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Stephen J Giovannoni - One of the best experts on this subject based on the ideXlab platform.
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Pelagibacter metabolism of diatom-derived volatile organic compounds imposes an energetic tax on photosynthetic carbon fixation.
Environmental microbiology, 2019Co-Authors: Eric R. Moore, Stephen J Giovannoni, Cleo L. Davie-martin, Kimberly H. HalseyAbstract:Volatile organic compounds (VOCs) produced by phytoplankton are molecules with high vapor pressures that can diffuse across cell membranes into the environment, where they become public goods. VOCs likely comprise a significant component of the marine dissolved organic carbon (DOC) pool utilized by microorganisms, but they are often overlooked as growth substrates because their diffusivity imposes analytical challenges. The roles of VOCs in the growth of the photoautotrophic diatom Thalassiosira pseudonana and heterotrophic bacterium Pelagibacter sp. HTCC1062 (SAR11) were examined using co-cultures and proton-transfer reaction time-of-flight mass spectrometry. VOCs at 82 m/z values were produced in the cultures, and the concentrations of 9 of these m/z values changed in co-culture relative to the diatom monoculture. Several of the m/z values were putatively identified, and their metabolism by HTCC1062 was confirmed by measuring ATP production. Diatom carbon fixation rates in co-culture with HTCC1062 were 20.3% higher than the diatom monoculture. Removal of VOCs from the T. pseudonana monoculture using a hydrocarbon trap caused a similar increase in carbon fixation (18.1%). These results show that a wide range of VOCs are cycled in the environment, and the flux of VOCs from phytoplankton to bacterioplankton imposes a large and unexpected tax on phytoplankton photosynthesis.
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SAR11 bacteria have a high affinity and multifunctional glycine betaine transporter.
Environmental microbiology, 2019Co-Authors: Stephen E. Noell, Stephen J GiovannoniAbstract:Marine bacterioplankton face stiff competition for limited nutrient resources. SAR11, a ubiquitous clade of very small and highly abundant Alphaproteobacteria, are known to devote much of their energy to synthesizing ATP-binding cassette periplasmic proteins that bind substrates. We hypothesized that their small size and relatively large periplasmic space might enable them to outcompete other bacterioplankton for nutrients. Using uptake experiments with 14 C-glycine betaine, we discovered that two strains of SAR11, Candidatus Pelagibacter sp. HTCC7211 and Cand. P. ubique HTCC1062, have extraordinarily high affinity for glycine betaine (GBT), with half-saturation (K s ) values around 1 nM and specific affinity values between 8 and 14 L mg cell-1 h-1 . Competitive inhibition studies indicated that the GBT transporters in these strains are multifunctional, transporting multiple substrates in addition to GBT. Both strains could use most of the transported compounds for metabolism and ATP production. Our findings indicate that Pelagibacter cells are primarily responsible for the high affinity and multifunctional GBT uptake systems observed in seawater. Maximization of whole-cell affinities may enable these organisms to compete effectively for nutrients during periods when the gross transport capacity of the heterotrophic plankton community exceeds the supply, depressing ambient concentrations.
