Biology subjects

Tang, S.-L.

Publications and source records attributed to Tang, S.-L..

At least 19 recordsLinked to original sources

bioRxiv2026

The missing part of the DMSP cycle in coral holobionts: Endozoicomonas exports acetate derived from DMSP degradation

Endozoicomonas, a dominant symbiotic bacterium in coral holobionts, is noted for its ability to degrade dimethylsulfoniopropionate (DMSP) so as to generate acetate. While acetate is a well-known short-chain fatty acid in metabolic cross-feeding relationships, it remains unclear whether acetate derived from bacterial DMSP degradation is available to corals and their other symbionts. In this study, we employed Endozoicomonas ruthgatesiae strain 8E (herein referred as 8E) as a model to examine availability of DMSP-derived acetate for other symbionts. Using gas chromatography-mass spectrometry (GC-MS), we observed a significant increase in acetate excretion in 8E upon exposure to DMSP. Stable isotope labeling further confirmed that this elevated acetate efflux originated directly from DMSP, suggesting a complete cycle of DMSP-derived carbon among coral symbionts. Transcriptomic analysis revealed that DMSP exposure upregulated dddD expression and triggered a systemic reconfiguration of metabolism, characterized by down-regulation of the TCA cycle and the Pta-AckA pathway, with carbon flux redirected to the glyoxylate shunt. These findings suggest that upon exposure to DMSP, metabolism of 8E shifts from biomass production to DMSP catabolism, resulting in acetate efflux. Notably, we found that elevated temperature diminishes DMSP cleavage activity of 8E, indicating thermal sensitivity of this bacterial metabolic activity. ImportanceEndozoicomonas is known for its dominance in coral holobionts and its ability to degrade DMSP, an important compound in the marine sulfur cycle. Acetate is one resulting product in microbial DMSP metabolism and a common cross-feeding molecule. Whether DMSP-derived acetate in coral-associated DMSP-degrading bacteria is employed for cross-feeding stands a critical step in making a complete carbon cycle of DMSP metabolism within coral holobionts. In this study, we employed GC-MS and RNA-sequencing techniques to offer the first evidence of acetate excretion in Endozoicomonas while metabolizing DMSP, as well as its underlying genetic mechanism. Furthermore, we demonstrate reduced genetic response and DMSP-degrading capability under an elevated temperature in Endozoicomonas ruthgatesiae strain 8E, the model bacterium employed in this study. These findings provide the missing puzzle of DMSP metabolism in coral holobionts and suggest a potential role of DMSP in modulating symbiotic interactions within coral holobionts.

microbiology↗

bioRxiv2026

Resilience and reassembly of redox-structured microbial functional networks after rare holomixis in a meromictic lake

Abstract-shortLand-locked meromictic lakes are characterized by long-term stratification and steep redox gradients that sustain vertically structured microbial communities and tightly coupled biogeochemical processes. Because complete overturns of the lake are rare, the dynamics of microbial reassembly after redox gradients collapse and subsequently recover remain poorly resolved. We investigated a mixing-restratification transition in Lake Shira (Siberia) with depth-stratified sampling of oxic, chemocline, anoxic, and water-sediment interface layers across four stages: intermittent holomictic (IH), complete holomictic (CH), developing meromictic (DM), and stable meromictic (M). 16S rRNA gene amplicons showed that CH homogenized the water column, dominated by Gamma- and Alphaproteobacteria, Campylobacteria, and Cyanobacteriia. As stratification re-formed (DM-M), communities became strongly depth-partitioned, with Desulfobacterota and other anaerobes re-established in sulfidic deep waters and assemblages concentrating near the redox transition. Nanopore metagenomics reconstructed 401 MAGs, revealing stage- and depth-specific functional repertoires consistent with redox zonation. Core MAGs, including Yoonia spp., persisted across phases, suggesting functional continuity underpinning rapid ecosystem recovery. These data provide a system-wide view of biogeochemical reassembly during collapse and restoration of stratification meromictic lake.

microbiology↗

bioRxiv2025

Bacteriophages of the predominant coral symbiont Endozoicomonas: novel models for coral holobiont interactions

