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Abstract
We found that the summer airborne bacterial community in the marine boundary layer over the Southern Ocean directly south of Australia is dominated by marine bacteria emitted in sea spray, originating primarily from the west in a zonal band at the latitude of collection. We found that airborne communities were more diverse to the north, and much less so toward Antarctica. These results imply that sea spray sources largely control the number concentrations of nuclei for liquid cloud droplets and limit ice nucleating particle concentrations to the low values expected in nascent sea spray. In the sampled region, the sources of summer cloud-active particles therefore are unlikely to have changed in direct response to perturbations in continental anthropogenic emissions. Microorganisms are ubiquitous and highly diverse in the atmosphere. Despite the potential impacts of airborne bacteria found in the lower atmosphere over the Southern Ocean (SO) on the ecology of Antarctica and on marine cloud phase, no previous region-wide assessment of bioaerosols over the SO has been reported. We conducted bacterial profiling of boundary layer shipboard aerosol samples obtained during an Austral summer research voyage, spanning 42.8 to 66.5°S. Contrary to findings over global subtropical regions and the Northern Hemisphere, where transport of microorganisms from continents often controls airborne communities, the great majority of the bacteria detected in our samples were marine, based on taxonomy, back trajectories, and source tracking analysis. Further, the beta diversity of airborne bacterial communities varied with latitude and temperature, but not with other meteorological variables. Limited meridional airborne transport restricts southward community dispersal, isolating Antarctica and inhibiting microorganism and nutrient deposition from lower latitudes to these same regions. A consequence and implication for this region’s marine boundary layer and the clouds that overtop it is that it is truly pristine, free from continental and anthropogenic influences, with the ocean as the dominant source controlling low-level concentrations of cloud condensation nuclei and ice nucleating particles.
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52
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Galili M, Tuller T. CSN: unsupervised approach for inferring biological networks based on the genome alone. BMC Bioinformatics 2020; 21:190. [PMID: 32414319 PMCID: PMC7227238 DOI: 10.1186/s12859-020-3479-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 03/31/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Most organisms cannot be cultivated, as they live in unique ecological conditions that cannot be mimicked in the lab. Understanding the functionality of those organisms' genes and their interactions by performing large-scale measurements of transcription levels, protein-protein interactions or metabolism, is extremely difficult and, in some cases, impossible. Thus, efficient algorithms for deciphering genome functionality based only on the genomic sequences with no other experimental measurements are needed. RESULTS In this study, we describe a novel algorithm that infers gene networks that we name Common Substring Network (CSN). The algorithm enables inferring novel regulatory relations among genes based only on the genomic sequence of a given organism and partial homolog/ortholog-based functional annotation. It can specifically infer the functional annotation of genes with unknown homology. This approach is based on the assumption that related genes, not necessarily homologs, tend to share sub-sequences, which may be related to common regulatory mechanisms, similar functionality of encoded proteins, common evolutionary history, and more. We demonstrate that CSNs, which are based on S. cerevisiae and E. coli genomes, have properties similar to 'traditional' biological networks inferred from experiments. Highly expressed genes tend to have higher degree nodes in the CSN, genes with similar protein functionality tend to be closer, and the CSN graph exhibits a power-law degree distribution. Also, we show how the CSN can be used for predicting gene interactions and functions. CONCLUSIONS The reported results suggest that 'silent' code inside the transcript can help to predict central features of biological networks and gene function. This approach can help researchers to understand the genome of novel microorganisms, analyze metagenomic data, and can help to decipher new gene functions. AVAILABILITY Our MATLAB implementation of CSN is available at https://www.cs.tau.ac.il/~tamirtul/CSN-Autogen.
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Affiliation(s)
- Maya Galili
- Biomedical Engineering Department, Tel Aviv University, Tel-Aviv, Israel
- Department of Molecular Microbiology & Biotechnology, Tel Aviv University, Tel-Aviv, Israel
| | - Tamir Tuller
- Biomedical Engineering Department, Tel Aviv University, Tel-Aviv, Israel
- The Sagol School of Neuroscience, Tel Aviv University, Tel-Aviv, Israel
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53
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Louca S, Astor YM, Doebeli M, Taylor GT, Scranton MI. Microbial metabolite fluxes in a model marine anoxic ecosystem. GEOBIOLOGY 2019; 17:628-642. [PMID: 31496030 DOI: 10.1111/gbi.12357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 04/11/2019] [Accepted: 06/23/2019] [Indexed: 06/10/2023]
Abstract
Permanently anoxic regions in the ocean are widespread and exhibit unique microbial metabolic activity exerting substantial influence on global elemental cycles and climate. Reconstructing microbial metabolic activity rates in these regions has been challenging, due to the technical difficulty of direct rate measurements. In Cariaco Basin, which is the largest permanently anoxic marine basin and an important model system for geobiology, long-term monitoring has yielded time series for the concentrations of biologically important compounds; however, the underlying metabolite fluxes remain poorly quantified. Here, we present a computational approach for reconstructing vertical fluxes and in situ net production/consumption rates from chemical concentration data, based on a 1-dimensional time-dependent diffusive transport model that includes adaptive penalization of overfitting. We use this approach to estimate spatiotemporally resolved fluxes of oxygen, nitrate, hydrogen sulfide, ammonium, methane, and phosphate within the sub-euphotic Cariaco Basin water column (depths 150-900 m, years 2001-2014) and to identify hotspots of microbial chemolithotrophic activity. Predictions of the fitted models are in excellent agreement with the data and substantially expand our knowledge of the geobiology in Cariaco Basin. In particular, we find that the diffusivity, and consequently fluxes of major reductants such as hydrogen sulfide, and methane, is about two orders of magnitude greater than previously estimated, thus resolving a long-standing apparent conundrum between electron donor fluxes and measured dark carbon assimilation rates.
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Affiliation(s)
- Stilianos Louca
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
- Department of Biology, University of Oregon, Eugene, OR, USA
| | - Yrene M Astor
- Estación de Investigaciones Marinas de Margarita, Fundación La Salle de Ciencias Naturales, Punta de Piedras, Venezuela
- Institute for Marine Remote Sensing, University of South Florida, Tampa, FL, USA
| | - Michael Doebeli
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Mathematics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, New York, NY, USA
| | - Mary I Scranton
- School of Marine and Atmospheric Sciences, Stony Brook University, New York, NY, USA
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54
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Potential Interactions between Clade SUP05 Sulfur-Oxidizing Bacteria and Phages in Hydrothermal Vent Sponges. Appl Environ Microbiol 2019; 85:AEM.00992-19. [PMID: 31492669 DOI: 10.1128/aem.00992-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/03/2019] [Indexed: 01/27/2023] Open
Abstract
In deep-sea hydrothermal vent environments, sulfur-oxidizing bacteria belonging to the clade SUP05 are crucial symbionts of invertebrate animals. Marine viruses, as the most abundant biological entities in the ocean, play essential roles in regulating the sulfur metabolism of the SUP05 bacteria. To date, vent sponge-associated SUP05 and their phages have not been well documented. The current study analyzed microbiomes of Haplosclerida sponges from hydrothermal vents in the Okinawa Trough and recovered the dominant SUP05 genome, designated VS-SUP05. Phylogenetic analysis showed that VS-SUP05 was closely related to endosymbiotic SUP05 strains from mussels living in deep-sea hydrothermal vent fields. Homology and metabolic pathway comparisons against free-living and symbiotic SUP05 strains revealed that the VS-SUP05 genome shared many features with the deep-sea mussel symbionts. Supporting a potentially symbiotic lifestyle, the VS-SUP05 genome contained genes involved in the synthesis of essential amino acids and cofactors that are desired by the host. Analysis of sponge-associated viral sequences revealed putative VS-SUP05 phages, all of which were double-stranded viruses belonging to the families Myoviridae, Siphoviridae, Podoviridae, and Microviridae Among the phage sequences, one contig contained metabolic genes (iscR, iscS, and iscU) involved in iron-sulfur cluster formation. Interestingly, genome sequence comparison revealed horizontal transfer of the iscS gene among phages, VS-SUP05, and other symbiotic SUP05 strains, indicating an interaction between marine phages and SUP05 symbionts. Overall, our findings confirm the presence of SUP05 bacteria and their phages in sponges from deep-sea vents and imply a beneficial interaction that allows adaptation of the host sponge to the hydrothermal vent environment.IMPORTANCE Chemosynthetic SUP05 bacteria dominate the microbial communities of deep-sea hydrothermal vents around the world, SUP05 bacteria utilize reduced chemical compounds in vent fluids and commonly form symbioses with invertebrate organisms. This symbiotic relationship could be key to adapting to such unique and extreme environments. Viruses are the most abundant biological entities on the planet and have been identified in hydrothermal vent environments. However, their interactions with the symbiotic microbes of the SUP05 clade, along with their role in the symbiotic system, remain unclear. Here, using metagenomic sequence-based analyses, we determined that bacteriophages may support metabolism in SUP05 bacteria and play a role in the sponge-associated symbiosis system in hydrothermal vent environments.
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55
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Abstract
In the ocean's major oxygen minimum zones (OMZs), oxygen is effectively absent from sea water and life is dominated by microorganisms that use chemicals other than oxygen for respiration. Recent studies that combine advanced genomic and chemical detection methods are delineating the different metabolic niches that microorganisms can occupy in OMZs. Understanding these niches, the microorganisms that inhabit them, and their influence on marine biogeochemical cycles is crucial as OMZs expand with increasing seawater temperatures.
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Affiliation(s)
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
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56
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Haas S, Desai DK, LaRoche J, Pawlowicz R, Wallace DWR. Geomicrobiology of the carbon, nitrogen and sulphur cycles in Powell Lake: a permanently stratified water column containing ancient seawater. Environ Microbiol 2019; 21:3927-3952. [PMID: 31314947 DOI: 10.1111/1462-2920.14743] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 07/12/2019] [Accepted: 07/13/2019] [Indexed: 11/30/2022]
Abstract
We present the first geomicrobiological characterization of the meromictic water column of Powell Lake (British Columbia, Canada), a former fjord, which has been stably stratified since the last glacial period. Its deepest layers (300-350 m) retain isolated, relict seawater from that period. Fine-scale vertical profiling of the water chemistry and microbial communities allowed subdivision of the water column into distinct geomicrobiological zones. These zones were further characterized by phylogenetic and functional marker genes from amplicon and shotgun metagenome sequencing. Binning of metagenomic reads allowed the linkage of function to specific taxonomic groups. Statistical analyses (analysis of similarities, Bray-Curtis similarity) confirmed that the microbial community structure followed closely the geochemical zonation. Yet, our characterization of the genetic potential relevant to carbon, nitrogen and sulphur cycling of each zone revealed unexpected features, including potential for facultative anaerobic methylotrophy, nitrogen fixation despite high ammonium concentrations and potential micro-aerobic nitrifiers within the chemocline. At the oxic-suboxic interface, facultative anaerobic potential was found in the widespread freshwater lineage acI (Actinobacteria), suggesting intriguing ecophysiological similarities to the marine SAR11. Evolutionary divergent lineages among diverse phyla were identified in the ancient seawater zone and may indicate novel adaptations to this unusual environment.
