Clonal integration promotes the growth of Phragmites australis populations in saline wetlands of the Yellow River Delta

Estuarine wetlands are highly heterogeneous due to strong interactions between freshwater input and seawater intrusion. However, little is known about how clonal plant populations adapt to heterogeneous salinity in soil environments. In the present study, the effects of clonal integration on Phragmites australis populations under salinity heterogeneity were studied using field experiments with 10 treatments in the Yellow River Delta. Clonal integration significantly increased plant height, aboveground biomass, underground biomass, root–shoot ratio, intercellular CO2 concentration, net photosynthetic rate, stomatal conductance, transpiration rate, and stem Na+ content under homogeneous treatment. Under the heterogeneous salt treatment, clonal integration significantly affected total aboveground and underground biomass, photosynthetic traits, and stem Na+ content under different salt gradients. The increase in salt concentration inhibited the physiological activity and growth of P. australis to varying degrees. Compared with the heterogeneous saline environment, clonal integration was more beneficial to P. australis populations in the homogeneous saline habitat. The results of the present study suggest that P. australis prefers homogeneous saline habitats; however, plants can adapt to heterogeneous salinity conditions via clonal integration

NMR-Based Metabolomic Investigations on the Differential Responses in Adductor Muscles from Two Pedigrees of Manila Clam Ruditapes philippinarum to Cadmium and Zinc

Manila clam Ruditapes philippinarum is one of the most important economic species in shellfishery in China due to its wide geographic distribution and high tolerance to environmental changes (e.g., salinity, temperature). In addition, Manila clam is a good biomonitor/bioindicator in “Mussel Watch Programs” and marine environmental toxicology. However, there are several pedigrees of R. philippinarum distributed in the marine environment in China. No attention has been paid to the biological differences between various pedigrees of Manila clams, which may introduce undesirable biological variation in toxicology studies. In this study, we applied NMR-based metabolomics to detect the biological differences in two main pedigrees (White and Zebra) of R. philippinarum and their differential responses to heavy metal exposures (Cadmium and Zinc) using adductor muscle as a target tissue to define one sensitive pedigree of R. philippinarum as biomonitor for heavy metals. Our results indicated that there were significant metabolic differences in adductor muscle tissues between White and Zebra clams, including higher levels of alanine, glutamine, hypotaurine, phosphocholine and homarine in White clam muscles and higher levels of branched chain amino acids (valine, leucine and isoleucine), succinate and 4-aminobutyrate in Zebra clam muscles, respectively. Differential metabolic responses to heavy metals between White and Zebra clams were also found. Overall, we concluded that White pedigree of clam could be a preferable bioindicator/biomonitor in marine toxicology studies and for marine heavy metals based on the relatively high sensitivity to heavy metals

Transcriptomics-based analysis of genes related to lead stress and their expression in the roots of Pogonatherum crinitum

Revealing plants’ tolerance and transport genes to heavy metal stress play an important role in exploring the potential of phytoremediation. Taking the heavy metal lead (Pb) hyperaccumulator plant Pogonatherum crinitum (Thunb.) Kunth as the research object, a hydroponic simulation stress experiment was set up to determine the physiological indicators such as antioxidant enzymes and non-enzymatic antioxidants in the roots of P. crinitum under different Pb concentrations (0, 300, 500, 1000, 2000 mg·L-1). RNA-Seq was performed, the Unigenes obtained by transcriptome sequencing were enriched and annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, and the differential expression genes (DEGs) of root were screened and verified by quantitative real-time polymerase chain reaction (qRT-PCR). The results are as follows: with the increase of Pb concentration, superoxide dismutase (SOD), catalase (CAT), and ascorbic acid (AsA) content increased. Peroxidase (POD), malondialdehyde (MDA), and ascorbic acid–glutathione (AsA-GSH) cycles showed low promotion with high inhibition. A total of 38.21 Gb of bases were obtained by transcriptome sequencing, and the base quality of each sample reached Q20 and Q30, accounting for 90%, making the sequencing results reliable. Combined with transcriptome sequencing, functional annotation, and qRT-PCR validation results, 17 root Pb-tolerant genes of P. crinitum were screened out, which were related to antioxidation, transportation, and transcription functions. Moreover, qRT-PCR verification results under different Pb stress concentrations were consistent with the transcriptome sequencing results and changes in physiological indicators. In brief, the root of P. crinitum can adapt to the Pb stress environment by up-regulating the expression of related genes to regulate the physiological characteristics

