Unsupervised biological integrity assessment by eDNA biomonitoring of multi-trophic aquatic taxa

The biological integrity of global freshwater ecosystems is threatened by ever-increasing environmental stressors due to increased human activities, such as land-use change, eutrophication, toxic pollutants, overfishing, and exploitation. Traditional ecological assessments of lake or riverine ecosystems often require human supervision of a pre-selected reference area, using the current state of the reference area as the expected state. However, selecting an appropriate reference area has become increasingly difficult with the expansion of human activities. Here, an unsupervised biological integrity assessment framework based on environmental DNA metabarcoding without a prior reference area is proposed. Taxon richness, species dominance, co-occurrence network density, and phylogenetic distance were used to assess the aquatic communities in the Taihu Lake basin. Multi-gene metabarcoding revealed comprehensive biodiversity at multiple trophic levels including algae, protists, zooplankton, and fish. Fish sequences were mainly derived from 12S, zooplankton mainly from mitochondrial cytochrome C oxidase subunit I, and algae and protists mainly from 18S. There were significant differences in community composition among lakes, rivers, and reservoirs but no significant differences in the four fundamental biological indicators. The algal and zooplankton integrities were positively correlated with protist and fish integrities, respectively. Additionally, the algal integrity of lakes was found to be significantly lower than that of rivers. The unsupervised assessment framework proposed in this study allows different ecosystems, including the same ecosystem in different seasons, to adopt the same indicators and assessment methods, which is more convenient for environmental management and decision-making.

Channel abandonment alters trophic characteristics of highland rivers

The Qinghai-Tibet Plateau (QTP) serves as a collection of unique ecosystems featured as oligotrophic and hypometabolic conditions, and is particularly vulnerable to threats posed by anthropogenic and natural disturbances. Active fluvial processes on the QTP, especially the lateral migration of rivers and channel abandonment accompanied by variations in the hydrological connectivity, and changes in river geomorphology, intensively modify this highland river-floodplain system. However, little is known about how these processes alter the trophic characteristics of highland river system on earth. In this study, we conducted field investigations on a typical meandering river, the Quanji River (QR), located in the northeastern QTP by sampling macroinvertebrates, surveying trophic sources, and measuring a range of environmental conditions. Based on the collected data, we identified four biotopes for the QR through hierarchical clustering, established the representative food web for each biotope through the allometric diet breadth model, and estimated the biomass storage and flux within food web for each biotope through the biomass balance model. Our results show that the identified biotopes differed markedly in hydrological connectivity. Biotopes 1 and 2, which were in the main river channel represented the condition of high connectivity, Biotope 3 in the open channel represented the median connectivity, while Biotope 4 in the semi-open/closed channel represented the low connectivity. In contrast to the unimodal pattern commonly observed in lowland rivers, indices for the highland QR, including the taxa richness, trophic group richness, biomass flux, biomass transfer efficiency, and trophic stability demonstrated a single-valley response pattern to the hydrological connectivity. We argue that the intermediate disturbance hypothesis still works on highland river ecosystems, whereas the optimal disturbance occurs in the low connectivity rather than median connectivity. We attribute this skewness to the low resistance and resilience of highland macroinvertebrate community in the face of hydrodynamic disturbances brought by flood events, and the biological disturbances from the predation by endemic migratory fish (Gymnocypris przewalskii) in QR. This study reveals that lateral migration and channel abandonment play important roles in highland river systems in the QTP in the context of biological and energetic perspectives and suggests that management strategies for highland rivers should be made different from those of lowland rivers.

