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Microbial diversity, producer-decomposer interactions and ecosystem processes: a theoretical model.

Interactions between the diversity of primary producers and that of decomposers--the two key functional groups that form the basis of all ecosystems--might have major consequences on the functioning of depauperate ecosystems. I present a simple ecosystem model in which primary producers (plants) and decomposers (microbes) are linked through material cycling. The model considers a diversity of plant organic compounds and a diversity of microbial species. Nutrient recycling efficiency from organic compounds to decomposers is then the key parameter that controls ecosystem processes (primary productivity, secondary productivity, producer biomass and decomposer biomass). The model predicts that microbial diversity has a positive effect on nutrient recycling efficiency and ecosystem processes through either greater intensity of microbial exploitation of organic compounds or functional niche complementarity, much like in plants. Microbial niche breadth and overlap should not affect ecosystem processes unless they increase the number of organic compounds that are decomposed. In contrast, the model predicts that plant organic compound diversity can only have a negative effect or, at best, no effect on ecosystem processes, at least in a constant environment. This creates a tension between the effects of plant diversity and microbial diversity on ecosystem functioning, which may explain some recent experimental results.

Bacteria↗

Dendritic cells and host resistance to infection.

Host defence against infection requires an integrated response of both the innate and adaptive arms of the immune system. Emerging data indicate that dendritic cells contribute an essential part to the initiation and regulation of adaptive immunity. Dendritic cells guard the sites of pathogen entry to the host and are uniquely suited to detect and capture invading microbes. Upon recognition of microbial structures and appropriate activation, a maturation programme is triggered and dendritic cells migrate to lymphoid organs to stimulate a primary cell-mediated immune response. Moreover, dendritic cells play a critical role in shaping the emerging response, thereby controlling the course of infection. They can discriminate between various types of microorganisms and are capable of producing different cytokines in response to different microbial stimuli. On the other hand, pathogens developed numerous strategies to evade and subvert dendritic cell functions. Elucidating the interactions of dendritic cells with microbial pathogens may lead to novel strategies for combating infectious diseases by dendritic cell-based vaccination and immunotherapy. This review highlights recent advances in our knowledge of the unique role of dendritic cells in counteracting microbial infections.

Animals↗

Epithelial antimicrobial peptides: review and significance for oral applications.

Epithelial tissues provide the first line of defense between an organism and the environment. Disruption of this barrier leads to bacterial invasion and subsequent inflammation. This is precisely the situation existing in the human oral cavity, where tissues are constantly exposed to a variety of microbial challenges that can lead to bacterially induced periodontal diseases, and to infections of the oral mucosa by bacteria, fungi, and viruses. With the recent discoveries of host-derived peptide antibiotics in mammalian mucosal epithelium, a new line of investigation is emerging to test the hypothesis that one class of these peptides, called "beta-defensins", functions to protect the host against microbial pathogenesis at these critical, confrontational sites. In that light, impairment of beta-defensin activity has recently been implicated in chronic bacterial infections in cystic fibrosis patients. The first direct evidence of expression of defensin peptides in the oral mucosa was the identification of a novel epithelial beta-defensin in mammalian tongue. It was shown to be upregulated in inflammation, suggesting that it participates in host defense. It is theorized that epithelial cell-derived antimicrobial peptides function to keep the natural flora of micro-organisms in a steady state in different niches such as the skin, the intestines, the airway, the endocervix, and the mouth. There is now evidence indicating that normal gingival epithelial cells and tissues express two beta-defensins, hBD-1 and the newly described hBD-2. In addition, a cathelin-class antimicrobial peptide, designated LL-37 and found in human neutrophils, is also expressed in skin and gingiva. It is highly likely that these and/or other epithelial antimicrobial peptides play an important role in determining the outcome of the host-pathogen interaction at the oral mucosal barrier, and that they may have important future applications in antibiotic treatment.

Amino Acid Sequence↗

Geomicrobiology: how molecular-scale interactions underpin biogeochemical systems.

