| microbial population dynamics associated with crude-oil biodegradation in diverse soils. | soil bacterial population dynamics were examined in several crude-oil-contaminated soils to identify those organisms associated with alkane degradation and to assess patterns in microbial response across disparate soils. seven soil types obtained from six geographically distinct areas of the united states (arizona, oregon, indiana, virginia, oklahoma, and montana) were used in controlled contamination experiments containing 2% (wt/wt) crude oil spiked with [1-(14)c]hexadecane. microbial populati ... | 2006 | 16957258 |
| pattern of elemental release during the granite dissolution can be changed by aerobic heterotrophic bacterial strains isolated from damma glacier (central alps) deglaciated granite sand. | colonisation and weathering of freshly deglaciated granite are key processes in initial soil formation and development. we have obtained 438 isolates from granite sand covering glacial toe, 284 isolates at 22°c and 154 at 4°c incubation temperatures, respectively, to obtain cultures for the investigation of their weathering capabilities under laboratory conditions. the isolation of bacteria from granite sand was performed on rich-, intermediate- and low-nutrient-content solid media. isolates wer ... | 2011 | 22105516 |
| dual transcriptional profiling of a bacterial/fungal confrontation: collimonas fungivorans versus aspergillus niger. | interactions between bacteria and fungi cover a wide range of incentives, mechanisms and outcomes. the genus collimonas consists of soil bacteria that are known for their antifungal activity and ability to grow at the expense of living fungi. in non-contact confrontation assays with the fungus aspergillus niger, collimonas fungivorans showed accumulation of biomass concomitant with inhibition of hyphal spread. through microarray analysis of bacterial and fungal mrna from the confrontation arena, ... | 2011 | 21614084 |
| glaciimonas immobilis gen. nov., sp. nov., a novel member of the family oxalobacteraceae isolated from alpine glacier cryoconite. | strains cr9-30(t) and cr9-12 were isolated from alpine glacier cryoconite. both strains were gram-negative, non-motile, rod-shaped and psychrophilic, showing good growth over a temperature range of 1-20°c. phylogenetic analysis of 16s rrna gene sequences revealed that the two strains formed a distinct branch within the family oxalobacteraceae and were most closely related to the members of the genus collimonas. the level of 16s rrna gene sequnce similarity between strains cr9-30(t) and cr9-12 wa ... | 2010 | 20935085 |
| violacein-producing collimonas sp. from the sea surface microlayer of costal waters in trøndelag, norway. | a new strain belonging to the genus collimonas was isolated from the sea surface microlayer off the coast of trøndelag, norway. the bacterium, designated collimonas ct, produced an antibacterial compound active against micrococcus luteus. subsequent studies using lc-ms identified this antibacterial compound as violacein, known to be produced by several marine-derived bacteria. fragments of the violacein biosynthesis genes vioa and viob were amplified by pcr from the collimonas ct genome and sequ ... | 2009 | 20098599 |
| the bacterial genus collimonas: mycophagy, weathering and other adaptive solutions to life in oligotrophic soil environments. | this minireview provides a synopsis of past and present research on the biology and ecology of members of the bacterial genus collimonas. from the distribution, abundance and functional behaviours of these so-called collimonads emerges a general picture of bacterial adaptation to low-nutrient soil environments. among these adaptations is the ability to extract nutrients from living fungi (mycophagy) and from rocks and minerals (weathering). this unique combination of properties will be discussed ... | 2010 | 19638176 |
| bacterial effects on arbuscular mycorrhizal fungi and mycorrhiza development as influenced by the bacteria, fungi, and host plant. | bacterial strains from mycorrhizal roots (three belonging to comamonadaceae and one to oxalobacteraceae) and from non-mycorrhizal roots (two belonging to comamonadaceae) of medicago truncatula and two reference strains (collimonas fungivorans ter331 and pseudomonas fluorescens c7r12) were tested for their effect on the in vitro saprophytic growth of glomus mosseae beg12 and on its colonization of m. truncatula roots. only the oxalobacteraceae strain, isolated from barrel medic mycorrhizal roots, ... | 2009 | 18941805 |
| 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 incre ... | 2009 | 18923455 |
| identification and characterization of genes underlying chitinolysis in collimonas fungivorans ter331. | through a combinatorial approach of plasposon mutagenesis, genome mining, and heterologous expression, we identified genes contributing to the chitinolytic phenotype of bacterium collimonas fungivorans ter331. one of five mutants with abolished ability to hydrolyze colloidal chitin carried its plasposon in the chii gene coding for an extracellular endochitinase. two mutants were affected in the promoter of chip-ii coding for an outer-membrane transporter of chitooligosaccharides. the remaining t ... | 2008 | 18671744 |
