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ANIMAL TRAFFIC: Lively Capital in the Global Exotic Pet Trade: By Rosemary-Claire Collard. First is the erasure of social relations that occurs in the commodity fetishism explained by traditional Marxian analyses, and second is Collard's assertion of the erasure of the animals' socio-ecological relations in their (former) biotic communities. These traits are what provide "use value" for humans, and Collard explains that for the commodity transformation to happen, exotic animals "are subject to a double fetishism" (p. 18). [Extracted from the article]

Soil erosion from steep slopes, bare soil, or construction sites is a problem that can create on-site gullies, make revegetation difficult, and adversely affect downstream water bodies and aquatic ecosystems. Mulches have been widely used to mitigate the effects of erosion. One common type of mulch, hydro-mulch, uses shredded wood or paper that is mixed with water and applied with an applicator gun. In this study, conventional wood and paper hydro-mulches were compared with cottonseed hulls and three types of processed cotton gin by-products. The mulches were applied at two rates, 1121 and 2242 kg/ha (1000 and 2000 lb/acre). Comparisons were made on the time to runoff, sediment loss, mulch loss, and mulch coverage (C-Factor). The cottonbased mulches (cottonseed hulls and cotton gin by-products) performed equal to or better than conventional wood and paper mulches in reducing soil loss during a simulated 6.35-cm/h (2.5-in/h) rainfall intensity event. Likewise, a lower percentage of the cotton-based mulches were washed-off during the rain event than with the conventional wood and paper hydro-mulches. The coverage factor and the time to runoff associated with the wood and paper mulches were higher than for any of the cotton-based mulches. Overall, the cotton-based mulches showed promise in erosion control applications. [ABSTRACT FROM AUTHOR]

Knowing what the highest-level mammalian carnivores and intermediate levels eat throughout the geography and how human activities may affect their community dynamics is relevant information to focusing and deciding on conservation efforts within a territory. In this review, we characterize geographically the accumulated knowledge about the trophic niche of terrestrial mammalian carnivore species and evaluate the spatial relationship between the species richness distribution and the geographical distribution of their trophic knowledge in Chile. We found 88 peer-reviewed papers that include trophic studies per se, theses, and short notes carried out in Chile, where at least one trophic element was reported for terrestrial mammalian carnivore species. We found a positive relationship between the species richness distribution pattern and the spatial distribution of accumulated trophic knowledge, i.e., most of the papers have been conducted in Central-southern Chile (Central Chile and Temperate Forest ecoregions) responding to the highest co-occurrence of carnivore species within the limits of the biodiversity hotspot, the most threatened area in the country. Despite this general relationship, we recognize gaps in knowledge regarding regions of the country that require more research effort, such as O'Higgins, Maule, and Ñuble regions, as well as focus efforts on certain species with no or almost no knowledge of their trophic ecology, such as Leopardus colocola, Lyncodon patagonicus and Conepatus chinga. Except for the northern Chilean ecosystems, there is a generalized report of high consumption of exotic mammals in the diet of carnivores in the center and south of the country. However, of the 98 localities recognized in the 88 papers, 20.4% correspond to an anthropized environment, while most (79.6%) correspond to a "non-anthropized" environment or protected area. We hope this review allows researchers and decision-makers to consider the knowledge and lack thereof of carnivore trophic interactions as an opportunity to conserve entire natural communities throughout the Chilean territory. [ABSTRACT FROM AUTHOR]

We respond to comments made in the opinion paper by Ainley et al. (Hydrobiologia, 10.1007/s10750-015-2607-4, ) regarding our recent publication on the biology, ecology and life history of Antarctic toothfish ( Dissostichus mawsoni) in the Ross Sea region. We focus in particular on the spatial and temporal extent of data collected from the fishery; results of research to date on changes in abundance and size of Antarctic toothfish at McMurdo Sound; and the subject of neutral buoyancy and inferences about vertical distribution. We conclude by re-iterating the need for well-designed, standardised research programmes to address remaining uncertainties in its life history. [ABSTRACT FROM AUTHOR]

Biodiversity is essential to the viability of ecological systems. Species diversity in ecosystems is promoted by cyclic, non-hierarchical interactions among competing populations. Central features of such non-transitive relations are represented by the ‘rock–paper–scissors’ game, in which rock crushes scissors, scissors cut paper, and paper wraps rock. In combination with spatial dispersal of static populations, this type of competition results in the stable coexistence of all species and the long-term maintenance of biodiversity. However, population mobility is a central feature of real ecosystems: animals migrate, bacteria run and tumble. Here, we observe a critical influence of mobility on species diversity. When mobility exceeds a certain value, biodiversity is jeopardized and lost. In contrast, below this critical threshold all subpopulations coexist and an entanglement of travelling spiral waves forms in the course of time. We establish that this phenomenon is robust; it does not depend on the details of cyclic competition or spatial environment. These findings have important implications for maintenance and temporal development of ecological systems and are relevant for the formation and propagation of patterns in microbial populations or excitable media. [ABSTRACT FROM AUTHOR]

Abstract: Archives and libraries all over the world suffer from biodeterioration of writings caused by microorganisms, especially fungi. With traditionally used culture-dependent methods, only a small amount of effectively colonising organisms is detected. Restoration and maintenance of written cultural heritage is therefore problematic due to incomplete knowledge of the deterioration agents. In the present study, culture-independent molecular methods were applied to identify fungal communities colonising paper samples of different composition and age. Nucleic-acid-based strategies targeting the internally transcribed spacer (ITS) regions, which are nested in the nuclear rDNA repeats, were selected to investigate the fungal diversity on paper. The ITS regions possess a high variation among taxonomically distinct fungal species and even within the species. With this aim, several molecular biological methods were optimised for working with paper materials. Here, we introduce a DNA extraction protocol, which allowed the direct extraction of PCR-amplifiable DNA from samples derived from different kinds of paper. The DNA extracts were used to amplify either the ITS1 or ITS2 region by using different fungi-specific primer sets. The ITS-amplified regions were subsequently analysed by denaturing gradient gel electrophoresis (DGGE). Conditions for DGGE analysis, gradient, voltage, and running time, were established to accurately discriminate different fungal species in complex communities. Pure fungal strains were used to constitute a marker for further comparative investigations of historic papers. [Copyright &y& Elsevier]

Background: The National Cancer Institute Informatics Technology for Cancer Research (ITCR) program provides a series of funding mechanisms to create an ecosystem of open-source software (OSS) that serves the needs of cancer research. As the ITCR ecosystem substantially grows, it faces the challenge of the long-term sustainability of the software being developed by ITCR grantees. To address this challenge, the ITCR sustainability and industry partnership working group (SIP-WG) was convened in 2019.Objective: The charter of the SIP-WG is to investigate options to enhance the long-term sustainability of the OSS being developed by ITCR, in part by developing a collection of business model archetypes that can serve as sustainability plans for ITCR OSS development initiatives. The working group assembled models from the ITCR program, from other studies, and from the engagement of its extensive network of relationships with other organizations (eg, Chan Zuckerberg Initiative, Open Source Initiative, and Software Sustainability Institute) in support of this objective.Methods: This paper reviews the existing sustainability models and describes 10 OSS use cases disseminated by the SIP-WG and others, including 3D Slicer, Bioconductor, Cytoscape, Globus, i2b2 (Informatics for Integrating Biology and the Bedside) and tranSMART, Insight Toolkit, Linux, Observational Health Data Sciences and Informatics tools, R, and REDCap (Research Electronic Data Capture), in 10 sustainability aspects: governance, documentation, code quality, support, ecosystem collaboration, security, legal, finance, marketing, and dependency hygiene.Results: Information available to the public reveals that all 10 OSS have effective governance, comprehensive documentation, high code quality, reliable dependency hygiene, strong user and developer support, and active marketing. These OSS include a variety of licensing models (eg, general public license version 2, general public license version 3, Berkeley Software Distribution, and Apache 3) and financial models (eg, federal research funding, industry and membership support, and commercial support). However, detailed information on ecosystem collaboration and security is not publicly provided by most OSS.Conclusions: We recommend 6 essential attributes for research software: alignment with unmet scientific needs, a dedicated development team, a vibrant user community, a feasible licensing model, a sustainable financial model, and effective product management. We also stress important actions to be considered in future ITCR activities that involve the discussion of the sustainability and licensing models for ITCR OSS, the establishment of a central library, the allocation of consulting resources to code quality control, ecosystem collaboration, security, and dependency hygiene. [ABSTRACT FROM AUTHOR]

