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)
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Animal Gut Nutrition and Greenhouse Gas Mitigation
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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.
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Harnessing plant microbiomes to improve performance and mechanistic understanding
This is a Cross-Journal Collection with Microbiome, Environmental Microbiome, npj Science of Plants, and npj Biofilms and Microbiomes. Please click here to see the collection page for npj Science of Plants and npj Biofilms and Microbiomes.
Modern agriculture needs to sustainably increase crop productivity while preserving ecosystem health. As soil degradation, climate variability, and diminishing input efficiency continue to threaten agricultural outputs, there is a pressing need to enhance plant performance through ecologically-sound strategies. In this context, plant-associated microbiomes represent a powerful, yet underexploited, resource to improve plant vigor, nutrient acquisition, stress resilience, and overall productivity.
The plant microbiome—comprising bacteria, fungi, and other microorganisms inhabiting the rhizosphere, endosphere, and phyllosphere—plays a fundamental role in shaping plant physiology and development. Increasing evidence demonstrates that beneficial microbes mediate key processes such as nutrient solubilization and uptake, hormonal regulation, photosynthetic efficiency, and systemic resistance to (a)biotic stresses. However, to fully harness these capabilities, a mechanistic understanding of the molecular dialogues and functional traits underpinning plant-microbe interactions is essential.
Recent advances in multi-omics technologies, synthetic biology, and high-throughput functional screening have accelerated our ability to dissect these interactions at molecular, cellular, and system levels. Yet, significant challenges remain in translating these mechanistic insights into robust microbiome-based applications for agriculture. Core knowledge gaps include identifying microbial functions that are conserved across environments and hosts, understanding the signaling networks and metabolic exchanges between partners, and predicting microbiome assembly and stability under field conditions.
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