Bacterial community structure and activity in different Cd-treated forest soils

In this study we compared indicators of Cd bioavailability (water extracts, Lakanen extracts, free ions) and ecotoxicity in forest soils with contrasting physico-chemical characteristics. Soil samples were treated with CdCl(2) solutions (0, 0.1, 1, 10 and 100 mM) and incubated for 30 days. Microbial activity indexes (acid phosphatase, beta-glucosidase, basal respiration) and changes in bacterial community structure using terminal restriction fragment length polymorphism (T-RFLP) fingerprinting were investigated. The Cd concentrations measured ranged from 1% to 37% of the total additions in water extracts, to higher levels in Lakanen extracts. Effects of Cd were observed at bioavailable concentrations exceeding United Nations/European Economic Commission UN/ECE guidelines for total Cd in the soil solution. Basal respiration was the most affected index, while enzymatic activities showed variable responses to the Cd treatments. We also noticed that soils with pH higher than 6.7 and clay content higher than 50% showed inhibition of basal respiration but no marked shift in bacterial community structure. Soils with lower pH (pH <5.8) with less clay content (<50%) showed in addition strong changes in the bacterial community structure. Our results provide evidence for the importance of relating the effects of Cd on the soil communities to soil properties and to bioavailability.     

Bacterial and fungal community structure in Arctic tundra tussock and shrub soils

Fungal and bacterial community structure in tussock, intertussock and shrub organic and mineral soils at Toolik Lake, Alaska were evaluated. Community structure was examined by constructing clone libraries of partial 16S and 18S rRNA genes. The soil communities were sampled at the end of the growing season in August 2004 and just after the soils thawed in June 2005. The communities differed greatly between vegetation types, although tussock and intertussock soil communities were very similar at the phyla level. The communities were relatively stable between sample dates at the phyla and subphyla levels, but differed significantly at finer phylogenetic scales. Tussock and intertussock bacterial communities were dominated by Acidobacteria, while shrub soils were dominated by Proteobacteria. These results appear consistent with previous work demonstrating that shrub soils contain an active, bioavailable C fraction, while tussock soils are dominated by more recalcitrant substrates. Tussock fungi communities had higher proportions of Ascomycota than shrub soils, while Zygomycota were more abundant in shrub soils. Recent documentation of increasing shrub abundance in the Arctic suggests that soil microbial communities and their functioning are likely to be altered by climate change.     

Bacterial community of very wet and acidic subalpine forest and fire-induced grassland soils

The subalpine forest and grassland ecosystems at Tatajia in Yushan National Park, Taiwan, at an elevation of 2,700 m, mean annual precipitation of 4,100 mm, mean annual temperature of 9.5°C, and soil pH near 3.5, represent land types whose bacterial communities have not been previously characterized. To this end, small subunit (SSU) rRNA libraries were prepared from environmental DNA, and 319 clones were sequenced and characterized. Despite differences in vegetation, Acidobacteria, Proteobacteria and Firmicutes were the most abundant phyla in soil communities from the forest and grassland. Although not significantly different, on the basis of Chao1, Shannon and other indices and rarefaction analyses, the diversity of the bacterial community of grassland appeared higher than that of the forest. The composition of the most abundant operational taxonomic units (OTUs) also differed between the grassland and forest communities. Because the grassland was formed by fire 30 years ago from forest, these results indicated a different bacterial community could form within that time. Moreover, most of the OTUs abundant in Tatajia soils had been previously detected in other studies, but in lower numbers. Therefore, the bacterial communities in Tatajia differed in relative abundance but not in types of bacteria present. However, one acidobacterial OTU abundant in Tatajia had previously been found to be abundant in soils from around the world. Thus, this OTU may represent a particularly abundant and cosmopolitan bacterial phylotype.     

Nitrous oxide reductase (nosZ) gene fragments differ between native and cultivated Michigan soils

