1
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Patin NV, Goodwin KD. Capturing marine microbiomes and environmental DNA: A field sampling guide. Front Microbiol 2023; 13:1026596. [PMID: 36713215 PMCID: PMC9877356 DOI: 10.3389/fmicb.2022.1026596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/22/2022] [Indexed: 01/15/2023] Open
Abstract
The expanding interest in marine microbiome and eDNA sequence data has led to a demand for sample collection and preservation standard practices to enable comparative assessments of results across studies and facilitate meta-analyses. We support this effort by providing guidelines based on a review of published methods and field sampling experiences. The major components considered here are environmental and resource considerations, sample processing strategies, sample storage options, and eDNA extraction protocols. It is impossible to provide universal recommendations considering the wide range of eDNA applications; rather, we provide information to design fit-for-purpose protocols. To manage scope, the focus here is on sampling collection and preservation of prokaryotic and microeukaryotic eDNA. Even with a focused view, the practical utility of any approach depends on multiple factors, including habitat type, available resources, and experimental goals. We broadly recommend enacting rigorous decontamination protocols, pilot studies to guide the filtration volume needed to characterize the target(s) of interest and minimize PCR inhibitor collection, and prioritizing sample freezing over (only) the addition of preservation buffer. An annotated list of studies that test these parameters is included for more detailed investigation on specific steps. To illustrate an approach that demonstrates fit-for-purpose methodologies, we provide a protocol for eDNA sampling aboard an oceanographic vessel. These guidelines can aid the decision-making process for scientists interested in sampling and sequencing marine microbiomes and/or eDNA.
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Affiliation(s)
- Nastassia Virginia Patin
- Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, National Oceanic and Atmospheric Administration, Miami, FL, United States,Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States,Stationed at Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, United States,*Correspondence: Nastassia Virginia Patin,
| | - Kelly D. Goodwin
- Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, National Oceanic and Atmospheric Administration, Miami, FL, United States,Stationed at Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, United States
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2
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Omics-Inferred Partitioning and Expression of Diverse Biogeochemical Functions in a Low-O 2 Cyanobacterial Mat Community. mSystems 2021; 6:e0104221. [PMID: 34874776 PMCID: PMC8651085 DOI: 10.1128/msystems.01042-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cyanobacterial mats profoundly influenced Earth’s biological and geochemical evolution and still play important ecological roles in the modern world. However, the biogeochemical functioning of cyanobacterial mats under persistent low-O2 conditions, which dominated their evolutionary history, is not well understood. To investigate how different metabolic and biogeochemical functions are partitioned among community members, we conducted metagenomics and metatranscriptomics on cyanobacterial mats in the low-O2, sulfidic Middle Island sinkhole (MIS) in Lake Huron. Metagenomic assembly and binning yielded 144 draft metagenome assembled genomes, including 61 of medium quality or better, and the dominant cyanobacteria and numerous Proteobacteria involved in sulfur cycling. Strains of a Phormidium autumnale-like cyanobacterium dominated the metagenome and metatranscriptome. Transcripts for the photosynthetic reaction core genes psaA and psbA were abundant in both day and night. Multiple types of psbA genes were expressed from each cyanobacterium, and the dominant psbA transcripts were from an atypical microaerobic type of D1 protein from Phormidium. Further, cyanobacterial transcripts for photosystem I genes were more abundant than those for photosystem II, and two types of Phormidium sulfide quinone reductase were recovered, consistent with anoxygenic photosynthesis via photosystem I in the presence of sulfide. Transcripts indicate active sulfur oxidation and reduction within the cyanobacterial mat, predominately by Gammaproteobacteria and Deltaproteobacteria, respectively. Overall, these genomic and transcriptomic results link specific microbial groups to metabolic processes that underpin primary production and biogeochemical cycling in a low-O2 cyanobacterial mat and suggest mechanisms for tightly coupled cycling of oxygen and sulfur compounds in the mat ecosystem. IMPORTANCE Cyanobacterial mats are dense communities of microorganisms that contain photosynthetic cyanobacteria along with a host of other bacterial species that play important yet still poorly understood roles in this ecosystem. Although such cyanobacterial mats were critical agents of Earth’s biological and chemical evolution through geological time, little is known about how they function under the low-oxygen conditions that characterized most of their natural history. Here, we performed sequencing of the DNA and RNA of modern cyanobacterial mat communities under low-oxygen and sulfur-rich conditions from the Middle Island sinkhole in Lake Huron. The results reveal the organisms and metabolic pathways that are responsible for both oxygen-producing and non-oxygen-producing photosynthesis as well as interconversions of sulfur that likely shape how much O2 is produced in such ecosystems. These findings indicate tight metabolic reactions between community members that help to explain the limited the amount of O2 produced in cyanobacterial mat ecosystems.
