What are archaebacteria: life's third domain or monoderm prokaryotes related to Gram-positive bacteria? A new proposal for the classification of prokaryotic organisms

The evolutionary relationship within prokaryotes is examined based on signature sequences (defined as conserved inserts or deletions shared by specific taxa) and phylogenies derived from different proteins. Archaebacteria are indicated as being monophyletic by a number of proteins related to the information transfer processes. In contrast, for several other highly conserved proteins, common signature sequences are present in archaebacteria and Gram-positive bacteria, whereas Gram-negative bacteria are indicated as being distinct. For these proteins, archaebacteria do not form a phylogenetically distinct clade but show polyphyletic branching within Gram-positive bacteria. A closer relationship of archaebacteria to Gram-positive bacteria in comparison with Gram-negative bacteria is generally seen for the majority of the available gene/protein sequences. To account for these results and the fact that both archaebacteria and Gram-positive bacteria are prokaryotes surrounded by a single cell membrane, I propose that the primary division within prokaryotes is between monoderm prokaryotes (surrounded by a single membrane) and diderm prokaryotes (i.e. all true Gram-negative bacteria containing both an inner cytoplasmic membrane and an outer membrane). This proposal is consistent with both cell morphology and signature sequences in different proteins. The monophyletic nature of archaebacteria for some genes, and their polyphyletic branching within Gram-positive bacteria as suggested by others, is critically examined, and several explanations, including derivation of archaebacteria from Gram-positive bacteria in response to antibiotic selection pressure, are proposed. Signature sequences in proteins also indicate that the low-G + C Gram-positive bacteria are phylogenetically distinct from the high-G + C Gram-positive group and that the diderm prokaryotes (i.e. Gram-negative bacteria) appear to have evolved from the latter group. Protein phylogenies and signature sequences also show that all eukaryotic cells have received significant gene contributions from both an archaebacterium and a Gram-negative eubacterium. Thus, the hypothesis that archaebacteria and eukaryotes shared a common ancestor exclusive of eubacteria is not supported. These observations provide evidence for an alternate view of the evolutionary relationship among living organisms that is different from the currently popular three-domain proposal.     

A new scenario of plastid evolution: plastid primary endosymbiosis before the divergence of the “Plantae,” emended

A recent hypothesis on the origin of eukaryotic phototrophs proposes that red algae, green plants (land plants plus green algae), and glaucophytes constitute the primary photosynthetic eukaryotes, whose plastids may have originated directly from a cyanobacterium-like prokaryote via primary endosymbiosis, whereas the plastids of other lineages of eukaryotic phototrophs appear to be the result of secondary endosymbiotic events involving a phototrophic eukaryote and a host cell. However, the phylogenetic relationships among the three lineages of primary photosynthetic eukaryotes remained unresolved because previous nuclear multigene phylogenies used incomplete red algal gene sequences derived mainly from Porphyra (Rhodophyceae, one of the two lineages of the Rhodophyta), and lacked sequences from the Cyanidiophyceae (the other red algal lineage). Recently, the complete nuclear genome sequences from the red alga Cyanidioschyzon merolae 10D of the Cyanidiophyceae were determined. Using this genomic information, nuclear multigene phylogenetic analyses of various lineages of mitochondrion-containing eukaryotes were conducted. Since bacterial and amitochondrial eukaryotic genes present serious problems to eukaryotic phylogenies, basal eukaryotes were deduced based on the paralogous comparison of the concatenated - and -tubulin. The comparison demonstrated that cellular slime molds (Amoebozoa) represent the most basal position within the mitochondrion-containing organisms. With the cellular slime molds as the outgroup, phylogenetic analyses based on a 1,525-amino acid sequence of four concatenated nuclear genes [actin, elongation factor-1( EF-1), -tubulin, and -tubulin] resolved the presence of two large, robust monophyletic groups and the basal eukaryotic lineages (Amoebozoa). One of the two groups corresponded to the Opisthokonta (Metazoa and Fungi), whereas the other included various lineages containing primary and secondary plastids (red algae, green plants, glaucophytes, euglenoids, heterokonts, and apicomplexans), Ciliophora, Kinetoplastida, dinoflagellates, and Heterolobosea, for which the red algae represented the most basal lineage. Therefore, the plastid primary endosymbiosis likely occurred once in the common ancestor of the latter group, and the primary plastids were subsequently lost in the ancestor(s) of organisms within the group that now lacks primary plastids. A new concept of Plantae was proposed for phototrophic and nonphototrophic organisms belonging to this group on the basis of their common history of plastid primary endosymbiosis. This new scenario of plastid evolution is discussed here, and is compared with recent genome information and findings on the secondary endosymbiosis of the Euglena plastid.     