The effect of standard agricultural management on the genetic heterogeneity of nitrous oxide reductase (nosZ) fragments from denitrifying prokaryotes in native and cultivated soil was explored. Thirty-six soil cores were composited from each of the two soil management conditions. nosZ gene fragments were amplified from triplicate samples, and PCR products were cloned and screened by restriction fragment length polymorphism (RFLP). The total nosZ RFLP profiles increased in similarity with soil sample size until triplicate 3-g samples produced visually identical RFLP profiles for each treatment. Large differences in total nosZ profiles were observed between the native and cultivated soils. The fragments representing major groups of clones encountered at least twice and four randomly selected clones with unique RFLP patterns were sequenced to verify nosZ identity. The sequence diversity of nosZ clones from the cultivated field was higher, and only eight patterns were found in clone libraries from both soils among the 182 distinct nosZ RFLP patterns identified from the two soils. A group of clones that comprised 32% of all clones dominated the gene library of native soil, whereas many minor groups were observed in the gene library of cultivated soil. The 95% confidence intervals of the Chao1 nonparametric richness estimator for nosZ RFLP data did not overlap, indicating that the levels of species richness are significantly different in the two soils, the cultivated soil having higher diversity. Phylogenetic analysis of deduced amino acid sequences grouped the majority of nosZ clones into an interleaved Michigan soil cluster whose cultured members are alpha-Proteobacteria. Only four nosZ sequences from cultivated soil and one from the native soil were related to sequences found in gamma-Proteobacteria. Sequences from the native field formed a distinct, closely related cluster (D(mean) = 0.16) containing 91.6% of the native clones. Clones from the cultivated field were more distantly related to each other (D(mean) = 0.26), and 65% were found outside of the cluster from the native soil, further indicating a difference in the two communities. Overall, there appears to be a relationship between use and richness, diversity, and the phylogenetic position of nosZ sequences, indicating that agricultural use of soil caused a shift to a more diverse denitrifying community.     

Young restored forests increase seedling recruitment in abandoned pastures in the Southern Atlantic rainforest

Planting seedlings is a common technique for abandoned pastures restoration in the tropics, supposedly by increasing the seedling recruitment and accelerating succession. In this study we evaluated the role of a young restored forest (one year old) in enhancing seedling establishment from two sources (seed rain and seed bank), in the Atlantic Rainforest region in Southern Brazil. We compared abandoned pasture, young restored forest and old-growth forest with respect to the seedlings recruited from different sources, by monitoring 40 permanent plots (0.5 m x 0.5 m) over 20 months. From the three studied areas a total of 392 seedlings of 53 species were recruited. Species were mainly herbaceous (85%), pioneers (88%), zoochorous (51%) and small-seeded species (60%). Seedling recruitment from the seed bank (density and species richness) was higher and dominated by herbaceous species in the abandoned pasture and in the young restored forest; on the other hand, the recruitment of woody species from seed rain was more pronounced in the old-growth forest. The young restored forest increased the species richness of woody seedlings recruitment from the seed bank (two-fold) and from seed rain (three-fold) compared to the abandoned pasture. Also, the seedling density in young restored forest was still higher than abandoned pastures (seed bank: four times; seed rain: ten times). Our results show that even young restored areas enhance the establishment of woody species and should be considered an important step for pasture restoration.     

Leaf respiration in Piper species native to a Mexican rainforest

We measured leaf respiration with a Clark-type oxygen-electrode in 6 species of the genus Piper (Piperaceae) growing naturally in wet evergreen rainforest, in microsites characterized by a broad range of light availabilities. Species normally found in large gaps and clearings ( Piper auritum and P. umbellatum ) had approximately twice the dark respiration per unit of leaf area or dry mass as species found predominantly in shaded understory sites ( P. aequale, P. lapathifolium and P. amalago ). within a species, dark respiration was lower in the individuals growing in low-light sites than in the individuals growing in high-light sites. Over all species, leaf respiration was positively correlated with the average daily photosynthetically active photon flux density (PFD) at each site, and negatively correlated with mean leaf longevity. Respiration was insensitive to leaf age in a shade species. ( P. lapathifolium ) and in a generalist ( P. hispidum ) but decreased with increasing leaf age in a gap specialist ( P. aurtium ).
In experiments on greenhouse-grown plants, we titrated respiration with potassium cyanide (KCN) and/or salicylhydroxamic acid (SHAM) to determine the cytochrome and alternative pathway components to respiration in 4 Piper species. All 4 species, representing gap, generalist and shade species, exhibited alternative pathway respiration. Engagement of the cytochrome pathway (ϱ_cyt) varied from 0.69 in P. auritum to 1.04 in P. lapathifolium and engagement of the alternative pathway (ϱ_alt varied from 0.41 to 1.02. Although the shade species had lower respiration rates than the gap species, the capacities for cytochrome and alternative pathway respiration made up similar or greater fractions of total respiration in shade species.     