Thermodynamics in Ecology-An Introductory Review

How to predict the evolution of ecosystems is one of the numerous questions asked of ecologists by managers and politicians. To answer this we will need to give a scientific definition to concepts like sustainability, integrity, resilience and ecosystem health. This is not an easy task, as modern ecosystem theory exemplifies. Ecosystems show a high degree of complexity, based upon a high number of compartments, interactions and regulations. The last two decades have offered proposals for interpretation of ecosystems within a framework of thermodynamics. The entrance point of such an understanding of ecosystems was delivered more than 50 years ago through Schrödinger's and Prigogine's interpretations of living systems as "negentropy feeders" and "dissipative structures", respectively. Combining these views from the far from equilibrium thermodynamics to traditional classical thermodynamics, and ecology is obviously not going to happen without problems. There seems little reason to doubt that far from equilibrium systems, such as organisms or ecosystems, also have to obey fundamental physical principles such as mass conservation, first and second law of thermodynamics. Both have been applied in ecology since the 1950s and lately the concepts of exergy and entropy have been introduced. Exergy has recently been proposed, from several directions, as a useful indicator of the state, structure and function of the ecosystem. The proposals take two main directions, one concerned with the exergy stored in the ecosystem, the other with the exergy degraded and entropy formation. The implementation of exergy in ecology has often been explained as a translation of the Darwinian principle of "survival of the fittest" into thermodynamics. The fittest ecosystem, being the one able to use and store fluxes of energy and materials in the most efficient manner. The major problem in the transfer to ecology is that thermodynamic properties can only be calculated and not measured. Most of the supportive evidence comes from aquatic ecosystems. Results show that natural and culturally induced changes in the ecosystems, are accompanied by a variations in exergy. In brief, ecological succession is followed by an increase of exergy. This paper aims to describe the state-of-the-art in implementation of thermodynamics into ecology. This includes a brief outline of the history and the derivation of the thermodynamic functions used today. Examples of applications and results achieved up to now are given, and the importance to management laid out. Some suggestions for essential future research agendas of issues that needs resolution are given.

Benchmarking successional progress in a quantitative food web

Central to ecology and ecosystem management, succession theory aims to mechanistically explain and predict the assembly and development of ecological communities. Yet processes at lower hierarchical levels, e.g. at the species and functional group level, are rarely mechanistically linked to the under-investigated system-level processes which drive changes in ecosystem properties and functioning and are comparable across ecosystems. As a model system for secondary succession, seasonal plankton succession during the growing season is readily observable and largely driven autogenically. We used a long-term dataset from large, deep Lake Constance comprising biomasses, auto- and heterotrophic production, food quality, functional diversity, and mass-balanced food webs of the energy and nutrient flows between functional guilds of plankton and partly fish. Extracting population- and system-level indices from this dataset, we tested current hypotheses about the directionality of successional progress which are rooted in ecosystem theory, the metabolic theory of ecology, quantitative food web theory, thermodynamics, and information theory. Our results indicate that successional progress in Lake Constance is quantifiable, passing through predictable stages. Mean body mass, functional diversity, predator-prey weight ratios, trophic positions, system residence times of carbon and nutrients, and the complexity of the energy flow patterns increased during succession. In contrast, both the mass-specific metabolic activity and the system export decreased, while the succession rate exhibited a bimodal pattern. The weighted connectance introduced here represents a suitable index for assessing the evenness and interconnectedness of energy flows during succession. Diverging from earlier predictions, ascendency and eco-exergy did not increase during succession. Linking aspects of functional diversity to metabolic theory and food web complexity, we reconcile previously disjoint bodies of ecological theory to form a complete picture of successional progress within a pelagic food web. This comprehensive synthesis may be used as a benchmark for quantifying successional progress in other ecosystems.

Spatio-temporal patterns of microbial communities in a hydrologically dynamic pristine aquifer

Seasonal patterns of groundwater and sediment microbial communities were explored in a hydrologically dynamic alpine oligotrophic porous aquifer, characterized by pronounced groundwater table fluctuations. Rising of the groundwater level in consequence of snow melting water recharge was accompanied by a dramatic drop of bacterial Shannon diversity in groundwater from H' = 3.22 ± 0.28 in autumn and winter to H' = 1.31 ± 0.35 in spring and summer, evaluated based on T-RFLP community fingerprinting. Elevated numbers of bacteria in groundwater in autumn followed nutrient inputs via recharge from summer rains and correlated well with highest concentrations of assimilable organic carbon. Sterile sediments incubated to groundwater in monitoring wells were readily colonized reaching maximum cell densities within 2 months, followed by a consecutive but delayed increase and leveling-off of bacterial diversity. After 1 year of incubation, the initially sterile sediments exhibited a similar number of bacteria and Shannon diversity when compared to vital sediment from a nearby river incubated in parallel. The river bed sediment microbial communities hardly changed in composition, diversity, and cell numbers during 1 year of exposure to groundwater. Summing up, the seasonal hydrological dynamics were found to induce considerable dynamics of microbial communities suspended in groundwater, while sediment communities seem unaffected and stable in terms of biomass and diversity.

