MOTILITY IN PROCARYOTIC ORGANISMS: PROBLEMS, POINTS OF VIEW, AND PERSPECTIVES

1. Procaryotic motility mechanisms are more difficult to investigate than those of the generally larger, hence more easily observable, eucaryotic forms. Furthermore, although the function—namely translational locomotion—is the same, the biomechanisms by which this end is accomplished may be, in fact, quite distinct in the two forms. 2. Observational techniques for studying procaryotic motility are relatively crude and qualitative. Progress toward a greater understanding of motility phenomena will be made correlative with advances derived from devising specific techniques involving approaches adapted from electrical engineering, biophysics and cybernetics. 3. There is a great amount of information at hand concerning the qualitative and quantitative chemical composition of procaryotic flagella, but there is no assurance that preparatory techniques include either the entire organelle on the one hand, or do not introduce subtle errors on the other hand. Similarly, the structural features of flagella as derived from electron-microscope studies of fixed preparations may be themselves influenced by the techniques employed to reveal them. 4. Chemotactic responses of bacteria have been noted almost since the beginning of bacteriology as a formal scientific endeavour, yet the study of transduction of environmental stimuli, using motile bacteria as experimental subjects, is a relatively recent development. We have proposed that the cytoplasmic membrane may act as a non-specific receptor-transmitter of such signals in motile bacteria. If this is found to be the case, perhaps a sensory code may be more amenable to discovery here than with more complex forms of organisms. 5. Knowledge of the physical aspects in procaryotic flagellar movement is extremely fragmentary. There is some information on the movements of living functional flagellar fascicles, but this form of movement of an individual flagellum is purely speculative. We have proposed that the procaryotic flagellum is a rigid or semi-rigid helix, which does not transmit helical waves of contraction, and that its movements are governed by a specialized area of the cytoplasmic membrane. The flagellum may rotate or wobble within the flagellar basal bulb to produce the motion necessary for propulsion. This view ‘explains’ many of the known properties of procaryotic flagella. 6. The basis of gliding motility remains unknown even after a great deal of experimental work. In our view, the secretion of slime is necessary for adhesion to a solid surface, and movement is believed to be mediated by a mechanism involving contractile waves. 7. Studies on procaryotic motility may yield valuable information on certain areas of general biological interest. Among these are: (a) the transduction of environmental stimuli and the sensory code; (b) the development of reproducible observational techniques for quantitative data on the hydrodynamic and biophysical parameters of cell motion in procaryotic forms; (c) the phenomenon of unicellular ‘behaviour’ and the survival value and evolutionary significance of motility; and (d) the elucidation of the mechanism of gliding with perhaps an assessment of its utility in a wide variety of micro-organisms. All of these areas are ripe for imaginative and innovative experimentation; let us hope it will be forthcoming!     

Family- and genus-level 16S rRNA-targeted oligonucleotide probes for ecological studies of methanotrophic bacteria

Methanotrophic bacteria play a major role in the global carbon cycle, degrade xenobiotic pollutants, and have the potential for a variety of biotechnological applications. To facilitate ecological studies of these important organisms, we developed a suite of oligonucleotide probes for quantitative analysis of methanotroph-specific 16S rRNA from environmental samples. Two probes target methanotrophs in the family Methylocystaceae (type II methanotrophs) as a group. No oligonucleotide signatures that distinguish between the two genera in this family, Methylocystis and Methylosinus, were identified. Two other probes target, as a single group, a majority of the known methanotrophs belonging to the family Methylococcaceae (type I/X methanotrophs). The remaining probes target members of individual genera of the Methylococcaceae, including Methylobacter, Methylomonas, Methylomicrobium, Methylococcus, and Methylocaldum. One of the family-level probes also covers all methanotrophic endosymbionts of marine mollusks for which 16S rRNA sequences have been published. The two known species of the newly described genus Methylosarcina gen. nov. are covered by a probe that otherwise targets only members of the closely related genus Methylomicrobium. None of the probes covers strains of the newly proposed genera Methylocella and "Methylothermus," which are polyphyletic with respect to the recognized methanotrophic families. Empirically determined midpoint dissociation temperatures were 49 to 57 degrees C for all probes. In dot blot screening against RNA from positive- and negative-control strains, the probes were specific to their intended targets. The broad coverage and high degree of specificity of this new suite of probes will provide more detailed, quantitative information about the community structure of methanotrophs in environmental samples than was previously available.     

