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Koblížek M, Ferrera I, Kolářová E, Duhamel S, Popendorf KJ, Gasol JM, Van Mooy BAS. Growth and mortality of aerobic anoxygenic phototrophs in the North Pacific Subtropical Gyre. Appl Environ Microbiol 2024; 90:e0003224. [PMID: 38551354 PMCID: PMC11022572 DOI: 10.1128/aem.00032-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/08/2024] [Indexed: 04/18/2024] Open
Abstract
Aerobic anoxygenic phototrophic (AAP) bacteria harvest light energy using bacteriochlorophyll-containing reaction centers to supplement their mostly heterotrophic metabolism. While their abundance and growth have been intensively studied in coastal environments, much less is known about their activity in oligotrophic open ocean regions. Therefore, we combined in situ sampling in the North Pacific Subtropical Gyre, north of O'ahu island, Hawaii, with two manipulation experiments. Infra-red epifluorescence microscopy documented that AAP bacteria represented approximately 2% of total bacteria in the euphotic zone with the maximum abundance in the upper 50 m. They conducted active photosynthetic electron transport with maximum rates up to 50 electrons per reaction center per second. The in situ decline of bacteriochlorophyll concentration over the daylight period, an estimate of loss rates due to predation, indicated that the AAP bacteria in the upper 50 m of the water column turned over at rates of 0.75-0.90 d-1. This corresponded well with the specific growth rate determined in dilution experiments where AAP bacteria grew at a rate 1.05 ± 0.09 d-1. An amendment of inorganic nitrogen to obtain N:P = 32 resulted in a more than 10 times increase in AAP abundance over 6 days. The presented data document that AAP bacteria are an active part of the bacterioplankton community in the oligotrophic North Pacific Subtropical Gyre and that their growth was mostly controlled by nitrogen availability and grazing pressure.IMPORTANCEMarine bacteria represent a complex assembly of species with different physiology, metabolism, and substrate preferences. We focus on a specific functional group of marine bacteria called aerobic anoxygenic phototrophs. These photoheterotrophic organisms require organic carbon substrates for growth, but they can also supplement their metabolic needs with light energy captured by bacteriochlorophyll. These bacteria have been intensively studied in coastal regions, but rather less is known about their distribution, growth, and mortality in the oligotrophic open ocean. Therefore, we conducted a suite of measurements in the North Pacific Subtropical Gyre to determine the distribution of these organisms in the water column and their growth and mortality rates. A nutrient amendment experiment showed that aerobic anoxygenic phototrophs were limited by inorganic nitrogen. Despite this, they grew more rapidly than average heterotrophic bacteria, but their growth was balanced by intense grazing pressure.
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Affiliation(s)
- Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology, Czech Academy of Science, Třeboň, Czechia
| | - Isabel Ferrera
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía (IEO-CSIC), Fuengirola, Málaga, Spain
| | - Eva Kolářová
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology, Czech Academy of Science, Třeboň, Czechia
| | - Solange Duhamel
- Department of Cellular and Molecular Biology, University of Arizona, Tucson, Arizona, USA
| | - Kimberly J. Popendorf
- Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Coral Gables, Florida, USA
| | - Josep M. Gasol
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Benjamin A. S. Van Mooy
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
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Meyneng M, Lemonnier H, Le Gendre R, Plougoulen G, Antypas F, Ansquer D, Serghine J, Schmitt S, Siano R. Subtropical coastal microbiome variations due to massive river runoff after a cyclonic event. ENVIRONMENTAL MICROBIOME 2024; 19:10. [PMID: 38291506 PMCID: PMC10829310 DOI: 10.1186/s40793-024-00554-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/23/2024] [Indexed: 02/01/2024]
Abstract
BACKGROUND Coastal ecosystem variability at tropical latitudes is dependent on climatic conditions. During the wet, rainy season, extreme climatic events such as cyclones, precipitation, and winds can be intense over a short period and may have a significant impact on the entire land‒sea continuum. This study focused on the effect of river runoff across the southwest coral lagoon ecosystem of Grand Terre Island of New Caledonia (South Pacific) after a cyclonic event, which is considered a pulse disturbance at our study site. The variability of coastal microbiomes, studied by the metabarcoding of V4 18S (protists) and V4-V5 16S (bacteria) rDNA genes, after the cyclone passage was associated with key environmental parameters describing the runoff impact (salinity, organic matter proxies, terrestrial rock origin metals) and compared to community structures observed during the dry season. RESULTS Microbiome biodiversity patterns of the dry season were destructured because of the runoff impact, and land-origin taxa were observed in the coastal areas. After the rainy event, different daily community dynamics were observed locally, with specific microbial taxa explaining these variabilities. Plume dispersal modeling revealed the extent of low salinity areas up to the coral reef area (16 km offshore), but a rapid (< 6 days) recovery to typical steady conditions of the lagoon's hydrology was observed. Conversely, during the same time, some biological components (microbial communities, Chl a) and biogeochemical components (particulate nickel, terrigenous organic matter) of the ecosystem did not recover to values observed during the dry season conditions. CONCLUSION The ecosystem resilience of subtropical ecosystems must be evaluated from a multidisciplinary, holistic perspective and over the long term. This allows evaluating the risk associated with a potential continued and long-term disequilibrium of the ecosystem, triggered by the change in the frequency and intensity of extreme climatic events in the era of planetary climatic changes.
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Affiliation(s)
- M Meyneng
- IFREMER, DYNECO, BP70, Plouzané, France
| | - H Lemonnier
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
| | - R Le Gendre
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
| | - G Plougoulen
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
| | - F Antypas
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
| | - D Ansquer
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
| | | | - S Schmitt
- IFREMER, DYNECO, BP70, Plouzané, France
| | - R Siano
- IFREMER, DYNECO, BP70, Plouzané, France.
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Li Y, Wang F, Yang H, Li H, Hu C. Balanced biogeographic and local environmental effects determine the patterns of microbial diversity in biocrusts at multi-scales. Front Microbiol 2023; 14:1284864. [PMID: 38029206 PMCID: PMC10666793 DOI: 10.3389/fmicb.2023.1284864] [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: 08/29/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Biodiversity maintenance and its underlying mechanisms are central issues of ecology. However, predicting the composition turnovers of microbial communities at multiple spatial scales remains greatly challenging because they are obscured by the inconsistent impacts of climatic and local edaphic conditions on the assembly process. Methods Based on the Illumina MeSeq 16S/18S rRNA sequencing technology, we investigated soil bacterial and eukaryotic communities in biocrusts with different successional levels at a subcontinental scale of Northern China. Results Results showed that irrespective of spatial scale, bacterial α diversity increased but eukaryotic diversity decreased with the primary succession, whereas both β diversities decreased at the subcontinental scale compared with smaller scales, indicating that the biogeographic pattern of soil microorganisms was balanced by successional convergence and distance decay effect. We found that the convergence of bacterial and eukaryotic communities was attributed to the turnovers of generalist and specialist species, respectively. In this process, edaphic and climatic factors showed unique roles in the changes of diversity at local/subcontinental scales. Moreover, the taxonomic diversity tended to be more susceptible to climatic and edaphic conditions, while biotic factors (photosynthesis and pigments) were more important to phylogenetic diversity. Conclusion Taken together, our study provided comprehensive insights into understanding the pattern of microbial diversity at multiple spatial scales of drylands.
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Affiliation(s)
- Yuanlong Li
- Hunan Provincial Key Laboratory of Carbon Neutrality and Intelligent Energy, School of Resource and Environment, Hunan University of Technology and Business, Changsha, China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Fengdi Wang
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Haijian Yang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Hua Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chunxiang Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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Simister RL, Iulianella Phillips BP, Wickham AP, Cayer EM, Hart CJR, Winterburn PA, Crowe SA. DNA sequencing, microbial indicators, and the discovery of buried kimberlites. COMMUNICATIONS EARTH & ENVIRONMENT 2023; 4:387. [PMID: 38665197 PMCID: PMC11041713 DOI: 10.1038/s43247-023-01020-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 09/19/2023] [Indexed: 04/28/2024]
Abstract
Population growth and technological advancements are placing growing demand on mineral resources. New and innovative exploration technologies that improve detection of deeply buried mineralization and host rocks are required to meet these demands. Here we used diamondiferous kimberlite ore bodies as a test case and show that DNA amplicon sequencing of soil microbial communities resolves anomalies in microbial community composition and structure that reflect the surface expression of kimberlites buried under 10 s of meters of overburden. Indicator species derived from laboratory amendment experiments were employed in an exploration survey in which the species distributions effectively delineated the surface expression of buried kimberlites. Additional indicator species derived directly from field observations improved the blind discovery of kimberlites buried beneath similar overburden types. Application of DNA sequence-based analyses of soil microbial communities to mineral deposit exploration provides a powerful illustration of how genomics technologies can be leveraged in the discovery of critical new resources.
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Affiliation(s)
- Rachel L. Simister
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T 1Z3 Canada
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Bianca P. Iulianella Phillips
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- MDRU-Mineral Deposit Research Unit, Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Andrew P. Wickham
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- MDRU-Mineral Deposit Research Unit, Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Erika M. Cayer
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- MDRU-Mineral Deposit Research Unit, Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Craig J. R. Hart
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- MDRU-Mineral Deposit Research Unit, Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Peter A. Winterburn
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- MDRU-Mineral Deposit Research Unit, Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Sean A. Crowe
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T 1Z3 Canada
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
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Zhang Z, Liu Y, Zhao W, Ji M. Radiation impacts gene redundancy and biofilm regulation of cryoconite microbiomes in Northern Hemisphere glaciers. MICROBIOME 2023; 11:228. [PMID: 37848997 PMCID: PMC10583317 DOI: 10.1186/s40168-023-01621-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/14/2023] [Indexed: 10/19/2023]
Abstract
BACKGROUND Glaciers harbor diverse microorganisms adapted to extreme conditions with high radiation, fluctuating temperature, and low nutrient availability. In glacial ecosystems, cryoconite granules are hotspots of microbial metabolic activity and could influences the biogeochemical cycle on glacier surface. Climate change could influence glacier dynamics by changing regional meteorological factors (e.g., radiation, precipitation, temperature, wind, and evaporation). Moreover, meteorological factors not only influence glacier dynamics but also directly or indirectly influence cryoconite microbiomes. However, the relationship of the meteorological factors and cryoconite microbiome are poorly understood. RESULTS Here, we collected 88 metagenomes from 26 glaciers distributed in the Northern Hemisphere with corresponding public meteorological data to reveal the relationship between meteorological factors and variation of cryoconite microbiome. Our results showed significant differences in taxonomic and genomic characteristics between cryoconite generalists and specialists. Additionally, we found that the biogeography of both generalists and specialists was influenced by solar radiation. Specialists with smaller genome size and lower gene redundancy were more abundant under high radiation stress, implying that streamlined genomes are more adapted to high radiation conditions. Network analysis revealed that biofilm regulation is a ubiquitous function in response to radiation stress, and hub genes were associated with the formation and dispersion of biofilms. CONCLUSION These findings enhance our understanding of glacier cryoconite microbiome variation on a hemispheric scale and indicate the response mechanisms to radiation stress, which will support forecasts of the ecological consequences of future climate change. Video Abstract.
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Affiliation(s)
- Zhihao Zhang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China.
| | - Weishu Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- SJTU Yazhou Bay Institute of Deepsea Sci-Tech, Yongyou Industrial Park, Sanya, 572024, China
- International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mukan Ji
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China
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Vipindas PV, Jabir T, Venkatachalam S, Yang EJ, Jain A, Krishnan KP. Vertical segregation and phylogenetic characterization of archaea and archaeal ammonia monooxygenase gene in the water column of the western Arctic Ocean. Extremophiles 2023; 27:24. [PMID: 37668803 DOI: 10.1007/s00792-023-01310-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/21/2023] [Indexed: 09/06/2023]
Abstract
Archaea constitute a substantial fraction of marine microbial biomass and play critical roles in the biogeochemistry of oceans. However, studies on their distribution and ecology in the Arctic Ocean are relatively scarce. Here, we studied the distributions of archaea and archaeal ammonia monooxygenase (amoA) gene in the western Arctic Ocean, using the amplicon sequencing approach from the sea surface to deep waters up to 3040 m depth. A total of five archaeal phyla, Nitrososphaerota, "Euryarchaeota", "Halobacteriota," "Nanoarchaeota", and Candidatus Thermoplasmatota, were detected. We observed a clear, depth-dependent vertical segregation among archaeal communities. Ca. Thermoplasmatota (66.8%) was the most dominant phylum in the surface waters. At the same time, Nitrososphaerota (55.9%) was dominant in the deep waters. Most of the amoA gene OTUs (99%) belonged to the Nitrosopumilales and were further clustered into five subclades ("NP-Alpha", "NP-Delta", "NP-Epsilon", "NP-Gamma", and "NP-Theta"). "NP-Epsilon" was the most dominant clade throughout the water column and "NP_Alpha" showed higher abundance only in the deeper water. Salinity and inorganic nutrient concentrations were the major factors that determined the vertical segregation of archaea. We anticipate that the observed differences in the vertical distribution of archaea might contribute to the compartmentalization of dark carbon fixation and nitrification in deeper water and organic matter degradation in surface waters of the Arctic Ocean.
