Francisco Dini-Andreote

Leaf bacterial communities shape plant defense and interactions with herbivores, yet how host filtering and stochastic processes assemble them remains unclear. We predicted that host identity, chemistry, and arthropods structure them, and that stochastic and deterministic contributions shift seasonally. Across one growing season we sampled leaf bacteria monthly and arthropods weekly on four Asclepias species (Apocynaceae: A. curassavica , A. incarnata , A. syriaca , A. tuberosa ) spanning a cardenolide gradient. We sequenced 16S rRNA genes and quantified selection and dispersal contributions to turnover using null models. Host identity shaped bacterial richness and composition, with A. tuberosa hosting the richest communities, and both richness and phylogenetic diversity rose through the season. Early on, homogenizing dispersal made communities more similar among plants; by mid-season no single process dominated turnover, and by late season dispersal limitation prevailed. Homogeneous selection was episodic, not sustained, and arthropod associations were host-specific, negatively so on A. syriaca. Phyllosphere assembly thus shifts from convergence to divergence in one season: young leaves recruit from a shared pool delivered by wind, rain, and arthropods, whereas exchange among ageing plants declines and communities drift apart. Herbivores arriving late meet plant-specific microbial environments, so microbial mediation of herbivory should be host-specific and seasonally contingent.

Mangroves are ecosystems located at land–sea transition zones, where they are continuously exposed to plant biomass and plastic pollution. Their soils harbor extensive microbial diversity with potential for discovering polymer-degrading enzymes. Here, we perform a microcosm experiment to examine how mangrove soil microbial communities respond to inputs of lignocellulose or polyethylene terephthalate (PET) in the presence and absence of seawater, and to explore the selection of putative PET-active enzymes (PETases) using gene- and genome-resolved metagenomics. Incubation conditions lead to a gradual increase in salinity, resulting in the enrichment of halophilic taxa, including spore-forming bacteria and archaeal species, particularly in seawater-depleted treatments. Lignocellulose input is the primary driver of soil microbial community restructuring, followed by seawater presence. In dry, lignocellulose-amended microcosms (L treatment), microbial diversity is significantly reduced, while lignocellulolytic taxa within the phyla Bacillota and Actinomycetota are enriched. Twelve potential PETases are identified in the L treatment, sharing >70% sequence similarity with known PETases, and three are predicted to be thermostable. Two putative PETases from Microbulbifer species display distinct sequence and structural features, thereby expanding the currently limited PETase sequence landscape. This study demonstrates that perturbing environmental microbiomes with plant-derived polymers represents a promising strategy for capturing novel PETases.

Microbial community coalescence (MCC), the mixing of distinct microbiomes, is increasingly recognized as an important process in natural and managed microbial systems. However, how MCC reorganizes species association architecture and whether this restructuring alters community stability remain poorly understood. Here, we investigated how MCC modifies microbial co-occurrence networks and whether resulting architectures deviate from expectations based on stochastic reshuffling or direct compositional mixing of donor communities. Using controlled soil microcosms, we manipulated pairwise coalescence scenarios across a gradient of biotic dilution and tracked community reassembly over 30 days. Empirical association networks were then compared to two reference frameworks: a stochastic balanced-averaging null model and a donor-preserving compositional mixing model. Across treatments, MCC produced extensive restructuring of species association architecture, with empirical networks exhibiting substantially higher node turnover and a predominance of novel correlations relative to both reference expectations. Higher-order network properties also frequently diverged from expected simulated outcomes, indicating that coalescence reshapes correlation architecture beyond stochastic or additive donor mixing. The consequences of this restructuring for network stability were strongly context-dependent. In one coalescence regime, reductions in biotic complexity led to coordinated declines in network complexity and robustness, accompanied by increased fragmentation and vulnerability, whereas other regimes remained insensitive to the biotic dilution gradient. Moreover, community diversity predicted network architecture only under specific coalescence contexts, revealing regime-specific relationships between community diversity, network complexity, and network stability. Together, these results demonstrate that MCC reorganizes microbial association networks in patterns consistent with context-dependent ecological processes that generate distinct complexity and stability patterns.

Coral holobionts acquire energy and nutrients from heterotrophic feeding, Symbiodiniaceae symbiosis, and additional metabolic functions (e.g. nitrogen (N) fixation) from associated bacterial communities. Since symbioses often require stable environmental conditions, corals in environments with seasonal variability have likely evolved adaptation strategies by either maintaining (i.e. regulating) or shifting (i.e. conforming) key functional traits, but empirical data is needed. We investigated carbon (C) and N elemental and stable isotope ratios alongside bacterial community composition in the hydrocoral Millepora dichotoma and the scleractinian coral Stylophora pistillata every two months over one year. These data were integrated with environmental parameters to investigate potential adaptation strategies of the coral holobionts over a seasonal cycle. S. pistillata showed temporal changes in δ13C, δ15N and C:N ratios in both host and Symbiodiniaceae tissues (indicating stable host-Symbiodiniaceae C/N cycling), in combination with stable bacterial communities. M. dichotoma, did not exhibit temporal changes in elemental and stable isotope ratios, but higher δ15N and C:N variability, and 61% higher C:N ratios in Symbiodiniaceae compared to host tissue. Temporal shifts in bacterial communities resulted in significantly enriched predicted metabolic functions for C, N, and sulfur cycling in winter. Stable C/N cycling and bacterial community composition suggest a regulator-like life history strategy of S. pistillata, whereas variable C/N cycling and flexible bacterial communities indicate a conformer-like life history strategy for M. dichotoma. Both contrasting adaptation strategies enable these organisms to succeed amid current environmental change, yet to what extent this can be maintained under future climate scenarios remains to be investigated.

Background: Bee bread is composed of a mixture of pollen and nectar used as the main source of proteins and lipids for the development of bee larvae. Despite its important role in honey bee food preservation, relatively little is known about the composition of bee bread microbiota and the potential impact of beekeeping management of hives on these microbial systems. Methods: Here, we evaluated whether (1) the bee bread of honey bees is characterized by a core microbiota and (2) miticide applications (formic acid and amitraz) affect the diversity and composition of the bee bread microbiota. We collected a total of 36 samples from six sites across two distinct geographic locations and sequenced the bee bread bacterial communities before and after miticide applications. Results: Our results revealed a conserved bee bread core microbiota comprised of 15 taxa belonging to the phyla Proteobacteria (11 taxa), Firmicutes (two taxa), Actinobacteriota (one taxon), and Bacteroidota (one taxon). In addition, we found weak evidence of miticide treatments impacting the diversity of the bee bread microbiota, with a general trend of a decrease in the diversity of non-core taxa following the application of organic miticides. Conclusion: Taken together, our results demonstrate that the bee bread of honey bees is characterized by a core microbiota despite variations associated with geographic location, sampling period, and miticide applications.