1
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Chen J, Jia Y, Sun Y, Liu K, Zhou C, Liu C, Li D, Liu G, Zhang C, Yang T, Huang L, Zhuang Y, Wang D, Xu D, Zhong Q, Guo Y, Li A, Seim I, Jiang L, Wang L, Lee SMY, Liu Y, Wang D, Zhang G, Liu S, Wei X, Yue Z, Zheng S, Shen X, Wang S, Qi C, Chen J, Ye C, Zhao F, Wang J, Fan J, Li B, Sun J, Jia X, Xia Z, Zhang H, Liu J, Zheng Y, Liu X, Wang J, Yang H, Kristiansen K, Xu X, Mock T, Li S, Zhang W, Fan G. Global marine microbial diversity and its potential in bioprospecting. Nature 2024:10.1038/s41586-024-07891-2. [PMID: 39232160 DOI: 10.1038/s41586-024-07891-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 07/31/2024] [Indexed: 09/06/2024]
Abstract
The past two decades has witnessed a remarkable increase in the number of microbial genomes retrieved from marine systems1,2. However, it has remained challenging to translate this marine genomic diversity into biotechnological and biomedical applications3,4. Here we recovered 43,191 bacterial and archaeal genomes from publicly available marine metagenomes, encompassing a wide range of diversity with 138 distinct phyla, redefining the upper limit of marine bacterial genome size and revealing complex trade-offs between the occurrence of CRISPR-Cas systems and antibiotic resistance genes. In silico bioprospecting of these marine genomes led to the discovery of a novel CRISPR-Cas9 system, ten antimicrobial peptides, and three enzymes that degrade polyethylene terephthalate. In vitro experiments confirmed their effectiveness and efficacy. This work provides evidence that global-scale sequencing initiatives advance our understanding of how microbial diversity has evolved in the oceans and is maintained, and demonstrates how such initiatives can be sustainably exploited to advance biotechnology and biomedicine.
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Affiliation(s)
- Jianwei Chen
- BGI Research, Qingdao, China
- BGI Research, Shenzhen, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Ying Sun
- BGI Research, Qingdao, China.
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China.
| | - Kun Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | | | - Chuan Liu
- BGI Research, Shenzhen, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Chengsong Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Tao Yang
- China National GeneBank, BGI Research, Shenzhen, China
- Guangdong Genomics Data Center, BGI Research, Shenzhen, China
| | | | - Yunyun Zhuang
- Key Laboratory of Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Dazhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | | | | | - Yang Guo
- BGI Research, Qingdao, China
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | | | - Inge Seim
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Simon Ming Yuen Lee
- Department of Food Science and Nutrition, and PolyU-BGI Joint Research Centre for Genomics and Synthetic Biology in Global Deep Ocean Resource, The Hong Kong Polytechnic University, Hong Kong, China
| | - Yujing Liu
- BGI Research, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
| | | | - Guoqiang Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | | | - Xiaofeng Wei
- China National GeneBank, BGI Research, Shenzhen, China
- Guangdong Genomics Data Center, BGI Research, Shenzhen, China
| | | | - Shanmin Zheng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | | | - Sen Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Chen Qi
- BGI Research, Shenzhen, China
| | - Jing Chen
- Guangdong Genomics Data Center, BGI Research, Shenzhen, China
| | - Chen Ye
- BGI Research, Shenzhen, China
| | | | | | - Jie Fan
- BGI Research, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
| | | | | | - Xiaodong Jia
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, China
| | - Zhangyong Xia
- Department of Neurology, The Second People's Hospital of Liaocheng, Liaocheng, China
| | - He Zhang
- BGI Research, Qingdao, China
- BGI Research, Shenzhen, China
| | | | | | - Xin Liu
- BGI Research, Qingdao, China
- BGI Research, Shenzhen, China
| | | | | | - Karsten Kristiansen
- BGI Research, Shenzhen, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xun Xu
- BGI Research, Qingdao, China
- BGI Research, Shenzhen, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
| | - Wenwei Zhang
- BGI Research, Shenzhen, China.
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China.
| | - Guangyi Fan
- BGI Research, Qingdao, China.
- BGI Research, Shenzhen, China.
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China.
- Department of Food Science and Nutrition, and PolyU-BGI Joint Research Centre for Genomics and Synthetic Biology in Global Deep Ocean Resource, The Hong Kong Polytechnic University, Hong Kong, China.
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China.
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2
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Stephens BM, Durkin CA, Sharpe G, Nguyen TTH, Albers J, Estapa ML, Steinberg DK, Levine NM, Gifford SM, Carlson CA, Boyd PW, Santoro AE. Direct observations of microbial community succession on sinking marine particles. THE ISME JOURNAL 2024; 18:wrad010. [PMID: 38365233 PMCID: PMC10811735 DOI: 10.1093/ismejo/wrad010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 11/10/2023] [Accepted: 11/15/2023] [Indexed: 02/18/2024]
Abstract
Microbial community dynamics on sinking particles control the amount of carbon that reaches the deep ocean and the length of time that carbon is stored, with potentially profound impacts on Earth's climate. A mechanistic understanding of the controls on sinking particle distributions has been hindered by limited depth- and time-resolved sampling and methods that cannot distinguish individual particles. Here, we analyze microbial communities on nearly 400 individual sinking particles in conjunction with more conventional composite particle samples to determine how particle colonization and community assembly might control carbon sequestration in the deep ocean. We observed community succession with corresponding changes in microbial metabolic potential on the larger sinking particles transporting a significant fraction of carbon to the deep sea. Microbial community richness decreased as particles aged and sank; however, richness increased with particle size and the attenuation of carbon export. This suggests that the theory of island biogeography applies to sinking marine particles. Changes in POC flux attenuation with time and microbial community composition with depth were reproduced in a mechanistic ecosystem model that reflected a range of POC labilities and microbial growth rates. Our results highlight microbial community dynamics and processes on individual sinking particles, the isolation of which is necessary to improve mechanistic models of ocean carbon uptake.
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Affiliation(s)
- Brandon M Stephens
- Department of Ecology, Evolution and Marine Biology, Marine Science Institute, University of California, Santa Barbara, CA 93106, United States
- Present address: Institute of Oceanography, National Taiwan University, Taipei 106, Taiwan
| | - Colleen A Durkin
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, United States
| | - Garrett Sharpe
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Trang T H Nguyen
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, United States
- Department of Integrated Sciences, Fulbright University Vietnam, Ho Chi Minh City 756000, Vietnam
| | - Justine Albers
- Department of Ecology, Evolution and Marine Biology, Marine Science Institute, University of California, Santa Barbara, CA 93106, United States
| | - Margaret L Estapa
- School of Marine Sciences, Darling Marine Center, University of Maine, Walpole, ME 04573, United States
| | - Deborah K Steinberg
- Coastal & Ocean Processes Section, Virginia Institute of Marine Science, William & Mary, Gloucester Point, VA 23062, United States
| | - Naomi M Levine
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, United States
| | - Scott M Gifford
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Craig A Carlson
- Department of Ecology, Evolution and Marine Biology, Marine Science Institute, University of California, Santa Barbara, CA 93106, United States
| | - Philip W Boyd
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Alyson E Santoro
- Department of Ecology, Evolution and Marine Biology, Marine Science Institute, University of California, Santa Barbara, CA 93106, United States
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3
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Deutschmann IM, Delage E, Giner CR, Sebastián M, Poulain J, Arístegui J, Duarte CM, Acinas SG, Massana R, Gasol JM, Eveillard D, Chaffron S, Logares R. Disentangling microbial networks across pelagic zones in the tropical and subtropical global ocean. Nat Commun 2024; 15:126. [PMID: 38168083 PMCID: PMC10762198 DOI: 10.1038/s41467-023-44550-y] [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: 04/10/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
Microbial interactions are vital in maintaining ocean ecosystem function, yet their dynamic nature and complexity remain largely unexplored. Here, we use association networks to investigate possible ecological interactions in the marine microbiome among archaea, bacteria, and picoeukaryotes throughout different depths and geographical regions of the tropical and subtropical global ocean. Our findings reveal that potential microbial interactions change with depth and geographical scale, exhibiting highly heterogeneous distributions. A few potential interactions were global, meaning they occurred across regions at the same depth, while 11-36% were regional within specific depths. The bathypelagic zone had the lowest proportion of global associations, and regional associations increased with depth. Moreover, we observed that most surface water associations do not persist in deeper ocean layers despite microbial vertical dispersal. Our work contributes to a deeper understanding of the tropical and subtropical global ocean interactome, which is essential for addressing the challenges posed by global change.
