Intraspecific sequence variation of chloroplast DNA among the component species of evergreen broad-leaved forests in Japan

For the purpose of phylogeographic study of lucidophyllous (evergreen broad-leaved) forests in Japan, we surveyed intraspecific chloroplast DNA (cpDNA) variation in 41 component species of such forests. Intraspecific cpDNA variations were detected in 14 species. In 15 species and one species group, 16 non-coding cpDNA regions were examined to find intraspecific sequence variation. The extent of variation in these regions was compared. The largest amount of intraspecific variation was detected in the rps16 region. A relatively large amount of intraspecific variation was detected in the petD-rpoA, rpl16, and trnL-F regions. It is suggested that these regions of cpDNA would be useful for detecting intraspecific variation in plant species, and could provide valuable information for various research purposes.     

Diversity and rarity hotspots and conservation of butterfly communities in and around the Aokigahara woodland of Mount Fuji,central Japan

In central Japan, Aokigahara woodland is considered to be one of the most natural areas around Mount Fuji and a core area in the conservation of the biodiversity of Mount Fuji. We chose butterflies as an indicator species of biodiversity and examined six communities in and around the woodland in 2000 using transect counts to examine and search for diversity and rarity hotspots and their associated landscapes. The results showed that butterfly species richness and species diversities H 1/ were significantly higher in forest-edge sites than in forest-interior and/or open-land sites, and variation in the total number of species among these three landscape types was well accounted for by ecologically specialist species, such as landscape specifics, oligovoltines, narrow diet feeders and low-density species. Thus, the species regarded as vulnerable to extinction, including Red List species, were observed more often in forest-edge sites than in forest-interior and/or open-land sites. As a result, in the study area, diversity and rarity hotspots were found in forest-edge landscapes. The reasons why butterfly diversity and rarity hotspots were established in forest-edge landscapes were analyzed and interpreted from several points of view, including disturbance level, landscape elements and plant species richness. From these results, and the fact that some species were confined to forest-interior sites, we conclude that it is very important to conserve and manage forest-edge habitats (considered to be semi-natural) as well as forest-interior habitats (considered to be the most natural) to maintain the diversity of butterfly communities and preserve the various types of threatened species in and around the Aokigahara woodland.     

Aerobic secondary utilization of a non-growth and inhibitory substrate 2,4,6-trichlorophenol by Sphingopyxis chilensis S37 and sphingopyxis-like strain S32

This paper reports 2,4,6-trichlorophenol (246TCP) degradation bySphingopyxis chilensis S37 and Sphingopyxis chilensis-like strain S32,which were unable to use 246TCP as the sole carbon and energy source. In R2A broth, the strainsdegraded 246TCP up to 0.5 mM. Results with mixtures of different 246TCP and glucose concentrations in mineral salt media demonstrated dependence on glucose to allow bacterial growth and degradation of 246TCP. Strain S32 degraded halophenol up to 0.2 mM when 5.33 mM glucose was simultaneously added, while strain S37 degraded the compound up to 0.1 mM when 1.33 mM glucose was added. These 246TCP concentrations were lethal for inocula in absence of glucose. Stoichiometricreleases of chloride and analysis by HPLC, GC-ECD and GC-MS indicated 246TCP mineralisation by both strains. To our knowledge, this is the first report of bacteriaable to mineralize a chlorophenol as a non-growth and inhibitory substrate. The concept of secondary utilization instead of cometabolism is proposed for this activity.     

Late glacial and Holocene vegetation,climate and fire history inferred from Lagoa Nova in the southeastern Brazilian lowland

The pollen and charcoal record of a 1,500-cm-long lake sediment core from Lagoa Nova allows a reconstruction of vegetation, climate and fire history in the Atlantic lowland of southeastern Brazil. Today the potential vegetation of the study region would be dense and tall semi-deciduous forest, related to a dry season of 4 months and 1,250 mm precipitation per year. The lowermost core section of Lagoa Nova is probably of late Glacial age and contains only few, poorly preserved pollen grains, indicating dry environmental conditions. Pollen preservation was good above 1,005-cm core depth. Extrapolating from four radiocarbon dates, this interval represents about the last 10,000 years. During the early Holocene (until about 8,500 b.p.), the landscape was dominated by savanna of the campo cerrado type (open shrub woodland), with frequent trees of Curatella americana and small areas of gallery forests along the drainage system. Savanna fires, probably natural, were frequent at that time. The palaeovegetation pattern is consistent with a long dry season of about 6 months and annual precipitation lower than today. Then, up to about 7,560 b.p., gallery forests expanded in the valleys, reflecting a shorter dry season of about 5 months and somewhat higher annual rainfall. Fire was less frequent during this wetter period. Between about 7,560 and 6,060 b.p., savanna expanded and gallery forests retreated, indicating a return to drier climatic conditions of probably between 5 and 6 months dry season and lower precipitation. Fire was again frequent, but not as frequent as during the early Holocene. During the mid to late Holocene period between about 6,060 and 2,180 b.p., the valleys were covered by semi-deciduous forest, but on the hills cerrado vegetation continued to grow. The dry season was probably around 5 months and rainfall was higher than in the preceding period. During the following period between about 2,810 and 600 b.p., the open cerrado on the hills changed to closed cerrado, reflecting wetter conditions with a shorter dry season than in the previous period. It was only after about 600 b.p. that dense semi-deciduous forests expanded throughout the study region, indicating the start of modern, wet climatic conditions with an annual dry season of about 4 months. Fire was nearly absent during this period. The reconstructed palaeoenvironment from the Lagoa Nova record is similar to that of Lago do Pires, indicating that changes in past vegetation, climate and fire frequency are regionally consistent in southeastern Brazil.     

