Predicting metabolic modules in incomplete bacterial genomes with MetaPathPredict.

The reconstruction of complete microbial metabolic pathways using 'omics data from environmental samples remains challenging. Computational pipelines for pathway reconstruction that utilize machine learning methods to predict the presence or absence of KEGG modules in incomplete genomes are lacking. Here, we present MetaPathPredict, a software tool that incorporates machine learning models to predict the presence of complete KEGG modules within bacterial genomic datasets. Using gene annotation data and information from the KEGG module database, MetaPathPredict employs deep learning models to predict the presence of KEGG modules in a genome. MetaPathPredict can be used as a command line tool or as a Python module, and both options are designed to be run locally or on a compute cluster. Benchmarks show that MetaPathPredict makes robust predictions of KEGG module presence within highly incomplete genomes.

Plasmid-Borne Biosynthetic Gene Clusters within a Permanently Stratified Marine Water Column.

Plasmids are mobile genetic elements known to carry secondary metabolic genes that affect the fitness and survival of microbes in the environment. Well-studied cases of plasmid-encoded secondary metabolic genes in marine habitats include toxin/antitoxin and antibiotic biosynthesis/resistance genes. Here, we examine metagenome-assembled genomes (MAGs) from the permanently-stratified water column of the Cariaco Basin for integrated plasmids that encode biosynthetic gene clusters of secondary metabolites (smBGCs). We identify 16 plasmid-borne smBGCs in MAGs associated primarily with Planctomycetota and Pseudomonadota that encode terpene-synthesizing genes, and genes for production of ribosomal and non-ribosomal peptides. These identified genes encode for secondary metabolites that are mainly antimicrobial agents, and hence, their uptake via plasmids may increase the competitive advantage of those host taxa that acquire them. The ecological and evolutionary significance of smBGCs carried by prokaryotes in oxygen-depleted water columns is yet to be fully elucidated.

Metagenomic profiles of archaea and bacteria within thermal and geochemical gradients of the Guaymas Basin deep subsurface.

Previous studies of microbial communities in subseafloor sediments reported that microbial abundance and diversity decrease with sediment depth and age, and microbes dominating at depth tend to be a subset of the local seafloor community. However, the existence of geographically widespread, subsurface-adapted specialists is also possible. Here, we use metagenomic and metatranscriptomic analyses of the hydrothermally heated, sediment layers of Guaymas Basin (Gulf of California, Mexico) to examine the distribution and activity patterns of bacteria and archaea along thermal, geochemical and cell count gradients. We find that the composition and distribution of metagenome-assembled genomes (MAGs), dominated by numerous lineages of Chloroflexota and Thermoproteota, correlate with biogeochemical parameters as long as temperatures remain moderate, but downcore increasing temperatures beyond ca. 45 ºC override other factors. Consistently, MAG size and diversity decrease with increasing temperature, indicating a downcore winnowing of the subsurface biosphere. By contrast, specific archaeal MAGs within the Thermoproteota and Hadarchaeota increase in relative abundance and in recruitment of transcriptome reads towards deeper, hotter sediments, marking the transition towards a specialized deep, hot biosphere.

Use of a Living Lab Approach to Implement a Smoke-Free Campus Policy.

While universities have increasingly become tobacco-/smoke-free, to our knowledge, no campus has reported 100% policy compliance. Innovative approaches to encourage compliance and ongoing data collection are needed. This paper describes actions undertaken, framed within a Living Lab (LL) approach, to implement smoke-free campus policies in an Irish university. The action research comprised student-collected data on observed smoking on campus to evaluate adherence and compliance, first to a smoke-free zones policy (June 2016-March 2018), and then to a smoke-free campus policy (March 2019-February 2020). From June 2016-February 2020, 2909 smokers were observed. Adherence, defined as the average reduction in number of observed smokers from baseline in May 2016, reduced by 79% from 5.7 to 4.9 . Compliance, defined as the proportion of smokers who complied when reminded of the policy, was 90% (2610/2909). Additional activities included development of a broader health promotion programme; identification of a pattern of 'social smoking'; and promoting increased awareness of the environmental harms of tobacco. Ongoing policy implementation is essential for smoke-free policies and should include data collection and evaluation. Actions framed within the characteristics of a LL achieved fewer observed smokers. A LL approach is recommended to encourage policy adherence and compliance.