Phages are important symbionts in corals that modulate the community and functions of other symbiotic bacteria. Although phages infecting coral pathogens have been reported, no phage targeting beneficial microorganisms in corals has been isolated to date. From seawater near Acropora and Stylophora corals, we isolated the first bacteriophages (designated EmPhiA and EmPhiS) that infect Endozoicomonas montiporae CL-33, a model strain of the coral-prevalent and predominant Endozoicomonas bacteria. Electron microscopic observations of both phages showed Myovirus-like morphology and head sizes characteristic of jumbophages, with cryo-electron microscopy reveals long whiskers unprecedent in known phages. Genetically, these phages shared 99.21% genome similarity and are distant from known prokaryotic viruses, suggesting that they represent a novel viral species, which we name Encorevirus taiwanensis, in a novel family Encoreviridae. The small burst sizes of these phages (13.14 PFU/cell for EmPhiA and 21.4 PFU/cell for EmPhiS) potentially enable continuous coexistence of them with host bacteria within corals, making them putative core members of coral holobionts. Furthermore, host range test showed that EmPhiA and EmPhiS infect both Endozoicomonas bacteria isolated from stony and soft corals, implying their presence in a broad spectrum of host marine invertebrates. Using EmPhiS, we also investigated phage-bacterium interaction during its infection of E. montiporae CL-33. Interestingly, in addition to modulation of host cellular machinery, we found expression of several tellurium resistance proteins by EmPhiS during infection, which may provide the host additional stress resistance. These phages provide a novel model that will greatly advance our understanding of coral-Endozoicomonas-phage interactions.

microbiology↗

bioRxiv2025

Microbial profiling and single-cell transcriptomics reveal probiotic mechanisms of coral thermal resilience

Probiotics hold promise for enhancing coral resilience under climate-driven thermal stress, yet their mechanisms remain poorly understood. Here, we evaluate two Endozoicomonas species as coral probiotics and characterize their effects on microbial communities and host gene expression. We show that E. acroporae Acr-14T enhances thermal tolerance in Stylophora pistillata, suppresses opportunistic pathogens, and promotes beneficial microbes. To facilitate transcriptomic profiling, we assembled a chromosome-level genome of S. pistillata clade 1 (Pacific lineage) and used it to reveal that E. acroporae Acr-14T mitigates heat-induced protein-folding stress and supports host energy homeostasis. Single-cell transcriptomics further uncovered enhanced pro-survival signaling and modulation of the S-adenosylmethionine (SAMe) synthesis pathway. Together, our findings identify E. acroporae Acr-14T as a robust coral probiotic and provide mechanistic insights into host-microbe interactions that promote coral resilience under thermal stress.

microbiology↗

bioRxiv2025

A high-quality chromosome-level genome of an undescribed Meretrix species using Nanopore and Hi-C technologies

Meretrix is a commercially valuable bivalve genus in Asia, but only one reference genome has hindered comprehensive genetic studies and germplasm resource evaluation. In this study, we present three reference genomes of Meretrix species: Meretrix sp. MF1, Meretrix sp. MT1, and Meretrix lamarckii JML1. Meretrix sp. MF1 was assembled at the chromosome level using Nanopore sequencing and Hi-C technologies, whereas Meretrix sp. MT1 and Meretrix lamarckii were assembled as scaffold-level assemblies. The chromosome-level genome of Meretrix sp. MF1 consists of 36 contigs, including 19 chromosomes and 17 scaffolds, with a total length of 883.3 Mb and a scaffold N50 of 46.87 Mb. Notably, the genome of Meretrix sp. MF1, a putative novel species, exhibits an Average Nucleotide Identity (ANI) of 94.33% with its closest relative, Meretrix lamarckii. These genomic resources not only provide a crucial foundation for genetic research on Meretrix but also contribute to the development of effective conservation strategies for its sustainable management.

