The in situ sinking rates of herbivore fecal pellets

The vertical flux of pigmented fecal pellets was measured forperiods of 4 h or less with closely spaced sediment traps. Thesettling of the nighttime injection resulting from macrozooplanktongrazing activity could be monitored as the pellets settled throughthe water column. Sinking rates of fecal pellets showed a rangeof 31 – 122 m d^–1 with an average of 87 m d^–1.Longer term experiments show that the vertical phaeopigmentflux is conservative, and that there is no significant lossof pigments en route to the sea floor. In Dabob Bay, coprophagyin the water column is most likely a minor consideration. Theamount of chlorophyll sinking out of the euphotic zone usuallyrepresents <1% of the standing crop, and is usually only5% or less than the phaeopigment flux. This suggests that grazingis the predominant process accounting for the major loss ofchlorophyll from the water column. ¹Contribution no. 1332 from the School of Oceanography, Universityof Washington, Seattle, WA 98195, USA. ²Present address: The Biological Laboratories, Harvard University,Cambridge, MA 02138, USA.     

Microbial colonization of soil aggregates as affected by temperature

Summary Sucrose-amended soil aggregates incubated at 15, 25 and 35°C exhibited quantitative and qualitative differences in microbial ecology. Numbers of bacteria and fungi showed a faster increase to the maximum level and a faster decrease with prolonged incubation the higher the temperature. Soil yeasts developed rapidly and extensively in aggregates incubated at 15 and 25 but not at 35°C.The fungal flora that developed on the aggregates varied with temperature: (a)M. silvaticus and anAlternaria species were the predominant primary flora at 15 and 25°C; (b)Sclerotium andPseudogymnoascus species developed in abundance in the later stages of incubation at 15 but were rare at 25°C; and (c)R. rhizopodiformis andA. fumigatus were virtually the only fungi observed on aggregates incubated at 35°C.Direct microscopic examination provided an estimate of the extent and type of fungal development that occurred on the aggregates. In general, dilution plate counts reflected accurately the growth and sporulation of the primary fungal flora of high sporulating capacity. But because spores of the primary flora remained viable in the soil and dominated the dilution plates long after the mycelia of these fungi had apparently decomposed, the plate counts provided little direct information regarding the development of the secondary fungal flora on the aggregates.     

Kinetic and thermodynamic stability of bacterial intracellular aggregates

Protein aggregation is related to many human disorders and constitutes a major bottleneck in protein production. However, little is known about the conformational properties of in vivo formed aggregates and how they relate to the specific polypeptides embedded in them. Here, we show that the kinetic and thermodynamic stability of the inclusion bodies formed by the Abeta42 Alzheimer peptide and its Asp19 alloform differ significantly and correlate with their amyloidogenic propensity and solubility inside the cell. Our results indicate that the nature of the polypeptide chain determines the specific conformational properties of intracellular aggregates. This implies that different protein inclusions impose dissimilar challenges to the cellular quality-control machinery.     

Phytoplankton sinking rates in the Rhine region of freshwater influence

According to Stokes’ law, colony formation in phytoplanktonwould lead to enhanced sinking rates and higher sedimentationlosses if colonies had the same densities as the phytoplanktoncells they contain. In the Dutch coastal zone of the North Sea,algae settling out of the water column are subject to zoobenthosgrazing or to physical mixing into the sediment and, therefore,the formation of colonies by common diatom species and the prymnesiophytePhaeocystis globosa seems paradoxical: it would increase theprobability that sedimentation becomes a significant loss factor.However, sinking rate measurements in the Rhine region of freshwaterinfluence (ROFI) using SetCol settling columns did not reveala straightforward relationship between phytoplankton sizes (<10to >1000 µm) and sinking rates (–0.4 to >2.2m day^-1) of 24 autotrophic phytoplankton species and groups.In fact, under nutrient-replete conditions, the sinking ratesof the diatoms Chaetoceros radicans, Rhizosolenia shrubsoleiand Rhizosolenia stolterfothii decreased with size. The sinkingrates of large colonies of the prymnesiophyte P. globosa werealso negatively correlated with their size and positive buoyancywas observed. Chlorophyll a sinking rates exceeded 1 m day^-1periodically, which is sufficient to cause significant surfacelayer loss rates over 0.2 day^-1. Under stratified conditions,both chlorophyll a concentrations and sinking rates in the bottomlayer were significantly higher (+49% and +16%, respectively)than in the surface layer. These observations are discussedin relation to Stokes’ law, together with a critical analysisof the SetCol technique. It is concluded that: (i) SetCol givesadequate results when incubations are performed at or near insitu irradiance and temperature; (ii) sinking rates are predominantlydetermined by cell or colony density rather than their size;(iii) periodic sedimentation is an important species-specificloss process for phytoplankton in the Dutch coastal zone. Itis speculated that for diatoms with low sinking rates, autolysisis an important loss factor.     

