New papers on microbiology of the built environment, July 17, 2016

Microbes in the clinic

Glove Contamination during Endodontic Treatment Is One of the Sources of Nosocomial Endodontic Propionibacterium acnes Infections – Sadia Ambreen Niazi – Journal of Endodontics ($35.95)

An endodontist operating on his patient, Wikipedia
An endodontist operating on his patient, Wikipedia

The opportunistic Propionibacterium acnes recovered frequently from failed endodontic treatments might be the result of nosocomial endodontic infections. The study was aimed to determine if gloves worn by dentists could be 1 of the sources of these nosocomial infections and to investigate the P. acnes phylotypes involved.(…) Contamination of the gloves was detected at the final stages of the treatment. P. acnesand S. epidermidis are the prevalent taxa on gloves and are opportunistic endodontic pathogens. Changing gloves frequently, after gaining access into the pulp space and also after taking the working length/master gutta-percha point radiographs, is likely to reduce the risk of root canal reinfection.

Microbes at the city dump

High-throughput sequencing of 16S rRNA Gene Reveals Substantial Bacterial Diversity on the Municipal Dumpsite – Kilaza Samson Mwaikono – BMC Microbiology (OA)

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Clustering of bacterial community from different solid wastes.

(…) This study focuses on a more comprehensive approach to study bacteria at the dumpsite (Note EB: Arusha, Tanzania). Since the site comprised of unsorted wastes, a qualitative survey was first performed to identify the variety of solid waste as this has influence on the microbial composition. Thus, domestic (Dom), biomedical (Biom), river sludge (Riv), and fecal material of pigs scavenging on the dumpsite (FecD) were sampled. Total DNA was extracted from 78 samples and the v4-16S rRNA amplicons was characterized using an Illumina MiSeq platform.(…) This study provides a comprehensive report on the abundance and diversity bacteria in municipal dumpsite. The species richness reported here shows the complexity of this man-made ecosystem and calls for further research to assess for a link between human diseases and the dumpsite. This would provide insight into proper disposal of the waste, as well as, limit the risks to human health associated with the dumpsite.

Microbes and urban influence

Biodiversity of green algae covering artificial hard substrate surfaces in a suburban environment: A case study using molecular approaches – Christine Hallmann – Journal of Phycology ($6 to rent, $38 to own)

Man-made artificial substrates covered by aero-terrestrial green algae
Man-made artificial substrates covered by aero-terrestrial green algae

In Middle European suburban environments green algae often cover open surfaces of artificial hard substrates. Microscopy reveals the Apatococcus/Desmococcus morphotype predominant over smaller coccoid forms. Adverse conditions as limited water availability connected with high PAR and UV irradiance may narrow the algal diversity to a few specialists in these subaerial habitats. We used rRNA gene cloning/sequencing from both, DNA extracts of the biofilms without culturing as well as cultures, for the unambiguous determination of the algal composition and to assess the algal diversity more comprehensively. The culture independent approach revealed in fact mainly just two genera (Apatococcus, Trebouxia) for all study sites and five molecular operational taxonomic units (OTUs) for a particular study site which based on microscopic observation was the one with the highest morphological diversity. The culture approach, however, revealed seven additional OTUs from five genera (Chloroidium, Coccomyxa, Coenochloris, Pabia, Klebsormidium) and an unidentified trebouxiophyte lineage for that same site; only two OTUs were shared by both approaches (…) Except for the streptophyte Klebsormidium only members of Trebouxiophyceae were detected suggesting these algae may be particularly well adapted to subaerial habitats.

Combined Flux Chamber and Genomics Approach Links Nitrous Acid Emissions to Ammonia Oxidizing Bacteria and Archaea in Urban and Agricultural Soil – Nicole K. Scharko – Environmental Science & Technology ($40 for 48h)

Relative abundance of archaea and bacteria
Relative abundance of archaea and bacteria

Nitrous acid (HONO) is a photochemical source of hydroxyl radical and nitric oxide in the atmosphere that stems from abiotic and biogenic processes, including the activity of ammonia-oxidizing soil microbes. HONO fluxes were measured from agricultural and urban soil in mesocosm studies aimed at characterizing biogenic sources and linking them to indigenous microbial consortia. (…) Genomic surveys of soil samples revealed that 1.5—6% of total expressed 16S rRNA sequences detected belonged to known ammonia oxidizing bacteria and archaea. (…) The results suggest that biogenic HONO emissions will be important in soil environments that exhibit high nitrification rates (e.g., agricultural soil) although the widespread occurrence of ammonia oxidizers implies that biogenic HONO emissions are also possible in the urban and remote environment.