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Affiliation(s)
- Puthiya Veettil Vipindas
- Arctic Ecology and Biogeochemistry Division, Ministry of Earth Sciences, National Centre for Polar and Ocean Research, Vasco-da-Gama, Goa, 403 804, India.
| | - Thajudeen Jabir
- Arctic Ecology and Biogeochemistry Division, Ministry of Earth Sciences, National Centre for Polar and Ocean Research, Vasco-da-Gama, Goa, 403 804, India
| | - Siddarthan Venkatachalam
- Arctic Ecology and Biogeochemistry Division, Ministry of Earth Sciences, National Centre for Polar and Ocean Research, Vasco-da-Gama, Goa, 403 804, India
| | - Eun Jin Yang
- Division of Ocean Sciences, Korea Polar Research Institute, 26 Songdo-dong, Yeonsu-gu, Incheon, 21990, Republic of Korea
| | - Anand Jain
- Arctic Ecology and Biogeochemistry Division, Ministry of Earth Sciences, National Centre for Polar and Ocean Research, Vasco-da-Gama, Goa, 403 804, India
| | - Kottekkatu Padinchati Krishnan
- Arctic Ecology and Biogeochemistry Division, Ministry of Earth Sciences, National Centre for Polar and Ocean Research, Vasco-da-Gama, Goa, 403 804, India
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From the Sunlit to the Aphotic Zone: Assembly Mechanisms and Co-Occurrence Patterns of Protistan-Bacterial Microbiotas in the Western Pacific Ocean. mSystems 2023; 8:e0001323. [PMID: 36847533 PMCID: PMC10134807 DOI: 10.1128/msystems.00013-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
We know little about the assembly processes and association patterns of microbial communities below the photic zone. In marine pelagic systems, there are insufficient observational data regarding why and how the microbial assemblies and associations vary from photic to aphotic zones. In this study, we investigated size-fractionated oceanic microbiotas, specifically free-living (FL; 0.22 to 3 μm) and particle-associated (PA; >3 μm) bacteria and protists (0.22 to 200 μm) collected from the surface to 2,000 m in the western Pacific Ocean, to see how assembly mechanisms and association patterns changed from photic to aphotic zones. Taxonomic analysis revealed a distinct community composition between photic and aphotic zones that was largely driven by biotic associations rather than abiotic factors. Aphotic community co-occurrence was less widespread and robust than its photic counterparts, and biotic associations were crucial in microbial co-occurrence, having a higher influence on photic than aphotic co-occurrences. The decrease in biotic associations and the increase in dispersal limitation from the photic to the aphotic zone affect the deterministic-stochastic balance, leading to a more stochastic-process-driven community assembly for all three microbial groups in the aphotic zone. Our findings significantly contribute to our understanding of how and why microbial assembly and co-occurrence vary from photic to aphotic zones, offering insight into the dynamics of the protistan-bacterial microbiota in the western Pacific's photic and aphotic zones. IMPORTANCE We know little about the assembly processes and association patterns of microbial communities below the photic zone in marine pelagic systems. We discovered that community assembly processes differed between photic and aphotic zones, with all three microbial groups studied (protists and FL and PA bacteria) being more influenced by stochastic processes than in the photic zone. The decrease in organismic associations and the increase in dispersal limitation from the photic to the aphotic zone both have an impact on the deterministic-stochastic balance, resulting in a more stochastic process-driven community assembly for all three microbial groups in the aphotic zone. Our findings significantly contribute to the understanding of how and why microbial assembly and co-occurrence change between photic and aphotic zones, offering insight into the dynamics of the protist-bacteria microbiota in the western Pacific oceans.
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Brock ML, Richardson R, Ederington-Hagy M, Nigro L, Snyder RA, Jeffrey WH. Temporal variability of microbial response to crude oil exposure in the northern Gulf of Mexico. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1096880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Abstract
Oil spills are common occurrences in the United States and can result in extensive ecological damage. The 2010 Deepwater Horizon oil spill in the Gulf of Mexico was the largest accidental spill recorded. Many studies were performed in deep water habitats to understand the microbial response to the released crude oil. However, much less is known about how planktonic coastal communities respond to oil spills and whether that response might vary over the course of the year. Understanding this temporal variability would lend additional insight into how coastal Florida habitats may have responded to the Deepwater Horizon oil spill. To assess this, the temporal response of planktonic coastal microbial communities to acute crude oil exposure was examined from September 2015 to September 2016 using seawater samples collected from Pensacola Beach, Florida, at 2-week intervals. A standard oil exposure protocol was performed using water accommodated fractions made from MC252 surrogate oil under photo-oxidizing conditions. Dose response curves for bacterial production and primary production were constructed from 3H-leucine incorporation and 14C-bicarbonate fixation, respectively. To assess drivers of temporal patterns in inhibition, a suite of biological and environmental parameters was measured including bacterial counts, chlorophyll a, temperature, salinity, and nutrients. Additionally, 16S rRNA sequencing was performed on unamended seawater to determine if temporal variation in the in situ bacterial community contributed to differences in inhibition. We observed that there is temporal variation in the inhibition of primary and bacterial production due to acute crude oil exposure. We also identified significant relationships of inhibition with environmental and biological parameters that quantitatively demonstrated that exposure to water-soluble crude oil constituents was most detrimental to planktonic microbial communities when temperature was high, when there were low inputs of total Kjeldahl nitrogen, and when there was low bacterial diversity or low phytoplankton biomass.
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Blumberg K, Miller M, Ponsero A, Hurwitz B. Ontology-driven analysis of marine metagenomics: what more can we learn from our data? Gigascience 2022; 12:giad088. [PMID: 37941395 PMCID: PMC10632069 DOI: 10.1093/gigascience/giad088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/30/2023] [Accepted: 09/28/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND The proliferation of metagenomic sequencing technologies has enabled novel insights into the functional genomic potentials and taxonomic structure of microbial communities. However, cyberinfrastructure efforts to manage and enable the reproducible analysis of sequence data have not kept pace. Thus, there is increasing recognition of the need to make metagenomic data discoverable within machine-searchable frameworks compliant with the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles for data stewardship. Although a variety of metagenomic web services exist, none currently leverage the hierarchically structured terminology encoded within common life science ontologies to programmatically discover data. RESULTS Here, we integrate large-scale marine metagenomic datasets with community-driven life science ontologies into a novel FAIR web service. This approach enables the retrieval of data discovered by intersecting the knowledge represented within ontologies against the functional genomic potential and taxonomic structure computed from marine sequencing data. Our findings highlight various microbial functional and taxonomic patterns relevant to the ecology of prokaryotes in various aquatic environments. CONCLUSIONS In this work, we present and evaluate a novel Semantic Web architecture that can be used to ask novel biological questions of existing marine metagenomic datasets. Finally, the FAIR ontology searchable data products provided by our API can be leveraged by future research efforts.
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Affiliation(s)
- Kai Blumberg
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ 85721, USA
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Matthew Miller
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Alise Ponsero
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ 85721, USA
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
| | - Bonnie Hurwitz
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ 85721, USA
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
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Muñoz-Marín MDC, Duhamel S, Björkman KM, Magasin JD, Díez J, Karl DM, García-Fernández JM. Differential Timing for Glucose Assimilation in Prochlorococcus and Coexistent Microbial Populations in the North Pacific Subtropical Gyre. Microbiol Spectr 2022; 10:e0246622. [PMID: 36098532 PMCID: PMC9602893 DOI: 10.1128/spectrum.02466-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 08/22/2022] [Indexed: 01/04/2023] Open
Abstract
The marine cyanobacterium Prochlorococcus can utilize glucose as a source of carbon. However, the relative importance of inorganic and organic carbon assimilation and the timing of glucose assimilation are still poorly understood in these numerically dominant cyanobacteria. Here, we investigated whole microbial community and group-specific primary production and glucose assimilation using incubations with radioisotopes combined with flow cytometry cell sorting. We also studied changes in the microbial community structure in response to glucose enrichments and analyzed the transcription of Prochlorocccus genes involved in carbon metabolism and photosynthesis. Our results showed a diel variation for glucose assimilation in Prochlorococcus, with maximum assimilation at midday and minimum at midnight (~2-fold change), which was different from that of the total microbial community. This suggests that the timing in glucose assimilation in Prochlorococcus is coupled to photosynthetic light reactions producing energy, it being more convenient for Prochlorococcus to show maximum glucose uptake precisely when the rest of microbial populations have their minimum glucose uptake. Many transcriptional responses to glucose enrichment occurred after 12- and 24-h periods, but community composition did not change. High-light Prochlorococcus strains were the most impacted by glucose addition, with transcript-level increases observed for genes in pathways for glucose metabolism, such as the pentose phosphate pathway, the Entner-Doudoroff pathway, glycolysis, respiration, and glucose transport. While Prochlorococcus C assimilation from glucose represented less than 0.1% of the bacterium's photosynthetic C fixation, increased assimilation during the day and glcH gene upregulation upon glucose enrichment indicate an important role of mixotrophic C assimilation by natural populations of Prochlorococcus. IMPORTANCE Several studies have demonstrated that Prochlorococcus, the most abundant photosynthetic organism on Earth, can assimilate organic molecules, such as amino acids, amino sugars, ATP, phosphonates, and dimethylsulfoniopropionate. This autotroph can also assimilate small amounts of glucose, supporting the hypothesis that Prochlorococcus is mixotrophic. Our results show, for the first time, a diel variability in glucose assimilation by natural populations of Prochlorococcus with maximum assimilation during midday. Based on our previous results, this indicates that Prochlorococcus could maximize glucose uptake by using ATP made during the light reactions of photosynthesis. Furthermore, Prochlorococcus showed a different timing of glucose assimilation from the total population, which may offer considerable fitness advantages over competitors "temporal niches." Finally, we observed transcriptional changes in some of the genes involved in carbon metabolism, suggesting that Prochlorococcus can use both pathways previously proposed in cyanobacteria to metabolize glucose.
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Affiliation(s)
- María del Carmen Muñoz-Marín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba, Spain
| | - Solange Duhamel
- Lamont-Doherty Earth Observatory of Columbia University, Division of Biology and Paleo Environment, Palisades, New York, USA
| | - Karin M. Björkman
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii at Manoa, C-MORE Hale, Honolulu, Hawaii, USA
| | - Jonathan D. Magasin
- Ocean Sciences Department, University of California, Santa Cruz, California, USA
| | - Jesús Díez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba, Spain
| | - David M. Karl
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii at Manoa, C-MORE Hale, Honolulu, Hawaii, USA
| | - José M. García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba, Spain
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11
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Guo B, Li W, Santibáñez P, Priscu JC, Liu Y, Liu K. Organic matter distribution in the icy environments of Taylor Valley, Antarctica. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 841:156639. [PMID: 35697215 DOI: 10.1016/j.scitotenv.2022.156639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/07/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Glaciers can accumulate and release organic matter affecting the structure and function of associated terrestrial and aquatic ecosystems. We analyzed 18 ice cores collected from six locations in Taylor Valley (McMurdo Dry Valleys), Antarctica to determine the spatial abundance and quality of organic matter, and the spatial distribution of bacterial density and community structure from the terminus of the Taylor Glacier to the coast (McMurdo Sound). Our results showed that dissolved and particulate organic carbon (DOC and POC) concentrations in the ice core samples increased from the Taylor Glacier to McMurdo Sound, a pattern also shown by bacterial cell density. Fluorescence Excitation Emission Matrices Spectroscopy (EEMs) and multivariate parallel factor (PARAFAC) modeling identified one humic-like (C1) and one protein-like (C2) component in ice cores whose fluorescent intensities all increased from the Polar Plateau to the coast. The fluorescence index showed that the bioavailability of dissolved organic matter (DOM) also decreased from the Polar Plateau to the coast. Partial least squares path modeling analysis revealed that bacterial abundance was the main positive biotic factor influencing both the quantity and quality of organic matter. Marine aerosol influenced the spatial distribution of DOC more than katabatic winds in the ice cores. Certain bacterial taxa showed significant correlations with DOC and POC concentrations. Collectively, our results show the tight connectivity among organic matter spatial distribution, bacterial abundance and meteorology in the McMurdo Dry Valley ecosystem.
