Prokaryotic-virus-encoded auxiliary metabolic genes throughout the global oceans
Published in Earth & Environment, Ecology & Evolution, and Microbiology
In the decades since sequencing technology and analytic advances have driven a surge in AMG studies across various ecosystems. Yet the lack of a systematically curated AMG catalog remained, thus hindering the integration of viruses into models to quantitatively assess their metabolic and biogeochemical impacts. Fortunately, five years prior to this study, global dsDNA catalog papers began to be published5,6,7, resulting in the identification of over 190,000 dsDNA viruses across the global oceans. For the first time, this presented a global ocean dataset that was deeply sequenced and curated for dsDNA viruses. It was against this backdrop that Funing Tian, then a PhD student in Microbiology who had received a University Fellowship from The Ohio State University, and James Wainaina, having just completed his graduate studies at the University of Western Australia (UWA), began working on this project.
Funing Tian (Left), Zhiping Zhong (Center), and James Wainaina (Right) during a poster presentation of the global AMG catalog work at the Center of Microbiome Science (CoMS) MidWest Conference May 2022
The Ocean AMG project faced numerous challenges. First, despite the increase in AMG studies, the lack of standards for what constitutes a 'bona fide' AMG has prevented cross-study comparisons. This necessitated the development of standards for what could be 'conservatively' assigned as AMGs, a process that took almost a year and was further aided by new analytical tools by Kelly Wrighton lab8. After identifying ~22,000 AMG gene clusters, the second challenge was determining how to narrow down to the most biogeochemical important AMGs,
There are several take-home messages from this paper. Firstly, given the avalanche of data from large consortia such as the Tara Ocean Expedition, it is crucial to have a systematic and scalable approach for analyzing the data and enabling cross-study comparisons. Secondly, reliable, updated, and maintained viral ecogenomics tools will be essential for continuously exploring and advancing omic data sets, especially within the marine ecosystem. Finally, this study would not have been possible without cross-disciplinary collaboration, teamwork, dogged determination despite scientific challenges, and an unwavering spirit; this was particularly important as it took over four years to get this work to publication.
What does the future hold for us, Funing Tian, now Dr. Tian is currently a Bioinformatician at the University of Chicago, where she focuses on bioinformatics analysis of single-cell multi-omics sequencing for asthma research. James has started his research group at the Woods Hole Oceanographic Institution Biology Department, where he continues exploring the ecology and evolution of marine viruses with a particular focus on corals.
1. Sullivan, M. B. et al. Prevalence and Evolution of Core Photosystem II Genes in Marine Cyanobacterial Viruses and Their Hosts. PLoS Biol. 4, e234 (2006).
2. Lindell, D. et al. Transfer of photosynthesis genes to and from Prochlorococcus viruses. Proc. Natl. Acad. Sci. U. S. A. 101, 11013–11018 (2004).
3. Lindell, D., Jaffe, J. D., Johnson, Z. I., Church, G. M. & Chisholm, S. W. Photosynthesis genes in marine viruses yield proteins during host infection. Nature 438, 86–89 (2005).
4. Bragg, J. G. & Chisholm, S. W. Modeling the fitness consequences of a cyanophage-encoded photosynthesis gene. PLoS One 3, 1–9 (2008).
5. Brum, J. R. et al. Ocean Viral Communities. Science (80-. ). 348, 1261498-1–11 (2015).
6. Roux, S. et al. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature 537, 689–693 (2016).
7. Gregory, A. C. et al. Marine DNA Viral Macro- and Microdiversity from Pole to Pole. Cell 177, 1109-1123.e14 (2019).
8. Shaffer, M. et al. DRAM for distilling microbial metabolism to automate the curation of microbiome function. Nucleic Acids Res. 48, 8883–8900 (2020).
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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.
This Research Topic welcomes Original Research, Reviews, Perspectives, and Meta-analyses that delve into the functional and mechanistic basis of plant-microbiome interactions. We are particularly interested in contributions that integrate molecular microbiology, systems biology, plant physiology, and computational modeling to unravel the mechanisms by which microbial communities enhance plant performance and/or mechanisms employed by plant hosts to assemble beneficial microbiomes. Studies ranging from controlled experimental systems to applied field trials are encouraged, especially those aiming to bridge the gap between fundamental understanding and translational outcomes such as microbial consortia, engineered strains, or microbiome-informed management practices.
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Microbiome and Reproductive Health
Microbiome is calling for submissions to our Collection on Microbiome and Reproductive Health.
Our understanding of the intricate relationship between the microbiome and reproductive health holds profound translational implications for fertility, pregnancy, and reproductive disorders. To truly advance this field, it is essential to move beyond descriptive and associative studies and focus on mechanistic research that uncovers the functional underpinnings of the host–microbiome interface. Such studies can reveal how microbial communities influence reproductive physiology, including hormonal regulation, immune responses, and overall reproductive health.
Recent advances have highlighted the role of specific bacterial populations in both male and female fertility, as well as their impact on pregnancy outcomes. For example, the vaginal microbiome has been linked to preterm birth, while emerging evidence suggests that gut microbiota may modulate reproductive hormone levels. These insights underscore the need for research that explores how and why these microbial influences occur.
Looking ahead, the potential for breakthroughs is immense. Mechanistic studies have the power to drive the development of microbiome-based therapies that address infertility, improve pregnancy outcomes, and reduce the risk of reproductive diseases. Incorporating microbiome analysis into reproductive health assessments could transform clinical practice and, by deepening our understanding of host–microbiome mechanisms, lay the groundwork for personalized medicine in gynecology and obstetrics.
We invite researchers to contribute to this Special Collection on Microbiome and Reproductive Health. Submissions should emphasize functional and mechanistic insights into the host–microbiome relationship. Topics of interest include, but are not limited to:
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This Collection supports and amplifies research related to SDG 3, Good Health and Well-Being.
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