Soil Microbial Bioassays: Quick and Relevant But Are They Useful?

Soil microorganisms are pivotal in ecological systems, it may not be possible to define an ecosystem where an impact on overall microorganism populations would not mean a severe impact on the ecosystem. They are as relevant to an ecosystem as any group of organisms could be. At the same time, it is very difficult to link impact on measurable microbial activities to ecological impacts. We lack the required understanding. The linkage fails because of: compensation processes—the ecological process is continued by organisms other than those measured; non-specific assays—the method used to measure activity may impose conditions that do not reflect ecological conditions and multiple and unknown interacting factors. Overall, the ambiguity in benefit/ detriment relationships for impacts on microbes is the largest problem. Here we describe several examples of successes and failures of soil microbial bioassays in applications related to soil cleanliness criteria and ecological risk assessment. The usefulness of the microbial bioassays remains in question.     

Red Fluorescing Phototrophic Picoplankton in the Laurentian Great Lakes: What Are They and What Are They Doing?

Epifluorescence microscopy, flow cytometry, and transmission electron microscopy were used to characterize the community of red fluorescing (emission >665 nm when excited with blue light) phototrophic picoplankton (RFPP) in lakes Huron and Michigan. A population of coccoid to ovate eukaryotic cells with a mean size of 1.2 μm dominated the RFPP community in both surface and deep water samples. Abundant prochlorophyte populations were not found in any samples. Comparisons of counts with epifluorescence microscopy and flow cytometry, revealed that RFPP were adequately enumerated with standard epifluorescence microscopy. These RFPP were significant contributors to total phototrophic picoplankton abundance in both lakes Michigan (24%) and Huron (18%), with maximum seasonal abundance during the May-June period (surface mixing layer temperatures, 3-9 °C). During thermal stratification, maximum vertical abundance was found in the metalimnion/hypolimnion at the 1-5% isolumes. RFPP were only minor contributors (1-7%) to total primary production. Growth rates of RFPP measured with dilution and small inocula growth experiments ranged from 0.05-1.0 d⁻¹. Microzooplankton grazing rates on RFPP measured with dilution experiments were similar to estimated growth rates, accounting for 52-280% of growth on any given date.     

Draining the Pool? Carbon Storage and Fluxes in Three Alpine Plant Communities

Shrub communities have expanded in arctic and alpine tundra during recent decades. Changes in shrub abundance may alter ecosystem carbon (C) sequestration and storage, with potential positive or negative feedback on global C cycling. To assess potential implications of shrub expansion in different alpine plant communities, we compared C fluxes and pools in one Empetrum-dominated heath, one herb- and cryptogam-dominated meadow, and one Salix-shrub community in Central Norway. Over two growing seasons, we measured Gross Ecosystem Photosynthesis, Ecosystem Respiration (ER), and C pools for above-ground vegetation, litter, roots, and soil separated into organic and mineral horizons. Both the meadow and shrub communities had higher rates of C fixation and ER, but the total ecosystem C pool in the meadow was twice that of the shrub community because of more C in the organic soil horizon. Even though the heath community had the lowest rates of C fixation, it stored one and a half times more C than the shrub community. The results indicate that the relatively high above-ground biomass sequestering C during the growing season is not associated with high C storage in shrub-dominated communities. Instead, shrub-dominated areas may be draining the carbon-rich alpine soils because of high rates of decomposition. These processes were not shown by mid-growing season C fluxes, but were reflected by the very different distribution of C pools in the three habitats.     

Carbon Mineralization in Peatlands: Does the Soil Microbial Community Composition Matter?

Peat from four geographically separated peatlands (up to 1,500 km apart) with distinct vegetation across North America was sterilized and inoculated with microbial consortia from either the home site or from the other sites. This reciprocal inoculation microcosm experiment examined how different microbial communities adapted to various peat substrates and how this in turn influenced C-mineralization patterns. The experimental approach allows distinctions to be made as to whether microbial community structure, peat properties, or imposed environmental conditions are primary drivers of peat C mineralization. Two additional inocula collected from other freshwater environments (industrially polluted harbor and lake sediments) were also added to each peat type to investigate the response of clearly disparate microbial communities. We hypothesized that the peat properties, such as substrate quality and physical structure, would dictate microbial community composition and activity, thus inoculations from different sites into the same peat soil would lead to the establishment of very similar microbial communities both phylogenetically and functionally. Post-incubation, the bacterial communities in each site converged towards a similar community regardless of the inoculum source, with the exception of peat inoculated with polluted harbor sediment. Inoculum type had no effect on C mineralization rates compared with controls, except for the two disparate inocula, which had lower rates in all peat types. Variation in microbial community structure measured as nonmetric multidimensional scaling axes scores or richness did not correlate significantly with microbial activity. Overall, these findings suggest that abiotic variables (e.g., pH, aeration, moisture content, and temperature) are the dominant control on peatland microbial activity and community composition, and in natural peatlands the microbial community can quickly adapt to future environmental change.     

