Global phylogeography of marine <i>Synechococcus</i> and <i>Prochlorococcus</i> reveals a distinct partitioning of lineages among oceanic biomes

Zwirglmaier, Katrin; Jardillier, Ludwig; Ostrowski, Martin; Mazard, Sophie; Garczarek, Laurence; Vaulot, Daniel; Not, Fabrice; Massana, Ramón; Ulloa, Osvaldo; Scanlan, David J.

doi:10.1111/j.1462-2920.2007.01440.x

Cited by 414 publications

(631 citation statements)

References 52 publications

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“…It has been shown that some prokaryotes, such as the SAR11 clade (Morris et al 2002), occur globally, whereas others, like the RCA (Roseobacter clade affiliated) phylogenetic cluster, exhibit distinct distribution patterns and appear to reflect features of distinct marine biomes or even regional systems (Selje et al 2004, Pommier et al 2005. Cyanobacterial lineages also distribute differentially across marine biomes (Zwirglmaier et al 2008). In fact, analysis of the metagenomic libraries of samples from the northwest Atlantic and eastern tropical Pacific 'Sorcerer II' global ocean sampling expedition revealed distinct regional patterns of the phylogenetic diversity (richness) of the prokaryotic communities (Rusch et al 2007).…”

Section: Refined Functional and Regional Resolutionmentioning

confidence: 99%

Towards a better understanding of microbial carbon flux in the sea*

Gasol¹,

Pinhassi²,

Alonso‐Sáez³

et al. 2008

Aquat. Microb. Ecol.

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We now have a relatively good idea of how bulk microbial processes shape the cycling of organic matter and nutrients in the sea. The advent of the molecular biology era in microbial ecology has resulted in advanced knowledge about the diversity of marine microorganisms, suggesting that we might have reached a high level of understanding of carbon fluxes in the oceans. However, it is becoming increasingly clear that there are large gaps in the understanding of the role of bacteria in regulating carbon fluxes. These gaps may result from methodological as well as conceptual limitations. For example, should bacterial production be measured in the light? Can bacterial production conversion factors be predicted, and how are they affected by loss of tracers through respiration? Is it true that respiration is relatively constant compared to production? How can accurate measures of bacterial growth efficiency be obtained? In this paper, we discuss whether such questions could (or should) be addressed. Ongoing genome analyses are rapidly widening our understanding of possible metabolic pathways and cellular adaptations used by marine bacteria in their quest for resources and struggle for survival (e.g. utilization of light, acquisition of nutrients, predator avoidance, etc.). Further, analyses of the identity of bacteria using molecular markers (e.g. subgroups of Bacteria and Archaea) combined with activity tracers might bring knowledge to a higher level. Since bacterial growth (and thereby consumption of DOC and inorganic nutrients) is likely regulated differently in different bacteria, it will be critical to learn about the life strategies of the key bacterial species to achieve a comprehensive understanding of bacterial regulation of C fluxes. Finally, some processes known to occur in the microbial food web are hardly ever characterized and are not represented in current food web models. We discuss these issues and offer specific comments and advice for future research agendas.

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Section: Refined Functional and Regional Resolutionmentioning

confidence: 99%

Towards a better understanding of microbial carbon flux in the sea*

Gasol¹,

Pinhassi²,

Alonso‐Sáez³

et al. 2008

Aquat. Microb. Ecol.

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“…However, noteworthy is that all three sites have comparatively high chlorophyll a concentrations (ranging between 0.28 and 1.37 mg m À 3 ) and moderate species richness determined by the Margalef index. Even so, resolving the combination of parameters responsible for structuring the PPE community is likely to be much more complex than for picocyanobacterial communities (Zwirglmaier et al, 2008) given the differences of taxonomic resolution between groups (picocyanobacteria have been studied at the genera level).…”