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Affiliation(s)
- Sebastian Haas
- Department of Oceanography, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, Canada
| | - Dhwani K Desai
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, Canada
| | - Julie LaRoche
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, Canada
| | - Rich Pawlowicz
- Department of Earth and Ocean Sciences, University of British Columbia, 6339 Stores Road, Vancouver, British Columbia, Canada
| | - Douglas W R Wallace
- Department of Oceanography, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, Canada
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57
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Dyksma S, Gallert C. Candidatus Syntrophosphaera thermopropionivorans: a novel player in syntrophic propionate oxidation during anaerobic digestion. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:558-570. [PMID: 30985964 DOI: 10.1111/1758-2229.12759] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 04/12/2019] [Indexed: 06/09/2023]
Abstract
Propionate is an important intermediate in the anaerobic mineralization of organic matter. In methanogenic environments, its degradation relies on syntrophic associations between syntrophic propionate-oxidizing bacteria (SPOB) and Archaea. However, only 10 isolated species have been identified as SPOB so far. We report syntrophic propionate oxidation in thermophilic enrichments of Candidatus Syntrophosphaera thermopropionivorans, a novel representative of the candidate phylum Cloacimonetes. In enrichment culture, methane was produced from propionate, while Ca. S. thermopropionivorans contributed 63% to total bacterial cells. The draft genome of Ca. S. thermopropionivorans encodes genes for propionate oxidation via methymalonyl-CoA. Phylogenetically, Ca. S. thermopropionivorans affiliates with the uncultured Cloacimonadaceae W5 and is more distantly related (86.4% 16S rRNA gene identity) to Ca. Cloacimonas acidaminovorans. Although Ca. S. thermopropionivorans was enriched from a thermophilic biogas reactor, Ca. Syntrophosphaera was in particular associated with mesophilic anaerobic digestion systems. 16S rRNA gene amplicon sequencng and a novel genus-specific quantitative PCR assay consistently identified Ca. Syntrophosphaera/Cloacimonadaceae W5 in 9 of 12 tested full-scale biogas reactors thereby outnumbering other SPOB such as Pelotomaculum, Smithella and Syntrophobacter. Taken together the ubiquity and abundance of Ca. Syntrophosphaera, those SPOB might be key players for syntrophic propionate metabolism that have been overlooked before.
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Affiliation(s)
- Stefan Dyksma
- Faculty of Technology, Microbiology - Biotechnology, University of Applied Sciences Emden/Leer, Emden, Germany
| | - Claudia Gallert
- Faculty of Technology, Microbiology - Biotechnology, University of Applied Sciences Emden/Leer, Emden, Germany
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58
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Morphological Plasticity in a Sulfur-Oxidizing Marine Bacterium from the SUP05 Clade Enhances Dark Carbon Fixation. mBio 2019; 10:mBio.00216-19. [PMID: 31064824 PMCID: PMC6509183 DOI: 10.1128/mbio.00216-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Identifying shifts in microbial metabolism across redox gradients will improve efforts to model marine oxygen minimum zone (OMZ) ecosystems. Here, we show that aerobic morphology and metabolism increase cell size, sulfur storage capacity, and carbon fixation rates in “Ca. Thioglobus autotrophicus,” a chemosynthetic bacterium from the SUP05 clade that crosses oxic-anoxic boundaries. Sulfur-oxidizing bacteria from the SUP05 clade are abundant in anoxic and oxygenated marine waters that appear to lack reduced sources of sulfur for cell growth. This raises questions about how these chemosynthetic bacteria survive across oxygen and sulfur gradients and how their mode of survival impacts the environment. Here, we use growth experiments, proteomics, and cryo-electron tomography to show that a SUP05 isolate, “Candidatus Thioglobus autotrophicus,” is amorphous in shape and several times larger and stores considerably more intracellular sulfur when it respires oxygen. We also show that these cells can use diverse sources of reduced organic and inorganic sulfur at submicromolar concentrations. Enhanced cell size, carbon content, and metabolic activity of the aerobic phenotype are likely facilitated by a stabilizing surface-layer (S-layer) and an uncharacterized form of FtsZ-less cell division that supports morphological plasticity. The additional sulfur storage provides an energy source that allows cells to continue metabolic activity when exogenous sulfur sources are not available. This metabolic flexibility leads to the production of more organic carbon in the ocean than is estimated based solely on their anaerobic phenotype.
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59
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Spietz RL, Lundeen RA, Zhao X, Nicastro D, Ingalls AE, Morris RM. Heterotrophic carbon metabolism and energy acquisition in Candidatus Thioglobus singularis strain PS1, a member of the SUP05 clade of marine Gammaproteobacteria. Environ Microbiol 2019; 21:2391-2401. [PMID: 30951247 DOI: 10.1111/1462-2920.14623] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 03/14/2019] [Accepted: 03/19/2019] [Indexed: 11/30/2022]
Abstract
A hallmark of the SUP05 clade of marine Gammaproteobacteria is the ability to use energy obtained from reduced inorganic sulfur to fuel autotrophic fixation of carbon using RuBisCo. However, some SUP05 also have the genetic potential for heterotrophic growth, raising questions about the roles of SUP05 in the marine carbon cycle. We used genomic reconstructions, physiological growth experiments and proteomics to characterize central carbon and energy metabolism in Candidatus Thioglobus singularis strain PS1, a representative from the SUP05 clade that has the genetic potential for autotrophy and heterotrophy. Here, we show that the addition of individual organic compounds and 0.2 μm filtered diatom lysate significantly enhanced the growth of this bacterium. This positive growth response to organic substrates, combined with expression of a complete TCA cycle, heterotrophic pathways for carbon assimilation, and methylotrophic pathways for energy conversion demonstrate strain PS1's capacity for heterotrophic growth. Further, our inability to verify the expression of RuBisCO suggests that carbon fixation was not critical for growth. These results highlight the metabolic diversity of the SUP05 clade that harbours both primary producers and consumers of organic carbon in the oceans and expand our understanding of specific pathways of organic matter oxidation by the heterotrophic SUP05.
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Affiliation(s)
- Rachel L Spietz
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - Rachel A Lundeen
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - Xiaowei Zhao
- Department of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Daniela Nicastro
- Department of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - Robert M Morris
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
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60
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Vallesi A, Sjödin A, Petrelli D, Luporini P, Taddei AR, Thelaus J, Öhrman C, Nilsson E, Di Giuseppe G, Gutiérrez G, Villalobo E. A New Species of the γ-Proteobacterium Francisella, F. adeliensis Sp. Nov., Endocytobiont in an Antarctic Marine Ciliate and Potential Evolutionary Forerunner of Pathogenic Species. MICROBIAL ECOLOGY 2019; 77:587-596. [PMID: 30187088 DOI: 10.1007/s00248-018-1256-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 08/29/2018] [Indexed: 06/08/2023]
Abstract
The study of the draft genome of an Antarctic marine ciliate, Euplotes petzi, revealed foreign sequences of bacterial origin belonging to the γ-proteobacterium Francisella that includes pathogenic and environmental species. TEM and FISH analyses confirmed the presence of a Francisella endocytobiont in E. petzi. This endocytobiont was isolated and found to be a new species, named F. adeliensis sp. nov.. F. adeliensis grows well at wide ranges of temperature, salinity, and carbon dioxide concentrations implying that it may colonize new organisms living in deeply diversified habitats. The F. adeliensis genome includes the igl and pdp gene sets (pdpC and pdpE excepted) of the Francisella pathogenicity island needed for intracellular growth. Consistently with an F. adeliensis ancient symbiotic lifestyle, it also contains a single insertion-sequence element. Instead, it lacks genes for the biosynthesis of essential amino acids such as cysteine, lysine, methionine, and tyrosine. In a genome-based phylogenetic tree, F. adeliensis forms a new early branching clade, basal to the evolution of pathogenic species. The correlations of this clade with the other clades raise doubts about a genuine free-living nature of the environmental Francisella species isolated from natural and man-made environments, and suggest to look at F. adeliensis as a pioneer in the Francisella colonization of eukaryotic organisms.
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Affiliation(s)
- Adriana Vallesi
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy.
| | - Andreas Sjödin
- Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
- Division of CBRN Defence and Security, Swedish Defence Research Agency, FOI, Umeå, Sweden
| | - Dezemona Petrelli
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy
| | - Pierangelo Luporini
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy
| | - Anna Rita Taddei
- Center of Large Equipment-section of Electron Microscopy, University of Tuscia, Largo dell'Università, snc, Viterbo, Italy
| | - Johanna Thelaus
- Division of CBRN Defence and Security, Swedish Defence Research Agency, FOI, Umeå, Sweden
| | - Caroline Öhrman
- Division of CBRN Defence and Security, Swedish Defence Research Agency, FOI, Umeå, Sweden
| | - Elin Nilsson
- Division of CBRN Defence and Security, Swedish Defence Research Agency, FOI, Umeå, Sweden
| | | | - Gabriel Gutiérrez
- Departamento de Genética, Universidad de Sevilla, Av Reina Mercedes 6, 41012, Seville, Spain
| | - Eduardo Villalobo
- Departamento de Microbiología, Universidad de Sevilla, Av Reina Mercedes 6, 41012, Seville, Spain.
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61
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Complete Genome Sequence of " Candidatus Thioglobus sp." Strain NP1, an Open-Ocean Isolate from the SUP05 Clade of Marine Gammaproteobacteria. Microbiol Resour Announc 2019; 8:8/11/e00097-19. [PMID: 30938321 PMCID: PMC6424205 DOI: 10.1128/mra.00097-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
“Candidatus Thioglobus sp.” strain NP1 is an open-ocean isolate from the SUP05 clade of Gammaproteobacteria. Whole-genome comparisons of strain NP1 to other sequenced isolates from the SUP05 clade indicate that it represents a new species of SUP05 that lacks the ability to fix inorganic carbon using the Calvin-Benson-Bassham cycle. “Candidatus Thioglobus sp.” strain NP1 is an open-ocean isolate from the SUP05 clade of Gammaproteobacteria. Whole-genome comparisons of strain NP1 to other sequenced isolates from the SUP05 clade indicate that it represents a new species of SUP05 that lacks the ability to fix inorganic carbon using the Calvin-Benson-Bassham cycle.
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62
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Decrypting the sulfur cycle in oceanic oxygen minimum zones. ISME JOURNAL 2018; 12:2322-2329. [PMID: 29884830 DOI: 10.1038/s41396-018-0149-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 01/30/2018] [Accepted: 02/28/2018] [Indexed: 11/08/2022]
Abstract
Here we present ecophysiological studies of the anaerobic sulfide oxidizers considered critical to cryptic sulfur cycling in oceanic oxygen minimum zones (OMZs). We find that HS- oxidation rates by microorganisms in the Chilean OMZ offshore from Dichato are sufficiently rapid (18 nM h-1), even at HS- concentrations well below 100 nM, to oxidize all sulfide produced during sulfate reduction in OMZs. Even at 100 nM, HS- is well below published half-saturation concentrations and we conclude that the sulfide-oxidizing bacteria in OMZs (likely the SUP05/ARTIC96BD lineage of the gammaproteobacteria) have high-affinity (>105 g-1 wet cells h-1) sulfur uptake systems. These specific affinities for sulfide are higher than those recorded for any other organism on any other substrate. Such high affinities likely allow anaerobic sulfide oxidizers to maintain vanishingly low sulfide concentrations in OMZs driving marine cryptic sulfur cycling. If more broadly distributed, such high-affinity sulfur biochemistry could facilitate sulfide-based metabolisms and prominent S-cycles in many other ostensibly sulfide-free environments.
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63
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Callbeck CM, Lavik G, Ferdelman TG, Fuchs B, Gruber-Vodicka HR, Hach PF, Littmann S, Schoffelen NJ, Kalvelage T, Thomsen S, Schunck H, Löscher CR, Schmitz RA, Kuypers MMM. Oxygen minimum zone cryptic sulfur cycling sustained by offshore transport of key sulfur oxidizing bacteria. Nat Commun 2018; 9:1729. [PMID: 29712903 PMCID: PMC5928099 DOI: 10.1038/s41467-018-04041-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 03/28/2018] [Indexed: 11/13/2022] Open
Abstract
Members of the gammaproteobacterial clade SUP05 couple water column sulfide oxidation to nitrate reduction in sulfidic oxygen minimum zones (OMZs). Their abundance in offshore OMZ waters devoid of detectable sulfide has led to the suggestion that local sulfate reduction fuels SUP05-mediated sulfide oxidation in a so-called “cryptic sulfur cycle”. We examined the distribution and metabolic capacity of SUP05 in Peru Upwelling waters, using a combination of oceanographic, molecular, biogeochemical and single-cell techniques. A single SUP05 species, UThioglobus perditus, was found to be abundant and active in both sulfidic shelf and sulfide-free offshore OMZ waters. Our combined data indicated that mesoscale eddy-driven transport led to the dispersal of UT. perditus and elemental sulfur from the sulfidic shelf waters into the offshore OMZ region. This offshore transport of shelf waters provides an alternative explanation for the abundance and activity of sulfide-oxidizing denitrifying bacteria in sulfide-poor offshore OMZ waters. The presence and activity of sulfide-oxidizing denitrifying bacteria in sulfide-poor offshore oxygen minimum zone waters remains unclear. Here, the authors combine oceanography, molecular, biogeochemical and single-cell techniques to examine their distribution, metabolic capacity, and origins.
