Taxonomic and phylogenetic evaluation of Limnothrix strains (Oscillatoriales, Cyanobacteria) by a... more Taxonomic and phylogenetic evaluation of Limnothrix strains (Oscillatoriales, Cyanobacteria) by adding Limnothrix planktonica strains isolated from central China
Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and loc... more Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types. We find that no single method is best for all cases. Instead, the optimal storage and extraction methods vary by taxa, by tissue, and by down-stream application. Therefore, we provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference gen...
Previous studies on the diversity and composition of nifH genes in the South China Sea (SCS) were... more Previous studies on the diversity and composition of nifH genes in the South China Sea (SCS) were mainly based on quantitative PCR and DNA clone methods. The pyrosequencing results of partial nifH gene fragments were used to study the spatiotemporal heterogeneity in composition and diversity of diazotrophs in the SCS. Seawater samples were collected throughout the upper ocean (<200-m depth) in different sites, as follows: the Pearl River Estuary; Taiwan and Luzon Straits (which are affected by the Kuroshio Current); a Trichodesmium bloom site; and two open ocean sites. Sample collection was conducted in four surveys from 2007 to 2010. A large dataset containing 217599 nifH reads from 27 samples was obtained. Putative diazotrophs in the SCS have reasonably low diversities, and the γ-proteobacteria and Trichodesmium were the two dominant nifH phylogenetic groups. No significant difference was observed among different regions and years. However, a significant difference existed amon...
Abstract2-Methylisoborneol (MIB), along with geosmin, has been frequently associated with taste a... more Abstract2-Methylisoborneol (MIB), along with geosmin, has been frequently associated with taste and odor (T&O) events in waters, and cyanobacterial species were considered the main producers in freshwater ecosystems. The detection and quantification of genes responsible for the synthesis of these odors on-site could be valuable for the prediction and treatment of T&O. In this study, SYBR Green and TaqMan real-time quantitative polymerase chain reaction (qPCR) assays were established on the basis of conserved regions in cyanobacterial MIB cyclase gene (mic) and applied to the quantification of potential MIB-producing cyanobacteria in waters. These two qPCR assays showed the prescribed values of amplification efficiency (0.976 and 1.023, respectively) with linearity (R2 > 0.99) in the range of 101 to 107mic copies. Examination on environmental samples and cyanobacterial cultures indicated that qPCRs were rarely inhibited by background biomass, and the limit of quantification was at the level of 103mic copies L−1 in natural waters. The seasonal variations of mic abundances in Lushui Reservoir, Donghu Lake, and Qinghai Lake of China were successfully quantified using the two qPCR protocols and indicated the applicability of these assays in field monitoring. Regression analysis revealed the positive correlation between mic abundance and MIB concentration, but no significant linear correlation was found between MIB-producing cyanobacteria and total cyanobacteria in investigated waters. The qPCR assays developed in this study could rapidly and reliably detect and quantify the abundance of potential cyanobacterial MIB producers, thereby providing a valuable tool for the prediction and early detection of T&O events.
Environmental Science and Pollution Research, 2014
Lake Erhai is the second largest lake of Southwest China and an important drinking water source. ... more Lake Erhai is the second largest lake of Southwest China and an important drinking water source. The lake is currently defined as the preliminary stage of eutrophic states, but facing a serious threat with transfer into intensive eutrophication. The present study examined the dynamics of Microcystis blooms and toxic Microcystis in Lake Erhai during 2010, based on quantitative real-time PCR method using 16S rRNA gene specific for Microcystis and microcystin systhesis gene (mcy), and chemical analysis on microcystin (MC) concentrations. Total Microcystis cell abundance at 16 sampling sites were shown as an average of 1.7 × 10(7) cells l(-1) (1.3 × 10(2)-3.8 × 10(9) cells l(-1)). Microcystin LR (MC-LR) and microcystin RR (MC-RR) were the main variants. The strong southwesterly winds, anticlockwise circular flows and geographical characteristics of lake and phytoplankton community succession impacted the distribution patterns of Chl a and MC in the lake. The concentration of Chl a and MC and abundances of total Microsytis and MC-producing Microsystis (MCM) were shown to be positively correlated with pH, DO and TP, negatively correlated with SD, NO₃-N, TN/Chl a and TN/TP, and not correlated with NH₄-N, TN, dissolved total nitrogen (DTN) and water temperatures. When TN/TP decrease, Microcystis tended to dominate and MC concentrations tended to increase, suggesting that the &amp;amp;quot;TN/TP rule&amp;amp;quot; can be partially applied to explain the correlation between the cyanobacterial blooms and nutrients N and P only within a certain nutrient level. It is speculated that N and P nutrients and the associated genes (e.g., mcy) may jointly drive MC concentration and toxigenicity of Microcystis in Lake Erhai.
During the process of terpene biosynthesis, C-C bond breaking and forming steps are subjected to ... more During the process of terpene biosynthesis, C-C bond breaking and forming steps are subjected to kinetic carbon isotope effects, leading to distinct carbon isotopic signatures of the products. Accordingly, carbon isotopic signatures could be used to reveal the "biosynthetic history" of the produced terpenoids. Five known sesquiterpene cyclases, regulating three different pathways, representing simple to complex biosynthetic sequences, were heterologously expressed and used for in vitro assays with farnesyl diphosphate as substrate. Compound specific IRMS measurements of the enzyme substrate farnesyl diphosphate (FDP) and the products of all the five cyclases were performed. The calculated δ(13) C value for FDP, based on δ(13) C values and the relative amounts of the products, was identical with its measured δ(13) C value, confirming the reliability of the approach and the precision of measurements. The different carbon isotope ratios of the products reflect the complexity ...
