Nitrification of mature sanitary landfill leachate with high-strength of N-NH(4) + (1080-2350 mg L(-1)) was performed in a 10 L continuous nitrification activated sludge reactor. The nitrification system was acclimatized with synthetic leachate during feed batch operation to avoid substrate inhibition before being fed with actual mature leachate. Successful nitrification was achieved with an approximately complete ammonium removal (99%) and 96% of N-NH(4) + conversion to N-NO(-) (3) . The maximum volumetric and specific nitrification rates obtained were 2.56 kg N-NH(4) (+) m(-3) day(-1) and 0.23 g N-NH(4) ( +) g(-1) volatile suspended solid (VSS) day(-1), respectively, at hydraulic retention time (HRT) of 12.7 h and solid retention time of 50 days. Incomplete nitrification was encountered when operating at a higher nitrogen loading rate of 3.14 kg N-NH(4) (+) m(-3) day(-1). The substrate overloading and nitrifiers competition with heterotrophs were believed to trigger the incomplete nitrification. Fluorescence in situ hybridization (FISH) results supported the syntrophic association between the ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria. FISH results also revealed the heterotrophs as the dominant and disintegration of some AOB cell aggregates into single cells which further supported the incomplete nitrification phenomenon.
Marine spatial planning tends to prioritise biological conservation targets over socio-economic considerations, which may incur lower user compliance and ultimately compromise management success. We argue for more inclusion of human dimensions in spatial management, so that outcomes not only fulfill biodiversity and conservation objectives, but are also acceptable to resource users. We propose a fuzzy logic framework that will facilitate this task- The protected area suitability index (PASI) combines fishers' spatial preferences with biological criteria to assess site suitability for protection from fishing. We apply the PASI in a spatial evaluation of a small-scale reef fishery in Sabah, Malaysia. While our results pertain to fishers specifically, the PASI can also be customized to include the interests of other stakeholders and resource users, as well as incorporate varying levels of protection.
A priori assessments of a site's biophysical and socio-economic capacity for accommodating tourism are less common than tourism impact studies. A priori evaluations can provide a contextual understanding of ecological, economic and socio-cultural forces, which shape the prospects for sustainable tourism development at the host destination, and can avert adverse impacts of tourism. We conduct an a priori assessment of the biophysical environment of Pulau Banggi, in the Malaysian state of Sabah for sustainable tourism development. We characterise baseline conditions of the island's marine biodiversity, seasonality, and infrastructure. We then evaluate how existing biophysical conditions will influence options for sustainable tourism development. In particular, we suggest conditions, if there are any, which constitute a limit to future tourism development in terms of compatibility for recreation and resilience to visitor impacts. We find that the biggest constraint is the lack of adequate water and sanitation infrastructure. Blast fishing, although occurring less than once per hour, can potentially destroy the major attraction for tourists. We conclude that while Pulau Banggi possesses natural qualities that are attractive for ecotourism, financial and institutional support must be made available to provide facilities and services that will enable local participation in environmental protection and enhance prospects for future sustainable tourism.
Selective logging and forest conversion to oil palm agriculture are rapidly altering tropical forests. However, functional responses of the soil microbiome to these land-use changes are poorly understood. Using 16S rRNA gene and shotgun metagenomic sequencing, we compared composition and functional attributes of soil biota between unlogged, once-logged and twice-logged rainforest, and areas converted to oil palm plantations in Sabah, Borneo. Although there was no significant effect of logging history, we found a significant difference between the taxonomic and functional composition of both primary and logged forests and oil palm. Oil palm had greater abundances of genes associated with DNA, RNA, protein metabolism and other core metabolic functions, but conversely, lower abundance of genes associated with secondary metabolism and cell-cell interactions, indicating less importance of antagonism or mutualism in the more oligotrophic oil palm environment. Overall, these results show a striking difference in taxonomic composition and functional gene diversity of soil microorganisms between oil palm and forest, but no significant difference between primary forest and forest areas with differing logging history. This reinforces the view that logged forest retains most features and functions of the original soil community. However, networks based on strong correlations between taxonomy and functions showed that network complexity is unexpectedly increased due to both logging and oil palm agriculture, which suggests a pervasive effect of both land-use changes on the interaction of soil microbes.