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Affiliation(s)
| | - Erwan Delage
- Nantes Université, CNRS UMR 6004, LS2N, F-44000, Nantes, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | | | | | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Javier Arístegui
- Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, ULPGC, Gran Canaria, Spain
| | - Carlos M Duarte
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal, Saudi Arabia
| | | | - Ramon Massana
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Josep M Gasol
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Damien Eveillard
- Nantes Université, CNRS UMR 6004, LS2N, F-44000, Nantes, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Samuel Chaffron
- Nantes Université, CNRS UMR 6004, LS2N, F-44000, Nantes, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain.
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4
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Liu S, Hu R, Strong PJ, Saleem M, Zhou Z, Luo Z, Wu Y, He Z, Wang C. Vertical connectivity of microbiome and metabolome reveals depth-dependent variations across a deep cold-seep water column. ENVIRONMENTAL RESEARCH 2023; 239:117310. [PMID: 37805181 DOI: 10.1016/j.envres.2023.117310] [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: 07/31/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
Deciphering the vertical connectivity of oceanic microbiome and metabolome is crucial for understanding the carbon sequestration and achieving the carbon neutrality. However, we lack a systematic view of the interplay among particle transport, microbial community, and metabolic trait across depths. Through integrating the biogeochemical, microbial, and metabolic characteristics of a deep cold-seep water column (∼1989 m), we find the altered connectivity of microbial community and dissolved organic matter (DOM) across depths. Both the microbial communities (bacteria and protists) and DOM show a clear compositional connectivity from surface to the depth of 1000 m, highlighting the controls of sinking particle over microbial connectivity from the epipelagic to mesopelagic zone. However, due to the biological migration and ocean mixing, the fecal-associated bacteria and protistan consumers unexpectedly emerge and the degradation index of DOM substantially alters around 1000-1200 m. Collectively, we unveil the significance of multi-faceted particle dispersion, which supports the connectivity and variability of deep ocean microbial communities.
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Affiliation(s)
- Songfeng Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - P J Strong
- School of Biology and Environmental Science, Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4001, Australia
| | - Muhammad Saleem
- Department of Biological Sciences, Alabama State University, Montgomery, AL, 36104, USA
| | - Zhengyuan Zhou
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhiwen Luo
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Yongjie Wu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, 510530, PR China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China.
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5
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Lee SH, Secchi E, Kang PK. Rapid formation of bioaggregates and morphology transition to biofilm streamers induced by pore-throat flows. Proc Natl Acad Sci U S A 2023; 120:e2204466120. [PMID: 36989304 PMCID: PMC10083537 DOI: 10.1073/pnas.2204466120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 02/28/2023] [Indexed: 03/30/2023] Open
Abstract
Bioaggregates are condensed porous materials comprising microbes, organic and inorganic matters, and water. They are commonly found in natural and engineered porous media and often cause clogging. Despite their importance, the formation mechanism of bioaggregates in porous media systems is largely unknown. Through microfluidic experiments and direct numerical simulations of fluid flow, we show that the rapid bioaggregation is driven by the interplay of the viscoelastic nature of biomass and hydrodynamic conditions at pore throats. At an early stage, unique flow structures around a pore throat promote the biomass attachment at the throat. Then, the attached biomass fluidizes when the shear stress at the partially clogged pore throat reaches a critical value. After the fluidization, the biomass is displaced and accumulated in the expansion region of throats forming bioaggregates. We further find that such criticality in shear stress triggers morphological changes in bioaggregates from rounded- to streamer-like shapes. This knowledge was used to control the clogging of throats by tuning the flow conditions: When the shear stress at the throat exceeded the critical value, clogging was prevented. The bioaggregation process did not depend on the detailed pore-throat geometry, as we reproduced the same dynamics in various pore-throat geometries. This study demonstrates that pore-throat structures, which are ubiquitous in porous media systems, induce bioaggregation and can lead to abrupt disruptions in flow.
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Affiliation(s)
- Sang Hyun Lee
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN55455
| | - Eleonora Secchi
- Institute of Environmental Engineering, ETH Zürich, Zürich8093, Switzerland
| | - Peter K. Kang
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN55455
- Saint Anthony Falls Laboratory, University of Minnesota, Minneapolis, MN55455
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6
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Geller-McGrath D, Mara P, Taylor GT, Suter E, Edgcomb V, Pachiadaki M. Diverse secondary metabolites are expressed in particle-associated and free-living microorganisms of the permanently anoxic Cariaco Basin. Nat Commun 2023; 14:656. [PMID: 36746960 PMCID: PMC9902471 DOI: 10.1038/s41467-023-36026-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/12/2023] [Indexed: 02/08/2023] Open
Abstract
Secondary metabolites play essential roles in ecological interactions and nutrient acquisition, and are of interest for their potential uses in medicine and biotechnology. Genome mining for biosynthetic gene clusters (BGCs) can be used for the discovery of new compounds. Here, we use metagenomics and metatranscriptomics to analyze BGCs in free-living and particle-associated microbial communities through the stratified water column of the Cariaco Basin, Venezuela. We recovered 565 bacterial and archaeal metagenome-assembled genomes (MAGs) and identified 1154 diverse BGCs. We show that differences in water redox potential and microbial lifestyle (particle-associated vs. free-living) are associated with variations in the predicted composition and production of secondary metabolites. Our results indicate that microbes, including understudied clades such as Planctomycetota, potentially produce a wide range of secondary metabolites in these anoxic/euxinic waters.
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Affiliation(s)
| | - Paraskevi Mara
- Geology & Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Elizabeth Suter
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA.,Biology, Chemistry and Environmental Studies Department, Molloy College, Rockville Centre, NY, USA
| | - Virginia Edgcomb
- Geology & Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| | - Maria Pachiadaki
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
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7
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Puigcorbé V, Ruiz-González C, Masqué P, Gasol JM. Impact of particle flux on the vertical distribution and diversity of size-fractionated prokaryotic communities in two East Antarctic polynyas. Front Microbiol 2023; 14:1078469. [PMID: 36910225 PMCID: PMC9995690 DOI: 10.3389/fmicb.2023.1078469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/27/2023] [Indexed: 02/25/2023] Open
Abstract
Antarctic polynyas are highly productive open water areas surrounded by ice where extensive phytoplankton blooms occur, but little is known about how these surface blooms influence carbon fluxes and prokaryotic communities from deeper waters. By sequencing the 16S rRNA gene, we explored the vertical connectivity of the prokaryotic assemblages associated with particles of three different sizes in two polynyas with different surface productivity, and we linked it to the magnitude of the particle export fluxes measured using thorium-234 (234Th) as particle tracer. Between the sunlit and the mesopelagic layers (700 m depth), we observed compositional changes in the prokaryotic communities associated with the three size-fractions, which were mostly dominated by Flavobacteriia, Alphaproteobacteria, and Gammaproteobacteria. Interestingly, the vertical differences between bacterial communities attached to the largest particles decreased with increasing 234Th export fluxes, indicating a more intense downward transport of surface prokaryotes in the most productive polynya. This was accompanied by a higher proportion of surface prokaryotic taxa detected in deep particle-attached microbial communities in the station with the highest 234Th export flux. Our results support recent studies evidencing links between surface productivity and deep prokaryotic communities and provide the first evidence of sinking particles acting as vectors of microbial diversity to depth in Antarctic polynyas, highlighting the direct influence of particle export in shaping the prokaryotic communities of mesopelagic waters.
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Affiliation(s)
- Viena Puigcorbé
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalunya, Spain.,Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Clara Ruiz-González
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalunya, Spain
| | - Pere Masqué
- Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, Joondalup, WA, Australia.,International Atomic Energy Agency, City of Monaco, Monaco
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalunya, Spain
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8
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Emiliania huxleyi-Bacteria Interactions under Increasing CO 2 Concentrations. Microorganisms 2022; 10:microorganisms10122461. [PMID: 36557715 PMCID: PMC9786219 DOI: 10.3390/microorganisms10122461] [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: 11/03/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
The interactions established between marine microbes, namely phytoplankton-bacteria, are key to the balance of organic matter export to depth and recycling in the surface ocean. Still, their role in the response of phytoplankton to rising CO2 concentrations is poorly understood. Here, we show that the response of the cosmopolitan Emiliania huxleyi (E. huxleyi) to increasing CO2 is affected by the coexistence with bacteria. Specifically, decreased growth rate of E. huxleyi at enhanced CO2 concentrations was amplified in the bloom phase (potentially also related to nutrient concentrations) and with the coexistence with Idiomarina abyssalis (I. abyssalis) and Brachybacterium sp. In addition, enhanced CO2 concentrations also affected E. huxleyi's cellular content estimates, increasing organic and decreasing inorganic carbon, in the presence of I. abyssalis, but not Brachybacterium sp. At the same time, the bacterial isolates only survived in coexistence with E. huxleyi, but exclusively I. abyssalis at present CO2 concentrations. Bacterial species or group-specific responses to the projected CO2 rise, together with the concomitant effect on E. huxleyi, might impact the balance between the microbial loop and the export of organic matter, with consequences for atmospheric carbon dioxide.
