A ridge-to-reef ecosystem microbial census reveals environmental reservoirs for animal and plant microbiomes.

Microbes are found in nearly every habitat and organism on the planet, where they are critical to host health, fitness, and metabolism. In most organisms, few microbes are inherited at birth; instead, acquiring microbiomes generally involves complicated interactions between the environment, hosts, and symbionts. Despite the criticality of microbiome acquisition, we know little about where hosts' microbes reside when not in or on hosts of interest. Because microbes span a continuum ranging from generalists associating with multiple hosts and habitats to specialists with narrower host ranges, identifying potential sources of microbial diversity that can contribute to the microbiomes of unrelated hosts is a gap in our understanding of microbiome assembly. Microbial dispersal attenuates with distance, so identifying sources and sinks requires data from microbiomes that are contemporary and near enough for potential microbial transmission. Here, we characterize microbiomes across adjacent terrestrial and aquatic hosts and habitats throughout an entire watershed, showing that the most species-poor microbiomes are partial subsets of the most species-rich and that microbiomes of plants and animals are nested within those of their environments. Furthermore, we show that the host and habitat range of a microbe within a single ecosystem predicts its global distribution, a relationship with implications for global microbial assembly processes. Thus, the tendency for microbes to occupy multiple habitats and unrelated hosts enables persistent microbiomes, even when host populations are disjunct. Our whole-watershed census demonstrates how a nested distribution of microbes, following the trophic hierarchies of hosts, can shape microbial acquisition.

The dimensionality of infection networks among viruses infecting microbial eukaryotes and bacteria.

Diverse viruses and their hosts are interconnected through complex networks of infection, which are thought to influence ecological and evolutionary processes, but the principles underlying infection network structure are not well understood. Here we focus on network dimensionality and how it varies across 37 networks of viruses infecting eukaryotic phytoplankton and bacteria. We find that dimensionality is often strikingly low, with most networks being one- or two-dimensional, although dimensionality increases with network richness, suggesting that the true dimensionality of natural systems is higher. Low-dimensional networks generally exhibit a mixture of host partitioning among viruses and nestededness of host ranges. Networks of bacteria-infecting and eukaryote-infecting viruses possess comparable distributions of dimensionality and prevalence of nestedness, indicating that fundamentals of network structure are similar among domains of life and different viral lineages. The relative simplicity of many infection networks suggests that coevolutionary dynamics are often driven by a modest number of underlying mechanisms.

Regional and fine-scale local adaptation in salinity tolerance in Daphnia inhabiting contrasting clusters of inland saline waters.

Understanding the spatial scales at which organisms can adapt to strong natural and human-induced environmental gradients is important. Salinization is a key threat to biodiversity, ecosystem functioning and the provision of ecosystem services of freshwater systems. Clusters of naturally saline habitats represent ideal test cases to study the extent and scale of local adaptation to salinization. We studied local adaptation of the water flea Daphnia magna, a key component of pond food webs, to salinity in two contrasting landscapes-a dense cluster of sodic bomb crater ponds and a larger-scale cluster of soda pans. We show regional differentiation in salinity tolerance reflecting the higher salinity levels of soda pans versus bomb crater ponds. We found local adaptation to differences in salinity levels at the scale of tens of metres among bomb crater pond populations but not among geographically more distant soda pan populations. More saline bomb crater ponds showed an upward shift of the minimum salt tolerance observed across clones and a consequent gradual loss of less tolerant clones in a nested pattern. Our results show evolutionary adaptation to salinity gradients at different spatial scales, including fine-tuned local adaptation in neighbouring habitat patches in a natural landscape.

Stability, resilience and eco-evolutionary feedbacks of mutualistic networks to rising temperature.