Depreissia is a little known genus comprising two hymenopteran-mimicking species, one found in Central Africa and one in the north of Borneo. The male of Depreissia decipiens is redescribed, the female is described for the first time. The carapace is elongated, dorsally flattened and rhombus-shaped, the rear of the thorax laterally depressed and transformed, with a pair of deep pits; the pedicel is almost as long as the abdomen. The male palp is unusual, characterized by the transverse deeply split membranous tegulum separating a ventral part which bears a sclerotized tegular apophysis and a large dagger-like retrodirected median apophysis. The female epigyne consists of one pair of large adjacent spermathecae and very long copulatory ducts arising posteriorly and rising laterally alongside the spermathecae continuing in several vertical and horizontal coils over the anterior surface. Relationships within the Salticidae are discussed and an affinity with the Cocalodinae is suggested. Arguments are provided for a hypothesis that Depreissia decipiens is not ant-mimicking as was previously believed, but is a mimic of polistinine wasps. The species was found in the canopy in the Kinabalu area only, in primary and old secondary rainforest at 200-700 m.a.s.l. Overlap of canopy-dwelling spider species with those in the understorey are discussed and examples of species richness and endemism in the canopy are highlighted. Canopy fogging is a very efficient method of collecting for most arthropods. The canopy fauna adds an extra dimension to the known biodiversity of the tropical rainforest. In southeast Asia, canopy research has been neglected, inhibiting evaluation of comparative results of this canopy project with that from other regions. More use of fogging as a collecting method would greatly improve insight into the actual species richness and species distribution in general.
Tomistoma schlegelii, also referred to as the "false gharial", is one of the most exclusive and least known of the world's fresh water crocodilians, limited to Southeast Asia. Indeed, lack of economic value for its skin has led to neglect the biodiversity of the species. The current study aimed to investigate the mentioned case using 40 simple sequence repeat (SSR) primer pairs and 45 inter-simple sequence repeat (ISSR) primers. DNA analysis of 17 T. schlegelii samples using the SSR and ISSR markers resulted in producing a total of 49 and 108 polymorphic bands, respectively. Furthermore, the SSR- and ISSR-based cluster analyses both generated two main clusters. However, the SSR based results were found to be more in line with the geographical distributions of the crocodile samples collected across the country as compared with the ISSR-based results. The observed heterozygosity (HO) and expected heterozygosity (HE) of the polymorphic SSRs ranged between 0.588-1 and 0.470-0.891, respectively. The present results suggest that the Malaysian T. schlegelii populations had originated from a core population of crocodiles. In cooperation with the SSR markers, the ISSRs showed high potential for studying the genetic variation of T. schlegelii, and these markers are suitable to be employed in conservation genetic programs of this endangered species. Both SSR- and ISSR-based STRUCTURE analyses suggested that all the individuals of T. schlegelii are genetically similar with each other.
In Amazonian tropical forests, recent studies have reported increases in aboveground biomass and in primary productivity, as well as shifts in plant species composition favouring fast-growing species over slow-growing ones. This pervasive alteration of mature tropical forests was attributed to global environmental change, such as an increase in atmospheric CO2 concentration, nutrient deposition, temperature, drought frequency, and/or irradiance. We used standardized, repeated measurements of over 2 million trees in ten large (16-52 ha each) forest plots on three continents to evaluate the generality of these findings across tropical forests. Aboveground biomass increased at seven of our ten plots, significantly so at four plots, and showed a large decrease at a single plot. Carbon accumulation pooled across sites was significant (+0.24 MgC ha(-1) y(-1), 95% confidence intervals [0.07, 0.39] MgC ha(-1) y(-1)), but lower than reported previously for Amazonia. At three sites for which we had data for multiple census intervals, we found no concerted increase in biomass gain, in conflict with the increased productivity hypothesis. Over all ten plots, the fastest-growing quartile of species gained biomass (+0.33 [0.09, 0.55] % y(-1)) compared with the tree community as a whole (+0.15 % y(-1)); however, this significant trend was due to a single plot. Biomass of slow-growing species increased significantly when calculated over all plots (+0.21 [0.02, 0.37] % y(-1)), and in half of our plots when calculated individually. Our results do not support the hypothesis that fast-growing species are consistently increasing in dominance in tropical tree communities. Instead, they suggest that our plots may be simultaneously recovering from past disturbances and affected by changes in resource availability. More long-term studies are necessary to clarify the contribution of global change to the functioning of tropical forests.