Are Antarctic aquatic invertebrates hitchhiking on your footwear?

The increasing number of humans who travel to and within Antarctic regions each year not only increases the risk of introducing non-native species but also of translocating native species within and between Antarctic biogeoregions and poses the potential for artificial, human-mediated introduction of native freshwater invertebrate species to newly ice-free areas of Antarctica. This study was designed to test the potential for transfer of native Antarctic freshwater invertebrates and their cysts on footwear. An average of 1.86 Anostraca cysts, 29.47 Copepoda cysts, 4.29 Nematoda, 0.40 Rotifera and 0.966 Tardigrada individuals per gram of sediment were found in samples taken from footwear after contact with freshwater sediment. The invertebrate cysts isolated from the samples that underwent drying at 27 °C were able to hatch in tap water, and representatives of the other systematic groups (Nematoda, Rotifera, and Tardigrada) also remained viable.     

A Multi Size-Level Assessment of Benthic Marine Communities in a Coastal Environment: Are They Different Sides of the Same Coin?

Organism body size has been demonstrated to be a discriminating element in shaping the response of living beings to environmental factors, thus playing a fundamental role in community structuring. Despite the importance of studies elucidating relations among communities of different size levels in ecosystems, the attempts that have been made in this sense are still very scarce and a reliable approach for these research still has to be defined. We characterized the benthic communities of bacteria, microbial eukaryotes, meiofauna and macrofauna in a coastal environment, encompassing a 10000-fold gradient in body size, testing and discussing a mixed approach of molecular fingerprinting for microbes and morphological observations for meio- and macrofauna. We found no correlation among structures of the different size-level communities: this suggests that community composition at one size-level could have no (or very low) influence on the community composition at other size-levels. Moreover, each community responds in a different way to the environmental parameters and with a degree of sensitivity which seems to increase with organism size. Therefore, our data indicate that the characterization of all the different size levels is clearly a necessity in order to study the dynamics really acting in a system.     

Are Antarctic suspension-feeding communities different from those elsewhere in the world?

This paper reviews the trophic ecology of benthic suspension feeders in Antarctic shelf communities, studied within SCAR's EASIZ Programme, in comparison with published information from other seas. Dense benthic suspension-feeder communities capture large quantities of particles and may directly regulate primary, and indirectly, secondary production in littoral food chains. Most work has been performed in temperate and tropical seas; however, little is known about suspension feeders in cold environments. Recent studies on Antarctic littoral benthic suspension feeders suggest the period of winter inactivity may last only a few weeks. This contrasts with the hypothesis that in Antarctic communities there is a prolonged period of minimal activity lasting at least 6 months during the austral winter. Results from other oceans may explain how dense benthic communities could develop under such conditions. Alternative food sources, i.e. the "fine fraction", sediment resuspension, lateral advection and efficient food assimilation may play a significant role in the development of suspension-feeder dominated, very diversified, high biomass and three-dimensionally structured communities on the Antarctic shelf.     

Research on Carbon Dioxide Fixation in Photosynthetic Microorganisms (1971–present)

This paper presents my personal account of research on CO(2) fixation from when I began these studies as a postdoctoral student in the early 1970s. It traces interests in microbial ribulose bisphosphate carboxylase/oxygenase (Rubisco) and considers early breakthroughs on the isolation, characterization, and significance of this enzyme from nonsulfur purple photosynthetic bacteria and other phototrophic organisms. This article also develops a historical perspective as to how recent efforts may lead to an understanding of molecular mechanisms by which the synthesis of this enzyme and other proteins of the pathway are regulated at the molecular level. In addition, how these studies impinge on the interactive control of CO(2) fixation, along with nitrogen fixation and hydrogen metabolism, is also considered. Finally, CO(2)-fixation studies in green sulfur photosynthetic bacteria and the discovery of the rather surprising Rubisco-like protein are described.     