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9
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Xiang N, Rädecker N, Pogoreutz C, Cárdenas A, Meibom A, Wild C, Gärdes A, Voolstra CR. Presence of algal symbionts affects denitrifying bacterial communities in the sea anemone Aiptasia coral model. ISME COMMUNICATIONS 2022; 2:105. [PMID: 37938763 PMCID: PMC9723753 DOI: 10.1038/s43705-022-00190-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/28/2022] [Accepted: 10/10/2022] [Indexed: 11/09/2023]
Abstract
The coral-algal symbiosis is maintained by a constant and limited nitrogen availability in the holobiont. Denitrifiers, i.e., prokaryotes reducing nitrate/nitrite to dinitrogen, could contribute to maintaining the nitrogen limitation in the coral holobiont, however the effect of host and algal identity on their community is still unknown. Using the coral model Aiptasia, we quantified and characterized the denitrifier community in a full-factorial design combining two hosts (CC7 and H2) and two strains of algal symbionts of the family Symbiodiniaceae (SSA01 and SSB01). Strikingly, relative abundance of denitrifiers increased by up to 22-fold in photosymbiotic Aiptasia compared to their aposymbiotic (i.e., algal-depleted) counterparts. In line with this, while the denitrifier community in aposymbiotic Aiptasia was largely dominated by diet-associated Halomonas, we observed an increasing relative abundance of an unclassified bacterium in photosymbiotic CC7, and Ketobacter in photosymbiotic H2, respectively. Pronounced changes in denitrifier communities of Aiptasia with Symbiodinium linucheae strain SSA01 aligned with the higher photosynthetic carbon availability of these holobionts compared to Aiptasia with Breviolum minutum strain SSB01. Our results reveal that the presence of algal symbionts increases abundance and alters community structure of denitrifiers in Aiptasia. Thereby, patterns in denitrifier community likely reflect the nutritional status of aposymbiotic vs. symbiotic holobionts. Such a passive regulation of denitrifiers may contribute to maintaining the nitrogen limitation required for the functioning of the cnidarian-algal symbiosis.
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Affiliation(s)
- Nan Xiang
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, 28359, Bremen, Germany.
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570, Bremerhaven, Germany.
| | - Nils Rädecker
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Claudia Pogoreutz
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Anny Cárdenas
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Anders Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
- Center for Advanced Surface Analysis (CASA), Institute of Earth Science, University of Lausanne, 1015, Lausanne, Switzerland
| | - Christian Wild
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, 28359, Bremen, Germany
| | - Astrid Gärdes
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570, Bremerhaven, Germany
- Hochschule Bremerhaven, Fachbereich 1, An der Karlstadt 8, 27568, Bremerhaven, Germany
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10
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Broman E, Izabel-Shen D, Rodríguez-Gijón A, Bonaglia S, Garcia SL, Nascimento FJA. Microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the Baltic benthic ecosystem. MICROBIOME 2022; 10:126. [PMID: 35965333 PMCID: PMC9377124 DOI: 10.1186/s40168-022-01321-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/05/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND Microorganisms in the seafloor use a wide range of metabolic processes, which are coupled to the presence of functional genes within their genomes. Aquatic environments are heterogenous and often characterized by natural physiochemical gradients that structure these microbial communities potentially changing the diversity of functional genes and its associated metabolic processes. In this study, we investigated spatial variability and how environmental variables structure the diversity and composition of benthic functional genes and metabolic pathways across various fundamental environmental gradients. We analyzed metagenomic data from sediment samples, measured related abiotic data (e.g., salinity, oxygen and carbon content), covering 59 stations spanning 1,145 km across the Baltic Sea. RESULTS The composition of genes and microbial communities were mainly structured by salinity plus oxygen, and the carbon to nitrogen (C:N) ratio for specific metabolic pathways related to nutrient transport and carbon metabolism. Multivariate analyses indicated that the compositional change in functional genes was more prominent across environmental gradients compared to changes in microbial taxonomy even at genus level, and indicate functional diversity adaptation to local environments. Oxygen deficient areas (i.e., dead zones) were more different in gene composition when compared to oxic sediments. CONCLUSIONS This study highlights how benthic functional genes are structured over spatial distances and by environmental gradients and resource availability, and suggests that changes in, e.g., oxygenation, salinity, and carbon plus nitrogen content will influence functional metabolic pathways in benthic habitats. Video Abstract.
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Affiliation(s)
- Elias Broman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Dandan Izabel-Shen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Alejandro Rodríguez-Gijón
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - Stefano Bonaglia
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Sarahi L. Garcia
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - Francisco J. A. Nascimento
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
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11
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Diverse Genomic Traits Differentiate Sinking-Particle-Associated versus Free-Living Microbes throughout the Oligotrophic Open Ocean Water Column. mBio 2022; 13:e0156922. [PMID: 35862780 PMCID: PMC9426571 DOI: 10.1128/mbio.01569-22] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Bacteria and archaea are central to the production, consumption, and remineralization of dissolved and particulate organic matter and contribute critically to carbon delivery, nutrient availability, and energy transformations in the deep ocean. To explore environmentally relevant genomic traits of sinking-particle-associated versus free-living microbes, we compared habitat-specific metagenome-assembled genomes recovered throughout the water column in the North Pacific Subtropical Gyre. The genomic traits of sinking-particle-associated versus free-living prokaryotes were compositionally, functionally, and phylogenetically distinct. Substrate-specific transporters and extracellular peptidases and carbohydrate-active enzymes were more enriched and diverse in particle-associated microbes at all depths than in free-living counterparts. These data indicate specific roles for particle-attached microbes in particle substrate hydrolysis, uptake, and remineralization. Shallow-water particle-associated microbes had elevated genomic GC content and proteome nitrogen content and reduced proteome carbon content in comparison to abyssal particle-associated microbes. An inverse trend was observed for their sympatric free-living counterparts. These different properties of attached microbes are postulated to arise in part due to elevated organic and inorganic nitrogen availability inside sinking particles. Particle-attached microbes also were enriched in genes for environmental sensing via two-component regulatory systems, and cell-cell interactions via extracellular secretion systems, reflecting their surface-adapted lifestyles. Finally, particle-attached bacteria had greater predicted maximal growth efficiencies than free-living bacterioplankton at all depths. All of these particle-associated specific genomic and proteomic features appear to be driven by microhabitat-specific elevated nutrient and energy availability as well as surface-associated competitive and synergistic ecological interactions. Although some of these characteristics have been previously postulated or observed individually, we report them together here in aggregate via direct comparisons of cooccurring free-living and sinking-particle-attached microbial genomes from the open ocean.
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12
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Luo E, Leu AO, Eppley JM, Karl DM, DeLong EF. Diversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean. THE ISME JOURNAL 2022; 16:1627-1635. [PMID: 35236926 PMCID: PMC9122931 DOI: 10.1038/s41396-022-01202-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/09/2022] [Accepted: 01/25/2022] [Indexed: 11/15/2022]
Abstract
Sinking particles and particle-associated microbes influence global biogeochemistry through particulate matter export from the surface to the deep ocean. Despite ongoing studies of particle-associated microbes, viruses in these habitats remain largely unexplored. Whether, where, and which viruses might contribute to particle production and export remain open to investigation. In this study, we analyzed 857 virus population genomes associated with sinking particles collected over three years in sediment traps moored at 4000 m in the North Pacific Subtropical Gyre. Particle-associated viruses here were linked to cellular hosts through matches to bacterial and archaeal metagenome-assembled genome (MAG)-encoded prophages or CRISPR spacers, identifying novel viruses infecting presumptive deep-sea bacteria such as Colwellia, Moritella, and Shewanella. We also identified lytic viruses whose abundances correlated with particulate carbon flux and/or were exported from the photic to abyssal ocean, including cyanophages. Our data are consistent with some of the predicted outcomes of the viral shuttle hypothesis, and further suggest that viral lysis of both autotrophic and heterotrophic prokaryotes may play a role in carbon export. Our analyses revealed the diversity and origins of prevalent viruses found on deep-sea sinking particles and identified prospective viral groups for future investigation into processes that govern particle export in the open ocean.
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Affiliation(s)
- Elaine Luo
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, HI, 96822, USA.
- Woods Hole Oceanographic Institution, 266 Woods Hole Road, MS 51, Woods Hole MA, 02543, Falmouth, USA.
| | - Andy O Leu
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, HI, 96822, USA
- Australia Center for Ecogenomics, University of Queensland, St. Lucia QLD, 4072, Australia
| | - John M Eppley
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, HI, 96822, USA
| | - David M Karl
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, HI, 96822, USA
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, HI, 96822, USA.
