Diversity and characterization of bacterial communities of five co‐occurring species at a hydrothermal vent on the Tonga Arc

Host–symbiont relationships in hydrothermal vent ecosystems, supported by chemoautotrophic bacteria as primary producers, have been extensively studied. However, the process by which densely populated co‐occurring invertebrate hosts form symbiotic relationships with bacterial symbionts remains unclear. Here, we analyzed gill‐associated symbiotic bacteria (gill symbionts) of five co‐occurring hosts, three mollusks (“Bathymodiolus” manusensis, B. brevior, and Alviniconcha strummeri) and two crustaceans (Rimicaris variabilis and Austinograea alayseae), collected together at a single vent site in the Tonga Arc. We observed both different compositions of gill symbionts and the presence of unshared operational taxonomic units (OTUs). In addition, the total number of OTUs was greater for crustacean hosts than for mollusks. The phylogenetic relationship trees of gill symbionts suggest that γ‐proteobacterial gill symbionts have coevolved with their hosts toward reinforcement of host specificity, while campylobacterial Sulfurovum species found across various hosts and habitats are opportunistic associates. Our results confirm that gill symbiont communities differ among co‐occurring vent invertebrates and indicate that hosts are closely related with their gill symbiont communities. Considering the given resources available at a single site, differentiation of gill symbionts seems to be a useful strategy for obtaining nutrition and energy while avoiding competition among both hosts and gill symbionts.     

The SARS‐unique domain (SUD) of SARS‐CoV and SARS‐CoV‐2 interacts with human Paip1 to enhance viral RNA translation

The ongoing outbreak of severe acute respiratory syndrome (SARS) coronavirus 2 (SARS‐CoV‐2) demonstrates the continuous threat of emerging coronaviruses (CoVs) to public health. SARS‐CoV‐2 and SARS‐CoV share an otherwise non‐conserved part of non‐structural protein 3 (Nsp3), therefore named as “SARS‐unique domain” (SUD). We previously found a yeast‐2‐hybrid screen interaction of the SARS‐CoV SUD with human poly(A)‐binding protein (PABP)‐interacting protein 1 (Paip1), a stimulator of protein translation. Here, we validate SARS‐CoV SUD:Paip1 interaction by size‐exclusion chromatography, split‐yellow fluorescent protein, and co‐immunoprecipitation assays, and confirm such interaction also between the corresponding domain of SARS‐CoV‐2 and Paip1. The three‐dimensional structure of the N‐terminal domain of SARS‐CoV SUD (“macrodomain II”, Mac2) in complex with the middle domain of Paip1, determined by X‐ray crystallography and small‐angle X‐ray scattering, provides insights into the structural determinants of the complex formation. In cellulo, SUD enhances synthesis of viral but not host proteins via binding to Paip1 in pBAC‐SARS‐CoV replicon‐transfected cells. We propose a possible mechanism for stimulation of viral translation by the SUD of SARS‐CoV and SARS‐CoV‐2.     

Putting the brakes on phagocytosis: “don't‐eat‐me” signaling in physiology and disease

Timely removal of dying or pathogenic cells by phagocytes is essential to maintaining host homeostasis. Phagocytes execute the clearance process with high fidelity while sparing healthy neighboring cells, and this process is at least partially regulated by the balance of “eat‐me” and “don''t‐eat‐me” signals expressed on the surface of host cells. Upon contact, eat‐me signals activate “pro‐phagocytic” receptors expressed on the phagocyte membrane and signal to promote phagocytosis. Conversely, don''t‐eat‐me signals engage “anti‐phagocytic” receptors to suppress phagocytosis. We review the current knowledge of don''t‐eat‐me signaling in normal physiology and disease contexts where aberrant don''t‐eat‐me signaling contributes to pathology.     

Effects of insularity on genetic diversity within and among natural populations

We conducted a quantitative literature review of genetic diversity (GD) within and among populations in relation to categorical population size and isolation (together referred to as “insularity”). Using populations from within the same studies, we were able to control for between‐study variation in methodology, as well as demographic and life histories of focal species. Contrary to typical expectations, insularity had relatively minor effects on GD within and among populations, which points to the more important role of other factors in shaping evolutionary processes. Such effects of insularity were sometimes seen—particularly in study systems where GD was already high overall. That is, insularity influenced GD in a study system when GD was high even in non‐insular populations of the same study system—suggesting an important role for the “scope” of influences on GD. These conclusions were more robust for within population GD versus among population GD, although several biases might underlie this difference. Overall, our findings indicate that population‐level genetic assumptions need to be tested rather than assumed in nature, particularly for topics underlying current conservation management practices.     

