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Friday, April 25, 2008

article : Why Forgive?

Johann Christoph Arnold

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Why Forgive?Forgiveness has become a buzzword, but people still don’t understand it. They don’t realize its rewards—or the cost of refusing to forgive. Many think forgiving means excusing, forgetting, or ignoring their pain. They view it as weakness. Why Forgive? brings together survivors of crime, betrayal, bigotry, and abuse—and ordinary men and women plagued by everyday strife. Not all are ready to forgive. But all are determined not to let anger, bitterness, and despair control their lives. Together, their stories will challenge and encourage others wherever they are on the road to healing.

In Why Forgive? Arnold lets the untidy experiences of ordinary people speak for themselves—people who have earned the right to talk about overcoming hurt, and about the peace of mind they have found in doing so.

“Hurt” is an understatement, actually, for many of these stories deal with the harrowing effects of violent crime, betrayal, abuse, bigotry, and war. But Why Forgive? examines life’s more mundane battle scars as well: the persistent hobgoblins of backbiting, gossip, strained family ties, marriages gone cold, and tensions in the workplace.

As in life, not every story has a happy ending—a fact Arnold refuses to skirt. The book also addresses the difficulty of forgiving oneself, the futility of blaming God, and the turmoil of those who simply cannot forgive, even though they try.

In his autobiography, Bill Clinton writes that Why Forgive?, formerly titled Seventy Times Seven, helped him through the darkest days of his presidency, following the Monica Lewinsky scandal.

Houston Chronicle
Arnold is thought-provoking and soul-challenging…He writes with an eye-opening simplicity that zings the heart.

Paul Brand
This is the book I would choose to give friends who are justifiably angry. A powerful statement on the importance of forgiveness in human psychology.

Madeleine L’Engle
Beautiful…We recognize ourselves in the poignant stories, and our recognition helps us to forgive. This is a book the whole world needs.

This book in other languages:
فن الغفران المفقود
Vergebung leben, Freiheit erfahren
Pourquoi Pardonner?
Setenta veces siete
잃어버린 기술 “용서”

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article : Sex, God and Marriage

Johann Christoph Arnold

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Sex, God and MarriageUnlike the vast majority of marriage books, Sex, God, and Marriage digs deeper than the usual “issues” and goes to the root: our relationship with God, and the defining power of that relationship over all others in our lives. Arnold addresses the deep pain resulting from the cycle of broken relationships and the misuse of sexual intimacy. His words offer healing, a new beginning, and a sense of hope to those who have experienced discouragement or failure.

Includes chapters on sex, alternatives to dating, parenthood, singleness, homosexuality, abortion, divorce and remarriage. Sex, God and Marriage carries a foreword by Mother Teresa and was formerly titled A Plea for Purity.

Also available, a free study guide to facilitate group discussion or personal study:
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This book in other languages:
Un llamado a la pureza
Sex, Gott und Ehe
아름다운 약속, 순결
الجنس والزواج في فكر الله

Francis Cardinal Arinze
Clear, incisive, and uplifting…this book should be very helpful in living the virtue of chastity, which is God’s will for all men and women.

Bill Beckman, Office of Catechetics, Archdiocese of Denver

An excellent biblical reflection on sex, marriage and God. Its message is clear, accessible and crucial. I recommend it as a good foundation for parents, teachers, catechists, couples preparing for marriage, and highschool and college students.

Paul Brand, M.D., author, Pain: The Gift Nobody Wants

A clear message for those who have seen the so-called freedom of sexual pleasure become a source of loneliness or pain….This book will help young people to hold on to purity.

Joan Brown Campbell, National Council of Churches
A cogent, well-reasoned approach to today’s troubling questions. Some may disagree with this or that conclusion, but all will acknowledge Arnold’s sincerity and his contribution to these debates.

Joseph M. Champlin, Cathedral of the Immaculate Conception, Syracuse, NY
Arnold writes with clarity, conviction, and compassion. His detailed analysis and very practical applications underscore the Catechism’s general principles.

Robert L. Cleath, California Polytechnic Univ.
A wise book…Arnold’s deep faith in Christ and the Bible shines through on every page as he faces the spiritual, emotional, and physical dimensions of marriage…Couples will find Arnold’s book a Spirit-led guide for true happiness in their life together.

William A. Dyrness, Fuller Theological Seminary
Striking for its clear and penetrating presentation of simple (and yet immensely profound) biblical truths about human sexuality. I wish everyone could read this call to cut through the complications of modern life by a holy and Christ-like life.

Bob Fryling, InterVarsity Christian Fellowship
Does a wonderful job of putting sex into the larger contexts of Creation, the church, and marriage. Not everyone will agree with all of Arnold’s specific conclusions, but every mature believer will benefit from the convictions reflected in this book.

Vernon Grounds, Denver Seminary
A sensitive yet forthright articulation of the basic biblical perspective on purity in sexual conduct. I am very grateful for its unabashed emphasis on holiness in this area of life. Arnold’s message bears a clear witness and will provoke serious soul-searching.

David P. Gushee, Southern Baptist Theological Seminary
Inspiring and challenging…suffused with a biblical reverence for human life. One does not have to agree with every stance articulated in the book to be edified by its moral vision.

William A. Heth, co-author, Jesus and Divorce
Sex, God and Marriage is about the Creator’s intentions for the human family….It is about loving, committed, honest relationships lived out in the midst of a world bewildered by its inability to deliver on promises of happiness….

Alice von Hildebrand, Hunter College/CUNY
Arnold’s beautiful presentation of the great virtue of purity should be in the hands of every educator and every teenager. It is a message that is desperately needed today, and I cannot recommend it strongly enough.

Jay Kesler, Taylor University
This book is a beacon in our midst, and it should make us to look at what we have become as a society in light of radical Christianity. Few will find everything in the book acceptable, but all who read it prayerfully will be challenged to purity. In a world where conviction is a rare thing, this book is a treasure in a field.

Peter Kreeft, Boston College
Clear, compassionate, uncompromisingly Christian, and straight from (and to) the heart…Pretty close, I think, to what Jesus would say if he were to write a book about sex today—and probably as socially acceptable as He was.

J. Carl Laney, Western Seminary
A clarion call to return to God’s high and holy standard regarding sex and marriage, and a rich resource of practical advice.

Steve de Mott, Maryknoll Magazine
Profoundly significant…While the moral demands of the book are strong and clear, the book is much more positive than negative. I found myself wishing that adults had spoken to me in such a positive vein about these matters when I was a child.