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13
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Nguyen TTH, Zakem EJ, Ebrahimi A, Schwartzman J, Caglar T, Amarnath K, Alcolombri U, Peaudecerf FJ, Hwa T, Stocker R, Cordero OX, Levine NM. Microbes contribute to setting the ocean carbon flux by altering the fate of sinking particulates. Nat Commun 2022; 13:1657. [PMID: 35351873 PMCID: PMC8964765 DOI: 10.1038/s41467-022-29297-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 03/02/2022] [Indexed: 11/25/2022] Open
Abstract
Sinking particulate organic carbon out of the surface ocean sequesters carbon on decadal to millennial timescales. Predicting the particulate carbon flux is therefore critical for understanding both global carbon cycling and the future climate. Microbes play a crucial role in particulate organic carbon degradation, but the impact of depth-dependent microbial dynamics on ocean-scale particulate carbon fluxes is poorly understood. Here we scale-up essential features of particle-associated microbial dynamics to understand the large-scale vertical carbon flux in the ocean. Our model provides mechanistic insight into the microbial contribution to the particulate organic carbon flux profile. We show that the enhanced transfer of carbon to depth can result from populations struggling to establish colonies on sinking particles due to diffusive nutrient loss, cell detachment, and mortality. These dynamics are controlled by the interaction between multiple biotic and abiotic factors. Accurately capturing particle-microbe interactions is essential for predicting variability in large-scale carbon cycling. Micro-scale microbial community dynamics can substantially alter the fate of sinking particulates in the ocean thus playing a key role in setting the vertical flux of particulate carbon in the ocean.
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14
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Can Aggregate-Associated Organisms Influence the Fouling in a SWRO Desalination Plant? Microorganisms 2022; 10:microorganisms10040682. [PMID: 35456734 PMCID: PMC9032733 DOI: 10.3390/microorganisms10040682] [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: 01/31/2022] [Revised: 03/17/2022] [Accepted: 03/17/2022] [Indexed: 12/10/2022] Open
Abstract
This pilot study investigates the formation of aggregates within a desalination plant, before and after pre-treatment, as well as their potential impact on fouling. The objective is to provide an understanding of the biofouling potential of the feed water within a seawater reverse osmosis (SWRO) desalination plant, due to the limited removal of fouling precursors. The 16S and 18S rRNA was extracted from the water samples, and the aggregates and sequenced. Pre-treatment systems, within the plant remove < 5 µm precursors and organisms; however, smaller size particles progress through the plant, allowing for the formation of aggregates. These become hot spots for microbes, due to their nutrient gradients, facilitating the formation of niche environments, supporting the proliferation of those organisms. Aggregate-associated organisms are consistent with those identified on fouled SWRO membranes. This study examines, for the first time, the factors supporting the formation of aggregates within a desalination system, as well as their microbial communities and biofouling potential.
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15
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Taxon-Specific Shifts in Bacterial and Archaeal Transcription of Dissolved Organic Matter Cycling Genes in a Stratified Fjord. mSystems 2021; 6:e0057521. [PMID: 34904860 PMCID: PMC8670421 DOI: 10.1128/msystems.00575-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A considerable fraction of organic matter derived from photosynthesis in the euphotic zone settles into the ocean’s interior and, as it progresses, is degraded by diverse microbial consortia that utilize a suite of extracellular enzymes and membrane transporters. Still, the molecular details that regulate carbon cycling across depths remain little explored. As stratification in fjords has made them attractive models to explore patterns in biological oceanography, we here analyzed bacterial and archaeal transcription in samples from five depth layers in the Gullmar Fjord, Sweden. Transcriptional variation over depth correlated with gradients in chlorophyll a and nutrient concentrations. Differences in transcription between sampling dates (summer and early autumn) were strongly correlated with ammonium concentrations, which potentially was linked with a stronger influence of (micro-)zooplankton grazing in summer. Transcriptional investment in carbohydrate-active enzymes (CAZymes) decreased with depth and shifted toward peptidases, partly a result of elevated CAZyme transcription by Flavobacteriales, Cellvibrionales, and Synechococcales at 2 to 25 m and a dominance of peptidase transcription by Alteromonadales and Rhodobacterales from 50 m down. In particular, CAZymes for chitin, laminarin, and glycogen were important. High levels of transcription of ammonium transporter genes by Thaumarchaeota at depth (up to 18% of total transcription), along with the genes for ammonia oxidation and CO2 fixation, indicated that chemolithoautotrophy contributed to the carbon flux in the fjord. The taxon-specific expression of functional genes for processing of the marine pool of dissolved organic matter and inorganic nutrients across depths emphasizes the importance of different microbial foraging mechanisms over spatiotemporal scales for shaping biogeochemical cycles. IMPORTANCE It is generally recognized that stratification in the ocean strongly influences both the community composition and the distribution of ecological functions of microbial communities, which in turn are expected to shape the biogeochemical cycling of essential elements over depth. Here, we used metatranscriptomics analysis to infer molecular detail on the distribution of gene systems central to the utilization of organic matter in a stratified marine system. We thereby uncovered that pronounced shifts in the transcription of genes encoding CAZymes, peptidases, and membrane transporters occurred over depth among key prokaryotic orders. This implies that sequential utilization and transformation of organic matter through the water column is a key feature that ultimately influences the efficiency of the biological carbon pump.
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16
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Jain A, Balmonte JP, Singh R, Bhaskar PV, Krishnan KP. Spatially resolved assembly, connectivity and structure of particle-associated and free-living bacterial communities in a high Arctic fjord. FEMS Microbiol Ecol 2021; 97:fiab139. [PMID: 34626180 PMCID: PMC8536490 DOI: 10.1093/femsec/fiab139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/07/2021] [Indexed: 01/08/2023] Open
Abstract
The assembly processes that underlie the composition and connectivity of free-living (FL) and particle-associated (PA) bacterial communities from surface to deep waters remain little understood. Here, using phylogenetic null modeling, we quantify the relative influence of selective and stochastic mechanisms that assemble FL and PA bacterial communities throughout the water column in a high Arctic fjord. We demonstrate that assembly processes acting on FL and PA bacterial communities are similar in surface waters, but become increasingly distinct in deep waters. As depth increases, the relative influence of homogeneous selection increases for FL but decreases for PA communities. In addition, dispersal limitation and variable selection increase with depth for PA, but not for FL communities, indicating increased residence time of taxa on particles and less frequent decolonization. As a consequence, beta diversity of PA communities is greater in bottom than in surface waters. The limited connectivity between these communities with increasing depth leads to highly distinct FL and PA bacterial communities in bottom waters. Finally, depth-related trends for FL and PA beta diversity and connectivity in this study are consistent with previous observations in the open ocean, suggesting that assembly processes for FL and PA bacterial communities may also be distinct in other aquatic environments.
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Affiliation(s)
- Anand Jain
- Arctic Ecology and Biogeochemistry, National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco da Gama 403 804, Goa, India
| | - John Paul Balmonte
- Department of Ecology and Genetics, Uppsala University, Uppsala 752 36, Sweden
- HADAL and NordCEE, Department of Biology, University of Southern Denmark, Odense, 5230, Denmark
| | - Richa Singh
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi 221 005, Uttar Pradesh, India
| | - Parli Venkateswaran Bhaskar
- Ocean Science Group, National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco da Gama 403 804, Goa, India
| | - Kottekkatu Padinchati Krishnan
- Arctic Ecology and Biogeochemistry, National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco da Gama 403 804, Goa, India
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17
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Wei W, Wang L, Fang J, Liu R. Population structure, activity potential and ecotype partitioning of Pseudoalteromonas along the vertical water column of the New Britain Trench. FEMS Microbiol Lett 2021; 368:6308368. [PMID: 34160584 DOI: 10.1093/femsle/fnab078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 06/21/2021] [Indexed: 11/14/2022] Open
Abstract
Microbial degradation of organic matter along the vertical profile of the water column is a major process driving the carbon cycle in the ocean. Pseudoalteromonas has been identified as a dominant genus in pelagic marine environments worldwide, playing important roles in the remineralization of organic carbon. However, the current understanding of Pseudoalteromonas was mainly based on shallow water populations or cultivated species. This study analyzed for the first time the structure, activity potential and ecotypes differentiation of Pseudoalteromonas in the water column of the New Britain Trench (NBT) down to 6000 m. Analysis on diversities of the 16S rRNA gene and their transcripts showed that Pseudoalteromonas was greatly enriched in deep-sea waters and showed high activity potentials. The deep-sea Pseudoalteromonas were significantly different from their shallow-water counterparts, suggesting an obvious ecotype division along with the vertical profile. Phylogenetic analysis on the 16S rRNA gene and hsp60 gene of 219 Pseudoalteromonas strains isolated from different depths further showed that the vertical ecotype division could even occur at the strain level, which might be a result of long-term adaptation to environmental conditions at different depths. The discovered depth-specific strains provide valuable models for further studies on adaptation, evolution and functions of the deep-sea Pseudoalteromonas.
