Displaying publications 21 - 40 of 394 in total

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  1. Fulltext Establishing the evidence base for maintaining biodiversity and ecosystem function in the oil palm landscapes of South East Asia
    Foster WA, Snaddon JL, Turner EC, Fayle TM, Cockerill TD, Ellwood MD, et al.
    Philos Trans R Soc Lond B Biol Sci, 2011 Nov 27;366(1582):3277-91.
    PMID: 22006968 DOI: 10.1098/rstb.2011.0041
    The conversion of natural forest to oil palm plantation is a major current threat to the conservation of biodiversity in South East Asia. Most animal taxa decrease in both species richness and abundance on conversion of forest to oil palm, and there is usually a severe loss of forest species. The extent of loss varies significantly across both different taxa and different microhabitats within the oil palm habitat. The principal driver of this loss in diversity is probably the biological and physical simplification of the habitat, but there is little direct evidence for this. The conservation of forest species requires the preservation of large reserves of intact forest, but we must not lose sight of the importance of conserving biodiversity and ecosystem processes within the oil palm habitat itself. We urgently need to carry out research that will establish whether maintaining diversity supports economically and ecologically important processes. There is some evidence that both landscape and local complexity can have positive impacts on biodiversity in the oil palm habitat. By intelligent manipulation of habitat complexity, it could be possible to enhance not only the number of species that can live in oil palm plantations but also their contribution to the healthy functioning of this exceptionally important and widespread landscape.
    Matched MeSH terms: Biodiversity*
  2. Fulltext Biotic and abiotic variables influencing plant litter breakdown in streams: a global study
    Boyero L, Pearson RG, Hui C, Gessner MO, Pérez J, Alexandrou MA, et al.
    Proc Biol Sci, 2016 Apr 27;283(1829).
    PMID: 27122551 DOI: 10.1098/rspb.2015.2664
    Plant litter breakdown is a key ecological process in terrestrial and freshwater ecosystems. Streams and rivers, in particular, contribute substantially to global carbon fluxes. However, there is little information available on the relative roles of different drivers of plant litter breakdown in fresh waters, particularly at large scales. We present a global-scale study of litter breakdown in streams to compare the roles of biotic, climatic and other environmental factors on breakdown rates. We conducted an experiment in 24 streams encompassing latitudes from 47.8° N to 42.8° S, using litter mixtures of local species differing in quality and phylogenetic diversity (PD), and alder (Alnus glutinosa) to control for variation in litter traits. Our models revealed that breakdown of alder was driven by climate, with some influence of pH, whereas variation in breakdown of litter mixtures was explained mainly by litter quality and PD. Effects of litter quality and PD and stream pH were more positive at higher temperatures, indicating that different mechanisms may operate at different latitudes. These results reflect global variability caused by multiple factors, but unexplained variance points to the need for expanded global-scale comparisons.
    Matched MeSH terms: Biodiversity
  3. Fulltext Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding
    Ji Y, Ashton L, Pedley SM, Edwards DP, Tang Y, Nakamura A, et al.
    Ecol Lett, 2013 Oct;16(10):1245-57.
    PMID: 23910579 DOI: 10.1111/ele.12162
    To manage and conserve biodiversity, one must know what is being lost, where, and why, as well as which remedies are likely to be most effective. Metabarcoding technology can characterise the species compositions of mass samples of eukaryotes or of environmental DNA. Here, we validate metabarcoding by testing it against three high-quality standard data sets that were collected in Malaysia (tropical), China (subtropical) and the United Kingdom (temperate) and that comprised 55,813 arthropod and bird specimens identified to species level with the expenditure of 2,505 person-hours of taxonomic expertise. The metabarcode and standard data sets exhibit statistically correlated alpha- and beta-diversities, and the two data sets produce similar policy conclusions for two conservation applications: restoration ecology and systematic conservation planning. Compared with standard biodiversity data sets, metabarcoded samples are taxonomically more comprehensive, many times quicker to produce, less reliant on taxonomic expertise and auditable by third parties, which is essential for dispute resolution.
