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.
Systematization and description of composition and structure of the monogeneans from the genus Dactylogyrus Diesing, 1850 mostly having five rayed ventral (additional) bar of the haptor and parasitizing mainly Palaearctic Barbinae and Leuciscinae, were carried out. These dactylogyrids have Palaearctic origin and occur in the north-western Africa, central and southern Europe, Transcaucasia, middle Asia, Mesopotamia and also in India and the Malacca Peninsula. Previously the analysis of dactylogyrids' distribution by continents (Gerasev et al., 1996), geographical regions (Gerasev, Timofeeva, 1997), taxonomic groups of hosts (Gerasev, 2008a, 6), and different taxonomic groups of host inside one geographical division (Kolpakov et al., 2007; Gerasev et al., 2007, 2008) was performed. This analysis have not been always resulted in the understanding of conjugate evolution of these parasites and their fish hosts, as well as in the resolving of problems concerned with speciation of monogeneans and phylogeography of their hosts. Therefore, in present work we consider more than one geographical region, different fish taxa, and the morphological groups of worms reflecting morphological variational series of types of copulatory organ and additional bar. Typification of copulatory organ, additional bar, anchors, and type of seating for 11 Palaearctic morphological groups of dactylogyrids mainly having five rayed additional ventral bar, were carried out. Four morphological groups of dactylogyrids of African, Indian, and different Palaearctic origin also parasitizing Palaearctic barbs were additionally included into analysis. In all, 92 species of dctylogyrids from 78 host species were considered. Analysis of speciation and phylogeny of dactylogyrids having five rayed additional ventral bar of haptor; conjugate evolution of these dactylogyrids and their fish hosts (mainly Barbinae); point of origin of Palaearctic polyploids Barbinae, and expansion of these fishes over the territory of Palaearctic will be discussed in next article.
Black flies (Simuliidae) are important biting insects and vectors of diseases agents of humans and livestock. Thus, understanding the taxonomy and biodiversity of these insects is crucial for control and management of these diseases. In this study, we used mitochondrial cytochrome c oxidase I sequences to examine genetic diversity of three human-biting and possible vector black fly taxa; the Simulium asakoae species-complex, S. chamlongi and S. nigrogilvum. High levels of genetic diversity (>3.5% intraspecific genetic divergence) were found in all three taxa. Phylogenetic analyses indicated that the S. asakoae complex can be divided into seven groups with the largest group consisting of specimens from Thailand, Malaysia and Myanmar. This group most likely represents true S. asakoae. The remaining haplotypes formed groups with conspecific haplotypes or with other closely related species. Among these groups, one including S. monglaense and another including S. myanmarense suggest that certain specimens identified as S. asakoae most likely belong to those species. Therefore, they constitute new locality records for Thailand and also represent new records of anthropophily. Members of S. chamlongi are not monophyletic as its clade also included S. hackeri. A median joining network revealed strong geographic associations of the haplotypes of S. nigrogilvum suggesting limitation of gene flow. Because this species occurs mainly in high elevation habitats, low land areas could present a barrier to gene flow.
Tropical peat swamp forest (PSF) is one of the most endangered ecosystems in the world. However, the impacts of
anthropogenic activities in PSF and its conversion area towards fish biodiversity are less understood. This study
investigates the influences of water physico-chemical parameters on fish occurrences in peat swamp, paddy field and
oil palm plantation in the North Selangor peat swamp forest (NSPSF), Selangor, Malaysia. Fish and water samples were
collected from four sites located in the peat swamps, while two sites were located in the paddy field and oil palm plantation
areas. Multivariate analyses were used to determine the associations between water qualities and fish occurrences in
the three habitats. A total of 1,382 individual fish, belonging to 10 families, 15 genera and 20 species were collected.
The family Cyprinidae had the highest representatives, followed by Bagridae and Osphronemidae. The most abundant
species was Barbonymus schwanefeldii (Bleeker 1854), while the least abundant was Wallago leerii Bleeker, 1851. The
paddy field and oil palm plantation area recorded significantly higher fish diversity and richness relative to peat swamp
(p<0.05). The water physico-chemical parameters, such as pH, DO, NH3
-N, PO4, SO4
, and Cl2 showed no significant
difference between paddy field and oil palm plantation (p>0.05), but was significantly different from the peat swamp
(p<0.05). However, no water quality parameter was consistently observed to be associated with fish occurrences in all
of the three habitats, but water temperature, NH3
-N, Cl2, SO4
, and EC were at least associated with fish occurrences in
two habitats studied. This study confirmed that each habitat possess different water quality parameters associated with
fish occurrences. Understanding all these ecological aspects could help future management and conservation of NSPSF.