Section: Ppe B-diversitymentioning

confidence: 99%

A global perspective on marine photosynthetic picoeukaryote community structure

et al. 2013

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A central goal in ecology is to understand the factors affecting the temporal dynamics and spatial distribution of microorganisms and the underlying processes causing differences in community structure and composition. However, little is known in this respect for photosynthetic picoeukaryotes (PPEs), algae that are now recognised as major players in marine CO 2 fixation. Here, we analysed dot blot hybridisation and cloning-sequencing data, using the plastid-encoded 16S rRNA gene, from seven research cruises that encompassed all four ocean biomes. We provide insights into global abundance, a-and b-diversity distribution and the environmental factors shaping PPE community structure and composition. At the class level, the most commonly encountered PPEs were Prymnesiophyceae and Chrysophyceae. These taxa displayed complementary distribution patterns, with peak abundances of Prymnesiophyceae and Chrysophyceae in waters of high (25:1) or low (12:1) nitrogen:phosphorus (N:P) ratio, respectively. Significant differences in phylogenetic composition of PPEs were demonstrated for higher taxonomic levels between ocean basins, using Unifrac analyses of clone library sequence data. Differences in composition were generally greater between basins (interbasins) than within a basin (intrabasin). These differences were primarily linked to taxonomic variation in the composition of Prymnesiophyceae and Prasinophyceae whereas Chrysophyceae were phylogenetically similar in all libraries. These data provide better knowledge of PPE community structure across the world ocean and are crucial in assessing their evolution and contribution to CO 2 fixation, especially in the context of global climate change.

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“…Previous investigations of Prochlorococcus biogeography have characterized phylogenetic diversity using specific genetic markers that reflect genome content to an unknown extent (Bouman et al, 2006;Johnson et al, 2006;Zwirglmaier et al, 2008). Metagenomics has also been employed to examine Prochlorococcus genomic diversity at smaller regional scales (Hewson et al, 2009;Rusch et al, 2010;Thompson et al, 2013) but not yet on a global scale.…”

Section: Introductionmentioning

confidence: 99%

“…Within the group, there are multiple phylogenetically distinct lineages and the distribution of this diversity has been linked to environmental factors, such as light, temperature and iron availability (Moore et al, 1998;West and Scanlan, 1999;Johnson et al, 2006;Zwirglmaier et al, 2008;Rusch et al, 2010). It has been suggested that pangenome variability allows Prochlorococcus as a genus to proliferate across many environments (Partensky et al, 1999;Kettler et al, 2007), but it is unclear how the mechanisms of descent contribute to their evolution and the diversity of local populations.…”

Section: Introductionmentioning

confidence: 99%

Global biogeography of Prochlorococcus genome diversity in the surface ocean

et al. 2016

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Prochlorococcus, the smallest known photosynthetic bacterium, is abundant in the ocean's surface layer despite large variation in environmental conditions. There are several genetically divergent lineages within Prochlorococcus and superimposed on this phylogenetic diversity is extensive gene gain and loss. The environmental role in shaping the global ocean distribution of genome diversity in Prochlorococcus is largely unknown, particularly in a framework that considers the vertical and lateral mechanisms of evolution. Here we show that Prochlorococcus field populations from a global circumnavigation harbor extensive genome diversity across the surface ocean, but this diversity is not randomly distributed. We observed a significant correspondence between phylogenetic and gene content diversity, including regional differences in both phylogenetic composition and gene content that were related to environmental factors. Several gene families were strongly associated with specific regions and environmental factors, including the identification of a set of genes related to lower nutrient and temperature regions. Metagenomic assemblies of natural Prochlorococcus genomes reinforced this association by providing linkage of genes across genomic backbones. Overall, our results show that the phylogeography in Prochlorococcus taxonomy is echoed in its genome content. Thus environmental variation shapes the functional capabilities and associated ecosystem role of the globally abundant Prochlorococcus.

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Global phylogeography of marine Synechococcus and Prochlorococcus reveals a distinct partitioning of lineages among oceanic biomes

Cited by 414 publications

References 52 publications

Towards a better understanding of microbial carbon flux in the sea*

Towards a better understanding of microbial carbon flux in the sea*

A global perspective on marine photosynthetic picoeukaryote community structure

Global biogeography of Prochlorococcus genome diversity in the surface ocean

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