Patch- and landscape-scale effects on howler monkey distribution and abundance in rainforest fragments

Variation at both the patch and landscape scale is known to influence the distribution and abundance of arboreal monkeys in rainforest fragments. However, few studies have examined the factors associated with these different scales of focus simultaneously. Using stepwise logistic-regression and generalized linear models (GLMs), howler monkey Alouatta palliata distribution and abundance were examined as a function of patch quality (fragment area, shape, tree DBH and canopy height) and landscape connectivity (isolation, total forest area, fragment and road abundance, corridor abundance and length) in 119 rainforest fragments in northern Chiapas, Mexico. The positive correlation observed between monkey distribution (presence/absence) and both fragment area and abundance may be explained by increased resources within larger fragments and those whose proximity allows greater exploration by monkeys. In contrast, GLM analysis indicated that monkey abundance in inhabited fragments was positively correlated with corridor abundance, canopy height and fragment area. These relationships could be explained by greater reproductive investments by monkeys in forest fragments whose size, degree of perturbation and degree of connectivity with other fragments suggest greater overall resource availability. Future studies should explicitly include a multi-scale approach to understanding the factors affecting patterns of monkey distribution and abundance, particularly as this relates to measures of and interactions between patch connectivity and resource availability.     

Ascomycete diversity in soil-feeding termite nests and soils from a tropical rainforest

Molecular microbial ecology has revealed remarkable biodiversity - prokaryotic and eukaryotic - in numerous soil environments. However, no culture-independent surveys of the termitosphere exists, although termites dominate tropical rainforests. Here, we focused on soil feeders, building nests with their soil-born faeces, enriched with clay-organic complexes, thus contributing to the improvement of soil fertility. In order to assess the fungal community composition of these termitaries compared with soils not foraged by termites, samples of the two types were collected in the Lopé rainforest, Gabon, and processed for generation of fungal internal transcribed spacer (ITS) clone libraries. Although primers were universal, most of the recovered sequences represented Ascomycete that were previously uncharacterized and the proportions of which reached 72.5% in soils and 80% in termitaries. Their affiliation with identified fungi was analysed in performing a phylogenetic tree based on 5.8S rDNA. Furthermore, the ascomycete communities of soil-feeding termitaries and soils shared only 6.3% of sequences. This discrepancy of composition between soil and nest may result from the building behaviour of termites, as the organic matter in the nest is chemically modified, and some vacant ecological microniches are available for more specialized fungi.     

The hummingbird community of a lowland Amazonian rainforest

Between October 1987 and September 1989, the British Ornithologists' Union Colombia Expedition recorded 16 species of hummingbird at Matamatá in the Amacayacu National Park, Amazonas, Colombia. Most of these species were resident breeders at the study site although two appeared to be local migrants. Six species of hermit hummingbirds (subfamily Phaethornithinae) occurred at Matamatá; although very similar in general morphology and behaviour, they showed different preferences for habitat, food plants and foraging technique. Hermits were predominant in the forest, but in areas of secondary vegetation and along riverine borders, "typical" hummingbirds (subfamily Trochilinae) were more common. The study site consisted of terra firme and várzea forest and an area of riverine secondary vegetation and contained around 60 species of flowering plants visited by hummingbirds. In contrast with most groups of organisms, hummingbirds and hummingbird-pollinated plants had similar species diversity in primary forest and secondary habitats. The overall abundance of hummingbirds and flowers was significantly higher in areas of riverine secondary growth. The hummingbird community at Matamatá is remarkably species rich when compared with study sites elsewhere in North and South America. However, random null model comparisons among Amazonian hummingbird communities reveal that they share many characteristics in their structure and show a high degree of species overlap.     

Bacterial diversity and community structure in polygonal tundra soils from Samoylov Island, Lena Delta, Siberia

During the Arctic summer, bacteria are active above the permafrost in an environment with sharp temperature and oxygen gradients. The present study addressed the diversity and abundance of bacteria in soil layers near the surface and above the permafrost of the rim and center of a low-centered polygon in the Lena Delta, Siberia. 16S rRNA gene clone libraries revealed the presence of all major soil bacterial groups and of the candidate divisions OD1, OP5, and OP11, and indicated a small-scale heterogeneity of these polygonal tundra soils. The diversity at the top of the elevated polygon rim was significantly different from that of the bottom and from both water-saturated sites of the polygon's center. The overall species-level diversity was very high (Shannon index of 5.3) but varied within the sites and decreased towards the permafrost table, coinciding with decreasing dissolved organic carbon (DOC) and phosphate concentrations. According to the number of operational taxonomical units (OTUs) and cells visualized by fluorescence in-situ hybridization, Bacteroidetes and Actinobacteria were the dominant members of the bacterial community in all sites. Bacteroidetes contributed almost 50% to all Bacteria cells while sequences affiliated with Bacteroidetes/Chlorobi represented on average 23% of all OTUs. Our results provide evidence of the extremely diverse bacterial communities present in permafrost soils and of the influence of nutrient concentrations, oxygen, and DOC on diversity.     