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Affiliation(s)
- Cameron M Callbeck
- Max Planck Institute for Marine Microbiology, Bremen, D-28359, Germany.,Swiss Federal Institute of Aquatic Science and Technology (Eawag), Kastanienbaum, 6047, Switzerland
| | - Gaute Lavik
- Max Planck Institute for Marine Microbiology, Bremen, D-28359, Germany
| | | | - Bernhard Fuchs
- Max Planck Institute for Marine Microbiology, Bremen, D-28359, Germany
| | | | - Philipp F Hach
- Max Planck Institute for Marine Microbiology, Bremen, D-28359, Germany
| | - Sten Littmann
- Max Planck Institute for Marine Microbiology, Bremen, D-28359, Germany
| | | | - Tim Kalvelage
- Max Planck Institute for Marine Microbiology, Bremen, D-28359, Germany
| | - Sören Thomsen
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, D-24148, Germany
| | - Harald Schunck
- Institute for General Microbiology, University of Kiel, Kiel, D-24418, Germany
| | - Carolin R Löscher
- Institute for General Microbiology, University of Kiel, Kiel, D-24418, Germany.,Nordcee and Danish Institute for Advanced Study, Dept. of Biology, University of Southern Denmark, Odense, DK-5230, Denmark
| | - Ruth A Schmitz
- Institute for General Microbiology, University of Kiel, Kiel, D-24418, Germany
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64
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Plominsky AM, Trefault N, Podell S, Blanton JM, De la Iglesia R, Allen EE, von Dassow P, Ulloa O. Metabolic potential andin situtranscriptomic profiles of previously uncharacterized key microbial groups involved in coupled carbon, nitrogen and sulfur cycling in anoxic marine zones. Environ Microbiol 2018; 20:2727-2742. [DOI: 10.1111/1462-2920.14109] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 02/27/2018] [Accepted: 03/07/2018] [Indexed: 01/05/2023]
Affiliation(s)
- Alvaro M. Plominsky
- Departamento de Oceanografía; Universidad de Concepción, P.O. Box 160-C; Concepción 4070386 Chile
- Instituto Milenio de Oceanografía, Universidad de Concepción; Concepción Chile
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor; Santiago 8580745 Chile
| | - Sheila Podell
- Marine Biology Research Division; Scripps Institution of Oceanography, University of California San Diego; San Diego CA 92093-0202 USA
| | - Jessica M. Blanton
- Marine Biology Research Division; Scripps Institution of Oceanography, University of California San Diego; San Diego CA 92093-0202 USA
| | - Rodrigo De la Iglesia
- Department of Molecular Genetics and Microbiology; Pontificia Universidad Católica de Chile; Santiago 8331150 Chile
| | - Eric E. Allen
- Marine Biology Research Division; Scripps Institution of Oceanography, University of California San Diego; San Diego CA 92093-0202 USA
- Division of Biological Sciences; University of California; San Diego CA USA
| | - Peter von Dassow
- Instituto Milenio de Oceanografía, Universidad de Concepción; Concepción Chile
- Department of Ecology; Pontificia Universidad Católica de Chile; Santiago 8331150 Chile
- Research Department UMI 3614, Evolutionary Biology and Ecology of Algae; CNRS UPMC; Roscoff 29680 France
| | - Osvaldo Ulloa
- Departamento de Oceanografía; Universidad de Concepción, P.O. Box 160-C; Concepción 4070386 Chile
- Instituto Milenio de Oceanografía, Universidad de Concepción; Concepción Chile
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65
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Pachiadaki MG, Sintes E, Bergauer K, Brown JM, Record NR, Swan BK, Mathyer ME, Hallam SJ, Lopez-Garcia P, Takaki Y, Nunoura T, Woyke T, Herndl GJ, Stepanauskas R. Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation. Science 2018; 358:1046-1051. [PMID: 29170234 DOI: 10.1126/science.aan8260] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 10/20/2017] [Indexed: 12/13/2022]
Abstract
Carbon fixation by chemoautotrophic microorganisms in the dark ocean has a major impact on global carbon cycling and ecological relationships in the ocean's interior, but the relevant taxa and energy sources remain enigmatic. We show evidence that nitrite-oxidizing bacteria affiliated with the Nitrospinae phylum are important in dark ocean chemoautotrophy. Single-cell genomics and community metagenomics revealed that Nitrospinae are the most abundant and globally distributed nitrite-oxidizing bacteria in the ocean. Metaproteomics and metatranscriptomics analyses suggest that nitrite oxidation is the main pathway of energy production in Nitrospinae. Microautoradiography, linked with catalyzed reporter deposition fluorescence in situ hybridization, indicated that Nitrospinae fix 15 to 45% of inorganic carbon in the mesopelagic western North Atlantic. Nitrite oxidation may have a greater impact on the carbon cycle than previously assumed.
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Affiliation(s)
| | - Eva Sintes
- Department of Limnology and Bio-Oceanography, University of Vienna, 1090 Vienna, Austria
| | - Kristin Bergauer
- Department of Limnology and Bio-Oceanography, University of Vienna, 1090 Vienna, Austria
| | - Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, USA
| | | | - Brandon K Swan
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, USA.,National Biodefense Analysis and Countermeasures Center, Frederick, MD 21702, USA
| | - Mary Elizabeth Mathyer
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, USA.,Division of Dermatology, Department of Internal Medicine, Center for Pharmacogenomics, and Center for the Study of Itch, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada.,Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada.,Peter Wall Institute for Advanced Studies, University of British Columbia, Vancouver, British Columbia, Canada.,ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Purificacion Lopez-Garcia
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
| | - Yoshihiro Takaki
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan.,Department of Subsurface Geobiology Analysis and Research, JAMSTEC, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Takuro Nunoura
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Gerhard J Herndl
- Department of Limnology and Bio-Oceanography, University of Vienna, 1090 Vienna, Austria.,Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, 1790 AB Den Burg, Netherlands
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66
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Buttigieg PL, Fadeev E, Bienhold C, Hehemann L, Offre P, Boetius A. Marine microbes in 4D-using time series observation to assess the dynamics of the ocean microbiome and its links to ocean health. Curr Opin Microbiol 2018; 43:169-185. [PMID: 29477022 DOI: 10.1016/j.mib.2018.01.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 01/30/2018] [Accepted: 01/31/2018] [Indexed: 02/07/2023]
Abstract
Microbial observation is of high relevance in assessing marine phenomena of scientific and societal concern including ocean productivity, harmful algal blooms, and pathogen exposure. However, we have yet to realise its potential to coherently and comprehensively report on global ocean status. The ability of satellites to monitor the distribution of phytoplankton has transformed our appreciation of microbes as the foundation of key ecosystem services; however, more in-depth understanding of microbial dynamics is needed to fully assess natural and anthropogenically induced variation in ocean ecosystems. While this first synthesis shows that notable efforts exist, vast regions such as the ocean depths, the open ocean, the polar oceans, and most of the Southern Hemisphere lack consistent observation. To secure a coordinated future for a global microbial observing system, existing long-term efforts must be better networked to generate shared bioindicators of the Global Ocean's state and health.
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Affiliation(s)
- Pier Luigi Buttigieg
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, D-27570 Bremerhaven, Germany; Max Planck Institut für Marine Mikrobiologie, Celsiusstr. 1, D-28359 Bremen, Germany.
| | - Eduard Fadeev
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, D-27570 Bremerhaven, Germany; Max Planck Institut für Marine Mikrobiologie, Celsiusstr. 1, D-28359 Bremen, Germany
| | - Christina Bienhold
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, D-27570 Bremerhaven, Germany; Max Planck Institut für Marine Mikrobiologie, Celsiusstr. 1, D-28359 Bremen, Germany
| | - Laura Hehemann
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, D-27570 Bremerhaven, Germany
| | - Pierre Offre
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, 1790 AB Den Burg, Texel, The Netherlands
| | - Antje Boetius
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, D-27570 Bremerhaven, Germany; Max Planck Institut für Marine Mikrobiologie, Celsiusstr. 1, D-28359 Bremen, Germany; MARUM-Center for Marine Environmental Sciences, University of Bremen, Leobener Str. 8, D-28334 Bremen, Germany.
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67
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Suter EA, Pachiadaki M, Taylor GT, Astor Y, Edgcomb VP. Free‐living chemoautotrophic and particle‐attached heterotrophic prokaryotes dominate microbial assemblages along a pelagic redox gradient. Environ Microbiol 2017; 20:693-712. [DOI: 10.1111/1462-2920.13997] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 11/09/2017] [Accepted: 11/13/2017] [Indexed: 01/28/2023]
Affiliation(s)
- Elizabeth A. Suter
- School of Marine and Atmospheric SciencesStony Brook UniversityStony Brook NY USA
- Department of Biological SciencesWagner CollegeStaten Island NY 10301 USA
| | - Maria Pachiadaki
- Woods Hole Oceanographic InstitutionWoods Hole MA USA
- Bigelow Laboratory for Ocean SciencesEast Boothbay ME USA
| | - Gordon T. Taylor
- School of Marine and Atmospheric SciencesStony Brook UniversityStony Brook NY USA
| | - Yrene Astor
- Fundación La Salle de Ciencias Naturales, EDIMARPorlamar Nueva Esparta Venezuela
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68
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Badapanda C, Metha SM. Advancing our understanding of the oxygen minimum zone microbial communities by an integrated metatranscriptomics approach. Meta Gene 2017. [DOI: 10.1016/j.mgene.2017.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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69
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Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients. Nat Commun 2017; 8:1507. [PMID: 29142241 PMCID: PMC5688066 DOI: 10.1038/s41467-017-01376-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 09/11/2017] [Indexed: 12/22/2022] Open
Abstract
Microbial communities drive biogeochemical cycles through networks of metabolite exchange that are structured along energetic gradients. As energy yields become limiting, these networks favor co-metabolic interactions to maximize energy disequilibria. Here we apply single-cell genomics, metagenomics, and metatranscriptomics to study bacterial populations of the abundant "microbial dark matter" phylum Marinimicrobia along defined energy gradients. We show that evolutionary diversification of major Marinimicrobia clades appears to be closely related to energy yields, with increased co-metabolic interactions in more deeply branching clades. Several of these clades appear to participate in the biogeochemical cycling of sulfur and nitrogen, filling previously unassigned niches in the ocean. Notably, two Marinimicrobia clades, occupying different energetic niches, express nitrous oxide reductase, potentially acting as a global sink for the greenhouse gas nitrous oxide.
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70
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Bertagnolli AD, Padilla CC, Glass JB, Thamdrup B, Stewart FJ. Metabolic potential and
in situ
activity of marine Marinimicrobia bacteria in an anoxic water column. Environ Microbiol 2017; 19:4392-4416. [DOI: 10.1111/1462-2920.13879] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 07/17/2017] [Accepted: 07/26/2017] [Indexed: 11/29/2022]
Affiliation(s)
| | - Cory C. Padilla
- School of Biological SciencesGeorgia Institute of TechnologyAtlanta GA USA
| | - Jennifer B. Glass
- School of Earth and Atmospheric SciencesGeorgia Institute of TechnologyAtlanta GA USA
| | - Bo Thamdrup
- Department of Biology and Nordic Center for Earth Evolution (NordCEE)University of Southern DenmarkOdense Denmark
| | - Frank J. Stewart
- School of Biological SciencesGeorgia Institute of TechnologyAtlanta GA USA
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71
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Hallam SJ, Torres-Beltrán M, Hawley AK. Monitoring microbial responses to ocean deoxygenation in a model oxygen minimum zone. Sci Data 2017; 4:170158. [PMID: 29087370 PMCID: PMC5663219 DOI: 10.1038/sdata.2017.158] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 09/19/2017] [Indexed: 11/09/2022] Open
Abstract
Today in Scientific Data, two compendia of geochemical and
multi-omic sequence information (DNA, RNA, protein) generated over almost a
decade of time series monitoring in a seasonally anoxic coastal marine setting
are presented to the scientific community. These data descriptors introduce a
model ecosystem for the study of microbial responses to ocean deoxygenation, a
phenotype that is currently expanding due to climate change. Public access to
this time series information is intended to promote scientific collaborations
and the generation of new hypotheses relevant to microbial ecology,
biogeochemistry and global change issues.
