Joseph Alexander Christie-Oleza

Bio: Joseph Alexander Christie-Oleza is an academic researcher from University of Warwick. The author has contributed to research in topics: Roseobacter & Proteogenomics. The author has an hindex of 20, co-authored 52 publications receiving 1672 citations. Previous affiliations of Joseph Alexander Christie-Oleza include University of the Balearic Islands & Spanish National Research Council.

Lost, but Found with Nile Red: A Novel Method for Detecting and Quantifying Small Microplastics (1 mm to 20 μm) in Environmental Samples

Abstract: Marine plastic debris is a global environmental problem. Surveys have shown that <5 mm plastic particles, known as microplastics, are significantly more abundant in surface seawater and on shorelines than larger plastic particles are. Nevertheless, quantification of microplastics in the environment is hampered by a lack of adequate high-throughput methods for distinguishing and quantifying smaller size fractions (<1 mm), and this has probably resulted in an underestimation of actual microplastic concentrations. Here we present a protocol that allows high-throughput detection and automated quantification of small microplastic particles (20-1000 μm) using the dye Nile red, fluorescence microscopy, and image analysis software. This protocol has proven to be highly effective in the quantification of small polyethylene, polypropylene, polystyrene, and nylon-6 particles, which frequently occur in the water column. Our preliminary results from sea surface tows show a power-law increase in small microplastics (i.e., <1 mm) with a decreasing particle size. Hence, our data help to resolve speculation about the "apparent" loss of this fraction from surface waters. We consider that this method presents a step change in the ability to detect small microplastics by substituting the subjectivity of human visual sorting with a sensitive and semiautomated procedure.

Marine Plastic Debris: A New Surface for Microbial Colonization.

Abstract: Plastics become rapidly colonized by microbes when released into marine environments. This microbial community-the Plastisphere-has recently sparked a multitude of scientific inquiries and generated a breadth of knowledge, which we bring together in this review. Besides providing a better understanding of community composition and biofilm development in marine ecosystems, we critically discuss current research on plastic biodegradation and the identification of potentially pathogenic "hitchhikers" in the Plastisphere. The Plastisphere is at the interface between the plastic and its surrounding milieu, and thus drives every interaction that this synthetic material has with its environment, from ecotoxicity and new links in marine food webs to the fate of the plastics in the water column. We conclude that research so far has not shown Plastisphere communities to starkly differ from microbial communities on other inert surfaces, which is particularly true for mature biofilm assemblages. Furthermore, despite progress that has been made in this field, we recognize that it is time to take research on plastic-Plastisphere-environment interactions a step further by identifying present gaps in our knowledge and offering our perspective on key aspects to be addressed by future studies: (I) better physical characterization of marine biofilms, (II) inclusion of relevant controls, (III) study of different successional stages, (IV) use of environmentally relevant concentrations of biofouled microplastics, and (V) prioritization of gaining a mechanistic and functional understanding of Plastisphere communities.

Understanding microbial community dynamics to improve optimal microbiome selection

Abstract: Artificial selection of microbial communities that perform better at a desired process has seduced scientists for over a decade, but the method has not been systematically optimised nor the mechanisms behind its success, or failure, determined. Microbial communities are highly dynamic and, hence, go through distinct and rapid stages of community succession, but the consequent effect this may have on artificially selected communities is unknown. Using chitin as a case study, we successfully selected for microbial communities with enhanced chitinase activities but found that continuous optimisation of incubation times between selective transfers was of utmost importance. The analysis of the community composition over the entire selection process revealed fundamental aspects in microbial ecology: when incubation times between transfers were optimal, the system was dominated by Gammaproteobacteria (i.e. main bearers of chitinase enzymes and drivers of chitin degradation), before being succeeded by cheating, cross-feeding and grazing organisms. The selection of microbiomes to enhance a desired process is widely used, though the success of artificially selecting microbial communities appears to require optimal incubation times in order to avoid the loss of the desired trait as a consequence of an inevitable community succession. A comprehensive understanding of microbial community dynamics will improve the success of future community selection studies.

Nutrient recycling facilitates long-term stability of marine microbial phototroph–heterotroph interactions

Abstract: Biological interactions underpin the functioning of marine ecosystems, be it via competition, predation, mutualism or symbiosis processes. Microbial phototroph-heterotroph interactions propel the engine that results in the biogeochemical cycling of individual elements, and they are critical for understanding and modelling global ocean processes. Unfortunately, studies thus far have focused on exponentially growing cultures in nutrient-rich media, meaning knowledge of such interactions under in situ conditions is rudimentary at best. Here, we have performed long-term phototroph-heterotroph co-culture experiments under nutrient-amended and natural seawater conditions, and show that it is not the concentration of nutrients but rather their circulation that maintains a stable interaction and a dynamic system. Using the Synechococcus-Roseobacter interaction as a model phototroph-heterotroph case study, we show that although Synechococcus is highly specialized for carrying out photosynthesis and carbon fixation, it relies on the heterotroph to remineralize the inevitably leaked organic matter, making nutrients circulate in a mutualistic system. In this sense we challenge the general belief that marine phototrophs and heterotrophs compete for the same scarce nutrients and niche space, and instead suggest that these organisms more probably benefit from each other because of their different levels of specialization and complementarity within long-term stable-state systems.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

Atmospheric transport and deposition of microplastics in a remote mountain catchment

Abstract: Plastic litter is an ever-increasing global issue and one of this generation’s key environmental challenges. Microplastics have reached oceans via river transport on a global scale. With the exception of two megacities, Paris (France) and Dongguan (China), there is a lack of information on atmospheric microplastic deposition or transport. Here we present the observations of atmospheric microplastic deposition in a remote, pristine mountain catchment (French Pyrenees). We analysed samples, taken over five months, that represent atmospheric wet and dry deposition and identified fibres up to ~750 µm long and fragments ≤300 µm as microplastics. We document relative daily counts of 249 fragments, 73 films and 44 fibres per square metre that deposited on the catchment. An air mass trajectory analysis shows microplastic transport through the atmosphere over a distance of up to 95 km. We suggest that microplastics can reach and affect remote, sparsely inhabited areas through atmospheric transport.

Microbial Surface Colonization and Biofilm Development in Marine Environments

Abstract: SUMMARY Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.

Methods for sampling and detection of microplastics in water and sediment: A critical review

Abstract: Microplastics are widespread contaminants, virtually present in all environmental compartments. However, knowledge on sources, fate and environmental concentration over time and space still is limited due to the laborious and varied analytical procedures currently used. In this work we critically review the methods currently used for sampling and detection of microplastics, identifying flaws in study design and suggesting promising alternatives. This work provides insights on bulk sample collection, separation, digestion, identification and quantification, and mitigation of cross-contamination. The sampling of microplastics will improve in representativeness and reproducibility through the determination of bulk sample volume, filter's pore size, density separation and digestion solutions, but also through use of novel methods, such as the enhancement of visual identification by staining dyes, and the generalized use of chemical characterization.