Species accumulation curves and incidence-based species richness estimators to appraise the diversity of cultivable yeasts from beech forest soils

Background

Yeast-like fungi inhabit soils throughout all climatic zones in a great abundance. While recent estimations predicted a plethora of prokaryotic taxa in one gram of soil, similar data are lacking for fungi, especially yeasts.

Methodology/Principal Findings

We assessed the diversity of soil yeasts in different forests of central Germany using cultivation-based techniques with subsequent identification based on rDNA sequence data. Based on experiments using various pre-cultivation sample treatment and different cultivation media we obtained the highest number of yeasts by analysing mixed soil samples with a single nutrient-rich medium. Additionally, several species richness estimators were applied to incidence-based data of 165 samples. All of them predicted a similar range of yeast diversity, namely 14 to 16 species. Randomized species richness curves reached saturation in all applied estimators, thus indicating that the majority of species is detected after approximately 30 to 50 samples analysed.

Conclusions/Significance

In this study we demonstrate that robust species identification as well as mathematical approaches are essential to reliably estimate the sampling effort needed to describe soil yeast communities. This approach has great potential for optimisation of cultivation techniques and allows high throughput analysis in the future.     

Underestimated spider diversity in a temperate beech forest

We used canopy fogging to study the high (20–26 m), intermediate (13–19 m) and low (5–6 m) strata in three European beech patches (Fagus sylvatica) in nine months (2005–2007) and estimate species richness and diversity of arboreal spiders. Eight species (10%) were previously unseen in European beech trees, and one of these is likely a new species. Moreover, two species are on the Bavarian red list. Our results revealed that the high stratum of the old-growth trees provided unique resources and possessed the greatest diversity and evenness, whereas intermediate and low strata had high similarity in respect to diversity, dominance, species, and family composition. Since the majority of beech forests consists of mature and young trees in Central Europe, and old-growth forests are rarely preserved, we recommend young beech be used in a sampling protocol for rapid biodiversity assessment. However, adding samples from the two higher strata to the lowest stratum (55 species), almost doubled the estimated species richness (102 species). This suggests that the lower stratum alone does not represent a true image of the total canopy fauna inventory in this, and likely other, beech stands. To complete this comprehensive inventory in European beeches, the Chao1 predicted that additional sampling would be needed in the highest stratum, where there is a high probability to find previously undetected species in a next survey. Our study clearly shows that neglecting the crowns of the largest, tallest trees risks underestimating the overall spider diversity in Central European forests.     

The species diversity of New Zealand forest birds: Some possible consequences of the modification of beech forests

The literature on forest birds in New Zealand is examined to see if the consequences of forest modification can be predicted. Forty‐four samples of birds, from North, South, and Stewart Islands, are classified according to four habitats of origin: virgin forest, modified forest, exotic forest, and suburban bush and gardens. An index of bird species diversity (BSD) is calculated for comparison, and where possible densities are tabulated.

Limited samples from modified forests in Westland suggest that the number of species is relatively smaller but the bird density is higher after modification. There do not seem to be any published quantitative data about birds in Westland exotic forests.

Data from the whole of New Zealand show that bird density increases as forest habitats change from virgin, to modified, to exotic, to suburban bush and gardens. BSD and equitability do not differ among these habitats. The number of species of native birds and their diversity decline as the habitat is more extensively altered, but their total density tends to remain constant. More productive forest habitats have the same BSD as other habitats. Diversity seems to be limited by the small variety of bird species available, and the more productive habitats could probably support more species. All habitats had a much higher diversity of birds before colonisation by the European.     

Population dynamics of four understorey shrub species in beech forest

Question: In the population dynamics of four understorey shrub species (Hp, Hydrangea paniculata Sieb, et Zucc.; Lu, Lindera umbellata Thunb. var. membranacea (Maxim.) Momiyama; Ms, Magnolia salicifolia (Sieb, et Zucc.) Maxim.; Vf, Viburnum furcatum Blume ex Maxim.), (1) What is the relative importance of seedling regeneration versus vegetative growth? (2) Can these shrubs persist stably for a long time in the understorey? (3) What kind of variation in demographic features is observed among these shrubs? Location: 780m a.s.l., north‐eastern Japan. Methods: Population dynamics were analyzed by using stage‐classified matrix models. Models were mainly constructed from five years stem‐census data, including current‐year seedlings and sprouts. Results: Current‐year sprouts emerged every year in every species. Current‐year seedlings emerged every year in Lu and Vf, but densities were very low. In every species, population growth rate (A) was close to the equilibrium value 1.0 and no statistical difference was found among species. The stable stage‐distribution predicted from the matrix model was similar to the observed distribution for Lu, Ms and Vf, but much different for Hp. Elasticity matrix was also similar among Lu, Ms and Vf, but was quite different for Hp. Conclusions: Lu, Ms and Vf were considered as climax shrubs that can regenerate and maintain their population stably in the understorey, even if canopy gaps form infrequently. Hp is a pioneer shrub that require more frequent formation of canopy gaps for long‐term persistence in the understorey.     

