Plastics in the North Atlantic garbage patch: a boat-microbe for hitchhikers and plastic degraders – REPOST!

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Debroas, D., Mone, A. and Ter Halle, A., 2017. Plastics in the North Atlantic garbage patch: a boat-microbe for hitchhikers and plastic degraders.  Science of the Total Environment,  599, pp.1222-1232.

Abstract:

Plastic is a broad name given to different polymers with high molecular weight that impact wildlife. Their fragmentation leads to a continuum of debris sizes (meso  to microplastics) entrapped in gyres and colonized by microorganisms. In the present work, the structure of eukaryotes, bacteria and Archaea was studied by a metabarcoding approach, and statistical analysis associated with network building was used to define a core microbiome at the plastic surface. Most of the bacteria significantly associated with the plastic waste originated from non-marine ecosystems, and numerous species can be considered as hitchhikers, whereas others act as keystone species (e.g., Rhodobacterales, Rhizobiales, Streptomycetales and Cyanobacteria) in the biofilm. The chemical analysis provides evidence for a specific colonization of the polymers. Alphaproteobacteria and Gammaproteobacteria significantly dominated mesoplastics consisting of poly(ethylene terephthalate) and polystyrene. Polyethylene was also dominated by these bacterial classes and Actinobacteria. Microplastics were made of polyethylene but differed in their crystallinity, and the majorities were colonized by Betaproteobacteria. Our study indicated that the bacteria inhabiting plastics harboured distinct metabolisms from those present in the surrounding water. For instance, the metabolic pathway involved in xenobiotic degradation was overrepresented on the plastic surface.

Justification:

I chose this paper because the accumulation of plastic in the ocean is a huge problem, and we generally think of plastics as very challenging to degrade.

Plastics in the North Atlantic garbage patch: A boat-microbe for hitchhikers and plastic degraders

Posted by On Filed under Biodegradation and bioremediation papers No Comments
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Debroas, D., Mone, A. and Ter Halle, A., 2017. Plastics in the North Atlantic garbage patch: a boat-microbe for hitchhikers and plastic degraders.  Science of the Total Environment,  599, pp.1222-1232.

Abstract:

Plastic is a broad name given to different polymers with high molecular weight that impact wildlife. Their fragmentation leads to a continuum of debris sizes (meso  to microplastics) entrapped in gyres and colonized by microorganisms. In the present work, the structure of eukaryotes, bacteria and Archaea was studied by a metabarcoding approach, and statistical analysis associated with network building was used to define a core microbiome at the plastic surface. Most of the bacteria significantly associated with the plastic waste originated from non-marine ecosystems, and numerous species can be considered as hitchhikers, whereas others act as keystone species (e.g., Rhodobacterales, Rhizobiales, Streptomycetales and Cyanobacteria) in the biofilm. The chemical analysis provides evidence for a specific colonization of the polymers. Alphaproteobacteria and Gammaproteobacteria significantly dominated mesoplastics consisting of poly(ethylene terephthalate) and polystyrene. Polyethylene was also dominated by these bacterial classes and Actinobacteria. Microplastics were made of polyethylene but differed in their crystallinity, and the majorities were colonized by Betaproteobacteria. Our study indicated that the bacteria inhabiting plastics harboured distinct metabolisms from those present in the surrounding water. For instance, the metabolic pathway involved in xenobiotic degradation was overrepresented on the plastic surface.

Justification:

I chose this paper because the accumulation of plastic in the ocean is a huge problem, and we generally think of plastics as very challenging to degrade.

Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system

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Citation:

Speth, D.R., Guerrero-Cruz, S., Dutilh, B.E. and Jetten, M.S., 2016. Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system.  Nature communications,  7, p.11172.

Abstract:

“Partial-nitritation anammox (PNA) is a novel wastewater treatment procedure for energy-efficient ammonium removal. Here we use genome-resolved metagenomics to build a genome-based ecological model of the microbial community in a full-scale PNA reactor. Sludge from the bioreactor examined here is used to seed reactors in wastewater treatment plants around the world; however, the role of most of its microbial community in ammonium removal remains unknown. Our analysis yielded 23 near-complete draft genomes that together represent the majority of the microbial community. We assign these genomes to distinct anaerobic and aerobic microbial communities. In the aerobic community, nitrifying organisms and heterotrophs predominate. In the anaerobic community, widespread potential for partial denitrification suggests a nitrite loop increases treatment efficiency. Of our genomes, 19 have no previously cultivated or sequenced close relatives and six belong to bacterial phyla without any cultivated members, including the most complete Omnitrophica (formerly OP3) genome to date.”

 

Justification:

I chose this article because I am interested in learning more about anammox and the role it plays in nitrogen cycling and wastewater treatment.

Microbial Communities of Mt. Prindle, AK — Permafrost soils!

