Prototypic SNARE Proteins Are Encoded in the Genomes of Heimdallarchaeota,Potentially Bridging the Gap between the Prokaryotes and Eukaryotes

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Looking through the Lens of the Ribosome Biogenesis Evolutionary History: Possible Implications for Archaeal Phylogeny and Eukaryogenesis

Our understanding of microbial diversity and its evolutionary relationships has increased substantially over the last decade. Such an understanding has been greatly fueled by culture-independent metagenomics analyses. However, the outcome of some of these studies and their biological and evolutionary implications, such as the origin of the eukaryotic lineage from the recently discovered archaeal Asgard superphylum, is debated. The sequences of the ribosomal constituents are amongst the most used phylogenetic markers. However, the functional consequences underlying the analysed sequence diversity and their putative evolutionary implications are essentially not taken into consideration. Here, we propose to exploit additional functional hallmarks of ribosome biogenesis to help disentangle competing evolutionary hypotheses. Using selected examples, such as the multiple origins of halophily in archaea or the evolutionary relationship between the Asgard archaea and Eukaryotes, we illustrate and discuss how function-aware phylogenetic framework can contribute to refining our understanding of archaeal phylogeny and the origin of eukaryotic cells.     

Distribution and Diversity of Microbial Eukaryotes in Bathypelagic Waters of the South China Sea

Little is known about the biodiversity of microbial eukaryotes in the South China Sea, especially in waters at bathyal depths. Here, we employed SSU rDNA gene sequencing to reveal the diversity and community structure across depth and distance gradients in the South China Sea. Vertically, the highest alpha diversity was found at 75‐m depth. The communities of microbial eukaryotes were clustered into shallow‐, middle‐, and deep‐water groups according to the depth from which they were collected, indicating a depth‐related diversity and distribution pattern. Rhizaria sequences dominated the microeukaryote community and occurred in all samples except those from less than 50‐m deep, being most abundant near the sea floor where they contributed ca. 64–97% and 40–74% of the total sequences and OTUs recovered, respectively. A large portion of rhizarian OTUs has neither a nearest named neighbor nor a nearest neighbor in the GenBank database which indicated the presence of new phylotypes in the South China Sea. Given their overwhelming abundance and richness, further phylogenetic analysis of rhizarians were performed and three new genetic clusters were revealed containing sequences retrieved from the deep waters of the South China Sea. Our results shed light on the diversity and community structure of microbial eukaryotes in this not yet fully explored area.     

Base compositional bias and phylogenetic analyses: a test of the "flying DNA" hypothesis

Phylogenetic methods can produce biased estimates of phylogeny when base composition varies along different lineages. Pettigrew (1994, Curr. Biol. 4:277-280) has suggested that base composition bias is responsible for the apparent support for the monophyly of bats (Chiroptera: megabats and microbats) from several different nuclear and mitochondrial genes. Pettigrew's "flying DNA" hypothesis makes several predictions: (1) that metabolic constraints associated with flying result in elevated levels of adenine and thymine throughout the genome of both megabats and microbats, (2) that the resulting base compositional bias in bats is sufficient to mislead phylogenetic methods and account for the support for bat monophyly from several nuclear and mitochondrial genes, and (3) that phylogenetic analysis using pairwise distances corrected for compositional bias should eliminate the support for bat monophyly. We tested these predictions by analyzing DNA sequences from two nuclear and three mitochondrial genes. The predicted base compositional bias does not appear to exist in some of the genes, and in other genes the differences in AT content are very small. Analyses under a wide diversity of criteria and models of evolution, including analyses that take base composition into account (using log-determinant distances), all strongly support bat monophyly. Moreover, simulation analyses indicate that even extreme bias toward AT-base composition in bats would be insufficient to explain the observed levels of support for bat monophyly. These analyses provide no support for the "flying DNA" hypothesis, whereas the monophyly of bats appears to be well supported by the DNA sequence data.     