Comparison of vascular plant diversity and species composition of coppice and high beech forest in the Banat region,Romania

Abandonment of coppicing is one of the main reasons of diversity decline in European temperate forests. To reverse this trend, coppicing has been reintroduced in several forests, especially in areas of high conservation value. However, empirical information on the effects of coppicing on plant diversity and composition is still scarce. By comparing vegetation data from active coppices and beech-dominated high forests in the Banat region in Romania, we tested the hypothesis that coppices have a higher plant diversity and different plant species composition than high forests. Data were collected in 60 randomly placed phytosociological relevés and were analysed using linear models and multivariate methods. As expected, we found differences in understorey plant composition. Herb species with various environmental demands–sciophytes-(hemi)-heliophytes and grassland species–were more frequent in coppices whereas high forests had more vernal species and sciophytes. Coppices also had slightly greater plant diversity but did not differ in herb species richness. Our results demonstrate that coppicing has a small positive effect on plant diversity but a large effect on species composition. Coppice restoration may be especially beneficial for populations of thermophilous and non-forest species.     

Spatial variability of NO and NO2 flux rates from soil of spruce and beech forest ecosystems

In order to evaluate differences in the magnitude of NO and NO₂ flux rates between soil areas in direct vicinity to tree stems and areas of increasing distance to tree stems, we followed in 1997 at the Höglwald Forest site with a fully automated measuring system a complete annual cycle of NO and NO₂ fluxes from soils of an untreated spruce stand, a limed spruce strand, and a beech stand using at each stand measuring chambers which were installed onto the soils in such a way that they formed a stem to stem gradient. Flux data obtained since the end of 1993 from measuring chambers placed at the interstem areas of the stands, which had been used for the calculation of the long year annual mean of NO and NO₂ flux rates from soils of the stands, are compared to both (a) those obtained from the interstem chambers in 1997 and (b) those from the stem to stem gradient chambers. Daily mean NO fluxes obtained in 1997 were in a range of 0.3 – 280.1 g NO-N m^–2 h^–1 at the untreated spruce stand, 0.5 – 273.2 g NO-N m^–2 h^–1 at the limed spruce stand and 0.5 - 368.8 g NO-N m^–2 h^–1 at the beech stand, respectively. Highest NO emission rates were observed during summer, lowest during winter. Daily mean NO₂ fluxes were in a range of –83.1 – 7.6 g NO₂-N m^–2 h^–1 at the untreated spruce stand, -85.1 – 2.1 g NO₂-N m^–2 h^–1 at the limed spruce stand and –77.9 to –2.0 g NO₂-N m^–2 h^–1 at the beech site, respectively. As had been observed for the years 1994–1996, also in 1997 NO emission rates were highest at the untreated spruce stand and lowest at the beech stand and liming of a spruce stand resulted in a significant decrease in NO emission rates. For NO₂ no marked differences in the magnitude of flux rates were found between the three different stands. Results obtained from the stem to stem gradient experiments revealed that at all stands studied NO emission rates were significantly higher (between 1.6- and 2.6-fold) from soil areas close to the tree stems and decreased – except at the beech stand - with increasing distance from the stems, while for NO₂ deposition no marked differences were found. Including the contribution of soil areas in direct vicinity to the beech stems in the estimation of the annual mean NO source strength revealed that the source strength has been underestimated by 40% in the past.     

