Tag Archives: Prokaryotes

Microbial Biogeography Of Public Restroom Surfaces

A very interesting paper recently appeared in the PLOS ONE journal, authored by Flores et al. entitled “Microbial Biogeography of Public Restroom Surfaces”.  This study, conducted by the Noah Fierer and Rob Knight labs at University of Colorado – Boulder, addressed the diversity of bacteria found at various places in public restrooms.  The novel aspect of this research is the use of culture-independent next-generation sequencing to determine bacterial species found in discriminating locations in public restrooms.

The restroom has been one of the greatest inventions in human history – especially from a public health perspective.  Without toilets and sinks – not failing to mention the plumbing infrastructure to get waste away from living spaces – disease causing bacteria (and let’s not forget other infectious organisms of the human gut, such as intestinal worms) associated with human waste easily spread from human to human, especially in close living quarters.  A fascinating brief overview of the microbial history of toilets (including some great anecdotes featuring toilet visionary Sir Thomas Crapper) and a commentary of this scientific paper, written by Rob Dunn, can be found on the Scientific American Blogs site.

Using barcoded pyrosequencing of the 16S rRNA gene marker, Flores et al. observed bacterial species on ten different surface types (door handles & stall handles – both in and out, faucet handles, soap dispenser, toilet seat, toilet flush handle, floor around toilet and floor around sink) in twelve different (six male and six female) restrooms on the UC-Boulder campus on a single day.

The researchers identified 19 different bacterial phyla on all of the surfaces sampled.  The majority of sequences (approximately 92%) could be placed within four phyla, including the Actinobacteria, Bacteriodetes, Firmicutes, and Proteobacteria.  Human-associated bacteria were found strongly associated with restroom surfaces, which is not surprising for indoor environments.

Bacterial communities could be categorized by the surfaces they inhabited.  On toilets, gut-associated bacteria were the dominant group.  Skin-associated bacteria were – not surprisingly – found on surfaces touched by hands, such as door handles.  The restroom floor held the greatest diversity of bacteria – some of which were found in low abundance – as these surfaces contained soil associated, as well as human associated, bacteria.  Quite interestingly, the researchers found that some of the toilet flush handles contained soil associated bacteria, implying that some restroom users flush toilets with their feet to avoid directly touching the handles.

There were no statistically significant differences between bacterial communities found in female and male restrooms, although the relative abundances of some bacterial groups were gender associated.  The bacterial family, Lactobacillaceae, found associated with vaginas, were – not surprisingly – more abundant in and around female restroom toilets than male counterparts.

The authors used the newly developed software package, Source Tracker, to determine the similarity of bathroom surfaces to communities from expected and previously published sources, such as human skin, the human gut, urine, soil, and faucet water.  It was predicted that human skin was the primary source of restroom surface bacteria.  Human gut was a source of bacteria found on and around toilets.  Despite the presence of many typical soil bacterial groups found on restroom floors, soil was not identified as a statistically significant source, probably because soil typically contains a highly diverse taxonomic array of species, many of which are rare.  The authors state that custodial mops and ventilation systems may also have some influence on the floor surfaces but were not directly addressed in this study.

The authors show here that human-associated bacteria are the most common microbes found in public restroom surfaces.  Human influenced source patterns can be determined from the bacterial community structure within the biogeography of restrooms.  This study underscores the importance of hand washing, particularly when using public restrooms, and the techniques used in this paper could be used to track or determine likely pathogenic bacteria found on surfaces during incidents of infectious outbreaks.

How Many Species Are There On Earth And In The Ocean?

This week, it’s been hard to miss the new paper, “How many species are there on Earth and in the Ocean?” published by Mora et al. in the August 2011 issue of the journal PLOS Biology.  There have been commentaries or news articles printed in the New York Times, The Economist, The Guardian, Damian Carrington’s Guardian Blog, National Geographic, Yahoo News, AlterNet, MSNBC, Reuters, UNEP, NewsDaily and Ed Yong has posted a commentary on his Google+ page.  Furthermore, some well respected scientists who study biological diversity have joined the debate too: Jonathan Eisen has devoted two blog posts to the paper (one about the actual paper in PLOS Biology and another on the National Geographic commentary) and there is a commentary from Robert May in PLOS Biology about the study and its significance.  Since there is ample information on the study elsewhere, let me communicate a brief summary of the study and some of my feelings about the paper.

