Dispersal homogenizes communities via immigration even at low rates in a simplified synthetic bacterial metacommunity

Fodelianakis, Stilianos; Lorz, Alexander; Valenzuela-Cuevas, Adriana; Barozzi, Alan; Booth, Jenny Marie; Daffonchio, Daniele

doi:10.1038/s41467-019-09306-7

Cited by 55 publications

(47 citation statements)

References 42 publications

(48 reference statements)

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“…S1). Finally, we verified that the levels of noise determined in this study are similar to the variability recorded from technical replicate samples taken during our previous experiment where we used the same bacterial system and instrument with identical settings [17]…”

Section: Assembling and Monitoring The Synthetic Bacterial Communitiessupporting

confidence: 79%

Direct quantification of ecological drift at the population level in synthetic bacterial communities

et al. 2020

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In community ecology, drift refers to random births and deaths in a population. In microbial ecology, drift is estimated indirectly via community snapshots but in this way, it is almost impossible to distinguish the effect of drift from the effect of other ecological processes. Controlled experiments where drift is quantified in isolation from other processes are still missing. Here we isolate and quantify drift in a series of controlled experiments on simplified and tractable bacterial communities. We detect drift arising randomly in the populations within the communities and resulting in a 1.4-2% increase in their growth rate variability on average. We further use our experimental findings to simulate complex microbial communities under various conditions of selection and dispersal. We find that the importance of drift increases under high selection and low dispersal, where it can lead to~5% of species loss and to~15% increase in β-diversity. The species extinct by drift are mainly rare, but they become increasingly less rare when selection increases, and dispersal decreases. Our results provide quantitative insights regarding the properties of drift in bacterial communities and suggest that it accounts for a consistent fraction of the observed stochasticity in natural surveys.

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Section: Assembling and Monitoring The Synthetic Bacterial Communitiessupporting

confidence: 79%

Direct quantification of ecological drift at the population level in synthetic bacterial communities

et al. 2020

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“…Microorganisms found in various sources, such as surface and groundwater supplies, act as inocula in drinking water systems ( Figure 6(a)) to propagate populations along the treatment procedure [99]. Microorganisms occurring on certain treatment systems, such as filters or reactor wall surfaces, can subsequently be released during or after processing [102] to the delivery units that depend on whether or not disinfection has occurred [103,104]. Bidirectional immigration amidst the water process and the biofilms on the inner pipe surface is feasible in the distribution network [105], which can further be elevated via stagnating the water [106].…”

Section: Quantifying the Contribution Of Microbial Immigration In Ecomentioning

confidence: 99%

RETRACTED ARTICLE: Metagenomics for taxonomy profiling: tools and approaches

et al. 2020

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The study of metagenomics is an emerging field that identifies the total genetic materials in an organism along with the set of all genetic materials like deoxyribonucleic acid and ribose nucleic acid, which play a key role with the maintenance of cellular functions. The best part of this technology is that it gives more flexibility to environmental microbiologists to instantly pioneer the immense genetic variability of microbial communities. However, it is intensively complex to identify the suitable sequencing measures of any specific gene that can exclusively indicate the involvement of microbial metagenomes and be able to advance valuable results about these communities. This review provides an overview of the metagenomic advancement that has been advantageous for aggregation of more knowledge about specific genes, microbial communities and its metabolic pathways. More specific drawbacks of metagenomes technology mainly depend on sequence-based analysis. Therefore, this 'targeted based metagenomics' approach will give comprehensive knowledge about the ecological, evolutionary and functional sequence of significantly important genes that naturally exist in living beings either human, animal and microorganisms from distinctive ecosystems.

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“…Our results revealed that microbial communities of water, shrimp intestine and sediment habitats in the SCPE had close relationships as communities of three habitats are connected to each other by various biological and ecological processes, including nutrient share, dispersal and microbial interactions [35,46,47]. For instance, dispersal is a key factor influencing the metacommunity and its associated community structure [48]. In this study, we observed that a high percentage of dispersal rates from sediment to the other two habitats in the SCPE, and especially, compared with water communities, shrimp intestine communities were more closely related to sediment communities.…”

Section: Discussionmentioning

confidence: 75%

Sediment microbial communities contribute to shrimp intestine microbiota in cultural pond ecosystems

Huang¹,

Hou²,

Zhou

et al. 2020

Preprint

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Background Microorganisms in a shrimp cultural pond ecosystem (SCPE) play important roles for animal and environmental health. While the microbial diversity and assembly mechanism, and how communities of multiple habitats contribute to the SCPE metacommunity are poorly understood. Here, we analyzed phylogenetic structure of 792 samples of three habitats (water, shrimp intestine and sediment) from 88 shrimp cultural ponds across six regional sites in China. Results We show that the microbial communities of three habitats in the SCPE contained 15,197 operational taxonomic units (OTUs), and the microbial community of sediment had the highest OTUs (14,857). Despite the high microbial diversity, the SCPE has small core taxa (13 OTUs) among three habitats, and 30, 15, 53 core OTUs in water, shrimp intestine, and sediment, respectively. Especially, some opportunistic pathogens or functional microbes were core taxa in shrimp intestine or water and sediment. Of the SCPE metacommunity, the microbial diversity of the SCPE was mainly contributed by‾αLocalCommunities (66.0%), and followed by βInterHabitats (29.0%). The sediment microbial communities had a larger contribution (56.8%) to shrimp intestine microbiota compared to water communities (18.1%), which was also corroborated by the Sloan neutral community model analysis. Further, microbial assembly of three habitats appeared to be largely driven by stochastic processes (over 78%) in the SCPE. Conclusions Our results demonstrate that those core microbial taxa of three habitats were distinct with each other, that sediment communities mainly contributed to shrimp intestine communities, and that the microbial assembly was largely driven by stochastic processes. Our study enhances the mechanistic understanding of the microbial diversity and assembly in the SCPE for further analyzing metacommunities, and has important implications for microbial ecology and shrimp culture strategies.

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Dispersal homogenizes communities via immigration even at low rates in a simplified synthetic bacterial metacommunity

Cited by 55 publications

References 42 publications

Direct quantification of ecological drift at the population level in synthetic bacterial communities

Direct quantification of ecological drift at the population level in synthetic bacterial communities

RETRACTED ARTICLE: Metagenomics for taxonomy profiling: tools and approaches

Sediment microbial communities contribute to shrimp intestine microbiota in cultural pond ecosystems

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