Maintenance of forest species diversity and latitudinal gradient

The species diversity of trees maintained in tropical rain forests is much higher than in temperate, boreal, or seasonally dry tropical forests. Many hypotheses have been proposed for higher diversity in tropical rain forests, including: (i) higher specialization of resource use, (ii) different mode of disturbance, (iii) smaller opportunity for competition on oligotrophic soil, (iv) higher productivity, (v) more active specific herbivores and pathogens, (vi) evolutionary/ecological history. In this paper we report mathematical models for tree-by-tree replacement. First the analysis of random drift model shows that the effect of gap size to species diversity is not very strong. Second we study phenological segregation model, which has the following assumptions: Basic mechanism for many species to coexist in the community is assumed given by the storage effect of lottery model, as species differ in seasonality in peak fruit production and in the subsequent period of high regeneration ability. Gaps formed during unfavorable season accumulate and become available for regeneration in the beginning of the growing season. The resulting synchronization of regeneration opportunity jeopardizes the coexistence of many similar species in seasonal environments. Analysis of a mathematical model shows: (1) the existence of unfavorable season can greatly reduce the diversity of coexisting species. (2) Diversity in the equilibrium community can be high when niche width of each species is broad and resource use is strongly overlapped. (3) Equilibrium community may include several distinct groups of species differing in phenology of regeneration. Effect of unequal niche width and frequency dependent regeneration are also examined.     

Evolutionary rates and species diversity in flowering plants

Genetic change is a necessary component of speciation, but the relationship between rates of speciation and molecular evolution remains unclear. We use recent phylogenetic data to demonstrate a positive relationship between species numbers and the rate of neutral molecular evolution in flowering plants (in both plastid and nuclear genes). Rates of protein and morphological evolution also correlate with the neutral substitution rate, but not with species numbers. Our findings reveal a link between the rate of neutral molecular change within populations and the evolution of species diversity.     

Landslide-facilitated species diversity in a beech-dominant forest

To evaluate the extent to which landslides affect community dynamics and consequent species diversity in a beech-dominated forest, differences in the composition and size structure of tree species were compared between landslide and adjacent stable (control) stands. Demography and changes in size were compared between the two stands over a 5-year period about 60 years after a landslide. In the control stand, replacement occurred even amongst late-successional species, with beech (Fagus crenata)—the most dominant species—increasing in relative abundance. In the landslide stand, very few large individuals of late-successional species occurred, whereas large individuals of early-successional species occurred only in the landslide stand. The traits indicate that the landslide strongly facilitated species diversity, not only by reducing the dominance of late-successional species, but also by promoting recruitment of early-successional species. However, new recruitment of early-successional species was inhibited in the landslide stand, although we observed succeeding regeneration and subsequent population growth of late-successional species there. As a result, the relative dominance of late-successional species increased with succession after the landslide, thus decreasing future species diversity. In beech-dominant forest landscapes in Japan that include communities with different developmental stages, the mosaic of serial stages may facilitate species diversity after a landslide.     

Molecular characterization of bacterial diversity from British Columbia forest soils subjected to disturbance

Bacteria from forest soils were characterized by DNA sequence analysis of cloned 16S rRNA gene fragments (16S clones). Surface organic matter and mineral soil samples from a British Columbia Ministry of Forests Long-Term Soil Productivity (LTSP) installation were collected during winter and summer from two disturbance treatments: whole-tree harvesting with no soil compaction (plot N) and whole-tree harvesting plus complete surface organic matter removal with heavy soil compaction (plot S). Phylogenetic analyses revealed that 87% of 580 16S clones were classified as Proteobacteria, Actinobacteria, Acidobacterium, Verrucomicrobia, Bacillus/Clostridium group, Cytophaga-Flexibacter-Bacteroides group, green nonsulfur bacteria, Planctomyces, and candidate divisions TM6 and OP10. Seventy-five 16S clones could not be classified into known bacterial divisions, and five 16S clones were related to chloroplast DNA. Members of Proteobacteria represented 46% of the clone library. A higher proportion of 16S clones affiliated with y-Proteobacteria were from plot N compared with plot S. 16S rRNA gene fragments amplified with Pseudomonas-specific primers and cloned (Ps clones) were examined from mineral-soil samples from plots N and S from three LTSP installations. A significantly greater proportion of sequenced Ps clones from plot N contained Pseudomonas 16S rRNA gene fragments compared with Ps clones from plot S.     

