Patrice Dion

Sources of Clostridia in Raw Milk on Farms

ABSTRACT A PCR-denaturing gradient gel electrophoresis (DGGE) method was used to examine on-farm sources of Clostridium cluster I strains in four dairy farms over 2 years. Conventional microbiological analysis was used in parallel to monitor size of clostridial populations present in various components of the milk production chain (soil, forage, grass silage, maize silage, dry hay, and raw milk). PCR amplification with Clostridium cluster I-specific 16S rRNA gene primers followed by DGGE separation yielded a total of 47 operational taxonomic units (OTUs), which varied greatly with respect to frequency of occurrence. Some OTUs were found only in forage, and forage profiles differed according to farm location (southern or northern Québec). More clostridial contamination was found in maize silage than in grass silage. Milk represented a potential environment for certain OTUs. No OTU was milk specific, indicating that OTUs originated from other environments. Most (83%) of the OTUs detected in raw milk were also found in grass or maize silage. Milk DGGE profiles differed according to farm and sampling year and fit into two distinct categories. One milk profile category was characterized by the presence of a few dominant OTUs, the presence of which appeared to be more related to farm management than to feed contamination. OTUs were more varied in the second profile category. The identities of certain OTUs frequently found in milk were resolved by cloning and sequencing. Clostridium disporicum was identified as an important member of clostridial populations transmitted to milk. Clostridium tyrobutyricum was consistently found in milk and was widespread in the other farm environments examined.

Construction of a Tn5 derivative encoding bioluminescence and its introduction in Pseudomonas, Agrobacterium and Rhizobium

SummaryA simple method based upon the use of a Tn5 derivative, Tn5-Lux, has been devised for the introduction and stable expression of the character of bioluminescence in a variety of gram-negative bacteria. In Tn5-Lux, the luxAB genes of Vibrio harveyi encoding luciferase are inserted on a SalI-BglII fragment between the kanamycin resistance (Kmr) gene and the right insertion sequence. The transposon derivative was placed on a transposition suicide vehicle by in situ recombination with the Tn5 suicide vector pGS9, to yield pDB30. Mating between Escherichia coli WA803 (pDB30) and a strain from our laboratory, Pseudomonas sp. RB100C, gave a Kmr transfer frequency of 10-6 per recipient, a value 10 times lower than that obtained with the original suicide vehicle pGS9. Tn5-Lux was also introduced by insertion mutagenesis in other strains of gram-negative soil bacteria. The bioluminescence marker was expressed in the presence of n-decanal, and was monitored as chemiluminescence in a liquid scintillation counter. The recorded light intensities were fairly comparable among the strains, and ranged between 0.2 to 1.8x106 cpm for a cell density of 103 colony forming units/ml. Nodules initiated by bioluminescent strains of Rhizobium leguminosarum on two different hosts were compared for intensity of the bioluminescence they produced.

Extreme Views on Prokaryote Evolution

Not two soils are identical. Not two bacteria are identical either, with perhaps even not two daughter cells as they emerge from symmetric division being rigorously the same (Stewart et al. 2005). However, it might be easier to draw generalizations from observations of Escherichia coli or Caulobacter crescentus than from soil studies. This might explain why the bacterial cell has been deemed a more popular object of theoretical reflections than has the soil environment, although remarkable concepts on soil biology have emerged (Wardle et al. 2004; Young and Crawford 2004). This being said, extreme soils may appear as a particularly fruitful ground for those of us who feel seduced by the “idea of the soil” and who wish to venture on such a ( admittedly slippery) terrain. Life constantly reinvents itself, under new aspects that owe much to ancient ones, to the point that nothing, at least microbial, can be said to have ever disappeared: the author is aware that this opinion may hold only if emphasis is placed on the modular construction of prokaryotic cells. In this sense, the last universal common ancestor or rather perhaps a set of basic processes acting on communally evolving primitive cells (Woese 2002), is still among us in a transformed and diversified form, and having seeded among its progeny many clues of its ancient organization. This apparent persistence of functional attributes over evolutionary time has been termed the “fecundity of function principle” (Staley 1997). Anecdotally, it might also be remarked that even the smallpox virus is still preserved somewhere behind well-locked doors. Life on Earth has been proposed to have originated in a hot (Di Giulio 2003; Schwartzman and Lineweaver 2004) or a cold (Price 2007) environment. As a reconciling alternative to these opposing possibilities, it has also been suggested that