Ecological networks comprising of mutualistic interactions can suddenly transition to undesirable states, such as collapse, due to small changes in environmental conditions such as a rise in local environmental temperature. However, little is known about the capacity of such interaction networks to adapt to a rise in temperature and the occurrence of critical transitions. Here, combining quantitative genetics and mutualistic dynamics in an eco-evolutionary framework, we evaluated the stability and resilience of mutualistic networks to critical transitions as environmental temperature increases. Specifically, we modelled the dynamics of an optimum trait that determined the tolerance of species to local environmental temperature as well as to species interaction. We then evaluated the impact of individual trait variation and evolutionary dynamics on the stability of feasible equilibria, the occurrence of threshold temperatures at which community collapses, and the abruptness of such community collapses. We found that mutualistic network architecture, that is the size of the community and the arrangement of species interactions, interacted with evolutionary dynamics to impact the onset of network collapses. Some networks had more capacity to track the rise in temperatures than others and thereby increased the threshold temperature at which the networks collapsed. However, such a result was modulated by the amount of heritable trait variation species exhibited, with high trait variation in the mean optimum phenotypic trait increasing the environmental temperature at which networks collapsed. Furthermore, trait variation not only increased the onset of temperatures at which networks collapsed but also increased the local stability of feasible equilibria. Our study argued that mutualistic network architecture interacts with species evolutionary dynamics and increases the capacity of networks to adapt to changes in temperature and thereby delayed the occurrence of community collapses.

Community connectivity and local heterogeneity explain animal species co-occurrences within pond communities.

Metacommunity processes have the potential to determine most features of the community structure. However, species diversity has been the dominant focus of studies. Nestedness, modularity and checkerboard distribution of species occurrences are main components of biodiversity organisation. Within communities, these patterns emerge from the interaction between functional diversity, spatial heterogeneity and resource availability. Additionally, the connectivity determines the pool of species for community assembly and, eventually, the pattern of species co-occurrence within communities. Despite the recognised theoretical expectations, the change in occurrence patterns within communities along ecological gradients has seldom been considered. Here, we analyse the spatial occurrence of animal species along sampling units within 18 temporary ponds and its relationship with pond environments and geographic isolation. Isolated ponds presented a nested organisation of species with low spatial segregation-modularity and checkerboard-and the opposite was found for communities with high connectivity. A pattern putatively explained by high functional diversity in ponds with large connectivity and heterogeneity, which determines that species composition tracks changes in microhabitats. On the contrary, nestedness is promoted in dispersal-limited communities with low functional diversity, where microhabitat filters mainly affect richness without spatial replacement between functional groups. Vegetation biomass promotes nestedness, probably due to the observed increase in spatial variance in biomass with the mean biomass. Similarly, the richness of vegetation reduced the spatial segregation of animals within communities. This result may be due to the high plant diversity of the pond that is observed similarly along all sampling units, which promotes the spatial co-occurrence of species at this scale. In the study system, the spatial arrangement of species within communities is related to local drivers as heterogeneity and metacommunity processes by means of dispersal between communities. Patterns of species co-occurrence are interrelated with community biodiversity and species interactions, and consequently with most functional and structural properties of communities. These results indicate that understanding the interplay between metacommunity processes and co-occurrence patterns is probably more important than previously thought to understand biodiversity assembly and functioning.

