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.

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

This review of 68 studies compares the methodologies used for the identification and quantification of microplastics from the marine environment. Three main sampling strategies were identified: selective, volume-reduced, and bulk sampling. Most sediment samples came from sandy beaches at the high tide line, and most seawater samples were taken at the sea surface using neuston nets. Four steps were distinguished during sample processing: density separation, filtration, sieving, and visual sorting of microplastics. Visual sorting was one of the most commonly used methods for the identification of microplastics (using type, shape, degradation stage, and color as criteria). Chemical and physical characteristics (e.g., specific density) were also used. The most reliable method to identify the chemical composition of microplastics is by infrared spectroscopy. Most studies reported that plastic fragments were polyethylene and polypropylene polymers. Units commonly used for abundance estimates are “items per m2” ...

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Microplastics in the Marine Environment: A Review of the Methods Used for Identification and Quantification

Communities of microscopic plant life, or phytoplankton, dominate the Earth's aquatic ecosystems. This important new book by Colin Reynolds covers the adaptations, physiology and population dynamics of phytoplankton communities in lakes and rivers and oceans. It provides basic information on composition, morphology and physiology of the main phyletic groups represented in marine and freshwater systems and in addition reviews recent advances in community ecology, developing an appreciation of assembly processes, co-existence and competition, disturbance and diversity. Although focussed on one group of organisms, the book develops many concepts relevant to ecology in the broadest sense, and as such will appeal to graduate students and researchers in ecology, limnology and oceanography.

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The Ecology of Phytoplankton

What is ecological speciation

Freshwater bacteria are at the hub of biogeochemical cycles and control water quality in lakes. Despite this, little is known about the identity and ecology of functionally significant lake bacteria. Molecular studies have identified many abundant lake bacteria, but there is a large variation in the taxonomic or phylogenetic breadths among the methods used for this exploration. Because of this, an inconsistent and overlapping naming structure has developed for freshwater bacteria, creating a significant obstacle to identifying coherent ecological traits among these groups. A discourse that unites the field is sorely needed. Here we present a new freshwater lake phylogeny constructed from all published 16S rRNA gene sequences from lake epilimnia and propose a unifying vocabulary to discuss freshwater taxa. With this new vocabulary in place, we review the current information on the ecology, ecophysiology, and distribution of lake bacteria and highlight newly identified phylotypes. In the second part of our review, we conduct meta-analyses on the compiled data, identifying distribution patterns for bacterial phylotypes among biomes and across environmental gradients in lakes. We conclude by emphasizing the role that this review can play in providing a coherent framework for future studies.

A Guide to the Natural History of Freshwater Lake Bacteria

Autotrophic picoplankton (APP) are distributed worldwide and are ubiquitous in all types of lakes of varying trophic state. APP are major players in carbon production in all aquatic ecosystems, including extreme environments such as cold ice-covered and/or warm tropical lakes and thermal springs. They often form the base of complex microbial food webs, becoming prey for a multitude of protozoan and micro-invertebrate grazers, that effectively channel APP carbon to higher trophic levels including fish. In this review we examine the existing literature on freshwater autotrophic picoplankton, setting recent findings and current ecological issues within an historic framework, and include a description of the occurrence and distribution of both single-cell and colonial APP (picocyanobacteria) in different types of lakes. In this review we place considerable emphasis on methodology and ecology, including sampling, counting, preservation, molecular techniques, measurement of photosynthesis, and include extensive comment on their important role in microbial food webs. The model outlined by Stockner of an increase of APP abundance and biomass and a decrease of its relative importance with the increase of phosphorus concentration in lakes has been widely accepted, and only recently confirmed in marine and freshwater ecosystems. Nevertheless the relationship which drives the APP presence and importance in lakes of differing trophic status appears with considerable variation so we must conclude that the success of APP in oligotrophic lakes worldwide is not a certainty but highly probable.

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Freshwater autotrophic picoplankton: a review

About 40 years have passed since the discovery of picophytoplankton; the present knowledge of the taxonomy physiology and ecology of these tiny photoautotrophic cells offers new perspectives on the importance of the microbial contribution to global biogeochemical cycles and food webs. This review focuses on the relationships among the components of picophytoplankton (picocyanobacteria and the picoplanktic eukaryotes) and biotic and abiotic environmental factors. The dynamics of picophytoplankton in aquatic ecosystems are strictly dependent upon basin size and trophy, temperature, and nutrient and light limitation, but they are also regulated by grazing and viral-induced lysis. The review considers: the pros and cons of the molecular approach to the study of the taxonomy of freshwater Synechococcus spp.; the importance of ecological aspects in understanding the puzzle of picophytoplankton phylogeny (genotype vs ecotype); and the role of biotic vs abiotic interactions in controlling picophytoplankt...