Animals can have both positive (e.g. via seed dispersal) and negative (e.g. via herbivory) impacts on plants. The net effects of these interactions remain difficult to predict and may be affected by overhunting and habitat disturbance, two widespread threats to tropical forests. Recent studies have documented their separate effects on plant recruitment but our understanding of how defaunation and logging interact to influence tropical tree communities is limited. From 2013 to 2016, we followed the fate of marked tree seedlings (n = 1489) from 81 genera in and outside experimental plots. Our plots differentially excluded small, medium and large-bodied mammal herbivores in logged and unlogged forest in Malaysian Borneo. We assessed the effects of experimental defaunation and logging on taxonomic diversity and plant trait (wood density, specific leaf area, fruit size) composition of seedling communities. Although seedling mortality was highest in the presence of all mammal herbivores (44%), defaunation alone did not alter taxonomic diversity nor plant trait composition. However, herbivores (across all body sizes) significantly reduced mean fruit size across the seedling community over time (95% confidence interval (CI): -0.09 to -0.01), particularly in logged forest (95% CI: -0.12 to -0.003). Our findings suggest that impacts of mammal herbivores on plant communities may be greater in forests with a history of disturbance and could subsequently affect plant functional traits and ecological processes associated with forest regeneration.
Southeast (SE) Asia is 1 of the most biodiverse regions in the world, and it holds approximately 20% of all mammal species. Despite this, the majority of SE Asia's genetic diversity is still poorly characterized. The growing interest in using environmental DNA to assess and monitor SE Asian species, in particular threatened mammals-has created the urgent need to expand the available reference database of mitochondrial barcode and complete mitogenome sequences. We have partially addressed this need by generating 72 new mitogenome sequences reconstructed from DNA isolated from a range of historical and modern tissue samples. Approximately 55 gigabases of raw sequence were generated. From this data, we assembled 72 complete mitogenome sequences, with an average depth of coverage of ×102.9 and ×55.2 for modern samples and historical samples, respectively. This dataset represents 52 species, of which 30 species had no previous mitogenome data available. The mitogenomes were geotagged to their sampling location, where known, to display a detailed geographical distribution of the species. Our new database of 52 taxa will strongly enhance the utility of environmental DNA approaches for monitoring mammals in SE Asia as it greatly increases the likelihoods that identification of metabarcoding sequencing reads can be assigned to reference sequences. This magnifies the confidence in species detections and thus allows more robust surveys and monitoring programmes of SE Asia's threatened mammal biodiversity. The extensive collections of historical samples from SE Asia in western and SE Asian museums should serve as additional valuable material to further enrich this reference database.
Little is known of the factors influencing soil archaeal community diversity and composition in the tropics. We sampled soils across a range of forest and nonforest environments in the equatorial tropics of Malaysia, covering a wide range of pH values. DNA was PCR-amplified for the V1-V3 region of the 16S rRNA gene, and 454-pyrosequenced. Soil pH was the best predictor of diversity and community composition of Archaea, being a stronger predictor than land use. Archaeal OTU richness was highest in the most acidic soils. Overall archaeal abundance in tropical soils (determined by qPCR) also decreased at higher pH. This contrasts with the opposite trend previously found in temperate soils. Thaumarcheota group 1.1b was more abundant in alkaline soils, whereas group 1.1c was only detected in acidic soils. These results parallel those found in previous studies in cooler climates, emphasizing niche conservatism among broad archaeal groups. Among the most abundant operational taxonomic units (OTUs), there was clear evidence of niche partitioning by pH. No individual OTU occurred across the entire range of pH values. Overall, the results of this study show that pH plays a major role in structuring tropical soil archaeal communities.
A recently developed rapid co-composting of oil palm empty fruit bunch (OPEFB) and palm oil mill effluent (POME) anaerobic sludge is beginning to attract attention from the palm oil industry in managing the disposal of these wastes. However, a deeper understanding of microbial diversity is required for the sustainable practice of the co-compositing process. In this study, an in-depth assessment of bacterial community succession at different stages of the pilot scale co-composting of OPEFB-POME anaerobic sludge was performed using 454-pyrosequencing, which was then correlated with the changes of physicochemical properties including temperature, oxygen level and moisture content. Approximately 58,122 of 16S rRNA gene amplicons with more than 500 operational taxonomy units (OTUs) were obtained. Alpha diversity and principal component analysis (PCoA) indicated that bacterial diversity and distributions were most influenced by the physicochemical properties of the co-composting stages, which showed remarkable shifts of dominant species throughout the process. Species related to Devosia yakushimensis and Desemzia incerta are shown to emerge as dominant bacteria in the thermophilic stage, while Planococcus rifietoensis correlated best with the later stage of co-composting. This study proved the bacterial community shifts in the co-composting stages corresponded with the changes of the physicochemical properties, and may, therefore, be useful in monitoring the progress of co-composting and compost maturity.