    Matched MeSH terms: Biodiversity*
  4. Fulltext Selective‐logging and oil palm: multitaxon impacts, biodiversity indicators, and trade‐offs for conservation planning
    Edwards DP, Magrach A, Woodcock P, Ji Y, Lim NT-, Edwards FA, et al.
    Ecol Appl, 2014;24(8):2029-49.
    PMID: 29185670 DOI: 10.1890/14-0010.1
    Strong global demand for tropical timber and agricultural products has driven large-scale logging and subsequent conversion of tropical forests. Given that the majority of tropical landscapes have been or will likely be logged, the protection of biodiversity within tropical forests thus depends on whether species can persist in these economically exploited lands, and if species cannot persist, whether we can protect enough primary forest from logging and conversion. However, our knowledge of the impact of logging and conversion on biodiversity is limited to a few taxa, often sampled in different locations with complex land-use histories, hampering attempts to plan cost-effective conservation strategies and to draw conclusions across taxa. Spanning a land-use gradient of primary forest, once- and twice-logged forests, and oil palm plantations, we used traditional sampling and DNA metabarcoding to compile an extensive data set in Sabah, Malaysian Borneo for nine vertebrate and invertebrate taxa to quantify the biological impacts of logging and oil palm, develop cost-effective methods of protecting biodiversity, and examine whether there is congruence in response among taxa. Logged forests retained high species richness, including, on average, 70% of species found in primary forest. In contrast, conversion to oil palm dramatically reduces species richness, with significantly fewer primary-forest species than found on logged forest transects for seven taxa. Using a systematic conservation planning analysis, we show that efficient protection of primary-forest species is achieved with land portfolios that include a large proportion of logged-forest plots. Protecting logged forests is thus a cost-effective method of protecting an ecologically and taxonomically diverse range of species, particularly when conservation budgets are limited. Six indicator groups (birds, leaf-litter ants, beetles, aerial hymenopterans, flies, and true bugs) proved to be consistently good predictors of the response of the other taxa to logging and oil palm. Our results confidently establish the high conservation value of logged forests and the low value of oil palm. Cross-taxon congruence in responses to disturbance also suggests that the practice of focusing on key indicator taxa yields important information of general biodiversity in studies of logging and oil palm.
    Matched MeSH terms: Biodiversity*
  5. Testing a global standard for quantifying species recovery and assessing conservation impact
    Grace MK, Akçakaya HR, Bennett EL, Brooks TM, Heath A, Hedges S, et al.
    Conserv Biol, 2021 12;35(6):1833-1849.
    PMID: 34289517 DOI: 10.1111/cobi.13756
    Recognizing the imperative to evaluate species recovery and conservation impact, in 2012 the International Union for Conservation of Nature (IUCN) called for development of a "Green List of Species" (now the IUCN Green Status of Species). A draft Green Status framework for assessing species' progress toward recovery, published in 2018, proposed 2 separate but interlinked components: a standardized method (i.e., measurement against benchmarks of species' viability, functionality, and preimpact distribution) to determine current species recovery status (herein species recovery score) and application of that method to estimate past and potential future impacts of conservation based on 4 metrics (conservation legacy, conservation dependence, conservation gain, and recovery potential). We tested the framework with 181 species representing diverse taxa, life histories, biomes, and IUCN Red List categories (extinction risk). Based on the observed distribution of species' recovery scores, we propose the following species recovery categories: fully recovered, slightly depleted, moderately depleted, largely depleted, critically depleted, extinct in the wild, and indeterminate. Fifty-nine percent of tested species were considered largely or critically depleted. Although there was a negative relationship between extinction risk and species recovery score, variation was considerable. Some species in lower risk categories were assessed as farther from recovery than those at higher risk. This emphasizes that species recovery is conceptually different from extinction risk and reinforces the utility of the IUCN Green Status of Species to more fully understand species conservation status. Although extinction risk did not predict conservation legacy, conservation dependence, or conservation gain, it was positively correlated with recovery potential. Only 1.7% of tested species were categorized as zero across all 4 of these conservation impact metrics, indicating that conservation has, or will, play a role in improving or maintaining species status for the vast majority of these species. Based on our results, we devised an updated assessment framework that introduces the option of using a dynamic baseline to assess future impacts of conservation over the short term to avoid misleading results which were generated in a small number of cases, and redefines short term as 10 years to better align with conservation planning. These changes are reflected in the IUCN Green Status of Species Standard.