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A Parasitic Arsenic Cycle That Shuttles Energy from Phytoplankton to Heterotrophic Bacterioplankton
mBio, 2019Co-Authors: Stephen J Giovannoni, Ben Temperton, Jing Sun, Kimberly H. Halsey, Jimmy H. Saw, Omran Muslin, Christopher P. Suffridge, Chih-ping Lee, Eric R. Moore, Stephen E. NoellAbstract:ABSTRACT In many regions of the world oceans, phytoplankton face the problem of discriminating between phosphate, an essential nutrient, and arsenate, a toxic analogue. Many phytoplankton, including the most abundant phytoplankton group known, Prochlorococcus, detoxify arsenate (AsV) by reduction to arsenite (AsIII), followed by methylation and excretion of the methylated arsenic products. We synthesized [14C]dimethyl arsenate (DMA) and used it to show that cultured Pelagibacter strain HTCC7211 (SAR11) cells oxidize the methyl group carbons of DMA, producing 14CO2 and ATP. We measured [14C]DMA oxidation rates in the P-depleted surface waters of the Sargasso Sea, a subtropical ocean gyre. [14C]DMA was oxidized to 14CO2 by Sargasso Sea plankton communities at a rate that would cause turnover of the estimated DMA standing stock every 8.1 days. SAR11 strain HTCC7211, which was isolated from the Sargasso Sea, has a pair of arsenate resistance genes and was resistant to arsenate, showing no growth inhibition at As/P ratios of >65:1. Across the global oceans, there was a strong inverse relationship between the frequency of the arsenate reductase (LMWPc_ArsC) in Pelagibacter genomes and phosphate concentrations. We propose that the demethylation of methylated arsenic compounds by Pelagibacter and possibly other bacterioplankton, coupled with arsenate resistance, results in the transfer of energy from phytoplankton to bacteria. We dub this a parasitic cycle because the release of arsenate by Pelagibacter in principle creates a positive-feedback loop that forces phytoplankton to continually regenerate arsenate detoxification products, producing a flow of energy to P-limited ocean regions. IMPORTANCE In vast, warm regions of the oceans, phytoplankton face the problem of arsenic poisoning. Arsenate is toxic because it is chemically similar to phosphate, a scarce nutrient that phytoplankton cells need for growth. Many phytoplankton, including the commonest phytoplankton type in warm oceans, Prochlorococcus, detoxify arsenate by adding methyl groups. Here we show that the most abundant non-photosynthetic plankton in the oceans, SAR11 bacteria, remove the methyl groups, releasing poisonous forms of arsenic back into the water. We postulate that the methylation and demethylation of arsenic compounds creates a cycle in which the phytoplankton can never get ahead and must continually transfer energy to the SAR11 bacteria. We dub this a parasitic process and suggest that it might help explain why SAR11 bacteria are so successful, surpassing all other plankton in their numbers. Field experiments were done in the Sargasso Sea, a subtropical ocean gyre that is sometimes called an ocean desert because, throughout much of the year, there is not enough phosphorous in the water to support large blooms of phytoplankton. Ocean deserts are expanding as the oceans absorb heat and grow warmer.
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A Parasitic Arsenic Cycle That Shuttles Energy from Phytoplankton to Heterotrophic Bacterioplankton
American Society for Microbiology, 2019Co-Authors: Stephen J Giovannoni, Ben Temperton, Jing Sun, Kimberly H. Halsey, Omran Muslin, Christopher P. Suffridge, Chih-ping Lee, Eric R. Moore, Jimmy Saw, Stephen E. NoellAbstract:In vast, warm regions of the oceans, phytoplankton face the problem of arsenic poisoning. Arsenate is toxic because it is chemically similar to phosphate, a scarce nutrient that phytoplankton cells need for growth. Many phytoplankton, including the commonest phytoplankton type in warm oceans, Prochlorococcus, detoxify arsenate by adding methyl groups. Here we show that the most abundant non-photosynthetic plankton in the oceans, SAR11 bacteria, remove the methyl groups, releasing poisonous forms of arsenic back into the water. We postulate that the methylation and demethylation of arsenic compounds creates a cycle in which the phytoplankton can never get ahead and must continually transfer energy to the SAR11 bacteria. We dub this a parasitic process and suggest that it might help explain why SAR11 bacteria are so successful, surpassing all other plankton in their numbers. Field experiments were done in the Sargasso Sea, a subtropical ocean gyre that is sometimes called an ocean desert because, throughout much of the year, there is not enough phosphorous in the water to support large blooms of phytoplankton. Ocean deserts are