Growth, biomass allocation and photosynthesis of invasive and native Hawaiian rainforest species

Growth, biomass allocation, and photosynthetic characteristics of seedlings of five invasive non-indigenous and four native species grown under different light regimes were studied to help explain the success of invasive species in Hawaiian rainforests. Plants were grown under three greenhouse light levels representative of those found in the center and edge of gaps and in the understory of Hawaiian rainforests, and under an additional treatment with unaltered shade. Relative growth rates (RGRs) of invasive species grown in sun and partial shade were significantly higher than those for native species, averaging 0.25 and 0.17 g g⁻¹ week⁻¹, respectively, while native species averaged only 0.09 and 0.06 g g⁻¹ week⁻¹, respectively. The RGR of invasive species under the shade treatment was 40% higher than that of native species. Leaf area ratios (LARs) of sun and partial-shade-grown invasive and native species were similar but the LAR of invasive species in the shade was, on average, 20% higher than that of native species. There were no differences between invasive and native species in biomass allocation to shoots and roots, or in leaf mass per area across light environments. Light-saturated photosynthetic rates (Pmax) were higher for invasive species than for native species in all light treatments. Pmax of invasive species grown in the sun treatment, for example, ranged from 5.5 to 11.9 μmol m⁻² s⁻¹ as compared with 3.0−4.5 μmol m⁻² s⁻¹ for native species grown under similar light conditions. The slope of the linear relationship between Pmax and dark respiration was steeper for invasive than for native species, indicating that invasive species assimilate more CO₂ at a lower respiratory cost than native species. These results suggest that the invasive species may have higher growth rates than the native species as a consequence of higher photosynthetic capacities under sun and partial shade, lower dark respiration under all light treatments, and higher LARs when growing under shade conditions. Overall, invasive species appear to be better suited than native species to capturing and utilizing light resources, particularly in high-light environments such as those characterized by relatively high levels of disturbance. Received: 30 December 1997 / Accepted: 1 September 1998     

Occurrence of nodulation in unexplored leguminous trees native to the West African tropical rainforest and inoculation response of native species useful in reforestation

Despite the abundance and diversity of timber tree legumes in the West African rainforest, their ability to form nitrogen-fixing nodules in symbiosis with rhizobia, and their response to rhizobial inoculation, remain poorly documented. In the first part of this study the occurrence of nodulation was determined in 156 leguminous species growing in six natural forest areas in Guinea, mostly mature trees. In the second part, an in situ experiment of rhizobial inoculation was performed on eight selected tree species belonging to three genera: Albizia, Erythrophleum and Millettia. Of the 97 plant species and 14 genera that had never been examined before this study, 31 species and four genera were reported to be nodulated. After 4 months of growing in a nursery and a further 11 months after transplantation of plants to the field, we observed a highly significant (P < 0.001) and positive effect of inoculation with Bradyrhizobium sp. strains on the growth of the eight tree species tested. The importance of determining the nodulation ability of unexplored local trees and subsequently using this information for inoculation in reforestation programmes was demonstrated.     

Determinants of mortality across a tropical lowland rainforest community

Tree mortality is an important process determining forest dynamics. However, in species‐rich tropical forests it is largely unknown, how species differ in their response of mortality to resource availability and individual condition. We use a hierarchical Bayesian approach to quantify the impact of light availability, tree size and past growth on mortality of 284 woody species in a 50‐ha long‐term forest census plot in Barro Colorado Island, Panama. Light reaching each individual tree was estimated from yearly vertical censuses of vegetation density. Across the community, 78% of the species showed increasing mortality with increasing light. Considering species individually, just 29 species showed a significant response to light, all with increasing mortality at high light. Past growth had a significant impact on all but three species, with higher growth leading to lower mortality. For the majority of species, mortality decreased sharply with diameter in saplings, then levelled off or increased slightly towards the maximum diameter of the species. Diameter had the biggest impact on mortality, followed by past growth and finally light availability. Our results challenge many previous reports of higher mortality in shade, and we suggest that it is crucial to control for size effects when assessing the impact of environmental conditions on mortality.     

