Hybrid networks reveal contrasting effects of agricultural intensification on antagonistic and mutualistic motifs 

Carlos Martínez‐Núñez, Pedro J. Rey, 2021

1. Anthropogenic‐driven perturbations such as agricultural intensification can affect simultaneously and distinctly several species groups and ecosystem functions. Unveiling these concurrent effects on interdependent species groups connected by different types of ecological interactions is a key challenge for ecologists. To this endeavor, hybrid ecological networks arise as a promising tool.
2. In this study, we used bee trap nests to sample hybrid networks that combined mutualistic and antagonistic interactions to explore agricultural intensification effects on the representation of network motifs (i.e., subnetworks showing different interaction types between a small number of species). Also, we assessed the variability of network motif’s frequencies on farms under similar management regimes and the dissimilarity between farms under different ones. For this, we implemented a novel approach, calculating network functional spaces based on probability density estimates of network motif’s frequencies, using network motifs as traits.
3. Results showed that environmentally‐friendly practices maximize the representation of mutualistic (cavity nesting bees‐plants) and predation (wasps‐prey and bees/wasps‐antagonists) motifs. In contrast, intensive agriculture favored generalist and intraguild predation interactions. Lastly, the frequency of motifs representing antagonistic interactions was more inconsistent and unpredictable across sites than mutualistic motifs, especially on intensified farms.
4. Our novel approach, dissecting hybrid networks into their motifs and analyzing the functional space defined by these, reported detailed and contrasting effects of agricultural intensification on network motifs that represent the mutualistic and antagonistic interactions in this system.
   

https://besjournals.onlinelibrary.wiley.com/doi/10.1111/1365-2435.13800

.

Juan Sanchez Cotán (1600)

.

Coexistence holes characterize the assembly and disassembly of multispecies systems

Angulo et al., 2021

A central goal of ecological research has been to understand the limits on the maximum number of species that can coexist under given constraints. However, we know little about the assembly and disassembly processes under which a community can reach such a maximum number, or whether this number is in fact attainable in practice. This limitation is partly due to the challenge of performing experimental work and partly due to the lack of a formalism under which one can systematically study such processes. Here, we introduce a formalism based on algebraic topology and homology theory to study the space of species coexistence formed by a given pool of species. We show that this space is characterized by ubiquitous discontinuities that we call coexistence holes (that is, empty spaces surrounded by filled space). Using theoretical and experimental systems, we aprovide direct evidence showing that these coexistence holes do not occur arbitrarily—their diversity is constrained by the internal structure of species interactions and their frequency can be explained by the external factors acting on these systems. Our work suggests that the assembly and disassembly of ecological systems is a discontinuous process that tends to obey regularities.

Coexistence holes characterize discontinuities in assembly and disassembly processes. a, A hypothetical pool of S = 3 species. b, When each of the 2S − 1 = 7 different species collection is assembled, it can either coexist (blue background) or not (white background). In this hypothetical example, species survive in isolation and coexist when assembled in pairs. However, the three species cannot coexist when assembled together. The corresponding assembly hypergraph is H =[[1], [2], [3], [1, 2], [2, 3], [3, 1]]. c, When embedded into a two-dimensional space (that is, a plane), the assembly hypergraph reveals the assembly hole h = [1, 2, 3]. d, The assembly hole reveals that coexistence abruptly brakes: in all assembly processes to obtain [1, 2, 3], all of the intermediate species collections coexist, but in the final step coexistence does not occur. e, In these hypothetical coexistence outcomes, only species 1 survives in isolation and coexistence is possible only if the species are assembled in a trio. The corresponding assembly hypergraph is H =[[1], [1, 2, 3]]. f, The associated disassembly hypergraph is D(H)=[[1], [2], [3], [1, 2], [2, 3], [3, 1]], calculated from the missing boundary of H. Each hyperedge of D is a sub-community that does not coexist, despite it having been disassembled from the species collection [1, 2, 3] that coexists. When embedded into the plane, D(H) uncovers the disassembly hole [1, 2, 3]. g, The disassembly hole reveals that coexistence abruptly brakes: despite [1, 2, 3] coexisting, in all disassembly processes starting from [1, 2, 3], not a single intermediate species collection with more than one species coexists.

https://www.nature.com/articles/s41559-021-01462-8

.