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Picophytoplankton in freshwater ecosystems: the importance of small-sized phototrophs

Studies on the picocyanobacteria, the major non-bloom forming group in lakes, have increased markedly in the past two decades.These cyanobacteria fall into two major groups, those that predominantly occur as solitary cells (here termed Pcy) and those that occur primarily as colonies (CPcy). The single-celled picoplankton have received most ecological study, though the colonial forms are better known taxonomically.The two groups are distributed worldwide and are ubiquitous in all types of lakes of varying trophic condition. The single-celled Pcy populations tend to be predominant in large, deep oligo-mesotrophic lakes, while the colonial species (CPcy) find optimal conditions in warmer, shallower and more nutrient rich (meso-eutrophic) lakes during the summer.The two groups are euryphotic and appear capable of adapting to a wide variety of light conditions, with CPcy more surface oriented and Pcy often reaching sub-surface peaks at irradiance levels 20–50% of surface values. Growth of the Pcy ranges from 0.1 d-1 to about 3.0 d-1 with doubling times from 7 h to 7 d.Their natural population growth rates are highly variable and appear in most cases to be in balance with loss rates, primarily from grazing. Pcy contribute substantially to total primary production within the euphotic zone, most significantly in ultra-oligotrophic lakes, but also in some meso- and eutrophic lakes, showing optimal growth at high N:P ratios (>20 molar) and more limitation by nitrogen than phosphorus.

Picoplankton and other non-bloom forming Cyanobacteria in lakes

Picocyanobacterial abundance and their contribution to the total phytoplankton biomass, estimated as chlorophyll a, was investigated in 32 deep and shallow lakes. The lake series covered a wide range of natural and artificial lakes, from high altitude clear lakes and deep, large subalpine lakes through large shallow lakes, small reservoirs and fish ponds. The chlorophyll a concentrations ranged between 0.2 and 390 μg 1−1. No simple relation existed between trophic state and the abundance of picocyanobacterial, mainly represented by Synechococcus spp. Below 10 μg Chl a 1−1 the percentage contribution of picocyanobacteria biomass to total phytoplankton biomass exceeded 70% in some cases, whereas above 100 μg Chl a l−1, the highest contribution was only 10%. At low chlorophyll a concentrations phycoerythrin-rich picocyanobacteria (PE) dominated almost exclusively but their contribution never exceeded 10% of the total picocyanobacterial abundance when chlorophyll a concentration was higher than 50 μg 1−1. Above this value there was high light attenuation and a shift of the maximum light penetration from the blue-green towards the red portion of the spectrum. In this underwater light climate phycocyanin-rich picocyanobacteria (PC) dominated. In the lakes chosen for their representation of ranges in trophy and light quality, PC cells prevailed over the PE when vertical attenuation coefficient of PAR was higher than 2.25 m−1 and red light penetrated farthest. PE cells were 100% when the vertical attenuation coefficient of PAR was lower than 0.55 m−1 and the green and blue were the most penetrating lights.

Freshwater picocyanobacteria along a trophic gradient and light quality range

A methodical approach for the assessment of pelagic biomass and the main carbon fluxes in remote and hardly accessible mountain lakes was elaborated and tested. Number and biomass of bacteria (BAC), autotrophic picoplankton (APP), heterotrophic nanoflagellates (HNF), ciliates (CIL), phytoplankton (PHY), zooplankton smaller than 40 μm (ZOOS) and zooplankton larger than 40 μm (ZOOL) were investigated regularly during two ice-free periods in 13 European mountain lakes (1st level approach – fixed samples elaborated in specialized laboratories). Carbon fluxes measured in 9 lakes included: primary production, exudation by PHY and BAC uptake of exudates, BAC production, elimination of BAC. These processes were measured in the field by specialized teams (2nd level approach). The ranges of values found in mountain lakes were evaluated and possible methodical and interpretative errors discussed. BAC were a significant component of pelagic biomass. The intercomparison between different partners showed differences in bacterial counts lower than 10%, whereas the mean cell volumes measured fluctuated by more than 40%. APP was never found in a significant quantity, except in one lake. HNF and CIL, though regularly found, were usually scarce and only occasionally significant in terms of biomass. The main components of pelagic biomass were BAC, PHY and ZOOL+ZOOS, except for acidified lakes, where zooplankton was very low. In oligotrophic mountain lakes, the percentage of extracellular production in the total primary production was considerable. Bacterial abundance and production often reached values quite comparable with the situation found in lowland mesotrophic lakes during winter.

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Cristiana Callieri

Papers

Freshwater autotrophic picoplankton: a review

Picophytoplankton in freshwater ecosystems: the importance of small-sized phototrophs

Picoplankton and other non-bloom forming Cyanobacteria in lakes

Freshwater picocyanobacteria along a trophic gradient and light quality range

Investigations on pelagic food webs in mountain lakes - aims and methods