Prokaryotes

The study of microbial fossils involves a broad array of disciplines and covers a vast diversity of topics, of which we review a select few, summarizing the state of the art. Microbes are found as body fossils preserved in different modes and have also produced recognizable structures in the rock record (microbialites, microborings). Study of the microbial fossil record and controversies arising from it have provided the impetus for the assembly and refining of powerful sets of criteria for recognition of bona fide microbial fossils. Different types of fossil evidence concur in demonstrating that microbial life was present in the Archean, close to 3.5 billion years ago. Early eukaryotes also fall within the microbial realm and criteria developed for their recognition date the oldest unequivocal evidence close to 2.0 billion years ago (Paleoproterozoic), but Archean microfossils >3 billion years old are strong contenders for earliest eukaryotes. In another dimension of their contribution to the fossil record, microbes play ubiquitous roles in fossil preservation, from facilitating authigenic mineralization to replicating soft tissue with extracellular polymeric substances, forming biofilms that inhibit decay of biological material, or stabilizing sediment interfaces. Finally, studies of the microbial fossil record are relevant to profound, perennial questions that have puzzled humanity and science—they provide the only direct window onto the beginnings and early evolution of life; and the methods and criteria developed for recognizing ancient, inconspicuous traces of life have yielded an approach directly applicable to the search for traces of life on other worlds.

A microbial composition study of sediments of contaminated (CWS) and uncontaminated (UWS) lentic ecosystems within Akwa Ibom State was carried out by analyzing the small-subunit rRNA genes to determine the effect of hydrocarbon contamination on its microbial composition and diversity. Analysis of the V4 region of the community DNA from both sediments revealed the presence of bacteria, archaea and microalgae. Bacterial sequences outnumbered archaea and microalgae. Abundance of Proteobacteria, Betaproteobacteria, Burholderiales, Alcaligenaceae, and Achrombacter were observed in the CWS and Actinobacteria, Actinomycetales, Bacillaceae, and Bacillus in the UWS. Crenarchaeota and Euryarchaeota were also observed to be present in both sediments. The genus Achromobacter and Bacillus dominated in the

TrfA is the only plasmid-encoded protein required for RK2 replication. We report here the construction and characterization of an RK2-based vector in which trfA is expressed from the inducible promoter Pm. The resulting construct, pJBSD1, was found to replicate in Escherichia coli DH5a (recA−) only in the presence of a Pm inducer. In two tested E. coli recA+ strains pJBSD1 could replicate in the absence of inducer, but a replication inducer-dependent phenotype was obtained in these strains by introducing a mutation known to reduce the trfA expression level. The plasmid construct could be used as a conditional suicide vector system for targeted chromosomal integration via homologous recombination. This feature may potentially be used for many types of studies in microbial molecular biology.

The southern-central Tyrrhenian Sea is a poorly studied area of the Mediterranean Sea, although its importance for the biological fluxes among the western and eastern basins is recognised. This note aimed at evaluating in the waters of the Southern Tyrrhenian Sea the efficiency of some steps of the organic matter processing (enzymatic hydrolysis, prokaryotic production and oxidation) and the role played by the prokaryotic community in this context. During the MEDBIO multidisciplinary cruise performed in July 2005, the distribution of prokaryotic abundance and activities (exoenzymatic activity, heterotrophic production and respiratory activity) was studied. The results showed the presence of high exoenzymatic activity rates (mostly leucine aminopeptidase) in the deep sea, while heterotrophic production and respiratory activity rates were high at surface. Some speculations on the different behaviors of the Carbon fluxes occurring among the different epi-, meso-and bathypelagic layers are reported. At the epipelagic layer both the decomposition and biomass production processes were high. At the mesopelagic layer the organic matter was quickly mobilised but not efficiently incorporated into biomass, therefore the dissolved monomers remained available in the water column for export to other trophic levels or utilization in other chemical processes (lateral advection, oxidation). The bathypelagic layer was characterised by high levels of hydrolytic activity coupled with relatively high prokaryotic production; in this layer, exoenzymatic activity levels fall in an order of magnitude similar to that observed at the epipelagic one. This finding highlights the importance of microbially mediated processes in sustaining life in the marine depths. Journal of Oceanography and Marine Research J o u rn al of Oc e a n o g ra p y h an d M a ri ne Res e a r c h

A microbial composition study of sediments of contaminated (CWS) and uncontaminated (UWS) lentic ecosystems within Akwa Ibom State was carried out by analyzing the small-subunit rRNA genes to determine the effect of hydrocarbon contamination on its microbial composition and diversity. Analysis of the V4 region of the community DNA from both sediments revealed the presence of bacteria, archaea and microalgae. Bacterial sequences outnumbered archaea and microalgae. Abundance of Proteobacteria, Betaproteobacteria, Burholderiales, Alcaligenaceae, and Achrombacter were observed in the CWS and Actinobacteria, Actinomycetales, Bacillaceae, and Bacillus in the UWS. Crenarchaeota and Euryarchaeota were also observed to be present in both sediments. The genus Achromobacter and Bacillus dominated in the

