Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2025.03.06.641946

Unusual Ecofunctional Traits of Endozoicomonas: A Pan-Genomic Perspective

Lim, S. L.·Chin, C.-H.·Chiou, Y.-J.·Hsu, M.-T.·Chiang, P.-W.·Chen, H.-J.·Tu, Y.-C.·Tang, S.-L.
View original source ↗Export metadata ↓

Abstract

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.

Explore related subjects

ecologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Lim, S. L., Chin, C.-H., Chiou, Y.-J., Hsu, M.-T., Chiang, P.-W., Chen, H.-J., Tu, Y.-C., Tang, S.-L.. 2025-03-11. Unusual Ecofunctional Traits of Endozoicomonas: A Pan-Genomic Perspective. https://doi.org/10.1101/2025.03.06.641946

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

PlanktonLake-CEREEP- A Freshwater Plankton Image Dataset with Semi-Automated Label Cleaning

Plankton plays a fundamental role in aquatic ecosystems, influencing biogeochemical cycles and serving as a key food source for many organisms. Recent high-throughput imaging technologies enable the rapid acquisition of large volumes of microscopic images, creating new opportunities for monitoring planktonic ecosystems. However, the manual processing and annotation of the vast amounts of data generated by these devices remain time-consuming tasks. In this context, machine learning-based classification models offer a promising solution. In this data paper, we introduce a new labeled freshwater plankton dataset comprising approximately 88,000 images distributed across 43 taxa. We also present the labeling assistance method we used to facilitate dataset annotation. Finally, we present a baseline based on a convolutional neural network (CNN), which achieves a classification accuracy of 93% on our dataset.

ecology↗
bioRxiv2026

A training protocol for human classification of Asian elephant images from trail cameras

Trail cameras have become ubiquitous tools for ecological data collection over recent decades. Despite progress in the development of automated algorithms and artificial intelligence for image classification, our ability to process large volumes of data remain limited by the need for trained human observers to make refined judgements. We provide guidance on placement of trail cameras for observing Asian elephants (Elephas maximus) and outline a protocol for training and testing naive human observers in performing image classifications (age/sex class and group composition) that cannot yet be automated. This process can be used to develop a high-throughput workflow capable of extracting useful data from large volumes of images. Our training material consisted of 14,007 images collected from 6 trail cameras around Udawalawe National Park in Sri Lanka from 2017-2019. In the first stage, expert observers (n=3) trained a group of inexperienced participants (n=4), who engaged in an iterative process to develop a protocol document. The document was then tested on a second set of subjects (n=6) each of whom classified 350 test images in four separate sequential batches using quantitative measures of precision and accuracy. The test set was sampled from 54,435 images from an additional 25 cameras. When compared to expert observers, they achieved a fair level of precision (Fleiss' kappa = 0.247) and 82.6% accuracy. Our approach can usefully be extended to other species and contexts.

ecology↗
bioRxiv2026

Forest belowground productivity and carbon allocation predominantly driven by soil properties rather than climate

Forests are threatened by a multitude of stressors, including anthropogenic disturbances and climate change. Assessing how forests will respond to these stressors requires a comprehensive understanding of net primary productivity (Npp), environmental constraints on growth, and adaptive capacity. A parameter of significant uncertainty is belowground Npp (bNpp), which can account for up to 80% of total Npp but is poorly estimated and rarely measured directly. We used a cross-biome dataset of direct, field-based measurements of aboveground and belowground primary productivity and 21 climatic and soil variables to identify potential constraints on bNpp and belowground carbon allocation in boreal and cold temperate forests. Soil variables, rather than climate variables, were the main drivers of bNpp and belowground allocation across biomes. The importance of soil variables suggests that soil nutrient dynamics, especially soil nutrient pool and flux variables, must be explicitly modeled to more accurately predict feedbacks between climate, productivity, and within-tree carbon allocation. Within biomes, environmental drivers of belowground allocation varied between low versus high allocation forests, indicating that environmental drivers are site-specific and the development of within-biome, site-scale classifications for forest ecosystems could be useful. Changes in soil variables, such as increasing soil nitrogen pools, caused abrupt and large decreases in bNpp for boreal, but not cold temperate forests. Threshold-like shifts indicate that boreal forests might have lower adaptive capacity and higher sensitivity to disturbances than cold temperate forests. With 70% of boreal forests characterized by low bNpp, disturbances such as anthropogenic nitrogen deposition could cause large-scale decreases in bNpp that could push these forests beyond their adaptive capacity.

ecology↗