.

Foto: @withnomoney

.

 .

Del perfume del mastranto y la tristeza del veguero, de un viaje a Camaguan haciendo de cabrestero. De los truenos de Octubre o en Junio los aguaceros, de amarrar cachilapos en la playa o en el estero. De un caballo machiro y un perro cachicamero.

Mi trasegar por el llano, Getulio Vargas Barón

.

Reinterpreting the relationship between number of species and number of links connects community structure and stability  

Carpentier et al., 2021 

For 50 years, ecologists have examined how the number of interactions (links) scales with the number of species in ecological networks. Here, we show that the way the number of links varies when species are sequentially removed from a community is fully defined by a single parameter identifiable from empirical data. We mathematically demonstrate that this parameter is network-specific and connects local stability and robustness, establishing a formal connection between community structure and two prime stability concepts. Importantly, this connection highlights a local stability–robustness trade-off, which is stronger in mutualistic than in trophic networks. Analysis of 435 empirical networks confirmed these results. We finally show how our network-specific approach relates to the classical across-network approach found in literature. Taken together, our results elucidate one of the intricate relationships between network structure and stability in community networks.

https://www.nature.com/articles/s41559-021-01468-2

.

 

Sequence from the movie "Tree of Life" from Rui Batista on Vimeo.

Plant holobiont interactions mediated by the type VI secretion system and the membrane vesicles: promising tools for a greener agriculture 

José Manuel Borrero de Acuña Patricia Bernal, 2021

A deeper understanding of the complex relationship between plants and their microbiota is allowing researchers to appreciate a plethora of possibilities to improve crops using chemical‐free alternatives based on beneficial microorganisms. An increase in crop yield from the promotion of plant growth or even simultaneous protection of the plants from the attack of phytopathogens can be achieved in the presence of different plant‐associated microorganisms known as plant‐growth‐promoting rhizobacteria (PGPR) and biocontrol agents (BCAs), respectively. Thus, the study of the great diversity of plant‐microbe and microbe‐microbe interactions is an attention‐grabbing topic covering studies of interactions since the plant seed and through all developmental stages, from root to shoot. The intricate communication systems that plant holobionts co‐evolved has resulted in many different strategies and interplays between these organisms shaping the bacterial communities and the plant fitness simultaneously. Herein, we emphasize two understudied delivery systems existing in plant‐associated bacteria: the type VI secretion system (T6SS) and the membrane vesicles with a huge potential to boost a highly demanded and necessary green agriculture.

 

https://sfamjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.15457 

.

Coordination of microbe–host homeostasis by crosstalk with plant innate immunity     

Ma et al., 2021.

Plants grown in natural soil are colonized by phylogenetically structured communities of microbes known as the microbiota. Individual microbes can activate microbe-associated molecular pattern (MAMP)-triggered immunity (MTI), which limits pathogen proliferation but curtails plant growth, a phenomenon known as the growth–defence trade-off. Here, we report that, in monoassociations, 41% (62 out of 151) of taxonomically diverse root bacterial commensals suppress Arabidopsis thaliana root growth inhibition (RGI) triggered by immune-stimulating MAMPs or damage-associated molecular patterns. Amplicon sequencing of bacterial 16S rRNA genes reveals that immune activation alters the profile of synthetic communities (SynComs) comprising RGI-non-suppressive strains, whereas the presence of RGI-suppressive strains attenuates this effect. Root colonization by SynComs with different complexities and RGI-suppressive activities alters the expression of 174 core host genes, with functions related to root development and nutrient transport. Furthermore, RGI-suppressive SynComs specifically downregulate a subset of immune-related genes. Precolonization of plants with RGI-suppressive SynComs, or mutation of one commensal-downregulated transcription factor, MYB15, renders the plants more susceptible to opportunistic Pseudomonas pathogens. Our results suggest that RGI-non-suppressive and RGI-suppressive root commensals modulate host susceptibility to pathogens by either eliciting or dampening MTI responses, respectively. This interplay buffers the plant immune system against pathogen perturbation and defence-associated growth inhibition, ultimately leading to commensal–host homeostasis.

https://doi.org/10.1038/s41477-021-00920-2

.