Los procesos metacomunitarios tienen el potencial de determinar la mayoría de las características de la estructura de las comunidades. Sin embargo, los trabajos se han enfocado principalmente en los patrones de diversidad de especies. El anidamiento, la modularidad y la distribución en damero de la ocurrencia espacial de las especies son propiedades básicas de las comunidades. Estos patrones surgen de la interacción entre la diversidad funcional, la heterogeneidad espacial y la disponibilidad de recursos dentro de las comunidades. Además, el pool de especies disponibles para el ensamblaje está determinado por la conectividad de la comunidad, afectando así su patrón de co­ocurrencia de especies. A pesar de las reconocidas expectativas teóricas, el cambio en los patrones de ocurrencia dentro de las comunidades a lo largo de gradientes ecológicos ha sido poco considerado. Aquí, analizamos la ocurrencia espacial de especies animales dentro de 18 charcos temporales y su relación con las características ambientales y el aislamiento geográfico de los charcos. Los charcos aislados presentaron alto anidamiento espacial mientras que los charcos de alta conectividad una distribución de ocurrencias modular y en damero. Por un lado, la baja diversidad funcional en charcos aislados, determinaría que los filtros microambientales afecten la riqueza de especies sin reemplazo espacial entre grupos funcionales, promoviendo un arreglo anidado de ocurrencias. Por otro lado, la alta diversidad funcional en charcos con alta conectividad y heterogeneidad permitiría el reemplazo espacial de especies en gradientes microambientales, determinando los patrones de segregación observados. La biomasa vegetal promueve el anidamiento, probablemente debido al aumento observado en la variación espacial de la biomasa con la biomasa media. La riqueza vegetal también redujo la segregación espacial de los animales dentro de las comunidades. Este resultado puede deberse a que la alta diversidad de plantas de los charcos es también observada a nivel de unidades muestreales, favoreciendo esto la coexistencia espacial de especies. El arreglo espacial de especies dentro de las comunidades estudiadas estaría determinado tanto por factores locales como la heterogeneidad, como por procesos regionales operando a través de la dispersión de individuos entre comunidades. Los patrones de co­ocurrencia de especies están interrelacionados con la diversidad comunitaria y las interacciones bióticas, y consecuentemente con la mayoría de las propiedades estructurales y funcionales de las comunidades. Este estudio evidencia la importancia de la conexión entre procesos metacomunitarios y la co­ocurrencia espacial de especies para comprender el ensamblaje y funcionamiento de la biodiversidad.

Ecto- and endoparasites of common reedbuck, Redunca arundinum, at 2 localities in KwaZulu-Natal Province, South Africa: community and network structure.

Parasite community structure is governed by functional traits of hosts and parasites. Notably, parasite populations and communities respond to host social and spatial behaviour. Many studies demonstrating these effects dealt with small-bodied host species, while the influence of host social patterns on parasite communities in large hosts remains understudied. In an earlier study on nyalas (Tragelaphus angasii), host age was more important than sex in structuring helminth communities and networks, but the influence of both was mediated by local environmental conditions, creating different locality patterns. Common reedbuck (Redunca arundinum) differ from nyalas in spatial and social behaviour. Based on helminth and ectoparasite data from 56 reedbuck examined at 2 localities in KwaZulu-Natal Province, we asked which patterns are similar and which differ between the 2 host species. Similar to nyalas, reedbuck age was more important than sex in structuring communities and networks. However, local environmental conditions exerted the strongest influence on transmission patterns, especially in ectoparasites. Complex interactions between reedbuck traits, parasite traits and local environmental conditions modulated the risk of infection differently at the 2 sites, confirming our earlier findings in nyalas that pooling data from different locations may obscure location-specific parasite community patterns. Similarities between patterns in reedbuck and nyalas, despite their behavioural differences, suggest some common patterns in parasite community ecology that, in turn, are determined mostly by parasite traits and population dynamics.

Nestedness of flea assemblages harboured by small mammalian hosts revisited: phylogenetic and functional nestedness do not follow compositional nestedness.

We studied compositional, phylogenetic, and functional nestedness in the flea assemblages of 14 host species across regions. Our main questions were (a) are a host's flea assemblages compositionally, phylogenetically, or functionally nested? (b) Do similar processes drive these nestedness facets? (d) Are a host's biological traits associated with nestedness of its flea assemblages? Rows of host matrices were ordered by decreasing species richness/the sum of the branch lengths of a phylogenetic tree/functional dendrogram or by decreasing region area or by increasing distance from the centre of a host's geographic range. None of the matrices sorted by species richness/sum of branch lengths were nested from a compositional perspective, but they were significantly nested from phylogenetic and functional perspectives. Compositional, phylogenetic, and functional nestedness of matrices sorted by region area or by distance from the host's geographic range centre varied between hosts. In some hosts, flea assemblages were nested from all three perspectives independently of how matrix rows were sorted, whereas in other hosts, the occurrence of significant nestedness depended on the order of the matrix rows. The degree of phylogenetic and functional nestedness for matrices sorted by the sum of branch lengths was associated with a host species' morphoecological traits and the latitude of its geographic range. We conclude that consideration of nestedness based solely on species composition does not allow a comprehensive understanding of the patterns of parasite community structure. Nestedness should also be considered from phylogenetic and functional perspectives.

