No abstract

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 method1 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.

Soil bacteria collectively known as rhizobia are able to convert atmospheric dinitrogen to ammonia while participating in a symbiotic association with legume plants. This capability has made the bacteria an attractive research subject at many levels of investigation, especially since physiological and metabolic specialization are central to this ecological niche. Dicarboxylate transport plays an important role in the operation of an effective, nitrogen-fixing symbiosis and considerable evidence suggests that dicarboxylates are a major energy and carbon source for the nitrogen-fixing rhizobia. The dicarboxylate transport (Dct) system responsible for importing these compounds generally consists of a dicarboxylate carrier protein, DctA, and a two component kinase regulatory system, DctB/DctD. DctA and DctB/D differ in the substrates that they recognize and a model for substrate recognition by DctA and DctB is discussed. In some rhizobia, DctA expression can be induced during symbiosis in the absence of DctB/DctD by an alternative, uncharacterized, mechanism. The DctA protein belongs to a subgroup of the glutamate transporter family now thought to have an unusual structure that combines aspects of permeases and ion channels. While the structure of C(4)-dicarboxylate transporters has not been analyzed in detail, mutagenesis of S. meliloti DctA has produced results consistent with the alignment of the rhizobial protein with the more characterized bacterial and eukaryotic glutamate transporters in this family.

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.

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.