    Matched MeSH terms: Biodiversity
  6. Fulltext The benefits of contributing to the citizen science platform iNaturalist as an identifier
    Callaghan CT, Mesaglio T, Ascher JS, Brooks TM, Cabras AA, Chandler M, et al.
    PLoS Biol, 2022 Nov;20(11):e3001843.
    PMID: 36355752 DOI: 10.1371/journal.pbio.3001843
    As the number of observations submitted to the citizen science platform iNaturalist continues to grow, it is increasingly important that these observations can be identified to the finest taxonomic level, maximizing their value for biodiversity research. Here, we explore the benefits of acting as an identifier on iNaturalist.
    Matched MeSH terms: Biodiversity
  7. Fulltext Succession of bacterial community structure and diversity in soil along a chronosequence of reclamation and re-vegetation on coal mine spoils in China
    Li Y, Wen H, Chen L, Yin T
    PLoS One, 2014;9(12):e115024.
    PMID: 25502754 DOI: 10.1371/journal.pone.0115024
    The growing concern about the effectiveness of reclamation strategies has motivated the evaluation of soil properties following reclamation. Recovery of belowground microbial community is important for reclamation success, however, the response of soil bacterial communities to reclamation has not been well understood. In this study, PCR-based 454 pyrosequencing was applied to compare bacterial communities in undisturbed soils with those in reclaimed soils using chronosequences ranging in time following reclamation from 1 to 20 year. Bacteria from the Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, Planctomycetes and Bacteroidetes were abundant in all soils, while the composition of predominant phyla differed greatly across all sites. Long-term reclamation strongly affected microbial community structure and diversity. Initial effects of reclamation resulted in significant declines in bacterial diversity indices in younger reclaimed sites (1, 8-year-old) compared to the undisturbed site. However, bacterial diversity indices tended to be higher in older reclaimed sites (15, 20-year-old) as recovery time increased, and were more similar to predisturbance levels nearly 20 years after reclamation. Bacterial communities are highly responsive to soil physicochemical properties (pH, soil organic matter, Total N and P), in terms of both their diversity and community composition. Our results suggest that the response of soil microorganisms to reclamation is likely governed by soil characteristics and, indirectly, by the effects of vegetation restoration. Mixture sowing of gramineae and leguminosae herbage largely promoted soil geochemical conditions and bacterial diversity that recovered to those of undisturbed soil, representing an adequate solution for soil remediation and sustainable utilization for agriculture. These results confirm the positive impacts of reclamation and vegetation restoration on soil microbial diversity and suggest that the most important phase of microbial community recovery occurs between 15 and 20 years after reclamation.
    Matched MeSH terms: Biodiversity*
  8. Forest conversion to oil palm compresses food chain length in tropical streams
    Wilkinson CL, Chua KWJ, Fiala R, Liew JH, Kemp V, Hadi Fikri A, et al.
    Ecology, 2021 01;102(1):e03199.
    PMID: 32969053 DOI: 10.1002/ecy.3199
    In Southeast Asia, biodiversity-rich forests are being extensively logged and converted to oil palm monocultures. Although the impacts of these changes on biodiversity are largely well documented, we know addition to samples we collected in 201 little about how these large-scale impacts affect freshwater trophic ecology. We used stable isotope analyses (SIA) to determine the impacts of land-use changes on the relative contribution of allochthonous and autochthonous basal resources in 19 stream food webs. We also applied compound-specific SIA and bulk-SIA to determine the trophic position of fish apex predators and meso-predators (invertivores and omnivores). There was no difference in the contribution of autochthonous resources in either consumer group (70-82%) among streams with different land-use type. There was no change in trophic position for meso-predators, but trophic position decreased significantly for apex predators in oil palm plantation streams compared to forest streams. This change in maximum food chain length was due to turnover in identity of the apex predator among land-use types. Disruption of aquatic trophic ecology, through reduction in food chain length and shift in basal resources, may cause significant changes in biodiversity as well as ecosystem functions and services. Understanding this change can help develop more focused priorities for mediating the negative impacts of human activities on freshwater ecosystems.
