Effect of dietary changes on the bacteriophage population in the rumen of sheep

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The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin

BACKGROUND: The hydrogenosomes of the anaerobic ciliate Nyctotherus ovalis show how mitochondria can evolve into hydrogenosomes because they possess a mitochondrial genome and parts of an electron-transport chain on the one hand, and a hydrogenase on the other hand. The hydrogenase permits direct reoxidation of NADH because it consists of a [FeFe] hydrogenase module that is fused to two modules, which are homologous to the 24 kDa and the 51 kDa subunits of a mitochondrial complex I. RESULTS: The [FeFe] hydrogenase belongs to a clade of hydrogenases that are different from well-known eukaryotic hydrogenases. The 24 kDa and the 51 kDa modules are most closely related to homologous modules that function in bacterial [NiFe] hydrogenases. Paralogous, mitochondrial 24 kDa and 51 kDa modules function in the mitochondrial complex I in N. ovalis. The different hydrogenase modules have been fused to form a polyprotein that is targeted into the hydrogenosome. CONCLUSION: The hydrogenase and their associated modules have most likely been acquired by independent lateral gene transfer from different sources. This scenario for a concerted lateral gene transfer is in agreement with the evolution of the hydrogenosome from a genuine ciliate mitochondrion by evolutionary tinkering

Groups without cultured representatives dominate eukaryotic picophytoplankton in the oligotrophic South East Pacific Ocean

Background: Photosynthetic picoeukaryotes (PPE) with a cell size less than 3 µm play a critical role in oceanic primary production. In recent years, the composition of marine picoeukaryote communities has been intensively investigated by molecular approaches, but their photosynthetic fraction remains poorly characterized. This is largely because the classical approach that relies on constructing 18S rRNA gene clone libraries from filtered seawater samples using universal eukaryotic primers is heavily biased toward heterotrophs, especially alveolates and stramenopiles, despite the fact that autotrophic cells in general outnumber heterotrophic ones in the euphotic zone. Methodology/Principal Findings: In order to better assess the composition of the eukaryotic picophytoplankton in the South East Pacific Ocean, encompassing the most oligotrophic oceanic regions on earth, we used a novel approach based on flow cytometry sorting followed by construction of 18S rRNA gene clone libraries. This strategy dramatically increased the recovery of sequences from putative autotrophic groups. The composition of the PPE community appeared highly variable both vertically down the water column and horizontally across the South East Pacific Ocean. In the central gyre, uncultivated lineages dominated: a recently discovered clade of Prasinophyceae (IX), clades of marine Chrysophyceae and Haptophyta, the latter division containing a potentially new class besides Prymnesiophyceae and Pavlophyceae. In contrast, on the edge of the gyre and in the coastal Chilean upwelling, groups with cultivated representatives (Prasinophyceae clade VII and Mamiellales) dominated. Conclusions/Significance: Our data demonstrate that a very large fraction of the eukaryotic picophytoplankton still escapes cultivation. The use of flow cytometry sorting should prove very useful to better characterize specific plankton populations by molecular approaches such as gene cloning or metagenomics, and also to obtain into culture strains representative of these novel groups

How and why DNA barcodes underestimate the diversity of microbial eukaryotes

Background: Because many picoplanktonic eukaryotic species cannot currently be maintained in culture, direct sequencing of PCR-amplified 18S ribosomal gene DNA fragments from filtered sea-water has been successfully used to investigate the astounding diversity of these organisms. The recognition of many novel planktonic organisms is thus based solely on their 18S rDNA sequence. However, a species delimited by its 18S rDNA sequence might contain many cryptic species, which are highly differentiated in their protein coding sequences. Principal Findings: Here, we investigate the issue of species identification from one gene to the whole genome sequence. Using 52 whole genome DNA sequences, we estimated the global genetic divergence in protein coding genes between organisms from different lineages and compared this to their ribosomal gene sequence divergences. We show that this relationship between proteome divergence and 18S divergence is lineage dependant. Unicellular lineages have especially low 18S divergences relative to their protein sequence divergences, suggesting that 18S ribosomal genes are too conservative to assess planktonic eukaryotic diversity. We provide an explanation for this lineage dependency, which suggests that most species with large effective population sizes will show far less divergence in 18S than protein coding sequences. Conclusions: There is therefore a trade-off between using genes that are easy to amplify in all species, but which by their nature are highly conserved and underestimate the true number of species, and using genes that give a better description of the number of species, but which are more difficult to amplify. We have shown that this trade-off differs between unicellular and multicellular organisms as a likely consequence of differences in effective population sizes. We anticipate that biodiversity of microbial eukaryotic species is underestimated and that numerous ''cryptic species'' will become discernable with the future acquisition of genomic and metagenomic sequences

