Accuracies of field CO2–H2O data from open-path eddy-covariance flux systems: assessment based on atmospheric physics and biological environment

Ecosystem CO2–H2O data measured by infrared gas analyzers in open-path eddy-covariance (OPEC) systems have numerous applications, such as estimations of CO2 and H2O fluxes in the atmospheric boundary layer. To assess the applicability of the data for these estimations, data uncertainties from analyzer measurements are needed. The uncertainties are sourced from the analyzers in zero drift, gain drift, cross-sensitivity, and precision variability. These four uncertainty sources are individually specified for analyzer performance, but so far no methodology exists yet to combine these individual sources into a composite uncertainty for the specification of an overall accuracy, which is ultimately needed. Using the methodology for closed-path eddy-covariance systems, this overall accuracy for OPEC systems is determined from all individual uncertainties via an accuracy model and further formulated into CO2 and H2O accuracy equations. Based on atmospheric physics and the biological environment, for EC150 infrared CO2–H2O analyzers, these equations are used to evaluate CO2 accuracy (±1.22 mgCO2 m−3, relatively ±0.19 %) and H2O accuracy (±0.10 gH2O m−3, relatively ±0.18 % in saturated air at 35 ∘C and 101.325 kPa). Both accuracies are applied to conceptual models addressing their roles in uncertainty analyses for CO2 and H2O fluxes. For the high-frequency air temperature derived from H2O density along with sonic temperature and atmospheric pressure, the role of H2O accuracy in its uncertainty is similarly addressed. Among the four uncertainty sources, cross-sensitivity and precision variability are minor, although unavoidable, uncertainties, whereas zero drift and gain drift are major uncertainties but are minimizable via corresponding zero and span procedures during field maintenance. The accuracy equations provide rationales to assess and guide the procedures. For the atmospheric background CO2 concentration, CO2 zero and CO2 span procedures can narrow the CO2 accuracy range by 40 %, from ±1.22 to ±0.72 mgCO2 m−3. In hot and humid weather, H2O gain drift potentially adds more to the H2O measurement uncertainty, which requires more attention. If H2O zero and H2O span procedures can be performed practically from 5 to 35 ∘C, the H2O accuracy can be improved by at least 30 %: from ±0.10 to ±0.07 gH2O m−3. Under freezing conditions, the H2O span procedure is impractical but can be neglected because of its trivial contributions to the overall uncertainty. However, the zero procedure for H2O, along with CO2, is imperative as an operational and efficient option under these conditions to minimize H2O measurement uncertainty.</p

The complete chloroplast genome sequence of Rhododendron fortunei: structural comparative and phylogenetic analysis in the Ericaceae family

Rhododendron fortunei (Ericaceae) possesses valuable horticultural and medicinal values. However, the genomic information on R. fortunei is very limited. In this study, the complete chloroplast genome (cp) of R. fortunei was assembled and annotated, SSR loci were characterised, comparative genomic analysis was carried out, and phylogenetic research was also performed. The results showed that the R. fortunei cp genome was of a typical quadripartite structure (200,997 bp). The lengths of the large single copy region (LSC), the inverted repeat regions (IR), and the small single copy region (SSC) were 109,151 bp, 2,604 bp, and 44,619 bp, respectively. A total of 147 unique genes were identified, including 99 protein-coding genes, 42 tRNA genes, and 6 rRNA genes, respectively. Leucine (11.51%) and cysteine (1.15%) were the highest and lowest representative amino acids, respectively. The total of 30 codons with obvious codon usage bias were all A/U-ending codons. Among the 77 simple sequence repeats, the majority were mononucleotide A/T repeats located in the intergenic spacer region. Five gene regions showed high levels of nucleotide diversity (Pi > 0.03). The comparative genome analysis revealed 7 hotspot intergenic regions (trnI-rpoB, trnTrpl16, rpoA-psbJ, rps7-rrn16, ndhI-rps16, rps16-rps19, and rrn16-trnI), showing great potential as molecular makers for species authentication. Expansion and contraction were detected in the IR region of the R. fortunei cp genome. In the phylogenetic tree, R. fortunei was closely related to R. platypodum. This research will be beneficial for evolutionary and genetic diversity studies of R. fortunei and related species among the Ericaceae family

Complete chloroplast genome sequence of Rhododendron mariesii and comparative genomics of related species in the family Ericaeae

