Microbes help plant fitness

By: Eileen Martinez

Changes in the environment, such as drought, flooding, introduction of animals, etc, often lead to evolutionary responses in organisms, and in this study, researches examine how the microbial community in soils play a role in plant changes over time in a stressed environment.  By studying the plant's response to soil moisture in both wet and dry soils, the scientists were able to measure flowering, growth, height, and fruits of the plant; nitrogen levels, ammonia levels, and carbon levels in the soil; and DNA changes in the microbes to determine the responses to the environment.  The scientists found that the microbes had rapid responses to their changing environments, and that these responses dictated/induced responses of the plants. Furthermore, the plants responded positively to the soil microbial community when the microbes had already adapted to the changes in the environment. Finally, the scientists concluded that plant adaptations to their environment is highly influenced by the microbial community in the soil and its interaction with the microbes.  This is important because it helps scientists understand the mechanisms behind organisms adapting and evolving to their environment as well as how future environmental changes will affect organisms, which in the long run can help us preserve these organisms.

Figure from Lau & Lennon (2012) depicts microbial communities effect on plant's number of flowers, number of fruits, and date of flowering in both dry and wet soil conditions over a period of time.   

Original article: Lau JA, Lennon JT. (2012). Rapid responses of soil microorganisms improve plant fitness in novel environments. PNAS Journal 109:14058-14062.

Building Design Versus Microbes

By: Melissa Saucedo

Microbes are everywhere! A recent study conducted in a hospital building showed how different methods of ventilation (mechanical and window ventilation) affected phylogenetic diversity (PD) of microbes when compared to microbe diversity found outdoors. Results showed a trend in which  PD was the highest in microbes found outdoors. Microbes found in rooms with window ventilation had intermediate PD; however, phylogeny exam showed a large similarity between microbes found outdoors to those in window ventilated rooms. Rooms with mechanical ventilation had the lowest PD and most importantly, microbes found in this rooms where largely pathogenic. This is important because it shows that ventilation systems can play a role in disease transmission in hospitals settings and at home.

Figure 1 from  Kembel et. al (2012) shows the difference in phylogenetic diversity (PD) between ventilation systems and microbes found outdoor. A significant difference was found between microbes in each setting (p<0.05).

Original article: Kembel, S.W., Jones, E., Kline, J., Northcutt, D., Stenson, J., Womack, A.M., Brendan, JM., Bohannan, Brown, G.Z., & Green, J.L. (2012). Architectural design influences the diversity and structure of the built environment microbiome. ISME Journal 6(8): 1469-1479.

Recharging aquifers with aerobic recycled water.

By: Bianca Rojas

Aquifers are anaerobic environments and are able to recharge when a rain event occurs near the recharge zone. But what if the recharge zone is fed aerobically treated recycled water? How is the microbe diversity affected? A study conducted in Western Australia conducted an assessment of the before and after microbiological counts and microbiological diversity when introducing aerobic treated recycled water into an aquifer through it's recharge zone. Even though elevated redox potentials and an increase in bacteria counts were observed, the microbiological diversity decreased as the depth increased. An increase in denitrifiers and sulfur-oxidizing populations is thought to be the reason for an increase in bacterial numbers and the decrease for microbiological diversity.

Figure from Ginige et. Al. (2013) The abundance of the 16S rRNA gene copy number of identified bacterial order relative to the total bacterial copy numbers before and after recharge.

 

Original Article:
Ginige M.P., Kaksonen A. H., Morris C., Shackelton M. Patterson B.M. (2013). Bacterial community and groundwater quality changes in an anaerobic aquifer during groundwater recharge with aerobic recycled water. FEMS Microbiology Ecology. Vol. 85. Issue 3: 553-567

Influential Microbes

Scientists from the University of California put to the test the ability of a microbial community to affect processes in estuarine sediments. They transplanted sediments from a low salinity location to a high salinity location and vice versa along the Nonesuch River. They placed the sediments in microbial “cages” to prevent microbial cross-contamination but still allowing the sediments to be exposed to the conditions of the new environment. They performed a short term experiment, which lasted a week, and a long term experiment that lasted 7 weeks. With these tests, scientists concluded that sediment processes, such as CO₂ production, CH₄ flux, nitrification, and enzyme activities resisted changes in the environment as long as the microbial composition remained the same. As microbial composition changed, functional processes in the sediments changed as well. 

