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 

 

 

Essential Oils: Nature's New Weapon Against Food Poisoning

By Ailyn De La O

Fig. The effects of essential oils on the enzymes that are engaged in the quorum-sensing pathway's degradation phases. Three kinds of enzymes can be overexpressed by some essential oils, which can impact the availability of acylhomoserine lactones (AHLs), which are signaling molecules in QS pathways.  (1) By hydrolyzing the ester bond in an aqueous environment, lactonases can open the homoserine lactone ring, preventing AHL molecules from attaching to their target transcriptional regulators and thereby facilitating quorum quenching.  (2) Oxidoreductases alter the way that AHLs interact with quorum receptors by promoting the oxidation or reduction of their acyl chain without breaking them down.  (3) To stop quorum signals, acilases hydrolyze the amide link that connects the acyl chain to the homoserine lactone ring.

The potential of plant-essential oils (EOs) and their nanoemulsions (such as oil and water) as natural food preservatives to combat dangerous foodborne pathogen proliferation in chicken and poultry meats, like Salmonella Heidelberg, and Listeria monocytogenes. What is particularly interesting is that these oils offer a tolerable and healthier alternative to synthetic preservatives and are important to enhancing food safety and shelf-life. It was found that essential oils extracted from plants such as cinnamon, clove, oregano, and rosemary are highly effective against a wide range of foodborne bacteria. This study focuses on how these EOs work by counteracting "bacterial virulence," which means they don't just kill the bacteria, but specifically interfere with the mechanisms that make them harmful.  According to research, EOs prevent to inhibit biofilm formation, a protective layer bacteria create to resist treatment, and quorum, the bacterial communication system that triggers collective attack behaviors. EOs also exert their effectiveness by disrupting bacterial cell membranes and inducing oxidative stress. By proving the effect of Eos and their nanoemulsions (ultrafine mixtures that improve stability and activity), the findings lay the groundwork for a significant shift in food preservation and safety. This can have a direct impact on food industry and agriculture, leading to a widespread adoption of natural, plant-based technologies for keeping meat, poultry, and dairy in production safer and fresher for longer, best benefiting public health. Of course, their usage in food must be carefully considered because misuse can result in toxicity, allergic reactions, and the emergence of bacterial resistance. 

Original Article:

Fidelis J, Bernardo YA de A, de Souza HCA, Conte-Junior CA, Paschoalin VMF. 2025. Modulating bacterial virulence: The role of food-plant essential oils in counteracting foodborne pathogen threats – A systematic review. International Journal of Food Microbiology. 442:111382. doi:https://doi.org/10.1016/j.ijfoodmicro.2025.111382. 

The Microbial Life on Wild Berries: A positive Influence or a Potential Health Risk?

By: Gissel De La Rosa

Distribution of bacterial microorganisms on lingonberries, rosehips, and rowanberries at phylum (A), class (B), and family (C) levels. (D) Heatmap of the most common genera of bacteria. RC, rosehip; SA, rowanberry; VVI, lingonberry. (Vepštaitė-Monstavičė et al. 2024)

In Northern Europe, wild berries like lingonberries, rowanberries, and rose hips gained recognition for their vitamins, antioxidants, and health benefits, but there is still limited information on the microbial communities of bacteria and fungi that live on them. Researchers discovered that each berry type hosts a unique population of microbes by using advanced DNA sequencing to analyze the microbes covering the fruits and grew yeasts in the lab to study them closely. On lingonberries, the main bacteria were Methylobacterium and Sphingomonas, which help protect the plant from disease and produce natural compounds that fight harmful germs. Rowanberries carried a broader mix, primarily with Sphingomonas, Hymenobacter, and Methylobacterium; microbes known for surviving in harsh conditions and possibly helping plants cope with stress. In contrast, rose hips were dominated by bacteria from the Enterobacteriaceae family and Pseudomonas, groups known to produce human infections and cause food spoilage, highlighting the need for careful handling. Regarding fungi, the populations differed. Lingonberries were mostly covered by fungi from the Exobasidium group, which attack plants. Rose hips carried fungi such as Dothiora and Aureobasidium, linked to food spoilage. Rowanberries, however, had a more diverse fungal community, including Aureobasidium and Vishniacozyma, some of which may help protect the fruit from disease. This research is vital for a better understanding of the microbial ecosystems on berries to improve handling, ensure food safety, and discover new biotechnological or health-related applications.