Richard John Neuhaus, First Things
Human sexuality is here drawn fully into the life of discipleship. The result is both demanding and exhilarating, which is what disciples of Jesus should expect.

J. I. Packer, Regent College
This is the work of a very wise man with a very clear vision of God’s ideal for marriage and family… Simple and short, but deep, this is one of the best books available on handling our sexuality in a way that honors God.

Chris Rice, author, More Than Equals
A passionate call back to standards that, in the long run, will lead to true joy and contentment.

William H. Willimon, Duke University Chapel

Arnold writes simply, eloquently, and faithfully. Sex, God and Marriage is a relentless, biblical, call for renewed Christian commitment. Advocates of accommodated, acculturated Christianity will find little comfort in these pages; struggling disciples, however, will be much encouraged.

Richard Rohr, O.F.M., Center for Action & Contemplation
Some Christians might not say it in the same way, or with the same emphasis on certain issues, but the underlying values in Sex, God and Marriage are strong, needed, and consistent. I admire and support such lived faith as I find in this book.

Fr. Kris Stubna, Diocese of Pittsburgh
A marvelous exposition on the true values of family life, the beauty of marriage, and human sexuality as God intended it to be…A great resource for Catholic educators.

Paul C. Vitz, New York University
To advocate an ideal of sexual purity is perhaps the last American taboo. But if anything will awaken our society from its decadent slumber, it may be the spectacle of large numbers of people actually living a life of sexual virtue. This book provides a wise spiritual guide on how, and why, to lead such a life.

The author makes his plea in an uncompromising way, and there is something here to offend almost everyone. Yet no one can doubt his sincerity and consistency.

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article : Love Letters

Eberhard Arnold and Emmy von Hollander

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Love LettersEveryone’s looking for true love, but few people seem willing to work at making it last. With separation and divorce so commonplace that most people see them as inevitable, it seems the very idea of marital commitment is fast becoming a foreign one. What’s gone wrong?

On Good Friday 1907, in the German university town of Halle, a young couple sealed their secret engagement with a kiss – and a vow to follow God wherever he led them. They were passionately in love, yet they rejected romance as the basis of their relationship, building instead on the promise of Jesus’ words, “Seek first the kingdom of God.” Circumstance (and scandalised parents) kept them separated for most of the next three years. But that separation bore its own fruit: an intense exchange of letters.

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Buy at Amazon UK

Anthony Tony Campolo, Eastern University
More than love letters. They show how a man and a woman can nurture each other toward spiritual maturity.

Frederica Mathewes-Green, author of The Lost Gospel of Mary
These letters disclose the writers’ burning commitment to the Lord above all else, and demonstrate how it became the foundation of the commitment they bore to each other. Such clarity and passion are rarely seen these days.

Father Philip K. Eichner, S.M. Catholic League for Religious and Civil Rights
A rare find. It is a privilege to be invited into such an intimate conversation.

Prof. John Briggs, Oxford University
Here are letters of both immense intensity and the deepest intimacy, almost too sacred for publication. They witness to a deeply based love nurtured in the context of an absolute commitment to Christ.

Prof. Lawrence S. Cunningham, The University of Notre Dame
These inspiring letters interweave a profound love for Jesus Christ with a deep love between two young people, as well as an utterly transparent search to do God’s will.

Denton Lotz, General Secretary, Baptist World Alliance

For modern secular humanity these Love Letters of Eberhard and Emmy Arnold must seem from another planet! But for Christian believers these letters are a powerful reminder of God’s transformation of ordinary human relationships into divine grace and the mystery of God’s love. Love Letters portrays the depth of human emotions that can be kindled by expressing through the written word the meaning and purpose of Christ’s love.

With enthusiasm I commend reading these letters for one’s own spiritual growth. In so doing one will also gain a greater appreciation for the tremendous spiritual movement that renewed the Church universal at the end of the 19th and beginning of the 20th century. This renewal raised up a generation of young men and women completely dedicated to Christ and the evangelisation of the world in their generation. The love story of Eberhard and Emmy is a thrilling testimony of what complete commitment and obedience to Christ can do. Read it, pray about it, and your marriage will take on new life and joy!

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article : Molecular pathogenicity of the oral opportunistic pathogen Actinobacillus actinomycetemcomitans.

Publication: Annual Review of Microbiology

Publication Date: 01-JAN-03

Author: Henderson, Brian ; Nair, Sean P. ; Ward, John M. ; Wilson, Michael

COPYRIGHT 2003 Annual Reviews, Inc.

* Abstract Periodontitis is mankind's most common chronic inflammatory disease. One severe form of periodontitis is localized aggressive periodontitis (LAP), a condition to which individuals of African origin demonstrate an increased susceptibility. The main causative organism of this disease is Actinobacillus actinomycetemcomitans. A member of the Pasteurellaceae, A. actinomycetemcomitans produces a number of interesting putative virulence factors including (a) an RTX leukotoxin that targets only neutrophils and monocytes and whose action is influenced by a novel type IV secretion system involved in bacterial adhesion; (b) the newly discovered toxin, cytolethal distending toxin (CDT); and (c) a secreted chaperonin 60 with potent leukocyte-activating and bone resorbing activities. This organism also produces a plethora of proteins able to inhibit eukaryotic cell cycle progression and proteins and peptides that can induce distinct forms of proinflammatory cytokine networks. A range of other proteins interacting with the host is currently being uncovered. In addition to these secreted factors, A. actinomycetemcomitans is invasive with an unusual mechanism for entering, and traveling within, eukaryotic cells. This review focuses on recent advances in our understanding of the molecular and cellular pathogenicity of this fascinating oral bacterium.

Key Words periodontitis, gingivitis, microbiota, cellular microbiology, bacterial virulence



Ninety percent of the cells in the human body are prokaryotic (170). The study of the human microbiota has largely centered on those organisms that live in the gastrointestinal tract. However, in the past few decades increasing attention has been devoted to the oral cavity. We now realize that this extremely complex organ, which is the center of one of our senses (taste) and is responsible for our capacity to communicate, contains an immensely complex population of bacteria (138) every bit as diverse as that found in the gut--and much more accessible. As recently argued by Rehnan & Falkow (143), there is a pressing need to understand how our microbiota interacts with us. This is particularly true of the oral microbiota, which is the source of significant human pathology.


The recent report of the Surgeon General has estimated that in the United States severe periodontal disease affects 14% of adults aged 45-54 and 23% of adults aged 65-74 (131a). Periodontitis is the result of the response of the periodontium to the presence of certain members of the oral microbiota. One of the most severe forms of periodontal disease is localized aggressive periodontitis (LAP), which is associated with the subject of this review.