Curing bacterial infections with protein aggregates

A growing number of human diseases seem to be associated with protein misfolding and deposition into aggregates. Bednarska and colleagues exploit the cytotoxic nature of protein aggregates to target bacterial infections. Protein aggregation is at the same time generic and sequence dependent; this allowed the authors to develop novel aggregation‐prone antimicrobial peptides that penetrate bacteria and induce a peptide specific proteostatic collapse that leads to fast bacterial death, without any observable effects on host cells. The applicability of this intriguing strategy was demonstrated by curing animal models from bacterial sepsis. Although the precise mechanisms underlying the bactericidal activity of the peptide aggregates are still not clear, there is no doubt that this approach offers an exciting therapeutic alternative to conventional antibiotics.     

Mechanisms controlling pathogen colonization of the gut

The intestinal microbiota can protect efficiently against colonization by many enteric pathogens ('colonization resistance', CR). This phenomenon has been known for decades, but the mechanistic basis of CR is incompletely defined. At least three mechanisms seem to contribute, that is direct inhibition of pathogen growth by microbiota-derived substances, nutrient depletion by microbiota growth and microbiota-induced stimulation of innate and adaptive immune responses. In spite of CR, intestinal infections are well known to occur. In these cases, the multi-faceted interactions between the microbiota, the host and the pathogen are shifted in favor of the pathogen. We are discussing recent progress in deciphering the underlying molecular mechanisms in health and disease.     

Clearance of picoplankton-sized partides and formation of rapidly sinking aggregates by the pteropod, Limacina reiroversa

Findings from experiments showed that the web-feeding euthecosomatouspteropod, Limacina retroversa, can produce rapidly sinking,mucous aggregates. It is suggested that, by adhesion, theseaggregates scavenged picoplankton-sized particles, which werethus effectively cleared from the medium. In contrast, Calanusfinmarchicus was not able to clear these particles in our experiments.Sedimentation velocities of 10 aggregates measured in vivo wereup to 1000 m day^–1, with an average of {small tilde}300m day^–1 (not including two aggegates with neutral buoyancy).Mean velocities measured for feces of C.finmarchicus, Calanushyperboreus and Thyssnoessa sp. were consider ably lower. Wesuggest that the sedimentation of L retroversa aggregates wasthe source of mucous flocs collected in sediment traps (Bathmannet al., Deep-Sea Res., 38,1341–1360,1991) and at the seafloor at 1200 m depth in the southern Norwegian Sea. This processmay be an important mediator of sedimentation to the deep sea,when these pteropods are present in surface waters in largeabundance.     

