Contribution of the Earthworm Lumbricus rubellus (Annelida, Oligochaeta) to the Establishment of Plasmids in Soil Bacterial Communities

Potential Effects of Horizontal Gene Exchange in the Human Gut

Many essential functions of the human body are dependent on the symbiotic microbiota, which is present at especially high numbers and diversity in the gut. This intricate host-microbe relationship is a result of the long-term coevolution between the two. While the inheritance of mutational changes in the host evolution is almost exclusively vertical, the main mechanism of bacterial evolution is horizontal gene exchange. The gut conditions, with stable temperature, continuous food supply, constant physicochemical conditions, extremely high concentration of microbial cells and phages, and plenty of opportunities for conjugation on the surfaces of food particles and host tissues, represent one of the most favorable ecological niches for horizontal gene exchange. Thus, the gut microbial system genetically is very dynamic and capable of rapid response, at the genetic level, to selection, for example, by antibiotics. There are many other factors to which the microbiota may dynamically respond including lifestyle, therapy, diet, refined food, food additives, consumption of pre- and probiotics, and many others. The impact of the changing selective pressures on gut microbiota, however, is poorly understood. Presumably, the gut microbiome responds to these changes by genetic restructuring of gut populations, driven mainly via horizontal gene exchange. Thus, our main goal is to reveal the role played by horizontal gene exchange in the changing landscape of the gastrointestinal microbiome and potential effect of these changes on human health in general and autoimmune diseases in particular.

Horizontal gene exchange in environmental microbiota

Horizontal gene transfer (HGT) plays an important role in the evolution of life on the Earth. This view is supported by numerous occasions of HGT that are recorded in the genomes of all three domains of living organisms. HGT-mediated rapid evolution is especially noticeable among the Bacteria, which demonstrate formidable adaptability in the face of recent environmental changes imposed by human activities, such as the use of antibiotics, industrial contamination, and intensive agriculture. At the heart of the HGT-driven bacterial evolution and adaptation are highly sophisticated natural genetic engineering tools in the form of a variety of mobile genetic elements (MGEs). The main aim of this review is to give a brief account of the occurrence and diversity of MGEs in natural ecosystems and of the environmental factors that may affect MGE-mediated HGT.

Solvent tolerance acquired by Brevibacillus brevis during an olive-waste vermicomposting process

In this work, a cultivable, Gram-positive, solvent-resistant bacterium was isolated from vermicomposted olive wastes (VOW). The highest 16S rRNA sequence similarity (99%) was found in Brevibacillus brevis. The genome of the isolate, selected for trichloroethylene (TCE)-tolerance, contained a nucleotide sequence encoding a conserved protein domain (ACR_tran) ascribable to the HAE1-RND family. Members of this family are hydrophobic/amphiphilic efflux pumps largely restricted to Gram-negative bacteria. No DNA sequences of HAE1 transporters were detected in the genome of a reference B. brevis strain isolated from natural soil. Since no cultivable solvent-tolerant bacterium was detected in the unvermicomposted olive waste, a transfer of solvent-resistance genes from Gram-negative bacteria during the vermicomposting process could explain the presence of HAE1 transporters in B. brevis isolated from the vermicompost. Under TCE stress conditions, the acquired nucleotide sequence could be translated into proteins, and the tolerance to solvents is conferred to the bacterium. The isolate was designated as strain BEA1 (EF079071).

Symbiotic microorganisms: untapped resources for insect pest control

Symbiotic microorganisms offer one route to meet the anticipated heightened demand for novel insect pest management strategies created by growing human populations and global climate change. Two approaches have particular potential: the disruption of microbial symbionts required by insect pests, and manipulation of microorganisms with major impacts on insect traits contributing to their pest status (e.g. capacity to vector diseases, natural enemy resistance). Specific research priorities addressed in this article include identification of molecular targets against which highly specific antagonists can be designed or discovered, and management strategies to manipulate the incidence and properties of facultative microorganisms that influence insect pest traits. Collaboration with practitioners in pest management will ensure that the research agenda is married to agricultural and public health needs.

The use of terrestrial and aquatic microcosms and mesocosms for the ecological risk assessment of veterinary medicinal products

In this paper, we investigate the applicability of experimental model ecosystems (microcosms and mesocosms) for the ecological risk assessment of veterinary medicinal products (VMPs). VMPs are used in large quantities, but the assessment of associated risks to the environment is limited, although they are continually infused into the environment via a number of routes. It is argued that the experience obtained by pesticide research largely can be used when evaluating VMPs, although there are several major differences between pesticides and pharmaceuticals (e.g., knowledge of their mechanisms of action on nontarget organisms). Also, because microorganisms are often the target organisms of VMPs, risk assessment should focus more on endpoints describing functional processes. This paper provides a review of the current risk assessment schemes of Europe and North America along with examples of experiments already performed with veterinary medicinal products in aquatic and terrestrial ecosystem models. We suggest that some of the approaches developed for pesticide risk assessment can be used for VMPs and offer suggestions for the development of a framework for ecological risk assessment of VMPs.

