Density dependence,spatial scale and patterning in sessile biota

Sessile biota can compete with or facilitate each other, and the interaction of facilitation and competition at different spatial scales is key to developing spatial patchiness and patterning. We examined density and scale dependence in a patterned, soft sediment mussel bed. We followed mussel growth and density at two spatial scales separated by four orders of magnitude. In summer, competition was important at both scales. In winter, there was net facilitation at the small scale with no evidence of density dependence at the large scale. The mechanism for facilitation is probably density dependent protection from wave dislodgement. Intraspecific interactions in soft sediment mussel beds thus vary both temporally and spatially. Our data support the idea that pattern formation in ecological systems arises from competition at large scales and facilitation at smaller scales, so far only shown in vegetation systems. The data, and a simple, heuristic model, also suggest that facilitative interactions in sessile biota are mediated by physical stress, and that interactions change in strength and sign along a spatial or temporal gradient of physical stress.     

The oral secretion of infectious scrapie prions occurs in preclinical sheep with a range of PRNP genotypes

Preclinical sheep with the highly scrapie-susceptible VRQ/VRQ PRNP genotype secrete prions from the oral cavity. In order to further understand the significance of orally available prions, buccal swabs were taken from sheep with a range of PRNP genotypes and analyzed by serial protein misfolding cyclic amplification (sPMCA). Prions were detected in buccal swabs from scrapie-exposed sheep of genotypes linked to high (VRQ/VRQ and ARQ/VRQ) and low (ARR/VRQ and AHQ/VRQ) lymphoreticular system involvement in scrapie pathogenesis. For both groups, the level of prion detection was significantly higher than that for scrapie-resistant ARR/ARR sheep which were kept in the same farm environment and acted as sentinel controls for prions derived from the environment which might contaminate the oral cavity. In addition, sheep with no exposure to the scrapie agent did not contain any measurable prions within the oral cavity. Furthermore, prions were detected in sheep over a wide age range representing various stages of preclinical disease. These data demonstrate that orally available scrapie prions may be a common feature in sheep incubating scrapie, regardless of the PRNP genotype and any associated high-level accumulation of PrP(Sc) within lymphoreticular tissues. PrP(Sc) was present in buccal swabs from a large proportion of sheep with PRNP genotypes associated with relatively low disease penetrance, indicating that subclinical scrapie infection is likely to be a common occurrence. The significance of positive sPMCA reactions was confirmed by the transmission of infectivity in buccal swab extracts to Tg338 mice, illustrating the likely importance of orally available prions in the horizontal transmission of scrapie.     

Microplastics as an emerging threat to terrestrial ecosystems

Microplastics (plastics <5 mm, including nanoplastics which are <0.1 μm) originate from the fragmentation of large plastic litter or from direct environmental emission. Their potential impacts in terrestrial ecosystems remain largely unexplored despite numerous reported effects on marine organisms. Most plastics arriving in the oceans were produced, used, and often disposed on land. Hence, it is within terrestrial systems that microplastics might first interact with biota eliciting ecologically relevant impacts. This article introduces the pervasive microplastic contamination as a potential agent of global change in terrestrial systems, highlights the physical and chemical nature of the respective observed effects, and discusses the broad toxicity of nanoplastics derived from plastic breakdown. Making relevant links to the fate of microplastics in aquatic continental systems, we here present new insights into the mechanisms of impacts on terrestrial geochemistry, the biophysical environment, and ecotoxicology. Broad changes in continental environments are possible even in particle‐rich habitats such as soils. Furthermore, there is a growing body of evidence indicating that microplastics interact with terrestrial organisms that mediate essential ecosystem services and functions, such as soil dwelling invertebrates, terrestrial fungi, and plant‐pollinators. Therefore, research is needed to clarify the terrestrial fate and effects of microplastics. We suggest that due to the widespread presence, environmental persistence, and various interactions with continental biota, microplastic pollution might represent an emerging global change threat to terrestrial ecosystems.     