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Metatranscriptomics by
In Situ
RNA Stabilization Directly and Comprehensively Revealed Episymbiotic Microbial Communities of Deep-Sea Squat Lobsters. mSystems 2020; 5:5/5/e00551-20. [PMID: 33024051 PMCID: PMC8534475 DOI: 10.1128/msystems.00551-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Shinkaia crosnieri is an invertebrate that inhabits an area around deep-sea hydrothermal vents in the Okinawa Trough in Japan by harboring episymbiotic microbes as the primary nutrition. To reveal physiology and phylogenetic composition of the active episymbiotic populations, metatranscriptomics is expected to be a powerful approach. However, this has been hindered by substantial perturbation (e.g., RNA degradation) during time-consuming retrieval from the deep sea. Here, we conducted direct metatranscriptomic analysis of S. crosnieri episymbionts by applying in situ RNA stabilization equipment. As expected, we obtained RNA expression profiles that were substantially different from those obtained by conventional metatranscriptomics (i.e., stabilization after retrieval). The episymbiotic community members were dominated by three orders, namely, Thiotrichales, Methylococcales, and Campylobacterales, and the Campylobacterales members were mostly dominated by the Sulfurovum genus. At a finer phylogenetic scale, the episymbiotic communities on different host individuals shared many species, indicating that the episymbionts on each host individual are not descendants of a few founder cells but are horizontally exchanged. Furthermore, our analysis revealed the key metabolisms of the community: two carbon fixation pathways, a formaldehyde assimilation pathway, and utilization of five electron donors (sulfide, thiosulfate, sulfur, methane, and ammonia) and two electron accepters (oxygen and nitrate/nitrite). Importantly, it was suggested that Thiotrichales episymbionts can utilize intercellular sulfur globules even when sulfur compounds are not usable, possibly also in a detached and free-living state. IMPORTANCE Deep-sea hydrothermal vent ecosystems remain mysterious. To depict in detail the enigmatic life of chemosynthetic microbes, which are key primary producers in these ecosystems, metatranscriptomic analysis is expected to be a promising approach. However, this has been hindered by substantial perturbation (e.g., RNA degradation) during time-consuming retrieval from the deep sea. In this study, we conducted direct metatranscriptome analysis of microbial episymbionts of deep-sea squat lobsters (Shinkaia crosnieri) by applying in situ RNA stabilization equipment. Compared to conventional metatranscriptomics (i.e., RNA stabilization after retrieval), our method provided substantially different RNA expression profiles. Moreover, we discovered that S. crosnieri and its episymbiotic microbes constitute complex and resilient ecosystems, where closely related but various episymbionts are stably maintained by horizontal exchange and partly by their sulfur storage ability for survival even when sulfur compounds are not usable, likely also in a detached and free-living state.
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Bastaraud A, Cecchi P, Handschumacher P, Altmann M, Jambou R. Urbanization and Waterborne Pathogen Emergence in Low-Income Countries: Where and How to Conduct Surveys? INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17020480. [PMID: 31940838 PMCID: PMC7013806 DOI: 10.3390/ijerph17020480] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 11/29/2022]
Abstract
A major forthcoming sanitary issue concerns the apparition and spreading of drug-resistant microorganisms, potentially threatening millions of humans. In low-income countries, polluted urban runoff and open sewage channels are major sources of microbes. These microbes join natural microbial communities in aquatic ecosystems already impacted by various chemicals, including antibiotics. These composite microbial communities must adapt to survive in such hostile conditions, sometimes promoting the selection of antibiotic-resistant microbial strains by gene transfer. The low probability of exchanges between planktonic microorganisms within the water column may be significantly improved if their contact was facilitated by particular meeting places. This could be specifically the case within biofilms that develop on the surface of the myriads of floating macroplastics increasingly polluting urban tropical surface waters. Moreover, as uncultivable bacterial strains could be involved, analyses of the microbial communities in their whole have to be performed. This means that new-omic technologies must be routinely implemented in low- and middle-income countries to detect the appearance of resistance genes in microbial ecosystems, especially when considering the new ‘plastic context.’ We summarize the related current knowledge in this short review paper to anticipate new strategies for monitoring and surveying microbial communities.
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Affiliation(s)
- Alexandra Bastaraud
- Laboratoire d’Hygiène des Aliments et de l’Environnement, Institut Pasteur de Madagascar, BP 1274, Antananarivo 101, Madagascar;
| | - Philippe Cecchi
- MARBEC (IRD, IFREMER, UM2 and CNRS), University Montpellier, 34095 Montpellier, France;
- Centre de Recherche Océanologique (CRO), Abidjan BPV 18, Ivory Coast
| | - Pascal Handschumacher
- IRD UMR 912 SESSTIM, INSERM-IRD-Université de Marseille II, 13000 Marseille, France;
| | - Mathias Altmann
- ISPED Université Victor Segalen Bordeaux II, 146 rue Leo Saignat, 33076 Bordeaux cedex, France;
| | - Ronan Jambou
- Département de Parasitologie et des insectes vecteurs, Institut Pasteur Paris, 75015 Paris, France
- Correspondence: ; Tel.: +33-622-10-72-96
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5
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Cooccurrence of Broad- and Narrow-Host-Range Viruses Infecting the Bloom-Forming Toxic Cyanobacterium Microcystis aeruginosa. Appl Environ Microbiol 2019; 85:AEM.01170-19. [PMID: 31324627 DOI: 10.1128/aem.01170-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/11/2019] [Indexed: 12/20/2022] Open
Abstract
Viruses play important roles in regulating the abundance and composition of bacterial populations in aquatic ecosystems. The bloom-forming toxic cyanobacterium Microcystis aeruginosa is predicted to interact with diverse cyanoviruses, resulting in Microcystis population diversification. However, current knowledge of the genomes from these viruses and their infection programs is limited to those of Microcystis virus Ma-LMM01. Here, we performed a time series sampling at a small pond in Japan during a Microcystis bloom and then investigated the genomic information and transcriptional dynamics of Microcystis-interacting viruses using metagenomic and metatranscriptomic approaches. We identified 15 viral genomic fragments classified into three groups, groups I (including Ma-LMM01), II (high abundance and transcriptional activity), and III (new lineages). According to the phylogenetic distribution of Microcystis strains possessing spacers against each viral group, the group II-original viruses interacted with all three phylogenetically distinct Microcystis population types (phylotypes), whereas the groups I and III-original viruses interacted with only one or two phylotypes, indicating the cooccurrence of broad- (group II) and narrow (groups I and III)-host-range viruses in the bloom. These viral fragments showed the highest transcriptional levels during daytime regardless of their genomic differences. Interestingly, M. aeruginosa expressed antiviral defense genes in the environment, unlike what was seen with an Ma-LMM01 infection in a previous culture experiment. Given that broad-host-range viruses often induce antiviral responses within alternative hosts, our findings suggest that such antiviral responses might inhibit viral multiplication, mainly that of broad-host-range viruses like those in group II.IMPORTANCE The bloom-forming toxic cyanobacterium Microcystis aeruginosa is thought to have diversified its population through the interactions between host and viruses in antiviral defense systems. However, current knowledge of viral genomes and infection programs is limited to those of Microcystis virus Ma-LMM01, which was a narrow host range in which it can escape from the highly abundant host defense systems. Our metagenomic approaches unveiled the cooccurrence of narrow- and broad-host-range Microcystis viruses, which included fifteen viral genomic fragments from Microcystis blooms that were classified into three groups. Interestingly, Microcystis antiviral defense genes were expressed against viral infection in the environment, unlike what was seen in a culture experiment with Ma-LMM01. Given that viruses with a broad host range often induce antiviral responses within alternative hosts, our findings suggest that antiviral responses inhibit viral reproduction, especially that of broad-range viruses like those in group II. This paper augments our understanding of the interactions between M. aeruginosa and its viruses and fills an important knowledge gap.
