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1. Inferring resource competition in microbial communities from time series

   https://doi.org/10.1101/2025.01.08.631910  

   Chen, Xiaowen; Crocker, Kyle; Kuehn, Seppe; Walczak, Aleksandra M; Mora, Thierry (January 2025, bioRxiv)

   The competition for resources is a defining feature of microbial communities. In many contexts, from soils to host-associated communities, highly diverse microbes are organized into metabolic groups or guilds with similar resource preferences. The resource preferences of individual taxa that give rise to these guilds are critical for understanding fluxes of resources through the community and the structure of diversity in the system. However, inferring the metabolic capabilities of individual taxa, and their competition with other taxa, within a community is challenging and unresolved. Here we address this gap in knowledge by leveraging dynamic measurements of abundances in communities. We show that simple correlations are often misleading in predicting resource competition. We show that spectral methods such as the cross-power spectral density (CPSD) and coherence that account for time-delayed effects are superior metrics for inferring the structure of resource competition in communities. We first demonstrate this fact on synthetic data generated from consumer-resource models with time-dependent resource availability, where taxa are organized into groups or guilds with similar resource preferences. By applying spectral methods to oceanic plankton time-series data, we demonstrate that these methods detect interaction structures among species with similar genomic sequences. Our results indicate that analyzing temporal data across multiple timescales can reveal the underlying structure of resource competition within communities. 

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2. Biotic interactions are the dominant drivers of phylogenetic and functional structure in bird communities along a tropical elevational gradient

   https://doi.org/10.1093/auk/ukz054  

   Boyce, Andy J; Shakya, Subir; Sheldon, Frederick H; Moyle, Robert G; Martin, Thomas E (October 2019, The Auk)

   Abstract Understanding how biotic and abiotic interactions influence community assembly and composition is a fundamental goal in community ecology. Addressing this issue is particularly tractable along elevational gradients in tropical mountains that feature substantial abiotic gradients and rates of species turnover. We examined elevational patterns of avian community structure on 2 mountains in Malaysian Borneo to assess changes in the relative strength of biotic interactions and abiotic constraints. In particular, we used metrics based on (1) phylogenetic relatedness and (2) functional traits associated with both resource acquisition and tolerance of abiotic challenges to identify patterns and causes of elevational differences in community structure. High elevation communities were composed of more phylogenetically and functionally similar species than would be expected by chance. Resource acquisition traits, in particular, were clustered at high elevations, suggesting low resource and habitat diversity were important drivers of those communities. Traits typically associated with tolerance of cold temperatures and low atmospheric pressure showed no elevational patterns. All traits were neutral or overdispersed at low elevations suggesting an absence of strong abiotic filters or an increased influence of interspecific competition. However, relative bill size, which is important for thermoregulation, was larger in low elevation communities, suggesting abiotic factors were also influential there. Regardless of metric, clustered and neutral communities were more frequent than overdispersed communities overall, implying that interspecific competition among close relatives may not be a pervasive driver of elevational distribution and community structure of tropical birds. Overall, our analyses reveal that a diverse set of predominantly biotic factors underlie elevational variation in community structure on tropical mountains. 

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3. Consequences of deforestation on functional community structure reverse at high elevations

   https://doi.org/10.1086/738326  

   Lertzman-Lepofsky, Gavia; Frishkoff, Luke O; Mahler, D Luke (August 2025, The American Naturalist)

   Functional diversity is expected to decrease following land conversion. Empirically, however, the consequences of such changes are highly variable. One possible explanation is that the magnitude and direction of functional diversity change depends on how agricultural land conversion interacts with the original determinants of community assembly (e.g., temperature and elevation gradients). We compared the functional structure of 50 Anolis lizard communities on the island of Hispaniola in both forested and deforested habitats along an elevation gradient, as elevation often determines community composition. We used morphological measurements of body size, limb and tail length, and toepad width to capture ecomorphological aspects of functional diversity. These traits are strongly linked to habitat use which has been shown to be the primary axis of niche partitioning in anoles. We found that deforestation had little effect on functional (morphological) richness at low elevations but increased functional richness and evenness at high elevations, where natural communities are depauperate due to thermal constraints. Simultaneously, deforestation reduced spatial turnover and eliminated morphologically peripheral species. These results suggest that how land conversion affects communities depends on whether it relaxes or reinforces a community’s dominant environmental filters: at high elevations, as deforestation increases daytime temperatures, the filters that typically shape these communities are relaxed, allowing them to functionally resemble low elevation communities. While this enriches high-elevation communities, it also removes morphologically unique species and homogenizes diversity across elevations. Our results highlight that how land conversion reorganizes the functional structure of a community depends on that community’s environmental context. 