The concept of the minimal cell has fascinated scientists for a long time, from both fundamental and applied points of view. This broad concept encompasses extreme reductions of genomes, the last universal common ancestor (LUCA), the creation of semiartificial cells, and the design of protocells and chassis cells. Here we review these different areas of research and identify common and complementary aspects of each one. We focus on systems biology, a discipline that is greatly facilitating the classical top-down and bottom-up approaches toward minimal cells. In addition, we also review the so-called middle-out approach and its contributions to the field with mathematical and computational models. Owing to the advances in genomics technologies, much of the work in this area has been centered on minimal genomes, or rather minimal gene sets, required to sustain life. Nevertheless, a fundamental expansion has been taking place in the last few years wherein the minimal gene set is viewed...

Actin has been described in all eukaryotic cells as the major microfilament cytoskeletal protein. Although prokaryotic cells do not have a cytoskeleton, proteins related to the latter have been found in different prokaryotic species. We have found prokaryotic actin-related proteins in the enterobacterium Escherichia coli and in the cyanobacteria Anabaena cylindrica and Anabaena variabilis. They were identified by the following criteria: (1) by cross-reaction with a fluorescent conjugated anti-actin (rat-brain) mAb by Western blot analysis (in total cellular extracts); (2) specific binding of acetone powder and soluble cellular extracts to DNase I; and (3) specific binding of cells and total cellular extracts to phalloidin. In E coli, specific binding of phalloidin labelled with rhodamine to cells was detected by spectrofluorometry. In total cellular extracts, three bands of 60, 43 and 35 kDa were weakly recognized by the mAb by Western blot analysis; this recognition increased when phalloidin was added to the extracts. Furthermore, three polypeptides of kDa were isolated by binding to DNase I, showing pI values of 6.7, 6.65 and 6.6, less acidic than all reported actin pI values. In A. cylindrica and A. variabilis, specific binding of phalloidin labelled with rhodamine to cells was also detected by spectrofluorometry. In total and soluble cellular extracts, the mAb recognized two bands of 45 and 40 kDa by Western blot analysis, but only the first was purified by binding to DNase I, and it showed three isoforms of pI values 6.8, 6.5 and 6.4. These results suggest the presence, in prokaryotes, of proteins with similar biochemical characteristics to eukaryotic actin.

Published 19 This paper reports an in vivo characterization technique to characterize dielectric proper-20 ties of living tissues and bio-molecules at microwave frequency using cavity perturbation 21 technique, where a slot ring resonant sensor has been used, that works at 8 GHz and 22 has been designed to enumerate the effective dielectric constant of Spirulina platensis 23 and chlorophyll molecule. Observed value of the dielectric constant of Spirulina platen-24 sis was 8 ± 0.04 in the absence of light and 14.575 ± 0.145 in the presence of light. 25 Molecular polarizability of chl a molecule was 5.07 ± 0.05 × 10 4Å3 . Experimentally cal-26 culated local electric field actually experienced by chl a molecule was 14.197±0.003 V/m 27 for applied field of 9.79 V/m across the slot ring, dipole moment of chl a molecule was 28

Appropriate detachment treatments are required to analyze prokaryotes associated with streambed sediments by flow cytometry. Using our previously optimized protocol, two groups of cells exhibiting different nucleic acid contents were easily detectable. However, the Nucleic Acid Double Staining assay proved that detachment procedures negatively affect the cell membrane integrity.

The composition of a cell in terms of macromolecular building blocks and other organic molecules underlies the metabolic needs and capabilities of a species. Although some core biomass components such as nucleic acids and proteins are evident for most species, the essentiality of the pool of other organic molecules, especially cofactors and prosthetic groups, is yet unclear. Here we integrate biomass compositions from 71 manually curated genome-scale models, 33 large-scale gene essentiality datasets, enzyme-cofactor association data and a vast array of publications, revealing universally essential cofactors for prokaryotic metabolism and also others that are specific for phylogenetic branches or metabolic modes. Our results revise predictions of essential genes in Klebsiella pneumoniae and identify missing biosynthetic pathways in models of Mycobacterium tuberculosis. This work provides fundamental insights into the essentiality of organic cofactors and has implications for minimal ...

The aquatic bacterial group SAR11 is one of the most abundant organisms on Earth, with an estimated global population size of 2.4 1028 cells in the oceans. Members of SAR11 have also been detected in brackish and fresh waters, but the evolutionary relationships between the species present in the different environments have been ambiguous. In particular, it was not clear how frequently this lineage has crossed the saline–freshwater boundary during its evolutionary diversification. Due to the huge population size of SAR11 and the potential of microbes for long-distance dispersal, we hypothesized that environmental transitions could have occurred repeatedly during the evolutionary diversification of this group. Here, we have constructed extensive 16S rDNA–based molecular phylogenies and undertaken metagenomic data analyses to assess the frequency of saline–freshwater transitions in SAR11 and to investigate the evolutionary implications of this process. Our analyses indicated that very ...