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6
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Charvet S, Riemann L, Alneberg J, Andersson AF, von Borries J, Fischer U, Labrenz M. AFISsys - An autonomous instrument for the preservation of brackish water samples for microbial metatranscriptome analysis. WATER RESEARCH 2019; 149:351-361. [PMID: 30469021 DOI: 10.1016/j.watres.2018.11.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 11/02/2018] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
Microbial communities are the main drivers of biogeochemical cycling of multiple elements sustaining life in the ocean. The rapidity of their response to stressors and abrupt environmental changes implies that even fast and infrequent events can affect local transformations of organic matter and nutrients. Modern molecular techniques now allow for monitoring of microbial activities and functions in the environment through the analysis of genes and expressed genes contained in natural microbial assemblages. However, messenger RNA turnover in cells can be as short as 30 seconds and stability varies greatly between transcripts. Sampling of in situ communities involves an inevitable delay between the collection of seawater and the extraction of its RNA, leaving the bacterial communities plenty of time to alter their gene expression. The characteristics of microbial RNA turnover make time-series very difficult because samples need to be processed immediately to limit alterations to the metatranscriptomes. To address these challenges we designed an autonomous in situ fixation multi-sampler (AFISsys) for the reliable sampling of microbial metatranscriptomes at frequent intervals, for refined temporal resolution. To advance the development of this instrument, we examined the minimal seawater volume necessary for adequate coverage of community gene expression, and the suitability of phenol/ethanol fixation for immediate and long-term preservation of transcripts from a microbial community. We then evaluated the field eligibility of the instrument itself, with two case studies in a brackish system. AFISsys is able to collect, fix, and store water samples independently at a predefined temporal resolution. Phenol/ethanol fixation can conserve metatranscriptomes directly in the environment for up to a week, for later analysis in the laboratory. Thus, the AFISsys constitutes an invaluable tool for the integration of molecular functional analyses in environmental monitoring in brackish waters and in aquatic environments in general.
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Affiliation(s)
- Sophie Charvet
- IOW - Leibniz Institute for Baltic Sea Research, Warnemuende, Germany
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Denmark
| | - Johannes Alneberg
- KTH - Royal Institute of Technology, Science for Life Laboratory, Sweden
| | - Anders F Andersson
- KTH - Royal Institute of Technology, Science for Life Laboratory, Sweden
| | | | - Uwe Fischer
- HYDRO-BIOS Apparatebau GmbH, Altenholz, Germany
| | - Matthias Labrenz
- IOW - Leibniz Institute for Baltic Sea Research, Warnemuende, Germany.
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7
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Morimoto D, Kimura S, Sako Y, Yoshida T. Transcriptome Analysis of a Bloom-Forming Cyanobacterium Microcystis aeruginosa during Ma-LMM01 Phage Infection. Front Microbiol 2018; 9:2. [PMID: 29403457 PMCID: PMC5780444 DOI: 10.3389/fmicb.2018.00002] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 01/03/2018] [Indexed: 01/21/2023] Open
Abstract
Microcystis aeruginosa forms massive blooms in eutrophic freshwaters, where it is constantly exposed to lytic cyanophages. Unlike other marine cyanobacteria, M. aeruginosa possess remarkably abundant and diverse potential antiviral defense genes. Interestingly, T4-like cyanophage Ma-LMM01, which is the sole cultured lytic cyanophage infecting M. aeruginosa, lacks the host-derived genes involved in maintaining host photosynthesis and directing host metabolism that are abundant in other marine cyanophages. Based on genomic comparisons with closely related cyanobacteria and their phages, Ma-LMM01 is predicted to employ a novel infection program that differs from that of other marine cyanophages. Here, we used RNA-seq technology and in silico analysis to examine transcriptional dynamics during Ma-LMM01 infection to reveal host transcriptional responses to phage infection, and to elucidate the infection program used by Ma-LMM01 to avoid the highly abundant host defense systems. Phage-derived reads increased only slightly at 1 h post-infection, but significantly increased from 16% of total cellular reads at 3 h post-infection to 33% of all reads by 6 h post-infection. Strikingly, almost none of the host genes (0.17%) showed a significant change in expression during infection. However, like other lytic dsDNA phages, including marine cyanophages, phage gene dynamics revealed three expression classes: early (host-takeover), middle (replication), and late (virion morphogenesis). The early genes were concentrated in a single ∼5.8-kb window spanning 10 open reading frames (gp054-gp063) on the phage genome. None of the early genes showed homology to the early genes of other T4-like phages, including known marine cyanophages. Bacterial RNA polymerase (σ70) recognition sequences were also found in the upstream region of middle and late genes, whereas phage-specific motifs were not found. Our findings suggest that unlike other known T4-like phages, Ma-LMM01 achieves three sequential gene expression patterns with no change in host promoter activity. This type of infection that does not cause significant change in host transcriptional levels may be advantageous in allowing Ma-LMM01 to escape host defense systems while maintaining host photosynthesis.