Base Compositional Bias and Phylogenetic Analyses: A Test of the “Flying DNA” Hypothesis

Phylogenetic methods can produce biased estimates of phylogeny when base composition varies along different lineages. Pettigrew (1994,Curr. Biol.4:277–280) has suggested that base composition bias is responsible for the apparent support for the monophyly of bats (Chiroptera: megabats and microbats) from several different nuclear and mitochondrial genes. Pettigrew's “flying DNA” hypothesis makes several predictions: (1) that metabolic constraints associated with flying result in elevated levels of adenine and thymine throughout the genome of both megabats and microbats, (2) that the resulting base compositional bias in bats is sufficient to mislead phylogenetic methods and account for the support for bat monophyly from several nuclear and mitochondrial genes, and (3) that phylogenetic analysis using pairwise distances corrected for compositional bias should eliminate the support for bat monophyly. We tested these predictions by analyzing DNA sequences from two nuclear and three mitochondrial genes. The predicted base compositional bias does not appear to exist in some of the genes, and in other genes the differences in AT content are very small. Analyses under a wide diversity of criteria and models of evolution, including analyses that take base composition into account (using log-determinant distances), all strongly support bat monophyly. Moreover, simulation analyses indicate that even extreme bias toward AT-base composition in bats would be insufficient to explain the observed levels of support for bat monophyly. These analyses provide no support for the “flying DNA” hypothesis, whereas the monophyly of bats appears to be well supported by the DNA sequence data.     

MicroRNA: Biogenesis, Function and Role in Cancer

MicroRNAs are small, highly conserved non-coding RNA molecules involved in the regulation of gene expression. MicroRNAs are transcribed by RNA polymerases II and III, generating precursors that undergo a series of cleavage events to form mature microRNA. The conventional biogenesis pathway consists of two cleavage events, one nuclear and one cytoplasmic. However, alternative biogenesis pathways exist that differ in the number of cleavage events and enzymes responsible. How microRNA precursors are sorted to the different pathways is unclear but appears to be determined by the site of origin of the microRNA, its sequence and thermodynamic stability. The regulatory functions of microRNAs are accomplished through the RNA-induced silencing complex (RISC). MicroRNA assembles into RISC, activating the complex to target messenger RNA (mRNA) specified by the microRNA. Various RISC assembly models have been proposed and research continues to explore the mechanism(s) of RISC loading and activation. The degree and nature of the complementarity between the microRNA and target determine the gene silencing mechanism, slicer-dependent mRNA degradation or slicer-independent translation inhibition. Recent evidence indicates that P-bodies are essential for microRNA-mediated gene silencing and that RISC assembly and silencing occurs primarily within P-bodies. The P-body model outlines microRNA sorting and shuttling between specialized P-body compartments that house enzymes required for slicer -dependent and -independent silencing, addressing the reversibility of these silencing mechanisms. Detailed knowledge of the microRNA pathways is essential for understanding their physiological role and the implications associated with dysfunction and dysregulation.     

Community assembly of bacteria and archaea in coastal waters governed by contrasting mechanisms: A seasonal perspective

Marine planktonic bacteria and archaea commonly exhibit pronounced seasonal succession in community composition. But the existence of seasonality in their assembly processes and between‐domain differences in underlying mechanism are largely unassessed. Using a high‐coverage sampling strategy (including single sample for each station during four cruises in different seasons), 16S rRNA gene sequencing, and null models, we investigated seasonal patterns in the processes governing spatial turnover of bacteria and archaea in surface coastal waters across a sampling grid over ~300 km in the East China Sea. We found that archaea only bloomed in prokaryotic communities during autumn and winter cruises. Seasonality mostly overwhelmed spatial variability in the compositions of both domains. Bacterial and archaeal communities were dominantly governed by deterministic and stochastic assembly processes, respectively, in autumn cruise, probably due to the differences in niche breadths (bacteria < archaea) and relative abundance (bacteria > archaea). Stochasticity dominated assembly mechanisms of both domains but was driven by distinct processes in winter cruise. Determinism‐dominated assembly mechanisms of bacteria rebounded in spring and summer cruises, reflecting seasonal variability in bacterial community assembly. This could be attributed to seasonal changes in bacterial niche breadths and habitat heterogeneity across the study area. There were seasonal changes in environmental factors mediating the determinism‐stochasticity balance of bacterial community assembly, holding a probability of the existence of unmeasured mediators. Our results suggest contrasting assembly mechanisms of bacteria and archaea in terms of determinism‐vs.‐stochasticity pattern and its seasonality, highlighting the importance of seasonal perspective on microbial community assembly in marine ecosystems.     