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Affiliation(s)
- Bixi Guo
- State Key Laboratory of Tibetan Plateau Earth System Science (LATPES), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; Polar Oceans Research Group, Sheridan, MT 59749, USA
| | - Wei Li
- Polar Oceans Research Group, Sheridan, MT 59749, USA; Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, CA 94550, USA
| | - Pamela Santibáñez
- Ministry of Science, Technology, Knowledge, & Innovation, Punta Arenas 6200000, Chile
| | - John C Priscu
- Polar Oceans Research Group, Sheridan, MT 59749, USA.
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System Science (LATPES), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System Science (LATPES), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
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12
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Comstock J, Nelson CE, James A, Wear E, Baetge N, Remple K, Juknavorian A, Carlson CA. Bacterioplankton communities reveal horizontal and vertical influence of an Island Mass Effect. Environ Microbiol 2022; 24:4193-4208. [PMID: 35691616 PMCID: PMC9796716 DOI: 10.1111/1462-2920.16092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 05/26/2022] [Accepted: 05/31/2022] [Indexed: 01/07/2023]
Abstract
Coral reefs are highly productive ecosystems with distinct biogeochemistry and biology nestled within unproductive oligotrophic gyres. Coral reef islands have often been associated with a nearshore enhancement in phytoplankton, a phenomenon known as the Island Mass Effect (IME). Despite being documented more than 60 years ago, much remains unknown about the extent and drivers of IMEs. Here we utilized 16S rRNA gene metabarcoding as a biological tracer to elucidate horizontal and vertical influence of an IME around the islands of Mo'orea and Tahiti, French Polynesia. We show that those nearshore oceanic stations with elevated chlorophyll a included bacterioplankton found in high abundance in the reef environment, suggesting advection of reef water is the source of altered nearshore biogeochemistry. We also observed communities in the nearshore deep chlorophyll maximum (DCM) with enhanced abundances of upper euphotic bacterioplankton that correlated with intrusions of low-density, O2 rich water, suggesting island influence extends into the DCM.
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Affiliation(s)
- Jacqueline Comstock
- Department of Ecology, Evolution and Marine Biology and Marine Science InstituteUniversity of California Santa BarbaraSanta BarbaraCAUSA
| | - Craig E. Nelson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College ProgramUniversity of Hawai'i at MānoaHonoluluHIUSA
| | - Anna James
- Department of Ecology, Evolution and Marine Biology and Marine Science InstituteUniversity of California Santa BarbaraSanta BarbaraCAUSA
| | - Emma Wear
- Department of Ecology, Evolution and Marine Biology and Marine Science InstituteUniversity of California Santa BarbaraSanta BarbaraCAUSA
| | - Nicholas Baetge
- Department of Ecology, Evolution and Marine Biology and Marine Science InstituteUniversity of California Santa BarbaraSanta BarbaraCAUSA
| | - Kristina Remple
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College ProgramUniversity of Hawai'i at MānoaHonoluluHIUSA
| | | | - Craig A. Carlson
- Department of Ecology, Evolution and Marine Biology and Marine Science InstituteUniversity of California Santa BarbaraSanta BarbaraCAUSA
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13
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Haber M, Roth Rosenberg D, Lalzar M, Burgsdorf I, Saurav K, Lionheart R, Lehahn Y, Aharonovich D, Gómez-Consarnau L, Sher D, Krom MD, Steindler L. Spatiotemporal Variation of Microbial Communities in the Ultra-Oligotrophic Eastern Mediterranean Sea. Front Microbiol 2022; 13:867694. [PMID: 35464964 PMCID: PMC9022036 DOI: 10.3389/fmicb.2022.867694] [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] [Received: 02/01/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Marine microbial communities vary seasonally and spatially, but these two factors are rarely addressed together. In this study, the temporal and spatial patterns of the bacterial and archaeal community were studied along a coast-to-offshore transect in the Eastern Mediterranean Sea (EMS) over six cruises, in three seasons of 2 consecutive years. Amplicon sequencing of 16S rRNA genes and transcripts was performed to determine presence and activity, respectively. The ultra-oligotrophic status of the Southeastern Mediterranean Sea was reflected in the microbial community composition dominated by oligotrophic bacterial groups such as SAR11, even at the most coastal station sampled, throughout the year. Seasons significantly affected the microbial communities, explaining more than half of the observed variability. However, the same few taxa dominated the community over the 2-year sampling period, varying only in their degree of dominance. While there was no overall effect of station location on the microbial community, the most coastal site (16 km offshore) differed significantly in community structure and activity from the three further offshore stations in early winter and summer. Our data on the microbial community compositions and their seasonality support previous notions that the EMS behaves like an oceanic gyre.
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Affiliation(s)
- Markus Haber
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel.,Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, České Budějovice, Czechia
| | - Dalit Roth Rosenberg
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Maya Lalzar
- Bioinformatics Service Unit, University of Haifa, Haifa, Israel
| | - Ilia Burgsdorf
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Kumar Saurav
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Regina Lionheart
- The Dr. Moses Strauss Department of Marine Geosciences, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Yoav Lehahn
- The Dr. Moses Strauss Department of Marine Geosciences, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Dikla Aharonovich
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Laura Gómez-Consarnau
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States.,Department of Biological Oceanography, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Mexico
| | - Daniel Sher
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Michael D Krom
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel.,Morris Kahn Marine Research Station, Environmental Geochemistry Lab., Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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14
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Blumberg KL, Ponsero AJ, Bomhoff M, Wood-Charlson EM, DeLong EF, Hurwitz BL. Ontology-Enriched Specifications Enabling Findable, Accessible, Interoperable, and Reusable Marine Metagenomic Datasets in Cyberinfrastructure Systems. Front Microbiol 2021; 12:765268. [PMID: 34956127 PMCID: PMC8692764 DOI: 10.3389/fmicb.2021.765268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/16/2021] [Indexed: 11/13/2022] Open
Abstract
Marine microbial ecology requires the systematic comparison of biogeochemical and sequence data to analyze environmental influences on the distribution and variability of microbial communities. With ever-increasing quantities of metagenomic data, there is a growing need to make datasets Findable, Accessible, Interoperable, and Reusable (FAIR) across diverse ecosystems. FAIR data is essential to developing analytical frameworks that integrate microbiological, genomic, ecological, oceanographic, and computational methods. Although community standards defining the minimal metadata required to accompany sequence data exist, they haven’t been consistently used across projects, precluding interoperability. Moreover, these data are not machine-actionable or discoverable by cyberinfrastructure systems. By making ‘omic and physicochemical datasets FAIR to machine systems, we can enable sequence data discovery and reuse based on machine-readable descriptions of environments or physicochemical gradients. In this work, we developed a novel technical specification for dataset encapsulation for the FAIR reuse of marine metagenomic and physicochemical datasets within cyberinfrastructure systems. This includes using Frictionless Data Packages enriched with terminology from environmental and life-science ontologies to annotate measured variables, their units, and the measurement devices used. This approach was implemented in Planet Microbe, a cyberinfrastructure platform and marine metagenomic web-portal. Here, we discuss the data properties built into the specification to make global ocean datasets FAIR within the Planet Microbe portal. We additionally discuss the selection of, and contributions to marine-science ontologies used within the specification. Finally, we use the system to discover data by which to answer various biological questions about environments, physicochemical gradients, and microbial communities in meta-analyses. This work represents a future direction in marine metagenomic research by proposing a specification for FAIR dataset encapsulation that, if adopted within cyberinfrastructure systems, would automate the discovery, exchange, and re-use of data needed to answer broader reaching questions than originally intended.
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Affiliation(s)
- Kai L Blumberg
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ, United States
| | - Alise J Ponsero
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ, United States
| | - Matthew Bomhoff
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ, United States
| | - Elisha M Wood-Charlson
- E.O. Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography, University of Hawai'i, Honolulu, HI, United States
| | - Bonnie L Hurwitz
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ, United States.,BIO5 Institute, University of Arizona, Tucson, AZ, United States
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15
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Tucker SJ, Freel KC, Monaghan EA, Sullivan CES, Ramfelt O, Rii YM, Rappé MS. Spatial and temporal dynamics of SAR11 marine bacteria across a nearshore to offshore transect in the tropical Pacific Ocean. PeerJ 2021; 9:e12274. [PMID: 34760357 PMCID: PMC8572523 DOI: 10.7717/peerj.12274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 09/19/2021] [Indexed: 01/04/2023] Open
Abstract
Surveys of microbial communities across transitions coupled with contextual measures of the environment provide a useful approach to dissect the factors determining distributions of microorganisms across ecological niches. Here, monthly time-series samples of surface seawater along a transect spanning the nearshore coastal environment within Kāneʻohe Bay on the island of Oʻahu, Hawaiʻi, and the adjacent offshore environment were collected to investigate the diversity and abundance of SAR11 marine bacteria (order Pelagibacterales) over a 2-year time period. Using 16S ribosomal RNA gene amplicon sequencing, the spatiotemporal distributions of major SAR11 subclades and exact amplicon sequence variants (ASVs) were evaluated. Seven of eight SAR11 subclades detected in this study showed distinct subclade distributions across the coastal to offshore environments. The SAR11 community was dominated by seven (of 106 total) SAR11 ASVs that made up an average of 77% of total SAR11. These seven ASVs spanned five different SAR11 subclades (Ia, Ib, IIa, IV, and Va), and were recovered from all samples collected from either the coastal environment, the offshore, or both. SAR11 ASVs were more often restricted spatially to coastal or offshore environments (64 of 106 ASVs) than they were shared among coastal, transition, and offshore environments (39 of 106 ASVs). Overall, offshore SAR11 communities contained a higher diversity of SAR11 ASVs than their nearshore counterparts, with the highest diversity within the little-studied subclade IIa. This study reveals ecological differentiation of SAR11 marine bacteria across a short physiochemical gradient, further increasing our understanding of how SAR11 genetic diversity partitions into distinct ecological units.
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Affiliation(s)
- Sarah J Tucker
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States.,Marine Biology Graduate Program, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States
| | - Kelle C Freel
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States
| | - Elizabeth A Monaghan
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States.,Marine Biology Graduate Program, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States
| | - Clarisse E S Sullivan
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States
| | - Oscar Ramfelt
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States
| | - Yoshimi M Rii
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States.,He'eia National Estuarine Research Reserve, Kāne'ohe, Hawai'i, United States
| | - Michael S Rappé
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States
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16
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Li F, Leu A, Poff K, Carlson LT, Ingalls AE, DeLong EF. Planktonic Archaeal Ether Lipid Origins in Surface Waters of the North Pacific Subtropical Gyre. Front Microbiol 2021; 12:610675. [PMID: 34589060 PMCID: PMC8473941 DOI: 10.3389/fmicb.2021.610675] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 08/23/2021] [Indexed: 01/04/2023] Open
Abstract
Thaumarchaeota and Thermoplasmatota are the most abundant planktonic archaea in the sea. Thaumarchaeota contain tetraether lipids as their major membrane lipids, but the lipid composition of uncultured planktonic Thermoplasmatota representatives remains unknown. To address this knowledge gap, we quantified archaeal cells and ether lipids in open ocean depth profiles (0–200 m) of the North Pacific Subtropical Gyre. Planktonic archaeal community structure and ether lipid composition in the water column partitioned into two separate clusters: one above the deep chlorophyll maximum, the other within and below it. In surface waters, Thermoplasmatota densities ranged from 2.11 × 106 to 6.02 × 106 cells/L, while Thaumarchaeota were undetectable. As previously reported for Thaumarchaeota, potential homologs of archaeal tetraether ring synthases were present in planktonic Thermoplasmatota metagenomes. Despite the absence of Thaumarchaeota in surface waters, measurable amounts of intact polar ether lipids were found there. Based on cell abundance estimates, these surface water archaeal ether lipids contributed only 1.21 × 10–9 ng lipid/Thermoplasmatota cell, about three orders of magnitude less than that reported for Thaumarchaeota cells. While these data indicate that even if some tetraether and diether lipids may be derived from Thermoplasmatota, they would only comprise a small fraction of Thermoplasmatota total biomass. Therefore, while both MGI Thaumarchaeota and MGII/III Thermoplasmatota are potential biological sources of archaeal GDGTs, the Thaumarchaeota appear to be the major contributors of archaeal tetraether lipids in planktonic marine habitats. These results extend and confirm previous reports of planktonic archaeal lipid sources, and further emphasize the need for Thermoplasmatota cultivation, to better characterize the membrane lipid constituents of marine planktonic Thermoplasmatota, and more precisely define the sources and patterns of archaeal tetraether lipid distributions in marine plankton.