expanding as the oceans absorb heat and grow warmer.In many regions of the world oceans, phytoplankton face the problem of discriminating between phosphate, an essential nutrient, and arsenate, a toxic analogue. Many phytoplankton, including the most abundant phytoplankton group known, Prochlorococcus, detoxify arsenate (AsV) by reduction to arsenite (AsIII), followed by methylation and excretion of the methylated arsenic products. We synthesized [14C]dimethyl arsenate (DMA) and used it to show that cultured Pelagibacter strain HTCC7211 (SAR11) cells oxidize the methyl group carbons of DMA, producing 14CO2 and ATP. We measured [14C]DMA oxidation rates in the P-depleted surface waters of the Sargasso Sea, a subtropical ocean gyre. [14C]DMA was oxidized to 14CO2 by Sargasso Sea plankton communities at a rate that would cause turnover of the estimated DMA standing stock every 8.1 days. SAR11 strain HTCC7211, which was isolated from the Sargasso Sea, has a pair of arsenate resistance genes and was resistant to arsenate, showing no growth inhibition at As/P ratios of >65:1. Across the global oceans, there was a strong inverse relationship between the frequency of the arsenate reductase (LMWPc_ArsC) in Pelagibacter genomes and phosphate concentrations. We propose that the demethylation of methylated arsenic compounds by Pelagibacter and possibly other bacterioplankton, coupled with arsenate resistance, results in the transfer of energy from phytoplankton to bacteria. We dub this a parasitic cycle because the release of arsenate by Pelagibacter in principle creates a positive-feedback loop that forces phytoplankton to continually regenerate arsenate detoxification products, producing a flow of energy to P-limited ocean regions
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Data_SAR11CNP
2018Co-Authors: Angelicque E. White, Stephen J Giovannoni, Yanlin Zhao, Kevin Vergin, Craig A. CarlsonAbstract:This file contains elemental data used to calculate C:N:P ratios for strains of Pelagibacter (SAR11). There are also tabs detailing the calculation of genomic phosphorus content and the potential contribution of SAR11 to gross primary production
Manuel Martinez-garcia - One of the best experts on this subject based on the ideXlab platform.
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Diel cycling of the cosmopolitan abundant Pelagibacter virus 37-F6: one of the most abundant viruses on earth.
Environmental microbiology reports, 2020Co-Authors: Francisco Martinez-hernandez, Edward F Delong, Elaine Luo, Kento Tominaga, Hiroyuki Ogata, Takashi Yoshida, Manuel Martinez-garciaAbstract:The spatiotemporal dynamics for marine viral populations has only recently been explored. However, nothing is known about temporal activities of the uncultured Pelagibacter virus vSAG 37-F6, which was discovered by single-virus genomics as potentially the most abundant marine virus. Here, we investigate the diel cycling of 37-F6 virus and the putative SAR11 host using coastal and oceanic transcriptomic and viromic time-series data from Osaka Bay and North Pacific Subtropical Gyre. Virus 37-F6 and relatives displayed diel cycling of transcriptional activities synchronized with its putative host. In both virus and host, the lowest transcription rates were observed at 14:00-15:00, coinciding roughly with maximum solar irradiance, while higher transcriptional rates were detected during the night/early morning and afternoon. Diel abundance of free viruses of 37-F6 in seawater roughly mirrored the transcriptional activities of both virus and host. In Osaka Bay, among viral relatives (genus level), virus 37-F6 specifically showed the highest ratio of transcriptional activity to virome abundance, a proxy for viral transcriptional activity relative to free viral particle abundance. This high ratio suggests high infection rate efficiencies in vSAG 37-F6 virus compared to viral relatives. Thus, time-series data revealed temporal transcript activities in one of the most abundant viruses in Earth.
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Droplet Digital PCR for Estimating Absolute Abundances of Widespread Pelagibacter Viruses.
Frontiers in microbiology, 2019Co-Authors: Francisco Martinez-hernandez, Monica Lluesma Gomez, Inmaculada Garcia-heredia, Lucia Maestre-carballa, Joaquín Martínez Martínez, Manuel Martinez-garciaAbstract:This work has been supported by Spanish Ministry of Economy and Competitiveness (Ref. RTI2018-094248-B-I00), Generalitat Valenciana (Ref. ACOM/2015/133 and ACIF/2015/332), and Gordon and Betty Moore Foundation (Grant 5334).
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Single-cell genomics uncover Pelagibacter as the putative host of the extremely abundant uncultured 37-F6 viral population in the ocean.
