Defining and quantifying the core microbiome: Challenges and prospects

The term “core microbiome” has become widely used in microbial ecology over the last decade. Broadly, the core microbiome refers to any set of microbial taxa, or the genomic and functional attributes associated with those taxa, that are characteristic of a host or environment of interest. Most commonly, core microbiomes are measured as the microbial taxa shared among two or more samples from a particular host or environment. Despite the popularity of this term and its growing use, there is little consensus about how a core microbiome should be quantified in practice. Here, we present a brief history of the core microbiome concept and use a representative sample of the literature to review the different metrics commonly used for quantifying the core. Empirical analyses have used a wide range of metrics for quantifying the core microbiome, including arbitrary occurrence and abundance cutoff values, with the focal taxonomic level of the core ranging from phyla to amplicon sequence variants. However, many of these metrics are susceptible to sampling and other biases. Developing a standardized set of metrics for quantifying the core that accounts for such biases is necessary for testing specific hypotheses about the functional and ecological roles of core microbiomes.

Genomic Comparisons of Two Armillaria Species with Different Ecological Behaviors and Their Associated Soil Microbial Communities

Armillaria species show considerable variation in ecological roles and virulence, from mycorrhizae and saprophytes to important root pathogens of trees and horticultural crops. We studied two Armillaria species that can be found in coniferous forests of northwestern USA and southwestern Canada. Armillaria altimontana is considered as a weak, opportunistic pathogen of coniferous trees, but it also appears to exhibit in situ biological control against A. solidipes, formerly North American A. ostoyae, which is considered a virulent pathogen of coniferous trees. Here, we describe their genome assemblies and present a functional annotation of the predicted genes and proteins for the two Armillaria species that exhibit contrasting ecological roles. In addition, the soil microbial communities were examined in association with the two Armillaria species within a 45-year-old plantation of western white pine (Pinus monticola) in northern Idaho, USA, where A. altimontana was associated with improved tree growth and survival, while A. solidipes was associated with reduced growth and survival.

Community assessment of crustose calcifying red algae as coral recruitment substrates

Successful recruitment of invertebrate larvae to reef substrates is essential to the health of tropical coral reef ecosystems and their capacity to recover from disturbances. Crustose calcifying red algae (CCRA) have been identified as important recruitment substrates for scleractinian corals. As such, CCRA as a whole or subgroups (e.g., crustose coralline algae, CCA) are often used at the functional group level in experimental, ecological, and monitoring studies. Species of CCRA, however, differ in their ecological roles and their value as coral recruitment substrates. Here, we (1) investigate the species richness and community composition of CCRA on experimental coral recruitment tiles, and (2) assess if there is a recruitment preference of the coral Acropora surculosa for any of these CCRA species. 27 species of two orders of CCRA (Corallinales and Peyssonneliales) were identified from the recruit tiles. None of the DNA sequences of these species matched released sequences in GenBank or sequences of CCRA collected from natural reef systems in Guam. The similarity in CCRA communities between the recruitment tiles was high. Two species of CCRA were significantly preferred as recruitment substrates over the other CCRA species. Both of these species belonged to the subfamily of the Lithophylloideae. These two species are closely related to Pacific species that have been referred to as Titanoderma -but probably have to be assigned to another genus- and many of the latter have been attributed to be preferred coral recruitment substrates. Of all CCRA, Lithophylloideae sp. 1 had the highest benthic cover on the recruitment tiles and was the most preferred recruitment substrate. These findings highlight the high taxonomic diversity of CCRA communities and provide insight into species-specific ecological roles of CCRA that are often overlooked.

Discovery of the Pseudomonas Polyyne Protegencin by a Phylogeny-Guided Study of Polyyne Biosynthetic Gene Cluster Diversity

Natural products bearing alkyne (triple carbon bond) or polyyne (multiple alternating single and triple carbon bonds) moieties exhibit a broad range of important biological activities. Polyyne metabolites have been implicated in important ecological roles such as cepacin mediating biological control of plant pathogens and caryoynencin protecting Lagriinae beetle eggs against pathogenic fungi.

Microbial Rhodopsins: The Last Two Decades

Microbial rhodopsins are diverse photoreceptive proteins containing a retinal chromophore and are found in all domains of cellular life and are even encoded in genomes of viruses. These rhodopsins make up two families: type 1 rhodopsins and the recently discovered heliorhodopsins. These families have seven transmembrane helices with similar structures but opposing membrane orientation. Microbial rhodopsins participate in a portfolio of light-driven energy and sensory transduction processes. In this review we present data collected over the last two decades about these rhodopsins and describe their diversity, functions, and biological and ecological roles. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Anabaenopeptins: What We Know So Far

Cyanobacteria are microorganisms with photosynthetic mechanisms capable of colonizing several distinct environments worldwide. They can produce a vast spectrum of bioactive compounds with different properties, resulting in an improved adaptative capacity. Their richness in secondary metabolites is related to their unique and diverse metabolic apparatus, such as Non-Ribosomal Peptide Synthetases (NRPSs). One important class of peptides produced by the non-ribosomal pathway is anabaenopeptins. These cyclic hexapeptides demonstrated inhibitory activity towards phosphatases and proteases, which could be related to their toxicity and adaptiveness against zooplankters and crustaceans. Thus, this review aims to identify key features related to anabaenopeptins, including the diversity of their structure, occurrence, the biosynthetic steps for their production, ecological roles, and biotechnological applications.