Microorganisms populate every habitable environment on Earth and, through their metabolic activity, affect the chemistry and physical properties of their surroundings. They have done this for billions of years. Over the past decade, genetic, biochemical, and genomic approaches have allowed us to document the diversity of microbial life in geologic systems without cultivation, as well as to begin to elucidate their function. With expansion of culture-independent analyses of microbial communities, it will be possible to quantify gene activity at the species level. Genome-enabled biogeochemical modeling may provide an opportunity to determine how communities function, and how they shape and are shaped by their environments.

Animals↗

Molecular aspects of intestinal epithelial cell-bacterial interactions that determine the development of intestinal inflammation.

The mechanisms by which intestinal epithelial cells perceive and respond to microbes, both pathogenic and commensal, is important to understand the pathogenesis of inflammatory diseases. Recent work has established that most eukaryotic cells possess families of receptors that can detect the structural signatures of prokaryotic life. Cells respond to the detection of microbes by activation of distinct cytoplasmic signaling cascades that ultimately result in the transcriptional activation of programs of genes with proinflammatory and anti-apoptotic function. These responses generally suffice to eliminate microbial threats. Also important are potential mechanisms by which microbes can influence the intestinal epithelial responses, influences with significant implications for the normal function of the intestine and inflammatory diseases.

Bacteria↗

Microbial lipopeptides stimulate dendritic cell maturation via Toll-like receptor 2.

The ability of dendritic cells (DC) to initiate immune responses in naive T cells is dependent upon a maturation process that allows the cells to develop their potent Ag-presenting capacity. Although immature DC can be derived in vitro by treatment of peripheral blood monocytes with GM-CSF and IL-4, additional signals such as those provided by TNF-alpha, CD40 ligand, or LPS are required for complete maturation and maximum APC function. Because we recently found that microbial lipoproteins can activate monocytes and DC through Toll-like receptor (TLR) 2, we also investigated whether lipoproteins can drive DC maturation. Immature DC were cultured with or without lipoproteins and were monitored for expression of cell surface markers indicative of maturation. Stimulation with lipopeptides increased expression of CD83, MHC class II, CD80, CD86, CD54, and CD58, and decreased CD32 expression and endocytic activity; these lipopeptide-matured DC also displayed enhanced T cell stimulatory capacity in MLR, as measured by T cell proliferation and IFN-gamma secretion. The lipid moiety of the lipopeptide was found to be essential for induction of maturation. Preincubation of maturing DC with an anti-TLR2 blocking Ab before addition of lipopeptide blocked the phenotypic and functional changes associated with DC maturation. These results demonstrate that lipopeptides can stimulate DC maturation via TLR2, providing a mechanism by which products of bacteria can participate in the initiation of an immune response.

Bacterial Outer Membrane Proteins↗

Metagenomic analysis reveals gene taxonomic and functional diversity response to microplastics and cadmium in an agricultural soil.

Both microplastics (MPs) and heavy metals are common soil pollutants and can interact to generate combined toxicity to soil ecosystems, but their impact on soil microbial communities (e.g., archaea and viruses) remains poorly studied. Here, metagenomic analysis was used to explore the response of soil microbiome in an agricultural soil exposed to MPs [i.e., polyethylene (PE), polystyrene (PS), and polylactic acid (PLA)] and/or Cd. Results showed that MPs had more profound effects on microbial community composition, diversity, and gene abundances when compared to Cd or their combination. Metagenomic analysis indicated that the gene taxonomic diversity and functional diversity of microbial communities varied with MPs type and dose. MPs affected the relative abundance of major microbial phyla and genera, while their coexistence with Cd influenced dominant fungi and viruses. Nitrogen-transforming and pathogenic genera, which were more sensitive to MPs variations, could serve as the indicative taxa for MPs contamination. High-dose PLA treatments (10%, w/w) not only elevated nitrogen metabolism and pathogenic genes, but also enriched copiotrophic microbes from the Proteobacteria phylum. Overall, MPs and Cd showed minimal interactions on soil microbial communities. This study highlights the microbial shifts due to co-occurring MPs and Cd, providing evidence for understanding their environmental risks.