Feeding appendages of the Euphausiacea (Crustacea)

The Euphausiacea comprises about 85 species and the structure of the feeding appendages of 68 of these species is discussed here. A considerable uniformity is apparent in the appendages throughout the order but generic, and even in some cases, specific differences are evident. It is concluded from the study of the morphology of the appendages and the analyses of stomach contents that the majority of species in the genera Bentheuphwsia, Thysanopoda, Meganyctiphanes, Nyctiphanes, Pseudeuphausia, Euphausia, Tessara-brachion and Thysanoessa are omnivorous; that is, they can feed by filtering material from the water and act as predators of small zooplankton, especially copepods. Species in the genera Nematoscelis, Nematobrachion and Stylocheiron can feed on bottom deposits and also by predation of zooplankton but the amount of filter-feeding which they do may be limited because their mouthparts are not so well adapted for filtering as those of the previous group of genera.
It is suggested, from the study of the appendages and several other features of the animals, that the genera Thysanopoda, Meganyctiphanes, and Euphausia are closely related to one another and that a similar relationship exists between the genera Nematoscelis, Nematobrachion and Stylocherion. The genera Nyctiphanes and Pseudeuphausia are probably more closely related to the Thysanopoda group of genera and the genera Tessarabrachion and Thysanoessa to the Nematoscelis group of genera.     

Streptococcus crista sp. nov., a viridans streptococcus with tufted fibrils, isolated from the human oral cavity and throat.

We studied strains of an unusual streptococcus that superficially resembles Streptococcus sanguis but has fibrils that are arranged in lateral tufts. These strains were originally isolated from human throats and oral cavities and have been referred to previously as "Streptococcus sanguis I," the "CR group," and the "tufted-fibril group." Until now, insufficient phenotypic data have been available to allow reliable differentiation of these strains from other viridans streptococcal species, particularly the species in the S. sanguis group. Recently, workers have proposed a scheme of phenetic tests that is based on 4-methylumbelliferyl-linked substrates and conventional biochemical tests and allows the tufted-fibril group to be differentiated; these organisms differ from other viridans species in being able to hydrolyze arginine but not esculin and in producing alpha-L-fucosidase but not beta-glucosidase or alkaline phosphatase. These data, together with the results of our DNA-DNA hybridization experiments and the unusual ultrastructure of the tufted-fibril strains as determined by electron microscopy, demonstrate that these organisms represent a new species, for which the name Streptococcus crista is proposed. The DNA base composition is 42.6 to 43.2 mol% G + C. The type strain is strain CR311 (= NCTC 12479).     

Biochemical studies on the mutagen, 6-N-hydroxylaminopurine. Synthesis of the deoxynucleoside triphosphate and its incorporation into DNA in vitro

The nucleotide analogue, 6-N-hydroxylaminopurine deoxynucleoside triphosphate (dHAPTP) has been synthesized from 6-chloropurine by a procedure involving both enzymatic and chemical reagents. In a series of experiments involving several different DNA polymerases including 3 procaryotic and 2 eucaryotic enzymes, it was shown that dHAPTP is ambiguous in its base-pairing characteristics, since it can replace both dATP and dGTP in DNA synthesis. It was also shown that different enzymes have different capacities to distinguish dHAPTP from the canonical deoxynucleoside triphosphates. These results are consistent with (but do not prove) the hypothesis that the mechanism of 6-N-hydroxylaminopurine mutagenesis seen in both eucaryotic and procaryotic organisms is due to its conversion, in vivo, to a deoxynucleoside triphosphate which is incorporated ambiguously for dATP and dGTP during DNA replication.     

Mesophilic aerobic Gram negative cellulose degrading bacteria from aquatic habitats and soils

New procedures have been developed for the isolation and purification of aerobic and facultatively anaerobic bacteria able to utilize cellulose as sole source of carbon and energy. Wood pulp medium was used for enrichment, and bacterial cellulose, obtained from cultures of Acetobacter aceti subsp. xylinus , was employed as carbon substrate during purification and for the rapid screening of colonies for cellulolytic activity. The methods have revealed several new groups of Gram negative cellulose-degrading bacteria, including organisms that form differentiated colonies superficially similar to myxobacterial sori. The organisms formed several phenetic clusters, three of which contained reference strains of Cellvibrio fulvus, Pseudomonas fluorescens var. cellulosa and Cytophaga hutchinsonii . No cellulose degrading cluster included non-cellulose degrading strains. Most of the cellulose degraders studied were flagellated and, of these, the majority had polar or lophotrichous flagella, although one cluster included peritrichously flagellated organisms. The cellulose degraders in this study included five organisms that grew on nitrate-free medium; these appeared in two different clusters. A few Gram positive isolates appeared to belong to the genera Streptomyces and Thermoactinomyces .     