Water pollution is a critical management issue, with many rivers and streams draining urban areas being polluted by the disposal of untreated solid waste and wastewater discharge, storm water and agricultural runoff. This has implications for biodiversity, and many rivers in the developing world are now considered compromised. We investigated benthic macroinvertebrate community structure and composition in relation to physico-chemical conditions of the water column and sediments. The study was conducted in an Austral catchment subject to both urban and agricultural pollutants in two different seasons. We assessed whether sediment characteristics were more important drivers of macroinvertebrate community composition than water column characteristics. We expected clear differences in macroinvertebrate community composition and in the associated community metrics due to distinct flow conditions between the two seasons. A combination of multivariate analyses (canonical correspondence analysis (CCA)) and biological indicator analysis were used to examine these patterns. Chironomidae was the most abundant family (>60%) in the upper mainstem river and stream sites. Stream sites were positively associated with CCA axis 2, being characterised by high turbidity and lower pH, salinity, phosphate concentration, channel width and canopy cover. Canopy cover, channel width, substrate embeddedness, phosphate concentration, pH, salinity and turbidity all had a significant effect on macroinvertebrate community composition. Using CCA variation partitioning, water quality was, however, a better predictor of benthic macroinvertebrate composition than sediment chemical conditions. Furthermore, our results suggest that seasonality had little effect on structuring benthic macroinvertebrate communities in this south-eastern zone of South Africa, despite clear changes in sediment chemistry. This likely reflects the relative lack of major variability in water chemistry compared to sediment chemistry between seasons and the relatively muted variability in precipitation between seasons than the more classic Austral temperate climates.
The increasing attention on Vietnam as a biodiversity hotspot prompted an investigation of the potential for cryptic diversity in black flies, a group well known elsewhere for its high frequency of isomorphic species. We analyzed the banding structure of the larval polytene chromosomes in the Simulium tuberosum species group to probe for diversity beyond the morphological level. Among 272 larvae, 88 different chromosomal rearrangements, primarily paracentric inversions, were discovered in addition to 25 already known in the basic sequences of the group in Asia. Chromosomal diversity in Vietnam far exceeds that known for the group in Thailand, with only about 5% of the rearrangements shared between the two countries. Fifteen cytoforms and nine morphoforms were revealed among six nominal species in Vietnam. Chromosomal evidence, combined with available molecular and morphological evidence, conservatively suggests that at least five of the cytoforms are valid species, two of which require formal names. The total chromosomal rearrangements and species (15) now known from the group in Vietnam far exceed those of any other area of comparable size in the world, supporting the country's status as a biodiversity hotspot. Phylogenetic inference based on uniquely shared, derived chromosomal rearrangements supports the clustering of cytoforms into two primary lineages, the Simulium tani complex and the Southeast Asian Simulium tuberosum subgroup. Some of these taxa could be threatened by habitat destruction, given their restricted geographical distributions and the expanding human population of Vietnam.
Vatica najibiana Ummul-Nazrah (Dipterocarpaceae), from the Relai Forest Reserve, Gua Musang, Kelantan and Gua Tanggang, Merapoh, Pahang, is described and illustrated. This species is Endangered and known from small populations restricted to two isolated karst limestone hills. The type locality, Relai Forest Reserve limestone, is currently under threat from encroaching oil palm plantations and ongoing logging, which, if it continues, will threaten the Kelantan population with extinction. The morphology of V. najibiana and the similar V. odorata subsp. odorata and V. harmandiana is compared.
