About

Juan A. Bonachela is a faculty member in the Department of Ecology, Evolution, and Natural Resources at Rutgers University. His area of expertise includes theoretical biology, ecology and evolution of spatial and temporal patterns, ecological network dynamics, and interactions ecology-evolution in microbes. His research focuses on understanding the complex interactions and patterns within ecological and evolutionary systems, particularly through the lens of theoretical models. As part of his academic role, he contributes to advancing knowledge in these fields and supports the department's mission of research and education in ecology, evolution, and natural resources.

Research topics

• Ecology
• Chemistry
• Biology
• Artificial Intelligence
• Computer Science
• Physics
• Process management
• Environmental science
• Virology
• Psychology
• Genetics
• Business
• Condensed matter physics
• Telecommunications

Selected publications

• Imbalance in gut microbial interactions as a marker of health and disease

  Science · 2026-02-26 · 3 citations

  articleCorresponding

  Imbalances in the human gut microbiome, or dysbioses, are associated with multiple diseases but remain poorly understood. Existing biomarkers of dysbiosis fail to capture the ecological mechanisms that differentiate healthy from diseased microbiomes. We have developed a metric, the ecological network balance index (ENBI), that quantifies the balance between positive and negative microbial interactions. This metric was inspired by the phenomenology observed in a model for gut microbiome dynamics that we introduce in this work, which revealed alternative stable states with distinct emergent microbial communities: a healthy state dominated by negative interactions and a dysbiotic state dominated by positive interactions. The ENBI robustly differentiates these states in both simulated and empirical datasets spanning multiple diseases and correlates with disease progression in conditions such as colorectal cancer, which underscores its potential as a diagnostic tool.

  PublisherDOI

• Spatial Trophic Dynamics Shape and are Shaped by Desertification Transitions

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-02-06

  articleSenior authorCorresponding

  Drylands, which sustain billions of people, face desertification driven by climate change and grazing pressures. From the bottom up, desertification is affected by water availability, with vegetation often self-organising into spatial patterns that vary with aridity levels. How these patterns and ultimately, desertification transitions, are affected by the spatial dynamics of higher trophic levels remain, however, poorly understood. Here, we introduce a spatially explicit tri-trophic model that links vegetation pattern formation to consumer-resource interactions and foraging behaviour. We find that the nature of vegetation spatial distribution and desertification transition strongly influence consumer spatial organisation, movement, and synchrony. Vegetation organised regularly in space generates "boom-bust" synchronised metapopulations, whereas fractal vegetation organisation generates scale-free consumer clustering and low synchrony. Our results reveal a reciprocal coupling between spatial trophic dynamics and ecosystem resilience, underscoring the need to integrate trophic interactions and behaviour into predictions informing management strategies for dryland ecosystems.

  PublisherDOI

• Imbalance in gut microbial interactions as a marker of health and disease

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-04-30 · 1 citations

  preprintOpen access

  Imbalances in the human gut microbiome (dysbioses) are linked to multiple diseases but remain poorly understood. Current biomarkers to identify dysbiosis are inconsistent and fail to capture the ecological mechanisms differentiating healthy from diseased microbiomes. We propose a general dysbiosis biomarker, inspired by phenomenology observed in a gut-microbiome theoretical model introduced here. The emergent communities show complex interaction networks and two distinct collective states, corresponding to healthy and dysbiotic microbiomes. Our robust metric for dysbiosis, by quantifying the balance between cooperation and competition, differentiates these states in both simulated and real datasets across diverse diseases. Moreover, it reveals that dysbiosis results from a shift toward greater cooperation in the community. Our metric further correlates with disease progression, highlighting its potential as a diagnostic tool.

