Wall growth in laboratory fermenters

The influence of microorganisms growing on the walls of laboratory fermenters was investigated and a model to describe of microbial lysis and the formation of growth inhibitory products in a continuous fermentation process was developed. The predictions were compared with results from an earlier model for growth of microorganisms on surfaces.     

Influence of DNA isolation on Q-PCR-based quantification of methanogenic Archaea in biogas fermenters

Quantitative real-time PCR (Q-PCR) is commonly applied for the detection of certain microorganisms in environmental samples. However, some environments, like biomass-degrading biogas fermenters, are enriched with PCR-interfering substances. To study the impact of the DNA extraction protocol on the results of Q-PCR-based analysis of the methane-producing archaeal community in biogas fermenters, nine different protocols with varying cell disruption and DNA purification approaches were tested.     

Evidence for Fossilized Subsurface Microbial Communities at the TAG Hydrothermal Mound

Scanning electron microscope examinations have revealed fossilized cell-like structures randomly distributed in near-surface oxidized deposits of red and gray Fe-rich chert and Fe-Si oxyhydroxides of the Trans-Atlantic Geotraverse (TAG) hydrothermal mound, Mid-Atlantic Ridge at 26°08'N. Chemically, these structures are carbon-based with the morphology of half-spheroids that are 2 to 3 w m in diameter and are mostly arranged in the form of clusters and long thread-like cellular masses that resemble single-celled microorganisms. The wide range of intracrystalline silica concentration, which seems to replace the original chemistry, suggests that the microorganisms were subjected to various degrees of silica mineralization, which was probably controlled by the thermal development of this hydrothermal site.     

Automatisiertes Laborfermentorsystem mit Mikrorechner „Elektronica-60”︁ gekoppelt

The microprocessor complex “Biotron-M” designed for automation of experiments in microorganisms cultivation carried out simultaneously on no more than 3 fermenters is described. The complex is based on KTS LIUS-2 and microcomputer “Elektronika-60”. Information and control functions as well as the complete system are considered. The operating system “Rafos” with double-task monitor is used as the system software. Special software is represented by a set of program modules performing the functions of the complex. An example is given concerning the operation of “Biotron-M” together with fermentation plant “FU-8”.     

Isolation,characterization and comparison of bacteria from swine faeces and manure storage pits

Storage of swine manure is associated with the microbiological production of a variety of odorous chemicals including ammonia, organic acids and alcohols, and sulphides. Although largely the product of microbiological activity, little is known about the microorganisms present in swine manure. In order to gain a better understanding of the types and activities of the microorganisms present, representative strains of microorganisms were isolated from faeces and stored manure slurry, identified, and physiologically characterized. For swine manure slurry samples, total anaerobe colony counts were greatest when a non-selective, habitat simulating medium containing clarified swine manure slurry was used whereas the highest counts for faecal anaerobes were obtained on rumen fluid containing medium. Faecal and slurry samples were also plated onto the appropriate medium containing the antibiotics tetracycline, erythromycin and tylosin (10 micro g ml-1, individually) and the proportional counts of organisms capable of growing in the presence of these antibiotics determined. Randomly selected isolates from the highest dilutions were identified by 16 s rDNA sequence analysis, and selected physiological characteristics were determined. The results of these examinations indicate that the predominant culturable microorganisms from these environments are obligately anaerobic, low mol percentage G + C Gram positive bacteria (Firmicutes) who are members of Clostridial, Eubacterial, and Lactobacillus/Streptococcus phylogenetic groups. Isolates similar to Sporomusa and Flexibacter/Cytophaga/Bacteroides (CFB or Bacteroidetes) groups were also obtained. Although similar overall, faecal and slurry samples differed in bacterial composition. Manure slurry samples were dominated by organisms similar to Clostridium coccoides and Enterococcus species whereas the distribution of species present in faeces appeared much broader. Whereas most of the pure cultures could be assigned to known phylogenetic groupings, few could be identified as known species. Examination of some growth and physiological characteristics of faecal and slurry isolates showed these to be primarily carbohydrate fermenters, although some were able to ferment lactate and amino acids. When the ability of manure and faecal isolates to ferment protein, peptides and amino acids was examined, a relatively small percentage of these were able to do so and most of these fermented carbohydrates in addition to the amino acid sources provided. The predominant amino acid fermenters were most closely related to C. coccoides and C. botulinum, but representatives of the Bacteroides, Staphylococcus, Enterococcus and other phylogenetic groups were also found. The results reported here are compared with those obtained from clone libraries prepared from the same environmental samples.     

