Catherine M. Yule

Freshwater biomonitoring with macroinvertebrates in East Asia

This paper summarizes the history and current status of efforts to implement macroinvertebrate biomonitoring protocols for surface water pollution in China, Japan, South Korea, Malaysia, Mongolia, Russia (Far East), and Thailand. Impediments to biomonitoring in some of these countries include: (1) lack of knowledge about macroinvertebrate fauna and their tolerance values, especially during the aquatic, immature stages; (2) the scarcity of research programs and formal training opportunities for biomonitoring offered in universities; (3) the shortage of high-quality microscopes and other necessary equipment; and (4) limited government understanding and support for biomonitoring, few skilled regulatory staff, and the persistence of old and unusable biomonitoring protocols. A recently established regional network, the Aquatic Entomological Society of East Asia (AESEA), and several major recent publications are helping to coordinate and promote science and technology in East Asia.

Keep wetlands wet: the myth of sustainable development of tropical peatlands – implications for policies and management

Pristine tropical peat swamp forests (PSFs) represent a unique wetland ecosystem of distinctive hydrology which support unique biodiversity and globally significant stores of soil carbon. Yet in Indonesia and Malaysia, home to 56% of the worlds tropical peatland, they are subject to considerable developmental pressures, including widespread drainage to support agricultural needs. In this article, we review the ecology behind the functioning and ecosystem services provided by PSFs, with a particular focus on hydrological processes as well as the role of the forest itself in maintaining those services. Drawing on this, we review the suitability of current policy frameworks and consider the efficacy of their implementation. We suggest that policies in Malaysia and Indonesia are often based around the narrative of oil palm and other major monocrops as drivers of prosperity and development. However, we also argue that this narrative is also being supported by a priori claims concerning the possibility of sustainability of peat swamp exploitation via drainage-based agriculture through the adherence to best management practices. We discuss how this limits their efficacy, uptake and the political will towards enforcement. Further, we consider how both narratives (prosperity and sustainability) clearly exclude important considerations concerning the ecosystem value of tropical PSFs which are dependent on their unimpacted hydrology. Current research clearly shows that the actual debate should be focused not on how to develop drainage-based plantations sustainably, but on whether the sustainable conversion to drainage-based systems is possible at all.

Burkholderia paludis sp. nov., an Antibiotic-Siderophore Producing Novel Burkholderia cepacia Complex Species, Isolated from Malaysian Tropical Peat Swamp Soil

A novel Gram negative rod-shaped bacterium, designated strain MSh1T, was isolated from Southeast Pahang tropical peat swamp forest soil in Malaysia and characterized using a polyphasic taxonomy approach. The predominant cellular fatty acids (>10.0%) were C16:0 (31.7%), C17:0 cyclo (26.6%), and C19:0 cyclo ω8c (16.1%). The polar lipids detected were phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol. The predominant ubiquinone was Q-8. This revealed that strain MSh1T belongs to the genus Burkholderia. The type strain MSh1T can be differentiated from other Burkholderia cepacia complex (Bcc) species by phylogenetic analysis of 16S rRNA gene sequence, multilocus sequence analysis (MLSA), average nucleotide identity (ANI) and biochemical tests. DNA–DNA relatedness values between strain MSh1T and closely related type strains were below the 70% threshold value. Based on this polyphasic study of MSh1T, it can be concluded that this strain represents a novel species within the Bcc, for which the name Burkholderia paludis sp. nov. is proposed. The type strain is MSh1T (= DSM 100703T = MCCC 1K01245T). The dichloromethane extract of MSh1T exhibited antimicrobial activity against four Gram positive bacteria (Enterococcus faecalis ATCC 29212, E. faecalis ATCC 700802, Staphylococcus aureus ATCC 29213, S. aureus ATCC 700699) and a Gram negative bacteria (Escherichia coli ATCC 25922). Further purification work has led to the isolation of Compound 1, pyochelin. Pyochelin demonstrated antimicrobial activity against four S. aureus strains and three E. faecalis strains with MIC-values of 3.13 μg/ml and 6.26 μg/ml, respectively. SEM analysis showed that the cellular morphology of E. faecalis ATCC 700802 was not affected by pyochelin; suggesting that it might target the intracellular components. Pyochelin, a siderophore with antimicrobial activity might be useful in treating bacterial infections caused by S. aureus and E. faecalis, however further work has to be done.

