Novel method to produce biofuel - by E.coli!

As an (originally) environmental microbiologist, I was very pleased when reading the news, delivered by BBC web site, tonight:

A novel biotech method, based on the growth of coliform bacteria, has recently been tested in laboratory conditions by British scientists. This sounds very promising because the simple nutritive requirements and rapid growth of coliforms. E.coli has the world record of growth rates: it can duplicate in 20 minutes when growth environment is optimal. In addition, coliforms can use sugars, derived from mechanical pulp manufacture - suits also to Finland?

http://www.bbc.co.uk/news/science-environment-22253746

From paper industry to mining environment

After my career as paper industry microbiologist (1983 - 2009) I have totally reoriented towards environmental problems of mining industry today.

 Reasons for the closure of the paper microbiology development is the depression of this industrial area. No interest in rapid control methods can be found anymore. Positive attitudes still exist (esp. in Finnish innovation organisations) but "money rules" today. No economical support can be found for e.g. luminometric ON LINE methods from paper companies - and it is really a pity.

Short summary of my career in paper microbiology:

I actually started as environmental microbiologist in HU / Dep.of Microbiology, Helsinki, Viikki. I recall shortly the most interesting projects in the beginning of 80's: cyanobacteria, nitrogen fixation, Bacillus-based insecticides, soil microbiology, coliform research..and then I found myself in the projects of prof. Seppo Niemelä. We were able to perform species analyses of different waste water types and found the best indicators of paper industry effluents which were led to Lake Lohjanjärvi. Growth temperature ranges of most important indicator coliforms were also determined by Tmax method. Several scientific analyses were written and I started my doctoral thesis about environmental and clinical species of a certain coliform. - Thank you, Leena, for your help to detect plasmid-bound antibiotic resistances!

A big chance of my career happened in Autumn 1986 when I was accepted to work as the research microbiologist for Enso-Gutzeit Ltd. I had to leave my doctoral work (all documents still in my book shelf!) but I got a job where I learned everything about paper industry microbiology - from raw materials up to waste waters! There were countless persons who helped me to understand the world of paper making - I will thank them all  because the name list would be too long to be published.

After some reorientation in my private life I headed towards Jyväskylä in 2006 and had the great chance to work with late prof. Christian Oker-Blom (R.I.P., Chrisse!). We constructed several project proposals for paper industry with several Finnish and foreign companies but it seemed that there were no money left for this kind of projects in paper companies anymore. Some interesting projects of air quality etc. then follows (thank you, Markus!) in the last years of 00's.

The last post of mine was the key account director of Samplion Ltd. No matter my title, I was able to perform real laboratory evaluations in JAMK laboratory and field tests in paper and paper additive companies - interesting!

In addition to the posts mentioned, I have worked as a part-time teacher for professional teaching organisations (especially TL, AEL, POHTO), companies and universities of applied sciences (especially Imatra, Jyväskylä, Kotka).

Today, as formally retired, I am more and more activated in environmental microbiology (greetings to Helge and BIOTECHTOUCH!). Coming back to those years in Viikki - the circle is now closed. I wonder if I have to reconstruct my blog but let it wait...I'll try to inform my readers in Twitter and Facebook about my reorientation. Please follow the key word "Talvivaara"...!

A new era in microbiology: back to Pasteur's times?

(first published April 25th 2010 by Juha V. Mentu)

The history of microbiology contains several eras with different targets. I will refer them in this way (based on my over 30 years experience as microbiologist and teacher of microbiology and biochemistry):

In the beginning, cultivation and observation of microorganisms was the main target. Doctors like Pasteur and Koch were very innovative and developed intelligent culture medias and vessels to perform very delicate experiments. The everlasting fight against pathogenic microbes was the primary target but Louis Pasteur started to help eg. wine producers to solve their quality problems, caused by microbes.

The combination of microbiology and biochemistry on the second era was very satisfying by solving questions concerning the huge amount of anabolic and catabolic processes included in microbial growth. More and more were also learned in the area of microbial ecology. Questions like "who? what? when? where? how? why?" were partially solved (ref. MADSEN,E.L. 2008. Environmental Microbiology. From Genomes to biochemistry. Blackwell Publishing).

"Third era" can be described by the novel methods to identify bacteria. Biochemical test kits (API etc.) were replaced by Fatty Acide Methylated Ester method (FAME) by Hewlett-Packard on 80's. After it, molecular biology methods, based on ribosomal RNA and DNA, helped to construct the development lines of microorganisms.

Today is the time of new era. We know the "family trees" of bacteria but we should now continue with environmental microbiology and microbial ecology to solve questions like "How, why, by whom and in which conditions will the raw materials of paper industry be biodeteriorated?", "How can we prevent these processes by setting the process conditions unsuitable for those biochemical processes?", "Can we prevent the growth of biofilms and slimes in an ecological way?", "How to prevent selectively the growth of toxin producers like Bacillus cereus in paper and board processes?", how to fight against Legionella in paper industry?".

Names are not the most important thing. Most important is, how the bacteria act in different ecological niches of a paper machine. This work has to be done by using simulations of paper processes which is possible by wet end simulators of research units (as an example: VTT in Jyväskylä, Finland) and laboratory/field instruments.

We are - and we shall - turn back to the era of Pasteur & Koch: the names are already known, and we shall now investigate, what the contaminating microbes are doing in the industrial processes and how to prevent losses of raw material, machine stops and poor quality of the products by simulating growth processes in small-scale tests, performed in the laboratory or in the field, by the machines themselves.

