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PubMed2003

Community composition and functioning of denitrifying bacteria from adjacent meadow and forest soils.

We investigated communities of denitrifying bacteria from adjacent meadow and forest soils. Our objectives were to explore spatial gradients in denitrifier communities from meadow to forest, examine whether community composition was related to ecological properties (such as vegetation type and process rates), and determine phylogenetic relationships among denitrifiers. nosZ, a key gene in the denitrification pathway for nitrous oxide reductase, served as a marker for denitrifying bacteria. Denitrifying enzyme activity (DEA) was measured as a proxy for function. Other variables, such as nitrification potential and soil C/N ratio, were also measured. Soil samples were taken along transects that spanned meadow-forest boundaries at two sites in the H. J. Andrews Experimental Forest in the Western Cascade Mountains of Oregon. Results indicated strong functional and structural community differences between the meadow and forest soils. Levels of DEA were an order of magnitude higher in the meadow soils. Denitrifying community composition was related to process rates and vegetation type as determined on the basis of multivariate analyses of nosZ terminal restriction fragment length polymorphism profiles. Denitrifier communities formed distinct groups according to vegetation type and site. Screening 225 nosZ clones yielded 47 unique denitrifying genotypes; the most dominant genotype occurred 31 times, and half the genotypes occurred once. Several dominant and less-dominant denitrifying genotypes were more characteristic of either meadow or forest soils. The majority of nosZ fragments sequenced from meadow or forest soils were most similar to nosZ from the Rhizobiaceae group in alpha-Proteobacteria species. Denitrifying community composition, as well as environmental factors, may contribute to the variability of denitrification rates in these systems.

Altitude↗
PubMed2006

Gene selection and classification of microarray data using random forest.

BACKGROUND: Selection of relevant genes for sample classification is a common task in most gene expression studies, where researchers try to identify the smallest possible set of genes that can still achieve good predictive performance (for instance, for future use with diagnostic purposes in clinical practice). Many gene selection approaches use univariate (gene-by-gene) rankings of gene relevance and arbitrary thresholds to select the number of genes, can only be applied to two-class problems, and use gene selection ranking criteria unrelated to the classification algorithm. In contrast, random forest is a classification algorithm well suited for microarray data: it shows excellent performance even when most predictive variables are noise, can be used when the number of variables is much larger than the number of observations and in problems involving more than two classes, and returns measures of variable importance. Thus, it is important to understand the performance of random forest with microarray data and its possible use for gene selection. RESULTS: We investigate the use of random forest for classification of microarray data (including multi-class problems) and propose a new method of gene selection in classification problems based on random forest. Using simulated and nine microarray data sets we show that random forest has comparable performance to other classification methods, including DLDA, KNN, and SVM, and that the new gene selection procedure yields very small sets of genes (often smaller than alternative methods) while preserving predictive accuracy. CONCLUSION: Because of its performance and features, random forest and gene selection using random forest should probably become part of the "standard tool-box" of methods for class prediction and gene selection with microarray data.

Algorithms↗
PubMed2005

Epidemiology of forest malaria in central Vietnam: a large scale cross-sectional survey.

In Vietnam, a large proportion of all malaria cases and deaths occurs in the central mountainous and forested part of the country. Indeed, forest malaria, despite intensive control activities, is still a major problem which raises several questions about its dynamics.A large-scale malaria morbidity survey to measure malaria endemicity and identify important risk factors was carried out in 43 villages situated in a forested area of Ninh Thuan province, south central Vietnam. Four thousand three hundred and six randomly selected individuals, aged 10-60 years, participated in the survey. Rag Lays (86%), traditionally living in the forest and practising "slash and burn" cultivation represented the most common ethnic group. The overall parasite rate was 13.3% (range [0-42.3] while Plasmodium falciparum seroprevalence was 25.5% (range [2.1-75.6]). Mapping of these two variables showed a patchy distribution, suggesting that risk factors other than remoteness and forest proximity modulated the human-vector interactions. This was confirmed by the results of the multivariate-adjusted analysis, showing that forest work was a significant risk factor for malaria infection, further increased by staying in the forest overnight (OR= 2.86; 95%CI [1.62; 5.07]). Rag Lays had a higher risk of malaria infection, which inversely related to education level and socio-economic status. Women were less at risk than men (OR = 0.71; 95%CI [0.59; 0.86]), a possible consequence of different behaviour. This study confirms that malaria endemicity is still relatively high in this area and that the dynamics of transmission is constantly modulated by the behaviour of both humans and vectors. A well-targeted intervention reducing the "vector/forest worker" interaction, based on long-lasting insecticidal material, could be appropriate in this environment.

