Prebiotics modulate the effects of antibiotics on gut microbial diversity and functioning in vitro

Intestinal bacteria carry out many fundamental roles, such as the fermentation of non-digestible dietary carbohydrates to produce short chain fatty acids (SCFAs), which can affect host energy levels and gut hormone regulation. Understanding how to manage this ecosystem to improve human health is an important but challenging goal. Antibiotics are the front line of defence against pathogens, but in turn they have adverse effects on indigenous microbial diversity and function. Here, we have investigated whether dietary supplementation—another method used to modulate gut composition and function—could be used to ameliorate the side effects of antibiotics. We perturbed gut bacterial communities with gentamicin and ampicillin in anaerobic batch cultures in vitro. Cultures were supplemented with either pectin (a non-fermentable fibre), inulin (a commonly used prebiotic that promotes the growth of beneficial bacteria) or neither. Although antibiotics often negated the beneficial effects of dietary supplementation, in some treatment combinations, notably ampicillin and inulin, dietary supplementation ameliorated the effects of antibiotics. There is therefore potential for using supplements to lessen the adverse effects of antibiotics. Further knowledge of such mechanisms could lead to better therapeutic manipulation of the human gut microbiota.

Carbon and nitrogen stock and fluxes in coastal Atlantic Forest of southeast Brazil: potential impacts of climate change on biogeochemical functioning

The Atlantic Forest is one of the most important biomes of Brazil. Originally covering approximately 1.5 million of km(2), today this area has been reduced to 12% of its original size. Climate changes may alter the structure and the functioning of this tropical forest. Here we explore how increases in temperature and changes in precipitation distribution could affect dynamics of carbon and nitrogen in coastal Atlantic Forest of the southeast region of Brazil The main conclusion of this article is that the coastal Atlantic Forest has high stocks of carbon and nitrogen above ground, and especially, below ground. An increase in temperature may transform these forests from important carbon sinks to carbon sources by increasing loss of carbon and nitrogen to the atmosphere. However, this conclusion should be viewed with caution because it is based on limited information. Therefore, more studies are urgently needed to enable us to make more accurate predictions.

Diversity Promotes Temporal Stability across Levels of Ecosystem Organization in Experimental Grasslands

The diversity–stability hypothesis states that current losses of biodiversity can impair the ability of an ecosystem to dampen the effect of environmental perturbations on its functioning. Using data from a long-term and comprehensive biodiversity experiment, we quantified the temporal stability of 42 variables characterizing twelve ecological functions in managed grassland plots varying in plant species richness. We demonstrate that diversity increases stability i) across trophic levels (producer, consumer), ii) at both the system (community, ecosystem) and the component levels (population, functional group, phylogenetic clade), and iii) primarily for aboveground rather than belowground processes. Temporal synchronization across studied variables was mostly unaffected with increasing species richness. This study provides the strongest empirical support so far that diversity promotes stability across different ecological functions and levels of ecosystem organization in grasslands

Moving forward on facilitation research: response to changing environments and effects on the diversity, functioning and evolution of plant communities

Once seen as anomalous, facilitative interactions among plants and their importance for community structure and functioning are now widely recognized. The growing body of modelling, descriptive and experimental studies on facilitation covers a wide variety of terrestrial and aquatic systems throughout the globe. However, the lack of a general body of theory linking facilitation among different types of organisms and biomes and their responses to environmental changes prevents further advances in our knowledge regarding the evolutionary and ecological implications of facilitation in plant communities. Moreover, insights gathered from alternative lines of inquiry may substantially improve our understanding of facilitation, but these have been largely neglected thus far. Despite over 15 years of research and debate on this topic, there is no consensus on the degree to which plant–plant interactions change predictably along environmental gradients (i.e. the stress-gradient hypothesis), and this hinders our ability to predict how plant–plant interactions may affect the response of plant communities to ongoing global environmental change. The existing controversies regarding the response of plant–plant interactions across environmental gradients can be reconciled when clearly considering and determining the species-specificity of the response, the functional or individual stress type, and the scale of interest (pairwise interactions or community-level response). Here, we introduce a theoretical framework to do this, supported by multiple lines of empirical evidence. We also discuss current gaps in our knowledge regarding how plant–plant interactions change along environmental gradients. These include the existence of thresholds in the amount of species-specific stress that a benefactor can alleviate, the linearity or non-linearity of the response of pairwise interactions across distance from the ecological optimum of the beneficiary, and the need to explore further how frequent interactions among multiple species are and how they change across different environments. We review the latest advances in these topics and provide new approaches to fill current gaps in our knowledge. We also apply our theoretical framework to advance our knowledge on the evolutionary aspects of plant facilitation, and the relative importance of facilitation, in comparison with other ecological processes, for maintaining ecosystem structure, functioning and dynamics. We build links between these topics and related fields, such as ecological restoration, woody encroachment, invasion ecology, ecological modelling and biodiversity–ecosystem-functioning relationships. By identifying commonalities and insights from alternative lines of research, we further advance our understanding of facilitation and provide testable hypotheses regarding the role of (positive) biotic interactions in the maintenance of biodiversity and the response of ecological communities to ongoing environmental changes.

