Fine scale prediction of ecological community composition using a two-step sequential Machine Learning ensemble.

Prediction is one of the last frontiers in ecology. Indeed, predicting fine-scale species composition in natural systems is a complex challenge as multiple abiotic and biotic processes operate simultaneously to determine local species abundances. On the one hand, species intrinsic performance and their tolerance limits to different abiotic pressures modulate species abundances. On the other hand, there is growing recognition that species interactions play an equally important role in limiting or promoting such abundances within ecological communities. Here, we present a joint effort between ecologists and data scientists to use data-driven models to predict species abundances using reasonably easy to obtain data. We propose a sequential data-driven modeling approach that in a first step predicts the potential species abundances based on abiotic variables, and in a second step uses these predictions to model the realized abundances once accounting for species competition. Using a curated data set over five years we predict fine-scale species abundances in a highly diverse annual plant community. Our models show a remarkable spatial predictive accuracy using only easy-to-measure variables in the field, yet such predictive power is lost when temporal dynamics are taken into account. This result suggests that predicting future abundances requires longer time series analysis to capture enough variability. In addition, we show that these data-driven models can also suggest how to improve mechanistic models by adding missing variables that affect species performance such as particular soil conditions (e.g. carbonate availability in our case). Robust models for predicting fine-scale species composition informed by the mechanistic understanding of the underlying abiotic and biotic processes can be a pivotal tool for conservation, especially given the human-induced rapid environmental changes we are experiencing. This objective can be achieved by promoting the knowledge gained with classic modelling approaches in ecology and recently developed data-driven models.

Artificial night light alters ecosystem services provided by biotic components.

The global catastrophe of natural biodiversity and ecosystem services are expedited with the growing human population. Repercussions of artificial light at night ALAN are much wider, as it varies from unicellular to higher organism. Subsequently, hastened pollution and over exploitation of natural resources accelerate the expeditious transformation of climatic phenomenon and further cause global biodiversity losses. Moreover, it has a crucial role in global biodiversity and ecosystem services losses via influencing the ecosystem biodiversity by modulating abundance, number and aggregation at every levels as from individual to biome levels. Along with these affects, it disturbs the population, genetics and landscape structures by interfering inter- and intra-species interactions and landscape formation processes. Furthermore, alterations in normal light/dark (diurnal) signalling disrupt the stable physiological, biochemical, and molecular processes and modulate the regulating, cultural and provisioning ecosystem services and ultimately disorganize the stable ecosystem structure and functions. Moreover, ALAN reshapes the abiotic component of the ecosystem, and as a key component of global warming via producing greenhouse gases via emitting light. By taking together the above facts, this review highlights the impact of ALAN on the ecosystem and its living and non-living components, emphasizing to the terrestrial and aquatic ecosystem. Further, we summarize the means of minimizing strategies of ALAN in the environment, which are very crucial to reduce the further spread of night light contamination in the environment and can be useful to minimize the drastic impacts on the ecosystem.

Functional biology in its natural context: A search for emergent simplicity.

The immeasurable complexity at every level of biological organization creates a daunting task for understanding biological function. Here, we highlight the risks of stripping it away at the outset and discuss a possible path toward arriving at emergent simplicity of understanding while still embracing the ever-changing complexity of biotic interactions that we see in nature.

Dynamic population stage structure due to juvenile-adult asymmetry stabilizes complex ecological communities.

Natural ecological communities are diverse, complex, and often surprisingly stable, but the mechanisms underlying their stability remain a theoretical enigma. Interactions such as competition and predation presumably structure communities, yet theory predicts that complex communities are stable only when species growth rates are mostly limited by intraspecific self-regulation rather than by interactions with resources, competitors, and predators. Current theory, however, considers only the network topology of population-level interactions between species and ignores within-population differences, such as between juvenile and adult individuals. Here, using model simulations and analysis, I show that including commonly observed differences in vulnerability to predation and foraging efficiency between juvenile and adult individuals results in up to 10 times larger, more complex communities than observed in simulations without population stage structure. These diverse communities are stable or fluctuate with limited amplitude, although in the model only a single basal species is self-regulated, and the population-level interaction network is highly connected. Analysis of the species interaction matrix predicts the simulated communities to be unstable but for the interaction with the population-structure subsystem, which completely cancels out these instabilities through dynamic changes in population stage structure. Common differences between juveniles and adults and fluctuations in their relative abundance may hence have a decisive influence on the stability of complex natural communities and their vulnerability when environmental conditions change. To explain community persistence, it may not be sufficient to consider only the network of interactions between the constituting species.