Rhododendron mariesii Hemsley et Wilson, 1907, a typical member of the family Ericaeae, possesses valuable medicinal and horticultural properties. In this research, the complete chloroplast (cp) genome of R. mariesii was sequenced and assembled, which proved to be a typical quadripartite structure with the length of 203,480 bp. In particular, the lengths of the large single copy region (LSC), small single copy region (SSC), and inverted repeat regions (IR) were 113,715 bp, 7,953 bp, and 40,918 bp, respectively. Among the 151 unique genes, 98 were protein-coding genes, 8 were tRNA genes, and 45 were rRNA genes. The structural characteristics of the R. mariesii cp genome was similar to other angiosperms. Leucine was the most representative amino acid, while cysteine was the lowest representative. Totally, 30 codons showed obvious codon usage bias, and most were A/U-ending codons. Six highly variable regions were observed, such as trnK-pafI and atpE-rpoB, which could serve as potential markers for future barcoding and phylogenetic research of R. mariesii species. Coding regions were more conserved than non-coding regions. Expansion and contraction in the IR region might be the main length variation in R. mariesii and related Ericaeae species. Maximum-likelihood (ML) phylogenetic analysis revealed that R. mariesii was relatively closed to the R. simsii Planchon, 1853 and R. pulchrum Sweet,1831. This research will supply rich genetic resource for R. mariesii and related species of the Ericaeae

The complete chloroplast genome sequence of Callitriche palustris (Plantaginaceae)

Callitriche palustris L. is an annual aquatic or marsh plant, wide spread in temperate regions throughout the world. In present study, we sequenced, assembled and annotated the complete chloroplast (cp) genome of C. palustris. The length of C. palustris complete cp genome was 150,138 bp, with a typical quadripartite structure comprising a pair of inverted repeat regions (IRs; 25,667 bp), a large single copy region (LSC; 81,432 bp) and a small single copy region (SSC; 17,372 bp). The whole cp genome contained 134 genes, including 89 protein-coding genes (PCGs), 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The maximum likelihood (ML) phylogenetic analysis indicated that C. palustris was a member of Plantaginaceae, but the relationships between subfamilies and tribes need more samplings. This cp genome would provide a valuable genetic resource for C. palustris’ phylogenetic study

Bidirectional natural hybridization between sympatric Ligularia vellerea and L. subspicata

Natural hybridization has been regarded as a crucial pathway of speciation and provides the raw materials for the evolution of biodiversity. The interspecific natural hybridization of the genus Ligularia Cass. is universal and has been considered to be an important factor driving the high diversity of Ligularia species in the Hengduan Mountains, China. Although the natural hybridization between L. vellerea and L. subspicata was reported previously, the direction of hybridization was uncertain due to the limitation of sampling. Thus, in this study, we sampled more individuals and increased two fragments of chloroplast DNA on the basis of the previous study to further verify the natural hybridization between L. vellerea and L. subspicata and confirm the direction of hybridization. Based on DNA sequences (atpB-rbcL, trnL-rpl32, trnQ-5'rps16, and nuclear ribosomal internal transcribed spacer region) data, we concluded that putative hybrids were primary products of hybridization between L. vellerea and L. subspicata and the hybridization was bidirectional. Moreover, sympatric L. tongolensis was not apparently involved in the hybridization. Surprisingly, some pure L. subspicata individuals showed the disaccordance between morphology and DNA data, which might indicate that introgression occurs between L. vellerea and L. subspicata

The complete chloroplast genome sequence of China Lindera praecox (Lauraceae) and intra-species diversity

Lindera praecox is a signature composition in the broadleaved deciduous forest of East China and Japan. Presently, the complete chloroplast (cp) genome of this species was sequenced, assembled, and annotated. It is 152,818 bp in length and encodes 85 protein-coding genes, 36 transfer RNA (tRNA) genes and eight ribosomal RNA (rRNA) genes. The phylogenetic analysis indicated intraspecific varieties within L. praecox species collected in China and Japan. This chloroplast genome sequencing offers genetic background for resources conservation and phylogenetic studies

Characterization of the complete chloroplast genome sequence of Limnophila sessiliflora Blume 1826 (Plantaginaceae)