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Affiliation(s)
- Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3.,Peter Wall Institute for Advanced Studies, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z2.,Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4.,Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada V6T 1Z4.,ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Mónica Torres-Beltrán
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Alyse K Hawley
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
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72
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Hawley AK, Torres-Beltrán M, Zaikova E, Walsh DA, Mueller A, Scofield M, Kheirandish S, Payne C, Pakhomova L, Bhatia M, Shevchuk O, Gies EA, Fairley D, Malfatti SA, Norbeck AD, Brewer HM, Pasa-Tolic L, del Rio TG, Suttle CA, Tringe S, Hallam SJ. A compendium of multi-omic sequence information from the Saanich Inlet water column. Sci Data 2017; 4:170160. [PMID: 29087368 PMCID: PMC5663217 DOI: 10.1038/sdata.2017.160] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 08/02/2017] [Indexed: 01/08/2023] Open
Abstract
Marine oxygen minimum zones (OMZs) are widespread regions of the ocean that are currently expanding due to global warming. While inhospitable to most metazoans, OMZs are hotspots for microbial mediated biogeochemical cycling of carbon, nitrogen and sulphur, contributing disproportionately to marine nitrogen loss and climate active trace gas production. Our current understanding of microbial community responses to OMZ expansion is limited by a lack of time-resolved data sets linking multi-omic sequence information (DNA, RNA, protein) to geochemical parameters and process rates. Here, we present six years of time-resolved multi-omic observations in Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island, British Columbia, Canada that undergoes recurring changes in water column oxygenation status. This compendium provides a unique multi-omic framework for studying microbial community responses to ocean deoxygenation along defined geochemical gradients in OMZ waters.
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Affiliation(s)
- Alyse K. Hawley
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Mónica Torres-Beltrán
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Elena Zaikova
- Department of Biology, Georgetown University,
Washington, District Of Columbia 20057,
USA
| | - David A. Walsh
- Department of Biology, Concordia University,
Montreal, Quebec, Canada H4B 1R6
| | - Andreas Mueller
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Melanie Scofield
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Sam Kheirandish
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Chris Payne
- Earth, Ocean and Atmospheric Sciences, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z4
| | - Larysa Pakhomova
- Earth, Ocean and Atmospheric Sciences, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z4
| | - Maya Bhatia
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Olena Shevchuk
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Esther A. Gies
- Department of Civil Engineering, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z4
| | - Diane Fairley
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | | | - Angela D. Norbeck
- Biological and Computational Sciences Division, Pacific
Northwest National Laboratory, Richland, Washington
99352, USA
| | - Heather M. Brewer
- Biological and Computational Sciences Division, Pacific
Northwest National Laboratory, Richland, Washington
99352, USA
| | - Ljiljana Pasa-Tolic
- Biological and Computational Sciences Division, Pacific
Northwest National Laboratory, Richland, Washington
99352, USA
| | | | - Curtis A. Suttle
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
- Earth, Ocean and Atmospheric Sciences, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z4
- Department of Botany, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z4
| | - Susannah Tringe
- Department of Energy Joint Genome Institute,
Walnut Creek, California 94598, USA
| | - Steven J. Hallam
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
- Peter Wall Institute for Advanced Studies, University of
British Columbia, Canada V6T 1Z2
- Genome Science and Technology Program, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z3
- Graduate Program in Bioinformatics, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z3
- ECOSCOPE Training Program, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z3
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73
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Torres-Beltrán M, Hawley AK, Capelle D, Zaikova E, Walsh DA, Mueller A, Scofield M, Payne C, Pakhomova L, Kheirandish S, Finke J, Bhatia M, Shevchuk O, Gies EA, Fairley D, Michiels C, Suttle CA, Whitney F, Crowe SA, Tortell PD, Hallam SJ. A compendium of geochemical information from the Saanich Inlet water column. Sci Data 2017; 4:170159. [PMID: 29087371 PMCID: PMC5663218 DOI: 10.1038/sdata.2017.159] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 06/21/2017] [Indexed: 11/13/2022] Open
Abstract
Extensive and expanding oxygen minimum zones (OMZs) exist at variable depths in
coastal and open ocean waters. As oxygen levels decline, nutrients and energy
are increasingly diverted away from higher trophic levels into microbial
community metabolism, resulting in fixed nitrogen loss and production of climate
active trace gases including nitrous oxide and methane. While ocean
deoxygenation has been reported on a global scale, our understanding of OMZ
biology and geochemistry is limited by a lack of time-resolved data sets. Here,
we present a historical dataset of oxygen concentrations spanning fifty years
and nine years of monthly geochemical time series observations in Saanich Inlet,
a seasonally anoxic fjord on the coast of Vancouver Island, British Columbia,
Canada that undergoes recurring changes in water column oxygenation status. This
compendium provides a unique geochemical framework for evaluating long-term
trends in biogeochemical cycling in OMZ waters.
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Affiliation(s)
- Mónica Torres-Beltrán
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Alyse K Hawley
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - David Capelle
- Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Elena Zaikova
- Department of Biology, Georgetown University, Washington, DC 20007, USA
| | - David A Walsh
- Department of Biology, Concordia University, Montreal, Quebec, Canada H4B 1R6
| | - Andreas Mueller
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Melanie Scofield
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Chris Payne
- Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Larysa Pakhomova
- Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Sam Kheirandish
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Jan Finke
- Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Maya Bhatia
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Olena Shevchuk
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Esther A Gies
- Department of Civil Engineering, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Diane Fairley
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Céline Michiels
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Curtis A Suttle
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3.,Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4.,Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Frank Whitney
- Department of Fisheries and Oceans Canada, Sidney, British Columbia, Canada V9L 6V9
| | - Sean A Crowe
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3.,Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4.,ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Philippe D Tortell
- Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4.,Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4.,Peter Wall Institute for Advanced Studies, University of British Columbia, Canada V6T 1Z2
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3.,ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4.,Peter Wall Institute for Advanced Studies, University of British Columbia, Canada V6T 1Z2.,Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada V6T 1Z4.,Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
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74
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Watanabe T, Miura A, Iwata T, Kojima H, Fukui M. Dominance of Sulfuritalea species in nitrate-depleted water of a stratified freshwater lake and arsenate respiration ability within the genus. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:522-527. [PMID: 28618172 DOI: 10.1111/1758-2229.12557] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/03/2017] [Indexed: 06/07/2023]
Abstract
Facultative autotrophs of the genus Sulfuritalea within the class Betaproteobacteria have been predicted to be an important bacterial population in stratified freshwater lakes based on previous PCR-based studies. Here, we designed a new probe specific for the genus Sulfuritalea and performed catalysed reporter deposition-fluorescence in situ hybridisation to enumerate cells of Sulfuritalea species throughout the water column in a stratified freshwater lake. The cells stained with the Sulfuritalea-specific probe were detected in all hypoxic water samples collected in different seasons and years. Their abundance ranged from 1.4 × 104 to 2.1 × 105 cells ml-1 , corresponding to 0.5-5.5% of the total DAPI-stained cells and 2.3-15% of the total bacterial cells. A high abundance of Sulfuritalea species was recorded in hypoxic water samples without nitrate, which is the only known anaerobic electron acceptor for Sulfuritalea. Nitrate-independent anaerobic respiration was further investigated using a single cultured representative of this genus, and its growth via arsenate respiration was experimentally demonstrated. In conclusion, Sulfuritalea species were found to be a major component of the planktonic bacterial community in nitrate-depleted hypoxic water, where arsenate respiration is one of the possible energy metabolisms of Sulfuritalea.
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Affiliation(s)
- Tomohiro Watanabe
- The Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Aya Miura
- The Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Tomoya Iwata
- Department of Environmental Sciences, University of Yamanashi, Kofu, Japan
| | - Hisaya Kojima
- The Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Manabu Fukui
- The Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
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75
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Rogge A, Vogts A, Voss M, Jürgens K, Jost G, Labrenz M. Success of chemolithoautotrophic SUP05 and Sulfurimonas GD17 cells in pelagic Baltic Sea redox zones is facilitated by their lifestyles as K- and r-strategists. Environ Microbiol 2017; 19:2495-2506. [PMID: 28464419 DOI: 10.1111/1462-2920.13783] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 04/25/2017] [Accepted: 04/25/2017] [Indexed: 11/27/2022]
Abstract
Chemolithoautotrophic sulfur-oxidizing and denitrifying Gamma- (particularly the SUP05 cluster) and Epsilonproteobacteria (predominantly Sulfurimonas subgroup GD17) are assumed to compete for substrates (electron donors and acceptors) in marine pelagic redox gradients. To elucidate their ecological niche separation we performed 34 S0 , 15 NO3- and H13 CO3- stable-isotope incubations with water samples from Baltic Sea suboxic, chemocline and sulfidic zones followed by combined phylogenetic staining and high-resolution secondary ion mass spectrometry of single cells. SUP05 cells were small-sized (0.06-0.09 µm3 ) and most abundant in low-sulfidic to suboxic zones, whereas Sulfurimonas GD17 cells were significantly larger (0.26-0.61 µm3 ) and most abundant at the chemocline and below. Together, SUP05 and GD17 cells accumulated up to 48% of the labelled substrates but calculation of cell volume-specific rates revealed that GD17 cells incorporated labelled substrates significantly faster throughout the redox zone, thereby potentially outcompeting SUP05 especially at high substrate concentrations. Thus, in synopsis with earlier described features of SUP05/GD17 we conclude that their spatially overlapping association in stratified sulfidic zones is facilitated by their different lifestyles: whereas SUP05 cells are streamlined, non-motile K-strategists adapted to low substrate concentrations, GD17 cells are motile r-strategists well adapted to fluctuating substrate and redox conditions.
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Affiliation(s)
- Andreas Rogge
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock-Warnemünde, Germany
| | - Angela Vogts
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock-Warnemünde, Germany
| | - Maren Voss
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock-Warnemünde, Germany
| | - Klaus Jürgens
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock-Warnemünde, Germany
| | - Günter Jost
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock-Warnemünde, Germany
| | - Matthias Labrenz
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock-Warnemünde, Germany
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76
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Global Distribution Patterns and Pangenomic Diversity of the Candidate Phylum "Latescibacteria" (WS3). Appl Environ Microbiol 2017; 83:AEM.00521-17. [PMID: 28314726 DOI: 10.1128/aem.00521-17] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 03/11/2017] [Indexed: 01/01/2023] Open
Abstract
We investigated the global distribution patterns and pangenomic diversity of the candidate phylum "Latescibacteria" (WS3) in 16S rRNA gene as well as metagenomic data sets. We document distinct distribution patterns for various "Latescibacteria" orders in 16S rRNA gene data sets, with prevalence of orders sediment_1 in terrestrial, PBSIII_9 in groundwater and temperate freshwater, and GN03 in pelagic marine, saline-hypersaline, and wastewater habitats. Using a fragment recruitment approach, we identified 68.9 Mb of "Latescibacteria"-affiliated contigs in publicly available metagenomic data sets comprising 73,079 proteins. Metabolic reconstruction suggests a prevalent saprophytic lifestyle in all "Latescibacteria" orders, with marked capacities for the degradation of proteins, lipids, and polysaccharides predominant in plant, bacterial, fungal/crustacean, and eukaryotic algal cell walls. As well, extensive transport and central metabolic pathways for the metabolism of imported monomers were identified. Interestingly, genes and domains suggestive of the production of a cellulosome-e.g., protein-coding genes harboring dockerin I domains attached to a glycosyl hydrolase and scaffoldin-encoding genes harboring cohesin I and CBM37 domains-were identified in order PBSIII_9, GN03, and MSB-4E2 fragments recovered from four anoxic aquatic habitats; hence extending the cellulosomal production capabilities in Bacteria beyond the Gram-positive Firmicutes In addition to fermentative pathways, a complete electron transport chain with terminal cytochrome c oxidases Caa3 (for operation under high oxygen tension) and Cbb3 (for operation under low oxygen tension) were identified in PBSIII_9 and GN03 fragments recovered from oxygenated and partially/seasonally oxygenated aquatic habitats. Our metagenomic recruitment effort hence represents a comprehensive pangenomic view of this yet-uncultured phylum and provides insights broader than and complementary to those gained from genome recovery initiatives focusing on a single or few sampled environments.IMPORTANCE Our understanding of the phylogenetic diversity, metabolic capabilities, and ecological roles of yet-uncultured microorganisms is rapidly expanding. However, recent efforts mainly have been focused on recovering genomes of novel microbial lineages from a specific sampling site, rather than from a wide range of environmental habitats. To comprehensively evaluate the genomic landscape, putative metabolic capabilities, and ecological roles of yet-uncultured candidate phyla, efforts that focus on the recovery of genomic fragments from a wide range of habitats and that adequately sample the intraphylum diversity within a specific target lineage are needed. Here, we investigated the global distribution patterns and pangenomic diversity of the candidate phylum "Latescibacteria" Our results document the preference of specific "Latescibacteria" orders to specific habitats, the prevalence of plant polysaccharide degradation abilities within all "Latescibacteria" orders, the occurrence of all genes/domains necessary for the production of cellulosomes within three "Latescibacteria" orders (GN03, PBSIII_9, and MSB-4E2) in data sets recovered from anaerobic locations, and the identification of the components of an aerobic respiratory chain, as well as occurrence of multiple O2-dependent metabolic reactions in "Latescibacteria" orders GN03 and PBSIII_9 recovered from oxygenated habitats. The results demonstrate the value of phylocentric pangenomic surveys for understanding the global ecological distribution and panmetabolic abilities of yet-uncultured microbial lineages since they provide broader and more complementary insights than those gained from single-cell genomic and/or metagenomic-enabled genome recovery efforts focusing on a single sampling site.
