the Built Environment Into the Design of Facilities”.  Kevin is an architect and he presented that perspective to the audience.  Talked about the possible tradeoff between energy and health and the need to harness the creativity of architects.  In a similar vein he talked about the need to excite people about our results and the importance of engaging architects, engineers, and industry.

Last talk (remote) of the meeting was Robin Guenther.  My computer died *and* her talk title wasn’t in the program so I don’t know the title.  But basically she posed 4 key questions, from a healthcare architect perspective, that she thinks should be answered.  She made the point that architects make choices that influence health, but don’t always think of it that way.   She discussed the move to “tight” buildings and wondered what effect that will have on the microbiome.  Informed us that hospitals are driving much of the product development in antimicrobial materials.

Meeting Report: Microbiomes of the Built Environment – Meeting #3: Day 1

Today was the first day of the 3rd meeting in the NAS-sponsored series of “Microbiomes of the Built Environment:  From Research to Application” meetings.  This meeting was held at UC Irvine and the goal was to provide information for the NAS committee that will subsequently produce a report on the status of the field.  For anyone that missed the talks, everything was recorded and will be available online.   We’ll post here at microBEnet when that happens.  The Storify of Twitter is at the end of this post.

Session #1 “How the Built Environment Microbiome Responds to Context and Perturbations”

The first speaker was Janet Jansson “Microbial Community Response to Environmental Conditions and the ‘Microbiomes in Transition (MinT)’ Initiative”.  She described a changing world (climate change, disease, chemical/drug exposure) where the impact on microbial communities is largely unknown.  Talked about a “multi-omics” approach for studying complex and changing environments.   Gave a few examples including permafrost and mice.

Next was Sarah Evans who talked about “Soil Microbial Responses to Climate Perturbations”.  Showed examples in soil, where manipulation of drought conditions causes a major shift in the microbiome.  Microbial communities show a change in ecological strategy, via taxonomic shifts.  Most of these shifts are caused by the arrival of new taxa to the system. Talked about rain microbial communities which I hadn’t though much about, however doesn’t see a large signature of those things in soils.

Last in the intro session was Shelly Miller “The Effect of Geographic Location on the Composition and Function of Indoor Microbiomes”.  Talked about their 1200 US homes study, their detailed Boulder dorm study, and the Boulder flood study.  Summarized part of their results with “If you want to change the fungi you live with, move somewhere else, preferably far away.  If you want to change the bacteria, change who you live with”.  Showing data that only a few fungi were more present inside homes than outside, more for bacteria but still only a few % of the total.  Broad scale metadata (climate, geography) predict fungal composition but not bacterial composition.  The dorm study showed that they could predict the sex of occupants from the bacterial communities.   The flood study showed that flood homes have different bacterial/fungal communities even after remediation.

Individual talks

Rob Knight gave a special talk called “The Current Toolkit for Studying Microbiome/Built Environment Interfaces”.  Talked about the big data aspect of microbiology and the dramatic changes in the field over the last 15 years.  Started with a lot of discovery data, early microbiome studies, etc.  Talked about the need for more accurate taxonomic assignments (examples of subway anthrax study, and the high abundance of platypus samples in Finland).  Hard to summarize his talk, he summarized the entire field!  Some data I hadn’t seen before about the spatial distribution of metabolic products and their relationship to bugs.

Another special talk about Scott Jackson “Microbiome and Metagenomic Standards at NIST”.  Gave some background on NIST.   Talked about various standards they’ve developed, including a human DNA standard for clinical diagnostics and an RNA spike-in standard for microarrary experiments.  They even have a highly characterized antibody molecule as a standard.  Describing the transition to a world where microbes themselves are therapeutics (as opposed to proteins or isolated molecules).  Talked about the fact that microbiome studies have so many places for error, from collection to extraction to analysis.  They are potentially interested in developing a mock community standard, but make the point that existing ones aren’t used.

Session #2 “Expanding the Toolkit: Studying Microbial Functions”

First talk was by Jay Lennon “A trait-based approach to microbial diversity”.  Pointing out the limitation of studying lists of taxa.  Asking about the phylogenetic conservation of traits, trade-offs between traits, and different kinds of traits.  Talked about bacterial persistence and longevity.  Claimed that 90% of skin bacteria were either dead or dormant.