Predicting distributions of Wolbachia strains through host ecological contact—Who's manipulating whom?

Reproductive isolation in response to divergent selection is often mediated via third‐party interactions. Under these conditions, speciation is inextricably linked to ecological context. We present a novel framework for understanding arthropod speciation as mediated by Wolbachia, a microbial endosymbiont capable of causing host cytoplasmic incompatibility (CI). We predict that sympatric host sister‐species harbor paraphyletic Wolbachia strains that provide CI, while well‐defined congeners in ecological contact and recently diverged noninteracting congeners are uninfected due to Wolbachia redundancy. We argue that Wolbachia provides an adaptive advantage when coupled with reduced hybrid fitness, facilitating assortative mating between co‐occurring divergent phenotypes—the contact contingency hypothesis. To test this, we applied a predictive algorithm to empirical pollinating fig wasp data, achieving up to 91.60% accuracy. We further postulate that observed temporal decay of Wolbachia incidence results from adaptive host purging—adaptive decay hypothesis—but implementation failed to predict systematic patterns. We then account for post‐zygotic offspring mortality during CI mating, modeling fitness clines across developmental resources—the fecundity trade‐off hypothesis. This model regularly favored CI despite fecundity losses. We demonstrate that a rules‐based algorithm accurately predicts Wolbachia infection status. This has implications among other systems where closely related sympatric species encounter adaptive disadvantage through hybridization.     

The early life of a leaf‐cutter ant colony constrains symbiont vertical transmission and favors horizontal transmission

Colonial organisms host a large diversity of symbionts (collectively, parasites, mutualists, and commensals) that use vertical transmission (from parent colony to offspring colony) and/or horizontal transmission to disperse between host colonies. The early life of some colonies, characterized by the dispersal and establishment of solitary individuals, may constrain vertical transmission and favor horizontal transmission between large established colonies. We explore this possibility with the miniature cockroach Attaphila fungicola, a symbiont of leaf‐cutter ants and the mutualist fungal gardens they cultivate. The early life of a leaf‐cutter colony is characterized by the dispersal of a female alate (winged “queen”) carrying a fungal pellet, and the subsequent establishment of a foundress (workerless “queen”) raising her incipient fungal garden and colony. Roaches hitchhike on female alates during leaf‐cutter nuptial flights, which strongly suggests that roaches are vertically transmitted to foundresses and their incipient colonies; however, weak compatibility between roaches and incipient gardens may constrain roach vertical transmission. Reciprocally, opportunities for horizontal transmission between large established colonies with abundant fungal gardens may weaken selection against roach‐induced harm (virulence) of incipient gardens. We use a laboratory experiment, behavioral observations, field surveys, and a transmission model to estimate the effect roaches have on the survivorship of incipient gardens and the frequency of roach vertical transmission. Contrary to traditional assumptions, our results indicate that roaches harm incipient gardens and predominantly use horizontal transmission between established leaf‐cutter colonies. Ultimately, “costs of generalism” associated with infecting disparate stages of a host''s lifecycle (e.g., incipient vs. established colonies) may constrain the vertical transmission of roaches and a broad range of symbionts.     

The formation of “mega‐flocks” depends on vegetation structure in montane coniferous forests of Taiwan

A mixed‐species bird flock is a social assemblage where two or more bird species are moving together while foraging and might benefit from increased foraging efficiency and antipredator vigilance. A “mega‐flock,” which includes flocking species from different vegetation strata, often exhibits high species diversity. Mechanisms for the formation of mega‐flocks have not yet been explored. In this study, we evaluated the influence of vegetation structure and bird species diversity in driving the occurrence of mega‐flocks. We investigated the composition of mixed‐species flocks, local bird communities, and vegetation structure in five vegetation types of two high‐elevation sites in central Taiwan. Mega‐flocks occurred more frequently in pine woodland than later successional stages of coniferous forests. However, species richness/diversity of local bird communities increased along successional stages. Therefore, vegetation variables exhibit more influence on the occurrence of mega‐flocks than local bird communities. Besides foliage height diversity, understory coverage also showed positive effects on flock size of mixed‐species flocks. Our results indicated that pine woodlands with more evenly distributed vegetation layers could facilitate the interactions of canopy and understory flocks and increase the formation of mega‐flocks and thus the complexity of mixed‐species flocks.     