Atmospheric changes could strongly influence how terrestrial ecosystems function by altering nutrient cycling. We examined how the dynamics of nutrient release from leaf litter responded to two important atmospheric changes: rising atmospheric CO2 and tropospheric O3. We evaluated the independent and combined effects of these gases on foliar litter nutrient dynamics in aspen ( Populus tremuloides Michx) and birch ( Betula papyrifera Marsh)/aspen communities at the Aspen FACE Project in Rhinelander, WI. Naturally senesced leaf litter was incubated in litter bags in the field for 735 days. Decomposing litter was sampled six times during incubation and was analyzed for carbon, and both macro (N, P, K, S, Ca, and Mg) and micro (Mn, B, Zn and Cu) nutrient concentrations. Elevated CO2 significantly decreased the initial litter concentrations of N (−10.7%) and B (−14.4%), and increased the concentrations of K (+23.7%) and P (+19.7%), with no change in the other elements. Elevated O3 significantly decreased the initial litter concentrations of P (−11.2%), S (−8.1%), Ca (−12.1%), and Zn (−19.5%), with no change in the other elements. Pairing concentration data with litterfall data, we estimated that elevated CO2 significantly increased the fluxes to soil of all nutrients: N (+12.5%), P (+61.0%), K (+67.1%), S (+28.0%), and Mg (+40.7%), Ca (+44.0%), Cu (+38.9%), Mn (+62.8%), and Zn (+33.1%). Elevated O3 had the opposite effect: N (−22.4%), P (−25.4%), K (−27.2%), S (−23.6%), Ca (−27.6%), Mg (−21.7%), B (−16.2%), Cu (−20.8%), and Zn (−31.6%). The relative release rates of the nine elements during the incubation was: K ≥ P ≥ mass ≥ Mg ≥ B ≥ Ca ≥ S ≥ N ≥ Mn ≥ Cu ≥ Zn. Atmospheric changes had little effect on nutrient release rates, except for decreasing Ca and B release under elevated CO2 and decreasing N and Ca release under elevated O3. We conclude that elevated CO2 and elevated O3 will alter nutrient cycling more through effects on litter production, rather than litter nutrient concentrations or release rates. [ABSTRACT FROM AUTHOR]

Human activities are increasing the concentrations of atmospheric carbon dioxide ([CO2]) and tropospheric ozone ([O3]), potentially leading to changes in the quantity and chemical quality of leaf litter inputs to forest soils. Because the quality and quantity of labile and recalcitrant carbon (C) compounds influence forest productivity through changes in soil organic matter content, characterizing changes in leaf litter in response to environmental change is critical to understanding the effects of global change on forests. We assessed the independent and combined effects of elevated [CO2] and elevated [O3] on foliar litter production and chemistry in aspen (Populus tremuloides Michx.) and birch–(Betula papyrifera Marsh.) aspen communities at the Aspen free-air CO2 enrichment (FACE) experiment in Rhinelander, WI. Litter was analyzed for concentrations of C, nitrogen (N), soluble sugars, lipids, lignin, cellulose, hemicellulose and C-based defensive compounds (soluble phenolics and condensed tannins). Concentrations of these chemical compounds in naturally senesced litter were similar in aspen and birch–aspen communities among treatments, except for N, the C:N ratio and lipids. Elevated [CO2] significantly increased C:N (+8.7%), lowered mean litter N concentration (–10.7%) but had no effect on the concentrations of soluble sugars, soluble phenolics and condensed tannins. Elevated [CO2] significantly increased litter biomass production (+33.3%), resulting in significant increases in fluxes of N, soluble sugars, soluble phenolics and condensed tannins to the soil. Elevated [O3] significantly increased litter concentrations of soluble sugars (+78.1%), soluble phenolics (+53.1%) and condensed tannins (+77.2%). There were no significant effects of elevated [CO2] or elevated [O3] on the concentrations of individual C structural carbohydrates (cellulose, hemicellulose and lignin). Elevated [CO2] significantly increased cellulose (+37.4%) input to soil, whereas elevated [O3] significantly reduced hemicellulose and lignin inputs to soil (–22.3 and –31.5%, respectively). The small changes in litter chemistry in response to elevated [CO2] and tropospheric [O3] that we observed, combined with changes in litter biomass production, could significantly alter the inputs of N, soluble sugars, condensed tannins, soluble phenolics, cellulose and lignin to forest soils in the future. [ABSTRACT FROM PUBLISHER]

The article offers news briefs in the U.S. Australian radiosondes monitor a large area of the Southern Hemisphere have experienced so many changes that unadjusted temperature trends of the bulk atmosphere computed from their soundings are suspect. Quantification of carbon exchange in forest ecosystems needs a unique sampling strategy. Strong vertical wind shear usually will weaken even mature hurricanes.

Nitrogen cycling in northern temperate forest ecosystems could change under increasing atmospheric CO2 and tropospheric O3 as a result of quantitative and qualitative changes in plant litter production. At the Aspen Free Air CO2–O3 Enrichment (FACE) experiment, we previously found that greater substrate inputs to soil under elevated CO2 did not alter gross N transformation rates in the first 3 years of the experiment. We hypothesized that greater litter production under elevated CO2 would eventually cause greater gross N transformation rates and that CO2 effects would be nullified by elevated O3. Following our original study, we continued measurement of gross N transformation rates for an additional four years. From 1999 to 2003, gross N mineralization doubled, N immobilization increased 4-fold, but changes in microbial biomass N and soil total N were not detected. We observed year-to-year variation in N transformation rates, which peaked during a period of foliar insect damage. Elevated CO2 caused equivalent increases in gross rates of N mineralization (+34%) and NH immobilization (+36%). These results indicate greater rates of N turnover under elevated CO2, but do not indicate a negative feedback between elevated CO2 and soil N availability. Elevated O3 decreased gross N mineralization (−16%) and had no effect on NH immobilization, indicating reduced N availability under elevated O3. The effects of CO2 and O3 on N mineralization rates were mainly related to changes in litter production, whereas effects on N immobilization were likely influenced by changes in litter chemistry and production. Our findings also indicate that concomitant increases in atmospheric CO2 and O3 could lead to a negative feedback on N availability. [ABSTRACT FROM AUTHOR]

The restoration of degraded ecosystems can be constrained by uncertainty over former conditions and the relevance of the past given recent changes. It can be difficult to differentiate among contrasting hypotheses about past ecosystem function, and restoration efforts can emphasize species reestablishment without integrating the ecological and cultural processes that once determined their occurrence. As a case study, we analyzed historical descriptions of an endangered oak grassland ecosystem in southwestern British Columbia, Canada, to determine former conditions and assess their validity for defining restoration targets. Twenty-three documents described this ecosystem from 1790 to 1951. Comparison of early survey records with contemporary occurrences suggests habitat loss of >95%. The identity and former range of most native plant species were poorly described, but accounts of ecosystem structure revealed a diversity of floral communities that has been much simplified. Fire, most likely set by indigenous peoples, interacted with edaphic and topographic factors to create this structural diversity. European settlers intensively modified the ecosystem with grazing, cultivation, and introduced flora. These transformations partly explain the current high levels of plant invasion. Restoration must target the ecosystems' former structural diversity and the ecological and cultural processes that maintained it. Given the recent impacts of fire suppression, habitat loss, and plant invasion, however, land managers must balance the reestablishment of historical processes with their potential negative effects in sites with numerous at-risk species. This ecosystem was, and remains, part of a culturally modified landscape, where human activity has maintained unforested areas for millennia but now promotes mostly exotic flora. Although pre-European conditions cannot be fully restored, the historical data provided restoration insights unobtainable from current biological studies emphasizing the end point of long-term ecological change. [ABSTRACT FROM AUTHOR]