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Affiliation(s)
- Fuyan Li
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Andy Leu
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Kirsten Poff
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Laura T Carlson
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mânoa, Honolulu, HI, United States
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17
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Boeuf D, Eppley JM, Mende DR, Malmstrom RR, Woyke T, DeLong EF. Metapangenomics reveals depth-dependent shifts in metabolic potential for the ubiquitous marine bacterial SAR324 lineage. MICROBIOME 2021; 9:172. [PMID: 34389059 PMCID: PMC8364033 DOI: 10.1186/s40168-021-01119-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 06/22/2021] [Indexed: 06/01/2023]
Abstract
BACKGROUND Oceanic microbiomes play a pivotal role in the global carbon cycle and are central to the transformation and recycling of carbon and energy in the ocean's interior. SAR324 is a ubiquitous but poorly understood uncultivated clade of Deltaproteobacteria that inhabits the entire water column, from ocean surface waters to its deep interior. Although some progress has been made in elucidating potential metabolic traits of SAR324 in the dark ocean, very little is known about the ecology and the metabolic capabilities of this group in the euphotic and twilight zones. To investigate the comparative genomics, ecology, and physiological potential of the SAR324 clade, we examined the distribution and variability of key genomic features and metabolic pathways in this group from surface waters to the abyss in the North Pacific Subtropical Gyre, one of the largest biomes on Earth. RESULTS We leveraged a pangenomic ecological approach, combining spatio-temporally resolved single-amplified genome, metagenomic, and metatranscriptomic datasets. The data revealed substantial genomic diversity throughout the SAR324 clade, with distinct depth and temporal distributions that clearly differentiated ecotypes. Phylogenomic subclade delineation, environmental distributions, genomic feature similarities, and metabolic capacities revealed strong congruence. The four SAR324 ecotypes delineated in this study revealed striking divergence from one another with respect to their habitat-specific metabolic potentials. The ecotypes living in the dark or twilight oceans shared genomic features and metabolic capabilities consistent with a sulfur-based chemolithoautotrophic lifestyle. In contrast, those inhabiting the sunlit ocean displayed higher plasticity energy-related metabolic pathways, supporting a presumptive photoheterotrophic lifestyle. In epipelagic SAR324 ecotypes, we observed the presence of two types of proton-pumping rhodopsins, as well as genomic, transcriptomic, and ecological evidence for active photoheterotrophy, based on xanthorhodopsin-like light-harvesting proteins. CONCLUSIONS Combining pangenomic and both metagenomic and metatranscriptomic profiling revealed a striking divergence in the vertical distribution, genomic composition, metabolic potential, and predicted lifestyle strategies of geographically co-located members of the SAR324 bacterial clade. The results highlight the utility of metapangenomic approaches employed across environmental gradients, to decipher the properties and variation in function and ecological traits of specific phylogenetic clades within complex microbiomes. Video abstract.
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Affiliation(s)
- Dominique Boeuf
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Manoa, Honolulu, HI 96822 USA
| | - John M. Eppley
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Manoa, Honolulu, HI 96822 USA
| | - Daniel R. Mende
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Manoa, Honolulu, HI 96822 USA
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Berkeley, CA 94720 USA
| | - Edward F. DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Manoa, Honolulu, HI 96822 USA
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18
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Biogeographical patterns and mechanisms of microbial community assembly that underlie successional biocrusts across northern China. NPJ Biofilms Microbiomes 2021; 7:15. [PMID: 33547284 PMCID: PMC7864921 DOI: 10.1038/s41522-021-00188-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 01/14/2021] [Indexed: 01/30/2023] Open
Abstract
Biocrusts play critical eco-functions in many drylands, however it is challenging to explore their community assembly, particularly within patched successional types and across climate zones. Here, different successional biocrusts (alga, lichen, and moss-dominated biocrusts) were collected across the northern China, and assembly of biocrust microbial communities was investigated by high-throughput sequencing combined with measurements of soil properties and microclimate environments. Bacterial and eukaryotic communities showed that the maximum and minimum community variation occurred across longitude and latitude, respectively. In the regions where all three stages of biocrusts were involved, the highest community difference existed between successional stages, and decreased with distance. The community assembly was generally driven by dispersal limitation, although neutral processes have controlled the eukaryotic community assembly in hyperarid areas. Along the succession, bacterial community had no obvious patterns, but eukaryotic community showed increasing homogeneity, with increased species sorting and decreased dispersal limitation for community assembly. Compared to early successional biocrusts, there were higher microbial mutual exclusions and more complex networks at later stages, with distinct topological features. Correlation analysis further indicated that the balance between deterministic and stochastic processes might be mediated by aridity, salinity, and total phosphorus, although the mediations were opposite for bacteria and eukaryotes.
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19
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Ponsero AJ, Bomhoff M, Blumberg K, Youens-Clark K, Herz NM, Wood-Charlson EM, Delong EF, Hurwitz BL. Planet Microbe: a platform for marine microbiology to discover and analyze interconnected 'omics and environmental data. Nucleic Acids Res 2021; 49:D792-D802. [PMID: 32735679 PMCID: PMC7778950 DOI: 10.1093/nar/gkaa637] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/23/2020] [Accepted: 07/20/2020] [Indexed: 12/27/2022] Open
Abstract
In recent years, large-scale oceanic sequencing efforts have provided a deeper understanding of marine microbial communities and their dynamics. These research endeavors require the acquisition of complex and varied datasets through large, interdisciplinary and collaborative efforts. However, no unifying framework currently exists for the marine science community to integrate sequencing data with physical, geological, and geochemical datasets. Planet Microbe is a web-based platform that enables data discovery from curated historical and on-going oceanographic sequencing efforts. In Planet Microbe, each ‘omics sample is linked with other biological and physiochemical measurements collected for the same water samples or during the same sample collection event, to provide a broader environmental context. This work highlights the need for curated aggregation efforts that can enable new insights into high-quality metagenomic datasets. Planet Microbe is freely accessible from https://www.planetmicrobe.org/.
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Affiliation(s)
- Alise J Ponsero
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ, USA.,BIO5 Institute, University of Arizona, Tucson, AZ, USA
| | - Matthew Bomhoff
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ, USA.,BIO5 Institute, University of Arizona, Tucson, AZ, USA
| | - Kai Blumberg
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ, USA.,BIO5 Institute, University of Arizona, Tucson, AZ, USA
| | - Ken Youens-Clark
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ, USA.,BIO5 Institute, University of Arizona, Tucson, AZ, USA
| | - Nina M Herz
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ, USA
| | - Elisha M Wood-Charlson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Edward F Delong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Manoa, Honolulu, HI 96822, USA
| | - Bonnie L Hurwitz
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ, USA.,BIO5 Institute, University of Arizona, Tucson, AZ, USA
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20
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Ares Á, Brisbin MM, Sato KN, Martín JP, Iinuma Y, Mitarai S. Extreme storms cause rapid but short-lived shifts in nearshore subtropical bacterial communities. Environ Microbiol 2021; 22:4571-4588. [PMID: 33448616 DOI: 10.1111/1462-2920.15178] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/27/2020] [Accepted: 07/24/2020] [Indexed: 01/04/2023]
Abstract
Climate change scenarios predict tropical cyclones will increase in both frequency and intensity, which will escalate the amount of terrestrial run-off and mechanical disruption affecting coastal ecosystems. Bacteria are key contributors to ecosystem functioning, but relatively little is known about how they respond to extreme storm events, particularly in nearshore subtropical regions. In this study, we combine field observations and mesocosm experiments to assess bacterial community dynamics and changes in physicochemical properties during early- and late-season tropical cyclones affecting Okinawa, Japan. Storms caused large and fast influxes of freshwater and terrestrial sediment - locally known as red soil pollution - and caused moderate increases of macronutrients, especially SiO2 and PO4 3-, with up to 25 and 0.5 μM respectively. We detected shifts in relative abundances of marine and terrestrially derived bacteria, including putative coral and human pathogens, during storm events. Soil input alone did not substantially affect marine bacterial communities in mesocosms, indicating that other components of run-off or other storm effects likely exert a larger influence on bacterial communities. The storm effects were short-lived and bacterial communities quickly recovered following both storm events. The early- and late-season storms caused different physicochemical and bacterial community changes, demonstrating the context-dependency of extreme storm responses in a subtropical coastal ecosystem.
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Affiliation(s)
- Ángela Ares
- Marine Biophysics Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
| | - Margaret Mars Brisbin
- Marine Biophysics Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
| | - Kirk N Sato
- Marine Biophysics Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan.,Friday Harbor Laboratories, University of Washington, WA, USA
| | - Juan P Martín
- Marine Biophysics Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
| | - Yoshiteru Iinuma
- Instrumental Analysis Section, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
| | - Satoshi Mitarai
- Marine Biophysics Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
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21
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Shahraki AH, Chaganti SR, Heath DD. Diel Dynamics of Freshwater Bacterial Communities at Beaches in Lake Erie and Lake St. Clair, Windsor, Ontario. MICROBIAL ECOLOGY 2021; 81:1-13. [PMID: 32621209 DOI: 10.1007/s00248-020-01539-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/08/2020] [Indexed: 06/11/2023]
Abstract
Bacteria play a key role in freshwater biogeochemical cycling as well as water safety, but short-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We sampled four public beaches in southern Ontario, Canada; in June, July, and August (2016) over a 24-h (diel) cycle at 2-h intervals. Using high-throughput sequencing of 16S rRNA gene, we found substantial bi-hourly and day/night variation in the bacterial communities with considerable fluctuation in the relative abundance of Actinobacteria and Proteobacteria phyla. Moreover, relative abundance of Enterobacteriaceae (associated with potential health risk) was significantly high at night in some dial cycles. Diversity was significantly high at night across most of the diel sampling events. qPCR assays showed a substantial bi-hourly variation of Escherichia coli levels with a significant high level of E. coli at night hours in comparison with day hours and the lowest levels at noon and during the afternoon hours. Taken together, these findings highlighted a considerable short-term temporal variation of bacterial communities which helps better understanding of freshwater bacterial dynamics and their ecology. E. coli monitoring showed that multiple samples in different hours will provide more accurate picture of freshwater safety and human health risk. Graphical abstract.
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Affiliation(s)
| | - Subba Rao Chaganti
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, N9B 3P4, Canada
- Cooperative Institute for Great Lakes Research, School of Environment and Sustainability, University of Michigan, Ann Arbor, MI, USA
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, N9B 3P4, Canada.
- Department of Integrative Biology, University of Windsor, Windsor, ON, Canada.