Soil Microbiology↗

The edaphic quantitative protargol stain: a sampling protocol for assessing soil ciliate abundance and diversity.

It has been suggested that species loss from microbial groups low in diversity that occupy trophic positions close to the base of the detrital food web could be critical for terrestrial ecosystem functioning. Among the protozoans within the soil microbial loop, ciliates are presumably the least abundant and of low diversity. However, the lack of a standardized method to quantitatively enumerate and identify them has hampered our knowledge about the magnitude of their active and potential diversity, and about the interactions in which they are involved. Thus, the Edaphic Quantitative Protargol Staining (EQPS) method is provided to simultaneously account for ciliate species richness and abundance in a quantitative and qualitative way. This direct method allows this rapid and simultaneous assessment by merging the Non-flooded Petri Dish (NFPD) method [Prog. Protistol. 2 (1987) 69] and the Quantitative Protargol Stain (QPS) method [Montagnes, D.J.S., Lynn, D.H., 1993. A quantitative protargol stain (QPS) for ciliates and other protists. In: Kemp, P.F., Sherr, B.F., Sherr, E.B., Cole, J.J. (Eds.), Handbook of Methods in Aquatic Microbial Ecology. Lewis Publishers, Boca Raton, FL, pp. 229-240]. The abovementioned protocols were refined by experiments examining the spatial distribution of ciliates under natural field conditions, sampling intensity, the effect of storage, and the use of cytological preparations versus live observations. The EQPS could be useful in ecological studies since it provides both a "snapshot" of the active and effective diversity and a robust estimate of the potential diversity.

Animals↗

Dynamic mathematical model to predict microbial growth and inactivation during food processing.

Many sigmoidal functions to describe a bacterial growth curve as an explicit function of time have been reported in the literature. Furthermore, several expressions have been proposed to model the influence of temperature on the main characteristics of this growth curve: maximum specific growth rate, lag time, and asymptotic level. However, as the predictive value of such explicit models is most often guaranteed only at a constant temperature within the temperature range of microbial growth, they are less appropriate in optimization studies of a whole production and distribution chain. In this paper a dynamic mathematical model--a first-order differential equation--has been derived, describing the bacterial population as a function of both time and temperature. Furthermore, the inactivation of the population at temperatures above the maximum temperature for growth has been incorporated. In the special case of a constant temperature, the solution coincides exactly with the corresponding Gompertz model, which has been validated in several recent reports. However, the main advantage of this dynamic model is its ability to deal with time-varying temperatures, over the whole temperature range of growth and inactivation. As such, it is an essential building block in (time-saving) simulation studies to design, e.g., optimal temperature-time profiles with respect to microbial safety of a production and distribution chain of chilled foods.

Bacteria↗

Short-term virus-host interactions and functional dynamics in recently deglaciated Antarctic tundra soils.

Long-term chronosequence studies have shown that, as glaciers retreat, newly exposed soils become colonized through primary succession. To determine the key drivers of this process and their vulnerability to climate change, the short-term responses of these pioneering microbial communities also need to be elucidated. Here, we investigated how the taxonomic and functional structure of microbial communities, including viruses, changed over a 7-year period in an Antarctic glacier forefield. Using metagenomics and metatranscriptomics we assessed the influence of both abiotic and biotic factors on these communities. Our results revealed a highly heterogeneous bacteria-dominated microbial community, with Pseudomonas as the most abundant genus, followed by Lysobacter, Devosia, Cellulomonas, and Brevundimonas. This community exhibited the capacity for aerobic anoxygenic phototrophy, carbon and nitrogen fixation, and sulfur cycling, processes vital for survival in nutrient-poor environments. 52 high-quality metagenome-assembled genomes (MAGs) were recovered, representing both transient and cosmopolitan taxa, some of which were able to rapidly respond to environmental changes. A diverse and highly dynamic collection of lytic and temperate viruses was identified across all samples, with high clonal viral genomes typically detected in only one of the eight samples analyzed. Metatranscriptomic analyses confirmed the activity of lytic viruses, while prophage genomes featured much lower expression levels. Prophages appeared to influence host fitness through the expression of genes encoding membrane transporters. Additionally, the abundance of genes linked to antimicrobial compound synthesis and resistance, along with antiphage defense systems, highlights the importance of biotic interactions in driving microbial community succession and shaping short-term responses to environmental fluctuations.