Other talk in this session was from Pieter Dorrestein “Chemistry of the human habitat…”.  Started off describing the significant lack of knowledge regarding indoor chemistry.  Need that groundwork before we can relate that to microbes and the whole system. Talked mostly about what I would call chemical forensics, matching chemical signatures on between people and the objects that surround them.

Session #3 “Expanding the Toolkit: Modeling the Microbiome”

First up was Jennifer Martiny “Microbial biogeography in light of traits”  As with Jay Lennon’s talk, an emphasis on traits versus lists of taxa.  Mentioned the Doolittle argument that because of HGT and rapid evolution, taxonomy might not be as informative as we hope.  However, she went on to show data that in fact there is a strong phylogenetic signal among microbes.  Gave some neat examples about microbial traits.

Next in session was Patricia Fabian (remotely) “Modeling the Built Environment, Indoor Air Quality, and Health: A Systems Science Approach”.  Talked about the challenges facing models, including multi-factorial nature, rare diseases, insufficient power in most studies, etc.  But, did show the advantages of the modeling approach… giving some interesting examples including influenza survival and impact of weatherization on low income multi family housing.

Session #4 “Analyzing What’s Known from Case Examples: Comparing and Contrasting Results”

Tiina Reponen “Microbiomes of the Built Environment: Homes”.  She started of by listing those attributes that make homes different from hospitals and the ISS (this is a comparative session).  Those were pets, influence of outdoor fungi, humidity, and building materials.  Showed the effects of various home characteristics on microbial richness, abundance, spores, etc.  Then made the point that what we really want to know is the relationship to health effects.  Talked in depth about the CCAAPS study, where they looked at homes over a long time. Also discussed the ERMI index (Environmental Relative Moldiness Index) which is a PCR-based assay that appears to be predictive in infants of later development of asthma.

Next was Brandon “Bubba” Brooks, “Reviewing major themes in hospital microbiome research”.  Gave a good background on hospital work.  Talked about the NICU as both and important and tractable study system.  Showed source-tracking data about where microbes on touch surfaces in the hospital come from.  Emphasized the need for genome sequencing, strain-level differences are important.  Summarized differences between hospitals and houses.  Hospitals are more sourced from humans, more spatial separation, etc.

Last talk in this group was Kasthuri Venkateswaran “Venkat” talking about “Environmental “omics on the ISS”.  Talking about Planetary Protection and why NASA cares about the microbiome.  NASA has access to some really cool closed systems, not just the ISS but various testing facilities including underwater.  Gave some geography of the ISS.  Talked about the results of a large-scale survey of the ISS, did both culture-dependent and culture-independent methods.  Looked at both bacteria and fungi.

Afterwards we had breakout sessions for discussing the status of the field and then a poster session.  Here is the Storify of tweet for the day:

Microbiologist Tatiana Travis reads a plate to check on a bacterium's resistance to a carbapenem antibiotic in an antimicrobial resistance and characterization lab within the Infectious Disease Laboratory at the federal Centers for Disease Control and Prevention, Monday, Nov. 25, 2013, in Atlanta. (AP Photo/David Goldman)

From @teamwaxman in STAT: pharma waste and antibiotic resistance

From STAT article. Original caption “Microbiologist Tatiana Travis reads a plate to check on a bacterium’s resistance to a carbapenem antibiotic at the Infectious Disease Laboratory at the CDC in Atlanta.” By DAVID GOLDMAN/AP.

Waste released from pharmaceutical plants in India and China is contributing to the spread of antibiotic-resistant superbugs.

So this is certainly interesting.  There is an opinion piece in STAT by Henry Waxman and Bill Corr from Waxman Strategies: Waste from pharmaceutical plants promotes antibiotic-resistant superbugs.  It is of interest both because we are almost certainly in need of more efforts to control the spread of antibiotic resistance and also because of who wrote it.  Waxman was in the US House of Representatives for many many many years and Corr was deputy secretary of Health and Human Services from 2009 to 2015.  So it is good they are emphasizing this.  Though I am not completely convinced by the references in here that we know a lot about how / if waste from pharma plants impact resistance.