Taxonomic and phylogenetic evaluation of Limnothrix strains (Oscillatoriales, Cyanobacteria) by a... more Taxonomic and phylogenetic evaluation of Limnothrix strains (Oscillatoriales, Cyanobacteria) by adding Limnothrix planktonica strains isolated from central China
Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and loc... more Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types. We find that no single method is best for all cases. Instead, the optimal storage and extraction methods vary by taxa, by tissue, and by down-stream application. Therefore, we provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference gen...
Previous studies on the diversity and composition of nifH genes in the South China Sea (SCS) were... more Previous studies on the diversity and composition of nifH genes in the South China Sea (SCS) were mainly based on quantitative PCR and DNA clone methods. The pyrosequencing results of partial nifH gene fragments were used to study the spatiotemporal heterogeneity in composition and diversity of diazotrophs in the SCS. Seawater samples were collected throughout the upper ocean (<200-m depth) in different sites, as follows: the Pearl River Estuary; Taiwan and Luzon Straits (which are affected by the Kuroshio Current); a Trichodesmium bloom site; and two open ocean sites. Sample collection was conducted in four surveys from 2007 to 2010. A large dataset containing 217599 nifH reads from 27 samples was obtained. Putative diazotrophs in the SCS have reasonably low diversities, and the γ-proteobacteria and Trichodesmium were the two dominant nifH phylogenetic groups. No significant difference was observed among different regions and years. However, a significant difference existed amon...
Abstract2-Methylisoborneol (MIB), along with geosmin, has been frequently associated with taste a... more Abstract2-Methylisoborneol (MIB), along with geosmin, has been frequently associated with taste and odor (T&O) events in waters, and cyanobacterial species were considered the main producers in freshwater ecosystems. The detection and quantification of genes responsible for the synthesis of these odors on-site could be valuable for the prediction and treatment of T&O. In this study, SYBR Green and TaqMan real-time quantitative polymerase chain reaction (qPCR) assays were established on the basis of conserved regions in cyanobacterial MIB cyclase gene (mic) and applied to the quantification of potential MIB-producing cyanobacteria in waters. These two qPCR assays showed the prescribed values of amplification efficiency (0.976 and 1.023, respectively) with linearity (R2 > 0.99) in the range of 101 to 107mic copies. Examination on environmental samples and cyanobacterial cultures indicated that qPCRs were rarely inhibited by background biomass, and the limit of quantification was at the level of 103mic copies L−1 in natural waters. The seasonal variations of mic abundances in Lushui Reservoir, Donghu Lake, and Qinghai Lake of China were successfully quantified using the two qPCR protocols and indicated the applicability of these assays in field monitoring. Regression analysis revealed the positive correlation between mic abundance and MIB concentration, but no significant linear correlation was found between MIB-producing cyanobacteria and total cyanobacteria in investigated waters. The qPCR assays developed in this study could rapidly and reliably detect and quantify the abundance of potential cyanobacterial MIB producers, thereby providing a valuable tool for the prediction and early detection of T&O events.
Environmental Science and Pollution Research, 2014
Lake Erhai is the second largest lake of Southwest China and an important drinking water source. ... more Lake Erhai is the second largest lake of Southwest China and an important drinking water source. The lake is currently defined as the preliminary stage of eutrophic states, but facing a serious threat with transfer into intensive eutrophication. The present study examined the dynamics of Microcystis blooms and toxic Microcystis in Lake Erhai during 2010, based on quantitative real-time PCR method using 16S rRNA gene specific for Microcystis and microcystin systhesis gene (mcy), and chemical analysis on microcystin (MC) concentrations. Total Microcystis cell abundance at 16 sampling sites were shown as an average of 1.7 × 10(7) cells l(-1) (1.3 × 10(2)-3.8 × 10(9) cells l(-1)). Microcystin LR (MC-LR) and microcystin RR (MC-RR) were the main variants. The strong southwesterly winds, anticlockwise circular flows and geographical characteristics of lake and phytoplankton community succession impacted the distribution patterns of Chl a and MC in the lake. The concentration of Chl a and MC and abundances of total Microsytis and MC-producing Microsystis (MCM) were shown to be positively correlated with pH, DO and TP, negatively correlated with SD, NO₃-N, TN/Chl a and TN/TP, and not correlated with NH₄-N, TN, dissolved total nitrogen (DTN) and water temperatures. When TN/TP decrease, Microcystis tended to dominate and MC concentrations tended to increase, suggesting that the &amp;amp;quot;TN/TP rule&amp;amp;quot; can be partially applied to explain the correlation between the cyanobacterial blooms and nutrients N and P only within a certain nutrient level. It is speculated that N and P nutrients and the associated genes (e.g., mcy) may jointly drive MC concentration and toxigenicity of Microcystis in Lake Erhai.
During the process of terpene biosynthesis, C-C bond breaking and forming steps are subjected to ... more During the process of terpene biosynthesis, C-C bond breaking and forming steps are subjected to kinetic carbon isotope effects, leading to distinct carbon isotopic signatures of the products. Accordingly, carbon isotopic signatures could be used to reveal the "biosynthetic history" of the produced terpenoids. Five known sesquiterpene cyclases, regulating three different pathways, representing simple to complex biosynthetic sequences, were heterologously expressed and used for in vitro assays with farnesyl diphosphate as substrate. Compound specific IRMS measurements of the enzyme substrate farnesyl diphosphate (FDP) and the products of all the five cyclases were performed. The calculated δ(13) C value for FDP, based on δ(13) C values and the relative amounts of the products, was identical with its measured δ(13) C value, confirming the reliability of the approach and the precision of measurements. The different carbon isotope ratios of the products reflect the complexity ...
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