The interaction of soil biota and soil structure under global change

The structural framework of soil mediates all soil processes, at all relevant scales. The spatio-temporal heterogeneity prevalent in most soils underpins the majority of biological diversity in soil, providing refuge sites for prey against predator, flow paths for biota to move, or be moved, and localized pools of substrate for biota to multiply. Just as importantly, soil biota play a crucial role in mediating soil structure: bacteria and fungi aggregate and stabilize structure at small scales (μm–cm) and earthworms and termites stabilize and create larger-scale structures (mm–m). The stability of this two-way interaction of structure and biota relations is crucial to the sustainability of the ecosystem. Soil is constantly reacting to changes in microclimates, and many of the soil–plant–microbe processes rely on the functioning of subtle chemical and physical gradients. The effect of global change on soil structure–biota interactions may be significant, through alterations in precipitation, temperature events, or land-use. Nonetheless, because of the complexity and the ubiquitous heterogeneity of these interactions, it is difficult to extrapolate from general qualitative predictions of the effects of perturbations to specific reactions. This paper reviews some of the main soil structure–biota interactions, particularly focusing on soil stability, and the role of biota mediating soil structures. The effect of alterations in climate and land-use on these interactions is investigated. Several case studies of the effect of land-use change are presented.     

Antarctic Sea Ice Biota

The sea ice surrounding Antarctica provides an extensive habitatfor organisms ranging in size from bacteria to marine birdsand mammals. Historically, most of the ecological work on theice biota has focused in the nearshore land-fast ice. Only inthe last decade have there been comparable studies in the deep-waterpack ice regions. These studies have indicated that there arefundamental differences in structural and physical characteristicsof fast and pack ice thatare a result of differing physicalregimes in nearshore and oceanic regions. Other physical processesact to create heterogeneity within the ice habitat that canrange from geographic and regional scales of patchiness to apronounced vertical gradient within ice floes. The conspicuouspatternsin the distribution of the ice biota can be explained largelyby these physical processes. Over 200 species have been reported living on, in, or in associationwith Antarctic sea ice.The ice biota includes bacteria, a varietyof algae, heterotrophic protozoans and small metazoans. Thediatom assemblages are the only taxonomic group that is knownwell enough to make comparisons among the various habitats.Studies by a number of workers suggest some specific diatomassemblages along with occurrence of species that are widelydistributedin both ice and plankton. Ice may also serve as a temporaryhabitat for species that also comprise planktonic communities,so that providing a "seed population" for ice edge planktonblooms may be an important role of the ice biota. Trophic interactionsamong organisms in ice suggest that the ice assemblage is atrue community with a welldeveloped microbial food web. Theice microbial community may be an important part of the Antarcticmarine food web because large consumers from the adjacent planktonicand benthic communities appear to feed on the ice biota.     

Recently discovered landlocked basins in Indonesia reveal high habitat diversity in anchialine systems

In this article, the variability of physical settings of anchialine systems in Indonesia is discussed together with the consequences these settings have for the environment and biota within the systems. Exploration in two karstic areas (Berau, East Kalimantan and Raja Ampat, West Papua) has resulted in the discovery of 20 previously unknown anchialine systems in Indonesia. Based on parameters such as bathymetry, size, coastline, salinity, water temperature, pH, degree of connection to the sea, and the presence-absence of selected key taxa we distinguish three types of (non-cave) anchialine systems in the Indo-Pacific: (1) Marine lakes with large and deep basins containing brackish to almost fully marine waters. Marine lakes show a range in the degree of connection to the sea with the result that the higher the connection the more the lake resembles a lagoon in both water chemistry and biota, while the more isolated lakes have brackish water and contain unique species that are rarely found in the adjacent sea. (2) Anchialine pools with small and shallow basins containing brackish water and low diversity of macrofauna. (3) Blue pools in chasms that contain water with a clear halocline and are possibly connected to anchialine caves. Study of the many unique features of anchialine systems will enhance our understanding of the physical and ecological processes responsible for diversification in tropical shallow marine environments.     