Figure 1. Dialysis tubing sediment cages with PVC collars. United States quarter dollar (24.26-mm diameter) shown for scale

Original article: 

Reed, H. E. and Martiny, J.B.H. (2012). Microbial composition affects the functioning of estuarine sediments. The ISME Journal 7: 868-879.

Microbes losing themselves in Heat

Microbes losing themselves in Heat

In this article presented by Nydahl, it is shown how the coastal zone is the productive area of the marine environment. In the article it is shown how climate change, increased temperature and precipitation are expected to influence the coastal food web. This experiment used a dark bottle as an incubation to show the short – term interactive effects of changes in salinity, temperature and riverine dissolved organic matter.in this there was found to be more microbial respiration, growth and abundance in the estuarine community. In the research, it was shown that when there was an increase in temperature, there was a reduction in bacterial abundance. Essentially, the study showed that hypoxia had the probability to increase in coastal zones due to respiration enhancement that are brought on by higher temperatures.

Table 1. Experimental design, including the environmental factors and their levels
Treatment	rDOM (μM)	Salinity (g kg−1)	Temperature (°C)
1.                   The in situ temperature 12 °C, 300 μM DOC and 3 g kg−1 salinity represent current levels.
1	300	1	12
2	300	1	15
3	300	3	12
4	300	3	15
5	600	1	12
6	600	1	15
7	600	3	12
8	600	3	15

Sampling and preparation of the media and inoculum

Original Article: Nydahl A and Panigrahi S. (2013) Increased Microbial activity in a warmer and wetter climate enhances the risk of coastal hypoxia. ISME J 85: 338-347

Vampires in Marine Environment!

By: Lizzette Alvarez

    Vampire amoebae or vampyrellids feed on algae, fungi, protozoa and small metazoans. Vampyrellids are much more diverse especially in marine habitats. A complementary approach of culturing and sequence database was used with ten new vampyrellid isolates, eight from marine or brackish sediments and two from soil or freshwater sediment. Samples were placed in artificial sea water and volvic mineral water. Samples were then checked on a regular basis for any vampyrellid- looking amoebae, once they had high density of vampyrellid- looking amoebae, the plates were photographed and DNA was collected before losing them. In this study ten new stains of vampyrellid- looking amoebae were identified, some of the forms were known as Leptophrys, Platyreta, and Theratromyxa weber.

Figure 1, 2, and 3 from Berney, C. et al, 2013. shows the new strains of vampyrellid- looking amoebae that were found in the study.



 

Original Article: Berney, C. et al (2013). Vampires in the oceans: predatory cercozoan amoebae in marine habitats. The ISME Journal.

 

 

Super Bread!

Scientist from the University of Alberta have discovered a way to replace artificial preservatives in bread and even possibly making it last longer than usual. Professor Michael Ganzle and a few other researchers were able to isolate natural compounds used to maintain a loaf of bread freshness while still keeping the same flavor as if it was just made. Preservatives are used to keep bread and other products fresh for long periods of time they also can alter the flavor of food; the compounds that were isolated can be found in fermented foods and are able to keep them fresh for a longer duration just like the usual preservatives we use. The compounds discovered also may have the potential to be used in or even as fungicides which are used on crop seeds.





Reference:

University of Alberta. "Scientist bake a better loaf of bread." ScienceDaily, 25 Feb. 2013. Web. 18 Nov, 2013.

Smells like Grape?