A binary effector module secreted by a type VI secretion system

Gram‐negative bacteria use type VI secretion systems (T6SSs) to deliver toxic effector proteins into neighboring cells. Cargo effectors are secreted by binding noncovalently to the T6SS apparatus. Occasionally, effector secretion is assisted by an adaptor protein, although the adaptor itself is not secreted. Here, we report a new T6SS secretion mechanism, in which an effector and a co‐effector are secreted together. Specifically, we identify a novel periplasm‐targeting effector that is secreted together with its co‐effector, which contains a MIX (marker for type sIX effector) domain previously reported only in polymorphic toxins. The effector and co‐effector directly interact, and they are dependent on each other for secretion. We term this new secretion mechanism “a binary effector module,” and we show that it is widely distributed in marine bacteria.     

Scent of a killer: How could killer yeast boost its dispersal?

Vector‐borne parasites often manipulate hosts to attract uninfected vectors. For example, parasites causing malaria alter host odor to attract mosquitoes. Here, we discuss the ecology and evolution of fruit‐colonizing yeast in a tripartite symbiosis—the so‐called “killer yeast” system. “Killer yeast” consists of Saccharomyces cerevisiae yeast hosting two double‐stranded RNA viruses (M satellite dsRNAs, L‐A dsRNA helper virus). When both dsRNA viruses occur in a yeast cell, the yeast converts to lethal toxin‑producing “killer yeast” phenotype that kills uninfected yeasts. Yeasts on ephemeral fruits attract insect vectors to colonize new habitats. As the viruses have no extracellular stage, they depend on the same insect vectors as yeast for their dispersal. Viruses also benefit from yeast dispersal as this promotes yeast to reproduce sexually, which is how viruses can transmit to uninfected yeast strains. We tested whether insect vectors are more attracted to killer yeasts than to non‑killer yeasts. In our field experiment, we found that killer yeasts were more attractive to Drosophila than non‐killer yeasts. This suggests that vectors foraging on yeast are more likely to transmit yeast with a killer phenotype, allowing the viruses to colonize those uninfected yeast strains that engage in sexual reproduction with the killer yeast. Beyond insights into the basic ecology of the killer yeast system, our results suggest that viruses could increase transmission success by manipulating the insect vectors of their host.     

Edge disturbance shapes liana diversity and abundance but not liana‐tree interaction network patterns in moist semi‐deciduous forests,Ghana

Edge disturbance can drive liana community changes and alter liana‐tree interaction networks, with ramifications for forest functioning. Understanding edge effects on liana community structure and liana‐tree interactions is therefore essential for forest management and conservation. We evaluated the response patterns of liana community structure and liana‐tree interaction structure to forest edge in two moist semi‐deciduous forests in Ghana (Asenanyo and Suhuma Forest Reserves: AFR and SFR, respectively). Liana community structure and liana‐tree interactions were assessed in 24 50 × 50 m randomly located plots in three forest sites (edge, interior and deep‐interior) established at 0–50 m, 200 m and 400 m from edge. Edge effects positively and negatively influenced liana diversity in forest edges of AFR and SFR, respectively. There was a positive influence of edge disturbance on liana abundance in both forests. We observed anti‐nested structure in all the liana‐tree networks in AFR, while no nestedness was observed in the networks in SFR. The networks in both forests were less connected, and thus more modular and specialised than their null models. Many liana and tree species were specialised, with specialisation tending to be symmetrical. The plant species played different roles in relation to modularity. Most of the species acted as peripherals (specialists), with only a few species having structural importance to the networks. The latter species group consisted of connectors (generalists) and hubs (highly connected generalists). Some of the species showed consistency in their roles across the sites, while the roles of other species changed. Generally, liana species co‐occurred randomly on tree species in all the forest sites, except edge site in AFR where lianas showed positive co‐occurrence. Our findings deepen our understanding of the response of liana communities and liana‐tree interactions to forest edge disturbance, which are useful for managing forest edge.     