To determine if non-native plant species are homogenizing species composition among widely dispersed plant communities. Twenty localities in North America. Species lists among localities were compared to measure the influence of non-native species richness at each locality on the Jaccard Index (JI) of similarity between localities. After removing the effects of distance, because shared native species decreased with distance, three (nonexclusive) lines of evidence indicate that non-native species promote homogenization. First, pairs of sites with a high combined total of non-native species tend to have higher similarity than those with a low total of non-natives. Second, for a given distance, more non-native than native species tended to be shared among localities. Third, whereas most of the site comparisons with high total non-native richness have a non-native/native JI ratio greater than 1 (often much greater), only half of the comparisons with low total non-native richness have a ratio greater than one. These findings provide quantitative support for the widely held, but rarely tested, notion that non-native species tend to homogenize biological communities because they are more commonly shared among communities. Such testing is important as non-native species could theoretically have no impact or even reduce homogenization among communities, if non-native colonizers consist of different species pools. [ABSTRACT FROM AUTHOR]

Extensive dieback of salt marsh dominated by the perennial grass Spartina alterniflora occurred throughout the Mississippi River deltaic plain during 2000. More than 100,000 ha were affected, with 43,000 ha severely damaged. The aim of this work was to determine if sudden dieback could have been caused by a coincident drought and to assess the significance of this event with respect to long-term changes in coastal vegetation. Multiple dieback sites and reference sites were established along 150 km of shoreline in coastal Louisiana, USA. Aerial and ground surveys were conducted from June 2000 to September 2001 to assess soil conditions and plant mortality and recovery. Dieback areas ranged in size from ∼300 m2−5 km2 in area with 50–100% mortality of plant shoots and rhizomes in affected zones. Co-occurring species such as Avicennia germinans (black mangrove) and Juncus roemerianus (needlegrass rush) were unaffected. Historical records indicate that precipitation, river discharge, and mean sea level were unusually low during the previous year. Although the cause of dieback is currently unknown, plant and soil characteristics were consistent with temporary soil desiccation that may have reduced water availability, increased soil salinity, and/or caused soil acidification (via pyrite oxidation) and increased uptake of toxic metals such as Fe or Al. Plant recovery 15 months after dieback was variable (0–58% live cover), but recovering plants were vigorous and indicated no long-lasting effects of the dieback agent. These findings have relevance for global change models of coastal ecosystems that predict vegetation responses based primarily on long-term increases in sea level and submergence of marshes. Our results suggest that large-scale changes in coastal vegetation may occur over a relatively short time span through climatic extremes acting in concert with sea-level fluctuations and pre-existing soil conditions. [ABSTRACT FROM AUTHOR]

In Canada, Environmental Effects Monitoring (EEM) programs exist within two regulations: the Pulp and Paper Effluent Regulations and the new Metal Mining Effluent Regulations under the Canadian Fisheries Act. EEM provides a biological, effects-based feedback loop to assess the effectiveness of technology-based regulations in protecting receiving environments. The promulgation of the Pulp and Paper Effluent Regulations, in 1992, represented a significant step forward in the Canadian regulatory approach by incorporating directly into a regulation a requirement to assess the effects of effluent discharges on receiving environments using proven scientific monitoring methodologies. Similarly, an assessment of the aquatic impacts of mines resulted in recommendations to amend the Metal Mining Effluent Regulations, recently promulgated in 2002, and includes an EEM program as a science-based feedback loop. As such, these regulations recognize the possibility that national, technology-based standards may not necessarily protect all receiving environments because of the diversity and variability of both discharges and receiving sites across the country. Since that time, EEM has improved its flexibility by considering both advances in science and the uniqueness of monitoring sites across Canada to allow the most appropriate and cost-effective monitoring approaches at each site while maintaining national consistency. This paper discusses the use of monitoring under two Canadian regulations to assess effects on aquatic ecosystems. As well, the National EEM approach to maintaining up-to-date scientific practices in a national regulatory program is discussed using examples. [ABSTRACT FROM AUTHOR]

This paper presents the application of the Linear Quadratic Optimal Control (LQOC) method for a parameter optimization problem in a marine ecosystem model. The ecosystem model simulates the distribution of nitrogen, phytoplankton, zooplankton and detritus in a water column with temperature and turbulent diffusivity profiles taken from a three-dimensional ocean circulation model.We present the linearization method which is based on the available observations. The linearization is necessary to apply the LQOC method on the nonlinear system of state equations. We show the form of the linearized time-variant problems and the resulting two algebraic Riccati Equations. By using the LQOC method, we are able to introduce temporally varying periodic model parameters and to significantly improve -- compared to the use of constant parameters -- the fit of the model output to given observational data. [ABSTRACT FROM AUTHOR]

A new generation of an Earth System Model now includes a number of land surface processes directly relevant to analyzing potential impacts of climate change. This model, HadGEM2-ES, allows us to assess the impacts of climate change, multiple interactions, and feedbacks as the model is run. This paper discusses the results of century-scale HadGEM2-ES simulations from an impacts perspective--specifically, terrestrial ecosystems and water resources--for four different scenarios following the Representative Concentration Pathways (RCPs), being used for next assessment report of the Intergovernmental Panel on Climate Change (IPCC). Over the 21st Century, simulated changes in global and continential-scale terrestrial ecosystems due to climate change appear to be very similar in all 4 RCPs, even though the level of global warming by the end of the 21st Century ranges from 2°C in the lowest scenario to 5.5°in the highest. A warming climate generally favours broadleaf trees over needleleaf, needleleaf trees over shrubs, and shrubs over herbaceous vegetation, resulting in a poleward shift of temperate and boreal forests and woody tundra in all scenarios. Although climate related changes are slightly larger in scenarios of greater warming, the largest differences between scenarios arise at regional scales as a consequence of different patterns of anthropogenic land cover change. In the model, the scenario with the lowest global warming results in the most extensive decline in tropical forest cover due to a large expansion of agriculture. Under all four RCPs, fire potential could increase across extensive land areas, particularly tropical and sub-tropical latitudes. River outflows are simulated to increase with higher levels of CO2 and global warming in all projections, with outflow increasing with mean temperature at the end of the 21st Century at the global scale and in North America, Asia, and Africa. In South America, Europe, and Australia, the relationship with climate warming and CO2 rise is less clear, probably as a result of land cover change exerting a dominant effect in those regions. [ABSTRACT FROM AUTHOR]

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We address the question why papers dealing with the ecology of primates are so sparsely represented in the general ecological literature. A literature analyses based on entries in Web of Science and PrimateLit reveals that despite a large number of papers published on primates in general and on the ecology of primates, only a very small fraction of these papers is published in high-ranking international ecological journals. We discuss a number of potential reasons for the disproportion and highlight the problems associated with experimental research on wild primates and constraints on sample size as major issues. [ABSTRACT FROM AUTHOR]

Coastal hypoxia and anoxia have become a global key stressor to marine ecosystems, with almost 500 dead zones recorded wordwide. By triggering cascading effects from the individual organism to the community and ecosystem-level, oxygen depletions threat marine biodiversity and can alter ecosystem structure and function. By integrating both physiological function and ecological processes, animal behaviour is ideal for assessing the stress state of benthic macrofauna to low dissolved oxygen. The initial response of organisms can serve as an early-warning signal, while the successive behavioural reactions of key species indicate hypoxia levels and help assess community degradation. Here we document the behavioural responses of a representative spectrum of benthic macrofauna in the natural setting in the Northern Adriatic Sea, Mediterranean. We experimentally induced small-scale anoxia with a benthic chamber in 24 m depth to overcome the difficulties in predicting the onset of hypoxia, which often hinders full documentation in the field. The behavioural reactions were documented with a time-lapse camera. Oxygen depletion elicited significant and re-peatable changes in general (visibility, locomotion, body movement and posture, location) and species-specific reactions in virtually all organisms (302 individuals from 32 species and 2 species groups). Most atypical (stress) behaviours were associated with specific oxygen thresholds: arm-tipping in the ophiuroid Ophiothrix quinquemac-ulata, for example, with the onset of mild hypoxia (<2mLO2L-1), the emergence of polychates on the sediment surface with moderate hypoxia (< 1 mLO2 L-1), the emergence of the infaunal sea urchin Schizaster canaliferus on the sediment with severe hypoxia (< 0.5mLO2L-1) and heavy body rotations in sea anemones with anoxia. Other species changed their activity patterns, i.e. circadian rhythm in the hermit crab Paguristes eremita or the bioherm-associated crab Pisidia longimana. Intra- and interspecific reactions were weakened or changed: decapods ceased defensive and territorial behaviour, and predator-prey interactions and relationships shifted. This nuanced scale of resolution is a useful tool to interpret present benthic community status (behaviour) and past mortalities (community composition, e.g. survival of tolerant species). This information on the sensitivity (onset of stress response), tolerance (mortality, survival), and characteristics (i.e. life habit, functional role) of key species also helps predict potential future changes in benthic structure and ecosystem functioning. This integrated approach can transport complex ecological processes to the public and decision-makers and help de?ne speci?c monitoring, assessment and conservation plans. [ABSTRACT FROM AUTHOR]