A. actinomycetemcomitans and Localized Aggressive Periodontitis

Adult periodontitis can affect all the teeth. In contrast, localized juvenile periodontitis (LJP), which has been recently renamed LAP (4), affects only certain teeth--the incisors and premolars. This predilection may be the result of selective colonization of the teeth. The disease tends to afflict younger individuals and, as its name implies, is associated with rapid destruction of the periodontal ligament and alveolar bone, which support the teeth. Evidence has accrued to support the hypothesis that A. actinomycetemcomitans is one of the key organisms responsible for the pathogenesis of LAP (159). The prevalence of LAP is not uniform among the world's populations. In the United States the mean prevalence was 0.53% among adolescents of all racial origins. Adolescents of African-American descent, in contrast, were found to have a 15-fold-higher incidence of disease than Caucasian Americans (96). In Brazil 3.7% of 15- to 16-year-old adolescents examined had LAP (42), while in Nigeria a prevalence of 0.8% was found (46, 97).

The possibility that LAP is a genetic disease has been under consideration since the early 1980s (110). Defects in neutrophil function have been a recurring theme (20, 155), and decreased neutrophil chemotaxis to the bacterial chemoattractant formyl-methionine-leucine-phenylalanine (FMLP) was an early finding (101). This bacterial peptide is a ligand for the N-formyl peptide receptor (FPR), a G-protein-coupled receptor (110). Currently, genes encoding three FPR proteins have been identified in Homo sapiens (93). Single nucleotide polymorphism analysis of 30 patients with LAP revealed that 29 had one of two point mutations in the FPR gene (43). Both mutations are associated with almost complete loss of receptor signaling in response to FMLP (150). If these results are substantiated, they raise the key question of why this major defect in recognition of FMLP does not result in general susceptibility to bacteria.

Extra-Oral Pathology Caused by A. actinomycetemcomitans

A. actinomycetemcomitans is occasionally responsible for non-oral infections including endocarditis, bacteremia, pericarditis, septicemia, pneumonia, infectious arthritis, osteomyelitis, synovitis, skin infections, urinary tract infections, and abscesses (178). It has been estimated that approximately 0.6% of cases of infective endocarditis are caused by A. actinomycetemcomitans (17).

Currently there is great interest in the possibility that periodontal diseases may be a risk factor for development of cardiovascular disease (41); A. actinomycetemcomitans has been detected in 18% of atherosclerotic plaque samples (45).


A. actinomycetemcomitans is a small nonmotile gram-negative coccobacillus that grows singly, in pairs, or in small clumps and is variously described as facultatively anaerobic, microaerophilic, and capnophilic. Growth is enhanced by the presence of 5% C[O.sub.2] (133) and the organism grows best at 37[degrees]C. The optimum pH range for growth is between 7.0 and 8.0 (163). In liquid media the organism forms isolated translucent granules that adhere to the sides and bottom of the tube with the broth itself remaining clear. On agar small translucent circular colonies (approximately 1-mm diameter after 2-3 days) with a slightly irregular edge are formed, and these tightly adhere to the agar surface. These "rough" colonies have a characteristic crossed-cigar or star-like appearance when viewed with a low-power microscope. Pitting of the agar occurs underneath the colony, resulting eventually in the colony becoming embedded in the agar medium. Ariel repeated subcultures the star-shape often disappears and the colonies become smooth and opaque and do not cause pitting of the agar. This transformation from rough to smooth phenotype is associated with the loss of fimbriae (62). Rough colony variants expressing fimbriae adhere better to hydroxyapatite and to saliva-coated hydroxyapatite than do the smooth colony variants (145).

The natural habitat of A. actinomycetemcomitans is the oral cavity of man and other mammals (5, 6, 8, 23). Within the human oral cavity A. actinomycetemcomitans has been isolated from a range of habitats including supragingival plaque, subgingival plaque, saliva, cheek mucosa, buccal mucosa, gingivae, tongue (dorsal and lateral surfaces), hard palate, and tonsils (5, 116). Furthermore, the organism can be detected in the oral cavity of periodontally healthy individuals as well as in those with periodontitis (57).

Significant advances have been made in understanding the molecular genetics of this bacterium. In a screening of wild-type isolates of A. actinomycetemcomitans for the presence of endogenous plasmids, only three plasmids were found out of 39 strains examined (94). The A. actinomycetemcomitans strain VT745 has the 25.42-kb plasmid pVT745, which has been completely sequenced (35). It contains 36 open reading frames (ORFs) and has a type IV secretion system, involved in conjugation of the plasmid, covering 12 kb of the plasmid (35, 130a). The plasmid carries no functional antibiotic resistance gene (it has an interrupted ROB [beta]-lactamase), hut derivatives with a cloned kanamycin resistance gene could transfer only to other A. actinomycetemcomitans strains. Such derivatives could mobilize the IncQ group plasmid pMMB67 into Escherichia coli. Derivatives of pVT745 with an integrated E. coli plasmid origin of replication could transfer to E. coli. The type IV secretion system from the plasmid is homologous to a type IV secretion system found on the chromosome of several A. actinomycetemcomitans strains (though not the parent strain from which pVT745 came), but it is not known what the chromosomally located type IV secretion systems can secrete.

The two other naturally occurring plasmids found in the screen of 39 strains were pVT736-1, which was only 2 kb, and pVT736-2, which was >30 kb. pVT736-2 is a rolling circle replicon, a type of plasmid more commonly associated with gram-positive bacteria (37-39). The small cryptic plasmid pVT736-1 has been made into shuttle replicons by fusing it to the E. coli plasmid ColEI(161), pUC, or p15a (120). A derivative of pVT736-1 with the E. coli plasmid p15a replicated in A. actinomycetemcomitans was used to propagate DNA from this bacterium, first in E. coli with subsequent transfer to A. actinomycetemcomitans (39). Structural instability was seen in a variety of the shuttle vectors, and those without an A. actinomycetemcomitans replicon or a broad-host-range replicon were lost after 100 generations of nonselective growth (39).

A. actinomycetemcomitans is a gram-negative bacterium, and as such, broad-host-range plasmids of the IncP, IncQ, and IncW group should replicate in it. Derivatives of the IncP group plasmid R995 were used to show that the IncC/KorB partition system of IncP group plasmids is effective in A. actinomycetemcomitans (157), and several reports have shown that IncQ group plasmids such as derivatives of pMMB67 (36, 39) replicate in A. actinomycetemcomitans.