Antarctica↗

The pneumococcal cell wall degrading enzymes: a modular design to create new lysins?

Autolysins are enzymes that degrade different bonds in the peptidoglycan and, eventually, cause the lysis and death of the cell. Streptococcus pneumoniae contains a powerful autolytic enzyme that has been characterized as an N-acetylmuramoyl-L-alanine amidase. We have cloned the lytA gene coding for this amidase and studied in depth the genetics and expression of this gene, which represented the first molecular analysis of a bacterial autolysin. Two observations have been fundamental in revealing further knowledge on the lytic systems of pneumococcus: (a) The well-documented dependence of the pneumococcal autolysin on the presence of choline in the cell wall for activity, and (b) the early observation that most pneumococcal phages also required the presence of this amino-alcohol in the growth medium to achieve a successful liberation of the phage progeny. We concluded that choline would serve as an element of strong selective pressure to preserve certain structures of the host and phage lytic enzymes which should lead to sequence homologies. We constructed active chimeras between the lytic enzymes of S. pneumoniae and its bacteriophages using genes that share sequence homology as well as genes that completely lack homologous regions. In this way, we demonstrated that the pneumococcal lytic enzymes are the result of the fusion of two independent functional modules where the carboxy-terminal domain might be responsible for the specific recognition of choline-containing cell walls whereas the active center of these enzymes should be localized in the N-terminal part of the protein. The modular design postulated for the pneumococcal lysins seems to be a widespread model for many types of microbial proteins and the construction of functional chimeric proteins between the lytic enzymes of pneumococcus and those of several gram-positive microorganisms, like Clostridium acetobutylicum or Lactococcus lactis, provided interesting clues on the modular evolution of proteins. The study of several genes coding for the lytic enzymes of temperate phages of pneumococcus also highlighted on some evolutionary relationships between microorganisms. We suggest that lysogenic relationships may represent a common mechanism by which pathogenic organisms like pneumococcus should undergo a rapid adaptation to an evolving environment.

Bacteriolysis↗

Layered murein revisited: a fundamentally new concept of bacterial cell wall structure, biogenesis and function.

The classical concept of the architecture of microbial murein assumes cross-linked glycan chains to be arranged in horizontal layers outside of the plasma membrane. It necessitates elaborate hypotheses to explain processes such as the biosynthesis, growth and division of the bacterial cell wall and provides no explanation for transenvelope macromolecular transport. Moreover, this model is difficult to reconcile with a number of basic chemical and electron microscopical data. According to a fundamentally distinct concept which is presented here, glycan strands in the microbial wall run perpendicular to the plasma membrane, each strand being cross-linked by peptide bridges with four other strands. This arrangement allows the formation of a structured matrix pierced with ordered ionophoric channels potentially harboring either lipoprotein or teichoic (lipoteichoic) acid molecules in Gram-negative and Gram-positive bacteria, respectively. New wall structures are synthesized in toto emerging from the cytoplasmic membrane as a condensed gel-like network below the old wall without being covalently attached to it, expanding due to inherent elasticity as the old wall is lyzed. This model reflects published genetic and biochemical data and offers a simple explanation for peptidoglycan biogenesis. As the biosynthesis is terminated by enzymic cleavage of all glycan strands, murein is irreversibly released from the membrane. The murein detachment prepares the membrane for de novo assembly of both the new wall synthesis machinery and the multicomponent factory for protein, DNA and phospholipid transfer. Being assembled in parallel, both new murein and the traffic complexes grow from the membrane together. This concept eliminates the necessity for the traffic complexes to penetrate intact murein. In the process of simultaneous assembly, the expanding murein functions as a lifting platform driven by the force of turgor pressure, transporting macromolecules through the perisplasmic space.

Cell Wall↗

Nitric oxide. Novel biology with clinical relevance.

