The Soil's Secret DNA

 The Soil's Secret DNA

Soils are among the most microbially diverse ecosystems on Earth, but most of the microbes living in them remain invisible to science because they cannot be cultured in the lab. A recent study in Environmental Microbiome highlights how new sequencing strategies can help overcome this challenge, bringing us closer to understanding the hidden roles of soil microbes. Researchers compared different approaches to reconstruct microbial genomes directly from complex soil samples, using cutting-edge sequencing technologies. Traditional short-read sequencing often struggles with the enormous diversity and uneven abundance of microbes in soils, making it hard to piece together full genomes. To address this, the team used hybrid methods that combine long-read and short-read data, plus advanced assembly pipelines. The result was higher-quality genomes, including from previously unknown microbial groups. Why does this matter? Soil microbes regulate critical processes like nutrient cycling, carbon storage, and plant health. By improving how we recover and analyze their genomes, scientists can better predict how soil communities respond to climate change, pollution, or farming practices. This work doesn’t just fill in gaps in our microbial “map” of soils — it opens the door to discovering novel metabolic pathways that could be applied in agriculture, biotechnology, or environmental restoration.

Figure 1: . Percent of metagenomic reads from soil and human samples mapping to the GEM and NCBI RefSeq databases as a function of Nonpareil k-mer diversity. Human microbiomes exhibit lower diversity and higher mapping rates (50–90%), whereas soil metagenomes are highly diverse with <5% of reads mapping, underscoring the limited genomic representation of soil microbes in current databases

Citations

Diamond, S., Crits-Christoph, A., Van Goethem, M. W., Simmons, S. L., Brown, C. T., Anantharaman, K., et al. 2024. From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology. Environmental Microbiome 19:69. https://doi.org/10.1186/s40793-024-00599-w

Microbes Solving Time-of-Death Enigmas

 By: Ashly M. Gutierrez

Figure 1. This image represents different viral families and the relationship between abundance and the amount of time taken for decomposition of rat cadavers.

Microbes play a significant role on a daily basis, at every corner, even in the decomposition of cadavers. This article, Yu 2025, proves that viruses are able to release nutrients and other components by being able to lyse or lysogenize the bacterial host. This helps accelerate the decomposition process by being able to understand the interactions among bacteria, viruses, and the nutrient cycle. A metagenomic analysis was performed to observe the viral succession over a 35-day period of the decomposition of rat cadavers which emphasized the abundance of microbes. The addition of different viral family biomarkers allowed the analysis to view the the PMI, postmortem interval, to identify and track changes in the microbial population towards the cadavers. The initial phase of decomposition demonstrated an increase in microbial abundance which may have been associated with the addition of resources produced by the cadavers. As more days went by the decline of microbial abundance was viewed to decline which may have been due to resources decline. Overall, being able to understand how microbes are able to decompose, act as a postmortem interval to specialized individuals that record decomposition, understand the components and resources required, and the relationship between viruses and bacterial hosts help have a better understanding for future and much larger projects instead of rat cadavers.

Original Article: Yu D. 2025. Viral community succession during cadaver decomposition and its potential for estimating postmortem intervals. Appl Environ Microbiol. doi:10.1128/aem.01453-25.

Natural Rocks are Richer in Microbial Communities than in Playgrounds

Fig 1. The gene copy numbers sampled from dust and dirt from artificial rubber mats (blue) and natural rock (red). The solid outline boxes are 16S rRNA gene copy in all samples and the dotted boxplots are paired samples. The mean is the midline and the upper and lower hinges are the minimum and maximum in order. This figure shows that natural rocks have a higher gene copy than the sampled rubber mat from playgrounds. https://doi.org/10.1128/spectrum.01930-24