  PublisherOA PDFDOI

• Zooplankton feeding behavioral signatures in the morphology of macroscale prey spatial distribution

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-31

  preprintOpen accessSenior author

  The problem of pattern and scale remains a central problem in ecology, bridging fundamental and applied questions. Marine microbial communities are a case in point. For instance, to understand the role of zooplankton in oceanic biogeochemistry, their response to changes in environmental conditions, and the implications for ecosystem services (e.g., fisheries), it is critical to understand zooplankton trophic interactions and how they change in a rapidly changing climate. This understanding, however, remains elusive because, unlike for phytoplankton, for which remote sensing of macroscale patterns can provide insight into their microscale dynamics and community composition, obtaining this information for zooplankton largely rests on quantifying the difficult-to-monitor microscale interactions among millions of individuals with different behaviors, and between individuals and their environment. Here, we investigate whether it is possible to obtain indirect information on zooplankton from the macroscale spatial distribution of their prey. To tackle this “problem of scale”, we develop a rigorous coarse-graining methodology that connects individual-level properties with macroscale spatial patterns. We demonstrate that the shape of the prey spatial distribution can indeed encode information about zooplankton feeding behavior and community dynamics. Specifically, we predict a change in dominant feeding behavior—from non-motile to motile feeding—as one moves from areas of high to areas of low prey density. These results thus suggest a novel application for remote sensing approaches: the potential tracking of consumer behavioral signatures in the large-scale patterns of the resource. Importantly, the scaling-up methodology that we developed to check whether those signatures exist is general, and can be used to link scales rigorously and systematically in any system in which the complexity of individual dynamics makes connecting scales intractable.

  PublisherOA PDFDOI

• Vegetation clump size and number as indicators for alternative stable states in semi-arid ecosystems

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-04

  preprintOpen accessSenior authorCorresponding

  Abstract Dryland ecosystems are vulnerable to desertification, a pressing issue in the face of global climate change. In these ecosystems, vegetation often grows in spatially periodic patterns that differ as aridity increases (gaps, labyrinths and clumps), which has been widely studied theoretically, aiming to assess the proximity of the system to desertification. While some theoretical models predict smooth desertification transitions, most typically predict an abrupt transition linked to the possibility of two alternative stable states (desert and vegetated states), predictions that are yet to be confirmed empirically. If this bistability of alternative stable states occurs, however, environmental fluctuations and the history of the ecosystem determine which state ultimately materializes. This uncertainty makes it harder to predict desertification, compounding the challenges posed by it. Here, we combine empirical data and theoretical methods to investigate the links between bistability and vegetation spatial organization, which can help identify the presence of alternative stable states. We found that, although the presence of vegetation clumps is not indicative of bistability, changes in clump morphology can provide reliable indicators of bistability and an impending desertification transition. Thus, our methodology indirectly identifies whether desertification will occur abruptly, and whether restoration efforts should consider a potential ecosystem history-dependence.

  PublisherOA PDFDOI

• Viral plasticity facilitates host diversity in challenging environments

  Nature Communications · 2024-08-29 · 15 citations

  articleOpen access1st authorCorresponding

  The antagonistic coevolution of microbes and viruses influences fundamentally the diversity of microbial communities. Information on how environmental variables interact with emergent defense-counterdefense strategies and community composition is, however, still scarce. Following biological intuition, diversity should increase with improved growth conditions, which offset evolutionary costs; however, laboratory and regional data suggest that microbial diversity decreases in nutrient-rich conditions. Moreover, global oceanic data show that microbial and viral diversity decline for high latitudes, although the underlying mechanisms are unknown. This article addresses these gaps by introducing an eco-evolutionary model for bacteria-virus antagonistic coevolution. The theory presented here harmonizes the observations above and identifies negative density dependence and viral plasticity (dependence of virus performance on host physiological state) as key drivers: environmental conditions selecting for slow host growth also limit viral performance, facilitating the survival of a diverse host community; host diversity, in turn, enables viral portfolio effects and bet-hedging strategies that sustain viral diversity. From marine microbes to phage therapy against antibiotic-resistant bacteria or cancer cells, the ubiquity of antagonistic coevolution highlights the need to consider eco-evolutionary interactions across a gradient of growth conditions.