The role of symbiosis in the first colonization of the seafloor by macrobiota: Insights from the oldest Ediacaran biota (Newfoundland, Canada).

The earliest record of animal life comes from the Ediacaran of Newfoundland, including dm scale fossil organisms, most of which are inferred to have been epibenthic immotile eumetazoans. This work introduces the palaeobiology of the major fossil groups in the Newfoundland assemblages including strange fractal-like taxa and addresses some of biogeochemical challenges such as sulfide buildup that could most easily have been overcome by symbiogenesis. Specifically, the epibenthic reclining nature of some of the Ediacaran biota-with their fractal-like high surface area lower surfaces-are considered to have been well designed for gaining nutriment from chemosynthetic, sulfur-oxidizing bacteria. This view constitutes a shift away from the view that most of the biota were anomalously large osmotrophs.

Evidences of the Oldest Trophic Interactions in the Riphean Biota (Lakhanda Lagerstätte, Southeastern Siberia).

Evidences of perforation of organic-walled fossil eukaryotes by other organisms has been found in the Lakhanda Lagerstätte (1030-1000 Ma, southeastern Siberia). The type of perforation is most similar to the type described from the Akademikerbren (750 Ma, Spitsbergen), Chuar (780-740 Ma, United States) and Shaler Supergroups (1150-900 Ma, Arctic Canada). The biogenic origin of the perforations has been substantiated. A hypothesis of perforation of fossils by zoosporic fungi found in the same deposits has been proposed. At the same time, the taxonomic diversity of eukaryotic "prey" taxa and the primitive morphology of such perforations do not allow us to qualify the perforators as distinct protists and do not point out the absolute certainty of selective predation among eukaryotes during the Riphean (Mesoproterozoic). Thus, the hypothesis of explosive diversification of eukaryotes in the Late Proterozoic driven by selective predation cannot yet be confirmed paleontologically.

Dynamical persistence in high-diversity resource-consumer communities.

We show how highly-diverse ecological communities may display persistent abundance fluctuations, when interacting through resource competition and subjected to migration from a species pool. These fluctuations appear, robustly and predictably, in certain regimes of parameter space. Their origin is closely tied to the ratio of realized species diversity to the number of resources. This ratio is set by competition, through the balance between species being pushed out and invading. When this ratio is smaller than one, dynamics will reach stable equilibria. When this ratio is larger than one, the competitive exclusion principle dictates that fixed-points are either unstable or marginally stable. If they are unstable, the system is repelled from fixed points, and abundances forever fluctuate. While marginally-stable fixed points are in principle allowed and predicted by some models, they become structurally unstable at high diversity. This means that even small changes to the model, such as non-linearities in how resources combine to generate species' growth, will result in persistent abundance fluctuations.

Symbiotic fouling of Vetulicola, an early Cambrian nektonic animal.

Here, we report the earliest fossil record to our knowledge of surface fouling by aggregates of small vermiform, encrusting and annulated tubular organisms associated with a mobile, nektonic host, the enigmatic Cambrian animal Vetulicola. Our material is from the exceptionally preserved early Cambrian (Epoch 2, Age 3), Chengjiang biota of Yunnan Province, southwest China, a circa 518 million-year old marine deposit. Our data show that symbiotic fouling relationships between species formed a component of the diversification of animal-rich ecosystems near the beginning of the Phanerozoic Eon, suggesting an early escalation of intimate ecologies as part of the Cambrian animal radiation.

Temperature increase altered Daphnia community structure in artificially heated lakes: a potential scenario for a warmer future.

