Investigating microbial associations from sequencing survey data with co‐correspondence analysis

Alric, Benjamin; Braak, Cajo J. F. ter; Desdevises, Yves; Lebredonchel, Hugo; Dray, Stéphane

doi:10.1111/1755-0998.13126

Cited by 6 publications

(4 citation statements)

References 107 publications

(147 reference statements)

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“…In addition, to test if the two microbial communities (i.e. water and guts) varied independently, we performed separate symmetric co-correspondence analyses (using the relative abundance of reads) for each sampling period using the cocorresp package (Simpson 2009), following Alric et al (2020).…”

Section: Statistical Analysesmentioning

confidence: 99%

A field experiment reveals seasonal variation in the Daphnia gut microbiome

Hegg

Radersma

Uller

2021

Oikos

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The gut microbiome is increasingly recognized for its impact on host fitness, but it remains poorly understood how naturally variable environments influence gut microbiome diversity and composition. We studied changes in the gut microbiome of ten genotypes of water fleas Daphnia magna in submerged mesocosm enclosures in a eutrophic lake over a period of 16 weeks, from early summer to autumn. The microbial diversity increased when Daphnia were reintroduced from the laboratory to the lake, and the composition of gut microbes drastically changed. Both gut microbiome diversity and composition continued to change over the 16‐week period, with alpha diversity peaking in late summer. The gut microbiome community was clearly distinct from that of the surrounding water, and temporal changes in the two communities were independent of each other. There were no consistent differences in the gut microbiomes among Daphnia genotypes in the lake environment. The change in gut microbiome over the season was accompanied by a decline in reproductive output and survival. There were weak, but statistically supported, effects of microbiota composition on Daphnia fitness, but there was no evidence that natural variation in microbiome diversity or composition was associated with tolerance to the cyanotoxin microcystin. We conclude that the gut microbiome of Daphnia is highly dynamic in a natural lake environment, but that host genetic effects on microbiome diversity and composition between genotypes within a population can be vanishingly small. These results emphasize that establishing the ecological effects of gut microbiota will require large‐scale experiments under natural conditions.

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Section: Statistical Analysesmentioning

confidence: 99%

A field experiment reveals seasonal variation in the Daphnia gut microbiome

Hegg

Radersma

Uller

2021

Oikos

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“…CoCA was performed on microbial and viral relative abundance profiles using the cocorresp package in symmetric mode. Significance and degree of covariance were computed and the ordination biplots were visualized using a method described previously by Alric et al (86). All permutation-based tests were conducted with 999 iterations.…”

Section: Prediction and Analysis Of Viral Scaffolds A Schematic Illustration Of Analyses Conducted Can Be Found Inmentioning

confidence: 99%

Diverse viruses carrying genes for microbial extremotolerance in the Atacama Desert hyperarid soil

Hwang

Rahlff

Schulze‐Makuch

et al. 2020

Preprint

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Viruses play an essential role in shaping microbial community structures and serve as reservoirs for genetic diversity in many ecosystems. In hyperarid desert environments, where life itself becomes scarce and loses diversity, the interactions between viruses and host populations have remained elusive. Here, we resolved host-virus interactions in the soil metagenomes of the Atacama Desert hyperarid core, one of the harshest terrestrial environments on Earth. We show dispersal of diverse and abundant viruses that infect a wide range of hosts over 205 km across the desert. Host genomes encoded both adaptive and innate immune systems, providing evidence of viral predation being a key selective pressure along with abiotic stresses. Viral genomes carried extremotolerance features (i.e. DNA repair proteins, enzymes against oxidative damage) and other auxiliary metabolic genes, indicating that viruses could mediate the spread of microbial resilience against environmental stress across the desert. Our results suggest that the host-virus interactions in the Atacama Desert soils are dynamic and complex, shaping uniquely adapted microbiomes in this highly selective and hostile environment.ImportanceDeserts are one of the largest and rapidly expanding terrestrial ecosystems characterized by low biodiversity and biomass. The hyperarid core of the Atacama Desert, previously thought to be devoid of life, is one of the harshest environments supporting only scant biomass of highly adapted microbes. While there is growing evidence that viruses play essential roles in shaping the diversity and structure of nearly every ecosystem, very little is known about the role of viruses in desert soils, especially where viral contact with viable hosts is significantly reduced. Our results indicate that viruses are abundant, diverse and widely dispersed across the desert, potentially spreading key stress resilience and metabolic genes to ensure host survival. The desertification accelerated by climate change expands both the ecosystem cover and the ecological significance of the desert virome. This study sheds light on the complex evolutionary dynamics that shape the unique and poorly understood host-virus relationships in desert soils.

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“…CoCA was performed on microbial and viral relative abundance profiles using the cocorresp package in both symmetric and predictive modes. Significance and degree of covariance in symmetric mode were computed, and the ordination biplots were visualized using a method described previously by Alric et al ( 85 ). All permutation-based tests were conducted with 999 iterations.…”

Section: Methodsmentioning

confidence: 99%

Diverse Viruses Carrying Genes for Microbial Extremotolerance in the Atacama Desert Hyperarid Soil

et al. 2021

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Viruses play an essential role in shaping microbial community structures and serve as reservoirs for genetic diversity in many ecosystems. In hyperarid desert environments, where life itself becomes scarce and loses diversity, the interactions between viruses and host populations have remained elusive. Here, we resolved host-virus interactions in the soil metagenomes of the Atacama Desert hyperarid core, one of the harshest terrestrial environments on Earth. We show evidence of diverse viruses infecting a wide range of hosts found in sites up to 205 km apart. Viral genomes carried putative extremotolerance features (i.e., spore formation proteins) and auxiliary metabolic genes, indicating that viruses could mediate the spread of microbial resilience against environmental stress across the desert. We propose a mutualistic model of host-virus interactions in the hyperarid core where viruses seek protection in microbial cells as lysogens or pseudolysogens, while viral extremotolerance genes aid survival of their hosts. Our results suggest that the host-virus interactions in the Atacama Desert soils are dynamic and complex, shaping uniquely adapted microbiomes in this highly selective and hostile environment. IMPORTANCE Deserts are one of the largest and rapidly expanding terrestrial ecosystems characterized by low biodiversity and biomass. The hyperarid core of the Atacama Desert, previously thought to be devoid of life, is one of the harshest environments, supporting only scant biomass of highly adapted microbes. While there is growing evidence that viruses play essential roles in shaping the diversity and structure of nearly every ecosystem, very little is known about the role of viruses in desert soils, especially where viral contact with viable hosts is significantly reduced. Our results demonstrate that diverse viruses are widely dispersed across the desert, potentially spreading key stress resilience and metabolic genes to ensure host survival. The desertification accelerated by climate change expands both the ecosystem cover and the ecological significance of the desert virome. This study sheds light on the complex virus-host interplay that shapes the unique microbiome in desert soils.

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Investigating microbial associations from sequencing survey data with co‐correspondence analysis

Cited by 6 publications

References 107 publications

A field experiment reveals seasonal variation in the Daphnia gut microbiome

A field experiment reveals seasonal variation in the Daphnia gut microbiome

Diverse viruses carrying genes for microbial extremotolerance in the Atacama Desert hyperarid soil

Diverse Viruses Carrying Genes for Microbial Extremotolerance in the Atacama Desert Hyperarid Soil

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