The playground environment stresses microbial communities that contribute to the risk of immune-mediated diseases. Children are more at risk of infection by poor microbial communities in playgrounds. In this study led by Juulia Manninen and other researchers, tested a total of 20 dirt and dust samples gather from 9 natural rocks and 19 playgrounds in Finland cities of Helsinki and Lahti. The natural rocks from dry natural habitats were used in this study were biotite paragneis, microcline granite, or quartzite. The rubber mats were made of steryene-buadiene and ethylene propylene diene monomer rubber. In their experiments they analyzed bacterial communities by using Illumina MiSeq 16S rRNA gene metabarcoding. They found that the 16S rRNA gene copy numbers were higher than the sampled rubber mats. Additionally, there was a more pronounced contrast when the mean values were in paired samples as shown in Fig.1. The importance of this study is to understand and be aware that playgrounds with poor microbial communities are creating avoidable situations that can be managed with proper strategies. Such as introducing rich organic soil and a diversity of vegetation. This certain introduction can increase the quality of children's immune system. Some concerns regarding this situation are that children being affected with immune-mediated diseases can develop antibiotic resistance from the antibiotics they are prescribed. Antibiotic resistance will become a challenge for treating immune-mediated diseases in the future.

Original article:

Manninen J., Saarenpaa M., Roslund M., Galitskaya P., Sinkkonen A. 2025. Microbial communities on dry natural rocks are richer and less stressed than those on man-made playgrounds. Microbiology Spectrum 13(5):1930 https://doi.org/10.1128/spectrum.01930-24

Window’s Within: Underground Microbial Diversity of Earth

 By Juanita Gonzalez

 Figure 1: Time-lapsed images of soil microorganisms encapsulated in microfluidic droplets.(Adapted from Dai et al.2025)

            Soil microbes were grown inside microfluidic droplets over 14 days. The images show how different culture media affected microbial growth, highlighting that the droplet method helps cultivate a wide variety of soil bacteria.

        In today’s World microbes are vital to everything we know today. From planting and growing food to curing and finding medicine for sickness, microbes aid in all aspects. Most microbes known by science are grown in a laboratory to be studied. Scientists, approximate 1% of microbes can be grown using typical batch culture. This implies that there is vital information on accounted for.

        In a study published in 2025, Dai’s team performed a new approach in soil microbes they believed would count for the 1% that usually go unobserved. They began using droplets of water to act like test tubes to hold microbes then to make this replication more ecologically precise they mimic the underground surroundings with the soil nutrients and other compounds microbes would encounter. Within water, microbes were free from competition and had controlled space. After growth scientist determined the bacteria present using sequencing. The results depicted 1.5 more species of microbe richness with more than 1.7 unique phyla And 11 more unique genrera compared to bulk culture. 

        This gives us a rare glimpse into the world of Microbial species of untypicality. By having access to these microbes, scientist can uncover mysteries surrounding these non-typical microbial. The next steps would be the application of this technique being Applied to various soils, then determining how certain functions apply to which microbe and focusing studies across ecosystems entirely of unseen, microbial diversity. This could change how we understand microbes and it’s use in climate, agriculture, technology and drug development.

Original Article:

Dai J, Ouyang Y, Gupte R, Liu XJ, Li Y, Yang F, Chen S, Provin T, Van Schaik E, Samuel JE, Jayaraman A, Zhou J, Han A. Microfluidic droplets with amended culture media cultivate a greater diversity of soil microorganisms. Appl Environ Microbiol. 91: e01794‑25 (2025).

Benefits of a social life: how it can help you when your microbiomes are wiped out!

By: Ximena Garcia 

There was an experiment done in Africa with gazelles on whether a difference between having a social life and not could affect if microbiomes grew in their stomachs. 

These researchers gave antibiotic shots to gazelles while also leaving some untreated. With time, they observed what animals were more social and which were more solitary. During this experiment, the researchers collected fecal samples of, before, 2-3 weeks after, and 1-3 months after the shot, to see how stomach microbes would change. 

Gazelles with a social life were able to gain their microbes back quicker than those who spent time alone. But, they found that this mix of microbes was different. 

Fig 2. Graph showed microbes change with time in 

gazelles' stomach who were treated vs. ones who weren't 

We use antibiotics when we’re sick, where medicine can also wipe out our good microbes that help us with digestion and the immune system. This study shows that being social is beneficial. It could help with recovery, but the new growth microbes will be different than before, who knows, maybe they're even stronger.

