Biomedical subjects

George A Kowalchuk

Publications and source records attributed to George A Kowalchuk.

8 recordsLinked to original sources

PubMed2006

Size and structure of bacterial, fungal and nematode communities along an Antarctic environmental gradient.

The unusually harsh environmental conditions of terrestrial Antarctic habitats result in ecosystems with simplified trophic structures, where microbial processes are especially dominant as drivers of soil-borne nutrient cycling. We examined soil-borne Antarctic communities (bacteria, fungi and nematodes) at five locations along a southern latitudinal gradient from the Falkland Islands (51 degrees S) to the base of the Antarctic Peninsula (72 degrees S), and compared principally vegetated vs. fell-field locations at three of these sites. Results of molecular (denaturing gradient gel electrophoresis, real-time PCR), biochemical (ergosterol, phospholipid fatty acids) and traditional microbiological (temperature- and medium-related CFU) analyses were related to key soil and environmental properties. Microbial abundance generally showed a significant positive relationship with vegetation and vegetation-associated soil factors (e.g. water content, organic C, total N). Microbial community structure was mainly related to latitude or location and latitude-dependent factors (e.g. mean temperature, NO3, pH). Furthermore, strong interactions between vegetation cover and location were observed, with the effects of vegetation cover being most pronounced in more extreme sites. These results provide insight into the main drivers of microbial community size and structure across a range of terrestrial Antarctic and sub-Antarctic habitats, potentially serving as a useful baseline to study the impact of predicted global warming on these unique and pristine ecosystems.

Animals↗

PubMed2006

Interplay between Senecio jacobaea and plant, soil, and aboveground insect community composition.

To elucidate the factors that affect the performance of plants in their natural environment, it is essential to study interactions with other neighboring plants, as well as with above- and belowground higher trophic organisms. We used a long-term field experiment to study how local plant community diversity influenced colonization by the biennial composite Senecio jacobaea in its native range in The Netherlands in Europe. We tested the effect of sowing later-succession plant species (0, 4, or 15 species) on plant succession and S. jacobaea performance. Over a period of eight years, the percent cover of S. jacobaea was relatively low in communities sown with 15 or 4 later-succession plant species compared to plots that were not sown, but that were colonized naturally. However, after four years of high abundance, the density of S. jacobaea in unsown plots started to decline, and the size of the individual plants was smaller than in the plots sown with 15 or 4 plant species. In the unsown plots, densities of aboveground leaf-mining, flower-feeding, and stem-boring insects on S. jacobaea plants were lower than on plants in sown plots, and there was a strong positive relationship between plant size and levels of herbivory. In a greenhouse experiment, we grew S. jacobaea in sterilized soil inoculated with soil from the different sowing treatments of the field experiment. Biomass production was lower when S. jacobaea test plants were grown in soil from the unsown plots than in soil from the sown plots (4 or 15 species). Molecular analysis of the fungal and bacterial communities revealed that the composition of fungal communities in unsown plots differed significantly from those in sown plots, suggesting that soil fungi could have been involved in the relative growth reduction of S. jacobaea in the greenhouse bioassay. Our results show that, in its native habitat, the abundance of S. jacobaea depends on the initial composition of the plant community and that, on a scale of almost a decade, its interactions with plant and soil communities and aboveground invertebrates may influence the dynamics of this colonizing species.

Animals↗

PubMed2005

Morphological, ontogenetic and molecular characterization of Scutellospora reticulata (Glomeromycota).

The arbuscular mycorrhizal (AM) fungus Scutellospora reticulata (CNPAB11) was characterized using morphological, ontogenetic and molecular approaches. Spore ontogenesis was studied using Ri T-DNA transformed carrot roots and observations were compared with those published for eight other, pot-cultured, Scutellospora species. The sporogenesis of S. reticulata exhibited an unreported pattern of outer spore wall differentiation. In addition, Denaturing Gradient Gel Electrophoresis (DGGE), targeting the V9 region of the SSU nrDNA, was used to differentiate S. reticulata from 16 other Scutellospora species and results were confirmed by sequencing analysis. Phylogenetic analyses, using nearly full length SSU nrDNA sequences, grouped S. reticulata in a cluster together with S. cerradensis and S. heterogama, species that share similar spore wall organization and also possess ornamented external walls. PCR-DGGE and sequence analysis revealed intragenomic SSU nrDNA polymorphisms in four out of six Scutellospora species tested, and demonstrated that SSU nrDNA intragenomic polymorphism could be used as a marker to differentiate several closely related Scutellospora species.