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Affiliation(s)
- Wenxia Wei
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai,201306, China.,National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, 201306, China
| | - Li Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai,201306, China.,National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, 201306, China
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai,201306, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao,266000, China.,Department of Natural Sciences, Hawaii Pacific University, Honolulu, HI 96813, USA
| | - Rulong Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai,201306, China.,National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, 201306, China
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18
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Baumas CMJ, Le Moigne FAC, Garel M, Bhairy N, Guasco S, Riou V, Armougom F, Grossart HP, Tamburini C. Mesopelagic microbial carbon production correlates with diversity across different marine particle fractions. THE ISME JOURNAL 2021; 15:1695-1708. [PMID: 33452475 PMCID: PMC8163737 DOI: 10.1038/s41396-020-00880-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 12/02/2020] [Accepted: 12/09/2020] [Indexed: 01/29/2023]
Abstract
The vertical flux of marine snow particles significantly reduces atmospheric carbon dioxide concentration. In the mesopelagic zone, a large proportion of the organic carbon carried by sinking particles dissipates thereby escaping long term sequestration. Particle associated prokaryotes are largely responsible for such organic carbon loss. However, links between this important ecosystem flux and ecological processes such as community development of prokaryotes on different particle fractions (sinking vs. non-sinking) are yet virtually unknown. This prevents accurate predictions of mesopelagic organic carbon loss in response to changing ocean dynamics. Using combined measurements of prokaryotic heterotrophic production rates and species richness in the North Atlantic, we reveal that carbon loss rates and associated microbial richness are drastically different with particle fractions. Our results demonstrate a strong negative correlation between prokaryotic carbon losses and species richness. Such a trend may be related to prokaryotes detaching from fast-sinking particles constantly enriching non-sinking associated communities in the mesopelagic zone. Existing global scale data suggest this negative correlation is a widespread feature of mesopelagic microbes.
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Affiliation(s)
- Chloé M. J. Baumas
- grid.500499.10000 0004 1758 6271Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO, UM 110), Marseille, France
| | - Frédéric A. C. Le Moigne
- grid.500499.10000 0004 1758 6271Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO, UM 110), Marseille, France
| | - Marc Garel
- grid.500499.10000 0004 1758 6271Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO, UM 110), Marseille, France
| | - Nagib Bhairy
- grid.500499.10000 0004 1758 6271Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO, UM 110), Marseille, France
| | - Sophie Guasco
- grid.500499.10000 0004 1758 6271Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO, UM 110), Marseille, France
| | - Virginie Riou
- grid.500499.10000 0004 1758 6271Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO, UM 110), Marseille, France
| | - Fabrice Armougom
- grid.500499.10000 0004 1758 6271Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO, UM 110), Marseille, France
| | - Hans-Peter Grossart
- grid.419247.d0000 0001 2108 8097Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany ,grid.11348.3f0000 0001 0942 1117Institute of Biochemistry and Biology, Postdam University, 14469 Potsdam, Germany
| | - Christian Tamburini
- grid.500499.10000 0004 1758 6271Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO, UM 110), Marseille, France
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19
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Fritts RK, McCully AL, McKinlay JB. Extracellular Metabolism Sets the Table for Microbial Cross-Feeding. Microbiol Mol Biol Rev 2021; 85:e00135-20. [PMID: 33441489 PMCID: PMC7849352 DOI: 10.1128/mmbr.00135-20] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The transfer of nutrients between cells, or cross-feeding, is a ubiquitous feature of microbial communities with emergent properties that influence our health and orchestrate global biogeochemical cycles. Cross-feeding inevitably involves the externalization of molecules. Some of these molecules directly serve as cross-fed nutrients, while others can facilitate cross-feeding. Altogether, externalized molecules that promote cross-feeding are diverse in structure, ranging from small molecules to macromolecules. The functions of these molecules are equally diverse, encompassing waste products, enzymes, toxins, signaling molecules, biofilm components, and nutrients of high value to most microbes, including the producer cell. As diverse as the externalized and transferred molecules are the cross-feeding relationships that can be derived from them. Many cross-feeding relationships can be summarized as cooperative but are also subject to exploitation. Even those relationships that appear to be cooperative exhibit some level of competition between partners. In this review, we summarize the major types of actively secreted, passively excreted, and directly transferred molecules that either form the basis of cross-feeding relationships or facilitate them. Drawing on examples from both natural and synthetic communities, we explore how the interplay between microbial physiology, environmental parameters, and the diverse functional attributes of extracellular molecules can influence cross-feeding dynamics. Though microbial cross-feeding interactions represent a burgeoning field of interest, we may have only begun to scratch the surface.
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Affiliation(s)
- Ryan K Fritts
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | | | - James B McKinlay
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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20
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DeLong EF. Genome-enabled exploration of microbial ecology and evolution in the sea: a rising tide lifts all boats. Environ Microbiol 2021; 23:1301-1321. [PMID: 33459471 PMCID: PMC8049014 DOI: 10.1111/1462-2920.15403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 11/26/2022]
Abstract
As a young bacteriologist just launching my career during the early days of the 'microbial revolution' in the 1980s, I was fortunate to participate in some early discoveries, and collaborate in the development of cross-disciplinary methods now commonly referred to as "metagenomics". My early scientific career focused on applying phylogenetic and genomic approaches to characterize 'wild' bacteria, archaea and viruses in their natural habitats, with an emphasis on marine systems. These central interests have not changed very much for me over the past three decades, but knowledge, methodological advances and new theoretical perspectives about the microbial world certainly have. In this invited 'How we did it' perspective, I trace some of the trajectories of my lab's collective efforts over the years, including phylogenetic surveys of microbial assemblages in marine plankton and sediments, development of microbial community gene- and genome-enabled surveys, and application of genome-guided, cultivation-independent functional characterization of novel enzymes, pathways and their relationships to in situ biogeochemistry. Throughout this short review, I attempt to acknowledge, all the mentors, students, postdocs and collaborators who enabled this research. Inevitably, a brief autobiographical review like this cannot be fully comprehensive, so sincere apologies to any of my great colleagues who are not explicitly mentioned herein. I salute you all as well!
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Affiliation(s)
- Edward F DeLong
- Daniel K. Inouye Centre for Microbial Oceanography: Research and Education, University of Hawaii, Manoa, Honolulu, HI, 96822, USA
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21
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Abstract
The ocean’s “biological pump” exports sinking particles containing carbon, nutrients, and energy to the deep sea, contributing centrally to the global carbon cycle. Here, we identify key organisms and biological processes associated with elevated carbon flux to the abyss. Our analyses reveal that, during summer export, specific populations of photosynthetic algae, heterotrophic protists, and bacteria reach the abyss on sinking particles. Deep-sea bacteria respond rapidly to this elevated nutrient delivery to the abyss in summer. During other seasons, different organisms and processes appear responsible for particle export to the deep sea. Our analyses reveal key biota and biological processes that interconnect surface productivity, particle export, and the deep-sea ecosystem, thereby influencing the function and efficiency of the ocean’s biological pump. In the open ocean, elevated carbon flux (ECF) events increase the delivery of particulate carbon from surface waters to the seafloor by severalfold compared to other times of year. Since microbes play central roles in primary production and sinking particle formation, they contribute greatly to carbon export to the deep sea. Few studies, however, have quantitatively linked ECF events with the specific microbial assemblages that drive them. Here, we identify key microbial taxa and functional traits on deep-sea sinking particles that correlate positively with ECF events. Microbes enriched on sinking particles in summer ECF events included symbiotic and free-living diazotrophic cyanobacteria, rhizosolenid diatoms, phototrophic and heterotrophic protists, and photoheterotrophic and copiotrophic bacteria. Particle-attached bacteria reaching the abyss during summer ECF events encoded metabolic pathways reflecting their surface water origins, including oxygenic and aerobic anoxygenic photosynthesis, nitrogen fixation, and proteorhodopsin-based photoheterotrophy. The abundances of some deep-sea bacteria also correlated positively with summer ECF events, suggesting rapid bathypelagic responses to elevated organic matter inputs. Biota enriched on sinking particles during a spring ECF event were distinct from those found in summer, and included rhizaria, copepods, fungi, and different bacterial taxa. At other times over our 3-y study, mid- and deep-water particle colonization, predation, degradation, and repackaging (by deep-sea bacteria, protists, and animals) appeared to shape the biotic composition of particles reaching the abyss. Our analyses reveal key microbial players and biological processes involved in particle formation, rapid export, and consumption, that may influence the ocean’s biological pump and help sustain deep-sea ecosystems.