Original article: Vepštaitė-Monstavičė I, Lukša J, Strazdaitė-Žielienė Ž, Serva S, Servienė E. 2024. Distinct microbial communities associated with health-relevant wild berries. Environmental Microbiology Reports 16(6):e70048. doi:10.1111/1758-2229.70048

The Big Impact of the Microscopic Blueberry Farmers

By Vielka Garcia  

Figure. The negative relationship between microbial cell density and nectar 

(A) shows the negative correlation as microbial cell density in the nectar samples increases, the sugar concentration of the nectar decreases. (B) depicts the sugar concentration of nectars containing no microbes, fungi, bacteria, or both fungi and bacteria. (Rering et al., 2024)

The nectar produced by plants is often regarded simply as sustenance for pollinators; however, it can harbor communities of microbes that largely affect the yield of the plants. The nectar produced by the blueberry plant species Vaccinium corymbosum and Vaccinium myrsinites were studied to determine the frequency of microbes in the nectar microbiome. The two cultivars of V. corymbosum studied were Meadowlark and Arcadia. Meadowlark was described as a low-yielding plant and Arcadia as high-yielding. Microbes were detected in 66% of the samples, with a higher frequency of microbes in Meadowlark, 88%, compared to 38% in Arcadia. Moreover, V. corymbosum and V. myrsinites had similar nectar, both V. myrsinites and Arcadia had similar nectar glucose, and both V. myrsinites and Arcadia produced more nectar glucose than Meadowlark. The differences in microbial incidence could be correlated to many factors such as location, farm management, flower age, and pollinator attraction based on nectar concentration or fungicide treatments. The effects of nectar microbes on blueberries can be inferred using the knowledge already known on the microbes detected in the nectars. Some microbes detected have been known to be plant pathogens, while others suppress plant pathogens and even help in attracting pollinators. Furthermore, microbe incidence had a negative correlation with pollinator visitations, suggesting that the amount of microbes present can have a significant effect on blueberry yields. 

Original article: 

Rering C, Rudolph A, Li QB, Read Q, Munoz P, Ternest J, Hunter C. 2024. A quantitative survey of the blueberry (Vaccinium spp.) culturable nectar microbiome: variation between cultivars, locations, and farm management approaches. FEMS Microbial Ecology. 100(3): https://doi.org/10.1093/femsec/fiae020 

Bathyarchaeia, The Deep Sea Microbes with a Hunger for Carbon

By: Viviana Valeria Rodriguez

The figure above is from the summarized article below. 
a) Here is a depiction of the BDGT-0 chemical structure. b) The LC-MS data showing peaks that confirm Bathyarchaeia producing unique BDGT lipids, with the placement of each peak identifying the lipid and height indicating its abundance.  (Dong et al., 2025) 

    When we think about ocean life, fish and coral reefs usually come to mind, but some of the most influential organisms cannot be seen with the human eye. Bathyarchaeia, a group of microbes deep in seafloor sediments, are among the most abundant archaea on Earth. Just recently, their role and importance in the carbon cycle have been properly understood. This study demonstrates that Bathyarchaeia can absorb carbon from both dissolved inorganic carbon (CO2) and organic matter from plants like lignin. They then can convert these carbons into a unique membrane lipid called butanetriol dialkyl glycerol tetraethers (BDGTs), which are structurally different from the more common lipids made by most other organisms known as glycerol. This dual strategy of two different resources allows them to be highly adaptable in nutrient limited environments. The importance of this discovery lies in how it reshapes our understanding of the carbon cycle. By recycling both "fresh" and "old" carbon into their cell structures, Bathyarchaeia play a crucial role in long term carbon storage in marine sediments. The distinctive lipids that they possess may also serve as a biomarker. Biomarkers help scientists track microbial activity in oceans and readjust carbon cycling in old environments. In short, these hidden microbes serve as powerful recyclers that silently impact Earth's climate system, reminding us that big change can come from the smallest things. 