Wet and Dry Atmospheric Depositions of Inorganic Nitrogen during Plant Growing Season in the Coastal Zone of Yellow River Delta

The ecological problems caused by dry and wet deposition of atmospheric nitrogen have been widespread concern in the world. In this study, wet and dry atmospheric depositions were monitored in plant growing season in the coastal zone of the Yellow River Delta (YRD) using automatic sampling equipment. The results showed that SO42- and Na+ were the predominant anion and cation, respectively, in both wet and dry atmospheric depositions. The total atmospheric nitrogen deposition was ~2264.24 mg m−2, in which dry atmospheric nitrogen deposition was about 32.02%. The highest values of dry and wet atmospheric nitrogen deposition appeared in May and August, respectively. In the studied area, NO3-–N was the main nitrogen form in dry deposition, while the predominant nitrogen in wet atmospheric deposition was NH4+–N with ~56.51% of total wet atmospheric nitrogen deposition. The average monthly attribution rate of atmospheric deposition of NO3-–N and NH4+–N was ~31.38% and ~20.50% for the contents of NO3-–N and NH4+–N in 0–10 cm soil layer, respectively, suggested that the atmospheric nitrogen was one of main sources for soil nitrogen in coastal zone of the YRD

A Meta-Analysis of the Bacterial and Archaeal Diversity Observed in Wetland Soils

This study examined the bacterial and archaeal diversity from a worldwide range of wetlands soils and sediments using a meta-analysis approach. All available 16S rRNA gene sequences recovered from wetlands in public databases were retrieved. In November 2012, a total of 12677 bacterial and 1747 archaeal sequences were collected in GenBank. All the bacterial sequences were assigned into 6383 operational taxonomic units (OTUs 0.03), representing 31 known bacterial phyla, predominant with Proteobacteria (2791 OTUs), Bacteroidetes (868 OTUs), Acidobacteria (731 OTUs), Firmicutes (540 OTUs), and Actinobacteria (418 OTUs). The genus Flavobacterium (11.6% of bacterial sequences) was the dominate bacteria in wetlands, followed by Gp1, Nitrosospira, and Nitrosomonas. Archaeal sequences were assigned to 521 OTUs from phyla Euryarchaeota and Crenarchaeota. The dominating archaeal genera were Fervidicoccus and Methanosaeta. Rarefaction analysis indicated that approximately 40% of bacterial and 83% of archaeal diversity in wetland soils and sediments have been presented. Our results should be significant for well-understanding the microbial diversity involved in worldwide wetlands.This study examined the bacterial and archaeal diversity from a worldwide range of wetlands soils and sediments using a meta-analysis approach. All available 16S rRNA gene sequences recovered from wetlands in public databases were retrieved. In November 2012, a total of 12677 bacterial and 1747 archaeal sequences were collected in GenBank. All the bacterial sequences were assigned into 6383 operational taxonomic units (OTUs 0.03), representing 31 known bacterial phyla, predominant with Proteobacteria (2791 OTUs), Bacteroidetes (868 OTUs), Acidobacteria (731 OTUs), Firmicutes (540 OTUs), and Actinobacteria (418 OTUs). The genus Flavobacterium (11.6% of bacterial sequences) was the dominate bacteria in wetlands, followed by Gp1, Nitrosospira, and Nitrosomonas. Archaeal sequences were assigned to 521 OTUs from phyla Euryarchaeota and Crenarchaeota. The dominating archaeal genera were Fervidicoccus and Methanosaeta. Rarefaction analysis indicated that approximately 40% of bacterial and 83% of archaeal diversity in wetland soils and sediments have been presented. Our results should be significant for well-understanding the microbial diversity involved in worldwide wetlands

Vegetative Ecological Characteristics of Restored Reed (Phragmites australis) Wetlands in the Yellow River Delta, China