Plant functional traits regulate ecosystem functions but little is known about how co-occurring gradients of land use and edaphic conditions influence their expression. We test how gradients of logging disturbance and soil properties relate to community-weighted mean traits in logged and old-growth tropical forests in Borneo. We studied 32 physical, chemical and physiological traits from 284 tree species in eight 1 ha plots and measured long-term soil nutrient supplies and plant-available nutrients. Logged plots had greater values for traits that drive carbon capture and growth, whilst old-growth forests had greater values for structural and persistence traits. Although disturbance was the primary driver of trait expression, soil nutrients explained a statistically independent axis of variation linked to leaf size and nutrient concentration. Soil characteristics influenced trait expression via nutrient availability, nutrient pools, and pH. Our finding, that traits have dissimilar responses to land use and soil resource availability, provides robust evidence for the need to consider the abiotic context of logging when predicting plant functional diversity across human-modified tropical forests. The detection of two independent axes was facilitated by the measurement of many more functional traits than have been examined in previous studies.
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.
Across the tropics, large-bodied mammals have been affected by selective logging in ways that vary with levels of timber extraction, collateral damage, species-specific traits and secondary effects of hunting, as facilitated by improved access through logging roads. In Peninsular Malaysia, 3.0 million hectares or 61 percent of its Permanent Reserved Forests is officially assigned for commercial selective logging. Understanding how wildlife adapts and uses logged forest is critical for its management and, for threatened species, their conservation. In this study, we quantify the population status of four tropical ungulate species in a large selectively logged forest reserve and an adjacent primary forest protected area. We then conduct finer scale analyses to identify the species-specific factors that determine their occurrence. A combined indirect sign-camera trapping approach with a large sampling effort (2,665 km and 27,780 trap nights surveyed) covering a wide area (560 km2) generated species-specific detection probabilities and site occupancies. Populations of wild boar were widespread across both logged and primary forests, whereas sambar and muntjac occupancy was lower in logged forest (48.4% and 19.2% respectively), with gaur showing no significant difference. Subsequent modelling revealed the importance of conserving lower elevation habitat in both habitat types, particularly <1,000 m asl, for which occupancies of sambar, muntjac and gaur were typically higher. This finding is important because 75 percent (~13,400 km2) of Peninsular Malaysia's Main Range Forest (Banjaran Titiwangsa) is under 1,000 m asl and therefore at risk of being converted to industrial timber plantations, which calls for renewed thinking around forest management planning.
Saffron (Crocus sativus L.) is an important plant in medicine. The Kashmir Valley (J&K, India) is one of the world's largest and finest saffron producing regions. However, over the past decade, there has been a strong declining trend in saffron production in this area. Plant Growth Promoting Rhizobacteria (PGPR) are free living soil bacteria that have ability to colonize the surfaces of the roots and ability to boost plant growth and development either directly or indirectly. Using the efficient PGPR as a bio-inoculant is another sustainable agricultural practice to improve soil health, grain yield quality, and biodiversity conservation. In the present study, a total of 13 bacterial strains were isolated from rhizospheric soil of saffron during the flowering stage of the tubers and were evaluated for various plant growth promoting characteristics under in vitro conditions such as the solubilization of phosphate, production of indole acetic acid, siderophore, hydrocyanic acid, and ammonia production and antagonism by dual culture test against Sclerotium rolfsii and Fusarium oxysporum. All the isolates were further tested for the production of hydrolytic enzymes such as protease, lipase, amylase, cellulase, and chitinase. The maximum proportions of bacterial isolates were gram-negative bacilli. About 77% of the bacterial isolates showed IAA production, 46% exhibited phosphate solubilization, 46% siderophore, 61% HCN, 100% ammonia production, 69% isolates showed protease activity, 62% lipase, 46% amylase, 85% cellulase, and 39% showed chitinase activity. Three isolates viz., AIS-3, AIS-8 and AIS-10 were found to have the most plant growth properties and effectively control the growth of Sclerotium rolfsii and Fusarium oxysporum. The bacterial isolates were identified as Brevibacterium frigoritolerans (AIS-3), Alcaligenes faecalis subsp. Phenolicus (AIS-8) and Bacillus aryabhattai (AIS-10) respectively by 16S rRNA sequence analysis. Therefore, these isolated rhizobacterial strains could be a promising source of plant growth stimulants to increase cormlets growth and increase saffron production.