Adolescent↗
PubMed2003

Forest cover of insular Southeast Asia mapped from recent satellite images of coarse spatial resolution.

The study provides an example of mapping tropical forest cover from SPOT-Vegetation satellite images of coarse spatial resolution (1 km) for the subregion of insular Southeast Asia. A satellite image mosaic has been generated from satellite images acquired for the period 1998 to 2000. Forest cover has been mapped by unsupervised digital classification. The mapping result has then been compared to selected forest maps from the subregion, demonstrating the potential to provide basic information on forest area extent and distribution, but also on massive forest cover change in the subregional context. Forest area estimates derived from the map for the subregion have been found comparable to those compiled by FAO. The results indicate that many of the remaining tropical forests in Southeast Asia, rich in timber resources and biodiversity, may be lost in the near future if deforestation continues at present or previous rates.

Asia, Southeastern↗
PubMed2006

Biotic and abiotic regulation of lightning fire initiation in the mixedwood boreal forest.

Lightning fire is the dominant natural disturbance of the western mixedwood boreal forest of North America. We quantified the independent effects of weather and forest composition on lightning fire initiation (a detected and recorded fire start) patterns in Alberta, Canada, to demonstrate how these biotic and abiotic components contribute to ecosystem dynamics in the mixedwood boreal forest. We used logistic regression to describe variation in annual initiation occurrence among 10,000-ha landscape units (voxels) covering a 9 million-ha study region over 11 years. At a voxel scale, forest composition explained more variation in annual initiation than did weather indices. Initiations occurred more frequently in landscapes with more conifer fuels (Picea spp.), and less in aspen-dominated (Populus spp.) ones. Initiations were less frequent in landscapes that had recently burned. Variation in initiation was also influenced by joint weather-lightning indices, but to a lesser degree. For each voxel, these indices quantified the number of days in the fire season when moisture levels were low and lightning was detected. Regional indices of fire weather severity explained substantial interannual variation of initiation, and the effect of forest composition was stronger in years with more severe fire weather. Our study is a conclusive demonstration of biotic and abiotic regulation of lightning fire initiation in the mixedwood boreal forest. The independent effects of forest composition emphasize that vegetation feedbacks strongly regulate disturbance dynamics in the region.

Alberta↗
PubMed2006

The value of small size: loss of forest patches and ecological thresholds in southern Madagascar.

Many services generated by forest ecosystems provide essential support for human well-being. However, the vulnerability of these services to environmental change such as forest fragmentation are still poorly understood. We present spatial modeling of the generation of ecosystem services in a human-dominated landscape where forest habitat patches, protected by local taboos, are located in a matrix of cultivated land in southern Madagascar. Two ecosystem services dependent on the forest habitats were addressed: (1) crop pollination services by wild and semidomesticated bees (Apoidea), essential for local crop production of, for example, beans, and (2) seed dispersal services based on the presence of ring-tailed lemurs (Lemur catta). We studied the vulnerability of these ecosystem services to a plausible scenario of successive destruction of the smallest habitat patches. Our results indicate that, in spite of the fragmented nature of the landscape, the fraction of the landscape presently covered by both crop pollination and seed dispersal services is surprisingly high. It seems that the taboo system, though indirectly and unintentionally, contributes to upholding the generation of these services by protecting the forest patches. Both services are, however, predicted to be very vulnerable to the successive removal of small patches. For crop pollination, the rate of decrease in cover was significant even when only the smallest habitat patches were removed. The capacity for seed dispersal across the landscape displayed several thresholds with habitat patch removal. Our results suggest that, in order to maintain capacity for seed dispersal across the landscape and crop pollination cover in southern Androy, the geographical location of the remaining forest patches is more crucial than their size. We argue that in heavily fragmented production landscapes, small forest patches should increasingly be viewed as essential for maintaining ecosystem services, such as agricultural production, and also should be considered in the ongoing process of tripling the area of protected habitats in Madagascar.