Phylogenetic analysis of 70 kD heat shock protein sequences suggests a chimeric origin for the eukaryotic cell nucleus

Background: The evolutionary relationships between archaebacteria, eubacteria and eukaryotic cells are of central importance in biology. The current view is that each of these three groups of organisms constitutes a monophyletic domain, and that eukaryotic cells have evolved from an archaebacterial ancestor. Recent studies on a number of highly conserved protein sequences do not, however, support this view and raise important questions concerning the evolutionary relationships between all extant organisms, particularly regarding the origin of eukaryotic cells.Results We have used sequences of 70 kD heat shock protein (hsp70) — the most conserved protein found to date in all species — to examine the evolutionary relationship between various species. We have obtained two new archaebacterial hsp70 sequences from the species, Thermoplasma acidophilum and Halobacterium cutirubrum. A global comparison of hsp70 sequences, including our two new sequences, shows that all known archaebacterial homologs share a number of sequence signatures with the Gram-positive group of bacteria that are not found in any other prokaryotic or eukaryotic species. In contrast, the eukaryotic homologs are shown to share a number of unique sequence features with the Gram-negative bacteria that are not present in any archaebacteria. Detailed phylogenetic analyses of hsp70 sequences strongly support a specific evolutionary relationship between archaebacteria and Gram-positive bacteria on the one hand, and Gram-negative bacteria and eukaryotes on the other. The phylogenetic analyses also indicate a polyphyletic branching of archaebacteria within the Gram-positive species. The possibility that the observed relationships are due to horizontal gene transfers can be excluded on the basis of sequence characteristics of different groups of homologs.Conclusion Our results do not support the view that archaebacteria constitute a monophyletic domain, but instead suggest a close evolutionary linkage between archaebacteria and Gram-positive bacteria. Furthermore, in contrast to the presently accepted view, eukaryotic hsp70s show a close and specific relationship to those from Gram-negative species. To explain the phylogenies based on different gene sequences, a chimeric model for the origin of the eukaryotic cell nucleus involving fusion between an archaebacterium and a Gram-negative eubacterium is proposed. Several predictions from the chimeric model are discussed.     

Evolutionary relationships among photosynthetic prokaryotes (Heliobacterium chlorum, Chloroflexus aurantiacus, cyanobacteria, Chlorobium tepidum and proteobacteria): implications regarding the origin of photosynthesis

The presence of shared conserved insertions or deletions in proteins (referred to as signature sequences) provides a powerful means to deduce the evolutionary relationships among prokaryotic organisms. This approach was used in the present work to deduce the branching orders of various eubacterial taxa consisting of photosynthetic organisms. For this purpose, portions of the Hsp60 and Hsp70 genes, covering known signature sequence regions, were PCR-amplified and sequenced from Heliobacterium chlorum, Chloroflexus aurantiacus and Chlorobium tepidum. This information was integrated with sequence data for several other proteins from numerous species to deduce the branching orders of different photosynthetic taxa. Based on signature sequences that are present in different proteins, it is possible to infer that the various eubacterial phyla evolved from a common ancestor in the following order: low G+C Gram-positive (H. chlorum) --> high G+C Gram-positive --> Deinococcus-Thermus --> green non-sulphur bacteria (Cf. aurantiacus ) --> cyanobacteria --> spirochaetes --> Chlamydia-Cytophaga-Aquifex-flavobacteria-green sulphur bacteria (Cb. tepidum) --> proteobacteria (alpha, delta and epsilon) and --> proteobacteria (beta and gamma). The members of the Heliobacteriaceae family that contain a Fe-S type of reaction centre (RC-1) and represent the sole photosynthetic phylum from the Gram-positive or monoderm group of prokaryotes are indicated to be the most ancestral of the photosynthetic lineages. Among the Gram-negative bacteria or diderm prokaryotes, green non-sulphur bacteria such as Cf. aurantiacus, which contains a pheophytin-quinone type of reaction centre (RC-2), are indicated to have evolved very early. Thus, the organisms containing either RC-1 or RC-2 existed before the evolution of cyanobacteria, which contain both these reaction centres to carry out oxygenic photosynthesis. The eubacterial divisions consisting of green sulphur bacteria and proteobacteria are indicated to have diverged after cyanobacteria. Some implications of these results concerning the origin of photosynthesis and the earliest prokaryotic fossils are discussed.     

