Biology subjects

Hoh, D. Z.

Publications and source records attributed to Hoh, D. Z..

5 recordsLinked to original sources

bioRxiv2026

What we miss shapes what we protect: sea turtles as a case study of grey literature and language bias in an evidence synthesis

Evidence-based approaches are increasingly advocated and applied in conservation to provide reliable recommendations for management and policymaking. Although substantial efforts have been undertaken to generate ecological knowledge across languages and publication types, many syntheses and meta-analyses fail to include relevant literature sources; drawing into question their reliability. To assess the extent of biases resulting from ignoring grey literature and non-English publications, we reviewed and synthesised movement and migratory connectivity data for green turtles across Southeast Asia from multiple literature types and eight languages. We identified substantial losses in connectivity information, with at least half of all locations losing more than 88% of their connections, and shifts in demographic representation and sampling techniques when grey literature was excluded from the evidence base. The exclusion of non-English literature had a comparatively smaller impact. The regional connectivity network generated through this study highlights the need for holistic reviews to develop evidence bases to underpin transboundary management of migratory species. Ignoring grey literature and, potentially, regional languages in the development may lead to misallocation of limited management resources. Holistic reviews can further support the establishment of Important Areas for migratory species and inform how we meet and report on global biodiversity commitments.

ecology↗

bioRxiv2023

An acidophilic fungus is integral to prey digestion in a carnivorous plant

Carnivorous plant leaves, such as those of the spoon-leaved sundew Drosera spatulata, secrete mucilage which hosts microorganisms potentially aiding in prey digestion. We characterised the mucilage microbial communities and identified the acidophilic fungus Acrodontium crateriforme as the ecologically dominant species. The fungus grows and sporulates on sundew glands as its preferred acidic environment. We show that the A. crateriforme has a reduced genome similar to that of other symbiotic fungi. Based on the transcriptomes when encountering prey insects, we revealed a high degree of genes co-option in each species during fungus-plant coexistence and digestion. Expression patterns of the holobiont during digestion further revealed synergistic effects in several gene families including fungal aspartic and sedolisin peptidases, facilitating the digestion of sundews prey, as well as transporters and dose-dependent responses in plant genes involved in jasmonate signalling pathway. This study establishes that botanical carnivory is defined by multidimensional adaptations correlated with interspecies interactions.

microbiology↗

bioRxiv2022

Fusarium solani species complex genomes reveal bases of compartmentalisation and animal pathogenesis

The Fusarium solani species complex (FSSC) comprises fungal pathogens responsible for mortality in a diverse range of animals and plants, but their genome diversity and transcriptome responses in animal pathogenicity remain to be elucidated. We sequenced and compared six chromosome-level FSSC clade 3 genomes of aquatic animal and plant host origins and revealed a spectrum of conservation patterns in chromosomes categorised into three compartments: core, fast-core (FC), and lineage-specific (LS). Each chromosome type varied in structural architectures, with FC and LS chromosomes containing significantly higher proportions of repetitive elements and methylation levels than core chromosomes, with genes exhibiting higher dN/dS and enriched in functions related to pathogenicity and niche expansion. Mesosynteny were detected between FC chromosomes of Fusarium genomes, indicating that these chromosomes were present in a common ancestor that predated FSSC species. These findings provide evidence that genome compartmentalisation was the outcome of multi-speed evolution amongst FSSC chromosomes. We further demonstrated that F. falciforme and F. keratoplasticum are opportunistic pathogens by inoculating Pelodiscus sinensis eggs and identified differentially expressed genes also associated with plant pathogenicity. These included the most upregulated genes encoding the CFEM (Common in Fungal Extracellular Membrane) domain. The study establishes genomic resources and an animal model for fungal pathogens of trans-kingdom hosts.

genomics↗

bioRxiv2021

The prevalence, predominance, and metabolic potentials of Candidatus Prochlorobium terpiosii in the coral-killing sponge, Terpios hoshinota

Terpios hoshinota is a ferocious, space-competing sponge that kills a variety of stony corals by overgrowth. Outbreaks of this species have led to intense coral reef damage and declines in living corals on the square kilometer scale in many geographical locations. Our large-scale 16S rRNA gene survey across three oceans revealed that the core microbiome of T. hoshinota included operational taxonomic units (OTUs) related to Prochloron, Endozoicomonas, Pseudospirillum, SAR116, Magnetospira, and Ruegeria. A Prochloron- related OTU was the most dominant cyanobacterium in T. hoshinota in the western Pacific Ocean, South China Sea, and Indian Ocean. The complete metagenome-assembled genome of the Prochloron-related cyanobacterium and our pigment analysis revealed that this bacterium had phycobiliproteins and phycobilins and lacked chlorophyll b, inconsistent with the iconic definition of Prochloron. Furthermore, the phylogenetic analyses based on 16S rRNA genes and 120 single-copy genes demonstrated that the bacterium was phylogenetically distinct to Prochloron, strongly suggesting that it should be a sister taxon to Prochloron; we therefore proposed this symbiotic cyanobacterium as a novel species under a new genus: Candidatus Paraprochloron terpiosii. With the recovery of the complete genome, we characterized the metabolic potentials of the novel cyanobacterium in carbon and nitrogen cycling and proposed a model for the interaction between Ca. Pp. terpiosi LD05 and T. hoshinota. In addition, comparative genomics analysis revealed that Ca. Paraprochloron and Prochloron showed distinct features in transporter systems and DNA replication. ImportanceThe finding that one species predominates cyanobacteria in T. hoshinota from different geographic locations indicates that this sponge and Ca. Pp. terpiosi LD05 share a tight relationship. This study builds the foundation for T. hoshinotas microbiome and paves a way for understanding the ecosystem, invasion mechanism, and causes of outbreak of this coral-killing sponge. Also, the first Prochloron-related complete genome enables us to study this bacterium with molecular approaches in the future and broadens our knowledge of the evolution of symbiotic cyanobacteria.

ecology↗

bioRxiv2019

Nest microbiota and pathogen abundance impact hatching success in sea turtle conservation

Hatchery practices are pivotal to conservation success. In sea turtle hatchery, reusing the same sand has been a norm but remains unclear whether such approach increases the risk of Fusarium solani species complex (FSSC) infection causing huge mortality in sea turtle eggs worldwide. We employed 16S and ITS amplicon sequencing in 123 sand samples and isolated fungal strains from diseased eggs across seven hatcheries and neighboring beaches in Malaysia. FSSC was isolated from all sampled hatcheries where F. solani/falciforme was the predominant species. A distinct microbial composition and higher abundance of FSSC (mean = 5.2 %) was found in all but one hatchery when compared to nesting beaches (mean = 1.3 %). Specifically, an ascomycetous fungus Pseudallescheria boydii consistently appeared in higher abundance (mean = 11.4 %) in FSSC-infected nests and was significantly associated with lower hatching success. The hatchery that maintained the most stringent practice by changing sand every nesting season had a microbiota resembling nesting beaches as well as lowest FSSC and P. boydii abundance. The results of current study imply the need to avoid reusing sand in sea turtle hatchery.

ecology↗