A. actinomycetemcomitans is transformable by electroporation when using plasmid DNA (33, 162) and there is a natural competence system analogous to the extensively studied Haemophilus influenzae DNA uptake system (179). The natural competence system involves the cleavage and processing of linear DNA fragments during uptake and this has been manipulated to generate an efficient method of gene replacement for A. actinomycetemcomitans (179). Another useful tool for the manipulation of A. actinomycetemcomitans is the inducible transposon IS903[phi]kan on the IncQ plasmid pVJT128 (173) that has been used to create libraries of random insertion mutants. From insertion libraries using this transposon, a catalase-deficient mutant was isolated (173) and the tight adherence operon (tad) was defined (69). A more conventional kind of gene knockout was used to generate a recA mutant of A. actinomycetemcomitans, SUNY 465 (111). A recombination deficient strain will have uses in propagating cloned segments of the A. actinomycetemcomitans chromosome for complementation studies.


Serological Diversity of A. actinomycetemcomitans

Currently six serotypes (a-f) are recognized (72). The immunodominant antigen is a high-molecular-mass O-polysaccharide of the lipopolysaccharide (LPS) (136). The O-polysaccharides of serotypes b, c, e, and f are the product of homologous gene clusters containing between 10 (serotype e) and 16 (serotype b) genes with highly conserved groups of genes at the proximal and distal ends and the central genes being unique to each cluster and containing a lower GC content (72). These serotype-specific gene clusters may have evolved from a common ancestral cluster by interspecific gene transfer from a...

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article : Sterilization in Microbiology

Sterilization (or sterilisation, see spelling differences) refers to any process that effectively kills or eliminates transmissible agents (such as fungi, bacteria, viruses, prions and spore forms etc.) from a surface, equipment, foods, medications, or biological culture medium. Sterilization can be achieved through application of heat, chemicals, irradiation, high pressure or filtration.


There are two types of sterilization: physical and chemical.

Physical sterilization includes:

  1. heat sterilization
  2. radiation sterilization

Chemical sterilization includes:

  1. ethylene oxide
  2. ozone
  3. chlorine bleach
  4. glutaraldehyde
  5. formaldehyde
  6. hydrogen peroxide
  7. peracetic acidv
  8. prions


Heat sterilization of medical instruments is known to have been used in Ancient Rome, but it mostly disappeared throughout the Middle Ages resulting in significant increases in disability and death following surgical procedures.

Preparation of injectable medications and intravenous solutions for fluid replacement therapy requires not only a high sterility assurance level, but well-designed containers to prevent entry of adventitious agents after initial sterilization.

Food sterilization is usually considered a harsher form of Pasteurization[1], and is carried out through heating, though other methods are available. Food sterilization is commonly a part of canning and is used in combination with or instead of preservatives, refrigeration, and other ways to preserve food.

Heat sterilization

Steam sterilization

Front-loading autoclaves are very common.
Front-loading autoclaves are very common.

A widely-used method for heat sterilization is the autoclave. Autoclaves commonly use steam heated to 121 °C or 134 °C. To achieve sterility, a holding time of at least 15 minutes at 121 °C or 3 minutes at 134 °C is required. Additional sterilizing time is usually required for liquids and instruments packed in layers of cloth, as they may take longer to reach the required temperature. After sterilization, autoclaved liquids must be cooled slowly to avoid boiling over when the pressure is released.

Proper autoclave treatment will inactivate all fungi, bacteria, viruses and also bacterial spores, which can be quite resistant. It will not necessarily eliminate all prions.

For prion elimination, various recommendations state 121–132 °C (270 °F) for 60 minutes or 134 °C (273 °F) for at least 18 minutes. The prion that causes the disease scrapie (strain 263K) is inactivated relatively quickly by such sterilization procedures; however, other strains of scrapie, as well as strains of CJD and BSE are more resistant. Using mice as test animals, one experiment showed that heating BSE positive brain tissue at 134-138 °C (273-280 °F) for 18 minutes resulted in only a 2.5 log decrease in prion infectivity. (The initial BSE concentration in the tissue was relatively low). For a significant margin of safety, cleaning should reduce infectivity by 4 logs, and the sterilization method should reduce it a further 5 logs.

To ensure the autoclaving process was able to cause sterilization, most autoclaves have meters and charts that record or display pertinent information such as temperature and pressure as a function of time. Indicator tape is often placed on packages of products prior to autoclaving. A chemical in the tape will change color when the appropriate conditions have been met. Some types of packaging have built-in indicators on them.

Biological indicators ("bioindicators") can also be used to independently confirm autoclave performance. Simple bioindicator devices are commercially available based on microbial spores. Most contain spores of the heat resistant microbe Bacillus stearothermophilus, among the toughest organisms for an autoclave to destroy. Typically these devices have a self-contained liquid growth medium and a growth indicator. After autoclaving an internal glass ampule is shattered, releasing the spores into the growth medium. The vial is then incubated (typically at 56 °C (132 °F)) for 48 hours. If the autoclave destroyed the spores, the medium will remain its original color. If autoclaving was unsuccessful the B. sterothermophilus will metabolize during incubation, causing a color change during the incubation.

For effective sterilization, steam needs to penetrate the autoclave load uniformly, so an autoclave must not be overcrowded, and the lids of bottles and containers must be left ajar. During the initial heating of the chamber, residual air must be removed. Indicators should be placed in the most difficult places for the steam to reach to ensure that steam actually penetrates there.

For autoclaving, as for all disinfection of sterilization methods, cleaning is critical. Extraneous biological matter or grime may shield organisms from the property intended to kill them, whether it physical or chemical. Cleaning can also remove a large number of organisms. Proper cleaning can be achieved by physical scrubbing. This should be done with detergent and warm water to get the best results. Cleaning instruments or utensils with organic matter, cool water must be used because warm or hot water may cause organic debris to coagulate. Treatment with ultrasound or pulsed air can also be used to remove debris.

Other methods

Other heat methods include flaming, incineration, boiling, tindalization, and using dry heat.

Flaming is done to loops and straight-wires in microbiology labs. Leaving the loop in the flame of a Bunsen burner or alcohol lamp until it glows red ensures that any infectious agent gets inactivated. This is commonly used for small metal or glass objects, but not for large objects (see Incineration below). However, during the initial heating infectious material may be "sprayed" from the wire surface before it is killed, contaminating nearby surfaces and objects. Therefore, special heaters have been developed that surround the inoculating loop with a heated cage, ensuring that such sprayed material does not further contaminate the area.