OBJECTIVE: The author provides the reader with a view of the regulation and function of nitric oxide (NO), based on the three distinct enzyme isoforms that synthesize NO. SUMMARY BACKGROUND DATA: Nitric oxide is a short-lived molecule exhibiting functions as diverse as neurotransmission and microbial killing. Recent advances in the characterization of the enzymes responsible for NO synthesis and in the understanding of how NO interacts with targets have led to new insights into the many facets of this diverse molecule. METHODS: Nitric oxide is produced by one of three enzyme isoforms of NO synthesis. These enzymes vary considerably in their distribution, regulation, and function. Accordingly, the NO synthesis or lack of NO production will have consequences unique to that isoform. Therefore, this review summarizes the regulation and function of NO generated by each of the three isoforms. RESULTS: Nitric oxide exhibits many unique characteristics that allow this molecule to perform so many functions. The amount, duration, and location of the NO synthesis will depend on the isoform of NO synthase expressed. For each isoform, there probably are disease processes in which deficiency states exist. For induced NO synthesis, states of overexpression exist. CONCLUSIONS: Understanding the regulation and function of the enzymes that produce NO and the unique characteristics of each enzyme isoform is likely to lead to therapeutic approaches to prevent or treat a number of diseases.

Amino Acid Oxidoreductases↗

Functional mapping of surfactant protein A.

Surfactant protein A (SP-A) is a highly ordered, oligomeric glycoprotein that is secreted into the airspaces of the lung by alveolar type II cells and Clara cells of the pulmonary epithelium. Although research has shown that SP-A is both a calcium-dependent phospholipid-binding protein that affects surfactant structure and function and a lectin that opsonizes diverse microbial species, our understanding of the physiologically relevant roles of SP-A in the lung remains incomplete. My review focuses on the putative biological functions of SP-A that are supported by experiments in mammals and on the structural basis of SP-A function.

Animals↗

Clinical and microscopic findings in edentulous patients 3 years after incorporation of osseointegrated implant-supported bridgework.

15 mandibular fixed prostheses supported by osseointegrated titanium implants were examined 3 years after insertion. No implants had been lost after 3 years and all prostheses were present and continuously functional. The morphotypic analysis of the microbial plaque taken from titanium implants adjacent to clinically inflamed tissues was different from that described of the dental plaque associated with sites of gingival inflammation. Radiographs demonstrated early horizontal bone loss adjacent to osseointegrated fixtures and occasional continuing horizontal bone loss at some sites during the 1st and 2nd years after prosthesis installation. All fixtures remained integrated after 3 years of function supporting fixed prostheses. Minor differences between the results of this study and earlier studies may reflect differences in surgical technique.

Adult↗

Valva ileocaecalis: preservation during ileocolonic surgery employing a rodent experimental model.

Experimental and clinical data suggest that the valva ileocaecalis under neurogenic and hormonal influences, modulates antegrade and retrograde flow of succus entericus. A priori reasoning suggests that this function may influence nutrient absorption by and intraluminal endogenous microbial flora within the ileum. The hypothesis to be tested was, can anatomical and functional integrity of the valva ileocaecalis be preserved during the performance of a right hemicolectomy with reestablishment of intestinal continuity via a cecocolostomy? The methodology involved utilization of Lewis male rats weighing approximately 500 gm. General anesthesia was induced for all procedures. The animals were randomly assigned to three groups (10 animals/group): (A) sham operation; (B) pericecal dissection (preservation of the arteria et vena ileocolica); and (C) periileal dissection (ligation of the aforementioned vessels). Celiotomy was performed employing standard clean techniques, and was accompanied by a right hemicolectomy and an end-to-end or end-to-side cecocolostomy. Function of the heterotopic valva ileocaecalis was assessed 6-12 weeks post-operatively employing radiographic criteria (fluoroscopic analysis after intraluminal instillation of barium sulfate). Light microscopic analysis was performed subsequent to the radiographic studies. Periileal dissection associated with ligation of the arteria et vena ileocolica uniformly resulted in anastomotic disruption. Pericecal dissection associated with preservation of those vessels resulted in uniform anastomotic integrity, although two animals succumbed secondary to pneumonitis within 5 post-operative days. Radiographic analysis of the heterotopic valva ileocaecalis revealed intermittent antegrade and no retrograde flow of contrast material, which suggested functional integrity. Qualitative light microscopic analysis revealed architectural integrity.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

Antibody regulation of Tcell immunity: implications for vaccine strategies against intracellular pathogens.