Diverse secondary metabolites are expressed in particle-associated and free-living microorganisms of the permanently anoxic Cariaco Basin.

Secondary metabolites play essential roles in ecological interactions and nutrient acquisition, and are of interest for their potential uses in medicine and biotechnology. Genome mining for biosynthetic gene clusters (BGCs) can be used for the discovery of new compounds. Here, we use metagenomics and metatranscriptomics to analyze BGCs in free-living and particle-associated microbial communities through the stratified water column of the Cariaco Basin, Venezuela. We recovered 565 bacterial and archaeal metagenome-assembled genomes (MAGs) and identified 1154 diverse BGCs. We show that differences in water redox potential and microbial lifestyle (particle-associated vs. free-living) are associated with variations in the predicted composition and production of secondary metabolites. Our results indicate that microbes, including understudied clades such as Planctomycetota, potentially produce a wide range of secondary metabolites in these anoxic/euxinic waters.

Developing a health promoting university in Trinity College Dublin-overview and outline process evaluation.

Higher Education Institutions (HEIs) have the potential to impact positively on the health and wellbeing of their staff and students. Using and expanding on the 'health promoting university' (HPU) platform within HEIs, this article provides a description of 'Healthy Trinity', which is an initiative underway in Trinity College Dublin, the University of Dublin. First, Healthy Trinity is contextualized in background literature including international and national policy and practice. Second, an overview of Healthy Trinity is provided including its vision and goals. Third, the article describes the steps taken relating to the identification of stakeholders and use of a network and a co-lead model. Within this approach, the article describes a partnership approach whereby responsibilities regarding health and wellbeing are shared by individuals and the institution. Fourth, the design and implementation of Healthy Trinity is discussed by taking a 'settings approach', in which the emphasis for change is placed on individual behaviours, environment, policy and organizational culture. Consideration is given to the interplay between intervention, implementation strategy and context for successful systemic implementation. The fifth element presented is the early-stage challenges encountered during implementation, such as the need to secure recurrent funding and the importance of having a direct input to the governance of the University to enable systemic change. The sixth and final component of the article is an outline of Healthy Trinity's intention to utilize a process evaluation of the early implementation phases of this complex intervention within a settings approach. Potential deliverables and impacts of this HPU initiative are presented and discussed.

Universities, such as Trinity College Dublin, the University of Dublin, can be looked at as a community of staff and students. The university community has needs in terms of health and wellbeing. 'Healthy Trinity' attempted to build strategies and practices to meet these needs for its community. The approach taken was from multiple angles and involved students and staff, focusing on both individual and organizational responsibility to promote and encourage healthy behaviours. Healthy Trinity achieved some successes as well as encountering some challenges. This article explores how the university might build upon the successes of Healthy Trinity in order to embed a culture which prioritizes health and wellbeing for the entire university community. The article also looks at the broader impact of achieving this goal, namely the University's contribution to a healthier community beyond the university setting.

c-Abl Activation Linked to Autophagy-Lysosomal Dysfunction Contributes to Neurological Impairment in Niemann-Pick Type A Disease.

