Bioremediation of contaminants by plants

Bioremediation of contaminants by plants

https://www.bbc.com/earth/story/20141111-plants-have-a-hidden-internet Introduction Whenever you see oil rigs or pollutants cover the soil, you must be pondering how much of a deal contaminants are to the environment. To put it into perspective, oil spills that come from industrial activities such as petroleum engineering and waste disposal is a problematic global issue for the environment. The conventional …

Mycoremediation potential of Pleurotus species for heavy metals: a review

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Abstract
Mycoremediation is one of the biotechniques that recruits fungi to remove toxic pollutants from environment in an efficient and economical manner. Mushrooms, macro-fungi, are among the nature’s most important mycoremediators. Pleurotus species (also called oyster mushrooms) are considered to be the most popular and widely cultivated varieties worldwide and this might be attributed to their low production cost and higher yields. Apart from their nutritive and therapeutic properties, Pleurotus species have high biosorption potential due to their extensive biomass, i.e. mycelial production. The genus has been reported to accumulate high levels of heavy metals. The current state-of-the art review mainly summarizes previous investigations carried out by researchers on different roles and mechanisms played by Pleurotus species on heavy metals mycoremediation.
I chose this paper because mycoremediation methods for removing contaminants have shown promise, at least in a similar fashion to phytoremediation. It is also because this article does a thorough job in explaining how and why they are able to absorb heavy metals from the soil and those contaminants are eventually accumulated into the fungi.
Kapahi, Meena, and Sarita Sachdeva. “Mycoremediation Potential of Pleurotus Species for Heavy Metals: A Review.’ Bioresources and Bioprocessing 4.1 (2017): 32.

Biodegradation of imidazolium ionic liquids by activated sludge microorganisms

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Biodegradation of imidazolium ionic liquids by activated sludge microorganisms
Abstract
Biological properties of ionic liquids (ILs) have been usually tested with the help of standard biodegradation or ecotoxicity tests. So far, several articles on the identification of intermediate metabolites of microbiological decay of ILs have been published. Simultaneously, the number of novel ILs with unrecognized characteristics regarding biodegradability and effect on organisms and environment is still increasing. In this work, seven imidazolium ionic liquids of different chemical structure were studied. Three of them are 1-alkyl-3-methyl-imidazolium bromides, while the other four are tetra- or completely substituted imidazolium iodides. This study focused on the identification of intermediate metabolites of the aforementioned ionic liquids subjected to biodegradation in a laboratory activated sludge system. Both fully substituted ionic liquids and 1-ethyl-3-methyl-imidazolium bromide were barely biodegradable. In the case of two of them, no biotransformation products were detected. The elongation of the alkyl side chain made the IL more susceptible for microbiological decomposition. 1-Decyl-3-methyl-imidazolium bromide was biotransformed most easily. Its primary biodegradation up to 100 % could be achieved. Nevertheless, the cleavage of the imidazolium ring has not been observed.
I thought that this paper would be fun to examine since the methods of wastewater treatment is such an important topic to society.
Liwarska-Bizukojc E, Maton C, Stevens CV. Biodegradation of imidazolium ionic liquids by activated sludge microorganisms. Biodegradation. 2015;26(6):453-463. doi:10.1007/s10532-015-9747-0.

Resource Recovery from Wastewater by Biological Technologies: Opportunities, Challenges, and Prospects