Comparative metagenome of a stream impacted by the urbanization phenomenon – Julliane Dutra Medeiros – Brazilian Journal of Microbiology (OA)

Metabolic pathways of from the metagenomes.
Metabolic pathways of methane, nitrogen and sulfur from the freshwater metagenomes.

(…) In the present study, we investigate the taxonomic and functional profile of the microbial community in an urban lotic environment. Samples of running water were collected at two points in the São Pedro stream: an upstream preserved and non-urbanized area, and a polluted urbanized area with discharged sewage. The metagenomic DNA was sequenced by pyrosequencing. Differences were observed in the community composition at the two sites. The non-urbanized area was overrepresented by genera of ubiquitous microbes that act in the maintenance of environments. In contrast, the urbanized metagenome was rich in genera pathogenic to humans. The functional profile indicated that the microbes act on the metabolism of methane, nitrogen and sulfur, especially in the urbanized area. It was also found that virulence/defense (antibiotic resistance and metal resistance) and stress response-related genes were disseminated in the urbanized environment. The structure of the microbial community was altered by uncontrolled anthropic interference, highlighting the selective pressure imposed by high loads of urban sewage discharged into freshwater environments.

Microbes and waste

Wastewater Enhanced Microbial Corrosion of Concrete Sewers – Guangming Jiang – Environmental Science & Technology ($40 for 48h)

Concrete pipes, County Materials, Wisconsin
Concrete pipes, County Materials, Wisconsin

Microbial corrosion of concrete in sewers is known to be caused by hydrogen sulfide, although the role of wastewater in regulating the corrosion processes is poorly understood. Flooding and splash of wastewater in sewers periodically inoculates the concrete surface in sewer pipes. No study has systematically investigated the impacts of wastewater inoculation on the corrosion of concrete in sewers. This study investigated the development of the microbial community, sulfide uptake activity and the change of the concrete properties for coupons subjected to periodic wastewater inoculation. (…)  The enhanced corrosion rate was due to the higher sulfide uptake rates induced by wastewater inoculation, although the increasing trend of sulfide uptake rates was slower with wastewater. Increased diversity in the corrosion layer microbial communities was detected when the corrosion rates were higher. This coincided with the environmental conditions of increased levels of gaseous H2S and the concrete type.

Microbes and drinking water

Microbiome profiling of drinking water in relation to incidence of inflammatory bowel disease – Jessica D. Forbes – Canadian Journal of Microbiology (Paywall, no price indicated)

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Cover of Canadian Journal of Microbiology

The etiology of inflammatory bowel disease (IBD) is unknown; current research is focused on determining environmental factors. One consideration is drinking water: water systems harbour considerable microbial diversity, with bacterial concentrations estimated at 106—108 cells/L. Perhaps differences in microbial ecology of water sources may impact differential incidence rates of IBD. Regions of Manitoba were geographically mapped according to incidence rates of IBD and identified as high (HIA) or low (LIA) incidence areas. Bulk water, filter material, and pipe wall samples were collected from public buildings in different jurisdictions and their population structure analyzed using 16S rDNA sequencing. (…) Particular microbes were found to associate with LIA or HIA, based on sample location and (or) type. This work lays out a basis for further studies exploring water as a potential environmental source for IBD triggers.

A modified weighted mixture model for the interpretation of spatial and temporal changes in the microbial communities in drinking water reservoirs using compositional phospholipid fatty acid data – I. Stanimirova – Talanta ($41.95)

Dendrogram and OTU heat map
Dendrogram and OTU heat map

The aim of this work was to check whether a methodology based on the analysis of data that contain the entire phospholipid fatty acid, PLFA, compositions of water samples can be successfully used to interpret spatial and temporal changes in the microbial communities in water reservoirs. The proposed methodology consists of the construction of a modified weighted multivariate mixture model for the PLFA profiles of the water samples collected in a given monitoring campaign and the identification of latent PLFA components through a comparison with the known PLFA profiles of some cultivated or non-cultivated microbial communities. A 16 S rDNA analysis of some of the selected water samples in the monitoring campaign was performed in order to verify the results of the PLFA analysis. The results showed that the proposed methodology can be useful for a dynamic and sensitive evaluation of changes in the microbial quality of water before and after flash flooding and can help in taking a decision regarding further risk assessment.

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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.