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1. Network motifs involving both competition and facilitation predict biodiversity in alpine plant communities

   https://doi.org/10.1073/pnas.2005759118  

   Losapio, Gianalberto; Schöb, Christian; Staniczenko, Phillip P.; Carrara, Francesco; Palamara, Gian Marco; De Moraes, Consuelo M.; Mescher, Mark C.; Brooker, Rob W.; Butterfield, Bradley J.; Callaway, Ragan M.; et al (February 2021, Proceedings of the National Academy of Sciences)

   null (Ed.)

   Biological diversity depends on multiple, cooccurring ecological interactions. However, most studies focus on one interaction type at a time, leaving community ecologists unsure of how positive and negative associations among species combine to influence biodiversity patterns. Using surveys of plant populations in alpine communities worldwide, we explore patterns of positive and negative associations among triads of species (modules) and their relationship to local biodiversity. Three modules, each incorporating both positive and negative associations, were overrepresented, thus acting as "network motifs." Furthermore, the overrepresentation of these network motifs is positively linked to species diversity globally. A theoretical model illustrates that these network motifs, based on competition between facilitated species or facilitation between inferior competitors, increase local persistence. Our findings suggest that the interplay of competition and facilitation is crucial for maintaining biodiversity. 

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2. Higher-order effects, continuous species interactions, and trait evolution shape microbial spatial dynamics

   https://doi.org/10.1073/pnas.2020956119  

   Swain, Anshuman; Fussell, Levi; Fagan, William F. (January 2022, Proceedings of the National Academy of Sciences)

   The assembly and maintenance of microbial diversity in natural communities, despite the abundance of toxin-based antagonistic interactions, presents major challenges for biological understanding. A common framework for investigating such antagonistic interactions involves cyclic dominance games with pairwise interactions. The incorporation of higher-order interactions in such models permits increased levels of microbial diversity, especially in communities in which antibiotic-producing, sensitive, and resistant strains coexist. However, most such models involve a small number of discrete species, assume a notion of pure cyclic dominance, and focus on low mutation rate regimes, none of which well represent the highly interlinked, quickly evolving, and continuous nature of microbial phenotypic space. Here, we present an alternative vision of spatial dynamics for microbial communities based on antagonistic interactions—one in which a large number of species interact in continuous phenotypic space, are capable of rapid mutation, and engage in both direct and higher-order interactions mediated by production of and resistance to antibiotics. Focusing on toxin production, vulnerability, and inhibition among species, we observe highly divergent patterns of diversity and spatial community dynamics. We find that species interaction constraints (rather than mobility) best predict spatiotemporal disturbance regimes, whereas community formation time, mobility, and mutation size best explain patterns of diversity. We also report an intriguing relationship among community formation time, spatial disturbance regimes, and diversity dynamics. This relationship, which suggests that both higher-order interactions and rapid evolution are critical for the origin and maintenance of microbial diversity, has broad-ranging links to the maintenance of diversity in other systems. 

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3. Niche partitioning of microbial communities in riverine floodplains

   https://doi.org/10.1038/s41598-019-52865-4  

   Peipoch, Marc; Miller, Scott R.; Antao, Tiago R.; Valett, H. Maurice (November 2019, Scientific Reports)

   Abstract Riverine floodplains exhibit high floral and faunal diversity as a consequence of their biophysical complexity. Extension of such niche partitioning processes to microbial communities is far less resolved or supported. Here, we evaluated the responses of aquatic biofilms diversity to environmental gradients across ten riverine floodplains with differing degrees of flow alteration and habitat diversity to assess whether complex floodplains support biofilm communities with greater biodiversity and species interactions. No significant evidence was found to support a central role for habitat diversity in promoting microbial diversity across 116 samples derived from 62 aquatic habitats, as neither α (H’: 2.8–4.1) nor β (Sørensen: 0.3–0.39) diversity were positively related to floodplain complexity across the ten floodplains. In contrast, our results documented the sensitivity of biofilm communities to regional templates manifested as gradients of carbon, nitrogen, and phosphorous availability. Large-scale conditions reflecting nitrogen limitation increased the relative abundance of N-fixing cyanobacteria (up to 0.34 as fraction of total reads), constrained the total number of interactions among bacterial taxa, and reinforced negative over positive interactions, generating unique microbial communities and networks that reflect large-scale species sorting in response to regional geochemical gradients. 