Incineration will also burn any b organism to ash. It is used to sanitize medical and other biohazardous waste before it is discarded with non-hazardous waste.

Boiling in water for 15 minutes will kill most vegetative bacteria and viruses, but boiling is ineffective against prions and many bacterial and fungal spores; therefore boiling is unsuitable for sterilization. However, since boiling does kill most vegetative microbes and viruses, it is useful for reducing viable levels if no better method is available. Boiling is a simple process, and is an option available to most people, requiring only water, enough heat, and a container that can withstand the heat; however, boiling can be hazardous and cumbersome.

Dry heat can be used to sterilize items, but as the heat takes much longer to be transferred to the organism, both the time and the temperature must usually be increased, unless forced ventilation of the hot air is used. The standard setting for a hot air oven is at least two hours at 160 °C (320 °F). A rapid method heats air to 190 °C (374 °F) for 6 minutes for unwrapped objects and 12 minutes for wrapped objects.[1][2] Dry heat has the advantage that it can be used on powders and other heat-stable items that are adversely affected by steam (for instance, it does not cause rusting of steel objects).

Prions can be inactivated by immersion in sodium hydroxide (NaOH 0.09N) for two hours plus one hour autoclaving (121 °C/250 °F). Several investigators have shown complete (>7.4 logs) inactivation with this combined treatment. However, sodium hydroxide may corrode surgical instruments, especially at the elevated temperatures of the autoclave.

Chemical sterilization

Chemicals are also used for sterilization. Although heating provides the most reliable way to rid objects of all transmissible agents, it is not always appropriate, because it will damage heat-sensitive materials such as biological materials, fiber optics, electronics, and many plastics.

Ethylene oxide (EO or EtO) gas is commonly used to sterilize objects sensitive to temperatures greater than 60 °C such as plastics, optics and electrics. Ethylene oxide treatment is generally carried out between 30 °C and 60 °C with relative humidity above 30% and a gas concentration between 200 and 800 mg/L for at least three hours. Ethylene oxide penetrates well, moving through paper, cloth, and some plastic films and is highly effective. Ethylene oxide sterilizers are used to process sensitive instruments which cannot be adequately sterilized by other methods. EtO can kill all known viruses, bacteria and fungi, including bacterial spores and is satisfactory for most medical materials, even with repeated use. However it is highly flammable, and requires a longer time to sterilize than any heat treatment. The process also requires a period of post-sterilization aeration to remove toxic residues. Ethylene oxide is the most common sterilization method, used for over 70% of total sterilizations, and for 50% of all disposable medical devices.

The two most important ethylene oxide sterilization methods are: (1) the gas chamber method and (2) the micro-dose method. To benefit from economies of scale, EtO has traditionally been delivered by flooding a large chamber with a combination of EtO and other gases used as dilutants (usually CFCs or carbon dioxide ). This method has drawbacks inherent to the use of large amounts of sterilant being released into a large space, including air contamination produced by CFCs and/or large amounts of EtO residuals, flammability and storage issues calling for special handling and storage, operator exposure risk and training costs. Because of these problems a micro-dose sterilization method was developed in the late 1950s, using a specially designed bag to eliminate the need to flood a larger chamber with EtO. This method is also known as gas diffusion sterilization, or bag sterilization. This method minimize the use of gas.[2]

Bacillus subtilis, a very resistant organism, is used as a rapid biological indicator for EO sterilizers. If sterilization fails, incubation at 37 °C causes a fluorescent change within four hours, which is read by an auto-reader. After 96 hours, a visible color change occurs. Fluorescence is emitted if a particular (EO resistant) enzyme is present, which means that spores are still active. The color change indicates a pH shift due to bacterial metabolism. The rapid results mean that the objects treated can be quarantined until the test results are available.

Ozone is used in industrial settings to sterilize water and air, as well as a disinfectant for surfaces. It has the benefit of being able to oxidize most organic matter. On the other hand, it is a toxic and unstable gas that must be produced on-site, so it is not practical to use in many settings.

Chlorine bleach is another accepted liquid sterilizing agent. Household bleach consists of 5.25% sodium hypochlorite. It is usually diluted to 1/10 immediately before use; however to kill Mycobacterium tuberculosis it should be diluted only 1/5. The dilution factor must take into account the volume of any liquid waste that it is being used to sterilize.[3] Bleach will kill many organisms immediately, but for full sterilization it should be allowed to react for 20 minutes. Bleach will kill many, but not all spores. It is highly corrosive and may corrode even stainless steel surgical instruments.

Glutaraldehyde and formaldehyde solutions (also used as fixatives) are accepted liquid sterilizing agents, provided that the immersion time is sufficiently long. To kill all spores in a clear liquid can take up to 12 hours with glutaraldehyde and even longer with formaldehyde. The presence of solid particles may lengthen the required period or render the treatment ineffective. Sterilization of blocks of tissue can take much longer, due to the time required for the fixative to penetrate. Glutaraldehyde and formaldehyde are volatile, and toxic by both skin contact and inhalation. Glutaraldehyde has a short shelf life (<2 href="" title="Methanol">methanol is added to inhibit polymerization to paraformaldehyde, but is much more volatile. Formaldehyde is also used as a gaseous sterilizing agent; in this case, it is prepared on-site by depolymerization of solid paraformaldehyde. Many vaccines, such as the original Salk polio vaccine, are sterilized with formaldehyde.

Ortho-phthalaldehyde (OPA) is a chemical sterilizing agent that received Food and Drug Administration (FDA) clearance in late 1999. Typically used in a 0.55% solution, OPA shows better myco-bactericidal activity than glutaraldehyde. It also is effective against glutaraldehyde-resistant spores. OPA has superior stability, is less volatile, and does not irritate skin or eyes, and it acts more quickly than glutaraldehyde. On the other hand, it is more expensive, and will stain proteins (including skin) gray in color.

Hydrogen peroxide is another chemical sterilizing agent. It is relatively non-toxic once diluted to low concentrations (although a dangerous oxidizer at high concentrations), and leaves no residue.

Low Temperature Plasma sterilization chambers use hydrogen peroxide vapor to sterilize heat-sensitive equipment such as rigid endoscopes. A recent model can sterilize most hospital loads in as little as 20 minutes. The Sterrad has limitations with processing certain materials such as paper/linens and long thin lumens. Paper products cannot be sterilized in the Sterrad system because of a process called cellulostics, in which the hydrogen peroxide would be completely absorbed by the paper product.