 Abstract
Limits in resource availability are driving a change in current societal production systems, changing the focus from residues treatment, such as wastewater treatment, toward resource recovery. Biotechnological processes offer an economic and versatile way to concentrate and transform resources from waste/wastewater into valuable products, which is a prerequisite for the technological development of a cradle-to-cradle bio-based economy. This review identifies emerging technologies that enable resource recovery across the wastewater treatment cycle. As such, bioenergy in the form of biohydrogen (by photo and dark fermentation processes) and biogas (during anaerobic digestion processes) have been classic targets, whereby, direct transformation of lipidic biomass into biodiesel also gained attention. This concept is similar to previous biofuel concepts, but more sustainable, as third generation biofuels and other resources can be produced from waste biomass. The production of high value biopolymers (e.g., for bioplastics manufacturing) from organic acids, hydrogen, and methane is another option for carbon recovery. The recovery of carbon and nutrients can be achieved by organic fertilizer production, or single cell protein generation (depending on the source) which may be utilized as feed, feed additives, next generation fertilizers, or even as probiotics. Additionlly, chemical oxidation-reduction and bioelectrochemical systems can recover inorganics or synthesize organic products beyond the natural microbial metabolism. Anticipating the next generation of wastewater treatment plants driven by biological recovery technologies, this review is focused on the generation and re-synthesis of energetic resources and key resources to be recycled as raw materials in a cradle-to-cradle economy concept.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5216025/
Puyol D, Batstone DJ, Hülsen T, Astals S, Peces M, Krömer JO. Resource Recovery from Wastewater by Biological Technologies: Opportunities, Challenges, and Prospects. Frontiers in Microbiology. 2016;7:2106. doi:10.3389/fmicb.2016.02106.
I thought that this paper was very cool to read because being able to recover materials from waste water in relation to microbial communities would prove to be crucial in the future.
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Microbial Community Profiles in Wastewaters from Onsite Wastewater Treatment Systems Technology

 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4725721/

JaÅ‚owiecki, Łukasz et al. “Microbial Community Profiles in Wastewaters from Onsite Wastewater Treatment Systems Technology.’ Ed. Andrew C Singer. PLoS ONE 11.1 (2016): e0147725. PMC. Web. 15 Feb. 2018.

Summary

The aim of the study was to determine the potential of community-level physiological profiles (CLPPs) methodology as an assay for characterization of the metabolic diversity of wastewater samples and to link the metabolic diversity patterns to efficiency of select onsite biological wastewater facilities. Metabolic fingerprints obtained from the selected samples were used to understand functional diversity implied by the carbon substrate shifts. Three different biological facilities of onsite wastewater treatment were evaluated: fixed bed reactor (technology A), trickling filter/biofilter system (technology B), and aerated filter system (the fluidized bed reactor, technology C). High similarities of the microbial community functional structures were found among the samples from the three onsite wastewater treatment plants (WWTPs), as shown by the diversity indices. Principal components analysis (PCA) showed that the diversity and CLPPs of microbial communities depended on the working efficiency of the wastewater treatment technologies. This study provided an overall picture of microbial community functional structures of investigated samples in WWTPs and discerned the linkages between microbial communities and technologies of onsite WWTPs used. The results obtained confirmed that metabolic profiles could be used to monitor treatment processes as valuable biological indicators of onsite wastewater treatment technologies efficiency. This is the first step toward understanding relations of technology types with microbial community patterns in raw and treated wastewaters.

I chose this paper because it gives a good insight on the diversity of microbes that are examined during wastewater treatment and it also elaborates on how exactly they were able to determine what microorganisms were found during the shifts in the substrate.

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Human Microbiome

Zachary Snelson

The Host Microbiome Regulates and Maintains Human Health: A Primer and Perspective for Non-Microbiologists

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5392374/

Summaries

General audience:

Human beings have always seen themselves as superior organisms that can operate on their own. However, would you ever think that even small parts of your body can have an entire ecosystem of microbes? Those interacting microbes can effect not just each other, but they can also have effects on the human host too. This research paper gives details on how the amount of diversity of microbes in the human microbiome can lead to adaptations against certain diseases and the changes in microbiome overtime can also help maintain the host’s development. Changes in the human host in terms of aging, diet and even what kind of environment that they are in have important roles in how the human microbiome is composed. The ongoing research over the diversity and composition of microbes on the human host can help us to further understand the molecular mechanics in disease.