Protozoan predation of bacterial cells in soil aggregates

Abstract The development and survival of Aerobacter aerogenes IAM11022 in the inner and outer zones of soil aggregates (1–2 mm) was investigated in relation to a protozoan ( Colpoda sp.). With different dilutions of the bacterial cell suspension, a constant partition ratio of these cells was observed between outer and inner zones of the aggregates. Protozoa inoculated in the same manner were generally recovered only from the outer zone of the aggregates.
In the presence of protozoa, prey cell numbers of the outer zone were reduced from more than 10⁸ to approx. 10⁴ cells · g soil⁻¹ in 12 days. In contrast, 10⁸ cells · g soil⁻¹ remained in the inner zone of the aggregates, even after 12 days.
The increase in predator cell number was proportional to initial prey densities in the outer zone of the aggregates. At a constant initial prey density (1.8 × 10⁷ cells · g soil⁻¹), Colpoda sp. multiplied in proportion to the initial number of predators. When the initial density of the predator was low more prey cells survived in the outer zone.
Prey persistence was associated with 3 different types of protection: (1) small pore necks of the inner zone space of the aggregates; (2) the division of the outer zone space into compartments; and (3) the distribution of protozoan cells among soil aggregates. The latter two were closely related to the moisture condition of the soil.     

Comparison of diffusion and reaction rates in anaerobic microbial aggregates

The ability of hydrogen diffusion to account for the rates of methane production in microbial aggregates was studied in a defined coculture consisting of a sulfate reducer grown as a syntrophic hydrogen producer in the absence of sulfate and a methanogen. The hydrogen uptake kinetics of the methanogen were determined using the infinite dilution technique. The maximum hydrogen uptake velocity was 7.1 nmol/min/μg protein and the half saturation constant for hydrogen uptake was 386 nmol/liter. A threshold of 28 nmol/liter below which no further hydrogen consumption occurred was observed. The reconstituted co-culture was shown to produce methane at rates similar to mixed culture enrichments grown on lactate. The diffusion model demonstrated that for the particular system studied, the rates of hydrogen diffusion could account for the overall rate of methane production.     

Weak rolling adhesion enhances bacterial surface colonization

Bacterial adhesion to and subsequent colonization of surfaces are the first steps toward forming biofilms, which are a major concern for implanted medical devices and in many diseases. It has generally been assumed that strong irreversible adhesion is a necessary step for biofilm formation. However, some bacteria, such as Escherichia coli when binding to mannosylated surfaces via the adhesive protein FimH, adhere weakly in a mode that allows them to roll across the surface. Since single-point mutations or even increased shear stress can switch this FimH-mediated adhesion to a strong stationary mode, the FimH system offers a unique opportunity to investigate the role of the strength of adhesion independently from the many other factors that may affect surface colonization. Here we compare levels of surface colonization by E. coli strains that differ in the strength of adhesion as a result of flow conditions or point mutations in FimH. We show that the weak rolling mode of surface adhesion can allow a more rapid spreading during growth on a surface in the presence of fluid flow. Indeed, an attempt to inhibit the adhesion of strongly adherent bacteria by blocking mannose receptors with a soluble inhibitor actually increased the rate of surface colonization by allowing the bacteria to roll. This work suggests that (i) a physiological advantage to the weak adhesion demonstrated by commensal variants of FimH bacteria may be to allow rapid surface colonization and (ii) antiadhesive therapies intended to prevent biofilm formation can have the unintended effect of enhancing the rate of surface colonization.     

Diet and bacterial colonization: role of probiotics and prebiotics

The intestinal mucosa functions as a defensive barrier that limits dietary antigen transport and microbial pathogens from colonizing enterocytes. The potential role of lactic acid bacteria, specifically Bifidobacteria, in probiotic and prebiotic functional food supplements is reviewed in the context of bacterial colonization, adherence, and disease prevention. This article reviews the mechanisms of action and optimization of methods that will lead to a new generation of biotic products with enhanced biologic properties and well-being foods.     

Death rates of bacterial mutants

We have studied the death rates of mutant and wild-type strains of Escherichia coli by two methods. One method involves microscopic estimations of the ability of bacteria to form microcolonies. The other method involves estimates of the numbers of bacteria permeable to a fluorescent dye. The results of both methods suggest that of the order of 0.1–0.3% of bacteria in an exponentially growing culture are dead according to the present criteria. When the death rates are compared with those for mutant bacteria with hyperaccurate or with error-prone ribosomes, no significant differences are observed. The results suggest that there is little or no relationship between death rate and the accuracy of gene expression in E. coli.     