    Matched MeSH terms: Biodiversity
  9. Fulltext Persistent mosquito fogging can be detrimental to non-target invertebrates in an urban tropical forest
    Lee NSM, Clements GR, Ting ASY, Wong ZH, Yek SH
    PeerJ, 2020;8:e10033.
    PMID: 33062440 DOI: 10.7717/peerj.10033
    Background: Human population growth has led to biodiversity declines in tropical cities. While habitat loss and fragmentation have been the main drivers of urban biodiversity loss, man-made interventions to reduce health risks have also emerged as an unintentional threat. For instance, insecticide fogging to control mosquito populations has become the most common method of preventing the expansion of mosquito-borne diseases such as Dengue. However, the effectiveness of fogging in killing mosquitoes has been called into question. One concern is the unintended effect of insecticide fogging on non-target invertebrates that are crucial for the maintenance of urban ecosystems. Here, we investigate the impacts of fogging on: (1) target invertebrate taxon (Diptera, including mosquitoes); (2) non-target invertebrate taxa; and (3) the foraging behavior of an invertebrate pollinator taxon (Lepidoptera) within an urban tropical forest.

    Methods: We carried out fogging with Pyrethroid insecticide (Detral 2.5 EC) at 10 different sites in a forest situated in the state of Selangor, Peninsular Malaysia. Across the sites, we counted the numbers of knocked-down invertebrates and identified them based on morphology to different taxa. We constructed Bayesian hierarchical Poisson regression models to investigate the effects of fogging on: (1) a target invertebrate taxon (Diptera) 3-h post-fogging; (2) selected non-target invertebrate taxa 3-h post-fogging; and (3) an invertebrate pollinator taxon (Lepidoptera) 24-h post-fogging.

    Results: A total of 1,874 invertebrates from 19 invertebrate orders were knocked down by the fogging treatment across the 10 sites. Furthermore, 72.7% of the invertebrates counted 3-h post-fogging was considered dead. Our regression models showed that given the data and prior information, the probability that fogging had a negative effect on invertebrate taxa 3-h post-fogging was 100%, with reductions to 11% of the pre-fogging count of live individuals for the target invertebrate taxon (Diptera), and between 5% and 58% of the pre-fogging count of live individuals for non-target invertebrate taxa. For the invertebrate pollinator, the probability that fogging had a negative effect 24-h post-fogging was also 100%, with reductions to 53% of the pre-fogging count of live individuals.

    Discussion: Our Bayesian models unequivocally demonstrate that fogging has detrimental effects on one pollinator order and non-target invertebrate orders, especially taxa that have comparatively lower levels of chitinisation. While fogging is effective in killing the target order (Diptera), no mosquitos were found dead in our experiment. In order to maintain urban biodiversity, we recommend that health authorities and the private sector move away from persistent insecticide fogging and to explore alternative measures to control adult mosquito populations.

    Matched MeSH terms: Biodiversity
  10. Fulltext Climate change considerations are fundamental to management of deep-sea resource extraction
    Levin LA, Wei CL, Dunn DC, Amon DJ, Ashford OS, Cheung WWL, et al.
    Glob Chang Biol, 2020 09;26(9):4664-4678.
