Competition and habitat filtering jointly explain phylogenetic structure of soil bacterial communities across elevational gradients

The importance of assembly processes in shaping biological communities is poorly understood, especially for microbes. Here, we report on the forces that structure soil bacterial communities along a 2000 m elevational gradient. We characterized the relative importance of habitat filtering and competition on phylogenetic structure and turnover in bacterial communities. Bacterial communities exhibited a phylogenetically clustered pattern and were more clustered with increasing elevation. Biotic factors (i.e., relative abundance of dominant bacterial lineages) appeared to be most important to the degree of clustering, evidencing the role of the competitive ability of entire clades in shaping the communities. Phylogenetic turnover showed the greatest correlation to elevation. After controlling the elevation, biotic factors showed greater correlation to phylogenetic turnover than all the habitat variables (i.e., climate, soil and vegetation). Structural equation modelling also identified that elevation and soil organic matter exerted indirect effects on phylogenetic diversity and turnover by determining the dominance of microbial competitors. Our results suggest that competition among bacterial taxa induced by soil carbon contributes to the phylogenetic pattern across elevational gradient in the Tibetan Plateau. This highlights the importance of considering not only abiotic filtering but also biotic interactions in soil bacterial communities across stressful elevational gradients.     

Direct and indirect effects of predatory young‐of‐year fishes in a dryland river food web

相似文献   

Conceptual Evaluation of Factors Potentially Affecting Restoration of Habitat Structure within the Channelized Kissimmee River Ecosystem

A critical element of the ongoing effort to restore the ecological integrity of Florida's Kissimmee River ecosystem is the reestablishment of pre-channelization habitat structure and function. Restoration of habitat will form the basis for responses by most biological components of the ecosystem and will provide a key indicator of the success of the restoration effort. This paper evaluates the relative importance of a range of abiotic and biotic habitat parameters in the existing and historic Kissimmee River ecosystem and provides a conceptual framework for predicting expected spatial and temporal responses of river and floodplain habitats to the restoration project. Among the ecological factors and process that influenced the development, dynamics, and maintenance of river and floodplain habitat structure, hydrology is expected to be of central importance in eliciting restoration responses in the Kissimmee River Ecosystem. Based on the assumption that the restoration plan will reestablish historic hydrologic characteristics, predictions are made of expected responses by geomorphic and vegetative components of the Kissimmee River's habitat structure. Recommendations are made regarding key habitat parameters requiring long term tracking and analysis and utilization of a geographic information system(GIS). A hierarchical habitat classification scheme is provided as a foundation for all components of the restoration evaluation program.     

Abiotic stress tolerance and competition‐related traits underlie phylogenetic clustering in soil bacterial communities

Soil bacteria typically coexist with close relatives generating widespread phylogenetic clustering. This has been ascribed to the abiotic filtering of organisms with shared ecological tolerances. Recent theoretical developments suggest that competition can also explain the phylogenetic similarity of coexisting organisms by excluding large low‐competitive clades. We propose that combining the environmental patterns of traits associated with abiotic stress tolerances or competitive abilities with phylogeny and abundance data, can help discern between abiotic and biotic mechanisms underlying the coexistence of phylogenetically related bacteria. We applied this framework in a model system composed of interspersed habitats of highly contrasted productivity and comparatively dominated by biotic and abiotic processes, i.e. the plant patch‐gap mosaic typical of drylands. We examined the distribution of 15 traits and 3290 bacterial taxa in 28 plots. Communities showed a marked functional response to the environment. Conserved traits related to environmental stress tolerance (e.g. desiccation, formation of resistant structures) were differentially selected in either habitat, while competition related traits (e.g. organic C consumption, formation of nutrient‐scavenging structures) prevailed under high resource availability. Phylogenetic clustering was stronger in habitats dominated by biotic filtering, suggesting that competitive exclusion of large clades might underlie the ecological similarity of co‐occurring soil bacteria.     