genomics↗

bioRxiv2025

Unusual Ecofunctional Traits of Endozoicomonas: A Pan-Genomic Perspective

BackgroundEndozoicomonas is a widely distributed genus of marine bacteria, associated with various marine organisms, and recognized for its ecological importance in host health, nutrient cycling, and disease dynamics. Despite its significance, genomic features of Endozoicomonas remain poorly characterized due to limited availability of high-quality genome assemblies. ResultsIn this study, we sequenced 5 novel Endozoicomonas strains and re-sequenced 1 known strain to improve genomic resolution. By integrating these 6 high-quality genomes with 31 others that were publicly available, we identified a distinct, coral-associated clade not recognized by the previous two-clade classification. Pan-genomic analysis revealed significant variation in genetic trait distribution among clades. Notably, Endozoicomonas lacks quorum sensing capabilities, suggesting resistance to quorum quenching mechanisms. It also lacks the ability to synthesize and transport vitamin B12, indicating that it is not a primary source of this nutrient for holobionts. A remarkable feature of Endozoicomonas is its abundance of giant proteins, ranging from 15 to 65 kbp. We identified 92 such proteins, which clustered into three major groups based on amino acid similarity, each associated with specialized functions, such as antimicrobial synthesis, exotoxin production, and cell adhesion. Additionally, we explored prophages and CRISPR-Cas systems. We found that Endozoicomonas acquired prophages from diverse sources via infection or other types of gene transfer. Notably, CRISPR-Cas sequences suggest independent evolutionary trajectories from both prophage acquisition and phylogenetic lineage, implying a potential influence of geographic or environmental pressures. ConclusionsThis study provides new insights into the genomic diversity of Endozoicomonas and its genetic adaptation to diverse hosts. Identification of novel genomic features, including deficiencies in B12 synthesis and quorum sensing, the presence of giant proteins, prophages, and CRISPR-Cas systems, underscores its ecological roles in various holobionts. These findings open new avenues for research on Endozoicomonas and its ecological interactions.

ecology↗

bioRxiv2024

Salinity impacted microbial carbonate precipitation mechanisms of modern microbialites in peritidal zone

Microbialites, ancient records of microbial activity, serve as significant indicators of environmental change. This study examined microbialites from the peritidal zone of three tide pools at Fongchueisha, Hengchun, Taiwan, to investigate the impact of salinity on microbial community composition and carbonate precipitation mechanisms. Microbial samples were collected across varying salinity gradients over multiple timepoints and analyzed using next-generation sequencing of bacterial 16S and eukaryotic 18S rRNA genes. Our findings reveal that the microbial communities in higher salinity environments exhibited significant shifts, with increased relative abundance of ureolytic bacteria and ammonifying microorganisms, such as Myxococcota and Actinobacteriota. This suggests the presence of diverse microbial carbonate precipitation mechanisms beyond photosynthesis, including ureolysis and ammonification. Furthermore, our results show that changes in the composition of cyanobacteria and diatoms were influenced by salinity, with heterocystous cyanobacteria (e.g., Nostocales) dominating low-salinity environments, and non-heterocystous cyanobacteria (e.g., Synechococcales) prevailing in higher salinity environments. Functional predictions reveal that microbial communities in high-salinity environments were enriched in anaerobic metabolic pathways, including pyruvate fermentation and the urea cycle. These findings highlight the significant role of salinity in influencing microbial composition and metabolic pathways, shaping carbonate precipitation processes in microbialites. ImportanceThe study focuses on the impact of environmental salinity on microbial community composition and carbonate precipitation mechanisms within modern microbialites, based on an analysis of samples from three tide pools with different salinity levels collected at five time points throughout the year. Using next-generation sequencing of bacterial 16S and eukaryotic 18S rRNA genes, we identified key shifts in microbial communities along salinity gradients and explored diverse microbial processes involved in carbonate precipitation. This work enhances our understanding of microbial ecosystems within modern microbialites and their response to environmental changes. Additionally, our study provides insight into ancient biogeochemical processes, with implications for interpreting microbial metabolism in carbonate precipitation across different salinity regimes.

microbiology↗

bioRxiv2024

CoPR: Collective Pattern Recognition-a Framework for Microbial Community Activity Analysis