Snake communities of moist rainforest and derived savanna sites of Nigeria: biodiversity patterns and conservation priorities

The taxonomic composition and the abundance of two communities of snakes were studied in two different areas of southern Nigeria. One community was studied in a derived savanna area (environs of Ejule, 06°54N, 07°23E), and one community was studied in a moist rainforest area (environs of Eket, 04°50N, 07°59E). Both the specific diversity and the mean frequency of observation of snakes were significantly higher in the forest area than in the savanna area, and the dominance index was higher in the savanna than in the forest site. However, most of the species were found in only one of the two areas, depending on their habitat requirements (e.g. Gastropyxis smaragdina, Dispholidus typus, Thelotornis kirtlandii, Dendroaspis jamesoni, Bitis nasicornis, Causus maculatus, etc). The forest community housed a significant number of arboreal and semiaquatic taxa, but in both sites most of the species were terrestrial. The commonest species in the forest area was an oviparous, semiaquatic, batracophagous natricine snake (Afronatrix anoscopus), whereas the commonest species in the savanna area was an oviparous terrestrial lacertophagous psammophine snake (Psammophis phillipsi). Some conservation implications of our biodiversity analyses are presented. It is suggested that the moist rainforest represents a critically endangered habitat, and should deserve special attention by the international scientific community. Oil industry activity is especially dangerous for snake communities, especially in the southernmost regions of Nigeria.     

The microbiology of ‘kunun-zaki’, a cereal beverage from northern Nigeria,during the fermentation (production) process

Kunun-zaki is a beverage produced by a fermentation process involving the steeping of millet grains and wetmilling. Initially, there is a wide range of microflora but, after steeping, the moulds are eliminated, leaving a 1:1 ratio of Gram-negative bacteria to Gram-positive bacteria. By the end of the fermentation, all Gram-negative bacteria are eliminated and Lactobacillus spp. predominate. Increase in acidity during the process also encourages growth of Saccharomyces cerevisiae. Fermentation for 8 h produces an acceptable product.     

Bacterial diversity of the Inner Mongolian Baer Soda Lake as revealed by 16S rRNA gene sequence analyses

Bacterial diversity associated with Baer Soda Lake in Inner Mongolia of China was investigated using a culture-independent method. Bacterial 16S rRNA gene libraries were generated using bacterial oligonucleotide primers, and 16S rRNA gene sequences of 58 clones were analyzed phylogenetically. The library was dominated by 16S rDNAs of Gram-negative bacteria (24% -Proteobacteria, 31% -Proteobacteria, 33% -Proteobacteria, and 2% -Proteobacteria), with a lower percentage of clones corresponding to Gram-positive bacteria. Forty cloned sequences were similar to that of known bacterial isolates (>97% sequence similarity), represented by the species of the genera Brevundimonas, Comamonas, Alcaligenes, Stenotrophomonas, and Klebsiella. Eighteen cloned sequences showed less affiliation with known taxa (<97% sequence similarity) and may represent novel taxa.Communicated by K. Horikoshi     

Moraxellae: Identification

According to published reports, all strains ofMoraxella osloensis and Moraxella (Oligella) urethralis grew on a mineral-base medium supplemented with 0.015M (0.123%) sodium acetate, but not all alkalinized a mineral-base medium supplemented with 0.008% bromthymol blue and 0.2% sodium acetate. This seeming discrepancy was examined. The growth of most strains ofM. urethralis was inhibited by 0.008% bromthymol blue, and some by 0.2% anhydrous sodium acetate. All (42) strains ofM. osloensis andM. urethralis alkalinized a mineral-base medium supplemented with 0.1% sodium acetate trihydrate and 0.001% bromthymol blue or phenol red.     