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Sophie Weaver
Technical summary: Permafrost and microbial functional diversity

Climate change is amplified in high latitudes, making areas with discontinuous permafrost especially susceptible to thaw. With the thaw and resulting processing of previously frozen soils through microbial decomposition, increased release of CO2 and CH4 into the atmosphere will occur. Permafrost currently stores approximately twice as much carbon as is in the atmosphere, making permafrost thaw and microbial processing an important topic of research in light of climate change. These authors asked (1) how are microbial communities and their functional composition and abundance affected by permafrost thaw and (2) what environmental shifts due to permafrost thaw (i.e. vegetation) might be leading to these changes. This study was carried out in Interior Alaska, where discontinuous permafrost creates an ideal location to study the impacts of permafrost thaw on soil biogeochemical cycling. They used GeoChip analyses to measure microbial functional genes present in minimally thawed, moderately thawed, and extensively thawed permafrost soil samples. They found that microbial community functional gene abundances (especially for C and N cycling genes) were highest at the moderately thawed sites and were associated with higher vascular plant growth. They found that along the thaw progression, microbial functional gene richness declined, but microbial community diversity actually increased. These results suggest that microbial communities and vascular plant growth might be correlated due to warming soils and permafrost thaw. As permafrost thaws, microbial decomposition and nutrient cycling will likely increase in these soils, and vascular plants could benefit from this, changing the tundra landscape and vegetation and suggesting that microbial and plant communities may co-evolve.

Non-technical Summary: What’s going on below this patch of vegetation??
Every environment surrounding us contains communities of microorganisms that perform important processes. These processes cycle elements, like carbon and nitrogen, throughout the biosphere (think – water cycle but more complex!). Soils, for example, are incredibly diverse environments that not only harbor plant growth, but are also home to millions of microbes. Soils have many characteristics that help define the community of plants and microbes that will be able to live there. Some soils are located in climates that are so cold they are continuously frozen for more than two years. This extreme soil habitat is called permafrost, and has its own unique microbial communities. When we think of climate change, we often picture starving polar bears and rising sea levels, but permafrost is also damaged by warming temperatures! As permafrost thaws, the plants growing on these soils can be impacted by increasing soil moisture and temperature. Microbial communities can also change, as some microbes are better fit to survive in the new, thawed,  conditions. So what might happen to these microbes that currently live in permafrost habitats that are starting to thaw? A study in central Alaska discovered that as permafrost thaws, plant growth changes, and the amount and the function of microbial communities present also changes! These scientists discovered that microbes found in more thawed soils had more abundant genes involved in the cycling of carbon and nitrogen, meaning that these microbes were better fit to process the carbon and nitrogen available in their environment. This change in soil conditions not only caused a change in microbial community, but also impacted the growth of the plants nearby! So what does this mean for microbes? As the Earth’s temperature continues to rise, more permafrost is expected to thaw, and microbes in Alaska are going to have to adapt in order to survive in novel soil conditions or they will be replaced by other microbes that are better fit for an unfrozen soil environment. While these microbes will likely benefit from thawing permafrost, the loss of permafrost will have huge implications for climate warming and plant growth, Microbes will contribute to climate change by increasing the prevalence of greenhouse gases (carbon dioxide, methane) in the atmosphere. The importance of microbial contributions to climate change should not be underestimated!

Microbial functional genes elucidate environmental drivers of biofilm metabolism in glacier-fed streams

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Citation:

Ren, Z., Gao, H., Elser, J. J., & Zhao, Q. (2017). Microbial functional genes elucidate environmental drivers of biofilm metabolism in glacier-fed streams.  Scientific reports,  7(1), 12668.

https://www.nature.com/articles/s41598-017-13086-9.pdf

Abstract:

Benthic biofilms in glacier-fed streams harbor diverse microorganisms driving biogeochemical cycles and, consequently, influencing ecosystem-level processes. Benthic biofilms are vulnerable to glacial retreat induced by climate change. To investigate microbial functions of benthic biofilms in glacier-fed streams, we predicted metagenomes from 16s rRNA gene sequence data using PICRUSt and identified functional genes associated with nitrogen and sulfur metabolisms based on KEGG database and explored the relationships between metabolic pathways and abiotic factors in glacier-fed streams in the Tianshan Mountains in Central Asia. Results showed that the distribution of functional genes was mainly associated with glacier area proportion, glacier source proportion, total nitrogen, dissolved organic carbon, and pH. For nitrogen metabolism, the relative abundance of functional genes associated with dissimilatory pathways was higher than those for assimilatory pathways. The relative abundance of functional genes associated with assimilatory sulfate reduction was higher than those involved with the sulfur oxidation system and dissimilatory sulfate reduction. Hydrological factors had more significant correlations with nitrogen metabolism than physicochemical factors and anammox was the most sensitive nitrogen cycling pathway responding to variation of the abiotic environment in these glacial-fed streams. In contrast, sulfur metabolism pathways were not sensitive to variations of abiotic factors in these systems.

 

I chose this article because I am very interested in biogeochemical cycling within stream biofilms, and how the diversity of microorganisms present can influence ecosystem processes. Adding glaciers to the mix just makes it more exciting! This article also uses methods we have learned about in class  (16srRNA gene sequencing), so the paper helped me better understand how these methods can be used in another environmental application.

 

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Intro Sophie Weaver

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Hi! My name is Sophie Weaver and I am currently a M.S. student studying stream biogeochemistry. My thesis project is focused on nutrient limitation of stream biofilms (i.e. algae, fungi, microbes), specifically looking at how permafrost thaw and increased nutrient concentrations can impact interactions between algae and heterotrophs in boreal streams! I’m taking this course to learn more about the microorganisms that are present in stream biofilms so I can gain a better understanding of important ecosystem processes (in or outside of streams) like metabolism and denitrification.

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