Original article:

Dong, L., Jing, Y., Hou, J., Zhou, J., Yu, T., Chen, S., Liang, L., Zhu, P., Zhu, P., Zhao, X., Hinrichs, K.-U., & Wang, F. (2025). A dominant subgroup of marine Bathyarchaeia assimilates organic and inorganic carbon into unconventional membrane lipids. Nature Microbiology.
https://doi.org/10.1038/s41564-025-02121-5

Environmental Pathway of Superbugs: Antibiotic Resistance Flowing through City Streams

 By Osvaldo J. Salazar

Fig 1. Study sites in Durban and Pietermaritzburg in South Africa, where surface water is near informal settlements.  

        As new antibiotics are becoming more challenging and expensive to manufacture, the emergence of antibiotic resistance (ABR) continues to become a global public health emergency that places an immense financial burden on the healthcare industry. The article focuses more on the harmful, antibiotic-resistant bacteria (ARB) that have spread throughout surface water (rivers and streams) close to two cities – Durban and Pietermaritzburg, South Africa – in informal settlements. The two types of bacteria that the article discussed were Escherichia coli (E. coli) and Enterococcus faecium. In this instance, the bacteria were carrying antibiotic-resistant genes (ARG) that make them non-susceptible to antibiotics, and they can cause serious illnesses, especially among those living in informal settlements. Researchers identified different strains of E. coli and E. fecium isolates that were susceptible and resistant, as well as related to other isolates in the waterways of both cities. This is important because the study highlights how these superbugs might threaten public health due to reservoirs of multi-resistant microorganisms that can infect humans and animals through tainted water and food from irrigated crops. However, the study also points to the potential for change. We can drastically lower the danger of ABRs in surface water and stop increasing antimicrobial infections by addressing poor waste management, sanitation, and access to proper facilities. 

Original Article:

Mukwevho FN, Mbanga J, Bester LA, Ismail A, Essack SY, Abia ALK. 2025. Potential environmental transmission of antibiotic-resistant Escherichia coli and Enterococcus faecium harbouring multiple antibiotic resistance genes and mobile genetic elements in surface waters close to informal settlements: A tale of two cities. Science of the Total Environment 976:179321.

Microbes vs. Neurotoxic methylmercury in farmlands and rice

 By: Ebie Rodriguez

The figure shows A and B graphical summaries of the microbial degradation of CH3Hg+concentration and the efficiency in C and D (Zhou et al. 2025).

Methylmercury is a neurotoxin produced from microbial conversion of inorganic mercury in rice paddy soils, which can accumulate in rice grains. Paddy and upland rotations are common in cropping systems that contribute CH3Hg+ to both soil types. This study aims to provide experimental evidence of the specific microbial taxa responsible for active CH3Hg+ degradation within the natural environment. The soil samples were collected from two agricultural regions known for Hg+ hotspots in Wanshan, Southwest China. The extent of degradation depended on the soil types, the initial background Hg levels, and ^13C enrichment to identify microbes involved in ^13C enrichment. After 28 days of incubation, the soils of high Hg-contaminated sites, paddy soil, High-P, and upland soil, High-Up, were calculated to have degradation efficiencies of CH3Hg+ were 86% and 37%, respectively, as illustrated in the figure above. The degradation efficiencies in the paddy soil (Low-P) and upland soil (Low-U) CH3Hg+ were 40% and 64%, respectively, as illustrated in the figure above. After using the 16S rRNA genes to determine the microorganisms degrading the ^13CH3Hg+, Xanthomonadaceae, Xanthobacteraceae, and Comamonadaceae were dominant families enriched in the ^13CH3Hg+ treatment in both High-P and Low-U soils. Overall, this study demonstrates the significant role of soil microorganisms in reducing the CH3Hg+ exposure risk to humans and wildlife.  

Original article:

Zhou X-Q, Chen K-H, Yu R-Q, Yang M, Liu Q, Hao Y-Y, Li J, Liu H-W, Feng J, Tan W, et al. 2025. Microbial potential to mitigate neurotoxic methylmercury accumulation in farmlands and rice. Nature 
Communications. 16(1). doi:http://doi.org/10.1038/s41467-025-60458-1. [accessed 2025 Sep 26]. https://www.nature.com/articles/s41467-025-60458-1#Fig1.