The ISME journal, 2018Co-Authors: Francisco Martinez-hernandez, Oscar Fornas, Monica Lluesma Gomez, Inmaculada Garcia-heredia, Lucia Maestre-carballa, Mario López-pérez, Jose M. Haro-moreno, Francisco Rodriguez-valera, Manuel Martinez-garciaAbstract:The identification of relevant virus-host pairs that globally account for a large pool of carbon and nutrients in the ocean is paramount to build accurate ecological models. A previous work using single-virus genomics led to the discovery of the uncultured single-virus vSAG 37-F6, originally sorted from the Mediterranean Sea (Blanes Bay Microbial Observatory), that represents one of the most abundant dsDNA viral population in the marine surface virosphere. Here, from same sampling site, we report that a Pelagibacter single-cell contained a viral member of vSAG 37-F6 population, by means of PCR screening of sorted, genome-amplified single cells with vSAG 37-F6-specific primers and whole-genome sequencing. Furthermore, viruses from this population were also found in three other Pelagibacter single cells from the South Pacific and Atlantic oceans. These new uncultured pelagiphages were genetically different from the previously characterized pelagiphage isolates. Data showed that the uncultured vSAG 37-F6 population represents the Pelagibacter phages that inhabit the sunlit ocean better, and contains a vast unrecognized microdiversity.
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Unveiling in situ interactions between marine protists and bacteria through single cell sequencing
The ISME journal, 2011Co-Authors: Manuel Martinez-garcia, Monica Lluesma Gomez, David M. Brazel, Nicole J. Poulton, Brandon K. Swan, Dashiell Masland, Michael E. Sieracki, Ramunas StepanauskasAbstract:Heterotrophic protists are a highly diverse and biogeochemically significant component of marine ecosystems, yet little is known about their species-specific prey preferences and symbiotic interactions in situ. Here we demonstrate how these previously unresolved questions can be addressed by sequencing the eukaryote and bacterial SSU rRNA genes from individual, uncultured protist cells collected from their natural marine environment and sorted by flow cytometry. We detected Pelagibacter ubique in association with a MAST-4 protist, an actinobacterium in association with a chrysophyte and three bacteroidetes in association with diverse protist groups. The presence of identical phylotypes among the putative prey and the free bacterioplankton in the same sample provides evidence for predator–prey interactions. Our results also suggest a discovery of novel symbionts, distantly related to Rickettsiales and the candidate divisions ZB3 and TG2, associated with Cercozoa and Chrysophyta cells. This study demonstrates the power of single cell sequencing to untangle ecological interactions between uncultured protists and prokaryotes.
Francisco Martinez-hernandez - One of the best experts on this subject based on the ideXlab platform.
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Diel cycling of the cosmopolitan abundant Pelagibacter virus 37-F6: one of the most abundant viruses on earth.
Environmental microbiology reports, 2020Co-Authors: Francisco Martinez-hernandez, Edward F Delong, Elaine Luo, Kento Tominaga, Hiroyuki Ogata, Takashi Yoshida, Manuel Martinez-garciaAbstract:The spatiotemporal dynamics for marine viral populations has only recently been explored. However, nothing is known about temporal activities of the uncultured Pelagibacter virus vSAG 37-F6, which was discovered by single-virus genomics as potentially the most abundant marine virus. Here, we investigate the diel cycling of 37-F6 virus and the putative SAR11 host using coastal and oceanic transcriptomic and viromic time-series data from Osaka Bay and North Pacific Subtropical Gyre. Virus 37-F6 and relatives displayed diel cycling of transcriptional activities synchronized with its putative host. In both virus and host, the lowest transcription rates were observed at 14:00-15:00, coinciding roughly with maximum solar irradiance, while higher transcriptional rates were detected during the night/early morning and afternoon. Diel abundance of free viruses of 37-F6 in seawater roughly mirrored the transcriptional activities of both virus and host. In Osaka Bay, among viral relatives (genus level), virus 37-F6 specifically showed the highest ratio of transcriptional activity to virome abundance, a proxy for viral transcriptional activity relative to free viral particle abundance. This high ratio suggests high infection rate efficiencies in vSAG 37-F6 virus compared to viral relatives. Thus, time-series data revealed temporal transcript activities in one of the most abundant viruses in Earth.