Animals↗
PubMed2006

Floristic conservation value, nested understory floras, and the development of second-growth forest.

Nestedness analysis can reveal patterns of plant composition and diversity among forest patches. For nested floral assemblages, the plants occupying any one patch are a nested subset of the plants present in successively more speciose patches. Elimination of sensitive understory plants with human disturbance is one of several mechanisms hypothesized to generate nonrandom, nested floral distributions. Hypotheses explaining distributions of understory plants remain unsubstantiated across broad landscapes of varying forest types and disturbance histories. We sampled the vegetation of 51 floodplain and 55 upland forests across Illinois (USA) to examine how the diversity, composition, and nestedness of understory floras related to their overstory growth and structure (basal area), and their overall floristic conservation value (mean C). We found that plant assemblages were nested with respect to site species richness, such that rare plants indicated diverse forests. Floras were also nested with respect to site mean C and basal area (BA). However, in an opposite pattern from what we had expected, floras of high-BA stands were nested subsets of those of low-BA stands. A set of early-successional plants restricted to low-BA stands, and more importantly, the absence of a set of true forest plants in high-BA stands, accounted for this pattern. Additionally, we observed a decrease in species richness with increasing BA. These results are consistent with the hypothesis that recovery of true forest plants does not occur concurrently with overstory regeneration following massive anthropogenic disturbance. Nestedness by site mean C indicates that high conservation value (conservative) plants co-occur in highly diverse stands; these forests are assumed to be less disturbed historically. Because site mean C was uncorrelated with BA, BA-neutral disturbances such as livestock usage are suggested as accounting for between-site differences in mean C. When considered individually, conservative plants were actually more likely to be found in low-BA stands (uplands only). This suggests that floras of historically more open-canopied oak-hickory uplands are being degraded by canopy closure from increasing density of "mesophytic, nonpyrogenic" trees. It also indirectly suggests that recent moderate logging is uncorrelated with floristic conservation values.

Conservation of Natural Resources↗
PubMedDate not supplied

Denitrification at a long-term forested land treatment system in the Piedmont of Georgia.

Spray irrigation of forested land can provide an effective system for nutrient removal and treatment of municipal wastewater. Evolution of N2 + N2O from denitrifying activity is an important renovation pathway for N applied to forested land treatment systems. Federal and state guidance documents for design of forested land treatment systems indicate the expected range for denitrification to be up to 25% of applied N, and most forest land treatment systems are designed using values from 15 to 20% of applied N. However, few measurements of denitrification following long-term wastewater applications at forested land treatment sites exist. In this study, soil N2 + N2O-N evolution was directly measured at four different landscape positions (hilltop, midslope, toe-slope, and riparian zone) in a forested land treatment facility in the Georgia Piedmont that has been operating for more than 13 yr. Denitrification rates within effluent-irrigated areas were significantly greater than rates in adjacent nonirrigated buffer zones. Rates of N2 + N2O-N evolved from soil in irrigated forests ranged from 5 to 10 kg ha(-1) yr(-1) N on the three upland landscape positions and averaged 38 kg ha(-1) yr(-1) N within the riparian zone. The relationship between measured riparian zone denitrification rates and soil physical and chemical properties was poor. The best relationship was with soil temperature, with an r2 of 0.18. Overall, on a landscape position weighted basis, only 2.4% of the wastewater-applied N was lost through denitrification.

