Researchers at Bigelow Laboratory for Ocean Sciences (East Boothbay, Maine, USA) have recently quantified a remarkable evolutionary process: a typical marine microorganism acquires and retains approximately 13% of its genes per million years through horizontal (lateral) gene transfer. This rate corresponds to roughly 250 genes exchanged and retained per litre of seawater each day
These transferred genes include those that provide either a selective advantage or are sufficiently neutral to persist via genetic drift—both well-established mechanisms of evolutionary change.
Some creationist arguments misapply Shannon Information Theory, claiming that gaining new genetic information violates the laws of thermodynamics. However, such arguments disregard key biological realities: cells are open systems capable of energy and material exchange; genome duplication and horizontal transfer are well-documented evolutionary processes; and substituting one nucleic acid for another does not create matter ex nihilo - facts of which any qualified biological scientists should be aware.
Furthermore, the successful retention and spread of horizontally acquired genes within microbial genomes provide clear, empirical evidence of Darwinian evolution in action. Although Charles Darwin formulated his theory without the concept of genes — speaking instead of 'heritable traits' — his mechanism of natural selection precisely explains how heritable variations can spread through populations over time.
This study also highlights that microorganisms can evolve not only through mutation and selection but also by acquiring pre-adapted genes from their environment, often from distantly related organisms. Consequently, these newly acquired genes can propagate rapidly within the recipient lineage.
The findings further challenge traditional microbial taxonomy, blurring species boundaries at the genetic level: horizontally transferred genes may function just as effectively in their new hosts as they did in their original genomes, thanks to the universality of underlying molecular machinery (e.g., replication and translation systems).
Examples of Horizontal Gene Transfer Across Life.This research was recently published in The ISME Journal and was highlighted in a Bigelow Laboratory news release.
- Bacteria & Archaea
- Escherichia coli: Frequently exchanges plasmids, including those carrying antibiotic resistance genes.
- Thermophilic archaea: Acquire metabolic genes from bacteria, enabling survival in extreme environments.
- Protists
- Euglena gracilis: Contains photosynthetic genes obtained from green algae, allowing it to switch between autotrophy and heterotrophy.
- Trichomonas vaginalis: Acquired bacterial genes for breaking down carbohydrates, aiding its parasitic lifestyle.
- Fungi
- Neurospora crassa: Shows evidence of transferred genes that help it metabolise new sugars.
- Pathogenic fungi (e.g., Fusarium species): Have acquired genes from bacteria that enhance virulence in plants.
- Plants
- Grasses (Poaceae): Some lineages have incorporated bacterial genes that improve stress tolerance and metabolic flexibility.
- Amborella trichopoda (a basal flowering plant): Carries dozens of mitochondrial genes from mosses, algae, and other plants.
- Sweet potatoes (Ipomoea batatas): Contain genes from Agrobacterium integrated into their genome, giving them natural transgenes.
- Animals
- Bdelloid rotifers (Adineta spp.): Incorporate foreign DNA from bacteria, fungi, and plants into their genomes, which helps them survive desiccation.
- Pea aphids (Acyrthosiphon pisum): Acquired fungal genes that allow them to synthesise carotenoids (hence their red and green colour forms).
- Coffee berry borer beetle (Hypothenemus hampei): Uses a bacterial gene to digest caffeine in coffee beans.
- Sea slugs (Elysia chlorotica): Incorporate algal genes for photosynthesis, enabling them to live partly like plants.
This demonstrates that HGT is not confined to microbes — it plays a role in shaping the genomes of fungi, plants, and animals as well, often conferring entirely new ecological abilities.
Researchers Quantify Rate of Essential Evolutionary Process
The movement of genetic material between organisms that aren’t directly related is a significant driver of evolution, especially among single-celled organisms like bacteria and archaea. A team led by researchers at Bigelow Laboratory for Ocean Sciences have now estimated that an average cell line acquires and retains roughly 13 percent of its genes every million years via this process of lateral gene transfer. That equates to about 250 genes swapped per liter of seawater every day.
The new study, recently published in The ISME Journal, provides the first quantitative analysis of gene transfer rates across an entire microbiome. It calls into question the strict classification lines drawn between individual species. It also confirms that many transferred genes have direct ecological benefits, highlighting how this process enables microbes to adapt to new environments and furnishes them with valuable capacities, such as the ability to access essential nutrients.
All the processes that microbes drive on our planet have evolved, and that evolution, to a large extent, is driven by lateral gene transfer, but the process is very difficult to study, and no one has been able to put numbers to the process. We know in general how it works, but we had no idea if you take a drop of seawater, are genes being exchanged once a minute or once a year or once a million years? That was completely unknown — until now.
Ramunas Stepanauskas, lead author.
Bigelow Laboratory for Ocean Sciences
East Boothbay, ME. USA.
Genes can be transferred laterally through multiple mechanisms, including the uptake of floating genetic material in the environment, direct transfer between cells, and the injection of foreign DNA into a host by a virus.