  PublisherOA PDFDOI

• Geometric effects of fragmentation are likely to mitigate diversity loss following habitat destruction in real‐world landscapes

  Global Ecology and Biogeography · 2024-03-13 · 4 citations

  articleOpen access

  Abstract Aim Habitat conversion is the number one threat to biodiversity. The loss of biodiversity due to habitat loss might be exacerbated if species are harmed by fragmentation per se—the breaking apart of natural habitat that remains (hereafter fragmentation ). However, the evidence that species are harmed by habitat fragmentation is mixed. Studies at the patch scale tend to show that fragmentation reduces diversity due to negative demographic effects on species' dispersal, survival and fecundity. In contrast, studies at the landscape scale tend to show that fragmentation increases diversity. This discrepancy may be partly due to geometric effects, defined as greater species turnover between patches in more fragmented landscapes. Although these effects have been demonstrated theoretically and are expected to be stronger across larger spatial extents, it is unclear whether they are likely to occur in real‐world settings with both realistic landscape patterns and communities. Here, we investigated the possibility of geometric effects using simulations combined with real‐world landscape and community data. Location New Jersey, northeastern USA. Time period Current. Taxa studied Bees. Methods We focused on landscape sizes within the typical range for protected areas (36–576 ha), simulated forest loss using real landscape patterns, and simulated forest‐bee communities based on field data we collected. Results We found weak but positive effects of fragmentation: immediately following forest destruction, the most fragmented forests harboured up to 7.3% more species than the least fragmented forests of the same area, in agreement with observational studies of biodiversity along fragmentation gradients. In contrast to expectations, however, the overall effects of fragmentation did not change with spatial extent. Conclusions Our results suggest that fragmentation can mitigate biodiversity loss immediately following habitat destruction, but that the benefits do not vary strongly with spatial extent in real‐world landscapes and at extents relevant to land management.

  PublisherOA PDFDOI

• Altered growth and death in dilution-based viral predation assays

  PLoS ONE · 2023-07-07 · 3 citations

  articleOpen accessCorresponding

  Viral lysis of phytoplankton is one of the most common forms of death on Earth. Building on an assay used extensively to assess rates of phytoplankton loss to predation by grazers, lysis rates are increasingly quantified through dilution-based techniques. In this approach, dilution of viruses and hosts are expected to reduce infection rates and thus increase host net growth rates (i.e., accumulation rates). The difference between diluted and undiluted host growth rates is interpreted as a measurable proxy for the rate of viral lytic death. These assays are usually conducted in volumes ≥ 1 L. To increase throughput, we implemented a miniaturized, high-throughput, high-replication, flow cytometric microplate dilution assay to measure viral lysis in environmental samples sourced from a suburban pond and the North Atlantic Ocean. The most notable outcome we observed was a decline in phytoplankton densities that was exacerbated by dilution, instead of the increased growth rates expected from lowered virus-phytoplankton encounters. We sought to explain this counterintuitive outcome using theoretical, environmental, and experimental analyses. Our study shows that, while die-offs could be partly explained by a 'plate effect' due to small incubation volumes and cells adhering to walls, the declines in phytoplankton densities are not volume-dependent. Rather, they are driven by many density- and physiology-dependent effects of dilution on predation pressure, nutrient limitation, and growth, all of which violate the original assumptions of dilution assays. As these effects are volume-independent, these processes likely occur in all dilution assays that our analyses show to be remarkably sensitive to dilution-altered phytoplankton growth and insensitive to actual predation pressure. Incorporating altered growth as well as predation, we present a logical framework that categorizes locations by the relative dominance of these mechanisms, with general applicability to dilution-based assays.