    PMID: 32531093 DOI: 10.1111/gcb.15223
    Climate change manifestation in the ocean, through warming, oxygen loss, increasing acidification, and changing particulate organic carbon flux (one metric of altered food supply), is projected to affect most deep-ocean ecosystems concomitantly with increasing direct human disturbance. Climate drivers will alter deep-sea biodiversity and associated ecosystem services, and may interact with disturbance from resource extraction activities or even climate geoengineering. We suggest that to ensure the effective management of increasing use of the deep ocean (e.g., for bottom fishing, oil and gas extraction, and deep-seabed mining), environmental management and developing regulations must consider climate change. Strategic planning, impact assessment and monitoring, spatial management, application of the precautionary approach, and full-cost accounting of extraction activities should embrace climate consciousness. Coupled climate and biological modeling approaches applied in the water and on the seafloor can help accomplish this goal. For example, Earth-System Model projections of climate-change parameters at the seafloor reveal heterogeneity in projected climate hazard and time of emergence (beyond natural variability) in regions targeted for deep-seabed mining. Models that combine climate-induced changes in ocean circulation with particle tracking predict altered transport of early life stages (larvae) under climate change. Habitat suitability models can help assess the consequences of altered larval dispersal, predict climate refugia, and identify vulnerable regions for multiple species under climate change. Engaging the deep observing community can support the necessary data provisioning to mainstream climate into the development of environmental management plans. To illustrate this approach, we focus on deep-seabed mining and the International Seabed Authority, whose mandates include regulation of all mineral-related activities in international waters and protecting the marine environment from the harmful effects of mining. However, achieving deep-ocean sustainability under the UN Sustainable Development Goals will require integration of climate consideration across all policy sectors.
    Matched MeSH terms: Biodiversity
  11. Fulltext Soil nitrogen concentration mediates the relationship between leguminous trees and neighbor diversity in tropical forests
    Xu H, Detto M, Fang S, Chazdon RL, Li Y, Hau BCH, et al.
    Commun Biol, 2020 06 19;3(1):317.
    PMID: 32561898 DOI: 10.1038/s42003-020-1041-y
    Legumes provide an essential service to ecosystems by capturing nitrogen from the atmosphere and delivering it to the soil, where it may then be available to other plants. However, this facilitation by legumes has not been widely studied in global tropical forests. Demographic data from 11 large forest plots (16-60 ha) ranging from 5.25° S to 29.25° N latitude show that within forests, leguminous trees have a larger effect on neighbor diversity than non-legumes. Where soil nitrogen is high, most legume species have higher neighbor diversity than non-legumes. Where soil nitrogen is low, most legumes have lower neighbor diversity than non-legumes. No facilitation effect on neighbor basal area was observed in either high or low soil N conditions. The legume-soil nitrogen positive feedback that promotes tree diversity has both theoretical implications for understanding species coexistence in diverse forests, and practical implications for the utilization of legumes in forest restoration.
    Matched MeSH terms: Biodiversity
  12. From Barcodes to Biomes: Special Issues from the 6th International Barcode of Life Conference
    Adamowicz SJ, Chain FJ, Clare EL, Deiner K, Dincă V, Elías-Gutiérrez M, et al.
    Genome, 2016 Sep;59(9):v-ix.
    PMID: 27611699 DOI: 10.1139/gen-2016-0159
    Matched MeSH terms: Biodiversity
  13. Seaweed and climate change: A mapping review
    Segaran TC, Azra MN, Handayani KS, Lananan F, Xu J
    Mar Environ Res, 2023 Nov;192:106216.