Evolutionary Change and Epistemology

This paper is concerned with the debate in evolutionary epistemology about the nature of the evolutionary process at work in the development of science: whether it is Darwinian or Lamarckian. It is claimed that if we are to make progress through the many arguments that have grown up around this issue, we must return to an examination of the concepts of change and evolution, and examine the basic kinds of mechanism capable of bringing evolution about. This examination results in two kinds of processes being identified, dubbed direct and indirect, and these are claimed to exhaust all possibilities. These ideas are then applied to a selection of the debates within evolutionary epistemology. It is shown that while arguments about the pattern and rate of evolutionary change are necessarily inconclusive, those concerning the origin of novel variations and the mode of inheritance can be resolved by means of the distinctions made here. It is claimed that the process of selection in the evolution of science can also be clarified. The conclusion is that the main process producing the evolution of science is a direct or Lamarckian one although, if realism is correct, an indirect or Darwinian process plays a vital role.     

Evolutionary relationships of bacterial and archaeal glutamine synthetase genes

Glutamine synthetase (GS), an essential enzyme in ammonia assimilation and glutamine biosynthesis, has three distinctive types: GSI, GSII and GSIII. Genes for GSI have been found only in bacteria (eubacteria) and archaea (archaebacteria), while GSII genes only occur in eukaryotes and a few soil-dwelling bacteria. GSIII genes have been found in only a few bacterial species. Recently, it has been suggested that several lateral gene transfers of archaeal GSI genes to bacteria may have occurred. In order to study the evolution of GS, we cloned and sequenced GSI genes from two divergent archaeal species: the extreme thermophile Pyrococcus furiosus and the extreme halophile Haloferax volcanii. Our phylogenetic analysis, which included most available GS sequences, revealed two significant prokaryotic GSI subdivisions: GSI-a and GSI-. GSIa-genes are found in the thermophilic bacterium, Thermotoga maritima, the low G+C Gram-positive bacteria, and the Euryarchaeota (includes methanogens, halophiles, and some thermophiles). GSI--type genes occur in all other bacteria. GSI-- and GSI--type genes also differ with respect to a specific 25-amino-acid insertion and adenylylation control of GS enzyme activity, both absent in the former but present in the latter. Cyanobacterial genes lack adenylylation regulation of GS and may have secondarily lost it. The GSI gene of Sulfolobus solfataricus, a member of the Crenarchaeota (extreme thermophiles), is exceptional and could not be definitely placed in either subdivision. The S. solfataricus GSI gene has a shorter GSI--type insertion, but like GSI-a-type genes, lacks conserved sequences about the adenylylation site. We suspect that the similarity of GSI- genes from Euryarchaeota and several bacterial species does not reflect a common phylogeny but rather lateral transmission between archaea and bacteria.Correspondence to: J.R. Brown 1073     

Gaining and losing the thermophilic adaptation in prokaryotes

We studied the evolution of thermophily in prokaryotes using the phylogenetic relationships between 279 bacteria and archaea and their thermophilic amino acid composition signature. Our findings suggest several examples in which the capacity of thermophilic adaptation has been gained or lost over relatively short evolutionary periods throughout the evolution of prokaryotes.     

Structure comparison and evolutionary relations between elongation factors EF-Tu (EF-1α) and SUP 2 proteins

On the basis of high homology and structural similarity, three genes, SUP2 Saccharomyces cerevisiae, SUP2 Pichia pinus and GST1 Homo sapiens, might be considered as members of one family named SUP2. Comparison of the primary structure of SUP2 proteins and elongation factors EF-Tu(EF-1) from 19 different species was performed. It was found that SUP2 proteins bear more homology to eukaryotic elongation factor than to procaryotic EF-Tu, though the degree of sequence conservation in SUP2 proteins is smaller than in EF-1 factors. The extensive phylogenetic analysis of SUP2 and EF-Tu(EF-1) genes was performed by means of 3 methods, 2 phenetic and one cladystic (maximal parsimony). The data support the close relation of SUP2 genes to other elongation factor genes.     