The role of patch area and habitat diversity in explaining native plant species richness in disturbed suburban forest patches in northern Belgium

Relatively easy measurable patch characteristics (especially habitat diversity measures) have proven to be valuable indicators of forest plant species richness in forest fragments of relatively undisturbed areas. Urban and suburban forest patches, however, are characterized by a specific landscape ecological context implying that specific processes may influence ecosystem functioning and hence that other abiotic indicators for plant diversity are more appropriate. We studied the relation between functional ecological plant species groups and suburban forest patch characteristics such as patch area, habitat diversity and isolation. Some components of species richness were related to the isolation of the patches. In contrast to previous similar large-scale fragmentation studies in more rural areas, further results stressed the overwhelming importance of patch area relative to habitat variables in determining species richness. This suggests (1) the occurrence of density-dependent species extinction processes in small forest patches; or (2) the existence of external deterministic factors which put a major constraint on species richness in small patches. We tend to support the latter hypothesis and propose forest disturbance and associated black cherry (Prunus serotina Ehrh.) invasion as such a possible external factor. Small forest patches may be more sensitive to disturbance and biological invasion due to various reasons. Hence large forest patches are to be preferred for plant conservation in the suburban area.     

Versatile habitat conditioning by damselfish cultivating turf algae on giant clams

In this paper, a monitoring and modelling concept for ecological optimized harbour dredging and fine sediment disposal in large rivers is presented. According to the concept, first a preliminary assessment should be performed previous to the dredging and dumping procedure to derive knowledge about the current status in hydrodynamics, morphology and instream habitat quality. During the performance of the maintenance work, a high-resolution monitoring program has to be organized to measure flow velocities, the suspended sediment concentrations and the extent of the occurring plume. These data can then be compared with natural suspended sediment conditions and serve as input data for numerical sediment transport modelling. Furthermore, bathymetric surveys and biotic sampling enable the detection of possible effects of dredging and disposal in the post-dumping stage. Based on sediment transport modelling approaches, short- to mid-term developments of the sediment plume can be predicted with an additional and final habitat evaluation at the end of the project. This concept was applied and optimized during the maintenance work at the case study winter harbour Linz at the Danube River. The findings of the presented study highlight the necessity of integrated monitoring and modelling approaches for harbour dredging especially in large river systems.     

Overview and quantification of the factors affecting the upstream and downstream movements of Gammarus pulex (Amphipoda)

Human activities have severely deteriorated the Flemish river systems, and many functions such as drinking water supply, fishing, ... are threatened. Because their restoration entails drastic social (e.g. change in habits with regard to water use and discharge, urban planning) and economical (e.g. investment in nature restoration, wastewater treatment system installation) consequences, the decisions should be taken with enough forethought. Ecosystem models can act as interesting tools to support decision-making in river restoration management. In particular models that can predict the habitat requirements of organisms are of considerable importance to ensure that the planned actions have the desired effects on the aquatic ecosystems. In preliminary studies, Artificial Neural Network (ANN) models were tested and optimized to obtain the best model configuration for the prediction of the habitat suitability for Gammarus pulex based on the abiotic characteristics of their aquatic environment in the Zwalm river basin (Flanders, Belgium). Although, these ANN models are in general quite robust with a rather high predictive reliability, the model performance has to be increased with regard to simulations for river restoration management. In particular, spatial-temporal expert-rules have to be included. Migration kinetics (downstream drift and upstream migration) of the organism and migration barriers along the river (weirs, impounded river sections, ...) can deliver important additional information on the effectiveness of the restoration plans, and also on the timing of the expected effects. This paper presents an overview and quantification of the factors affecting the upstream and downstream movements of Gammarus pulex. During further research, ANN models will be used to predict the habitat suitability for Gammarus pulex after several restoration options. The migration models, implemented in a Geographical Information System (GIS), are applied to calculate the migration time to the restored parts of the river. In this way, decision makers have an idea whether and when a selected restoration option has the desired effect.     

The role of biotic interactions in shaping distributions and realised assemblages of species: implications for species distribution modelling