Hydrogen peroxide and formic acid are mixed as needed in the Endoclens device for sterilization of endoscopes. This device has two independent asynchronous bays, and cleans (in warm detergent with pulsed air), sterilizes and dries endoscopes automatically in 30 minutes. Studies with synthetic soil with bacterial spores showed the effectiveness of this device.

Dry sterilization process (DSP) uses hydrogen peroxide at a concentration of 30-35% under low pressure conditions. This process achieves bacterial reduction of 10-6...10-8. The complete process cycle time is just 6 seconds, and the surface temperature is increased only 10-15 °C (18 to 27 °F). Originally designed for the sterilization of plastic bottles in the beverage industry, because of the high germ reduction and the slight temperature increase the dry sterilization process is also useful for medical and pharmaceutical applications.

Peracetic acid (0.2%) is used to sterilize instruments in the Steris system.

Prions are highly resistant to chemical sterilization. Treatment with aldehydes (e.g., formaldehyde) have actually been shown to increase prion resistance. Hydrogen peroxide (3%) for one hour was shown to be ineffective, providing less than 3 logs (10-3) reduction in contamination. Iodine, formaldehyde, glutaraldehyde and peracetic acid also fail this test (one hour treatment). Only chlorine, a phenolic compound, guanidinium thiocyanate, and sodium hydroxide (NaOH) reduce prion levels by more than 4 logs. Chlorine and NaOH are the most consistent agents for prions. Chlorine is too corrosive to use on certain objects. Sodium hydroxide has had many studies showing its effectiveness.

Radiation sterilization

Methods exist to sterilize using radiation such as electron beams, X-rays, gamma rays, or subatomic particles.

  • Gamma rays are very penetrating and are commonly used for sterilization of disposable medical equipment, such as syringes, needles, cannulas and IV sets. Gamma radiation requires bulky shielding for the safety of the operators; they also require storage of a radioisotope (usually Cobalt-60), which continuously emits gamma rays (it cannot be turned off, and therefore always presents a hazard in the area of the facility).
  • Electron beam processing is also commonly used for medical device sterilization. Electron beams use an on-off technology and provide a much higher dosing rate then gamma or x-rays. Due to the higher dose rate, less exposure time is needed and thereby any potential degradation to polymers is reduced. A limitation is that electron beams are less penetrating than either gamma or x-rays.
  • X-rays are less penetrating than gamma rays and tend to require longer exposure times, but require less shielding, and are generated by an X-ray machine that can be turned off for servicing and when not in use.
  • Ultraviolet light irradiation (UV, from a germicidal lamp) is useful only for sterilization of surfaces and some transparent objects. Many objects that are transparent to visible light absorb UV. UV irradiation is routinely used to sterilize the interiors of biological safety cabinets between uses, but is ineffective in shaded areas, including areas under dirt (which may become polymerized after prolonged irradiation, so that it is very difficult to remove). It also damages many plastics, such as polystyrene foam.
Further information: Ultraviolet Germicidal Irradiation
  • Subatomic particles may be more or less penetrating, and may be generated by a radioisotope or a device, depending upon the type of particle.

Irradiation with X-rays or gamma rays does not make materials radioactive. Irradiation with particles may make materials radioactive, depending upon the type of particles and their energy, and the type of target material: neutrons and very high-energy particles can make materials radioactive, but have good penetration, whereas lower energy particles (other than neutrons) cannot make materials radioactive, but have poorer penetration.

Irradiation is used by the United States Postal Service to sterilize mail in the Washington, DC area. Some foods (e.g. spices, ground meats) are irradiated for sterilization (see food irradiation).

Sterile filtration

Clear liquids that would be damaged by heat, irradiation or chemical sterilization can be sterilized by mechanical filtration. This method is commonly used for sensitive pharmaceuticals and protein solutions in biological research. A filter with pore size 0.2 µm will effectively remove bacteria. If viruses must also be removed, a much smaller pore size around 20 nm is needed. Solutions filter slowly through membranes with smaller pore diameters. Prions are not removed by filtration. The filtration equipment and the filters themselves may be purchased as presterilized disposable units in sealed packaging, or must be sterilized by the user, generally by autoclaving at a temperature that does not damage the fragile filter membranes. To ensure sterility, the filtration system must be tested to ensure that the membranes have not been punctured prior to or during use.

To ensure the best results, pharmaceutical sterile filtration is performed in a room with highly filtered air (HEPA filtration) or in a laminar flow cabinet or "flowbox", a device which produces a laminar stream of HEPA filtered air.

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article : Biofilm in Microbiology

A biofilm is a complex aggregation of microorganisms marked by the excretion of a protective and adhesive matrix. Biofilms are also often characterized by surface attachment, structural heterogeneity, genetic diversity, complex community interactions, and an extracellular matrix of polymeric substances.

Single-celled organisms generally exhibit two distinct modes of behavior. The first is the familiar free floating, or planktonic, form in which single cells float or swim independently in some liquid medium. The second is an attached state in which cells are closely packed and firmly attached to each other and usually form a solid surface. A change in behavior is triggered by many factors, including quorum sensing, as well as other mechanisms that vary between species. When a cell switches modes, it undergoes a phenotypic shift in behavior in which large suites of genes are up- and down- regulated.


5 stages of biofilm development. Stage 1, initial attachment; stage 2, irreversible attachment; stage 3, maturation I; stage 4, maturation II; stage 5, dispersion. Each stage of development in the diagram is paired with a photomicrograph of a developing P. aeruginosa biofilm. All photomicrographs are shown to same scale.
5 stages of biofilm development. Stage 1, initial attachment; stage 2, irreversible attachment; stage 3, maturation I; stage 4, maturation II; stage 5, dispersion. Each stage of development in the diagram is paired with a photomicrograph of a developing P. aeruginosa biofilm. All photomicrographs are shown to same scale.

Formation of a biofilm begins with the attachment of free-floating microorganisms to a surface. These first colonists adhere to the surface initially through weak, reversible van der Waals forces. If the colonists are not immediately separated from the surface, they can anchor themselves more permanently using cell adhesion molecules such as pili.[1]

The first colonists facilitate the arrival of other cells by providing more diverse adhesion sites and beginning to build the matrix that holds the biofilm together. Some species are not able to attach to a surface on their own but are often able to anchor themselves to the matrix or directly to earlier colonists. It is during this colonization that the cells are able to communicate via quorum sensing. Once colonization has begun, the biofilm grows through a combination of cell division and recruitment. The final stage of biofilm formation is known as development, and is the stage in which the biofilm is established and may only change in shape and size. This development of biofilm allows for the cells to become more antibiotic resistant.