It’s quite embarrassing that we have really no clue how much biological diversity is found on this planet.  Adding insult to injury is the fact that we have no concept of the current magnitude of the loss of diversity due to human induced mass extinctions.  This paper seeks to predict total global biological diversity by documenting current taxonomic numbers and extrapolating consistent patterns to estimate the number of species that have yet to be identified.

The methods of the authors essentially consisted of three parts.  First, the authors compiled a list of approximately 1.2 million species pulled from numerous biological databases.  Second, they surveyed a little over 500 taxonomists who were asked to identify the validity of current scientific names and comment on the intensity of current taxonomic efforts to describe new species.  Third, the authors analyzed this data to find the estimated global numbers of biological taxa for each phylum.

The authors show a predictable pattern in the classification of species (at the phylum, class, order, family, and genus level) at least consistently for animals.  By evaluating these patterns using regression, the authors validated this by closely examining 18 taxonomic groups that we think we understand their total biological diversity.  By doing this, the authors come up with a total estimate of 7.7 million species of animals (mostly insects), close to 300,000 species of plants, more than 600,000 species of fungi, and a total estimate of roughly 9 million eukaryotes on Earth.  The authors estimate that 86% of species on Earth and 91% of species in the oceans still have not been formally described.  Previous estimates of species diversity have been wide: anywhere between 3 million to a 100 million species.

This paper is a novel and worthwhile attempt to determine the total amount of species diversity on this planet.  Despite this, I think – and the authors have their own reservations – that there are some serious problems with some of their calculations.

One problem is that the study is based mainly on using animals, and vertebrates for that matter – which are the best described of any phylum, as the baseline for measuring the completeness of species diversity.  I would argue that plants and fungi, and obviously bacteria, archaea, and “the protists” are clearly not well known enough to extrapolate any serious estimate species numbers especially when considering vertebrate animals as a baseline and whose numbers are largely skewed.

Another problem is in our collective definition of species, as well as taxonomic subjectivity of the categorization of other taxonomic hierarchies, which are based on the on the homology of shared characters and, I would argue, are largely incomparable outside of each phylum.  For example, what one taxonomist calls an order in one grouping may not be equivalent to what another taxonomist calls a completely different order in another completely different grouping.

I should point out that the authors don’t ignore these caveats, but they still exist in their study.  In any event, this paper is important because it adds to the dialogue concerning species diversity, the need to estimate, inventory and preserve the massive amount of diversity we share on the planet.

UPDATE: More commentaries in the news can be found here, here, and here.

Jacques Monod Conference: Integrative Ecological Genomics

Ecological genomics is thriving as a discipline, evidenced by the number of research papers published in this area, and this is due to the large amounts of genomic data now available to researchers.  Information from individual genomes, “pan-genomes”, and large scale environmental genome sequencing is giving us a more complete picture of biological diversity.

Some of the top researchers in this newly emerging discipline will be speaking at the Jacques Monod Conference “Integrative Ecological Genomics.”  The meeting is held in Roscoff, Brittany, France.  Registration is by application (the submission deadline is June 20th 2011) and the number of attendees is capped at 115 people.  Information regarding the meeting and registration can be found here and here.

Raiders Of The Lost Domain

Metagenomics, the process of acquiring the genomes – or pieces of genomes – of all the microorganisms in a single environmental sample and then analyzing their composition, has developed in recent years with the advent of next-generation sequencing techniques.  Metagenomic studies are increasing our knowledge about microbial life by providing vast amounts of data on the overall diversity of organisms found in soil, aquatic habitats, the human body, and even what is splattered across car windshields (see here).  Unknown organisms found in metagenomic studies correspond to the three domains of life: Bacteria, Archaea, and Eukaryotes, but scientists have wondered if other domains of life exist, but have gone unnoticed.

A paper authored by Wu et al., entitled “Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees“, recently published in the PLoS One journal and from the laboratory of Jonathan Eisen at UC Davis (see here and here), ponders the presence of novel lineages of life by searching for genes with presumed deep origins in the tree of life.  By using metagenomic sequences from Craig Venter’s Global Ocean Sampling (GOS) initiative, the authors searched for novel life by probing for genes – those associate with ribosomal RNA – assumed to have early origins in the evolution of life.  Image link from a commentary from the Economist.