Biofilms and biocides

Biofilm is a ubiquitous material generated by microorganisms proliferating on solid surfaces in water exposed to appropriate aqueous nutrients. It is suggested that model biofilm fermenters will be useful in investigating and in the end controlling biofilm formation. The Cardiff constant depth film fermenter is described. The growth of cutting fluid organisms on a model amine: carboxylate medium in this system is discussed. A simple film model based on a dominant metal-working fluid organism Pseudomonas aeruginosa was investigated and preliminary results using formaldehyde as a biocide are presented.     

Fast sampling and quenching procedures for microbial metabolic profiling

A reliable quantification of intracellular concentrations of intermediates in microorganisms depends on a proper sampling procedure and the subsequent fast inactivation of metabolism via quenching. A single device integrating both operations was developed and simultaneously the quenching procedure on cells was assessed too, without finding negative effects on viability or metabolite leakage. Moreover, supported by an experimental design, the influences of process parameters in its dynamic operation were characterized and optimized. The novel in-situ rapid sampling and quenching apparatus can be employed on any laboratory glass fermenters accessible from the top of the bioreactor.     

Marine sponges as microbial fermenters

The discovery of phylogenetically complex, yet highly sponge-specific microbial communities in marine sponges, including novel lineages and even candidate phyla, came as a surprise. At the same time, unique research opportunities opened up, because the microorganisms of sponges are in many ways more accessible than those of seawater. Accordingly, we consider sponges as microbial fermenters that provide exciting new avenues in marine microbiology and biotechnology. This review covers recent findings regarding diversity, biogeography and population dynamics of sponge-associated microbiota, and the data are discussed within the larger context of the microbiology of the ocean.     

群体和单细胞微囊藻对短期高光胁迫的生理响应

为了探讨不同形态的微囊藻（Microcystis）对光的耐受能力及其应对机制,研究比较了短期高光强条件下群体微囊藻和单细胞微囊藻的生理响应,结果表明,在高光强胁迫下,群体和单细胞微囊藻的叶绿素含量、最大电子传递速率（ETR_max）均降低,但与单细胞微囊藻相比,群体微囊藻的下降幅度较小;在高光强胁迫下,群体微囊藻的过氧化氢酶（CAT）与超氧化物歧化酶（SOD）的活性均显著增加,而单细胞微囊藻只有CAT活性增加;在短期高光胁迫下,群体微囊藻的死亡率没有显著变化。这些结果表明群体微囊藻比单细胞微囊藻能耐受更高的光强,也暗示了群体微囊藻在野外高光强条件下更具竞争优势。     

Catabolism of dimethylsulphoniopropionate: microorganisms, enzymes and genes

The compatible solute dimethylsulphoniopropionate (DMSP) has important roles in marine environments. It is an anti-stress compound made by many single-celled plankton, some seaweeds and a few land plants that live by the shore. Furthermore, in the oceans it is a major source of carbon and sulphur for marine bacteria that break it down to products such as dimethyl sulphide, which are important in their own right and have wide-ranging effects, from altering animal behaviour to seeding cloud formation. In this Review, we describe how recent genetic and genomic work on the ways in which several different bacteria, and some fungi, catabolize DMSP has provided new and surprising insights into the mechanisms, regulation and possible evolution of DMSP catabolism in microorganisms.     