Biofilms are usually found on solid substrates submerged in or exposed to some aqueous solution, although they can form as floating mats on liquid surfaces and also on the surface of leaves, particularly in high humidity climates. Given sufficient resources for growth, a biofilm will quickly grow to be macroscopic. Biofilms can contain many different types of microorganism, e.g. bacteria, archaea, protozoa, fungi and algae; each group performing specialized metabolic

functions. However, some organisms will form monospecies films under certain conditions.

Extracellular matrix

The biofilm is held together and protected by a matrix of excreted polymeric compounds called EPS. EPS is an abbreviation for either extracellular polymeric substance or exopolysaccharide. This matrix protects the cells within it and facilitates communication among them through biochemical signals. Some biofilms have been found to contain water channels that help distribute nutrients and signalling molecules. This matrix is strong enough that under certain conditions, biofilms can become fossilized.

Bacteria living in a biofilm usually have significantly different properties from free-floating bacteria of the same species, as the dense and protected environment of the film allows them to cooperate and interact in various ways. One benefit of this environment is increased resistance to detergents and antibiotics, as the dense extracellular matrix and the outer layer of cells protect the interior of the community. In some cases antibiotic resistance can be increased 1000 fold.[2]


Biofilm in Yellowstone National Park. Longest raised mat area is about half a meter long.
Biofilm in Yellowstone National Park. Longest raised mat area is about half a meter long.

Biofilms are ubiquitous. Nearly every species of microorganism, not only bacteria and archaea, have mechanisms by which they can adhere to surfaces and to each other.

  • Biofilms can be found on rocks and pebbles at the bottom of most streams or rivers and often form on the surface of stagnant pools of water. In fact, biofilms are important components of foodchains in rivers and streams and are grazed by the aquatic invertebrates upon which many fish feed.
  • In industrial environments, biofilms can develop on the interiors of pipes, which can lead to clogging and corrosion. Biofilms on floors and counters can make sanitation difficult in food preparation areas. Biofilms in cooling water systems are known to reduce heat transfer[3] and harbour Legionella bacteria[4].
  • Biofilms can also be harnessed for constructive purposes. For example, many sewage treatment plants include a treatment stage in which waste water passes over biofilms grown on filters, which extract and digest organic compounds. In such biofilms, bacteria are mainly responsible for removal of organic matter (BOD); whilst protozoa and rotifers are mainly responsible for removal of suspended solids (SS), including pathogens and other microorganisms. Slow sand filters rely on biofilm development in the same way to filter surface water from lake, spring or river sources for drinking purposes.
  • Biofilms can help eliminate petroleum oil from contaminated oceans or marine systems. The oil is eliminated by the hydrocarbon-degrading activities of microbial communities, in particular by a remarkable recently discovered group of specialists, the so-called hydrocarbonoclastic bacteria (HCB).[5]

Biofilms and infectious diseases

Biofilms have been found to be involved in a wide variety of microbial infections in the body, by one estimate 80% of all infections.[6] Infectious processes in which biofilms have been implicated include common problems such as urinary tract infections, catheter infections, middle-ear infections, formation of dental plaque[7], gingivitis[7], coating contact lenses[8], and less common but more lethal processes such as endocarditis, infections in cystic fibrosis, and infections of permanent indwelling devices such as joint prostheses and heart valves.[9][10]

It has recently been shown that biofilms are present on the removed tissue of 80% of patients undergoing surgery for chronic sinusitis. The patients with biofilms were shown to have been denuded of cilia and goblet cells, unlike the controls without biofilms who had normal cilia and goblet cell morphology.[11] Biofilms were also found on samples from two of 10 healthy controls mentioned. The species of bacteria from interoperative cultures did not correspond to the bacteria species in the biofilm on the respective patient's tissue. In other words, the cultures were negative though the bacteria were present.[12]

New staining techniques are being developed to differentiate bacterial cells growing in living animals, e.g. from tissues with allergy-inflammations .[13]

Pseudomonas aeruginosa biofilms

The achievements of medical care in industrialised societies are markedly impaired due to chronic opportunistic infections that have become increasingly apparent in immunocompromised patients and the aging population. Chronic infections remain a major challenge for the medical profession and are of great economic relevance because traditional antibiotic therapy is usually not sufficient to eradicate these infections. One major reason for persistence seems to be the capability of the bacteria to grow within biofilms that protects them from adverse environmental factors. Pseudomonas aeruginosa is not only an important opportunistic pathogen and causative agent of emerging nosocomial infections but can also be considered a model organism for the study of diverse bacterial mechanisms that contribute to bacterial persistence. In this context the elucidation of the molecular mechanisms responsible for the switch from planctonic growth to a biofilm phenotype and the role of inter-bacterial communication in persistent disease should provide new insights in P. aeruginosa pathogenicity, contribute to a better clinical management of chronically infected patients and should lead to the identification of new drug targets for the development of alternative anti-infective treatment strategies.[14]

Dental plaque

Dental plaque is the material that adheres to the teeth and consists of bacterial cells (mainly Streptococcus mutans and Streptococcus sanguis), salivary polymers and bacterial extracellular products. Plaque is a biofilm on the surfaces of the teeth. This accumulation of microorganisms subject the teeth and gingival tissues to high concentrations of bacterial metabolites which results in dental disease.[7

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article : Human microbiome project

Human microbiome project (HMP) is a National Institutes of Health initiative with the goal of identifying and characterizing the microorganisms which are found in association with both healthy and diseased humans. It is a five-year project, best characterized as a feasibility study, and has a total budget of 115 million dollars. The ultimate goal of this and similar NIH-sponsored microbiome projects is a demonstration (or refutation) that currently poorly characterized changes in the human microbiome can be associated with human health or disease.

Important components of the Human microbiome project will be culturing-independent methods of microbial community characterization, such as metagenomics (which provides a broad genetic perspective on a single microbial community), as well as extensive whole-genome sequencing (which provides a "deep" genetic perspective on certain aspects of a given microbial community, i.e., of individual bacterial species). The latter will serve as reference genomic sequences — 600 such sequences of individual bacterial isolates are currently planned — for comparison purposes during subsequent metagenomic analysis. The microbiology of five body sites will be emphasized: oral, skin, vagina, gut, and nasal/lung.

