Holobionts and their hologenomes: Evolution with mixed modes of inheritance

Bacterial communities of the psyllid pest Bactericera cockerelli (Hemiptera: Triozidae) Central haplotype of tomato crops cultivated at different locations of Mexico

Background

The psyllid, Bactericera cockerelli, is an insect vector of 'Candidatus Liberibacter' causing "Zebra chip" disease that affects potato and other Solanaceae crops worldwide. In the present study, we analyzed the bacterial communities associated with the insect vector Bactericera cockerelli central haplotype of tomato crop fields in four regions from Mexico.

Methods

PCR was used to amplify the mitochondrial cytochrome oxidase I gene (mtCOI) and then analyze the single nucleotide polymorphisms (SNP) and phylogenetic analysis for haplotype identification of the isolated B. cockerelli. Moreover, we carried out the microbial diversity analysis of several B. cockerelli collected from four regions of Mexico through the NGS sequencing of 16S rRNA V3 region. Finally, Wolbachia was detected by the wsp gene PCR amplification, which is the B. cockerelli facultative symbiont. Also we were able to confirm the relationship with several Wolbachia strains by phylogenetic analysis.

Results

Our results pointed that B. cockerelli collected in the four locations from Mexico (Central Mexico: Queretaro, and Northern Mexico: Sinaloa, Coahuila, and Nuevo Leon) were identified, such as the central haplotype. Analyses of the parameters of the composition, relative abundance, and diversity (Shannon index: 1.328 ± 0.472; Simpson index 0.582 ± 0.167), showing a notably relatively few microbial species in B. cockerelli. Analyses identified various facultative symbionts, particularly the Wolbachia (Rickettsiales: Anaplasmataceae) with a relative abundance higher. In contrast, the genera of Sodalis and 'Candidatus Carsonella' (Gammaproteobacteria: Oceanospirillales: Halomonadaceae) were identified with a relatively low abundance. On the other hand, the relative abundance for the genus 'Candidatus Liberibacter' was higher only for some of the locations analyzed. PCR amplification of a fragment of the gene encoding a surface protein (wsp) of Wolbachia and phylogenetic analysis corroborated the presence of this bacterium in the central haplotype. Beta-diversity analysis revealed that the presence of the genus 'Candidatus Liberibacter' influences the microbiota structure of this psyllid species.

Conclusions

Our data support that the members with the highest representation in microbial community of B. cockerelli central haplotype, comprise their obligate symbiont, Carsonella, and facultative symbionts. We also found evidence that among the factors analyzed, the presence of the plant pathogen affects the structure and composition of the bacterial community associated with B. cockerelli.

Patterns of Plant Salinity Adaptation Depend on Interactions with Soil Microbes

AbstractAs plant-microbe interactions are both ubiquitous and critical in shaping plant fitness, patterns of plant adaptation to their local environment may be influenced by these interactions. Identifying the contribution of soil microbes to plant adaptation may provide insight into the evolution of plant traits and their microbial symbioses. To this end, we assessed the contribution of soil microbes to plant salinity adaptation by growing 10 populations of Bromus tectorum, collected from habitats differing in their salinity, in the greenhouse under either high-salinity or nonsaline conditions and with or without soil microbial partners. Across two live soil inoculum treatments, we found evidence for adaptation of these populations to their home salinity environment. However, when grown in sterile soils, plants were slightly maladapted to their home salinity environment. As plants were on average more fit in sterile soils, pathogenic microbes may have been significant drivers of plant fitness herein. Consequently, we hypothesized that the plant fitness advantage in their home salinity may have been due to increased plant resistance to pathogenic attack in those salinity environments. Our results highlight that plant-microbe interactions may partially mediate patterns of plant adaptation as well as be important selective agents in plant evolution.

Population dynamics of Brachionus calyciflorus driven by the associated natural bacterioplankton

Zooplankton provides bacteria with a complex microhabitat richen in organic and inorganic nutrients, and the bacteria community also changes the physiochemical conditions for zooplankton, where the symbiotic relationship between them plays an important role in the nutrient cycle. However, there are few studies on the effect of associated bacteria on the population dynamics of rotifers. In order to make clear their relationships, we reconstructed the associated bacterial community in Brachionus calyciflorus culture, and examined the life history and population growth parameters, and analyzed the diversity and community composition of the associated bacteria at different growth stages of B. calyciflorus. The results showed that the addition of bacteria from natural water can promote the population growth and asexual reproduction of B. calyciflorus, but has no significant effect on sexual reproduction, exhibited by the improvement of its life expectancy at hatching, net reproduction rates and intrinsic growth rate, no significant effects on the generation time and mixis ratio of offspring. It was found that the B. calyciflorus-associated bacterial community was mainly composed of Proteobacteria, Bacteroidota, Actinobacteriota, Cyanobacteria and Firmicutes. Through correlation network analysis, the members of Burkholderiales, Pseudomonadales, Micrococcales, Caulobacterales and Bifidobacteriales were the keystone taxa of B. calyciflorus-associated bacteria. In addition, the relative abundance of some specific bacteria strains increased as the population density of B. calyciflorus increased, such as Hydrogenophaga, Acidovorax, Flavobacterium, Rheinheimera, Novosphingobium and Limnobacter, and their relative abundance increased obviously during the slow and exponential phases of population growth. Meanwhile, the relative abundance of adverse taxa (such as Elizabethkingia and Rickettsiales) decreased significantly with the increase in rotifer population density. In conclusion, the closely associated bacteria are not sufficient for the best growth of B. calyciflorus, and external bacterioplankton is necessary. Furthermore, the function of keystone and rare taxa is necessary for further exploration. The investigation of the symbiotic relationship between zooplankton-associated bacterial and bacterioplankton communities will contribute to monitoring their roles in freshwater ecosystems, and regulate the population dynamics of the micro-food web.

