Suitable microscopic entropy for the origin of microbial life: Microbiological methods are challenges

A hypothesis is proposed that the first living microbial cell(s) on Earth assembled about 3.6-4 billion years ago when an environmental microscopic entropy (balance between order and disorder; suitable amount of randomness) was within a range suitable for the origin of microbial cell(s) in a hydrogel environment. An earlier origin of microbial life was not possible as the elements, molecules and entropy conditions necessary for life were not available at the microscopic level. Methodology limitations to study postulated past origin of microbial life events and to mimic these events in the laboratory, are still obstacles to understanding the origin of life.     

Hypothesized origin of microbial life in a prebiotic gel and the transition to a living biofilm and microbial mats

This article hypothesizes that the origin of the first microbial cell(s) occurred as a series of increasing levels of organization within a prebiotic gel attached to a mineral surface, which made the transition to a biofilm composed of the first cell(s) capable of growth and division. A gel microenvironment attached to a surface for the origin of life, and subsequent living cells offers numerous advantages. These include acting as a water and nutrient trap on a surface, physical protection as well as protection from UV radiation. The prebiotic gel and the living biofilm contained the necessary water, does not impede diffusion of molecules including gases, provides a structured gel microscopic location for biochemical interactions and polymerisation reactions, where the necessary molecules for life need to be present and not limiting. The composition of the first gel environment may have been an oily-water mixture (or the interface between an oily-water mixture) of microscopic dimensions, but large enough for the organization of the first cell(s). The living biofilm then made the evolutionary transition to a microbial mat.     

Herbivore influence on soil microbial biomass and nitrogen mineralization in a northern grassland ecosystem: Yellowstone National Park

Microorganisms are largely responsible for soil nutrient cycling and energy flow in terrestrial ecosystems. Although soil microorganisms are affected by topography and grazing, little is known about how these two variables may interact to influence microbial processes. Even less is known about how these variables influence microorganisms in systems that contain large populations of free-roaming ungulates. In this study, we compared microbial biomass size and activity, as measured by in situ net N mineralization, inside and outside 35- to 40-year exclosures across a topographic gradient in northern Yellowstone National Park. The objective was to determine the relative effect of topography and large grazers on microbial biomass and nitrogen mineralization. Microbial C and N varied by almost an order of magnitude across sites. Topographic depressions that contained high plant biomass and fine-textured soils supported the greatest microbial biomass. We found that plant biomass accurately predicted microbial biomass across our sites suggesting that carbon inputs from plants constrained microbial biomass. Chronic grazing neither depleted soil C nor reduced microbial biomass. We hypothesize that microbial populations in grazed grasslands are sustained mainly by inputs of labile C from dung deposition and increased root turnover or root exudation beneath grazed plants. Mineral N fluxes were affected more by grazing than topography. Net N mineralization rates were highest in grazed grassland and increased from dry, unproductive to mesic, highly productive communities. Overall, our results indicate that topography mainly influences microbial biomass size, while mineral N fluxes (microbial activity) are affected more by grazing in this grassland ecosystem. Received: 4 June 1997 / Accepted: 16 December 1997     

Nanomaterials‐based biosensors for detection of microorganisms and microbial toxins

Detection of microorganisms and microbial toxins is important for health and safety. Due to their unique physical and chemical properties, nanomaterials have been extensively used to develop biosensors for rapid detection of microorganisms with microbial cells and toxins as target analytes. In this paper, the design principles of nanomaterials‐based biosensors for four selected analyte categories (bacteria cells, toxins, mycotoxins, and protozoa cells), closely associated with the target analytes' properties is reviewed. Five signal transducing methods that are less equipment intensive (colorimetric, fluorimetric, surface enhanced Raman scattering, electrochemical, and magnetic relaxometry methods) is described and compared for their sensory performance (in term oflimit of detection, dynamic range, and response time) for all analyte categories. In the end, the suitability of these five sensing principles for on‐site or field applications is discussed. With a comprehensive coverage of nanomaterials, design principles, sensing principles, and assessment on the sensory performance and suitability for on‐site application, this review offers valuable insight and perspective for designing suitable nanomaterials‐based microorganism biosensors for a given application.     

Environmental restraints and life strategies: a habitat templet matrix

Summary Four basic environmental restraints on life are deduced from the requirements of life's inherent order laws. Possible life strategies to contend with these restraints are listed. The various combinations of the restraints are subsequently investigated, and appropriate combinations of life strategies are fitted. This model is finally tested against insect case histories in various environments, and is demonstrated to explain some combinations of characteristics of insects in ecosystems not covered by the r-K or r-K-A continua. The role of heterochrony in achieving appropriate life strategies is briefly discussed.     