Life forms of organisms as patterns of organization and spatial ecological factors

Tectological and archaetectonical approaches which are conventionally used in morphology are discussed. The similarity of these approaches to some views on the structure and organization of nature systems was shown. These wiews were originated within the framework of the modern system-cybernetic conception. The morphology particularities of natural object of any rank (from organism to biosphere) allow determination of environment influence character. In some cases intensity of the influence can be determined. This, morphological-geometrical approach of nature investigation acquires high prognostic value. The aspects of "pattern organization" concept and its perspectives are discussed. The patterns of organization of organisms could be characterized only in the context of their interactions with environment. Therefore it is necessary to distinguish new group of ecological factors: spatial or chorological one. It was suggested that spatial ecological factors is predominant if all other physical factors have no extreme values.     

Polarizable force fields

Standard force fields used in biomolecular computing describe electrostatic interactions in terms of fixed, usually atom-centered, charges. Real physical systems, however, polarize substantially when placed in a high-dielectric medium such as water--or even when a strongly charged system approaches a neutral body in the gas phase. Such polarization strongly affects the geometry and energetics of molecular recognition. First introduced more than 20 years ago, polarizable force fields seek to account for appropriate variations in charge distribution with dielectric environment. Over the past five years, an accelerated pace of development of such force fields has taken place on systems ranging from liquid water to metalloenzymes. Noteworthy progress has been made in better understanding the capabilities and limitations of polarizable models for water and in the formulation and utilization of complete specifically parameterized polarizable force fields for peptides and proteins.     

Linking soil biodiversity and vegetation: implications for a changing planet

Soil biota are intimately tied to plant communities through herbivory and symbiosis and indirectly by the decomposition of dead organic plant material. Through both roots and aboveground organic material (e.g., leaves and wood), plants provide substantial inputs of organic matter to soil systems. Plants are the basis for most biotic soil food webs that comprise an enormous diversity of species whose multiple interactions function to help regulate nutrient cycling, which in turn influences plant growth. Many factors govern the biogeography of soil biota, including the physical and chemical properties of soil, climate, the composition and type of vegetation, and interactions with other soil biota. Despite awareness of factors influencing soil communities, no single factor allows predictions of soil animal diversity or distribution. However, research is showing that plants can have unique soil biotic communities. Degradation of soil, which removes predators and biotic regulation that occurs in less managed ecosystems, can result in increased pathogens and pests that affect humans, other animals and plants. Global changes such as land use, desertification, and soil pollution all have been shown to alter soil animal diversity and abundance. Because of our dependence on soils and plant production, studies linking soil biotic communities to primary productivity are needed to assure long-term soil sustainability.     

What is river health?

1. Traditionally the assessment of river water quality has been based solely on the measurement of physical, chemical and some biological characteristics. While these measurements may be efficient for regulating effluent discharges and protecting humans, they are not very useful for large-scale management of catchments or for assessing whether river ecosystems are being protected. 2. Measurements of aquatic biota, to identify structural or functional integrity of ecosystems, have recently gained acceptance for river assessment. Empirical evidence from studies of river ecosystems under stress suggests that a small group of biological ecosystem-level indicators can assess river condition. However, physical and chemical features of the environment affect these indicators, the structure and function of which may be changed by human activities. 3. The term ‘river health’, applied to the assessment of river condition, is often seen as being analogous with human health, giving many a sense of understanding. Unfortunately, the meaning of ‘river health’ remains obscure. It is not clear what aspects of river health sets of ecosystem-level indicators actually identify, nor how physical, chemical and biological characteristics may be integrated into measures rather than just observations of cause and effect. 4. Increased examination of relationships between environmental variables that affect aquatic biota, such as habitat structure, flow regime, energy sources, water quality and biotic interactions and biological condition, are required in the study of river health.     