Bats are important flagship species for biodiversity research; however, diversity in Southeast Asia is considerably underestimated in the current checklists and field guides. Incorporation of DNA barcoding into surveys has revealed numerous species-level taxa overlooked by conventional methods. Inclusion of these taxa in inventories provides a more informative record of diversity, but is problematic as these species lack formal description. We investigated how frequently documented, but undescribed, bat taxa are encountered in Peninsular Malaysia. We discuss whether a barcode library provides a means of recognizing and recording these taxa across biodiversity inventories. Tissue was sampled from bats trapped at Pasir Raja, Dungun Terengganu, Peninsular Malaysia. The DNA was extracted and the COI barcode region amplified and sequenced. We identified 9 species-level taxa within our samples, based on analysis of the DNA barcodes. Six specimens matched to four previously documented taxa considered candidate species but currently lacking formal taxonomic status. This study confirms the high diversity of bats within Peninsular Malaysia (9 species in 13 samples) and demonstrates how DNA barcoding allows for inventory and documentation of known taxa lacking formal taxonomic status.
Two new species of diminutive, sympatric, lowland, leaf-litter skinks of the genus Tytthoscincus Linkem, Diesmos Brown from the Sekayu region of Hulu Terengganu, Terengganu State in northeastern Peninsular Malaysia are described on the basis genetic and morphological data. One of the new species, T. monticolus sp. nov., was collected in a hilly riparian area along Sungai (=river) Bubu and is most closely related to an undescribed species from the Tembak Reservoir area. The other, T. keciktuek sp. nov. collected along Sungai Peres, is most closely related to T. perhentianensis Grismer, Wood, Grismer from Pulau (=island) Perhentian Besar. Sympatry and syntopy of multiple, specialized, unrelated, leaf-litter species of Tytthoscincus was previously only known from upland areas and these new species represent the first example of lowland of sympatry. More importantly, however, these endemic species add to a growing body of research and discoveries that continue to underscore the unrealized biodiversity of the riparian systems of Hulu Terengganu and the Sekayu region and their need for protection and continued study.
Two new species of black flies, Simulium (Simulium) srisukai and S. (S.) kiewmaepanense, are described from specimens collected in Thailand. Both species are assigned to the Simulium variegatum species-group of the subgenus Simulium (Simulium) Latreille. They are characterized by the darkened female femora and tibiae and six inflated pupal gill filaments, and the darkened female tibiae and six ordinary thread-like pupal gill filaments, respectively. Taxonomic notes are given to separate these new species from 10 related species among the group. These new species represent the third and fourth species of the S. variegatum species-group from Thailand.
The dominant factors controlling soil bacterial community variation within the tropics are poorly known. We sampled soils across a range of land use types--primary (unlogged) and logged forests and crop and pasture lands in Malaysia. PCR-amplified soil DNA for the bacterial 16S rRNA gene targeting the V1-V3 region was pyrosequenced using the 454 Roche machine. We found that land use in itself has a weak but significant effect on the bacterial community composition. However, bacterial community composition and diversity was strongly correlated with soil properties, especially soil pH, total carbon, and C/N ratio. Soil pH was the best predictor of bacterial community composition and diversity across the various land use types, with the highest diversity close to neutral pH values. In addition, variation in phylogenetic structure of dominant lineages (Alphaproteobacteria, Beta/Gammaproteobacteria, Acidobacteria, and Actinobacteria) is also significantly correlated with soil pH. Together, these results confirm the importance of soil pH in structuring soil bacterial communities in Southeast Asia. Our results also suggest that unlike the general diversity pattern found for larger organisms, primary tropical forest is no richer in operational taxonomic units of soil bacteria than logged forest, and agricultural land (crop and pasture) is actually richer than primary forest, partly due to selection of more fertile soils that have higher pH for agriculture and the effects of soil liming raising pH.
Tropical rainforests are subject to extensive degradation by commercial selective logging. Despite pervasive changes to forest structure, selectively logged forests represent vital refugia for global biodiversity. The ability of these forests to buffer temperature-sensitive species from climate warming will be an important determinant of their future conservation value, although this topic remains largely unexplored. Thermal buffering potential is broadly determined by: (i) the difference between the "macroclimate" (climate at a local scale, m to ha) and the "microclimate" (climate at a fine-scale, mm to m, that is distinct from the macroclimate); (ii) thermal stability of microclimates (e.g. variation in daily temperatures); and (iii) the availability of microclimates to organisms. We compared these metrics in undisturbed primary forest and intensively logged forest on Borneo, using thermal images to capture cool microclimates on the surface of the forest floor, and information from dataloggers placed inside deadwood, tree holes and leaf litter. Although major differences in forest structure remained 9-12 years after repeated selective logging, we found that logging activity had very little effect on thermal buffering, in terms of macroclimate and microclimate temperatures, and the overall availability of microclimates. For 1°C warming in the macroclimate, temperature inside deadwood, tree holes and leaf litter warmed slightly more in primary forest than in logged forest, but the effect amounted to <0.1°C difference between forest types. We therefore conclude that selectively logged forests are similar to primary forests in their potential for thermal buffering, and subsequent ability to retain temperature-sensitive species under climate change. Selectively logged forests can play a crucial role in the long-term maintenance of global biodiversity.