Cultivation-dependent characterization of bacterial diversity from British Columbia forest soils subjected to disturbance

Bacteria from forest surface organic matter and mineral soil horizons were cultivated using four methods and characterized by fatty acid methyl ester (FAME) analysis. Soil samples from a British Columbia Ministry of Forests Long-Term Soil Productivity (LTSP) installation were collected during winter and summer from two disturbance treatments (whole-tree harvesting with no soil compaction (plot N) and whole-tree harvesting plus complete surface organic matter removal with heavy soil compaction (plot S)) and from an unlogged reference plot (REF). Seventy-five percent of 1795 bacterial isolates were affiliated with 42 genera representing beta- and gamma-Proteobacteria, Actinobacteria, the Bacillus/Clostridium group, and the Cytophaga-Flexibacter-Bacteroides group. Approximately half of the culture collection represented genetic diversity confined to four bacterial genera: Pseudomonas, Bacillus, Paenibacillus, and Arthrobacter. A significantly higher proportion of bacterial isolates belonging to Actinobacteria, and the member genus Arthrobacter, were isolated from plot S soil samples compared with soil samples from plots N and REF. Twenty-five percent of bacterial isolates were not conclusively identified to genus with FAME analysis. Sherlock Tracker cluster analysis and partial 16S rRNA gene sequence analysis enabled classification of a subset of these isolates.     

亚热带两种森林土壤担子菌漆酶基因多样性比较

漆酶是降解森林凋落物中木质素的关键酶之一,直接影响着森林生态系统碳循环过程.运用TA克隆、测序技术,研究了两种亚热带森林(原生常绿落叶阔叶混交林和人工马尾松林)凋落物层(O层)和土壤表层(A层,0～20 cm)降解木质素的担子菌漆酶基因多样性.结果表明:同一土壤层位,原生林土壤中担子菌漆酶基因多样性和种群丰富度高于马尾松林;同一森林生态系统,原生林土壤O层中担子菌漆酶基因多样性和种群丰富度略高于土壤A层,而马尾松林则O层明显低于A层;两森林土壤具有相同含漆酶基因的担子菌优势种群,且大部分优势种群与伞菌目小菇属或侧耳属有较高的氨基酸相似性;与原生林土壤A层和马尾松林土壤O层相比,原生林土壤O层和马尾松林土壤A层中含漆酶基因的担子菌种群分布相对均匀;马尾松林O层与A层之间漆酶基因核苷酸序列的相似性较原生林土壤O层与A层之间的高.表明植被和土壤层位显著影响漆酶基因多样性和群落结构,而植被和土壤层位引起的担子菌可利用底物和土壤pH值的差异可能直接驱动这种影响.     

Torulopsis pampelonensis sp. nov. A new species of yeast isolated from beech forest soil

A new yeast species, Torulopsis pampelonensis is described. Six strains were recovered from a gleyic Andosol under a beech forest and two other strains from the surface of fallen leaves of Fagus silvatica L. Although it showed some morphological and physiological similarities with Torulopsis tannotolerans Jacob and Torulopsis navarrensis Ramírez and Moriyón, it differed from all Torulopsis species presently known.     

Seasonality and resource availability control bacterial and archaeal communities in soils of a temperate beech forest

It was hypothesized that seasonality and resource availability altered through tree girdling were major determinants of the phylogenetic composition of the archaeal and bacterial community in a temperate beech forest soil. During a 2-year field experiment, involving girdling of beech trees to intercept the transfer of easily available carbon (C) from the canopy to roots, members of the dominant phylogenetic microbial phyla residing in top soils under girdled versus untreated control trees were monitored at bimonthly intervals through 16S rRNA gene-based terminal restriction fragment length polymorphism profiling and quantitative PCR analysis. Effects on nitrifying and denitrifying groups were assessed by measuring the abundances of nirS and nosZ genes as well as bacterial and archaeal amoA genes. Seasonal dynamics displayed by key phylogenetic and nitrogen (N) cycling functional groups were found to be tightly coupled with seasonal alterations in labile C and N pools as well as with variation in soil temperature and soil moisture. In particular, archaea and acidobacteria were highly responsive to soil nutritional and soil climatic changes associated with seasonality, indicating their high metabolic versatility and capability to adapt to environmental changes. For these phyla, significant interrelations with soil chemical and microbial process data were found suggesting their potential, but poorly described contribution to nitrification or denitrification in temperate forest soils. In conclusion, our extensive approach allowed us to get novel insights into effects of seasonality and resource availability on the microbial community, in particular on hitherto poorly studied bacterial phyla and functional groups.     