The diverse variety of microbes in the human microbiome consists of not only bacteria and viruses, but also archaea and fungi as well. What kinds of benefits the microbes in the human microbiome can offer in terms of survival can range from The microbiome changes as the host ages, such as when a newborn is introduced to a foreign environment and when it eventually grows up to be an adult. When a baby is born, it can have a different structure in its microbiome depending on how it was born. For example, when born vaginally, the baby will have bacteria that helps aid in the digestion of lactose in milk products due to microbes in the vaginal cavity coming into contact with the baby during birth. Even other types of interaction with the human host can alter the microbial communities in the microbiome. In this case, the human host having a different diet can promote changes in the gut microbiota, an example such as animal products can increase the abundance of bile resistant bacteria in the gut. The human microbiome can play a crucial role in providing other benefits that can help maintain the host’s health. Such examples are the gut microbiome acting as a safeguard against cardiovascular disease, Inflammatory Bowel Syndrome, and pathogens. Cancer is also another threat to the health of the human host and negatively impact the microbiome. Changes in the gut microbiome from foreign bacteria, antibiotics, and age related symptoms can lead to the development of cancer in the human host’s gut.

Microbes in the human host that were genetically engineered have potential that can even assist with cancer prevention. It is important to help assess the advances in the diversity of microbes in the human microbiome to accommodate the emerging methods of surveillance and detection of different strains of microbes on the human body. Looking into how and why the interacting microorganisms in the human microbiome will be able to help us further understand the implication that microbes have on important medical fields such as disease management, cancer research, and even aging.

Scientists/engineers:

To emphasize the size and scale of microbes, the amount of eukaryotic cells in the human body is estimated to be 3 × 1013   and there are about 3.9 × 1013 colonizing microorganisms, in which would imply that the amount of microbes is larger than the human host. There is compelling evidence that the interaction between microorganisms in the human biome and the host is important to maintaining the individual host’s survival. The diversity of the microbiome is determined using metagenomic data. The bioinformatic results from the targeted metagenomic sequencing are available from various sources such as the Human Oral Microbiome Database, SILVA, and the Ribosomal Database Project. Prokaryotic microbes such as bacteria, archaea, fungi and even viruses like Bacteriophages play a role in the ecology and community of prokaryotes and eukaryotes in the human gut. Even eukaryotic microbes such as fungi, Protozoa, algae, and nematodes are prevalent in the skin microbiota.

The human microbiome in terms of diversity can change over time as the host develops and ages during its lifetime. When it comes to the development microbiota of babies, for instance, changes depending on the human host being exposed to a different environment over time. When the human baby is born, for instance, the microbiome can change depending on how the host is born and what types of microbes are related to those types of exposure. Babies that were born through the Cesarean section method were found to have Streptococcus spp. and other bacteria that were associated with the mother’s skin, while babies born vaginally have Lactobacillus which can aid in the digestion of milk. Aging over time can lead susceptibility to disease that correlates with changes in the immune system such as increase in inflammatory states in the gut, Lactobacillus bacteria increasing with low fat diets and oxidative stress that encourages virulence of anaerobic bacteria. The human microbiome can play a role in the health of the heart in regards to cardiovascular health, obesity and even behavior. The human microbiome, especially the gut microbiota, are vital for the metabolic potential to alter the chance of the human host having cancer. The microbiome can be changed by dysbiosis, which is the disruption of interactions between the gut flora and the human host. Smoking, foreign pathogens, and immunosenescence from aging are major factors that can disrupt the gut microbiome, and can eventually result in negative results such as tumor progression.

