Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience

Mandaković, Dinka; Rojas, Claudia; Maldonado, Jonathan; Latorre, Mauricio; Travisany, Dante; Delage, Erwan; Bihouée, Audrey; Jean, Géraldine; Díaz, Francisco Javier Mato; Fernández-Gómez, Beatriz; Cabrera, Pablo J.; Gaete, Alexis; Latorre, Claudio; Gutiérrez, Rodrigo A.; Maass, Alejandro; Cambiazo, Verónica; Navarrete, Sergio A.; Eveillard, Damien; González, Maurício

doi:10.1038/s41598-018-23931-0

Cited by 125 publications

(115 citation statements)

References 53 publications

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“…The Atacama Desert is the oldest and driest desert on Earth. In recent years, it has become one of the principal areas for the study of microbial diversity, biogeochemistry and natural products potential 19,41 . Based on the particular soil scenario present in the Atacama Desert, two Gram-positive, rod-shaped and yellow-pigmented Microbacterium strains (CGR1 and CGR2) were isolated from soil samples collected from the Andes mountain range in the central region of the Atacama Desert (Fig.…”

Section: Resultsmentioning

confidence: 99%

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Genome-scale metabolic models of Microbacterium species isolated from a high altitude desert environment

Mandaković

Cintolesi

Maldonado

et al. 2020

Sci Rep

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The Atacama Desert is the most arid desert on Earth, focus of important research activities related to microbial biodiversity studies. In this context, metabolic characterization of arid soil bacteria is crucial to understand their survival strategies under extreme environmental stress. We investigated whether strain-specific features of two Microbacterium species were involved in the metabolic ability to tolerate/ adapt to local variations within an extreme desert environment. Using an integrative systems biology approach we have carried out construction and comparison of genome-scale metabolic models (GEMs) of two Microbacterium sp., CGR1 and CGR2, previously isolated from physicochemically contrasting soil sites in the Atacama Desert. Despite CGR1 and CGR2 belong to different phylogenetic clades, metabolic pathways and attributes are highly conserved in both strains. However, comparison of the GEMs showed significant differences in the connectivity of specific metabolites related to pH tolerance and co 2 production. The latter is most likely required to handle acidic stress through decarboxylation reactions. We observed greater GEM connectivity within Microbacterium sp. CGR1 compared to CGR2, which is correlated with the capacity of CGR1 to tolerate a wider pH tolerance range. Both metabolic models predict the synthesis of pigment metabolites (β-carotene), observation validated by HPLC experiments. Our study provides a valuable resource to further investigate global metabolic adaptations of bacterial species to grow in soils with different abiotic factors within an extreme environment. In recent years, there has been increased interest in the study of Actinobacteria from desert areas. As noted by previous researchers, this class possess bacteria with a variety of attractive metabolic qualities that make them good candidates to survive in desert areas 1 , including their extensive metabolic capability to degrade and utilize compounds from nutrient poor environments and their ability to synthesize secondary metabolites and natural antibiotics 2. In fact, Actinobacteria is the dominant class present in desert locations 3 , and their ability to adapt to this kind of environment is the focus of intense research. For example, Lynch and collaborators found that over 98% of the lineages present in the vicinity of a volcano in the Atacama Desert corresponded to Actinobacteria, and that their metabolisms were adapted to utilize atmospheric gases present in this ecosystem 4. One genus that

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Section: Resultsmentioning

confidence: 99%

“…Electrical conductivity (EC) was determined in a 1:5 soil/water extract. Total elemental profiles from soluble soil extracts were determinate by Total Reflection X-ray Fluorescence (TXRF) 19 .…”

Section: Soils Condition Tolerance Assays and Elemental Content Ph Amentioning

confidence: 99%

Genome-scale metabolic models of Microbacterium species isolated from a high altitude desert environment

Mandaković

Cintolesi

Maldonado

et al. 2020

Sci Rep

Self Cite

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“…Compared with that in the emerged areas, the bacterial co-occurrence network in the inundated areas was more complex, which could have been caused by the continuous hydrological connection in the inundated areas during the whole year 47,48 . Previous studies have also indicated that positive correlations between nodes in co-occurrence networks of desert soil bacterial communities could be the result of functional interdependencies among bacterial taxa under extreme environmental conditions [49][50][51] . In our study, high proportions of positive correlations between nodes in the two networks suggested the interdependencies among bacterial taxa under environmental disturbance.…”

