Conserved bacterial genomes from two geographically distinct peritidal stromatolite formations shed light on potential functional guilds

Waterworth, Samantha C.; Isemonger, Eric W.; Rees, Evan R.; Dorrington, Rosemary A.; Kwan, Jason C.

doi:10.1101/818625

Cited by 4 publications

(4 citation statements)

References 101 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A few model mat systems were used for comparison at both taxonomic and functional levels. These included hypersaline mats from Shark Bay (Australia) [66], marine mats from Highbourne Cay (Bahamas) [67] stromatolites from Cape Recife and Schoenmakerskop (South Africa) [68], oligotrophic mats from Cuatro Ciénagas (Mexico) [69], and two HAAL mats: a rare archaeal biofilm from Diamante lake [19] and the hypersaline mats from Socompa [18]. Functional analysis based on COG markers for carbon fixation confirmed the KEGG-based observations for BM and TM.…”

Section: Plos Onementioning

confidence: 54%

Carbon fixation and rhodopsin systems in microbial mats from hypersaline lakes Brava and Tebenquiche, Salar de Atacama, Chile

et al. 2021

View full text Add to dashboard Cite

In this work, molecular diversity of two hypersaline microbial mats was compared by Whole Genome Shotgun (WGS) sequencing of environmental DNA from the mats. Brava and Tebenquiche are lakes in the Salar de Atacama, Chile, where microbial communities are growing in extreme conditions, including high salinity, high solar irradiance, and high levels of toxic metals and metaloids. Evaporation creates hypersaline conditions in these lakes and mineral precipitation is a characteristic geomicrobiological feature of these benthic ecosystems. The mat from Brava was more rich and diverse, with a higher number of different taxa and with species more evenly distributed. At the phylum level, Proteobacteria, Cyanobacteria, Chloroflexi, Bacteroidetes and Firmicutes were the most abundant, including ~75% of total sequences. At the genus level, the most abundant sequences were affilitated to anoxygenic phototropic and cyanobacterial genera. In Tebenquiche mats, Proteobacteria and Bacteroidetes covered ~70% of the sequences, and 13% of the sequences were affiliated to Salinibacter genus, thus addressing the lower diversity. Regardless of the differences at the taxonomic level, functionally the two mats were similar. Thus, similar roles could be fulfilled by different organisms. Carbon fixation through the Wood-Ljungdahl pathway was well represented in these datasets, and also in other mats from Andean lakes. In spite of presenting less taxonomic diversity, Tebenquiche mats showed increased abundance and variety of rhodopsin genes. Comparison with other metagenomes allowed identifying xantorhodopsins as hallmark genes not only from Brava and Tebenquiche mats, but also for other mats developing at high altitudes in similar environmental conditions.

show abstract

Section: Plos Onementioning

confidence: 54%

Carbon fixation and rhodopsin systems in microbial mats from hypersaline lakes Brava and Tebenquiche, Salar de Atacama, Chile

et al. 2021

View full text Add to dashboard Cite

show abstract

“…With this approach, Automappa has been used in our group to manually curate 242 MAGs from fourteen metagenomic samples across a diverse range of environments, including stromatolites, marine sponges and beetles which have been successfully published in scientific literature [8,[27][28][29]. Moreover, this tool has been used to produce an additional 376 final clusters from 13 more unpublished metagenomes derived from a similar diverse range of environments.…”

Section: Resultsmentioning

confidence: 99%

“…Automappa assisted in gaining these insights by enabling expert curation of metabolic pathways respective to each of the Tethybacterales MAGs. Similarly, microbiomes from geographically distinct stromatolite formations were curated using Automappa allowing comparison of the conserved MAGs' functional gene sets recovered [28].…”

