Diversity of an uncommon elastic hypersaline microbial mat along a small-scale transect

Espinosa-Asuar, Laura; Monroy, Camila; Madrigal-Trejo, David; Navarro-Miranda, Marisol; Sánchez-Pérez, Jazmín; Muñoz, J.L Canales; Villar, Juan Diego; Cifuentes, Julián Felipe; Kalambokidis, Maria; Esquivel-Hernández, Diego; Viladomat, Mariette; Escalante-Hernández, Ana Elena; Vélez, Patricia; Figueroa, Mario; Ramírez‐Barahona, Santiago; Gasca-Pineda, Jaime; Eguiarte, Luis E.; Souza, Valeria

doi:10.1101/2021.03.04.433984

Cited by 4 publications

(22 citation statements)

References 140 publications

(198 reference statements)

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“…S1: Supplementary material). This site was discovered in 2016, and was firstly described by Medina-Chávez et al (2019) [unpublished], andEspinosa-Asuar et al (2021) [unpublished]. During the rainy season, mostly during the months of August to September, the pond fills with water up to ∼20 cm.…”

Section: Study Site and Sample Collectionmentioning

confidence: 80%

Modern microbial mats from the Chihuahuan Desert provide insights into ecological stability throughout Earth’s history

Madrigal-Trejo

Sánchez-Pérez

Espinosa-Asuar

et al. 2021

Preprint

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Microbial mats are complex ecological assemblages that are found in the Precambrian fossil record and in extant extreme environments. Hence, these structures are regarded as highly stable ecosystems. In this work, we assess the ecological stability in a modern, fluctuating, hypersaline pond from the Cuatro Ciénegas Basin. From the 2016 to 2019 metagenomic sampling of this site, we found that this microbial site is sensitive to disturbances, which leads to high taxonomic replacement. Additionally, the mats have shown to be functionally stable throughout time, and could be differentiated between dry and rainy seasonal states. We speculate that this microbial system could represent modern analogs of ancient microbial mats where functions were preserved over time, whereas composition was subject to diversification in the face of local and planetary perturbations.

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Section: Study Site and Sample Collectionmentioning

confidence: 80%

Modern microbial mats from the Chihuahuan Desert provide insights into ecological stability throughout Earth’s history

Madrigal-Trejo

Sánchez-Pérez

Espinosa-Asuar

et al. 2021

Preprint

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“…This dataset comes from a microbial mat located in the Cuatro Ciénegas Basin (CCB), Coahuila, Mexico (coordinates 26º49'41.7'' N, 102º01'28.7'' W). The sampling used in this case study, which consists of ten samples along a 1.5 m transect, represents a natural community with more than 6,000 ASVs [80]. Compositional data was acquired as raw reads form 16S amplicon sequencing.…”

Section: Biological Validation: Kombucha Consortiummentioning

confidence: 99%

“…Compositional data was acquired as raw reads form 16S amplicon sequencing. Reads were filtered and processed for clustering and taxonomic annotation in QIIME 2 platform, as shown by the authors [80]. Singletons and unique counts were subsequently filtered as suggested, and consequently, 2,600 ASVs remained [25].…”

Section: Biological Validation: Kombucha Consortiummentioning

confidence: 99%

“…To further evaluate the performance of MicNet as a high-throughput toolbox capable of analyzing a highly diverse and complex environment, we tested it on a compositional dataset of ten samples from a microbial mat in Cuatro Ciénegas, Mexico, in the Chihuahuan Desert [80]. This microbial mat, The Archean Domes , thrives in a fluctuating hypersaline pond which has been previously described as hyperdiverse [80,101]. Like every microbial mat, it is a stratified community with an intricate metabolic interplay between their organisms [102].…”

Section: Case Study: Archean Domes Microbial Matsmentioning

confidence: 99%

“…To set SparCC parameter values, we perform a parameter search in our more complex study case from the communities reported by Espinosa-Asuar et al (2021) [80]. We performed an independent parameter sweep on each parameter, varying the exclusion threshold from 0 to 1 in steps of 0.1, the number of iterations from 10 to 100 in steps of 10 and the exclusion number from 10 to 100 in steps of 10.…”