A bioassay for insect deterrent compounds found in plant and animal tissues

A general field bioassay for detecting biologically active compounds in plants and insects has been developed and tested for efficacy and sensitivity. Methanolic extracts, in sucrose solution, of 20 plant and six caterpillar species were offered to the ponerine ant Paraponera clavata and the feeding preferences observed. The bioassay resulted in the detection of nine plant and three caterpillar species with ant-deterrent extracts, and 11 plant and three caterpillar species with neutral or attractant extracts. All of the plants showing ant-deterrent characteristics which had been chemically investigated in our laboratory, or for which chemical literature was available, contained secondary metabolites of known deterrence. Both naturally occurring and artificial differences in chemical concentrations could be detected using the bioassay. The method provides a means of screening plants and insects for compounds that are insect anti-feedants or that can modify insect behaviour.     

Sulfur isotope inventories of atmospheric deposition, spruce forest floor and living Sphagnum along a NW–SE transect across Europe

At five European sites, differing in atmospheric Sinputs by a factor of 6, and differing in S isotope signatures ofthese inputs by up to 14 (CDT), we investigated thedirection and magnitude of an assimilation-related ³⁴S shiftand the relationship between atmospheric deposition and Sretention in selected ecosystem compartments. Bulk precipitationand spruce throughfall were collected between 1994 and 1996 inthe Isle of Mull (Scotland), Connemara (Ireland), Thorne Moors(England), Rybárenská slat' and Oceán (both Czech Republic) andanalyzed for sulfate concentrations and ³⁴S ratios. Eighteenreplicate samples per site of living Sphagnum collected inunforested peatlands and 18 samples of spruce forest floorcollected near each of the peatlands were also analyzed for Sconcentrations and ³⁴S ratios. Assimilation of S was associatedwith a negative ³⁴S shift. Plant tissues systematicallypreferred the light isotope ³²S, on average by 2. There wasa strong positive correlation between the non-marine portion ofthe atmospheric S input and total S concentration in forest floorand Sphagnum, respectively (R = 0.97 and R = 0.85). Elevated Sinputs lead to higher S retention in these two organic-richcompartments of the ecosystem. It follows that equal emphasismust be placed on organic S as on adsorption/desorption ofinorganic sulfate when studying acidification reversal inecosystems. The sea-shore sites had rainfall enriched in theheavy isotope ³⁴S due to an admixture of sea-spray. The inlandsites had low ³⁴S reflecting ³⁴S of sulfur emitted from localcoal-burning power stations. Sphagnum had always lower S contentsand higher ³⁴S ratios compared to forest floor. The within-siterange of ³⁴S ratios of Sphagnum and forest floor was wide (upto 12) suggesting that at least six replicate samples shouldbe taken when using ³⁴S as a tracer.     

Phosphorus cycling in a Mexican tropical dry forest ecosystem

The study was conducted in five contiguous small watersheds (12–28 ha) gauged for long-term ecosystem research. Five 80 × 30 m plots were used for the study. We quantified inputs from the atmosphere, dissolved and particulate-bound losses, throughfall and litterfall fluxes, standing crop litter and soil available P pools. Mean P input and output for a six-year period was 0.16 and 0.06 kgha^–1yr^–1, respectively. Phosphorus concentration increased as rainfall moved through the canopy. Annual P returns in litterfall (3.88 kg/ha) represented more than 90% of the total aboveground nutrient return to the forest floor. Phosphorus concentration in standing litter (0.08%) was lower than that in litterfall (0.11%). Phosphorus content in the litterfall was higher at Chamela than at other tropical dry forests. Mean residence time on the forest floor was 1.2 yr for P and 1.3 yr for organic matter. Together these results suggest that the forest at Chamela may not be limited by P availability and suggest a balance between P immobilization and uptake. Comparison of P losses in stream water with input rates from the atmosphere for the six-year period showed that inputs were higher than outputs. Balances calculated for a wet and a dry year indicated a small P accumulation in both years.     

Secondary structure prediction and folding of globular protein: refolding of ferredoxin

The physicochemical mechanism of protein folding has been elucidated by the island model, describing a growth type of folding. The folding pathway is closely related with nucleation on the polypeptide chain and thus the formation of small local structures or secondary structures at the earliest stage of folding is essential to all following steps. The island model is applicable to any protein, but a high precision of secondary structure prediction is indispensable to folding simulation. The secondary structures formed at the earliest stage of folding are supposed to be of standard form, but they are usually deformed during the folding process, especially at the last stage, although the degree of deformation is different for each protein. Ferredoxin is an example of a protein having this property. According to X-ray investigation (1FDX), ferredoxin is not supposed to have secondary structures. However, if we assumed that in ferredoxin all the residues are in a coil state, we could not attain the correct structure similar to the native one. Further, we found that some parts of the chain are not flexible, suggesting the presence of secondary structures, in agreement with the recent PDB data (1DUR). Assuming standard secondary structures (-helices and -strands) at the nonflexible parts at the early stage of folding, and deforming these at the final stage, a structure similar to the native one was obtained. Another peculiarity of ferredoxin is the absence of disulfide bonds, in spite of its having eight cysteines. The reason cysteines do not form disulfide bonds became clear by applying the lampshade criterion, but more importantly, the two groups of cysteines are ready to make iron complexes, respectively, at a rather later stage of folding. The reason for poor prediction accuracy of secondary structure with conventional methods is discussed.