Analysis of single root tip microbiomes suggests that distinctive bacterial communities are selected by Pinus sylvestris roots colonized by different ectomycorrhizal fungi

Abstract

Symbiotic ectomycorrhizal tree roots represent an important niche for interaction with bacteria since the fungi colonizing them have a large surface area and receive a direct supply of photosynthetically derived carbon. We examined individual root tips of Pinus sylvestris at defined time points between 5 days and 24 weeks, identified the dominant fungi colonizing each root tip using Sanger sequencing and the bacterial communities colonizing individual root tips by 454 pyrosequencing. Bacterial colonization was extremely dynamic with statistically significant variation in time and increasing species richness until week 16 (3477 operational taxonomic units). Bacterial community structure of roots colonized by Russula sp. 6 GJ-2013b, Piloderma spp., Meliniomyces variabilis and Paxillus involutus differed significantly at weeks 8 and 16 but diversity declined and significant differences were no longer apparent at week 24. The most common genera were Burkholderia, Sphingopyxsis, Dyella, Pseudomonas, Acinetobacter, Actinospica, Aquaspirillum, Acidobacter Gp1, Sphingomonas, Terriglobus, Enhydrobacter, Herbaspirillum and Bradyrhizobium. Many genera had high initial abundance at week 8, declining with time but Dyella and Terriglobus increased in abundance at later time points. In roots colonized by Piloderma spp. several other bacterial genera, such as Actinospica, Bradyrhizobium, Acidobacter Gp1 and Rhizomicrobium appeared to increase in abundance at later sampling points.

Bacterial Communities in Boreal Forest Mushrooms Are Shaped Both by Soil Parameters and Host Identity

“…These results point to some level of habitat specificity and possibly specific functions of certain bacteria depending on the taxonomy and lifestyle of mushrooms. Indeed, a strong selection of specific bacterial communities has been observed in the ectomycorrhizosphere of truffles and other EcM fungi (Marupakula et al, 2015; Deveau et al, 2016). Similar to what has been observed in plants (Bulgarelli et al, 2013; Vandenkoornhuyse et al, 2015), variation of mushroom carbon-compounds or differential carbon allocation across different fungal groups (Boersma et al, 2009, 2010; Warmink et al, 2009) may mediate bacterial–fungus associations.…”

Bacterial microbiomes of individual ectomycorrhizal Pinus sylvestris roots are shaped by soil horizon and differentially sensitive to nitrogen addition

“…(). Other laboratory studies of bacteria associated with ectomycorrhizal roots growing in organic soil (Marupakula et al ., – 5694 OTUs) and field studies of ectomycorrhizal P . muricata roots (Nguyen and Bruns, – 1224 OTUs) or of ectomycorrhizal herb Bistorta vivipara (Vik et al ., – 4419 OTUs) have all revealed lower bacterial diversity.…”

“…Roots were cleaned meticulously using the methods described by Marupakula et al . (). A total of 323 root tips from all the treatments were harvested and stored at −20°C prior to DNA extraction.…”

“…Marupakula et al . () (see Deveau, ) overcame this problem by examining individual root tips of Pinus sylvestris in laboratory microcosms containing natural soil but sampled at defined time points and identifying the dominant fungi colonizing each root tip using Sanger sequencing, before identifying the bacterial communities colonizing individual roots using 454 pyrosequencing. These authors were able to show strongly significant effects of different ectomycorrhizal fungi on bacterial communities associated with root tips in the organic horizon, but no roots growing in the mineral soil horizons were investigated.…”

DNA accumulation on ventilation system filters in university buildings in Singapore

“…To our knowledge, genera Gp1, Gp4, Gp6 and Gp16 have not been reported in previous indoor bioaerosol studies. These genera belong to phylum Acidobacteria, which are commonly found in soil or plant roots [29–30]. These bacteria likely originate outdoors.…”