One major limitation of microbial community marker gene sequencing is that it does not provide direct information on the functional composition of sampled communities. Here, we present PICRUSt2 ( https://github.com/picrust/picrust2 ), which expands the capabilities of the original PICRUSt method ¹ to predict the functional potential of a community based on marker gene sequencing profiles. This updated method and implementation includes several improvements over the previous algorithm: an expanded database of gene families and reference genomes, a new approach now compatible with any OTU-picking or denoising algorithm, and novel phenotype predictions. Upon evaluation, PICRUSt2 was more accurate than PICRUSt1 and other current approaches overall. PICRUSt2 is also now more flexible and allows the addition of custom reference databases. We highlight these improvements and also important caveats regarding the use of predicted metagenomes, which are related to the inherent challenges of analyzing metagenome data in general.

Fungal pathogens pose a major threat to food production worldwide. Traditionally, chemical fungicides have been the primary means of controlling these pathogens, but many of these fungicides have recently come under increased scrutiny due to their negative effects on the health of humans, animals, and the environment. Furthermore, the use of chemical fungicides can result in the development of resistance in populations of phytopathogenic fungi. Therefore, new environmentally friendly alternatives that provide adequate levels of disease control are needed to replace chemical fungicides—if not completely, then at least partially. A number of alternatives to conventional chemical fungicides have been developed, including plant defence elicitors (PDEs); biological control agents (fungi, bacteria, and mycoviruses), either alone or as consortia; biochemical fungicides; natural products; RNA interference (RNAi) methods; and resistance breeding. This article reviews the conventional and alternative methods available to manage fungal pathogens, discusses their strengths and weaknesses, and identifies potential areas for future research.

A complex network of functions and symbiotic interactions between a eukaryotic host and its microbiome is a the foundation of the ecological unit holobiont. However, little is known about how the non-fungal eukaryotic microorganisms fit in this complex network of host–microbiome interactions. In this study, we employed a unique wild blueberry ecosystem to evaluate plant-associated microbiota, encompassing both eukaryotic and bacterial communities. We found that, while soil microbiome serves as a foundation for root microbiome, plant-influenced species sorting had stronger effect on eukaryotes than on bacteria. Our study identified several fungal and protist taxa, which are correlated with decreased fruit production in wild blueberry agricultural ecosystems. The specific effect of species sorting in root microbiome resulted in an increase in relative abundance of fungi adapted to plant-associated life-style, while the relative abundance of non-fungal eukaryotes was decreased along the soil-endosphere continuum in the root, probably because of low adaptation of these microorganisms to host–plant defense responses. Analysis of community correlation networks indicated that bacterial and eukaryotic interactions became more complex along the soil-endosphere continuum and, in addition to extensive mutualistic interactions, co-exclusion also played an important role in shaping wild blueberry associated microbiome. Our study identified several potential hub taxa with important roles in soil fertility and/or plant–microbe interaction, suggesting the key role of these taxa in the interconnection between soils and plant health and overall microbial community structure. This study also provides a comprehensive view of the role of non-fungal eukaryotes in soil ecosystem.

Agricultural soils are inherently disturbed systems where organic matter additions are considered to enhance microbial community structure and resilience. High-throughput sequencing of community was applied to soils receiving annual applications of an alkaline stabilized biosolid (ATB), at four increasing rates over 10 years, as an environmental stressor in contrast to a one-time application of ATB ten years prior. Bacterial community structure was more greatly influenced by annual ATB applications relative to fungi and eukaryotes. Specifically, higher relative abundances of Proteobacteria, Acidobacteria, Bacteroidetes, and Chloroflexi were measured in annual ATB rates relative to the single ATB rates and the control. High rates of annual ATB applications resulted in lower bacterial alpha-diversity, as well as fungal and eukaryotic Shannon diversity, but single ATB or lower rates of ATB applied annually showed increased alpha -diversity relative to the control. Soil microbiome responses to annual ATB and single ATB rates were also examined using co-occurrence network analysis. High rates and frequency of ATB application resulted in a decrease in network interactions, lower average number of neighbors, and reduced network density compared to control soils. A concomitant increase in network diameter and characteristic path length further suggests annual additions of ATB led to a more adapted, but less cooperative, state in the microbiome. The data suggest a more universal functional response of microbiomes to the stressors compared to community structure and local diversity. In particular, beta-analysis and network analysis were both able to resolve significant effects on soil microbiomes 10 years post-application of low rates of ATB. Community complexity and stability were increased by single low rate of ATB additions and decreased by single high rate and annual moderate rates of ATB additions. These results provide insights into the effects that ATB additions have on soil community after only one-time use and after annual additions over a decade.

We examined the differences between bacterial and eukaryotic soil communities associated with natural and managed habitats of wild blueberry, Vaccinium angustifolium. In total, 138 bacterial and 130 eukaryotic soil and rhizosphere communities across seven blueberry fields, all established at least 30 years ago and from two forest areas adjacent to some of these fields, were analyzed. We analyzed correlations between soil chemical factors and the structure of eukaryotic and bacterial communities, including differences in the microbiome between bulk and rhizosphere soils, and between rhizospheres of plants growing in natural and managed habitats. Characterization of a broad selection of fields across the province of Nova Scotia, Canada, allowed us to tentatively identify specific signatures from several distinct soil niches. Our data indicate that bacterial and eukaryotic communities differ in how they correlate with soil chemical properties. Also, while eukaryotic communities correlate stronger with soil fertility than bacterial communities, plant selection had a stronger effect on bacterial microbiomes than on eukaryote microbiomes. Additionally, we found that the composition of root-associated bacterial communities differs between managed and natural wild blueberry habitats, confirming previous reports that management can affect rhizosphere microbiomes.

Little is known about the ecology of microbial plastic degradation. In this study, we employed next generation amplicon sequencing to assess the effect of low-density polyethylene (LDPE) films on the structure of bacterial and fungal communities in four mature compost piles with age ranging between 2 and 10 years. While, bacterial Proteobacteria, Bacteroidetes, Actinobacteria and fungi Ascomycota were most abundant across all facilities, our data indicated significant differences in compost microbiomes between compost facilities, which might be related to compost chemical parameters, age of piles and characteristics of the feedstock. In addition, a substantial shift in the interaction pattern within microbial communities from bulk and plastic-associated (PA) compost was detected. For example, cooperation between Firmicutes Bacillaceae and Thermoactinomycetaceae was detected only in PA compost. However, based on the analysis of the diversity indices and the relative abundances of microbial taxa we can conclude that the presence of plastics in compost had no significant effect on the structure of microbial community.