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Affiliation(s)
- Daichi Morimoto
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Shigeko Kimura
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- School of Environmental Science, University of Shiga Prefecture, Hikone, Japan
| | - Yoshihiko Sako
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Takashi Yoshida
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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8
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Pochon X, Zaiko A, Fletcher LM, Laroche O, Wood SA. Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications. PLoS One 2017; 12:e0187636. [PMID: 29095959 PMCID: PMC5667844 DOI: 10.1371/journal.pone.0187636] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 10/23/2017] [Indexed: 11/19/2022] Open
Abstract
High-throughput sequencing metabarcoding studies in marine biosecurity have largely focused on targeting environmental DNA (eDNA). DNA can persist extracellularly in the environment, making discrimination of living organisms difficult. In this study, bilge water samples (i.e., water accumulating on-board a vessel during transit) were collected from 15 small recreational and commercial vessels. eDNA and eRNA molecules were co-extracted and the V4 region of the 18S ribosomal RNA gene targeted for metabarcoding. In total, 62.7% of the Operational Taxonomic Units (OTUs) were identified at least once in the corresponding eDNA and eRNA reads, with 19.5% unique to eDNA and 17.7% to eRNA. There were substantial differences in diversity between molecular compartments; 57% of sequences from eDNA-only OTUs belonged to fungi, likely originating from legacy DNA. In contrast, there was a higher percentage of metazoan (50.2%) and ciliate (31.7%) sequences in the eRNA-only OTUs. Our data suggest that the presence of eRNA-only OTUs could be due to increased cellular activities of some rare taxa that were not identified in the eDNA datasets, unusually high numbers of rRNA transcripts in ciliates, and/or artefacts produced during the reverse transcriptase, PCR and sequencing steps. The proportions of eDNA/eRNA shared and unshared OTUs were highly heterogeneous within individual bilge water samples. Multiple factors including boat type and the activities performed on-board, such as washing of scientific equipment, may play a major role in contributing to this variability. For some marine biosecurity applications analysis, eDNA-only data may be sufficient, however there are an increasing number of instances where distinguishing the living portion of a community is essential. For these circumstances, we suggest only including OTUs that are present in both eDNA and eRNA data. OTUs found only in the eRNA data need to be interpreted with caution until further research provides conclusive evidence for their origin.
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Affiliation(s)
- Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
- * E-mail:
| | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
- Marine Science and Technology Centre, Klaipeda University, Klaipeda, Lithuania
| | | | - Olivier Laroche
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Susanna A. Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Environmental Research Institute, University of Waikato, Hamilton, New Zealand
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9
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Alberti A, Poulain J, Engelen S, Labadie K, Romac S, Ferrera I, Albini G, Aury JM, Belser C, Bertrand A, Cruaud C, Da Silva C, Dossat C, Gavory F, Gas S, Guy J, Haquelle M, Jacoby E, Jaillon O, Lemainque A, Pelletier E, Samson G, Wessner M, Acinas SG, Royo-Llonch M, Cornejo-Castillo FM, Logares R, Fernández-Gómez B, Bowler C, Cochrane G, Amid C, Hoopen PT, De Vargas C, Grimsley N, Desgranges E, Kandels-Lewis S, Ogata H, Poulton N, Sieracki ME, Stepanauskas R, Sullivan MB, Brum JR, Duhaime MB, Poulos BT, Hurwitz BL, Pesant S, Karsenti E, Wincker P. Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition. Sci Data 2017; 4:170093. [PMID: 28763055 PMCID: PMC5538240 DOI: 10.1038/sdata.2017.93] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/05/2017] [Indexed: 02/01/2023] Open
Abstract
A unique collection of oceanic samples was gathered by the Tara Oceans
expeditions (2009–2013), targeting plankton organisms ranging from viruses to
metazoans, and providing rich environmental context measurements. Thanks to recent advances in
the field of genomics, extensive sequencing has been performed for a deep genomic analysis of
this huge collection of samples. A strategy based on different approaches, such as
metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for
analysis of size-fractionated plankton communities. Here, we provide detailed procedures
applied for genomic data generation, from nucleic acids extraction to sequence production, and
we describe registries of genomics datasets available at the European Nucleotide Archive (ENA,
www.ebi.ac.uk/ena). The association of these metadata to the experimental
procedures applied for their generation will help the scientific community to access these data
and facilitate their analysis. This paper complements other efforts to provide a full
description of experiments and open science resources generated from the Tara
Oceans project, further extending their value for the study of the world’s planktonic
ecosystems.