Oil-Degrading Microorganisms Join Forces with Spill Treating Agents to Fight Oil Spills!

by: Francheska Nicole Rodriguez 

Figure 1. Biodegradation rates by ANS, ANS+Cytosol, and ANS + Thick Slick treatments on (a) Total alkanes, (b) total PAHs, (c) alkanes C30-C35, (d) EPA Priority PAHs monitored by quantifying the remaining concentrations of pollutants over time. 

                    

When most people think about the Deepwater Horizon Spill, they might think or say to themselves, “Yes! It was a long time ago. What happened again?”. This question can expose that the general public is not aware of the  environmental impacts this oil spill had 15 years later. Environmental impacts of oil spills are detrimental because it increases the concentration of environmental pollutants such as n-alkanes and polycyclic aromatic hydrocarbons (PAHs). One of the most significant advances towards combating these pollutants includes bioremediation which uses microorganisms to reduce the concentration of hazardous wastes in the environment. A study by Kiara L. Lech and colleagues determined if spill treating agents (STAs) or if a family of microorganisms, Sphingomonadaceae and Rhodobacteraceae, facilitated the degradation of oil pollutants at better rates. They conducted their study by monitoring N-alkane and PAH degradation rates using  three treatments of Alaskan Northern Crude Oil (ANS) incorporated with an oil-degrading microorganism and a STA. The control, ANS stand alone, did not contain a STA. Surprisingly, results showcased PAHs and n-alkanes were degraded at higher rates by a treatment that contained a STA and oil-degrading microorganism. These findings highlight the importance of using oil degrading microorganisms and STAs together in order to amplify biodegradation rates. Considering this, the next time someone brings to remembrance an oil spill that occurred, one can ask themselves a different question and think, “What bioremediation methods are being used to treat it?”

Lech KL, Sundaravadivelu D, Grosser RJ, Trutschel LR, Brinkman NE, Conmy RN. 2025. Oil spill surface washing agents and chemical herders drive microbial community structure impacting biodegradation. Appl Environ Microbiol. 91(5):e0233424. [about 16 p.]. https://doi.org/10.1128/aem.02334-24 

More Than Just a Fungus, a Cleanser: Ustilago maydis

 By: Leah Lopez

              

           The figure shows corn smut, a fungus that grows onto the outside of corn. Photo taken by John Cowell/Grant Heilman Photography

Ustilago maydis is typically known as corn smut and is used for dishes in some Mexican cuisines. However, it has been shown to have other beneficial qualities to it that can help industries. Ustilago maydis can create compounds that are surface-active and antimicrobial in nature. Due to these properties, which are derived from the compounds mannosylerythritol lipids (MELs) and cellobiose lipids (CBLs), they can be used to make a non-toxic, beneficial, and effective alternative to the harsh antimicrobial cleaners that are used today. In order to obtain the desired amount and effect of the compounds, special steps are taken to get max efficiency and output. To do this, a two strategy growth process was used to help biomass formation in both compounds. The first strategy was to put the samples under neutral pH and nitrogen dense conditions. The second strategy used was to put the same samples under a  glycolipid pandering environment. These strategies had a much better output compared to a single step strategy, helping MELs to a 190% increase and a 108% CBL increase. Something interesting that was discovered is that sugarcane molasses could be used as an alternative carbon source for growth. This further goes to show that there is a possibility that other forms of industrial waste can be used to help aid in the research of using Ustilago maydis as a source needed to create the alternative to harsh cleansers, all the while lowering the build-up of industrial waste. 

Original article:

    

Valkenburg AD, Teke GM, Eugéne van Rensburg, Pott RWM. 2025. Harnessing industrial waste for the co-production of mannosylerythritol and cellobiose lipids by Ustilago maydis. Biomass and Bioenergy. 197:107812–107812. doi:https://doi.org/10.1016/j.biombioe.2025.107812

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The Chesapeake Bay Bacteria You Didn’t Know About

 

Fig: These graph shows how V. parahaemolyticus levels in the Chesapeake Bay change with salinity, water clarity, and temperature across different seasons. Warmer and cloudier waters generally support more bacteria.

