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Verifying the applicability of SWAT to simulate fecal contamination for watershed management of Selangor River, Malaysia

Kondo T, Sakai N, Yazawa T, Shimizu Y

Sci Total Environ, 2021 Jun 20;774:145075.
PMID: 33609845 DOI: 10.1016/j.scitotenv.2021.145075

The Soil and Water Assessment Tool (SWAT) ecohydrological model was utilized to simulate fecal contamination in the 1937 km2 Selangor River Watershed in Malaysia. The watershed conditions posed considerable challenges owing to data scarcity and tropical climate conditions, which are very different from the original conditions that SWAT was developed and tested for. Insufficient data were compensated by publicly available data (e.g., land cover, soil, and weather) to run SWAT. In addition, field monitoring and interviews clarified representative situations of pollution sources and loads, which were used as input for the model. Model parameters determined by empirical analyses in the USA (e.g., surface runoff, evapotranspiration, and temperature adjustment for bacteria die-off) are thoroughly discussed. In particular, due consideration was given to tropical climate characteristics such as intense rainfall, high potential evapotranspiration, and high temperatures throughout the year. As a result, the developed SWAT successfully simulated fecal contamination ranging several orders of magnitude along with its spatial distribution (i.e., Nash-Sutcliffe Efficiency (NSE) = 0.64, Root Mean Square Error-Observations Standard Deviation Ratio (RSR) = 0.64 at six mainstem sites, and NSE = 0.67 and RSR = 0.57 at 12 major tributaries). Moreover, mitigation countermeasures for future worsening of fecal contamination (i.e., E.coli concentration > 20,000 CFU/100 mL for 690 days during nine years at a raw water intake point for Kuala Lumpur [KL] residents) were analyzed through scenario simulations, thereby contributing to discussing effective watershed management. The results propose improving decentralized sewage treatment systems and treating chicken manure with effective microorganisms in order to guarantee water safety for KL residents (i.e., E.coli concentrations <20,000 CFU/100 mL throughout the period, considering Malaysian standards). Accordingly, this study verified the applicability of SWAT to simulate fecal contamination in areas that are difficult to model and suggests solutions for watershed management based on quantitative evidence.
Electrotransformation of thermophilic bacterium Caldimonas manganoxidans

Arai T, Aikawa S, Sudesh K, Kondo T, Kosugi A

J Microbiol Methods, 2022 01;192:106375.
PMID: 34793853 DOI: 10.1016/j.mimet.2021.106375

Caldimonas manganoxidans is a Gram-negative, thermophilic, bioplastic-producing bacterium that is a promising strain to overcome the drawbacks of existing bioplastic manufacturing methods. However, genetic manipulation of this species has not previously been studied. Here, we developed an optimized electrotransformation protocol for C. manganoxidans by screening conditions, including the bacterial growth phase, electroporation buffer, pulse strength, and recovery time. The optimized transformation protocol obtained (3.1 ± 0.78) × 108 colony-forming units/μg DNA of plasmid pBBR1MCS-2. High transformation efficiency was observed when using plasmid DNA isolated from C. manganoxidans. The DNA methylases of Escherichia coli did not affect the transformation efficiency of C. manganoxidans. The electrotransformation technique proposed here will be beneficial for the genetic manipulation of thermophilic Caldimonas species.
Fulltext Non-density dependent pollen dispersal of Shorea maxwelliana (Dipterocarpaceae) revealed by a Bayesian mating model based on paternity analysis in two synchronized flowering seasons

Masuda S, Tani N, Ueno S, Lee SL, Muhammad N, Kondo T, et al.