Ecosystem↗
PubMedDate not supplied

Ion cycling in hemlock-northern hardwood forests of the southern Lake Superior region: a preliminary study.

Upland forests of the southern Lake Superior region are diverse and contain a shifting mosaic of eastern hemlock [Tsuga canadensis (L.) Carr.] and northern hardwood forests dominated by sugar maple (Acer saccharum Marsh.). In this study, we survey the relative effects of management practice (old growth vs. managed), forest cover type (hemlock vs. northern hardwood), and soil great group (Entic Haplorthod vs. Alfic Oxyaquic Fragiorthod) on ion cycling as a precursor to a longer-term, more detailed study. Bulk precipitation, throughfall, and soil leachates at three depths were collected for two growing seasons in eight stands on the Ottawa National Forest in the Upper Peninsula of Michigan. A total of 1210 solutions were analyzed for pH, Na, K, Mg, Ca, Cl, NO3, and SO4. Losses of base cations (Ca, Mg, K) and SO4 from the bottom of the rooting zone generally were greater in old-growth than in managed northern hardwoods on both fragic and nonfragic soils. Leaching losses of base cations and NO3 usually were greater beneath old-growth northern hardwoods than beneath old-growth hemlock on both soil types and for both forest cover types and management practices on fragic than nonfragic soils. Management practice, forest cover type, and soil type all appear to affect ion cycling within these forests. All of the stands featured striking losses of base cations that probably are influenced strongly by NO3 and SO4 in atmospheric deposition.

Acer↗
PubMed2001

Scale correlation between vegetation and soil in larch forest, NE China.

After the analysis on the linages of species, the fractal dimensions of vegetation and soil in a managed larch(Larix gmelini) forest in Daxingan Mountains, NE China were estimated separately, and their scale correlation was discussed. (1) The dominant species of the larch forest, larch and the important accompany species, birch(Betula platyphylla) were homogeneously distributed along the transect. The other species were heterogeneous, and can be divided into three groups located on the right, left and central parts of the transect respectively. The transect can be separated into two parts at the position for the 29th quadrat(580 m). (2) The fractal dimension in the large scale range from 200 to 400 m was lower than that in the small scale range from 0 to 200 m in the forest, indicating the different variation regularities of spatial heterogeneity in different scale ranges. The inflection point at 200 m was one of the key scales of spatial hierarchy of the larch forest. (3) The scale variation of the forest was correlated with that of soil pH on large scales, which reflected the indirect control of the dominant species to the spatial pattern and species distribution of understorey by changing soil acidity in the forest and the indirect effects of forest management.

China↗
PubMed2000

[Neural network based on modified simplex method and its application in studying forest self-thinning].

The mechanism of forest self-thinning is generally nonlinear and dynamic, and the artificial neural network has the characteristic of expressing arbitrary nonlinear mapping. In this paper, the feasibility and limitation of artificial neural network used to simulating forest self-thinning was expounded, and the principle and algorithms of the neural network model based on modified simplex method (BP-MSM mixed algorithms) for modeling forest self-thinning were described. Its applications in self-thinning of Populus tremula natural forest Cunninghamia lanceolata plantation were illustrated. The results of forest self-thinning examples show the BP-MSM mixed algorithms were satisfactory in simulating forest self-thinning, and its precision was higher, which develops the method and theory of artificial neural network, and enriches the simulating method of forest self-thinning.

Algorithms↗
PubMed2002

[Regulation effect of forest vegetation on watershed runoff in the Loess Plateau].