Biogeography and Limno-terrestrial Tardigrades: Are They Truly Incompatible Binomials?

Due to the passive dispersal, tardigrades have been traditionally considered unsuitable for biogeographical studies. However, this paper provides some biogeographical and biological data supporting the possibility of using those animals to solve biogeographical problems at continental level.     

Endothelial Vesicles in the Blood–Brain Barrier: Are They Related to Permeability?

1. Macromolecules cross capillary walls via large vascular pores that are thought to be formed by plasmalemmal vesicles. Early hypotheses suggested that vesicles transferred plasma constituents across the endothelial wall either by a shuttle mechanism or by fusing to form transient patent channels for diffusion. Recent evidence shows that the transcytotic pathway involves both movement of vesicles within the cell and a series of fusions and fissions of the vesicular and cellular membranes.2. The transfer of macromolecules across the capillary wall is highly specific and is mediated by receptors incorporated into specific membrane domains. Therefore, despite their morphological similarity, endothelial vesicles form heterogeneous populations in which the predominant receptor proteins incorporated in their membranes define the functions of individual vesicles.3. Blood–brain barrier capillaries have very low permeabilities to most hydrophilic molecules. Their low permeability to macromolecules has been presumed to be due to an inhibition of the transcytotic mechanism, resulting in a low density of endothelial vesicles.4. A comparison of vesicular densities and protein permeabilities in a number of vascular beds shows only a very weak correlation, therefore vesicle numbers alone cannot be used to predict permeability to macromolecules.5. Blood–brain barrier capillaries are fully capable of transcytosing specific proteins, for example, insulin and transferrin, although the details are still somewhat controversial.6. It has recently been shown that the albumin binding protein gp60 (also known as albondin), which facilitates the transcytosis of native albumin in other vascular beds, is virtually absent in brain capillaries.7. It seems likely that the low blood–brain barrier permeability to macromolecules may be due to a low level of expression of specific receptors, rather than to an inhibition of the transcytosis mechanism.     

Alpha-, Delta- and PP-cells: Are They the Architectural Cornerstones of Islet Structure and Co-ordination?

Islet non-β-cells, the α- δ- and pancreatic polypeptide cells (PP-cells), are important components of islet architecture and intercellular communication. In α-cells, glucagon is found in electron-dense granules; granule exocytosis is calcium-dependent via P/Q-type Ca²⁺-channels, which may be clustered at designated cell membrane sites. Somatostatin-containing δ-cells are neuron-like, creating a network for intra-islet communication. Somatostatin 1-28 and 1-14 have a short bioactive half-life, suggesting inhibitory action via paracrine signaling. PP-cells are the most infrequent islet cell type. The embryologically separate ventral pancreas anlage contains PP-rich islets that are morphologically diffuse and α-cell deficient. Tissue samples taken from the head region are unlikely to be representative of the whole pancreas. PP has anorexic effects on gastro-intestinal function and alters insulin and glucagon secretion. Islet architecture is disrupted in rodent diabetic models, diabetic primates and human Type 1 and Type 2 diabetes, with an increased α-cell population and relocation of non-β-cells to central areas of the islet. In diabetes, the transdifferentiation of non-β-cells, with changes in hormone content, suggests plasticity of islet cells but cellular function may be compromised. Understanding how diabetes-related disordered islet structure influences intra-islet cellular communication could clarify how non-β-cells contribute to the control of islet function.     

PCR-Based Methods for the Diagnosis of Invasive Candidiasis: Are They Ready for Use in the Clinic?

Purpose of Review

We review the performance of Candida PCR and the T2Candida panel (T2Biosystems, Lexington, MA) in diagnosing invasive candidiasis, consider how these tests may be incorporated into patient care, and determine if they are ready to be used in the clinic.

Recent Findings

PCR and T2Candida sensitivity/specificity for diagnosing candidemia are ~?90%/90% and ~?90%/98%, respectively. Limited data for intra-abdominal candidiasis suggest PCR sensitivity of ~?85–90%, but specificity has varied from 33 to 97%. T2Candida data are lacking for infections other than candidemia.

