Whole-ecosystem experimental manipulations of tropical forests

Attaining freshwater and estuarine-water soil saturation in an ecosystem-scale coastal flooding experiment

Coastal upland forests are facing widespread mortality as sea-level rise accelerates and precipitation and storm regimes change. The loss of coastal forests has significant implications for the coastal carbon cycle; yet, predicting mortality likelihood is difficult due to our limited understanding of disturbance impacts on coastal forests. The manipulative, ecosystem-scale Terrestrial Ecosystem Manipulation to Probe the Effects of Storm Treatments (TEMPEST) experiment addresses the potential for freshwater and estuarine-water disturbance events to alter tree function, species composition, and ecosystem processes in a deciduous coastal forest in MD, USA. The experiment uses a large-unit (2000 m²), un-replicated experimental design, with three 50 m × 40 m plots serving as control, freshwater, and estuarine-water treatments. Transient saturation (5 h) of the entire soil rooting zone (0-30 cm) across a 2000 m² coastal forest was attained by delivering 300 m³ of water through a spatially distributed irrigation network at a rate just above the soil infiltration rate. Our water delivery approach also elevated the water table (typically ~ 2 m belowground) and achieved extensive, low-level inundation (~ 8 cm standing water). A TEMPEST simulation approximated a 15-cm rainfall event and based on historic records, was of comparable intensity to a 10-year storm for the area. This characterization was supported by showing that Hurricane Ida's (~ 5 cm rainfall) hydrologic impacts were shorter (40% lower duration) and less expansive (80% less coverage) than those generated through experimental manipulation. Future work will apply TEMPEST treatments to evaluate coastal forest resilience to changing hydrologic disturbance regimes and identify conditions that initiate ecosystem state transitions.

Nine actions to successfully restore tropical agroecosystems

Well-designed approaches to ecological restoration can benefit nature and society. This is particularly the case in tropical agroecosystems, where restoration can provide substantial socioecological benefits at relatively low costs. To successfully restore tropical agroecosystems and maximise benefits, initiatives must begin by considering 'who' should be involved in and benefit from restoration, and 'what', 'where', and 'how' restoration should occur. Based on collective experience of restoring tropical agroecosystems worldwide, we present nine actions to guide future restoration of these systems, supported by case studies that demonstrate our actions being used successfully in practice and highlighting cases where poorly designed restoration has been damaging. We call for increased restoration activity in tropical agroecosystems during the current UN Decade on Ecosystem Restoration.

Ecology: Mammals, interaction networks and the relevance of scale

A new study shows that large mammals in an African savanna not only modify the vegetation but also strongly alter interaction networks between plants and pollinators. These insights raise fundamental yet unresolved questions about spatial dimensions of experiments, species interaction networks and ecosystems.

Effects of Large-Scale Nitrogen Fertilization on Insect–Plant Interactions in the Canopy of Tall Alder Trees with N2-Fixing Traits in a Cool Temperate Forest

Nitrogen (N) deposition is expected to influence forests. The effects of large-scale N fertilization on canopy layer insect–plant interactions in stands of tall, atmospheric nitrogen (N2)-fixing tree species have never been assessed. We conducted a large-scale fertilization experiment (100 kg N ha−1 year−1 applied to approximately 9 ha) over three years (2012–2014) in a cool temperate forest in northern Japan. Our goal was to evaluate relational responses between alder (Alnus hirsuta [Turcz.]) and their insect herbivores to N deposition. Specifically, we assessed leaf traits (N concentration, C:N ratio, condensed tannin concentration, and leaf mass per unit area (LMA)) and herbivory by three feeding guilds (leaf damage by chewers and the densities of gallers and miners) between the fertilized site and an unfertilized control. Fertilization led to increased galler density in spring 2013 and increased leaf damage by chewers in late summer 2014. For leaf traits, the LMA decreased in spring 2013 and late summer 2014, and the C:N ratio decreased in late summer 2013. The N and condensed tannin concentrations remained unchanged throughout the study period. There was a negative correlation between LMA and leaf damage by chewers, but LMA was not correlated with galler density. These results show that large-scale N fertilization had a positive plant-mediated (i.e., indirect) effect on leaf damage by chewers via a decrease in LMA in the canopy layer. Changes in physical defenses in canopy leaves may be a mechanism by which N fertilization affects the herbivory in tall N2-fixing trees.