Predicting which species will occur together in the future, and where, remains one of the greatest challenges in ecology, and requires a sound understanding of how the abiotic and biotic environments interact with dispersal processes and history across scales. Biotic interactions and their dynamics influence species' relationships to climate, and this also has important implications for predicting future distributions of species. It is already well accepted that biotic interactions shape species' spatial distributions at local spatial extents, but the role of these interactions beyond local extents (e.g. 10 km² to global extents) are usually dismissed as unimportant. In this review we consolidate evidence for how biotic interactions shape species distributions beyond local extents and review methods for integrating biotic interactions into species distribution modelling tools. Drawing upon evidence from contemporary and palaeoecological studies of individual species ranges, functional groups, and species richness patterns, we show that biotic interactions have clearly left their mark on species distributions and realised assemblages of species across all spatial extents. We demonstrate this with examples from within and across trophic groups. A range of species distribution modelling tools is available to quantify species environmental relationships and predict species occurrence, such as: (i) integrating pairwise dependencies, (ii) using integrative predictors, and (iii) hybridising species distribution models (SDMs) with dynamic models. These methods have typically only been applied to interacting pairs of species at a single time, require a priori ecological knowledge about which species interact, and due to data paucity must assume that biotic interactions are constant in space and time. To better inform the future development of these models across spatial scales, we call for accelerated collection of spatially and temporally explicit species data. Ideally, these data should be sampled to reflect variation in the underlying environment across large spatial extents, and at fine spatial resolution. Simplified ecosystems where there are relatively few interacting species and sometimes a wealth of existing ecosystem monitoring data (e.g. arctic, alpine or island habitats) offer settings where the development of modelling tools that account for biotic interactions may be less difficult than elsewhere.     

Characterization of hydraulic habitat and retention across different channel types; introducing a new field-based technique

Understanding the interactions between physical habitat and aquatic biodiversity has become a key research objective in river management. River research and management practitioners are increasingly seeking new methodologies and techniques for characterizing physical habitat heterogeneity. The physical biotope has been widely employed as the standard mesoscale unit in river surveys. However, few surveys have quantified the combined physical heterogeneity at the meso- and microscale scale via a single technique. This paper describes a new field methodology for assessing variations in hydraulic habitat and retention across different channel types (e.g. step-pool, bedrock, plane-bed and pool-riffle). Hydraulic habitat and retention was measured by timing 100 flow tracers across a 100-m stream length, and recording the types of trapping structures. The pattern of flow tracers and retention varied significantly between channel types and structures. Rocks (boulders and cobbles) were more important retentive structures than eddies and snags (woody material and vegetation). The results indicate the importance of a diverse hydraulic environment, woody material and channel substrate character in increasing physical heterogeneity within a stream reach. The findings suggest that the field methodology may be an effective tool to assess differences in physical heterogeneity pre and post river restoration activities.     

Effects of hydromorphological integrity on biodiversity and functioning of river ecosystems

River channels tend to a dynamic equilibrium driven by the dynamics of water and sediment discharge. The resulting fluctuating pattern of channel form is affected by the slope, the substrate erodibility, and the vegetation in the river corridor and in the catchment. Geomorphology is basic to river biodiversity and ecosystem functioning since the channel pattern provides habitat for the biota and physical framework for ecosystem processes. Human activities increasingly change the natural drivers of channel morphology on a global scale (e.g. urbanization increases hydrological extremes, and clearing of forests for agriculture increases sediment yield). In addition, human actions common along world rivers impact channel dynamics directly, e.g. river regulation simplifies and fossilizes channel form. River conservation and restoration must incorporate mechanisms of channel formation and ecological consequences of channel form and dynamics. This article (1) summarizes the role of channel form on biodiversity and functioning of river ecosystems, (2) describes spatial complexity, connectivity and dynamism as three key hydromorphological attributes, (3) identifies prevalent human activities that impact these key components and (4) analyzes gaps in current knowledge and identifies future research topics.     

A review of cephalopod–environment interactions in European Seas

Cephalopods are highly sensitive to environmental conditions and changes at a range of spatial and temporal scales. Relationships documented between cephalopod stock dynamics and environmental conditions are of two main types: those concerning the geographic distribution of abundance, for which the mechanism is often unknown, and those relating to biological processes such as egg survival, growth, recruitment and migration, where mechanisms are sometimes known and in a very few cases demonstrated by experimental evidence. Cephalopods seem to respond to environmental variation both ‘actively’ (e.g. migrating to areas with more favoured environmental conditions for feeding or spawning) and ‘passively’ (growth and survival vary according to conditions experienced, passive migration with prevailing currents). Environmental effects on early life stages can affect life history characteristics (growth and maturation rates) as well as distribution and abundance. Both large-scale atmospheric and oceanic processes and local environmental variation appear to play important roles in species–environment interactions. While oceanographic conditions are of particular significance for mobile pelagic species such as the ommastrephid squids, the less widely ranging demersal and benthic species may be more dependent on other physical habitat characteristics (e.g. substrate and bathymetry). Coastal species may be impacted by variations in water quality and salinity (related to rainfall and river flow). Gaps in current knowledge and future research priorities are discussed. Key research goals include linking distribution and abundance to environmental effects on biological processes, and using such knowledge to provide environmental indicators and to underpin fishery management.     