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Droplet Digital PCR for Estimating Absolute Abundances of Widespread Pelagibacter Viruses.
Frontiers in microbiology, 2019Co-Authors: Francisco Martinez-hernandez, Monica Lluesma Gomez, Inmaculada Garcia-heredia, Lucia Maestre-carballa, Joaquín Martínez Martínez, Manuel Martinez-garciaAbstract:This work has been supported by Spanish Ministry of Economy and Competitiveness (Ref. RTI2018-094248-B-I00), Generalitat Valenciana (Ref. ACOM/2015/133 and ACIF/2015/332), and Gordon and Betty Moore Foundation (Grant 5334).
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Single-cell genomics uncover Pelagibacter as the putative host of the extremely abundant uncultured 37-F6 viral population in the ocean.
The ISME journal, 2018Co-Authors: Francisco Martinez-hernandez, Oscar Fornas, Monica Lluesma Gomez, Inmaculada Garcia-heredia, Lucia Maestre-carballa, Mario López-pérez, Jose M. Haro-moreno, Francisco Rodriguez-valera, Manuel Martinez-garciaAbstract:The identification of relevant virus-host pairs that globally account for a large pool of carbon and nutrients in the ocean is paramount to build accurate ecological models. A previous work using single-virus genomics led to the discovery of the uncultured single-virus vSAG 37-F6, originally sorted from the Mediterranean Sea (Blanes Bay Microbial Observatory), that represents one of the most abundant dsDNA viral population in the marine surface virosphere. Here, from same sampling site, we report that a Pelagibacter single-cell contained a viral member of vSAG 37-F6 population, by means of PCR screening of sorted, genome-amplified single cells with vSAG 37-F6-specific primers and whole-genome sequencing. Furthermore, viruses from this population were also found in three other Pelagibacter single cells from the South Pacific and Atlantic oceans. These new uncultured pelagiphages were genetically different from the previously characterized pelagiphage isolates. Data showed that the uncultured vSAG 37-F6 population represents the Pelagibacter phages that inhabit the sunlit ocean better, and contains a vast unrecognized microdiversity.
H. James Tripp - One of the best experts on this subject based on the ideXlab platform.
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The unique metabolism of SAR11 aquatic bacteria
Journal of Microbiology, 2013Co-Authors: H. James TrippAbstract:The deeply branching clade of abundant, globally distributed aquatic α-Proteobacteria known as “SAR11”, are adapted to nutrient-poor environments such as the surface waters of the open ocean. Unknown prior to 1990, uncultured until 2002, members of the SAR11 clade can now be cultured in artificial, defined media to densities three orders of magnitude higher than in unamended natural media. Cultivation in natural and defined media has confirmed genomic and metagenomic predictions such as an inability to reduce sulfate to sulfide, a requirement for pyruvate, an ability to oxidize a wide variety of methylated and one-carbon compounds for energy, and an unusual form of conditional glycine auxotrophy. Here we describe the metabolism of the SAR11 type strain Candidatus “Pelagibacter ubique” str. HTCC1062, as revealed by genome-assisted studies of laboratory cultures. We also describe the discovery of SAR11 and field studies that have been done on natural populations.
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SAR11 marine bacteria require exogenous reduced sulphur for growth
Nature, 2008Co-Authors: H. James Tripp, Larry J. Wilhelm, Michael S. Schwalbach, Joshua B. Kitner, John W. H. Dacey, Stephen J GiovannoniAbstract:Sulphur is a universally required cell nutrient found in two amino acids and other small organic molecules. All aerobic marine bacteria are known to use assimilatory sulphate reduction to supply sulphur for biosynthesis, although many can assimilate sulphur from organic compounds that contain reduced sulphur atoms. An analysis of three complete 'Candidatus Pelagibacter ubique' genomes, and public ocean metagenomic data sets, suggested that members of the ubiquitous and abundant SAR11 alphaproteobacterial clade are deficient in assimilatory sulphate reduction genes. Here we show that SAR11 requires exogenous sources of reduced sulphur, such as methionine or 3-dimethylsulphoniopropionate (DMSP) for growth. Titrations of the algal osmolyte DMSP in seawater medium containing all other macronutrients in excess showed that 1.5 x 10(8) SAR11 cells are produced per nanomole of DMSP. Although it has been shown that other marine alphaproteobacteria use sulphur from DMSP in preference to sulphate, our results indicate that 'Cand. P. ubique' relies exclusively on reduced sulphur compounds that originate from other plankton.