Increasing importance of small phytoplankton in a warmer ocean

Author Posting. © The Author(s), 2009. This is the author's version of the work. It is posted here by permission of Blackwell Publishing for personal use, not for redistribution. The definitive version was published in Global Change Biology 16 (2010): 1137-1144, doi:10.1111/j.1365-2486.2009.01960.x.The macroecological relationships between marine phytoplankton total cell density, community size structure and temperature have lacked a theoretical explanation. The tiniest members of this planktonic group comprise cyanobacteria and eukaryotic algae smaller than 2 μm in diameter, collectively known as picophytoplankton. We combine here two ecological rules, the temperature-size relationship with the allometric size-scaling of population abundance to explain a remarkably consistent pattern of increasing picophytoplankton biomass with temperature over the -0.6 to 22ºC range in a merged dataset obtained in the eastern and western temperate North Atlantic Ocean across a diverse range of environmental conditions. Our results show that temperature alone was able to explain 73% of the variance in the relative contribution of small cells to total phytoplankton biomass regardless of differences in trophic status or inorganic nutrient loading. Our analysis predicts a gradual shift towards smaller primary producers in a warmer ocean. Since the fate of photosynthesized organic carbon largely depends on phytoplankton size we anticipate future alterations in the functioning of oceanic ecosystems.X.A.G.M., A.C.-D. and Á.L.-U. acknowledge the financial support of research grants VARIPLACA (REN2001-0345/MAR), PERPLAN (CTM2006-04854/MAR) and the RADIALES time-series program of the Instituto Español de Oceanografía. W.K.W.L. was supported by the Canadian Department of Fisheries and Oceans Strategic Science Fund in the Ocean Climate Program and the Atlantic Zone Monitoring Program. This work was partially funded by Theme 6 of the EU Seventh Framework Programme through the Marine Ecosystem Evolution in a Changing Environment (MEECE No 212085) Collaborative Project

Photosynthetic pigments of oceanic chlorophyta belonging to prasinophytes clade VII

Preprin

Sampling bias misrepresents the biogeographical significance of constitutive mixotrophs across global oceans

Aim Most protist plankton are mixotrophic, with potential to engage in photoautotrophy and phagotrophy; however, the ecology of these organisms has been misdiagnosed for over a century. A large proportion of these organisms are constitutive mixotrophs (CMs), with an innate ability to photosynthesize. Here, for the first time, an analysis is presented of the biogeography of CMs across the oceans. Location Global marine ecosystems. Time period 1970–2018. Major taxa studied Marine planktonic protists. Methods Records for CM species, primarily from the Ocean Biogeographic Information System (OBIS), were grouped by taxonomy and size to evaluate sampling efforts across Longhurst's oceanic provinces. Biases were evaluated through nonparametric tests and multivariate analysis. Biogeographies of CMs from OBIS data were compared with data from studies that specifically targeted these organisms. Results Constitutive mixotrophs of different taxonomic groups, across all size ranges, are ubiquitous. However, strong database biases were detected with respect to organism size, taxonomic groups and region. A strong bias was seen towards dinophytes. Species Main conclusions Constitutive mixotrophs are dominant members of organisms traditionally termed “phytoplankton”. However, lack of routine protocols for measuring phagotrophy in “phytoplankton” protists has led to widespread misrepresentation of the fundamental nature of marine planktonic primary producers; most express both “animal‐like” and “plant‐like” nutrition. Our results have implications for studies of the global biogeography of plankton, of food web dynamics (including models) and of biogeochemical cycling in the oceans