Quantitative contributions of TNF receptor superfamily members to CD8+ T‐cell responses

T‐cell responses to infections and cancers are regulated by co‐signalling receptors grouped into the binary categories of co‐stimulation or co‐inhibition. The co‐stimulation TNF receptor superfamily (TNFRSF) members 4‐1BB, CD27, GITR and OX40 have similar signalling mechanisms raising the question of whether they have similar impacts on T‐cell responses. Here, we screened for the quantitative impact of these TNFRSFs on primary human CD8⁺ T‐cell cytokine production. Although both 4‐1BB and CD27 increased production, only 4‐1BB was able to prolong the duration over which cytokine was produced, and both had only modest effects on antigen sensitivity. An operational model explained these different phenotypes using shared signalling based on the surface expression of 4‐1BB being regulated through signalling feedback. The model predicted and experiments confirmed that CD27 co‐stimulation increases 4‐1BB expression and subsequent 4‐1BB co‐stimulation. GITR and OX40 displayed only minor effects on their own but, like 4‐1BB, CD27 could enhance GITR expression and subsequent GITR co‐stimulation. Thus, different co‐stimulation receptors can have different quantitative effects allowing for synergy and fine‐tuning of T‐cell responses.     

Degrees of compositional shift in tree communities vary along a gradient of temperature change rates over one decade: Application of an individual‐based temporal beta‐diversity concept

Temporal patterns in communities have gained widespread attention recently, to the extent that temporal changes in community composition are now termed “temporal beta‐diversity.” Previous studies of beta‐diversity have made use of two classes of dissimilarity indices: incidence‐based (e.g., Sørensen and Jaccard dissimilarity) and abundance‐based (e.g., Bray–Curtis and Ružička dissimilarity). However, in the context of temporal beta‐diversity, the persistence of identical individuals and turnover among other individuals within the same species over time have not been considered, despite the fact that both will affect compositional changes in communities. To address this issue, I propose new index concepts for beta‐diversity and the relative speed of compositional shifts in relation to individual turnover based on individual identity information. Individual‐based beta‐diversity indices are novel dissimilarity indices that consider individual identity information to quantitatively evaluate temporal change in individual turnover and community composition. I applied these new indices to individually tracked tree monitoring data in deciduous and evergreen broad‐leaved forests across the Japanese archipelago with the objective of quantifying the effect of climate change trends (i.e., rates of change in both annual mean temperature and annual precipitation) on individual turnover and compositional shifts at each site. A new index explored the relative contributions of mortality and recruitment processes to temporal changes in community composition. Clear patterns emerged showing that an increase in the temperature change rate facilitated the relative contribution of mortality components. The relative speed of compositional shift increased with increasing temperature change rates in deciduous forests but decreased with increasing warming rates in evergreen forests. These new concepts provide a way to identify novel and high‐resolution temporal patterns in communities.     

Symbiosis and Insect Diversification: an Ancient Symbiont of Sap-Feeding Insects from the Bacterial Phylum Bacteroidetes

Several insect groups have obligate, vertically transmitted bacterial symbionts that provision hosts with nutrients that are limiting in the diet. Some of these bacteria have been shown to descend from ancient infections. Here we show that the large group of related insects including cicadas, leafhoppers, treehoppers, spittlebugs, and planthoppers host a distinct clade of bacterial symbionts. This newly described symbiont lineage belongs to the phylum Bacteroidetes. Analyses of 16S rRNA genes indicate that the symbiont phylogeny is completely congruent with the phylogeny of insect hosts as currently known. These results support the ancient acquisition of a symbiont by a shared ancestor of these insects, dating the original infection to at least 260 million years ago. As visualized in a species of spittlebug (Cercopoidea) and in a species of sharpshooter (Cicadellinae), the symbionts have extraordinarily large cells with an elongate shape, often more than 30 μm in length; in situ hybridizations verify that these correspond to the phylum Bacteroidetes. “Candidatus Sulcia muelleri” is proposed as the name of the new symbiont.     