I generally agree with the sentiments – such as this:

This is all-hands-on-deck time. In the US, the Centers for Disease Control and Prevention estimate that more than 2 million people become infected with bacteria that are resistant to antibiotics and at least 23,000 die as a result of those infections. Globally, superbugs are estimated to cause 700,000 deaths annually, a number that could top 10 million by 2050 if we don’t take effective action.

Reducing antibiotic-laden pollution from pharmaceutical manufacturing plants is a relatively easy, affordable part of the solution.

Again, not sure about the degree of evidence at this point for a connection between pharma waste and resistance.  Regardless, it makes sense that this is a simple action we can take with a likely benefit.

New papers on Microbiology of the Built Environment, October 15, 2016

Microbes indoors

ReviewMicroorganisms in Confined Habitats: Microbial Monitoring and Control of Intensive Care Units, Operating Rooms, Cleanrooms and the International Space Station – Maximilian Mora – Frontiers in Microbiology (OA)

Graphical display of the confined habitats addressed in this review
Graphical display of the confined habitats addressed in this review

Indoor environments, where people spend most of their time, are characterized by a specific microbial community, the indoor microbiome. Most indoor environments are connected to the natural environment by high ventilation, but some habitats are more confined: intensive care units, operating rooms, cleanrooms and the international space station (ISS) are extraordinary living and working areas for humans, with a limited exchange with the environment. (…) In this article, we summarize the available data on the microbiome of aforementioned confined habitats. By comparing the different operating, maintenance and monitoring procedures as well as microbial communities therein, we emphasize the importance to properly understand the effects of confinement on the microbial diversity, the possible risks represented by some of these microorganisms and by the evolution of (antibiotic) resistances in such environments – and the need to reassess the current hygiene standards.

Receipt of Antibiotics in Hospitalized Patients and Risk for Clostridium difficile Infection in Subsequent Patients Who Occupy the Same Bed – Daniel E. Freedberg – JAMA (paywalled)

Multiple risk factors were identified related to the subsequent patient
Multiple risk factors were identified related to the subsequent patient

To assess whether receipt of antibiotics by prior hospital bed occupants is associated with increased risk for CDI in subsequent patients who occupy the same bed. This is a retrospective cohort study of adult patients hospitalized in any 1 of 4 facilities between 2010 and 2015. Among 100 615 pairs of patients who sequentially occupied a given hospital bed, there were 576 pairs (0.57%) in which subsequent patients developed CDI. Receipt of antibiotics in prior patients was significantly associated with incident CDI in subsequent patients (log-rank P < .01). (…) Receipt of antibiotics by prior bed occupants was associated with increased risk for CDI in subsequent patients. Antibiotics can directly affect risk for CDI in patients who do not themselves receive antibiotics.

Press: Antibiotics Encourage Spread of C.diff To Subsequent Patients Who Occupy the Same Bed and Haven’t Received Antibiotics: Interview with Daniel Freedberg – Medical Research

Bioaerosol assessment in the library of Istanbul University and fungal flora associated with paper deterioration – Duygu Göksay Kadaifciler – Aerobiologia ($39.95)

Map of the library of Istanbul University, Ground Floor
Map of the library of Istanbul University, Ground Floor

Health problems in people who are in indoor environments with poor ventilation have resulted in an increase in the number of studies regarding air quality. Microorganisms and inferior indoor air-climatic conditions not only affect human health but also cause decay of invaluable materials present in libraries. Therefore, this study aimed to assess the culturable bioaerosol composition and concentration in the library of Istanbul University. The culturable fungal flora, a biodeterioration agent, of the damaged archival materials was also examined. The air was sampled for a year, as were the surfaces of 207 biologically damaged books. (…). The highest amount of fungus was determined in Archive 3, which contained damaged books. The fungal species isolated from the air and books were essentially the same. Therefore, it is important to determine not only the numeric values but also the microbiological composition of fungal colonies because the variety of fungal species is indicative of a deterioration process in effect over a long period. The deterioration of books must be remedied.

