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The Evolutionary Role of Microbial Communities: Unveiling the Hidden World of Microbiomes

From the symmetry of beehives to the bright colors of coral reefs, every living thing in the natural world has evolved under the often-invisible pressures of natural selection. But to understand exactly what evolutionary processes have shaped the natural world, it is essential to understand exactly how forces of natural selection and adaptation have impacted organisms of the biosphere in the past and present. In recent decades, scientists have only just begun to study one of the most prominent and impactful of these invisible processes—the microbiome.

The microbiome refers to the community of microbial organisms, or microbes, that are nearly omnipresent in the environment and within organisms. Every human, for example, is believed to host around 39 trillion microbes within their body. Just like larger animals, these microbes exist within delicate ecologies, with different community compositions that are impacted by living conditions in their habitat. Importantly, these microbes produce a massive and poorly understood diversity of biochemicals through diverse metabolic processes, and these can have important impacts at individual, ecosystem, and evolutionary levels.1

Given the multifaceted roles of microbial communities in evolution and biodiversity, understanding their co-evolution with eukaryotes is paramount for grasping broader evolutionary principles. However, studying microbial diversity and its effects on host organisms poses significant challenges, particularly in natural environments where microbial communities can comprise thousands, or even millions, of taxa. Traditional methods based on morphological identification are insufficient for such complexity—these tiny, invisible microbes, cannot be picked up, measured, and counted like Darwin’s finches.

This is where Next-Generation Sequencing (NGS) methods have revolutionized microbiome research. NGS allows scientists to obtain comprehensive genetic information from microbial communities, providing insights into their composition, diversity, and functional potential. Through NGS, researchers can study the vast and diverse world of microorganisms in a much more nuanced way, allowing for a deeper understanding of their evolutionary relationships and ecological roles. The question, then, becomes which organisms to study.

Learning from Marine Invertebrates

One way to study the role that microbes have played in the evolution of animals is to start from the beginning.

Sea sponges and cnidarians, are two highly diverse phyla that are believed to have been some of the first animals on the tree of life, with lineages dating back hundreds of millions of years. These animals also typically have very simple body plans—sponges have almost none of the unique types of cells that are common among other animals, and while cnidarians are slightly more complicated, including diverse groups such as jellyfish, anemones, and corals, they don’t come anywhere close to the complexity of many other invertebrates.2 But despite their simplicity, these taxa have managed to survive longer than any other animals, and provide critical habitat and ecological functions in all of the world’s oceans.

Many sponges and corals in particular have accomplished this feat of life through particularly strong symbioses with microbes. Most corals, for example, live through a process called obligate symbiosis, in which the depend completely on symbiosis with microbes called Zooxanthellae, photosynthetic algae that provide the corals with energy in exchange for protection, and are also what give many corals their color. This service of photosynthesis has resulted in co-evolutionary dynamics in corals and Zooxanthellae over time, and has broadened the ecological niche of corals, allowing them to thrive in many tropical, nutrient-poor waters.3

Coral Reef

Corals depend heavily on symbiosis with photosynthetic microbes that also give them their brilliant colors. "Coral Reef" by NOAA’s National Ocean Service is marked with Public Domain Mark 1.0.

Sponges, on the other hand, are filter feeders but also rely on the metabolic activity of microbes so much so that some species are actually 70% microbe by body weight. The functions that these symbioses provide are highly diverse and vary across taxa. One notable service that microbes provide is influence on host phenotype, that is, the physical qualities of the animal. In many animals, this can impact traits such as growth, reproduction, and resistance to environmental stressors. In some sponges, this phenotypic plasticity can be a catalyst for natural selection, leading to enhanced survival and adaptation in changing environments.

Sea Sponge

Sea sponges rely on microbes for important metabolic processes and disease resistance. "Sea Sponge" by Anna Barnett is licensed under CC BY 2.0.

