Microbiological broad classification

Microbiology one of the most intersting subject no one can really hate the subject it is basically a subject deals with microbes(micro-organisms).Microorganism plays a vital role in human life.

There are two types of microbes harmful an harmless.

Harmful are the organisms which cause disease in humans and it can also cause death to humans

ex., AIDS,Cholera,Malaria etc.,

Harmless organisms are the organisms which does not harm human and it can also be auseful agent to humans in their day today life. for ex., lactobacillus in curd, yeast in dough and wine.

Harmful and harmless belongs to different types of organisms. MIcrobes are further classified into bacteria, virus,algae,fungi and protozoans.

In this bacteria and virus plays a vital role in life and to certain extend fungus.

Algae are less causative in humans

Continuation of the chapter Three

4. PRINCIPLES FOR THE DETERMINATION OF RELATIONSHIPS
What are the characters on which the recognition and separation of natural groups may be based? In the classification of higher plants and animals, systematists have relied almost exclusively on morphology. Nevertheless, some exceptions to this rule may be found, particularly in the treatment of the thallophytes, where an increasing reliance appears to be placed on physiological characters. For example, Smith (1938) in breaking up the algae into seven new divisions, places as much weight on physiological characters (reserve products, nature of the cell wall, pigments) as on morphological ones. It is above all in bacterial systematics that extensive use of physiological criteria has been made. This is understandable
enough in view of the paucity of morphological data but, as pointed out by Kluyver and van Niel (1936), the injudicious use of physiology without a clear understanding of what constitute important physiological characters, has led to much confusion. A good example of this is the order Thiobacteriales of Buchanan, which is based on the presence of "bacteriopurpurin and/or
sulfur granules" in the cells. In addition to uniting exceedingly heterogeneous morphological groups, these characters also bring together two radically different physiological groups, the photosynthetic purple bacteria and some of the chemosynthetic colorless sulfur-oxidizing bacteria. Furthermore, extreme physiological systems have often neglected obvious morphological relationships, with the result that natural morphological groups have been split up or forced into assemblages with which they have little in common save certain aspects of metabolism. The Thiobacteriales again are a good example of this; other even more glaring ones may be found in the system of Orla-Jensen (1909) where, for example, the genera Mycobacterium, Corynebacterium and Actinomyces are placed among the cephalotrichous bacteria in one family with the genus Rhizobium! The chief stumbling block in attempting to draw up a phylogenetic system on a primarily physiological basis is the necessity of making a large number of highly speculative assumptions as to what constitute primitive and advanced metabolic types.Orla-Jensen, for example, regarded the chemosynthetic bacteria as the most primitive group because they can live in the complete absence of organic matter and hence are independent of other living forms. This overlooks the fact that a chemosynthetic metabolism
necessarily presupposes a rather highly specialized synthetic ability such as one would not expect to find in metabolically primitive forms. Furthermore, this reasoning was based at least
in part on the hypothesis that living forms arose at a time when the earth was devoid of organic matter, an hypothesis which has been effectively challenged by Oparin (1938) in his book on the
origin of life. According to Oparin, it is probable that a long period of chemical synthesis of organic material preceded the emergence of life, and that consequently the earliest living forms
were heterotrophs. On this reasoning, the development of autotrophism was a later adaptation to an environment in which organic materials had become scarce through the activities of heterotrophs.Thus, the basic assumption used by Orla-Jensen in erecting aphysiological phylogenetic system has been rendered, to say the least, highly doubtful. The physiological reasoning on which the further development of the system is founded is also open to serious
criticisms.
In spite of the comparative simplicity of bacteria it is rather naive to believe that in the distribution of their metabolic characters one can discern the trend of physiological evolution. For these reasons, a phylogenetic system based solely or largely on physiological grounds seems unsound. It is our belief that the greatest weight in making the major subdivisions in the Schizomycetes should be laid on morphological characters, although correlative physiological characters may also be used. What, then, are the basically important morphological characters which we can use? Clearly paramount is the structure of the individual vegetative cell, including such points as the nature of the cell wall, the presence and location of chromatin material, the functional structures (e.g., of locomotion), the method of cell division, and the shape of the cell. A closelyallied character is the type of organization of cells into larger structures. In addition, the nature and structure of reproductive or resting cells or cell masses deserve due consideration. In the following sections we will examine the major bacterial groups which we can discern by the application of these criteria, elucidating as far as possible the relationships of these groups to each other and to other microorganisms.

