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Fulltext Mangrove-Associated Fungal Communities Are Differentiated by Geographic Location and Host Structure

Lee NLY, Huang D, Quek ZBR, Lee JN, Wainwright BJ

Front Microbiol, 2019;10:2456.
PMID: 31736902 DOI: 10.3389/fmicb.2019.02456

Marine fungi on the whole remain understudied, especially in the highly diverse Southeast Asian region. We investigated the fungal communities associated with the mangrove tree Avicennia alba throughout Singapore and Peninsular Malaysia. At each sampling location, we examined ten individual trees, collecting leaves, fruits, pneumatophores, and an adjacent sediment sample from each plant. Amplicon sequencing of the fungal internal transcribed spacer 1 and subsequent analyses reveal significant differences in fungal communities collected from different locations and host structures. Mantel tests and multiple regression on distance matrices show a significant pattern of distance decay with samples collected close to one another having more similar fungal communities than those farther away. Submergence appears to drive part of the variation as host structures that are never submerged (leaves and fruits) have more similar fungal communities relative to those that are covered by water during high tide (pneumatophores and sediment). We suggest that fungi of terrestrial origins dominate structures that are not inundated by tidal regimes, while marine fungi dominate mangrove parts and sediments that are submerged by the incoming tide. Given the critical functions fungi play in all plants, and the important role they can have in determining the success of restoration schemes, we advocate that fungal community composition should be a key consideration in any mangrove restoration or rehabilitation project.
Biogeographic structure of fungal communities in seagrass Halophilia ovalis across the Malay Peninsula

Quek ZBR, Zahn G, Lee NLY, Ooi JLS, Lee JN, Huang D, et al.

Environ Microbiol Rep, 2021 Dec;13(6):871-877.
PMID: 34438473 DOI: 10.1111/1758-2229.13003

Distributed across both the tropical Atlantic and Pacific oceans, the seagrass Halophilia ovalis stabilizes coastal sediment, thereby preventing shoreline erosion and is also an important food source for megaherbivores such as dugongs. However, seagrass meadows globally are under severe duress due to both climate change and anthropogenic activities. We characterized the mycobiome of Halophilia ovalis at seven sites in the Malay Peninsula using ITS1 rDNA amplicon sequences and investigated differences in fungal community structure. We found that geographic location was a significant factor shaping fungal communities and that marine sediment harboured significantly higher diversity when compared to H. ovalis leaves, roots and rhizomes. Taken together, it is likely that locality rather than specific plant structure determines fungal community structure in H. ovalis. Because the plant mycobiome is known to exert a strong effect on plant health, to maximize the success of future seagrass transplantation and restoration work we propose that these efforts consider the importance of seagrass mycobiomes at all stages.
Diversity and Distribution of Microbial Communities Associated with Reef Corals of the Malay Peninsula

Kanisan DP, Quek ZBR, Oh RM, Afiq-Rosli L, Lee JN, Huang D, et al.

Microb Ecol, 2023 Jan;85(1):37-48.
PMID: 35043221 DOI: 10.1007/s00248-022-01958-1

Coral-associated bacteria play critical roles in the regulation of coral health and function. Environmental perturbations that alter the bacterial community structure can render the coral holobiont more susceptible and less resilient to disease. Understanding the natural variation of the coral microbiome across space and host species provides a baseline that can be used to distinguish shifts in community structure. Using a 16S rRNA gene metabarcoding approach, this study examines bacterial community structure across three scleractinian coral hosts. Our results show that corals of three regions-eastern and western Peninsular Malaysia and Singapore-host distinct bacterial communities; despite these differences, we were able to identify a core microbiome shared across all three species. This core microbiome was also present in samples previously collected in Thailand, suggesting that these core microbes play an important role in promoting and maintaining host health. For example, several have been identified as dimethylsulfoniopropionate (DMSP) metabolizers that have roles in sulfur cycling and the suppression of bacterial pathogens. Pachyseris speciosa has the most variable microbiome, followed by Porites lutea, with the composition of the Diploastrea heliopora microbiome the least variable throughout all locations. Microbial taxa associated with each region or site are likely shaped by local environmental conditions. Taken together, host identity is a major driver of differences in microbial community structure, while environmental heterogeneity shapes communities at finer scales.
Fulltext Distinct fungal communities associated with different organs of the mangrove Sonneratia alba in the Malay Peninsula

