Methane Presence in Aquifers

 By: Jacqueline Martinez

In the methane and famine diagram, there is a big amount of methanotrophs demonstrated in the high methane portion. In the Gracilibacteria diagram, what is shown is growth in the two different populations of the bacteria.

Microbes found in aquifers may affect the release of methane into the atmosphere. To lessen methane emissions, methane can be broken down by microbes, which is also known as bioremediation. In a study, there were several tests made in a contaminated environment where there were different conditions to investigate methanotrophs with different gases, including nitrate, methane, and oxygen. This was made to test methanotrophic and methylotrophic populations and their response to stray gas leakage while observing the bioremediation of methane potential. According to the typical functions of a methylotroph, the observations from the study aligned with what was expected of it, and what was found was the stimulation of growth of Gracilibacteria that showed interactions between the environmental conditions and bacteria in groundwater are active and serve as evidence of the groundwater no longer being contaminated by methane. While the study by Kuloyo and colleagues found that specific microbes feed off of other sources when methane is not present, this allows for the research to be used for future studies and to have a better understanding of the functions of the microbes within groundwater.

Journal article:

Kuloyo, O., Ruff, S. E., Cahill, A., Connors, L., Zorz, J. K., Hrabe de Angelis, I., Nightingale, M., Mayer, B., & Strous, M. (2020). Methane oxidation and methylotroph population dynamics in groundwater mesocosms. Environmental Microbiology, 22(4), 1222–1237. https://doi.org/10.1111/1462-2920.14929 

Global Warming Could have Effects on Underwater Plants and its Microbes

 By. Sangwon Sloman-Moll

Figure. Significant variations of bacterial genera at the surface of seaweed collected from combination of low, ambient, and high temperature and irradiance taken from the article Beniot et al. 2021. 

  

When we think about climate change, we think about the changes that we can see on the territorial environment. However, the changes are also happening in the underwater environment. The article shows synergistic effects of temperature and light on seaweed and its epibacterial community. The research team took Taonia atomaria, a seaweed speice to check the global warming effects on the underwater plants and its microbes. The experiment was designed to check the synergistic effect of temperature and irradiance on the seaweed microbes for 14 days. As we can see in the figure, the middle part with ambient temperature and irradiance has the most microbes. The microbes’ environment provides protection, growth benefits for, and other essential functions of the plant. When the temperature and irradiance gets high the microbes' environment would not be able to stay with seaweed, the result of that would eventually kill the seaweed. Based on the research article, global warming with higher temperature and high irradiation would provide an immoblie environment for microbes on underwater plants. The plants would not survive without the microbes. The microbiome is not visible in our eyes, but it has significant functions on plants and animals; therefore, we have to look over the changes in microbiome from global warming.

Original article:

Paix, B., Potin, P., Schires, G., Le, P. C., Misson, B., Leblanc, C., Culioli, G., & Briand, J. F. (2021). Synergistic effects of temperature and light affect the relationship between taonia atomaria and its epibacterial community: a controlled conditions study. Environmental Microbiology, 2021 Sep 07. https://doi.org/10.1111/1462-2920.15758

Viruses in Wastewater Treatment Plants

 Miroslava Hernandez,

   One of the most important inovations in the world is the biotechnological application of activated sludge (AS) systems in waterwaste treatment plants (WWTPs). The AS system utilities microbes to facilitate the disinfection process by controlling the microbial communities. WWTps have enourmous amounts of microbes; however, the viral of the AS systems has not been studied enough. In a study six WWTPs in Hong Kong were used to obtain samples. Using a mentagenomic sequence, the final data showed 50,037 viral contigs, which were further analyzed and classified into 8756 viral clusters. podoviridae was among the most prevalent of the family viruses.in the study, it was also determined that these viruses affectef the microbial community of WWTPs. Basef on the results, Proteobacteria, Actinobacteria, and Firmicutes were amomh the most abundant bacteria hosts used by viruses to multiply. These findings show a rising issue in WWTPs. Viruses can alter the role of bacteria; thus, alterning the disinfection process. This is alarming because this means that communities will not get clean water for their cosumption. Having clean water is one of the best methods to prevent diseases. It is important to keep researching about WWTPs to avoid future diseases.

