Ecology of mycophagous collimonas bacteria in soil

Bacteria belonging to the genus Collimonas consist of soil bacteria that can grow at expense of living fungal hyphae i.e. they are mycophagous. This PhD studies deals with the ecology of mycophagous bacteria in soil using collimonads as model organisms. Collimonads were found to be widely distributed in different types of soils albeit at low densities. Highest numbers were present in fungal-rich grassland soils and lowest numbers in fungal-poor arable soils. Yet, no significant positive correlation between numbers of collimonads and fungal biomass densities was obtained when all soils were included in the analysis. Actual growth of indigenous collimonads in soils upon invasion by fungal hyphae was demonstrated using a newly, developed Collimonas-specific qPCR assay. The fungal-induced increase in numbers of collimonads was moderate and did not result in an increased turn-over of fungal biomass. In contrast to the effects on fungal-biomass turn-over, effects of presence of collimonads on soil fungal community composition were strong. This implies that collimonads can change the competitive relationships between soil fungal species. Hence, our conclusion is that a small component of the soil microbial community can have a huge impact on this community.NWO-ALW:813.04.009UBL - phd migration 201

Mycophagous growth of Collimonas bacteria in natural soils, impact on fungal biomass turnover and interactions with mycophagous Trichoderma fungi

Bacteria of the genus Collimonas are widely distributed in soils, although at low densities. In the laboratory, they were shown to be mycophagous, that is, they are able to grow at the expense of living hyphae. However, so far the importance of mycophagy for growth and survival of collimonads in natural soil habitats is unknown. Using a Collimonas-specific real-time PCR assay, we show here that the invasion of field soils by fungal hyphae (Absidia sp.) resulted in a short-term, significant increase (average fourfold) of indigenous collimonads. No such responses were observed for other soil bacteria studied (Pseudomonas, Burkholderia, PCR-denaturing gradient gel electrophoresis patterns of total bacteria and Burkholderia). Hence, it appears that the stimulation of growth of Collimonas bacteria by fungal hyphae is not common among other soil bacteria. In the same field soils, Trichoderma, a fungal genus known for mycophagous (mycoparasitic) growth, increased upon introduction of Absidia hyphae. Hence, mycophagous growth by Collimonas and Trichoderma can occur in the same soils. However, in controlled experiments (sand microcosms), collimonads appeared to have a negative effect on mycophagous growth of a Trichoderma strain. The effect of mycophagous growth of collimonads on fungal biomass dynamics was studied in sand microcosms using the same Absidia sp. as a test fungus. The growth of collimonads did not cause a significant reduction in the Absidia biomass. Overall, the study indicates that mycophagous nutrition may be important for collimonads in natural soils, but the impact on fungal biomass turnover is likely to be minor.

Impact of Collimonas bacteria on community composition of soil fungi

The genus Collimonas consists of soil bacteria that have the potential to grow at the expense of living fungal hyphae. However, the consequences of this mycophagous ability for soil fungi are unknown. Here we report on the development of fungal communities after introduction of collimonads in a soil that had a low abundance of indigenous collimonads. Development of fungal communities was stimulated by addition of cellulose or by introducing plants (Plantago lanceolata). Community composition of total fungi in soil and rhizosphere and of arbuscular mycorrhizal fungi in roots was examined by PCR-DGGE. The introduction of collimonads altered the composition of all fungal communities studied but had no effects on fungal biomass increase, cellulose degrading activity or plant performance. The most likely explanation for these results is that differences in sensitivity of fungal species to the presence of collimonads result in competitive replacement of species. The lab and greenhouse experiments were complemented with a field experiment. Mesh bags containing sterile sand with or without collimonads were buried in an ex-arable field and a forest. The presence of collimonads had an effect on the composition of fungi invading these bags in the ex-arable site but not in the forest site.

Collimonas arenae sp. nov. and Collimonas pratensis sp. nov., isolated from (semi-) natural grassland soils

A polyphasic taxonomic study was performed to compare 26 novel bacterial isolates obtained from (semi-)natural grassland soils and a heathland soil in the Netherlands with 16 strains that had previously been assigned to the genus Collimonas. Genomic fingerprinting (BOX-PCR), whole-cell protein electrophoresis, matrix-assisted laser desorption ionization time-of-flight mass spectrometry of intact cells and physiological characterization (Biolog) of the isolates confirmed the existence of different strain clusters (A–D) within the genus Collimonas. Until now, only cluster C strains have been formally classified, as Collimonas fungivorans. In this study, DNA–DNA hybridizations were performed with a selection of strains representing the four clusters. The results showed that cluster B strains also belong to C. fungivorans and that strains of clusters A and D represent two novel species within the genus Collimonas. The latter novel species could be differentiated by means of phenotypic and genotypic characteristics and are classified as Collimonas arenae sp. nov. (cluster A; type strain Ter10T =LMG 23964T =CCUG 54727T) and Collimonas pratensis sp. nov. (cluster D; type strain Ter91T =LMG 23965T =CCUG 54728T).

Identification et suivi des bactéries et gènes impliqués dans l’altération des minéraux et la fertilité des sols forestiers

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