应用指示种预测森林管理对物种多样性及群落组成的影响

采用指示种分析方法,研究了会同亚热带森林物种多样性和群落组成对森林管理的响应.从357个林下种中鉴定出显著性指示种94个,并构造新的指示种数据集,检验指示种数据集和源群落数据集之间的关联,评估指示种对林下植被管理效应的预测潜能.结果表明:指示种数据集和源群落数据集之间存在极显著的关联(Mantel r=0.898),指示种数据集很好地预测了生物多样性的变化(回归分析,R2>0.74);指示种很好地预测了群落组成对森林管理的响应(ANOVA,F>16.79);非度量多尺度排序(NMDS)以及K-means聚类分析表明,对于不同森林管理的样地类型,指示种数据集的识别能力和源群落数据集是一致的.从物种多样性、群落组成以及在森林类型的识别上,指示种数据集和源群落数据集有一致性规律,作用几乎相同,因此森林评估可以利用指示种代替源群落预测森林管理效应,以减少森林全面调查的成本.     

Organic carbon stocks and sequestration rates of forest soils in Germany

The National Forest Soil Inventory (NFSI) provides the Greenhouse Gas Reporting in Germany with a quantitative assessment of organic carbon (C) stocks and changes in forest soils. Carbon stocks of the organic layer and the mineral topsoil (30 cm) were estimated on the basis of ca. 1.800 plots sampled from 1987 to 1992 and resampled from 2006 to 2008 on a nationwide grid of 8 × 8 km. Organic layer C stock estimates were attributed to surveyed forest stands and CORINE land cover data. Mineral soil C stock estimates were linked with the distribution of dominant soil types according to the Soil Map of Germany (1 : 1 000 000) and subsequently related to the forest area. It appears that the C pool of the organic layer was largely depending on tree species and parent material, whereas the C pool of the mineral soil varied among soil groups. We identified the organic layer C pool as stable although C was significantly sequestered under coniferous forest at lowland sites. The mineral soils, however, sequestered 0.41 Mg C ha^?1 yr^?1. Carbon pool changes were supposed to depend on stand age and forest transformation as well as an enhanced biomass input. Carbon stock changes were clearly attributed to parent material and soil groups as sandy soils sequestered higher amounts of C, whereas clayey and calcareous soils showed small gains and in some cases even losses of soil C. We further showed that the largest part of the overall sample variance was not explained by fine‐earth stock variances, rather by the C concentrations variance. The applied uncertainty analyses in this study link the variability of strata with measurement errors. In accordance to other studies for Central Europe, the results showed that the applied method enabled a reliable nationwide quantification of the soil C pool development for a certain period.     

Acetate synthesis in soil from a bavarian beech forest

Soil obtained from a beech forest formed significant amounts of acetate when incubated in a bicarbonate-buffered, mineral salt solution under anaerobic conditions at both 5 and 20 degrees C (21 and 38 g of acetate per kg [dry weight] of soil, respectively). At 20 degrees C, following an 18-day lag period, rates of 0.07 mmol of acetate synthesized per g (dry weight) of soil per day were observed. Acetate was not subject to immediate turnover; methane and hydrogen were not formed during the time intervals (5 degrees C, 335 days; 20 degrees C, 95 days) evaluated. The synthesis of acetate from endogenous materials was coincident with acetogenic potentials, i.e., the capacity to catalyze the H(2)-dependent synthesis of acetate. Hydrogen consumption was not directed towards the synthesis of methane. Collectively, these results suggest that acetogenesis may be an underlying microbial activity of this forest soil.     

Heavy metal accumulation and distribution in forest understory herb species of Carpathian beech ecosystems

Abstract

This study addresses the issue of heavy metal (HM) accumulation and distribution for three different plant species, Carex pilosa, Dentaria bulbifera, Galium odoratum, in Carpathian beech ecosystems. Data are presented on HM concentrations in forest understory vegetation and a preliminary insight into different HM allocation patterns is provided. Bioaccumulation factors (BCFs) and shoot/root ratios differed considerably among the species and between polluted and unpolluted regions. HMs were accumulated in forest plants as follows: Cu > Zn > Cd >Pb in unpolluted areas and Zn> Cd > Cu >Pb in polluted areas. Zn was preferentially distributed to roots and Cu to shoots. The distribution of Cd and Pb in different plant parts was specific in terms of the species-dependence. Cd and Pb levels in Carex pilosaand Galium odoratumwere more strictly controlled in the transfer zone of root-shoot, compared to Dentaria bulbifera.The highest BCFs were found in Carex pilosafor Cu (5.9) and in Dentaria bulbiferawas found the highest shoot/root ratio for Cd (3.1).