Environmental DNA detection has emerged as a powerful tool to monitor aquatic species without the need for capture or visual identification and is particularly useful for rare or elusive species. Our objective was to develop an eDNA approach for detecting the southern river terrapin (Batagur affinis) in Malaysia. We designed species-specific primers for a fragment of B. affinis mtDNA and evaluated their effectiveness in silico, in vitro and in situ. The primers amplified 110 bp of the cytochrome b mtDNA sequence of B. affinis from aquarium water samples housing nine juvenile B. affinis. We also successfully detected B. affinis eDNA from river samples taken from a site where turtles were known to be in the vicinity. Prospects and challenges of using an eDNA approach to help determine the distribution of B. affinis, essential information for an effective conservation plan, are discussed.
Three new megophryid species, Leptolalax melanoleucus, L. fuliginosus, and L. solus, are described from southwestern and southern Thailand on the bases of acoustic and morphological characteristics. Leptolalax melanoleucus and L. fuliginosus are similar to L. pelodytoides from northern Thailand, but differ from it completely in advertisement call characteristics and ventral color. Leptolalax solus is similar to L. heteropus from peninsular Malaysia, but differs from it by advertisement call, as well as by some body proportions. The distributional pattern of Leptolalax within Thailand is discussed.
The recent advent of carbon crediting has led to a rapid rise in biosequestration projects that seek to remove carbon from the atmosphere through afforestation and forest rehabilitation. Such projects also present an important potential opportunity to reverse biodiversity losses resulting from deforestation and forest degradation, but the biodiversity benefits of different forms of biosequestration have not been considered adequately. We captured birds in mist nets to examine the effects of rehabilitation of logged forest on birds in Sabah, Borneo, and to test the hypothesis that rehabilitation restores avian assemblages within regenerating forest to a condition closer to that seen in unlogged forest. Species richness and diversity were similar in unlogged and rehabilitated forest, but significantly lower in naturally regenerating forest. Rehabilitation resulted in a relatively rapid recovery of populations of insectivores within logged forest, especially those species that forage by sallying, but had a marked adverse effect on frugivores and possibly reduced the overall abundance of birds within regenerating forest. In view of these results, we advocate increased management for heterogeneity within rehabilitated forests, but we strongly urge an increased role for forest rehabilitation in the design and implementation of a biodiversity-friendly carbon-offsetting market.
One of the main environmental threats in the tropics is selective logging, which has degraded large areas of forest. In southeast Asia, enrichment planting with seedlings of the dominant group of dipterocarp tree species aims to accelerate restoration of forest structure and functioning. The role of tree diversity in forest restoration is still unclear, but the 'insurance hypothesis' predicts that in temporally and spatially varying environments planting mixtures may stabilize functioning owing to differences in species traits and ecologies. To test for potential insurance effects, we analyse the patterns of seedling mortality and growth in monoculture and mixture plots over the first decade of the Sabah biodiversity experiment. Our results reveal the species differences required for potential insurance effects including a trade-off in which species with denser wood have lower growth rates but higher survival. This trade-off was consistent over time during the first decade, but growth and mortality varied spatially across our 500 ha experiment with species responding to changing conditions in different ways. Overall, average survival rates were extreme in monocultures than mixtures consistent with a potential insurance effect in which monocultures of poorly surviving species risk recruitment failure, whereas monocultures of species with high survival have rates of self-thinning that are potentially wasteful when seedling stocks are limited. Longer-term monitoring as species interactions strengthen will be needed to more comprehensively test to what degree mixtures of species spread risk and use limited seedling stocks more efficiently to increase diversity and restore ecosystem structure and functioning.