An Entropic Analysis of Social Demonstrations.

Social media has dramatically influenced how individuals and groups express their demands, concerns, and aspirations during social demonstrations. The study of X or Twitter hashtags during those events has revealed the presence of some temporal points characterised by high correlation among their participants. It has also been reported that the connectivity presents a modular-to-nested transition at the point of maximum correlation. The present study aims to determine whether it is possible to characterise this transition using entropic-based tools. Our results show that entropic analysis can effectively find the transition point to the nested structure, allowing researchers to know that the transition occurs without the need for a network representation. The entropic analysis also shows that the modular-to-nested transition is characterised not by the diversity in the number of hashtags users post but by how many hashtags they share.

Range restricted old and young lineages show the southern Western Ghats to be both a museum and a cradle of diversity for woody plants.

The Western Ghats (WG) mountain chain is a global biodiversity hotspot with high diversity and endemicity of woody plants. The latitudinal breadth of the WG offers an opportunity to determine the evolutionary drivers of latitudinal diversity patterns. We examined the spatial patterns of evolutionary diversity using complementary phylogenetic diversity and endemism measures. To examine if different regions of the WG serve as a museum or cradle of evolutionary diversity, we examined the distribution of 470 species based on distribution modelling and occurrence locations across the entire region. In accordance with the expectation, we found that the southern WG is both a museum and cradle of woody plant evolutionary diversity, as a higher proportion of both old and young evolutionary lineages are restricted to the southern WG. The diversity gradient is likely driven by high geo-climatic stability in the south and phylogenetic niche conservatism for moist and aseasonal sites. This is corroborated by persistent lineage nestedness at almost all evolutionary depths (10-135 million years), and a strong correlation of evolutionary diversity with drought seasonality, precipitation and topographic heterogeneity. Our results highlight the global value of the WG, demonstrating, in particular, the importance of protecting the southern WG-an engine of plant diversification and persistence.

Orchid-mycorrhizal fungi interactions reveal a duality in their network structure in two European regions differing in climate.

Network analysis is an effective tool to describe and quantify the ecological interactions between plants and root-associated fungi. Mycoheterotrophic plants, such as orchids, critically rely on mycorrhizal fungi for nutrients to survive, so investigating the structure of those intimate interactions brings new insights into the plant community assembly and coexistence. So far, there is little consensus on the structure of those interactions, described either as nested (generalist interactions), modular (highly specific interactions) or of both topologies. Biotic factors (e.g., mycorrhizal specificity) were shown to influence the network structure, while there is less evidence of abiotic factor effects. By using next-generation sequencing of the orchid mycorrhizal fungal (OMF) community associated to with plant individuals belonging to 17 orchid species, we assessed the structure of four orchid-OMF networks in two European regions under contrasting climatic conditions (Mediterranean vs. Continental). Each network contained four to 12 co-occurring orchid species, including six species shared among the regions. All four networks were both nested and modular, and fungal communities were different between co-occurring orchid species, despite multiple sharing of fungi across some orchids. Co-occurring orchid species growing in Mediterranean climate were associated with more dissimilar fungal communities, consistent with a more modular network structure compared to the Continental ones. OMF diversity was comparable among orchid species since most orchids were associated with multiple rarer fungi and with only a few highly dominant ones in the roots. Our results provide useful highlights into potential factors involved in structuring plant-mycorrhizal fungus interactions in different climatic conditions.