Not That Close to Mommy: Horizontal Transmission Seeds the Microbiome Associated with the Marine Sponge Plakina cyanorosea

Marine sponges are excellent examples of invertebrate-microbe symbioses. In this holobiont, the partnership has elegantly evolved by either transmitting key microbial associates through the host germline and/or capturing microorganisms from the surrounding seawater. We report here on the prokaryotic microbiota during different developmental stages of Plakina cyanorosea and their surrounding environmental samples by a 16S rRNA metabarcoding approach. In comparison with their source adults, larvae housed slightly richer and more diverse microbial communities, which are structurally more related to the environmental microbiota. In addition to the thaumarchaeal Nitrosopumilus, parental sponges were broadly dominated by Alpha- and Gamma-proteobacteria, while the offspring were particularly enriched in the Vibrionales, Alteromonodales, Enterobacterales orders and the Clostridia and Bacteroidia classes. An enterobacterial operational taxonomic unit (OTU) was the dominant member of the strict core microbiota. The most abundant and unique OTUs were not significantly enriched amongst the microbiomes from host specimens included in the sponge microbiome project. In a wider context, Oscarella and Plakina are the sponge genera with higher divergence in their associated microbiota compared to their Homoscleromorpha counterparts. Our results indicate that P. cyanorosea is a low microbial abundance sponge (LMA), which appears to heavily depend on the horizontal transmission of its microbial partners that likely help the sponge host in the adaptation to its habitat.

Origins of human milk microbiota: new evidence and arising questions

Human milk contains a diverse community of bacteria. The growing appreciation of commensal microbes and increasing availability of high-throughput technology has set the stage for a theory-driven approach to the study of milk microbiota, and translation of this knowledge to improve maternal and child health. We recently profiled the milk microbiota of healthy Canadian mothers and applied theory-driven causal modeling, finding that mode of breast milk feeding (nursing directly at the breast vs. pumping and feeding breast milk from a bottle) was significantly associated with milk microbiota composition. This observation could reflect an increased exposure to pumps and/or a decreased exposure to the infant mouth. Either way, it provides evidence for the retrograde mechanism of milk inoculation. Here, we discuss the implications of this research and related controversies, and raise new questions about the origins and function of milk bacteria.

The Catenulida flatworm can express genes from its microbiome or from the DNA it ingests

Stenostomum are tiny planarians of the phylum Platyhelminthes that reproduce asexually. We transfected these worms using plasmids containing a gfp reporter gene. Here we show that they can express genes present in plasmids carried by bacteria and those that are encoded by naked DNA, such as plasmids or PCR fragments, transfected by electroporation; they can also express genes taken up during feeding. The microbiome associated with worm maintenance was evaluated, and the results indicated that when a plasmid is maintained in the microbiome, gfp gene expression is stable. When genes originate from naked DNA or bacteria not maintained in the microbiome, GFP expression is transient. Therefore, changes in the microbiome can modify the ability of worms to express foreign genes. In stable GFP-expressing worms, NSG showed that the gfp gene was maintained in the plasmid and was not integrated into the chromosome. These results suggest that, at least for some organisms such as flatworms, the expression of genes provided by the microbiome or the environment can be considered among the potential sources of phenotypic plasticity, which can have implications for evolvability.

Holobiont chronobiology: mycorrhiza may be a key to linking aboveground and underground rhythms

Circadian clocks are nearly ubiquitous timing mechanisms that can orchestrate rhythmic behavior and gene expression in a wide range of organisms. Clock mechanisms are becoming well understood in fungal, animal, and plant model systems, yet many of these organisms are surrounded by a complex and diverse microbiota which should be taken into account when examining their biology. Of particular interest are the symbiotic relationships between organisms that have coevolved over time, forming a unit called a holobiont. Several studies have now shown linkages between the circadian rhythms of symbiotic partners. Interrelated regulation of holobiont circadian rhythms seems thus important to coordinate shifts in activity over the day for all the partners. Therefore, we suggest that the classical view of "chronobiological individuals" should include "a holobiont" rather than an organism. Unfortunately, mechanisms that may regulate interspecies temporal acclimation and the evolution of the circadian clock in holobionts are far from being understood. For the plant holobiont, our understanding is particularly limited. In this case, the holobiont encompasses two different ecosystems, one above and the other below the ground, with the two potentially receiving timing information from different synchronizing signals (Zeitgebers). The arbuscular mycorrhizal (AM) symbiosis, formed by plant roots and fungi, is one of the oldest and most widespread associations between organisms. By mediating the nutritional flux between the plant and the many microbes in the soil, AM symbiosis constitutes the backbone of the plant holobiont. Even though the importance of the AM symbiosis has been well recognized in agricultural and environmental sciences, its circadian chronobiology remains almost completely unknown. We have begun to study the circadian clock of arbuscular mycorrhizal fungi, and we compile and here discuss the available information on the subject. We propose that analyzing the interrelated temporal organization of the AM symbiosis and determining its underlying mechanisms will advance our understanding of the role and coordination of circadian clocks in holobionts in general.