While evidence for the interplay is not fully understood, there have been evidence to show that microbes can affect the rate of carcinogenesis, the progression of tumors and the overall response to immunotherapy treatment. Through the co-evolution between the human host and the microbiome, the immune system is inherently modulated by microorganisms that inhabit the human host from selective pressure from invading pathogens in the environment. The applications of microbes in the gut microbiome can help provide insight on how microbes can help benefit the human host in preventing irritable bowel syndrome and In order to help improve cancer treatments, researchers will need to keep thoroughly examining the human microbiome. While there have been astounding achievements in developing the taxonomy of the human microbiome, there are still challenges in Studying the human microbiome can help us become more familiar with the genetics, biology, physiology and immunologic effects of the interacting microorganisms in the human host.

An Integrated Study to Analyze Soil Microbial Community Structure and Metabolic Potential in Two Forest Types

Abstract

Soil microbial metabolic potential and ecosystem function have received little attention owing to difficulties in methodology. In this study, we selected natural mature forest and natural secondary forest and analyzed the soil microbial community and metabolic potential combing the high-throughput sequencing and GeoChip technologies. Phylogenetic analysis based on 16S rRNA sequencing showed that one known archaeal phylum and 15 known bacterial phyla as well as unclassified phylotypes were presented in these forest soils, and  Acidobacteria,  Protecobacteria, and  Actinobacteria  were three of most abundant phyla. The detected microbial functional gene groups were related to different biogeochemical processes, including carbon degradation, carbon fixation, methane metabolism, nitrogen cycling, phosphorus utilization, sulfur cycling, etc. The Shannon index for detected functional gene probes was significantly higher (P<0.05) at natural secondary forest site. The regression analysis showed that a strong positive (P<0.05) correlation was existed between the soil microbial functional gene diversity and phylogenetic diversity. Mantel test showed that soil oxidizable organic carbon, soil total nitrogen and cellulose, glucanase, and amylase activities were significantly linked (P<0.05) to the relative abundance of corresponded functional gene groups. Variance partitioning analysis showed that a total of 81.58% of the variation in community structure was explained by soil chemical factors, soil temperature, and plant diversity. Therefore, the positive link of soil microbial structure and composition to functional activity related to ecosystem functioning was existed, and the natural secondary forest soil may occur the high microbial metabolic potential. Although the results can’t directly reflect the actual microbial populations and functional activities, this study provides insight into the potential activity of the microbial community and associated feedback responses of the terrestrial ecosystem to environmental changes.

Zhang, Yuguang et al. “An Integrated Study to Analyze Soil Microbial Community Structure and Metabolic Potential in Two Forest Types.’ Ed. A. Mark Ibekwe.  PLoS ONE  9.4 (2014): e93773.  PMC. Web. 8 Feb. 2018.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3990527/

I picked this article because I’m interested in ecosystem processes, especially when they are related to the development of forests.

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Colonization Habitat Controls Biomass, Composition, and Metabolic Activity of Attached Microbial Communities in the Columbia River Hyporheic Corridor

Abstract

Hydrologic exchange plays a critical role in biogeochemical cycling within the hyporheic zone (the interface between river water and groundwater) of riverine ecosystems. Such exchange may set limits on the rates of microbial metabolism and impose deterministic selection on microbial communities that adapt to dynamically changing dissolved organic carbon (DOC) sources. This study examined the response of attached microbial communities (in situ  colonized sand packs) from groundwater, hyporheic, and riverbed habitats within the Columbia River hyporheic corridor to “cross-feeding’ with either groundwater, river water, or DOC-free artificial fluids. Our working hypothesis was that deterministic selection during  in situ  colonization would dictate the response to cross-feeding, with communities displaying maximal biomass and respiration when supplied with their native fluid source. In contrast to expectations, the major observation was that the riverbed colonized sand had much higher biomass and respiratory activity, as well as a distinct community structure, compared with those of the hyporheic and groundwater colonized sands. 16S rRNA gene amplicon sequencing revealed a much higher proportion of certain heterotrophic taxa as well as significant numbers of eukaryotic algal chloroplasts in the riverbed colonized sand. Significant quantities of DOC were released from riverbed sediment and colonized sand, and separate experiments showed that the released DOC stimulated respiration in the groundwater and piezometer colonized sand. These results suggest that the accumulation and degradation of labile particulate organic carbon (POC) within the riverbed are likely to release DOC, which may enter the hyporheic corridor during hydrologic exchange, thereby stimulating microbial activity and imposing deterministic selective pressure on the microbial community composition.