Niemann-Pick type A (NPA) disease is a fatal lysosomal neurodegenerative disorder caused by the deficiency in acid sphingomyelinase (ASM) activity. NPA patients present severe and progressive neurodegeneration starting at an early age. Currently, there is no effective treatment for this disease and NPA patients die between 2 and 3 years of age. NPA is characterized by an accumulation of sphingomyelin in lysosomes and dysfunction in the autophagy-lysosomal pathway. Recent studies show that c-Abl tyrosine kinase activity downregulates autophagy and the lysosomal pathway. Interestingly, this kinase is also activated in other lysosomal neurodegenerative disorders. Here, we describe that c-Abl activation contributes to the mechanisms of neuronal damage and death in NPA disease. Our data demonstrate that: 1) c-Abl is activated in-vitro as well as in-vivo NPA models; 2) imatinib, a clinical c-Abl inhibitor, reduces autophagy-lysosomal pathway alterations, restores autophagy flux, and lowers sphingomyelin accumulation in NPA patient fibroblasts and NPA neuronal models and 3) chronic treatment with nilotinib and neurotinib, two c-Abl inhibitors with differences in blood-brain barrier penetrance and target binding mode, show further benefits. While nilotinib treatment reduces neuronal death in the cerebellum and improves locomotor functions, neurotinib decreases glial activation, neuronal disorganization, and loss in hippocampus and cortex, as well as the cognitive decline of NPA mice. Our results support the participation of c-Abl signaling in NPA neurodegeneration and autophagy-lysosomal alterations, supporting the potential use of c-Abl inhibitors for the clinical treatment of NPA patients.

Institutional effects on ecological outcomes of community-based management of fisheries in the Amazon.

Communities throughout the globe are increasingly being given the responsibility of resource management, making it necessary to understand the factors that lead to success in community-based management (CBM). Here, we assessed whether and how institutional design principles affect the ecological outcomes of CBM schemes for Arapaima sp., an important common-pool fishery resource of the Amazon Basin. We quantified the degree of presence of Ostrom's (Science 325:419-422, 1990) institutional design principles in 83 communities using a systematic survey, and quantitatively linked the design principles to a measure of ecological outcome (arapaima density) in a subset of 39 communities to assess their influence. To understand regional patterns of institutional capacity for CBM, we evaluated the degree of presence of each principle in all 83 communities. The principle scores were positively related to arapaima density in the 39 CBM schemes, explaining about half of the variation. Design principles related to defined boundaries and graduated sanctions exerted the strongest influence on the capacity of CBM to increase arapaima density. The degree to which most principles were present in all 83 communities was generally low, however, with the two most influential principles (defined boundaries and graduated sanctions) being the least present of all. Although the roles of the other principles (management rules, conflict resolution, collective action, and monitoring systems) are probably important, our results indicate that efforts aimed at strengthening the presence of defined boundaries and graduated sanctions in communities hold promise to improve the effectiveness of arapaima CBM regionally.

Development and proposed evaluation of an eHealth learning tool for undergraduate university students in Ireland.

Undergraduate university students are at a critical stage of development in terms of their academic, social, psychological and behavioural health. Patterns established during these formative years can last a lifetime. eHealth tools have the potential to be engaging, convenient and accessible to a wide range of students by providing health information and enhancing the uptake of positive health behaviours. The 'Healthy Trinity Online Tool' (H-TOT) was developed in collaboration with students and a transdisciplinary team with decades of experience between them in terms of research, clinical responsibility and service delivery. Developmental steps undertaken included: a literature review to formulate the topic content choices; a survey of students to check the relevance and suitability of topics identified; and, the tacit experience of the development team. This co-design model led to the development of content encompassing academic life, healthy eating, physical activity, mood, financial matters, alcohol, tobacco, drugs and relaxation. Qualitative focus groups were subsequently conducted for in-depth exploration of the usage and functionality of H-TOT. The theoretical underpinnings include the locus of control and social cognitive theory. Evidence-based behavioural change techniques are embedded throughout. During early pre-piloting of H-TOT, the team identified and solved content functionality problems. The tone of the content was also revised to ensure it was non-judgemental. To make the H-TOT as interactive as possible, video scenarios were included and all content was audio-recorded to allow playback for students with visual or learning difficulties. Evaluation plans for the pilot year of H-TOT are outlined.

On the diversity and distribution of a data deficient habitat in a poorly mapped region: The case of Sabellaria alveolata L. in Ireland.