This document is a special issue of the journal "Plants" that focuses on the soil-plant-water system and its interactions. The articles in this issue cover a wide range of topics, including climate change and soil water deficits, forest and woody plant ecosystems, and alternative crop production methods. The studies explore the effects of drought on plant growth and development, the impact of different inter-row soil management techniques on soil water content, and the response of plants to phosphorus addition. The issue also includes research on zero discharge cultivation of cucumbers and indoor vegetable production methods. The authors highlight the importance of studying the soil-plant-water system as an interconnected system and identify areas for further research. [Extracted from the article]

Network analysis provides a powerful framework to study the complexity underlying the structure, dynamics and function of ecological systems. By now, analysing single‐layered networks is a common practice with clear guidelines and well‐established computational tools. Nevertheless, ecological communities are multilayered because they vary over space and time and contain multiple types of interactions. In recent years, the analysis of ecological multilayer networks (EMLNs) has allowed researchers to include such multilayered complexity. However, there is a paucity of practical guidelines and standardised tools to handle EMLN data, even before downstream analysis.In this article, we accomplish three objectives: (1) We provide practical guidelines for handling EMLN data. (2) We developed the EMLN R package to standardise the workflow of creating, storing and working with EMLN objects. The package also enables conversion between multiple formats for downstream analysis with other standard packages. (3) We provide EMLN data sets for research and training purposes.A dedicated website with explanations, detailed examples and code accompanies our paper. This website is a gateway for novice and experienced network ecologists who want to include EMLNs in their research.By simplifying the analysis of multilayer networks and promoting standardised approaches, we facilitate the analysis of EMLNs. This paves the road towards gaining deeper insights into functioning and resilience of natural ecosystems. [ABSTRACT FROM AUTHOR]

Soils are a crucial component of the Earth System; they comprise a large portion of terrestrial carbon stocks, mediate the supply and demand of nutrients, and influence the overall response of terrestrial ecosystems to perturbations. In this paper, we develop a new soil biogeochemistry model for the Community Land Model, version 4 (CLM4). The new model includes a vertical dimension to carbon (C) and nitrogen (N) pools and transformations, a more realistic treatment of mineral N pools, flexible treatment of the dynamics of decomposing carbon, and a radiocarbon (14C) tracer. We describe the model structure, comparison against site-level and global observations, and overall effect of the revised soil model on CLM carbon dynamics. Site-level comparisons to radiocarbon and bulk soil C observations support the idea that soil C turnover is reduced at depth beyond what is expected from environmental controls by temperature, moisture, and oxygen that are considered in the model. The revised soil model predicts substantially more and older soil C, particularly at high latitudes, where it resolves a permafrost soil C pool, in better agreement with observations. In addition the 20th century C dynamics of the model are more realistic than the baseline model, with more terrestrial C uptake over the 20th century due to reduced N downregulation and longer turnover times of decomposing C. [ABSTRACT FROM AUTHOR]

Based on a wide range of empirical data we investigated surface and vegetation dynamics in the artificial initial ecosystem "Chicken Creek" (Lusatia, Germany) in the years 2008-2011. We scrutinized three different hypotheses concerning (1) the relations between initial geomorphological and substrate characteristics with surface structure and terrain properties, (2) the effects of the latter on the occurrence of grouped plant species, and (3) vegetation density effects on terrain surface change. Our data comprise annual vegetation monitoring results, terrestrial laser scans twice a year, annual groundwater levels, and initially measured soil characteristics. Using Generalized Linear Models (GLMM) and Generalized Additive Mixed Models (GAMM) we can mostly confirm our hypotheses, revealing statistically significant relations that partly reflect object or period specific effects but also more general processes which mark the transition from a geo-hydro towards a bio-geo-hydro system, where pure geomorphology or substrate feedbacks are changing into vegetation-substrate feedback processes. [ABSTRACT FROM AUTHOR]

In this paper, we investigate similarities of effects of soil environmental drivers on year-round daily soil fluxes of nitrous oxide and methane for three distinct semi-natural or natural ecosystems: temperate spruce forest, Germany; tropical rain forest, Queensland, Australia; and ungrazed semi-arid steppe, Inner Mongolia, China. Annual cumulative fluxes of nitrous oxide and methane varied markedly among ecosystems, with nitrous oxide fluxes being highest for the tropical forest site (tropical forest: 0.96 kg N ha-1 yr-1; temperate forest: 0.67 kg N ha-1 yr-1; steppe: 0.22 kg N ha-1 yr-1), while rates of soil methane uptake were approximately equal for the temperate forest (3.45 kg C ha-1 yr-1) and the steppe (3.39 kg C ha-1 yr-1), but lower for the tropical forest site (2.38 kg C ha-1 yr-1). In order to allow for cross-site comparison of effects of changes in soil moisture and soil temperature on fluxes of methane and nitrous oxide, we used a normalization approach. Data analysis with normalized data revealed that across sites, optimum rates of methane uptake are found at environmental conditions representing approximately average site environmental conditions. This might have rather important implications for understanding effects of climate change on soil methane uptake potential, since any shift in environmental conditions is likely to result in a reduction of soil methane uptake ability. For nitrous oxide, our analysis revealed expected patterns: highest nitrous oxide emissions under moist and warm conditions and large nitrous oxide fluxes if soils are exposed to freeze-thawing effects at sufficient high soil moisture contents. However, the explanatory power of relationships of soil moisture or soil temperature to nitrous oxide fluxes remained rather poor (≤ 0.36). When combined effects of changes in soil moisture and soil temperature were considered, the explanatory power of our empirical relationships with regard to temporal variations in nitrous oxide fluxes were at maximum about 50%. This indicates that other controlling factors such as N and C availability or microbial community dynamics might exert a significant control on the temporal dynamic of nitrous oxide fluxes. Though underlying microbial processes such as nitrification and denitrification are sensitive to changes in the environmental regulating factors, important regulating factors like moisture and temperature seem to have both synergistic and antagonistic effects on the status of other regulating factors. Thus we cannot expect a simple relationship between them and the pattern in the rate of emissions, associated with denitrification or nitrification in the soils. In conclusion, we hypothesize that our approach of data generalization may prove beneficial for the development of environmental response models which can be used across sites, and which are needed to help better understanding climate change feed-backs on biospheric sinks or sources of nitrous oxide and methane. [ABSTRACT FROM AUTHOR]

In this study, we investigate the phytoplankton community response, with emphasis on ecophysiology and succession, after two experimental additions of Saharan dust in the surface layer of a low-nutrient low-chlorophyll ecosystem in the Mediterranean Sea. Three mesocosms were amended with evapocondensed dust to simulate realistic Saharan dust events while three additional mesocosms were kept unamended and served as controls. Experiments consisted in two consecutive dust additions and samples were daily collected at different depths (-0.1, -5 and -10m) during one week, starting before each addition occurred. Data concerning HPLC pigment analysis on two size classes (<3 and >3 µm), electron transport rate (ETR) versus irradiance curves, non-photochemical fluorescence quenching (NPQ) and phytoplankton cell abundance (measured by flow cytometry), are presented and discussed in this paper. Results show that picophytoplankton mainly respond to the first dust addition, while the second addition leads to an increase of both pico- and nano-/microphytoplankton. Ecophysiological changes in the phytoplankton community are revealed, and an increase in NPQ development, as well as in pigment concentration per cell, follows the dust additions. ETR does not show large variations between dust-amended and control conditions, while biomass increases in response to the dust additions. Furthermore, the biomass increase observed during this mesocosm experiment allows us to attempt a quantitative assessment and parameterization of the onset of a phytoplankton bloom in a nutrient-limited ecosystem. These results are discussed focusing on the adaptation of picophytoplankton to such a nutrient-limited mixed layer system, as well as on size-dependent competition ability in phytoplankton. [ABSTRACT FROM AUTHOR]