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Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data
Biology direct, 2007Co-Authors: Larry J. Wilhelm, Daniel P. Smith, H. James Tripp, Scott A. Givan, Stephen J GiovannoniAbstract:Background One objective of metagenomics is to reconstruct information about specific uncultured organisms from fragmentary environmental DNA sequences. We used the genome of an isolate of the marine alphaproteobacterium SAR11 ('Candidatus Pelagibacter ubique'; strain HTCC1062), obtained from the cold, productive Oregon coast, as a query sequence to study variation in SAR11 metagenome sequence data from the Sargasso Sea, a warm, oligotrophic ocean gyre.
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High intraspecific recombination rate in a native population of Candidatus Pelagibacter ubique (SAR11)
Environmental microbiology, 2007Co-Authors: Kevin L. Vergin, Larry J. Wilhelm, H. James Tripp, Michael S. Rappé, Dee R. Denver, Stephen J GiovannoniAbstract:Summary Recombination is an important process in microbial evolution. Rates of recombination with extracellular DNA matter because models of microbial population structure are profoundly influenced by the degree to which recombination is occurring within the population. Low rates of recombination may be suffi- cient to ensure the lateral propagation of genes that have a high selective advantage without disrupting the clonal pattern of inheritance for other genes. High rates of recombination potentially can obscure clonal patterns, leading to linkage equilibrium, and give microbial populations a population genetic structure more akin to sexually interbreeding eukaryotic populations. We examined eight loci from nine strains of candidatus Pelagibacter ubique (SAR11), isolated from a single 2L niskin sample of natural seawater, for evidence of genetic recombination between strains. The Shimodaira-Hasegawa test revealed significant phylogenetic incongruence in seven of the genes, indicating that frequent recombination obscures phy- logenetic signals from the linear inheritance of genes in this population. Statistical evidence for intragenic recombination was found for six loci. An informative sites matrix showed extensive evidence for a widespread breakdown of linkage disequilibrium. Although the mechanisms of genetic transfer in native SAR11 populations are unknown, we measured recombination rates, r, that are much higher than point mutation rates, q, as a source of genetic diver- sity in this clade. The eukaryotic model of species sharing a common pool of alleles is more apt for this SAR11 population than a strictly clonal model of
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Proteorhodopsin in the ubiquitous marine bacterium SAR11
Nature, 2005Co-Authors: Stephen J Giovannoni, Jang-cheon Cho, Lisa Bibbs, Martha Stapels, Russell A. Desiderio, Kevin L. Vergin, Michael S. Rappé, Samuel R. Laney, Lawrence J. Wilhelm, H. James TrippAbstract:Proteorhodopsin genes were discovered, as DNA fragments in sea water, long before anybody knew what organisms they came from. They encode light-dependent proton pumps that are thought to have a central role in ocean ecology by supplying the energy for microbial metabolism, and now the intact proteorhodopsin system has been tracked down. It is found in SAR11, one of the most abundant organisms on the planet. SAR11, recently renamed Pelagibacter ubique, was synonymous with uncultured microbial diversity until it was first cultured in 2002. These organisms have proteorhodopsin proton pumps and have the odd (for a light-gatherer) ability to grow equally as well in the dark as in the light. SAR11 is out there in the oceans competing with the likes of cyanobacteria for a niche amongst the bacterioplankton. Now it seems that the cyanobacteria may have outside assistance. Viruses (or phages) that infect the ubiquitous cyanobacteria Prochlorococcus do more than just use their DNA to force the host to make more phage. The viral genome contains photosynthesis genes, possibly captured from cyanobacterial hosts long ago. These encode proteins that combine with host photosynthetic machinery to ensure that the host provides the phage with the energy necessary to produce phage progeny. Proteorhodopsins are light-dependent proton pumps that are predicted to have an important role in the ecology of the oceans by supplying energy for microbial metabolism1,2. Proteorhodopsin genes