Microbialite genetic diversity and composition relate to environmental variables

Centeno, Carla M.; Legendre, Pierre; Beltrán, Yislem; Alcántara-Hernández, Rocı́o; Lidström, Ulrika E.; Ashby, Matthew N.; Falcón, Luisa I.

doi:10.1111/j.1574-6941.2012.01447.x

Cited by 48 publications

(45 citation statements)

References 60 publications

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“…As stromatolites are highly novel communities, a subsampled open‐reference OTU picking approach in qiime to be inclusive of unique taxa was needed (Rideout et al ., ); therefore, we targeted only 16S rRNA gene libraries that had overlapping amplicons (V2‐V4 regions). Unfortunately, this approach prohibited the inclusion of several prominent microbialite studies, such as the 16S rRNA gene analyses of microbialites collected throughout Mexico (Cuatros Ciénegas, Alchichica, Sian Ka'an and Bacalar; Centeno et al ., ), which targeted the V5–6 region. Additionally, several earlier studies that used clone libraries to survey stromatolites from across the globe (e.g.…”

Section: Resultsmentioning

confidence: 99%

Characterization of the stromatolite microbiome from Little Darby Island, The Bahamas using predictive and whole shotgun metagenomic analysis

Casaburi

Duscher

Reid

et al. 2015

Environmental Microbiology

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Modern stromatolites represent ideal ecosystems to understand the biological processes required for the precipitation of carbonate due to their long evolutionary history and occurrence in a wide range of habitats. However, most of the prior molecular work on stromatolites has focused on understanding the taxonomic complexity and not fully elucidating the functional capabilities of these systems. Here, we begin to characterize the microbiome associated with stromatolites of Little Darby Island, The Bahamas using predictive metagenomics of the 16S rRNA gene coupled with direct whole shotgun sequencing. The metagenomic analysis of the Little Darby stromatolites revealed many shared taxa and core pathways associated with biologically induced carbonate precipitation, suggesting functional convergence within Bahamian stromatolites. A comparison of the Little Darby stromatolites with other lithifying microbial ecosystems also revealed that although factors, such as geographic location and salinity, do drive some differences within the population, there are extensive similarities within the microbial populations. These results suggest that for stromatolite formation, 'who' is in the community is not as critical as metabolic activities and environmental interactions. Together, these analyses help improve our understanding of the similarities among lithifying ecosystems and provide an important first step in characterizing the shared microbiome of modern stromatolites.

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Section: Resultsmentioning

confidence: 99%

Characterization of the stromatolite microbiome from Little Darby Island, The Bahamas using predictive and whole shotgun metagenomic analysis

Casaburi

Duscher

Reid

et al. 2015

Environmental Microbiology

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“…() and Centeno et al . (). The high Mg : Ca ratio (48.1 : 69.3) of Alchichica water is reflected in the microbialite mineralogy, where uncommon hydromagnesite‐magnesite minerals are present (Kaźmierczak et al ., ).…”

Section: Methodsmentioning

confidence: 97%

Alkaline phosphatases in microbialites and bacterioplankton from Alchichica soda lake, Mexico

Valdespino-Castillo

Alcántara-Hernández

Alcocer³

et al. 2014

FEMS Microbiol Ecol

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Dissolved organic phosphorus utilization by different members of natural communities has been closely linked to microbial alkaline phosphatases whose affiliation and diversity is largely unknown. Here we assessed genetic diversity of bacterial alkaline phosphatases phoX and phoD, using highly diverse microbial consortia (microbialites and bacterioplankton) as study models. These microbial consortia are found in an oligo-mesotrophic soda lake with a particular geochemistry, exhibiting a low calcium concentration and a high Mg : Ca ratio relative to seawater. In spite of the relative low calcium concentration in the studied system, our results highlight the diversity of calcium-based metallophosphatases phoX and phoD-like in heterotrophic bacteria of microbialites and bacterioplankton, where phoX was the most abundant alkaline phosphatase found. phoX and phoD-like phylotypes were more numerous in microbialites than in bacterioplankton. A larger potential community for DOP utilization in microbialites was consistent with the TN : TP ratio, suggesting P limitation within these assemblages. A cross-system comparison indicated that diversity of phoX in Lake Alchichica was similar to that of other aquatic systems with a naturally contrasting ionic composition and trophic state, although no phylotypes were shared among systems.

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“…Lake Bacalar, the largest freshwater habitat in the Yucatan Peninsula, is renowned for its striking blue color, the clarity of its water, and for the world’s largest occurrence of microbialites. With a length of more than 10 km [33–35], it occupies a larger fault basin [36] (50 km long, 2 to 3 km wide). With sediments derived from karst limestone, it represents the world’s largest freshwater lens system [37].…”

Section: Methodsmentioning

confidence: 99%

Using eDNA to biomonitor the fish community in a tropical oligotrophic lake

Valdéz-Moreno

Ivanova

Elías‐Gutiérrez

et al. 2018

Preprint

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Environmental DNA (eDNA) is an effective approach for detecting vertebrates and plants, especially in aquatic ecosystems, but prior studies have largely examined eDNA in cool temperate settings. By contrast, this study employs eDNA to survey the fish fauna in tropical Lake Bacalar (Mexico) with the additional goal of assessing the possible presence of invasive fishes, such as Amazon sailfin catfish. Sediment and water samples were collected from eight stations in Lake Bacalar on three occasions over a 4-month interval. Each sample was stored in the presence or absence of lysis buffer to compare eDNA recovery. Short fragments (184-187 bp) of the cytochrome c oxidase I (COI) gene were amplified using fusion primers and then sequenced on Ion Torrent PGM and S5 before their source species were determined using a custom reference sequence database constructed on BOLD. In total, eDNA sequences were recovered from 75 species of vertebrates including 47 fishes, 15 birds, 7 mammals, 5 reptiles, and 1 amphibian. Although all species are known from this region, 6 fish species represent new records for the study area, while 2 require verification. Sequences for five species (2 birds, 2 mammals, 1 reptile) were only detected from sediments, while sequences from 52 species were only recovered from water. Because DNA from the Amazon sailfin catfish was not detected, we used a mock eDNA experiment to confirm our methods were appropriate for its detection. We developed protocols that enabled the recovery of eDNA from tropical oligotrophic aquatic ecosystems, and confirmed their effectiveness in detecting diverse species of vertebrates including an invasive species of Amazon catfish.

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Microbialite genetic diversity and composition relate to environmental variables

Cited by 48 publications

References 60 publications

Characterization of the stromatolite microbiome from Little Darby Island, The Bahamas using predictive and whole shotgun metagenomic analysis

Characterization of the stromatolite microbiome from Little Darby Island, The Bahamas using predictive and whole shotgun metagenomic analysis

Alkaline phosphatases in microbialites and bacterioplankton from Alchichica soda lake, Mexico

Using eDNA to biomonitor the fish community in a tropical oligotrophic lake

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