Biology subjects

Sim, C. W. H.

Publications and source records attributed to Sim, C. W. H..

6 recordsLinked to original sources

bioRxiv2026

Successful coral microbiome transplant from high to low heat tolerant corals requires antibiotic pretreatment

Microbiome transplantation, used to treat human disease, can enhance thermal and pathogen resilience in bleaching-susceptible corals via coral microbiome transplantation (CMT), though success is donor- and recipient-dependent. In this study, less thermally tolerant Pachyseris speciosa fragments were exposed to ciprofloxacin or an antibiotic cocktail for 24 h, then received CMT from the thermally tolerant Acropora millepora from Singapore's turbid reef system. Alpha diversity increased only in antibiotic-treated, CMT fragments, demonstrating that antibiotic-induced dysbiosis enhanced bacterial uptake. Coral microbiome assemblage shifted significantly at 1 and 10 d, regardless of antibiotic treatment or Acropora inoculum. Antibiotic-induced dysbiosis did not enhance uptake of donor's core ASVs (e.g., Endozoicomonas spp.). However, early uptake favoured potential pathogens like Vibrio spp., while longer inoculation allowed for uptake of unculturable environmental taxa. Our approach of using antibiotic pretreatment followed by whole microbiome transplant parallels human faecal microbiota transplantation to restore gut health.

microbiology↗

bioRxiv2026

A beneficial megaplasmid transforms an opportunistic bacterial pathogen to benefit coral by extending their thermal range

Resilient turbid coral reefs, found 1{degrees} north of the equator, experience fewer and less intense bleaching events despite being situated within the worlds busiest shipping port in highly urbanised Singapore. We hypothesised that bacteria within the coral holobiont play a role in maintaining coral diversity within this extreme environment by conferring traits that enhance host tolerance. Eleven Pseudovibrio isolates, whose genomes differ by only four SNPs, were isolated from the scleractinian coral Pachyseris speciosa. A [~]490 kbp megaplasmid (pCJH) was found in 7 of the 11 Pseudovibrio isolates. This study identified an opportunistic Pseudovibrio sp. pathogen of P. speciosa, accelerating bleaching disease. However, presence of the megaplasmid alters the ecological strategy of Pseudovibrio sp. toward mutualism, delaying coral bleaching. The megaplasmid enhances Pseudovibrios host colonisation and establishment of symbiosis through increased attachment and extends its bioactive genetic potential, but reduces fecundity. The Pseudovibrio genomes and megaplasmid encode several diffusible antibiotic biosynthetic gene clusters and contact-dependent inhibition mechanisms, with both types of inhibitory activity shown against local (i.e. P. speciosa) and type-strain Vibrio spp. Interaction analyses in experimentally heat-stressed corals revealed negative associations between Pseudovibrio and Vibrio ASVs corresponding to these cultured isolates. They also showed increased coral thermal tolerance by a full degree (1{degrees}C) when it is associated with the megaplasmid-bearing strain. Together, these findings support the Coral Probiotic Hypothesis that bacteria enhance coral resilience through chemical defense and identifies additional aspects to this symbiosis by a mobile genetic element which could play an important role in coral reef resilience.

microbiology↗

bioRxiv2026

Labyrinthula merlionensis sp. nov.: a novel labyrinthulid infecting marine diatoms

Labyrinthulomycetes are a class of fungus-like heterotrophic protists from the Stramenopiles lineage, recognized for their ecological role as decomposers and contributors to nutrient cycling. They colonize various substrates, from seaweed to terrestrial environments, utilizing ectoplasmic networks for nutrient absorption. This study characterized a novel Labyrinthula strain associated with the marine diatom Biddulphia. Phylogenetic analysis of the full-length 18S rRNA gene positioned this strain as a new species, Labyrinthula merlionensis sp. nov. Scanning electron and light microscopy observations revealed bi-flagellated zoospores and spindle-shaped vegetative cells with ectoplasmic networks. Time-series observations of the interactions between L. merlionensis and Biddulphia were categorised into different phases: establishment, infection, and aggregation. Scanning electron and confocal microscopy observations during the infection phase established the use of ectoplasmic nets to target the marginal ridge regions between diatoms, and the detection of labyrinthulid cells within diatom frustules. These findings enhance the understanding of the diversity, morphology, and ecological roles of Labyrinthulomycetes, particularly their intra- and extra-cellular interactions with diatom hosts.