Litterfall production and chemistry of Koompassia malaccensis and Shorea uliginosa in a tropical peat swamp forest: plant nutrient regulation and climate relationships

Key messageThis study shows that two emergent tree species growing in a nutrient-limited tropical peat swamp forest use different mechanisms for nutrient regulation.AbstractThe main aim of this study is to understand the contribution of litterfall to nutrient supply and regulation of two emergent tree species in a tropical peat swamp forest (TPSF) in Peninsular Malaysia. The questions posed by this study include: (1) Do coexisting tree species in TPSF differ in terms of litter production, physico-chemical traits and litterfall patterns? (2) How do these relate to possible nutrient regulation mechanisms of the tree species and do the strategies involved differ between a nitrogen (N) fixing legume (Koompassia malaccensis, Family Fabaceae) and a dipterocarp (Shorea uliginosa, Family Dipterocarpaceae)? (3) Is litterfall timing of the selected tree species driven by climatic variables? Litterfall was collected from litter traps placed under the selected trees in the Sungai Karang TPSF. Green leaves of the selected tree species were also collected. Both leaf litter and green leaves were assessed for their physico-chemical properties (toughness, total phenols, total tannins, proximate fibre–cellulose–lignin and a range of nutrients) and compared. Results obtained indicate that K. malaccensis relies on a combination of high litter quality (higher N coupled with lower amount of tannins, fibre and cellulose) and low annual litterfall mass (388.17xa0gxa0m−2) for nutrient regulation while the opposite strategy is used by S. uliginosa, which was found to produce an annual litterfall mass of 918.14xa0gxa0m−2. Due to the aseasonal environment, no significant relationships were observed between climatic variables and litterfall. Therefore, litterfall characteristics in aseasonal tropical regions may depend more on species-specific physico-chemical properties than on climatic variables.

The caddisflies (Trichoptera) from a tropical peat swamp in Selangor, Peninsular Malaysia, including two new species

Five species of caddisfly were identified in several small collections from a peat swamp at Selangor in Peninsular Malaysia. They included a widespread South-East Asian leptocerid species, Oecetis meghadouta Schmid, 1958 – described from Sri Lanka; two ecnomid species, Ecnomus crepidulus Mosely, 1932 – described from Malaysia, and Ecnomus selangor sp. nov.; one hydroptilid species, Oxyethira paludicola sp. nov.; and an unidentified female hydropsychid species. The distribution and special features of tropical peat swamps are summarised, the new species are described, and comments are given on the trophic groups represented in the caddisfly fauna.

Newly Isolated Paenibacillus tyrfis sp. nov., from Malaysian Tropical Peat Swamp Soil with Broad Spectrum Antimicrobial Activity

Emergence of antimicrobial resistance coupled with the slowdown in discovery of new antimicrobial compounds points to serious consequences for human health. Therefore, scientists are looking for new antimicrobial compounds from unique and understudied ecosystems such as tropical peat swamp forests. Over the course of isolating antimicrobial producing bacteria from North Selangor tropical peat swamp forest, Malaysia, a Gram variable, rod shaped, endospore forming, facultative anaerobic novel strain MSt1T that exerts potent and broad spectrum antimicrobial activity was isolated. Phylogenetic analysis using 16S rRNA gene sequences showed that strain MSt1T belonged to the genus Paenibacillus with the highest similarity to Paenibacillus elgii SD17T (99.5%). Whole genome comparison between strain MSt1T with its closely related species using average nucleotide identity (ANI) revealed that similarity between strain MSt1T with P. elgii B69 (93.45%) and Paenibacillus ehimensis A2 (90.42%) was below the recommended threshold of 95%. Further analysis using in silico pairwise DDH also showed that similarity between strain MSt1T with P. elgii B69 (55.4%) and P. ehimensis A2 (43.7%) was below the recommended threshold of 70%. Strain MSt1T contained meso-diaminopilemic acid in the cell wall and MK-7 as the major menaquinone. The major fatty acids of strain MSt1T were anteiso-C15:0 (48.2%) and C16:0 (29.0%) whereas the polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, one unknown lipid, two unknown glycolipids, and one unknown phospholipid. Total DNA G+C content of strain MSt1T was 51.5 mol%. The extract from strain MSt1T exerted strong antimicrobial activity against Escherichia coli ATCC 25922 (MIC = 1.5 μg/mL), MRSA ATCC 700699 (MIC = 25 μg/mL) and Candida albicans IMR (MIC = 12.5 μg/mL). Partially purified active fraction exerted a strong effect against E. coli ATCC 25922 resulting in cell rupture when viewed with SEM. Based on distinctive taxonomic differences between strain MSt1T when compared to its closely related type species, we propose that strain MSt1T represents a novel species within the genus of Paenibacillus, for which the name Paenibacillus tyrfis sp. nov. (= DSM 100708T = MCCC 1K01247T) is proposed.