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77
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Ponnudurai R, Kleiner M, Sayavedra L, Petersen JM, Moche M, Otto A, Becher D, Takeuchi T, Satoh N, Dubilier N, Schweder T, Markert S. Metabolic and physiological interdependencies in the Bathymodiolus azoricus symbiosis. ISME JOURNAL 2016; 11:463-477. [PMID: 27801908 PMCID: PMC5270565 DOI: 10.1038/ismej.2016.124] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 07/28/2016] [Accepted: 08/10/2016] [Indexed: 12/28/2022]
Abstract
The hydrothermal vent mussel Bathymodiolus azoricus lives in an intimate
symbiosis with two types of chemosynthetic Gammaproteobacteria in its gills: a
sulfur oxidizer and a methane oxidizer. Despite numerous investigations over the
last decades, the degree of interdependence between the three symbiotic
partners, their individual metabolic contributions, as well as the mechanism of
carbon transfer from the symbionts to the host are poorly understood. We used a
combination of proteomics and genomics to investigate the physiology and
metabolism of the individual symbiotic partners. Our study revealed that key
metabolic functions are most likely accomplished jointly by B. azoricus
and its symbionts: (1) CO2 is pre-concentrated by the host for carbon
fixation by the sulfur-oxidizing symbiont, and (2) the host replenishes
essential biosynthetic TCA cycle intermediates for the sulfur-oxidizing
symbiont. In return (3), the sulfur oxidizer may compensate for the host's
putative deficiency in amino acid and cofactor biosynthesis. We also identified
numerous ‘symbiosis-specific' host proteins by comparing
symbiont-containing and symbiont-free host tissues and symbiont fractions. These
proteins included a large complement of host digestive enzymes in the gill that
are likely involved in symbiont digestion and carbon transfer from the symbionts
to the host.
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Affiliation(s)
- Ruby Ponnudurai
- Institute of Pharmacy, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Manuel Kleiner
- Department of Geoscience, University of Calgary, Calgary, Canada
| | - Lizbeth Sayavedra
- Department of Symbiosis, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jillian M Petersen
- Department of Symbiosis, Max Planck Institute for Marine Microbiology, Bremen, Germany.,Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Martin Moche
- Institute of Microbiology, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Andreas Otto
- Institute of Microbiology, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Dörte Becher
- Institute of Microbiology, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Nicole Dubilier
- Department of Symbiosis, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Thomas Schweder
- Institute of Pharmacy, Ernst-Moritz-Arndt-University, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
| | - Stephanie Markert
- Institute of Pharmacy, Ernst-Moritz-Arndt-University, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
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78
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Petersen JM, Kemper A, Gruber-Vodicka H, Cardini U, van der Geest M, Kleiner M, Bulgheresi S, Mußmann M, Herbold C, Seah BKB, Antony CP, Liu D, Belitz A, Weber M. Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation. Nat Microbiol 2016; 2:16195. [PMID: 27775707 PMCID: PMC6872982 DOI: 10.1038/nmicrobiol.2016.195] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 09/07/2016] [Indexed: 12/04/2022]
Abstract
Chemosynthetic symbioses are partnerships between invertebrate animals
and chemosynthetic bacteria. The latter are the primary producers, providing most of
the organic carbon needed for the animal host's nutrition. We sequenced genomes of
the chemosynthetic symbionts from the lucinid bivalve Loripes lucinalis and the stilbonematid nematode Laxus oneistus. The symbionts of both host species
encoded nitrogen fixation genes. This is remarkable as no marine chemosynthetic
symbiont was previously known to be capable of nitrogen fixation. We detected
nitrogenase expression by the symbionts of lucinid clams at the transcriptomic and
proteomic level. Mean stable nitrogen isotope values of Loripes lucinalis were within the range expected for fixed atmospheric
nitrogen, further suggesting active nitrogen fixation by the symbionts. The ability
to fix nitrogen may be widespread among chemosynthetic symbioses in oligotrophic
habitats, where nitrogen availability often limits primary productivity. The chemosynthetic symbionts of the bivalve Loripes lucinalis and nematode Laxus
oneistus are found to encode nitrogen fixation genes, with evidence for
active nitrogen fixation.
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Affiliation(s)
- Jillian M Petersen
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria.,Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen 28359, Germany
| | - Anna Kemper
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen 28359, Germany
| | - Harald Gruber-Vodicka
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen 28359, Germany
| | - Ulisse Cardini
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria
| | - Matthijs van der Geest
- Centre for Marine Biodiversity, Exploitation and Conservation (MARBEC), UMR 9190, IRD-IFREMER-CNRS-UM, Université de Montpellier, Montpellier Cedex 5 34095, France.,Department of Coastal Systems and Utrecht University, NIOZ Royal Netherlands Institute for Sea Research, PO Box 59, 1790 AB Den Burg, Texel, The Netherlands
| | - Manuel Kleiner
- Department of Geoscience, University of Calgary, 2500 University Drive Northwest, Alberta T2N 1N4, Canada
| | - Silvia Bulgheresi
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria
| | - Marc Mußmann
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria
| | - Craig Herbold
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria
| | - Brandon K B Seah
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen 28359, Germany
| | - Chakkiath Paul Antony
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen 28359, Germany
| | - Dan Liu
- Department of Geoscience, University of Calgary, 2500 University Drive Northwest, Alberta T2N 1N4, Canada
| | - Alexandra Belitz
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria
| | - Miriam Weber
- HYDRA Institute for Marine Sciences, Elba Field Station, Campo nell'Elba, Livorno 54037, Italy
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79
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Louca S, Hawley AK, Katsev S, Torres-Beltran M, Bhatia MP, Kheirandish S, Michiels CC, Capelle D, Lavik G, Doebeli M, Crowe SA, Hallam SJ. Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone. Proc Natl Acad Sci U S A 2016; 113:E5925-E5933. [PMID: 27655888 PMCID: PMC5056048 DOI: 10.1073/pnas.1602897113] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Microorganisms are the most abundant lifeform on Earth, mediating global fluxes of matter and energy. Over the past decade, high-throughput molecular techniques generating multiomic sequence information (DNA, mRNA, and protein) have transformed our perception of this microcosmos, conceptually linking microorganisms at the individual, population, and community levels to a wide range of ecosystem functions and services. Here, we develop a biogeochemical model that describes metabolic coupling along the redox gradient in Saanich Inlet-a seasonally anoxic fjord with biogeochemistry analogous to oxygen minimum zones (OMZs). The model reproduces measured biogeochemical process rates as well as DNA, mRNA, and protein concentration profiles across the redox gradient. Simulations make predictions about the role of ubiquitous OMZ microorganisms in mediating carbon, nitrogen, and sulfur cycling. For example, nitrite "leakage" during incomplete sulfide-driven denitrification by SUP05 Gammaproteobacteria is predicted to support inorganic carbon fixation and intense nitrogen loss via anaerobic ammonium oxidation. This coupling creates a metabolic niche for nitrous oxide reduction that completes denitrification by currently unidentified community members. These results quantitatively improve previous conceptual models describing microbial metabolic networks in OMZs. Beyond OMZ-specific predictions, model results indicate that geochemical fluxes are robust indicators of microbial community structure and reciprocally, that gene abundances and geochemical conditions largely determine gene expression patterns. The integration of real observational data, including geochemical profiles and process rate measurements as well as metagenomic, metatranscriptomic and metaproteomic sequence data, into a biogeochemical model, as shown here, enables holistic insight into the microbial metabolic network driving nutrient and energy flow at ecosystem scales.
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Affiliation(s)
- Stilianos Louca
- Institute of Applied Mathematics, University of British Columbia, Vancouver, BC, Canada V6T1Z2
| | - Alyse K Hawley
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T1Z3
| | - Sergei Katsev
- Large Lakes Observatory, University of Minnesota Duluth, Duluth, MN 55812; Department of Physics and Astronomy, University of Minnesota Duluth, Duluth, MN 55812
| | - Monica Torres-Beltran
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T1Z3
| | - Maya P Bhatia
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T1Z3; Canadian Institute for Advanced Research Program in Integrated Microbial Biodiversity, Canadian Institute for Advanced Research, Toronto, ON, Canada M5G1Z8
| | - Sam Kheirandish
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T1Z3
| | - Céline C Michiels
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T1Z3
| | - David Capelle
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada V6T1Z4
| | - Gaute Lavik
- Biogeochemistry Group, Max Planck Institute for Marine Microbiology, Bremen D-28359, Germany
| | - Michael Doebeli
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada V6T1Z4; Department of Mathematics, University of British Columbia, Vancouver, BC, Canada V6T1Z4
| | - Sean A Crowe
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T1Z3; Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada V6T1Z4; Ecosystem Services, Commercialization Platforms, and Entrepreneurship (ECOSCOPE) Training Program, University of British Columbia, Vancouver, BC, Canada V6T1Z3;
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T1Z3; Canadian Institute for Advanced Research Program in Integrated Microbial Biodiversity, Canadian Institute for Advanced Research, Toronto, ON, Canada M5G1Z8; Ecosystem Services, Commercialization Platforms, and Entrepreneurship (ECOSCOPE) Training Program, University of British Columbia, Vancouver, BC, Canada V6T1Z3; Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada V6T1Z3; Peter Wall Institute for Advanced Studies, University of British Columbia, Vancouver, BC, Canada V6T1Z2
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80
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Rastelli E, Corinaldesi C, Petani B, Dell'Anno A, Ciglenečki I, Danovaro R. Enhanced viral activity and dark CO2
fixation rates under oxygen depletion: the case study of the marine Lake Rogoznica. Environ Microbiol 2016; 18:4511-4522. [DOI: 10.1111/1462-2920.13484] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/02/2016] [Accepted: 08/04/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Eugenio Rastelli
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
- Stazione Zoologica Anton Dohrn, Villa Comunale; Naples 80121 Italy
| | - Cinzia Corinaldesi
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
| | - Bruna Petani
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
| | - Antonio Dell'Anno
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
| | - Irena Ciglenečki
- Division for Marine and Environmental Research, Bijenicka 54; Rudjer Bošković Institute; Zagreb 10001 Croatia
| | - Roberto Danovaro
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
- Stazione Zoologica Anton Dohrn, Villa Comunale; Naples 80121 Italy
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81
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Orsi WD, Barker Jørgensen B, Biddle JF. Transcriptional analysis of sulfate reducing and chemolithoautotrophic sulfur oxidizing bacteria in the deep subseafloor. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:452-460. [PMID: 26991974 DOI: 10.1111/1758-2229.12387] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Sulfate reducing bacteria (SRB) oxidize a significant proportion of subseafloor organic carbon, but their metabolic activities and subsistence mechanisms are poorly understood. Here, we report in depth phylogenetic and metabolic analyses of SRB transcripts in the Peru Margin subseafloor and interpret these results in the context of sulfate reduction activity in the sediment. Relative abundance of overall SRB gene transcripts declines strongly whereas relative abundance of ribosomal protein transcripts from sulfate reducing δ-Proteobacteria peak at 90 m below seafloor (mbsf) within a deep sulfate methane transition zone. This coincides with isotopically heavy δ(34) S values of pore water sulfate (70‰), indicating active subseafloor microbial sulfate reduction. Within the shallow sulfate reduction zone (0-5 mbsf), a transcript encoding the beta subunit of dissimilatory sulfite reductase (dsrB) was related to Desulfitobacterium dehalogenans and environmental sequences from Aarhus Bay (Denmark). At 159 mbsf we discovered a transcript encoding the reversely operating dissimilatory sulfite reductase α-subunit (rdsrA), with basal phylogenetic relation to the chemolithoautotrophic SUP05 Group II clade. A diversity of SRB transcripts involved in cellular maintenance point toward potential subsistence mechanisms under low-energy over long time periods, and provide a detailed new picture of SRB activities underlying sulfur cycling in the deep subseafloor.