DNA, Fungal↗

PubMed2004

Collimonas fungivorans gen. nov., sp. nov., a chitinolytic soil bacterium with the ability to grow on living fungal hyphae.

A polyphasic approach was used to describe the phylogenetic position of 22 chitinolytic bacterial isolates that were able to grow at the expense of intact, living hyphae of several soil fungi. These isolates, which were found in slightly acidic dune soils in the Netherlands, were strictly aerobic, Gram-negative rods. Cells grown in liquid cultures were flagellated and possessed pili. A wide range of sugars, alcohols, organic acids and amino acids could be metabolized, whereas several di- and trisaccharides could not be used as substrates. The major cellular fatty acids were C(16 : 0), C(16 : 1)omega7c and C(18 : 1)omega7c. DNA G+C contents were 57-62 mol%. Analysis of nearly full-length 16S rDNA sequences showed that the isolates were related closely to each other (>98.6 % sequence similarity) and could be assigned to the beta-Proteobacteria, family 'Oxalobacteraceae', order 'Burkholderiales'. The most closely related species belonged to the genera Herbaspirillum and Janthinobacterium, exhibiting 95.9-96.7 % (Herbaspirillum species) and 94.3-95.6 % (Janthinobacterium species) 16S rDNA sequence similarity to the isolates. Several physiological and biochemical properties indicated that the isolates could be distinguished clearly from both of these genera. Therefore, it is proposed that the isolates described in this study are representatives of a novel genus, Collimonas gen. nov. Genomic fingerprinting (BOX-PCR), detailed analysis of 16S rDNA patterns and physiological characterization (Biolog) of the isolates revealed the existence of four subclusters. The name Collimonas fungivorans gen. nov., sp. nov. has been given to one subcluster (four isolates) that appears to be in the centre of the novel genus; isolates in the other subclusters have been tentatively named Collimonas sp. The type strain of Collimonas fungivorans gen. nov., sp. nov. is Ter6(T) (=NCCB 100033(T)=LMG 21973(T)).

Base Composition↗

PubMed2004

PCR-denaturing gradient gel electrophoresis profiling of inter- and intraspecies 18S rRNA gene sequence heterogeneity is an accurate and sensitive method to assess species diversity of arbuscular mycorrhizal fungi of the genus Gigaspora.

Despite the importance of arbuscular mycorrhizal fungi in the majority of terrestrial ecosystems, their ecology, genetics, and evolution are poorly understood, partly due to difficulties associated with detecting and identifying species. We explored the inter- and intraspecies variations of the 18S rRNA genes of the genus Gigaspora to assess the use of this marker for the discrimination of Gigaspora isolates and of Gigasporaceae populations from environmental samples. Screening of 48 Gigaspora isolates by PCR-denaturing gradient gel electrophoresis (DGGE) revealed that the V3-V4 region of the 18S rRNA gene contained insufficient variation to discriminate between different Gigaspora species. In contrast, the patterns of 18S ribosomal DNA (rDNA) heterogeneity within the V9 region of this marker could be used for reliable identification of all recognized species within this genus. PCR-DGGE patterns provided insight into some putative misidentifications and could be used to differentiate geographic isolates of G. albida, G. gigantea, and G. margarita but not G. rosea. Two major clusters were apparent based upon PCR-DGGE ribotype patterns, one containing G. albida, G. candida, G. ramisporophora, and G. rosea and the other containing G. decipiens and G. margarita. Dissection of the DGGE patterns by cloning, DGGE screening, and sequencing confirmed these groupings and revealed that some ribotypes were shared across species boundaries. Of the 48 isolates examined, only two displayed any spore-to-spore variation, and these exceptions may be indicative of coisolation of more than one species or subspecies within these cultures. Two Brazilian agricultural soils were also analyzed with a Gigasporaceae-specific nested PCR approach, revealing a dominance of G. margarita within this family.

Base Sequence↗

PubMed2003

Microbial community composition affects soil fungistasis.