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22
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Wang M, Ma Y, Feng C, Cai L, Li W. Diversity of Pelagic and Benthic Bacterial Assemblages in the Western Pacific Ocean. Front Microbiol 2020; 11:1730. [PMID: 33071990 PMCID: PMC7533643 DOI: 10.3389/fmicb.2020.01730] [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: 02/24/2020] [Accepted: 07/02/2020] [Indexed: 12/28/2022] Open
Abstract
Despite numerous studies on marine prokaryotes, the vertical distribution patterns of bacterial community, either on the taxonomic composition or the functional structure, remains relatively unexplored. Using HiSeq-derived 16S rRNA data, the depth-related distribution patterns of taxonomic diversity and functional structure predicted from diversity data in the water column and sediments of the Western Pacific Ocean were explored. The OTU richness declined along the water column after peaking between 100 to 200 m deep. Relative abundance of Cyanobacteria and SAR11 decreased significantly with depth, while Actinobacteria and Gammaproteobacteria increased. This clearly mirrors the vertical distribution pattern of the predicted functional composition with the shift between phototrophic to chemoheterotrophic groups from the surface to the deeper layers. In terms of community composition and functional structure, the epipelagic zone differed from other deeper ones (i.e., meso-, bathy-, and abyssopelagic zones) where no obvious differences were detected. For the epipelagic zone, temperature, dissolved oxygen, and salinity were recognized as the crucial factors shaping both community composition and the functional structure of bacteria. Compared with water samples, benthic sediment samples harbored unexpectedly higher read abundance of Proteobacteria, presenting distinguishable taxonomic and functional compositions. This study provides novel knowledge on the vertical distribution of bacterial taxonomic and functional compositions in the western Pacific.
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Affiliation(s)
- Mengmeng Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yiyuan Ma
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Chunhui Feng
- Beihai Ocean Engineering Survey Research Institute, State Oceanic Administration, Qingdao, China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
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23
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Puigcorbé V, Ruiz-González C, Masqué P, Gasol JM. Sampling Device-Dependence of Prokaryotic Community Structure on Marine Particles: Higher Diversity Recovered by in situ Pumps Than by Oceanographic Bottles. Front Microbiol 2020; 11:1645. [PMID: 32760385 PMCID: PMC7373737 DOI: 10.3389/fmicb.2020.01645] [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: 03/29/2020] [Accepted: 06/24/2020] [Indexed: 01/24/2023] Open
Abstract
Microbes associated with sinking marine particles play key roles in carbon sequestration in the ocean. The sampling of particle-attached microorganisms is often done with sediment traps or by filtration of water collected with oceanographic bottles, both involving a certain time lapse between collection and processing of samples that may result in changes in particle-attached microbial communities. Conversely, in situ water filtration through submersible pumps allows a faster storage of sampled particles, but it has rarely been used to study the associated microbial communities and has never been compared to other particle-sampling methods in terms of the recovery of particle microbial diversity. Here we compared the prokaryotic communities attached to small (1–53 μm) and large (>53 μm) particles collected from the mesopelagic zone (100–300 m) of two Antarctic polynyas using in situ pumps (ISP) and oceanographic bottles (BTL). Each sampling method retrieved largely different particle-attached communities, suggesting that they capture different kinds of particles. These device-driven differences were greater for large particles than for small particles. Overall, the ISP recovered 1.5- to 3-fold more particle-attached bacterial taxa than the BTL, and different taxonomic groups were preferentially recovered by each method. In particular, typical particle-attached groups such as Planctomycetes and Deltaproteobacteria recovered with ISP were nearly absent from BTL samples. Our results suggest that the method used to sample marine particles has a strong influence in our view of their associated microbial communities.
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Affiliation(s)
- Viena Puigcorbé
- School of Science, Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA, Australia
| | - Clara Ruiz-González
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - Pere Masqué
- School of Science, Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA, Australia.,Institut de Ciència i Tecnologia Ambientals (ICTA), Bellaterra, Spain.,Department of Physics, Autonomous University of Barcelona, Barcelona, Spain.,International Atomic Energy Agency, Monaco City, Monaco
| | - Josep M Gasol
- School of Science, Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA, Australia.,Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
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24
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Manna V, Malfatti F, Banchi E, Cerino F, De Pascale F, Franzo A, Schiavon R, Vezzi A, Del Negro P, Celussi M. Prokaryotic Response to Phytodetritus-Derived Organic Material in Epi- and Mesopelagic Antarctic Waters. Front Microbiol 2020; 11:1242. [PMID: 32582131 PMCID: PMC7296054 DOI: 10.3389/fmicb.2020.01242] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/14/2020] [Indexed: 12/31/2022] Open
Abstract
Particulate organic matter (POM) export represents the underlying principle of the biological carbon pump, driving the carbon flux from the sunlit to the dark ocean. The efficiency of this process is tightly linked to the prokaryotic community, as >70% of POM respiration is carried out by particle-associated prokaryotes. In the Ross Sea, one of the most productive areas of the Southern Ocean, up to 50% of the surface primary production is exported to the mesopelagic ocean as POM. Recent evidence suggests that a significant fraction of the POM in this area is composed of intact phytoplankton cells. During austral summer 2017, we set up bottle enrichment experiments in which we amended free-living surface and deep prokaryotic communities with organic matter pools generated from native microplankton, mimicking the particle export that may derive from mild (1 μg of Chlorophyll a L-1) and intense (10 μg of Chlorophyll a L-1) phytoplankton bloom. Over a course of 4 days, we followed free-living and particle-attached prokaryotes' abundance, the degradation rates of polysaccharides, proteins and lipids, heterotrophic production as well as inorganic carbon utilization and prokaryotic community structure dynamics. Our results showed that several rare or undetected taxa in the initial community became dominant during the time course of the incubations and that different phytodetritus-derived organic matter sources induced specific changes in microbial communities, selecting for peculiar degradation and utilization processes spectra. Moreover, the features of the supplied detritus (in terms of microplankton taxa composition) determined different colonization dynamics and organic matter processing modes. Our study provides insights into the mechanisms underlying the prokaryotic utilization of phytodetritus, a significant pool of organic matter in the dark ocean.
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Affiliation(s)
- Vincenzo Manna
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale – OGS, Trieste, Italy
- Department of Life Sciences, Università degli Studi di Trieste, Trieste, Italy
| | - Francesca Malfatti
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale – OGS, Trieste, Italy
- Scripps Institution of Oceanography, University of California, San Diego, San Diego, CA, United States
| | - Elisa Banchi
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale – OGS, Trieste, Italy
| | - Federica Cerino
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale – OGS, Trieste, Italy
| | - Fabio De Pascale
- Department of Biology, Università degli Studi di Padova, Padua, Italy
| | - Annalisa Franzo
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale – OGS, Trieste, Italy
| | - Riccardo Schiavon
- Department of Biology, Università degli Studi di Padova, Padua, Italy
| | - Alessandro Vezzi
- Department of Biology, Università degli Studi di Padova, Padua, Italy
| | - Paola Del Negro
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale – OGS, Trieste, Italy
| | - Mauro Celussi
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale – OGS, Trieste, Italy
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25
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Ruiz-González C, Mestre M, Estrada M, Sebastián M, Salazar G, Agustí S, Moreno-Ostos E, Reche I, Álvarez-Salgado XA, Morán XAG, Duarte CM, Sala MM, Gasol JM. Major imprint of surface plankton on deep ocean prokaryotic structure and activity. Mol Ecol 2020; 29:1820-1838. [PMID: 32323882 DOI: 10.1111/mec.15454] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 03/12/2020] [Accepted: 04/16/2020] [Indexed: 01/06/2023]
Abstract
Deep ocean microbial communities rely on the organic carbon produced in the sunlit ocean, yet it remains unknown whether surface processes determine the assembly and function of bathypelagic prokaryotes to a larger extent than deep-sea physicochemical conditions. Here, we explored whether variations in surface phytoplankton assemblages across Atlantic, Pacific and Indian ocean stations can explain structural changes in bathypelagic (ca. 4,000 m) free-living and particle-attached prokaryotic communities (characterized through 16S rRNA gene sequencing), as well as changes in prokaryotic activity and dissolved organic matter (DOM) quality. We show that the spatial structuring of prokaryotic communities in the bathypelagic strongly followed variations in the abundances of surface dinoflagellates and ciliates, as well as gradients in surface primary productivity, but were less influenced by bathypelagic physicochemical conditions. Amino acid-like DOM components in the bathypelagic reflected variations of those components in surface waters, and seemed to control bathypelagic prokaryotic activity. The imprint of surface conditions was more evident in bathypelagic than in shallower mesopelagic (200-1,000 m) communities, suggesting a direct connectivity through fast-sinking particles that escape mesopelagic transformations. Finally, we identified a pool of endemic deep-sea prokaryotic taxa (including potentially chemoautotrophic groups) that appear less connected to surface processes than those bathypelagic taxa with a widespread vertical distribution. Our results suggest that surface planktonic communities shape the spatial structure of the bathypelagic microbiome to a larger extent than the local physicochemical environment, likely through determining the nature of the sinking particles and the associated prokaryotes reaching bathypelagic waters.
