The interplay between host plants and priority effects in community assembly processes of arbuscular mycorrhizal fungi

Plants and arbuscular mycorrhizal fungi (AMF) form a symbiosis for mutualistic benefits. AMF rely on host plants as carbon sources, whereas the plants benefit from the development of an extensive hyphal network in the soil that delivers water and nutrients to the plant roots. The assembly of species into a community is governed by several biotic and abiotic factors and predicting the outcomes of community assembly is regarded as the holy grail of community ecology. The relative importance of the mechanisms underlying the assembly of AMF communities in plant roots is still a matter of discussion, with impacts by the host plant itself, effects exerted by the plant neighbourhood, soil conditions and dispersal processes as candidates for highly relevant determinants of the AMF assembly. To elucidate the interplay between some of these influences on the fungal assembly, and to reveal their relative importance as determinants of assembly mechanisms, I determined the generalism and specialism in the interaction of separately grown pasture plants with AMF by characterising several numeric and phylogenetic interaction properties. I also examined the plant-AMF interaction of these plants grown in a plant community, in which I experimentally manipulated their order of arrival. My objectives were: 1) to examine if and how pasture plants differ in their inherent interaction strategies with AMF; 2) to assess if the plants’ interaction strategies with AMF influence the carbon allocation to the microbial community (AMF and bacteria) as measured by their differences in biomass and community composition, and if, due to priority effects, these differences had consequences for the further development of the rhizosphere community; 3) to examine the relative effects of plant neighbours and the order of arrival on the plant-AMF interaction of plants differing in their interaction niche strategies; and 4) to evaluate the interplay between inherent interaction niche strategy, neighbour plants, and priority of arrival on the bipartite plant-AMF interaction network structure. By quantifying the plants’ niche width in their interaction with AMF and their specificity for AMF species, I revealed that the pasture plant species were characterised by distinct inherent interaction strategies, suggesting partitioning of the plant-AMF interaction traits among the members of a plant community. When these plants were grown in a plant community, they still tended to employ their inherent interaction strategy, with some exceptions. In contrast, all studied plant species showed significant changes in their AMF abundances due to the influence of neighbouring plants in comparison to their single growth. I found that while the relative impact of the neighbourhood on a plant’s AMF community assembly changed with the order of arrival of the host plant in the plant community, the direction and strength of that change was affected by the plants’ inherent interaction strategy. My results suggest that the inherent interaction strategy of an early arriving focal plant can be a determinant of the AMF assembly of the late arrivals. However, the impact of the focal plant pertained entirely to changes in AMF α- and β-diversities, whereas the topology (i.e., nestedness and modularity) of the bipartite plant-AMF interaction network remained unresponsive to these changes. My findings suggest that the combination of order of arrival and interaction strategies of the plants are relevant determinants of the AMF community assembly of the plant-AMF interaction with possible consequences for the succession of the system as well as for its stability and productivity. However, that the topology of the bipartite interaction network, which is seen as an indicator of its stability and persistence, remained mostly unchanged suggests a high robustness of the plant community against changes in the diversity of its AMF mutualists. This network consistency might, in turn, offer robustness against perturbation of the system.</p

Phospholipid fatty acid (PLFA) analysis as a tool to estimate absolute abundances from compositional 16S rRNA bacterial metabarcoding data

Microbial biodiversity monitoring through the analysis of DNA extracted from environmental samples is increasingly popular because it is perceived as being rapid, cost-effective, and flexible concerning the sample types studied. DNA can be extracted from diverse media before high-throughput sequencing of the prokaryotic 16S rRNA gene is used to characterize the taxonomic diversity and composition of the sample (known as metabarcoding). While sources of bias in metabarcoding methodologies are widely acknowledged, previous studies have focused mainly on the effects of these biases within a single substrate type, and relatively little is known of how these vary across substrates. We investigated the effect of substrate type (water, microbial mats, lake sediments, stream sediments, soil and a mock microbial community) on the relative performance of DNA metabarcoding in parallel with phospholipid fatty acid (PLFA) analysis. Quantitative estimates of the biomass of different taxonomic groups in samples were made through the analysis of PLFAs, and these were compared to the relative abundances of microbial taxa estimated from metabarcoding. Furthermore, we used the PLFA-based quantitative estimates of the biomass to adjust relative abundances of microbial groups determined by metabarcoding to provide insight into how the biomass of microbial taxa from PLFA analysis can improve understanding of microbial communities from environmental DNA samples. We used two sets of PLFA biomarkers that differed in their number of PLFAs to evaluate how PLFA biomarker selection influences biomass estimates. Metabarcoding and PLFA analysis provided significantly different views of bacterial composition, and these differences varied among substrates. We observed the most notable differences for the Gram-negative bacteria, which were overrepresented by metabarcoding in comparison to PLFA analysis. In contrast, the relative biomass and relative sequence abundances aligned reasonably well for Cyanobacteria across the tested freshwater substrates. Adjusting relative abundances of microbial taxa estimated by metabarcoding with PLFA-based quantification estimates of the microbial biomass led to significant changes in the microbial community compositions in all substrates. We recommend including independent estimates of the biomass of microbial groups to increase comparability among metabarcoding libraries from environmental samples, especially when comparing communities associated with different substrates.publishe