Improving occupancy estimation when two types of observational error occur: non-detection and species misidentification

Efforts to draw inferences about species occurrence frequently account for false negatives, the common situation when individuals of a species are not detected even when a site is occupied. However, recent studies suggest the need to also deal with false positives, which occur when species are misidentified so that a species is recorded as detected when a site is unoccupied. Bias in estimators of occupancy, colonization, and extinction can be severe when false positives occur. Accordingly, we propose models that simultaneously account for both types of error. Our approach can be used to improve estimates of occupancy for study designs where a subset of detections is of a type or method for which false positives can be assumed to not occur. We illustrate properties of the estimators with simulations and data for three species of frogs. We show that models that account for possible misidentification have greater support (lower AIC for two species) and can yield substantially different occupancy estimates than those that do not. When the potential for misidentification exists, researchers should consider analytical techniques that can account for this source of error, such as those presented here.     

Flux capacities and acclimation costs in Trichodesmium from the Gulf of Mexico

Phytoplankton function and acclimation are driven by catalytic protein complexes that mediate key physiological transformations, including generation of photosynthetic ATP and reductant, and carbon and nitrogen fixation. Quantitation of capacities for these processes allows estimation of rates for key ecosystem processes, and identification of factors limiting primary productivity. We herein present molar quantitations of PSI, PSII, ATP synthase, RuBisCO and the Fe protein of nitrogenase of Trichodesmium collected from the Gulf of Mexico, in comparison to determinations for a range of cyanobacteria growing in culture. Using these measurements, estimates were generated for Trichodesmium capacities for carbon fixation of 1–3.4 g C g chl a ⁻¹ h⁻¹ and nitrogen fixation of 0.06–0.17 g N g chl a ⁻¹ h⁻¹, with diel variations in capacities. ATP synthase levels show that ATP synthesis capacity is sufficient to support these levels of carbon and nitrogen fixation, and that ATP synthase levels change over the day in accordance with the ATP demands of nitrogenase and RuBisCO activity. Levels of measured complexes indicate that Trichodesmium manifests n-type diel light acclimation through rapid changes in RuBisCO:PSII, supported by significant investment of cellular nitrogen. The plasticity in the levels and stoichiometry of these core complexes show that changes in the abundance of core protein complexes are an important component of acclimation and regulation of metabolic function by Trichodesmium populations. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Monitoring a changing Arctic: Recent advancements in the study of sea ice microbial communities

Sea ice continues to decline across many regions of the Arctic, with remaining ice becoming increasingly younger and more dynamic. These changes alter the habitats of microbial life that live within the sea ice, which support healthy functioning of the marine ecosystem and provision of resources for human-consumption, in addition to influencing biogeochemical cycles (e.g. air–sea CO₂ exchange). With the susceptibility of sea ice ecosystems to climate change, there is a pressing need to fill knowledge gaps surrounding sea ice habitats and their microbial communities. Of fundamental importance to this goal is the development of new methodologies that permit effective study of them. Based on outcomes from the DiatomARCTIC project, this paper integrates existing knowledge with case studies to provide insight on how to best document sea ice microbial communities, which contributes to the sustainable use and protection of Arctic marine and coastal ecosystems in a time of environmental change.Supplementary InformationThe online version contains supplementary material available at 10.1007/s13280-021-01658-z.     

Muskox status,recent variation,and uncertain future

Ambio - Muskoxen (Ovibos moschatus) are an integral component of Arctic biodiversity. Given low genetic diversity, their ability to respond to future and rapid Arctic change is unknown, although...     

Integrated emergy,energy and economic evaluation of rice and vegetable production systems in alluvial paddy fields: Implications for agricultural policy in China

China is the largest rice producing and consuming country in the world, but rice production has given way to the production of vegetables during the past twenty years. The government has been trying to stop this land-use conversion and increase the area in rice-vegetable rotation. Important questions that must be answered to determine what strategy is best for society are, “What is the reason behind this conversion?”; “Which system is more productive and which is more sustainable?”; and “How can economic policy be used to adjust the pattern of farmland use to attain sustainable development?” To answer these questions, a combined evaluation of these agricultural production systems was done using emergy, energy and economic methods. An economic analysis clearly showed that the reason for this conversion was simply that the economic output/input ratio and the benefit density of the vegetable production system were greater than that of rice. However, both energy and emergy evaluations showed that long-term rice was the best choice for sustainable development, followed by rotation systems. The current price of rice is lower than the em-value of rice produced from the long-term rice system, but higher than that of rice produced from the rotation system. Scenario analysis showed that if the government increases the price of rice to the em-value of rice produced from the long-term rice system, US$0.4/kg, and takes the value of soil organic matter into account, the economic output/input ratios of both the rice and rotation systems will be higher than that of the vegetable system. The three methods, energy, emergy and economics, are different but complementary, each revealing a different aspect of the same system. Their combined use shows not only the reasons behind a system’s current state or condition, but also the way to adjust these systems to move toward more sustainable states.     