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Affiliation(s)
| | - Mireia Mestre
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain.,Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile.,Centro de Investigación Oceanográfica COPAS Sur-Austral, Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile
| | - Marta Estrada
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - Marta Sebastián
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain.,Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria (ULPGC), Las Palmas, Spain
| | - Guillem Salazar
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain.,Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Susana Agustí
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Enrique Moreno-Ostos
- Department of Ecology and Geology, Marine Ecology and Limnology Research Group, CEIMAR, University of Málaga, Málaga, Spain
| | - Isabel Reche
- Departamento de Ecología and Research Unit Modeling Nature (MNat), Universidad de Granada, Granada, Spain
| | | | - Xosé Anxelu G Morán
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Carlos M Duarte
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | | | - Josep M Gasol
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain.,Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, Joondalup, WA, Australia
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26
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Chen ML, Becraft ED, Pachiadaki M, Brown JM, Jarett JK, Gasol JM, Ravin NV, Moser DP, Nunoura T, Herndl GJ, Woyke T, Stepanauskas R. Hiding in Plain Sight: The Globally Distributed Bacterial Candidate Phylum PAUC34f. Front Microbiol 2020; 11:376. [PMID: 32226422 PMCID: PMC7081726 DOI: 10.3389/fmicb.2020.00376] [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: 11/19/2019] [Accepted: 02/20/2020] [Indexed: 12/31/2022] Open
Abstract
Bacterial candidate phylum PAUC34f was originally discovered in marine sponges and is widely considered to be composed of sponge symbionts. Here, we report 21 single amplified genomes (SAGs) of PAUC34f from a variety of environments, including the dark ocean, lake sediments, and a terrestrial aquifer. The diverse origins of the SAGs and the results of metagenome fragment recruitment suggest that some PAUC34f lineages represent relatively abundant, free-living cells in environments other than sponge microbiomes, including the deep ocean. Both phylogenetic and biogeographic patterns, as well as genome content analyses suggest that PAUC34f associations with hosts evolved independently multiple times, while free-living lineages of PAUC34f are distinct and relatively abundant in a wide range of environments.
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Affiliation(s)
- Michael L Chen
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States.,Department of Biology, Williams College, Williamstown, MA, United States
| | - Eric D Becraft
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States.,Department of Biology, University of North Alabama, Florence, AL, United States
| | - Maria Pachiadaki
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States.,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Jessica K Jarett
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Josep M Gasol
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain.,Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA, Australia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Duane P Moser
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, United States
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Gerhard J Herndl
- Department of Limnology and Bio-Oceanography, University of Vienna, Vienna, Austria.,Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Tanja Woyke
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, United States
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27
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Li W, Wang M, Burgaud G, Yu H, Cai L. Fungal Community Composition and Potential Depth-Related Driving Factors Impacting Distribution Pattern and Trophic Modes from Epi- to Abyssopelagic Zones of the Western Pacific Ocean. MICROBIAL ECOLOGY 2019; 78:820-831. [PMID: 30993370 DOI: 10.1007/s00248-019-01374-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/22/2019] [Indexed: 06/09/2023]
Abstract
Fungi play an important role in cycling organic matter and nutrients in marine ecosystems. However, the distribution of fungal communities in the ocean, especially the vertical distribution along depth in the water column, remained poorly understood. Here, we assess the depth-related distribution pattern of fungal communities along the water column from epi- to abyssopelagic zones of the Western Pacific Ocean using internal transcribed spacer 2 (ITS2) metabarcoding. Majority of the assigned OTUs were affiliated to Ascomycota, followed by three other minor phyla (Basidiomycota, Chytridiomycota, and Mucoromycota). The epipelagic zone harbored a higher OTU richness with distinct fungal communities as compared with meso-, bathy-, and abyssopelagic zones. Across the whole water column, depth appears as a key parameter for both fungal α- and β-diversity. However, when the dataset was split into the upper (5-500 m) and deeper (below 500 m) layers, no significant correlation was observed between depth and community compositions. In the upper layer, temperature and dissolved oxygen were recognized as the primary environmental factors shaping fungal α- and β- diversity. By parsing fungal OTUs into ecological categories, multi-trophic mode of nutrition was found to be more prevalent with increasing depth, suggesting a potential adaptation to the extreme conditions of the deep sea. This study provides new and meaningful information on the depth-stratified fungal diversity, community structure, and putative ecological roles in the open sea.
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Affiliation(s)
- Wei Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Mengmeng Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Gaëtan Burgaud
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise, 29280, Plouzané, France
| | - Huaming Yu
- College of Oceanic and Atmospheric Sciences, Ocean University of China, Qingdao, China
- Key Laboratory of Physical Oceanography, MOE, Qingdao, China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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28
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Shoemaker KM, Duhamel S, Moisander PH. Copepods promote bacterial community changes in surrounding seawater through farming and nutrient enrichment. Environ Microbiol 2019; 21:3737-3750. [PMID: 31222878 DOI: 10.1111/1462-2920.14723] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 05/21/2019] [Accepted: 06/18/2019] [Indexed: 12/11/2022]
Abstract
Bacteria living in the oligotrophic open ocean have various ways to survive under the pressure of nutrient limitation. Copepods, an abundant portion of the mesozooplankton, release nutrients through excretion and sloppy feeding that can support growth of surrounding bacteria. We conducted incubation experiments in the North Atlantic Subtropical Gyre to investigate the response of bacterial communities in the presence of copepods. Bacterial community composition and abundance measurements indicate that copepods have the potential to influence the microbial communities surrounding and associating with them - their 'zoosphere', in two ways. First, copepods may attract and support the growth of copiotrophic bacteria including representatives of Vibrionaceae, Oceanospirillales and Rhodobacteraceae in waters surrounding them. Second, copepods appear to grow specific groups of bacteria in or on the copepod body, particularly Flavobacteriaceae and Pseudoalteromonadaceae, effectively 'farming' them and subsequently releasing them. These distinct mechanisms provide a new view into how copepods may shape microbial communities in the open ocean. Microbial processes in the copepod zoosphere may influence estimates of oceanic bacterial biomass and in part control bacterial community composition and distribution in seawater.
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Affiliation(s)
- Katyanne M Shoemaker
- Department of Biology, University of Massachusetts Dartmouth, North Dartmouth, MA, 02747, USA
| | - Solange Duhamel
- Lamont-Doherty Earth Observatory, Division of Biology and Paleo Environment, Columbia University, NY, 10964, USA
| | - Pia H Moisander
- Department of Biology, University of Massachusetts Dartmouth, North Dartmouth, MA, 02747, USA
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29
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Biological composition and microbial dynamics of sinking particulate organic matter at abyssal depths in the oligotrophic open ocean. Proc Natl Acad Sci U S A 2019; 116:11824-11832. [PMID: 31127042 PMCID: PMC6575173 DOI: 10.1073/pnas.1903080116] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Sinking particles composed of both organic and inorganic material feed the deep-sea ecosystem and contribute centrally to ocean carbon sequestration. Despite their importance, little is known about the biological composition of sinking particles reaching the deep sea. Time-series analyses of sinking particles unexpectedly revealed bacterial assemblages that were simple and homogeneous over time. Particle-associated eukaryote assemblages, however, were more variable and complex. Several modes of export were observed, including summer inputs from the surface, more stochastic export of surface-derived protists and animals, and contributions from midwater animals and deep-sea bacteria. In summary, sinking particles exhibited temporally variable, heterogeneous biological sources and activities that reflected their important roles in the downward transport and transformation of organic matter in the deep sea. Sinking particles are a critical conduit for the export of organic material from surface waters to the deep ocean. Despite their importance in oceanic carbon cycling and export, little is known about the biotic composition, origins, and variability of sinking particles reaching abyssal depths. Here, we analyzed particle-associated nucleic acids captured and preserved in sediment traps at 4,000-m depth in the North Pacific Subtropical Gyre. Over the 9-month time-series, Bacteria dominated both the rRNA-gene and rRNA pools, followed by eukaryotes (protists and animals) and trace amounts of Archaea. Deep-sea piezophile-like Gammaproteobacteria, along with Epsilonproteobacteria, comprised >80% of the bacterial inventory. Protists (mostly Rhizaria, Syndinales, and ciliates) and metazoa (predominantly pelagic mollusks and cnidarians) were the most common sinking particle-associated eukaryotes. Some near-surface water-derived eukaryotes, especially Foraminifera, Radiolaria, and pteropods, varied greatly in their abundance patterns, presumably due to sporadic export events. The dominance of piezophile-like Gammaproteobacteria and Epsilonproteobacteria, along with the prevalence of their nitrogen cycling-associated gene transcripts, suggested a central role for these bacteria in the mineralization and biogeochemical transformation of sinking particulate organic matter in the deep ocean. Our data also reflected several different modes of particle export dynamics, including summer export, more stochastic inputs from the upper water column by protists and pteropods, and contributions from sinking mid- and deep-water organisms. In total, our observations revealed the variable and heterogeneous biological origins and microbial activities of sinking particles that connect their downward transport, transformation, and degradation to deep-sea biogeochemical processes.
