The influence of migratory Paraburkholderia on growth and competition of wood-decay fungi

Certain bacteria are capable of migrating along fungal hyphae, using them as a dispersal mechanism to cross otherwise-prohibitory distances. Three strains of fungal-migratory Paraburkholderia were isolated from the mycelium of wood-decay fungi, and inoculated onto ten strains of wood-decay fungi growing on solid agar medium. Two of the three bacteria were able to migrate along the hyphae of all fungi, although to differing extents. No bacteria-associated growth inhibition was observed with eight of the ten fungi, but mycelial extension rate of two strains of Phanerochaete was significantly reduced. Bacteria were also introduced into fungus-fungus competitive pairings, and significantly reduced the competitive performance of one of the Phanerochaete strains. Additionally, in several cases, introducing bacteria into competitive interactions made the outcome unpredictable, whereas in the absence of bacteria one fungus was consistently dominant. This is the first time that bacteria have been shown to influence fungal inter-specific competition

The Genome Sequences of Three Paraburkholderia sp. Strains Isolated from Wood-Decay Fungi Reveal Them as Novel Species with Antimicrobial Biosynthetic Potential.

Three strains of fungus-associated Burkholderiales bacteria with antagonistic activity against Gram-negative plant pathogens were genome sequenced to investigate their taxonomic placement and potential for antimicrobial specialized metabolite production. The selected strains were identified as novel taxa belonging to the genus Paraburkholderia and carry multiple biosynthetic gene clusters

Threesomes destabilise certain relationships: multispecies interactions between wood decay fungi in natural resources

Understanding interspecific interactions is key to explaining and modelling community development and associated ecosystem function. Most interactions research has focused on pairwise combinations, overlooking the complexity of multispecies communities. This study investigated three-way interactions between saprotrophic fungi in wood and across soil, and indicated that pairwise combinations are often inaccurate predictors of the outcomes of multispecies competition in wood block interactions. This inconsistency was especially true of intransitive combinations, resulting in increased species coexistence within the resource. Further, the addition of a third competitor frequently destabilised the otherwise consistent outcomes of pairwise combinations in wood blocks, which occasionally resulted in altered resource decomposition rates, depending on the relative decay abilities of the species involved. Conversely, interaction outcomes in soil microcosms were unaffected by the presence of a third combatant. Multispecies interactions promoted species diversity within natural resources, and made community dynamics less consistent than could be predicted from pairwise interaction studies

Application of bacterial genomics and culture-free microbiota diagnostics to respiratory infections

Polymicrobial infections drive the progression of chronic lung diseases and can dramatically affect clinical outcomes. Clinical laboratories routinely employ culture-based tools to diagnose lung infection. Nevertheless, culture cannot capture the full extent of bacterial diversity and is prone to misidentification. The suitability of 16S rRNA gene sequencing and ribosomal intergenic spacer analysis (RISA) was explored in context of respiratory infection diagnosis in the Public Health Wales (PHW) microbiology service. Optimised RISA and PCR protocols were used to analyse mock communities simulating respiratory bacterial pathogen assemblages. Sequence-based community abundance and diversity was distinct between each mock community, although community composition substantially deviated from expected proportions. RISA proved useful in predicting species identification. A genomic DNA extraction protocol was then validated for microbiota analysis using silica-based gDNA extraction employing bead-beating. These optimised protocols were applied to profile bronchiectasis, cystic fibrosis, and chronic obstructive pulmonary disease sputa, and the results compared to PHW routine culture-based analyses. Respiratory microbiota was highly individualised, and bacterial diversity did not statistically correlate with reduced lung function. Combining both culture-free and culture-dependent methodologies proved beneficial in the identification of potentially pathogenic microorganisms missed in culture and for resolving poor sequence identification in a minority of samples. Whole genome sequencing (WGS) was deployed for the accurate characterisation of the emerging cystic fibrosis pathogens Achromobacter spp., and was compared to conventional MALDI-TOF. WGS was instrumental in determining sources of Achromobacter insuavis acquisition and the multidrug-resistant nature of these species, suggesting the presence of previously unreported metallo-beta-lactamases. Phenotypic traits suggest that Achromobacter xylosoxidans’ competitive fitness was demonstrably similar to traditional CF Gram-negative species. These results also suggested these species interacted as an intransitive hierarchy. Overall, these DNA-based methods show promise for routinisation in the PHW however WGS is still largely a research tool in context of lung infection

The Genome Sequences of Three Paraburkholderia sp. Strains Isolated from Wood-Decay Fungi Reveal Them as Novel Species with Antimicrobial Biosynthetic Potential.

Three strains of fungus-associated Burkholderiales bacteria with antagonistic activity against Gram-negative plant pathogens were genome sequenced to investigate their taxonomic placement and potential for antimicrobial specialized metabolite production. The selected strains were identified as novel taxa belonging to the genus Paraburkholderia and carry multiple biosynthetic gene clusters

Fifty important research questions in microbial ecology.

Microbial ecology provides insights into the ecological and evolutionary dynamics of microbial communities underpinning every ecosystem on Earth. Microbial communities can now be investigated in unprecedented detail, although there is still a wealth of open questions to be tackled. Here we identify 50 research questions of fundamental importance to the science or application of microbial ecology, with the intention of summarising the field and bringing focus to new research avenues. Questions are categorised into seven themes: host-microbiome interactions; health and infectious diseases; human health and food security; microbial ecology in a changing world; environmental processes; functional diversity; and evolutionary processes. Many questions recognise that microbes provide an extraordinary array of functional diversity that can be harnessed to solve real-world problems. Our limited knowledge of spatial and temporal variation in microbial diversity and function is also reflected, as is the need to integrate micro- and macro-ecological concepts, and knowledge derived from studies with humans and other diverse organisms. Although not exhaustive, the questions presented are intended to stimulate discussion and provide focus for researchers, funders and policy makers, informing the future research agenda in microbial ecology.This work was supported by contributions from the British Ecological Society and the University of Salford towards funding the workshop. KMF was funded by the Finnish Cultural Foundation, NLMF Colciencias, MCM by Earth and Life Systems Alliance, and WJS by Arcadi