Intracellular microbial pathogens cause a plethora of diseases that pose a huge public health challenge. Efficacious prophylactic vaccines are needed to protect the population from this myriad of infectious diseases. Contemporary approaches to vaccine design are guided by the immunobiological paradigm that extracellular pathogens are controlled principally by humoral immunity, involving specific antibodies, whereas host protection against intracellular pathogens requires effectors of cell-mediated immunity. However, this distinct T-helper (Th) type 1 and 2 paradigm of host defense has encountered a major challenge due to the reality that most antigens or vaccines induce mixed immune responses comprising of both humoral and CMI effectors. Besides, the true functional independence of antibodies and T-cells under in vivo physiologic conditions is uncertain. Recent findings have revealed that antibodies exert a significant immunoregulatory effect on T-cell immunity. Thus, a robust and protective T-cell memory response against microbial pathogens such as Chlamydia and Mycobacteria require an effective primary humoral immune response characterized by specific antibody isotypes whose role is to modulate Th1 activation via Fc receptors (FcR) by facilitating a rapid uptake, processing and presentation of pathogen-derived antigens for an enhanced T-cell response. These findings have crystallized into a paradigm shift in host defense wherein different components of the apparently disparate mixed immune responses elicited against a microbial pathogen function concertedly to maximize the principal effector mechanism. This review focuses on the essential role of both arms of the immune system in controlling intracellular microbial pathogens, especially the regulatory role of FcR-mediated antibody function in optimizing the induction of a protective Th1 response. The immunobiological implications are discussed in the context of vaccine design, delivery and evaluation against intracellular microbial pathogens of bacteria, fungi and parasitic origin.

Animals↗

Toll-like receptor 2, 3, and 4 expression and function in human airway smooth muscle.

BACKGROUND: Host defense against microbial pathogens is elicited through the innate immune system by means of Toll-like receptors (TLRs). Airway smooth muscle cells (ASMCs) display proinflammatory and immunomodulatory functions. ASMCs might participate in airway inflammatory responses associated with innate immune activation. OBJECTIVES: We determined the effects of cytokines, TLR ligands, and corticosteroids on TLR expression and function in human ASMCs. METHODS: Real-time PCR and flow cytometry were used to assess TLR mRNA and protein expression, respectively. ASMCs were stimulated with TLR ligands, and chemokine release was measured by means of ELISA. RESULTS: ASMCs expressed TLR1 to TLR10 mRNA, and TLR2 and TLR3 protein expression was demonstrated. TNF-alpha and double-stranded RNA (dsRNA; TLR3 ligand) were potent inducers of TLR2 and TLR3 mRNA expression, and both stimuli had additive or synergistic effects with IFN-gamma on TLR2 and TLR4, but not TLR3, mRNA expression. Peptidoglycan (TLR2 ligand) and LPS (TLR4 ligand) weakly enhanced TLR2 mRNA expression. Peptidoglycan, dsRNA, and LPS induced IL-8 and eotaxin release, with dsRNA being most potent. dsRNA also modulated cytokine-induced chemokine release in a differential manner. Dexamethasone inhibited cytokine- and ligand-induced TLR2, TLR3, and TLR4 expression and chemokine release. However, dexamethasone potentiated TLR2 expression induced by combined IFN-gamma and TNF-alpha stimulation. CONCLUSION: Expression of TLR2, TLR3, and TLR4 is regulated by cytokines and TLR ligands, and their activation mediates chemokine release in ASMCs. CLINICAL IMPLICATIONS: Proinflammatory responses mediated by activation of pathogen-recognition receptors in ASMCs might contribute to infectious exacerbations of airway inflammatory conditions, such as asthma and chronic obstructive pulmonary disease.

Bronchi↗