Evaluating Impact Using Time-Series Data

Humanity's impact on the environment is increasing, as are strategies to conserve biodiversity, but a lack of understanding about how interventions affect ecological and conservation outcomes hampers decision-making. Time series are often used to assess impacts, but ecologists tend to compare average values from before to after an impact; overlooking the potential for the intervention to elicit a change in trend. Without methods that allow for a range of responses, erroneous conclusions can be drawn, especially for large, multi-time-series datasets, which are increasingly available. Drawing on literature in other disciplines and pioneering work in ecology, we present a standardised framework to robustly assesses how interventions, like natural disasters or conservation policies, affect ecological time series.

Moderate phosphorus additions consistently affect community composition of arbuscular mycorrhizal fungi in tropical montane forests in southern Ecuador

Anthropogenic atmospheric deposition can increase nutrient supply in the most remote ecosystems, potentially affecting soil biodiversity. Arbuscular mycorrhizal fungal (AMF) communities rapidly respond to simulated soil eutrophication in tropical forests. Yet the limited spatio-temporal extent of such manipulations, together with the often unrealistically high fertilization rates employed, impedes generalization of such responses. We sequenced mixed root AMF communities within a seven year-long fully factorial nitrogen (N) and phosphorus (P) addition experiment, replicated at three tropical montane forests in southern Ecuador with differing environmental characteristics. We hypothesized: strong shifts in community composition and species richness after long-term fertilization, site- and clade-specific responses to N vs P additions depending on local soil fertility and clade life history traits respectively. Fertilization consistently shifted AMF community composition across sites, but only reduced richness of Glomeraceae. Compositional changes were mainly driven by increases in P supply while richness reductions were observed only after combined N and P additions. We conclude that moderate increases of N and P exert a mild but consistent effect on tropical AMF communities. To predict the consequences of these shifts, current results need to be supplemented with experiments that characterize local species-specific AMF functionality.

Digging mammal reintroductions reduce termite biomass and alter assemblage composition along an aridity gradient

Invasions can trigger cascades in ecological communities by altering species interactions. Following the introduction of cats and foxes into Australia, one tenth of Australia's terrestrial mammal species became extinct, due to predation, while many continue to decline. The broader consequences for Australian ecosystems are poorly understood. Soil-dwelling invertebrates are likely to be affected by the loss of fossorial native mammals, which are predators and disturbance agents. Using reintroductions as a model for ecosystems prior to species loss, we tested the hypothesis that mammal reintroduction leads to reduced vegetation cover and altered termite assemblages, including declines in abundance and biomass and changed species composition. We hypothesised that the magnitude of mammal reintroduction effects would diminish with increasing aridity, which affects resource availability. We compared six paired sites inside and outside three reintroduction sanctuaries across an aridity gradient. We sampled termite assemblages using soil trenches and measured habitat availability. Reintroductions were associated with increased bare ground and reduced vegetation, compared with controls. Aridity also had an underlying influence on vegetation cover by limiting water availability. Termite abundance and biomass were lower where mammals were reintroduced and the magnitude of this effect decreased with increasing aridity. Termite abundance was highest under wood, and soil-nesting wood-feeders were most affected inside sanctuaries. Ecological cascades resulting from exotic predator invasions are thus likely to have increased termite biomass and altered termite assemblages, but impacts may be lower in less-productive habitats. Our findings have implications for reserve carrying capacities and understanding of assemblage reconstruction following ecological cascades.