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4. Substrate complexity buffers negative interactions in a synthetic community of leaf litter degraders

   https://doi.org/10.1093/femsec/fiae102  

   Abdoli, Parmis; Vulin, Clément; Lepiz, Miriam; Chase, Alexander_B; Weihe, Claudia; Rodríguez-Verdugo, Alejandra (July 2024, FEMS Microbiology Ecology)

   Abstract Leaf litter microbes collectively degrade plant polysaccharides, influencing land–atmosphere carbon exchange. An open question is how substrate complexity—defined as the structure of the saccharide and the amount of external processing by extracellular enzymes—influences species interactions. We tested the hypothesis that monosaccharides (i.e. xylose) promote negative interactions through resource competition, and polysaccharides (i.e. xylan) promote neutral or positive interactions through resource partitioning or synergism among extracellular enzymes. We assembled a three-species community of leaf litter-degrading bacteria isolated from a grassland site in Southern California. In the polysaccharide xylan, pairs of species stably coexisted and grew equally in coculture and in monoculture. Conversely, in the monosaccharide xylose, competitive exclusion and negative interactions prevailed. These pairwise dynamics remained consistent in a three-species community: all three species coexisted in xylan, while only two species coexisted in xylose, with one species capable of using peptone. A mathematical model showed that in xylose these dynamics could be explained by resource competition. Instead, the model could not predict the coexistence patterns in xylan, suggesting other interactions exist during biopolymer degradation. Overall, our study shows that substrate complexity influences species interactions and patterns of coexistence in a synthetic microbial community of leaf litter degraders. 

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5. Amplicon Sequencing Analysis of Submerged Plant Microbiome Diversity and Screening for ACC Deaminase Production by Microbes

   https://doi.org/10.3390/ijms252413330  

   Mohan, Binoop; Majeed, Aqsa; Thingujam, Doni; Burton, Sethson Silton; Cowart, Katie E; Pajerowska-Mukhtar, Karolina M; Mukhtar, M Shahid (December 2024, International Journal of Molecular Sciences)

   Submerged plants can thrive entirely underwater, playing a crucial role in maintaining water quality, supporting aquatic organisms, and enhancing sediment stability. However, they face multiple challenges, including reduced light availability, fluctuating water conditions, and limited nutrient access. Despite these stresses, submerged plants demonstrate remarkable resilience through physiological and biochemical adaptations. Additionally, their interactions with microbial communities are increasingly recognized as pivotal in mitigating these environmental stresses. Understanding the diversity of these microbial communities is crucial for comprehending the complex interactions between submerged plants and their environments. This research aims to identify and screen microbes from submerged plant samples capable of producing 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase and to explore microbial diversity through metagenomic analysis. Microbes were isolated and screened for ACC deaminase production, and metagenomic techniques, including co-occurrence network analysis, were used to examine microbial diversity and interactions within the communities. ACC deaminase-producing microbes can significantly enhance plant metabolism under stress conditions. The identification of the culturable bacteria revealed that most of these microbes belong to the genera Pseudomonas, Bacillus, and Acinetobacter. A total of 177 microbial strains were cultured, with molecular identification revealing 79 reductant, 86 non-reductant, and 12 uncultured strains. Among 162 samples screened for ACC deaminase activity, 50 tested positive. To further understand microbial dynamics, samples were collected from both natural sources and artificial pond reservoirs to assess the impact of the location on flood-associated microbiomes in submerged plants. Metagenomic analysis was conducted on both the epiphytic and endophytic samples. By exploring the overall composition and dynamics of microbial communities associated with submerged plants, this research seeks to deepen our understanding of plant–microbe interactions in aquatic environments. The microbial screening helped to identify the diverse microbes associated with ACC deaminase activity in submerged plants and amplicon sequencing analysis paved the way towards identifying the impact of the location in shaping the microbiome and the diversity associated with endophytic and epiphytic microbes. Co-occurrence network analysis further highlighted the intricate interactions within these microbial communities. Notably, ACC deaminase activity was observed in plant-associated microbes across different locations, with distinct variations between epiphytic and endophytic populations as identified through co-occurrence network analysis. 

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