    PMID: 37891025 DOI: 10.1016/j.marenvres.2023.106216
    Seaweed has garnered increasing interest due to its capacity to mitigate climate change by curbing carbon emissions from agriculture, as well as its potential to serve as a supplement or alternative for dietary, livestock feed, or fuel source production. Moreover, seaweed is regarded as one of the earliest plant forms to have evolved on Earth. Owing to the extensive body of literature available and the uncertainty surrounding the future trajectory of seaweed research under evolving climate conditions, this review scrutinizes the structure, dynamics, and progression of the literature pertaining to seaweed and climate change. This analysis is grounded in the Web of Science Core Collection database, augmented by CiteSpace software. Furthermore, we discuss the productivity and influence of individual researchers, research organizations, countries, and scientific journals. To date, there have been 8047 articles published globally (after a series of filters and exclusions), with a notable upswing in publication frequency since 2018. The USA, China, and Australia are among the leading countries contributing to this research area. Our findings reveal that current research on seaweed and climate change encompasses 13 distinct research clusters, including "marine heatwave", "temperate estuary", "ocean acidification", and "macroalgal bloom". The most frequently cited keywords are "climate change", "biomass", "community", and "photosynthesis". The seaweed species most commonly referenced in relation to climate change include Gracilaria sp., Sargassum sp., Ecklonia maxima, and Macrocystis pyrifera. These results provide valuable guidance for shaping the direction of specialized topics concerning marine biodiversity under shifting climate conditions. We propose that seaweed production may be compromised during prolonged episodes of reduced water availability, emphasizing the need to formulate strategies to guarantee its continued viability. This article offers fresh perspectives on the analysis of seaweed research in the context of impending climate change.
    Matched MeSH terms: Biodiversity
  14. Temporal coexistence mechanisms contribute to the latitudinal gradient in forest diversity
    Usinowicz J, Chang-Yang CH, Chen YY, Clark JS, Fletcher C, Garwood NC, et al.
    Nature, 2017 10 05;550(7674):105-108.
    PMID: 28953870 DOI: 10.1038/nature24038
    The tropical forests of Borneo and Amazonia may each contain more tree species diversity in half a square kilometre than do all the temperate forests of Europe, North America, and Asia combined. Biologists have long been fascinated by this disparity, using it to investigate potential drivers of biodiversity. Latitudinal variation in many of these drivers is expected to create geographic differences in ecological and evolutionary processes, and evidence increasingly shows that tropical ecosystems have higher rates of diversification, clade origination, and clade dispersal. However, there is currently no evidence to link gradients in ecological processes within communities at a local scale directly to the geographic gradient in biodiversity. Here, we show geographic variation in the storage effect, an ecological mechanism that reduces the potential for competitive exclusion more strongly in the tropics than it does in temperate and boreal zones, decreasing the ratio of interspecific-to-intraspecific competition by 0.25% for each degree of latitude that an ecosystem is located closer to the Equator. Additionally, we find evidence that latitudinal variation in climate underpins these differences; longer growing seasons in the tropics reduce constraints on the seasonal timing of reproduction, permitting lower recruitment synchrony between species and thereby enhancing niche partitioning through the storage effect. Our results demonstrate that the strength of the storage effect, and therefore its impact on diversity within communities, varies latitudinally in association with climate. This finding highlights the importance of biotic interactions in shaping geographic diversity patterns, and emphasizes the need to understand the mechanisms underpinning ecological processes in greater detail than has previously been appreciated.
    Matched MeSH terms: Biodiversity*
  15. Diversity of pollination ecology in the Schismatoglottis Calyptrata Complex Clade (Araceae)
    Hoe YC, Gibernau M, Wong SY
    Plant Biol (Stuttg), 2018 May;20(3):563-578.