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22
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Wu W, Xu Z, Dai M, Gan J, Liu H. Homogeneous selection shapes free‐living and particle‐associated bacterial communities in subtropical coastal waters. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13193] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Wenxue Wu
- School of Marine Sciences Sun Yat‐sen University Zhuhai China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Zhuhai China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering Sun Yat‐sen University Zhuhai China
| | - Zhimeng Xu
- Department of Ocean Science The Hong Kong University of Science and Technology Kowloon Hong Kong SAR China
| | - Minhan Dai
- State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Jianping Gan
- Department of Ocean Science The Hong Kong University of Science and Technology Kowloon Hong Kong SAR China
| | - Hongbin Liu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Zhuhai China
- Department of Ocean Science The Hong Kong University of Science and Technology Kowloon Hong Kong SAR China
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23
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Seasonality in Spatial Turnover of Bacterioplankton Along an Ecological Gradient in the East China Sea: Biogeographic Patterns, Processes and Drivers. Microorganisms 2020; 8:microorganisms8101484. [PMID: 32992545 PMCID: PMC7600760 DOI: 10.3390/microorganisms8101484] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/18/2020] [Accepted: 09/18/2020] [Indexed: 11/16/2022] Open
Abstract
Seasonal succession in bacterioplankton is a common process in marine waters. However, seasonality in their spatial turnover is largely unknown. Here, we investigated spatial turnover of surface bacterioplankton along a nearshore-to-offshore gradient in the East China Sea across four seasons. Although seasonality overwhelmed spatial variability of bacterioplankton composition, we found significant spatial turnover of bacterioplankton along the gradient as well as overall seasonal consistency in biogeographic patterns (including distance-decay relationship and covariation of community composition with distance to shore) with subtle changes. Bacterioplankton assembly was consistently dominated by deterministic mechanisms across seasons, with changes in specific processes. We found overall seasonal consistency in abiotic factors (mainly salinity and nitrogen and phosphorus nutrients) shaping bacterioplankton composition, while phytoplankton showed a similar influence as abiotic factors only in spring. Although key taxa responsible for bacterioplankton spatial turnover showed certain season-specificity, seasonal switching between closely related taxa occurred within most dominant families. Moreover, many close relatives showed different responding patterns to the environmental gradients in different seasons, suggesting their differences in both seasonally climatic and spatially environmental preferences. Our results provide insights into seasonal consistency and variability in spatial turnover of bacterioplankton in terms of biogeographic patterns, ecological processes, and external and internal drivers.
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24
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Mena C, Reglero P, Balbín R, Martín M, Santiago R, Sintes E. Seasonal Niche Partitioning of Surface Temperate Open Ocean Prokaryotic Communities. Front Microbiol 2020; 11:1749. [PMID: 32849378 PMCID: PMC7399227 DOI: 10.3389/fmicb.2020.01749] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 07/03/2020] [Indexed: 12/20/2022] Open
Abstract
Surface microbial communities are exposed to seasonally changing environmental conditions, resulting in recurring patterns of community composition. However, knowledge on temporal dynamics of open ocean microbial communities remains scarce. Seasonal patterns and associations of taxa and oligotypes from surface and chlorophyll maximum layers in the western Mediterranean Sea were studied over a 2-year period. Summer stratification versus winter mixing governed not only the prokaryotic community composition and diversity but also the temporal dynamics and co-occurrence association networks of oligotypes. Flavobacteriales, Rhodobacterales, SAR11, SAR86, and Synechococcales oligotypes exhibited contrasting seasonal dynamics, and consequently, specific microbial assemblages and potential inter-oligotype connections characterized the different seasons. In addition, oligotypes composition and dynamics differed between surface and deep chlorophyll maximum (DCM) prokaryotic communities, indicating depth-related environmental gradients as a major factor affecting association networks between closely related taxa. Taken together, the seasonal and depth specialization of oligotypes suggest temporal dynamics of community composition and metabolism, influencing ecosystem function and global biogeochemical cycles. Moreover, our results indicate highly specific associations between microbes, pointing to keystone ecotypes and fine-tuning of the microbes realized niche.
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Affiliation(s)
- Catalina Mena
- Instituto Español de Oceanografía (IEO), Centre Oceanogràfic de les Balears, Ecosystem Oceanography Group (GRECO), Palma, Spain
| | - Patricia Reglero
- Instituto Español de Oceanografía (IEO), Centre Oceanogràfic de les Balears, Ecosystem Oceanography Group (GRECO), Palma, Spain
| | - Rosa Balbín
- Instituto Español de Oceanografía (IEO), Centre Oceanogràfic de les Balears, Ecosystem Oceanography Group (GRECO), Palma, Spain
| | - Melissa Martín
- Instituto Español de Oceanografía (IEO), Centre Oceanogràfic de les Balears, Ecosystem Oceanography Group (GRECO), Palma, Spain
| | - Rocío Santiago
- Instituto Español de Oceanografía (IEO), Centre Oceanogràfic de les Balears, Ecosystem Oceanography Group (GRECO), Palma, Spain
| | - Eva Sintes
- Instituto Español de Oceanografía (IEO), Centre Oceanogràfic de les Balears, Ecosystem Oceanography Group (GRECO), Palma, Spain
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25
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Djurhuus A, Closek CJ, Kelly RP, Pitz KJ, Michisaki RP, Starks HA, Walz KR, Andruszkiewicz EA, Olesin E, Hubbard K, Montes E, Otis D, Muller-Karger FE, Chavez FP, Boehm AB, Breitbart M. Environmental DNA reveals seasonal shifts and potential interactions in a marine community. Nat Commun 2020; 11:254. [PMID: 31937756 PMCID: PMC6959347 DOI: 10.1038/s41467-019-14105-1] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 12/12/2019] [Indexed: 02/02/2023] Open
Abstract
Environmental DNA (eDNA) analysis allows the simultaneous examination of organisms across multiple trophic levels and domains of life, providing critical information about the complex biotic interactions related to ecosystem change. Here we used multilocus amplicon sequencing of eDNA to survey biodiversity from an eighteen-month (2015–2016) time-series of seawater samples from Monterey Bay, California. The resulting dataset encompasses 663 taxonomic groups (at Family or higher taxonomic rank) ranging from microorganisms to mammals. We inferred changes in the composition of communities, revealing putative interactions among taxa and identifying correlations between these communities and environmental properties over time. Community network analysis provided evidence of expected predator-prey relationships, trophic linkages, and seasonal shifts across all domains of life. We conclude that eDNA-based analyses can provide detailed information about marine ecosystem dynamics and identify sensitive biological indicators that can suggest ecosystem changes and inform conservation strategies. Increasingly, eDNA is being used to infer ecological interactions. Here the authors sample eDNA over 18 months in a marine environment and use co-occurrence network analyses to infer potential interactions among organisms from microbes to mammals, testing how they change over time in response to oceanographic factors.
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Affiliation(s)
- Anni Djurhuus
- University of South Florida, College of Marine Science, 140 7th Avenue South, St. Petersburg, FL, 33701, USA.
| | - Collin J Closek
- Stanford Center for Ocean Solutions, Stanford University, 473 Via Ortega, Stanford, CA, 94305, USA. .,Department of Civil and Environmental Engineering, Stanford University, 473 Via Ortega, Stanford, CA, 94305, USA.
| | - Ryan P Kelly
- University of Washington, School of Marine and Environmental Affairs, 3707 Brooklyn Ave, Seattle, WA, 98105, USA
| | - Kathleen J Pitz
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA, 95039, USA
| | - Reiko P Michisaki
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA, 95039, USA
| | - Hilary A Starks
- Stanford Center for Ocean Solutions, Stanford University, 473 Via Ortega, Stanford, CA, 94305, USA.,Department of Civil and Environmental Engineering, Stanford University, 473 Via Ortega, Stanford, CA, 94305, USA
| | - Kristine R Walz
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA, 95039, USA
| | - Elizabeth A Andruszkiewicz
- Department of Civil and Environmental Engineering, Stanford University, 473 Via Ortega, Stanford, CA, 94305, USA
| | - Emily Olesin
- Florida Fish and Wildlife Research Conservation-Fish and Wildlife Research Institute, 100 8th Avenue SE, St. Petersburg, FL, 33701, USA
| | - Katherine Hubbard
- Florida Fish and Wildlife Research Conservation-Fish and Wildlife Research Institute, 100 8th Avenue SE, St. Petersburg, FL, 33701, USA
| | - Enrique Montes
- University of South Florida, College of Marine Science, 140 7th Avenue South, St. Petersburg, FL, 33701, USA
| | - Daniel Otis
- University of South Florida, College of Marine Science, 140 7th Avenue South, St. Petersburg, FL, 33701, USA
| | - Frank E Muller-Karger
- University of South Florida, College of Marine Science, 140 7th Avenue South, St. Petersburg, FL, 33701, USA
| | - Francisco P Chavez
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA, 95039, USA
| | - Alexandria B Boehm
- Department of Civil and Environmental Engineering, Stanford University, 473 Via Ortega, Stanford, CA, 94305, USA
| | - Mya Breitbart
- University of South Florida, College of Marine Science, 140 7th Avenue South, St. Petersburg, FL, 33701, USA.
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26
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Niu A, Song LY, Xiong YH, Lu CJ, Junaid M, Pei DS. Impact of water quality on the microbial diversity in the surface water along the Three Gorge Reservoir (TGR), China. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 181:412-418. [PMID: 31220781 DOI: 10.1016/j.ecoenv.2019.06.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/05/2019] [Accepted: 06/07/2019] [Indexed: 06/09/2023]
Abstract
The Three Gorges Reservoir (TGR), one of the world's largest reservoirs, has crucial roles in flood control, power generation, and navigation. The TGR is contaminated because of the human activities, and how the contaminated water influences the distribution of the microbial community have not been well studied. In this study, we collected 41 freshwater samples from 13 main dwelling districts along the TGR to investigate the water quality, the distribution of the microbial community, and how water quality affects the microbial community structure. The sampling sites cover the whole TGR along the stream, with 670 km distance. Our results show that both water quality and the compositions of bacterial community vary along the TGR. The distribution of bacterial community is closely related to the local water quality. There is the highest concentration of chemical oxygen demand (COD), the highest relative abundance of Firmicutes, and the highest relative abundance of Bacillus in the upstream, compared to the middle and down streams. Redundancy analysis (RDA) showed that PO43- and COD were the main environmental factors influencing on the structure of bacterial community. The relative abundance of nitrification and denitrification functional genes also altered along the streams. These findings provide the basic data for water quality, the distribution of bacterial community, the link of environmental factors, and the bacterial community structure along the TGR, which guides the local environmental protection agency to launch protection strategy for maintaining the ecosystem health of the TGR.
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Affiliation(s)
- Aping Niu
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Yan Song
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang-Hui Xiong
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chun-Jiao Lu
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Muhammad Junaid
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - De-Sheng Pei
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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27
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Mende DR, Boeuf D, DeLong EF. Persistent Core Populations Shape the Microbiome Throughout the Water Column in the North Pacific Subtropical Gyre. Front Microbiol 2019; 10:2273. [PMID: 31632377 PMCID: PMC6779783 DOI: 10.3389/fmicb.2019.02273] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 09/18/2019] [Indexed: 01/23/2023] Open
Abstract
Marine microbial communities are responsible for many important ecosystem processes in the oceans. Their variability across time and depths is well recognized, but mostly at a coarse-grained taxonomic resolution. To gain a deeper perspective on ecological patterns of bacterioplankton diversity in the North Pacific Subtropical Gyre, we characterized bacterioplankton communities throughout the water column at a fine-grained taxonomic level with a focus on temporally persistent (core) populations. Considerable intra-clade microdiversity was evident in virtually every microbial clade examined. While some of the most abundant populations comprised only a small fraction of the intra-clade microdiversity, they formed a temporally persistent core within a more diverse array of less abundant ephemeral populations. The depth-stratified population structure within many phylogenetically disparate clades suggested that ecotypic variation was the rule among most planktonic bacterial and archaeal lineages. Our results suggested that the abundant, persistent core populations comprised the bulk of the biomass within any given clade. As such, we postulate that these core populations are largely responsible for microbially driven ecosystem processes, and so represent ideal targets for elucidating key microbial processes in the open-ocean water column.
