In marine environments, including coral reef ecosystems, all biomes are fundamentally dependent on their microbial constituents (Azam and Worden 2004). About 98% of reef-building corals contain endolithic microbes (Le Campion-Alsumard et al. 1995), and those endoliths contribute to the high biomass of corals (Odum and Odum 1955, Rosenberg et al. 2007, Schönberg and Wisshak 2012).
Among the endoliths in coral skeleton, aerobic microbes and green algae Ostreobium has been found in diverse live corals and is considered a coral symbiont because of its role of both microborer and primary producer (Schlichter et al. 1995, Del Campo et al. 2017). Besides, the endolithic microbes are related to new nitrogen input and process nutrient regeneration in coral reefs (Shashar et al. 1994, O’Neil and Capone 2008, Cardini et al. 2014).
In addition to aerobic endolithic microorganisms, anaerobic photoautotrophic green sulfur bacteria (GSB) Prosthecochloris has been constantly found in the skeleton of coral Isopora palifera with a relative high abundance (Yang et al. 2016). Recently, anaerobic microbes are considered as one of the major contributors to the high diversity characteristics of the coral holobiont. However, due to technical challenges, their distribution, as well as their functions, remains poorly characterized despite considerable belief on the critical role they may play in the coral physiology and response to environmental stressors.
Why can GSB prevail in the skeleton of Isopora palifera? What are their functions? These are core questions of this study. Hence, we conducted multi-level approaches—including metagenomic, anaerobic cultivation, pigment analysis, ultrathin-section transmission electron microscopy, fluorescence in situ hybridization, nanoscale secondary ion mass spectrometry (FISH-NanoSIMS) and acetylene reduction assay (ARA)—to understand and clarify the role of the endolithic GSB in the nutrient cycle.
(Green Iayer in the coral, Isopora palifera)
With culture-independent and culture-dependent methods, we discovered putative functions of nitrogen, sulfur and carbon metabolisms of GSB and other endolithic microbes in the coral skeleton. In addition, the results from FISH-NanoSIMS and ARA also demonstrated the ability of nitrogen uptake by endolithic GSB in the coral skeleton, indicating the dominant GSB in coral skeletons has important role in fixing nitrogen. Furthermore, we found that the dominant endolithic GSB in the green layer are new species of marine GSB Prosthecochloris. Interestingly, the new strains of Prosthecochloris from coral skeletons showed phylogenetic distance from other free-living marine Prosthecochloris isolates. Therefore, we propose a group of coral-associated Prosthecochloris (CAP).
We suggest that the composition of endolithic microbes is more likely to be diverse and dynamic than previous understanding, and special micro-environmental factors in the skeleton should be paid more attention. Besides, the growth conditions and physiological, cellular and genomic features of the GSB are strongly linked with specific environmental factors: that is, light and oxygen although there can be other environmental factors as well. We believe that this study pointed out the value of anaerobic metabolisms when studying coral holobionts and the evolution of CAP and their coral hosts. The further information can be found in our paper (Yang et al., 2019, Microbiome 7:3)
(Dr. Shan-Hua Yang, the first author, and the culture of endolithic GSB)
Follow the Topic
-
Microbiome
This journal hopes to integrate researchers with common scientific objectives across a broad cross-section of sub-disciplines within microbial ecology. It covers studies of microbiomes colonizing humans, animals, plants or the environment, both built and natural or manipulated, as in agriculture.
Related Collections
With Collections, you can get published faster and increase your visibility.
Oncobiome
This collection of papers delves into the burgeoning field of oncobiome research, exploring the intricate relationship between cancer and the microbiome. The oncobiome encompasses the diverse microbial communities residing in and on the human body, which influence cancer development, progression, and treatment responses. By examining these interactions, our aim is to unravel the complex mechanisms through which the microbiome impacts oncogenesis and therapeutic outcomes.
This compilation highlights cutting-edge research, offering insights into potential diagnostic markers and novel therapeutic strategies, thereby advancing our understanding of cancer biology and paving the way for innovative, microbiome-targeted cancer treatments.
This is a cross-journal collection between:
Experimental Hematology and Oncology
Articles will undergo the standard peer-review process of the journal to which they are submitted and are subject to either the BMC editorial policies or those of BJC Reports. Articles will be added to the Collection as they are published. The Editors have no competing interests with the submissions which they handle through the peer review process. The peer review of any submissions for which the Editors have competing interests is handled by another Editorial Board Member who has no competing interests.
Publishing Model: Open Access
Deadline: Ongoing
Animal Gut Nutrition and Greenhouse Gas Mitigation
Animal Microbiome, Journal of Animal Science and Biotechnology and Microbiome call for submissions to the collection on Animal Gut Nutrition and Greenhouse Gas Mitigation.
Efforts to reduce greenhouse gas emissions from livestock systems increasingly hinge on innovations in animal gut nutrition. The dynamic relationship between the gut microbiome and nutrient utilization plays a pivotal role in shaping methane output, feed efficiency, and overall sustainability. Advances in microbial ecology—particularly in understanding the role of gut microbiome in nutrient metabolism—are opening new pathways for mitigating emissions while enhancing productivity. These developments support the implementation of climate-smart agricultural strategies to address climate change and its impacts.
Looking ahead, continued research in this field has the potential to yield innovative solutions such as targeted probiotic supplementation, which could further optimize gut function and enhance nutrient absorption. These advancements may lead to reduced greenhouse gas emissions while improving animal health and productivity. By deepening our understanding of the animal gut microbiome, we can contribute significantly to sustainable agricultural practices that benefit both the environment and food security.
We invite researchers to contribute to this special Collection on Animal Gut Nutrition and Greenhouse Gas Mitigation. Topics of interest include but are not limited to:
- Animal Gut Microbiome and Feed Efficiency
- Greenhouse Gas Mitigation Strategies
- Rumen Fermentation Dynamics
- Nutrient Utilization in Livestock
- Probiotic Supplementation Effects
- Sustainable Livestock Production Practices
- Climate-Smart Agriculture Innovations
This Collection supports and amplifies research related to SDG 13, Climate action.
All submissions in this collection undergo the relevant journal’s standard peer review process. Similarly, all manuscripts authored by a Guest Editor(s) will be handled by the Editor-in-Chief of the relevant journal. As an open access publication, participating journals levy an article processing fee (Animal Microbiome fees, Journal of Animal Science and Biotechnology fees, Microbiome fees). We recognize that many key stakeholders may not have access to such resources and are committed to supporting participation in this issue wherever resources are a barrier. For more information about what support may be available, please visit OA funding and support, or email OAfundingpolicy@springernature.com or the Editor-in-Chief of the journal where the article is being submitted.
Publishing Model: Open Access
Deadline: Sep 04, 2026
Please sign in or register for FREE
If you are a registered user on Research Communities by Springer Nature, please sign in