Have you ever wondered why eating raw or undercooked seafood sometimes makes people sick? One reason is a bacterium called Vibrio parahaemolyticus which is naturally occurring in brackish and marine waters and is one of the leading causes of seafood borne illnesses. A 2017 study led by Benjamin J.K. Davis explores what environmental conditions promote or limit this bacterium in the Chesapeake Bay's Water. They collected various water samples from various spots across four years. They tested these samples for things like temperature, saltiness (salinity), cloudiness (turbidity), and oxygen levels. Moreover, they checked if the versions that cause food poisoning were present. What they found was that V. parahaemolyticus thrives in warm, cloudy water, and it struggles to survive in saltier water. However, salt is not a big factor if the water is already warm or murky. Something interesting was that most water samples that contained this bacterium did not contain the genetic markers that cause virulence, meaning that the bacteria is not considered a harmful strain. Researchers noted, though, that figuring out how and when it becomes virulent is still an ongoing investigation. They also pointed out that shellfish can carry high levels of the disease-causing strains. This study is important because it shows how environmental conditions in the Chesapeake Bay influence the growth of V. parahaemolyticus. This can later be used to predict when seafood might be riskier to eat, helping protect both people who enjoy seafood and the industries that depend on it.

Article:

Davis BJK, Jacobs JM, Davis MF, Schwab KJ, DePaola A, Curriero FC. 2017. Environmental Determinants of Vibrio parahaemolyticus in the Chesapeake Bay. Applied and Environmental Microbiology. 83(21). doi:10.1128/aem.01147-17. https://doi.org/10.1128/aem.01147-17.

Identification of Aerobic and Anaerobic Bacteria in Tattoo and Permanent Makeup Inks

By: Kenya Dominguez

Figure 1 illustrates a co-occurrence network of 36 bacteria from tattoo and PMU inks where red is pathogenic and green is non-pathogenic. This Figure was taken by Yoon et al. 2024.

Tattoo and permanent makeup (PMU) inks are man-made products that are utilized to apply pigment, which is inserted into the dermis of the skin permanently. Over the past years, these products have gained recognition and popularity, leading to reports of ink-related infections (Yoon et al. 2024). For this reason, microbial contamination is the major contributor to tattoo and PMU ink. This research was the first to examine the presence of both aerobic and anaerobic bacteria in tattoo and PMU inks. The results of this study indicate that both aerobic and anaerobic bacteria were present in opened and sealed inks from different manufacturers and even those labeled as sterile. Furthermore, the study tested 75 tattoo and PMU inks from 14 different manufacturers. These inks were examined using serial dilution methods and agar plating into 3 different agars: Anaerobe agar (no oxygen), Blood agar (low oxygen), and Modified Letheen Agar MLA (atmospheric oxygen). As a result, 26 out of the 76 ink samples were contaminated with 34 bacterial isolates. The 34 bacteria isolates were categorized into three groups based on their different growth conditions. For instance, group 1 contained six bacteria isolates with anaerobic growth patterns, such as obligate anaerobic C. acnes and facultative anaerobic S. epidermis. Whereas,  Groups 2 and 3 are composed of 28 oxygen-requiring bacteria (aerobes) such as P. putida, S. saprophyticus, and S. maltophilia (Yoon et al. 2024). Overall, determining the anaerobic and aerobic bacteria in tattoo and PMU inks can improve contamination hazards and future microbial research.

                                  Article:

Yoon S, Kondakala S, Foley SL, Moon MS,Huang MJ, Periz G, Zang J, Katz LM, Kim S,Kweon O.2024.Detection of anaerobic and aerobic bacteria from commercial tattoo and permanent makeup inks. Appl Environ

The Disruption of Ecosystem Dynamics Due to Biological Anomalies

 By Janitssa Rodoli

This photo displays a variety of phenological anomalies; i.e., plants blooming in their off season. Photo Credit: Living things are showing increasing anomalies in their seasonal activity, which could disrupt the dynamics of biodiversity and ecosystems

Global warming and climate change are topics often spoken about with a sense of urgency, and for good reason. It has been made clear that the past decade, circa 2015, has increasingly become hotter temperature-wise. The article discusses the sudden abnormal shift in the blooming of flowers and other vegetation in their respective ecosystems, and the greater consequences this could bring. Ecosystems are made up of more than just plants, containing other living inhabitants including humans, animals, and insects. Early blooms of flowers in the Fall, for example, could spell trouble for certain crops that grow perennially and require specific pollinators to produce. Researchers observed flowers and plants blooming later than expected during the Winter season, and deduced they would be more vulnerable to pathogen and herbivore attacks as they would be weaker structurally. The desynchronization affects humans in the aspects of health, agriculture, and ecotourism as well. The way we tolerate pollen, the food we consume, and the economic tourism drawn in from cherry blossom viewing become just a few aspects of life that could change if these conditions continue to occur. Researchers are still unsure as to how long this change could last, but call for more monitoring and analysis of ecosystems in order to gain more of an understanding of this phenomena.