Controls on Soil Carbon Sequestration and Dynamics: Lessons from Land-use Change

Soil carbon (C) dynamics and sequestration are controlled by interactions of chemical, physical and biological factors. These factors include biomass quantity and quality, physical environment and the biota. Management can alter these factors in ways that alter C dynamics. We have focused on a range of managed sites with documented land use change from agriculture or grassland to forest. Our results suggest that interactions of soil type, plant and environment impact soil C sequestration. Above and below ground C storage varied widely across sites. Results were related to plant type and calcium on sandy soils in our Northern sites. Predictors of sequestration were more difficult to detect over the temperature range of 12.4°C in the present study. Accrual of litter under pines in the moist Mississippi site limited C storage in a similar manner to our dry Nebraska site. Pre-planting heterogeneity of agricultural fields such as found in Illinois influences C contents. Manipulation of controls on C sequestration such as species planted or amelioration of soil quality before planting within managed sites could increase soil C to provide gains in terrestrial C storage. Cost effective management would also improve soil C pools positively affecting soil fertility and site productivity.     

Estimating the Toxicity of Pesticide Mixtures to Aquatic Organisms: A Review

A major difficulty in addressing chemical mixtures through legislation or regulations revolves around our limited understanding of their potential impacts. This review provides an overview of recent research on pesticide mixture toxicity to aquatic biota and the methods employed to predict toxic effects. The most common approaches are to assume concentration-addition or independent action of chemicals in a mixture. There are a number of cases in the literature of interactions between pesticides. However, models accounting for possible interactions between mixture components are used infrequently. Although results are limited, studies investigating the effects of pesticide mixtures have not demonstrated significant synergism at environmentally relevant concentrations. Based on the results of our review, we conclude that the concentration-addition model is a generally conservative and practical first-tier model for the ecological assessment of pesticide mixtures in aquatic systems.     

Ecological impacts of feral pigs in the Hawaiian Islands

The foraging habits of exotic ungulate species can directly and indirectly affect native plant and animal distribution and abundance patterns. Most of the studies on feral pig interactions with other biota in the Hawaiian Islands have been published as difficult to access reports to governmental and nongovernmental organizations, graduate student theses, and a few in peer reviewed journals. In this paper we discuss the origins of pig introductions to Hawaii, their feralization process, population expansion, and interactions with native and non-native biota. We also consider the environmental effects triggered by pigs on local ecosystems and biotic communities. Feral pig activities can reduce the abundance of native plant species, enhance conditions for the establishment of invasive non-indigenous plants, and perhaps indirectly negatively impact native forest bird species. Pig foraging and traveling patterns may also lead to physical alteration of ecosystems by increasing soil erosion that may lead to watershed degradation. However, much remains to be learned about the strength and significance of aforementioned interactions and their long-term effects on Hawaiian biota and ecosystems due to some confounding events. Elucidating the dynamics and long-term ecological effects generated by pigs is a crucial step towards increasing our understanding of and more effectively managing biotic interactions.     

Nanopore analysis reveals differences in structural stability of ovine PrPC proteins corresponding to scrapie susceptible (VRQ) and resistance (ARR) genotypes

Species, as well as individuals within species, have unique susceptibilities to prion infection that are likely based on sequence differences in cellular prion protein (PrP^C). Species barriers to transmission also reflect PrP^C sequence differences. Defining the structure-activity relationship of PrP^C/PrP^Sc with respect to infectivity/susceptibility will benefit disease understanding and assessment of transmission risks. Here, nanopore analysis is employed to investigate genotypes of sheep PrP^C corresponding to differential susceptibilities to scrapie infection. Under non-denaturing conditions scrapie resistant (ARR) and susceptible (VRQ) genotypes display similar, type I (bumping) predominant event profiles, suggesting a conserved folding pattern. Under increasingly denaturing conditions both proteins shift to type II (intercalation/translocation) events but with different sensitivities to unfolding. Specifically, when pre-incubated in 2M Gdn-HCl, the VRQ variant had more of type II events as compared with the ARR protein, suggesting a more flexible unfolding pattern. Addition of PrP^Sc-specific polyclonal antibody (YML) to the ARR variant, pre-incubated in 2M Gdn-HCl, reduced the number of type II events with no clear intercalation/translocation peak, whereas for VRQ, type II events above blockades of 90 pA bound YML. A second PrP^Sc-specific antibody (SN6b) to a different cryptic epitope reduced type II events for VRQ but not the ARR variant. Collectively, the event patterns associated with sequential denaturation, as well as interactions with PrP^Sc-specific antibodies, support unique patterns and/or propensities of misfolding between the genotypes. Overall, nanopore analysis identifies intermediate conformations that occur during the unfolding pathways of ARR and VRQ genotypes and may help to understand the correlation of structural properties that induce protein misfolding.     