Optimal temperature for microbes in an acetate fed microbial electrolysis cell (MEC)

Temperature is one of the important parameters which can significantly effect on the activity/selection of microorganism and subsequently on the reactor's performance. Two microbial electrolysis cells (MECs) were operated at different temperature settings with acetate as a carbon source. On average, COD removal rates of 16.8, 24.7, 34.0, 36.2 and 18.1 mg/l/h were recorded at 25, 29, 30, 31 and 35 °C, respectively. The results of volatile suspended solids analysis indicated that biomass concentration continued to drop at all temperatures, but the drop was the lowest at 30 °C. Consideration of biomass drop and specific COD removal rate showed 31 °C as the optimum temperature. These significant results imply that effect of temperature and change in biomass concentration should be considered in future experiments when expressing the removal rates.     

The arbuscular mycorrhizal fungus Rhizophagus intraradices and other microbial groups affect plant species in a copper-contaminated post-mining soil

Background and aimArbuscular mycorrhizal fungi (AMF) have an important role in plant-microbe interactions. But, there are few studies in which the combined effect of AMF with a stress factor, such as the presence of a metal, on plant species were assessed. This study investigated the effect of arbuscular mycorrhizal (AM) fungus Rhizophagus intraradices and other soil microbial groups in the presence of copper on three plant species in a microcosm experiment.MethodsTwo grass species Poa compressa and Festuca rubra and one herb species Centaurea jacea were selected as model plants in a pot-design test in which soils were artificially contaminated with copper. Treatments were bacteria (control), saprophytic fungi, protists, and a combined treatment of saprophytic fungi and protists, all in the presence or absence of the AM fungal species. After sixty days, plants were harvested and the biomass of grass and herb species and microbial respiration were measured.ResultsThe results showed almost equal above- and belowground plant biomass and microbial respiration in the treatments in the presence or absence of R. intraradices. The herb species C. jecea responded significantly to the soil inoculation with AM fungus, while grass species showed inconsistent patterns. Significant effect of AMF and copper and their interactions was observed on plant biomass when comparing contaminated vs. non-contaminated soils.ConclusionStrong effect of AMF on the biomass of herb species and slight changes in plant growth with the presence of this fungal species in copper-spiked test soils indicates the importance of mycorrhizal fungi compared to other soil microorganisms in our experimental microcosms.     

Insects on Hog weed Flowers: a Suggestion for a Student Project

The current Bullock debate has focused attention on the role of language in learning and challenges us to consider the linguistic competence of our pupils. This article describes how students' knowledge and interest in their own subject was used to start them thinking through ideas about language. For a group of biology graduates taking a postgraduate education course, biology became the vehicle for integrating more widely ranging educational issues.

After a preliminary introduction to the topic, opportunities were created for the students to gather school experience, and then in the light of this to extend their appreciation of available theory. The value of such an approach is discussed, and also the problems inherent in it, for example the division of tutorial responsibilities within the university department.     

Partners for life: building microbial consortia for the future

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Biodegradation of polyalcohol ethoxylate by a wastewater microbial consortium

Polyalcohol ethoxylate (PAE), an anionic surfactant, is the primary component in most laundry and dish wash detergents and is therefore highly loaded in domestic wastewater. Its biodegradation results in the formation of several metabolites and the fate of these metabolites through wastewater treatment plants, graywater recycling processes, and in the environment must be clearly understood. Biodegradation pathways for PAE were investigated in this project with a municipal wastewater microbial consortium. A microtiter-based oxygen sensor system was utilized to determine the preferential use of potential biodegradation products. Results show that while polyethylene glycols (PEGs) were readily degraded by PAE acclimated microorganisms, most of the carboxylic acids tested were not degraded. Biodegradation of PEGs suggests that hydrophobe–hydrophile scission was the dominant pathway for PAE biodegradation in this wastewater community. Ethylene glycol (EG) and diethylene glycol (DEG) were not utilized by microbial populations capable of degrading higher molecular weight EGs. It is possible that EG and DEG may accumulate. The microtiter-based oxygen sensor system was successfully utilized to elucidate information on PAE biodegradation pathways and could be applied to study biodegradation pathways for other important contaminants.     