Most soils inhibit fungal germination and growth to a certain extent, a phenomenon known as soil fungistasis. Previous observations have implicated microorganisms as the causal agents of fungistasis, with their action mediated either by available carbon limitation (nutrient deprivation hypothesis) or production of antifungal compounds (antibiosis hypothesis). To obtain evidence for either of these hypotheses, we measured soil respiration and microbial numbers (as indicators of nutrient stress) and bacterial community composition (as an indicator of potential differences in the composition of antifungal components) during the development of fungistasis. This was done for two fungistatic dune soils in which fungistasis was initially fully or partly relieved by partial sterilization treatment or nutrient addition. Fungistasis development was measured as restriction of the ability of the fungi Chaetomium globosum, Fusarium culmorum, Fusarium oxysporum, and Trichoderma harzianum to colonize soils. Fungistasis did not always reappear after soil treatments despite intense competition for carbon, suggesting that microbial community composition is important in the development of fungistasis. Both microbial community analysis and in vitro antagonism tests indicated that the presence of pseudomonads might be essential for the development of fungistasis. Overall, the results lend support to the antibiosis hypothesis.

Antibiosis↗

PubMed2002

Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms.

A coupling of above-ground plant diversity and below-ground microbial diversity has been implied in studies dedicated to assessing the role of macrophyte diversity on the stability, resilience, and functioning of ecosystems. Indeed, above-ground plant communities have long been assumed to drive below-ground microbial diversity, but to date very little is known as to how plant species composition and diversity influence the community composition of micro-organisms in the soil. We examined this relationship in fields subjected to different above-ground biodiversity treatments and in field experiments designed to examine the influence of plant species on soil-borne microbial communities. Culture-independent strategies were applied to examine the role of wild or native plant species composition on bacterial diversity and community structure in bulk soil and in the rhizosphere. In comparing the influence of Cynoglossum officinale (hound's tongue) and Cirsium vulgare (spear thistle) on soil-borne bacterial communities, detectable differences in microbial community structure were confined to the rhizosphere. The colonisation of the rhizosphere of both plants was highly reproducible, and maintained throughout the growing season. In a separate experiment, effects of plant diversity on bacterial community profiles were also only observed for the rhizosphere. Rhizosphere soil from experimental plots with lower macrophyte diversity showed lower diversity, and bacterial diversity was generally lower in the rhizosphere than in bulk soil. These results demonstrate that the level of coupling between above-ground macrophyte communities and below-ground microbial communities is related to the tightness of the interactions involved. Although plant species composition and community structure appear to have little discernible effect on microbial communities inhabiting bulk soil, clear and reproducible changes in microbial community structure and diversity are observed in the rhizosphere.

Bacteria↗

PubMed2002

Community analysis of arbuscular mycorrhizal fungi associated with Ammophila arenaria in Dutch coastal sand dunes.

A polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) approach for the detection and characterization of arbuscular mycorrhizal fungi (AMF) 18S ribosomal DNA (rDNA) was developed and applied to the study of AMF communities associated with the main sand-stabilizing plant species of the Dutch sand dunes, marram grass (Ammophila arenaria, L.). DNA was extracted directly from plant roots, soil or isolated AMF spores, and prominent bands resulting from AMF-specific DGGE profiles were excised for sequence analysis. This strategy provided a robust means of detecting and identifying AMF-like species without the use of trap plant cultivation methods. A number of Glomus-like and Scutellospora-like sequences was detected, including a putatively novel Glomus species, and differences were observed in the dominant AMF-like populations detected in healthy vs. degenerating stands of A. arenaria and in bulk sand dune soil. It has previously been suggested that plant pathogens, such as fungi and nematodes, may contribute to the decline of A. arenaria. Although no causal relationship can be drawn between the observed differences in the dominantly detected AMF-like populations and the vitality of plant growth, these results indicate that mutualistic interactions between this plant and AMF should not be overlooked when examining the role of soil-borne microorganisms in vegetation dynamics. In addition, there were discrepancies observed between the AMF-like groups detected in spore populations vs. direct 18S rDNA analysis of root material, corroborating previous suggestions that spore inspection alone may poorly represent actual AMF population structure.

DNA, Fungal↗