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Affiliation(s)
- Adriana Alberti
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Julie Poulain
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Stefan Engelen
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Karine Labadie
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Sarah Romac
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Isabel Ferrera
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Guillaume Albini
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Jean-Marc Aury
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Caroline Belser
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Alexis Bertrand
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Corinne Cruaud
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Corinne Da Silva
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Carole Dossat
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Frédérick Gavory
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Shahinaz Gas
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Julie Guy
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Maud Haquelle
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - E'krame Jacoby
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Olivier Jaillon
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France.,CNRS, UMR 8030, Evry CP5706, France.,Université d'Evry, UMR 8030, Evry CP5706, France
| | - Arnaud Lemainque
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Eric Pelletier
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France.,CNRS, UMR 8030, Evry CP5706, France.,Université d'Evry, UMR 8030, Evry CP5706, France
| | - Gaëlle Samson
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Mark Wessner
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | | | - Silvia G Acinas
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Marta Royo-Llonch
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Francisco M Cornejo-Castillo
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Ramiro Logares
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Beatriz Fernández-Gómez
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain.,FONDAP Center for Genome Regulation, Moneda 1375, Santiago 8320000, Chile.,Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Libano Macul, Santiago 5524, Chile
| | - Chris Bowler
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, Paris F-75005, France
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genomes Campus, Hinxton, Cambridge CB10 1 SD, UK
| | - Clara Amid
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genomes Campus, Hinxton, Cambridge CB10 1 SD, UK
| | - Petra Ten Hoopen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genomes Campus, Hinxton, Cambridge CB10 1 SD, UK
| | - Colomban De Vargas
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Nigel Grimsley
- CNRS UMR 7232, BIOM, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France.,Sorbonne Universités Paris 06, OOB UPMC, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France
| | - Elodie Desgranges
- CNRS UMR 7232, BIOM, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France.,Sorbonne Universités Paris 06, OOB UPMC, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France
| | - Stefanie Kandels-Lewis
- Directors' Research European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg 69117, Germany.,Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg 69117, Germany
| | - Hiroyuki Ogata
- for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Nicole Poulton
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine 04544, USA
| | - Michael E Sieracki
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine 04544, USA.,National Science Foundation, Arlington, Virginia 22230, USA
| | | | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, Ohio 43210, USA.,Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Jennifer R Brum
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Bonnie L Hurwitz
- Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, Arizona 85719, USA
| | | | - Stéphane Pesant
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Str. 8, Bremen 28359, Germany.,PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Leobener Str. 8, Bremen 28359, Germany
| | - Eric Karsenti
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, Paris F-75005, France.,Directors' Research European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg 69117, Germany.,Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'oceanographie de Villefranche (LOV), Observatoire Océanologique, 181 Chemin du Lazaret, Villefranche-sur-mer F-06230, France
| | - Patrick Wincker
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France.,CNRS, UMR 8030, Evry CP5706, France.,Université d'Evry, UMR 8030, Evry CP5706, France
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10
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Díez-Vives C, Moitinho-Silva L, Nielsen S, Reynolds D, Thomas T. Expression of eukaryotic-like protein in the microbiome of sponges. Mol Ecol 2017; 26:1432-1451. [PMID: 28036141 DOI: 10.1111/mec.14003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 12/08/2016] [Accepted: 12/09/2016] [Indexed: 01/04/2023]
Abstract
Eukaryotic-like proteins (ELPs) are classes of proteins that are found in prokaryotes, but have a likely evolutionary origin in eukaryotes. ELPs have been postulated to mediate host-microbiome interactions. Recent work has discovered that prokaryotic symbionts of sponges contain abundant and diverse genes for ELPs, which could modulate interactions with their filter-feeding and phagocytic host. However, the extent to which these ELP genes are actually used and expressed by the symbionts is poorly understood. Here, we use metatranscriptomics to investigate ELP expression in the microbiomes of three different sponges (Cymbastella concentrica, Scopalina sp. and Tedania anhelens). We developed a workflow with optimized rRNA removal and in silico subtraction of host sequences to obtain a reliable symbiont metatranscriptome. This showed that between 1.3% and 2.3% of all symbiont transcripts contain genes for ELPs. Two classes of ELPs (cadherin and tetratricopeptide repeats) were abundantly expressed in the C. concentrica and Scopalina sp. microbiomes, while ankyrin repeat ELPs were predominant in the T. anhelens metatranscriptome. Comparison with transcripts that do not encode ELPs indicated a constitutive expression of ELPs across a range of bacterial and archaeal symbionts. Expressed ELPs also contained domains involved in protein secretion and/or were co-expressed with proteins involved in extracellular transport. This suggests these ELPs are likely exported, which could allow for direct interaction with the sponge. Our study shows that ELP genes in sponge symbionts represent actively expressed functions that could mediate molecular interaction between symbiosis partners.
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Affiliation(s)
- C Díez-Vives
- Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, Australia
| | - L Moitinho-Silva
- Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, Australia
| | - S Nielsen
- Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, Australia
| | - D Reynolds
- Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, Australia
| | - T Thomas
- Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, Australia
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11
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Vincent AT, Derome N, Boyle B, Culley AI, Charette SJ. Next-generation sequencing (NGS) in the microbiological world: How to make the most of your money. J Microbiol Methods 2016; 138:60-71. [PMID: 26995332 DOI: 10.1016/j.mimet.2016.02.016] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 01/26/2016] [Accepted: 02/24/2016] [Indexed: 12/16/2022]
Abstract
The Sanger sequencing method produces relatively long DNA sequences of unmatched quality and has been considered for long time as the gold standard for sequencing DNA. Many improvements of the Sanger method that culminated with fluorescent dyes coupled with automated capillary electrophoresis enabled the sequencing of the first genomes. Nevertheless, using this technology to sequence whole genomes was costly, laborious and time consuming even for genomes that are relatively small in size. A major technological advance was the introduction of next-generation sequencing (NGS) pioneered by 454 Life Sciences in the early part of the 21th century. NGS allowed scientists to sequence thousands to millions of DNA molecules in a single machine run. Since then, new NGS technologies have emerged and existing NGS platforms have been improved, enabling the production of genome sequences at an unprecedented rate as well as broadening the spectrum of NGS applications. The current affordability of generating genomic information, especially with microbial samples, has resulted in a false sense of simplicity that belies the fact that many researchers still consider these technologies a black box. In this review, our objective is to identify and discuss four steps that we consider crucial to the success of any NGS-related project. These steps are: (1) the definition of the research objectives beyond sequencing and appropriate experimental planning, (2) library preparation, (3) sequencing and (4) data analysis. The goal of this review is to give an overview of the process, from sample to analysis, and discuss how to optimize your resources to achieve the most from your NGS-based research. Regardless of the evolution and improvement of the sequencing technologies, these four steps will remain relevant.