The Most Conserved Genome Segments for Life Detection on Earth and Other Planets

On Earth, very simple but powerful methods to detect and classify broad taxa of life by the polymerase chain reaction (PCR) are now standard practice. Using DNA primers corresponding to the 16S ribosomal RNA gene, one can survey a sample from any environment for its microbial inhabitants. Due to massive meteoritic exchange between Earth and Mars (as well as other planets), a reasonable case can be made for life on Mars or other planets to be related to life on Earth. In this case, the supremely sensitive technologies used to study life on Earth, including in extreme environments, can be applied to the search for life on other planets. Though the 16S gene has become the standard for life detection on Earth, no genome comparisons have established that the ribosomal genes are, in fact, the most conserved DNA segments across the kingdoms of life. We present here a computational comparison of full genomes from 13 diverse organisms from the Archaea, Bacteria, and Eucarya to identify genetic sequences conserved across the widest divisions of life. Our results identify the 16S and 23S ribosomal RNA genes as well as other universally conserved nucleotide sequences in genes encoding particular classes of transfer RNAs and within the nucleotide binding domains of ABC transporters as the most conserved DNA sequence segments across phylogeny. This set of sequences defines a core set of DNA regions that have changed the least over billions of years of evolution and provides a means to identify and classify divergent life, including ancestrally related life on other planets.     

Perspective: Time scales in scientific research with an emphasis on microbial cellular and molecular research

Scientists use time to describe and research the universe in which humans live. Geologists and evolutionary biologists often use time scales in the millions to billions of years while biochemists and molecular biologists use time scales in the milliseconds or less. The atom smashers use time scales that are almost the speed of light. However, in some areas of research such as molecular-based activities in cells, it is very challenging to obtain data sets in molecular time scales. This has been a challenge to obtaining accurate and precise measurements at the cell and molecular levels of organization in living organisms. Measurements of specific cellular and molecular activities are often made over time scales longer than the actual molecular events. The data sets obtained become estimates over seconds, minutes and hours and not measurements over milli- and nanoseconds. The question can then be posed — how representative and accurate are our data sets when the time scales are not synchronized with the actual living events? In this article, the role of time scales in scientific research and our understanding of living microorganisms are examined with an emphasis on cell and molecular time scales.     

The non-coding genome: a universe in expansion for fine-tuning the coding world

A report on the EMBO/EMBL Symposium on The Non-Coding Genome, held in Heidelberg, Germany, 9-12 October, 2013.We share 98% coding genome similarity with mouse and have about the same number of protein coding genes as worms, yet the differences in complexity are obvious. Where is this complexity encoded? A huge change in our understanding of genome evolution and regulation of gene expression arrived with the development of high-throughput sequencing technologies. It turns out that most of our genome is transcribed, but only a small percentage has coding information imbedded. The rest of the genome, the non-coding genome, mistakenly labeled as ‘junk DNA’, is where evolutionary complexity resides. In The Non-Coding Genome meeting, several research studies delved deeper into the importance of the non-coding genome, identifying novel classes of non-coding RNAs (ncRNAs) and novel regulatory functions, and expanding our knowledge about this new world, opening more exciting questions to study and answer.     

The alien flora of Greece: taxonomy,life traits and habitat preferences

The aim of the paper is the state-of-the-art assessment of the alien flora of Greece and its traits. The dataset consists of a total of 343 alien taxa, including 49 archaeophytes. The taxonomy, life traits and habitat of the 294 neophytes are analysed vs their naturalisation status. Out of the 122 (41%) naturalised neophytes, 50 are identified as exhibiting invasive behaviour. Poaceae, Asteraceae, Amaranthaceae, Solanaceae, Fabaceae, and Polygonaceae are the plant families richest in alien taxa. The majority of them are of American origin, followed by those of Asiatic and Mediterranean origin. The neophytes are predominantly herbs, most of them annuals. Yet, the perennial life cycle is equally frequent with the annual one and the proportion of phanerophytes in the alien flora is increased compared to the one of the native flora. Regarding flowering traits, most of the aliens have a long flowering period (over 1 month) and flower in late spring, summer and autumn, when few of the native plants are in bloom. Vertebrate zoochory and anemochory are the two dispersal modes mostly utilised by the alien plants (43 and 28%, respectively), while more than one dispersal mechanisms are functional for 56% of them. Artificial habitats have the highest frequencies of alien plants. The natural habitats with the highest numbers of aliens are the coastal ones and inland surface waters. Opuntia ficus-barbarica, Ailanthus altissima, Oxalis pes-caprae, Erigeron bonariensis, Amaranthus albus and Symphyotrichum squamatum are typical cases of plants characterised as invasive, having established in almost all the habitat groups identified. The diversity of the ecological characteristics of the plants suggests a potential of impacts that needs to be further assessed.