Molecular Identification and Biofilm-Forming Ability of Culturable Aquatic Bacteria In Microbial Biofilms Formed in Drinking Water Distribution Networks

Drinking water distribution networks are known to harbor microbial biofilms. The aim of the present work is to (i) identify the culturable bacteria presented in the drinking-water distribution network, (ii) investigate the ability of isolated bacteria to form biofilm under some environmental stress conditions and some eliminating or removing treatments. To achieve it, 57 strains were isolated from biofilm (43 isolates) and water samples (14 isolates) collected from five stations in drinking-water distribution network in Taif city, Kingdom of Saudi Arabia (KSA). Partial sequences of 16S rRNA gene in the 57 isolates ensured the presence of only 22 different strains in biofilm samples. Among these strains, only 14 strains were also detected in water samples. Gram-negative Aeromonas hydrophila was the most occurred bacterium in the microbial biofilm obtained from the purified-water storage tanks followed by Gram-negative Pseudomonas sp. Gram-positive Bacillus subtilis was the most occurred bacterium in the microbial biofilm collected from the ends of the distribution pipes. Among the 22 isolated strains, 13 strains were strong biofilm producers at 30 and 37°C. The effects of environmental stresses including nutrient starvation (diluted TSB, 20:1), heating (100°C for 10 min), UV-treatment (240 nm for 10 min) and dynamic incubation (150 rpm min^?1) on the formation of biofilm were also investigated. These conditions affected the biofilm formation ability of the isolated strains at different levels. Nutrient starvation enhanced biofilm formation by most of the isolates. Among some biofilm deforming treatments, SDS and trypsin had considerable effects on preventing biofilm formation by most of the isolated strains. In conclusion, the results of the present work indicated that not all biofilm strains released from biofilm to the drinking water. Also, not all biofilm strains were able to form biofilm. Most of isolated bacteria had ability to form biofilm at suboptimum temperature of growth. These results may provide basic information on formation of microbial biofilms and overcome the problem of deteriorating of water quality in the drinking-water distribution networks.     

小脆柄菇属微小脆柄菇支系的一个新种及两个中国新记录种

依据形态学及ITS、LSU、β-tub和tef-1α等4个片段系统发育分析结果,描述了产自中国的小脆柄菇属微小脆柄菇支系下1个新种及2个中国新记录种,即翘鳞小脆柄菇Psathyrella squarrosa、斑褶菇状小脆柄菇P.panaeoloides和皂味小脆柄菇P.saponacea.翘鳞小脆柄菇发现于广东省,群生...     

Ecological Patterns and Biological Invasions: Using Regional Species Inventories in Macroecology

Macroecology depends heavily on a comparative methodology in order to identify large-scale patterns and to test alternative hypotheses that might generate such patterns. With the advent and accessibility of large electronic databases of species and their life history and ecological attributes, ecologists have begun seeking generalities, and examining large-scale ecological hypotheses involving core themes of range, abundance and diversity. For example, combinations of ecological, life history and phylogenetic data have been analysed using large species sets to test hypotheses in invasion biology. Analysis of regional species inventories can contribute cogently to our understanding of invasions. Here we examine several ways in which database analysis is effective. We review 19 studies of comparative invasions biology, each using >100 species of plants in their analyses, and show that invader success is linked to seven correlates: short life cycle, abiotic (mostly wind) dispersal, large native range size, non-random taxonomic patterns (emphasizing certain families or orders), presence of clonal organs, occupying disturbed habitats, and earlier time of introduction. These phylogenetically influenced, comparative analyses using regional species inventories are only just beginning and have much potential.     