BackgroundMicrobial community activities provide essential information on understanding bacterial communities. Unfortunately, they are generally not directly observable. We rely on longitudinal abundance profiles to get insight into microbial community activities. Often datasets do not have sufficient longitudinal sampling points to successfully apply our algorithms. Hence, in this paper, we are interested in analysing multiple datasets from similar environments to alleviate the aforementioned problem. Furthermore, we wish to see whether collective pattern recognition would enhance our understanding of microbial community activities. ResultsIn this paper, we present CoPR, a framework for collective microbial longitudinal abundance data. Our visualisation shows that a single pattern for temporal abundance variation does not exist. However, it also indicates that even complete individuality does not exist. Consequently, our visualisation highlights the individuality and conformity in the temporal variation of abundance profiles of similar host environments. We also identify different characteristics in the TVAP (Temporal Variation of Abundance Profile) patterns with regards to cohesion and separation. ConclusionsCoPR helps gain essential insights into the microbial communities and their heterogeneity through visualisation tools. This paper also highlights the choice between individuality and conformity in microbial community data analysis.

bioinformatics↗

bioRxiv2022

Microbial mat compositions and localization patterns explain the virulence of black band disease in corals

Black band disease (BBD) in corals is characterized by a distinctive, band-like microbial mat, which spreads across the tissues and often kills infected colonies. The microbial mat is dominated by cyanobacteria but also commonly contains sulfide-oxidizing bacteria (SOB), sulfate-reducing bacteria (SRB), and other microbes. The migration rate in BBD varies across different environmental conditions including temperature, light, and pH. However, whether variations in the migration rates reflect differences in the microbial consortium within the BBD mat remains unknown. Here, we show that the micro-scale surface structure, bacterial composition, and spatial distribution differed across BBD lesions with different migration rates. The migration rate was positively correlated with the relative abundance of potential SOBs belonging to Arcobacteraceae localized in the middle layer within the mat and negatively correlated with the relative abundance of other potential SOBs belonging to Rhodobacteraceae. Our study highlights the microbial composition in BBD as an important determinant of virulence.

microbiology↗

bioRxiv2022

The soil microbiome may offer solutions to ginger cultivation

The Taitung region is one of Taiwans main places for ginger agriculture. Due to issues with disease and nutrient, farmers cannot use continuous cropping techniques on ginger, meaning that the ginger industry is constantly searching for new lands. Continuous cropping increases the risk of infection by Pythium myriotylum and Ralstonia solanacearum, which cause soft rot disease and bacterial wilt, respectively. In addition, fertilizer additives cannot recover the soil when using continuous cropping on ginger, even when there is no decrease in trace elements observed in the soil. Although there may be other reasons for the reduction in production, such as soil microbes, we know little about the soil microbiome associated with ginger cultivation. Hence, in this study, we used the bacterial 16S V3-V4 hypervariable region of the 16S ribosomal RNA region to investigate microbe compositions in ginger soil to identify the difference between ginger soil with and without disease. Later, to investigate the influence of the well-known biocontrol agent-B. velezensis and fungicide Etridiazole on soil microbes and ginger productivity, we designed an experiment that collected the soil samples according to the different ginger cultivation periods to examine the microbial community dynamics in the rhizome and bulk soil. We demonstrated that B. velezensis is beneficial to ginger reproduction and suggest that it may influence the plant by adjusting its soil microbial composition. Etridiazole, on the other hand, may have some side effects on the ginger or beneficial bacteria in the soils, inhibiting ginger reproduction.

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

Microbiome restructuring: dominant coral bacterium Endozoicomonas species display differential adaptive capabilities to environmental changes

Bacteria in the coral microbiome play a crucial role in determining coral health and fitness, and the coral host often restructures its microbiome composition in response to external factors. An important but often neglected factor determining this microbiome restructuring is the capacity of microbiome members to adapt to a new environment. To address this issue, we examined how the microbiome structure of Acropora muricata corals changed over 9 months following a reciprocal transplant experiment. Using a combination of metabarcoding, genomics, and comparative genomics approaches, we found that coral colonies separated by a small distance harbored different dominant Endozoicomonas related phylotypes belonging to two different species, including a novel species, Candidatus Endozoicomonas penghunesis 4G, whose chromosome level (complete) genome was also sequenced in this study. Furthermore, the two dominant Endozoicomonas species showed varied adaptation capabilities when coral colonies were transplanted in a new environment. The differential adaptation capabilities of dominant members of the microbiome can a) provide distinct advantages to coral hosts when subjected to changing environmental conditions and b) have positive implications for future reefs.