were first discovered through the cloning and sequencing of large genomic DNA fragments from seawater1. They were later shown to be widely distributed, phylogenetically diverse, and active in the oceans3,4,5,6,7. Proteorhodopsin genes have not been found in cultured bacteria, and on the basis of environmental sequence data, it has not yet been possible to reconstruct the genomes of uncultured bacterial strains that have proteorhodopsin genes. Although the metabolic effect of proteorhodopsins is uncertain, they are thought to function in cells for which the primary mode of metabolism is the heterotrophic assimilation of dissolved organic carbon. Here we report that SAR11 strain HTCC1062 (‘Pelagibacter ubique’)8, the first cultivated member of the extraordinarily abundant SAR11 clade, expresses a proteorhodopsin gene when cultured in autoclaved seawater and in its natural environment, the ocean. The Pelagibacter proteorhodopsin functions as a light-dependent proton pump. The gene is expressed by cells grown in either diurnal light or in darkness, and there is no difference between the growth rates or cell yields of cultures grown in light or darkness.
Francisco Rodriguez-valera - One of the best experts on this subject based on the ideXlab platform.
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Microorganisms of Lake Baikal—the deepest and most ancient lake on Earth
Applied Microbiology and Biotechnology, 2020Co-Authors: Tamara I. Zemskaya, Pedro J. Cabello-yeves, Olga N. Pavlova, Francisco Rodriguez-valeraAbstract:Lake Baikal (Russia) is the largest (by volume) and deepest lake on Earth. The lake remains relatively pristine due to the low population density around its basin. Being very distant from any marine water body but having a remarkable number of similarities to oceans (depth, oxygen content, oligotrophy) provides a unique model of pelagic microbiota that is submitted to marine-like conditions minus the salt content of the water. It is also a model of lakes located at high latitudes and submitted to yearly ice cover (from January to April). The analysis by different approaches has indeed provided a view of the microbiota of this lake. It contains novel microbes that are closely related to marine groups not known to be present in freshwater like Chloroflexi or Pelagibacter . The deep water mass contains large communities of chemolithotrophs that use ammonia generated in the photic zone or methane from the sediments. Key Points • The chemical composition and limnic features of the deepest lake on Earth determine the vital activity of microorganisms. • The diversity, ecology, and role of individual taxa of microorganisms were studied using cultivation and molecular methods. • Data of large metagenomic datasets in the epipelagic and bathypelagic layers of the water column in southern Baikal were discussed.
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Microorganisms of Lake Baikal-the deepest and most ancient lake on Earth.
Applied microbiology and biotechnology, 2020Co-Authors: Tamara I. Zemskaya, Pedro J. Cabello-yeves, Olga N. Pavlova, Francisco Rodriguez-valeraAbstract:Lake Baikal (Russia) is the largest (by volume) and deepest lake on Earth. The lake remains relatively pristine due to the low population density around its basin. Being very distant from any marine water body but having a remarkable number of similarities to oceans (depth, oxygen content, oligotrophy) provides a unique model of pelagic microbiota that is submitted to marine-like conditions minus the salt content of the water. It is also a model of lakes located at high latitudes and submitted to yearly ice cover (from January to April). The analysis by different approaches has indeed provided a view of the microbiota of this lake. It contains novel microbes that are closely related to marine groups not known to be present in freshwater like Chloroflexi or Pelagibacter. The deep water mass contains large communities of chemolithotrophs that use ammonia generated in the photic zone or methane from the sediments. KEY POINTS: • The chemical composition and limnic features of the deepest lake on Earth determine the vital activity of microorganisms. • The diversity, ecology, and role of individual taxa of microorganisms were studied using cultivation and molecular methods. • Data of large metagenomic datasets in the epipelagic and bathypelagic layers of the water column in southern Baikal were discussed.