Data that can be used to monitor biodiversity through time are essential for conservation and management. The reef-forming worm, Sabellaria alveolata (L. 1767) is currently classed as 'Data Deficient' due to an imbalance in the spread of data on its distribution. Little is known about the distribution of this species around Ireland. Using data archaeology, we collated past and present distribution records and discovered that S. alveolata has a discontinuous distribution with large gaps between populations. Many regions lack data and should be targeted for sampling. Biodiversity surveys revealed that S. alveolata supported diverse epibiotic algal communities. Retrograding (declining) reefs supported greater infaunal diversity than prograding (growing) reefs or sand, suggesting that S. alveolata is a dynamic ecosystem engineer that has a lasting legacy effect. Similar research should be carried out for other Data Deficient species, habitats and regions. Such data are invaluable resources for management and conservation.

Aerobic fitness and isokinetic knee strength of semi-professional rugby union players: a comparison between backs and forwards.

BACKGROUND: This study aimed to describe the physical fitness characteristics of semi-professional rugby union (RU) players using VO2max (mL. min-1. kg-1), knee peak torque (PT), mean power (MP), hamstring: quadriceps (H:Q) ratio and basic anthropometrics characteristics and to compare backs and forwards across these same characteristics. METHODS: VO2max and ventilatory threshold (VT) as a percentage of VO2max were measured using the Bruce protocol maximal graded test. Knee strength test PT, MP and H:Q were analyzed using the isokinetic dynamometer test. Basic anthropometrics measures were obtained by measures of body mass, height (from Tanita Body Composition Analysis; Tanita Corp., Tokyo, Japan). While fat mass was measured using skinfold thicknesses taking from different body parts. Twenty-five semi-professional players aged (26.3±0.9 years) from the same team were recruited for the study. Mean experimental values from maximal graded test and isokinetic dynamometer test were analyzed using t-tests from the SigmaStat 3.11 program (Systat Software Inc., San Jose, CA, USA). RESULTS: The results showed that forwards were significant taller (P=0.036), heavier (P=0.01), with greater fat mass (P=0.001) than backs. Backs had a greater VO2max (P=0.02) than forwards. With forwards having a greater (P=0.01) eccentric H PT. CONCLUSIONS: This study presents important information for players and athletic coordinators as to the differences between backs and forwards across physiological and strength measures. This information can greatly inform the individualized training protocol and preparation of current and future players across different positions and different levels.

Not really a smoker? A study on the prevalence of and attitudes to occasional social smoking in a third level institution in Ireland.

BACKGROUND: Occasional smoking is defined as any smoking occurring on a less than daily basis. Social smoking, i.e. smoking primarily in social contexts, is a sub-group of occasional smoking. Data on occasional cigarette smoking and the subset of social smoking among third level students are limited. OBJECTIVES: (1) To determine prevalence of occasional/social smoking among third level students in an Irish university; (2) to evaluate students' attitudes to occasional/social smoking, including perceived benefits and harm; (3) to explore when students commenced occasional/social smoking, their reasons and continued smoking habits; and (4) to determine any influence of other factors, e.g. alcohol consumption, on occasional/social smoking. METHODS: An anonymous online survey was distributed to undergraduates and postgraduates, using SurveyMonkey. Data were analysed in Microsoft Excel. RESULTS: Of 18,407 students surveyed, 1310 (7.1%) responded;1267 (96.7%) provided adequate data for analysis. Of the 1267 students, 423 (33.4%) self-reported as current smokers of whom 106/1267 (8.4%) self-classified as daily smokers and 317/1267 (25%) as occasional smokers. The 25% of occasional smokers comprised 266/1267 (21%) social smokers and 51/1267 (4%) non-social smokers. Occasional smokers tended to start smoking earlier and think less about quitting than daily smokers. Of 423 current smokers, 386 (97.2%) reported that alcohol increased their smoking habits. CONCLUSION: Prevalence of self-reported occasional smoking among university students was higher than daily smoking. Most occasional smokers primarily smoked in social contexts. All current smokers reported that alcohol increased cigarette intake. Effective intervention campaigns tailored to determinants of occasional/social smoking are needed as part of induction to third level.