Transformation du lactosérum déprotéiné en milieu de culture pour la levure de boulangerie

Abstract A process is described to produce bakers yeast, a biological product of high value, from protein-free whey obtained by ultrafiltration. The process includes a lactic fermentation of protein-free whey, the separation of the bacterial biomass by ultrafiltration, and the fermentation of the permeate by bakers yeast. The reported results are of two kinds, those on the behavior of yeast in presence of lactic acid, and those on whey fermentation. The growth of yeast in lactic acid medium was particularly affected by aeration rate and acid concentration. The lactic fermentation of whey produced a substrate suitable for bakers yeast.

The Microbiological Promises of Extreme Soils

Whereas the notion of extreme environment has received much attention from microbiologists, this generalization does not systematically include extreme soils. There may be at least two reasons for this. First, any soil may be considered as extreme for the colonizing microbes constantly facing starvation, desiccation, predation, and other attacks. In this sense, the notion of “extreme soil” would appear pleonastic. A second reason for the uncommon use of the term “extreme soil” might be the opinion that there is little to be gained from it, inasmuch as every soil has its particularities and, in its very nature, is refractory to human efforts at unification and simplification. In this sense, any grouping of soils from, say, the Antarctic or hot deserts into a common category designated as “extreme” would appear futile, if not detrimental to a precise understanding of soils and their microbial populations. However, one might take the stance that, although it certainly serves to be aware of these difficulties, there is still much to be learned from running into them. Hence, it is hoped that the present book will be a demonstration of the usefulness of the extreme soil concept to microbiologists. Various extreme soils have been the topic of numerous and fruitful studies dealing with the characterization of microbial communities and processes. These studies have done much to enrich our understanding of microbial diversity and of biogeochemical and other biological mechanisms. They allow us to grasp microbial adaptability and to envision practical applications. Reading the enclosed collection of chapters will make it clear that unifying these studies under the general theme of “extreme soils,” and associating this concept with the broader notion of “extreme environments” leads to essential theoretical and practical advances. We qualify a soil as “extreme” when it supports colonization by organisms presenting a specific and common adaptation. The specifying character of an extreme soil may be physical in nature, and correspond to extreme values of temperature, or

Reconstructing Soil Biology

Soil bacteria and archaea first evolved as principal inhabitants of primordial environments, and then in association with fungi, plants and animals as new environments emerged. Thus, transitions occurred, which did not correspond to a replacement of ancient processes by new ones, but to a superposition or accretion of processes. The maintenance of primordial environments depends on the development of complexity to compensate for the effects of increasing diversity. Much of the persistence that is observed along the biological history of soils depends on symbiogenesis, which might be understood in terms, not of natural selection among biological systems, but of natural maintenance. Soil microbial diversity has no equivalent in other environments carrying heavy microbial loads, such as aquatic or human gut systems. Variability and complexity of soil microbial communities originate in part from heterogeneous distribution of water, oxygen and nutrients within the structured soil matrix (Young and Ritz 2000). Evolutionary change also has the potential to contribute to soil microbial diversity, insofar as it occurs without replacement. In the present review, the biological history of soil will be presented as a cumulative succession of colonizations. Under the combined influence of biological variation and global environmental changes, new groups of microbes and multicellular organisms have colonized land without necessarily replacing previously established soil inhabitants. New soil organisms might have appeared suddenly, in a punctuated equilibrium pattern (Eldredge and Gould 1972). Such sudden releases from species homeostasis might have generated waves of new soil colonists, organisms from one such wave collectively

Towards a New Purpose for Traditional and Other Forms of Soil Knowledge

The various forms of traditional and scientific soil knowledge may be organized as a continuum set between two polar extremes. Enchantment resides at one of these extremes and leads to superstition and irrationalism, whereas the other extreme is the preserve of disenchantment, which in turn invites to reductionism and even a regressive form of systematized knowledge. In practice, enchantment and disenchantment contribute in various proportions to the generation and the instantiation of soil knowledge.