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Affiliation(s)
- William D Orsi
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Germany
| | - Bo Barker Jørgensen
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, 8000, Aarhus, Denmark
| | - Jennifer F Biddle
- College of Earth, Ocean and Environment, University of Delaware, Lewes, DE, 19958, USA
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82
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Cultivation of a chemoautotroph from the SUP05 clade of marine bacteria that produces nitrite and consumes ammonium. ISME JOURNAL 2016; 11:263-271. [PMID: 27434424 PMCID: PMC5315479 DOI: 10.1038/ismej.2016.87] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 03/02/2016] [Accepted: 05/20/2016] [Indexed: 11/10/2022]
Abstract
Marine oxygen minimum zones (OMZs) are expanding regions of intense nitrogen cycling. Up to half of the nitrogen available for marine organisms is removed from the ocean in these regions. Metagenomic studies have identified an abundant group of sulfur-oxidizing bacteria (SUP05) with the genetic potential for nitrogen cycling and loss in OMZs. However, SUP05 have defied cultivation and their physiology remains untested. We cultured, sequenced and tested the physiology of an isolate from the SUP05 clade. We describe a facultatively anaerobic sulfur-oxidizing chemolithoautotroph that produces nitrite and consumes ammonium under anaerobic conditions. Genetic evidence that closely related strains are abundant at nitrite maxima in OMZs suggests that sulfur-oxidizing chemoautotrophs from the SUP05 clade are a potential source of nitrite, fueling competing nitrogen removal processes in the ocean.
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83
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Meyerhof MS, Wilson JM, Dawson MN, Michael Beman J. Microbial community diversity, structure and assembly across oxygen gradients in meromictic marine lakes, Palau. Environ Microbiol 2016; 18:4907-4919. [PMID: 27312889 DOI: 10.1111/1462-2920.13416] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 06/13/2016] [Indexed: 11/29/2022]
Abstract
Microbial communities consume oxygen, alter biogeochemistry and compress habitat in aquatic ecosystems, yet our understanding of these microbial-biogeochemical-ecological interactions is limited by a lack of systematic analyses of low-oxygen ecosystems. Marine lakes provide an ideal comparative system, as they range from well-mixed holomictic lakes to stratified, anoxic, meromictic lakes that vary in their vertical extent of anoxia. We examined microbial communities inhabiting six marine lakes and one ocean site using pyrosequencing of 16S rRNA genes. Microbial richness and evenness was typically highest in the anoxic monimolimnion of meromictic lakes, with common marine bacteria present in mixolimnion communities replaced by anoxygenic phototrophs, sulfate-reducing bacteria and SAR406 in the monimolimnion. These sharp changes in community structure were linked to environmental gradients (constrained variation in redundancy analysis = 68%-76%) - particularly oxygen and pH. However, in those lakes with the steepest oxygen gradients, salinity and dissolved nutrients were important secondary constraining variables, indicating that subtle but substantive differences in microbial communities occur within similar low-oxygen habitats. Deterministic processes were a dominant influence on whole community assembly (all nearest taxon index values >4), demonstrating that the strong environmental gradients present in meromictic marine lakes drive microbial community assembly.
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Affiliation(s)
- Matthew S Meyerhof
- Life and Environmental Sciences, University of California, Merced, CA, 95343, USA
| | - Jesse M Wilson
- Life and Environmental Sciences, University of California, Merced, CA, 95343, USA
| | - Michael N Dawson
- Life and Environmental Sciences, University of California, Merced, CA, 95343, USA
| | - J Michael Beman
- Life and Environmental Sciences, University of California, Merced, CA, 95343, USA
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84
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Lüke C, Speth DR, Kox MAR, Villanueva L, Jetten MSM. Metagenomic analysis of nitrogen and methane cycling in the Arabian Sea oxygen minimum zone. PeerJ 2016; 4:e1924. [PMID: 27077014 PMCID: PMC4830246 DOI: 10.7717/peerj.1924] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 03/21/2016] [Indexed: 01/24/2023] Open
Abstract
Oxygen minimum zones (OMZ) are areas in the global ocean where oxygen concentrations drop to below one percent. Low oxygen concentrations allow alternative respiration with nitrate and nitrite as electron acceptor to become prevalent in these areas, making them main contributors to oceanic nitrogen loss. The contribution of anammox and denitrification to nitrogen loss seems to vary in different OMZs. In the Arabian Sea, both processes were reported. Here, we performed a metagenomics study of the upper and core zone of the Arabian Sea OMZ, to provide a comprehensive overview of the genetic potential for nitrogen and methane cycling. We propose that aerobic ammonium oxidation is carried out by a diverse community of Thaumarchaeota in the upper zone of the OMZ, whereas a low diversity of Scalindua-like anammox bacteria contribute significantly to nitrogen loss in the core zone. Aerobic nitrite oxidation in the OMZ seems to be performed by Nitrospina spp. and a novel lineage of nitrite oxidizing organisms that is present in roughly equal abundance as Nitrospina. Dissimilatory nitrate reduction to ammonia (DNRA) can be carried out by yet unknown microorganisms harbouring a divergent nrfA gene. The metagenomes do not provide conclusive evidence for active methane cycling; however, a low abundance of novel alkane monooxygenase diversity was detected. Taken together, our approach confirmed the genomic potential for an active nitrogen cycle in the Arabian Sea and allowed detection of hitherto overlooked lineages of carbon and nitrogen cycle bacteria.
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Affiliation(s)
- Claudia Lüke
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Daan R Speth
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Martine A R Kox
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Laura Villanueva
- Department of Marine Organic Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), 't Horntje (Texel), Netherlands
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, Netherlands.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands.,Soehngen Institute of Anaerobic Microbiology, Nijmegen, Netherlands
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85
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He T, Zhang X. Characterization of Bacterial Communities in Deep-Sea Hydrothermal Vents from Three Oceanic Regions. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:232-241. [PMID: 26626941 DOI: 10.1007/s10126-015-9683-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 11/15/2015] [Indexed: 06/05/2023]
Abstract
Deep-sea hydrothermal vents are considered to be one of the most spectacular ecosystems on Earth. Microorganisms form the basis of the food chain in vents controlling the vent communities. However, the diversity of bacterial communities in deep-sea hydrothermal vents from different oceans remains largely unknown. In this study, the pyrosequencing of 16S rRNA gene was used to characterize the bacterial communities of the venting sulfide, seawater, and tubeworm trophosome from East Pacific Rise, South Atlantic Ridge, and Southwest Indian Ridge, respectively. A total of 23,767 operational taxonomic units (OTUs) were assigned into 42 different phyla. Although Proteobacteria, Actinobacteria, and Bacteroidetes were the predominant phyla in all vents, differences of bacterial diversity were observed among different vents from three oceanic regions. The sulfides of East Pacific Rise possessed the most diverse bacterial communities. The bacterial diversities of venting seawater were much lower than those of vent sulfides. The symbiotic bacteria of tubeworm Ridgeia piscesae were included in the bacterial community of vent sulfides, suggesting their significant ecological functions as the primary producers in the deep-sea hydrothermal vent ecosystems. Therefore, our study presented a comprehensive view of bacterial communities in deep-sea hydrothermal vents from different oceans.
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Affiliation(s)
- Tianliang He
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Xiaobo Zhang
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China.
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86
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Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent. ISME JOURNAL 2016; 10:1925-38. [PMID: 26872039 PMCID: PMC5029171 DOI: 10.1038/ismej.2015.258] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 12/07/2015] [Accepted: 12/10/2015] [Indexed: 01/13/2023]
Abstract
The chemolithoautotrophic microbial community of the rocky subseafloor potentially provides a large amount of organic carbon to the deep ocean, yet our understanding of the activity and metabolic complexity of subseafloor organisms remains poorly described. A combination of metagenomic, metatranscriptomic, and RNA stable isotope probing (RNA-SIP) analyses were used to identify the metabolic potential, expression patterns, and active autotrophic bacteria and archaea and their pathways present in low-temperature hydrothermal fluids from Axial Seamount, an active submarine volcano. Metagenomic and metatranscriptomic results showed the presence of genes and transcripts for sulfur, hydrogen, and ammonium oxidation, oxygen respiration, denitrification, and methanogenesis, as well as multiple carbon fixation pathways. In RNA-SIP experiments across a range of temperatures under reducing conditions, the enriched 13C fractions showed differences in taxonomic and functional diversity. At 30 °C and 55 °C, Epsilonproteobacteria were dominant, oxidizing hydrogen and primarily reducing nitrate. Methanogenic archaea were also present at 55 °C, and were the only autotrophs present at 80 °C. Correspondingly, the predominant CO2 fixation pathways changed from the reductive tricarboxylic acid (rTCA) cycle to the reductive acetyl-CoA pathway with increasing temperature. By coupling RNA-SIP with meta-omics, this study demonstrates the presence and activity of distinct chemolithoautotrophic communities across a thermal gradient of a deep-sea hydrothermal vent.
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87
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Jiang Y, Xiong X, Danska J, Parkinson J. Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality. MICROBIOME 2016; 4:2. [PMID: 26757703 PMCID: PMC4710996 DOI: 10.1186/s40168-015-0146-x] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/19/2015] [Indexed: 05/11/2023]
Abstract
BACKGROUND Metatranscriptomics is emerging as a powerful technology for the functional characterization of complex microbial communities (microbiomes). Use of unbiased RNA-sequencing can reveal both the taxonomic composition and active biochemical functions of a complex microbial community. However, the lack of established reference genomes, computational tools and pipelines make analysis and interpretation of these datasets challenging. Systematic studies that compare data across microbiomes are needed to demonstrate the ability of such pipelines to deliver biologically meaningful insights on microbiome function. RESULTS Here, we apply a standardized analytical pipeline to perform a comparative analysis of metatranscriptomic data from diverse microbial communities derived from mouse large intestine, cow rumen, kimchi culture, deep-sea thermal vent and permafrost. Sequence similarity searches allowed annotation of 19 to 76% of putative messenger RNA (mRNA) reads, with the highest frequency in the kimchi dataset due to its relatively low complexity and availability of closely related reference genomes. Metatranscriptomic datasets exhibited distinct taxonomic and functional signatures. From a metabolic perspective, we identified a common core of enzymes involved in amino acid, energy and nucleotide metabolism and also identified microbiome-specific pathways such as phosphonate metabolism (deep sea) and glycan degradation pathways (cow rumen). Integrating taxonomic and functional annotations within a novel visualization framework revealed the contribution of different taxa to metabolic pathways, allowing the identification of taxa that contribute unique functions. CONCLUSIONS The application of a single, standard pipeline confirms that the rich taxonomic and functional diversity observed across microbiomes is not simply an artefact of different analysis pipelines but instead reflects distinct environmental influences. At the same time, our findings show how microbiome complexity and availability of reference genomes can impact comprehensive annotation of metatranscriptomes. Consequently, beyond the application of standardized pipelines, additional caution must be taken when interpreting their output and performing downstream, microbiome-specific, analyses. The pipeline used in these analyses along with a tutorial has been made freely available for download from our project website: http://www.compsysbio.org/microbiome .
