Stand stratification and woody species diversity of a subtropical forest in limestone habitat in the northern part of Okinawa Island

Stand stratification and woody species diversity were studied in a subtropical forest in limestone habitat in the northern part of Okinawa Island, Japan. The forest stand consisted of four architectural layers. Cinnamomum japonicum Sieb. was the most dominant species as it had the highest importance value in all layers, especially in the lower three layers. Although Rhus succedanea L. was a major top-layer species, it might disappear because of its absence in the lower two layers. The lower two layers had similar floristic composition, while the composition of the top layer differed greatly from that of the lower two layers. The value of H′ in each layer increased from the bottom to the second layer and then decreased, and the value of J′ in each layer consistently increased from the bottom layer upward. The values of Shannon’s index H′ and Pielou’s index J′ were 4.27 bit and 0.74, respectively, at the stand level. The trends of H′ and J′ based on the cumulative height range from the top layer downward were, respectively, the same as those in each layer for the present forest in limestone habitat. However, these trends were opposite from those of a nearby subtropical forest in silicate habitat, where the values of H′ and J′ based on the cumulative height range decreased steadily from the bottom layer upward.     

Comparison of green and albino individuals of the partially mycoheterotrophic orchid Epipactis helleborine on molecular identities of mycorrhizal fungi,nutritional modes and gene expression in mycorrhizal roots

Some green orchids obtain carbon from their mycorrhizal fungi, as well as from photosynthesis. These partially mycoheterotrophic orchids sometimes produce fully achlorophyllous, leaf‐bearing (albino) variants. Comparing green and albino individuals of these orchids will help to uncover the molecular mechanisms associated with mycoheterotrophy. We compared green and albino Epipactis helleborine by molecular barcoding of mycorrhizal fungi, nutrient sources based on ¹⁵N and ¹³C abundances and gene expression in their mycorrhizae by RNA‐seq and cDNA de novo assembly. Molecular identification of mycorrhizal fungi showed that green and albino E. helleborine harboured similar mycobionts, mainly Wilcoxina. Stable isotope analyses indicated that albino E. helleborine plants were fully mycoheterotrophic, whereas green individuals were partially mycoheterotrophic. Gene expression analyses showed that genes involved in antioxidant metabolism were upregulated in the albino variants, which indicates that these plants experience greater oxidative stress than the green variants, possibly due to a more frequent lysis of intracellular pelotons. It was also found that some genes involved in the transport of some metabolites, including carbon sources from plant to fungus, are higher in albino than in green variants. This result may indicate a bidirectional carbon flow even in the mycoheterotrophic symbiosis. The genes related to mycorrhizal symbiosis in autotrophic orchids and arbuscular mycorrhizal plants were also upregulated in the albino variants, indicating the existence of common molecular mechanisms among the different mycorrhizal types.     

Proembryo culture: in vitro development of early globular-stage zygotic embryos from Brassica juncea

We have systematically investigated the nutritional requirements for in vitro culture of zygotic proembryos of Brassica juncea. Normal embryo development in vitro was achieved in a new embryo culture medium (ECM) which contains mineral salts, sugars, amino acids, organic acids and coconut water. The culture system is comprised of two agar layers, with the top layer containing a higher osmolality than the bottom layer. Proembryos were embedded in the top layer in which the osmotic pressure decreased gradually during culture because of the diffusion of osmotically active compounds into the bottom layer. Using such a double-layer culture system and the ECM, proembryos as small as 35 μm (8–36 cells) could be cultured and developed into normal, mature embryos with an efficiency of at least 75%. In contrast to previous findings, we found that the removal of the suspensor had only a small effect on the development of embryos 55 μm or smaller, but no effect on larger proembryos. We expect this system to be very useful for investigations of the mechanism of plant embryogenesis.     

UV-B radiation and selenium affected energy availability in green alga <Emphasis Type="Italic">Zygnema</Emphasis>

Green alga Zygnema was exposed to three concentrations of selenium and two levels of UV-B radiation. The combined effects of both treatments on energy availability; photochemical quantum yield and respiratory potential were studied. Our findings show that traces of selenium enhance metabolic process connected with photochemical quantum yield and mitochondrial respiration. Surprisingly, selenium does not diminish the effects of UV-B radiation; on the contrary, the combined action of UV-B radiation and traces of selenium leads to pronounced negative effects on photochemical quantum yield and the respiratory potential. Selenium is involved in the activation of energy resources in green alga Zygnema. The importance of selenium for activity of the mitochondria is possibly an evolutionary recollection from an endosymbiotic bacterium.     