The lagoon of Setiu Wetlands has high biodiversity of bivalve’s species. The majority of villagers are fisherman and bivalves are one of their income-generating activities. Studies on parasites of bivalves are important to our knowledge for maintenance of natural resources. This study investigated the parasite prevalence among four commercially exploited shellfish species from Setiu Wetland, Malaysia. A total of 120 samples were collected during the low tide time for four shellfish species which were Polymesoda expansa, Meretrix meretrix, Anadara sp. and Crassostrea iredalei. The bivalve specimens were measured on its length with and without shell, width, height, weight and microscopically examined on the presence of parasites focused at gills, muscle and digestive tract. The discovered macroparasite were fixed into 70% ethanol solution for preservation. In this study, Anadara sp. was highest infestation of parasites, while Polymesoda expansa has the least infestation of parasites. There were occurrence of copepod and Nematopsis sp. in Anadara sp., M. meretrix and C. iredalei. Apart from that, there were other parasites observed in four bivalve species such as metacercaria, cestode larvae, Panopeus sp., Pinnotheres sp., Balanus sp. and unidentified ciliates. Ecological factors, feeding activity, season and abundance of definitive host were known to be elements that altered the prevalence of parasites in host. Upon the observation, a high prevalence of Nematopsis sp. were observed in three species of bivalves except P. expansa. Whereas for other parasites were occurred in low prevalence and intensity, without causing significant damage towards host.
Humanity will soon define a new era for nature-one that seeks to transform decades of underwhelming responses to the global biodiversity crisis. Area-based conservation efforts, which include both protected areas and other effective area-based conservation measures, are likely to extend and diversify. However, persistent shortfalls in ecological representation and management effectiveness diminish the potential role of area-based conservation in stemming biodiversity loss. Here we show how the expansion of protected areas by national governments since 2010 has had limited success in increasing the coverage across different elements of biodiversity (ecoregions, 12,056 threatened species, 'Key Biodiversity Areas' and wilderness areas) and ecosystem services (productive fisheries, and carbon services on land and sea). To be more successful after 2020, area-based conservation must contribute more effectively to meeting global biodiversity goals-ranging from preventing extinctions to retaining the most-intact ecosystems-and must better collaborate with the many Indigenous peoples, community groups and private initiatives that are central to the successful conservation of biodiversity. The long-term success of area-based conservation requires parties to the Convention on Biological Diversity to secure adequate financing, plan for climate change and make biodiversity conservation a far stronger part of land, water and sea management policies.
A 14-months survey was carried out to identify the species composition of Anopheles mosquitoes from Kampung Bongor, Grik, Perak. Adding to that, a preliminary one month mosquito population screening was done at Kampung Tepin, Serian, Sarawak. Consequently, the insecticide susceptibility status of a pyrethroid was tested against two selected species of Anopheles collected from these two locations in Malaysia. A total of 4,497 Anopheles from 11 species were identified from collections in Kampung Bongor, whereas 2,654 An. letifer were collected from Kampung Tepin. The An. maculatus of Kampung Bongor and An. letifer of Kampung Tepin were then selected and tested using WHO standard diagnostic test kits and impregnated papers with 0.75% permethrin. The response values of KT50 and KT95 for An. maculatus were recorded at 28.09 minutes and 62.98 minutes respectively. Anopheles letifer recorded much slower response values of KT50 and KT95, which was at 35.09 minutes and 73.03 minutes respectively. Both An. maculatus and An. letifer showed 100% mortality after 24 hours holding period. The results indicate that both species were still susceptible to the tested pyrethroid. For effective vector control and resistance management, accurate and periodic insecticide resistance monitoring should be undertaken especially in rural areas with agricultural usage of insecticides.
Extant Canis lupus genetic diversity can be grouped into three phylogenetically distinct clades: Eurasian and American wolves and domestic dogs.1 Genetic studies have suggested these groups trace their origins to a wolf population that expanded during the last glacial maximum (LGM)1-3 and replaced local wolf populations.4 Moreover, ancient genomes from the Yana basin and the Taimyr peninsula provided evidence of at least one extinct wolf lineage that dwelled in Siberia during the Pleistocene.35 Previous studies have suggested that Pleistocene Siberian canids can be classified into two groups based on cranial morphology. Wolves in the first group are most similar to present-day populations, although those in the second group possess intermediate features between dogs and wolves.67 However, whether this morphological classification represents distinct genetic groups remains unknown. To investigate this question and the relationships between Pleistocene canids, present-day wolves, and dogs, we resequenced the genomes of four Pleistocene canids from Northeast Siberia dated between >50 and 14 ka old, including samples from the two morphological categories. We found these specimens cluster with the two previously sequenced Pleistocene wolves, which are genetically more similar to Eurasian wolves. Our results show that, though the four specimens represent extinct wolf lineages, they do not form a monophyletic group. Instead, each Pleistocene Siberian canid branched off the lineage that gave rise to present-day wolves and dogs. Finally, our results suggest the two previously described morphological groups could represent independent lineages similarly related to present-day wolves and dogs.