Inhibition of post-termination ribosome recycling at premature termination codons in UPF1 ATPase mutants.

Recognition and rapid degradation of mRNA harboring premature translation termination codons (PTCs) serves to protect cells from accumulating non-functional and potentially toxic truncated polypeptides. Targeting of PTC-containing transcripts is mediated by the nonsense-mediated mRNA decay (NMD) pathway and requires a conserved set of proteins including UPF1, an RNA helicase whose ATPase activity is essential for NMD. Previously, we identified a functional interaction between the NMD machinery and terminating ribosomes based on 3' RNA decay fragments that accrue in UPF1 ATPase mutants. Herein, we show that those decay intermediates originate downstream of the PTC and harbor 80S ribosomes that migrate into the mRNA 3' UTR independent of canonical translation. Accumulation of 3' RNA decay fragments is determined by both RNA sequence downstream of the PTC and the inactivating mutation within the active site of UPF1. Our data reveal a failure in post-termination ribosome recycling in UPF1 ATPase mutants.

Microbial communities across a hillslope-riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock.

Watersheds are important suppliers of freshwater for human societies. Within mountainous watersheds, microbial communities impact water chemistry and element fluxes as water from precipitation events discharge through soils and underlying weathered rock, yet there is limited information regarding the structure and function of these communities. Within the East River, CO watershed, we conducted a depth-resolved, hillslope to riparian zone transect study to identify factors that control how microorganisms are distributed and their functions. Metagenomic and geochemical analyses indicate that distance from the East River and proximity to groundwater and underlying weathered shale strongly impact microbial community structure and metabolic potential. Riparian zone microbial communities are compositionally distinct, from the phylum down to the species level, from all hillslope communities. Bacteria from phyla lacking isolated representatives consistently increase in abundance with increasing depth, but only in the riparian zone saturated sediments we found Candidate Phyla Radiation bacteria. Riparian zone microbial communities are functionally differentiated from hillslope communities based on their capacities for carbon and nitrogen fixation and sulfate reduction. Selenium reduction is prominent at depth in weathered shale and saturated riparian zone sediments and could impact water quality. We anticipate that the drivers of community composition and metabolic potential identified throughout the studied transect will predict patterns across the larger watershed hillslope system.

The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms.

BACKGROUND: The neonatal intensive care unit (NICU) contains a unique cohort of patients with underdeveloped immune systems and nascent microbiome communities. Patients often spend several months in the same room, and it has been previously shown that the gut microbiomes of these infants often resemble the microbes found in the NICU. Little is known, however, about the identity, persistence, and absolute abundance of NICU room-associated bacteria over long stretches of time. Here, we couple droplet digital PCR (ddPCR), 16S rRNA gene surveys, and recently published metagenomics data from infant gut samples to infer the extent to which the NICU microbiome is shaped by its room occupants. RESULTS: Over 2832 swabs, wipes, and air samples were collected from 16 private-style NICU rooms housing very low birth weight (< 1500 g), premature (< 31 weeks' gestation) infants. For each infant, room samples were collected daily, Monday through Friday, for 1 month. The first samples from the first infant and the last samples from the last infant were collected 383 days apart. Twenty-two NICU locations spanning room surfaces, hands, electronics, sink basins, and air were collected. Results point to an incredibly simple room community where 5-10 taxa, mostly skin-associated, account for over 50% of the amplicon reads. Biomass estimates reveal four to five orders of magnitude difference between the least to the most dense microbial communities, air, and sink basins, respectively. Biomass trends from bioaerosol samples and petri dish dust collectors suggest occupancy to be a main driver of suspended biological particles within the NICU. Using a machine learning algorithm to classify the origin of room samples, we show that each room has a unique microbial fingerprint. Several important taxa driving this model were dominant gut colonizers of infants housed within each room. CONCLUSIONS: Despite regular cleaning of hospital surfaces, bacterial biomass was detectable at varying densities. A room-specific microbiome signature was detected, suggesting microbes seeding NICU surfaces are sourced from reservoirs within the room and that these reservoirs contain actively dividing cells. Collectively, the data suggests that hospitalized infants, in combination with their caregivers, shape the microbiome of NICU rooms.

Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface.

An enormous diversity of previously unknown bacteria and archaea has been discovered recently, yet their functional capacities and distributions in the terrestrial subsurface remain uncertain. Here, we continually sampled a CO2-driven geyser (Colorado Plateau, Utah, USA) over its 5-day eruption cycle to test the hypothesis that stratified, sandstone-hosted aquifers sampled over three phases of the eruption cycle have microbial communities that differ both in membership and function. Genome-resolved metagenomics, single-cell genomics and geochemical analyses confirmed this hypothesis and linked microorganisms to groundwater compositions from different depths. Autotrophic Candidatus "Altiarchaeum sp." and phylogenetically deep-branching nanoarchaea dominate the deepest groundwater. A nanoarchaeon with limited metabolic capacity is inferred to be a potential symbiont of the Ca. "Altiarchaeum". Candidate Phyla Radiation bacteria are also present in the deepest groundwater and they are relatively abundant in water from intermediate depths. During the recovery phase of the geyser, microaerophilic Fe- and S-oxidizers have high in situ genome replication rates. Autotrophic Sulfurimonas sustained by aerobic sulfide oxidation and with the capacity for N2 fixation dominate the shallow aquifer. Overall, 104 different phylum-level lineages are present in water from these subsurface environments, with uncultivated archaea and bacteria partitioned to the deeper subsurface.

Running and Metabolic Demands of Elite Rugby Union Assessed Using Traditional, Metabolic Power, and Heart Rate Monitoring Methods.

The aims of this study were (1) to analyze elite rugby union game demands using 3 different approaches: traditional, metabolic and heart rate-based methods (2) to explore the relationship between these methods and (3) to explore positional differences between the backs and forwards players. Time motion analysis and game demands of fourteen professional players (24.1 ± 3.4 y), over 5 European challenge cup games, were analyzed. Thresholds of 14.4 km·h-1, 20 W.kg-1 and 85% of maximal heart rate (HRmax) were set for high-intensity efforts across the three methods. The mean % of HRmax was 80.6 ± 4.3 % while 42.2 ± 16.5% of game time was spent above 85% of HRmax with no significant differences between the forwards and the backs. Our findings also show that the backs cover greater distances at high-speed than forwards (% difference: +35.2 ± 6.6%; p<0.01) while the forwards cover more distance than the backs (+26.8 ± 5.7%; p<0.05) in moderate-speed zone (10-14.4 km·h-1). However, no significant difference in high-metabolic power distance was found between the backs and forwards. Indeed, the high-metabolic power distances were greater than high-speed running distances of 24.8 ± 17.1% for the backs, and 53.4 ± 16.0% for the forwards with a significant difference (+29.6 ± 6.0% for the forwards; p<0.001) between the two groups. Nevertheless, nearly perfect correlations were found between the total distance assessed using the traditional approach and the metabolic power approach (r = 0.98). Furthermore, there is a strong association (r = 0.93) between the high-speed running distance (assessed using the traditional approach) and the high-metabolic power distance. The HR monitoring methods demonstrate clearly the high physiological demands of professional rugby games. The traditional and the metabolic-power approaches shows a close correlation concerning their relative values, nevertheless the difference in absolute values especially for the high-intensity thresholds demonstrates that the metabolic power approach may represent an interesting alternative to the traditional approaches used in evaluating the high-intensity running efforts required in rugby union games.

How livestock and flooding mediate the ecological integrity of working forests in Amazon River floodplains.

