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Characterization of Trichodesmium spp. by genetic techniques.

ABSTRACT: The genetic diversity of Trichodesmium spp. from natural populations (off Bermuda in the Sargasso Sea and off North Australia in the Arafura and Coral Seas) and of culture isolates from two regions (Sargasso Sea and Indian Ocean) was investigated. Three independent techniques were used, including a DNA fingerprinting method based on a highly iterated palindrome (HIP1), denaturing gradient gel electrophoresis of a hetR fragment, and sequencing of the internal transcribed spacer (ITS) of the 16S-23S rDNA region. Low genetic diversity was observed in natural populations of Trichodesmium spp. from the two hemispheres. Culture isolates of Trichodesmium thiebautii, Trichodesmium hildebrandtii, Trichodesmium tenue, and Katagnymene spiralis displayed remarkable similarity when these techniques were used, suggesting that K. spiralis is very closely related to the genus TRICHODESMIUM: The largest genetic variation was found between Trichodesmium erythraeum and all other species of Trichodesmium, including a species of KATAGNYMENE: Our data obtained with all three techniques suggest that there are two major clades of Trichodesmium spp. The HIP1 fingerprinting and ITS sequence analyses allowed the closely related species to be distinguished. This is the first report of the presence of HIP1 in marine cyanobacteria.

SUBMITTER: Orcutt KM

PROVIDER: S-EPMC127538 | biostudies-literature | 2002 May

REPOSITORIES: biostudies-literature

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Characterization of Trichodesmium spp. by genetic techniques.

Orcutt K M KM Rasmussen U U Webb E A EA Waterbury J B JB Gundersen K K Bergman B B

Applied and environmental microbiology 20020501 5

The genetic diversity of Trichodesmium spp. from natural populations (off Bermuda in the Sargasso Sea and off North Australia in the Arafura and Coral Seas) and of culture isolates from two regions (Sargasso Sea and Indian Ocean) was investigated. Three independent techniques were used, including a DNA fingerprinting method based on a highly iterated palindrome (HIP1), denaturing gradient gel electrophoresis of a hetR fragment, and sequencing of the internal transcribed spacer (ITS) of the 16S-2 ...[more]

PMID: 11976093

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Project description:Trichodesmium, a filamentous bloom-forming marine cyanobacterium, plays a key role in the biogeochemistry of oligotrophic ocean regions because of the ability to fix nitrogen. Naturally occurring in the Great Barrier Reef (GBR), the contribution of Trichodesmium to the nutrient budget may be of the same order as that entering the system via catchment runoff. However, the cyclicity of Trichodesmium in the GBR is poorly understood and sparsely documented because of the lack of sufficient observations. This study provides the first systematic analysis of Trichodesmium spatial and temporal occurrences in the GBR over the decade-long MERIS ocean color mission (2002-2012). Trichodesmium surface expressions were detected using the Maximum Chlorophyll Index (MCI) applied to MERIS satellite imagery of the GBR lagoonal waters. The MCI performed well (76%), albeit tested on a limited set of images (N = 25) coincident with field measurements. A north (Cape York) to south (Fitzroy) increase in the extent, frequency and timing of the surface expressions characterized the GBR, with surface expressions extending over several hundreds of kilometers. The two southernmost subregions Mackay and Fitzroy accounted for the most (70%) bloom events. The bloom timing of Trichodesmium varied from May in the north to November in the south, with wet season conditions less favorable to Trichodesmium aggregations. MODIS-Aqua Sea Surface Temperature (SST) datasets, wind speed and field measurements of nutrient concentrations were used in combination with MCI positive instances to assess the blooms' driving factors. Low wind speed (<6 m.s-1) and SST > 24°C were associated with the largest surface aggregations. Generalized additive models (GAM) indicated an increase in bloom occurrences over the 10-year period with seasonal bloom patterns regionally distinct. Interannual variability in SST partially (14%) explained bloom occurrences, and other drivers, such as the subregion and the nutrient budget, likely regulate Trichodesmium surface aggregations in the GBR.

Project description:BACKGROUND:Mosquitoes are the potential vectors for a variety of viruses that can cause diseases in the human and animal populations. Viruses in the order Picornavirales infect a broad range of hosts, including mosquitoes. In this study, we aimed to characterize a novel picorna-like virus from the Culex spp. of mosquitoes from the Zambezi Valley of Mozambique. METHODS:The extracted RNA from mosquito pools was pre-amplified with the sequence independent single primer amplification (SISPA) method and subjected to high-throughput sequencing using the Ion Torrent platform. Reads that are classified as Iflaviridae, Picornaviridae and Dicistroviridae were assembled by CodonCode Aligner and SPAdes. Gaps between the viral contigs were sequenced by PCR. The genomic ends were analyzed by 5' and 3' RACE PCRs. The ORF was predicted with the NCBI ORF finder. The conserved domains were identified with ClustalW multiple sequence alignment, and a phylogenetic tree was built with MEGA. The presence of the virus in individual mosquito pools was detected by RT-PCR assay. RESULTS:A near full-length viral genome (9740 nt) was obtained in Culex mosquitoes that encoded a complete ORF (3112 aa), named Culex picorna-like virus (CuPV-1). The predicted ORF had 38% similarity to the Hubei picorna-like virus 35. The sequence of the conserved domains, Helicase-Protease-RNA-dependent RNA polymerase, were identified by multiple sequence alignment and found to be at the 3' end, similar to iflaviruses. Phylogenetic analysis of the putative RdRP amino acid sequences indicated that the virus clustered with members of the Iflaviridae family. CuPV-1 was detected in both Culex and Mansonia individual pools with low infection rates. CONCLUSIONS:The study reported a highly divergent, near full-length picorna-like virus genome from Culex spp. mosquitoes from Mozambique. The discovery and characterization of novel viruses in mosquitoes is an initial step, which will provide insights into mosquito-virus interaction mechanisms, genetic diversity and evolution.

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Characterization of Trichodesmium spp. by genetic techniques.

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Characterization of Trichodesmium spp. by genetic techniques.

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