Monitoring of microbial growth and sporulation

pH, temperature, nutrients and biocides are usually observed when the risks of microbial growth and sporulation inside paper machines should be estimated. Fourth important factor, time, will be often ignored, no matter it plays a most significant role in paper process microbiology. The simple figure above shows two important parameters which reveal the microbiological status of the white water in an anonymous paper machine (my personal data ca. 2006): Colony Count (CC, indicating the count of vegetative bacterial cells per ml) and Spore Count (SC, indicating the count of bacterial spores per ml). It is obvious that this very sample contains relatively high amounts of nutrients to secure the rapid growth of bacteria (the growth rates of bacteria, carried by white water, are usually much lower but bacterial densities, in opposite, on a very high, stabile levels). What is especially important in this case is the rapid increase of bacterial spores - producers of process biofilms after their outgrowth and risks for product hygiene in their original form - which seems to take place after ca. 0,5 days storage time. This event takes place practically always when the flow of white water, pulp and broke have been stopped during the delays of constant machine operation. The hygiene status of the total process would then be very important to know - how much spoiled water and broke can be supplied from towers to the process, are there risks to have biodeteriorated raw materials from the storage tanks, is there any need to use shock dosing of biocides in some sites etc. - but it cannot be done by using CC, SC or any other cultivation technique which give analytical results only after several days' incubation periods. Long analytical delays in colony count analyses also totally prevent the efficient application of HACCP hygiene control procedures into paper machine environment. - These are the facts which motivate me personally to continue planning rapid, ON LINE process hygiene methods.

Microbiology Services for Paper Industry by BIOTECHTOUCH

BIOTECHTOUCH is a group of consulting specialists for process industry and environmental research. Our main competence areas are biocides, microbiology and toxicology. We have focused especially on the problems of paper industry (raw material, process and product hygiene as well as effects of waste waters on recipients). This is also my own area of activity today, after my departure from my previous post in SAMPLION Ltd.

Future methods for P&P microbiology.

It seems that new methods for P&P microbiology are needed.

After discussions in PulPaper Congress in Helsinki, June 2010, it is obvious that traditional colony count methods cannot tell the truth about process problems.

These methods, originally developed for clinical microbiology, seem to have too high nutrient content. They cannot, therefore, select the "troublemakers" from the process samples. Bacteria like Gram-negative rods and Bacillus sp. are overestimated in these analyses but eg. filamentous bacteria cannot grow on common, commercial agar media.

Identification of bacteria can be important in some cases. Food poisoning species from the genuses Bacillus, Staphylococcus and Clostridia and hygiene indicators like coliforms, E.coli and Enterococci should be found in raw material control in the production of high hygiene products (LPB, other food-grade cartonboards and papers as well as tissue-type products). If not covered by other bacteria, they can be found with CC analyses. PCR also gives a good way to distinct them among other bacteria.

These methods cannot reveal some severe problems, however. Biofilm formation and comparative biocide testing are two types of investigations which cannot be performed with agar cultivations or molecular biology methods. They should be done either in machine trials or simulations. PMEU methods seem to be the best alternatives for rapid evaluation of biofilm formation and biocide testing today because they exclude all artefacts, caused by artificial growth medium (in colony counts) or too high selection of microorganisms (in PCR). CC's and PCR can be adopted to certain tests but when the subject of the study is to see, what happens in the real paper processes, simulation methods like PMEU shall be chosen.

Trends in environmental microbiology with references from paper industry microbiology

The history of microbiology contains several eras with different targets. I will refer them in this way (based on my over 30 years experience as microbiologist and teacher of microbiology and biochemistry):

In the beginning, cultivation and observation of microorganisms was the main target. Doctors like Pasteur and Koch were very innovative and developed intelligent culture medias and vessels to perform very delicate experiments. The everlasting fight against pathogenic microbes was the primary target but Louis Pasteur started to help eg. wine producers to solve their quality problems, caused by microbes.

The combination of microbiology and biochemistry on the second era was very satisfying by solving questions concerning the huge amount of anabolic and catabolic processes included in microbial growth. More and more were also learned in the area of microbial ecology. Questions like "who? what? when? where? how? why?" were partially solved (ref. MADSEN,E.L. 2008. Environmental Microbiology. From Genomes to biochemistry. Blackwell Publishing).

"Third era" can be described by the novel methods to identify bacteria. Biochemical test kits (API etc.) were replaced by Fatty Acide Methylated Ester method (FAME) by Hewlett-Packard on 80's. After it, molecular biology methods, based on ribosomal RNA and DNA, helped to construct the development lines of microorganisms.

Today is the time of new era. We know the "family trees" of bacteria but we should now continue with environmental microbiology and microbial ecology to solve questions like "How, why, by whom and in which conditions will the raw materials of paper industry be biodeteriorated?", "How can we prevent these processes by setting the process conditions unsuitable for those biochemical processes?", "Can we prevent the growth of biofilms and slimes in an ecological way?", "How to prevent selectively the growth of toxin producers like Bacillus cereus in paper and board processes?", how to fight against Legionella in paper industry?".

Names are not the most important thing. Most important is, how the bacteria act in different ecological niches of a paper machine. This work has to be done by using simulations of paper processes which is possible by wet end simulators of research units (as an example: VTT in Jyväskylä, Finland) and laboratory/field instruments (like biofilm detectors in the processes or PMEU incubators by Samplion Ltd.).

The role of PMEU is getting more and more important because this method helps to detect microbial growth of different types (biofilms included) in a very short period of time as well as to test simultaneously the effects of alternative biocides in small-scale tests whose growth parameters match with the growth conditions in the real processes.

We are - and we shall - turn back to the era of Pasteur & Koch: the names are already known, and we shall now investigate, what the contaminating microbes are doing in the industrial processes and how to prevent losses of raw material, machine stops and poor quality of the products by simulating growth processes in small-scale tests, performed in the laboratory or in the field, by the machies themselves.