Molecular evidence for the evolution of metal homeostasis genes by lateral gene transfer in bacteria from the deep terrestrial subsurface

Lateral gene transfer (LGT) plays a vital role in increasing the genetic diversity of microorganisms and promoting the spread of fitness-enhancing phenotypes throughout microbial communities. To date, LGT has been investigated in surface soils, natural waters, and biofilm communities but not in the deep terrestrial subsurface. Here we used a combination of molecular analyses to investigate the role of LGT in the evolution of metal homeostasis in lead-resistant subsurface bacteria. A nested PCR approach was employed to obtain DNA sequences encoding P(IB)-type ATPases, which are proteins that transport toxic or essential soft metals such as Zn(II), Cd(II), and Pb(II) through the cell wall. Phylogenetic incongruencies between a 16S rRNA gene tree and a tree based on 48 P(IB)-type ATPase amplicons and sequences available for complete bacterial genomes revealed an ancient transfer from a member of the beta subclass of the Proteobacteria (beta-proteobacterium) that may have predated the diversification of the genus Pseudomonas. Four additional phylogenetic incongruencies indicate that LGT has occurred among groups of beta- and gamma-proteobacteria. Two of these transfers appeared to be recent, as indicated by an unusual G+C content of the P(IB)-type ATPase amplicons. This finding provides evidence that LGT plays a distinct role in the evolution of metal homeostasis in deep subsurface bacteria, and it shows that molecular evolutionary approaches may be used for investigation of this process in microbial communities in specific environments.

Population dynamics and gene transfer in genetically modified bacteria in a model microcosm

The horizontal transfer and effects on host fitness of a neutral gene cassette inserted into three different genomic loci of a plant-colonizing pseudomonad was assessed in a model ecosystem. The KX reporter cassette (kanamycin resistance, aph, and catechol 2, 3, dioxygenase, xylE) was introduced on the disarmed transposon mini-Tn5 into: (I) the chromosome of a spontaneous rifampicin resistant mutant Pseudomonas fluorescens SBW25R; (II) the chromosome of SBW25R in the presence of a naturally occurring lysogenic-phage (phage Phi101); and (III) a naturally occurring plasmid pQBR11 (330 kbp, tra+, Hgr) introduced into SBW25R. These bacteria were applied to Stellaria media (chickweed) plants as seed dressings [c. 5 x 104 colony-forming units (cfu)/seed] and the seedlings planted in 16 microcosm chambers containing model plant and animal communities. Gene transfer to pseudomonads in the phyllosphere and rhizosphere was found only in the plasmid treatment (III). Bacteria in the phage treatment (II) initially declined in density and free phage was detected, but populations partly recovered as the plants matured. Surprisingly, bacteria in the chromosome insertion treatment (I) consistently achieved higher population densities than the unmanipulated control and other treatments. Plasmids were acquired from indigenous bacterial populations in the control and chromosome insertion treatments. Plasmid acquisition, plasmid transfer from inocula and selection for plasmid carrying inocula coincided with plant maturation.

The hidden lifestyles of Bacillus cereus and relatives

Bacillus cereus sensu lato, the species group comprising Bacillus anthracis, Bacillus thuringiensis and B. cereus (sensu stricto), has previously been scrutinized regarding interspecies genetic correlation and pathogenic characteristics. So far, little attention has been paid to analysing the biological and ecological properties of the three species in their natural environments. In this review, we describe the B. cereus sensu lato living in a world on its own; all B. cereus sensu lato can grow saprophytically under nutrient-rich conditions, which are only occasionally found in the environment, except where nutrients are actively collected. As such, members of the B. cereus group have recently been discovered as common inhabitants of the invertebrate gut. We speculate that all members disclose symbiotic relationships with appropriate invertebrate hosts and only occasionally enter a pathogenic life cycle in which the individual species infects suitable hosts and multiplies almost unrestrained.

Horizontal gene transfer in the phytosphere

Here, the ecological aspects of gene transfer processes between bacteria in the phytosphere are examined in the context of emerging evidence for the dominant role that horizontal gene transfer (HGT) has played in the evolutionary shaping of bacterial communities. Moreover, the impact of the putative capture of genetic material by bacteria from plants is discussed. Examples are provided that illustrate how mobile genetic elements (MGEs) influence the behaviour of bacteria in their natural habitat, especially in structured communities such as biofilms on plant surfaces. This community behaviour is used as a framework to pose questions on the evolutionary role and significance of gene transfer processes in plant-associated habitats. Selection within the highly structured phytosphere is likely to represent a dominant force shaping the genetic make-up of plant-associated bacterial communities. Current understanding of the triggering and impact of horizontal gene transfer, however, remains limited by our lack of understanding of the nature of the selective forces that act on bacteria in situ. The individual, colony, population and community level selection benefits imposed by the ability to use specific carbon sources or survive selective compounds are clear, but it is not always possible to assess what drives gene transfer and persistence. The role of HGT in the adaptation of host bacteria to their environmental niche is still not fully understood.

Intergeneric transfer of chromosomal and conjugative plasmid genes between Ralstonia solanacearum and Acinetobacter sp. BD413

Conjugative transfer of a broad-host range plasmid and transformation-mediated transfer of chromosomal genes were found to occur at significant frequencies between Ralstonia solanacearum and Acinetobacter sp. in planta. These intergeneric gene transfers are related to the conditions provided by the infected plant, including the extensive multiplication of these two bacteria in planta and the development of a competence state in Acinetobacter sp. Although interkingdom DNA transfer from nuclear transgenic plants to these bacteria was not detectable, plants infected by pathogens (e.g., Ralstonia solanacearum) and co-colonized by soil saprophyte bacteria (e.g., Acinetobacter sp.) can be considered as potential "hot spots" for gene transfer, even between phylogenetically remote organisms.