Brain Evolution: Mammals,Primates, Chimpanzees,and Humans

Though many modern techniques are available for studying brains, they are difficult to use in evolutionary contexts that require examination of large numbers of specimens and species, and all major parts of the brain. Thus, evolutionary studies of many species and of whole brains still tend to be based upon simpler data such as sizes of brains and brain components. Such investigations, carried out over many decades, have usually employed univariate and bivariate analyses, though a few investigators used early multivariate methods. In mammals, these studies generally show the primacy of the relationship between brain and brain-part sizes with overall body size. More recent multivariate applications have confirmed this (Finlay, B. L., and Darlington, R. B. (1995). Science 268: 1578–1584) and some have also separated the highest level phylogenetic groups: strepsirrhines and haplorrhines (Barton, R. A., and Harvey, P. H. (2000). Nature 405: 1055–1058). Both findings were, in fact, evident in earlier multivariate studies (Holloway, R. L. (1979). In Hahn, M. E., Jensen C., and Dudek, B. C. (eds.), Development and Evolution of Brain Size: Behavioral Implications, Academic Press, New York, pp. 59–88; Sacher, G. A. (1970). In Noback, C. R., and Montagna, W. (eds.), The Primate Brain: Advances in Primatology. Vol. 1, Appleton-Century-Crofts, Educational Division, Meredith Corporation, New York, pp. 245–287). However, new studies employing proportional data aimed at conveying input/output relationships between brain components show further groupings of species that share convergences in lifestyles (de Winter, W., and Oxnard, C. E. (2001). Nature 409: 710–714). The convergences are brought about by combinations of brain variables that seem to be associated with brain functions implied by the specific lifestyles. Our most recent results demonstrate that chimpanzees and humans are especially different from one another, and the difference is not due to size alone. Part of this difference is merely a continuation, from chimpanzees towards humans, of a trend already present across all other primates that relates mainly to neocortical increase. But several other large and independent differences are not in the direction of the overall primate trend, but are differences of humans from all other mammals examined including all nonhuman primates. The combinations of brain variables associated with the latter differences are not related simply to enhancement of the neocortex, but seem to reflect other internal relationships. The overall separation of humans and chimpanzees is so large that it goes far beyond the conventional 98.6% commonality in their DNAs. It fits better with more recent molecular, developmental and evolutionary studies implying a considerably greater difference between chimpanzees and humans than usually recognized.     

A Resurgence in Field Research is Essential to Better Understand the Diversity,Ecology, and Evolution of Microbial Eukaryotes

The discovery and characterization of protist communities from diverse environments are crucial for understanding the overall evolutionary history of life on earth. However, major questions about the diversity, ecology, and evolutionary history of protists remain unanswered, notably because data obtained from natural protist communities, especially of heterotrophic species, remain limited. In this review, we discuss the challenges associated with “field protistology”, defined here as the exploration, characterization, and interpretation of microbial eukaryotic diversity within the context of natural environments or field experiments, and provide suggestions to help fill this important gap in knowledge. We also argue that increased efforts in field studies that combine molecular and microscopical methods offer the most promising path toward (1) the discovery of new lineages that expand the tree of eukaryotes; (2) the recognition of novel evolutionary patterns and processes; (3) the untangling of ecological interactions and functions, and their roles in larger ecosystem processes; and (4) the evaluation of protist adaptations to a changing climate.     

Compartments in a marine food web associated with phylogeny, body mass, and habitat structure

A long-standing question in community ecology is whether food webs are organized in compartments, where species within the same compartment interact frequently among themselves, but show fewer interactions with species from other compartments. Finding evidence for this community organization is important since compartmentalization may strongly affect food web robustness to perturbation. However, few studies have found unequivocal evidence of compartments, and none has quantified the suite of mechanisms generating such a structure. Here, we combine computational tools from the physics of complex networks with phylogenetic statistical methods to show that a large marine food web is organized in compartments, and that body size, phylogeny, and spatial structure are jointly associated with such a compartmentalized structure. Sharks account for the majority of predatory interactions within their compartments. Phylogenetically closely related shark species tend to occupy different compartments and have divergent trophic levels, suggesting that competition may play an important role structuring some of these compartments. Current overfishing of sharks has the potential to change the structural properties, which might eventually affect the stability of the food web.     

Phylogenetic Analysis of Phaeosphaeria Species Using Mating Type Genes and Distribution of Mating Types in Iran

Phaeosphaeria species are pathogenic on wheat, barley and a wide range of wild grasses. To analyze mating type loci of the Phaeosphaeria species and investigate mating type distribution in Iran, we sequenced mating type loci of 273 Phaeosphaeria isolates including 67 isolates obtained from symptomatic leaves and ears of wheat, barley, and wild grasses from two wheat-growing region in Iran as well as 206 isolates from our collection from other regions in Iran which were isolated in our previous studies. Mating type genes phylogeny was successfully used to determine the species identity and relationships among isolates within the Phaeosphaeria spp. complex. In this study, we reported seven new host records for Phaeosphaeria species and the Phaeosphaeria avenaria f. sp. tritici 3 group was first reported from Iran in this study. Mating type distribution among Phaeosphaeria species was determined. Both mating types were present in all sampling regions from Iran. We observed skewed distribution of mating types in one region (Kohgiluyeh va Boyer-Ahmad) and equal distribution in the other region (Bushehr). However, when considering our entire dataset of 273 Iranian Phaeosphaeria isolates, the ratio of mating types was not deviated significantly from 1:1 suggesting possibilities for isolates of opposite mating type to interact and reproduce sexually, although the sexual cycle may infrequently occur in some regions especially when the climatic conditions are unfavorable for teleomorph development.     