PLoS One, 2013;8(12):e82039.
PMID: 24391712 DOI: 10.1371/journal.pone.0082039

Pollinator syndrome is one of the most important determinants regulating pollen dispersal in tropical tree species. It has been widely accepted that the reproduction of tropical forest species, especially dipterocarps that rely on insects with weak flight for their pollination, is positively density-dependent. However differences in pollinator syndrome should affect pollen dispersal patterns and, consequently, influence genetic diversity via the mating process. We examined the pollen dispersal pattern and mating system of Shorea maxwelliana, the flowers of which are larger than those of Shorea species belonging to section Mutica which are thought to be pollinated by thrips (weak flyers). A Bayesian mating model based on the paternity of seeds collected from mother trees during sporadic and mass flowering events revealed that the estimated pollen dispersal kernel and average pollen dispersal distance were similar for both flowering events. This evidence suggests that the putative pollinators - small beetles and weevils - effectively contribute to pollen dispersal and help to maintain a high outcrossing rate even during sporadic flowering events. However, the reduction in pollen donors during a sporadic event results in a reduction in effective pollen donors, which should lead to lower genetic diversity in the next generation derived from seeds produced during such an event. Although sporadic flowering has been considered less effective for outcrossing in Shorea species that depend on thrips for their pollination, effective pollen dispersal by the small beetles and weevils ensures outcrossing during periods of low flowering tree density, as occurs in a sporadic flowering event.
Fulltext Small temperature variations are a key regulator of reproductive growth and assimilate storage in oil palm (Elaeis guineensis)

Tani N, Abdul Hamid ZA, Joseph N, Sulaiman O, Hashim R, Arai T, et al.

Sci Rep, 2020 01 20;10(1):650.
PMID: 31959766 DOI: 10.1038/s41598-019-57170-8

Oil palm is an important crop for global vegetable oil production, and is widely grown in the humid tropical regions of Southeast Asia. Projected future climate change may well threaten palm oil production. However, oil palm plantations currently produce large amounts of unutilised biological waste. Oil palm stems - which comprise two-thirds of the waste - are especially relevant because they can contain high levels of non-structural carbohydrates (NSC) that can serve as feedstock for biorefineries. The NSC in stem are also considered a potent buffer to source-sink imbalances. In the present study, we monitored stem NSC levels and female reproductive growth. We then applied convergent cross mapping (CCM) to assess the causal relationship between the time-series. Mutual causal relationships between female reproductive growth and the stem NSC were detected, with the exception of a relationship between female reproductive organ growth and starch levels. The NSC levels were also influenced by long-term cumulative temperature, with the relationship showing a seven-month time lag. The dynamic between NSC levels and long-term cumulative rainfall showed a shorter time lag. The lower temperatures and higher cumulative rainfall observed from October to December identify this as a period with maximum stem NSC stocks.
Unravelling proximate cues of mass flowering in the tropical forests of South-East Asia from gene expression analyses

Yeoh SH, Satake A, Numata S, Ichie T, Lee SL, Basherudin N, et al.

Mol Ecol, 2017 Oct;26(19):5074-5085.
PMID: 28749031 DOI: 10.1111/mec.14257

Elucidating the physiological mechanisms of the irregular yet concerted flowering rhythm of mass flowering tree species in the tropics requires long-term monitoring of flowering phenology, exogenous and endogenous environmental factors, as well as identifying interactions and dependencies among these factors. To investigate the proximate factors for floral initiation of mast seeding trees in the tropics, we monitored the expression dynamics of two key flowering genes, meteorological conditions and endogenous resources over two flowering events of Shorea curtisii and Shorea leprosula in the Malay Peninsula. Comparisons of expression dynamics of genes studied indicated functional conservation of FLOWERING LOCUS T (FT) and LEAFY (LFY) in Shorea. The genes were highly expressed at least 1 month before anthesis for both species. A mathematical model considering the synergistic effect of cool temperature and drought on activation of the flowering gene was successful in predicting the observed gene expression patterns. Requirement of both cool temperature and drought for floral transition suggested by the model implies that flowering phenologies of these species are sensitive to climate change. Our molecular phenology approach in the tropics sheds light on the conserved role of flowering genes in plants inhabiting different climate zones and can be widely applied to dissect the flowering processes in other plant species.
Complex pollination of a tropical Asian rainforest canopy tree by flower-feeding thrips and thrips-feeding predators

Kondo T, Nishimura S, Tani N, Ng KK, Lee SL, Muhammad N, et al.