By: Luz A. Rodriguez

Pseudomonas aeruginosa is an infamous bacterium that is a known as a pathogen and has a characteristic smell of grape when grown in vitro. Recently, P. aeruginosa made it aboard two space shuttle missions and showed growth! This innovative study tries to show the benefits and downsides of microbes in space due to the concern of decreased immunity of humans and increased virulence of microbes during space missions. The study focuses on biofilm development and physiology of this bacterial community under microgravity. Results show that spaceflight actually increased number of cells, biofilm production and thickness. The microbes even exhibited a “column-and-canopy” structure that has not been seen on Earth.

 

Figure from Kim et al. (2013) shows the difference in biofilm structure in normal gravity and under the influence of microgravity. 

Original Article: Kim, W., Tengra, F. K., Young, Z., Shong, J., Marchand, N., Chan, H., & Collins, C. H. (2013). Spaceflight promotes biofilm formation by pseudomonas aeruginosa. Plos One 8: 1-8. 

More biofuel from biofuel-waste

By Maxwell Addo

For a long term sustainability of biofuel production, there would be the need to consider producing more biofuels from glycerol, a biofuel waste. Glycerol is one of the byproducts of bioethanol production. Carbon atoms in glycerol can easily be reduced with higher efficiency to produce more bioethanol.

Several natural and engineered species of genera Escherichia, Clostridium, Lactobacillus, Bacillus, Propionibacterium and Anaerobiospirillum will be important in this new industry of fermentative metabolism of glycerol into bioethanol. Research has found out that theoretically, glycerol will produce more biofuel than the traditional fermentation of glucose.

Production of glycerol-waste from biofuel production has increased since 2004. With the view of reducing the quantity of corn use for bioethanol production in order to reduce of cost of animal feedstock (since corn is also use to feed farm animals) there is the need to consider converting more of the glycerol produced in bioethanol production from corn into more bioethanol.

 

 

 

Figure from the review by Clomburg, J M, & Gonzalez R. showing US biodiesel production and crude glycerol price (www.thejacobsen.com) published in Trends in Biotechnology Journal, January 2013 edition.

Original Article: Clomburg, J M, & Gonzalez R. (2013). Anaerobic fermentation of glycerol: a platform for renewable fuels and chemicals. Trends in Biotechnology Journal, Vol.31 No. 1

 

 

 

 

 

 

 

Food-Borne Phatogens Resistant to Disinfectants

By Luis Duron

                 Food-borne diseases are currently a dilemma in foods and food processing plants. Listeria monocytogenes causes listeriosis a rare but severe food-borne disease. Listeriosis has a fatality rate of 16% and affects primarily elderly, pregnant women, and compromised immune systems individuals. A recent study, investigated 138 isolates from foods and food processing plants, and determined different trends associated in frequency of L. monocytogenes resistance to benzalkonium chloride (BC), cadmium, and arsenic. Resistance to cadmium and BC was common among all the isolates, while, combination of resistant of arsenic and cadmium were found in only certain isolates from foods and food processing plants. Developing new disinfectants to eliminate food-borne pathogens from foods is essential, since; this recent study has shown L. monocytogenes becoming resistant to current disinfectants used in food processing plants.

Figure 1. The bar graph (Ratani et al. 2012) illustrates the serotype-associated trends of resistance to BC, cadmium, and arsenic in L. monocytogenes isolates from food and environmental sources.

Ratani SS, Siletsky RM, Dutta V, Yildirim S, Osborne JA, Lin W. et al. 2012. Heavy Metal and Disinfectant Resistant of Listeria monocytogenes from Foods and Food Processing Plants. Applied and Environmental Microbiology. 19:6938 – 6945.

 

 

Swimming toward the hydrogen: Methanococcus maripaludis

Based on the knowledge of free microbe movement in response to external stimuli, the idea of biological cells moving toward hydrogen gas has been thought before; however is still need to be demonstrated in the lab. In this study, Methanococcus maripaludis was used to measure the swimming velocity toward the source of hydrogen gas. The results suggested that methanogen reacts to hydrogen concentration. These events represent a new approach for microbes to get hydrogen gas which at the same time may influence the nitrogen, carbon and sulfide cycles.