Scientists have struggled to quantify those processes, though, given the immense diversity of microbial life. Traditional “evolutionary tree” approaches can be used to study the transfer of specific, widespread genes — a handful at a time — but are impractical for studying an entire ecosystem. Likewise, the common method for studying microbial genomes, metagenomics, works by stitching together assemblies of related, “typical” genes, meaning it actively excludes transferred genes that are rare or come from unrelated organisms.
Advances in computational modeling and single-cell genomics, though, have allowed scientists to begin answering these questions.
The team used genomes of 12,000 randomly-sampled microbial cells from the tropical and subtropical surface ocean sequenced by Stepanauskas’s team at the Single Cell Genomics Center (SCGC). The unique dataset is one of the largest compilations of microbial genomes ever produced. They compared the distribution of shared genes in that real-world data with a computer model that assumed that genes can only be transferred vertically between parents and offspring, not laterally.
This project was an exciting opportunity to think differently about how to measure an essential yet elusive evolutionary process that shapes the microbial component of ecosystems globally.
Professor Siavash Mirarab, co-author
Department of Electrical and Computer Engineering
University of California; San Diego
La Jolla, California, USA.
The approach confirmed that most genes are exchanged between closely related cells, but not all. Some genes with obvious ecological value can be successfully transferred between microbes that are as distantly related to each other as humans to kangaroos. For example, they found evidence of microbes acquiring novel genes that enable them to uptake new sources of phosphorus in the phosphorus-limited Sargasso Sea.
The findings also show evidence of the exchange of genes that encode ribosomal RNA, the cellular machinery responsible for protein synthesis. That, Stepanauskas said, was surprising given that those genes are often used as metrics for biological diversity exactly because scientists assumed they were not engaged in lateral transfer.
In the future, the team hopes to expand this approach into new environments and tease apart differences between lineages, transfer mechanisms, and ecosystems. That work could have significant biotechnology implications by revealing how nature effectively and rapidly engineers cells for different environments and processes. To that end, SCGC is continually improving and scaling up its analytical capabilities to enable the large-scale studies that work will require.
Answering these questions may have become possible, but only if we can continue to improve our modeling toolkit.
Professor Siavash Mirarab.
I see this as just the beginning. We finally have sufficient data to start doing this kind of quantitative analysis, but we still need to go much further to say how frequently specific kinds of microbes do it, what processes are involved, and how we can use this knowledge in environmental stewardship and bioeconomy.
Ramunas Stepanauskas.
Funding for this work was provided by the Simons Foundation, National Science Foundation, and the National Institutes of Health. The study also features researchers from Woods Hole Oceanographic Institution, University of Pretoria, Wellesley College, and Massachusetts Institute of Technology. From Bigelow Laboratory, co-authors include Julia Brown and Greg Gavelis.
Publication:
AbstractThis discovery is yet another example of how the natural world constantly defies creationist claims that organisms are somehow fixed, immutable, and incapable of innovation. Horizontal gene transfer shows that genetic novelty can arise in multiple ways, not only by mutation but also by borrowing useful sequences from neighbours—sometimes even across wide evolutionary distances. The Bible's authors clearly knew nothing of micro-organisms or genetics let alone the origins of heritable genetic information.
Lateral gene transfer is a major evolutionary process in Bacteria and Archaea. Despite its importance, lateral gene transfer quantification in nature using traditional phylogenetic methods has been hampered by the rarity of most genes within the enormous microbial pangenomes. Here, we estimated lateral gene transfer rates within the epipelagic tropical and subtropical ocean using a global, randomized collection of single amplified genomes and a non-phylogenetic computational approach. By comparing the fraction of shared genes between pairs of genomes against a lateral gene transfer-free model, we show that an average cell line laterally acquires and retains ~13% of its genes every 1 million years. This translates to a net lateral gene transfer rate of ~250 genes L−1 seawater day−1 and involves both “flexible” and “core” genes. Our study indicates that whereas most genes are exchanged among closely related cells, the range of lateral gene transfer exceeds the contemporary definition of bacterial species, thus providing prokaryoplankton with extensive genetic resources for lateral gene transfer-based adaptation to environmental stressors. This offers an important starting point for the quantitative analysis of lateral gene transfer in natural settings and its incorporation into evolutionary and ecosystem studies and modeling.
INTRODUCTION
Lateral gene transfer (LGT) is a major evolutionary process in Bacteria and Archaea, with impacts spanning the spread of antibiotic resistance among human pathogens, the emergence of new capabilities in planetary biogeochemical cycles, and serving as a fundamental driver of microbial speciation [1-3]. Recent discoveries the repertoire of classical LGT mechanisms - natural transformation, conjugation, and transduction - with a plethora previously unknown processes and vectors, such as gene transfer agents, phage-inducible chromosomal islands, extracellular vesicles, tycheposons, and likely other, yet undiscovered modes [4-6]. However, quantification of in situ rates of LGT has proven challenging. Existing estimates of LGT rates are primarily based on studies of model bacterial cultures grown under laboratory conditions [7, 8], model genetic elements employed in the field [9], or inferences about a limited set of genes in genomes of cultured isolates [10 12]. Due to biases inherent in these approaches, current rate estimates are likely not fully representative of the diversity of microorganisms and evolutionary processes in nature.
