The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing.

Microbial ecology is plagued by problems of an abstract nature. Cell sizes are so small and population sizes so large that both are virtually incomprehensible. Niches are so far from our everyday experience as to make their very definition elusive. Organisms that may be abundant and critical to our survival are little understood, seldom described and/or cultured, and sometimes yet to be even seen. One way to confront these problems is to use data of an even more abstract nature: molecular sequence data. Massive environmental nucleic acid sequencing, such as metagenomics or metatranscriptomics, promises functional analysis of microbial communities as a whole, without prior knowledge of which organisms are in the environment or exactly how they are interacting. But sequence-based ecological studies nearly always use a comparative approach, and that requires relevant reference sequences, which are an extremely limited resource when it comes to microbial eukaryotes. In practice, this means sequence databases need to be populated with enormous quantities of data for which we have some certainties about the source. Most important is the taxonomic identity of the organism from which a sequence is derived and as much functional identification of the encoded proteins as possible. In an ideal world, such information would be available as a large set of complete, well curated, and annotated genomes for all the major organisms from the environment in question. Reality substantially diverges from this ideal, but at least for bacterial molecular ecology, there is a database consisting of thousands of complete genomes from a wide range of taxa, supplemented by a phylogeny-driven approach to diversifying genomics [2]. For eukaryotes, the number of available genomes is far, far fewer, and we have relied much more heavily on random growth of sequence databases, raising the question as to whether this is fit for purpose

Sources, Distribution, and Fate of Microscopic Plastics in Marine Environments

Microplastics are pieces of plastic debris <5 mm in diameter. They enter the environment from a variety of sources including the direct input of small pieces such as exfoliating beads used in cosmetics and as a consequence of the fragmentation of larger items of debris. A range of common polymers, including polyethylene, polypropylene, polystyrene, and polyvinyl chloride, are present in the environment as microplastic particles. Microplastics are widely distributed in marine and freshwater habitats. They have been reported on shorelines from the poles to the equator; they are present at the sea surface and have accumulated in ocean systems far from land. Microplastics are also present in substantial quantities on the seabed. A wide range of organisms including birds, fish, and invertebrates are known to ingest microplastics and for some species it is clear that a substantial proportion of the population have microplastic in their digestive tract. The extent to which this might have harmful effects is not clear; however, the widespread encounter rate indicates that substantial quantities of microplastic may be distributed within living organisms themselves as well as in the habitats in which they live. Our understanding about the long-term fate of microplastics is relatively limited. Some habitats such as the deep sea may be an ultimate sink for the accumulation of plastic debris at sea; indeed, some recent evidence indicates quantities in the deep sea can be greater than at the sea surface. It has also been suggested that microplastics might be susceptible to biodegradation by microorganisms; however, this is yet to be established and the prevailing view is that even if emissions of debris to the environment are substantially reduced, the abundance of microplastics will increase over the next few decades. However, it is also clear that the benefits which plastics bring to society can be realized without the need for emissions of end-of-life plastics to the ocean. To some extent the accumulation of microplastic debris in the environment is a symptom of an outdated business model. There are solutions at hand and many synergistic benefits can be achieved in terms of both waste reduction and sustainable use of resources by moving toward a circular economy

Understanding How Microplastics Affect Marine Biota on the Cellular Level Is Important for Assessing Ecosystem Function: A Review

Plastic has become indispensable for human life. When plastic debris is discarded into waterways, these items can interact with organisms. Of particular concern are microscopic plastic particles (microplastics) which are subject to ingestion by several taxa. This review summarizes the results of cutting-edge research about the interactions between a range of aquatic species and microplastics, including effects on biota physiology and secondary ingestion. Uptake pathways via digestive or ventilatory systems are discussed, including (1) the physical penetration of microplastic particles into cellular structures, (2) leaching of chemical additives or adsorbed persistent organic pollutants (POPs), and (3) consequences of bacterial or viral microbiota contamination associated with microplastic ingestion. Following uptake, a number of individual-level effects have been observed, including reduction of feeding activities, reduced growth and reproduction through cellular modifications, and oxidative stress. Microplastic-associated effects on marine biota have become increasingly investigated with growing concerns regarding human health through trophic transfer. We argue that research on the cellular interactions with microplastics provide an understanding of their impact to the organisms’ fitness and, therefore, its ability to sustain their functional role in the ecosystem. The review summarizes information from 236 scientific publications. Of those, only 4.6% extrapolate their research of microplastic intake on individual species to the impact on ecosystem functioning. We emphasize the need for risk evaluation from organismal effects to an ecosystem level to effectively evaluate the effect of microplastic pollution on marine environments. Further studies are encouraged to investigate sublethal effects in the context of environmentally relevant microplastic pollution conditions

A review of microscopy and comparative molecular-based methods to characterize 'plastisphere' communities

Plastic is currently the most abundant form of debris in the ocean. Since the early 70's, investigators have recognized the presence of life such as pennate diatoms, bryozoans and bacteria on plastic debris, sometimes referred to as the "Plastisphere". This review provides an overview of molecular and visualization techniques used to characterize life in the Plastisphere, presents a new data portal located on the Visual Analysis of Microbial Population Structures (VAMPS) website to illustrate how one can compare plastic debris datasets collected using different high-throughput sequencing strategies, and makes recommendations on standardized operating procedures that will facilitate future comparative studies

The periodontal pathogen Porphyromonas gingivalis cleaves apoB-100 and increases the expression of apoM in LDL in whole blood leading to cell proliferation

Objective: Several studies support an association between periodontal disease and atherosclerosis with a crucial role for the pathogen Porphyromonas gingivalis. This study aims to investigate the proteolytic and oxidative activity of P. gingivalis on LDL in a whole blood system by using a proteomic approach and analyze the effects of P. gingivalis-modifed LDL on cell proliferation. Methods: The cellular effects of P. gingivalis in human whole blood were assessed using lumi-aggregometry analyzing reactive oxygen species (ROS) production and aggregation. Blood was incubated for 30 min with P. gingivalis, whereafter LDL was isolated and a proteomic approach was applied to examine protein expression. LDL-oxidation was determined by analyzing the formation of protein carbonyls. The effects of P. gingivalis-modifed LDL on fibroblast proliferation were studied using the MTS-assay. Results: Incubation of whole blood with P. gingivalis caused an extensive aggregation and ROS-production, indicating platelet and leukocyte activation. LDL prepared from the bacteria-exposed blood showed an increased protein oxidation, elevated levels of apoM and formation of two apoB-100 N-terminal fragments. P. gingivalis-modified LDL markedly increased the growth of fibroblasts. Inhibition of gingipain R suppressed the modification of LDL by P. gingivalis. Conclusions: The ability of P. gingivalis to change the protein expression and the proliferative capacity of LDL may represent a crucial event in periodontitis-associated atherosclerosis.The definitive version is available at www.blackwell-synergy.com: Torbjörn Bengtsson, Helen Karlsson, Patrik Gunnarsson, Caroline Skoglund, Charlotte Elison, Per Leanderson and Mats Lindahl, The periodontal pathogen Porphyromonas gingivalis cleaves apoB-100 and increases the expression of apoM in LDL in whole blood leading to cell proliferation, 2008, Journal of Internal Medicine, (263), 5, 558-571. http://dx.doi.org/10.1111/j.1365-2796.2007.01917.x. Copyright: Blackwell Publishing www.blackwell-synergy.com</p