Rare microbial taxa emerge when communities collide: freshwater and marine microbiome responses to experimental mixing

Rocca, Jennifer D.; Simonin, Marie; Bernhardt, Emily S.; Washburne, Alex D.; Wright, Justin P.

doi:10.1002/ecy.2956

Cited by 79 publications

(75 citation statements)

References 58 publications

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“…In our study we tried to mimic natural dispersal events of bacterial communities which are often complex and involve mixing or coalescence of entire communities (Rillig et al, 2015; Rocca et al, 2020). This study provides experimental evidence that temperature‐dependency of invasion (immigration) success can occur in complex pelagic bacterial communities wherein different bacterial groups are involved in different ways.…”

Section: Discussionmentioning

confidence: 99%

“…In the latter case, dispersal initiates species sorting processes even at very low rates of dispersal (Declerck et al, 2013), which eventually selects species that are better adapted to the given environment. All these processes can play an important role whenever mixing of communities (known as “community coalescence”) occurs (Rocca et al, 2020). Such community interchange events vary in the extent to which the environments of the coalescing communities are involved in the exchange, the mixing ratio of the communities, as well as temporal aspects of the event, which then all influence the resulting species establishments, exchanges and extinctions (Rillig et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

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Warming mediates the resistance of aquatic bacteria to invasion during community coalescence

et al. 2021

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The immigration history of communities can profoundly affect community composition. For instance, early‐arriving species can have a lasting effect on community structure by reducing the invasion success of late‐arriving ones through priority effects. This can be particularly important when early‐arriving communities coalesce with another community during dispersal (mixing) events. However, the outcome of such community coalescence is unknown as we lack knowledge on how different factors influence the persistence of early‐arriving communities and the invasion success of late‐arriving taxa. Therefore, we implemented a full‐factorial experiment with aquatic bacteria where temperature and dispersal rate of a better adapted community were manipulated to test their joint effects on the resistance of early‐arriving communities to invasion, both at community and population level. Our 16S rRNA gene sequencing‐based results showed that invasion success of better adapted late‐arriving bacteria equaled or even exceeded what we expected based on the dispersal ratios of the recipient and invading communities suggesting limited priority effects on the community level. Patterns detected at the population level, however, showed that resistance of aquatic bacteria to invasion might be strengthened by warming as higher temperatures (a) increased the sum of relative abundances of persistent bacteria in the recipient communities, and (b) restricted the total relative abundance of successfully established late‐arriving bacteria. Warming‐enhanced resistance, however, was not always found and its strengths differed between recipient communities and dispersal rates. Nevertheless, our findings highlight the potential role of warming in mitigating the effects of invasion at the population level.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Warming mediates the resistance of aquatic bacteria to invasion during community coalescence

et al. 2021

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“…The emergence of rare taxa seems to be a shared coalescence outcome between different ecosystems, i.e. for the mixing of freshwater and marine microbiome (29), the unequal mixing of two soils with different physicochemical and microbial compositions (69) or the mixing of soils for the outcome of rhizobial communities on rooibos nodules (70). Rare taxa becoming dominant can provide essential or new functions in nutrient cycling or plant growth, which replace or compensate for the function deficiency of abundant species (71).…”

Section: Discussionmentioning

confidence: 99%

“…The encounter between two microbial communities and how they then evolve together has been called community coalescence (27–29). The outcomes of community coalescence can vary in a continuum between two categories from symmetric to asymmetric outcomes (30).…”

Section: Introductionmentioning

confidence: 99%

Asymmetric outcome of community coalescence of seed and soil microbiota during early seedling growth

Rochefort

Simonin

Marais

et al. 2020

Preprint

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Seed microbial community constitutes a primary inoculum for plant microbiota assembly. Still, the persistence of seed microbiota when seeds encounter soil during plant emergence and early growth is barely documented. Here, we characterized the interchange event or coalescence of seed and soil microbiota and how it structured seedling bacterial and fungal communities. We performed eight contrasted coalescence events to identify drivers influencing seedling microbiota assembly: four seed lots of two Brassica napus genotypes were sown in two soils of contrasted diversity. We found that seedling root and stem microbiota were influenced by soil diversity but not by initial seed microbiota composition. A strong selection on the two-source communities occurred during microbiota assembly, with only 8-32% of soil taxa and 0.8-1.4% of seed-borne taxa colonizing seedlings. The recruitment of seedling microbiota came mainly from soil (35-72% of diversity) and not from seeds (0.3-15%). The outcome of seed and soil microbiota coalescence is therefore strongly asymmetrical with a dominance of soil taxa. Interestingly, seedling microbiota was primarily composed of initially rare taxa (from seed, soil or unknown origin) and sub-dominant soil taxa. Our results suggest that plant microbiome engineering success based on native seed or soil microbiota will rely on rare and sub-dominant taxa in source communities.

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“…Recently, a growing body of research has emphasized the ecological importance of rare taxa (Lynch and Neufeld, 2015;Jousset et al, 2017), and distinct succession patterns and functional characteristics were found in abundant and rare taxa (Jia et al, 2018;Jiao and Lu, 2020b;Rocca et al, 2020). The abundant taxa are usually perceived as the most active category in biogeochemical cycles, especially carbohydrate metabolism, and take up the coring niche (Jiao et al, 2017;Kurm et al, 2019;Liang et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Distinct Functions and Assembly Mechanisms of Soil Abundant and Rare Bacterial Taxa Under Increasing Pyrene Stresses

Dong

Deng

et al. 2021

Front. Microbiol.

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Elucidating the relative importance of species interactions and assembly mechanisms in regulating bacterial community structure and functions, especially the abundant and rare subcommunities, is crucial for understanding the influence of environmental disturbance in shaping ecological functions. However, little is known about how polycyclic aromatic hydrocarbon (PAH) stress alters the stability and functions of the abundant and rare taxa. Here, we performed soil microcosms with gradient pyrene stresses as a model ecosystem to explore the roles of community assembly in determining structures and functions of the abundant and rare subcommunities. The dose–effect of pyrene significantly altered compositions of abundant and rare subcommunities. With increasing pyrene stresses, diversity increased in abundant subcommunities, while it decreased in the rare. Importantly, the abundant taxa exhibited a much broader niche width and environmental adaptivity than the rare, contributing more to pyrene biodegradation, whereas rare taxa played a key role in improving subcommunity resistance to stress, potentially promoting community persistence and stability. Furthermore, subcommunity co-occurrence network analysis revealed that abundant taxa inclined to occupy the core and central position in adaptation to the pyrene stresses. Stochastic processes played key roles in the abundant subcommunity rather than the rare subcommunity. Overall, these findings extend our understanding of the ecological mechanisms and interactions of abundant and rare taxa in response to pollution stress, laying a leading theoretical basis that abundant taxa are core targets for biostimulation in soil remediation.

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Rare microbial taxa emerge when communities collide: freshwater and marine microbiome responses to experimental mixing

Cited by 79 publications

References 58 publications

Warming mediates the resistance of aquatic bacteria to invasion during community coalescence

Warming mediates the resistance of aquatic bacteria to invasion during community coalescence

Asymmetric outcome of community coalescence of seed and soil microbiota during early seedling growth

Distinct Functions and Assembly Mechanisms of Soil Abundant and Rare Bacterial Taxa Under Increasing Pyrene Stresses

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