In Situ Tropical Peatland Fire Emission Factors and Their Variability, as Determined by Field Measurements in Peninsula Malaysia

Fires in tropical peatlands account for >25% of estimated total greenhouse gas emissions from deforestation and degradation. Despite significant global and regional impacts, our understanding of specific gaseous fire emission factors (EFs) from tropical peat burning is limited to a handful of studies. Furthermore, there is substantial variability in EFs between sampled fires and/or studies. For example, methane EFs vary by 91% between studies. nHere we present new fire EFs for the tropical peatland ecosystem; the first EFs measured for Malaysian peatlands, and only the second comprehensive study of EFs in this crucial environment. During August 2015 (under El Nino conditions) and July 2016, we embarked on field campaigns to measure gaseous emissions at multiple peatland fires burning on deforested land in Southeast Pahang (2015) and oil palm plantations in North Selangor (2016), Peninsula Malaysia. Gaseous emissions were measured using open-path Fourier transform infrared spectroscopy. The IR spectra were used to retrieve mole fractions of twelve different gases present within the smoke (including carbon dioxide and methane), and these measurements used to calculate EFs. Peat samples were taken at each burn site for physicochemical analysis and to explore possible relationships between specific physicochemical properties and fire EFs. Here we present the first evidence to indicate that substrate bulk density affects methane fire EFs reported here. This novel explanation of inter-plume, within-biome variability should be considered by those undertaking greenhouse gas accounting and haze forecasting in this region, and is of importance to peatland management, particularly with respect to artificial compaction.

Draft Genome Sequences of Two Antimicrobial-Producing Burkholderia sp. Strains, MSh1 and MSh2, Isolated from Malaysian Tropical Peat Swamp Forest Soil

ABSTRACT We report the draft genome sequences of two antimicrobial-producing isolates, Burkholderia sp. strains MSh1 and MSh2, which were isolated from tropical peat swamp forest soil. Putative genes related to different antimicrobial production have been annotated in both genome sequences.

The contribution of leaching to nutrient release from leaf litter of two emergent tree species in a Malaysian tropical peat swamp forest

To understand the role of abiotic leaching in nutrient release within the nutrient-deficit tropical peat swamp forest (TPSF), an experiment was conducted over 30xa0days using leaf litter from two common emergent TPSF trees, Koompassia malaccensis and Shorea uliginosa. The main objectives were to determine leaf litter nutrient leaching dynamics, and the effect of water pH and potential microbial influence on nutrient release. Leaf litter (single species and combined) was subjected to 3 treatments: peat water (natural acidic conditions), poisoned peat water (NaN3 as microbial poison) and deionized water (control). Despite loss of nutrients from the leaves, this was not associated with the loss of mass or carbon (C) from the leaves because they are resistant to decomposition. Nutrient loss occurred in the order of phosphorus (P)xa0>xa0nitrogen (N)xa0>xa0C whereby litter P content was quickly exhausted. Microbial activity only affected the bioavailable P (PO4−) whereby initial litter P release stimulated microbial growth, which resulted in the subsequent immobilization of P. Lastly, the effect of pH was not profound in this study. In conclusion, abiotic leaching from leaf litter releases considerable amounts of nutrients (notably PO43−) and functions as an important autochthonous nutrient source for the TPSF.

First High-Quality Draft Genome Sequence of Pasteurella multocida Sequence Type 128 Isolated from Infected Bone.

ABSTRACT We report here the first high-quality draft genome sequence of Pasteurella multocida sequence type 128, which was isolated from the infected finger bone of an adult female who was bitten by a domestic dog. The draft genome will be a valuable addition to the scarce genomic resources available for P. multocida.