Am J Bot, 2016 Nov;103(11):1912-1920.
PMID: 27797714

PREMISE OF THE STUDY: In tropical rainforests of Southeast Asia, a highly fecund thrips (Thrips spp.) responds rapidly to the mass flowering at multiple-year intervals characteristic of certain species such as the canopy tree studied here, Shorea acuminata, by feeding on flower resources. However, past DNA analyses of pollen adherent to thrips bodies revealed that the thrips promoted a very high level of self-pollination. Here, we identified the pollinator that contributes to cross-pollination and discuss ways that the pollination system has adapted to mass flowering.
METHODS: By comparing the patterns of floral visitation and levels of genetic diversity in adherent pollen loads among floral visitors, we evaluated the contribution of each flower visitor to pollination.
KEY RESULTS: The big-eyed bug, Geocoris sp., a major thrips predator, was an inadvertent pollinator, and importantly contributed to cross-pollination. The total outcross pollen adhering to thrips was approximately 30% that on the big-eyed bugs. Similarly, 63% of alleles examined in S. acuminata seeds and seedlings occurred in pollen adhering to big-eyed bugs; about 30% was shared with pollen from thrips.
CONCLUSIONS: During mass flowering, big-eyed bugs likely travel among flowering S. acuminata trees, attracted by the abundant thrips. Floral visitation patterns of big-eyed bugs vs. other insects suggest that these bugs can maintain their population size between flowering by preying upon another thrips (Haplothrips sp.) that inhabits stipules of S. acuminata throughout the year and quickly respond to mass flowering. Thus, thrips and big-eyed bugs are essential components in the pollination of S. acuminata.
Nuclear and chloroplast DNA phylogeography reveals Pleistocene divergence and subsequent secondary contact of two genetic lineages of the tropical rainforest tree species Shorea leprosula (Dipterocarpaceae) in South-East Asia

Ohtani M, Kondo T, Tani N, Ueno S, Lee LS, Ng KK, et al.

Mol Ecol, 2013 Apr;22(8):2264-79.
PMID: 23432376 DOI: 10.1111/mec.12243

Tropical rainforests in South-East Asia have been affected by climatic fluctuations during past glacial eras. To examine how the accompanying changes in land areas and temperature have affected the genetic properties of rainforest trees in the region, we investigated the phylogeographic patterns of a widespread dipterocarp species, Shorea leprosula. Two types of DNA markers were used: expressed sequence tag-based simple sequence repeats and chloroplast DNA (cpDNA) sequence variations. Both sets of markers revealed clear genetic differentiation between populations in Borneo and those in the Malay Peninsula and Sumatra (Malay/Sumatra). However, in the south-western part of Borneo, genetic admixture of the lineages was observed in the two marker types. Coalescent simulation based on cpDNA sequence variation suggested that the two lineages arose 0.28-0.09 million years before present and that following their divergence migration from Malay/Sumatra to Borneo strongly exceeded migration in the opposite direction. We conclude that the genetic structure of S. leprosula was largely formed during the middle Pleistocene and was subsequently modified by eastward migration across the subaerially exposed Sunda Shelf.
Fulltext An ecological transcriptome approach to capture the molecular and physiological mechanisms of mass flowering in Shorea curtisii

Suhaimi AH, Kobayashi MJ, Satake A, Ng CC, Lee SL, Muhammad N, et al.

PeerJ, 2023;11:e16368.
PMID: 38047035 DOI: 10.7717/peerj.16368

Climatic factors have commonly been attributed as the trigger of general flowering, a unique community-level mass flowering phenomenon involving most dipterocarp species that forms the foundation of Southeast Asian tropical rainforests. This intriguing flowering event is often succeeded by mast fruiting, which provides a temporary yet substantial burst of food resources for animals, particularly frugivores. However, the physiological mechanism that triggers general flowering, particularly in dipterocarp species, is not well understood largely due to its irregular and unpredictable occurrences in the tall and dense forests. To shed light on this mechanism, we employed ecological transcriptomic analyses on an RNA-seq dataset of a general flowering species, Shorea curtisii (Dipterocarpaceae), sequenced from leaves and buds collected at multiple vegetative and flowering phenological stages. We assembled 64,219 unigenes from the transcriptome of which 1,730 and 3,559 were differentially expressed in the leaf and the bud, respectively. Differentially expressed unigene clusters were found to be enriched with homologs of Arabidopsis thaliana genes associated with response to biotic and abiotic stresses, nutrient level, and hormonal treatments. When combined with rainfall data, our transcriptome data reveals that the trees were responding to a brief period of drought prior to the elevated expression of key floral promoters and followed by differential expression of unigenes that indicates physiological changes associated with the transition from vegetative to reproductive stages. Our study is timely for a representative general flowering dipterocarp species that occurs in forests that are under the constant threat of deforestation and climate change as it pinpoints important climate sensitive and flowering-related homologs and offers a glimpse into the cascade of gene expression before and after the onset of floral initiation.