The runoff and rainfall data of typical forested and non-forested watersheds in Ziwuling region, which is located in the hinterland of the Loess Plateau, were used to analyze their annual runoff variation comparatively. The result showed that the annual distribution of runoff in forested watersheds was uniform, compared with that in non-forested watersheds. The total runoff in flood season decreased by 8.88 mm and 7.1 mm. Regression analyses between runoff in dried-up season and rainfall in flood season or in dried-up season showed that the rainfall in flood season in forested watersheds could be changed into underground runoff by forest vegetation, and increased the runoff in dried-up season. The annual variation of runoff also indicated that the total effect of forest vegetation on dried-up runoff complement from October to December was 1.69 mm and 0.5 mm, and that from January to May was not significant.

China↗
PubMed2004

[Snow/wind damage in natural secondary forests in Liaodong mountainous regions of Liaoning Province].

In early spring of 2003, the secondary forests at the Qingyuan Experimental Forests (QEF) of the Institute of Applied Ecology, Chinese Academy of Sciences suffered from the damage caused by snow and wind (snow/wind damage). This damage occurred at 800 m above sea level was the most serious one since 1949. In order to make clear its occurrence and process and to analyze its possible influences on the secondary forest system, comprehensive investigations were conducted soon after the snow/wind damage. The results showed that the occurrence of this damage was due to the special site conditions (higher sea level and steeper slopes) and air temperature, which suited the wet snow formation and the snow accumulation on trees after a large scale of precipitation. The more seriously damaged areas were those with the stands of Acer mono, Juglans mandshurica, Populus spp. and so on. The ratio of damaged trees was negatively correlated with stand density, soil depth and size class of diameter, and positively correlated with tree height. Based on these results, the likely influences of snow/wind damage, i. e., the happening of diseases and insect pests, the vegetation changing under forests, and the factors of habitat and dominant species in natural secondary forests were also discussed. It is significant that to do observation and basic research on damaged forests will provide reasonable strategies for management of natural secondary forests.

China↗
PubMed2004

[Effect of Jinggang Mountain forests on regional ecological environment].

Based on the late years' data of forest resources, climate, hydrology and atmosphere in Jinggang Mountain region and by the methods of canonical correlation analysis and multiple linear stepwise regression, this paper analyzed the influence of forests on the climate, water quality and atmosphere of this region. The results showed that forest volume had an evident effect on maximum daily precipitation, extreme highest air temperature and atmospheric SO2 concentration, and on COD(cr) and ammonic nitrogen contents in river water. The greater the regional forest volume, the less maximum daily precipitation and the lower extreme highest air temperature, atmospheric SO2 concentration and water COD(cr) and ammonic nitrogen contents. Forest cover percentage could remarkably affect soil erosion modulus and atmospheric NOx concentration: the two latter were decreased as forest cover percentage increased. These results will provide theoretic foundation for the evaluation of the environmental value and ecological benefit of forest.

Atmosphere↗
PubMed2004

[Dynamics of litters in artificial restoration process of subalpine coniferous forest].

By adopting the concept of space as a substitute for time and taking the primitive subalpine coniferous forests as a reference, this paper investigated the forest litters in 10, 30, 40, 50 and 60-years subalpine Picea asperata stands to study the development process of litters in subalpine coniferous plantations with different restoration stages. The difference in litter development in artificial and natural stands was also discussed. The results indicated that in Picea asperata plantations with different ages, the litter pool on forest floor and the nutrient storage and maximum moisture holding capacity of litters showed a general trend of decrease at their earlier restoration stages, and of increase at the later stages. The trend of increase reached the maximum around 50 years of restoration, and then gradually leveled off or even slightly decreased. The observed litter pool (70.21 x 10(3) kg x hm(-2)), nutrient storage (4.73 x 10(3) kg x hm(-2)) and maximum moisture holding capacity (89.98 x 10(3) kg x hm(-2)) of 60-years plantations were considerably small, only accounted for 48.40%, 46.79% and 46.99% of the primitive forests, respectively. After 40 years of restoration, both artificial stands and naturally regenerated secondary forests showed similarity in litter dynamics, annual litterfall, and amount of annual nutrient returning to the soils, while a big difference in litter components, litter pool and structure on the forest floor, nutrient storage, and maximum moisture holding capacity. The difference which accounts for the difference in ecological functioning of the subalpine coniferous plantations lagging behind that of the secondary forests might be mainly caused by the less species diversity of the former.