Yiqiang, C., Yulin , W., David, P, Martin, and Thong, Z (2021). Prokaryotic viruses impact functionai microorganisms in nutrient removal and carbon cycle in wastewater treatment plants. Nature communications 12, 5398.

Silver Shows to Assist Antibiotic in the Treatment of Infect Burn Wounds

By: Samantha Johnson

Stages of healing from mice in the study. Photo from Khalil, M. A., et al. 2021. 

This study researched the effectiveness of silver nanoparticles, Ag-NPs, combined with the different antibiotics to treat burn wounds infected with the bacteria Pseudomonas aeruginosa. Burn wound infections have a high mortality so they are a constant concern in patients that suffer from burn wounds. Many of the bacteria species, such as the P. aeruginosa, exhibit high levels of antibiotic resistance. Silver ions have been used to treat skin infections in the past but they had not previously been used in combination with neomycin. In most of the samples, the treatment of antibiotics combined with Ag-NPs showed healing. The photo above shows G6 which is the healing after the topical application of neomycin and Ag-NPs gel. G7 is healing after the topical application of neomycin and Ag-NPs spray. The other pictures are without the combination. Based off the results in this study the topical application of an antibiotic-nanoparticle spray does assist in healing burn wound infections. More research needs to be done in this field and more research needs to be done to see how nanoparticles can be used to treat other bacterial infections.

Original Article:

Khalil, M. A., El Maghraby, G. M., Sonbol, F. I., Allam, N. G., Ateya, P. S., and Ali, S.S. (2021) Enhanced efficacy of some antibiotics in presence of silver nanoparticles against multidrug resistant Pseudomonas aeruginosa recovered from burn wound infections. Front. Microbiol. 12:648560. doi: 10.3389/fmicb.2021.648560 

Viral Diversity in Hadal Biospheres

 By Karla Hinojosa

A. Diagram figure shows the locations of samples and types of samples used in the research article. B. Venn diagram figure shows the overall number of vOUTs that compose the OTVGD. C. Specific vOTUs and protein cluster percentages in seawater and sediment with the three public databases. D. Bar chart figure represents the taxonomic compositions of viruses grouped in types of samples and ocean trenches. The bars on the right side indicate the number of viral taxa in viruses. E. Bar graph figure shows the bacterial and archaeal hosts of viruses in ocean trenches. The bars located on the top and the bottom represent the ocean zone. The heatmap on the right lower side indicated the vOTUs with hosts. Figure taken from Jian et al. 2021. 

Viruses have a considerable influence and portray a big role in seawater and sediment-water. The diversity of viruses has been examined in surface water, but little to no research has been done in the hadal biosphere, the deepest section of the ocean with depths that exceed 6000 meters. The distribution, genetic characteristics, way of life, and ecological function of viruses found in seawater and sediment that inhabit the hadal biosphere were analyzed. Nineteen metagenomic samples were obtained from three Pacific Ocean trenches: Mariana, Yap, and Kermadec. From hadal ocean water and sediment samples, 108 archaeal and bacterial genomes, which included microbial isolate genomes, metagenomic bins, and single-cell genomes were collected. The Mariana Trench samples ranged from 0 to 10,500 meters deep, the Yap Trench samples were obtained from a depth of 6000 meters or deeper. To display sample locations and types, an oceanic trench viral genome dataset (OTVGD) was used. Additionally, viral contigs were categorized into virus operational taxonomic units or vOTUs. The vOTUs composed the OTGD. Three public databases, RefSeq Virus database, Global Ocean Viromes 2.0 (GOV), and IMG/VR were used in this study to investigate the novelty of OTVGD, vOTUs, and protein clustering. The link between various viruses and their hosts suggests that viruses manage microbial communities in seawater hadal biospheres. The results conclude a high number of viruses enriched in oceanic trenches have not been discovered yet. Thaumarchaeota, an archaeal phylum found in hadal environments, and Oleibacer, an abundant bacterial genus, are infected by hadal viruses. Hadal viruses were identified to adopt a lysogenic lifestyle as a result of hadopelagic water. AMGs (auxiliary metabolic genes) found in hadal virus genomes have been shown to play a role in host metabolism and biogeochemical cycles. Microbial metabolism, fatality, and nutrient recycling are all aided by viral populations in oceanic trenches, which have an impact on hadal ecosystems and overall marine life. There is further research to be done to gain a better understanding of hadal viruses. 