Second part of staniers Book

3. A CRITIQUE OF BERGEY'S SYSTEM

Admittedly it is a difficult task to frame a definition of the Schizomycetes adequate to include all organisms which belong here but sufficiently specific to exclude other groups of microorganisms.
Nevertheless, a more inadequate definition than that given by Bergey would be hard to conceive. Bacterial cells are described as "relatively primitive in organization," but one looks in vain for an explicit statement of the absence of true nuclei, which is perhaps the most important single morphological characteristic of these organisms. In describing cell shape, the word filamentous is used in a most confusing manner; apparently it is applied indiscriminately to the usually non-septate mycelium of the actinomycetes, to chains of individual cells such as occur
in the Bacilleae and to the truly filamentous (i.e. multicellular) arrangement found in the Beggiatoaceae. Multiplication is given as being typically by "cell fission," but there is no mention of its wellnigh universal transverse nature. The absence of sexual reproduction is not noted. The formation of endospores and conidia is mentioned but not the formation of myxobacterial
spores and cysts. Next comes the astonishing statement,"Chlorophyll is produced by none of the bacteria (with the possible exception of a single genus)." The occurrence of a true chlorophyll-though chemically slightly different from the green plant chlorophylls a and b-in all the purple bacteria, both Thioand Athiorhodaceae, invalidates the inclusion of this character.

In the description of motility, the peculiar locomotion so characteristic of the Myxobacteriales goes unmentioned; the motility of the Spirochaetales is described as flexuouss," which certainly does not characterize the mode of locomotion of these forms in any adequate manner. In order to appreciate the complete inadequacy of this definition of the class Schizomycetes one has only to realize that there is nothing in it which would exclude the fungi and most of the protozoa, whereas th statement about the absence of chlorophyll (clearly put in originally to keep out the algae) now also excludes a whole family of the Thiobacteriales. The differentiation of the seven orders used in the Manual is no more satisfactory. The first order of the Eubacteriales is carefully segregated from the rest as containing "simple and undifferentiated forms." No mention is made of the flagellar nature of motility or the rigidity of the cell wall, which are really
important characters in this ordr. The statement that "iron (is) not stored as visible particles" applies equally well to all other living organisms. The remaining orders are described as "specialized or differentiated"; in the absence of a definition of these two terms the characterization becomes entirely meaningless. Even if, from a consideration of the organisms thus grouped together, it would seem possible to sense the implication of these terms, it must be pointed out that forms no more "specialized or differentiated" than members of the Eubacteriales have been incorporated in these orders. To mention an example: in the second order of the Actinomycetales (which is separated from the following orders as being "mold-like") one finds the genera Mycobacterium and Corynebacterium. It is clearly illogical to describe these genera either as "mold-like" or as "specialized and differentiated," an opinion which is substantiated by the fact that in the fifth edition one can find indubitable Corynebacterium species described in no less than three families of the Eubacteriales (Rhizobiaceae, Pseudomonadaceae and Bacteriaceae). The third, fourth and fifth orders Chlamydobacteriales, Caulobacteriales and Thiobacteriales are collectively described as "alga-like." Clearly the recognition of the relationship of organisms such as the Beggiatoaceae, Clonothrix, etc., to representatives of the order Hormogonales of the Myxophyta has prompted the inclusion of this
character in the descriptive diagnosis of these orders. But the term "alga-like" is entirely too general since it implies some unspecified resemblance (such as habit of growth?) to some organisms included in some of the seven divisions of the algae. Furthermore, this statement applies only to some of the organisms in each order, certainly not to all; in the Caulobacteriales one can find organisms morphologically very similar to the Eubacteriales except for the possession of a stalk or holdfast (Nevskia pediculata, Caulobacter vibrioides), while the representatives of the entire family Rhodobacteriaceae (Thiobacteriales) are morphologically
indistinguishable from their colorless counterparts in the Eubacteriales. The artificiality of the Chlamydobacteriales, Caulobacteriales and Thiobacteriales is clearly shown by the fact that the important differential characteristic for each order is also exhibited by species which have been placed in one of the other two orders. Thus, a sheath, which is the key character of the Chlamydobacteriales, occurs in the genus Thioploca (Thiobacteriales); several Leptothrix (Chlamydobacteriales) and Thiothrix (Thiobacteriales) species are attached to the substratum by a holdfast (Caulobacteriales: "in some species the stalks may be very short or absent, the cells connected directly to the substrate or to each other by holdfasts"); and finally, the species Nevskia ramosa (Caulobacteriales) shows evidence of containing sulfur globules, which might suggest an alternative position in the Thiobacteriales. Even if these species can be placed in the order to which they have been assigned on the basis of other characters, such a situation is apt to cause confusion.

