Benefits and limitations of three-dimensional printing technology for ecological research.

BACKGROUND: Ecological research often involves sampling and manipulating non-model organisms that reside in heterogeneous environments. As such, ecologists often adapt techniques and ideas from industry and other scientific fields to design and build equipment, tools, and experimental contraptions custom-made for the ecological systems under study. Three-dimensional (3D) printing provides a way to rapidly produce identical and novel objects that could be used in ecological studies, yet ecologists have been slow to adopt this new technology. Here, we provide ecologists with an introduction to 3D printing. RESULTS: First, we give an overview of the ecological research areas in which 3D printing is predicted to be the most impactful and review current studies that have already used 3D printed objects. We then outline a methodological workflow for integrating 3D printing into an ecological research program and give a detailed example of a successful implementation of our 3D printing workflow for 3D printed models of the brown anole, Anolis sagrei, for a field predation study. After testing two print media in the field, we show that the models printed from the less expensive and more sustainable material (blend of 70% plastic and 30% recycled wood fiber) were just as durable and had equal predator attack rates as the more expensive material (100% virgin plastic). CONCLUSIONS: Overall, 3D printing can provide time and cost savings to ecologists, and with recent advances in less toxic, biodegradable, and recyclable print materials, ecologists can choose to minimize social and environmental impacts associated with 3D printing. The main hurdles for implementing 3D printing-availability of resources like printers, scanners, and software, as well as reaching proficiency in using 3D image software-may be easier to overcome at institutions with digital imaging centers run by knowledgeable staff. As with any new technology, the benefits of 3D printing are specific to a particular project, and ecologists must consider the investments of developing usable 3D materials for research versus other methods of generating those materials.

Validation of a Noninvasive Hair Trapping Method for Extractive-Foraging Primates.

Hair is a useful source of biological information. For example, the bulb can be a source of high-quality genetic material, whereas the shaft can be useful for measuring heavy metals and some hormones, such as cortisol. The stable isotope composition of hair is another valuable source of biological information. Consequently, noninvasive methods of hair sampling have become important research tools. Several hair-trapping methods have been developed for use on mammals, but these are rarely deployed on primates in part because their travel patterns can be difficult to predict and because many species are averse to novel objects in their environments. Yet if a species has a natural propensity to envision, manipulate, and withdraw extractable food resources, then a baited receptacle lined with double-sided tape may prove successful as a hair trap. Recently, researchers demonstrated the success of such a contraption with tufted capuchins, a Neotropical monkey species with a high degree of somatosensory intelligence and a proclivity for extractive foraging. Here, we replicate this method in a population of tool-using long-tailed macaques (Macaca fascicularis). Our trials validate the effectiveness of the method, suggesting that it is suitable for long-tailed macaques and other extractive-foraging primates.

Actogram analysis of free-flying migratory birds: new perspectives based on acceleration logging.

The use of accelerometers has become an important part of biologging techniques for large-sized birds with accelerometer data providing information about flight mode, wing-beat pattern, behaviour and energy expenditure. Such data show that birds using much energy-saving soaring/gliding flight like frigatebirds and swifts can stay airborne without landing for several months. Successful accelerometer studies have recently been conducted also for free-flying small songbirds during their entire annual cycle. Here we review the principles and possibilities for accelerometer studies in bird migration. We use the first annual actograms (for red-backed shrike Lanius collurio) to explore new analyses and insights that become possible with accelerometer data. Actogram data allow precise estimates of numbers of flights, flight durations as well as departure/landing times during the annual cycle. Annual and diurnal rhythms of migratory flights, as well as prolonged nocturnal flights across desert barriers are illustrated. The shifting balance between flight, rest and different intensities of activity throughout the year as revealed by actogram data can be used to analyse exertion levels during different phases of the life cycle. Accelerometer recording of the annual activity patterns of individual birds will open up a new dimension in bird migration research.

Maize Cropping Systems Mapping Using RapidEye Observations in Agro-Ecological Landscapes in Kenya.

Cropping systems information on explicit scales is an important but rarely available variable in many crops modeling routines and of utmost importance for understanding pests and disease propagation mechanisms in agro-ecological landscapes. In this study, high spatial and temporal resolution RapidEye bio-temporal data were utilized within a novel 2-step hierarchical random forest (RF) classification approach to map areas of mono- and mixed maize cropping systems. A small-scale maize farming site in Machakos County, Kenya was used as a study site. Within the study site, field data was collected during the satellite acquisition period on general land use/land cover (LULC) and the two cropping systems. Firstly, non-cropland areas were masked out from other land use/land cover using the LULC mapping result. Subsequently an optimized RF model was applied to the cropland layer to map the two cropping systems (2nd classification step). An overall accuracy of 93% was attained for the LULC classification, while the class accuracies (PA: producer's accuracy and UA: user's accuracy) for the two cropping systems were consistently above 85%. We concluded that explicit mapping of different cropping systems is feasible in complex and highly fragmented agro-ecological landscapes if high resolution and multi-temporal satellite data such as 5 m RapidEye data is employed. Further research is needed on the feasibility of using freely available 10-20 m Sentinel-2 data for wide-area assessment of cropping systems as an important variable in numerous crop productivity models.