Biodiversity↗
PubMed2005

[Resource and ecological distribution of ectomycorrhizal fungi under pine forests of Huangshan Mountain district].

Pinus massoniana and Pinus taiwanensis are the most common and important tree species in the Huangshan Mountain district, and ectomycorrhizae plays an important role in their forestation. Our investigations in 1998-2003 showed that under the pine forests of this district, there were 43 species of ectomycorrhizal fungi belonging to 10 families and 17 genera, of which, 43 were under Pinus massoniana forest, and 12 under Pinus taiwanensis forest. Only a few species were found under young Pinus massoniana forest, with the dominant of Pisolithus tinctorius (Pers.) Coken and Rhizopogon spp., but under mature Pinus massoniana forest, there were plentiful species, with the dominant of Russulaceae, Amanitaceae, Boletaceae and Canthurellaceae. The relationships between woody species and ectomycorrhizal fungi, and between fungi distribution and temperature, moisture and soil condition were discussed in this paper, which would benefit to the further studies on the effects of different ectomyrrhizal fungi to Pinus massoniana and Pinus taiwanensis forests.

China↗
PubMed2005

[Effects of artificial seabuckthorn forest on soil and water conservation in loess hilly region].

Seabuckthorn is regarded as a main eco-economical tree species, and plays an increasing important role in eco-environmental construction in Northwest, Northeast and North China. Our study on artificial seabuckthorn forest in loess hilly region showed that the average rainfall interception rate of 7-10 ages seabuckthorn canopy was 8.5%, and the litter layer of 5-10 ages seabuckthorn forest could intercept 0.89 mm rainfall. Seabuckthorn forest could improve soil infiltration and anti-strike ability through improving soil physical and chemical properties, and the numbers of its hair roots and the depth of its litter layer were the main indices of soil anti-strike ability. The effects of seabuckthorn forest on soil and water conservation increased with its increasing age. In 2-3 ages stage, the effects were weak, and the runoff and sediment were mainly affected by the characters of rainfall. In 4-5 ages stage when the forest became maturing, the annual runoff depth and annual erosion modulus were 1.8-3.2 mm and 24.64 t x km(-2), respectively. In 6-12 ages stage when the forest matured, the runoff and sediment on seabuckthorn woodland changed slowly, the annual runoff depth and annual erosion modulus being 0.3 -3.4 mm and 0-6.75 t x km(-2), respectively, and the characters of rainfall had much less effect on them. In the stage from young (2-5 ages) to mature forest, the sediment charge in runoff changed sharply, ranged from 77. 31 kg x m(-3) to 9.12 kg x m(-3), but in 6-12 ages stage, the sediment content in runoff changed very slowly, and the range was 0-5.09 kg x m(-3).

Conservation of Natural Resources↗
PubMed2005

[Carbon storage and its dynamics of forest vegetations in Heilongjiang Province].

Forest is the leading sink of carbon on the earth, while the forest resources of Heilongjiang Province take an important position in China. Based on the national forest inventory data from 1973 to 2003, the carbon storage of forests in Heilongjiang Province was estimated by the linear relationship between stand biomass and volume. The results showed that the total carbon storage of forests in 1973-1976, 1977-1981, 1985-1988, 1989-1993, 1994-1998 and 1999-2003 was 7.916 x 10(8), 5.413 x 10(8), 5.661 x 10(8), 5.880 x 10(8), 6.216 x 10(8) and 6.011 x 10(8) t, respectively, with an increasing trend since 1977, indicating that the forests in this Province played a role as a sink of atmospheric carbon dioxide, and this functioning was strengthened during the last 20 years. If the current forest is managed well, it would become a huge potential carbon sink in the future.

Atmosphere↗