Jian, H., Yi, Y., Wang, J. et al. (2021). Diversity and distribution of viruses inhabiting the deepest ocean on Earth. ISME J 15, 3094-3110. https://doi.org/10.1038/s41396-021-00994-y

It's all downhill from here, antibiotic runoff that is

 By Angelica Leos

A figure showing the patterns observed of total antibiotic concentration at different sampling sites on the hillslope. The black dots are those with manure and the white dots show the control (no manure treatment). Figure taken from Zhao et al. 2020

Large amounts of antibiotics enter the soil environment through the application of animal manure in agricultural fields to improve nutrient levels. These antibiotics typically enter water sources via runoff or they are drained away from the soil by rainwater. A study by Zhao and colleagues explores the patterns of these antibiotics in the soil in response to rainfall events on a hillside scale. The researchers used a hillslope in the Zhangxi watershed where pig manure was applied in one area and another hillside was used without any manure application. The hillslopes were divided into three areas: cropland, peach orchard, and forestland. For each area, five subsamples of soil were collected and three samples of the surface were collected for each of the plots. The study found that after rainfall events, antibiotics were rich in areas where manure was applied and antibiotic concentration in the soil increased from the top to the bottom of the hills. The researchers also discovered that the soil aggregate, organic matter, and clay content played important roles in the drainage of antibiotics by rainwater. This research impacts how farmers should adapt their manure applications with respect to the type of terrain they are using in order to prevent high concentrations in their crops. 

Original article:

Zhao, Fangkai, et al. "Effects of Land Use and Rainfall on Sequestration of Veterinary Antibiotics in Soils at the Hillslope Scale." Environmental Pollution, vol. 260, 2020, doi:10.1016/j.envpol.2020.114112

Bacterial resistance genes found in Women and infants in Australia

 By: Andrea Martinez

This figure shows (A) the major and (B) the minor types of antimicrobial resistance genes that were found in the fecal samples of healthy women and infants in Australia. This is simply the overview that was found when the researchers used the shotgun metagenomics sequencing method. Figure from Guernier-Cambert et. al.

    
    Over the last couple of years, there has been a rise in the number of bacteria and other microorganisms that develop antimicrobial resistance. This has led to nearly 700,000 deaths a year due to these drug-resistant diseases. The human gut contains a large variety of bacteria which can differ due to one's age, diet, genetic background, culture, pregnancy, and a variety of other factors. Recently it was found that human gut resistomes can be diverse due to the country we live in. In this study, there were fecal samples collected from seven adults and two infants who are from southeast Australia since Australia was ranked seventh when it came to high rates of systematic antimicrobial use within the 26 European countries. The samples were collected from women that were pregnant at about their 36 week period. There were two types of sequencing methods used in this study, non-targeted sequencing: Shotgun Metagenomic Sequencing, and targeted sequencing: IonAmpliSeq Panels. With these methods, it was found that a total of 64 antimicrobial resistance genes (ARGs) are seen to be identified with the phenotypic resistance to 12 types of antibiotics. Overall the number of ARGs that were found in infants at the mean base depth per 5 million reads (BD5M) was a total mean of 13.7, this figure is significantly lower than that of what was found in adults which is a mean total of 24.4. This study is important to the general public because it provides information about how antimicrobials can become ineffective and why it is important to ensure that we always have treatments that are effective towards bacterial infections.