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Affiliation(s)
- Antony T Vincent
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC G1V 0A6, Canada; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, QC G1V 4G5, Canada
| | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada; Département de biologie, Faculté des sciences et de génie, Université Laval, Quebec City G1V 0A6, Canada
| | - Brian Boyle
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Alexander I Culley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC G1V 0A6, Canada; Groupe de Recherche en Écologie Buccale (GREB), Faculté de médecine dentaire, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Steve J Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC G1V 0A6, Canada; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, QC G1V 4G5, Canada.
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12
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Tuorto SJ, Brown CM, Bidle KD, McGuinness LR, Kerkhof LJ. BioDry: An Inexpensive, Low-Power Method to Preserve Aquatic Microbial Biomass at Room Temperature. PLoS One 2015; 10:e0144686. [PMID: 26710122 PMCID: PMC4692454 DOI: 10.1371/journal.pone.0144686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 11/23/2015] [Indexed: 02/01/2023] Open
Abstract
This report describes BioDry (patent pending), a method for reliably preserving the biomolecules associated with aquatic microbial biomass samples, without the need of hazardous materials (e.g. liquid nitrogen, preservatives, etc.), freezing, or bulky storage/sampling equipment. Gel electrophoresis analysis of nucleic acid extracts from samples treated in the lab with the BioDry method indicated that molecular integrity was protected in samples stored at room temperature for up to 30 days. Analysis of 16S/18S rRNA genes for presence/absence and relative abundance of microorganisms using both 454-pyrosequencing and TRFLP profiling revealed statistically indistinguishable communities from control samples that were frozen in liquid nitrogen immediately after collection. Seawater and river water biomass samples collected with a portable BioDry “field unit", constructed from off-the-shelf materials and a battery-operated pumping system, also displayed high levels of community rRNA preservation, despite a slight decrease in nucleic acid recovery over the course of storage for 30 days. Functional mRNA and protein pools from the field samples were also effectively conserved with BioDry, as assessed by respective RT-PCR amplification and western blot of ribulose-1-5-bisphosphate carboxylase/oxygenase. Collectively, these results demonstrate that BioDry can adequately preserve a suite of biomolecules from aquatic biomass at ambient temperatures for up to a month, giving it great potential for high resolution sampling in remote locations or on autonomous platforms where space and power are limited.
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Affiliation(s)
- Steven J. Tuorto
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Chris M. Brown
- Environmental Proteomics N.B. Inc, Sackville, New Brunswick, Canada
| | - Kay D. Bidle
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Lora R. McGuinness
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Lee J. Kerkhof
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
- * E-mail:
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13
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Glass JB, Kretz CB, Ganesh S, Ranjan P, Seston SL, Buck KN, Landing WM, Morton PL, Moffett JW, Giovannoni SJ, Vergin KL, Stewart FJ. Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones. Front Microbiol 2015; 6:998. [PMID: 26441925 PMCID: PMC4585252 DOI: 10.3389/fmicb.2015.00998] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 09/07/2015] [Indexed: 11/13/2022] Open
Abstract
Iron (Fe) and copper (Cu) are essential cofactors for microbial metalloenzymes, but little is known about the metalloenyzme inventory of anaerobic marine microbial communities despite their importance to the nitrogen cycle. We compared dissolved O2, NO[Formula: see text], NO[Formula: see text], Fe and Cu concentrations with nucleic acid sequences encoding Fe and Cu-binding proteins in 21 metagenomes and 9 metatranscriptomes from Eastern Tropical North and South Pacific oxygen minimum zones and 7 metagenomes from the Bermuda Atlantic Time-series Station. Dissolved Fe concentrations increased sharply at upper oxic-anoxic transition zones, with the highest Fe:Cu molar ratio (1.8) occurring at the anoxic core of the Eastern Tropical North Pacific oxygen minimum zone and matching the predicted maximum ratio based on data from diverse ocean sites. The relative abundance of genes encoding Fe-binding proteins was negatively correlated with O2, driven by significant increases in genes encoding Fe-proteins involved in dissimilatory nitrogen metabolisms under anoxia. Transcripts encoding cytochrome c oxidase, the Fe- and Cu-containing terminal reductase in aerobic respiration, were positively correlated with O2 content. A comparison of the taxonomy of genes encoding Fe- and Cu-binding vs. bulk proteins in OMZs revealed that Planctomycetes represented a higher percentage of Fe genes while Thaumarchaeota represented a higher percentage of Cu genes, particularly at oxyclines. These results are broadly consistent with higher relative abundance of genes encoding Fe-proteins in the genome of a marine planctomycete vs. higher relative abundance of genes encoding Cu-proteins in the genome of a marine thaumarchaeote. These findings highlight the importance of metalloenzymes for microbial processes in oxygen minimum zones and suggest preferential Cu use in oxic habitats with Cu > Fe vs. preferential Fe use in anoxic niches with Fe > Cu.