Environmental diversity: on the best-possible use of surrogate data for assessing the relative biodiversity of sets of areas

The conservation goal of representation of biodiversity (in the broad sense of all species) in protected areas requires best-possible use of available surrogate information. One standard approach is based on indicator groups of taxa. A minimum set of areas having at least one representation of each indicator species is taken to be representative of other organisms. This same minimum-set approach is adapted to other attributes of biodiversity, for example, derived environmental clusters. A weakness of these approaches is that useful information is lost; for example, for environmental clusters, there is no distinction made either among or within clusters. A more powerful surrogate approach can use some expression of environmental and/or biotic pattern so that variation among areas is seen as part of a continuum rather than partitioned into arbitrary clusters/attributes. The challenge in using pattern effectively is to adopt a robust model for the relationship between pattern and the underlying units of biodiversity, i.e. species. An environmental space (a continuum or ordination pattern), combined with the standard ecological continuum model relating species to environmental space, has advantages over other patterns based on hierarchy or distance matrices. Because an environmental space can be estimated either directly (observed environmental data) or indirectly (data on indicator groups), the corresponding surrogate-measure of biodiversity, environmental diversity (ED) makes best-possible use of either kind of data. We conclude that the arbitrariness of the attribute approach can be replaced by a robust surrogate pattern approach that is flexible and avoids unwarranted assumptions.     

A method for the estimation of gene flow parameters from a population structure caused by restricted gene flow and genetic drift

Summary A method has been developed which enables the estimation of the plant gene flow parameters _p (pollen dispersal), _s (seed dispersal) and t (outcrossing rate) from a selection-free continuously structured population in equilibrium. The method uses Wright's F-coefficients and introduces a new F-function which describes the genetic similarity as a function of the spatial distance. The method has been elaborated for wind pollinated plant species but can be modified for insect pollination and for animal species. In practice allozymes will provide for the necessary neutral genetic variation. The more loci used and the more intermediate the gene frequencies, the more reliable the results. For the estimation of _p and t together (when the outcrossing rate is not known) at least two chromosomally unlinked loci are required. The method for estimating _s depends on whether the plant species is annual or perennial. The mechanism of selfing has been analysed by the explanation of the value of t by three components: population density (d), pollen flow (_p) and relative fertilization potential of own pollen (Z). The concepts of neighbourhood size and isolation by distance, developed by Wright, who used a single gene flow parameter , have been extended to the situation which is realistic for seed plants, using all three parameters _p, _s and t. When _p is large with respect to _s, _s largely determines the value of the neighbourhood size, whereas _p is the most dominating factor in isolation by distance. The use of local effective population size and mean gene transport per generation instead of neighbourhood size and neighbourhood area, respectively, is proposed to avoid confusion. Computer simulations have been carried out to check the validity and the reliability of the method. Populations of 200 plants, using two or three loci with intermediate allele frequencies, gave good results in the calculation of _p with known value of t and of _s and N_e. With unknown t, especially with lower values of t, larger populations of at least 1,000 plants are necessary to obtain reasonably accurate results for _p and mean gene transport per generation M.Grassland Species Research Group Publication No. 81     

Bacterial diversity in deep-sea sediments from different depths

Seven sediment samples have been examined, taken from different depths of the deep-sea in the range of 1159m to 6482m. A total of 75 different 16S rDNA sequences (149 clones) analyzed clustered into the Proteobacteria, Gram-positive bacteria, Cytophaga, Planctomyces, and Actinomycetes and many sequences were from microorganisms that showed no phylogenetic affiliation with known bacteria. Clones identical to 16S rDNA sequences of members of the genus Pseudomonas were observed in all of the sediments examined. The second group of common sequences cloned from six sediment samples was related to the 16S rDNA sequence of a chemoautotrophic bacterium, the Solemya velum symbiont. Five 16S rDNA sequences from three sediments were related to those of the Alvinella pompejana epibiont which is a member of the -Proteobacteria. Only one sequence was obtained that was closely related to the 16S rDNA of the barophilic bacterium, Shewanella benthica, which might be a minor population in the deeper sediments. -Proteobacteria-related sequences were cloned from sediments obtained from sites near man-made garbage deposits and a Calyptogena community. These environments obviously would be richer in nutrients than other sites, and might be expected to show more types of bacteria than other deep-sea sediments. A large number of cloned sequences in this study showed very low identity to known sequences. These sequences may represent communities of as-yet-uncultivated microorganisms in the sediments.     