Summary

PCR and T2Candida will have the greatest value if their use is restricted to cases in which positive and negative predictive values differ in a clinically meaningful way from the pre-test likelihood. Studies are needed to establish that patient care and stewardship strategies incorporating Candida PCR or T2Candida improve patients’ outcomes, reduce unnecessary antifungal usage, limit emergence of resistance, and are cost-effective. The development and validation of standardized PCR assays is a top priority.

     

Levels of Intervention: How Are They Used in Quebec Hospitals?

In order to promote better practices and communication around end-of-life decision-making, several Canadian hospitals in the province of Quebec have developed a tool called “Levels of Intervention” (LOI). No work to date has been published demonstrating improvement since these forms were implemented. The purpose of the present study was to obtain information about the use of LOI forms across Quebec hospitals and to identify gaps in practice as well as areas for improvement. A retrospective study was undertaken of 299 charts of patients who had died in three Quebec hospitals with a LOI ordered. Results were analysed through a principlism ethical framework. High compliance with the level of intervention ordered at the time of death was recorded, as well as high involvement of patient and/or family, demonstrating the efficiency of LOI in promoting respect for autonomy. Other results show delays in end-of-life care discussions in the course of the hospitalization. Only a small proportion of patients who died had a palliative care consultation, which may reflect equity issues in access to care. This study highlights the importance of the LOI in Quebec and the role it is playing in respect for end-of-life preferences as well as in the involvement of patients and families in the decision-making process. Training specific to end-of-life decision-making conversations would help support the LOI form’s use, as would developing provincial or national guidelines on the use of LOI to standardize organizational policies and practice around end-of-life care.     

Intrinsically Disordered Regions in Serum Albumin: What Are They For?

Serum albumin is a major plasma protein in mammalian blood. The importance of this protein lies in its roles in both bioregulation and transport phenomena. Serum albumin binds various metal ions and participates in the transport and storage of fatty acids, bilirubin, steroids amino acids, and many other ligands, usually with regions of hydrophobic surface. Although the primary role of serum albumin is to transport various ligand, its versatile binding capacities and high concentration mean that it can assume a number of additional functions. The major goal of this article is to show how intrinsic disorder is encoded in the amino acid sequence of serum albumin, and how intrinsic disorder is related to functions of this important serum protein.     

How Microbes Shape Their Communities? A Microbial Community Model Based on Functional Genes

Exploring the mechanisms of maintaining microbial community structure is important to understand biofilm development or microbiota dysbiosis. In this paper, we propose a functional gene-based composition prediction(FCP) model to predict the population structure composition within a microbial community. The model predicts the community composition well in both a low-complexity community as acid mine drainage(AMD) microbiota, and a complex community as human gut microbiota. Furthermore, we define community structure shaping(CSS) genes as functional genes crucial for shaping the microbial community. We have identified CSS genes in AMD and human gut microbiota samples with FCP model and find that CSS genes change with the conditions. Compared to essential genes for microbes, CSS genes are significantly enriched in the genes involved in mobile genetic elements, cell motility, and defense mechanisms, indicating that the functions of CSS genes are focused on communication and strategies in response to the environment factors. We further find that it is the minority, rather than the majority, which contributes to maintaining community structure. Compared to health control samples, we find that some functional genes associated with metabolism of amino acids, nucleotides, and lipopolysaccharide are more likely to be CSS genes in the disease group. CSS genes may help us to understand critical cellular processes and be useful in seeking addable gene circuitries to maintain artificial self-sustainable communities. Our study suggests that functional genes are important to the assembly of microbial communities.     

Microbial control in Asia: a bellwether for the future?

Advances and barriers faced by microbial control efforts in Asia offer instructive insights for microbial control in general. The papers in this series, which are based on plenary lectures given at the Society for Invertebrate Pathology 2006 meeting in Wuhan, China, explore the history and current status of microbial control in China, Japan, and Southeast Asia, and in doing so, bring to light the following key assumptions that deserve further examination; (1) the adoption rate of microbial control is well documented; (2) microbial control agents can compete directly with conventional insecticides; (3) microbial control agents are relatively easy and inexpensive to produce and develop; (4) patents will promote innovation and investor interest in microbial control. Alternative viewpoints are presented that can hopefully aid in future efforts to develop more safe and effective microbial control agents.