Under conditions of global warming, organisms are expected to track their thermal preferences, invading new habitats at higher latitudes and altitudes and altering the structure of local communities. To fend off potential invaders, indigenous communities/populations will have to rapidly adapt to the increase in temperature. In this study, we tested if decades of artificial water heating changed the structure of communities and populations of the Daphnia longispina species complex. We compared the species composition of contemporary Daphnia communities inhabiting five lakes heated by power plants and four non-heated control lakes. The heated lakes are ca. 3-4 °C warmer, as all lakes are expected to be by 2100 according to climate change forecasts. We also genotyped subfossil resting eggs to describe past shifts in Daphnia community structure that were induced by lake heating. Both approaches revealed a rapid replacement of indigenous D. longispina and D. cucullata by invader D. galeata immediately after the onset of heating, followed by a gradual recovery of the D. cucullata population. Our findings clearly indicate that, in response to global warming, community restructuring may occur faster than evolutionary adaptation. The eventual recolonisation by D. cucullata indicates that adaptation to novel conditions can be time-lagged, and suggests that the long-term consequences of ecosystem disturbance may differ from short-term observations.

Abiotic and biotic context dependency of perennial crop yield.

Perennial crops in agricultural systems can increase sustainability and the magnitude of ecosystem services, but yield may depend upon biotic context, including soil mutualists, pathogens and cropping diversity. These biotic factors themselves may interact with abiotic factors such as drought. We tested whether perennial crop yield depended on soil microbes, water availability and crop diversity by testing monocultures and mixtures of three perennial crop species: a novel perennial grain (intermediate wheatgrass-Thinopyrum intermedium-- that produces the perennial grain Kernza®), a potential perennial oilseed crop (Silphium intregrifolium), and alfalfa (Medicago sativa). Perennial crop performance depended upon both water regime and the presence of living soil, most likely the arbuscular mycorrhizal (AM) fungi in the whole soil inoculum from a long term perennial monoculture and from an undisturbed native remnant prairie. Specifically, both Silphium and alfalfa strongly benefited from AM fungi. The presence of native prairie AM fungi had a greater benefit to Silphium in dry pots and alfalfa in wet pots than AM fungi present in the perennial monoculture soil. Kernza did not benefit from AM fungi. Crop mixtures that included Kernza overyielded, but overyielding depended upon inoculation. Specifically, mixtures with Kernza overyielded most strongly in sterile soil as Kernza compensated for poor growth of Silphium and alfalfa. This study identifies the importance of soil biota and the context dependence of benefits of native microbes and the overyielding of mixtures in perennial crops.

Effects of arthropod inquilines on growth and reproductive effort among metacommunities of the purple pitcher plant (Sarracenia purpurea var. montana).

Many plant species harbor communities of symbionts that release nutrients used by their host plants. However, the importance of these nutrients to plant growth and reproductive effort is not well understood. Here, we evaluate the relationship between the communities that colonize pitcher plant phytotelmata and the pitcher plants' vegetative growth and flower production to better understand the symbiotic role played by phytotelma communities. We focus on the mountain variety purple pitcher plant (Sarracenia purpurea var. montana), which occurs in small and isolated populations in Western North Carolina. We found that greater symbiont community diversity is associated with higher flower production the following season. We then examined geographic variation in communities and found that smaller plant populations supported less diverse symbiont communities. We relate our observations to patterns of community diversity predicted by community ecology theory.

[Interactions among soil biota and their applications in synergistic bioremediation of heavy-metal contaminated soils].

Soil is the material basis for human survival. However, in China, soils are wildly polluted by heavy metals, which poses serious health risks to humans. Bioremediation of heavy-metal contaminated soil is widely considered as a sustainable remediation strategy, but low remediation efficiency is still a scientific bottleneck of bioremediation. There are abundant microorganisms, plants and animals living in soils. Among these soil biota, there are complex interactions to form an intricate food web through material circulation and energy transfer. These interactions among soil biota affect the transportation and transformation of pollutants in soil, and consequently influence the bioremediation efficiency. The synergistic remediation by soil biota combines the advantages of diferent organisms to enhance the efficiency of bioremediation. In this paper, the interactions among soil biota and their influence on heavy-metal transportation and transformation, as well as bioremediation efficiency are reviewed. We also propose perspectives for future researches, including targeted regulating the structure of soil food web, improving the bioremediation efficiency of heavy-metal contaminated soil, and building a synergistic remediation technology with multi-organisms based on food web.

Biotic and abiotic sounds affect calling activity but not plasma testosterone levels in male frogs (Batrachyla taeniata) in the field and in captivity.