Stand scale variability of topsoil organic matter composition in a high-elevation Norway spruce forest ecosystem

Our knowledge about the effect of single-tree influence areas on the physicochemical properties of the underlying mineral soil in forest ecosystems is still limited. This restricts our ability to adequately estimate future changes in soil functioning due to forest management practices. We studied the stand scale spatial variation of different soil organic matter species investigated by 13C NMR spectroscopy, lignin phenol and neutral sugar analysis under an unmanaged mountainous high-elevation Norway spruce (Picea abies L.) forest in central Europe. Multivariate geostatistical approaches were applied to relate the spatial patterns of the different soil organic matter species to topographic parameters, bulk density, oxalate- and dithionite-extractable iron, pH, and the impact of tree distribution. Soil samples were taken from the mineral top soil. Generally, the stand scale distribution patterns of different soil organic matter compounds could be divided into two groups: Those compounds, which were significantly spatially correlated with topography/altitude and those with small scale spatial pattern (range ≤ 10 m) that was closely related to tree distribution. The concentration of plant-derived soil organic matter components, such as lignin, at a given sampling point was significantly spatially related to the distance of the nearest tree (p ≤ 0.05). In contrast, the spatial distribution of mainly microbial-derived compounds (e.g. galactose and mannose) could be attributed to the dominating impact of small-scale topography and the contribution of poorly crystalline iron oxides that were significantly larger in the central depression of the study site compared to crest and slope positions. Our results demonstrate that topographic parameters dominate the distribution of overall topsoil organic carbon (OC) stocks at temperate high-elevation forest ecosystems, particularly in sloped terrain. However, trees superimpose topography-controlled OC biogeochemistry beneath their crown by releasing litter and changing soil conditions in comparison to open areas. This may lead to distinct zones with different mechanisms of soil organic matter degradation and also stabilization in forest stands.

Contribution of woody habitat islands to the conservation of birds and their potential ecosystem services in an extensive Colombian rangeland

The conservation of birds and their habitats is essential to maintain well-functioning ecosystems including human-dominated habitats. In simplified or homogenized landscapes, patches of natural and semi-natural habitat are essential for the survival of plant and animal populations. We compared species composition and diversity of trees and birds between gallery forests, tree islands and hedges in a Colombian savanna landscape to assess how fragmented woody plant communities affect forest bird communities and how differences in habitat characteristics influenced bird species traits and their potential ecosystem function. Bird and tree diversity was higher in forests than in tree islands and hedges. Soil depth influenced woody species distribution, and canopy cover and tree height determined bird species distribution, resulting in plant and bird communities that mainly differed between forest and non-forest habitat. Bird and tree species and traits widely co-varied. Bird species in tree islands and hedges were on average smaller, less specialized to habitat and more tolerant to disturbance than in forest, but dietary differences did not emerge. Despite being less complex and diverse than forests, hedges and tree islands significantly contribute to the conservation of forest biodiversity in the savanna matrix. Forest fragments remain essential for the conservation of forest specialists, but hedges and tree islands facilitate spillover of more tolerant forest birds and their ecological functions such as seed dispersal from forest to the savanna matrix.

