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Yu M, Zhang M, Zeng R, Cheng R, Zhang R, Hou Y, Kuang F, Feng X, Dong X, Li Y, Shao Z, Jin M. Diversity and potential host-interactions of viruses inhabiting deep-sea seamount sediments. Nat Commun 2024; 15:3228. [PMID: 38622147 PMCID: PMC11018836 DOI: 10.1038/s41467-024-47600-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 04/04/2024] [Indexed: 04/17/2024] Open
Abstract
Seamounts are globally distributed across the oceans and form one of the major oceanic biomes. Here, we utilized combined analyses of bulk metagenome and virome to study viral communities in seamount sediments in the western Pacific Ocean. Phylogenetic analyses and the protein-sharing network demonstrate extensive diversity and previously unknown viral clades. Inference of virus-host linkages uncovers extensive interactions between viruses and dominant prokaryote lineages, and suggests that viruses play significant roles in carbon, sulfur, and nitrogen cycling by compensating or augmenting host metabolisms. Moreover, temperate viruses are predicted to be prevalent in seamount sediments, which tend to carry auxiliary metabolic genes for host survivability. Intriguingly, the geographical features of seamounts likely compromise the connectivity of viral communities and thus contribute to the high divergence of viral genetic spaces and populations across seamounts. Altogether, these findings provides knowledge essential for understanding the biogeography and ecological roles of viruses in globally widespread seamounts.
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Affiliation(s)
- Meishun Yu
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Menghui Zhang
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Runying Zeng
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Ruolin Cheng
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Yanping Hou
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Fangfang Kuang
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Xuejin Feng
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Xiyang Dong
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Yinfang Li
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China.
| | - Min Jin
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China.
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Li H, Zhang H, Li H, Duan L, Zhang X, Gao Y, Hall IR, Hemming SR, LeVay LJ. Sedimentary DNA reveals the link between microbial community dynamics and climate during the late last glaciation in the offshore region of the Zambezi River, Southwest Indian Ocean. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167787. [PMID: 37844644 DOI: 10.1016/j.scitotenv.2023.167787] [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: 06/29/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 10/18/2023]
Abstract
Reconstructing the relationship between microbial communities and past abrupt climate change is of great importance for understanding current biodiversity patterns and predicting changes under future climate scenarios. However, little is currently known about how microbial communities respond to changes in key environmental stages due to a lack of research in this area. Here, we examine the variability in the communities of bacteria, archaea, and fungi from sediments deposited offshore region of the Zambezi River between 21.7 and 9.6 thousand years ago (ka) (covering the last glacial maximum, or LGM, and the early Holocene) using DNA metabarcoding approach via high-throughput sequencing. The results showed that (1) microbial assemblages differed across three key time intervals, with the last deglaciation having the most homogeneous prokaryotic assemblages, while for fungal communities in the LGM, and the early Holocene and LGM differing the most; (2) the warm early Holocene showed the highest diversity, whereas the lowest diversity was found in the LGM; and (3) the selected indicator species better reflected the climatic characteristics of different environmental stages. These results highlight the power of ancient sedimentary DNA to refine our understanding of microbial dynamics in marine sedimentary systems near large rivers, thus providing a basis for better modeling ecological processes in further research.
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Affiliation(s)
- Haoyu Li
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, 650500 Kunming, China
| | - Hucai Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, 650500 Kunming, China.