Shortnose sturgeon (Acipenser brevirostrum) of the Saco River Estuary: Assessment of a unique habitat

The shortnose sturgeon (Acipenser brevirostrum; SNS) is an endangered fish that thrives in large river systems along the U.S. east coast. Despite the endangered status, our understanding of this species’ ecology is limited, especially regarding the importance of smaller river systems to their recovery. In 2010, the first sighting of SNS occurred in the Saco River estuary (SRE), Maine, a proportionately smaller system to other known drainages. To investigate the habitat usage of SNS within the SRE, an on‐going acoustic tagging study was initiated in 2011. In 2016, the collection of SRE abiotic data was coupled with the acoustic tagging study in an effort to establish which environmental parameters were most influential to SNS habitat preferences using Poisson regression. Aggregations of SNS in the SRE were concentrated rkm 6–8 and regression analyses revealed that water temperature, conductivity, acidity, and dissolved oxygen content were influential to these aggregations. Furthermore, SNS prey appears to be present and abundant throughout the estuary, and thus we hypothesize that SNS use the SRE as a foraging ground, but aggregate upriver due to the physiologically preferable and energetically optimal abiotic conditions.     

Techniques for evaluating the spatial behaviour of river fish

Radio-tagging is widely used for studies of movements, resource use and demography of land vertebrates, with potential to combine such data for predictive modelling of populations from individuals. Such modelling requires standard measures of individual space use, for combination with data on resources, survival, dispersal and breeding. This paper describes how protocols for efficient collection of space-use data can be developed during a pilot study, and reviews the ways in which such data can be used for space-use indices that help answer biological questions, with examples from a study of riverine pike (Esox lucius). Analyses of diurnal activity and spatio-temporal correlation were used to assess when to record locations, and analyses of home range increments were used to define the number of location records necessary to assess seasonal ranges. We stress the importance of developing protocols that use minimal numbers of locations from each individual, so that analyses can be based on samples of many individuals. The efficacy of link-distance (e.g. cluster analysis) and location density (e.g. contouring) techniques for spatial analysis for river fish were compared, and the utility of clipping off areas to river banks was assessed. In addition, a new automated analysis was used to estimate distances along river mid-lines. These techniques made it possible to quantify interactions between individuals and their habitat: including a significant increase in core range size during floods, significant preference for deep pools, and a lack of exclusive territories.     

Tree-based ensembles unveil the microhabitat suitability for the invasive bleak (Alburnus alburnus L.) and pumpkinseed (Lepomis gibbosus L.): Introducing XGBoost to eco-informatics

Random Forests (RFs) and Gradient Boosting Machines (GBMs) are popular approaches for habitat suitability modelling in environmental flow assessment. However, both present some limitations theoretically solved by alternative tree-based ensemble techniques (e.g. conditional RFs or oblique RFs). Among them, eXtreme Gradient Boosting machines (XGBoost) has proven to be another promising technique that mixes subroutines developed for RFs and GBMs. To inspect the capabilities of these alternative techniques, RFs and GBMs were compared with: conditional RFs, oblique RFs and XGBoost by modelling, at the micro-scale, the habitat suitability for the invasive bleak (Alburnus alburnus L.) and pumpkinseed (Lepomis gibbosus L.). XGBoost outperformed the other approaches, particularly conditional and oblique RFs, although there were no statistical differences with standard RFs and GBMs. The partial dependence plots highlighted the lacustrine origins of pumpkinseed and the preference for lentic habitats of bleak. However, the latter depicted a larger tolerance for rapid microhabitats found in run-type river segments, which is likely to hinder the management of flow regimes to control its invasion. The difference in the computational burden and, especially, the characteristics of datasets on microhabitat use (low data prevalence and high overlapping between categories) led us to conclude that, in the short term, XGBoost is not destined to replace properly optimised RFs and GBMs in the process of habitat suitability modelling at the micro-scale.     