Wolbachia in the spittlebug Prosapia ignipectus: Variable infection frequencies,but no apparent effect on host reproductive isolation

Animals serve as hosts for complex communities of microorganisms, including endosymbionts that live inside their cells. Wolbachia bacteria are perhaps the most common endosymbionts, manipulating host reproduction to propagate. Many Wolbachia cause cytoplasmic incompatibility (CI), which results in reduced egg hatch when uninfected females mate with infected males. Wolbachia that cause intense CI spread to high and relatively stable frequencies, while strains that cause weak or no CI tend to persist at intermediate, often variable, frequencies. Wolbachia could also contribute to host reproductive isolation (RI), although current support for such contributions is limited to a few systems. To test for Wolbachia frequency variation and effects on host RI, we sampled several local Prosapia ignipectus (Fitch) (Hemiptera: Cercopidae) spittlebug populations in the northeastern United States over two years, including closely juxtaposed Maine populations with different monomorphic color forms, “black” and “lined.” We discovered a group‐B Wolbachia (wPig) infecting P. ignipectus that diverged from group‐A Wolbachia—like model wMel and wRi strains in Drosophila—6 to 46 MYA. Populations of the sister species Prosapia bicincta (Say) from Hawaii and Florida are uninfected, suggesting that P. ignipectus acquired wPig after their initial divergence. wPig frequencies were generally high and variable among sites and between years. While phenotyping wPig effects on host reproduction is not currently feasible, the wPig genome contains three divergent sets of CI loci, consistent with high wPig frequencies. Finally, Maine monomorphic black and monomorphic lined populations of P. ignipectus share both wPig and mtDNA haplotypes, implying no apparent effect of wPig on the maintenance of this morphological contact zone. We hypothesize P. ignipectus acquired wPig horizontally as observed for many Drosophila species, and that significant CI and variable transmission produce high but variable wPig frequencies.     

Differential effects of ecosystem engineering by the superb lyrebird Menura novaehollandiae and herbivory by large mammals on floristic regeneration and structure in wet eucalypt forests

Ecosystem engineers that modify the soil and ground‐layer properties exert a strong influence on vegetation communities in ecosystems worldwide. Understanding the interactions between animal engineers and vegetation is challenging when in the presence of large herbivores, as many vegetation communities are simultaneously affected by both engineering and herbivory. The superb lyrebird Menura novaehollandiae, an ecosystem engineer in wet forests of south‐eastern Australia, extensively modifies litter and soil on the forest floor. The aim of this study was to disentangle the impacts of engineering by lyrebirds and herbivory by large mammals on the composition and structure of ground‐layer vegetation. We carried out a 2‐year, manipulative exclusion experiment in the Central Highlands of Victoria, Australia. We compared three treatments: fenced plots with simulated lyrebird foraging; fenced plots excluding herbivores and lyrebirds; and open controls. This design allowed assessment of the relative impacts of engineering and herbivory on germination rates, seedling density, vegetation cover and structure, and community composition. Engineering by lyrebirds enhanced the germination of seeds in the litter layer. After 2 years, more than double the number of germinants were present in “engineered” than “non‐engineered” plots. Engineering did not affect the density of seedlings, but herbivory had strong detrimental effects. Herbivory also reduced the floristic richness and structural complexity (<0.5 m) of forest vegetation, including the cover of herbs. Neither process altered the floristic composition of the vegetation within the 2‐year study period. Ecosystem engineering by lyrebirds and herbivory by large mammals both influence the structure of forest‐floor vegetation. The twofold increase in seeds stimulated to germinate by engineering may contribute to the evolutionary adaptation of plants by allowing greater phenotypic expression and selection than would otherwise occur. Over long timescales, engineering and herbivory likely combine to maintain a more‐open forest floor conducive to ongoing ecosystem engineering by lyrebirds.     