In animals, the expression of diverse reproductive behaviors is hormonally regulated. In particular, vocalizing during courtship has been related to circulating androgen levels, and reciprocally, conspecific vocalizations are known to modulate androgen secretion in vertebrates. The effect of natural sounds of abiotic origin on hormonal status has virtually not received attention. Therefore, we evaluated the vocal responses of male Batrachyla taeniata frogs to conspecific chorus and rainfall sounds in natural and controlled laboratory settings, measuring the testosterone levels of exposed individuals. In field and laboratory conditions, testosterone levels of frogs exposed to 31.5 min of chorus and rain sounds and non-exposed individuals were similar. In the field, frogs increased their call rate in response to playbacks of chorus and rain sound, but the evoked calling activity was unrelated to plasma testosterone. In contrast to the field, frogs showed limited responsiveness to 31.5-min acoustic exposures in the laboratory. Similarly to the field, for vocally active males tested in the laboratory there was no association between call rate and testosterone levels. Additionally, in this group, testosterone levels were higher in vocally active males relative to non-calling individuals. Overall, these results indicate that in B. taeniata testosterone levels are not altered following a short-term exposure to conspecific biotic and to abiotic sounds. Our results are suggestive of a threshold influence of testosterone on the vocal activity of the species studied. Further explorations of the influence of abiotic sounds on endocrine activation are required to understand how animals respond to variable acoustic environmental conditions.

Potential impact of small hydroelectric power plants on river biota: a case study on macroinvertebrates associated to basaltic knickzones / Potencial impacto de pequenas centrais hidreléticas sobre a biota aquática: um estudo de caso sobre macroinvertebrados associados a pedrais basálticos

Abstract Small hydroelectric power plants (SHP) have been considered as an alternative for the generation of electricity with reduced environmental impacts. Nevertheless, no studies have addressed changes in a particular kind of river macrohabitat commonly affected by SHPs, the knickzones. This study aimed to assess the impact of a SHP construction on the aquatic macroinvertebrate fauna associated with two basaltic knickzones located in Sapucaí-Mirim River, Southeast Brazil. The first, considered as a functional knickzone, follows the natural dynamics of the river flow and preserves the original rock substrate. The second, considered as non-functional knickzone, was permanently flooded after the SHP construction and the consolidated rock substrate was changed by fine sediment. Sampling was carried out in two seasonal periods and the data were analysed through multivariate analysis. It was observed differences in composition and structure of the macroinvertebrates community between the knickzones and periods. The functional knickzone exhibited a much higher richness, 72 taxa compared to 44 in the non-functional, as well as a large number of exclusive taxa (38, being only nine exclusive to the non-functional). Diversity, equitability and density mean values were also higher in the functional knickzone. The limnological parameters varied significantly between dry and rainy seasons but not between the distinct knickzones. This kind of macrohabitats and its potential role for the rivers biodiversity is practically unknown. In the scenery of fast SHP expansion, further studies and protection measures are necessary.

Resumo Atualmente, a instalação de pequenas centrais hidrelétricas (PCHs) tem sido a alternativa mais visada quando a questão é suprir a demanda energética, considerando-se os menores impactos ambientais possíveis. Contudo, são escassos os trabalhos que avaliam as alterações causadas por esses empreendimentos, principalmente no que se diz respeito a um tipo de macro-habitat de rios, os pedrais. Assim, este estudo teve como objetivo avaliar o impacto da construção de uma PCH na fauna de macroinvertebrados aquáticos associada a dois pedrais basálticos, localizados no rio Sapucaí-Mirim, no Sudeste do Brasil. O primeiro, considerado como um pedral funcional, segue a dinâmica natural do fluxo do rio e possui o substrato rochoso original. O segundo, considerado como pedral não funcional, foi permanentemente inundado após a construção da PCH e o substrato consolidado foi alterado por sedimentos finos. A amostragem foi realizada em dois períodos sazonais e os dados foram analisados através de análise multivariada. Foram observadas diferenças na composição e estrutura da comunidade de macroinvertebrados entre os pedrais e períodos. O pedral funcional apresentou uma riqueza muito maior, 72 táxons em comparação com 44 no não funcional, bem como um grande número de táxons exclusivos (38, sendo apenas nove exclusivos do não-funcional). Os valores médios da diversidade, equitabilidade e densidade também foram maiores no pedral funcional. Os parâmetros limnológicos variaram significativamente entre as estações seca e chuvosa, mas não entre os diferentes pedrais. Este tipo de macro-habitat e seu potencial papel para a biodiversidade dos rios são praticamente desconhecidos. Assim, mais estudos e medidas de proteção são necessários, principalmente diante do atual cenário de rápida expansão das PCHs.