Monitoring the bacterial community of maize silage stored in a bunker silo inoculated with Enterococcus faecium, Lactobacillus plantarum and Lactobacillus buchneri

Aims: To monitor variations in the bacterial community and fermentation products of maize silage within and between bunker silos. Methods and Results: Silage samples were collected in 2008 and 2009 from three dairy farms, wherein the farmers arranged for a contractor to produce maize silage using bunker silos. Silage was prepared using a lactic acid bacteria (LAB) inoculant consisting of Enterococcus faecium, Lactobacillus plantarum and Lactobacillus buchneri. Eight samples were collected from each bunker silo; 4 ‘outer’ and 4 ‘inner’ samples were collected from near the top and the bottom of the silo. The dry matter, lactic acid, acetic acid, ethanol, 1‐propanol and 1,2‐propanediol contents differed between bunker silos in both sampling years. Higher acetic acid, 1‐propanol and 1,2‐propanediol contents were found in the bottom than the top layers in the 2008 samples, and higher lactic acid content was found in the top than the bottom layers in the 2009 samples. The bacterial community varied more between bunker silos than within a bunker silo in the 2008 samples, whereas differences between the top and the bottom layers were seen across bunker silos in the 2009 samples. The inoculated LAB were uniformly distributed, while several nonconventional silage bacteria were also detected. Lactobacillus acetotolerans, Lactobacillus panis and Acetobacter pasteurianus were detected in both years. Stenotrophomonas maltophilia was detected in the 2008 samples, and Lactobacillus reuteri, Acinetobacter sp. and Rahnella sp. were detected in the 2009 samples. Conclusions: Although differences were seen within and between bunker silos, the bacterial community may indicate a different relationship between bunker silos and sampling locations within a bunker silo from that indicated by the fermentation products. Significance and Impact of the Study: Analysis of bacterial community can help understand how diverse non‐LAB and LAB species are involved in the ensiling process of bunker‐made maize silage.     

Stand structure and woody species diversity in relation to stand stratification in a subtropical evergreen broadleaf forest, Okinawa Island

Stand structure and woody species diversity in a subtropical evergreen broadleaf forest grown in a silicate habitat, Okinawa Island, have been investigated on the basis of stand stratification. The forest stand consisted of four layers. The floristic composition of the top and the lower three layers was only slightly similar, although approximately one-third of the species were common to them. Mean tree weight decreased from the top toward the bottom layer whereas tree density increased from the top downward. This trend resembled the mean weight–density trajectory of self-thinning plant populations. The relationship between mean tree height and tree density for the upper two layers supported Yamakuras quasi –1/2 power law of tree height. The values of the Shannon–Wiener index, H, and the equitability index, J, tended to increase from the top layer downward except for the bottom layer. The values of H and J were, respectively, 4.83 bit and 0.82 for trees taller than 0.10 m. The lower layers contained many species of smaller height. High species diversity of the forest depended on small trees in the lower layers. Conservation of small trees in the lower layers, especially the bottom layer, is indispensable for sound maintenance of Okinawan evergreen broadleaf forests.     