Polyphasic approach of bacterial classification — An overview of recent advances

Classification of microorganisms on the basis of traditional microbiological methods (morphological, physiological and biochemical) creates a blurred image about their taxonomic status and thus needs further clarification. It should be based on a more pragmatic approach of deploying a number of methods for the complete characterization of microbes. Hence, the methods now employed for bacterial systematics include, the complete 16S rRNA gene sequencing and its comparative analysis by phylogenetic trees, DNA-DNA hybridization studies with related organisms, analyses of molecular markers and signature pattern(s), biochemical assays, physiological and morphological tests. Collectively these genotypic, chemotaxonomic and phenotypic methods for determining taxonomic position of microbes constitute what is known as the ‘polyphasic approach’ for bacterial systematics. This approach is currently the most popular choice for classifying bacteria and several microbes, which were previously placed under invalid taxa have now been resolved into new genera and species. This has been possible owing to rapid development in molecular biological techniques, automation of DNA sequencing coupled with advances in bioinformatic tools and access to sequence databases. Several DNA-based typing methods are known; these provide information for delineating bacteria into different genera and species and have the potential to resolve differences among the strains of a species. Therefore, newly isolated strains must be classified on the basis of the polyphasic approach. Also previously classified organisms, as and when required, can be reclassified on this ground in order to obtain information about their accurate position in the microbial world. Thus, current techniques enable microbiologists to decipher the natural phylogenetic relationships between microbes.     

Bacillus and relatives in foodborne illness

Species of Bacillus and related genera have long been troublesome to food producers on account of their resistant endospores. These organisms have undergone huge taxonomic changes in the last 30 years, with numbers of genera and species now standing at 56 and over 545, respectively. Despite this expansion, relatively few new species have been isolated from infections, few are associated with food and no important new agents of foodborne illness have been reported. What has changed is our knowledge of the established agents. Bacillus cereus is well known as a cause of food poisoning, and much more is now understood about its toxins and their involvement in infections and intoxications. Also, although B. licheniformis, B. subtilis and B. pumilus have occasionally been isolated from cases of food‐associated illness, their roles were usually uncertain. Much more is now known about the toxins that strains of these species may produce, so that their significances in such episodes are clearer; however, it is still unclear why such cases are so rarely reported. Another important development is the use of aerobic endosporeformers as probiotics, as the potentials of such organisms to cause illness or to be sources of antibiotic resistance need to be borne in mind.     

Nutritional studies on Chloroflexus,a filamentous photosynthetic,gliding bacterium

Nutritional studies on four different strains of Chloroflexus, a new genus of filamentous, photosynthetic bacteria are described. This organism appears to be related to several different procaryotic groups, and in particular to the green sulfur bacteria and blue-green algae. Unlike these autotrophs, however, Chloroflexus is nutritionally diverse, being able to grow aerobically as a light-independent heterotroph, and anaerobically as a photoautotroph or photoheterotroph. Numerous organic carbon sources including hexoses, amino acids, short chain fatty acids, organic acids, and some alcohols are utilized under various growth conditions. These results suggest that this organism may be among the most nutritionally versatile organisms known.     

Bacterial decolorization and degradation of azo dyes

Azo compounds constitute the largest and the most diverse group of synthetic dyes and are widely used in a number of industries such as textile, food, cosmetics and paper printing. They are generally recalcitrant to biodegradation due to their xenobiotic nature. However microorganisms, being highly versatile, have developed enzyme systems for the decolorization and mineralization of azo dyes under certain environmental conditions. Several genera of Basidomycetes have been shown to mineralize azo dyes. Reductive cleavage of azo bond, leading to the formation of aromatic amines, is the initial reaction during the bacterial metabolism of azo dyes. Anaerobic/anoxic azo dye decolorization by several mixed and pure bacterial cultures have been reported. Under these conditions, this reaction is non-specific with respect to organisms as well as dyes. Various mechanisms, which include enzymatic as well as low molecular weight redox mediators, have been proposed for this non-specific reductive cleavage. Only few aerobic bacterial strains that can utilize azo dyes as growth substrates have been isolated. These organisms generally have a narrow substrate range. Degradation of aromatic amines depends on their chemical structure and the conditions. It is now known that simple aromatic amines can be mineralized under methanogenic conditions. Sulfonated aromatic amines, on the other hand, are resistant and require specialized aerobic microbial consortia for their mineralization. This review is focused on the bacterial decolorization of azo dyes and mineralization of aromatic amines, as well as the application of these processes for the treatment of azo-dye-containing wastewaters.     