The researchers began looking for novelty across the small subunit rRNA gene, a common gene for phylogenetics at the level of bacteria and archaea, but were unable to resolve these phylogenies at deep levels due to a lack of robust sequence alignments for novel sequences.  The researchers ended up focusing on two rRNA associated genes also with assumed deep origins: RecA, a gene involved in DNA recombination, and RpoB, a gene involved in translating DNA into RNA.  Jonathan Eisen has written a very detailed and elucidating blog post of the background of the methodology, in supplement to the methodology found in this paper. The following figure comes from Norm Pace’s excellent 2009 review article on the tree of life and shows how the basal nodes of many lineages remain unresolved.

When constructing phylogenetic trees of the RecA and RpoB sequences, the authors found specific novel branches that could not be easily identified.  The authors describe four explanations concerning the characterization of these sequences.  One explanation is that these novel clades come from undescribed viruses not previously observed.  A second possibility is that the sequences represent recombinations of previously identified genes, which the authors rule out due to phylogenetic uniqueness.  A third explanation is the presence of ancient paralogous genes from organisms lacking gene data or information.  Lastly, a fourth possibility is that the novel sequences come from yet unknown lineages of organisms and their phylogenetic novelty actually represents novel organisms.  The authors stress that this study needs more data and more rigorous research in order to investigate these possibly novel clades, but this study is the first of, hopefully, many to address this interesting research question.  If you would like to read more about this research there are numerous commentaries available for your reading pleasure (see here, here, and here).

XV International Congress on Molecular Plant-Microbe Interactions

The XV International Congress on Molecular Plant-Microbe Interactions has shaped up to be an amazing meeting.  A stellar group of researchers will be presenting at the meeting.  Registration is open now.

Directly from the meeting website:  “The XV International Congress on Molecular Plant-Microbe Interactions is recognized as the most important international meeting for plant-microbe interactions to discuss research and network with colleagues from around the world.  This meeting is the global venue for presenting and discussing new research and developments in molecular plant-microbe interactions.  Through plenary lectures, concurrent sessions, special workshops and various events, attendees experience innovative plant-microbe interactions research.  The meeting features hundreds of abstracts and provides networking and professional development opportunities.”

First Steps Toward Learning the Language of Mycorrhizal Communication

I’ve already talked about mycorrhizal associations numerous times (here and here), so if you’re not already used to hearing about mycorrhizae, you will if you continue to read this blog.  In this recent paper, entitled “Fungal lipochitooligosaccharide symbiotic signals in arbuscular mycorrhiza“, published online in the journal Nature, the authors Maillet et al address plant and fungal interactions of arbuscular mycorrhizal associations.  Using the Glomus intraradicesMedicago truncatula model system, the researchers identify diffusible chemical signals produced by the fungus during initiation of the mycorrhizal association with the plant.

It has been hypothesized that both fungi and bacteria interacting with plant roots do so using similar genetic mechanisms.  It has already been shown that rhizobial bacteria – particularly the nitrogen fixing microbes associated with leguminous plants – produce lipochitooligosaccharide (LCO) signals used in the  communication with host plants.  The authors of this study discovered that the fungus Glomus intraradices, like the nitrogen-fixing bacteria, secretes an array of sulfated and non-sulfated simple LCOs which stimulated the formation of arbuscular mycorrhizae in disparately related plants, such as Medicago (Fabaceae), Daucus carota (Wild Carrot; Apiaceae), and Tagetes patula (French Marigold; Asteraceae).  These compounds were found in Glomus intraradices both interacting with plant roots and in free-living resting spores in the soil.

Comparing the genes involved in the transduction of the LCO signals in both rhizobial bacteria associated with legumes and arbuscular mycorrhizal fungi associated with land plants yielded similar gene expression pathways.  In order to validate the role of LCOs in mycorrhizae formation, the researchers genetically engineered non-plant interacting bacteria to produce the LCOs from Glomus.  These engineered bacteria increased mycorrhizae formation in plants already associated with Glomus.  Fungal LCOs were also found to induce root branching, a trait long associated with the formation of mycorrhizae in plants.  There is a nice commentary on this research article located here.