New papers on microbiology of the built environment, March 26, 2016

Your weekend update:

Microbes and drinking water

Diversity of ribosomal 16S DNA- and RNA-based bacterial community in an office building drinking water system – Jenni Inkinen – Journal of Applied Microbiology  (See also their 2014 Water Research paper about same system)

Screen Shot 2016-03-25 at 05.44PM, Mar 25Next-generation sequencing of 16S ribosomal RNA genes (rDNA) and ribosomal RNA (rRNA) was used to characterize water and biofilm microbiome collected from a drinking water distribution system of an office building after its first year of operation. (…) Microbial communities differed between water and biofilms, between cold and hot water systems, locations in the building and between water rRNA and rDNA libraries, as shown by clear clusters in principal component analysis (PcoA). By using the rRNA method, we found that not all bacterial community members were active (e.g. Legionella spp.) while other members showed increased activity in some locations; e.g. Pseudomonas spp. in hot water circulations’ biofilm and order Rhizobiales and Limnohabitans spp. in stagnated locations’ water and biofilm. (…) rRNA-based methods may be better than rDNA-based methods for evaluating human health implications as rRNA methods can be used to describe the active bacterial fraction. This study indicates that copper as a pipeline material might have an adverse impact on the occurrence of Mycobacterium spp. The activity of Legionella spp. maybe questionable when detected solely by using DNA-based methods.

Microbes and Antarctic camps

Imported anthropogenic bacteria may survive the Antarctic winter and introduce new genes into local bacterial communities – Kristian Brat – Polish Polar Research (OA)

Screen Shot 2016-03-25 at 05.36PM, Mar 25We studied dynamic changes in anthropogenic bacterial communities at a summer-operated Czech research base (the Mendel Research Station) in the Antarctic during 2012 and 2013. We observed an increase in total numbers of detected bacteria between the beginning and the end of each stay in the Antarctic. (…) 16S rRNA sequencing showed high rates of accordance between nucleotide sequences among the tested strains. Three conclusions were drawn: (1) Number of anthropogenic bacteria were able to survive the harsh conditions of the Antarctic winter (inside and outside the polar station). Under certain circumstances (e.g. impaired immunity), the surviving bacteria might pose a health risk to the participants of future expeditions or to other visitors to the base. (2) The bacteria released into the outer environment might have impacts on local ecosystems. (3) New characteristics (e.g. resistance to antibiotics) may be introduced into local bacterial communities.

Microbes and platinum mining

Biological role in the transformation of platinum-group mineral grains – Frank Reith – Nature Geoscience

Screen Shot 2016-03-25 at 05.41PM, Mar 25Platinum-group elements are strategically important metals. Finding new deposits is becoming increasingly difficult owing to our limited understanding of the processes that affect their mobility in surface environments. Microorganisms have been shown to promote the mobility of metals around ore deposits. Here we show that microorganisms influence the mobility of platinum-group elements in mineral grains collected from Brazil, Australia and Colombia. Scanning electron microscopy showed biofilms covering the platinum-group mineral grains. (…) We conclude that biofilms are capable of forming or transforming platinum-group mineral grains, and may play an important role for platinum-group element dispersion and re-concentration in surface environments.

Microbes and pollution

Response and resilience of soil microbial communities inhabiting in edible oil stress/contamination from industrial estates – Vrutika Patel – BMC Microbiology (OA)

Screen Shot 2016-03-25 at 05.47PM, Mar 25(…) To understand the impact of long-term oil contamination on microbial community structure soil samples were taken from oil fields located in different industrial regions across Kadi, near Ahmedabad, India. Soil collected was hence used for metagenomic DNA extraction to study the capabilities of intrinsic microbial community in tolerating the oil perturbation. (…) Our results indicated that soil microbial diversity (Shannon diversity index) decreased significantly with contamination. Further, assignment of obtained metagenome reads to Clusters of Orthologous Groups (COG) of protein and Kyoto Encyclopedia of Genes and Genomes (KEGG) hits revealed metabolic potential of indigenous microbial community. Enzymes were mapped on fatty acid biosynthesis pathway to elucidate their roles in possible catalytic reactions. To the best of our knowledge this is first study for influence of edible oil on soil microbial communities via shotgun sequencing. The results indicated that long-term oil contamination significantly affects soil microbial community structure by acting as an environmental filter to decrease the regional differences distinguishing soil microbial communities.

Microbes and archaeology

Complications in the study of ancient tuberculosis: Presence of environmental bacteria in human archaeological remains – Romy Müller – Journal of Archaeological Science

Screen Shot 2016-03-25 at 05.50PM, Mar 25There are many reports of ancient DNA from bacteria of the Mycobacterium tuberculosis complex (MTBC) being present in skeletons with and without osteological indications of tuberculosis. A possible complication in these studies is that extracts might also contain DNA from the microbiome of the individual whose remains are being analysed and/or from environmental bacteria that have colonised the skeleton after death. These contaminants might include ‘mycobacteria other than tuberculosis’ (MOTT), which are common in the environment, but which are not normally associated with clinical cases of tuberculosis. In this paper we show that MOTT of various types, as well as bacteria of related genera, are present in most if not all archaeological remains.(…) Our results also illustrate the challenges faced when assembling MTBC genome sequences from ancient DNA samples, as misidentification of MOTT sequence reads as MTBC would lead to errors in the assembly. Identifying such errors would be particularly difficult, if not impossible, if the MOTT DNA content is greater than that of the authentic MTBC. The difficulty in identifying and excluding MOTT sequences is exacerbated by the fact that many MOTT are still uncharacterized and hence their sequence features are unknown.



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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.