Haemoglobin synthesis in 28 obligatory cases for α-thalassemia traits

Summary In the Far East two types of -thalassemia genes, namely -thalassemia₁ (-thal₁) and -thalassemia₂ (-thal₂) exist. Definite diagnosis of the -thal₁ and -thal₂ traits is very difficult because their hematological findings are minimally abnormal or normal. This study attempts to characterize the heterozygotes by hemoglobin chain synthesis in reticulocytes from obligatory cases of the -thal₁ and -thal₂ traits. Twelve parents of babies with hemoglobin Bart's hydrops fetalis (obligatory -thal₁ trait) had the mean total radioactivity / ratio of 0.76±SD 0.04, while that of 7 normal controls was 1.06±SD 0.04. The / globin chain ratios of 16 cases, who were either parents or offspring of patients with hemoglobin H disease, were found to segregate into 2 groups, i.e. 0.78±SD 0.03 (10 cases) and 0.92±SD 0.03 (6 cases), probably representing the -thal₁ and -thal₂ traits respectively. The hematological data of the first group showed definite hypochromic microcytic red cells, similar to thoseof the parents of the hydrops. The second group had significantly higher mean corpuscular hemoglobin than the first group, compatible with -thal₂ trait. Our globin chain synthesis study thus appears to be capable of discriminating normal, -thal₁ and -thal₂ traits.A preliminary report of the results was presented at the XV Congress of the International Society of Haematology, Israel, September, 1974.     

The taxonomic significance of the trunk limbs of the chydoridae (Cladocera)

Summary The differences in the structure of the trunk limbs allow to outline three sections of Chydoridae (see table I and fig. 1), coinciding with the sections distinguished according to the structure of the head pores.

---

Chydoridae (Cladocera)

Chydoridae (. ), , .

     

Bacterial symbionts on green hydra and their effect on phosphate uptake

Gram-negative rod-shaped bacteria (1.5–2m long and 0.5m wide) have been found associated with green hydra. They are always present on the hydra surface delineating the ectodermal cells, on animals in culture, and also on those sampled from a natural habitat. The bacteria could be removed by a 30-min treatment with antibiotics (50/ml polymyxin B and 50/ml streptomycin). Antibiotic-treated hydra took up 55% less phosphate from the medium than control hydra. The nutritional relationship between the bacteria and green hydra and possible routes of infection of the hydra by these prokaryotic symbionts are discussed. Their importance in interpreting results of certain types of physiological experiments using aquatic organisms is emphasized.     

Distribution of glutathione transferases in Gram-positive bacteria and Archaea

Glutathione transferases (GSTs) have been widely studied in Gram-negative bacteria and the structure and function of several representatives have been elucidated. Conversely, limited information is available about the occurrence, classification and functional features of GSTs both in Gram-positive bacteria and in Archaea. An analysis of 305 fully-sequenced Gram-positive genomes highlights the presence of 49 putative GST genes in the genera of both Firmicutes and Actinobacteria phyla. We also performed an analysis on 81 complete genomes of the Archaea domain. Eleven hits were found in the Halobacteriaceae family of the Euryarchaeota phylum and only one in the Crenarchaeota phylum. A comparison of the identified sequences with well-characterized GSTs belonging to both Gram-negative and eukaryotic GSTs sheds light on their putative function and the evolutionary relationships within the large GST superfamily. This analysis suggests that the identified sequences mainly cluster in the new Xi class, while Beta class GSTs, widely distributed in Gram-negative bacteria, are under-represented in Gram-positive bacteria and absent in Archaea.     

Relationships of Agropyron intermedium chromosomes determined by chromosome pairing and alcohol dehydrogenase isozymes in common wheat background

Summary The relationships of Agropyron intermedium chromosomes in two wheat-Agropyron addition series were determined. Chromosome pairing behaviour revealed that the alien chromosome in lines TAF-2 and L7 of Vilmorin-A. intermedium set are homologous to the alien chromosomes in lines P and C of the Caribo-A. intermedium set respectively. Localization of alcohol dehydrogenase isozyme genes in Vilmorin-Agropyron addition line L4 and in Caribo-Agropyron line O indicated relationships with wheat chromosomes of homoeologous group 4.