To assess the responses of nitrogen and greenhouse gas emissions to pan-European changes in land cover, land management and climate, an integrated dynamic model, INTEGRATOR, has been developed. This model includes both simple process-based descriptions and empirical relationships, and uses detailed GIS-based environmental and farming data in combination with various downscaling methods. This paper analyses the propagation of uncertainties in model inputs and model parameters to outputs of INTEGRATOR, using a Monte Carlo analysis. Uncertain model inputs and parameters were represented by probability distributions, while spatial correlation in these uncertainties was taken into account by assigning correlation coefficients at various spatial scales. The uncertainty propagation was analysed for the emissions of NH3, N2O and NOx and N leaching to groundwater and N surface runoff to surface water for the entire EU27 and for individual countries. Results show large uncertainties for N leaching and N runoff (relative errors of ~19% for Europe as a whole), and smaller uncertainties for emission of N2O, NH3 and NOx (relative errors of ~12%). Uncertainties for Europe as a whole were much smaller compared to uncertainties at Country level, because errors partly cancelled out due to spatial aggregation. [ABSTRACT FROM AUTHOR]

Land models, which have been developed by the modeling community in the past two decades to predict future states of ecosystems and climate, have to be critically evaluated for their performance skills of simulating ecosystem responses and feedback to climate change. Benchmarking is an emerging procedure to measure and evaluate performance of models against a set of defined standards. This paper proposes a benchmarking framework for evaluation of land models. The framework includes (1) targeted aspects of model performance to be evaluated; (2) a set of benchmarks as defined references to test model performance; (3) metrics to measure and compare performance skills among models so as to identify model strengths and deficiencies; and (4) model improvement. Component 4 may or may not be involved in a benchmark analysis but is an ultimate goal of general modeling research. Land models are required to simulate exchange of water, energy, carbon and sometimes other trace gases between the atmosphere and the land-surface, and should be evaluated for their simulations of biophysical processes, biogeochemical cycles, and vegetation dynamics across timescales in response to both weather and climate change. Benchmarks that are used to evaluate models generally consist of direct observations, data-model products, and data-derived patterns and relationships. Metrics of measuring mismatches between models and benchmarks may include (1) a priori thresholds of acceptable model performance and (2) a scoring system to combine data-model mismatches for various processes at different temporal and spatial scales. The benchmark analyses should identify clues of weak model performance for future improvement. Iterations between model evaluation and improvement via benchmarking shall demonstrate progress of land modeling and help establish confidence in land models for their predictions of future states of ecosystems and climate. [ABSTRACT FROM AUTHOR]

Background: Using next-generation sequencing technologies, scientists can sequence complex microbial communities directly from the environment. Significant insights into the structure, diversity, and ecology of microbial communities have resulted from the study of metagenomics. The assembly of reads into longer contigs, which are then binned into groups of contigs that correspond to different species in the metagenomic sample, is a crucial step in the analysis of metagenomics. It is necessary to organize these contigs into operational taxonomic units (OTUs) for further taxonomic profiling and functional analysis. For binning, which is synonymous with the clustering of OTUs, the tetra-nucleotide frequency (TNF) is typically utilized as a compositional feature for each OTU. Results: In this paper, we present AFIT, a new l-mer statistic vector for each contig, and AFITBin, a novel method for metagenomic binning based on AFIT and a matrix factorization method. To evaluate the performance of the AFIT vector, the t-SNE algorithm is used to compare species clustering based on AFIT and TNF information. In addition, the efficacy of AFITBin is demonstrated on both simulated and real datasets in comparison to state-of-the-art binning methods such as MetaBAT 2, MaxBin 2.0, CONCOT, MetaCon, SolidBin, BusyBee Web, and MetaBinner. To further analyze the performance of the purposed AFIT vector, we compare the barcodes of the AFIT vector and the TNF vector. Conclusion: The results demonstrate that AFITBin shows superior performance in taxonomic identification compared to existing methods, leveraging the AFIT vector for improved results in metagenomic binning. This approach holds promise for advancing the analysis of metagenomic data, providing more reliable insights into microbial community composition and function. Availability: A python package is available at: https://github.com/SayehSobhani/AFITBin. [ABSTRACT FROM AUTHOR]

To explore complex biological questions, it is often necessary to access various data types from public data repositories. As the volume and complexity of biological sequence data grow, public repositories face significant challenges in ensuring that the data is easily discoverable and usable by the biological research community. To address these challenges, the National Center for Biotechnology Information (NCBI) has created NCBI Datasets. This resource provides straightforward, comprehensive, and scalable access to biological sequences, annotations, and metadata for a wide range of taxa. Following the FAIR (Findable, Accessible, Interoperable, and Reusable) data management principles, NCBI Datasets offers user-friendly web interfaces, command-line tools, and documented APIs, empowering researchers to access NCBI data seamlessly. The data is delivered as packages of sequences and metadata, thus facilitating improved data retrieval, sharing, and usability in research. Moreover, this data delivery method fosters effective data attribution and promotes its further reuse. This paper outlines the current scope of data accessible through NCBI Datasets and explains various options for exploring and downloading the data. [ABSTRACT FROM AUTHOR]

Heavy metals (HMs) in aquatic environments are characterized by high toxicity, a propensity for bioaccumulation, and non-degradability, and pose significant risks to biological communities. Previous studies of HMs in lakes have shown that the physical and chemical characteristics of the lake water may control both the migration of HMs in the sediments and the concentration of heavy metals in the lake water. In fact, the change in aquatic environments changes the heavy metal fraction in the sediment, which controls the release of HMs. In this paper, we investigated the effects of the pH, temperature, and salinity levels of overlying water on the chemical fraction of Cu and Zn in Wuliangsuhai Lake surface sediments. The results show that lower water pH and higher water salinity and temperature could increase Cu and Zn release from the sediment. An increase in pH led to changes in the speciation of solid fractions of Zn, namely increases in the residual fraction and decreases in the organic matter and sulfide, whereas acid-extractable and Fe-Mn oxide fractions remained largely the same. Increases in temperature and salinity led to opposite changes in the speciation of solid fractions, namely decreases in the residual fraction and increases in the organic matter and sulfide and Fe-Mn oxide fractions, whereas acid-extractable fractions remained largely the same. The effect of pH, temperature, and salinity on Cu fractions in the solids was much smaller. According to the ratio of the secondary phase to the primary phase (RSP), acidic, high-temperature, and high-salt conditions increase the release risks of Zn. Changes in water temperature have the greatest influence on the risk of Zn and Cu release from sediments, followed by the influence of salinity changes. [ABSTRACT FROM AUTHOR]

The stochastic nature of ecological systems is fundamental to their modeling and understanding. In this paper, we introduce a comprehensive algae-zooplankton model that incorporates general interaction rate and second-order independent stochastic components. Our model’s perturbation component encompasses both white noise and jump processes, enabling us to account for various sources of variability and capture a wide range of potential fluctuations in the system. By utilizing an auxiliary equation, we establish a global threshold for the stochastic system, distinguishing between scenarios of extinction and ergodicity. This threshold serves as a critical determinant of the system’s long-term behavior and sheds light on the delicate balance between population persistence and decline in ecological communities. To elucidate the impact of noise on the dynamics of algae and zooplankton, we present a series of numerical illustrations. Through these simulations, we highlight how noise influences not only the extinction time but also the shape of the stationary distribution. Our findings underscore the significant role of stochasticity in shaping ecological dynamics and emphasize the importance of considering noise effects in ecological modeling and management practices. [ABSTRACT FROM AUTHOR]