The Ionian Sea represents a suitable basin for studying the biogeochemical processes mediated by microbial activities. Because of its characteristics as a crossing region between the western and eastern Mediterranean Sea, it is one of the sites most affected by changes in water mass composition and dynamics, caused by the Eastern Mediterranean Transient (EMT). To date, relatively few data exist on microbial activities in pelagic areas of the Ionian Sea. From 1998 to 2004, during different research cruises, prokaryotic parameters (abundance, extracellular enzyme activities leucine aminopeptidase, β-glucosidase, alkaline phosphatase, bacterial production and respiration) were measured together with culturable bacteria and the main physical, chemical and trophic parameters (temperature, salinity, nutrients, particulated organic matter). The aim of the study was to describe the spatial and temporal variability in microbial activities involved in the carbon and phosphorus cycles, in diff...

A microbial composition study of sediments of contaminated (CWS) and uncontaminated (UWS) lentic ecosystems within Akwa Ibom State was carried out by analyzing the small-subunit rRNA genes to determine the effect of hydrocarbon contamination on its microbial composition and diversity. Analysis of the V4 region of the community DNA from both sediments revealed the presence of bacteria, archaea and microalgae. Bacterial sequences outnumbered archaea and microalgae. Abundance of Proteobacteria, Betaproteobacteria, Burholderiales, Alcaligenaceae, and Achrombacter were observed in the CWS and Actinobacteria, Actinomycetales, Bacillaceae, and Bacillus in the UWS. Crenarchaeota and Euryarchaeota were also observed to be present in both sediments. The genus Achromobacter and Bacillus dominated in the

E. coli fumarate nitrate reductase (FNR) binds
to conserved FNR sites to regulate transcription under
anaerobic condition. L. lactis subsp. cremoris MG1363
strain contains two FNR-like proteins (FlpA and B) encoded
by flpA and flpB genes and the rcfA gene–encoded RcfA
in L. lactis subsp. lactis IL1403 strain. Potential FNRbinding
sites were located upstream of these genes. The flpA
promoter is expressed in MG1363 anaerobically and aerobically.
The flpB and rcfA promoters have typical class II
FNR-dependent promoters and are activated anaerobically
in MG1363 and IL1403, respectively. Despite their strong
homology, the Flp and RcfA proteins cannot substitute for
each other and control these promoters in the heterologous
strains. The flpA and flpB promoters require FlpA and FlpB
for activation in the MG1363 background. This was confirmed
by expressing FlpB under nisin control in flp mutants
and monitoring flpA promoter expression. In flpB– backgrounds,
both FlpA and FlpB were required for flpA
promoter expression. FlpB could not complement for the
lack of FlpA protein in flpA- backgrounds.

ABSTRACT: A new genus, Desserobdella, is described to accommodate the leech Clepsine picta Verrill, 1872 which feeds exclusively on amphibians of northern and central North America. This leech belongs to the subfamily Glossiphoniinae and therefore deposits cocoons directly onto the substrate. The genus Desserobdella n.gen. has the following diagnostic characteristics: (i) two pairs of coalesced eyes; (ii) one pair of diffuse salivary glands; and (iii) a single pair of saccular mycetomes containing prokaryotic endosymbionts. Members of the new genus are distinguished from species of the closely related genus Placobdella Blanchard, 1893 on the basis of their salivary gland structure; Placobdella species have two pairs of compact salivary glands versus the single pair of diffuse salivary glands of the genus Desserobdella n.gen. Congenitors of the new genus are Desserobdella cryptobranchii (Johnson and Klemm, 1977) n.comb., Desserobdella michiganensis (Sawyer, 1972) n.comb., and Desserobdella phalera (Graf, 1899) Jones and Woo, 1990. Desserobdella picta n.gen. et comb. exhibited a stereotypical sequence of feeding behaviours on Rana catesbeiana tadpoles which involved picking at the site of proboscis insertion prior to probing, probing, and finally blood-feeding with the posterior sucker released.

Several strains of bacteria unusually highly resistant to mercury were isolated from seawater and marine sediment samples and identified by 16S rDNA sequencing and were also characterized by a battery of biochemical and morphological tests. The bacterial isolates were identified to belong to the genera Pseudomonas, Alcaligenes, Brevibacterium and Bacillus. Many of the chosen isolates were tested for growth in the presence of different heavy metals and a variety of xenobiotics. Growth curves of all six bacteria highly resistant to mercury examined for growth at different concentrations of Hg exhibited prolonged lag phase,
during which time necessary physiological adaptations to toxic milieu were undergone. All the strains tested for antibiotic resistance showed little to no effect of antibiotics on their normal growth. Results of this study demonstrate the occurrence of
diverse groups of marine prokaryotes capable of high tolerance to mercury with a potential to degrade a variety of toxic heavy
metals and xenobiotics.