Untangling the oxidative cost of reproduction: An analysis in wild banded mongooses

The cost of reproduction plays a central role in evolutionary theory, but the identity of the underlying mechanisms remains a puzzle. Oxidative stress has been hypothesized to be a proximate mechanism that may explain the cost of reproduction. We examine three pathways by which oxidative stress could shape reproduction. The “oxidative cost” hypothesis proposes that reproductive effort generates oxidative stress, while the “oxidative constraint” and “oxidative shielding” hypotheses suggest that mothers mitigate such costs through reducing reproductive effort or by pre‐emptively decreasing damage levels, respectively. We tested these three mechanisms using data from a long‐term food provisioning experiment on wild female banded mongooses (Mungos mungo). Our results show that maternal supplementation did not influence oxidative stress levels, or the production and survival of offspring. However, we found that two of the oxidative mechanisms co‐occur during reproduction. There was evidence of an oxidative challenge associated with reproduction that mothers attempted to mitigate by reducing damage levels during breeding. This mitigation is likely to be of crucial importance, as long‐term offspring survival was negatively impacted by maternal oxidative stress. This study demonstrates the value of longitudinal studies of wild animals in order to highlight the interconnected oxidative mechanisms that shape the cost of reproduction.     

Intraspecific trait variability and community assembly in hawkmoths (Lepidoptera: Sphingidae) across an elevational gradient in the eastern Himalayas,India

1. We investigated some aspects of hawkmoth community assembly at 13 elevations along a 200‐ to 2770‐m transect in the eastern Himalayas, a little studied biodiversity hot spot of global importance. We measured the morphological traits of body mass, wing loading, and wing aspect ratio of 3,301 free‐ranging individuals of 76 species without having to collect or even constrain them. We used these trait measurements and T‐statistic metrics to assess the strength of intracommunity (“internal") and extra‐community (“external”) filters which determine the composition of communities vis‐a‐vis the regional pool of species.
2. The trait distribution of constituent species turned out to be nonrandom subsets of the community‐trait distribution, providing strong evidence for internal filtering in all elevational communities. The external filter metric was more ambiguous. However, the elevational dependence of many metrics including that of the internal filter provided evidence for external (i.e., environmental) filtering. On average, a species occupied as much as 50%–75% of the total community‐trait space, yet the T‐statistic metric for internal filter was sufficiently sensitive to detect a strong nonrandom structure in the trait distribution.
3. We suggest that the change in T‐statistic metrics along the environmental gradient may provide more clues to the process of community assembly than previously envisaged. A large, smoothly varying and well‐sampled environmental span would make it easier to discern them. Developing T‐statistics for combined analysis of multiple traits will perhaps provide a more accurate picture of internal/filtering and niche complementarity. Moths are a hyperdiverse taxon and a very important component of many ecosystems. Our technique for accurately measuring body and wing dimensions of free‐ranging moths can generate trait database for a large number of individuals in a time‐ and resource‐efficient manner for a variety of community assembly studies using this important taxon.

     

Plant history and soil history jointly influence the selection environment for plant species in a long‐term grassland biodiversity experiment

Long‐term biodiversity experiments have shown increasing strengths of biodiversity effects on plant productivity over time. However, little is known about rapid evolutionary processes in response to plant community diversity, which could contribute to explaining the strengthening positive relationship. To address this issue, we performed a transplant experiment with offspring of seeds collected from four grass species in a 14‐year‐old biodiversity experiment (Jena Experiment). We used two‐ and six‐species communities and removed the vegetation of the study plots to exclude plant–plant interactions. In a reciprocal design, we transplanted five “home” phytometers (same origin and actual environment), five “away‐same” phytometers (same species richness of origin and actual environment, but different plant composition), and five “away‐different” phytometers (different species richness of origin and actual environment) of the same species in the study plots. In the establishment year, plants transplanted in home soil produced more shoots than plants in away soil indicating that plant populations at low and high diversity developed differently over time depending on their associated soil community and/or conditions. In the second year, offspring of individuals selected at high diversity generally had a higher performance (biomass production and fitness) than offspring of individuals selected at low diversity, regardless of the transplant environment. This suggests that plants at low and high diversity showed rapid evolutionary responses measurable in their phenotype. Our findings provide first empirical evidence that loss of productivity at low diversity is not only caused by changes in abiotic and biotic conditions but also that plants respond to this by a change in their micro‐evolution. Thus, we conclude that eco‐evolutionary feedbacks of plants at low and high diversity are critical to fully understand why the positive influence of diversity on plant productivity is strengthening through time.