ReviewObservation-based metrics for residential dampness and mold with dose–response relationships to health: A review – M. J. Mendell – Indoor Air ($6 to rent, $38 to own)

Associations between health effects and three-level index #23 for moisture damage and visible mold
Associations between health
effects and three-level index #23 for
moisture damage and visible mold

An important proportion of respiratory illness is considered attributable to residential dampness or mold (D/M). Developing health-protective D/M guidelines has been challenging, in part because unhealthy levels of indoor D/M cannot be defined using available microbiological measurements. This review paper explores reported multilevel, observation-based (eg visual or olfactory) D/M metrics for potential in defining unhealthy levels of residential D/M. For many of the 33 multilevel residential D/M metrics identified, health risks generally increased as observed D/M increased. Although some metrics seemed too complex for practical use, simple metrics had among the strongest associations with health outcomes. Available findings suggest the feasibility of setting observation-based D/M thresholds to trigger remedial action, using further improved D/M metrics without microbiological measurements (at least until the actual dampness-related agents that cause illness are better quantified). Additional data would allow setting health-protective D/M thresholds more precisely. Also, metrics could better reflect hidden D/M by more strongly emphasizing mold odor, which has demonstrated strong associations with health effects.

Popular press: Mapping the Subway’s Microbiome – Grégory Fléchet – CNRS News France (OA)

H. Richard, A. Carbone/LCQB
H. Richard, A. Carbone/LCQB

A vast international study is being undertaken to classify, using metagenomics, the bacteria that dwell in the underground transport systems of 50 cities across the globe. (…)  The aim of the operation, repeated several times throughout the day of June 21, 2016, at the entrances of several Paris metro stations, was strictly scientific: to identify the microorganisms that have taken up residence in this suburban environment. This unprecedented study is part of an international consortium framework dubbed MetaSUB (link is external).1 The project, which will be used to create microbial maps of the underground transit networks of the world’s largest cities, already includes 53 international megalopolises including New York, London, São Paulo, Tokyo, Berlin and Shanghai.

Microbes in space

Popular press: What radiation-resistant space fungus can do for drug discovery – Shayla Love – STAT News (OA)

Chernobyl fungi sent to ISS are grown in petri dishes in the lab at NASA’s Jet Propulsion Laboratory.
Chernobyl fungi sent to ISS are grown in petri dishes in the lab at NASA’s Jet Propulsion Laboratory.

On Aug. 26, the Dragon space capsule dropped into the Pacific Ocean somewhere off the coast of Baja California, Mexico. Onboard were payloads containing fungi that had now grown in two of the most extreme conditions known to man: outer space and the Chernobyl Atomic Energy Station. These fungi are radiation resistant. Thirty years ago, they survived when a routine test led to an explosion that blasted radioactive material throughout northern Ukraine. By sending these fungi to the International Space Station, Kasthuri Venkateswaran, a research scientist at NASA’s Jet Propulsion Lab, and Clay Wang, a professor at the USC School of Pharmacy, have tried to push them to adapt again.

Microbes and food production

Ultrasound improves chemical reduction of natural contaminant microbiota and Salmonella enterica subsp. enterica on strawberries – Denes Kaic Alves do Rosário – International Journal of Food Microbiology ($35.95)

Strawberries  Source:

New sanitization methods have been evaluated to improve food safety and food quality and to replace chlorine compounds. However, these new methods can lead to physicochemical and sensory changes in fruits and vegetables. The present study evaluated the effects of acetic acid, peracetic acid, and sodium dodecylbenzenesulfonate isolated or combined with 5 min of ultrasound treatment (40 kHz, 500 W) on strawberry quality over 9 days of storage at 8 °C. The strawberry natural contaminant microbiota (molds and yeasts, mesophilic aerobic and lactic acid bacteria), physicochemical quality (pH, total titratable acidity, total soluble solids, vitamin C, and color), sensory quality (triangle test) and inactivation of Salmonella enterica subsp. enterica intentionally inoculated onto strawberries were analyzed. (…)  Moreover, synergistic effects were observed in contaminant natural microbiota inactivation for all tested compounds during storage, without any major physicochemical or sensory alteration to the strawberries. Therefore, ultrasound treatment can improve the effect of sanitizers that are substitutes of chlorine compounds without altering the quality of strawberries during storage.