| comparative genomics of the pipo2/psb102 family of environmental plasmids: sequence, evolution, and ecology of pter331 isolated from collimonas fungivorans ter331. | plasmid pter331 from the bacterium collimonas fungivorans ter331 is a new member of the pipo2/psb102 family of environmental plasmids. the 40 457-bp sequence of pter331 codes for 44 putative orfs, most of which represent genes involved in replication, partitioning and transfer of the plasmid. we confirmed that pter331 is stably maintained in its native host. deletion analysis identified a mini-replicon capable of replicating autonomously in escherichia coli and pseudomonas putida. furthermore, p ... | 2008 | 18355297 |
| 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 differen ... | 2008 | 18218941 |
| collimonas fungivorans, an unpredicted in vitro but efficient in vivo biocontrol agent for the suppression of tomato foot and root rot. | although bacteria from the genus collimonas have demonstrated in vitro antifungal activity against many different fungi, they appeared inactive against the plant-pathogenic fungus fusarium oxysporum f.sp. radicis-lycopersici (forl), the causal agent of tomato foot and root rot (tfrr). visualization studies using fluorescently labelled organisms showed that bacterial cells attached extensively to the fungal hyphae under nutrient-poor conditions but not in glucose-rich armstrong medium. collimonas ... | 2007 | 17504497 |
| specific detection and real-time pcr quantification of potentially mycophagous bacteria belonging to the genus collimonas in different soil ecosystems. | the bacterial genus collimonas has the remarkable characteristic that it grows at the expense of living fungal hyphae under laboratory conditions. here, we report the first field inventory of the occurrence and abundance of collimonas in soils (n = 45) with naturally different fungal densities, which was performed in order to test the null hypothesis that there is a relationship between the presence of collimonas and fungal biomass. estimates of fungal densities were based on ergosterol measurem ... | 2007 | 17483278 |
| effect of the mycorrhizosphere on the genotypic and metabolic diversity of the bacterial communities involved in mineral weathering in a forest soil. | to date, several bacterial species have been described as mineral-weathering agents which improve plant nutrition and growth. however, the possible relationships between mineral-weathering potential, taxonomic identity, and metabolic ability have not been investigated thus far. in this study, we characterized a collection of 61 bacterial strains isolated from scleroderma citrinum mycorrhizae, the mycorrhizosphere, and the adjacent bulk soil in an oak forest. the ability of bacteria to weather bi ... | 2007 | 17351101 |
| characterization of psychrotolerant heterotrophic bacteria from finnish lapland. | a total of 331 aerobic heterotrophic bacterial strains were isolated from various ecosystems of finnish lapland (68-69 degrees n) including forest soil, arctic alpine-tundra soil, stream water, lake and mire sediments, lichen and snow algae. whole cell fatty acid and 16s rrna gene sequence analysis and microscopy indicated that the isolates were dominated by gram-negative bacteria, while only 20 gram-positive strains were isolated. based on 16s rrna gene sequences the isolates were members of al ... | 2006 | 16564959 |
| genomic flank-sequencing of plasposon insertion sites for rapid identification of functional genes. | plasposons are modified mini-tn5 transposons for random mutagenesis of gram-negative bacteria. their unique design allows for the rescue cloning and sequencing of dna that flanks insertion sites in plasposon mutants. however, this process can be laborious and time-consuming, as it involves genomic dna isolation, restriction endonuclease treatment, subsequent religation, transformation of religated dna into an escherichia coli host, and re-isolation as a plasmid, which is then used as a template ... | 2006 | 16457898 |
| a soil-based microbial biofilm exposed to 2,4-d: bacterial community development and establishment of conjugative plasmid pjp4. | a soil suspension was used as a source to initiate the development of microbial communities in flow cells irrigated with 2,4-dichlorophenoxyacetic acid (2,4-d) (25 microg ml(-1)). culturable bacterial members of the community were identified by 16s rrna gene sequencing and found to be members of the genera pseudomonas, burkholderia, collimonas and rhodococcus. a 2,4-d degrading donor strain, pseudomonas putida sm1443 (pjp4::gfp), was inoculated into flow cell chambers containing 2-day old biofil ... | 2005 | 16332330 |
| phylogeny-function analysis of (meta)genomic libraries: screening for expression of ribosomal rna genes by large-insert library fluorescent in situ hybridization (lil-fish). | we assessed the utility of fluorescent in situ hybridization (fish) in the screening of clone libraries of (meta)genomic or environmental dna for the presence and expression of bacterial ribosomal rna (rrna) genes. to establish proof-of-principle, we constructed a fosmid-based library in escherichia coli of large-sized genomic dna fragments of the mycophagous soil bacterium collimonas fungivorans, and hybridized 768 library clones with the collimonas-specific fluorescent probe cte998-1015. criti ... | 2004 | 15305924 |
| 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 tri ... | 2004 | 15143036 |
| 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 ... | 2009 | 19260938 |