Neighborhood effects explain increasing asynchronous seedling survival in a subtropical forest

Biotic interactions play a critical role in mediating community responses to temporal environmental variation, but the importance of these effects relative to the direct effects of environmental change remains poorly understood, particularly in diverse forest communities. Here we combine a neighborhood modeling approach with insights from coexistence theory to assess the effects of temporal variation in species interactions and environmental conditions (e.g., precipitation, temperature, and understory light availability) on seedling survival over nine census years in a subtropical forest. We find significant temporal shifts in the magnitude of neighborhood effects on both community-wide and species-level seedling survival (statistically significant random effects of neighborhood × year and neighborhood × species × year interactions). These results are consistent with the idea that environmental change will play a fundamental role on forest regeneration dynamics by altering biotic interactions at the neighborhood scale. Moreover, differences among species in response to neighbors over time contribute to a pattern of temporal decoupling of seedling survival between species, which can help to promote diversity in certain contexts. In separate analyses of multiple regression on distance matrices (MRM), altered interactions with neighbors are much stronger predictors of asynchronous seedling survival among species than the pure effects of climate and plant functional traits, explaining twice as much variation (43.9% vs. 22.2%). In sum, these results reveal that divergent species responses to interannual environmental variability detected are driven primarily by indirect effects mediated by changing biotic environments. This highlights the importance of including indirect effects from local biotic (neighborhood) interactions in forecasts of forest community responses to global change.

Termites mitigate the effects of drought in tropical rainforest

Termites perform key ecological functions in tropical ecosystems, are strongly affected by variation in rainfall, and respond negatively to habitat disturbance. However, it is not known how the projected increase in frequency and severity of droughts in tropical rainforests will alter termite communities and the maintenance of ecosystem processes. Using a large-scale termite suppression experiment, we found that termite activity and abundance increased during drought in a Bornean forest. This increase resulted in accelerated litter decomposition, elevated soil moisture, greater soil nutrient heterogeneity, and higher seedling survival rates during the extreme El Niño drought of 2015–2016. Our work shows how an invertebrate group enhances ecosystem resistance to drought, providing evidence that the dual stressors of climate change and anthropogenic shifts in biotic communities will have various negative consequences for the maintenance of rainforest ecosystems.

A global database and "state of the field" review of research into ecosystem engineering by land animals

Ecosystem engineers have been widely studied for terrestrial systems, but global trends in research encompassing the range of taxa and functions have not previously been synthesised. We reviewed contemporary understanding of engineer fauna in terrestrial habitats and assessed the methods used to document patterns and processes, asking: (a) which species act as ecosystem engineers and with whom do they interact? (b) What are the impacts of ecosystem engineers in terrestrial habitats and how are they distributed? (c) What are the primary methods used to examine engineer effects and how have these developed over time? We considered the strengths, weaknesses and gaps in knowledge related to each of these questions and suggested a conceptual framework to delineate "significant impacts" of engineering interactions for all terrestrial animals. We collected peer-reviewed publications examining ecosystem engineer impacts and created a database of engineer species to assess experimental approaches and any additional covariates that influenced the magnitude of engineer impacts. One hundred and twenty-two species from 28 orders were identified as ecosystem engineers, performing five ecological functions. Burrowing mammals were the most researched group (27%). Half of all studies occurred in dry/arid habitats. Mensurative studies comparing sites with and without engineers (80%) were more common than manipulative studies (20%). These provided a broad framework for predicting engineer impacts upon abundance and species diversity. However, the roles of confounding factors, processes driving these patterns and the consequences of experimentally adjusting variables, such as engineer density, have been neglected. True spatial and temporal replication has also been limited, particularly for emerging studies of engineer reintroductions. Climate change and habitat modification will challenge the roles that engineers play in regulating ecosystems, and these will become important avenues for future research. We recommend future studies include simulation of engineer effects and experimental manipulation of engineer densities to determine the potential for ecological cascades through trophic and engineering pathways due to functional decline. We also recommend improving knowledge of long-term engineering effects and replication of engineer reintroductions across landscapes to better understand how large-scale ecological gradients alter the magnitude of engineering impacts.