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Affiliation(s)
- Daniel R Mende
- Daniel K. Inouye Center for Microbial Oceanography, Research and Education, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, United States
| | - Dominique Boeuf
- Daniel K. Inouye Center for Microbial Oceanography, Research and Education, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, United States
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography, Research and Education, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, United States
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28
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Wang Z, Juarez DL, Pan J, Blinebry SK, Gronniger J, Clark JS, Johnson ZI, Hunt DE. Microbial communities across nearshore to offshore coastal transects are primarily shaped by distance and temperature. Environ Microbiol 2019; 21:3862-3872. [DOI: 10.1111/1462-2920.14734] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/05/2019] [Accepted: 07/05/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Zhao Wang
- Duke University Marine Lab Beaufort NC
| | | | - Jin‐Fen Pan
- Duke University Marine Lab Beaufort NC
- College of Environmental Science Ocean University of China Qingdao China
| | | | | | - James S. Clark
- Environmental Sciences and Policy Duke University Durham NC
- Biology Department Duke University Durham NC
| | - Zackary I. Johnson
- Duke University Marine Lab Beaufort NC
- Biology Department Duke University Durham NC
| | - Dana E. Hunt
- Duke University Marine Lab Beaufort NC
- Biology Department Duke University Durham NC
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29
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Ushio M. Use of a filter cartridge combined with intra‐cartridge bead‐beating improves detection of microbial DNA from water samples. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13204] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Masayuki Ushio
- Hakubi Center, Kyoto University Kyoto Japan
- Center for Ecological Research Kyoto University Otsu Japan
- PRESTO Japan Science and Technology Agency Kawaguchi Japan
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30
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Jing X, Gou H, Gong Y, Ji Y, Su X, Zhang J, Han M, Xu L, Wang T. Seasonal dynamics of the coastal bacterioplankton at intensive fish-farming areas of the Yellow Sea, China revealed by high-throughput sequencing. MARINE POLLUTION BULLETIN 2019; 139:366-375. [PMID: 30686439 DOI: 10.1016/j.marpolbul.2018.12.052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 12/23/2018] [Accepted: 12/30/2018] [Indexed: 06/09/2023]
Abstract
Marine aquaculture areas are facing stressed environmental challenges, especially the degradation of coastal ecosystems. Here a coordinated time-series study was used to investigate the coastal bacterioplankton biodiversity dynamics of the Yellow Sea, China. Bacterial 16S rRNA gene sequencing revealed a temporal pattern of decreasing of diversity in summer. Functional prediction indicated that metabolic pathways related to the adenosine triphosphate (ATP)-binding cassette transporters and other membrane transporters were significantly enriched in May, while the genetic information processing category was most abundant in March. The May microbiomes showed most significant positive correlation with phosphate concentration, while the August and November microbiomes correlated with temperature and chemical oxygen demand (COD) most, and the March microbiomes showed significant correlation with Cu2+ level, pH and salinity. The correlations between representative bacteria and environmental parameters revealed in this study may provide insights into the potential influences of human aquaculture activities, on the biodiversity of coastal bacterioplankton.
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Affiliation(s)
- Xiaoyan Jing
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China; University of Chinese Academy of Sciences, Beijing, China
| | - Honglei Gou
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Yanhai Gong
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Yuetong Ji
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Xiaolu Su
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Jia Zhang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Maozhen Han
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - La Xu
- Shandong Key Laboratory of Disease Control in Mariculture, Marine Biology Institute of Shandong Province, Qingdao, Shandong, China.
| | - Tingting Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.
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31
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Parallel Evolution of Genome Streamlining and Cellular Bioenergetics across the Marine Radiation of a Bacterial Phylum. mBio 2018; 9:mBio.01089-18. [PMID: 30228235 PMCID: PMC6143742 DOI: 10.1128/mbio.01089-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Understanding long-term patterns of microbial evolution is critical to advancing our knowledge of past and present role microbial life in driving global biogeochemical cycles. Historically, it has been challenging to study the evolution of environmental microbes due to difficulties in obtaining genome sequences from lineages that could not be cultivated, but recent advances in metagenomics and single-cell genomics have begun to obviate many of these hurdles. Here we present an evolutionary genomic analysis of the Marinimicrobia, a diverse bacterial group that is abundant in the global ocean. We demonstrate that distantly related Marinimicrobia species that reside in similar habitats have converged to assume similar genome architectures and cellular bioenergetics, suggesting that common factors shape the evolution of a broad array of marine lineages. These findings broaden our understanding of the evolutionary forces that have given rise to microbial life in the contemporary ocean. Diverse bacterial and archaeal lineages drive biogeochemical cycles in the global ocean, but the evolutionary processes that have shaped their genomic properties and physiological capabilities remain obscure. Here we track the genome evolution of the globally abundant marine bacterial phylum Marinimicrobia across its diversification into modern marine environments and demonstrate that extant lineages are partitioned between epipelagic and mesopelagic habitats. Moreover, we show that these habitat preferences are associated with fundamental differences in genomic organization, cellular bioenergetics, and metabolic modalities. Multiple lineages present in epipelagic niches independently acquired genes necessary for phototrophy and environmental stress mitigation, and their genomes convergently evolved key features associated with genome streamlining. In contrast, lineages residing in mesopelagic waters independently acquired nitrate respiratory machinery and a variety of cytochromes, consistent with the use of alternative terminal electron acceptors in oxygen minimum zones (OMZs). Further, while epipelagic clades have retained an ancestral Na+-pumping respiratory complex, mesopelagic lineages have largely replaced this complex with canonical H+-pumping respiratory complex I, potentially due to the increased efficiency of the latter together with the presence of the more energy-limiting environments deep in the ocean’s interior. These parallel evolutionary trends indicate that key features of genomic streamlining and cellular bioenergetics have occurred repeatedly and congruently in disparate clades and underscore the importance of environmental conditions and nutrient dynamics in driving the evolution of diverse bacterioplankton lineages in similar ways throughout the global ocean.
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32
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Jin D, Kong X, Cui B, Jin S, Xie Y, Wang X, Deng Y. Bacterial communities and potential waterborne pathogens within the typical urban surface waters. Sci Rep 2018; 8:13368. [PMID: 30190569 PMCID: PMC6127328 DOI: 10.1038/s41598-018-31706-w] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 05/10/2018] [Indexed: 12/11/2022] Open
Abstract
Waterborne pathogens have attracted a great deal of attention in the public health sector over the last several decades. However, little is known about the pathogenic microorganisms in urban water systems. In this study, the bacterial community structure of 16 typical surface waters in the city of Beijing were analyzed using Illumina MiSeq high-throughput sequencing based on 16S rRNA gene. The results showed that Bacteroidetes, Proteobacteria and Actinobacteria were the dominant groups in 16 surface water samples, and Betaproteobacteria, Alphaproteobacteria, Flavobacteriia, Sphingobacteriia and Actinobacteria were the most dominant classes. The dominant genus across all samples was Flavobacterium. In addition, fifteen genus level groups of potentialy pathogenic bacteria were detected within the 16 water samples, with Pseudomonas and Aeromonas the most frequently identified. Spearman correlation analysis demonstrated that richness estimators (OTUs and Chao1) were correlated with water temperature, nitrate and total nitrogen (p < 0.05), while ammonia-nitrogen and total nitrogen were significantly correlated with the percent of total potential pathogens (p ≤ 0.05). These results could provide insight into the ecological function and health risks of surface water bacterial communities during the process of urbanization.
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Affiliation(s)
- Decai Jin
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China. .,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiao Kong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bingjian Cui
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shulan Jin
- School of History Geography and Tourism, Shangrao Normal University, Shangrao, 334000, China
| | - Yunfeng Xie
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Xingrun Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China. .,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Phoma S, Vikram S, Jansson JK, Ansorge IJ, Cowan DA, Van de Peer Y, Makhalanyane TP. Agulhas Current properties shape microbial community diversity and potential functionality. Sci Rep 2018; 8:10542. [PMID: 30002454 PMCID: PMC6043601 DOI: 10.1038/s41598-018-28939-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 06/28/2018] [Indexed: 11/21/2022] Open
Abstract
Understanding the impact of oceanographic features on marine microbial ecosystems remains a major ecological endeavour. Here we assess microbial diversity, community structure and functional capacity along the Agulhas Current system and the Subtropical Front in the South Indian Ocean (SIO). Samples collected from the epipelagic, oxygen minimum and bathypelagic zones were analysed by 16S rRNA gene amplicon and metagenomic sequencing. In contrast to previous studies, we found high taxonomic richness in surface and deep water samples, but generally low richness for OMZ communities. Beta-diversity analysis revealed significant dissimilarity between the three water depths. Most microbial communities were dominated by marine Gammaproteobacteria, with strikingly low levels of picocyanobacteria. Community composition was strongly influenced by specific environmental factors including depth, salinity, and the availability of both oxygen and light. Carbon, nitrogen and sulfur cycling capacity in the SIO was linked to several autotrophic and copiotrophic Alphaproteobacteria and Gammaproteobacteria. Taken together, our data suggest that the environmental conditions in the Agulhas Current system, particularly depth-related parameters, substantially influence microbial community structure. In addition, the capacity for biogeochemical cycling of nitrogen and sulfur is linked primarily to the dominant Gammaproteobacteria taxa, whereas ecologically rare taxa drive carbon cycling.
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Affiliation(s)
- Sandra Phoma
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2, University of Pretoria, Pretoria, 0028, South Africa
| | - Surendra Vikram
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2, University of Pretoria, Pretoria, 0028, South Africa
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratories, P.O. Box 999, Richland, WA, USA
| | - Isabelle J Ansorge
- Department of Oceanography and Marine Research Institute (Ma-Re), University of Cape Town, Rondebosch, 7701, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2, University of Pretoria, Pretoria, 0028, South Africa
| | - Yves Van de Peer
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2, University of Pretoria, Pretoria, 0028, South Africa
- VIB Centre for Plant Systems Biology, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2, University of Pretoria, Pretoria, 0028, South Africa.
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Vertical and horizontal biogeographic patterns and major factors affecting bacterial communities in the open South China Sea. Sci Rep 2018; 8:8800. [PMID: 29891895 PMCID: PMC5995897 DOI: 10.1038/s41598-018-27191-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/24/2018] [Indexed: 11/15/2022] Open
Abstract
Microorganisms display diverse biogeographic patterns in the three-dimensional contiguous seawater. The distance-decay relationship, the change in species composition similarity between different communities over a geographic distance, is a commonly observed biogeographic pattern. To study biogeographic patterns and the corresponding driving forces, the bacterial distance-decay patterns along the horizontal and vertical dimensions in the South China Sea (SCS) were investigated through the sequencing of partial 16 S rRNA gene regions. Along the horizontal geographical distances (up to ~1000 km), no significant distance-decay pattern in community compositions was observed in any of the tested seawater layers. However, vertical depths (up to ~4 km) had strong effects on bacterial community variation, which was apparently governed by dispersal barriers due to limited water mass mixing. In addition, community variations in the vertical direction were strongly correlated with the prominent variation of environmental factors. Apparently, the changes in bacterial community compositions along vertical distances were much greater than those along horizontal distances. The results showed that the distance-decay relationship in bacterial communities at the medium spatial scale was associated with vertical depth rather than with horizontal distance, even though the horizontal distance is much larger than the vertical distance in the open SCS.
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Abstract
Artificial habitats for animals have high commercial and societal value. Microbial communities (microbiomes) in such habitats may play ecological roles similar to those in nature. However, this hypothesis remains largely untested. Georgia Aquarium's Ocean Voyager (OV) exhibit is a closed-system aquatic habitat that mimics the oligotrophic open ocean and houses thousands of large marine animals, including fish, sea turtles, and whale sharks. We present a 14-month time series characterizing the OV water column microbiome. The composition and stability of the microbiome differed from those of natural marine environments with similar chemical features. The composition shifted dramatically over the span of 2 weeks and was characterized by bloom events featuring members of two heterotrophic bacterial lineages with cosmopolitan distributions in the oceans. The relative abundances of these lineages were inversely correlated, suggesting an overlap in ecological niches. Transcript mapping to metagenome-assembled genomes (MAGs) of these taxa identified unique characteristics, including the presence and activity of genes for the synthesis and degradation of cyanophycin, an amino acid polymer linked to environmental stress and found frequently in cyanobacteria but rarely in heterotrophic bacteria. The dominant MAGs also contained and transcribed plasmid-associated sequences, suggesting a role for conjugation in adaptation to the OV environment. These findings indicate a highly dynamic microbiome despite the stability of the physical and chemical parameters of the water column. Characterizing how such fluctuations affect microbial function may inform our understanding of animal health in closed aquaculture systems. IMPORTANCE Public aquariums play important societal roles, for example, by promoting science education and helping conserve biodiversity. The health of aquarium animals depends on interactions with the surrounding microbiome. However, the extent to which aquariums recreate a stable and natural microbial ecosystem is uncertain. This study describes the taxonomic composition of the water column microbiome over 14 months in a large indoor aquatic habitat, the Ocean Voyager exhibit at the Georgia Aquarium. Despite stable water column conditions, the exhibit experienced blooms in which the abundance of a single bacterial strain increased to over 65% of the community. Genome analysis indicated that the OV's dominant strains share unique adaptations, notably genes for storage polymers associated with environmental stress. These results, interpreted alongside data from natural ocean systems and another artificial seawater aquarium, suggest a highly dynamic aquarium microbiome and raise questions of how microbiome stability may affect the ecological health of the habitat.