microbiology↗

bioRxiv2021

Response of Endozoicomonas montiporae to heat stress and coral host lysates

Endozoicomonas, a core bacterial group in corals, may also be a coral symbiont. Endozoicomonas communities often decrease rapidly in corals under heat stress. However, how the bacteria respond to changes in temperature and coral host during heat stress is unknown. Here, we employed the cultivable, dominant species E. montiporae as a working organism to explore how Endozoicomonas responds to heat stress. We designed two experiments to clarify the extent to which E. montiporae is influenced by temperature and coral host. We detected differentially expressed protein (DEP) profiles in this bacterium at 31{degrees}C and 33{degrees}C compared to 25{degrees}C by tandem mass tags-based quantitative proteome analysis. Fifty DEPs, including many heat shock proteins, were detected when the temperature changed. The expression of antioxidant defense proteins and key pyruvate synthase proteins decreased, suggesting that E. montiporae were in a physiology of stress at 33{degrees}C. Furthermore, some proteins were differentially expressed because of the heat-stress-treated coral lysate specifically, suggesting that not only heat but also heat-induced host factors can affect the protein expression of the bacterium. This study provides an in-depth analysis of how the molecular mechanisms of Endozoicomonas are affected by heat stress and coral host.

microbiology↗

bioRxiv2021

Complete and high-quality genomes of novel microbial species from a meromictic lake using a workflow combining long- and short-read sequencing platforms

BackgroundMost of Earths bacteria have yet to be cultivated. The metabolic and functional potentials of these uncultivated microorganisms thus remain mysterious, and the metagenome-assembled genome (MAG) approach is the most robust method for uncovering these potentials. However, MAGs discovered by conventional metagenomic assembly and binning methods are usually highly fragmented genomes with heterogeneous sequence contamination, and this affects the accuracy and sensitivity of genomic analyses. Though the maturation of long-read sequencing technologies provides a good opportunity to fix the problem of highly fragmented MAGs as mentioned above, the methods error-prone nature causes severe problems of long-read-alone metagenomics. Hence, methods are urgently needed to retrieve MAGs by a combination of both long- and short-read technologies to advance genome-centric metagenomics. ResultsIn this study, we combined Illumina and Nanopore data to develop a new workflow to reconstruct 233 MAGs--six novel bacterial orders, 20 families, 66 genera, and 154 species--from Lake Shunet, a secluded meromictic lake in Siberia. Those new MAGs were underrepresented or undetectable in other MAGs studies using metagenomes from human or other common organisms or habitats. Using this newly developed workflow and strategy, the average N50 of reconstructed MAGs greatly increased 10-40-fold compared to when the conventional Illumina assembly and binning method were used. More importantly, six complete MAGs were recovered from our datasets, five of which belong to novel species. We used these as examples to demonstrate many novel and intriguing genomic characteristics discovered in these newly complete genomes and proved the importance of high-quality complete MAGs in microbial genomics and metagenomics studies. ConclusionsThe results show that it is feasible to apply our workflow with a few additional long reads to recover numerous complete and high-quality MAGs from short-read metagenomes of high microbial diversity environment samples. The unique features we identified from five complete genomes highlight the robustness of this method in genome-centric metagenomic research. The recovery of 154 novel species MAGs from a rarely explored lake greatly expands the current bacterial genome encyclopedia and broadens our knowledge by adding new genomic characteristics of bacteria. It demonstrates a strong need to recover MAGs from diverse unexplored habitats in the search for microbial dark matter.