The PrP genotype of sheep of the improved Valachian breed

In a worldwide majority of sheep breeds an excessive susceptibility to scrapie associated with the PrP gene alleles coding for valine (V; at the 136 codon) and glutamine (Q; at the 171 codon) (e.g., VRQ/VRQ, VRQ/ARQ, or ARQ/ARQ) was demonstrated. Particularly the PrPVRQ allele is closely associated with the high-risk development of the disease; the PrPARQ allele can also fulfill this function but under certain limited conditions. Polymorphism in the PrP gene sequences (conclusively related to the increased susceptibility of sheep to scrapie) of improved Valachian sheep from two Slovak regions, Orava and Spis, was determined. Examination of 735 sheep showed that ARR/ARQ was the most frequent genotype (45.2%). High-risk genotypes were determined in 32.4% of sheep (ARQ/ARQ 19.3, ARR/VRQ 9.0, ARR/VRQ 3.5, VRQ/VRQ 0.3, ARR/VRR 0.3). Low-risk genotypes were found in 67.7% of sheep (ARR/ARQ 45.2, ARR/ARR 10.9, ARR/AHQ 5.7, ARQ/ARQ 4.9, AHQ/AHQ 0.7, ARR/AHR 0.3). Despite the geographically distant flocks of improved Valachian sheep investigated no difference in the occurrence of individual PrP genotypes was observed.     

Plant: soil interactions in temperate multi-cropping production systems

Background and scope

Multi-cropping approaches in production systems, where more than one crop cultivar or species are grown simultaneously, are gaining increased attention and application. Benefits can include increased production, effective pest, disease and weed control, and improved soil health. The effects of such practices on the range of interactions within the plant-soil system are manifest via plant interspecific competition, pest and disease attenuation, soil community composition and structure, nutrient cycling, and soil structural dynamics. Interplant diversity and competition effectively increases the nature and extent of root networks, tending to lead to more efficient resource use in time and space. Increased competitive ability at a system level, and allelopathic interactions, can reduce weed, pest and disease severity. Soil biotic communities are affected by plant diversity, which can increase abundance, diversity and activity of functional groups. Attendant rhizosphere-located processes can facilitate nutrient uptake between component crops. Whilst there are few studies into multi-cropping effects on soil structure, it is hypothesised that such processes are manifest particularly via the role which the belowground biota play in soil structural dynamics. A deeper understanding of eco-physiological processes affecting weed, pest and disease dynamics in the context of multiple cropping scenarios, and breeding cultivars to optimise mutualistic and allelopathic traits of crop mixtures could significantly increase productivity and adoption of more sustainable farming practices.

Conclusions

Wider consideration needs to be given to plant: soil interactions when crop plants are grown in the context of mixtures, i.e. as communities as opposed to monotonous populations. In particular, a better understanding is required of how root systems develop in the context of mixtures and the extent to which resultant interactions with the soil biota are context-dependent. A significant challenge is that crop cultivars or production systems optimised for monocultural circumstances should not be assumed to be most suited for multi-cropping scenarios, and hence alternative strategies for developing new production systems need to take this into account.     