In this study, we compared ecological characteristics of wetland vegetation in a series of restoration projects that were carried out in the wetlands of Yellow River Delta. The investigated characteristics include plant composition structure, species diversity and community similarity in three kinds of Phragmites australis wetlands, i.e. restored P. australis wetlands (R1, R2, R3 and R4: restored in 2002, 2005, 2007 and 2009, respectively), natural P. australis wetland (N) and degraded P. australis wetland (D) to assess the process of wetlands restoration. The coverage of the R1 was 99%, which was similar to natural wetland. Among all studied wetlands, the highest and lowest stem density was observed in R1 and R2, respectively, Plant height and stem diameter show the same trend as N > R2 > R1 > R3 > D > R4. Species diversity of restored P. australis wetlands became closed to natural wetland. Both species richness and Shannon–Wiener index had similar tendency: increased first and then decreased with restored time. The highest species richness and species diversity were observed in R2, while the lowest values of those parameters were found in natural P. australis wetland. Similarity indexes between restored wetlands and natural wetland increased with the restoration time, but they were still less than 50%. The results indicate that the vegetation of P. australis wetlands has experienced a great improvement after several years’ restoration, and it is feasible to restored degraded P. australis wetlands by pouring fresh water into those wetlands in the Yellow River Delta. However, it is notable that costal degraded P. australis wetland in this region may take years to decades to reach the status of natural wetland

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Regulation of Metabolites, Gene Expression, and Antioxidant Enzymes to Environmentally Relevant Lead and Zinc in the Halophyte Suaeda salsa

As a pioneer halophyte, Suaeda salsa can grow in the intertidal zones, which are often polluted by heavy metals from both terrigenous wastewater and tidewater containing high concentrations of heavy metals. Therefore S. salsa is potentially suitable as a biomonitor for heavy-metal pollution in the intertidal zones. In this study, regulation of metabolites, gene expression, and antioxidant status of environmentally relevant lead and zinc were characterized using NMR-based metabolomics, real-time quantitative reverse transcription polymerase chain reaction, and antioxidant enzyme activities. In Pb-exposed S. salsa samples, only decreased tyrosine was observed, with statistical significance approaching 0.05. Metabolic biomarkers in Zn-exposed S. salsa samples included increased amino acids (valine, isoleucine, leucine, threonine, asparagine, and phenylalanine), and decreased acetate, glucose, ferulate, and fumarate. Increased succinate, aspartate, and malonate and decreased fructose were uniquely found in mixed Pb- and Zn-exposed samples in addition to the similar metabolic changes such as alanine, glucose, fumarate, and ferulate in Zn-exposed samples. Based on the metabolic biomarkers, gene expressions, and antioxidant enzyme activities, both Zn and mixed Pb and Zn induced significant oxidative stress and disturbances in energy metabolism, photosynthesis/glucogenesis, and protein biodegradation in S. salsa. However, environmentally relevant Pb could induce slight oxidative stress in S. salsa as indicated by increased catalase gene expression levels and catalase activities.As a pioneer halophyte, Suaeda salsa can grow in the intertidal zones, which are often polluted by heavy metals from both terrigenous wastewater and tidewater containing high concentrations of heavy metals. Therefore S. salsa is potentially suitable as a biomonitor for heavy-metal pollution in the intertidal zones. In this study, regulation of metabolites, gene expression, and antioxidant status of environmentally relevant lead and zinc were characterized using NMR-based metabolomics, real-time quantitative reverse transcription polymerase chain reaction, and antioxidant enzyme activities. In Pb-exposed S. salsa samples, only decreased tyrosine was observed, with statistical significance approaching 0.05. Metabolic biomarkers in Zn-exposed S. salsa samples included increased amino acids (valine, isoleucine, leucine, threonine, asparagine, and phenylalanine), and decreased acetate, glucose, ferulate, and fumarate. Increased succinate, aspartate, and malonate and decreased fructose were uniquely found in mixed Pb- and Zn-exposed samples in addition to the similar metabolic changes such as alanine, glucose, fumarate, and ferulate in Zn-exposed samples. Based on the metabolic biomarkers, gene expressions, and antioxidant enzyme activities, both Zn and mixed Pb and Zn induced significant oxidative stress and disturbances in energy metabolism, photosynthesis/glucogenesis, and protein biodegradation in S. salsa. However, environmentally relevant Pb could induce slight oxidative stress in S. salsa as indicated by increased catalase gene expression levels and catalase activities