The description of the sixth order Myxobacteriales as "slimemold-like" would hardly appeal to anyone familiar with the organisms belonging to the two groups. The absence of true nuclei, of sexual reproduction, and of amoeboid cell form in the Myxobacteriales shows quite clearly the fundamental lack of similarity to the Myxomycetae. Scientific descriptive keys should not contain such misleading comparisons. On the other hand, the two most important characters of the Myxobacteriales, the type of locomotion and the absence of rigid cell walls, are not mentioned in the key.

After this, it is not surprising to find the seventh order Spirochaetales differentiated from the rest as "protozoan-like." The further characterization is so diffuse that it gives no helpful information concerning this group of organisms. Certainly the determinative significance of the statement "Some forms transmitted by insect vectors" is not apparent. The stress laid on these

points may seem unnecessary. However, the fact that the definitions and segregations of the various orders have remained unchanged through five consecutive editions of Bergey's Manual shows that its weaknesses (not only from the scientific, but even from the determinative standpoint) have not been generally realized.

THE MAIN OUTLINES OF BACTERIAL CLASSIFICATION

THE MAIN OUTLINES OF BACTERIAL CLASSIFICATION
R. Y. STANIER AND C. B. VAN NIEL
Hopkins Marine Station, Pacific Grove, California
Received for publication February 8, 1941

"Was diese Wissenschaft betrifft,
Es ist so schwer, den falschen Weg zu meiden,
Es liegt in ihr so viel verborgnes Gift,
Und von der Arzenei ist's kaum zu unterscheiden."

-GOETHE

1. INTRODUCTION
Although a great deal has been written on bacterial taxonomy during the past few decades, a perusal of the literature shows that for the most part this work has been restricted to the classification of the Eubacteriales alone. Since the early days of microbiology, comparatively little attention has been paid to the broader problem of delimiting and defining the Schizomycetes as a whole and the major groups contained therein. Nevertheless, it can hardly be contended that this is an unimportant aspect of bacterial taxonomy; on the contrary, a clear recognition of the larger natural groups of bacteria, their characteristics and relationships, would seem to be an indispensable basis for more detailed work. The increased use of Bergey's Manual of Determinative Bacteriology for purposes of identification, together with the obvious attempts made by the present Board of Editors to seek collaboration with specialists on various groups, make it likely that this Manual will ultimately become the internationally recognized and authoritative handbook on bacterial taxonomy. Nevertheless, in its main outlines the system used in Bergey's Manual is still far from satisfactory. There will in due course be a succeeding edition, and it is with the hope of contributing some constructive suggestions for its outline that the present essay is offered.

