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Whether an ecological community is controlled from above or below remains a popular framework that continues generating interesting research questions and takes on especially important meaning in agroecosystems. We describe the regulation from above of three coffee herbivores, a leaf herbivore (the green coffee scale, Coccus viridis), a seed predator (the coffee berry borer, Hypothenemus hampei), and a plant pathogen (the coffee rust disease, caused by Hemelia vastatrix) by various natural enemies, emphasizing the remarkable complexity involved. We emphasize the intersection of this classical question of ecology with the burgeoning field of complex systems, including references to chaos, critical transitions, hysteresis, basin or boundary collision, and spatial self-organization, all aimed at the applied question of pest control in the coffee agroecosystem.

Temperate phages are viruses of bacteria that can establish two types of infection: a lysogenic infection in which the virus replicates with the host cell without producing virions, and a lytic infection where the host cell is eventually destroyed, and new virions are released. While both lytic and lysogenic infections are routinely observed in the environment, the ecological and evolutionary processes regulating these viral dynamics are still not well understood, especially for uncultivated virus-host pairs. Here, we characterized the long-term dynamics of uncultivated viruses infecting green sulfur bacteria (GSB) in a model freshwater lake (Trout Bog Lake, TBL). As no GSB virus has been formally described yet, we first used two complementary approaches to identify new GSB viruses from TBL; one in vitro based on flow cytometry cell sorting, the other in silico based on CRISPR spacer sequences. We then took advantage of existing TBL metagenomes covering the 2005–2018 period to examine the interactions between GSB and their viruses across years and seasons. From our data, GSB populations in TBL were constantly associated with at least 2-8 viruses each, including both lytic and temperate phages. The dominant GSB population in particular was consistently associated with two prophages with a nearly 100% infection rate for >10 years. We illustrate with a theoretical model that such an interaction can be stable given a low, but persistent, level of prophage induction in low-diversity host populations. Overall, our data suggest that lytic and lysogenic viruses can readily co-infect the same host population, and that host strain-level diversity might be an important factor controlling virus-host dynamics including lytic/lysogeny switch.

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13 1. The animal gut is a complex ecosystem containing many interacting species. A major 14 objective of microbiota research is to identity the scale at which gut taxa shape hosts. 15However, most studies focus solely on pairwise interactions and ignore higher-order 16interactions involving three or more component taxa. Higher-order interactions 17 represent non-additive effects that cannot be predicted from first-order or pairwise 18interactions. 192. Possible reasons as to why studies of higher higher-order interactions have been 20 scarce is that many host-associated systems are experimentally intractable, gut 21 microbiota are prohibitively species rich, and the influence of any given taxon on 22hosts is often context-dependent. Furthermore, quantifying emergent effects that 23 represent higher-order interactions that are not simply the result of lower-order 24 interactions, present a combinatorial challenge for which there are few well-25 developed statistical approaches in host-microbiota studies. 263. In this perspective, our goal is to quantify the existence of emerging higher-order 27 effects and characterize their prevalence in the microbiota. To do so, we adapt a 28 method from evolutionary genetics used to quantify epistatic effects between 29 mutations and use it to quantify the effects of higher-order microbial interactions on 30 host infection risk. 31 4. We illustrate this approach by applying it to an in silico dataset generated to resemble 32 a population of hosts with gut-associated microbial communities. We assign each host 33 a pathogen load, and then determine how emergent interactions between gut taxa 34 influence this host trait. 35 5. We find that the effect of higher-order interactions generally increases in magnitude 36with the number of species in the gut community. Based on the average magnitude of 37 interaction for each order, we find that 9 th order interactions have the largest non-38 linear effect on determining host infection risk. 39 6. Our approach illustrates how incorporating the effects of higher-order interactions 40 among gut microbiota can be essential for understanding their effects on host 41 infection risk. We conclude that insofar as higher-order interactions between taxa may 42 profoundly shape important organismal phenotypes (such as susceptibility to 43 infection), that they deserve greater attention in microbiome studies. 44 1 45 46 Introduction 47 Animal guts contain complex microbial communities whose structure and function 48 depend upon the interactions among microbes and the host. Gut microbiota serve as 49 key actors in host health, impacting development, metabolism, and pathogen 50 susceptibility (Brugman et al., 2018). The development of microbe-free (also known as 51 germ-free) model hosts has made it possible to experimentally study how the 52 microbiota influences host susceptibility to infection (Goodman et al., 2011; Ridaura et 53 al., 2013). However, most studies rely on correlations between the relative abundances 54 of individual bacterial taxa an...

Many of the choices humans make with regard to infrastructure, urban planning and other phenomena have impacts that will last thousands of years. This can readily be seen in modern cities in which contemporary streets run along street grids that were laid out thousands of years prior or even in which ancient viaducts still play a role. However, rarely do evolutionary biologists explicitly consider the future of life likely to be associated with the decisions we are making today. Here, we consider the evolutionary future of species in cities with a focus on the origin of lineages and species. We do so by adjusting evolutionary predictions from the theory of island biogeography so as to correspond to the unique features of cities as islands. Specifically, the species endemic to cities tend to be associated with the gray habitats in cities. Those habitats tend to be dominated by human bodies, pet bodies and stored food. It is among such species where the origin of new lineages is most likely, although most research on evolution in cities has focused on green habitats. We conclude by considering a range of scenarios for the far future and their implications for the origin of lineages and species.

Aim: Understanding the ecological conditions that determine invasive success requires information on the ecological dynamics in both the native and introduced range of exotic species. While numerous studies of the little fire ant, Wasmannia auropunctata, have focused on the evolutionary aspects of invasiveness, we know little about possible ecological dynamics that might contribute to the remarkable invasiveness of this species.Location: We investigate the ecological differences in resource discovery and recruitment by W. auropunctata within its native range (Mexico) and introduced range (Puerto Rico). Methods:We conducted experimental trials on coffee plants by comparing: (1) the rate of resource discovery by W. auropunctata at various distances from main foraging trails; and (2) the recruitment rate between W. auropunctata in the introduced range of Puerto Rico. Results:Our experiments revealed that W. auropunctata took nearly twice as long to discover baits in Puerto Rico, as compared to Mexico. W. auropunctata was relatively slower at recruiting workers than other dominant ants. Main conclusion:We conclude that competitive traits such as resource discovery and recruitment are not necessarily indicative of invasive success, but contradict traditional expectations. We propose that W. auropunctata behaves as an insinuator species in Mexico (i.e. workers maintain a low profile), while in Puerto Rico it acts as an aggressive dominator. The switch in foraging strategy might explain the astounding success of this exotic species. K E Y W O R D Sbiogeography, biological invasions, discovery-dominance-insinuator trade-off, invasive ants, tropical ecology

The tragedy of the commons posits that depletion of common resources harms all stakeholders. Although such a downward spiral is plausible, the potential outcomes are far more complex. In the present article, we report on this coupled feedback between resource strategies and the environment from the perspective of Blackologists. We fully embrace that our understanding and appreciation for nature are inherently shaped by our identity, culture, and lived experiences. First, we deconstruct the uses and beneficiaries of the shared resource. Then, we identify potential cascades of conflict through the lens of resource partitioning, plasticity, and mitigation strategies recognizing the inherent human dimension nested within these dynamics. We emphasize that who studies these processes can alter the framing and outcome of the tragedy through several case studies. We recommend that avoidance of environmental tragedies is possible with inclusive engagement, interdisciplinarity, and oversight at different spatial and temporal scales.