Isotope and fatty acid trends along continental shelf depth gradients: Inshore versus offshore hydrological influences on benthic trophic functioning

Anthropogenic activities and land-based inputs into the sea may influence the trophic structure and functioning of coastal and continental shelf ecosystems, despite the numerous opportunities and services the latter offer to humans and wildlife. In addition, hydrological structures and physical dynamics potentially influence the sources of organic matter (e.g., terrestrial versus marine, or fresh material versus detrital material) entering marine food webs. Understanding the significance of the processes that influence marine food webs and ecosystems (e.g., terrestrial inputs, physical dynamics) is crucially important because trophic dynamics are a vital part of ecosystem integrity. This can be achieved by identifying organic matter sources that enter food webs along inshore–offshore transects. We hypothesised that regional hydrological structures over wide continental shelves directly control the benthic trophic functioning across the shelf. We investigated this issue along two transects in the northern ecosystem of the Bay of Biscay (north-eastern Atlantic). Carbon and nitrogen stable isotope analysis (SIA) and fatty acid analysis (FAA) were conducted on different complementary ecosystem compartments that include suspended particulate organic matter (POM), sedimentary organic matter (SOM), and benthic consumers such as bivalves, large crustaceans and demersal fish. Samples were collected from inshore shallow waters (at ∼1 m in depth) to more than 200 m in depth on the offshore shelf break. Results indicated strong discrepancies in stable isotope (SI) and fatty acid (FA) compositions in the sampled compartments between inshore and offshore areas, although nitrogen SI (δ15N) and FA trends were similar along both transects. Offshore the influence of a permanently stratified area (described previously as a “cold pool”) was evident in both transects. The influence of this hydrological structure on benthic trophic functioning (i.e., on the food sources available for consumers) was especially apparent across the northern transect, due to unusual carbon isotope compositions (δ13C) in the compartments. At stations under the cold pool, SI and FA organism compositions indicated benthic trophic functioning based on a microbial food web, including a significant contribution of heterotrophic planktonic organisms and/or of SOM, notably in stations under the cold pool. On the contrary, inshore and shelf break areas were characterised by a microalgae-based food web (at least in part for the shelf break area, due to slope current and upwelling that can favour fresh primary production sinking on site). SIA and FAA were relevant and complementary tools, and consumers better medium- to long-term system integrators than POM samples, for depicting the trophic functioning and dynamics along inshore–offshore transects over continental shelves.

Ecosystem Engineering Effects On Species Diversity Across Ecosystems: A Meta-analysis.

Ecosystem engineering is increasingly recognized as a relevant ecological driver of diversity and community composition. Although engineering impacts on the biota can vary from negative to positive, and from trivial to enormous, patterns and causes of variation in the magnitude of engineering effects across ecosystems and engineer types remain largely unknown. To elucidate the above patterns, we conducted a meta-analysis of 122 studies which explored effects of animal ecosystem engineers on species richness of other organisms in the community. The analysis revealed that the overall effect of ecosystem engineers on diversity is positive and corresponds to a 25% increase in species richness, indicating that ecosystem engineering is a facilitative process globally. Engineering effects were stronger in the tropics than at higher latitudes, likely because new or modified habitats provided by engineers in the tropics may help minimize competition and predation pressures on resident species. Within aquatic environments, engineering impacts were stronger in marine ecosystems (rocky shores) than in streams. In terrestrial ecosystems, engineers displayed stronger positive effects in arid environments (e.g. deserts). Ecosystem engineers that create new habitats or microhabitats had stronger effects than those that modify habitats or cause bioturbation. Invertebrate engineers and those with lower engineering persistence (<1 year) affected species richness more than vertebrate engineers which persisted for >1 year. Invertebrate species richness was particularly responsive to engineering impacts. This study is the first attempt to build an integrative framework of engineering effects on species diversity; it highlights the importance of considering latitude, habitat, engineering functional group, taxon and persistence of their effects in future theoretical and empirical studies.

Isotopic view of vegetation and carbon and nitrogen cycles in a cerrado ecosystem, southeastern Brazil

Carbon and nitrogen biogeochemical cycles in savannas are strongly regulated by the seasonal distribution of precipitation and pulses of nutrients released during the wetting of the dry soil and are critical to the dynamics of microorganisms and vegetation. The objective of this study was to investigate the spatial and temporal variability of C and N isotope ratios as indicators of the cycling of these elements in a cerrado sensu stricto area, within a protected area in a State Park in the state of São Paulo, Brazil. The foliar δ13C and δ15N values varied from -33.6 to -24.4 ‰ and -2.5 to 4.5 ‰, respectively. The δ13C values showed a consistent relationship with canopy height, revealing the importance of structure of the canopy over the C isotopic signature of the vegetation. Carbon isotopic variations associated with the length of the dry season indicated the importance of recent fixed C to the integrated isotopic signature of the leaf organic C. The studied Cerrado species showed a depleted foliar δ15N, but a wide range of foliar Nitrogen with no difference among canopy heights. However, seasonal variability was observed, with foliar δ15N values being higher in the transition period between dry and rainy seasons. The variation of the foliar C and N isotope ratios presented here was consistent with highly diverse vegetation with high energy available but low availability of water and N.

