1
|
Quantification of Marine Picocyanobacteria on Water Column Particles and in Sediments Using Real-Time PCR Reveals Their Role in Carbon Export. mSphere 2022; 7:e0049922. [PMID: 36472446 PMCID: PMC9769826 DOI: 10.1128/msphere.00499-22] [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] [Indexed: 12/12/2022] Open
Abstract
Picocyanobacteria are the most abundant primary producers in the ocean and play a fundamental role in marine carbon cycling. Quantification of picocyanobacteria on sinking particles and in sediments is essential to understanding their contribution to the biological carbon pump. We designed a primer set targeting the 16S-23S rRNA internal transcribed spacer (ITS) sequence of cyanobacteria and established a quantitative PCR (qPCR) method for quantifying the ITS sequence abundance. High-throughput sequencing confirmed that this primer set can cover broad diversities of marine picocyanobacteria and avoid amplification of other marine cyanobacteria such as Trichodesmium and Crocosphaera. Amplification efficiencies were slightly different when seven marine Synechococcus and Prochlorococcus strains were assayed. The qPCR results were comparable with flow cytometry for water samples. Using this method, we found that, in the dark ocean, picocyanobacterial ITS sequence abundances were 10 to 100 copies/mL in the size fraction of 0.2 to 3 μm, which were 1 to 3 orders of magnitude more abundant than on the >3-μm particles. We also found that picocyanobacterial ITS abundance in sediment ranged from 105 to 107 copies/g along two nearshore-to-offshore transects in the northern South China Sea. These results further explain the important role of picocyanobacteria in carbon export. Collectively, we provide a qPCR method quantifying the total abundance of marine picocyanobacteria on water column particles and in sediments. Moreover, this newly designed primer set can be also applied to investigate the community of picocyanobacteria via high-throughput sequencing. IMPORTANCE Picocyanobacteria are the most abundant primary producers in the ocean. However, quantification of picocyanobacteria on the sinking particles and in sediments remains challenging using flow cytometry or epifluorescence microscopy. Here, we developed a real-time PCR method to quantify picocyanobacteria using a newly designed primer set specifically targeting the 16S-23S rRNA ITS sequence of cyanobacteria. We showed that in the dark ocean, picocyanobacteria are 1 to 3 orders of magnitude more abundant in small particles (0.2 to 3 μm) than in larger particles (>3 μm). This result supports the important role of direct sinking free-living picocyanobacteria cells in the carbon export to deep ocean. We also found that the picocyanobacterial ITS sequence abundance were 105 to 107 copies per gram in sediments, suggesting significant accumulation of sinking picocyanobacteria in the benthic ecosystem. This qPCR method can be used to quantify the contribution of picocyanobacteria to the biological carbon pump.
Collapse
|
2
|
Van Cauwenberghe J, Santamaría RI, Bustos P, Juárez S, Ducci MA, Figueroa Fleming T, Etcheverry AV, González V. Spatial patterns in phage-Rhizobium coevolutionary interactions across regions of common bean domestication. THE ISME JOURNAL 2021; 15:2092-2106. [PMID: 33558688 PMCID: PMC8245606 DOI: 10.1038/s41396-021-00907-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 01/14/2021] [Accepted: 01/21/2021] [Indexed: 01/30/2023]
Abstract
Bacteriophages play significant roles in the composition, diversity, and evolution of bacterial communities. Despite their importance, it remains unclear how phage diversity and phage-host interactions are spatially structured. Local adaptation may play a key role. Nitrogen-fixing symbiotic bacteria, known as rhizobia, have been shown to locally adapt to domesticated common bean at its Mesoamerican and Andean sites of origin. This may affect phage-rhizobium interactions. However, knowledge about the diversity and coevolution of phages with their respective Rhizobium populations is lacking. Here, through the study of four phage-Rhizobium communities in Mexico and Argentina, we show that both phage and host diversity is spatially structured. Cross-infection experiments demonstrated that phage infection rates were higher overall in sympatric rhizobia than in allopatric rhizobia except for one Argentinean community, indicating phage local adaptation and host maladaptation. Phage-host interactions were shaped by the genetic identity and geographic origin of both the phage and the host. The phages ranged from specialists to generalists, revealing a nested network of interactions. Our results suggest a key role of local adaptation to resident host bacterial communities in shaping the phage genetic and phenotypic composition, following a similar spatial pattern of diversity and coevolution to that in the host.
Collapse
Affiliation(s)
- Jannick Van Cauwenberghe
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Mexico, Mexico.
- Department of Integrative Biology, University of California, Berkeley, CA, USA.
| | - Rosa I Santamaría
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Mexico, Mexico
| | - Patricia Bustos
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Mexico, Mexico
| | - Soledad Juárez
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Mexico, Mexico
| | - Maria Antonella Ducci
- Instituto Nacional de Tecnología Agropecuaria, Universidad Nacional de Salta, Salta, Argentina
| | | | | | - Víctor González
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Mexico, Mexico.
| |
Collapse
|
3
|
Xue C, Liu X, Wang Q, Lin T, Wang M, Liu Q, Shao H, Jiang Y. The isolation and genome sequencing of a novel cyanophage S-H68 from the Bohai Sea, China. Mar Genomics 2020; 53:100739. [PMID: 32883437 DOI: 10.1016/j.margen.2019.100739] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 10/06/2019] [Accepted: 12/20/2019] [Indexed: 11/24/2022]
Abstract
Cyanobacteria, also known as bule-green algae, are capable of photosynthesis and have a fixed carbon and nitrogen effect. The virus that specifically infects cyanobacteria is called the cyanophage. Cyanophages play a key role in building microbial communities. However, only a small number of cyanophages have been reported so far. In this study, a novel Synechococcus cyanophage S-H68 was isolated from the Bohai Sea of China. Transmission electron microscope observations showed that S-H68 has an icosahedral head, 66 ± 1 nm in diameter, and a tail with a length of 107 ± 1 nm, and should be grouped into the family Siphoviridae. To better understand the genetic diversity of this cyanophage, the complete genome was characterized. It consists of 79,639 -bp -length double-stranded DNA with a GC content of 59.8% and is predicted to have 117 open reading frames (ORFs) with an average length of 655 nucleotides. Using the BLASTN tool in the NCBI database for genome comparison, there was no significant similarity between S-H68 and other known cyanophages. So the present study added a new Siphoviridae cyanophage to the marine phage dataset.
Collapse
Affiliation(s)
- Chenglong Xue
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Xinxin Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Qi Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Tongtong Lin
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Min Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
| | - Qian Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Hongbing Shao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yong Jiang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China.
| |
Collapse
|