| | - Huayong Li
- School of Resource Environment and Tourism, Anyang Normal University, Anyang 455000, China
| | - Lizeng Duan
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, 650500 Kunming, China
| | - Xiaonan Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, 650500 Kunming, China
| | - Youhong Gao
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, 650500 Kunming, China
| | - Ian R Hall
- Department of Earth Sciences, Cardiff University, Main College, Park Place, PO Box 914, Cardiff, Wales CF10 3AT, United Kingdom
| | - Sidney R Hemming
- Lamont-Doherty Earth Observatory, Columbia University, 61 Route 9W, Palisades, NY, 10964, USA
| | - Leah J LeVay
- International Ocean Discovery Program, Texas A&M University, College Station, TX 77845, USA
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Sun J, Zhou H, Cheng H, Chen Z, Yang J, Wang Y, Jing C. Depth-Dependent Distribution of Prokaryotes in Sediments of the Manganese Crust on Nazimov Guyots of the Magellan Seamounts. MICROBIAL ECOLOGY 2023; 86:3027-3042. [PMID: 37792089 DOI: 10.1007/s00248-023-02305-8] [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: 05/17/2023] [Accepted: 09/04/2023] [Indexed: 10/05/2023]
Abstract
Deep ocean polymetallic nodules, rich in cobalt, nickel, and titanium which are commonly used in high-technology and biotechnology applications, are being eyed for green energy transition through deep-sea mining operations. Prokaryotic communities underneath polymetallic nodules could participate in deep-sea biogeochemical cycling, however, are not fully described. To address this gap, we collected sediment cores from Nazimov guyots, where polymetallic nodules exist, to explore the diversity and vertical distribution of prokaryotic communities. Our 16S rRNA amplicon sequencing data, quantitative PCR results, and phylogenetic beta diversity indices showed that prokaryotic diversity in the surficial layers (0-8 cm) was > 4-fold higher compared to deeper horizons (8-26 cm), while heterotrophs dominated in all sediment horizons. Proteobacteria was the most abundant taxon (32-82%) across all sediment depths, followed by Thaumarchaeota (4-37%), Firmicutes (2-18%), and Planctomycetes (1-6%). Depth was the key factor controlling prokaryotic distribution, while heavy metals (e.g., iron, copper, nickel, cobalt, zinc) can also influence significantly the downcore distribution of prokaryotic communities. Analyses of phylogenetic diversity showed that deterministic processes governing prokaryotic assembly in surficial layers, contrasting with stochastic influences in deep layers. This was further supported from the detection of a more complex prokaryotic co-occurrence network in the surficial layer which suggested more diverse prokaryotic communities existed in the surface vs. deeper sediments. This study expands current knowledge on the vertical distribution of benthic prokaryotic diversity in deep sea settings underneath polymetallic nodules, and the results reported might set a baseline for future mining decisions.
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Affiliation(s)
- Jianxing Sun
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, People's Republic of China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, People's Republic of China
- Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, People's Republic of China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, People's Republic of China
- Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, People's Republic of China
| | - Zhu Chen
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, People's Republic of China
- Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, People's Republic of China
| | - Jichao Yang
- College of Marine Science and Engineering, Shandong University of Science and Technology, Qingdao, 266590, Shandong, People's Republic of China
| | - Yuguang Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, People's Republic of China.
- Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, People's Republic of China.
| | - Chunlei Jing
- National Deepsea Center, Ministry of Natural Resources, Qingdao, 266237, Shandong, People's Republic of China.
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Ngema SS, Khumalo SH, Ojo MC, Pooe OJ, Malilehe TS, Basson AK, Madoroba E. Evaluation of Antimicrobial Activity by Marine Nocardiopsis dassonvillei against Foodborne Listeria monocytogenes and Shiga Toxin-Producing Escherichia coli. Microorganisms 2023; 11:2539. [PMID: 37894198 PMCID: PMC10609338 DOI: 10.3390/microorganisms11102539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/12/2023] [Accepted: 09/30/2023] [Indexed: 10/29/2023] Open
Abstract
The emergence of multidrug-resistant pathogens creates public health challenges, prompting a continuous search for effective novel antimicrobials. This study aimed to isolate marine actinomycetes from South Africa, evaluate their in vitro antimicrobial activity against Listeria monocytogenes and Shiga toxin-producing Escherichia coli, and characterize their mechanisms of action. Marine actinomycetes were isolated and identified by 16S rRNA sequencing. Gas chromatography-mass spectrometry (GC-MS) was used to identify the chemical constituents of bioactive actinomycetes' secondary metabolites. Antibacterial activity of the secondary metabolites was assessed by the broth microdilution method, and their mode of actions were predicted using computational docking. While five strains showed antibacterial activity during primary screening, only Nocardiopsis dassonvillei strain SOD(B)ST2SA2 exhibited activity during secondary screening for antibacterial activity. GC-MS identified five major bioactive compounds: 1-octadecene, diethyl phthalate, pentadecanoic acid, 6-octadecenoic acid, and trifluoroacetoxy hexadecane. SOD(B)ST2SA2's extract demonstrated minimum inhibitory concentration and minimum bactericidal concentration, ranging from 0.78-25 mg/mL and 3.13 to > 25 mg/mL, respectively. Diethyl phthalate displayed the lowest bacterial protein-binding energies (kcal/mol): -7.2, dihydrofolate reductase; -6.0, DNA gyrase B; and -5.8, D-alanine:D-alanine ligase. Thus, marine N. dassonvillei SOD(B)ST2SA2 is a potentially good source of antibacterial compounds that can be used to control STEC and Listeria monocytogenes.