Lee NLY, Huang D, Quek ZBR, Lee JN, Wainwright BJ

IMA Fungus, 2020;11:17.
PMID: 32974121 DOI: 10.1186/s43008-020-00042-y

Mangrove forests are key tropical marine ecosystems that are rich in fungi, but our understanding of fungal communities associated with mangrove trees and their various organs remains limited because much of the diversity lies within the microbiome. In this study, we investigated the fungal communities associated with the mangrove tree Sonneratia alba throughout Peninsular Malaysia and Singapore. At each sampling location, we collected leaves, fruits, pneumatophores and sediment samples and performed amplicon sequencing of the ribosomal internal transcribed spacer 1 to characterise the associated communities. Results show distinct fungal communities at each sampled location with further differentiation according to the plant part. We find a significant distance decay of similarity, particularly for sediment samples due to the greater variability of sediment environments relative to the more stable fungal habitats provided by living plant organs. We are able to assign taxonomy to the majority of sequences from leaves and fruits, but a much larger portion of the sequences recovered from pneumatophores and sediment samples could not be identified. This pattern underscores the limited mycological research performed in marine environments and demonstrates the need for a concerted research effort on multiple species to fully characterise the coastal microbiome and its role in the functioning of marine ecosystems.
Fulltext Seagrass-associated fungal communities show distance decay of similarity that has implications for seagrass management and restoration

Wainwright BJ, Zahn GL, Zushi J, Lee NLY, Ooi JLS, Lee JN, et al.

Ecol Evol, 2019 Oct;9(19):11288-11297.
PMID: 31641473 DOI: 10.1002/ece3.5631

Marine fungal biodiversity remains vastly understudied, and even less is known of their biogeography and the processes responsible for driving these distributions in marine environments. We investigated the fungal communities associated with the seagrass Enhalus acoroides collected from Singapore and Peninsular Malaysia to test the hypothesis that fungal communities are homogeneous throughout the study area. Seagrass samples were separated into different structures (leaves, roots, and rhizomes), and a sediment sample was collected next to each plant. Amplicon sequencing of the fungal internal transcribed spacer 1 and subsequent analysis revealed significant differences in fungal communities collected from different locations and different structures. We show a significant pattern of distance decay, with samples collected close to each other having more similar fungal communities in comparison with those that are more distant, indicating dispersal limitations and/or differences in habitat type are contributing to the observed biogeographic patterns. These results add to our understanding of the seagrass ecosystem in an understudied region of the world that is also the global epicenter of seagrass diversity. This work has implications for seagrass management and conservation initiatives, and we recommend that fungal community composition be a consideration for any seagrass transplant or restoration programme.
The core mangrove microbiome reveals shared taxa potentially involved in nutrient cycling and promoting host survival

Wainwright BJ, Millar T, Bowen L, Semon L, Hickman KJE, Lee JN, et al.

Environ Microbiome, 2023 Jun 01;18(1):47.
PMID: 37264467 DOI: 10.1186/s40793-023-00499-5

BACKGROUND: Microbes have fundamental roles underpinning the functioning of our planet, they are involved in global carbon and nutrient cycling, and support the existence of multicellular life. The mangrove ecosystem is nutrient limited and if not for microbial cycling of nutrients, life in this harsh environment would likely not exist. The mangroves of Southeast Asia are the oldest and most biodiverse on the planet, and serve vital roles helping to prevent shoreline erosion, act as nursery grounds for many marine species and sequester carbon. Despite these recognised benefits and the importance of microbes in these ecosystems, studies examining the mangrove microbiome in Southeast Asia are scarce.cxs RESULTS: Here we examine the microbiome of Avicenia alba and Sonneratia alba and identify a core microbiome of 81 taxa. A further eight taxa (Pleurocapsa, Tunicatimonas, Halomonas, Marinomonas, Rubrivirga, Altererythrobacte, Lewinella, and Erythrobacter) were found to be significantly enriched in mangrove tree compartments suggesting key roles in this microbiome. The majority of those identified are involved in nutrient cycling or have roles in the production of compounds that promote host survival.
CONCLUSION: The identification of a core microbiome furthers our understanding of mangrove microbial biodiversity, particularly in Southeast Asia where studies such as this are rare. The identification of significantly different microbial communities between sampling sites suggests environmental filtering is occurring, with hosts selecting for a microbial consortia most suitable for survival in their immediate environment. As climate change advances, many of these microbial communities are predicted to change, however, without knowing what is currently there, it is impossible to determine the magnitude of any deviations. This work provides an important baseline against which change in microbial community can be measured.