Reiterated DNA sequences in Rhizobium and Agrobacterium spp.

Repeated DNA sequences are a general characteristic of eucaryotic genomes. Although several examples of DNA reiteration have been found in procaryotic organisms, only in the case of the archaebacteria Halobacterium halobium and Halobacterium volcanii [C. Sapienza and W. F. Doolittle, Nature (London) 295:384-389, 1982], has DNA reiteration been reported as a common genomic feature. The genomes of two Rhizobium phaseoli strains, one Rhizobium meliloti strain, and one Agrobacterium tumefaciens strain were analyzed for the presence of repetitive DNA. Rhizobium and Agrobacterium spp. are closely related soil bacteria that interact with plants and that belong to the taxonomical family Rhizobiaceae. Rhizobium species establish a nitrogen-fixing symbiosis in the roots of legumes, whereas Agrobacterium species is a pathogen in different plants. The four strains revealed a large number of repeated DNA sequences. The family size was usually small, from 2 to 5 elements, but some presented more than 10 elements. Rhizobium and Agrobacterium spp. contain large plasmids in addition to the chromosomes. Analysis of the two Rhizobium strains indicated that DNA reiteration is not confined to the chromosome or to some plasmids but is a property of the whole genome.     

Unique ribosome structure of Leptospira interrogans is composed of four rRNA components

All known ribosomes of procaryotic organisms are made up of three rRNA components that are 23, 16, and 5S in size. We now report that in some Leptospira interrogans strains, the classical 23S rRNA is further processed to generate 14 and 17S rRNAs. This processing step was previously known to occur only in some eucaryotes and in a small group of procaryotes. The implications of this finding are discussed.     

Isolation of new actinomycete strains for the screening of new bioactive compounds

In order to facilitate the discovery of novel bioactive compounds from microorganisms, various techniques for isolation of new actinomycete strains have been attempted. Studies of the vertical distribution of actinomycetes in soil, isolation of actinomycetes from desert soils or fallen leaves, selective isolation of Kitasatospora strains using novobiocin or Actinoplanes strains using the chemotactic method, and the use of gellan gum as a solidifying agent were carried out. We discovered 9 novel bioactive compounds from actinomycete strains isolated under unusual conditions, and proposed two new genera, five new species and one new subspecies.     

Bioremediation potential of glyphosate-degrading microorganisms in eutrophicated Ecuadorian water bodies

Phosphonate compounds are the basis of many xenobiotic pollutants, such as Glyphosate (N-(phosphonomethyl-glycine). Only procaryotic microorganisms and the lower eukaryotes are capable of phosphonate biodegradation through C–P lyase pathways. Thus, the aim of this study was to determine the presence of C–P lyase genes in Ecuadorian freshwater systems as a first step towards assessing the presence of putative glyphosate degraders. To that end, two Nested PCR assays were designed to target the gene that codifies for the subunit J (phnJ), which breaks the C-P bond that is critical for glyphosate mineralization. The assays designed in this study led to the detection of phnJ genes in 7 out of 8 tested water bodies. The amplified fragments presented 85–100% sequence similarity with phnJ genes that belong to glyphosate-degrading microorganisms. Nine sequences were not reported previously in the GenBank. The presence of phosphonate degraders was confirmed by isolating three strains able to grow using glyphosate as a unique carbon source. According to the 16S sequence, these strains belong to the Pantoea, Pseudomonas, and Klebsiella genera. Performing a Nested PCR amplification of phnJ genes isolated from eutrophicated water bodies, prior to isolation, may be a cost-effective strategy for the bioprospection of new species and/or genes that might have new properties for biotech industries, laying the groundwork for additional research.     

