Biology subjects

Huang, Y. M.

Publications and source records attributed to Huang, Y. M..

3 recordsLinked to original sources

bioRxiv2023

Humic substances mitigate adverse effects of elevated temperature with potentially critical repercussions for coral reef resilience

Previous observational studies have suggested that terrestrially-derived compounds, most notably humic substances (HS) can protect coral reefs from thermal stress. No study hitherto has, however, tested this hypothesis. In the present study, we used a randomised-controlled microcosm setup to test to what extent HS are able to mitigate the adverse effects of elevated temperature and intense UVB radiation on coral photosynthetic activity, and environmental and host-associated bacterial ercommunities. Our results clearly demonstrate a significant protective effect of HS. Corals in HS-supplemented microcosms had significantly higher photosynthetic activities than those in microcosms subjected to elevated heat and intense UVB radiation. Our results, furthermore, showed that coral reef organisms in HS-supplemented microcosms contained unique bacterial communities enriched with known groups of potentially beneficial bacteria. Our findings have significant repercussions for reef resilience in the face of increasing climate-induced stressors and highlight the importance of restoring coastal forests and the land-sea interface in order to protect coral reefs.

ecology↗

bioRxiv2023

Development and validation of an experimental life support system to study the impact of ultraviolet B radiation and temperature on coral reef microbial communities

In the present study, we developed and validated an experimental life support system (ELSS) designed to investigate the response of coral reef associated bacterial communities to increases in temperature and UVB intensity. The ELSS consisted of 32 independent microcosms, which enables researchers to study the individual and interactive effects of up to three factors using a full factorial experimental design. Temperature can be controlled using water-baths. UV exposure was introduced to the system using UV fluorescent lights. Individual UVB-opaque polyester films were added to the microcosms using a random design. In the validation experiment (stable temperature and no UVB), a coral reef environment was simulated using a layer of coral reef sediment, synthetic seawater, and specimens from five benthic reef species. The species used were two hard corals Montipora digitata and Montipora capricornis, a soft coral Sarcophyton glaucum, a zoanthid Zoanthus sp., and a sponge Chondrilla sp.. To validate the system, we assessed physical and chemical parameters and characterised host and free-living bacterial communities of the ELSS over 34 days and compared these data to those observed in natural reef ecosystems. Water temperature, dissolved oxygen, pH, salinity and dissolved nutrients in the ELSS were similar to those at shallow coral reef sites. Sediment bacterial diversity and composition were more similar to natural-type communities at day 29 and 34 than at day 8 after transfer to the microcosms, indicating a return to natural-type conditions following an initial, apparent perturbation phase. Transplantation significantly altered the bacterial community composition of M. digitata and Chondrilla sp. and increased coral photosynthetic efficiency compared to before transplantation. These results highlight the importance of M. digitata and Chondrilla sp. microbiomes to host adaptation following potential stress events.. Altogether, our results validated the suitability of the ELLS developed in this study as a model system to investigate the responses of coral reef associated bacterial communities to shifts of temperature and UVB radiation and potentially other environmental conditions (e.g., environmental pollution).

microbiology↗

bioRxiv2021

SALTS: SURFR (small noncoding RNA) And LAGOOn (long noncoding RNA) Transcriptomics Suite

The widespread utilization of high-throughput sequencing technologies has unequivocally demonstrated that eukaryotic transcriptomes consist primarily (>98%) of non-coding RNA (ncRNA) transcripts significantly more diverse than their protein-coding counterparts. ncRNAs are typically divided into two categories based on their length. (1) ncRNAs less than 200 nucleotides (nt) long are referred as small non-coding RNAs (sncRNAs) and include microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), transfer ribonucleic RNAs (tRNAs), etc., and the majority of these are thought to function primarily in controlling gene expression. That said, the full repertoire of sncRNAs remains fairly poorly defined as evidenced by two entirely new classes of sncRNAs only recently being reported, i.e., snoRNA-derived RNAs (sdRNAs) and tRNA-derived fragments (tRFs). (2) ncRNAs longer than 200 nt long are known as long ncRNAs (lncRNAs). lncRNAs represent the 2nd largest transcriptional output of the cell (behind only ribosomal RNAs), and although functional roles for several lncRNAs have been reported, most lncRNAs remain largely uncharacterized due to a lack of predictive tools aimed at guiding functional characterizations. Importantly, whereas the cost of high-throughput transcriptome sequencing is now feasible for most active research programs, tools necessary for the interpretation of these sequencings typically require significant computational expertise and resources markedly hindering widespread utilization of these datasets. In light of this, we have developed a powerful new ncRNA transcriptomics suite, SALTS, which is highly accurate, markedly efficient, and extremely user-friendly. SALTS stands for SURFR (sncRNA) And LAGOOn (lncRNA) Transcriptomics Suite and offers platforms for comprehensive sncRNA and lncRNA profiling and discovery, ncRNA functional prediction, and the identification of significant differential expressions among datasets. Notably, SALTS is accessed through an intuitive Web-based interface, can be used to analyze either user-generated, standard next-generation sequencing (NGS) output file uploads (e.g., FASTQ) or existing NCBI Sequence Read Archive (SRA) data, and requires absolutely no dataset pre-processing or knowledge of library adapters/oligonucleotides. SALTS constitutes the first publically available, Web-based, comprehensive ncRNA transcriptomic NGS analysis platform designed specifically for users with no computational background, providing a much needed, powerful new resource capable of enabling more widespread ncRNA transcriptomic analyses. The SALTS WebServer is freely available online at http://salts.soc.southalabama.edu.

bioinformatics↗