microbiology↗

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↗

bioRxiv2021

Population Differentiation of Rhodobacteraceae Along Coral Compartments

Coral mucus, tissue and skeleton harbor compositionally different microbiota, but how these coral compartments shape the microbial evolution remains unexplored. Here, we focused on the Rhodobacteraceae, which represents a significant but variable proportion (5-50%) of the coral microbiota. We sequenced 234 genomes constituting two divergent populations inhabiting a prevalent coral species Platygyra acuta. One population diverged into two clades colonizing the mucus and skeleton respectively. We reconstructed the ancestral gene changing events that potentially drove the split, and found that the affected genes matched well with the distinct physicochemical features of the mucus and skeleton. Specifically, the mucus clade acquired functions involved in the utilization of coral osmolytes abundant in the mucus (e.g., methylamines, DMSP, taurine and L-proline), whereas the skeleton clade uniquely harbored traits that may promote adaptation to the low-energy and diurnally anoxic skeleton (e.g., sulfur oxidation and swimming motility). These between-clade genetic differences were largely supported by physiological assays. Expanded analyses by including relatives isolated from various marine environments suggest that the mucus and skeleton clades may have diversified in non-coral habitats, but they also consolidated a key role of distinct coral compartments in diversifying many of the above-mentioned traits. The second population varied only at a few dozen nucleotide sites across the whole genomes, and the Slatkin-Maddison test supported that dispersal limitation between coral compartments is another key mechanism driving microbial population differentiation. Collectively, our results suggest that different coral compartments represent ecologically distinct and microgeographically separate habitats that drive the evolution of the coral microbiota.

microbiology↗

bioRxiv2020

A universal subcuticular bacterial symbiont of a coral predator, the crown-of-thorns starfish

BackgroundPopulation outbreaks of the crown-of-thorns starfish (Acanthaster planci sensu lato; COTS), a primary predator of reef-building corals in the Indo-Pacific Ocean, are major concerns in coral reef management. While biological and ecological knowledge of COTS has been accumulating since the 1960s, little is known about its associated bacteria. The aim of this study was to provide fundamental information on dominant COTS-associated bacteria through a multifaceted molecular approach. MethodsA total of 205 COTS individuals from 17 locations throughout the Indo-Pacific Ocean were examined for the presence of COTS-associated bacteria. We conducted 16S rRNA metabarcoding of COTS to determine the bacterial profiles of different parts of the body, and generated a full-length 16S rRNA gene sequence from a single dominant bacterium, which we designated COTS27. We performed phylogenetic analysis to determine the taxonomy, screening of COTS27 across the Indo-Pacific, FISH to visualize it within the COTS tissues, and reconstruction of the chromosome from the hologenome sequence data. ResultsWe discovered that a single bacterium exists at high densities in the subcuticular space in COTS forming a biofilm-like structure between the cuticle and the epidermis. COTS27 belongs to a clade that presumably represents a distinct order (so-called marine spirochetes) in the phylum Spirochaetes and is universally present in COTS throughout the Indo-Pacific Ocean. The reconstructed genome of COTS27 includes some genetic traits that are probably linked to adaptation to marine environments and evolution as an extracellular endosymbiont in subcuticular spaces. ConclusionsCOTS27 can be found in three allopatrically speciated COTS species, ranging from northern Red Sea to the Pacific, implying that symbiotic relationship arose before the speciation (approximately 2 million years ago). The universal association of COTS27 with COTS and nearly mono-specific association at least with the Indo-Pacific COTS potentially provides a useful model system for studying symbiont-host interactions in marine invertebrates.

microbiology↗

bioRxiv2020

Reciprocal transplant experiment in lakes with disparate trophic states show resolution dependent partial functional redundancy

Microbial communities are considered to be functionally redundant, but few studies have tested this hypothesis empirically. In this study, we performed an in situ reciprocal transplant experiment on the surface and bottom waters of two lakes with disparate trophic states and tracked changes in their microbial community and functional attributes for 6 weeks using high-throughput sequencing and functional approaches. The communities from both lakes were resistant to changes in composition after the reciprocal transplant, but their functions tended to become similar to the incubating lakes functional profiles. A significant linear positive relationship was observed between the microbial community and functional attributes, though with varying scales of similarity, suggesting partial functional redundancy. Furthermore, the entropy-based L-divergence measure quantified the scale of partial functional redundancy in the lakes surface and bottom waters. This study establishes and quantifies the scale of partial functional redundancy in the freshwater ecosystem through empirical investigation.

ecology↗