Linking photoacclimation responses and microbiome shifts between depth-segregated sibling species of reef corals

Metazoans host complex communities of microorganisms that include dinoflagellates, fungi, bacteria, archaea, and viruses. Interactions among members of these complex assemblages allow hosts to adjust their physiology and metabolism to cope with environmental variation and occupy different habitats. Here, using reciprocal transplantation across depths, we studied adaptive divergence in the Caribbean corals Orbicella annularis and O. franksi. When transplanted from deep to shallow, O. franksi experienced fast photoacclimation, low mortality, and maintained a consistent bacterial community. In contrast, O. annularis experienced higher mortality, and limited photoacclimation when transplanted from shallow to deep. The photophysiological collapse of O. annularis in the deep environment was associated with an increased microbiome variability and reduction of some bacterial taxa. Differences in the symbiotic algal community were more pronounced between coral species than between depths. Our study suggests that these sibling species are adapted to distinctive light environments partially driven by the algae photoacclimation capacity and the microbiome robustness, highlighting the importance of niche specialization in symbiotic corals for the maintenance of species diversity. Our findings have implications for the management of these threatened Caribbean corals and the effectiveness of coral reef restoration efforts.

Two New Russula Species (Fungi) from Dry Dipterocarp Forest in Thailand Suggest Niche Specialization to This Habitat Type

Dry dipterocarp forests are among the most common habitat types in Thailand. Russulaceae are known as common ectomycorrhizal symbionts of Dipterocarpaceae trees in this type of habitat. The present study aims to identify collections of Russula subsection Amoeninae Buyck from dry dipterocarp forests in Thailand. A multi-locus phylogenetic analysis placed Thai Amoeninae collections in two novel lineages, and they are described here as Russula bellissima sp. nov. and R. luteonana sp. nov. The closest identified relatives of both species were sequestrate species suggesting that they may belong to drought-adapted lineages. The analysis of publicly available ITS sequences in R. subsect. Amoeninae did not confirm evidence of any of the new species occurring in other Asian regions, indicating that dry dipterocarp forests might harbor a novel community of ectomycorrhizal fungi. Macromorphological characters are variable and are not totally reliable for distinguishing the new species from other previously described Asian Amoeninae species. Both new species are defined by a combination of differentiated micromorphological characteristics in spore ornamentation, hymenial cystidia and hyphal terminations in the pileipellis. The new Amoeninae species may correspond to some Russula species collected for consumption in Thailand, and the detailed description of the new species can be used for better identification of edible species and food safety in the region.

The effect of sugar concentration on yeast growth associated with floral nectar and honey

Background: Floral nectar and honey vary in sugar concentration, from low concentration in nectar to high concentration in honey. Variation in sugar concentration is a gradient that determines yeast growth and can lead to its ecological niche specialization. Objective: Evaluate the effect of a sugar concentration gradient on the growth kinetics and cell size of yeasts isolated from the floral nectar and honey of Melipona beecheii. Methods: Four strains identified as Metschnikowia koreensis and Sympodiomycopsis paphiopedili, isolated from floral nectar, and Starmerella apicola and Starmerella apicola 2, isolated from honey of Melipona beecheii were grown in artificial media with a gradient of 2, 10, 20, 40 and 60% glucose. We evaluated culture density (cells / µL), growth parameters, and cell size in each strain. Results and Conclusions: Strains isolated from honey had high growth rates at the highest glucose concentrations, while strains isolated from floral nectar grew best at low concentrations. Cell size decreased as glucose concentration increased in all strains. The data supports the hypothesis that sugar concentration gradient is an ecological filter that modifies the growth and morphology of yeasts associated with flowers and honey and leads to niche specialization in yeasts that colonize plant-bee environments.

Whole genome sequencing reveals possible host species adaptation of Streptococcus dysgalactiae

Streptococcusdysgalactiae (SD) is an emerging pathogen in human and veterinary medicine, and is associated with several host species, disease phenotypes and virulence mechanisms. SD has traditionally been divided into the subspecies dysgalactiae (SDSD) and subsp.equisimilis (SDSE), but recent molecular studies have indicated that the phylogenetic relationships are more complex. Moreover, the genetic basis for the niche versatility of SD has not been extensively investigated. To expand the knowledge about virulence factors, phylogenetic relationships and host-adaptation strategies of SD, we analyzed 78 SDSD genomes from cows and sheep, and 78 SDSE genomes from other host species. Sixty SDSD and 40 SDSE genomes were newly sequenced in this study. Phylogenetic analysis supported SDSD as a distinct taxonomic entity, presenting a mean value of the average nucleotide identity of 99%. Bovine and ovine associated SDSD isolates clustered separately on pangenome analysis, but no single gene or genetic region was uniquely associated with host species. In contrast, SDSE isolates were more heterogenous and could be delineated in accordance with host. Although phylogenetic clustering suggestive of cross species transmission was observed, we predominantly detected a host restricted distribution of the SD-lineages. Furthermore, lineage specific virulence factors were detected, several of them located in proximity to hotspots for integration of mobile genetic elements. Our study indicates that SD has evolved to adapt to several different host species and infers a potential role of horizontal genetic transfer in niche specialization.