Complex microbiomes carry millions of genes that collectively comprise the enormous pangenomes of constituent lineages, and most of these genes are exceedingly rare [13, 14]. Comprehensive tracking of lateral transfers of such rare genes using traditional phylogenetic approaches requires bias-free genome sampling at scales that remain unattainable in contemporary microbiology. Another challenge is the complex and poorly understood microbial biogeography, which exhibits structure from microscopic to global scales and obscures the discrimination of biological (e.g., evolutionary distance) and physical (e.g., cell encounter rate) factors impacting the distribution and exchange of genetic material [15, 16]. Subsequently, even approximate LGT rates and phylogenetic range in natural, complex microbiomes remain largely unknown, representing a major knowledge gap in microbiology [1-3].
Marine planktonic Bacteria and Archaea (prokaryoplankton) constitute two-thirds of the ocean’s biomass and play essential roles in the global carbon cycle, nutrient remineralization, and climate formation [17]. Prior studies have suggested that LGT is important in the evolutionary patterns of specific prokaryoplankton lineages [18-20]. The global mixing of the ocean by thermohaline circulation every 1,000–2,000 years and surface currents acting at much shorter time scales [21] minimize the impact of dispersal limitations on long-term evolutionary processes of prokaryoplankton. Prokaryoplankton sister cells are estimated to separate by several kilometers each week, on average [20]. Although environmental factors can drive regional differences in the lineages’ relative abundances [22], cells inhabiting epipelagic environments in tropical and subtropical latitudes are efficiently dispersed within this zone globally and differ genetically from cells inhabiting higher latitudes and greater depths, with the physicochemical environment driving these biogeographic patterns [14, 23]. Genomic sequencing of 6,236 individual prokaryoplankton cells from a single 0.4 mL seawater sample recovered a substantial fraction of the total coding potential of prokaryoplankton inhabiting this zone [14]. It is likely that prokaryoplankton inhabiting the tropical and subtropical epipelagic have been experiencing a rather stable environment for tens of millions of years [24]. This offers a less complex and more stable system for studies of microbiome-wide evolutionary processes compared to the more compartmentalized and temporary environments, such as soils and host-associated holobionts.
A recently reported collection of 12,715 randomly sampled single amplified genomes (SAGs) from 28 globally distributed samples of tropical and subtropical, epipelagic ocean water, collectively called Global Ocean Reference Genomes - Tropics (GORG-Tropics), offers a unique opportunity for quantitative, microbiome-wide tracking of gene distribution at the resolution of individual cells [14, 25]. No two GORG-Tropics cells were found to contain identical gene content, and extensive LGT was hypothesized as a plausible explanation for this observation. Here, we harness GORG-Tropics and a novel computational approach, which we call Discrepancy in Gene Share (DIGS), to estimate in situ rates of net LGT in the epipelagic zone of tropical and subtropical ocean. First, we determined the fraction of highly similar genes in each pair of GORG-Tropics genomes and compared it against data derived from an LGT-free model.
Then, we used discrepancies between the observed and modeled data in the context of evolutionary distances of compared genomes to estimate the average net rate of LGT in this microbiome. Our analyses indicated that marine prokaryoplankton acquire and retain ~13% of their genes through LGT every 1 million years, translating to a net rate of ~250 genes L-1 day-1, with most transfers occurring among closely related cells. Subsequently, we applied established methods to identify examples of LGT in GORG-Tropics. We explored how these events impact DIGS, which revealed LGT of both ecologically relevant “flexible” genes as well as “core” genes that are frequently used as phylogenetic anchors, including the 16S rRNA gene.
Ramunas Stepanauskas, Julia M Brown, Shayesteh Arasti, Uyen Mai, Gregory Gavelis, Maria Pachiadaki, Oliver Bezuidt, Jacob H Munson-McGee, Tianyi Chang, Steven J Biller, Paul M Berube, Siavash Mirarab
Net rate of lateral gene transfer in marine prokaryoplankton
The ISME Journal, 2025;, wraf159, https://doi.org/10.1093/ismejo/wraf159 [PDF}
Copyright: © 2025 International Society for Microbial Ecology.
Published by Oxford University Press. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)
What we see here is Darwinian evolution at work on a microscopic scale, adding layer upon layer of genetic variety that fuels adaptation and diversification. Far from violating any scientific principles, these processes are firmly grounded in observable biology, biochemistry, and physics.
Over the course of millions of years, the cumulative effect of these exchanges has been to reshape microbial genomes and blur the boundaries of species, while also reminding us of life’s shared origins. In the universality of the genetic code, we find both the mechanism and the evidence: a common inheritance that allows a gene from one organism to function seamlessly in another.
As this research illustrates, the story of life on Earth is not one of rigid design but of dynamic, evolving systems—messy, inventive, and endlessly adaptive. Horizontal gene transfer is simply one of the many ways evolution has equipped living things to survive, thrive, and share their successes with others in the great web of life.
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