Bee communities (Hymenoptera: Anthophila) of the "Cerrado" ecosystem in Sao Paulo State, Brazil

Five surveys of the bee communities in four "Cerrado" ecosystem reserves in Sao Paulo State were compared for species richness and similarity. These areas are fragment vegetation reser-reserves located in the Cerrado Corumbata Reserve (Corumbata), Jata Ecological Park (Luiz Antonio), Cajuru (Cajuru), and Vassununga State Park - ""Gleba de Cerrado de Pe-de-Gigante"" (Santa Rita do Passa Quatro). The methodology consisted of capturing bees foraging on flowers along transects, though with small differences between surveys. These ""cerrado"" areas have a large number of species of native bees, which are important pollinators in several Brazilian ecosystems. The community of bees varied among these different fragments. Based on 500 individuals (standardized by rarefaction), Cajuru, Corumbata 1 and Corumbata 2 were the areas with highest species richness, and Jata and Pe-de-Gigante had the lowest species richness in the bee communities. The bee faunas of Corumbata 2 and Pe-de-Gigante had the highest similarity, forming a group with the bee fauna of Cajuru. The bee faunas of Corumbata 1 and Jata were isolated from this group. We found that the bee species richness and similarity found in these ""cerrado"" areas cannot be explained by general factors such as the size of the fragment, the species richness of plants and the distance between the areas. Therefore, we suppose that local factors that differ among areas, such as interactions between populations, and competition and interference from surrounding areas influence and determine bee species richness and similarity in these reserves.

Nitrogen dynamics during ecosystem development in tropical forest restoration

We considered whether ecological restoration using high diversity of native tree species serves to restore nitrogen dynamics in the Brazilian Atlantic Forest. We measured delta(15)N and N content in green foliage and soil; vegetation N:P ratio; and soil N mineralization in a preserved natural forest and restored forests of ages 21 and 52 years. Green foliage delta(15)N values, N content, N:P ratio, inorganic N and net mineralization and nitrification rates were all higher, the older the forest. Our findings indicate that the recuperation of N cycling has not been achieved yet in the restored forests even after 52 years, but show that they are following a trajectory of development that is characterized by their N cycling intensity becoming similar to a natural mature forest of the same original forest formation. This study demonstrated that some young restored forests are more limited by N compared to mature natural forests. We document that the recuperation of N cycling in tropical forests can be achieved through ecological restoration actions. (C) 2011 Elsevier B.V. All rights reserved.

Stable isotopes of bulk organic matter to trace carbon and nitrogen dynamics in an estuarine ecosystem in Babitonga Bay (Santa Catarina, Brazil)

The biogeochemical processes affecting the transport and cycling of terrestrial organic carbon in coastal and transition areas are still not fully understood One means of distinguishing between the sources of organic materials contributing to particulate organic matter (POM) in Babitonga Bay waters and sediments is by the direct measurement of delta(13)C of dissolved inorganic carbon (DIC) and delta(13)C and delta(15)N in the organic constituents. An isotopic survey was taken from samples collected in the Bay in late spring of 2004. The results indicate that the delta(13)C and delta(15)N compositions of OM varied from -21.7 parts per thousand to -26 2 parts per thousand. and from + 9 2 parts per thousand. to -0 1 parts per thousand, respectively. delta(13)C from DIC ranges from +0.04 parts per thousand to -12.7 parts per thousand The difference in the isotope compositions enables the determination of three distinct end-members terrestrial, marine and urban Moreover, the evaluation of source contribution to the particulate organic matter (POM) in the Bay, enables assessment of the anthropogenic impact. Comparing the depleted values of delta(13)C(DIC) and delta(13)C(POC) it is possible to further understand the carbon dynamic within Babitonga Bay (C) 2010 Elsevier BV All rights reserved