    PMID: 29316090 DOI: 10.1111/plb.12687
    Field studies integrating pollination investigations with an assessment of floral scent composition and thermogenesis in tropical aroids are rather few. Thus, this study aimed to investigate the pollination biology of nine species belonging to Schismatoglottis Calyptrata Complex Clade. The flowering mechanism, visiting insect activities, reproductive system, thermogenesis and floral scent composition were examined. Anthesis for all species started at dawn and lasted 25-29 h. Colocasiomyia (Diptera, Drosophilidae) are considered the main pollinators for all the investigated species. Cycreon (Coleoptera, Hydrophilidae) are considered secondary pollinators as they are only present in seven of the nine host plants, despite the fact that they are the most effective pollen carrier, carrying up to 15 times more pollen grains than Colocasiomyia flies. However, the number of Colocasiomyia individuals was six times higher than Cycreon beetles. Chaloenus (Chrysomelidae, Galeuricinae) appeared to be an inadvertent pollinator. Atheta (Coleoptera, Staphylinidae) is considered a floral visitor in most investigated species of the Calyptrata Complex Clade in Sarawak, but a possible pollinator in S. muluensis. Chironomidae midges and pteromalid wasps are considered visitors in S. calyptrata. Thermogenesis in a biphasic pattern was observed in inflorescences of S. adducta, S. calyptrata, S. giamensis, S. pseudoniahensis and S. roh. The first peak occurred during pistillate anthesis; the second peak during staminate anthesis. Inflorescences of all investigated species of Calyptrata Complex Clade emitted four types of ester compound, with methyl ester-3-methyl-3-butenoic acid as a single major VOC (volatile organic compound). The appendix, pistillate zone, staminate zone and spathe emitted all these compounds. A mixed fly-beetle pollination system is considered an ancestral trait in the Calyptrata Complex Clade, persisting in Sarawak taxa, whereas the marked reduction of interpistillar staminodes in taxa from Peninsular Malaysia and especially, Ambon, Indonesia, is probably linked to a shift in these taxa to a fly-pollinated system.
    Matched MeSH terms: Biodiversity
  16. Effects of simulated warming on bacterial diversity and abundance in tropical soils from East Malaysia using open top chambers
    Chua CY, Wong CMVL
    Can J Microbiol, 2021 Jan;67(1):64-74.
    PMID: 33084348 DOI: 10.1139/cjm-2019-0461
    The effects of global warming are increasingly evident, where global surface temperatures and atmospheric concentration of carbon dioxide have increased in past decades. Given the role of terrestrial bacteria in various ecological functions, it is important to understand how terrestrial bacteria would respond towards higher environmental temperatures. This study aims to determine soil bacterial diversity in the tropics and their response towards in situ warming using an open-top chamber (OTC). OTCs were set up in areas exposed to sunlight throughout the year in the tropical region in Malaysia. Soil samples were collected every 3 months to monitor changes in bacterial diversity using V3-V4 16S rDNA amplicon sequencing inside the OTCs (treatment plots) and outside the OTCs (control plots). After 12 months of simulated warming, an average increase of 0.81 to 1.15 °C was recorded in treatment plots. Significant changes in the relative abundance of bacterial phyla such as Bacteroidetes and Chloroflexi were reported. Increases in the relative abundance of Actinobacteria were also observed in treatment plots after 12 months. Substantial changes were observed at the genus level, where most bacterial genera decreased in relative abundance after 12 months. This study demonstrated that warming can alter soil bacteria in tropical soils from Kota Kinabalu.
    Matched MeSH terms: Biodiversity
  17. Fulltext Habitat degradation and indiscriminate hunting differentially impact faunal communities in the Southeast Asian tropical biodiversity hotspot
    Tilker A, Abrams JF, Mohamed A, Nguyen A, Wong ST, Sollmann R, et al.
    Commun Biol, 2019;2:396.
    PMID: 31701025 DOI: 10.1038/s42003-019-0640-y
    Habitat degradation and hunting have caused the widespread loss of larger vertebrate species (defaunation) from tropical biodiversity hotspots. However, these defaunation drivers impact vertebrate biodiversity in different ways and, therefore, require different conservation interventions. We conducted landscape-scale camera-trap surveys across six study sites in Southeast Asia to assess how moderate degradation and intensive, indiscriminate hunting differentially impact tropical terrestrial mammals and birds. We found that functional extinction rates were higher in hunted compared to degraded sites. Species found in both sites had lower occupancies in the hunted sites. Canopy closure was the main predictor of occurrence in the degraded sites, while village density primarily influenced occurrence in the hunted sites. Our findings suggest that intensive, indiscriminate hunting may be a more immediate threat than moderate habitat degradation for tropical faunal communities, and that conservation stakeholders should focus as much on overhunting as on habitat conservation to address the defaunation crisis.
    Matched MeSH terms: Biodiversity*
  18. Fulltext Alternative futures for Borneo show the value of integrating economic and conservation targets across borders
    Runting RK, Meijaard E, Abram NK, Wells JA, Gaveau DL, Ancrenaz M, et al.