Citations: 

Brown BRP, Kalema-Zikusoka G, Abrahms B, Macdonald DW, Seidel DP, Lloyd-Smith JO, et al. 2024. Social behaviour mediates the microbiome response to antibiotic treatment in a wild mammal. Proc R Soc B. 291:20241756. https://doi.org/10.1098/rspb.2024.1756

Image from Brown BRP, Kalema-Zikusoka G, Abrahms B, Macdonald DW, Seidel DP, Lloyd-Smith JO, et al. 2024. Social behaviour mediates the microbiome response to antibiotic treatment in a wild mammal. Proc R Soc B. 291:20241756. https://doi.org/10.1098/rspb.2024.1756

Enter Enterobacter to delete plastic pollution

 By Julia Amerith Flores 

Selvakumar Santhosh, Jayaraman Narenkumar, Kayeen Vadakkan, Nandini MS, Aruliah Rajasekar, Rajaram Rajamohan. 2025. Enterobacter hormaechei mediated biodegradation of PET: a sustainable approach to plastic waste. Biodegradation. 36(5).https://doi.org/10.1007/s10532-025-10183-9 

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Figure (1) shows how untreated PET (a) looks vs the crystalline changes that happen after it was treated with the bacteria (b) from 

Selvakumar Santhosh, Jayaraman Narenkumar, Kayeen Vadakkan, Nandini MS, Aruliah Rajasekar, Rajaram Rajamohan. 2025. Enterobacter hormaechei mediated biodegradation of PET: a sustainable approach to plastic waste. Biodegradation. 36(5).https://doi.org/10.1007/s10532-025-10183-9 

Plastic pollution is notoriously hard to get rid of within the environment. Enter Enterbacter hormaechei, who has the ability to biodegrade or breakdown a type of plastic known as PET (polymer polyethylene terephthalate). Bacteria, like all living things, need a carbon source to have energy. E. hormaechei is able to use the plastic to do so by excreting an enzyme that breaks down the hydrogen bonds within the plastic. The bacteria is able to create biofilms on the plastic, which means that they are able to grow on the plastic without needing an alternate source for energy. This gradually breaks up the edges of the plastic and even suggests that the bacteria make the plastic brittle and more prone to further degradation. The bacteria break down the plastic by modifying the molecular structure, specifically by using it as a carbon source. This was observed through several different ways; spectroscopy, particle size analysis, and X-ray. These techniques tell through various ways if the plastic has been affected; rearrangements in the atomic structure, bonds breaking or forming in the chemical structure, and if it changes sizes. This is important because plastic is a serious pollutant. It takes a very long time to break down naturally and most of the time, negatively affects the ecosystems it pollutes. Perhaps, E. hormaechei may help remedy the issues that plastic pollution presents.

Does Plastic Make E. coli Stronger? Effects of Microplastics on Escherichia coli Antibiotic Resistance

By Miguel Rubio

Why are microplastics becoming common in today's world? The answer is that humans discard a lot of plastic. With time, plastic breaks into smaller pieces, eventually becoming microplastics. There has been discussion of the potential harm of microplastics. However, Boston University performed research that poses a new question: can microplastics be beneficial to some organisms? Based on an experiment conducted by the university, they found that exposing Escherichia coli to microplastics (polyethylene, polystyrene, and polypropylene) of various sizes and concentrations led biofilm-attached cells to become more antibiotic resistant than those grown on control surfaces such as glass. Microplastics were effective at proliferation and resistance, likely due to their characteristics which include their hydrophobic nature, adsorptive surfaces, and surface chemistry. The bacteria that grew as biofilms on plastic surfaces became resistant to multiple antibiotics, even when no microplastics were present during growth. The effect depended on the plastic’s properties and size, with polystyrene spheres and higher particle numbers generally increasing resistance. The researchers suggested that plastics provide protected surfaces, promoted increased biofilm sizes, and alter how antibiotics make contact with cells. This study has implications for treatment in healthcare as the interactions between the antibiotic resistant bacteria and microplastics can be used to develop effective strategies to address the challenges posed by MPs increasing antibiotic resistance.

 

 

Figure 2. Displaying increase in resistance to antibiotics (ampicillin, ciprofloxacin, doxycycline, and streptomycin) in media containing microplastics (MPs).

References:

Gross N, Muhvich J, Ching C, Gomez B, Horvath E, Nahum Y, Zaman MH. 2025. Effects of microplastic concentration, composition, and size on Escherichia coli biofilm-associated antimicrobial resistance. Appl Environ Microbiol. 91(4):e02282-24. https://doi.org/10.1128/aem.02282-24