Effects of Earthworms and Agricultural Plant Species on the Soil Nematode Community in a Microcosm Experiment.

Both earthworms and plants may affect the soil nematode community. However, the effects of earthworms and plant species interactions on soil nematode community are poorly understood. We explored how an epigeic earthworm Eisenia fetida affects the soil nematode community in systems with three representative plants (wheat, cotton and cabbage) which were grown in pots with or without added earthworms under greenhouse conditions. Earthworm presence decreased the abundance of total nematode and all four nematode trophic groups, except for the fungivore and predator/omnivore nematodes in wheat systems, but increased the genus richness of nematode in all treatments. Due to plant identity and different root exudates, plants had significant effects on soil nematode abundance. Compared with the no plant and without earthworm treatment, wheat and cabbage had the higher stimulation of the abundance of total nematode, bacterivores and fungivores, and cotton had the higher stimulation of the abundance of fungivores and predators-omnivores; whereas earthworm presence mostly weakened the stimulation effects of plant species on soil nematode abundance which indicated earthworms had the enhanced effects in the presence of plants. The interaction affected soil nematode abundance (total nematodes, bacterivore, fungivore and omnivore-predators) and community diversity indices (diversity index H', evenness index J', community maturity index ∑MI, Simpson dominance index λ and nematode channel ratio NCR). Principal component analysis showed that plant species affected soil nematode community composition. Redundancy analysis indicated plant species and biomass accounted for 41.60% and 34.13% of the variation in soil nematode community structure, respectively; while earthworms explained only 6.13%. Overall, current study suggest that earthworm could inhibit nematode abundance; whereas, plants have exerted greater influences on nematode community structure than earthworm presence due to their species-specific effects on different trophic groups of nematodes.

Plant communities control long term carbon accumulation and biogeochemical gradients in a Patagonian bog.

Peat carbon accumulation is controlled by both large scale factors, such as climate and hydrological setting, and small scale factors, such as microtopography and plant community. These small scale factors commonly vary within peatlands and can cause variation in biogeochemical traits and carbon accumulation within the same site. To understand these within-site variations, we investigated long term carbon accumulation, peat decomposition, biogeochemistry of pore water and plant macrofossils along a transect in an ombrotrophic bog in southern Patagonia. An additional question we addressed is how historical deposition of volcanic ash on the peatland has affected its carbon balance. Variability in plant community and water table led to differences in long term peat and carbon accumulation (peat moss > cushion plant), organic matter decomposition (cushion plant > peat moss), and methane production (peat moss > cushion plant). Macrofossil analysis and radiocarbon dating indicated a relationship between plant community and carbon accumulation or decomposition during the historical succession of vegetation in the peatland. C/N ratio and isotopic signatures reflected variability in plant community as litter source, and DOC concentrations were controlled by humification level. Volcanic ash deposition had only limited effect on plant composition, but it was associated with increased decomposition in overlying peat layers. This study highlights the importance of understanding how plant communities develop, as changes in communities could significantly affect the potential of ombrotrophic peatlands as C sink.

Effects of oil sands process water mixtures on the mayfly Hexagenia and field-collected aquatic macroinvertebrate communities.