Predicting the continuum between corridors and barriers to animal movements using Step Selection Functions and Randomized Shortest Paths.

The loss, fragmentation and degradation of habitat everywhere on Earth prompts increasing attention to identifying landscape features that support animal movement (corridors) or impedes it (barriers). Most algorithms used to predict corridors assume that animals move through preferred habitat either optimally (e.g. least cost path) or as random walkers (e.g. current models), but neither extreme is realistic. We propose that corridors and barriers are two sides of the same coin and that animals experience landscapes as spatiotemporally dynamic corridor-barrier continua connecting (separating) functional areas where individuals fulfil specific ecological processes. Based on this conceptual framework, we propose a novel methodological approach that uses high-resolution individual-based movement data to predict corridor-barrier continua with increased realism. Our approach consists of two innovations. First, we use step selection functions (SSF) to predict friction maps quantifying corridor-barrier continua for tactical steps between consecutive locations. Secondly, we introduce to movement ecology the randomized shortest path algorithm (RSP) which operates on friction maps to predict the corridor-barrier continuum for strategic movements between functional areas. By modulating the parameter Ѳ, which controls the trade-off between exploration and optimal exploitation of the environment, RSP bridges the gap between algorithms assuming optimal movements (when Ѳ approaches infinity, RSP is equivalent to LCP) or random walk (when Ѳ → 0, RSP → current models). Using this approach, we identify migration corridors for GPS-monitored wild reindeer (Rangifer t. tarandus) in Norway. We demonstrate that reindeer movement is best predicted by an intermediate value of Ѳ, indicative of a movement trade-off between optimization and exploration. Model calibration allows identification of a corridor-barrier continuum that closely fits empirical data and demonstrates that RSP outperforms models that assume either optimality or random walk. The proposed approach models the multiscale cognitive maps by which animals likely navigate real landscapes and generalizes the most common algorithms for identifying corridors. Because suboptimal, but non-random, movement strategies are likely widespread, our approach has the potential to predict more realistic corridor-barrier continua for a wide range of species.

Microfluidic-based photocatalytic microreactor for environmental application: a review of fabrication substrates and techniques, and operating parameters.

Photochemical technology with microfluidics is emerging as a new platform in environmental science. Microfluidic technology has various advantages, like better mixing and a shorter diffusion distance for the reactants and products; and uniform distribution of light on the photocatalyst. Depending on the material type and related applications, several fabrication techniques have been adopted by various researchers. Microreactors have been prepared by various techniques, such as lithography, etching, mechanical microcutting technology, etc. Lithography can be classified into photolithography, soft lithography and X-ray lithography techniques whereas the etching process is divided into wet etching (chemical etching) and dry etching (plasma etching) techniques. Several substrates, like polymers, such as polydimethyl-siloxane (PDMS), polymethyle-methacrylate (PMMA), hydrogel, etc.; metals, such as stainless steel, titanium foil, etc.; glass, such as silica capillary, glass slide, etc.; and ceramics have been used for microchannel fabrication. During degradation in a microreactor, the degradation efficiency is affected by few important parameters such as flow rate, initial concentration of the target compound, microreactor dimensions, light intensity, photocatalyst structure and catalyst support. The present paper discusses and critically reviews fabrication techniques and substrates used for microchannel fabrication and critical operating parameters for organics, especially dye degradation in the microreactor. The kinetics of degradation has also been discussed.

Aqueous Mesocosm Techniques Enabling the Real-Time Measurement of the Chemical and Isotopic Kinetics of Dissolved Methane and Carbon Dioxide.

Previous studies of microbially mediated methane oxidation in oceanic environments have examined the many different factors that control the rates of oxidation. However, there is debate on what factor(s) are limiting in these types of environments. These factors include the availability of methane, O2, trace metals, nutrients, the density of cell population, and the influence that CO2 production may have on pH. To look at this process in its entirety, we developed an automated mesocosm incubation system with a Dissolved Gas Analysis System (DGAS) coupled to a myriad of analytical tools to monitor chemical changes during methane oxidation. Here, we present new high temporal resolution techniques for investigating dissolved methane and carbon dioxide concentrations and stable isotopic dynamics during aqueous mesocosm and pure culture incubations. These techniques enable us to analyze the gases dissolved in solution and are nondestructive to both the liquid media and the analyzed gases enabling the investigation of a mesocosm or pure culture experiment in a completely closed system, if so desired.

BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology.