Section: New Implementation Of Sparccmentioning

confidence: 99%

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MicNet Toolbox: visualizing and deconstructing a microbial network

Favila¹,

Madrigal-Trejo

Legorreta³

et al. 2021

Preprint

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Understanding both global and local patterns in the structure and interplay of microbial communities has been a fundamental question in ecological research. In this paper, we present a python toolbox that combines two emerging techniques that have been proposed as useful when analyzing compositional microbial data. On one hand, we introduce a visualization module that incorporates the use of UMAP, a recent dimensionality reduction technique that focuses on local patterns, and HDBSCAN, a clustering technique based on density. On the other hand, we have included a module that runs an enhanced version of the SparCC code, sustaining larger datasets than before, and we couple this with network theory analyses to describe the resulting co-occurrence networks, including several novel analyses, such as structural balance metrics and a proposal to discover the underlying topology of a co-occurrence network. We validated the proposed toolbox on 1) a simple and well described biological network of kombucha, consisting of 48 ASVs, and 2) using simulated community networks with known topologies to show that we are able to discern between network topologies. Finally, we showcase the use of the MicNet toolbox on a large dataset from Archean Domes, consisting of more than 2,000 ASVs. Our toolbox is freely available as a github repository (https://github.com/Labevo/MicNetToolbox), and it is accompanied by a web dashboard (http://micnetapplb-1212130533.us-east-1.elb.amazonaws.com) that can be used in a simple and straightforward manner with relative abundance data.Author SummaryMicrobial communities are complex systems that cannot be wholly understood when studied by its individual components. Hence, global pattern analyses seem to be a promising complement to highly focused local approaches. Here, we introduce the MicNet toolbox, an open-source collection of several analytical methods for visualizing abundance data and creating co-occurrence networks for further analysis. We include two modules: one for visualization and one for network analysis based on graph theory. Additionally, we introduce an enhanced version of SparCC, a method to estimate correlations for co-occurrence network construction, that is faster and can support larger datasets. We performed method validations using simulated data and a simple biological network. Our toolbox is freely available in a github repository at https://github.com/Labevo/MicNetToolbox, and it is accompanied by a web dashboard that could be easily accessed and manipulated by non-specialist users. With this implementation, we attempt to provide a simple and straightforward way to explore and analyze microbial relative abundance data.

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Metabolomic Diversity in Microbial Mats Under Different Environmental Conditions: A Tool to Test Microbial Ecosystem Chemical Change

Buenrostro‐Muñoz,

Jarmusch,

Souza

et al. 2023

Chemistry & Biodiversity

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Microbial mats are microbial communities capable of recycling the essential elements of life and considered to be the oldest evidence of microbial communities on Earth. Due to their uniqueness and limited sampling material, analyzing their metabolomic profile in different seasons or conditions is challenging. In this study, microbial mats from a small pond in the Cuatro Cienegas Basin in Coahuila, Mexico, were collected in wet and dry seasons. In addition to these samples, mesocosm experiments from the wet samples were set. These mats are elastic and rise after heavy rainfall by forming gas domes structures known as “Archean domes”, by the outgassing of methanogenic bacteria, archaea, and sulfur bacteria. Extracts from all mats and mesocosms were subjected to untargeted mass spectrometry‐based metabolomics and molecular networking analysis. Interestingly, each mat showed high chemical diversity that may be explained by the temporal dynamic processes in which they were sampled.

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Diversity of an uncommon elastic hypersaline microbial mat along a small-scale transect

Cited by 4 publications

References 140 publications

Modern microbial mats from the Chihuahuan Desert provide insights into ecological stability throughout Earth’s history

Modern microbial mats from the Chihuahuan Desert provide insights into ecological stability throughout Earth’s history

MicNet Toolbox: visualizing and deconstructing a microbial network

Metabolomic Diversity in Microbial Mats Under Different Environmental Conditions: A Tool to Test Microbial Ecosystem Chemical Change

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