Moreover, microbial communities play a crucial role in disease prevalence and resistance. The presence of specific microbes can bolster an organism’s immune response, helping to fend off pathogens. Conversely, imbalances in microbial communities, or dysbiosis, can predispose hosts to diseases. In corals, a lack of Zooxanthellae leads to coral bleaching and often death, while in some sponges microbial symbiosis fosters extraordinary powers of regeneration. Understanding these dynamics offers insights into the evolutionary arms race between hosts and pathogens, highlighting the role of microbes in shaping health and disease outcomes.

The Deep Sea: A case study

So, what processes do scientists use to study these types of microbial symbiosis?

Sample Collection

The first step in all zoological research is sample collection. Sponges and cnidarians living in deep regions of the oceans are particularly interesting study subjects because of their remarkable adaptions to unique environments, such as hydrothermal vents, cold seeps, whalefalls and extreme conditions. This environment necessitates special collection techniques, such as by remotely operated vehicles (ROVs), which have robotic arms and tools that can be used to collected sterile tissue samples and surrounding water samples.4

Extraction, Amplification, and Sequencing

Once these samples are brought back to the lab, scientists then have to employ protocols that can be used with the latest NGS techniques, and which depend on the desired downstream analysis. The first decisions that should be made is whether RNA or DNA will be sequenced and what genetic markers will be sequenced.

After extracting DNA and RNA using commercial kits, the segments of interested can then be sequenced for metagenomic or metatranscriptomic sequencing. For sponge and coral microbiomes, this is traditionally done using the 16S rRNA markers, for which Novogene can provide standard in-house primers or custom primers.

However, an alternative, more advanced method for differentiating taxa is metagenomic shotgun sequencing, which is also offered by Novogene metagenomic shotgun sequencing services. Unlike traditional 16S rRNA gene sequencing, this method sequences many random sections of genomes, allowing researchers to differentiate between taxa at the species and subspecies levels while providing genome-wide information on individuals.

For metatranscriptomics, RNA libraries can be prepped and sequenced on NGS technology, such as Illumina NovaSeq X Plus Sequencing System, through Novogene’s Metatranscriptomic Services. While metagenomic sequencing provides researchers with an idea of what organisms are present in microbiome samples, metatransriptomic sequencing tells them exactly what these microbes are doing. In this manner, researchers are able to sequence the full functional diversity of microbial communities.

Bioinformatic Analysis

NGS technology and services offered by Novogene provides users with millions of datapoints characterizing the genetic and functional diversity of their samples. This amount of data requires intensive bioinformatic analysis in order to successfully interpret biological realities. For 16S rRNA gene sequencing data, Novogene offers bioinformatic analysis using the established Qiime pipeline in order to classify and quantify taxa present. For metatranscriptomic sampling, Novogene also offers analyses based on Trinity suite software.

Conclusions

The advent of NGS technology has opened the door for scientists to learn about how microbes have shaped the biodiversity and evolution of life in all its forms. In the context of marine life, there is still much to explore, but many scientists have already begun to piece together the role that the microbiome plays in the evolution and ecology of fundamentally important taxa, such as sponges and corals. As further studies continue to characterize the microbiomes of hard-to-reach places, such as the deep sea, scientists will continue to improve our fundamental understanding of evolution, biodiversity, and the interconnectedness of all living organisms.

References

1. Rosenberg, E., & Zilber-Rosenberg, I. (2016). Microbes drive evolution of animals and plants: the hologenome concept. MBio7(2), 10-1128.

2. Nielsen, C. (2019). Early animal evolution: a morphologist’s view. Royal Society open science6(7), 190638.

3. Muscatine, L., Falkowski, P. G., Dubinsky, Z., Cook, P. A., & McCloskey, L. R. (1989). The effect of external nutrient resources on the population dynamics of zooxanthellae in a reef coral. Proceedings of the Royal Society of London. B. Biological Sciences236(1284), 311-324.

4. Osman, E. O., & Weinnig, A. M. (2022). Microbiomes and obligate symbiosis of deep-sea animals. Annual review of animal biosciences10(1), 151-176.