    Nat Commun, 2015 04 14;6:6819.
    PMID: 25871635 DOI: 10.1038/ncomms7819
    Balancing economic development with international commitments to protect biodiversity is a global challenge. Achieving this balance requires an understanding of the possible consequences of alternative future scenarios for a range of stakeholders. We employ an integrated economic and environmental planning approach to evaluate four alternative futures for the mega-diverse island of Borneo. We show what could be achieved if the three national jurisdictions of Borneo coordinate efforts to achieve their public policy targets and allow a partial reallocation of planned land uses. We reveal the potential for Borneo to simultaneously retain ∼50% of its land as forests, protect adequate habitat for the Bornean orangutan (Pongo pygmaeus) and Bornean elephant (Elephas maximus borneensis), and achieve an opportunity cost saving of over US$43 billion. Such coordination would depend on enhanced information sharing and reforms to land-use planning, which could be supported by the increasingly international nature of economies and conservation efforts.
    Matched MeSH terms: Biodiversity*
  19. DNA metabarcoding of insects and allies: an evaluation of primers and pipelines
    Brandon-Mong GJ, Gan HM, Sing KW, Lee PS, Lim PE, Wilson JJ
    Bull. Entomol. Res., 2015 Dec;105(6):717-27.
    PMID: 26344799 DOI: 10.1017/S0007485315000681
    Metabarcoding, the coupling of DNA-based species identification and high-throughput sequencing, offers enormous promise for arthropod biodiversity studies but factors such as cost, speed and ease-of-use of bioinformatic pipelines, crucial for making the leapt from demonstration studies to a real-world application, have not yet been adequately addressed. Here, four published and one newly designed primer sets were tested across a diverse set of 80 arthropod species, representing 11 orders, to establish optimal protocols for Illumina-based metabarcoding of tropical Malaise trap samples. Two primer sets which showed the highest amplification success with individual specimen polymerase chain reaction (PCR, 98%) were used for bulk PCR and Illumina MiSeq sequencing. The sequencing outputs were subjected to both manual and simple metagenomics quality control and filtering pipelines. We obtained acceptable detection rates after bulk PCR and high-throughput sequencing (80-90% of input species) but analyses were complicated by putative heteroplasmic sequences and contamination. The manual pipeline produced similar or better outputs to the simple metagenomics pipeline (1.4 compared with 0.5 expected:unexpected Operational Taxonomic Units). Our study suggests that metabarcoding is slowly becoming as cheap, fast and easy as conventional DNA barcoding, and that Malaise trap metabarcoding may soon fulfill its potential, providing a thermometer for biodiversity.
    Matched MeSH terms: Biodiversity
  20. Diversity and human perceptions of bees (Hymenoptera: Apoidea) in Southeast Asian megacities
    Sing KW, Wang WZ, Wan T, Lee PS, Li ZX, Chen X, et al.
    Genome, 2016 Oct;59(10):827-839.
    PMID: 27327818
    Urbanization requires the conversion of natural land cover to cover with human-constructed elements and is considered a major threat to biodiversity. Bee populations, globally, are under threat; however, the effect of rapid urban expansion in Southeast Asia on bee diversity has not been investigated. Given the pressing issues of bee conservation and urbanization in Southeast Asia, coupled with complex factors surrounding human-bee coexistence, we investigated bee diversity and human perceptions of bees in four megacities. We sampled bees and conducted questionnaires at three different site types in each megacity: a botanical garden, central business district, and peripheral suburban areas. Overall, the mean species richness and abundance of bees were significantly higher in peripheral suburban areas than central business districts; however, there were no significant differences in the mean species richness and abundance between botanical gardens and peripheral suburban areas or botanical gardens and central business districts. Urban residents were unlikely to have seen bees but agreed that bees have a right to exist in their natural environment. Residents who did notice and interact with bees, even though being stung, were more likely to have positive opinions towards the presence of bees in cities.
    Matched MeSH terms: Biodiversity
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