The Amazon rainforest has sustained human existence for more than 10,000 years. Part of this has been the way that the forest controls regional climate including precipitation important for the ecosystem as well as agroforestry and farming. In addition, the Amazon also affects the global weather systems, so cutting down the rainforest significantly increases the effects of climate change, threatening the world's biodiversity and causing local desertification and soil erosion. The current fire activities and deforestation in the Amazon rainforest therefore have consequences for global sustainability. In the light of this, the current decisions made in Brazil regarding an increase in Amazon deforestation require policy changes if the global ecosystems and biodiversity are not to be set to collapse. There is only one way to move forward and that is to increase efforts in sustainable development of the region including limitation in deforestation and to continuously measure and monitor the development. The G7 countries have offered Brazil financial support for at least 20 million euros for fighting the forest fires but the president denies receiving such financial support and says that it is more relevant to raise new forests in Europe. In fact, this is exactly what is happening in Denmark and China in order to reduce climate change. Such activities should be global and include South America, Europe, Africa and Asia where deforestation is important issue. Forest restoration reduces climate change, desertification, and preserves both the regional tropical and global environment if the wood is not burned at a later stage but instead used in e.g. roads as filling material. Changes are therefore needed through improved international understanding and agreements to better avoid the global climate changes, from cutting down the precious rainforest before it is too late as rainforest cannot be re-planted.
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.
Tropical forests are being rapidly altered by logging, and cleared for agriculture. Understanding the effects of these land use changes on soil fungi, which play vital roles in the soil ecosystem functioning and services, is a major conservation frontier. Using 454-pyrosequencing of the ITS1 region of extracted soil DNA, we compared communities of soil fungi between unlogged, once-logged, and twice-logged rainforest, and areas cleared for oil palm, in Sabah, Malaysia. Overall fungal community composition differed significantly between forest and oil palm plantation. The OTU richness and Chao 1 were higher in forest, compared to oil palm plantation. As a proportion of total reads, Basidiomycota were more abundant in forest soil, compared to oil palm plantation soil. The turnover of fungal OTUs across space, true β-diversity, was also higher in forest than oil palm plantation. Ectomycorrhizal (EcM) fungal abundance was significantly different between land uses, with highest relative abundance (out of total fungal reads) observed in unlogged forest soil, lower abundance in logged forest, and lowest in oil palm. In their entirety, these results indicate a pervasive effect of conversion to oil palm on fungal community structure. Such wholesale changes in fungal communities might impact the long-term sustainability of oil palm agriculture. Logging also has more subtle long term effects, on relative abundance of EcM fungi, which might affect tree recruitment and nutrient cycling. However, in general the logged forest retains most of the diversity and community composition of unlogged forest.
An assemblage of beetle specimens from family Carabidae (ground beetles) was carried out at Kenyir water catchment as an indicator to measure disturbance. The samplings were conducted from 30th July to 1st August 2007 at limestone forest of Teluk Bewah and the dipterocarp forest of Sungai Cicir. 28 individuals from 13 species were collected from Teluk Bewah whereas 54 individuals from ten species was sampled from Sungai Cicir. The carabids were more specious (Simpson Diversity index: 0.97) and more abundant (Margalef index: 5.35) at Teluk Bewah compared to Sungai Cicir (Simpson Diversity index, 0.72: Margalefindex, 2.22). Light trapping was most efficient assembling 97.56% of ground beetles compared to Malaise trap, pitfall and net sweeping. This is the first record of beetle assemblage at Kenyir water catchment, Malaysia. New records for Kenyir, Terengganu, Malaysia are Abacetus sp. 1, Abacetus sp. 2, Acupalpus rectifrotis, Aephnidius adelioides, Dischissus notulatus, Dolichoctis sp., Dolichoctis sp. 2, Dolichoctis straitus, Ophinoea bimaculata, Perigona sp., Pheropsophus piciccollis, Pheropsophus occipitalis, Stenolophus quinquepustulatus, Stenolophus smaragdulus, Stenolophus sp., Tachys coracinus, Casnoidea sp., Orthogonius sp. Seven species coded as Cara C, Cara J, Cara M, Cara N, Cara O, Cara R and Cara S were unidentified and are probably new species to be described in another report. There is moderately high diversity (Simpson Diversity index: 0.846) of Carabidae indicating that ecotourism does not affect diversity of ground beetle at Kenyir Lake.