Degradation of coastal ecosystems by eutrophication is largely defined by nitrogen loading from land via surface and groundwater flows. However, indicators of water quality are highly variable due to a myriad of other drivers, including temperature and precipitation. To evaluate these drivers, we examined spatial and temporal trends in a 22 year record of summer water quality data from 122 stations in 17 embayments within Buzzards Bay, MA (USA), collected through a citizen science monitoring program managed by Buzzards Bay Coalition. To identify spatial patterns across Buzzards Bay's embayments, we used a principle component and factor analysis and found that rotated factor loadings indicated little correlation between inorganic nutrients and organic matter and chlorophyll a (Chl a) concentration. Factor scores showed that embayment geomorphology in addition to nutrient loading was a strong driver of water quality, where embayments with surface water inputs showed larger biological impacts than embayments dominated by groundwater influx. A linear regression analysis of annual summertime water quality indicators over time revealed that from 1992 to 2013, most embayments (15 of 17) exhibited an increase in temperature (mean rate of 0.082 ± 0.025 (SD) °C yr-1) and Chl a (mean rate of 0.0171 ± 0.0088 log10 (Chl a; mgm-3)yr-1, equivalent to a 4.0% increase per year). However, only 7 embayments exhibited an increase in total nitrogen (TN) concentration (mean rate 0.32 ± 0.47 (SD)μM yr-1). Average summertime log10 (TN) and log10 (Chl a) were correlated with an indication that yield of Chl a per unit total nitrogen increased with time suggesting the estuarine response to TN may have changed because of other stressors such as warming, altered precipitation patterns, or changing light levels. These findings affirm that nitrogen loading and physical aspects of embayments are essential in explaining observed ecosystem response. However, climate-related stressors may also need to be considered by managers because increased temperature and precipitation may worsen water quality and partially offset benefits achieved by reducing nitrogen loading. [ABSTRACT FROM AUTHOR]

Oceanic upwelling velocities are too small to be measured directly. The surface disequilibrium of the ³He/4He ratio provides an indirect method to infer vertical velocities at the base of the mixed layer. Samples of helium isotopes were taken from two coastal upwelling regions, off Peru on cruise M91, and off Mauritania on 3 cruises. The helium- 3 flux into the mixed layer also depends on the diapycnal mixing. Direct observations of the vertical diffusivity have been performed on all 4 cruises and are also used in this study. The resulting upwelling velocities in the coastal regions vary between 1.1x10-5 and 2.8x10-5ms-1 for all cruises. Vertical velocities off the equator can also be inferred from the divergence of the wind driven Ekman transport. In the coastal regimes, the agreement between wind and helium derived upwelling is fairly good at least for the mean values. Further offshore, the helium derived upwelling still reaches 1x10-5ms-1, whereas the wind driven upwelling from Ekman suction is smaller by at least one order of magnitude. One reason for this difference might be eddy induced upwelling. Both advective and diffusive nutrient fluxes into the mixed layer are calculated based on the helium derived vertical velocities and the measured vertical diffusivities. The advective part of these fluxes makes up at least 50% of the total. The nutrient flux into the mixed layer in the coastal upwelling regimes is equivalent to a net community production (NCP) of 1.3gCm² d-1 off Peru and 1.6-1.9 gCm² d-1 off Mauritania. [ABSTRACT FROM AUTHOR]

The successful movement of individuals is fundamental to life. Facilitating these movements by promoting ecological connectivity has become a central theme in ecology and conservation. Urban areas contain more than half of the world's human population, and their potential to support biodiversity and to connect their citizens to nature is increasingly recognized. Promoting ecological connectivity within these areas is essential to reaching this potential. However, our current understanding of ecological connectivity within urban areas appears limited., We reviewed the published scientific literature to assess the state-of-the-art of ecological connectivity research in urban areas, summarized trends in study attributes and highlighted knowledge gaps., We found 174 papers that investigated ecological connectivity within urban areas. These papers addressed either structural (48) or functional connectivity (111), and some addressed both (15), but contained substantial geographic and taxonomic biases. These papers rarely defined the aspect of connectivity they were investigating and objective descriptions of the local urban context were uncommon. Formulated hypotheses or a priori predictions were typically unstated and many papers used suboptimal study designs and methods., We suggest future studies explicitly consider and quantify the landscape within their analyses and make greater use of available and rapidly developing tools and methods for measuring functional connectivity (e.g. biotelemetry or landscape genetics). We also highlight the need for studies to clearly define how the terms ' urban' and ' connectivity' have been applied., Knowledge gaps in ecological connectivity in urban areas remain, partly because the field is still in its infancy and partly because we must better capitalize on the state-of-the-art technological and analytical techniques that are increasingly available. Well-designed studies that employed high-resolution data and powerful analytical techniques highlight our abilities to quantify ecological connectivity in urban areas. These studies are exemplary, setting the standards for future research to facilitate data-driven and evidence-based biodiversity-friendly infrastructure planning in urban areas. [ABSTRACT FROM AUTHOR]

Cities are critical to a sustainable future for our planet; still, the construction and operation of cities rely on intensive resource and energy use and transformation, leading to the generation of waste, effluents, and pollution, representing negative externalities outside and inside the city. Within every process, transformation implies the use of energy and the increase of entropy. In an urban system, the transformation of energy and materials will trigger the creation of entropic landscapes, mainly in the informal city and in unguarded natural landscapes, even hundreds of kilometers away, which generates substantial economic, social, and environmental impacts. In this sense, cities are significant contributors to the environmental crisis. Upstream, degradation of landscapes and ecosystems is frequent. Cities' externalities and exogenous consumptions are directly linked with entropy and entropic landscapes, which are recognized as pollution (in the air, water, and land) or waste and in the degradation of natural ecosystems and communities. Through a systematic review of existing literature, this paper first outlines briefly how entropy has been applied in different disciplines and then focuses on presenting recent developments of how entropy has been defined, used, and characterized in urban studies concerning sustainability in cities and architecture, and presents a definition of the concept in relation to urban systems and key aspects to consider. [ABSTRACT FROM AUTHOR]

Drought has been a concern of global and regional water, carbon and energy cycles. From 1999 to 2011, North China experienced a multiyear precipitation reduction, which decreased significantly water availability as indicated by decreased soil moisture and Palmer Drought Severity Index. In this study, three light use efficiency models (CASA, MODIS-GPP and EC-LUE) and one dynamic vegetation model (IBIS) were used to characterize the impacts of long-term drought on terrestrial carbon fluxes over the North China. All of four models showed the reduction in averaged GPP of 0.026-0.047 Pg C yr-1 from 1999 to 2011 compared to 1982-2011. Based on IBIS model, simulated ecosystem respiration fell from 1999 to 2011 by 0.016 Pg C yr-1. Multiple precipitation reduction changed the regional carbon uptake of 0.0014 Pg C yr-1 from 1982 to 1998 to a net source of 0.018 Pg C yr-1. Moreover, a pronounced decrease of maize yield was found ranging from 1999 to 2011 versus the average of 1978-2011 at almost all provinces over the study region. The largest reduction of maize yield occurred in the Beijing (2499 kg ha-1 yr-1), Jilin (2180 kg ha-1 yr-1), Tianjing (1923 kg ha-1 yr-1) and Heilongjiang (1791 kg ha-1 yr-1), and maize yield anomaly was significantly correlated with the precipitation through May and September over the entire study area. Our results revealed that recent climate change, and especially drought-induced water stress, is the dominant cause of the reduction in the terrestrial carbon sink. [ABSTRACT FROM AUTHOR]