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4. Competition for fluctuating resources reproduces statistics of species abundance over time across wide-ranging microbiotas

   https://doi.org/10.7554/eLife.75168  

   Ho, Po-Yi; Good, Benjamin H; Huang, Kerwyn Casey (April 2022, eLife)

   Across diverse microbiotas, species abundances vary in time with distinctive statistical behaviors that appear to generalize across hosts, but the origins and implications of these patterns remain unclear. Here, we show that many of these macroecological patterns can be quantitatively recapitulated by a simple class of consumer-resource models, in which the metabolic capabilities of different species are randomly drawn from a common statistical distribution. Our model parametrizes the consumer-resource properties of a community using only a small number of global parameters, including the total number of resources, typical resource fluctuations over time, and the average overlap in resource-consumption profiles across species. We show that variation in these macroscopic parameters strongly affects the time series statistics generated by the model, and we identify specific sets of global parameters that can recapitulate macroecological patterns across wide-ranging microbiotas, including the human gut, saliva, and vagina, as well as mouse gut and rice, without needing to specify microscopic details of resource consumption. These findings suggest that resource competition may be a dominant driver of community dynamics. Our work unifies numerous time series patterns under a simple model, and provides an accessible framework to infer macroscopic parameters of effective resource competition from longitudinal studies of microbial communities. 

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5. Long-Term Cellulose Enrichment Selects for Highly Cellulolytic Consortia and Competition for Public Goods

   https://doi.org/10.1128/msystems.01519-21  

   Lewin, Gina R.; Davis, Nicole M.; McDonald, Bradon R.; Book, Adam J.; Chevrette, Marc G.; Suh, Steven; Boll, Ardina; Currie, Cameron R. (April 2022, mSystems)

   Mackelprang, Rachel (Ed.)

   ABSTRACT The complexity of microbial communities hinders our understanding of how microbial diversity and microbe-microbe interactions impact community functions. Here, using six independent communities originating from the refuse dumps of leaf-cutter ants and enriched using the plant polymer cellulose as the sole source of carbon, we examine how changes in bacterial diversity and interactions impact plant biomass decomposition. Over up to 60 serial transfers (∼8 months) using Whatman cellulose filter paper, cellulolytic ability increased and then stabilized in four enrichment lines and was variable in two lines. Bacterial community characterization using 16S rRNA gene amplicon sequencing showed community succession differed between the highly cellulolytic enrichment lines and those that had slower and more variable cellulose degradation rates. Metagenomic and metatranscriptomic analyses revealed that Cellvibrio and/or Cellulomonas dominated each enrichment line and produced the majority of cellulase enzymes, while diverse taxa were retained within these communities over the duration of transfers. Interestingly, the less cellulolytic communities had a higher diversity of organisms competing for the cellulose breakdown product cellobiose, suggesting that cheating slowed cellulose degradation. In addition, we found competitive exclusion as an important factor shaping all of the communities, with a negative correlation of Cellvibrio and Cellulomonas abundance within individual enrichment lines and the expression of genes associated with the production of secondary metabolites, toxins, and other antagonistic compounds. Our results provide insights into how microbial diversity and competition affect the stability and function of cellulose-degrading communities. IMPORTANCE Microbial communities are a key driver of the carbon cycle through the breakdown of complex polysaccharides in diverse environments including soil, marine systems, and the mammalian gut. However, due to the complexity of these communities, the species-species interactions that impact community structure and ultimately shape the rate of decomposition are difficult to define. Here, we performed serial enrichment on cellulose using communities inoculated from leaf-cutter ant refuse dumps, a cellulose-rich environment. By concurrently tracking cellulolytic ability and community composition and through metagenomic and metatranscriptomic sequencing, we analyzed the ecological dynamics of the enrichment lines. Our data suggest that antagonism is prevalent in these communities and that competition for soluble sugars may slow degradation and lead to community instability. Together, these results help reveal the relationships between competition and polysaccharide decomposition, with implications in diverse areas ranging from microbial community ecology to cellulosic biofuels production. 

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