Concentrations of mobile source air pollutants in urban microenvironments

Human exposures to criteria and hazardous air pollutants (HAPs) in urban areas vary greatly due to temporal-spatial variations in emissions, changing meteorology, varying proximity to sources, as well as due to building, vehicle, and other environmental characteristics that influence the amounts of ambient pollutants that penetrate or infiltrate into these microenvironments. Consequently, the exposure estimates derived from central-site ambient measurements are uncertain and tend to underestimate actual exposures. The Exposure Classification Project (ECP) was conducted to measure pollutant concentrations for common urban microenvironments (MEs) for use in evaluating the results of regulatory human exposure models. Nearly 500 sets of measurements were made in three Los Angeles County communities during fall 2008, winter 2009, and summer 2009. MEs included in-vehicle, near-road, outdoor, and indoor locations accessible to the general public. Contemporaneous 1- to 15-min average personal breathing zone concentrations of carbon monoxide (CO), carbon dioxide (CO₂), volatile organic compounds (VOCs), nitric oxide (NO), nitrogen oxides (NO_x), particulate matter (<2.5 μm diameter; PM_2.5) mass, ultrafine particle (UFP; <100 nm diameter) number, black carbon (BC), speciated HAPs (e.g., benzene, toluene, ethylbenzene, xylenes [BTEX], 1,3-butadiene), and ozone (O₃) were measured continuously. In-vehicle and inside/outside measurements were made in various passenger vehicle types and in public buildings to estimate penetration or infiltration factors. A large fraction of the observed pollutant concentrations for on-road MEs, especially near diesel trucks, was unrelated to ambient measurements at nearby monitors. Comparisons of ME concentrations estimated using the median ME/ambient ratio versus regression slopes and intercepts indicate that the regression approach may be more accurate for on-road MEs. Ranges in the ME/ambient ratios among ME categories were generally greater than differences among the three communities for the same ME category, suggesting that the ME proximity factors may be more broadly applicable to urban MEs.

Implications:Estimates of population exposure to air pollutants extrapolated from ambient measurements at ambient fixed site monitors or exposure surrogates are prone to uncertainty. This study measured concentrations of mobile source air toxics (MSAT) and related criteria pollutants within in-vehicle, outdoor near-road, and indoor urban MEs to provide multipollutant ME measurements that can be used to calibrate regulatory exposure models.     

The Financial Impact of Different Stormwater Fee Types: A Case Study of Two Municipalities in Virginia

Eight stormwater user fees (SUFs) were applied to the City of Roanoke and the Town of Blacksburg, Virginia, to determine the effect each has on how land use type impacts the sources of revenue. Roanoke is larger and includes more industrial areas, but less multifamily impervious areas than Blacksburg, which translates differently in the SUFs. Residential parcels comprise the highest percentage of the revenue in all eight SUFs in Blacksburg and four in Roanoke. For both municipalities, two specific SUFs consistently comprised the highest percentage burden for residential homeowners while three other SUFs demonstrated the highest burden for commercial parcels. Open space parcels contain little impervious area, yet account for up to 27% of the revenue in the Blacksburg Area fee structure. Industrial parcels comprise more revenue in Roanoke, averaging 10.1‐4.5% in Blacksburg. Fee types that are easier to administer (e.g., Flat fees) may not fully represent the stormwater contribution from the parcels. SUF types that more accurately represent the stormwater burden on the municipality are also more administratively intensive and are more variable with fee factors.     

Simulated management effects on ammonia emissions from field applied manure

A need exists to improve the utilization of manure nutrients by minimizing NH₃ emissions from land application of manure. Management strategies to reduce NH₃ emissions are available; however, few have been validated under Canadian conditions. A well tested and accurate simulation model, however, can help overcome this challenge by determining appropriate management strategies for a given set of field conditions.     

Measuring the effectiveness of landscape approaches to conservation and development

Landscape approaches attempt to achieve balance amongst multiple goals over long time periods and to adapt to changing conditions. We review project reports and the literature on integrated landscape approaches, and found a lack of documented studies of their long-term effectiveness. The combination of multiple and potentially changing goals presents problems for the conventional measures of impact. We propose more critical use of theories of change and measures of process and progress to complement the conventional impact assessments. Theories of change make the links between project deliverables, outputs, outcomes, and impacts explicit, and allow a full exploration of the landscape context. Landscape approaches are long-term engagements, but short-term process metrics are needed to confirm that progress is being made in negotiation of goals, meaningful stakeholder engagement, existence of connections to policy processes, and effectiveness of governance. Long-term impact metrics are needed to assess progress on achieving landscapes that deliver multiple societal benefits, including conservation, production, and livelihood benefits. Generic criteria for process are proposed, but impact metrics will be highly situation specific and must be derived from an effective process and a credible theory of change.     

Investigation of the Ultraviolet Photolysis Method for the Determination of Organic Nitrogen in Aerosol Samples

Abstract

The research objective was to adapt the ultraviolet (UV)photolysis method to determine dissolved organic nitrogen (DON) in aqueous extracts of aerosol samples. DON was assumed to be the difference in total concentration of inorganic nitrogen forms before and after sample irradiation. Using a 2² factorial design the authors found that the optimal conversion of urea, amino acids (alanine, aspartic acid, glycine, and serine), and methylamine for a reactor temperature of 44 °C occurred at pH 2.0 with a 24-hr irradiance period at concentrations < µM of organic nitrogen. Different decomposition mechanisms were evident: the photolysis of amino acids and methylamine released mainly ammonium (NH₄ ⁺), but urea released a near equimolar ratio of NH₄ ⁺ and nitrate (NO₃ ^?). The method was applied to measure DON in the extracts of aerosol samples from Tampa, FL, over a 32-day sampling period. Average dissolved inorganic (DIN) and DON concentrations in the particulate matter fraction PM₁₀ were 78.1 ± 29.2 nmol-Nm^?3and 8.3 ± 4.9 nmol-Nm^?3, respectively. The ratio between DON and total dissolved nitrogen ([TDN] = DIN + DON) was 10.1 ± 5.7%, and the majority of the DON (79.1 ± 18.2%) was found in the fine particulate matter (PM_2.5) fraction. The average concentrations of DIN and DON in the PM_2.5 fraction were 54.4 ± 25.6 nmol-Nm^?3 and 6.5 ± 4.4 nmol-Nm^?3, respectively.