Scale Expansion of Community Investigations and Integration of the Effects of Abiotic and Biotic Processes on Maintenance of Species Diversity

Information on the maintenance of diversity patterns from regional to local scales is dispersed among academic fields due to the local focus of community ecology. To better understand these patterns, the study of ecological communities needs to be expanded to larger scales and the various processes affecting them need to be integrated using a suitable quantitative method. We determined a range of communities on a flora-subregional scale in Yunnan province, China (383210.02 km2). A series of species pools were delimited from the regional to plot scales. Plant diversity was evaluated and abiotic and biotic processes identified at each pool level. The species pool effect was calculated using an innovative model, and the contribution of these processes to the maintenance of plant species diversity was determined and integrated: climate had the greatest effect at the flora-subregional scale, with historical and evolutionary processes contributing ∼11%; climate and human disturbance had the greatest effect at the local site pool scale; competition exclusion and stress limitation explained strong filtering at the successional stage pool scale; biotic processes contributed more on the local community scale than on the regional scale. Scale expansion combined with the filtering model approach solves the local problem in community ecology.

Natural enemy diversity reduces temporal variability in wasp but not bee parasitism

Biodiversity may enhance and stabilise ecosystem functioning, but little evidence exists for diversity–function relationships involving multitrophic interactions in real landscapes. In multitrophic communities diversity may vary at different trophic levels, with either synergistic or antagonistic effects on ecosystem functioning. Intensification of land-use systems is often found to reduce diversity, which in turn may lead to reduced associated ecological functions in natural food webs, such as host-parasite interactions. In this study we investigated the relationship between the number of natural enemy and host species and the mean rate and temporal variability of parasitism (inverse of stability), along an intensification gradient of coffee agroforests in Ecuador. We used standardised trap nests for bees and wasps and their natural enemies in 14 agroforests, and evaluated these monthly over a period of 17 months. We found that parasitism rates of wasps and bees increased with increasing number of enemy species and decreased with increasing number of host species. Temporal variability in parasitism rates decreased with increasing number of enemy species and increased with temporal variability in enemy species richness; however, these effects were restricted to wasp hosts. Intensification of agroforests did not significantly affect species richness of hosts or enemies or their relation to parasitism and its temporal variability. We conclude that high enemy diversity may enhance parasitism rates and that high host diversity may provide resistance against consumption. Furthermore, we show that a diverse and stable enemy community may also have a stabilizing effect on parasitism rates. However, these effects may be host-guild specific, as these relations were restricted to wasps.

Modeling energy flow in a large Neotropical reservoir: a tool do evaluate fishing and stability

Recently, there is an increasing perception that the ecosystem approach gives important insights to support fisheries stock assessment and management. This paper aims to quantify energy flows in the Itaipu Reservoir (Brazil) and to simulate increase of the fishing effort of some species, using Ecopath with Ecosim software, which could allow inferences on stability. Therefore, two steady-state Itaipu models were built (1983-87 and 1988-92). Results showed that: a) there are no differences between models, and results on aging trends do not vary over time indicating that fishery does not alter the ecosystem as a whole; b) results of fisheries simulations are approximate to mono-specific stock assessment for the same species and periods; c) many authors believe that tropical ecosystems are environments where biotic and abiotic oscillations are annual and sometimes unexpected, but the results found for the Itaipu Reservoir indicate that stability was met after 16 years.

Trophic interactions and the relationship between species diversity and ecosystem stability

Several theoretical studies propose that biodiversity buffers ecosystem functioning against environmental fluctuations, but virtually all of these studies concern a single trophic level, the primary producers. Changes in biodiversity also affect ecosystem processes through trophic interactions. Therefore, it is important to understand how trophic interactions affect the relationship between biodiversity and the stability of ecosystem processes. Here we present two models to investigate this issue in ecosystems with two trophic levels. The first is an analytically tractable symmetrical plant-herbivore model under random environmental fluctuations, while the second is a mechanistic ecosystem model under periodic environmental fluctuations. Our analysis shows that when diversity affects net species interaction strength, species interactions--both competition among plants and plant-herbivore interactions--have a strong impact on the relationships between diversity and the temporal variability of total biomass of the various trophic levels. More intense plant competition leads to a stronger decrease or a lower increase in variability of total plant biomass, but plant-herbivore interactions always have a destabilizing effect on total plant biomass. Despite the complexity generated by trophic interactions, biodiversity should still act as biological insurance for ecosystem processes, except when mean trophic interaction strength increases strongly with diversity.