ecology↗

bioRxiv2026

Uncoupling of seagrass host selection and succession for microbial guilds in meadow chronosequence

Succession is an ecosystem building process in which a habitat and its community interact predictably by increasing diversity, habitat engineering, and ultimately reaching a climax community, where other ecological processes influence its dynamic. Key to succession is the establishment of primary producing habitat forming species, which drives niche differentiation leading to increasing diversity. Here, we use the primary colonizing and habitat forming seagrass, Halophila ovalis, to demonstrate that it drives bacterial succession in a meadow ecosystem, and its microbiome, both rhizoplane and phylloplane, are under host selection. Many of the characteristics attributed to plants for habitat modification are microbial processes such as nitrogen fixation and sulfide detoxification and succession is often extrapolated to such processes. To determine if succession (increasing diversity) or selection (reducing diversity) drives changes in diversity (16S rRNA gene) or habitat modifying processes (nifH, soxB, aprA, dsrA), molecular analysis was performed along chronosequences (as a proxy for succession) of seagrass patches. Bacterial communities were sampled within the meadow ecosystem and the microbiomes of H. ovalis (both rhizoplane and phylloplane). Genes involved in biogeochemical cycling are differentially impacted within the microbiome and meadow sediments, with only nifH under succession. All genes from all niches sampled for community analysis are under directional community trajectories, despite being subjected to distinct ecological processes, signifying that many ecological processes, including succession and host association, drive community assemblage.

ecology↗

bioRxiv2024

Temporal dynamics and biogeography of sympagic and planktonic autotrophic microbial eukaryotes during the under-ice Arctic bloom

Photosynthetic microbial eukaryotes play a pivotal role as primary producers in the Arctic Ocean, where seasonal blooms within and below the ice are crucial phenomena, contributing significantly to global primary production and biogeochemical cycling. In this study, we investigated the taxonomic composition of sympagic algae and phytoplankton communities during the Arctic under-ice spring bloom using metabarcoding of the 18S rRNA gene. Samples were obtained from three size fractions over a period of nearly three months at an ice camp deployed on landfast ice off the coast of Baffin Island as part of the Green Edge project. We classified the major sympagic and phytoplankton taxa found in this study into biogeographical categories using publicly available metabarcoding data from more than 2 800 oceanic and coastal marine samples. This study demonstrated the temporal succession of taxonomic groups during the development of the under-ice bloom, illustrated by an overall transition from polar to polar-temperate taxa, in particular in the smallest size fraction. Overlooked classes such as Pelagophyceae (undescribed Pelagomonadales clade A1 and the genus Ankylochrysis), Bolidophyceae (Parmales environmental clade 2), and Cryptophyceae (Baffinella frigidus) might play a greater role than anticipated within the pico-sized communities in and under the ice pack during the pre-bloom period. Finally, we emphasize the importance of microdiversity, taking the example of B. frigidus for which a new strain isolated during Green Edge represents an ice ecotype while the type strain is clearly linked to marine waters.

ecology↗

bioRxiv2022

metaPR2: a database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists.

In recent years, metabarcoding has become the method of choice for investigating the composition and assembly of microbial eukaryotic communities, and an increasing number of environmental datasets are being published. Although unprocessed sequence files are often publicly available, processed data, i.e. sequences clustered as operational taxonomic units (OTUs) or amplicon sequence variants (ASVs) are rarely at hand in a comparable format. This hampers comparative studies between different environments and datasets, for example examining the biogeographical patterns of specific groups/species, as well analysing the micro-genetic diversity within these groups. Here, we present a newly-assembled database of processed 18S rRNA metabarcodes that are annotated with the PR2 reference sequence database. This database, called metaPR2, contains 41 datasets corresponding to more than 4,000 samples and 73,000 ASVs. The database is accessible through both a web-based interface (https://shiny.metapr2.org) and as an R package, and should prove very useful to all researchers working on protist diversity in a variety of systems.

ecology↗