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Affiliation(s)
- Yue Jiang
- Program in Molecular Structure and Function, The Hospital for Sick Children, Peter Gilgan Center for Research and Learning, 686 Bay Street, Toronto, ON, M5G 0A4, Canada.
| | - Xuejian Xiong
- Program in Molecular Structure and Function, The Hospital for Sick Children, Peter Gilgan Center for Research and Learning, 686 Bay Street, Toronto, ON, M5G 0A4, Canada.
| | - Jayne Danska
- Department of Immunology, University of Toronto, Toronto, ON, Canada.
- Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
| | - John Parkinson
- Program in Molecular Structure and Function, The Hospital for Sick Children, Peter Gilgan Center for Research and Learning, 686 Bay Street, Toronto, ON, M5G 0A4, Canada.
- Departments of Biochemistry, Computer Science and Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- Centre for the Analysis of Genome Evolution, University of Toronto, Toronto, ON, Canada.
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88
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Yilmaz P, Yarza P, Rapp JZ, Glöckner FO. Expanding the World of Marine Bacterial and Archaeal Clades. Front Microbiol 2016; 6:1524. [PMID: 26779174 PMCID: PMC4705458 DOI: 10.3389/fmicb.2015.01524] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/18/2015] [Indexed: 12/18/2022] Open
Abstract
Determining which microbial taxa are out there, where they live, and what they are doing is a driving approach in marine microbial ecology. The importance of these questions is underlined by concerted, large-scale, and global ocean sampling initiatives, for example the International Census of Marine Microbes, Ocean Sampling Day, or Tara Oceans. Given decades of effort, we know that the large majority of marine Bacteria and Archaea belong to about a dozen phyla. In addition to the classically culturable Bacteria and Archaea, at least 50 “clades,” at different taxonomic depths, exist. These account for the majority of marine microbial diversity, but there is still an underexplored and less abundant portion remaining. We refer to these hitherto unrecognized clades as unknown, as their boundaries, names, and classifications are not available. In this work, we were able to characterize up to 92 of these unknown clades found within the bacterial and archaeal phylogenetic diversity currently reported for marine water column environments. We mined the SILVA 16S rRNA gene datasets for sequences originating from the marine water column. Instead of the usual subjective taxa delineation and nomenclature methods, we applied the candidate taxonomic unit (CTU) circumscription system, along with a standardized nomenclature to the sequences in newly constructed phylogenetic trees. With this new phylogenetic and taxonomic framework, we performed an analysis of ICoMM rRNA gene amplicon datasets to gain insights into the global distribution of the new marine clades, their ecology, biogeography, and interaction with oceanographic variables. Most of the new clades we identified were interspersed by known taxa with cultivated members, whose genome sequences are available. This result encouraged us to perform metabolic predictions for the novel marine clades using the PICRUSt approach. Our work also provides an update on the taxonomy of several phyla and widely known marine clades as our CTU approach breaks down these randomly lumped clades into smaller objectively calculated subgroups. Finally, all taxa were classified and named following standards compatible with the Bacteriological Code rules, enhancing their digitization, and comparability with future microbial ecological and taxonomy studies.
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Affiliation(s)
- Pelin Yilmaz
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | | | - Josephine Z Rapp
- HGF-MPG Joint Research Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, Bremen and the Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Bremerhaven, Germany
| | - Frank O Glöckner
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine MicrobiologyBremen, Germany; Life Sciences and Chemistry, Jacobs UniversityBremen, Germany
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89
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Genome Sequence of "Candidatus Thioglobus autotrophica" Strain EF1, a Chemoautotroph from the SUP05 Clade of Marine Gammaproteobacteria. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01156-15. [PMID: 26494660 PMCID: PMC4616170 DOI: 10.1128/genomea.01156-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Chemoautotrophic marine bacteria from the SUP05 clade of marine gammaproteobacteria often dominate low-oxygen waters in upwelling regions, fjords, and hydrothermal systems. Here, we announce the complete genome sequence of "Candidatus Thioglobus autotrophica" strain EF1, the first cultured chemoautotrophic representative from the SUP05 clade.
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90
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Genome Sequence of "Candidatus Thioglobus singularis" Strain PS1, a Mixotroph from the SUP05 Clade of Marine Gammaproteobacteria. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01155-15. [PMID: 26494659 PMCID: PMC4616169 DOI: 10.1128/genomea.01155-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Mixotrophic marine bacteria from the SUP05 clade are ubiquitous in the ocean. Here, we announce the complete genome sequence of “Candidatus Thioglobus singularis” strain PS1, the first cultured mixotrophic representative from the SUP05 clade.
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91
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Ikuta T, Takaki Y, Nagai Y, Shimamura S, Tsuda M, Kawagucci S, Aoki Y, Inoue K, Teruya M, Satou K, Teruya K, Shimoji M, Tamotsu H, Hirano T, Maruyama T, Yoshida T. Heterogeneous composition of key metabolic gene clusters in a vent mussel symbiont population. ISME JOURNAL 2015; 10:990-1001. [PMID: 26418631 PMCID: PMC4796938 DOI: 10.1038/ismej.2015.176] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 08/10/2015] [Accepted: 08/13/2015] [Indexed: 11/09/2022]
Abstract
Chemosynthetic symbiosis is one of the successful systems for adapting to a wide range of habitats including extreme environments, and the metabolic capabilities of symbionts enable host organisms to expand their habitat ranges. However, our understanding of the adaptive strategies that enable symbiotic organisms to expand their habitats is still fragmentary. Here, we report that a single-ribotype endosymbiont population in an individual of the host vent mussel, Bathymodiolus septemdierum has heterogeneous genomes with regard to the composition of key metabolic gene clusters for hydrogen oxidation and nitrate reduction. The host individual harbours heterogeneous symbiont subpopulations that either possess or lack the gene clusters encoding hydrogenase or nitrate reductase. The proportions of the different symbiont subpopulations in a host appeared to vary with the environment or with the host's development. Furthermore, the symbiont subpopulations were distributed in patches to form a mosaic pattern in the gill. Genomic heterogeneity in an endosymbiont population may enable differential utilization of diverse substrates and confer metabolic flexibility. Our findings open a new chapter in our understanding of how symbiotic organisms alter their metabolic capabilities and expand their range of habitats.
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Affiliation(s)
- Tetsuro Ikuta
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Yukiko Nagai
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Shigeru Shimamura
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Miwako Tsuda
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Shinsuke Kawagucci
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Yui Aoki
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Koji Inoue
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Morimi Teruya
- Okinawa Industrial Technology Center, 12-2 Suzaki, Uruma, Okinawa, Japan
| | - Kazuhito Satou
- Okinawa Institute of Advanced Sciences (OIAS), 5-1 Suzaki, Uruma, Okinawa, Japan
| | - Kuniko Teruya
- Okinawa Institute of Advanced Sciences (OIAS), 5-1 Suzaki, Uruma, Okinawa, Japan
| | - Makiko Shimoji
- Okinawa Institute of Advanced Sciences (OIAS), 5-1 Suzaki, Uruma, Okinawa, Japan
| | - Hinako Tamotsu
- Okinawa Institute of Advanced Sciences (OIAS), 5-1 Suzaki, Uruma, Okinawa, Japan
| | - Takashi Hirano
- Okinawa Institute of Advanced Sciences (OIAS), 5-1 Suzaki, Uruma, Okinawa, Japan.,Okinawa Science and Technology Promotion Center (OSTC), 112-18 Asahimachi, Naha, Okinawa, Japan
| | - Tadashi Maruyama
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Takao Yoshida
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
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92
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Cao H, Shao Z, Li J, Zhang W, Qian PY. Phylogenetic diversity of nitrogen-utilizing genes in hydrothermal chimneys from 3 middle ocean ridges. Extremophiles 2015; 19:1173-82. [PMID: 26369648 DOI: 10.1007/s00792-015-0788-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Accepted: 08/30/2015] [Indexed: 10/23/2022]
Abstract
Nitrogen-metabolizing genes, including nitrogenase (nifH), periplasmic nitrate reductase (napA), and cytochrome cd 1-type nitrite reductase (nirS), were collected from hydrothermal chimney sulfides on 3 middle ocean ridges and compared for the first time. There was a clear phylogenetic distinction of these nifH genes between different hydrothermal ecosystems, which supported the colonization and potential adaptation by different nitrogen fixing microbes in those sulfides. In particular, in sulfides from low-temperature hydrothermal vents of the Southwest Indian Ocean Ridge, the prevalence of nifH genes appears to be attributed to sulfate-reducing bacteria, suggesting their ecological significance. Phylogenetic analysis of nitrate/nitrite reductase genes indicated that nitrate was a critical electron acceptor for sulfur- or metal-oxidizing bacteria in these hydrothermal ecosystems. Our results provided information about the compositions and diversity of the 3 important genes involved in nitrogen fixation and nitrate/nitrite reduction processes in hydrothermal ecosystems and is the first comprehensive genetic repertoire of genes related to potential nitrogen fixation and denitrification processes in various hydrothermal environments.
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Affiliation(s)
- Huiluo Cao
- Division of Life Sciences, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, The Third Institute of Oceanography, State of Oceanic Administration, Xiamen, China
| | - Jiangtao Li
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Weipeng Zhang
- Division of Life Sciences, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Pei-Yuan Qian
- Division of Life Sciences, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
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93
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Sayavedra L, Kleiner M, Ponnudurai R, Wetzel S, Pelletier E, Barbe V, Satoh N, Shoguchi E, Fink D, Breusing C, Reusch TBH, Rosenstiel P, Schilhabel MB, Becher D, Schweder T, Markert S, Dubilier N, Petersen JM. Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels. eLife 2015; 4:e07966. [PMID: 26371554 PMCID: PMC4612132 DOI: 10.7554/elife.07966] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 09/14/2015] [Indexed: 01/06/2023] Open
Abstract
Bathymodiolus mussels live in symbiosis with intracellular sulfur-oxidizing (SOX) bacteria that provide them with nutrition. We sequenced the SOX symbiont genomes from two Bathymodiolus species. Comparison of these symbiont genomes with those of their closest relatives revealed that the symbionts have undergone genome rearrangements, and up to 35% of their genes may have been acquired by horizontal gene transfer. Many of the genes specific to the symbionts were homologs of virulence genes. We discovered an abundant and diverse array of genes similar to insecticidal toxins of nematode and aphid symbionts, and toxins of pathogens such as Yersinia and Vibrio. Transcriptomics and proteomics revealed that the SOX symbionts express the toxin-related genes (TRGs) in their hosts. We hypothesize that the symbionts use these TRGs in beneficial interactions with their host, including protection against parasites. This would explain why a mutualistic symbiont would contain such a remarkable 'arsenal' of TRGs.
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Affiliation(s)
| | - Manuel Kleiner
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Ruby Ponnudurai
- Institute of Pharmacy, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Silke Wetzel
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Eric Pelletier
- Genoscope - Centre National de Séquençage, Commissariat à l'énergie atomique et aux énergies alternatives, Evry, France
- Metabolic Genomics Group, Commissariat à l'énergie atomique et aux énergies alternatives, Evry, France
- University of Évry-Val d'Essonne, Evry, France
| | - Valerie Barbe
- Genoscope - Centre National de Séquençage, Commissariat à l'énergie atomique et aux énergies alternatives, Evry, France
| | - Nori Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology, Onna, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology, Onna, Japan
| | - Dennis Fink
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Corinna Breusing
- Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Thorsten BH Reusch
- Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | | | | | - Dörte Becher
- Institute of Marine Biotechnology, Greifswald, Germany
- Institute of Microbiology, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Thomas Schweder
- Institute of Pharmacy, Ernst-Moritz-Arndt-University, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Stephanie Markert
- Institute of Pharmacy, Ernst-Moritz-Arndt-University, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- University of Bremen, Bremen, Germany
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94
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Colatriano D, Ramachandran A, Yergeau E, Maranger R, Gélinas Y, Walsh DA. Metaproteomics of aquatic microbial communities in a deep and stratified estuary. Proteomics 2015. [PMID: 26223443 DOI: 10.1002/pmic.201500079] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Here we harnessed the power of metaproteomics to assess the metabolic diversity and function of stratified aquatic microbial communities in the deep and expansive Lower St. Lawrence Estuary, located in eastern Canada. Vertical profiling of the microbial communities through the stratified water column revealed differences in metabolic lifestyles and in carbon and nitrogen processing pathways. In productive surface waters, we identified heterotrophic populations involved in the processing of high and low molecular weight organic matter from both terrestrial (e.g. cellulose and xylose) and marine (e.g. organic compatible osmolytes) sources. In the less productive deep waters, chemosynthetic production coupled to nitrification by MG-I Thaumarchaeota and Nitrospina appeared to be a dominant metabolic strategy. Similar to other studies of the coastal ocean, we identified methanol oxidation proteins originating from the common OM43 marine clade. However, we also identified a novel lineage of methanol-oxidizers specifically in the particle-rich bottom (i.e. nepheloid) layer. Membrane transport proteins assigned to the uncultivated MG-II Euryarchaeota were also specifically detected in the nepheloid layer. In total, these results revealed strong vertical structure of microbial taxa and metabolic activities, as well as the presence of specific "nepheloid" taxa that may contribute significantly to coastal ocean nutrient cycling.