Biotechnology, environmental forcing, and unintended trophic cascades

A long ongoing discussion between scientists and policy decision-makers seems to have entered recently into a new phase. The consequences of release of transgenic crops into the environment are being discussed not only by scientists but also by farmers, environmental groups and politicians, while an increasing amount of data is becoming available at all biological scales, including the field level. However, data still rely on experiments designed to capture direct consumer–resource interactions. Here we argue that we should attempt to concentrate on the ecosystem functioning of soil biota under genetically-modified (GM) plants, because functional and mechanistic analysis of the multitrophic effects of GM plants on soil biota is still lacking. It is our opinion that we should avoid addressing taxa and soil communities separately, but link them at their functional level. We shall explain why, using examples from ecosystem services, allometric scaling, and soil food webs. The energy flow of any food web under stress incorporates several factors and pooled information on ecosystem services and on the different responses of soil invertebrates to induced perturbations in other trophic levels. Therefore, we will systematically focus on the complementarities of these approaches. Handling editor: Sam Cook     

Lack of Prion Accumulation in Lymphoid Tissues of PRNP ARQ/ARR Sheep Intracranially Inoculated with the Agent of Scrapie

Sheep scrapie is a transmissible spongiform encephalopathy that can be transmitted horizontally. The prion protein gene (PRNP) profoundly influences the susceptibility of sheep to the scrapie agent and the tissue levels and distribution of PrP^Sc in affected sheep. The purpose of this study was to compare the survival time and PrP^Sc tissue distribution in sheep with highly resistant and highly susceptible PRNP genotypes after intracranial inoculation of the agent of scrapie. Five sheep each of genotype VRQ/VRQ, VRQ/ARR or ARQ/ARR were inoculated. Sheep were euthanized when clinical signs of scrapie became severe. Clinical signs, microscopic lesions, and western blot profiles were uniform across genotypes and consistent with manifestations of classical scrapie. Mean survival time differences were associated with the 171 polymorphic site with VRQ/VRQ sheep surviving 18 months, whereas VRQ/ARR and ARQ/ARR sheep survived 60 and 56 months, respectively. Labeling of PrP^Sc by immunohistochemistry revealed similar accumulations in central nervous system tissues regardless of host genotype. Immunoreactivity for PrP^Sc in lymphoid tissue was consistently abundant in VRQ/VRQ, present but confined to tonsil or retropharyngeal lymph node in 4/5 VRQ/ARR, and totally absent in ARQ/ARR sheep. The results of this study demonstrate the susceptibility of sheep with the ARQ/ARR genotype to scrapie by the intracranial inoculation route with PrP^Sc accumulation in CNS tissues, but prolonged incubation times and lack of PrP^Sc in lymphoid tissue.     

Disturbance influences the outcome of plant–soil biota interactions in the invasive Acacia longifolia and in native species

Interrelated causes of plant invasion have been gaining increasing recognition. However, research on this subject has mainly focused around conceptual models. Here we explore whether plant–soil biota feedbacks and disturbance, two major factors capable of facilitating invasive plants in introduced ranges, interact to preferentially benefit exotics compared to native plants. We investigated the influence of fire disturbance on plant–soil biota interactions for the invasive Acacia longifolia and two dominant natives (Cytisus striatus and Pinus pinaster) in Portuguese dune systems. In the first experiment, we grew exotic and native plants in soil inoculated with soil biota from unburned or recently burned soils collected in an area with small invasion intensity by A. longifolia. Soil biota effects on the exotic legume A. longifolia changed from neutral to positive after fire, whereas the opposite outcome was observed in the native legume C. striatus, and a change from negative to neutral effects after fire occurred in the native P. pinaster. Fire reduced mycorrhizal colonization in all species and rhizobial colonization in C. striatus but not in A. longifolia. In the second experiment, we grew the exotic and native plants with conspecific and heterospecific soil biota from undisturbed soils (area with low invasion intensity by A. longifolia), and from post‐fire soils (area affected by a fire ～12 years ago and currently heavily invaded by A. longifolia). The exotic benefited more from post‐fire than from undisturbed soil biota, particularly from those associated with natives. Natives did not experience detrimental effects with invasive‐associated soil biota. Our results show that fire disturbance affected the functional interactions between soil biota and plants that may benefit more the exotic than some native species. Disturbance may open a window of opportunity that promotes invader success by altering soil enemy and mutualistic impacts.