Section: Resultsmentioning

confidence: 99%

Automappa: An interactive interface for metagenome-derived genome bins

Rees,

Waterworth,

Chanana

et al. 2023

Preprint

View full text Add to dashboard Cite

BackgroundStudies attempting to observe microbes commonly considered uncultivable under standard laboratory conditions are turning to so-called “deep” environmental sequencing approaches whereby they may access these unculturable organisms’ genomes viain silicoapproaches. A typical workflow involves metagenome assembly, annotation, and binning for reconstruction of each respective organism’s genome (or metagenome-assembled genome, MAG). Many automated genome binning approaches have been developed and have displayed a wide range of variation in performance. Therefore, refinement methods have been developed in order to aid manual curation following the automated genome binning process. Current manual curation tools were developed with a focus towards teaching metagenomics concepts and may fail when handling complex datasets containing many microbes. Automappa was developed with a focus on overlaying a variety of annotations such as taxonomy, coverage and marker-gene prevalence while maintaining an implementation that may scale to the complexity of environmental samples.ResultsWe present Automappa, a companion tool and interactive interface for exploration and refinement of Autometa taxon and genome binning results from metagenomes. Selections provide real-time updates of MAG metrics to aid manual curation. Furthermore, researchers may detect unbinned MAGs as well as manually improve their draft-quality MAGs with contigs that closely match the MAG’s genome characteristics. Automappa’s utility has previously been demonstrated on host-associated, marine and terrestrial systems with a total of 242 curated MAGs across fourteen published metagenomes. Of these refined MAGs, the number of high-quality and medium-quality bins increased, consequently lowering the number of low-quality bins and decreasing the amount of data discarded from downstream analyses. The recovery of higher quality MAGs improved the confidence in results and strengthened the resultant conclusions of these respective studies. Automappa consists of three tabs, one for uploading a user’s metagenome data, another for exploration and refinement and the last for providing an overall summary of the refined MAG results.ConclusionsAutomappa is an open source software package that allows researchers to easily assess and refine undetected or draft-quality MAGs from their respective metagenomes. It is freely available under the GPLv3 license athttps://github.com/WiscEvan/Automappaand through Figshare (doi: 10.6084/m9.figshare.22593235).

show abstract

“…The copyright holder for this preprint this version posted August 20, 2023. ; https://doi.org/10.1101/2023.08.19.553462 doi: bioRxiv preprint reported in High-Bourne Cay (Khodadad & Foster, 2012). In Lake Magadi (Kambura et al, 2016) and Hamelin Pool (Ruvindy et al, 2015), only members of Euryarchaeota and TACK have been reported, whereas in Cape Recife (Waterworth et al, 2020), members of Asgard and DPANN have been reported. However, other analyses often report only the dominant relative abundance of some specific members of a single phylum, such as in Lake Tyrrel (Andrade et al, 2015), Euryarchaeota and Nanohaloarchaeota dominate in the Dead Sea (Jacob et al, 2017), and within the phylum Euryarchaeota, only members of of the family Halobacteriaceae.…”

Section: Discussionmentioning

confidence: 99%

Unveiling Local Radiation Events through Metagenome Assembled Genomes of Archaea and Bacteria in Hypersaline Microbial Mats from the Archean Domes Site, Cuatro Cienegas, Coahuila, Mexico

Rodríguez Cruz,

Castelán-Sánchez,

Madrigal-Trejo

et al. 2023

Preprint

View full text Add to dashboard Cite

A comprehensive study was conducted in the Cuatro Cienegas Basin (CCB) in Coahuila, Mexico, known for its remarkable microbiological diversity and unique physicochemical properties. The ″Archaean Domes″(DA) in the CCB are hypersaline, non-lithifying microbial mats. This study focused on analyzing the small domes and circular structures formed in DA through metagenome assembly genomes (MAGs) with the aim of finding new microorganisms and providing information on the tree of life in a place as diverse as the CCB. In total, 329 MAGs were identified, including 52 archaea and 277 bacteria. Remarkably, 30 Archaea and 154 Bacteria could not be classified at the genus level, highlighting the remarkable diversity of CCB. The CCBs showed significant diversity at the phylum level, with Proteobacteria being the most abundant, followed by Euryarchaeota, Firmicutes, Bacteroidetes, Actinobacteria, Cyanobacteria, Spirochaetes, Chloroflexi, Planctomycetes, Candidatus Parvarchaeota, Verrucomicrobia, Balneolaeota, Nitrospirae, and Tenericutes. Subsequently, the MAGs were classified into a phylogenetic tree. In Archaea, monophyletic groups MAGs belonged to the phyla Archaeoglobi, Candidatus Aenigmarchaeota, Candidatus Nanoarchaeota, Candidatus Lokiarchaeota, and Halobacteriota. Among the Bacteria, monophyletic groups were identified as well, including Spirochaetes, Proteobacteria, Planctomycetota, Actinobacteria, Verrucomicrobiota, Bacteroidetes, Bipolaricaulota, Desulfobacterota, and Cyanobacteria. These monophyletic clusters may indicate radiation events that are likely influenced by geographical isolation as well as extreme environmental conditions reported in AD pond like phosphorus deficiency (122:42:1 C:N:P) , fluctuating pH and a salinity of 5.28%

show abstract

Conserved bacterial genomes from two geographically distinct peritidal stromatolite formations shed light on potential functional guilds

Cited by 4 publications

References 101 publications

Carbon fixation and rhodopsin systems in microbial mats from hypersaline lakes Brava and Tebenquiche, Salar de Atacama, Chile

Carbon fixation and rhodopsin systems in microbial mats from hypersaline lakes Brava and Tebenquiche, Salar de Atacama, Chile

Automappa: An interactive interface for metagenome-derived genome bins

Unveiling Local Radiation Events through Metagenome Assembled Genomes of Archaea and Bacteria in Hypersaline Microbial Mats from the Archean Domes Site, Cuatro Cienegas, Coahuila, Mexico

Contact Info

Product

Resources

About