Entamoeba histolytica Schaudinn, 1903 and Entamoeba dispar Brumpt, 1925: differences in their cell surfaces and in the bacteria-containing vacuoles

Entamoeba histolytica Schaudinn, 1903 and Entamoeba dispar Brumpt. 1925 are two of eight species of Entamoeba that sometimes inhabit the human colon. The former is an invasive organism capable of causing life-threatening intestinal and extra-intestinal disease: the latter appears not to be invasive. Because the two species, when viewed by light microscopy appear morphologically similar, they were long regarded as a single species. However, recent biochemical. immunological, and genetic studies provided convincing evidence that they belong to separate species. Our ultrastructural studies revealed distinct differences in at least two features of the trophozoites. 1) The cell surfaces of the trophozoites of each species differ with regard to structures exposed on the surface, and the distribution and arrangement of intra-membranous proteins. 2) The phagocytosis of bacteria differs in respect to the formation of the phagocytic vacuoles. Loose vacuoles containing several bacteria were seen in E. histolytica whereas tight vacuoles containing a single bacterium were observed in E. dispar. Furthermore, bacteria were found only within vacuoles in E. histolytica; in E. dispar, bacteria were found within vacuoles and some were found free in the cytoplasm.     

Microbial diversity and complexity in hypersaline environments: A preliminary assessment

The microbial communities in solar salterns and a soda lake have been characterized using two techniques: BIOLOG, to estimate the metabolic potential, and amplicon length heterogeneity analysis, to estimate the molecular diversity of these communities. Both techniques demonstrated that the halophilic Bacteria and halophilic Archaea populations in the Eilat, Israel saltern are dynamic communities with extensive metabolic potentials and changing community structures. Halophilic Bacteria were detected in Mono Lake and the lower salinity ponds at the Shark Bay saltern in Western Australia, except when the crystallizer samples were stressed by exposure to Acid Green Dye #9899. At Shark Bay, halophilic Archaea were found only in the crystallizer samples. These data confirm both the metabolic diversity and the phylogenetic complexity of the microbial communities and assert the need to develop more versatile media for the cultivation of the diversity of bacteria in hypersaline environments. Journal of Industrial Microbiology & Biotechnology (2002) 28, 48–55 DOI: 10.1038/sj/jim/7000175 Received 20 May 2001/ Accepted in revised form 15 June 2001     

Effect of Glycinebetaine on Chloroplast Ultrastructure, Chlorophyll and Protein Content, and RuBPCO Activities in Tomato Grown under Drought or Salinity

The effect of foliar-applied glycinebetaine (GB) on chloroplast ultrastructure, the amount of chlorophyll and proteins and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBPCO) activity in stressed tomato leaves were analysed. Initial, and total activity and activation state state of RuBPCO were also measured. RuBPCO activities, chloroplast area, and the number of plastoglobuli remained unaffected, while the relative area of starch granules increased in GB-treated, salt-stressed tomato leaflets. Under drought-stress, the relative area of plastoglobuli increased upon GB application. The primary effect of GB was, however, the increased protein and chlorophyll content.     

Hyperhalophilic archaeal biofilms: growth kinetics,structure, and antagonistic interaction in continuous culture

Biofilms by the hyperhalophilic archaea Halorubrum sp. and Halobacterium sp. were analyzed, and for the first time the progression of structural features and the developmental parameters of these sessile populations are described. Optical slicing and digital analysis of sequential micrographs showed that their three dimensional structure was microorganism dependent. Biofilms of Halobacterium sp. developed in clusters that covered about 30% of the supporting surface at the interface level and expanded over about 86?±?4 μm in thickness, while Halorubrum sp. biofilms covered less than 20% of the surface and reached a thickness of 41?±?1 μm. The kinetics of growth was lower in biofilms, with generation times of 27?±?1 and 36?±?2 h for Halobacterium sp. and Halorubrum sp., respectively, as compared to 8.4?±?0.3 and 14?±?1 h in planktonic cultures. Differences between microorganisms were also observed at the cell morphology level. The interaction between the two microorganisms was also evaluated, showing that Halobacterium sp. can outcompete already established Halorubrum sp. biofilms by a mechanism that might include the combined action of tunnelling swimmers and antimicrobial compounds.