In order to investigate the mechanism of spatial dynamics of picoplankton community (bacteria and Synechococcus spp.) and estimate the carbon flux of the microbial food web in the oligotrophic Taiwan Warm Current Water of subtropical marine pelagic ecosystem, we conducted size-fractionation experiments in five cruises by the R/V Ocean Research II during the summers of 2010 and 2011 in the southern East China Sea. We carried out culture experiments using surface water which, according to a temperature-salinity (T-S) diagram, is characterized as oligotrophic Taiwan Current Warm Water. We found a negative correlation between bacteria growth rate and temperature, indicating that the active growth of heterotrophic bacteria might be induced by nutrients lifted from deep layer by cold upwelling water. This finding suggests that the area we studied was a bottom-up control pelagic ecosystem. We suggest that the microbial food web of an oligotrophic ecosystem may be changed from top-down control to resource supply (bottom-up control) when a physical force brings nutrient into the oligotrophic ecosystem. Upwelling brings nutrient-rich water to euphotic zone and promotes bacteria growth, increasing the picoplankton biomass which increased the consumption rate of nanoflagellate. The net growth rate (growth rate--grazing rate) becomes negative when the densities of bacteria and Synechococcus spp. are lower than the threshold values. The interaction between growth and grazing will limit the abundances of bacteria (105 -106 cells mL -1) and Synechococcus spp. (104 -105 cells mL-1) within a narrow range, forming a predator-prey eddy. Meanwhile, 62% of bacteria production and 55% of Synechococcus spp. production are transported to higher trophic level (nanoflagellate), though the cascade effect might cause an underestimation of both percentages of transported carbon. Based on the increasing number of sizes we found in the size-fractionation experiments, we estimated that the predation values were underestimated by 28.3% for bacteria and 34.6% for Synechococcus spp. Taking these corrections into consideration, we conclude that picoplankton production is balanced by nonoflagellate grazing and the diet of nanoflagellate is composed of 64% bacteria and 36% Synechococcus spp. [ABSTRACT FROM AUTHOR]

To model phytoplankton primary production from remotely sensed data a method to estimate photosynthetic parameters describing the photosynthetic rates per unit biomass is required. Variability in these parameters must be related to environmental variables that are measurable remotely. In the Arctic, a limited number of measurements of photosynthetic parameter have been carried out with the concurrent environmental variables needed. Therefore, to improve the accuracy of remote estimates of phytoplankton primary production as well as our ability to predict changes in the future such measurements and relationship to environmental variables are required. During the MALINA cruise, a large dataset of these parameters were obtained. Together with previously published datasets, we use environmental and trophic variables to provide functional relationships for these parameters. In particular, we describe several specific aspects: the maximum rate of photosynthesis (Pmaxchl) normalized to chlorophyll decreases with depth and is higher for communities composed of large cells; the saturation parameter (Ek) decreases with depth but is independent of the community structure; and the initial slope of the photosynthesis versus irradiance curve (αchl) normalized to chlorophyll is independent of depth but is higher for communities composed of larger cells. The photosynthetic parameters were not influenced by temperature over the range encountered during the cruise (-2 to 8 °C). [ABSTRACT FROM AUTHOR]

We conducted high frequency measurements of the δ18 O value of atmospheric CO2 from a juniper (Juniperus monosperma) woodland in New Mexico, USA, over a four- year period to investigate climatic and physiological regulation of the δ18O value of ecosystem respiration (δR). Rain pulses reset δR with the dominant water source isotope composition, followed by progressive enrichment of δR. Transpiration (ET) was significantly related to post-pulse δR enrichment because leaf water δ18O value showed strong enrichment with increasing vapor pressure deficit that occurs following rain. Post-pulse δR enrichment was correlated with both ET and the ratio of ET to soil evaporation (ET/ES). In contrast, soil water δ18O value was relatively stable and δR enrichment was not correlated with ES. Model simulations captured the large post-pulse δR enrichments only when the offset between xylem and leaf water δ18O value was modeled explicitly and when a gross flux model for CO2 retro-diffusion was included. Drought impacts δR through the balance between evaporative demand, which enriches δR, and low soil moisture availability, which attenuates δR enrichment through reduced ET. The net result, observed throughout all four years of our study, was a negative correlation of post-precipitation δR enrichment with increasing drought. [ABSTRACT FROM AUTHOR]

We compared the functional response of a biogeochemical data assimilation model versus an empirical satellite-derived algorithm in describing the variation of four phytoplankton (diatoms, cyanobacteria, coccolithophores and chlorophytes) groups globally and in 12 major oceanographic basins. Global mean differences of all groups were within ~15% of an independent observation data base for both approaches except for satellite-derived chlorophytes. Diatoms and cyanobacteria concentrations were significantly (p < 0.05) correlated with the independent observation data base for both methods. Coccolithophore concentrations were only correlated with the in situ data for the model approach and the chlorophyte concentration was only significantly correlated to the in situ data for the satellite-derived approach. Using monthly means from 1998–2007, the seasonal variation from the satellite-derived approach and model were significantly correlated in 11 regions for diatoms and in 9 for coccolithophores but only in 3 and 2 regions for cyanobacteria and chlorophytes. Most disagreement on the seasonal variation of phytoplankton composition occurred in the North Pacific and Antarctic where, except for diatoms, no significant correlation could be found between the monthly mean concentrations derived from both approaches. In these two regions there was also an overestimate of diatom concentration by the model of ~60% whereas the satellite-derived approach was closer to in situ data (8-26% underestimate). Chlorophytes were the group for which both approaches differed most and that was furthest from the in situ data. These results highlight the strengths and weaknesses of both approaches and allow us to make some suggestions to improve our approaches to understanding phytoplankton dynamics and distribution. [ABSTRACT FROM AUTHOR]

We investigated the production of ammonium via photodegradation of dissolved organic matter (DOM) in the coastal upwelling system off central Chile (36° S). Photoam-monification experiments were carried out using exudates obtained from representative diatom species (Chaetoceros muelleri and Thalassiosira minuscule) and natural marine DOM under simulated solar radiation conditions. Additionally, we evaluated the use of photoproduced ammonium by natural microbial communities and separated ammonium oxidizing archaea and bacteria by using GC-7 as an inhibitor of the archaeal community. We found photoammonification operating at two levels: via the transformation of DOM by UV radiation (abiotic ammonification) and via the simultaneous occurrence of abiotic phototransformation and biological remineralization of DOM into NH4+ (referred as gross photoproduction of NH4+). The maximum rates of abiotic ammonification reached 0.057 µmol L-1 h-1, whereas maximum rates of gross photopro- duction reached 0.746 µmol L-1 h-1. Our results also suggest that ammonium oxidizing archaea could dominate the biotic remineralization induced by photodegradation of organic matter and consequently play an important role in the local N cycle. Abiotic ammonium photoproduction in coastal upwelling systems could support between 7 and 50%of the spring-summer phytoplankton NH4+ demand. Surprisingly, gross ammonium photoproduction (remineralization induced by abiotic ammonification) might support 50 to 180% of spring-summer phytoplankton NH4+ assimilation. [ABSTRACT FROM AUTHOR]

We present a Simple Diagnostic Photosynthesis and Respiration Model (SDPRM) that has been developed based on pre-existing formulations. The photosynthesis model is based on the light use efficiency logic, suggested by Monteith (1977), for calculating the Gross Primary Production (GPP) while the ecosystem respiration (Reco) model is based on the formulations introduced by Lloyd and Taylor (1994) and modified by Reichstein et al. (2003). SDPRM is driven by satellite-derived fAPAR (fraction of Absorbed Photosynthetically Active Radiation) and climate data from NCEP/NCAR. The model estimates 3-hourly values of GPP for seven major biomes and daily Reco. The motivation is to provide a-priori fields of surface CO2 fluxes with fine temporal and spatial scales, and their derivatives with respect to adjustable model parameters, for atmospheric CO2 inversions. The estimated fluxes from SDPRM showed that the model is capable of producing flux estimates consistent with the ones inferred from atmospheric CO2 inversion or simulated from process-based models. In this Technical Note, different analyses were carried out to test the sensitivity of the estimated fluxes of GPP and Reco to their driving forces. The spatial patterns of the climatic controls (temperature, precipitation, water) on the interannual variability of GPP are consistent with previous studies even though SDPRM has a very simple structure and few adjustable parameters, and hence it is much easier to modify than more sophisticated process-based models used in these previous studies. According to SDPRM, the results show that temperature is a limiting factor for the interannual variability of Reco over the cold boreal forest, while precipitation is the main limiting factor of Reco over the tropics and the southern hemisphere, consistent with previous regional studies. [ABSTRACT FROM AUTHOR]