Comparative nutrient extraction from forages by grazing bovids and equids: a test of the nutritional model of equid/bovid competition and coexistence

Summary Ruminants are unevenly distributed across the range of body sizes observed in herbivorous mammals; among extant East African species they predominate, in numbers and species richness, in the medium body sizes (10–600 kg). The small and the large species are all hind-gut fermenters. Some medium-sized hind-gut fermenters, equid perissodactyls, coexist with the grazing ruminants, principally bovid artiodactyls, in grassland ecosystems. These patterns have been explained by two complementary models based on differences between the digestive physiology of ruminants and hind-gut fermenters. The Demment and Van Soest (1985) model accounts for the absence of ruminants among the small and large species, while the Bell/Janis/Foose model accounts both for the predominance of ruminants, and their co-existence with equids among the medium-sized species (Bell 1971; Janis 1976; Foose 1982). The latter model assumes that the rumen is competitively superior to the hind-gut system on medium quality forages, and that hind-gut fermenters persist because of their ability to eat more, and thus to extract more nutrients per day from high fibre, low quality forages. Data presented here demonstrate that compared to similarly sized grazing ruminants (bovids), hind-gut fermenters (equids) have higher rates of food intake which more than compensate for their lesser ability to digest plant material. As a consequence equids extract more nutrients per day than bovids not only from low quality foods, but from the whole range of forages eaten by animals of this size. Neither of the current nutritional models, nor refinements of them satisfactorily explain the preponderance of the bovids among medium-sized ungulates; alternative hypotheses are presented.     

Soil Microbial Communities of Eastern Antarctica

Investigation of microbial communities of Antarctica soils is a very important field of research that expands our knowledge of microbial participation in primary soil formation and specific features of their communities in extreme habitats, and it is of considerable interest in directed search of for microorganisms as potential biotechnological objects. The results of long-term (2012–2017) complex studies on soil microbial communities of the Russian East Antarctica polar stations at Shirmakher oasis (Novolazarevskaya station), the Larsemann Hills (Progress station), and the Tala Hills (Molodezhnaya station) are presented in this review. The assessment of biomass of soil microorganisms by the methods of direct microscopy has been carried out for the first time for this region. The general amount of microbial biomass is small; the fungi dominate (77–99%). The unique features of Antarctic soils are the high content and morphological diversity of small forms of microorganisms: fungi are presented by mainly single-celled structures (small spores and yeasts), while bacteria by ultrafine (filtering) forms. At the same time, microorganisms can significantly contribute to such important ecological functions of soil as the emission of greenhouse gases, especially during the warm season with the stable positive temperatures of the soil. This should be considered during creation of models and forecasts of global warming. The use of various isolation techniques for the analysis of the soil microbial population, together with the succession approach, significantly expand the information about taxonomic diversity of cultivated fungi and bacteria in Antarctica soils.     

Characterization of the microflora of high acid submerged vinegar fermenters by distinct plasmid profiles

Summary Since isolation of the Acetobacter strains responsible for ethanol oxidation in high acid, submerged vinegar fermentations is still extremely difficult, characterization of the vinegar microflora was approached by isolation and gel electrophoresis of plasmids extractable from the harvested microorganisms. Distinct plasmid profiles have been detected in all of 19 investigated fermenters from 5 different locations. Plasmid sizes varied between 1.3 and 133 Megadalton. Between 3 and 11 different plasmids were recognized in particular profiles. Comparison of these profiles from different sources proves that the plasmid profile of a vinegar fermenter is a unique property of the inherent microflora which allows definite conclusions regarding its stability, origin, identity and composition.     

The energetics of coprophagy: a theoretical analysis

Lagomorphs, many rodents and some other small mammals eat their faeces during the part of the day when they are not foraging for fresh food. One of the possible benefits of this habit of coprophagy is that it may enable them to extract more energy from their food. A computer model is used to assess the likely benefits and explore their relationships to food, feeding rate and gut morphology. The predicted benefits are much larger for hindgut fermenters than for foregut fermenters, and especially large for hindgut fermenters with relatively small fermentation chambers. They are larger for poor foods (with lower proportions of cell contents) than for richer ones. At low feeding rates the energetic advantage of coprophagy may disappear if the faeces from food eaten during one feeding period emerge largely during the next, but this can be avoided by adjusting the rate of passage of gut contents during the intervening rest period.     