Original Article: Chuine, I., Garcia de Cortazar-Atauri, I., Jean, F. et al. Living things are showing increasing anomalies in their seasonal activity, which could disrupt the dynamics of biodiversity and ecosystems. Sci Rep 15, 32860 (2025). https://doi.org/10.1038/s41598-025-16585-2

Koji fermentation: The Moldy Microbes That Make Chocolate And Relations All The Sweeter

By: Lorena Celest Razo 

This image is of the fermentation process cacao goes through with koji yeast before becoming chocolate
picture by: https://www.tandfonline.com/doi/figure/10.1080/15528014.2024.2447663?scroll=top&needAccess=true

    Koji is a mold spore that is commonly used in fermentation. This article will cover how the use of mold spores is being implemented to enhance flavors. Koji is an often found in some Japanese cuisines such as miso and sake, but this mold sore has grown in popularity due to being named the “powerhouse of enzymes” due to its high concentration of amylase and proteases. In this experiment Koji is being used in the fermentation of cacao, conventional chocolate relies on bacteria that is acid producing along with yeast to make cacao into the chocolate. The koji fermentation process relies on the fungus being directly introduced to the cacaos pulp by being sprinkled onto the beans and left to ferment with banana leaves until made into chocolate. Koji fermented coffee which in India was the starting point with a few experiments until the thought of koji covered cacao was brought up, it was the perfect blend of Japan and India being able to connect. Although the introduction to the public was a shaky one with koji being an unfamiliar term and mold, it was also known as the “a magical microbe” giving the final product of koji chocolate its wonderful flavor profile. Koji though a mold lives up to its magical microbe name as it has elevated tastes, helped reduce waste in other products such as mayo, and have even helped with not only cultural-economic relations but human-microbe relations as well just through their enzymatic work in chocolate alone. 

Original Article: 

Hey M, Michael E. 2025. “A Whole New World of Possibilities”: Koji Uses and Ambiguities on the Global Marketplace. Food, Culture & Society. 28(2):365–386. doi:10.1080/15528014.2024.2447663. https://dx.doi.org/10.1080/15528014.2024.2447663.

Greenspaces in Dry Cities: How Landscaping Shapes Microbial and Viral Communities

 By: Francisco Montaner

This image illustrates an urban greenspace. Picture by: https://www.scientificamerican.com/article/cities-pledge-more-green-space-to-combat-urban-heat

Urban greenspaces are open space areas that provide natural or landscaped environments within cities, such as parks and gardens, offering ecological, social, and health benefits to residents. However, in arid environments these greenspaces are designed using a global model which are not suitable for arid environments. These models when applied potentially affects microbial communities and favors certain genes. In this experiment, the authors will assess bacterial and viral genomic data to determine difference within both environments. The authors collected soil samples from two urban parks and twelve ecosystem-representative sites. They then extracted DNA from these samples and were sequenced for bacterial and viral characterization. The results showed that viral abundance was higher in natural soils; however, the ratio of virulent to temperate viruses was slightly higher in urban soils. On the other hand, bacteria in urban soils had overall smaller genome sizes, and the abundance of heavy metal resistance genes was higher compared to natural soils. Contrary to this, the abundance of antibiotic resistance genes was not marginally different between both urban and natural soils. Additionally, in urban soils bacterial DNA had a higher abundance of denitrification genes than natural soils. This research is important because it highlights how bacteria and viruses differ between natural and landscaped environments, and how human activity can influence the way these communities are shaped.

Original article :

Touceda-Suárez M, Ponsero AJ, Barberán A. 2025 Jul 15. Differences in the genomic potential of soil bacterial and viral communities between urban greenspaces and natural arid soils. Spear JR, editor. Applied and Environmental Microbiology. doi:https://doi.org/10.1128/aem.02124-24.