Engineered ecosystem for sustainable on-site wastewater treatment

A Pilot-Scale Engineered Ecosystem (PSEE) operated for over two years in sub-tropical conditions, produced an effluent with COD (median 38 mg/L) and TSS (median 3 mg/L) levels comparable to that required by the AS/NZS 1547:2000 Onsite Domestic Wastewater Management standard. Only partial nitrification was achieved as dissimilatory nitrate reduction to ammonia occurred; however the level of NH4-N was reduced by 75% and total inorganic nitrogen by 53%. Phosphorus was not removed by the system due to the lack of regular sludge removal. Mass balances around the system showed that bacteria removed 36% of the influent nitrogen and 76% of the influent COD. Algae and plants were shown to remove 5% of the influent nitrogen, and 6% of the influent phosphorus. Challenges in developing a sustainable on-site wastewater treatment system were largely met by minimising chemical, energy and labour inputs, eliminating the need for frequent sludge handling, and creating an effluent quality suitable for re-use in non-potable applications. However, the sludge removal from the system needs to be adequately managed to avoid excessive accumulation as this can cause a range of negative impacts.

Ecosystem dynamics at disturbed and undisturbed sites in North Queensland wet tropical rain forest. III. Nutrient returns to the forest floor through litterfall

The nutrient contents and accessions in litterfall over a period of 3 y are reported for undisturbed areas and at two sites disturbed by selective harvesting in tropical rain forest in North Queensland, Australia. Mean concentrations (mg g(-1) dry weight) of nutrients in litterfall ranged from 10 to 12 for nitrogen; 0.33 to 0.43 for phosphorus; 3.6 to 4.3 for potassium; 6.0 to 10.5 for calcium and 1.7 to 2.6 for magnesium. These concentrations are in the middle to lower part of the spectrum of values recorded for tropical forest. Accessions of nutrients in litterfall (kg ha(-1) y(-1)) ranged from 59 to 64 N; 1.9 to 2.4 P; 20 to 24K; 34 to 63 Ca; and 9 to 16 Mg. These rates, particularly for IN and P, are among the lowest recorded for tropical forests. There were no consistent between-site differences in total nutrient accessions in small litterfall. In terms of the contribution of litterfall to the accessions of nutrients to the forest floor, this suggests that the logged sites have recovered from the effects of selective harvesting within 25 y. Nutrient accessions at each site were distinctly seasonal, with maximum accessions occurring in the late dry season to late in the wet season. Leaf-fall accounted for the largest proportion of nutrient accessions over the study period, although at certain times accessions in both reproductive material and wood were significant. A cyclone which crossed the coast near the study sites resulted in large nutrient accessions over a short period but had little effect on the total annual accession. A comparison with previous studies of litterfall in Australian tropical rainforests indicates that nutrient return in litterfall is directly related to soil fertility.

Subantarctic Macquarie Island - a model ecosystem for studying animal-derived nitrogen sources using N-15 natural abundance

Plants collected from diverse sites on subantarctic Macquarie Island varied by up to 30 parts per thousand in their leaf delta(15)N values. N-15 natural abundance of plants, soils, animal excrement and atmospheric ammonia suggest that the majority of nitrogen utilised by plants growing in the vicinity of animal colonies or burrows is animal-derived. Plants growing near scavengers and animal higher in the food chain had highly enriched delta(15)N values (mean = 12.9 parts per thousand), reflecting the highly enriched signature of these animals' excrement, while plants growing near nesting penguins and albatross, which have an intermediate food chain position, had less enriched delta(15)N values (> 6 parts per thousand). Vegetation in areas affected by rabbits had lower delta(15)N values (mean = 1.2 parts per thousand), while the highly depleted delta(15)N values (below -5 parts per thousand) of plants at upland plateau sites inland of penguin colonies, suggested that a portion of their nitrogen is derived from ammonia (mean N-15 = -10 parts per thousand) lost during the degradation of penguin guano. Vegetation in a remote area had delta(15)N values near -2 parts per thousand. These results contrast with arctic and subarctic studies that attribute large variations in plant N-15 values to nitrogen partitioning in nitrogen-limited environments. Here, plant N-15 reflects the N-15 Of the likely nitrogen sources utilised by plants.