NaCl胁迫下哈茨木霉ACCC32524的转录组和代谢组分析

【目的】通过分析NaCl胁迫下哈茨木霉(Trichoderma harzianum)ACCC32524转录组和代谢组数据,研究差异表达基因及次级代谢产物的变化情况,初步探索响应NaCl胁迫的分子机制。【方法】利用Illumina HiSeq XTen高通量测序平台完成0、0.4、0.6 mol/L NaCl浓度胁迫培养下哈茨木霉ACCC32524的转录组测序,GC-TOF-MS技术完成对0mol/L和0.6mol/LNaCl胁迫培养下的差异次级代谢产物检测,利用相关软件及数据库对差异表达基因(DEGs)和次级代谢产物的注释、筛选和分类,并进行RT-qPCR验证。【结果】本研究分别得到0.4 mol/L和0.6 mol/L NaCl胁迫下417和733条差异表达基因;GO富集分析显示,分别有318和582条差异表达基因注释到生物学过程、分子功能和细胞组分3个一级分类和40个二级分类;COG分类结果表明分别有232和414条转录本为20个类别,涉及差异表达基因最多的分别为氨基酸的转运和代谢、一般功能预测、碳水化合物的转运和代谢;KEGG代谢途径分析结果表明,分别有75和96条基因归到25个代谢通路中(P≤0.05),其中涉及差异基因最多的是氨基酸的生物合成和2-氧代羧酸代谢通路。从转录组数据中共筛选出与渗透调节、离子转运、活性氧清除等22个耐盐相关基因。0 mol/L和0.6 mol/L NaCl胁迫下的代谢组数据中共筛选出101个差异次级代谢产物,包括8种积累量上调和93种下调物质,其中36个得到定性,分属于糖类、有机酸和氨基酸等9个分类中。RT-qPCR验证挑选的差异表达基因的表达量变化,均与RNA-seq分析结果一致。【结论】NaCl胁迫下引起哈茨木霉ACCC32524基因及次级代谢产物发生明显变化,细胞代谢途径发生明显偏移,这些进程共同作用减少NaCl对细胞的毒害作用,为木霉菌的耐盐机理研究提供重要信息。     

Methylation of protein phosphatase 2A—Influence of regulators and environmental stress factors

Protein phosphatase 2A catalytic subunit (PP2A‐C) has a terminal leucine subjected to methylation, a regulatory mechanism conserved from yeast to mammals and plants. Two enzymes, LCMT1 and PME1, methylate and demethylate PP2A‐C, respectively. The physiological importance of these posttranslational modifications is still enigmatic. We investigated these processes in Arabidopsis thaliana by mutant phenotyping, by global expression analysis, and by monitoring methylation status of PP2A‐C under different environmental conditions. The lcmt1 mutant, possessing essentially only unmethylated PP2A‐C, had less dense rosettes, and earlier flowering than wild type (WT). The pme1 mutant, with 30% reduction in unmethylated PP2A‐C, was phenotypically comparable with WT. Approximately 200 overlapping genes were twofold upregulated, and 200 overlapping genes were twofold downregulated in both lcmt1 and pme1 relative to WT. Differences between the 2 mutants were also striking; 97 genes were twofold upregulated in pme1 compared with lcmt1, indicating that PME1 acts as a negative regulator for these genes. Analysis of enriched GO terms revealed categories of both abiotic and biotic stress genes. Furthermore, methylation status of PP2A‐C was influenced by environmental stress, especially by hypoxia and salt stress, which led to increased levels of unmethylated PP2A‐C, and highlights the importance of PP2A‐C methylation/demethylation in environmental responses.     

Spatial heterogeneity recognition in estuarine intertidal benthic macrofaunal communities: influence of sieve mesh-size and sampling depth

Estuarine intertidal soft-bottom macrobenthic infauna of the Tagus estuary was characterised using different mesh size sieves and sediment sampling depth. The study sampled 105 sites using a hand held 0.01 m² corer. The top layer (0–5 cm) was sieved through nested 1.0 and 0.5 mm meshes whereas the bottom layer (5–20 cm) was through a 1 mm mesh. The total survey took 26 taxa of more than 5800 individuals and a total wet weight biomass of over 650 g. The top layer, using both sieves, gathered 23 taxa (92% of the total), more than 5600 specimens (96%) but less than 8 g of biomass (1%) whereas the 1.0 mm sieve retained 21 taxa (91%), more than 1700 specimens (31%) and almost 7 g of biomass (1%). Abundance was dominated by small annelids, of which Streblospio shrubsolii was 68%, whereas biomass was dominated by molluscs, with the bivalve Scrobicularia plana representing 98%. Multivariate analyses showed an abundance pattern where the top layer data was very similar to that obtained with both layers. The bottom layer data were needed to accurately represent the total biomass pattern. The macrofaunal spatial pattern identified with the 0.5 mm sieve data differed from that identified by the 1.0 mm and was essential to discriminate a faunal assemblage located along the upper part of the shore. It was concluded that in order to characterize the macrofauna community structure, based on the presence/absence of taxa, the top layer and a 1.0 mm sieve would be sufficient. An abundance-based characterization requires the top layer and a 0.5 mm sieve whereas a biomass-based characterization requires data for both layers but it is sufficient to use the 1.0 mm sieve. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.