The contribution of working forests to tropical conservation and development depends upon the maintenance of ecological integrity under ongoing land use. Assessment of ecological integrity requires an understanding of the structure, composition, and function and major drivers that govern their variability. Working forests in tropical river floodplains provide many goods and services, yet the data on the ecological processes that sustain these services is scant. In flooded forests of riverside Amazonian communities, we established 46 0.1-ha plots varying in flood duration, use by cattle and water buffalo, and time since agricultural abandonment (30-90 yr). We monitored three aspects of ecological integrity (stand structure, species composition, and dynamics of trees and seedlings) to evaluate the impacts of different trajectories of livestock activity (alleviation, stasis, and intensification) over nine years. Negative effects of livestock intensification were solely evident in the forest understory, and plots alleviated from past heavy disturbance increased in seedling density but had higher abundance of thorny species than plots maintaining low activity. Stand structure, dynamics, and tree species composition were strongly influenced by the natural pulse of seasonal floods, such that the defining characteristics of integrity were dependent upon flood duration (3-200 d). Forests with prolonged floods ≥ 140 d had not only lower species richness but also lower rates of recruitment and species turnover relative to forests with short floods <70 d. Overall, the combined effects of livestock intensification and prolonged flooding hindered forest regeneration, but overall forest integrity was largely related to the hydrological regime and age. Given this disjunction between factors mediating canopy and understory integrity, we present a subset of metrics for regeneration and recruitment to distinguish forest condition by livestock trajectory. Although our study design includes confounded factors that preclude a definitive assessment of the major drivers of ecological change, we provide much-needed data on the regrowth of a critical but poorly studied ecosystem. In addition to its emphasis on the dynamics of tropical wetland forests undergoing anthropogenic and environmental change, our case study is an important example for how to assess of ecological integrity in working forests of tropical ecosystems.

Slowing Amazon deforestation through public policy and interventions in beef and soy supply chains.

The recent 70% decline in deforestation in the Brazilian Amazon suggests that it is possible to manage the advance of a vast agricultural frontier. Enforcement of laws, interventions in soy and beef supply chains, restrictions on access to credit, and expansion of protected areas appear to have contributed to this decline, as did a decline in the demand for new deforestation. The supply chain interventions that fed into this deceleration are precariously dependent on corporate risk management, and public policies have relied excessively on punitive measures. Systems for delivering positive incentives for farmers to forgo deforestation have been designed but not fully implemented. Territorial approaches to deforestation have been effective and could consolidate progress in slowing deforestation while providing a framework for addressing other important dimensions of sustainable development.

Dependence of hydropower energy generation on forests in the Amazon Basin at local and regional scales.

Tropical rainforest regions have large hydropower generation potential that figures prominently in many nations' energy growth strategies. Feasibility studies of hydropower plants typically ignore the effect of future deforestation or assume that deforestation will have a positive effect on river discharge and energy generation resulting from declines in evapotranspiration (ET) associated with forest conversion. Forest loss can also reduce river discharge, however, by inhibiting rainfall. We used land use, hydrological, and climate models to examine the local "direct" effects (through changes in ET within the watershed) and the potential regional "indirect" effects (through changes in rainfall) of deforestation on river discharge and energy generation potential for the Belo Monte energy complex, one of the world's largest hydropower plants that is currently under construction on the Xingu River in the eastern Amazon. In the absence of indirect effects of deforestation, simulated deforestation of 20% and 40% within the Xingu River basin increased discharge by 4-8% and 10-12%, with similar increases in energy generation. When indirect effects were considered, deforestation of the Amazon region inhibited rainfall within the Xingu Basin, counterbalancing declines in ET and decreasing discharge by 6-36%. Under business-as-usual projections of forest loss for 2050 (40%), simulated power generation declined to only 25% of maximum plant output and 60% of the industry's own projections. Like other energy sources, hydropower plants present large social and environmental costs. Their reliability as energy sources, however, must take into account their dependence on forests.