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30
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Enke TN, Datta MS, Schwartzman J, Cermak N, Schmitz D, Barrere J, Pascual-García A, Cordero OX. Modular Assembly of Polysaccharide-Degrading Marine Microbial Communities. Curr Biol 2019; 29:1528-1535.e6. [PMID: 31031118 DOI: 10.1016/j.cub.2019.03.047] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/27/2019] [Accepted: 03/21/2019] [Indexed: 02/05/2023]
Abstract
Understanding the principles that govern the assembly of microbial communities across earth's biomes is a major challenge in modern microbial ecology. This pursuit is complicated by the difficulties of mapping functional roles and interactions onto communities with immense taxonomic diversity and of identifying the scale at which microbes interact [1]. To address this challenge, here, we focused on the bacterial communities that colonize and degrade particulate organic matter in the ocean [2-4]. We show that the assembly of these communities can be simplified as a linear combination of functional modules. Using synthetic polysaccharide particles immersed in natural bacterioplankton assemblages [1, 5], we showed that successional particle colonization dynamics are driven by the interaction of two types of modules: a first type made of narrowly specialized primary degraders, whose dynamics are controlled by particle polysaccharide composition, and a second type containing substrate-independent taxa whose dynamics are controlled by interspecific interactions-in particular, cross-feeding via organic acids, amino acids, and other metabolic byproducts. We show that, as a consequence of this trophic structure, communities can assemble modularly-i.e., by a simple sum of substrate-specific primary degrader modules, one for each complex polysaccharide in the particle, connected to a single broad-niche range consumer module. Consistent with this model, a linear combination of the communities on single-polysaccharide particles accurately predicts community composition on mixed-polysaccharide particles. Our results suggest that the assembly of heterotrophic communities that degrade complex organic materials follows simple design principles that could be exploited to engineer heterotrophic microbiomes.
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Affiliation(s)
- Tim N Enke
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Environmental Systems Science, ETH Zurich, 8093 Zurich, Switzerland
| | - Manoshi S Datta
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Julia Schwartzman
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nathan Cermak
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Désirée Schmitz
- Department of Environmental Systems Science, ETH Zurich, 8093 Zurich, Switzerland
| | - Julien Barrere
- Department of Environmental Systems Science, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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31
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Richert I, Yager PL, Dinasquet J, Logares R, Riemann L, Wendeberg A, Bertilsson S, Scofield DG. Summer comes to the Southern Ocean: how phytoplankton shape bacterioplankton communities far into the deep dark sea. Ecosphere 2019. [DOI: 10.1002/ecs2.2641] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Inga Richert
- Department of Ecology and Genetics: Limnology Uppsala University Uppsala Sweden
- Department of Environmental Microbiology Helmholtz Centre for Environmental Research – UFZ Leipzig Germany
| | - Patricia L. Yager
- Department of Marine Science University of Georgia Athens Georgia USA
| | - Julie Dinasquet
- Department of Biology University of Copenhagen Helsingør Denmark
- Scripps Institution of Oceanography UCSD San Diego California USA
| | | | - Lasse Riemann
- Department of Biology University of Copenhagen Helsingør Denmark
| | - Annelie Wendeberg
- Department of Environmental Microbiology Helmholtz Centre for Environmental Research – UFZ Leipzig Germany
| | - Stefan Bertilsson
- Department of Ecology and Genetics: Limnology Uppsala University Uppsala Sweden
- Science for Life Laboratory Uppsala University Uppsala Sweden
| | - Douglas G. Scofield
- Department of Ecology and Genetics: Evolutionary Biology Uppsala University Uppsala Sweden
- Uppsala Multidisciplinary Center for Advanced Computational Science Uppsala University Uppsala Sweden
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32
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Podell S, Blanton JM, Neu A, Agarwal V, Biggs JS, Moore BS, Allen EE. Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles. ISME JOURNAL 2018; 13:468-481. [PMID: 30291328 DOI: 10.1038/s41396-018-0292-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/12/2018] [Accepted: 09/15/2018] [Indexed: 01/10/2023]
Abstract
Candidatus Poribacteria is a little-known bacterial phylum, previously characterized by partial genomes from a single sponge host, but never isolated in culture. We have reconstructed multiple genome sequences from four different sponge genera and compared them to recently reported, uncharacterized Poribacteria genomes from the open ocean, discovering shared and unique functional characteristics. Two distinct, habitat-linked taxonomic lineages were identified, designated Entoporibacteria (sponge-associated) and Pelagiporibacteria (free-living). These lineages differed in flagellar motility and chemotaxis genes unique to Pelagiporibacteria, and highly expanded families of restriction endonucleases, DNA methylases, transposases, CRISPR repeats, and toxin-antitoxin gene pairs in Entoporibacteria. Both lineages shared pathways for facultative anaerobic metabolism, denitrification, fermentation, organosulfur compound utilization, type IV pili, cellulosomes, and bacterial proteosomes. Unexpectedly, many features characteristic of eukaryotic host association were also shared, including genes encoding the synthesis of eukaryotic-like cell adhesion molecules, extracellular matrix digestive enzymes, phosphoinositol-linked membrane glycolipids, and exopolysaccharide capsules. Complete Poribacteria 16S rRNA gene sequences were found to contain multiple mismatches to "universal" 16S rRNA gene primer sets, substantiating concerns about potential amplification failures in previous studies. A newly designed primer set corrects these mismatches, enabling more accurate assessment of Poribacteria abundance in diverse marine habitats where it may have previously been overlooked.
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Affiliation(s)
- Sheila Podell
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA
| | - Jessica M Blanton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA
| | - Alexander Neu
- Division of Biological Sciences, University of California, La Jolla, San Diego, CA, USA
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA
| | - Jason S Biggs
- University of Guam Marine Laboratory, UOG Station, Mangilao, Guam, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA, USA
| | - Eric E Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA. .,Division of Biological Sciences, University of California, La Jolla, San Diego, CA, USA. .,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA.
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33
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Farnelid H, Turk-Kubo K, Ploug H, Ossolinski JE, Collins JR, Van Mooy BAS, Zehr JP. Diverse diazotrophs are present on sinking particles in the North Pacific Subtropical Gyre. ISME JOURNAL 2018; 13:170-182. [PMID: 30116043 PMCID: PMC6299005 DOI: 10.1038/s41396-018-0259-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/03/2018] [Accepted: 07/26/2018] [Indexed: 11/09/2022]
Abstract
Sinking particles transport carbon and nutrients from the surface ocean into the deep sea and are considered hot spots for bacterial diversity and activity. In the oligotrophic oceans, nitrogen (N2)-fixing organisms (diazotrophs) are an important source of new N but the extent to which these organisms are present and exported on sinking particles is not well known. Sinking particles were collected every 6 h over a 2-day period using net traps deployed at 150 m in the North Pacific Subtropical Gyre. The bacterial community and composition of diazotrophs associated with individual and bulk sinking particles was assessed using 16S rRNA and nifH gene amplicon sequencing. The bacterial community composition in bulk particles remained remarkably consistent throughout time and space while large variations of individually picked particles were observed. This difference suggests that unique biogeochemical conditions within individual particles may offer distinct ecological niches for specialized bacterial taxa. Compared to surrounding seawater, particle samples were enriched in different size classes of globally significant N2-fixing cyanobacteria including Trichodesmium, symbionts of diatoms, and the unicellular cyanobacteria Crocosphaera and UCYN-A. The particles also contained nifH gene sequences of diverse non-cyanobacterial diazotrophs suggesting that particles could be loci for N2 fixation by heterotrophic bacteria. The results demonstrate that diverse diazotrophs were present on particles and that new N may thereby be directly exported from surface waters on sinking particles.
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Affiliation(s)
- Hanna Farnelid
- Ocean Sciences Department, University of California at Santa Cruz, Santa Cruz, CA, USA. .,Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden.
| | - Kendra Turk-Kubo
- Ocean Sciences Department, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Helle Ploug
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Justin E Ossolinski
- Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - James R Collins
- Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.,MIT/WHOI Joint Program in Oceanography, University of Washington, Seattle, WA, USA.,School of Oceanography and eScience Institute, University of Washington, Seattle, WA, USA
| | - Benjamin A S Van Mooy
- Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California at Santa Cruz, Santa Cruz, CA, USA
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