The Arctic Ocean (AO) undergoes profound changes of its physical and biotic environments due to climate change. The greater light exposure and stratification alter its plankton ecosystem structure, functioning and productivity promoting oligotrophy in some areas as the Beaufort Sea. A one-dimension (1-D) physical-biological coupled model based on the large multiparametric database of the Malina project in the Beaufort Sea was used (i) to infer the functioning and nitrogen fluxes within the summer plankton ecosystem and (ii) to assess the model sensitivity to key light-associated processes involved in nutrient recycling and phytoplankton growth. The coupled model suggested that ammonium photochemically produced from photosensitive dissolved organic nitrogen (i.e. photoammonification process) was a necessary nitrogen source to achieve the observed levels of microbial biomass and production. It contributed to ca. two-thirds and one-third of the simulated surface (0-10 m) and depth-integrated primary and bacterial production, respectively. The model also suggested that carbon to chlorophyll ratios for small (<5 µm) phytoplankton (ca. 15-45 gg-1) lower than those commonly used in biogeochemical models applied to the AO were required to simulate the observed herbivorous versus microbial food web competition and realistic nitrogen fluxes in the Beaufort Sea oligotrophic waters. In face of accelerating Arctic warming, more attention should be paid in the future to the mechanistic processes involved in food webs and functional groups competition, nutrient recycling and primary production in poorly productive waters of the AO as they are expected to expand rapidly. [ABSTRACT FROM AUTHOR]

Microbial respiration depends on microclimatic variables and carbon (C) substrate availability, all of which are altered when ecosystems experience major disturbance. Widespread tree mortality, currently affecting piñon-juniper ecosystems in Southwestern North America, may affect C substrate availability in several ways; for example, via litterfall pulses and loss of root exudation. To determine piñnon mortality effects on C and water limitation of microbial respiration, we applied field amendments (sucrose and water) to two piñnon-juniper sites in central New Mexico, USA: one with a recent (<1 yr), experimentally-induced mortality event and a nearby site with live canopy. We monitored the respiration response to water and sucrose applications to the litter surface and to the underlying mineral soil surface, testing the following hypotheses: (1) soil respiration in a piñnon-juniper woodland is water- and labile C-limited in both the litter layer and mineral soil; (2) water and sucrose applications increase temperature sensitivity of respiration; (3) the mortality-affected site will show a reduction in C limitation in the litter; (4) the mortality-affected site will show an enhancement of C limitation in the mineral soil. Litter respiration at both sites responded to increased water availability, yet surprisingly, mineral soil respiration was not limited by water. Temperature sensitivity was enhanced by some of the sucrose and water treatments. Consistent with hypothesis 3, C limitation of litter respiration was lower at the recent mortality site compared to the intact canopy site. Results following applications to the mineral soil 20 suggest the presence of abiotic effects of increasing water availability, precluding our ability to measure labile C limitation in soil. Widespread piñon mortality may decrease labile C limitation of litter respiration, at least during the first growing season following mortality. [ABSTRACT FROM AUTHOR]

Present and future levels of primary production (PP) in the Arctic Ocean (AO) depend on nutrient inputs to the photic zone via vertical mixing, upwelling and external sources. In this regard, the importance of horizontal river supply relative to oceanic processes is poorly constrained at the panarctic scale. We compiled extensive historical (1954-2012) data on discharge and nutrient concentrations to estimate fluxes of nitrate, soluble reactive phosphate (SRP), silicate, DOC, DON, PON and POC from 9 large Arctic rivers and assess their potential impact on the biogeochemistry of shelf waters. Several key points can be emphasized from this analysis. The contribution of riverine nitrate to new PP (PPnew) is very small at the regional scale (<1% to ca. 6.2 %) and negligible at the panarctic scale (ca. 0.73%), in agreement with recent studies. By consuming all this nitrate, oceanic phytoplankton would be able to use only ca. 13.5%and 6.6-17.5% of the river supply of silicate at the panarctic and regional scales, respectively. Corresponding figures for SRP are ca. 27.8% and 18.4-44.4 %. On the Beaufort and Bering shelves, riverine SRP cannot fulfil phytoplankton requirements. On a seasonal basis, the removal of riverine nitrate, silicate and SRP would be the highest in spring and not in summer when AO shelf waters are nitrogen-limited. Riverine DON is potentially an important nitrogen source for the planktonic ecosystem in summer, when ammonium supplied through the photoammonification of refractory DON (ca. 3.9x109 mol N) may exceed the combined riverine supply of nitrate and ammonium (ca. 2.9x109 mol N). Nevertheless, overall nitrogen limitation of AO phytoplankton is expected to persist even when projected increases of riverine DON and nitrate supply are taken into account. This analysis underscores the need to better contrast oceanic nutrient supply processes with the composition and fate of changing riverine nutrient deliveries in future scenarios of plankton community structure, function and production in the coastal AO. [ABSTRACT FROM AUTHOR]

Here we report a time series of experiments performed in a microcosm to test the response of hypersaline microbial mats to diverse atmospheric CO2 conditions. Different from most part of the literature, our study used a sample chamber were carbon dioxide concentration was controlled. Our aim was to test the effect of different atmospheric CO2 conditions in benthic gross and net primary production, and respiration. This study showed for the first time to our knowledge absolute carbon limitation in a microbial mat. Oxygen concentration profile varied from a flattened shape to almost linear when atmospheric CO2 at the chamber reached 0 ppm, with NPP reaching 0 nmol cm-3 s-1 throughout most part of the profile. In this conditions sediment community respiration represented 100% of GPP. Extreme close coupling between primary production and respiration in microbial mats can be even self-sustainable in environments with temporally no atmospheric CO2 available. When submitted to even high CO2 concentrations (550 ppm), our sample showed a characteristic shape that indicate limitation composed by a more rectilinear oxygen profile, and NPP peaks mainly restricted to deeper layers. Therefore, we suggest that phototrophic communities in aquatic shallow ecosystems can be carbon limited. This limitation could be common especially in ecosystems submitted to variable water depth conditions, like coastal lagoons and intertidal sediments. [ABSTRACT FROM AUTHOR]

Net community production (NCP) and ratios of carbon to nutrient consumption were studied during a large-scale mesocosm experiment on ocean acidification in Kongsfjorden, West Spitsbergen, during June-July 2010. Nutrient-deplete fjord water with natural phyto- and bacteriaplankton assemblages, enclosed in nine mesocosms of ∼50m³ volume, was exposed to pCO2 levels ranging from 185 to 1420 µatm on initial state. Mean values of pCO2 levels during experiment ranged from 175 to 1085 µatm in different mesocosms. Phytoplankton growth was stimulated by nutrient addition. In this study NCP is estimated as a cumulative change in dissolved inorganic carbon concentrations. Stoichiometric couping between inorganic carbon and nutrient is shown as a ratio of a cumulative NCP to a cumulative change in inorganic nutrients. Three peaks of chlorophyll a concentration occurred during the experiment. Accordingly the experiment was divided in three phases. Overall cumulative NCP was similar in all mesocosms by the final day of experiment. However, NCP varied among phases, showing variable response to CO2 perturbation. Carbon to nitrogen (C:N) and carbon to phosphorus (C: P) uptake ratios were estimated only for the period after nutrient addition (post-nutrient period). For the total post-nutrient period ratios were close to Redfield proportions, however varied from it in different phases. The response of C:N and C: P uptake ratios to CO2 perturbation was different for three phases of the experiment, reflecting variable NCP and dependence on changing microbial community. Through the variable NCP, C:N and C: P uptake ratios for 31 days of the experiment we show a flexibility of biogeochemical response establishing a strong microbial loop in Kongsfjorden under different CO2 scenarios. [ABSTRACT FROM AUTHOR]

The article presents a study that demonstrates the applications of the Biogeochemical Transport and Reactions (CLM4-BeTR) in regional and global biogeochemistry modeling and climate predictability. It outlines the functions of the model in which its transport code are evaluated through several analytical test cases. The study shows that the method provides detailed comparison between ecosystem observation and predictions.