Reference:

Guernier-Cambert, V., Chamings, A., Collier, F., & Alexandersen, S. (1AD, January 1). Diverse bacterial resistance GENES detected in fecal samples From Clinically healthy women and infants IN Australia-A DESCRIPTIVE pilot study. Frontiers. Retrieved from https://www.frontiersin.org/articles/10.3389/fmicb.2021.596984/full.

Asgard archaeal cells and interactions of ribosomes and DNA

 By: Alejandra Pena

A. Likelihood phylogeny of Loki- and hemidallarchaeota operational taxonomic units and their related sequences from SILVA database. Specificities of FISH probes and the amount of sequence in each OTU are shown. B. Relative abundances of Loki- and Hemidallarchaeota sequences shown at different sediment depths. Figure taken from Avci et al. 2021

Asgard archaea are known prokaryotes, yet are known to be the most similar form of prokaryotes that show eukaryotic properties. This particular type of archaea shows similar genomes to signature eukaryotic proteins found in the first eukaryotic cell. Asgard archaea are very diverse, making the visualization of these cells in the environment crucial in the understanding of their structure and diversity. A primer free sequence was used in order to retrieve rRNA sequences from Loki- and Heimdallarchaeota to later design oligonucleotide probes and properly visualize cells in the marine sediments. The results show that the genomic material of both Loki- and Hemidallarchaeota detected in the cells are condensed and distinct in the riboplasm. This proved that the role of asgard archaea can be indicative of cellular compartmentalization. This method could be used in future research in order to use a reliable method of in situ imagine of rare microorganisms in environmental samples, as well as using the ultrastructure of asgard archaeal cells by using electron microscopy for insight on the complex structure of eukaryotic cells.

Reference:

Avcı, B., Brandt, J., Nachmias, D. et al. Spatial separation of ribosomes and DNA in Asgard archaeal cells. ISME J (2021). https://doi.org/10.1038/s41396-021-01098-3

Disinfectant use may endanger aquatic ecosystems

 

By: Juan Vega

 

 

Figure: the chemical structures of disinfectant by-products and their effects on aquatic organisms. Figure from Cui et al. (2021)

Disinfection is a process that is key to several industries and services in countries, as well as being an activity that has intensified due to the COVID-19 pandemic. However, many of the products used for disinfection may pose a risk in aquatic environments due to “disinfection by-products” (also known a “DBPs”) that stems from wastewater effluent. A study conducted in Tsinghua University located in Shenzhen, China tested the effects of 17 different contaminants within three groups: haloacetic acids (HAAs), haloacetonitriles (HANs), and trihalomethanes (THMs). The effects of these contaminants were tested on phytoplankton, zooplankton, as well as fish. The results of the experiment showed that all three groups of contaminants had unique detrimental effects in the health of the groups tested. Phytoplankton had its photosynthetic processes interrupted, while zooplankton experienced immobilization. Fish embryos showed abnormal development or even death at higher concentrations of these contaminants. The experiment also showed evidence for many contaminants negatively affecting a species at a much lower concentration that it would need to induce detrimental effects on others. Although disinfection of premises and equipment is necessary to prevent the spread of infectious diseases, moderation in its use can prevent further harm in already struggling ecosystems.

 

Original article:

Cui, H., Chen, B., Jiang, Y., Tao, Y., Zhu, X. & Cai, Z. (2021)  Toxicity of 17 Disinfection By-products to Different Trophic Levels of Aquatic Organisms: Ecological Risks and Mechanisms. Environ. Sci. Technol. 55 (15), 10534-10541