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Affiliation(s)
- Jennifer B Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology Atlanta, GA, USA ; School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Cecilia B Kretz
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology Atlanta, GA, USA
| | - Sangita Ganesh
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Piyush Ranjan
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | | | - Kristen N Buck
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
| | - William M Landing
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University Tallahassee, FL, USA
| | - Peter L Morton
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University Tallahassee, FL, USA
| | - James W Moffett
- Department of Biological Sciences, University of Southern California Los Angeles, CA, USA
| | | | - Kevin L Vergin
- Department of Microbiology, Oregon State University Corvallis, OR, USA
| | - Frank J Stewart
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology Atlanta, GA, USA ; School of Biology, Georgia Institute of Technology Atlanta, GA, USA
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14
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Padilla CC, Ganesh S, Gantt S, Huhman A, Parris DJ, Sarode N, Stewart FJ. Standard filtration practices may significantly distort planktonic microbial diversity estimates. Front Microbiol 2015; 6:547. [PMID: 26082766 PMCID: PMC4451414 DOI: 10.3389/fmicb.2015.00547] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/13/2015] [Indexed: 02/01/2023] Open
Abstract
Fractionation of biomass by filtration is a standard method for sampling planktonic microbes. It is unclear how the taxonomic composition of filtered biomass changes depending on sample volume. Using seawater from a marine oxygen minimum zone, we quantified the 16S rRNA gene composition of biomass on a prefilter (1.6 μm pore-size) and a downstream 0.2 μm filter over sample volumes from 0.05 to 5 L. Significant community shifts occurred in both filter fractions, and were most dramatic in the prefilter community. Sequences matching Vibrionales decreased from ~40 to 60% of prefilter datasets at low volumes (0.05–0.5 L) to less than 5% at higher volumes, while groups such at the Chromatiales and Thiohalorhabdales followed opposite trends, increasing from minor representation to become the dominant taxa at higher volumes. Groups often associated with marine particles, including members of the Deltaproteobacteria, Planctomycetes, and Bacteroidetes, were among those showing the greatest increase with volume (4 to 27-fold). Taxon richness (97% similarity clusters) also varied significantly with volume, and in opposing directions depending on filter fraction, highlighting potential biases in community complexity estimates. These data raise concerns for studies using filter fractionation for quantitative comparisons of aquatic microbial diversity, for example between free-living and particle-associated communities.
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Affiliation(s)
- Cory C Padilla
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Sangita Ganesh
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Shelby Gantt
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Alex Huhman
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Darren J Parris
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Neha Sarode
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Frank J Stewart
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
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15
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Dalsgaard T, Stewart FJ, Thamdrup B, De Brabandere L, Revsbech NP, Ulloa O, Canfield DE, DeLong EF. Oxygen at nanomolar levels reversibly suppresses process rates and gene expression in anammox and denitrification in the oxygen minimum zone off northern Chile. mBio 2014; 5:e01966. [PMID: 25352619 PMCID: PMC4217175 DOI: 10.1128/mbio.01966-14] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
UNLABELLED A major percentage (20 to 40%) of global marine fixed-nitrogen loss occurs in oxygen minimum zones (OMZs). Concentrations of O2 and the sensitivity of the anaerobic N2-producing processes of anammox and denitrification determine where this loss occurs. We studied experimentally how O2 at nanomolar levels affects anammox and denitrification rates and the transcription of nitrogen cycle genes in the anoxic OMZ off Chile. Rates of anammox and denitrification were reversibly suppressed, most likely at the enzyme level. Fifty percent inhibition of N2 and N2O production by denitrification was achieved at 205 and 297 nM O2, respectively, whereas anammox was 50% inhibited at 886 nM O2. Coupled metatranscriptomic analysis revealed that transcripts encoding nitrous oxide reductase (nosZ), nitrite reductase (nirS), and nitric oxide reductase (norB) decreased in relative abundance above 200 nM O2. This O2 concentration did not suppress the transcription of other dissimilatory nitrogen cycle genes, including nitrate reductase (narG), hydrazine oxidoreductase (hzo), and nitrite reductase (nirK). However, taxonomic characterization of transcripts suggested inhibition of narG transcription in gammaproteobacteria, whereas the transcription of anammox narG, whose gene product is likely used to oxidatively replenish electrons for carbon fixation, was not inhibited. The taxonomic composition of transcripts differed among denitrification enzymes, suggesting that distinct groups of microorganisms mediate different steps of denitrification. Sulfide addition (1 µM) did not affect anammox or O2 inhibition kinetics but strongly stimulated N2O production by denitrification. These results identify new O2 thresholds for delimiting marine nitrogen loss and highlight the utility of integrating biogeochemical and metatranscriptomic analyses. IMPORTANCE The removal of fixed nitrogen via anammox and denitrification associated with low O2 concentrations in oceanic oxygen minimum zones (OMZ) is a major sink in oceanic N budgets, yet the sensitivity and dynamics of these processes with respect to O2 are poorly known. The present study elucidated how nanomolar O2 concentrations affected nitrogen removal rates and expression of key nitrogen cycle genes in water from the eastern South Pacific OMZ, applying state-of-the-art (15)N techniques and metatranscriptomics. Rates of both denitrification and anammox responded rapidly and reversibly to changes in O2, but denitrification was more O2 sensitive than anammox. The transcription of key nitrogen cycle genes did not respond as clearly to O2, although expression of some of these genes decreased. Quantifying O2 sensitivity of these processes is essential for predicting through which pathways and in which environments, from wastewater treatment to the open oceans, nitrogen removal may occur.