New data on the systematics of the Limnocytheridae (Ostracoda,Cytheracea)

A new grouping of genera having fossil as well as recent representatives of the family Limnocytheridae (Ostracoda, Cytheracea) is proposed using morphological characteristics of the appendages, of the shell and of the evolutionary trends observed in this family.     

Baetimyces, a new genus of Harpellales, and first report of Legeriomyces ramosus from the northeastern Iberian Peninsula

Baetimyces, belonging to the Legeriomycetaceae, is described here as a new genus. Its single species, B. ancorae, has been found growing in the hindgut of mayfly nymphs of the genus Baetis (Ephemeroptera, Baetidae) inhabiting a Pyrenean Mountains canal-stream from the northeastern region of the Iberian Peninsula. The new genus is characterized by having trichospores with two thick appendages of unequal length, and by zygospores perpendicularly and medially attached to the zygosporophore. The new genus may be related to Glotzia, Legeriomyes, and Zygopolaris, and similarities with these and other genera are compared and discussed. The new species often coexists in the same gut with Legeriomyces ramosus, which is reported for the first time in Spain.     

Two new species of Pseudogymnoascus with Geomyces anamorphs and their phylogenetic relationship with Gymnostellatospora

Two new psychrophilic Pseudogymnoascus species with Geomyces anamorphs are described from a Sphagnum bog in Alberta, Canada. Pseudogymnoascus appendiculatus has long, branched, orange appendages and smooth, fusoid to ellipsoidal ascospores with a faint longitudinal rim. Pseudogymnoascus verrucosus has short, subhyaline appendages and warty peridial hyphae and ascospores, and both smooth to asperulate and irregularly warty conidia. Both species produce asci in chains, a feature that supports the distinction between this group and Myxotrichum, which produces asci singly. The discovery of species intermediate between Pseudogymnoascus and Gymnostellatospora, in having both ornamented ascospores and Geomyces anamorphs, prompted a re-evaluation of the genera. Sequence analysis of the internal transcribed spacer regions (ITS) of the nuclear ribosomal DNA indicates that the two genera remain distinct and comprise a monophyletic group. Pseudogymnoascus species have smooth to warty or lobate-reticulate ascospores while species of Gymnostellatospora have walnut-shaped spores with distinct longitudinal crests and striations. Anamorphs assignable to the form genus Geomyces are allied with both genera. A key is provided to the four species and varieties of Pseudogymnoascus.     

Identification of New Sphingomyelinases D in Pathogenic Fungi and Other Pathogenic Organisms

Sphingomyelinases D (SMases D) or dermonecrotic toxins are well characterized in Loxosceles spider venoms and have been described in some strains of pathogenic microorganisms, such as Corynebacterium sp. After spider bites, the SMase D molecules cause skin necrosis and occasional severe systemic manifestations, such as acute renal failure. In this paper, we identified new SMase D amino acid sequences from various organisms belonging to 24 distinct genera, of which, 19 are new. These SMases D share a conserved active site and a C-terminal motif. We suggest that the C-terminal tail is responsible for stabilizing the entire internal structure of the SMase D Tim barrel and that it can be considered an SMase D hallmark in combination with the amino acid residues from the active site. Most of these enzyme sequences were discovered from fungi and the SMase D activity was experimentally confirmed in the fungus Aspergillus flavus. Because most of these novel SMases D are from organisms that are endowed with pathogenic properties similar to those evoked by these enzymes alone, they might be associated with their pathogenic mechanisms.     

A redescription of Cythere japonica Hanai, 1959 (Podocopida: Ostracoda)

Cythere japonica was proposed by Hanai (1959) as a new species of the genus Cythere , from the Pleistocene Sawane Formation in Sado Island, Niigata Prefecture, Japan. The characters of carapace were already known, but the appendages have not been previously described. The authors formerly considered that this species should be separate from the genus Cythere sensu stricto because it has twice as many sieve-type pore systems as typical Cythere species, and a markedly higher carapace. The existence of living Cythere japonica in the tidal zone of north-west Japan is confirmed, and its taxonomic position re-examined on the basis of its appendages and the ontogeny of pore systems. The appendages, except for the copulatory organ, are almost identical with those of other Cythere species, and their pore systems share the same pattern in and before the A-4 moult stage. On the basis of these features this species should be retained in the genus Cythere. Phylogenetic relationships are considered on the basis of the ontogeny of pore systems.
The abdominal segments of podocopid Ostracoda, which have always been regarded as difficult to observe because of their fusion, are shown clearly by the SEM.