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Olson DK, Yoshizawa S, Boeuf D, Iwasaki W, DeLong EF. Proteorhodopsin variability and distribution in the North Pacific Subtropical Gyre. ISME JOURNAL 2018; 12:1047-1060. [PMID: 29476140 PMCID: PMC5864233 DOI: 10.1038/s41396-018-0074-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/21/2017] [Accepted: 12/05/2017] [Indexed: 11/17/2022]
Abstract
Proteorhodopsin is a light-activated retinal-containing proton pump found in many marine bacteria. These photoproteins are globally distributed in the ocean’s photic zone and are capable of generating a proton motive force across the cell membrane. We investigated the phylogenetic diversity, distribution, and abundance of proteorhodopsin encoding genes in free-living bacterioplankton in the North Pacific Subtropical Gyre, leveraging a gene catalog derived from metagenomic samples from the ocean’s surface to 1000 m depth. Proteorhodopsin genes were identified at all depths sampled, but were most abundant at depths shallower than 200 m. The majority of proteorhodopsin gene sequences (60.9%) belonged to members of the SAR11 lineage, with remaining sequences distributed among other diverse taxa. We observed variations in the conserved residues involved in ion pumping and spectral tuning, and biochemically confirmed four different proton pumping proteorhodopsin motifs, including one unique to deep-water SAR11. We also identified a new group of putative proteorhodopsins having unknown function. Our results reveal a broad organismal and unexpected depth distribution for different proteorhodopsin types, as well as substantial within-taxon variability. These data provide a framework for exploring the ecological relevance of proteorhodopsins and their spatiotemporal variation and function in heterotrophic bacteria in the open ocean.
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Affiliation(s)
- Daniel K Olson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography, University of Hawaii, Honolulu, HI, 96822, USA
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan
| | - Dominique Boeuf
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography, University of Hawaii, Honolulu, HI, 96822, USA
| | - Wataru Iwasaki
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography, University of Hawaii, Honolulu, HI, 96822, USA.
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Abstract
Bacteriophages are numerically the most abundant DNA-containing entities in the oligotrophic ocean, yet how specific phage populations vary over time and space remains to be fully explored. Here, we conducted a metagenomic time-series survey of double-stranded DNA phages throughout the water column in the North Pacific Subtropical Gyre, encompassing 1.5 years from depths of 25 to 1,000 m. Viral gene sequences were identified in assembled metagenomic samples, yielding an estimated 172,385 different viral gene families. Viral marker gene distributions suggested that lysogeny was more prevalent at mesopelagic depths than in surface waters, consistent with prior prophage induction studies using mitomycin C. A total of 129 ALOHA viral genomes and genome fragments from 20 to 108 kbp were selected for further study, which represented the most abundant phages in the water column. Phage genotypes displayed discrete population structures. Most phages persisted throughout the time-series and displayed a strong depth structure that mirrored the stratified depth distributions of co-occurring bacterial taxa in the water column. Mesopelagic phages were distinct from surface water phages with respect to diversity, gene content, putative life histories, and temporal persistence, reflecting depth-dependent differences in host genomic architectures and phage reproductive strategies. The spatiotemporal distributions of the most abundant open-ocean bacteriophages that we report here provide new insight into viral temporal persistence, life history, and virus-host-environment interactions throughout the open-ocean water column. The North Pacific Subtropical Gyre represents one of the largest biomes on the planet, where microbial communities are central mediators of ecosystem dynamics and global biogeochemical cycles. Critical members of these communities are the viruses of marine bacteria, which can alter microbial metabolism and significantly influence their survival and productivity. To better understand these viral assemblages, we conducted genomic analyses of planktonic viruses over a seasonal cycle to ocean depths of 1,000 m. We identified 172,385 different viral gene families and 129 unique virus genotypes in this open-ocean setting. The spatiotemporal distributions of the most abundant open-ocean viruses that we report here provide new insights into viral temporal variability, life history, and virus-host-environment interactions throughout the water column.
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Xia X, Guo W, Liu H. Basin Scale Variation on the Composition and Diversity of Archaea in the Pacific Ocean. Front Microbiol 2017; 8:2057. [PMID: 29109713 PMCID: PMC5660102 DOI: 10.3389/fmicb.2017.02057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 10/06/2017] [Indexed: 01/09/2023] Open
Abstract
The Archaea are a widely distributed group of prokaryotes that inhabit and thrive in many different environments. In the sea, they play key roles in various global biogeochemical processes. Here, in order to investigate the vertical profiles of archaeal community across a large geographic distance, the compositions of archaeal communities in seven seawater columns in the Pacific Ocean were investigated using high throughput 454 pyrosequencing of the 16S rRNA gene. The surface archaeal communities showed lower diversity and greater variability than those in the deeper layers. Two of the major archaeal phyla that displayed different depth preferences were Thaumarchaeota and Euryarchaeota. The majority of Thaumarchaeota belonged to Marine Group I (MGI), which had high relative abundance in deep water. In contrast, Euryarchaeota, which mainly consisted of Marine Group II (MGII) and III (MGIII), were dominant in the surface layer. Compared with MGI and MGII, MGIII were less abundant in seawater and generally absent from the surface water of the subarctic Pacific. In addition, niche separation in the MGI, MGII, and MGIII subgroups was also observed. For example, MGI.C and MGII.A (the major subgroups of MGI and MGII, respectively) displayed a strong negative correlation with each other. The highest level of archaeal diversity was found in the core of an oxygen minimum zone (OMZ) located off Costa Rica, which resulted from the co-occurrence of both anaerobic and aerobic archaea. For example, methanotrophic archaea ANME-2, methanogenic archaea and several sediment origin archaea, such as Marine Benthic Group A (MBGA) and Bathyarchaeota, were all detected at relatively high abundance in the OMZ. Together, our findings indicate that vertical heterogeneities along water columns and latitudinal differentiation in the surface waters are ubiquitous features of archaeal communities in the Pacific Ocean, and the OMZ off Costa Rica is an archaeal biodiversity hot-spot.
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Affiliation(s)
| | | | - Hongbin Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, Hong Kong
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39
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Abstract
Marine microbial communities exert a large influence on ocean ecosystem processes, and viruses in these communities play key roles in controlling microbial abundances, nutrient cycling, and productivity. We show here that dominant viruses in the open ocean persist for long time periods and that many appear tightly locked in coordinated diel oscillations with their bacterial hosts. The persistent structure of viral assemblages, as well as synchronized daily oscillations of viruses and hosts, are in part the result of the regular diurnal coupling of viral and host replication cycles. Collectively, our results suggest that viruses, as key components of marine ecosystems, are intrinsically synchronized with the daily rhythms of microbial community processes in the ocean’s photic zone. Viruses are fundamental components of marine microbial communities that significantly influence oceanic productivity, biogeochemistry, and ecosystem processes. Despite their importance, the temporal activities and dynamics of viral assemblages in natural settings remain largely unexplored. Here we report the transcriptional activities and variability of dominant dsDNA viruses in the open ocean’s euphotic zone over daily and seasonal timescales. While dsDNA viruses exhibited some fluctuation in abundance in both cellular and viral size fractions, the viral assemblage was remarkably stable, with the most abundant viral types persisting over many days. More extended time series indicated that long-term persistence (>1 y) was the rule for most dsDNA viruses observed, suggesting that both core viral genomes as well as viral community structure were conserved over interannual periods. Viral gene transcription in host cell assemblages revealed diel cycling among many different viral types. Most notably, an afternoon peak in cyanophage transcriptional activity coincided with a peak in Prochlorococcus DNA replication, indicating coordinated diurnal coupling of virus and host reproduction. In aggregate, our analyses suggested a tightly synchronized diel coupling of viral and cellular replication cycles in both photoautotrophic and heterotrophic bacterial hosts. A surprising consequence of these findings is that diel cycles in the ocean’s photic zone appear to be universal organizing principles that shape ecosystem dynamics, ecological interactions, and biogeochemical cycling of both cellular and acellular community components.
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Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment. Sci Rep 2017; 7:12240. [PMID: 28947818 PMCID: PMC5612959 DOI: 10.1038/s41598-017-12501-5] [Citation(s) in RCA: 173] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/11/2017] [Indexed: 11/08/2022] Open
Abstract
Effective marine management requires comprehensive data on the status of marine biodiversity. However, efficient methods that can document biodiversity in our oceans are currently lacking. Environmental DNA (eDNA) sourced from seawater offers a new avenue for investigating the biota in marine ecosystems. Here, we investigated the potential of eDNA to inform on the breadth of biodiversity present in a tropical marine environment. Directly sequencing eDNA from seawater using a shotgun approach resulted in only 0.34% of 22.3 million reads assigning to eukaryotes, highlighting the inefficiency of this method for assessing eukaryotic diversity. In contrast, using 'tree of life' (ToL) metabarcoding and 20-fold fewer sequencing reads, we could detect 287 families across the major divisions of eukaryotes. Our data also show that the best performing 'universal' PCR assay recovered only 44% of the eukaryotes identified across all assays, highlighting the need for multiple metabarcoding assays to catalogue biodiversity. Lastly, focusing on the fish genus Lethrinus, we recovered intra- and inter-specific haplotypes from seawater samples, illustrating that eDNA can be used to explore diversity beyond taxon identifications. Given the sensitivity and low cost of eDNA metabarcoding we advocate this approach be rapidly integrated into biomonitoring programs.
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41
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Environmental drivers of a microbial genomic transition zone in the ocean's interior. Nat Microbiol 2017; 2:1367-1373. [PMID: 28808230 DOI: 10.1038/s41564-017-0008-3] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 07/04/2017] [Indexed: 01/01/2023]
Abstract
The core properties of microbial genomes, including GC content and genome size, are known to vary widely among different bacteria and archaea 1,2 . Several hypotheses have been proposed to explain this genomic variability, but the fundamental drivers that shape bacterial and archaeal genomic properties remain uncertain 3-7 . Here, we report the existence of a sharp genomic transition zone below the photic zone, where bacterial and archaeal genomes and proteomes undergo a community-wide punctuated shift. Across a narrow range of increasing depth of just tens of metres, diverse microbial clades trend towards larger genome size, higher genomic GC content, and proteins with higher nitrogen but lower carbon content. These community-wide changes in genome features appear to be driven by gradients in the surrounding environmental energy and nutrient fields. Collectively, our data support hypotheses invoking nutrient limitation as a central driver in the evolution of core bacterial and archaeal genomic and proteomic properties.
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Goldberg SJ, Nelson CE, Viviani DA, Shulse CN, Church MJ. Cascading influence of inorganic nitrogen sources on DOM production, composition, lability and microbial community structure in the open ocean. Environ Microbiol 2017; 19:3450-3464. [PMID: 28618153 DOI: 10.1111/1462-2920.13825] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 05/26/2017] [Accepted: 05/29/2017] [Indexed: 12/22/2022]
Abstract
Nitrogen frequently limits oceanic photosynthesis and the availability of inorganic nitrogen sources in the surface oceans is shifting with global change. We evaluated the potential for abrupt increases in inorganic N sources to induce cascading effects on dissolved organic matter (DOM) and microbial communities in the surface ocean. We collected water from 5 m depth in the central North Pacific and amended duplicate 20 liter polycarbonate carboys with nitrate or ammonium, tracking planktonic carbon fixation, DOM production, DOM composition and microbial community structure responses over 1 week relative to controls. Both nitrogen sources stimulated bulk phytoplankton, bacterial and DOM production and enriched Synechococcus and Flavobacteriaceae; ammonium enriched for oligotrophic Actinobacteria OM1 and Gammaproteobacteria KI89A clades while nitrate enriched Gammaproteobacteria SAR86, SAR92 and OM60 clades. DOM resulting from both N enrichments was more labile and stimulated growth of copiotrophic Gammaproteobacteria (Alteromonadaceae and Oceanospirillaceae) and Alphaproteobacteria (Rhodobacteraceae and Hyphomonadaceae) in weeklong dark incubations relative to controls. Our study illustrates how nitrogen pulses may have direct and cascading effects on DOM composition and microbial community dynamics in the open ocean.