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Affiliation(s)
| | - Frank J Stewart
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Bo Thamdrup
- Department of Biology and Nordic Center for Earth Evolution (NordCEE), University of Southern Denmark, Odense, Denmark
| | - Loreto De Brabandere
- Department of Biology and Nordic Center for Earth Evolution (NordCEE), University of Southern Denmark, Odense, Denmark
| | | | - Osvaldo Ulloa
- Departamento de Oceanografía & Instituto Mileno de Oceanografía, Universidad de Concepción, Concepción, Chile
| | - Don E Canfield
- Department of Biology and Nordic Center for Earth Evolution (NordCEE), University of Southern Denmark, Odense, Denmark
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16
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Alberti A, Belser C, Engelen S, Bertrand L, Orvain C, Brinas L, Cruaud C, Giraut L, Da Silva C, Firmo C, Aury JM, Wincker P. Comparison of library preparation methods reveals their impact on interpretation of metatranscriptomic data. BMC Genomics 2014; 15:912. [PMID: 25331572 PMCID: PMC4213505 DOI: 10.1186/1471-2164-15-912] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 10/13/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Metatranscriptomics is rapidly expanding our knowledge of gene expression patterns and pathway dynamics in natural microbial communities. However, to cope with the challenges of environmental sampling, various rRNA removal and cDNA synthesis methods have been applied in published microbial metatranscriptomic studies, making comparisons arduous. Whereas efficiency and biases introduced by rRNA removal methods have been relatively well explored, the impact of cDNA synthesis and library preparation on transcript abundance remains poorly characterized. The evaluation of potential biases introduced at this step is challenging for metatranscriptomic samples, where data analyses are complex, for example because of the lack of reference genomes. RESULTS Herein, we tested four cDNA synthesis and Illumina library preparation protocols on a simplified mixture of total RNA extracted from four bacterial species. In parallel, RNA from each microbe was tested individually. cDNA synthesis was performed on rRNA depleted samples using the TruSeq Stranded Total RNA Library Preparation, the SMARTer Stranded RNA-Seq, or the Ovation RNA-Seq V2 System. A fourth experiment was made directly from total RNA using the Encore Complete Prokaryotic RNA-Seq. The obtained sequencing data were analyzed for: library complexity and reproducibility; rRNA removal efficiency and bias; the number of genes detected; coverage uniformity; and the impact of protocols on expression biases. Significant variations, especially in organism representation and gene expression patterns, were observed among the four methods. TruSeq generally performed best, but is limited by its requirement of hundreds of nanograms of total RNA. The SMARTer method appears the best solution for smaller amounts of input RNA. For very low amounts of RNA, the Ovation System provides the only option; however, the observed biases emphasized its limitations for quantitative analyses. CONCLUSIONS cDNA and library preparation methods may affect the outcome and interpretation of metatranscriptomic data. The most appropriate method should be chosen based on the available quantity of input RNA and the quantitative or non-quantitative objectives of the study. When low amounts of RNA are available, as in most metatranscriptomic studies, the SMARTer method seems to be the best compromise to obtain reliable results. This study emphasized the difficulty in comparing metatranscriptomic studies performed using different methods.
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Affiliation(s)
- Adriana Alberti
- />CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706 F-91057, Evry Cedex, France
| | - Caroline Belser
- />CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706 F-91057, Evry Cedex, France
| | - Stéfan Engelen
- />CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706 F-91057, Evry Cedex, France
| | - Laurie Bertrand
- />CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706 F-91057, Evry Cedex, France
| | - Céline Orvain
- />CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706 F-91057, Evry Cedex, France
| | - Laura Brinas
- />CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706 F-91057, Evry Cedex, France
| | - Corinne Cruaud
- />CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706 F-91057, Evry Cedex, France
| | - Laurène Giraut
- />CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706 F-91057, Evry Cedex, France
| | - Corinne Da Silva
- />CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706 F-91057, Evry Cedex, France
| | - Cyril Firmo
- />CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706 F-91057, Evry Cedex, France
| | - Jean-Marc Aury
- />CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706 F-91057, Evry Cedex, France
| | - Patrick Wincker
- />CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706 F-91057, Evry Cedex, France
- />Université d’Evry, UMR 8030, CP5706 Evry, France
- />Centre National de la Recherche Scientifique (CNRS), UMR 8030, CP5706 Evry, France
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17
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Moitinho-Silva L, Seridi L, Ryu T, Voolstra CR, Ravasi T, Hentschel U. Revealing microbial functional activities in the Red Sea sponge Stylissa carteri by metatranscriptomics. Environ Microbiol 2014; 16:3683-98. [PMID: 24920529 DOI: 10.1111/1462-2920.12533] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/15/2014] [Accepted: 04/15/2014] [Indexed: 01/26/2023]
Abstract
Sponges are important components of marine benthic environments and are associated with microbial symbionts that carry out ecologically relevant functions. Stylissa carteri is an abundant, low-microbial abundance species in the Red Sea. We aimed to achieve the functional and taxonomic characterization of the most actively expressed prokaryotic genes in S. carteri. Prokaryotic mRNA was enriched from sponge total RNA, sequenced using Illumina HiSeq technology and annotated using the metagenomics Rapid Annotation using Subsystem Technology (MG-RAST) pipeline. We detected high expression of archaeal ammonia oxidation and photosynthetic carbon fixation by members of the genus Synechococcus. Functions related to stress response and membrane transporters were among the most highly expressed by S. carteri symbionts. Unexpectedly, gene functions related to methylotrophy were highly expressed by gammaproteobacterial symbionts. The presence of seawater-derived microbes is indicated by the phylogenetic proximity of organic carbon transporters to orthologues of members from the SAR11 clade. In summary, we revealed the most expressed functions of the S. carteri-associated microbial community and linked them to the dominant taxonomic members of the microbiome. This work demonstrates the applicability of metatranscriptomics to explore poorly characterized symbiotic consortia and expands our knowledge of the ecologically relevant functions carried out by coral reef sponge symbionts.
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Affiliation(s)
- Lucas Moitinho-Silva
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Wuerzburg, Julius-von-Sachs Platz 3, 97082, Wuerzburg, Germany
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