Direct and indirect effects of predation on tadpole community structure in the Amazon rainforest

Abstract The relationship between the distribution of predators (fish, odonates and water beetles) and prey assemblages (amphibian larvae) was investigated in the tropical rainforest of central Amazonas, Brasil. The anuran community uses a variety of waterbodies for reproduction, ranging from streams and streamside ponds to isolated forest ponds. Predators in this system include fish in streams and streamside ponds, and invertebrates (primarily odonate naiads and beetles) in forest ponds. Tadpole species richness and assemblage structure were related to fish density and species richness. No relationships between tadpole assemblages and abiotic pond characteristics were detected. The presence offish explained much of the variation in both species composition and species richness within and among ponds. Some species of tadpole were consistently found to coexist with high densities of fish. Path analyses suggest that while fish have a strong direct effect on tadpole associations and species richness, they also have an indirect effect through invertebrate predators (odonate larvae and coleopteran beetles). Prey survival-strategies such as palatability and behaviour may explain how tadpole species composition is affected by predators at the community level. These findings suggest that the observed patterns of habitat use by larval anurans may be structured in response to the distribution of key predators (fish) in this system.     

Local and landscape correlates of non‐native species invasion in restored wetlands

Vulnerability of natural communities to invasion by non‐native plants has been linked to factors such as recent disturbance and high resource availability, suggesting that recently restored habitats may be especially invasible. Because non‐native plants can interfere with restoration goals, monitoring programs should anticipate which sites are most susceptible to invasion and which species are likely to become problematic at a site. Restored sites of larger area and those with high rates of propagule input should have higher species richness of both natives and non‐natives, leading to a positive correlation between the two. However, in restored wetlands, urbanization, riparian landscape settings, and nitrogen enrichment likely favor non‐native relative to native species. We sampled 28 restored wetlands in Illinois, USA, modeled the responses of native richness, non‐native richness and non‐native cover to local and landscape predictors with linear regression, and modeled the presence/absence of 21 non‐native species with logistic regressions. Unexpectedly, native and non‐native richness were uncorrelated, suggesting different responses to environmental factors. Native richness declined with increasing available soil nitrogen and urbanization in the surrounding landscape. Non‐native richness, the richness of non‐natives relative to natives, and the likelihood of invasion by several individual invasive species decreased with increasing distance from the city of Chicago, likely in response to decreasing non‐native propagule pressure. Total cover of non‐natives, however, as well as cover by non‐native Phalaris arundinacea, increased with nitrogen availability. Our results indicate that although non‐native richness was better predicted by factors related to propagule pressure, non‐native species dominance was more closely related to local abiotic factors. Non‐native richness in restoration sites may be beyond the control of restoration practitioners, and furthermore, may be of limited relevance for conservation goals. In contrast, limiting the relative dominance of non‐natives should be a restoration priority and may be achievable through management of nutrient availability.     

Enrichment planting to improve habitat quality and conservation value of tropical rainforest fragments

Many areas of tropical rainforest have been fragmented and the habitat quality of fragments is often poor. For example, on Borneo, many forest fragments are highly degraded by repeated logging of Dipterocarpaceae trees prior to fragmentation, and we examined the viability of enrichment planting as a potential management tool to enhance the conservation value of these forest fragments. We planted seedlings of three dipterocarp species with contrasting light demands and tolerances (Parashorea malaanonan (light demander), Dryobalanops lanceolata (intermediate), Hopea nervosa (shade tolerant)) in eight forest fragment sites (3–3529 ha), and compared seedling performance with four sites in continuous forest. Eighteen months after planting, survival rates of seedlings were equally high in fragment sites (mean survival = 63 %), and in continuous forest sites (mean survival = 68 %). By contrast, seedling growth and herbivory rates were considerably higher in fragments (by 60 % for growth and 45 % for herbivory) associated with higher light environments in degraded forest fragments compared with continuous forest sites. Among the three study species, H. nervosa seedlings had the highest survival rates overall, and P. malaanonan seedlings generally grew fastest and suffered highest herbivory rates. There were no interactions between species performance and the effects of fragment site area, forest structure or soil characteristics of sites suggesting that the three species responded similarly to fragmentation effects. High survival of planted seedlings implies that enrichment planting would be a successful forest management strategy to improve forest quality, and hence conservation value, of fragments.     

Seasonal cycles of diversity and similarity in a Central American rainforest butterfly community

Despite the importance of understanding the effects of tropical seasonality on ecological diversity, few studies have investigated the influence of environmental factors on seasonal community composition, and even fewer use standardized sampling and robust analytical methods that are directly comparable. Our 104 months of sampling in Costa Rican lowland rainforest yielded 12 757 individuals of 106 fruit‐feeding butterfly species demonstrated biannual cycles in species diversity, but community similarity showed an annual cycle that peaked in the driest months. We found that community diversity and similarity did not decline with increasing time lag, which we attribute to lack of long‐term changes in species abundances. Our findings differ from a similar study in Ecuador, where cycles in weather and community diversity were annual. Long‐term intensive monitoring and robust statistical analysis of changes in community composition in relation to environmental factors can help to elucidate the dynamics of communities, and their response to climate change.