Stern, Noah et al. “Colonization Habitat Controls Biomass, Composition, and Metabolic Activity of Attached Microbial Communities in the Columbia River Hyporheic Corridor.’ Ed. Joel E. Kostka.  Applied and Environmental Microbiology  83.16 (2017): e00260—17.  PMC. Web. 8 Feb. 2018.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5541231/

 

This paper shows an intriguing concept on riverine microbial community composition and the effects that their biogeochemical cycling processes have on the freshwater environment.

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Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies

Abstract

The hyporheic zone (HZ) is the active ecotone between the surface stream and groundwater, where exchanges of nutrients and organic carbon have been shown to stimulate microbial activity and transformations of carbon and nitrogen. To examine the relationship between sediment texture, biogeochemistry, and biological activity in the Columbia River HZ, the grain size distributions for sediment samples were characterized to define geological facies, and the relationships among physical properties of the facies, physicochemical attributes of the local environment, and the structure and activity of associated microbial communities were examined. Mud and sand content and the presence of microbial heterotrophic and nitrifying communities partially explained the variability in many biogeochemical attributes such as C:N ratio and %TOC. Microbial community analysis revealed a high relative abundance of putative ammonia-oxidizing Thaumarchaeota and nitrite-oxidizing Nitrospirae. Network analysis showed negative relationships between sets of co-varying organisms and sand and mud contents, and positive relationships with total organic carbon. Our results indicate grain size distribution is a good predictor of biogeochemical properties, and that subsets of the overall microbial community respond to different sediment texture. Relationships between facies and hydrobiogeochemical properties enable facies-based conditional simulation/mapping of these properties to inform multiscale modeling of hyporheic exchange and biogeochemical processes.

Hou, Z. et al. “Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies.’  Scientific Reports  7 (2017): 12006.  PMC. Web. 8 Feb. 2018.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5607297/

This paper presents an interesting perspective on how microbes can function in different types of sediments.

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Microbial Ecology of the Dark Ocean above, at, and below the Seafloor

Abstract

Summary: The majority of life on Earth–notably, microbial life–occurs in places that do not receive sunlight, with the habitats of the oceans being the largest of these reservoirs. Sunlight penetrates only a few tens to hundreds of meters into the ocean, resulting in large-scale microbial ecosystems that function in the dark. Our knowledge of microbial processes in the dark ocean–the aphotic pelagic ocean, sediments, oceanic crust, hydrothermal vents, etc.–has increased substantially in recent decades. Studies that try to decipher the activity of microorganisms in the dark ocean, where we cannot easily observe them, are yielding paradigm-shifting discoveries that are fundamentally changing our understanding of the role of the dark ocean in the global Earth system and its biogeochemical cycles. New generations of researchers and experimental tools have emerged, in the last decade in particular, owing to dedicated research programs to explore the dark ocean biosphere. This review focuses on our current understanding of microbiology in the dark ocean, outlining salient features of various habitats and discussing known and still unexplored types of microbial metabolism and their consequences in global biogeochemical cycling. We also focus on patterns of microbial diversity in the dark ocean and on processes and communities that are characteristic of the different habitats.

Orcutt, Beth N. et al. “Microbial Ecology of the Dark Ocean Above, At, and below the Seafloor.’  Microbiology and Molecular Biology Reviews’¯: MMBR  75.2 (2011): 361—422.  PMC. Web. 8 Feb. 2018.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3122624/

I chose this paper because it gives a broad but easy to understand explanation on how and why the biogeochemical cycling of microbes in marine environments is important to study.

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