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Affiliation(s)
- S J Goldberg
- Center for Microbial Oceanography: Research and Education, Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, 1950 East West Road, Honolulu, HI 96822, USA
| | - C E Nelson
- Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, 1950 East West Road, Honolulu, HI 96822, USA
| | - D A Viviani
- Center for Microbial Oceanography: Research and Education, Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, 1950 East West Road, Honolulu, HI 96822, USA
| | - C N Shulse
- Center for Microbial Oceanography: Research and Education, Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, 1950 East West Road, Honolulu, HI 96822, USA
| | - M J Church
- Center for Microbial Oceanography: Research and Education, Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, 1950 East West Road, Honolulu, HI 96822, USA
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43
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Marine Bacterioplankton Seasonal Succession Dynamics. Trends Microbiol 2017; 25:494-505. [DOI: 10.1016/j.tim.2016.12.013] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/13/2016] [Accepted: 12/21/2016] [Indexed: 01/08/2023]
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Fundamental differences in diversity and genomic population structure between Atlantic and Pacific Prochlorococcus. ISME JOURNAL 2017; 11:1997-2011. [PMID: 28524867 DOI: 10.1038/ismej.2017.64] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 03/09/2017] [Accepted: 03/17/2017] [Indexed: 01/09/2023]
Abstract
The Atlantic and Pacific Oceans represent different biogeochemical regimes in which the abundant marine cyanobacterium Prochlorococcus thrives. We have shown that Prochlorococcus populations in the Atlantic are composed of hundreds of genomically, and likely ecologically, distinct coexisting subpopulations with distinct genomic backbones. Here we ask if differences in the ecology and selection pressures between the Atlantic and Pacific are reflected in the diversity and genomic composition of their indigenous Prochlorococcus populations. We applied large-scale single-cell genomics and compared the cell-by-cell genomic composition of wild populations of co-occurring cells from samples from Station ALOHA off Hawaii, and from Bermuda Atlantic Time Series Station off Bermuda. We reveal fundamental differences in diversity and genomic structure of populations between the sites. The Pacific populations are more diverse than those in the Atlantic, composed of significantly more coexisting subpopulations and lacking dominant subpopulations. Prochlorococcus from the two sites seem to be composed of mostly non-overlapping distinct sets of subpopulations with different genomic backbones-likely reflecting different sets of ocean-specific micro-niches. Furthermore, phylogenetically closely related strains carry ocean-associated nutrient acquisition genes likely reflecting differences in major selection pressures between the oceans. This differential selection, along with geographic separation, clearly has a significant role in shaping these populations.
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Mackey KRM, Post AF, McIlvin MR, Saito MA. Physiological and proteomic characterization of light adaptations in marine Synechococcus. Environ Microbiol 2017; 19:2348-2365. [PMID: 28371229 DOI: 10.1111/1462-2920.13744] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 03/23/2017] [Accepted: 03/24/2017] [Indexed: 10/19/2022]
Abstract
Marine Synechococcus thrive over a range of light regimes in the ocean. We examined the proteomic, genomic and physiological responses of seven Synechococcus isolates to moderate irradiances (5-80 μE m-2 s-1 ), and show that Synechococcus spans a continuum of light responses ranging from low light optimized (LLO) to high light optimized (HLO). These light responses are linked to phylogeny and pigmentation. Marine sub-cluster 5.1A isolates with higher phycouribilin: phycoerythrobilin ratios fell toward the LLO end of the continuum, while sub-cluster 5.1B, 5.2 and estuarine Synechococcus with less phycouribilin fell toward the HLO end of the continuum. Global proteomes were highly responsive to light, with > 50% of abundant proteins varying more than twofold between the lowest and highest irradiance. All strains downregulated phycobilisome proteins with increasing irradiance. Regulation of proteins involved in photosynthetic electron transport, carbon fixation, oxidative stress protection (superoxide dismutases) and iron and nitrogen metabolism varied among strains, as did the number of high light inducible protein (Hlip) and DNA photolyase genes in their genomes. All but one LLO strain possessed the photoprotective orange carotenoid protein (OCP). The unique combinations of light responses in each strain gives rise to distinct photophysiological phenotypes that may affect Synechococcus distributions in the ocean.
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Affiliation(s)
| | - Anton F Post
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, 02882, USA
| | - Matthew R McIlvin
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02536, USA
| | - Mak A Saito
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02536, USA
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46
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Haro-Moreno JM, Rodriguez-Valera F, López-García P, Moreira D, Martin-Cuadrado AB. New insights into marine group III Euryarchaeota, from dark to light. ISME JOURNAL 2017; 11:1102-1117. [PMID: 28085158 DOI: 10.1038/ismej.2016.188] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 11/25/2016] [Accepted: 12/05/2016] [Indexed: 01/29/2023]
Abstract
Marine Euryarchaeota remain among the least understood major components of marine microbial communities. Marine group II Euryarchaeota (MG-II) are more abundant in surface waters (4-20% of the total prokaryotic community), whereas marine group III Euryarchaeota (MG-III) are generally considered low-abundance members of deep mesopelagic and bathypelagic communities. Using genome assembly from direct metagenome reads and metagenomic fosmid clones, we have identified six novel MG-III genome sequence bins from the photic zone (Epi1-6) and two novel bins from deep-sea samples (Bathy1-2). Genome completeness in those genome bins varies from 44% to 85%. Photic-zone MG-III bins corresponded to novel groups with no similarity, and significantly lower GC content, when compared with previously described deep-MG-III genome bins. As found in many other epipelagic microorganisms, photic-zone MG-III bins contained numerous photolyase and rhodopsin genes, as well as genes for peptide and lipid uptake and degradation, suggesting a photoheterotrophic lifestyle. Phylogenetic analysis of these photolyases and rhodopsins as well as their genomic context suggests that these genes are of bacterial origin, supporting the hypothesis of an MG-III ancestor that lived in the dark ocean. Epipelagic MG-III occur sporadically and in relatively small proportions in marine plankton, representing only up to 0.6% of the total microbial community reads in metagenomes. None of the reconstructed epipelagic MG-III genomes were present in metagenomes from aphotic zone depths or from high latitude regions. Most low-GC bins were highly enriched at the deep chlorophyll maximum zones, with the exception of Epi1, which appeared evenly distributed throughout the photic zone worldwide.
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Affiliation(s)
- Jose M Haro-Moreno
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Purificación López-García
- Unité d'Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Orsay Cedex, France
| | - David Moreira
- Unité d'Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Orsay Cedex, France
| | - Ana-Belen Martin-Cuadrado
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
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Diversity and Activity of Communities Inhabiting Plastic Debris in the North Pacific Gyre. mSystems 2016; 1:mSystems00024-16. [PMID: 27822538 PMCID: PMC5069773 DOI: 10.1128/msystems.00024-16] [Citation(s) in RCA: 238] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 04/12/2016] [Indexed: 01/08/2023] Open
Abstract
Marine plastic debris has become a significant concern in ocean ecosystems worldwide. Little is known, however, about its influence on microbial community structure and function. In 2008, we surveyed microbial communities and metabolic activities in seawater and on plastic on an oceanographic expedition through the "great Pacific garbage patch." The concentration of plastic particles in surface seawater within different size classes (2 to 5 mm and >5 mm) ranged from 0.35 to 3.7 particles m-3 across sampling stations. These densities and the particle size distribution were consistent with previous values reported in the North Pacific Ocean. Net community oxygen production (NCP = gross primary production - community respiration) on plastic debris was positive and so net autotrophic, whereas NCP in bulk seawater was close to zero. Scanning electron microscopy and metagenomic sequencing of plastic-attached communities revealed the dominance of a few metazoan taxa and a diverse assemblage of photoautotrophic and heterotrophic protists and bacteria. Bryozoa, Cyanobacteria, Alphaproteobacteria, and Bacteroidetes dominated all plastic particles, regardless of particle size. Bacteria inhabiting plastic were taxonomically distinct from the surrounding picoplankton and appeared well adapted to a surface-associated lifestyle. Genes with significantly higher abundances among plastic-attached bacteria included che genes, secretion system genes, and nifH genes, suggesting enrichment for chemotaxis, frequent cell-to-cell interactions, and nitrogen fixation. In aggregate, our findings suggest that plastic debris forms a habitat for complex microbial assemblages that have lifestyles, metabolic pathways, and biogeochemical activities that are distinct from those of free-living planktonic microbial communities. IMPORTANCE Marine plastic debris is a growing concern that has captured the general public's attention. While the negative impacts of plastic debris on oceanic macrobiota, including mammals and birds, are well documented, little is known about its influence on smaller marine residents, including microbes that have key roles in ocean biogeochemistry. Our work provides a new perspective on microbial communities inhabiting microplastics that includes its effect on microbial biogeochemical activities and a description of the cross-domain communities inhabiting plastic particles. This study is among the first molecular ecology, plastic debris biota surveys in the North Pacific Subtropical Gyre. It has identified fundamental differences in the functional potential and taxonomic composition of plastic-associated microbes versus planktonic microbes found in the surrounding open-ocean habitat. Author Video: An author video summary of this article is available.
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Milici M, Deng ZL, Tomasch J, Decelle J, Wos-Oxley ML, Wang H, Jáuregui R, Plumeier I, Giebel HA, Badewien TH, Wurst M, Pieper DH, Simon M, Wagner-Döbler I. Co-occurrence Analysis of Microbial Taxa in the Atlantic Ocean Reveals High Connectivity in the Free-Living Bacterioplankton. Front Microbiol 2016; 7:649. [PMID: 27199970 PMCID: PMC4858663 DOI: 10.3389/fmicb.2016.00649] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/18/2016] [Indexed: 12/04/2022] Open
Abstract
We determined the taxonomic composition of the bacterioplankton of the epipelagic zone of the Atlantic Ocean along a latitudinal transect (51°S–47°N) using Illumina sequencing of the V5-V6 region of the 16S rRNA gene and inferred co-occurrence networks. Bacterioplankon community composition was distinct for Longhurstian provinces and water depth. Free-living microbial communities (between 0.22 and 3 μm) were dominated by highly abundant and ubiquitous taxa with streamlined genomes (e.g., SAR11, SAR86, OM1, Prochlorococcus) and could clearly be separated from particle-associated communities which were dominated by Bacteroidetes, Planktomycetes, Verrucomicrobia, and Roseobacters. From a total of 369 different communities we then inferred co-occurrence networks for each size fraction and depth layer of the plankton between bacteria and between bacteria and phototrophic micro-eukaryotes. The inferred networks showed a reduction of edges in the deepest layer of the photic zone. Networks comprised of free-living bacteria had a larger amount of connections per OTU when compared to the particle associated communities throughout the water column. Negative correlations accounted for roughly one third of the total edges in the free-living communities at all depths, while they decreased with depth in the particle associated communities where they amounted for roughly 10% of the total in the last part of the epipelagic zone. Co-occurrence networks of bacteria with phototrophic micro-eukaryotes were not taxon-specific, and dominated by mutual exclusion (~60%). The data show a high degree of specialization to micro-environments in the water column and highlight the importance of interdependencies particularly between free-living bacteria in the upper layers of the epipelagic zone.
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Affiliation(s)
- Mathias Milici
- Group Microbial Communication, Helmholtz-Center for Infection Research Braunschweig, Germany
| | - Zhi-Luo Deng
- Group Microbial Communication, Helmholtz-Center for Infection Research Braunschweig, Germany
| | - Jürgen Tomasch
- Group Microbial Communication, Helmholtz-Center for Infection Research Braunschweig, Germany
| | - Johan Decelle
- UMR 7144 - Sorbonne Universités, UPMC Univ Paris 06Roscoff, France; Centre National de la Recherche Scientifique, UMR 7144Roscoff, France
| | - Melissa L Wos-Oxley
- Group Microbial Interactions and Processes, Helmholtz-Center for Infection Research Braunschweig, Germany
| | - Hui Wang
- Group Microbial Communication, Helmholtz-Center for Infection Research Braunschweig, Germany
| | - Ruy Jáuregui
- Group Microbial Interactions and Processes, Helmholtz-Center for Infection Research Braunschweig, Germany
| | - Iris Plumeier
- Group Microbial Interactions and Processes, Helmholtz-Center for Infection Research Braunschweig, Germany
| | - Helge-Ansgar Giebel
- Biology of Geological Processes, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg Oldenburg, Germany
| | - Thomas H Badewien
- Biology of Geological Processes, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg Oldenburg, Germany
| | - Mascha Wurst
- Biology of Geological Processes, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg Oldenburg, Germany
| | - Dietmar H Pieper
- Group Microbial Interactions and Processes, Helmholtz-Center for Infection Research Braunschweig, Germany
| | - Meinhard Simon
- Biology of Geological Processes, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg Oldenburg, Germany
| | - Irene Wagner-Döbler
- Group Microbial Communication, Helmholtz-Center for Infection Research Braunschweig, Germany
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