Extraction of Canada's oil sands has created 1 billion m3 of tailings, which are stored in on-site tailings ponds. Due to limited storage capacity, the planned release of tailings into the surrounding environment may be required. This represents an environmental management challenge, as the tailings contain contaminants that are known toxins to aquatic communities. Of particular concern are naphthenic acids and their metallic counterparts, as they are the principal toxic components of tailings, are relatively soluble, and are persistent in aquatic environments. This study examines the acute toxicity of environmentally relevant 10:1 mixtures of two process water components: naphthenic acid and sodium naphthenate. We assess the effects of these simplified oil sands process water (OSPW) mixtures under planned and unplanned tailings release scenarios, using traditional and cutting-edge bioindicators for aquatic invertebrate taxa. We found that safe concentrations for mayflies and other aquatic macroinvertebrates were less than 1 mg/l, as no mayfly taxa survived repeated exposure to this dose in either the 48-h or 72-h acute toxicity test. In the 72-h test, no mayflies survived treatment levels greater than 0.5 mg sodium naphthenate/l. In the mesocosm study, even a 90% dilution of the OSPW mixture was not sufficient to protect sensitive macroinvertebrate communities. The results of this study highlight the potential environmental damage that will occur if OSPW is not carefully managed. This information will aid with the development of a management plan for oil sands tailings ponds, which will provide insight into the potential for process water release into the surrounding environment while conserving unique ecosystems downstream of development in the oil sands region.

Chronic nutrient inputs affect stream macroinvertebrate communities more than acute inputs: An experiment manipulating phosphorus, nitrogen and sediment.

Freshwaters worldwide are affected by multiple stressors. Timing of inputs and pathways of delivery can influence the impact stressors have on freshwater communities. In particular, effects of point versus diffuse nutrient inputs on stream macroinvertebrates are poorly understood. Point-source inputs tend to pose a chronic problem, whereas diffuse inputs tend to be acute with short concentration spikes. We manipulated three key agricultural stressors, phosphorus (ambient, chronic, acute), nitrogen (ambient, chronic, acute) and fine sediment (ambient, high), in 112 stream mesocosms (26 days colonisation, 18 days of manipulations) and determined the individual and combined effects of these stressors on stream macroinvertebrate communities (benthos and drift). Chronic nutrient treatments continuously received high concentrations of P and/or N. Acute channels received the same continuous enrichment, but concentrations were doubled during two 3-hour periods (day 6, day 13) to simulate acute nutrient inputs during rainstorms. Sediment was the most pervasive stressor in the benthos, reducing total macroinvertebrate abundance and richness, EPT (mayflies, stoneflies, caddisflies) abundance and richness. By contrast, N or P enrichment did not affect any of the six studied community-level metrics. In the drift assemblage, enrichment effects became more prevalent the longer the experiment went on. Sediment was the dominant driver of drift responses at the beginning of the experiment. After the first acute nutrient pulse, sediment remained the most influential stressor but its effects started to fade. After the second pulse, N became the dominant stressor. In general, impacts of either N or P on the drift were due to chronic exposure, with acute nutrient pulses having no additional effects. Overall, our findings imply that cost-effective management should focus on mitigating sediment inputs first and tackle chronic nutrient inputs second. Freshwater managers should also take into account the length of exposure to high nutrient concentrations, rather than merely the concentrations themselves.

The composition of British bird communities is associated with long-term garden bird feeding.

There is a multi-billion dollar global industry dedicated to feeding wild birds in residential gardens. This extraordinary boost to food resources is almost certainly reshaping entire bird communities, yet the large-scale, long-term impacts on community ecology remain unknown. Here we reveal a 40-year transformation of the bird communities using garden bird feeders in Britain, and provide evidence to suggest how this may have contributed to national-scale population changes. We find that increases in bird diversity at feeders are associated with increasing community evenness, as species previously rarely observed in gardens have increasingly exploited the growing variety of foods on offer over time. Urban areas of Britain are consequently nurturing growing populations of feeder-using bird species, while the populations of species that do not use feeders remain unchanged. Our findings illustrate the on-going, gross impact people can have on bird community structure across large spatial scales.

Reconciling cooperation, biodiversity and stability in complex ecological communities.

Empirical evidences show that ecosystems with high biodiversity can persist in time even in the presence of few types of resources and are more stable than low biodiverse communities. This evidence is contrasted by the conventional mathematical modeling, which predicts that the presence of many species and/or cooperative interactions are detrimental for ecological stability and persistence. Here we propose a modelling framework for population dynamics, which also include indirect cooperative interactions mediated by other species (e.g. habitat modification). We show that in the large system size limit, any number of species can coexist and stability increases as the number of species grows, if mediated cooperation is present, even in presence of exploitative or harmful interactions (e.g. antibiotics). Our theoretical approach thus shows that appropriate models of mediated cooperation naturally lead to a solution of the long-standing question about complexity-stability paradox and on how highly biodiverse communities can coexist.