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Affiliation(s)
- David Colatriano
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | | | - Etienne Yergeau
- National Research Council Canada, Energy, Mining and Environment, Montreal, Quebec, Canada
| | - Roxane Maranger
- Département des Sciences Biologiques, Université de Montréal, Montréal, Quebec, Canada.,Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Montreal, Quebec, Canada
| | - Yves Gélinas
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, Canada.,Geochemistry and Geodynamics Research Center (GEOTOP), Montreal, Quebec, Canada
| | - David A Walsh
- Department of Biology, Concordia University, Montreal, Quebec, Canada.,Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Montreal, Quebec, Canada.,Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program, Toronto ON, Canada
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95
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Tian M, Zhao F, Shen X, Chu K, Wang J, Chen S, Guo Y, Liu H. The first metagenome of activated sludge from full-scale anaerobic/anoxic/oxic (A2O) nitrogen and phosphorus removal reactor using Illumina sequencing. J Environ Sci (China) 2015; 35:181-190. [PMID: 26354707 DOI: 10.1016/j.jes.2014.12.027] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 12/01/2014] [Accepted: 12/09/2014] [Indexed: 06/05/2023]
Abstract
The anaerobic/anoxic/oxic (A2O) process is globally one of the widely used biological sewage treatment processes. This is the first report of a metagenomic analysis using Illumina sequencing of full-scale A2O sludge from a municipal sewage treatment plant. With more than 530,000 clean reads from different taxa and metabolic categories, the metagenome results allow us to gain insight into the functioning of the biological community of the A2O sludge. There are 51 phyla and nearly 900 genera identified from the A2O activated sludge ecosystem. Proteobacteria, Bacteroidetes, Nitrospirae and Chloroflexi are predominant phyla in the activated sludge, suggesting that these organisms play key roles in the biodegradation processes in the A2O sewage treatment system. Nitrospira, Thauera, Dechloromonas and Ignavibacterium, which have abilities to metabolize nitrogen and aromatic compounds, are most prevalent genera. The percent of nitrogen and phosphorus metabolism in the A2O sludge is 2.72% and 1.48%, respectively. In the current A2O sludge, the proportion of Candidatus Accumulibacter is 1.37%, which is several times more than that reported in a recent study of A2O sludge. Among the four processes of nitrogen metabolism, denitrification related genes had the highest number of sequences (76.74%), followed by ammonification (15.77%), nitrogen fixation (3.88%) and nitrification (3.61%). In phylum Planctomycetes, four genera (Planctomyces, Pirellula, Gemmata and Singulisphaera) are included in the top 30 abundant genera, suggesting the key role of ANAMMOX in nitrogen metabolism in the A2O sludge.
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Affiliation(s)
- Mei Tian
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou 221116, China; College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, China
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Xin Shen
- College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, China
| | - Kahou Chu
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Jinfeng Wang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuai Chen
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Guo
- Lianyungang Jinzhao Water Co., Ltd., Lianyungang 222005, China
| | - Hanhu Liu
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou 221116, China.
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96
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Variations in Microbial Community Structure through the Stratified Water Column in the Tyrrhenian Sea (Central Mediterranean). JOURNAL OF MARINE SCIENCE AND ENGINEERING 2015. [DOI: 10.3390/jmse3030845] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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97
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Noguerola I, Picazo A, Llirós M, Camacho A, Borrego CM. Diversity of freshwaterEpsilonproteobacteriaand dark inorganic carbon fixation in the sulphidic redoxcline of a meromictic karstic lake. FEMS Microbiol Ecol 2015. [PMID: 26195601 DOI: 10.1093/femsec/fiv086] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Imma Noguerola
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, Universitat de Girona, Campus de Montilivi, E-17071 Girona, Spain
| | - Antonio Picazo
- Cavanilles Institute for Biodiversity and Evolutionary Biology and Department of Microbiology and Ecology, Edificio de Investigación 'Jeroni Muñoz', Campus de Burjassot, Universitat de Valencia, E-46100, Burjassot, Valencia, Spain
| | - Marc Llirós
- Université Catholique de Louvain, Institut des Sciences de la Vie, Place Croix du Sud, 4/5 L07.07.06, B-1348 Louvain-La-Neuve, Belgium
| | - Antonio Camacho
- Cavanilles Institute for Biodiversity and Evolutionary Biology and Department of Microbiology and Ecology, Edificio de Investigación 'Jeroni Muñoz', Campus de Burjassot, Universitat de Valencia, E-46100, Burjassot, Valencia, Spain
| | - Carles M Borrego
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, Universitat de Girona, Campus de Montilivi, E-17071 Girona, Spain Water Quality and Microbial Diversity, Catalan Institute for Water Research (ICRA), H2O Building, Scientific and Technological Park of the University of Girona, Emili Grahit 101, E-17003 Girona, Spain
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98
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Metagenomic resolution of microbial functions in deep-sea hydrothermal plumes across the Eastern Lau Spreading Center. ISME JOURNAL 2015; 10:225-39. [PMID: 26046257 DOI: 10.1038/ismej.2015.81] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 03/05/2015] [Accepted: 04/09/2015] [Indexed: 11/08/2022]
Abstract
Microbial processes within deep-sea hydrothermal plumes affect ocean biogeochemistry on global scales. In rising hydrothermal plumes, a combination of microbial metabolism and particle formation processes initiate the transformation of reduced chemicals like hydrogen sulfide, hydrogen, methane, iron, manganese and ammonia that are abundant in hydrothermal vent fluids. Despite the biogeochemical importance of this rising portion of plumes, it is understudied in comparison to neutrally buoyant plumes. Here we use metagenomics and bioenergetic modeling to describe the abundance and genetic potential of microorganisms in relation to available electron donors in five different hydrothermal plumes and three associated background deep-sea waters from the Eastern Lau Spreading Center located in the Western Pacific Ocean. Three hundred and thirty one distinct genomic 'bins' were identified, comprising an estimated 951 genomes of archaea, bacteria, eukarya and viruses. A significant proportion of these genomes is from novel microorganisms and thus reveals insights into the energy metabolism of heretofore unknown microbial groups. Community-wide analyses of genes encoding enzymes that oxidize inorganic energy sources showed that sulfur oxidation was the most abundant and diverse chemolithotrophic microbial metabolism in the community. Genes for sulfur oxidation were commonly present in genomic bins that also contained genes for oxidation of hydrogen and methane, suggesting metabolic versatility in these microbial groups. The relative diversity and abundance of genes encoding hydrogen oxidation was moderate, whereas that of genes for methane and ammonia oxidation was low in comparison to sulfur oxidation. Bioenergetic-thermodynamic modeling supports the metagenomic analyses, showing that oxidation of elemental sulfur with oxygen is the most dominant catabolic reaction in the hydrothermal plumes. We conclude that the energy metabolism of microbial communities inhabiting rising hydrothermal plumes is dictated by the underlying plume chemistry, with a dominant role for sulfur-based chemolithoautotrophy.
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Carolan MT, Smith JM, Beman JM. Transcriptomic evidence for microbial sulfur cycling in the eastern tropical North Pacific oxygen minimum zone. Front Microbiol 2015; 6:334. [PMID: 26029168 PMCID: PMC4426714 DOI: 10.3389/fmicb.2015.00334] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 04/03/2015] [Indexed: 01/06/2023] Open
Abstract
Microbial communities play central roles in ocean biogeochemical cycles, and are particularly important in in oceanic oxygen minimum zones (OMZs). However, the key carbon, nitrogen, and sulfur (S) cycling processes catalyzed by OMZ microbial communities are poorly constrained spatially, temporally, and with regard to the different microbial groups involved. Here we sample across dissolved oxygen (DO) gradients in the oceans’ largest OMZ by volume—the eastern tropical North Pacific ocean, or ETNP—and quantify 16S rRNA and functional gene transcripts to detect and constrain the activity of different S-cycling groups. Based on gene expression profiles, putative dissimilatory sulfite reductase (dsrA) genes are actively expressed within the ETNP OMZ. dsrA expression was limited almost entirely to samples with elevated nitrite concentrations, consistent with previous observations in the Eastern Tropical South Pacific OMZ. dsrA and ‘reverse’ dissimilatory sulfite reductase (rdsrA) genes are related and the associated enzymes are known to operate in either direction—reducing or oxidizing different S compounds. We found that rdsrA genes and soxB genes were expressed in the same samples, suggestive of active S cycling in the ETNP OMZ. These data provide potential thresholds for S cycling in OMZs that closely mimic recent predictions, and indicate that S cycling may be broadly relevant in OMZs.
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Affiliation(s)
- Molly T Carolan
- Life and Environmental Sciences and Sierra Nevada Research Institute, University of California at Merced Merced, CA, USA
| | - Jason M Smith
- Monterey Bay Aquarium Research Institute Moss Landing, CA, USA
| | - J M Beman
- Monterey Bay Aquarium Research Institute Moss Landing, CA, USA
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Chow CET, Winget DM, White RA, Hallam SJ, Suttle CA. Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions. Front Microbiol 2015; 6:265. [PMID: 25914678 PMCID: PMC4392320 DOI: 10.3389/fmicb.2015.00265] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 03/17/2015] [Indexed: 11/13/2022] Open
Abstract
Viral diversity and virus-host interactions in oxygen-starved regions of the ocean, also known as oxygen minimum zones (OMZs), remain relatively unexplored. Microbial community metabolism in OMZs alters nutrient and energy flow through marine food webs, resulting in biological nitrogen loss and greenhouse gas production. Thus, viruses infecting OMZ microbes have the potential to modulate community metabolism with resulting feedback on ecosystem function. Here, we describe viral communities inhabiting oxic surface (10 m) and oxygen-starved basin (200 m) waters of Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island, British Columbia using viral metagenomics and complete viral fosmid sequencing on samples collected between April 2007 and April 2010. Of 6459 open reading frames (ORFs) predicted across all 34 viral fosmids, 77.6% (n = 5010) had no homology to reference viral genomes. These fosmids recruited a higher proportion of viral metagenomic sequences from Saanich Inlet than from nearby northeastern subarctic Pacific Ocean (Line P) waters, indicating differences in the viral communities between coastal and open ocean locations. While functional annotations of fosmid ORFs were limited, recruitment to NCBI's non-redundant “nr” database and publicly available single-cell genomes identified putative viruses infecting marine thaumarchaeal and SUP05 proteobacteria to provide potential host linkages with relevance to coupled biogeochemical cycling processes in OMZ waters. Taken together, these results highlight the power of coupled analyses of multiple sequence data types, such as viral metagenomic and fosmid sequence data with prokaryotic single cell genomes, to chart viral diversity, elucidate genomic and ecological contexts for previously unclassifiable viral sequences, and identify novel host interactions in natural and engineered ecosystems.
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Affiliation(s)
- Cheryl-Emiliane T Chow
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia Vancouver, BC, Canada
| | - Danielle M Winget
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia Vancouver, BC, Canada
| | - Richard A White
- Department of Microbiology and Immunology, University of British Columbia Vancouver, BC, Canada
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia Vancouver, BC, Canada ; Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research Toronto, ON, Canada ; Graduate Program in Bioinformatics, University of British Columbia Vancouver, BC, Canada
| | - Curtis A Suttle
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia Vancouver, BC, Canada ; Department of Microbiology and Immunology, University of British Columbia Vancouver, BC, Canada ; Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research Toronto, ON, Canada ; Department of Botany, University of British Columbia Vancouver, BC, Canada
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