Members of the flavobacterial genus Polaribacter thrive in response to North Sea spring phytoplankton blooms. We analyzed two respective Polaribacter species by whole genome sequencing, comparative genomics, substrate tests and proteomics. Both can degrade algal polysaccharides but occupy distinct niches. The liquid culture isolate Polaribacter sp. strain Hel1_33_49 has a 3.0-Mbp genome with an overall peptidase:CAZyme ratio of 1.37, four putative polysaccharide utilization loci (PULs) and features proteorhodopsin, whereas the agar plate isolate Polaribacter sp. strain Hel1_85 has a 3.9-Mbp genome with an even peptidase:CAZyme ratio, eight PULs, a mannitol dehydrogenase for decomposing algal mannitol-capped polysaccharides but no proteorhodopsin. Unlike other sequenced Polaribacter species, both isolates have larger sulfataserich PULs, supporting earlier assumptions that Polaribacter take part in the decomposition of sulfated polysaccharides. Both strains grow on algal laminarin and the sulfated polysaccharide chondroitin sulfate. For strain Hel1_33_49, we identified by proteomics (i) a laminarin-induced PUL, (ii) chondroitin sulfate-induced CAZymes and (iii) a chondroitin-induced operon that likely enables chondroitin sulfate recognition. These and other data suggest that strain Hel1_33_49 is a planktonic flavobacterium feeding on proteins and a small subset of algal polysaccharides, while the more versatile strain Hel1_85 can decompose a broader spectrum of polysaccharides and likely associates with algae.

In recent years, representatives of the Bacteroidetes have been increasingly recognized as specialists for the degradation of macromolecules. Formosa constitutes a Bacteroidetes genus within the class Flavobacteria, and the members of this genus have been found in marine habitats with high levels of organic matter, such as in association with algae, invertebrates, and fecal pellets. Here we report on the generation and analysis of the genome of the type strain of Formosa agariphila (KMM 3901 T ), an isolate from the green alga Acrosiphonia sonderi. F. agariphila is a facultative anaerobe with the capacity for mixed acid fermentation and denitrification. Its genome harbors 129 proteases and 88 glycoside hydrolases, indicating a pronounced specialization for the degradation of proteins, polysaccharides, and glycoproteins. Sixty-five of the glycoside hydrolases are organized in at least 13 distinct polysaccharide utilization loci, where they are clustered with TonB-dependent receptors, SusD-like proteins, sensors/ transcription factors, transporters, and often sulfatases. These loci play a pivotal role in bacteroidetal polysaccharide biodegradation and in the case of F. agariphila revealed the capacity to degrade a wide range of algal polysaccharides from green, red, and brown algae and thus a strong specialization of toward an alga-associated lifestyle. This was corroborated by growth experiments, which confirmed usage particularly of those monosaccharides that constitute the building blocks of abundant algal polysaccharides, as well as distinct algal polysaccharides, such as laminarins, xylans, and -carrageenans.

To investigate the changes in the morphology and polysaccharide content of Microcystis aeruginosa (Kütz.) Kütz. during flagellate grazing, cultures of M. aeruginosa were exposed to grazing Ochromonas sp. for a period of 9 d under controlled laboratory conditions. M. aeruginosa responded actively to flagellate grazing and formed colonies, most of which were made up of several or dozens of cells, suggesting that flagellate grazing may be one of the biotic factors responsible for colony formation in M. aeruginosa. When colonies were formed, the cell surface ultrastructure changed, and the polysaccharide layer on the surface of the cell wall became thicker. This change indicated that synthesis and secretion of extracellular polysaccharide (EPS) of M. aeruginosa cells increased under flagellate grazing pressure. The contents of soluble extracellular polysaccharide (sEPS), bound extracellular polysaccharide (bEPS), and total polysaccharide (TPS) in colonial cells of M. aeruginosa increased significantly compared with those in single cells. This finding suggested that the increased amount of EPS on the cell surface may play a role in keeping M. aeruginosa cells together to form colonies.