Global organellar proteomics

Cataloging the proteomes of single-celled microorganisms, cells, biological fluids, tissue and whole organisms is being undertaken at a rapid pace as advances are made in protein and peptide separation, detection and identification. For metazoans, subcellular organelles represent attractive targets for global proteome analysis because they represent discrete functional units, their complexity in protein composition is reduced relative to whole cells and, when abundant cytoskeletal proteins are removed, lower abundance proteins specific to the organelle are revealed. Here, we review recent literature on the global analysis of subcellular organelles and briefly discuss how that information is being used to elucidate basic biological processes that range from cellular signaling pathways through protein-protein interactions to differential expression of proteins in response to external stimuli. We assess the relative merits of the different methods used and discuss issues and future directions in the field.     

Plant-induced cell death in the oomycete pathogen Phytophthora parasitica

The activation of programmed cell death in the host during plant-pathogen interactions is an important component of the plant disease resistance mechanism. In this study we show that activation of programmed cell death in microorganisms also regulates plant-pathogen interactions. We found that a form of vacuolar cell death is induced in the oomycete Phytophthora parasitica--the agent that causes black shank disease in Nicotiana tabacum--by extracellular stimuli from resistant tobacco. The single-celled zoospores underwent cell death characterized by dynamic membrane rearrangements, cell shrinkage, formation of numerous large vacuoles in the cytoplasm and degradation of cytoplasmic components before plasma membrane disruption. Phytophthora cell death required protein synthesis but not caspase activation, and was associated with the production of intracellular reactive oxygen species. This characterization of plant-mediated cell death signalling in pathogens will enhance our understanding of the biological processes regulating plant-pathogen interactions, and improve our ability to control crop diseases.     

Fate of bioterrorism-relevant viruses and bacteria, including spores, aerosolized into an indoor air environment

An aerosol physics test facility was used in a series of eight experiments to gather an integrated comprehensive broad base of data on the fate of surrogates of microorganisms that cause smallpox, plague, glanders, anthrax, and viral hemorrhagic fevers. The results are directly relevant to the public health issue of how to protect the occupants of buildings against bioterrorism. The test conditions were directly relevant to the indoor air environment situation, and the results can be generalized to buildings that are now occupied. The reductions in concentrations of relevant viruses and bacteria--including gram-negative fermenters and nonfermenters, gram-positive cocci and bacilli, and spores--were substantial and statistically robust. The data show that the bioterrorism-relevant aerosolized viruses and bacteria, including spores, respond like small particulates to the primary (electrical) forces that control the distribution of small particulates in a room. Further, these relevant microorganisms respond like small particulates to means designed to control airborne particulates. The results could be used to anticipate the effects of a bioterrorist attack on the public health, provide information on means that can be used to minimize such effects, and used to make decisions on how best to protect occupants of specific buildings at minimal cost and with assurance of success.     

Ultrastructure and molecular phylogenetic position of a novel euglenozoan with extrusive episymbiotic bacteria: <Emphasis Type="Italic">Bihospites bacati</Emphasis> n. gen. et sp. (Symbiontida)

Background  

Poorly understood but highly diverse microbial communities exist within anoxic and oxygen-depleted marine sediments. These communities often harbour single-celled eukaryotes that form symbiotic associations with different prokaryotes. During low tides in South-western British Columbia, Canada, vast areas of marine sand become exposed, forming tidal pools. Oxygen-depleted sediments within these pools are distinctively black at only 2-3 cm depth; these layers contain a rich variety of microorganisms, many of which are undescribed. We discovered and characterized a novel (uncultivated) lineage of heterotrophic euglenozoan within these environments using light microscopy, scanning and transmission electron microscopy, serial sectioning and ultrastructural reconstruction, and molecular phylogenetic analyses of small subunit rDNA sequences.     

Model for the growth of aerobic microorganisms under oxygen limiting conditions

A simple dynamic model is proposed which will allow fermenters to be run at throughputs which fully utilize the mass transfer capabilities of the fermenters while not decreasing the yield from the substrate. The model is compared with one previously proposed, which was originally formulated for double substrate limitation when both substrates were supplied in the feed. Computer solutions of the model are given which show the effects of the parameters used. Experimental results from growing Candida utilis on a high concentration of glucose were found to be similar to those predicted by the model.