Disruption of the odorant coreceptor Orco impairs foraging and host finding behaviors in the New World screwworm fly

The evolution of obligate ectoparasitism in blowflies (Diptera: Calliphoridae) has intrigued scientists for over a century, and surprisingly, the genetics underlying this lifestyle remain largely unknown. Blowflies use odors to locate food and oviposition sites; therefore, olfaction might have played a central role in niche specialization within the group. In insects, the coreceptor Orco is a required partner for all odorant receptors (ORs), a major gene family involved in olfactory-evoked behaviors. Hence, we characterized the Orco gene in the New World screwworm, Cochliomyia hominivorax, a blowfly that is an obligate ectoparasite of warm-blooded animals. In contrast, most of the closely related blowflies are scavengers that lay their eggs on dead animals. We show that the screwworm Orco orthologue (ChomOrco) is highly conserved within Diptera, showing signals of strong purifying selection. Expression of ChomOrco is broadly detectable in chemosensory appendages, and is related to morphological, developmental, and behavioral aspects of the screwworm biology. We used CRISPR/Cas9 to disrupt ChomOrco and evaluate the consequences of losing the OR function on screwworm behavior. In two-choice assays, Orco mutants displayed an impaired response to floral-like and animal host-associated odors, suggesting that OR-mediated olfaction is involved in foraging and host-seeking behaviors in C. hominivorax. These results broaden our understanding of the chemoreception basis of niche occupancy by blowflies.

Isotopic Niche Partitioning and Individual Specialization in an Arctic Raptor Guild

Intra- and inter-specific resource partitioning within predator communities is a fundamental component of trophic ecology, and one proposed mechanism for how populations partition resources is through individual niche variation. The Niche Variation Hypothesis (NVH) predicts that interindividual trait variation leads to functional trade-offs in foraging efficiency, resulting in populations comprised of individual dietary specialists. A modified version of the NVH [mNVH] predicts niche specialization is plastic and responsive to fluctuating resource availability. We quantified niche overlap and tested the mNVH within an Arctic raptor guild, focusing on three species that employ different foraging strategies: Golden Eagles (generalists); Gyrfalcons (facultative specialists); and Rough-legged Hawks (specialists). Tundra ecosystems exhibit cyclic populations of arvicoline rodents (lemmings and voles), providing a unique system under which to examine interannual fluctuations in predator resource availability. Using blood δ13C & δ15N values from 189 raptor nestlings on Alaska’s Seward Peninsula (2014–2019), we calculated isotopic niche width and used Bayesian stable isotope mixing models (BSIMMs) to characterize individual specialization and test the mNVH. We observed a high degree of isotopic niche overlap between the three species and variable trophic responses to different stages of the arvicoline rodent cycle. Elevated arvicoline rodent abundance corresponded to reduced niche overlap among species and increased individual specialization in Golden Eagles and Gyrfalcons. Further, Gyrfalcons displayed a positive relationship between individual specialization and population niche width on an interannual basis consistent with the mNVH. Our findings suggest plasticity in niche specialization may reduce intra- and inter-specific resource competition under dynamic ecological conditions.

Network Properties of Local Fungal Communities Reveal the Anthropogenic Disturbance Consequences of Farming Practices in Vineyard Soils

ABSTRACT Agroecosystems are human-managed ecosystems subject to generalized ecological rules. Understanding the ecology behind the assembly and dynamics of soil fungal communities is a fruitful way to improve management practices and plant productivity. Thus, monitoring soil health would benefit from the use of metrics that arise from ecological explanations that can also be informative for agricultural management. Beyond traditional biodiversity descriptors, community-level properties have the potential of informing about particular ecological situations. Here we assess the impact of different farming practices in a survey of 350 vineyard soils from the United States and Spain by estimating network properties based on spatial associations. Our observations using traditional approaches show results concurring with previous literature: the influence of geographic and climatic factors on sample distributions, or different operational taxonomic unit (OTU) compositions depending on agricultural managements. Furthermore, using network properties, we observe that fungal communities ranged from dense arrangements of associations to a sparser structure of associations, indicating differential levels of niche specialization. We detect fungal arrangements capable of thriving in wider or smaller ranges of temperature, revealing that niche specialization may be a critical soil process impacting soil health. Low-intervention practices (organic and biodynamic managements) promoted densely clustered networks, describing an equilibrium state based on mixed collaborative communities. In contrast, conventionally managed vineyards had highly modular sparser communities, supported by a higher coexclusion proportion. Thus, we hypothesize that network properties at the community level may help to understand how the environment and land use can affect community structure and ecological processes in agroecosystems. IMPORTANCE Soil fungal communities play a key role in agroecosystem sustainability. The complexity of fungal communities, at both taxonomic and functional levels, makes it difficult to find clear patterns connecting community composition with ecosystem function and to understand the impact of biotic (interspecies interactions) and abiotic (e.g., climate or anthropogenic disturbances) factors on it. Here we combine network analysis methods and properties, proposing a novel analytical approach: to infer ecological properties from local networks, which we apply to the study of fungal communities in vineyard soils. We conclude that different levels of farming intensification may lead to different ecological strategies in soil fungal communities settled by particular association arrangements.