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min of submission holiday season done difficult task i don t wish to think about constipation and faecal flora during my holidays the peaceful atmosphere between christmas and new year was transiently disrupted by reading this manuscript merry x mas first my recommendation was reject with new submission because it is necessary to investigate further but reading a well written manuscript before x mas makes me feel like santa claus season s greetings i apologise for my slow response but a roast goose prevented me from answering emails for a few days technical issues maybe some beetle took a pee on one or the other of the samples you call the sample fresh water this is confusing as it is saline water the trees are crap but besides this excellent work writing style you know there is something important there but the language is so inaccessible that you cannot make up your mind if they are trying to hide something or they actually think that is a good style of writing this manuscript gets the title worst written manuscript of the year reviewed by dj the writing style is flowery and has an air of oscar wilde about it great manuscripts this is a long but excellent report it hurts me a little to have so little criticism of a manuscript i perused this manuscript while in the hotel prior to a friend s wedding i was suspicious that a state of relaxation had influenced my enjoyment of a paper on soil formation so i read it again this time squashed between two large people on the delayed flight home and still enjoyed reading it very much enjoyed reading this one and do not have any significant comments wish i had thought of this one it is always a joy to review manuscripts such as this well conceived well executed well edited clean pristine from start to finish links referees quotes 2010 environmental microbiology 2010 12 3303 3304 referees quotes 2009 environmental microbiology 2009 11 3309 3310 image credits image desperate schoolboy modified from a photo by patrick bell source flickr this image is licensed under a creative commons attribution 3 0 unported license read the rest of the article posted by cesar sanchez at 12 36 pm view comments share more oct 6 2010 microbial pigments an untapped resource for teachers artists and researchers the journal plos biology has launched a new series of articles on education to present innovative approaches to teaching critical concepts developments and methods in biology the title of the first article in the series is in living color bacterial pigments as an untapped resource in the classroom and beyond from the article soil bacteria from the streptomyces genus represent a source of interesting natural products that have been largely overlooked by artists researchers and teachers this article is intended to encourage amateurs and professionals alike to explore this overflowing source of biopigments not only does this endeavor have the potential to lead us toward a fertile nexus between art and science it may also lead to a more sustainable and environmentally friendly way to color the world around us in the future the relevance of biopigments to many facets of science technology and society makes this material an outstanding tool to engage students of varying academic interests across multiple age groups therefore we encourage teachers of all levels to consider using biopigments as a vehicle to introduce the scientific method to their students to facilitate the implementation of biopigments into science and art curricula we have provided a list of useful online resources and information about procuring materials as well as recommend ways to evaluate the effectiveness of the lesson original article and image source charkoudian lk fitzgerald jt khosla c champlin a 2010 in living color bacterial pigments as an untapped resource in the classroom and beyond plos biol 8 10 e1000510 doi 10 1371 journal pbio 1000510 image elvis lives painted on agar media plates using the bacterium streptomyces coelicolor related links microbial art a collection of unique artworks created using living bacteria fungi and protists painting with penicillin alexander fleming s germ art the scientist created works of art using microbes but did his artwork help lead him to his greatest discovery by rob dunn smithsonian com july 12 2010 streptomyces they re twisted twisted bacteria aug 10 2007 read the rest of the article posted by cesar sanchez at 12 42 pm view comments share more aug 19 2010 a voyage from molecular genetics to microbial ecology includes a fish tank and some cartoons the march issue of international microbiology included a very nice article by roberto kolter professor of microbiology and molecular genetics at harvard medical school the title is biofilms in lab and nature a molecular geneticist s voyage to microbial ecology freely available as pdf in the article the author gives an entertaining account of the path that lead him to the study of biofilms that is aggregations of microbes growing on solid substrates he also highlights some of his recent research on the ecology of microbial islands there is also a fish tank anecdote and i added a couple of microbial cartoons just for fun microbes are excellent model organisms at least for studies on basic cellular processes as jacques monod put it ce qui est vrai pour le colibacille est vrai pour l éléphant what is true for the colibacillus is true for the elephant that is why roberto kolter and many other researchers soon fell under the spell of bacteria and in particular the colibacillus escherichia coli for some time kolter studied the regulation of cell growth in e coli under the right conditions cells divide to yield daughter cells which grow and divide quickly again and so on and the bacterial population undergoes exponential growth this exponential phase of growth a k a log phase is typically followed by a stationary phase when the growth rate slows down due to a scarcity of nutrients and accumulation of toxic products eventually the bacterial population shrinks in what is known as death phase you can visit cells alive or wikipedia for basic information on bacterial growth these processes are typically studied in the laboratory using shaken cultures the shaking of flasks and test tubes keeps the broth composition uniform throughout the flask and provides a continuous supply of fresh air that helps microbes grow fast as a result the cells are in a planktonic state that is they grow in suspension in the broth from these shaker sick cultures kolter and coworkers learnt a few interesting things about what happens during the stationary and death phases in the international microbiology article he summarizes their findings as follows and what we found through genetic analyses was rather extraordinary death allowed new life we were witnessing evolution in real time underlying the usually observed death phase was a dynamic world of dying and growing bacteria there were constant population takeovers such that pre existing fitter bacterial mutants grew as the original population met its demise evolutionary cheating we would call it later on in other words the adverse conditions occurring in the e coli cultures during the death phase toxic products little food appeared to have two contrasting effects it was obvious that many cells were dying but at the same time successive waves of different spontaneous mutants were able to thrive and outgrow their dying siblings in this less