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Plankton samples were collected from six remote freshwater and saline lakes located at altitudes of 3,204 to 4,718 m and 1,000 km apart within an area of ca. 1 million km 2 on the eastern Tibetan Plateau to comparatively assess how environmental factors influence the diversity of bacterial communities in high-altitude lakes. The composition of the bacterioplankton was investigated by analysis of large clone libraries of 16S rRNA genes. Comparison of bacterioplankton diversities estimated for the six Tibetan lakes with reference data previously published for lakes located at lower altitudes indicated relatively low taxon richness in the Tibetan lakes. The estimated average taxon richness in the four Tibetan freshwater lakes was only one-fifth of the average taxon richness estimated for seven low-altitude reference lakes. This cannot be explained by low coverage of communities in the Tibetan lakes by the established libraries or by differences in habitat size. Furthermore, a comparison of the taxonomic compositions of bacterioplankton across the six Tibetan lakes revealed low overlap between their community compositions. About 70.9% of the operational taxonomic units (99% similarity) were specific to single lakes, and a relatively high percentage (11%) of sequences were <95% similar to publicly deposited sequences of cultured or uncultured bacteria. This beta diversity was explained by differences in salinity between lakes rather than by distance effects. Another characteristic of the investigated lakes was the predominance of Cyanobacteria (Synechococcus) and Bacteroidetes. These features of bacterioplankton diversity may reflect specific adaptation of various lineages to the environmental conditions in these highaltitude lakes.

Bacterial communities comprise large numbers of species and normally include a few abundant taxa and many rare taxa. These two subcommunities may have fundamentally different ecological roles, and it is not clear whether their diversity patterns along elevation gradients vary. In this study, we investigated the diversity of bacterioplankton and their subcommunities, i.e., abundant and rare bacterioplankton, in lakes across gradual elevations from 525 m to 4652 m at Siguniang Mountain in western China via the high-throughput sequencing of bacterial 16S rRNA genes. Elevation showed strong influence on bacterioplankton community composition (BCC) and that the dissimilarity of BCC increased with increasing differences in elevation. However, the elevational distance-decay rate of abundant bacterioplankton was higher than that of rare bacterioplankton. Abundant bacterioplankton were more sensitive to changes of environmental factors than rare bacterioplankton. We observed a marginal increase in alpha diversity, estimated as operational taxonomic unit richness and phylogenetic diversity, of overall bacterioplankton with increasing elevation. The alpha diversity of abundant bacterioplankton decreased monotonically with elevation; in contrast, the alpha diversity of rare bacterioplankton increased monotonically with elevation. Null model tests indicated that environmental filtering played a dominant role in overall bacterioplankton community assembly along the elevation gradient, while there was decreased contribution of environmental selection to rare bacterioplankton in smaller lakes at higher elevation. Our results revealed that abundant bacterioplankton followed the general elevation diversity theory commonly found for plants and animals in freshwater lakes, whereas rare bacterioplankton did not follow this tenet.

c pH is an important factor that shapes the structure of bacterial communities. However, we have very limited information about the patterns and processes by which overall bacterioplankton communities assemble across wide pH gradients in natural freshwater lakes. Here, we used pyrosequencing to analyze the bacterioplankton communities in 25 discrete freshwater lakes in Denmark with pH levels ranging from 3.8 to 8.8. We found that pH was the key factor impacting lacustrine bacterioplankton community assembly. More acidic lakes imposed stronger environmental filtering, which decreased the richness and evenness of bacterioplankton operational taxonomic units (OTUs) and largely shifted community composition. Although environmental filtering was determined to be the most important determinant of bacterioplankton community assembly, the importance of neutral assembly processes must also be considered, notably in acidic lakes, where the species (OTU) diversity was low. We observed that the strong effect of environmental filtering in more acidic lakes was weakened by the enhanced relative importance of neutral community assembly, and bacterioplankton communities tended to be less phylogenetically clustered in more acidic lakes. In summary, we propose that pH is a major environmental determinant in freshwater lakes, regulating the relative importance and interplay between niche-related and neutral processes and shaping the patterns of freshwater lake bacterioplankton biodiversity. Bacterioplankton are a crucial component of aquatic ecosystems, and they play an important role in the ecological processes of freshwater lakes (1, 2). Understanding the mechanisms governing bacterioplankton community assembly (e.g., community composition, diversity, and phylogenetic structure) in natural freshwater lakes is a longstanding challenge in microbial community ecology. There is increasing evidence that the community structure of freshwater lake bacterioplankton is influenced by niche-related (deterministic) and neutral (stochastic) processes (2-4). Niche-related processes (5) include selection imposed by the abiotic environment (environmental filtering) and species interactions (competition, facilitation, mutualism, and predation), whereas neutral effects (6) include stochastic processes, such as unpredictable disturbances, probabilistic dispersal, and random birth/death events (7,8). Neutral processes likely result in random fluctuations in community composition along a given environmental gradient (9). The observation that both niche and neutral processes are important in shaping bacterioplankton community assembly raises the question of what affects the relative contributions and interplay between stochastic and deterministic processes in structuring lacustrine bacterioplankton assembly.Multiple environmental factors regulate the distribution of bacterioplankton communities in freshwater lakes (10-16). pH is proposed to be an important environmental factor influencing both overall bacterioplankton community composition (BCC) (2, ...

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