Limnophila sessiliflora Blume 1826 is a perennial amphibious herb with ornamental and water purification value that is widespread in temperate and tropical Asia. In the present study, we sequenced, assembled, and annotated the complete chloroplast (cp) genome of L. sessiliflora. It is 152,395 bp in length, with a typical quadripartite structure, comprising a pair of inverted repeat regions (IRs; 25,545 bp), a large single-copy region (LSC; 83,163 bp), and a small single-copy (SSC; 18,142 bp) region. The whole cp genome contained 135 genes, including 89 protein-coding genes (PCGs), 38 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The maximum-likelihood (ML) phylogenetic analysis indicated that L. sessiliflora was closely related to the genera Bacopa and Scoparia in the tribe Gratioleae of Plantaginaceae. This cp genome provides a valuable genetic resource for phylogenetic study

The complete chloroplast genome sequence of Disanthus cercidifolius Subsp. Longipes (Hamamelidaceae)

Disanthus cercidifolius Maximowicz subsp. longipes (H. T. Chang) K. Y. Pan is a rare and Endangered species endemic to central China. Here, we assembled and annotated the complete chloroplast (cp) genome. It is 158,148 bp in length and encodes 87 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. This chloroplast genome sequencing offers a useful resource for future conservation genetics and phylogenetic studies

Natural Hybridization and Introgression between <i>Ligularia cymbulifera</i> and <i>L. tongolensis</i> (Asteraceae, Senecioneae) in Four Different Locations

<div><p>Natural hybridization has been considered to represent an important factor influencing the high diversity of the genus <i>Ligularia</i> Cass. in the Hengduan Mountains, China. Natural hybridization has been confirmed to occur frequently in <i>Ligularia</i>. To date, however, it has been demonstrated only within a single population. In this paper, we present evidence of natural hybridization in <i>Ligularia</i> from four different locations. The internal transcribed spacer (ITS) region of the nuclear ribosomal DNA and three chloroplast intergenic spacers (<i>trn</i>K-<i>rps</i>16, <i>trn</i>L-<i>rpl</i>32 and <i>trn</i>Q-5'<i>rps</i>16) of 149 accessions of putative hybrids and their putative parents (<i>L. cymbulifera</i> and <i>L. tongolensis</i>) were analyzed for evidence of hybridization. The ITS data clearly distinguished two putative parental species and sympatric <i>L. vellerea</i> and supported the hypothesis that those morphological intermediates were products of natural hybridization between <i>L. cymbulifera</i> and <i>L. tongolensis</i>. Moreover, several identified morphological parents were actual introgressed products. Because of hybridization and introgression, chloroplast DNA sequences generated a poorly resolved network. The present results indicate that varying degrees of hybridization and introgression occur differently depending on the habitat context. We conclude that gene flow caused by natural hybridization in <i>Ligularia</i> indeed plays an important role in the species diversity.</p></div

Changes in soil phosphorus fractions after 9 years of continuous nitrogen addition in a Larix gmelinii plantation

International audienceThe key message N addition decreased soil inorganic P availability, microbial biomass P, and acid phosphatase activity in the larch plantation. Soil inorganic P availability decreased after N addition due to the changes in both microbial properties and plant uptake.• Context Soil phosphorus (P) availability is considered an important factor in influencing the biomass production of plants. Sustained inputs of nitrogen (N) through atmospheric deposition or N fertilizers, particularly in temperate forests, may change the composition and availability of P and thus affect long-term forest productivity.• Aims The objective of this study was to assess soil P availability, P fractions, and microbial properties including microbial biomass P and acid phosphatase activity after 9 consecutive years of N addition in a larch (Larix gmelinii) plantation, northeastern China.• Methods From 2003 to 2011, NH4NO3 was added to replicate plots (three 20 m × 30 m plots) in the larch plantation each year at a rate of 100 kg N ha−1 year−1. Soil samples from 0–10-cm and 10–20-cm depths were collected in N addition plots and control (no N addition) plots.• Results N addition significantly decreased soil NaHCO3-Pi (Pi is inorganic P), microbial biomass P, and acid phosphatase activity but increased the NaOH-Pi concentration. N addition appeared to induce a decrease in soil inorganic P availability by changing pH and P uptake by trees. In addition, N addition significantly decreased the NaOH-Po (Po is organic P) concentration, possibly because of increased P mineralization. However, the total P and other P fractions were unaffected by N fertilization.• Conclusion Our results suggested that N addition enhanced P uptake by trees, whereas it reduced soil inorganic P availability as well as microbial biomass and activity related to soil P cycling in the larch plantation