Social amoebae establish a protective interface with their bacterial associates by lectin agglutination

Both animals and amoebae use phagocytosis and DNA-based extracellular traps as anti-bacterial defense mechanisms. Whether, like animals, amoebae also use tissue-level barriers to reduce direct contact with bacteria has remained unclear. We have explored this question in the social amoeba Dictyostelium discoideum, which forms plaques on lawns of bacteria that expand as amoebae divide and bacteria are consumed. We show that CadA, a cell adhesion protein that functions in D. discoideum development, is also a bacterial agglutinin that forms a protective interface at the plaque edge that limits exposure of vegetative amoebae to bacteria. This interface is important for amoebal survival when bacteria-to-amoebae ratios are high, optimizing amoebal feeding behavior, and protecting amoebae from oxidative stress. Lectins also control bacterial access to the gut epithelium of mammals to limit inflammatory processes; thus, this strategy of antibacterial defense is shared across a broad spectrum of eukaryotic taxa.

Chromatin Evolution-Key Innovations Underpinning Morphological Complexity

The history of life consists of a series of major evolutionary transitions, including emergence and radiation of complex multicellular eukaryotes from unicellular ancestors. The cells of multicellular organisms, with few exceptions, contain the same genome, however, their organs are composed of a variety of cell types that differ in both structure and function. This variation is largely due to the transcriptional activity of different sets of genes in different cell types. This indicates that complex transcriptional regulation played a key role in the evolution of complexity in eukaryotes. In this review, we summarize how gene duplication and subsequent evolutionary innovations, including the structural evolution of nucleosomes and chromatin-related factors, contributed to the complexity of the transcriptional system and provided a basis for morphological diversity.

Is Host Filtering the Main Driver of Phylosymbiosis across the Tree of Life?

Host-associated microbiota composition can be conserved over evolutionary time scales. Indeed, closely related species often host similar microbiota; i.e., the composition of their microbiota harbors a phylogenetic signal, a pattern sometimes referred to as "phylosymbiosis." Elucidating the origins of this pattern is important to better understand microbiota ecology and evolution. However, this is hampered by our lack of theoretical expectations and a comprehensive overview of phylosymbiosis prevalence in nature. Here, we use simulations to provide a simple expectation for when we should expect this pattern to occur and then review the literature to document the prevalence and strength of phylosymbiosis across the host tree of life. We demonstrate that phylosymbiosis can readily emerge from a simple ecological filtering process, whereby a given host trait (e.g., gut pH) that varies with host phylogeny (i.e., harbors a phylogenetic signal) filters preadapted microbes. We found marked differences between methods used to detect phylosymbiosis, so we proposed a series of practical recommendations based on using multiple best-performing approaches. Importantly, we found that, while the prevalence of phylosymbiosis is mixed in nature, it appears to be stronger for microbiotas living in internal host compartments (e.g., the gut) than those living in external compartments (e.g., the rhizosphere). We show that phylosymbiosis can theoretically emerge without any intimate, long-term coevolutionary mechanisms and that most phylosymbiosis patterns observed in nature are compatible with a simple ecological process. Deviations from baseline ecological expectations might be used to further explore more complex hypotheses, such as codiversification. IMPORTANCE Phylosymbiosis is a pattern defined as the tendency of closely related species to host microbiota whose compositions resemble each other more than host species drawn at random from the same tree. Understanding the mechanisms behind phylosymbiosis is important because it can shed light on rules governing the assembly of host-associated microbiotas and, potentially, their coevolutionary dynamics with hosts. For example, is phylosymbiosis a result of coevolution, or can it be generated by simple ecological filtering processes? Beyond qualitative theoretical models, quantitative theoretical expectations can provide new insights. For example, deviations from a simple baseline of ecological filtering may be used to test more-complex hypotheses (e.g., coevolution). Here, we use simulations to provide evidence that simple host-related ecological filtering can readily generate phylosymbiosis, and we contrast these predictions with real-world data. We find that while phylosymbiosis is widespread in nature, phylosymbiosis patterns are compatible with a simple ecological model in the majority of taxa. Internal compartments of hosts, such as the animal gut, often display stronger phylosymbiosis than expected from a purely ecological filtering process, suggesting that other mechanisms are also involved.