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Associations between depth and micro-diversity within marine viral communities revealed through metagenomics
2019Co-Authors: Felipe H. Coutinho, Riccardo Rosselli, Francisco Rodriguez-valeraAbstract:Abstract Viruses are extremely abundant and diverse biological entities that contribute to the functioning of marine ecosystems. Despite their recognized importance no studies have addressed trends of micro-diversity in marine viral communities across depth gradients. To fill this gap we obtained metagenomes from both the cellular and viral fractions of Mediterranean seawater samples spanning the epipelagic to the bathypelagic zone at 15, 45, 60 and 2000 meters deep. The majority of viral genomic sequences obtained were derived from bacteriophages of the order Caudovirales, and putative host assignments suggested that they infect some of the most abundant bacteria in marine ecosystems such as Pelagibacter, Puniceispirillum and Prochlorococcus. We evaluated micro-diversity patterns by measuring the accumulation of synonymous and non-synonymous mutations in viral genes. Our results demonstrated that the degree of micro-diversity differs among genes encoding metabolic, structural, and replication proteins and that the degree of micro-diversity increased with depth. These trends of micro-diversity were linked to the changes in environmental conditions observed throughout the depth gradient, such as energy availability, host densities and proportion of actively replicating viruses. These observations allowed us to generate hypotheses regarding the selective pressures acting upon marine viruses from the epipelagic to the bathypelagic zones.
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Marine-freshwater prokaryotic transitions require extensive changes in the proteome
2019Co-Authors: Pedro J. Cabello-yeves, Francisco Rodriguez-valeraAbstract:Abstract The comparison of microbial genomes found in either freshwater or marine habitats indicated that in some cases (Synechococcus and Ca. Pelagibacter) there were notable differences in the global isoelectric point (pI) of proteins. We have analysed global metagenomic proteomes and have added more prokaryotes to extend the pI comparison. Without exception, in a set that included archaea and multiple bacterial phyla, the proteome pI distribution varied, with more acidic values in marine and neutral/basic in freshwater microbes. Four pairs of highly related prokaryotes of marine and freshwater origin revealed marked differences manifested mostly in the residues located at the protein surface. This study has also shown that the magnitude of the change depended on protein location (secreted > cytoplasmic > transmembrane) and affected proteins encoded at both core and flexible genome. Our results point to a very extensive variation taking place in microbes when they move from marine (salt-rich) to freshwater habitats. These adaptations would require long evolutionary times to produce changes involving many genes in the core genome. They also point to significant differences in the physiology, probably at the level of membrane functioning, bioenergetics, intracellular ion concentration and pH (or all of them).
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Single-cell genomics uncover Pelagibacter as the putative host of the extremely abundant uncultured 37-F6 viral population in the ocean.
The ISME journal, 2018Co-Authors: Francisco Martinez-hernandez, Oscar Fornas, Monica Lluesma Gomez, Inmaculada Garcia-heredia, Lucia Maestre-carballa, Mario López-pérez, Jose M. Haro-moreno, Francisco Rodriguez-valera, Manuel Martinez-garciaAbstract:The identification of relevant virus-host pairs that globally account for a large pool of carbon and nutrients in the ocean is paramount to build accurate ecological models. A previous work using single-virus genomics led to the discovery of the uncultured single-virus vSAG 37-F6, originally sorted from the Mediterranean Sea (Blanes Bay Microbial Observatory), that represents one of the most abundant dsDNA viral population in the marine surface virosphere. Here, from same sampling site, we report that a Pelagibacter single-cell contained a viral member of vSAG 37-F6 population, by means of PCR screening of sorted, genome-amplified single cells with vSAG 37-F6-specific primers and whole-genome sequencing. Furthermore, viruses from this population were also found in three other Pelagibacter single cells from the South Pacific and Atlantic oceans. These new uncultured pelagiphages were genetically different from the previously characterized pelagiphage isolates. Data showed that the uncultured vSAG 37-F6 population represents the Pelagibacter phages that inhabit the sunlit ocean better, and contains a vast unrecognized microdiversity.