Growth interactions during bacterial colonization of seedling rootlets

Rootlet elongation and bacterial growth on rootlets were determined after inoculation of cucumber and spinach seedlings with Pseudomonas strains differing in production of siderophores and HCN. Siderophore producers grew more profusely than nonproducers on both species and promoted rootlet elongation on cucumber. Coinoculation of siderophore producers and nonproducers resulted in restricted growth of the latter. The total populations of nonproducers of HCN in the presence of HCN producers were not decreased, but the tenacity of their association with the rootlet surface was altered.     

Mechanisms of bacterial biocide and antibiotic resistance

Resistance to antibiotics is increasingly commonplace amongst important human pathogens. Although the mechanism(s) of resistance vary from agent to agent they typically involve one or more of: alteration of the drug target in the bacterial cell, enzymatic modification or destruction of the drug itself, or limitation of drug accumulation as a result of drug exclusion or active drug efflux. While most of these are agent specific, providing resistance to a single antimicrobial or class of antimicrobial, there are currently numerous examples of efflux systems that accommodate and, thus, provide resistance to a broad range of structurally unrelated antimicrobials--so-called multidrug efflux systems. Resistance to biocides is less common and likely reflects the multiplicity of targets within the cell as well as the general lack of known detoxifying enzymes. Resistance typically results from cellular changes that impact on biocide accumulation, including cell envelope changes that limit uptake, or expression of efflux mechanisms. Still, target site mutations leading to biocide resistance, though rare, are known. Intriguingly, many multidrug efflux systems also accommodate biocides (e.g. triclosan) such that strains expressing these are both antibiotic- and biocide-resistant. Indeed, concern has been expressed regarding the potential for agents such as triclosan to select for strains resistant to multiple clinically-relevant antibiotics. Some of the better characterized examples of such multidrug efflux systems can be found in the opportunistic pathogen Pseudomonas aeruginosa where they play an important role in the noted intrinsic and acquired resistance of this organism to antibiotics and triclosan. These tripartite pumps include an integral inner membrane drug-proton antiporter, an outer membrane- and periplasm-spanning channel-forming protein and a periplasmic link protein that joins these two. Expression of efflux genes is governed minimally by the product of a linked regulatory gene that is in most cases the target for mutation in multidrug resistant strains hyperexpressing these efflux systems. Issues for consideration include the natural function of these efflux systems and the therapeutic potential of targeting these systems in combating acquired multidrug resistance.     

Effects of burn wound excision on bacterial colonization and invasion

Rates of survival after thermal injury have improved in the past two decades, and rates of wound infections and sepsis have decreased during the same period. Early excision has been advocated as one of the major factors, but its safety and efficacy and the exact timing of burn excision are still under debate. It was hypothesized that acute burn wound excision (in the first 24 hours after burning) would be superior to conservative treatment and delayed excision in preventing bacterial colonization and invasion. Twenty consecutive patients with thermal injuries were studied. Twelve patients underwent acute burn wound excision, and eight patients underwent conservative treatment and delayed excision. The second group of patients received topical treatments in another facility and underwent delayed excision after transfer to our service, on postburn day 6. Quantitative bacteriological assessments of the excised wound and biopsy samples of the wound bed, obtained before autografting and/or homografting, were performed. The effects of time on bacterial counts, differences between superficial and deep biopsy samples, and the effects of early versus late debridement were studied. Patients admitted early exhibited bacterial counts of less than 10 bacteria per gram of tissue. Patients in this group did not experience infection or graft loss. Patients admitted late exhibited counts of more than 10 bacteria (p = 0.001, compared with early admission). Three patients in the late excision group experienced infection and graft loss (p < 0.05, compared with the early excision group). Burn wound excision significantly decreased bacterial colonization for all patients (p < 0.001). Greater bacterial colonization and higher rates of infection were correlated with topical treatment and late excision (p < 0.001). It is concluded that burn wound excision significantly reduces bacterial colonization. Patients who undergo topical treatment and delayed burn wound excision exhibit greater bacterial colonization and increased rates of infection. Acute burn wound excision should be considered for all full-thickness burns.