than optimal environment these findings were reviewed in two papers with memorable titles life after log and gasping for life in stationary phase isn t that a fascinating microcosms the little creatures in the test tube were not just dying they were evolving and now the fish tank anecdote or in kolter s own words the epiphany of the fish tank the years that followed represented for me a dramatic turn of direction in my research one might ascribe the change to some sort of post tenure depression i refer to it as the epiphany of the fish tank now microbial life on surfaces for decades studied by bill costerton and other intrepid pioneers of the biofilm field had been long ignored by most microbial physiologists and molecular geneticists myself included however things changed for me in 1994 when noticing my depressed state members of my laboratory gave me a fish tank in a effort to draw me out of the blues as i sat locked up in the office staring at the tank i realized that by studying shaken cultures of e coli i had been barking up the wrong tree the water in the fish tank remained crystal clear it was on the surfaces where most microbial activity was occurring that observation applies well beyond fish tanks it is possible that the majority of microbes on earth spend most of their lives in aggregates attached to surfaces and therefore not in a free floating or swimming planktonic state obviously they are not solitary guys we could view biofilms in nature as quite complex societies or cities where different types of microorganisms inhabit buildings made out of sticky macromolecules polysaccharides proteins dna importantly microbes in biofilms are sometimes resistant to the action of antibiotics to which the same organisms are sensitive when in planktonic state so have microbiologists been barking up the wrong tree all this time well not exactly experiments using shaken cultures have been and will continue to be extremely useful they are without doubt highly valuable to learn about the biochemistry genetics and many other aspects of the biology of microbes and they have been instrumental in providing us with antibiotics and vaccines to fight infectious disease but it is true that shaken cultures are sometimes not the best research models especially if we try to understand the real life of a microbe in its natural environment the fish tank epiphany lead kolter into biofilm research a first approach he and his collaborators took was to study the biofilms formed by certain bacillus subtilis strain the accompanying image shows on the left a beaker with a floating film that the microbe forms when grown in a standing not shaken liquid culture and on the right a magnified view of a colony grown on an agar plate although these biofilms consist only of a single organism they are actually highly structured with several layers composed of different cell types engaged in various activities some cells are actively producing the matrix not the wachowskis movie but the glue that keeps the biofilm together others are swimming around and there are also some cells in the process of becoming spores how close is that to a multicellular organism the b subtilis biofilm is a very useful model but you may well think that a beaker containing a single microbial species is a very artificial setting then how can scientists study biofilms in natural environments for kolter the inspiration came no fish tank involved from the writings of biologist e o wilson in collaboration with robert macarthur wilson developed in the 1960s the theory of island biogeography which has become fundamental in ecology and evolutionary biology the theory tries to explain the factors that control the number of species in a natural community it was originally developed for islands but now it is applied to any ecosystem that is surrounded by other ecosystems kolter was fascinated by the ways wilson studied newly formed islands to put the theory to the test what wilson actually did was to fumigate some small islands to kill all arthropods and then observe how the islands were recolonized however kolter was wise enough and did not try to make free from microbes any islands that would be tough his approach much less destructive consisted of studying two natural microbial islands the pitchers of a carnivorous plant and the human lungs the first island is sarracenia purpurea a carnivorous plant feeding on the insects and spiders that fall into its water filled pitchers kolter and collaborators found that the inside of unopened newly formed pitchers was sterile there you go a microbial island is born this allowed them to analyse the composition of the nascent bacterial population in the pitchers during the season as microbes colonized the island among other results the researchers found that pitchers containing certain mosquito larvae keystone predators had a greater bacterial diversity the second microbial island studied by kolter and coworkers is the respiratory tract of humans suffering from cystic fibrosis cf as long as you are healthy your lungs are supposed to be mostly sterile however respiratory diseases such as cf or asthma open the gates to outside microbial colonizers which can make a lot of harm in cf the major microbial pathogen is the bacterium pseudomonas aeruginosa which forms biofilms inside the lungs and can easily become resistant to antibiotics using culture independent methods kolter s laboratory compared the microbial communities in the lungs of different cf patients the researchers showed that the presence of p aeruginosa was correlated with lower microbial diversity worse lung function and patient age in other words it appears that the arrival of p aeruginosa an invasive species greatly affects the microbial community in cf lungs resulting in a decrease in diversity the researchers suggest that the composition of the microbial community could be a better predictor of disease progression than the presence of p aeruginosa alone well that was a long post please read roberto kolter s article it is free which includes a few more interesting thoughts and quotes the concept of microbial islands is fascinating and the growing interaction between the long time isolated fields of ecology and microbiology is i think changing the way microbiologists view their study subjects hopefully ecologists will also become more aware of the organisms that rule the planet which are not humans you know reference for roberto kolter s article roberto kolter 2010 biofilms in lab and nature a molecular geneticist s voyage to microbial ecology int microbiol 13 1 7 doi 10 2436 20 1501 01 105 pdf related links biology of microbial communities interview to roberto kolter video jove may 2007 roberto kolter bacillus subtilis and bacteria as multicellular organisms podcast meet the scientist episode 20 march 2009 microbeworld the evolution of the biofilm concept a long and winding road free pdf by j w costerton sartoniana 2008 21 59 67 about the existence of microbes viruses in healthy and diseased human lungs metagenomic analysis of respiratory tract dna viral communities in cystic fibrosis and non cystic fibrosis individuals 2009 plos one 4 10 e7370 doi 10 1371 journal pone 0007370 free article image credits cartoons by sanja saftic many thanks to her for allowing me to use the cartoons for this blog post source biotoon com microbiological edutainment color enhanced scanning electron microscope sem image of a biofilm formed by desulfovibrio desulfuricans ba...