  PublisherOA PDFDOI

• Inferring Long-term Dynamics of Ecological Communities Using Combinatorics

  arXiv (Cornell University) · 2023-09-01

  preprintOpen access

  In an increasingly changing world, predicting the fate of species across the globe has become a major concern. Understanding how the population dynamics of various species and communities will unfold requires predictive tools that experimental data alone can not capture. Here, we introduce our combinatorial framework, Widespread Ecological Networks and their Dynamical Signatures (WENDyS) which, using data on the relative strengths of interactions and growth rates within a community of species predicts all possible long-term outcomes of the community. To this end, WENDyS partitions the multidimensional parameter space (formed by the strengths of interactions and growth rates) into a finite number of regions, each corresponding to a unique set of coarse population dynamics. Thus, WENDyS ultimately creates a library of all possible outcomes for the community. On the one hand, our framework avoids the typical ``parameter sweeps'' that have become ubiquitous across other forms of mathematical modeling, which can be computationally expensive for ecologically realistic models and examples. On the other hand, WENDyS opens the opportunity for interdisciplinary teams to use standard experimental data (i.e., strengths of interactions and growth rates) to filter down the possible end states of a community. To demonstrate the latter, here we present a case study from the Indonesian Coral Reef. We analyze how different interactions between anemone and anemonefish species lead to alternative stable states for the coral reef community, and how competition can increase the chance of exclusion for one or more species. WENDyS, thus, can be used to anticipate ecological outcomes and test the effectiveness of management (e.g., conservation) strategies.

  PublisherOA PDFDOI

• Multiple co‐occurring bioeconomic drivers of overexploitation can accelerate rare species extinction risk

  Journal of Applied Ecology · 2023-02-27 · 8 citations

  articleOpen access

  Abstract The unsustainable harvest of species for the global wildlife trade is a major cause of vertebrate extinction. Through the anthropogenic Allee effect (AAE), overexploitation to extinction can occur when a species' rarity drives up its market price, enabling profitable harvest of all remaining individuals. Even in the absence of rarity value, however, the harvest of other species can subsidize the overexploitation of a rare species to the point of extinction, a phenomenon termed opportunistic exploitation. These two pathways to extinction have been considered independently, but many traded species experience them simultaneously. In this study, we develop a simple model that incorporates these mechanisms simultaneously and demonstrate that including multiple harvest strategies with market‐based feedbacks fundamentally alters rare species extinction risk and the rate at which overexploitation occurs. As a pertinent case study, we consider the harvest of ground pangolins Smutsia temminckii . Our results show that pangolin extinction was generally associated with high rarity value, the use of multiple harvest strategies and the simultaneous harvest of a common species that has a fast life history. Pangolin population depletion and short‐term extinction risk were greatest when harvesters used a combination of pursuit and opportunistic (i.e. multi‐species) harvest strategies. Policy implications. Our results suggest that feedbacks between multiple financial incentives to overharvest can exacerbate the risk of extinction of rare species. As a result, continuing to address AAE and opportunistic exploitation as separate extinction pathways may insufficiently capture extinction risk for many exploited species. Criteria for assessing extinction risk or harvest sustainability of exploited species should incorporate multiple drivers of harvest pressure, with an expanded focus on including species with high rarity value that are exploited in multi‐species harvest regimes.

  PublisherOA PDFDOI

Recent grants

• Characterizing Ecological Transitions in Systems with Regularity

  NSF · $210k · 2021–2026

Frequent coauthors

• Miguel A. Muñoz

  23 shared

• Simon A. Levin

  Princeton University

  18 shared

• Corina E. Tarnita

  Princeton University

  10 shared

• Ricardo Martínez‐García

  Universidade Estadual Paulista (Unesp)

  9 shared

• Carey D. Nadell

  Dartmouth College

  9 shared

• Kay Jörg Wiese

  Université Paris Cité

  8 shared

• Adam C. Martiny

  University of California, Irvine

  8 shared

• Melinda Choua

  8 shared