BACKGROUND: Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as "Web services") and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust "in silico" science. However, use of this approach in biodiversity science and ecology has thus far been quite limited. RESULTS: BioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on-line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible 'virtual laboratory', free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity. CONCLUSIONS: Our work shows we can deliver an operational, scalable and flexible Internet-based virtual laboratory to meet new demands for data processing and analysis in biodiversity science and ecology. In particular, we have successfully integrated existing and popular tools and practices from different scientific disciplines to be used in biodiversity and ecological research.

A novel method for capturing and monitoring a small neotropical primate, the squirrel monkey (Saimiri collinsi).

Squirrel monkeys (genus Saimiri) are agile, arboreal primates that are seldom captured in the wild due to their small body size (<1 kg) and large, non-cohesive social groups (40-50 individuals). However, long-term studies on these primates often require captures and permanent identification of individuals, in order to monitor their behavior and health. Here we report on a novel trapping method successfully used to capture Saimiri collinsi, in Eastern Amazonia, Brazil. Our objective was to capture as many individuals as possible from one social group of approximately 50 individuals, ranging over 150 ha of terra firme forest. Captures occurred in November and December 2013. We habituated animals to feed on a large platform located in a 123.5 m(2) area enclosed by a green net (3 m high). Multiple individuals could freely enter and exit the area via four ropes affixed from surrounding trees to the platform. Once individuals were feeding inside the netted area on selected trapping days, the ropes were dropped remotely, eliminating their escape routes. We successfully trapped 21 different individuals of the social group (14 adults and 7 immatures) with this method. We conclude that this is a conceptually simple, effective method for trapping squirrel monkeys in most habitats, and possibly other small arboreal primates that live in large social groups. The present method was more effective than previous methods utilized to capture squirrel monkeys in the field, and has the advantages of: allowing for safe capture of several individuals simultaneously; enabling re-captures; releasing of animals as a group at the site of capture; use of soft netting which facilitates safe capture of the monkeys.

Siting algae cultivation facilities for biofuel production in the United States: trade-offs between growth rate, site constructability, water availability, and infrastructure.

Locating sites for new algae cultivation facilities is a complex task. The climate must support high growth rates, and cultivation ponds require appropriate land and water resources, as well as transportation and utility infrastructure. We employ our spatiotemporal Biomass Assessment Tool (BAT) to select promising locations based on the open-pond cultivation of Arthrospira sp. and strains of the order Sphaeropleales. A total of 64,000 sites across the southern United States were evaluated. We progressively applied screening criteria and tracked their impact on the number of potential sites, geographic location, and biomass productivity. Both strains demonstrated maximum productivity along the Gulf of Mexico coast, with the highest values on the Florida peninsula. In contrast, sites meeting all selection criteria for Arthrospira were located along the southern coast of Texas and for Sphaeropleales were located in Louisiana and southern Arkansas. Results were driven mainly by the lack of oil pipeline access in Florida and elevated groundwater salinity in southern Texas. The requirement for low-salinity freshwater (<400 mg L(-1)) constrained Sphaeropleales locations; siting flexibility is greater for salt-tolerant species like Arthrospira. Combined siting factors can result in significant departures from regions of maximum productivity but are within the expected range of site-specific process improvements.

Climate and atmosphere simulator for experiments on ecological systems in changing environments.

Grand challenges in global change research and environmental science raise the need for replicated experiments on ecosystems subjected to controlled changes in multiple environmental factors. We designed and developed the Ecolab as a variable climate and atmosphere simulator for multifactor experimentation on natural or artificial ecosystems. The Ecolab integrates atmosphere conditioning technology optimized for accuracy and reliability. The centerpiece is a highly contained, 13-m(3) chamber to host communities of aquatic and terrestrial species and control climate (temperature, humidity, rainfall, irradiance) and atmosphere conditions (O2 and CO2 concentrations). Temperature in the atmosphere and in the water or soil column can be controlled independently of each other. All climatic and atmospheric variables can be programmed to follow dynamical trajectories and simulate gradual as well as step changes. We demonstrate the Ecolab's capacity to simulate a broad range of atmospheric and climatic conditions, their diurnal and seasonal variations, and to support the growth of a model terrestrial plant in two contrasting climate scenarios. The adaptability of the Ecolab design makes it possible to study interactions between variable climate-atmosphere factors and biotic disturbances. Developed as an open-access, multichamber platform, this equipment is available to the international scientific community for exploring interactions and feedbacks between ecological and climate systems.

Working upstream: how far can you go with sewage-based drug epidemiology?

The field of drug epidemiology based upon sewer sampling has only emerged in the last 10 years and has great potential to aid in drug epidemiological studies. This rapidly expanding field can provide an unbiased look into the illicit drug habits of large populations as well as specific, smaller groups. How far the field has evolved is discussed as well as where the future for these types of monitoring studies could go.