Context and importance of HMP

Total microbial cells found in association with humans may exceed the total number of cells making up the human body by a factor of ten-to-one. The total number of genes associated with the human microbiome could exceed the total number of human genes by a factor of 100-to-one. Many of these organisms have not been successfully cultured, identified, or otherwise characterized. Organisms expected to be found in the human microbiome, however, may generally be categorized as bacteria (the majority), members of domain Archaea, yeasts, and single-celled eukaryotes as well as various helminth parasites and viruses, the latter including viruses that infect the cellular microbiome organisms (e.g., bacteriophages, the viruses of bacteria).

"The HMP will address some of the most inspiring, vexing and fundamental scientific questions today. Importantly, it also has the potential to break down the artificial barriers between medical microbiology and environmental microbiology. It is hoped that the HMP will not only identify new ways to determine health and predisposition to diseases but also define the parameters needed to design, implement and monitor strategies for intentionally manipulating the human microbiota, to optimize its performance in the context of an individual's physiology."[1]

The HMP has been described as "a logical conceptual and experimental extension of the Human Genome Project"[2]. In 2007 the Human microbiome project was listed on the NIH Roadmap for Medical Research as one of the New Pathways to Discovery. Organized characterization of the human microbiome is also being done internationally under the auspices of the International Human Microbiome Consortium.

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article : Environmental microbiology

Environmental microbiology is the study of the composition and physiology of microbial communities in the environment. The environment in this case means the soil, water, air and sediments covering the planet and can also include the animals and plants that inhabit these areas. Environmental microbiology also includes the study of microorganisms that exist in artificial environments such as bioreactors.

Microbial life is amazingly diverse and microorganisms literally cover the planet. It is estimated that we know fewer than 1% of the microbial species on Earth. Microorganisms can survive in some of the most extreme environments on the planet and some, for example the Archaea, can survive high temperatures, often above 100°C, as found in geysers, black smokers, and oil wells. Some are found in very cold habitats and others in highly saline, acidic, or alkaline water.[1]

An average gram of soil contains approximately one billion (1,000,000,000) microbes representing probably several thousand species. Microorganisms have special impact on the whole biosphere. They are the backbone of ecosystems of the zones where light cannot approach. In such zones, chemosynthetic bacteria are present which provide energy and carbon to the other organisms there. Some microbes are decomposers which have ability to recycle the nutrients. Microbes have a special role in biogeochemical cycles. Microbes, especially bacteria, are of great importance because their symbiotic relationship (either positive or negative) have special effects on the ecosystem.

Microorganisms are used for in-situ microbial biodegradation or bioremediation of domestic, agricultural and industrial wastes and subsurface pollution in soils, sediments and marine environments. The ability of each microorganism to degrade toxic waste depends on the nature of each contaminant. Since most sites typically have multiple pollutant types, the most effective approach to microbial biodegradation is to use a mixture of bacterial species and strains, each specific to the biodegradation of one or more types of contaminants. It is vital to monitor the composition of the indigenous and added bacteria in order to evaluate the activity level and to permit modifications of the nutrients and other conditions for optimizing the bioremediation process.[2]

Oil biodegradation

Petroleum oil is toxic, and pollution of the environment by oil causes major ecological concern. Oil spills of coastal regions and the open sea are poorly containable and mitigation is difficult; much of the oil can, however, be eliminated by the hydrocarbon-degrading activities of microbial communities, in particular the hydrocarbonoclastic bacteria (HCB). These organisms can help remedy the ecological damage caused by oil pollution of marine habitats. HCB also have potential biotechnological applications in the areas of bioplastics and biocatalysis.[3]

Degradation of aromatic compounds by Acinetobacter

Acinetobacter strains isolated from the environment are capable of the biodegradation of a wide range of aromatic compounds. The predominant route for the final stages of assimilation to central metabolites is through catechol or protocatechuate (3,4-dihydroxybenzoate) and the beta-ketoadipate pathway and the diversity within the genus lies in the channelling of growth substrates, most of which are natural products of plant origin, into this pathway.[4]

Analysis of waste biotreatment

Biotreatment, the processing of wastes using living organisms, is an environmentally friendly alternative to other options for treating waste material. Bioreactors] have been designed to overcome the various limiting factors of biotreatment processes in highly controlled systems. This versatility in the design of bioreactors allows the treatment of a wide range of wastes under optimized conditions. It is vital to consider various microorganisms and a great number of analyses are often required.[5]

Environmental genomics of Cyanobacteria

The application of molecular biology and genomics to environmental microbiology has led to the discovery of a huge complexity in natural communities of microbes. Diversity surveying, community fingerprinting and functional interrogation of natural populations have become common, enabled by a range of molecular and bioinformatics techniques. Recent studies on the ecology of Cyanobacteria have covered many habitats and have demonstrated that cyanobacterial communities tend to be habitat-specific and that much genetic diversity is concealed among morphologically simple types. Molecular, bioinformatics, physiological and geochemical techniques have combined in the study of natural communities of these bacteria.[6]


Corynebacteria are a diverse group Gram-positive bacteria found in a range of different ecological niches such as soil, vegetables, sewage, skin, and cheese smear. Some, such as Corynebacterium diphtheriae, are important pathogens while others, such as Corynebacterium glutamicum, are of immense industrial importance. C. glutamicum is one of the biotechnologically most important bacterial species with an annual production of more than two million tons of amino acids, mainly L-glutamate and L-lysine.[7]


Legionella is common in many environments, with at least 50 species and 70 serogroups identified. Legionella is commonly found in aquatic habitats where its ability to survive and to multiply within different protozoa equips the bacterium to be transmissible and pathogenic to humans.[8]


Originally, Archaea were once thought of as extremophiles existing only in hostile environments but have since been found in all habitats and may contribute up to 20% of total biomass. Archaea are particularly common in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet. Archaea are subdivided into four phyla of which two, the Crenarchaeota and the Euryarchaeota, are most intensively studied.[1]


In the late 1800s and early 1900s, Sergei Winogradsky, Russian microbiologist, pioneered the investigation of microbial auto trophy, and initiated the field of Environmental Microbiology. He was a strong supporter of examining freshly-isolated organisms rather than 'domesticated' laboratory strains.One of the methods he developed for the study of microbial nutrient cycling in the environment is what is now known as the "Windogradsky column". These can be set up in an amazing variety of ways to study sulfur, nitrogen, carbon, phosphorus, or other nutrients, most often cycling between the upper aerobic zone and the lower anaerobic zone. [9][10]

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