Microbes, waste, and pollution

Experimental Climate Change Modifies Degradative Succession in Boreal Peatland Fungal Communities – Asma Asemaninejad – Microbial Ecology ($39.95)

PCA biplot of fungi under increased temperature, elevated atmospheric CO2, and altered water table conditions
PCA biplot of fungi under increased temperature, elevated atmospheric CO2, and altered water table conditions

Peatlands play an important role in global climate change through sequestration of atmospheric CO2. Climate-driven changes in the structure of fungal communities in boreal peatlands that favor saprotrophic fungi can substantially impact carbon dynamics and nutrient cycling in these crucial ecosystems. In a mesocosm study using a full factorial design, 100 intact peat monoliths, complete with living Sphagnum and above-ground vascular vegetation, were subjected to three climate change variables (increased temperature, reduced water table, and elevated CO2 concentrations). (…)  Since fungi play a central role in peatland communities, increased abundances of saprotrophic fungi under warming conditions, at the expense of reduced fungal richness overall, may increase decomposition rates under future climate scenarios and could potentially aggravate the impacts of climate change.

Response of Core Microbial Consortia to Chronic Hydrocarbon Contaminations in Coastal Sediment Habitats – Mathilde Jeanbille – Frontiers in Microbiology (OA)

Co-occurrence OTU network based on correlation analysis.
Co-occurrence OTU network based on correlation analysis.

(…) Here, we investigated the ecological relationships between the three domains of life (i.e., Bacteria, Archaea, and Eukarya) using 454 pyrosequencing on the 16S rRNA and 18S rRNA genes from chronically impacted and pristine sediments, along the coasts of the Mediterranean Sea (Gulf of Lion, Vermillion coast, Corsica, Bizerte lagoon and Lebanon) and the French Atlantic Ocean (Bay of Biscay and English Channel). (…) OTUs forming the core microbial community showed the highest sensitivity to changes in environmental and contaminant variations, with salinity, latitude, temperature, particle size distribution, total organic carbon (TOC) and PAH concentrations as main drivers of community assembly. (…)  Comparison of network topological properties between contaminated and non-contaminated samples showed substantial differences in the network structure and indicated a higher vulnerability to environmental perturbations in the contaminated sediments.

Nitrogen transforming bacteria within a full-scale partially saturated vertical subsurface flow constructed wetland treating urban wastewater – Catiane Pelissari – Science of the Total Environment ($41.95)

Graphical abstract, detail
Graphical abstract, detail

The aim of this study was to characterize the nitrogen transforming bacterial communities within a partially saturated vertical subsurface flow constructed wetland (VF) treating urban wastewater in southern Brazil.(…)  The nitrifying and denitrifying bacterial communities were characterized in wetland cell 3 (764 m2 surface area) over a period of 12 months by using the FISH technique. (…) Based on the identified bacterial dynamics, the partially saturated VF wetland operated under low OLR enabled favorable conditions for simultaneous nitrification and denitrification.

Quality of greywater treated in biochar filter and risk assessment of gastroenteritis due to household exposure during maintenance and irrigation – S.S. Dalahmeh – Journal of Applied Microbiology ($6 to rent, $38 to own)

Concentration of E. coli in the influent (■) and effluent (□) of the studied pilot biochar filter treating household greywater
Concentration of E. coli in the influent (■) and
effluent (□) of the studied pilot biochar filter treating household greywater

This study evaluated treatment of greywater (GW) by a biochar filter in Jordan and assessed the annual risks of infection (Pi-annual), annual risk of disease (Pd-annual) and disease burden (in disability-adjusted life years; DALYs) of gastroenteritis caused by Salmonella spp. and rotavirus due to ingestion of GW during system maintenance and consumption of green onions irrigated with treated and nontreated GW.(…)  The highest risks of gastrointestinal disease were thus associated mainly with direct ingestion of GW when maintaining the system. Garden produce irrigated with GW treated in biochar filter did not display intolerable risks of rotavirus‒based gastroenteritis during summer season in the study area given that the produce is harvested 1 to 2 days, and washed, before consumption.