Section: Discussionmentioning

confidence: 99%

Microbial community structure and functional properties in permanently and seasonally flooded areas in Poyang Lake

Liu

Ren

et al. 2020

Sci Rep

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Water level fluctuations are an inherent feature regulating the ecological structures and functions of lakes. It is vital to understand the effects of water level fluctuations on bacterial communities and metabolic characteristics in freshwater lakes in a changing world. However, information on the microbial community structure and functional properties in permanently and seasonally flooded areas are lacking. Poyang Lake is a typical seasonal lake linked to the Yangtze River and is significantly affected by water level fluctuations. Bottom water was collected from 12 sampling sites: seven inundated for the whole year (inundated areas) and five drained during the dry season (emerged areas). High-throughput 16S rRNA gene sequencing was used to identify the bacterial communities. The results showed that the taxonomic structure and potential functions of the bacterial communities were significantly different between the inundated and emerged areas. Cyanobacteria was dominant in both areas, but the relative abundance of Cyanobacteria was much higher in the emerged areas than in the inundated areas. Bacterial communities were taxonomically sensitive in the inundated areas and functionally sensitive in the emerged areas. Nitrogen, phosphorus, and dissolved organic carbon concentrations and their ratios, as well as dissolved oxygen, played important roles in promoting the bacterial taxonomic and functional compositional patterns in both areas. According to the metabolic predictions based on 16S rRNA gene sequences, the relative abundance of functional genes related to assimilatory nitrate reduction in the emerged areas was higher than in the inundated areas, and the relative abundance of functional genes related to dissimilatory nitrate reduction in the inundated areas was higher. These differences might have been caused by the nitrogen differences between the permanently and seasonally flooded areas caused by intra-annual water level fluctuations. The relative abundance of functional genes associated with denitrification was not significantly different in the inundated and emerged areas. This study improved our knowledge of bacterial community structure and nitrogen metabolic processes in permanently and seasonally flooded areas caused by water level fluctuations in a seasonal lake.Microbial assemblages are fundamental components of aquatic ecosystems and play important roles in driving global energy fluxes and biogeochemical cycling 1 . Microbial communities have high species diversity and genetic diversity 2-5 , which make them sensitive to environmental perturbations 6,7 . The relative balance of external nutrient loading influences microbial functional genes and associated metabolic processes in lake ecosystems 8 . Understanding the taxonomic and functional compositions of microbial communities is essential to elucidating the responses of natural bacterial communities to environmental perturbations, such as hydrological fluctuations and nutrient pollution 9-11 . Poyang Lake (PYL) is a seasonal lake characterized by ...

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“…A comparison of the microbial community structure in the disease with the healthy can hence be achieved by construction of microbial association networks corresponding to each state, known as the 'case' and 'control' network respectively. This 'case' and 'control' networks can be further evaluated and compared based on their constituent network properties [21,[30][31][32][33][34]. However, meaningful insights can only be obtained when such pair of networks is comparable.…”

Section: Introductionmentioning

confidence: 99%

‘NetShift’: a methodology for understanding ‘driver microbes’ from healthy and disease microbiome datasets

et al. 2018

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The combined effect of mutual association within the co-inhabiting microbes in human body is known to play a major role in determining health status of individuals. The differential taxonomic abundance between healthy and disease are often used to identify microbial markers. However, in order to make a microbial community based inference, it is important not only to consider microbial abundances, but also to quantify the changes observed among inter microbial associations. In the present study, we introduce a method called 'NetShift' to quantify rewiring and community changes in microbial association networks between healthy and disease. Additionally, we devise a score to identify important microbial taxa which serve as 'drivers' from the healthy to disease. We demonstrate the validity of our score on a number of scenarios and apply our methodology on two real world metagenomic datasets. The 'NetShift' methodology is also implemented as a web-based application available at https://web.rniapps.net/netshift

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Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience

Cited by 125 publications

References 53 publications

Genome-scale metabolic models of Microbacterium species isolated from a high altitude desert environment

Genome-scale metabolic models of Microbacterium species isolated from a high altitude desert environment

Microbial community structure and functional properties in permanently and seasonally flooded areas in Poyang Lake

‘NetShift’: a methodology for understanding ‘driver microbes’ from healthy and disease microbiome datasets

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