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Application of ancient DNA to the reconstruction of past microbial assemblages and for the detection of toxic cyanobacteria in subtropical freshwater ecosystems.
Mol Ecol. 2014 Dec; 23(23):5791-802.ME

Abstract

Ancient DNA (aDNA) analysis of lake sediments is a promising tool for detecting shifts in past microbial assemblages in response to changing environmental conditions. We examined sediment core samples from subtropical, freshwater Laguna Blanca (Uruguay), which has been severely affected by cultural eutrophication since 1960 and where cyanobacterial blooms, particularly those of the saxitoxin-producer Cylindrospermopsis raciborskii, have been reported since the 1990s. Samples corresponding to ~1846, 1852, 2000 and 2007 AD were selected to perform denaturing gradient gel electrophoresis (DGGE) analysis of the 16S-23S rRNA intergenic transcribed spacer (ribosomal ITS) to compare their prokaryotic assemblage composition. Each stratum showed different ITS patterns, but the composition of 21st century samples was clearly different than those of mid-19th century. This compositional change was correlated with shifts in sediment organic matter and chlorophyll a content, which were significantly higher in recent samples. The presence of saxitoxin-producing cyanobacteria was addressed by quantitative real-time PCR of the sxtU gene involved in toxin biosynthesis. This gene was present only in recent samples, for which clone libraries and ITS sequencing indicated the presence of Cyanobacteria. Phylogenetic analyses identified C. raciborskii only in the 2000 sample, shortly after several years when blooms were recorded in the lake. These data suggest the utility of aDNA for the reconstruction of microbial assemblage shifts in subtropical lakes, at least on centennial scales. The application of aDNA analysis to genes involved in cyanotoxin synthesis extends the applicability of molecular techniques in palaeolimnological studies to include key microbial community characteristics of great scientific and social interest.

Authors+Show Affiliations

Departamento de Microbiología, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Avenida Italia 3318, 11600, Montevideo, Uruguay; Ecology and Physiology of Phytoplankton Group, CSIC, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay.No affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

25346253

Citation

Martínez de la Escalera, Gabriela, et al. "Application of Ancient DNA to the Reconstruction of Past Microbial Assemblages and for the Detection of Toxic Cyanobacteria in Subtropical Freshwater Ecosystems." Molecular Ecology, vol. 23, no. 23, 2014, pp. 5791-802.
Martínez de la Escalera G, Antoniades D, Bonilla S, et al. Application of ancient DNA to the reconstruction of past microbial assemblages and for the detection of toxic cyanobacteria in subtropical freshwater ecosystems. Mol Ecol. 2014;23(23):5791-802.
Martínez de la Escalera, G., Antoniades, D., Bonilla, S., & Piccini, C. (2014). Application of ancient DNA to the reconstruction of past microbial assemblages and for the detection of toxic cyanobacteria in subtropical freshwater ecosystems. Molecular Ecology, 23(23), 5791-802. https://doi.org/10.1111/mec.12979
Martínez de la Escalera G, et al. Application of Ancient DNA to the Reconstruction of Past Microbial Assemblages and for the Detection of Toxic Cyanobacteria in Subtropical Freshwater Ecosystems. Mol Ecol. 2014;23(23):5791-802. PubMed PMID: 25346253.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Application of ancient DNA to the reconstruction of past microbial assemblages and for the detection of toxic cyanobacteria in subtropical freshwater ecosystems. AU - Martínez de la Escalera,Gabriela, AU - Antoniades,Dermot, AU - Bonilla,Sylvia, AU - Piccini,Claudia, Y1 - 2014/11/21/ PY - 2014/03/05/received PY - 2014/10/02/revised PY - 2014/10/06/accepted PY - 2014/10/28/entrez PY - 2014/10/28/pubmed PY - 2015/2/24/medline KW - ancient DNA KW - bacterial community composition KW - lake sediment KW - ribosomal ITS KW - saxitoxin-encoding genes SP - 5791 EP - 802 JF - Molecular ecology JO - Mol Ecol VL - 23 IS - 23 N2 - Ancient DNA (aDNA) analysis of lake sediments is a promising tool for detecting shifts in past microbial assemblages in response to changing environmental conditions. We examined sediment core samples from subtropical, freshwater Laguna Blanca (Uruguay), which has been severely affected by cultural eutrophication since 1960 and where cyanobacterial blooms, particularly those of the saxitoxin-producer Cylindrospermopsis raciborskii, have been reported since the 1990s. Samples corresponding to ~1846, 1852, 2000 and 2007 AD were selected to perform denaturing gradient gel electrophoresis (DGGE) analysis of the 16S-23S rRNA intergenic transcribed spacer (ribosomal ITS) to compare their prokaryotic assemblage composition. Each stratum showed different ITS patterns, but the composition of 21st century samples was clearly different than those of mid-19th century. This compositional change was correlated with shifts in sediment organic matter and chlorophyll a content, which were significantly higher in recent samples. The presence of saxitoxin-producing cyanobacteria was addressed by quantitative real-time PCR of the sxtU gene involved in toxin biosynthesis. This gene was present only in recent samples, for which clone libraries and ITS sequencing indicated the presence of Cyanobacteria. Phylogenetic analyses identified C. raciborskii only in the 2000 sample, shortly after several years when blooms were recorded in the lake. These data suggest the utility of aDNA for the reconstruction of microbial assemblage shifts in subtropical lakes, at least on centennial scales. The application of aDNA analysis to genes involved in cyanotoxin synthesis extends the applicability of molecular techniques in palaeolimnological studies to include key microbial community characteristics of great scientific and social interest. SN - 1365-294X UR - https://www.unboundmedicine.com/medline/citation/25346253/Application_of_ancient_DNA_to_the_reconstruction_of_past_microbial_assemblages_and_for_the_detection_of_toxic_cyanobacteria_in_subtropical_freshwater_ecosystems_ L2 - https://doi.org/10.1111/mec.12979 DB - PRIME DP - Unbound Medicine ER -