A framework for modelling soil structure dynamics induced by biological activity

Soil degradation is a worsening global phenomenon driven by socio‐economic pressures, poor land management practices and climate change. A deterioration of soil structure at timescales ranging from seconds to centuries is implicated in most forms of soil degradation including the depletion of nutrients and organic matter, erosion and compaction. New soil–crop models that could account for soil structure dynamics at decadal to centennial timescales would provide insights into the relative importance of the various underlying physical (e.g. tillage, traffic compaction, swell/shrink and freeze/thaw) and biological (e.g. plant root growth, soil microbial and faunal activity) mechanisms, their impacts on soil hydrological processes and plant growth, as well as the relevant timescales of soil degradation and recovery. However, the development of such a model remains a challenge due to the enormous complexity of the interactions in the soil–plant system. In this paper, we focus on the impacts of biological processes on soil structure dynamics, especially the growth of plant roots and the activity of soil fauna and microorganisms. We first define what we mean by soil structure and then review current understanding of how these biological agents impact soil structure. We then develop a new framework for modelling soil structure dynamics, which is designed to be compatible with soil–crop models that operate at the soil profile scale and for long temporal scales (i.e. decades, centuries). We illustrate the modelling concept with a case study on the role of root growth and earthworm bioturbation in restoring the structure of a severely compacted soil.     

Edge effects and tropical forest canopy invertebrates

The term edge effect can be used to encompass a wide range of both biotic and abiotic trends associated with boundaries between adjacent habitat types, whether these be natural or anthropogenic. Edge effects have been shown to represent significant forces affecting both faunal and floral assemblages in fragmented ecosystems. Specific studies of faunal assemblages associated with habitat edges have revealed trends at all levels of biological organisation from individuals to communities.Studies of edge effects on invertebrates in tropical forests have been relatively scarce. In this paper we review the nature and organisation of edge effects, focusing upon the processes which may lead to detrimental consequences for both forest canopy invertebrates and the forests themselves. We present as a case study data illustrating the very large amount of variance (over 50%) in community structure that is predicted simply by abiotic (microclimatic) variables in both a tropical and a temperate forest edge. We summarise major features of edge effects amongst forest invertebrates, stress the inter-relatedness of edge and canopy biology, and present an agenda for study of the canopy as an edge.     

Harmonising the bioassessment of large rivers in the absence of near‐natural reference conditions – a case study of the Danube River

1. International river catchments pose challenges for effective water resource management. Catchment‐wide strategies are often complicated by differences in national bioassessment and quality classification. Intercalibration efforts aim to harmonise these differences, but rely on the consistent delineation of near‐natural reference sites that are almost unavailable in today’s landscape, especially for large rivers. 2. We introduce the concept of alternative benchmarking that is based on the notion of aquatic communities at similar (low) levels of impairment associated with least‐disturbed conditions (LDC) as defined by abiotic criteria. Using data acquired during the second Joint Danube Survey, we defined LDC sites based on a multivariate gradient of anthropogenic pressures, mostly related to morphological deterioration, that spans the entire navigable Danube. 3. The river was subdivided into four stretches, each featuring homogeneous biological assemblages. Indirect gradient analysis revealed relationships between the pressure gradient and selected features of the macroinvertebrate and macrophyte community but not for diatoms or phytoplankton. 4. We identified biological metrics suitable for the quality classification of individual stretches or the entire river. Impoundment is the major hydromorphological alteration on the Danube but various metrics still responded significantly to differences in the morphological condition of sites not affected by impoundment. 5. A comparison of macroinvertebrate sampling techniques (airlift versus kick‐and‐sweep) revealed differences in how the acquired data reflect the effects of anthropogenic pressure. Biological metrics based only on kick‐and‐sweep sample data were insensitive to habitat deterioration in the heavily modified Upper Danube. 6. This study exemplifies the empirical approach of alternative benchmarking in intercalibration and offers practical solutions to some of the challenges of large river bioassessment.     

Nutrient composition of soil and plants may predict the distribution and abundance of specialist insect herbivores: implications for agent selection in weed biological control

Abstract  Refining the process of selecting specialist herbivores that are used as biological control agents to maximise effects on the targets can diminish the risk to non-target species. While biotic factors (e.g. plant demography and agent–host interactions) have been explored for clues to improve the way we make agent selection decisions, recent ecological research indicates that abiotic factors related to the habitat (e.g. plant and soil nutrient composition, and soil characteristics) are important predictors of insect herbivore community composition. In this paper we explore the relevance of plant nutrient composition to aid in selecting agents for the invasive Eurasian perennial Euphorbia esula (leafy spurge) in Illinois, USA. We propose that an approach that compares such abiotic factors across the native and invaded ranges of plants in conjunction with the community composition of specialist herbivores in the native range may yield valuable clues in selecting agents that are most likely to establish and regulate populations of the target weed.