2. PHYLOGENY AND EMPIRICISM IN BACTERIAL SYSTEMATICS

In most biological fields it is considered a truism to state that the only satisfactory basis for the construction of a rational system of classification is the phylogenetic one. Nevertheless, "realistic" bacteriologists show a curious aversion to the attempted use of phylogeny in bacterial systematics. This is well illustrated, for example, by the statement of Breed (1939): Realistic workers have on their side been impatient with idealists who have introduced many ... unjustified speculations regarding relationships between the various groups of bacteria. To what may we ascribe this distrust of phylogeny? In part it is undoubtedly due to the unsatisfactory nature of certain systems, purportedly based on phylogeny, which have been proposed in the past. However, the mere fact that a particular phylogenetic scheme has been shown to be unsound by later work is not a valid reason for total rejection of the phylogenetic approach. Another important reason for the "realistic" attitude is the widespread belief that bacteria present too few characters on which schemes of relationships (and hence a natural system) can
be based. It is our belief that such pessimism is not entirely justified, and that at present some relationships can be recognized which can well be incorporated in a system of classification. Even granting that the true course of evolution can never be known and that any phylogenetic system has to be based to some extent on hypothesis, there is good reason to prefer an admittedly imperfect natural system to a purely empirical one. A phylogenetic system has at least a rational basis, and can be altered and improved as new facts come to light; its very weaknesses will suggest the type of experimental work necessary for improvement. On the other hand, an empirical system is largely unmodifiable because the differential characters employed are arbitrarily chosen and usually cannot be altered to any great extent without disrupting the whole system. Its sole ostensible advantage is its greater immediate practical utility; but if the differential characters used are not mutually exclusive (and suchmutual exclusiveness may be difficult to attain when the criteria employed are purely arbitrary) even this advantage disappears. The wide separation of closely related groups caused by the use of arbitrary differential characters naturally enough shocks "idealists," but when these characters make it impossible to tell with certainty in what order a given organism belongs, an empirical system loses its value even for "realists." It seems unnecessary to give here an exhaustive review of bacterial systematics. The reader is referred to Buchanan's scholarly treatise on general systematic bacteriology for an excellent survey of this field up to 1925. More recent literature has been briefly reviewed by Breed in the latest edition of Bergey's Manual. We shall, therefore, restrict ourselves to a critique of Bergey's system which illustrates well the weaknesses of the empirical approach.

Bacterial Classification

The taxonomy of bacteria is not very definitively worked out yet, especially the higher levels of classification. Some authorities believe that the degree of variance between different bacterial groups is sufficient to give them each 'Kingdom Status' of their own. Thus in the 9th edition of "Brock: Biology of Microorganism" you will find reference to 13 Kingdoms of Bacteria. From the point of view of these pages it is not really important whether you think of the different categories as Phyla or Kingdoms as long as you are aware that the bacteria are an incredible diverse group of organisms. Here I have followed the classification scheme laid out in the 2nd edition of "Bergey's Manual of Systematic Biology".

Gram Staining

You will find bacteria referred to as 'Gram +' or 'Gram Positive' and 'Gram -' or 'Gram Negative' this is a reference to how the bacteria responds to the Gram staining method. Staining methods are designed to make a staining agent bind to the cell wall of the bacteria. The Gram staining method is named after Christian Gram who invented the method in 1884.

In testing for gram stain response, microbiologists first spread some bacteria on a slide, then fire it by passing the slide through a flame briefly. The next step is to flood the slide with crystal violet solution for 1 minute. Then they add iodine solution for 3 minutes - at this stage all cells are purple. Adding alcohol for 20 seconds results in Gram negative cells becoming clear again, ie they lose their purple staining. Lastly, the cells are restained with safranin. This results in gram positive cells remaining purple and gram negative ones being red or pink. Gram staining is nearly always the first step in identifying a new sample or species of bacteria. Nowadays, gram staining can be done in one step using a fluorescent dye and a fluorescence microscope.

Microbiology Basic Principles

MicroBiology:

The Science That deals with the study of micro organisms.

Micro organism:

Organism which cannot seen through our naked eye.

Classification:

These Microorganism is mainly classified into

• Bacteria
• Virus
• Fungi
• Algae