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Affiliation(s)
- Siyanda S. Ngema
- Department of Biochemistry and Microbiology, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa; (S.S.N.); (S.H.K.); (M.C.O.); (A.K.B.)
| | - Solomuzi H. Khumalo
- Department of Biochemistry and Microbiology, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa; (S.S.N.); (S.H.K.); (M.C.O.); (A.K.B.)
| | - Michael C. Ojo
- Department of Biochemistry and Microbiology, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa; (S.S.N.); (S.H.K.); (M.C.O.); (A.K.B.)
| | - Ofentse J. Pooe
- Discipline of Biochemistry, School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa;
| | - Tsolanku S. Malilehe
- Department of Water and Sanitation, University of Limpopo, Private Bag X1106, Polokwane 0727, South Africa;
| | - Albertus K. Basson
- Department of Biochemistry and Microbiology, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa; (S.S.N.); (S.H.K.); (M.C.O.); (A.K.B.)
| | - Evelyn Madoroba
- Department of Biochemistry and Microbiology, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa; (S.S.N.); (S.H.K.); (M.C.O.); (A.K.B.)
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Akter S, Rahman MS, Ali H, Minch B, Mehzabin K, Siddique MM, Galib SM, Yesmin F, Azmuda N, Adnan N, Hasan NA, Rahman SR, Moniruzzaman M, Ahmed MF. Phylogenetic diversity and functional potential of the microbial communities along the Bay of Bengal coast. Sci Rep 2023; 13:15976. [PMID: 37749192 PMCID: PMC10520010 DOI: 10.1038/s41598-023-43306-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/21/2023] [Indexed: 09/27/2023] Open
Abstract
The Bay of Bengal, the world's largest bay, is bordered by populous countries and rich in resources like fisheries, oil, gas, and minerals, while also hosting diverse marine ecosystems such as coral reefs, mangroves, and seagrass beds; regrettably, its microbial diversity and ecological significance have received limited research attention. Here, we present amplicon (16S and 18S) profiling and shotgun metagenomics data regarding microbial communities from BoB's eastern coast, viz., Saint Martin and Cox's Bazar, Bangladesh. From the 16S barcoding data, Proteobacteria appeared to be the dominant phylum in both locations, with Alteromonas, Methylophaga, Anaerospora, Marivita, and Vibrio dominating in Cox's Bazar and Pseudoalteromonas, Nautella, Marinomonas, Vibrio, and Alteromonas dominating the Saint Martin site. From the 18S barcoding data, Ochrophyta, Chlorophyta, and Protalveolata appeared among the most abundant eukaryotic divisions in both locations, with significantly higher abundance of Choanoflagellida, Florideophycidae, and Dinoflagellata in Cox's Bazar. The shotgun sequencing data reveals that in both locations, Alteromonas is the most prevalent bacterial genus, closely paralleling the dominance observed in the metabarcoding data, with Methylophaga in Cox's Bazar and Vibrio in Saint Martin. Functional annotations revealed that the microbial communities in these samples harbor genes for biofilm formation, quorum sensing, xenobiotics degradation, antimicrobial resistance, and a variety of other processes. Together, these results provide the first molecular insight into the functional and phylogenetic diversity of microbes along the BoB coast of Bangladesh. This baseline understanding of microbial community structure and functional potential will be critical for assessing impacts of climate change, pollution, and other anthropogenic disturbances on this ecologically and economically vital bay.
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Affiliation(s)
- Salma Akter
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Hazrat Ali
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Benjamin Minch
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Coral Gables, FL, USA
| | - Kaniz Mehzabin
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Md Moradul Siddique
- Department of Computer Science and Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Syed Md Galib
- Department of Computer Science and Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Farida Yesmin
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Nafisa Azmuda
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Nihad Adnan
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Nur A Hasan
- University of Maryland, College Park, MD, USA
| | | | - Mohammad Moniruzzaman
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Coral Gables, FL, USA.
| | - Md Firoz Ahmed
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh.
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