Original Article: Brileya K. A, Connolly J.M, Downey C, Gerlanch R, Fields M.W. (2013) Taxis Toward Hydrogen Gas by Methanococcus maripaludis .Nature. 3140

Microbes: Our life-long companions

Most of the microbes that live within us are located within the gastrointestinal tract and form a mutualistic relationship. The gastrointestinal microbiota is usually stable during our adult years but once we begin aging this homeostasis starts to be affected by pathophysiological processes. Some age-related changes of the gut microbiota influence the risk of elderly to develop several diseases such as colon cancer. Pro/prebiotics are dietary supplements that target the intestinal microbiota and have been associated with health maintenance of elderly. The manipulation of this gut microbiota through the use of pro/prebiotics may be a strategy used to prevent and treat diseases as we begin aging. 

Figure from Biagi et al. (2013) shows the health impact of age-related modifications in gut microbiota composition

Original article: Biagi E, Candela M, Turroni S, Garagnani P, Franceschi C, Brigidi P (2013). Ageing and gut microbes: perspectives for health maintenance and longevity. Pharmacol Res 69: 11-20. 

Lignin-consuming Microbe Unlocks Promise for Biofuels

The extraction of cellulose sugars for the production of biofuels has always been a difficult task, due to the presence of lignin in the cell walls of plants. Lignin which is considered as being a strong, woody polymer, binds and protects the cellulose sugars which plants use for energy. However, in an effort to overcome such lignin challenge, researchers have characterized a  rainforest microbe that is able to break down such complex polymer by simply breathing it. The microbe which has been identified as E. lignolyticus SCF1 is an anaerobic bacteria which was isolated from tropical forest soils. The unique enzymatic activity of such microbe makes its capable of degrading up to 56 percent of lignin within a period of 48 hours under anaerobic conditions. The results from this study suggest that the enzymes found in E. lignolyticus SCF1 could be used to deconstruct lignin, and in exchange improve the production of advanced biofuels.

Figure from DeAngelis et al. (2013). Graph showing the degradation percentages of lignin by the bacteria E. lignolyticus SCF1. Also the SCF1 growth curves are shown in the additional graph provided.

Original Article: DeAngelis KM, Sharma D, Varney R, Simmons B, Isern NG, Markillie LM, Nicora C, Norbeck AD, Taylor RC, Aldrich JT and Robinson EW (2013) Evidence supporting dissimilatory and assimilatory lignin degrdation of Enterobacter lignolyticus SCF1. Front. Microbiol. 4:280. doi: 10.3389/fmicb. 2013.00280

The resistant sheep

The resistant sheep

by Maria Gallegos

Antibiotic use in animals and crops has yielded multi-drug resistance causing concern due to lack of efficient treatments in the future.  Agricultural use of streptomycin in apple and pear orchards in order to combat fire blight lead to a study examining the levels of resistance that developed in Escherichia coli and Staphylococcus species found in intestinal and nasal cavities of sheep.  Findings demonstrated an increase in antibiotic multi-resistance particularly in Escherichia coli of sheep grazing in orchards exposed to streptomycin.

 

Fig 1. Streptomycin-resistant E. coli isolated from sheep.  Graph shows a three month multi-drug resistance analysis of control and test group sheep concerning E. coli. 

Human use of antibiotics in the future requires careful consideration. This is the first known study conducted in sheep concerning this topic however certainly not the only species with this dilemma.

Original article by: Scherer A, Vogt H, Vilei E, Frey J, Perreten V. (2013). Enhanced antibiotic multi-resistance in nasal and faecal bacteria after agricultural use of streptomycin. Environmental Microbiology. 15(1), 297–304.