The impacts of recurrent fires on diversity of fruit-feeding butterflies in a south-eastern Amazon forest

In the south-eastern Amazon, positive feedbacks between land use and severe weather events are increasing the frequency and intensity of fires, threatening local biodiversity. We sampled fruit-feeding butterflies in experimental plots in a south-eastern Amazon forest: one control plot, one plot burned every 3 y, one plot burned yearly. We also measured environmental parameters (canopy cover, temperature, humidity). Our results show no significant differences in overall species richness between plots (34, 37 and 33 species respectively), although richness was lower in burned plots during the dry season. We found significant differences in community composition and structure between control and burned plots, but not between burned treatments. In the control plot, forest-specialist species represented 64% of total abundance, decreasing to 50% in burned every 3 y and 54% in yearly burned plots. Savanna specialist species were absent in the control plot, but represented respectively 8% and 3% of total abundance in burned plots. The best predictor of the change in spatial community patterns and abundance of forest specialists was canopy cover. Although we found high resilience to forest burning in many species, our study suggests that fire disturbance can still be a threat to forest specialists due to changes in microclimate.

Increasing Metagenomic Resolution of Microbiome Interactions Through Functional Phylogenomics and Bacterial Sub-Communities

The genomic composition of the microbiome and its relationship with the environment is an exciting open question in biology. Metagenomics is a useful tool in the discovery of previously unknown taxa, but its use to understand the functional and ecological capacities of the microbiome is limited until taxonomy and function are understood in the context of the community. We suggest that this can be achieved using a combined functional phylogenomics and co-culture-based experimental strategy that can increase our capacity to measure sub-community interactions. Functional phylogenomics can identify and partition the genome such that hidden gene functions and gene clusters with unique evolutionary signals are revealed. We can test these phylogenomic predictions using an experimental model based on sub-community populations that represent a subset of the diversity directly obtained from environmental samples. These populations increase the detection of mechanisms that drive functional forces in the assembly of the microbiome, in particular the role of metabolites from key taxa in community interactions. Our combined approach leverages the potential of metagenomics to address biological questions from ecological systems.

Analyses between Reproductive Behavior, Genetic Diversity and Pythium Responsiveness in Zingiber spp. Reveal an Adaptive Significance for Hemiclonality

Mode of reproduction is generally considered to have long-range evolutionary implications on population survival. Because sexual reproduction produces genetically diverse genotypes, this mode of reproduction is predicted to positively influence the success potential of offspring in evolutionary arms race with parasites (Red queen) whereas, without segregation and recombination, the obligate asexual multiplication may push a species into extinction due to the steady accumulation of deleterious mutations (Muller's ratchet). However, the extent of linearity between reproductive strategies, genetic diversity and population fitness, and the contributions of different breeding strategies to population fitness are yet to be understood clearly. Genus Zingiber belonging to the pan-tropic family Zingiberaceae represents a good system to study contributions of different breeding behavior on genetic diversity and population fitness, as this genus comprises species with contrasting breeding systems. In this study, we analyzed breeding behavior, amplified fragment length polymorphism diversity and response to the soft-rot pathogen Pythium aphanidermatum in 18 natural populations of three wild Zingiber spp.: Z. neesanum, Z. nimmonii, and Z. zerumbet, together with the obligately asexual cultivated congener, ginger (Z. officinale). Ginger showed an exceptionally narrow genetic base, and adding to this, all the tested cultivars were uniformly susceptible to soft-rot. Concordant with the postulates of Muller's ratchet, the background selection may be continuously pushing ginger into the ancestral state, rendering it inefficient in host-pathogen coevolution. Z. neesanum and Z. nimmonii populations were sexual and genetically diverse; however, contrary to Red Queen expectations, the populations were highly susceptible to soft-rot. Z. zerumbet showed a hemiclonal breeding behavior. The populations inhabiting forest understory were large and continuous, sexual and genetically diverse, but were susceptible, whereas populations inhabiting the revenue land were fragmented and monoclonal, but were resistant. It may be possible that, when genetic recombination becomes at a premium due to the genetic constraints imparted by habitat fragmentation or pathogen pressure, Z. zerumbet.